diff --git a/.gitattributes b/.gitattributes deleted file mode 100644 index 9a84ebf9..00000000 --- a/.gitattributes +++ /dev/null @@ -1,6 +0,0 @@ -resources/grch37.simpleRepeat.truvari.bed.gz filter=lfs diff=lfs merge=lfs -text -resources/grch37.simpleRepeat.truvari.bed.gz.tbi filter=lfs diff=lfs merge=lfs -text -resources/grch38.simpleRepeat.truvari.bed.gz filter=lfs diff=lsf merge=lfs -text -resources/grch38.simpleRepeat.truvari.bed.gz.tbi filter=lfs diff=lsf merge=lfs -text -resources/chm13.simpleRepeat.truvari.bed.gz filter=lfs diff=lsf merge=lfs -text -resources/chm13.simpleRepeat.truvari.bed.gz.tbi filter=lfs diff=lsf merge=lfs -text diff --git a/.github/workflows/func_tests.yml b/.github/workflows/func_tests.yml index dcf6f496..29535e46 100644 --- a/.github/workflows/func_tests.yml +++ b/.github/workflows/func_tests.yml @@ -26,6 +26,7 @@ jobs: pip install pylint pip install anybadge pip install coverage + sudo apt-get install bcftools samtools tabix python -m pip install . - name: Running ssshtest run: | diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 00000000..00c23dab --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,29 @@ +# .readthedocs.yaml +# Read the Docs configuration file +# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details + +# Required +version: 2 + +# Set the version of Python and other tools you might need +build: + os: ubuntu-20.04 + tools: + python: "3.9" + # You can also specify other tool versions: + # nodejs: "16" + # rust: "1.55" + # golang: "1.17" + +# Build documentation in the docs/ directory with Sphinx +sphinx: + configuration: docs/api/conf.py + +# If using Sphinx, optionally build your docs in additional formats such as PDF +# formats: +# - pdf + +# Optionally declare the Python requirements required to build your docs +python: + install: + - requirements: docs/requirements.txt diff --git a/README.md b/README.md index 07026c7b..ab61c3ea 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,3 @@ -``` -████████╗██████╗ ██╗ ██╗██╗ ██╗ █████╗ ██████╗ ██╗ -╚══██╔══╝██╔══██╗██║ ██║██║ ██║██╔══██╗██╔══██╗██║ - ██║ ██████╔╝██║ ██║██║ ██║███████║██████╔╝██║ - ██║ ██╔══██╗██║ ██║╚██╗ ██╔╝██╔══██║██╔══██╗██║ - ██║ ██║ ██║╚██████╔╝ ╚████╔╝ ██║ ██║██║ ██║██║ - ╚═╝ ╚═╝ ╚═╝ ╚═════╝ ╚═══╝ ╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ -``` [![PyPI version](https://badge.fury.io/py/Truvari.svg)](https://badge.fury.io/py/Truvari) [![pylint](imgs/pylint.svg)](https://github.com/acenglish/truvari/actions/workflows/pylint.yml) [![FuncTests](https://github.com/acenglish/truvari/actions/workflows/func_tests.yml/badge.svg?branch=develop&event=push)](https://github.com/acenglish/truvari/actions/workflows/func_tests.yml) @@ -13,20 +5,21 @@ [![develop](https://img.shields.io/github/commits-since/acenglish/truvari/v3.5.0)](https://github.com/ACEnglish/truvari/compare/v3.5.0...develop) [![Downloads](https://pepy.tech/badge/truvari)](https://pepy.tech/project/truvari) +![Logo](https://raw.githubusercontent.com/ACEnglish/truvari/develop/imgs/BoxScale1_DarkBG.png) Toolkit for benchmarking, merging, and annotating Structrual Variants -[WIKI page](https://github.com/acenglish/truvari/wiki) has detailed documentation. -See [Updates](https://github.com/acenglish/truvari/wiki/Updates) on new versions. -Read our [Paper](https://doi.org/10.1101/2022.02.21.481353) for more details. +📚 [WIKI page](https://github.com/acenglish/truvari/wiki) has detailed documentation. +📈 See [Updates](https://github.com/acenglish/truvari/wiki/Updates) on new versions. +📝 Read our [Paper](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02840-6) to learn more. -## Installation +## 💻 Installation Truvari uses Python 3.6+ and can be installed with pip: ``` python3 -m pip install Truvari ``` For details and more installation options, see [Installation](https://github.com/acenglish/truvari/wiki/Installation) on the wiki. -## Quick Start +## ⏩ Quick Start Each sub-command contains help documentation. Start with `truvari -h` to see available commands. @@ -34,17 +27,19 @@ The current most common Truvari use case is for structural variation benchmarkin ``` truvari bench -b base.vcf.gz -c comp.vcf.gz -o output_dir/ ``` -## Truvari Commands +## 🧬 Truvari Commands - [bench](https://github.com/acenglish/truvari/wiki/bench) - Performance metrics from comparison of two VCFs - [collapse](https://github.com/acenglish/truvari/wiki/collapse) - Collapse possibly redundant VCF entries - [anno](https://github.com/acenglish/truvari/wiki/anno) - Add SV annotations to a VCF - - [vcf2df](https://github.com/acenglish/truvari/wiki/vcf2df) - Turn a VCF into a pandas DataFrame - [consistency](https://github.com/acenglish/truvari/wiki/consistency) - Consistency report between multiple VCFs - - [divide](https://github.com/ACEnglish/truvari/wiki/divide) - Divide a VCF into independent parts + - [vcf2df](https://github.com/acenglish/truvari/wiki/vcf2df) - Turn a VCF into a pandas DataFrame - [segment](https://github.com/acenglish/truvari/wiki/segment) - Normalization of SVs into disjointed genomic regions + - [stratify](https://github.com/acenglish/truvari/wiki/stratify) - Count variants per-region in vcf + - [divide](https://github.com/ACEnglish/truvari/wiki/divide) - Divide a VCF into independent shards - [phab](https://github.com/ACEnglish/truvari/wiki/phab) - Harmonize variant representations using MSA + - [refine](https://github.com/ACEnglish/truvari/wiki/refine) - Automated bench result refinement with phab -## More Information +## 🔎 More Information -Find more details and discussions about Truvari on the [WIKI page](https://github.com/acenglish/truvari/wiki). +All documentation about Truvari is on the [WIKI](https://github.com/acenglish/truvari/wiki). Additional information about using Truvari can be found in [Discussions](https://github.com/ACEnglish/truvari/discussions) diff --git a/Singularity.def b/Singularity.def index 535deb02..663250b9 100644 --- a/Singularity.def +++ b/Singularity.def @@ -6,20 +6,32 @@ Stage: spython-base . /opt/truvari-source %post -apt-get -qq update && apt-get install -yq \ -python3-pip \ -python3-dev \ -curl \ -&& \ -rm -rf /var/lib/apt/lists/* + +apt-get -qq update \ + && DEBIAN_FRONTEND=noninteractive apt-get install -yq \ + bcftools \ + curl \ + python3-dev \ + python3-pip \ + samtools \ + tabix \ + vcftools \ + wget \ + && \ + rm -rf /var/lib/apt/lists/* cd /opt/truvari-source +wget https://mafft.cbrc.jp/alignment/software/mafft_7.505-1_amd64.deb \ + && dpkg -i mafft_7.505-1_amd64.deb && rm mafft_7.505-1_amd64.deb + python3 -m pip install --upgrade pip && \ -python3 -m pip install setproctitle pylint anybadge coverage && \ -python3 -m pip install --upgrade setuptools && \ -python3 -m pip install ./ + python3 -m pip install setproctitle pylint anybadge coverage && \ + python3 -m pip install --upgrade setuptools && \ + python3 -m pip install ./ + +mkdir /data cd /data %runscript diff --git a/docs/api/conf.py b/docs/api/conf.py index 6180d136..9384a268 100644 --- a/docs/api/conf.py +++ b/docs/api/conf.py @@ -9,12 +9,15 @@ # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. +import os +import sys +sys.path.insert(0, os.path.abspath('../../')) # -- Project information ----------------------------------------------------- project = 'Truvari' -copyright = '2021, Adam English' +copyright = '2023, Adam English' author = 'Adam English' diff --git a/docs/api/index.rst b/docs/api/index.rst index 8bc3349e..0cce639f 100644 --- a/docs/api/index.rst +++ b/docs/api/index.rst @@ -8,10 +8,10 @@ Welcome to Truvari's documentation! This documentation is aimed at developers looking to reuse truvari's code. -For those looking to use truavari as a tool for analysis, full documentation -is available via the github page +For those looking to use truvari for analysis, full documentation +is available via the github wiki -https://github.com/ACEnglish/truvari +https://github.com/ACEnglish/truvari/wiki .. toctree:: :maxdepth: 2 diff --git a/docs/api/local_build.sh b/docs/api/local_build.sh index af51d8b9..b958e835 100644 --- a/docs/api/local_build.sh +++ b/docs/api/local_build.sh @@ -1,7 +1,6 @@ -#sphinx-apidoc -f -F ../../truvari/ -o /data/docs/api/ --ext-autodoc -M -# requires pip install sphinx & sphinx_rtd_theme DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" -# will overwrite your python +python3 -m pip install sphinx sphinx_rtd_theme +# will overwrite your current environment's truvari cd ../../ python3 setup.py install cd - diff --git a/docs/api/truvari.rst b/docs/api/truvari.rst index 90443191..d26f867d 100644 --- a/docs/api/truvari.rst +++ b/docs/api/truvari.rst @@ -8,48 +8,12 @@ Overview :undoc-members: :show-inheritance: -Objects -------- -GT -^^ -.. autoclass:: GT - :members: - -RegionVCFIterator -^^^^^^^^^^^^^^^^^ -.. autoclass:: RegionVCFIterator - :members: - -LogFileStderr -^^^^^^^^^^^^^ -.. autoclass:: LogFileStderr - :members: - -MatchResult -^^^^^^^^^^^ -.. autoclass:: MatchResult - :members: - -Matcher -^^^^^^^ -.. autoclass:: Matcher - :members: - -SV -^^ -.. autoclass:: SV - :members: - VariantRecord Methods --------------------- entry_boundaries ^^^^^^^^^^^^^^^^ .. autofunction:: entry_boundaries -entry_create_haplotype -^^^^^^^^^^^^^^^^^^^^^^ -.. autofunction:: entry_create_haplotype - entry_distance ^^^^^^^^^^^^^^ .. autofunction:: entry_distance @@ -66,10 +30,6 @@ entry_is_present ^^^^^^^^^^^^^^^^ .. autofunction:: entry_is_present -entry_pctsim -^^^^^^^^^^^^ -.. autofunction:: entry_pctsim - entry_reciprocal_overlap ^^^^^^^^^^^^^^^^^^^^^^^^ .. autofunction:: entry_reciprocal_overlap @@ -78,6 +38,10 @@ entry_same_variant_type ^^^^^^^^^^^^^^^^^^^^^^^ .. autofunction:: entry_same_variant_type +entry_seq_similarity +^^^^^^^^^^^^^^^^^^^^^^^^^ +.. autofunction:: entry_seq_similarity + entry_size ^^^^^^^^^^ .. autofunction:: entry_size @@ -86,9 +50,9 @@ entry_size_similarity ^^^^^^^^^^^^^^^^^^^^^ .. autofunction:: entry_size_similarity -entry_to_haplotype -^^^^^^^^^^^^^^^^^^ -.. autofunction:: entry_to_haplotype +entry_to_hash +^^^^^^^^^^^^^ +.. autofunction:: entry_to_hash entry_to_key ^^^^^^^^^^^^ @@ -98,8 +62,12 @@ entry_variant_type ^^^^^^^^^^^^^^^^^^ .. autofunction:: entry_variant_type +entry_shared_ref_context +^^^^^^^^^^^^^^^^^^^^^^^^ +.. autofunction:: entry_shared_ref_context + Extra Methods ---------------------- +------------- allele_freq_annos ^^^^^^^^^^^^^^^^^ .. autofunction:: allele_freq_annos @@ -120,6 +88,10 @@ calc_hwe ^^^^^^^^ .. autofunction:: calc_hwe +compress_index_vcf +^^^^^^^^^^^^^^^^^^ +.. autofunction:: compress_index_vcf + create_pos_haplotype ^^^^^^^^^^^^^^^^^^^^ .. autofunction:: create_pos_haplotype @@ -156,6 +128,10 @@ phab ^^^^ .. autofunction:: phab +phab_multi +^^^^^^^^^^ +.. autofunction:: phab_multi + reciprocal_overlap ^^^^^^^^^^^^^^^^^^ .. autofunction:: reciprocal_overlap @@ -180,12 +156,12 @@ vcf_ranges ^^^^^^^^^^ .. autofunction:: vcf_ranges -weighted_score -^^^^^^^^^^^^^^ -.. autofunction:: weighted_score - Dev methods ----------- +benchdir_count_entries +^^^^^^^^^^^^^^^^^^^^^^ +.. autofunction:: benchdir_count_entries + chunker ^^^^^^^ .. autofunction:: chunker @@ -194,6 +170,18 @@ cmd_exe ^^^^^^^ .. autofunction:: cmd_exe +consolidate_phab_vcfs +^^^^^^^^^^^^^^^^^^^^^ +.. autofunction:: consolidate_phab_vcfs + +count_entries +^^^^^^^^^^^^^ +.. autofunction:: count_entries + +fchain +^^^^^^ +.. autofunction:: fchain + file_zipper ^^^^^^^^^^^ .. autofunction:: file_zipper @@ -214,6 +202,10 @@ optimize_df_memory ^^^^^^^^^^^^^^^^^^ .. autofunction:: optimize_df_memory +performance_metrics +^^^^^^^^^^^^^^^^^^^ +.. autofunction:: performance_metrics + restricted_float ^^^^^^^^^^^^^^^^ .. autofunction:: restricted_float @@ -234,6 +226,49 @@ vcf_to_df ^^^^^^^^^ .. autofunction:: vcf_to_df +Objects +------- + +Bench +^^^^^ +.. autoclass:: Bench + :members: + +BenchOutput +^^^^^^^^^^^ +.. autoclass:: BenchOutput + :members: + +GT +^^ +.. autoclass:: GT + :members: + +RegionVCFIterator +^^^^^^^^^^^^^^^^^ +.. autoclass:: RegionVCFIterator + :members: + +LogFileStderr +^^^^^^^^^^^^^ +.. autoclass:: LogFileStderr + :members: + +MatchResult +^^^^^^^^^^^ +.. autoclass:: MatchResult + :members: + +Matcher +^^^^^^^ +.. autoclass:: Matcher + :members: + +SV +^^ +.. autoclass:: SV + :members: + Data ---- HEADERMAT diff --git a/docs/requirements.txt b/docs/requirements.txt index f5ce90d0..1d378653 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,9 +1,7 @@ sphinx==4.2.0 sphinx_rtd_theme==1.0.0 readthedocs-sphinx-search==0.1.1 -python-Levenshtein==0.12.2 edlib>=1.3.8.post2 -progressbar2>=3.41.0 pysam>=0.15.2 intervaltree>=3.0 joblib>=1.0.1 diff --git a/docs/v4.0.0/Citations.md b/docs/v4.0.0/Citations.md new file mode 100644 index 00000000..d600b860 --- /dev/null +++ b/docs/v4.0.0/Citations.md @@ -0,0 +1,30 @@ +# Citing Truvari + +English, A.C., Menon, V.K., Gibbs, R.A. et al. Truvari: refined structural variant comparison preserves allelic diversity. Genome Biol 23, 271 (2022). https://doi.org/10.1186/s13059-022-02840-6 + +# Citations + +List of publications using Truvari. Most of these are just pulled from a [Google Scholar Search](https://scholar.google.com/scholar?q=truvari). Please post in the [show-and-tell](https://github.com/spiralgenetics/truvari/discussions/categories/show-and-tell) to have your publication added to the list. +* [A robust benchmark for detection of germline large deletions and insertions](https://www.nature.com/articles/s41587-020-0538-8) +* [Leveraging a WGS compression and indexing format with dynamic graph references to call structural variants](https://www.biorxiv.org/content/10.1101/2020.04.24.060202v1.abstract) +* [Duphold: scalable, depth-based annotation and curation of high-confidence structural variant calls](https://academic.oup.com/gigascience/article/8/4/giz040/5477467?login=true) +* [Parliament2: Accurate structural variant calling at scale](https://academic.oup.com/gigascience/article/9/12/giaa145/6042728) +* [Learning What a Good Structural Variant Looks Like](https://www.biorxiv.org/content/10.1101/2020.05.22.111260v1.full) +* [Long-read trio sequencing of individuals with unsolved intellectual disability](https://www.nature.com/articles/s41431-020-00770-0) +* [lra: A long read aligner for sequences and contigs](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009078) +* [Samplot: a platform for structural variant visual validation and automated filtering](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02380-5) +* [AsmMix: A pipeline for high quality diploid de novo assembly](https://www.biorxiv.org/content/10.1101/2021.01.15.426893v1.abstract) +* [Accurate chromosome-scale haplotype-resolved assembly of human genomes](https://www.nature.com/articles/s41587-020-0711-0) +* [Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome](https://www.nature.com/articles/s41587-019-0217-9) +* [NPSV: A simulation-driven approach to genotyping structural variants in whole-genome sequencing data](https://academic.oup.com/bioinformatics/article-abstract/37/11/1497/5466452) +* [SVIM-asm: structural variant detection from haploid and diploid genome assemblies](https://academic.oup.com/bioinformatics/article/36/22-23/5519/6042701?login=true) +* [Readfish enables targeted nanopore sequencing of gigabase-sized genomes](https://www.nature.com/articles/s41587-020-00746-x) +* [stLFRsv: A Germline Structural Variant Analysis Pipeline Using Co-barcoded Reads](https://internal-journal.frontiersin.org/articles/10.3389/fgene.2021.636239/full) +* [Long-read-based human genomic structural variation detection with cuteSV](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02107-y) +* [An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates](https://f1000research.com/articles/10-246) +* [Paragraph: a graph-based structural variant genotyper for short-read sequence data](https://link.springer.com/article/10.1186/s13059-019-1909-7) +* [Genome-wide investigation identifies a rare copy-number variant burden associated with human spina bifida](https://www.nature.com/articles/s41436-021-01126-9) +* [TT-Mars: Structural Variants Assessment Based on Haplotype-resolved Assemblies](https://www.biorxiv.org/content/10.1101/2021.09.27.462044v1.abstract) +* [An ensemble deep learning framework to refine large deletions in linked-reads](https://www.biorxiv.org/content/10.1101/2021.09.27.462057v1.abstract) +* [MAMnet: detecting and genotyping deletions and insertions based on long reads and a deep learning approach](https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbac195/6587170)](https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbac195/6587170) +* [Automated filtering of genome-wide large deletions through an ensemble deep learning framework](https://www.sciencedirect.com/science/article/pii/S1046202322001712#b0110) diff --git a/docs/v4.0.0/Comparing-two-SV-programs.md b/docs/v4.0.0/Comparing-two-SV-programs.md new file mode 100644 index 00000000..6463f90d --- /dev/null +++ b/docs/v4.0.0/Comparing-two-SV-programs.md @@ -0,0 +1,67 @@ +A frequent application of comparing SVs is to perform a 'bakeoff' of performance +between two SV programs against a single set of base calls. + +Beyond looking at the Truvari results/report, you may like to investigate what calls +are different between the programs. + +Below is a set of scripts that may help you generate those results. For our examples, +we'll be comparing arbitrary programs Asvs and Bsvs aginst base calls Gsvs. + +*_Note_* - This assumes that each record in Gsvs has a unique ID in the vcf. + +Generate the Truvari report for Asvs and Bsvs +============================================= + +```bash +truvari bench -b Gsvs.vcf.gz -c Asvs.vcf.gz -o cmp_A/ ... +truvari bench -b Gsvs.vcf.gz -c Bsvs.vcf.gz -o cmp_B/ ... +``` +Consistency +=========== +The simplest way to compare the programs is to get the intersection of TPbase calls from the two reports. +```bash +truvari consistency cmp_A/tp-base.vcf cmp_B/tp-base.vcf +``` +See [[consistency wiki|consistency]] for details on the report created. + +Below are older notes to manually create a similar report to what one can make using `truvari consistency` + +Combine the TPs within each report +================================== + +```bash +cd cmp_A/ +paste <(grep -v "#" tp-base.vcf) <(grep -v "#" tp-comp.vcf) > combined_tps.txt +cd ../cmp_B/ +paste <(grep -v "#" tp-base.vcf) <(grep -v "#" tp-comp.vcf) > combined_tps.txt +``` + +Grab the FNs missed by only one program +======================================= + +```bash +(grep -v "#" cmp_A/fn.vcf && grep -v "#" cmp_B/fn.vcf) | cut -f3 | sort | uniq -c | grep "^ *1 " | cut -f2- -d1 > missed_names.txt +``` + +Pull the TP sets' difference +============================ + +```bash +cat missed_names.txt | xargs -I {} grep -w {} cmp_A/combined_tps.txt > missed_by_B.txt +cat missed_names.txt | xargs -I {} grep -w {} cmp_B/combined_tps.txt > missed_by_A.txt +``` + +To look at the base-calls that Bsvs found, but Asvs didn't, run `cut -f1-12 missed_by_A.txt`. + +To look at the Asvs that Bsvs didn't find, run `cut -f13- missed_by_B.txt`. + +Shared FPs between the programs +=============================== + +All of the work above has been about how to analyze the TruePositives. If you'd like to see which calls are shared between Asvs and Bsvs that aren't in Gsvs, simply run Truvari again. + +```bash +bgzip cmp_A/fp.vcf && tabix -p vcf cmp_A/fp.vcf.gz +bgzip cmp_B/fp.vcf && tabix -p vcf cmp_B/fp.vcf.gz +truvari bench -b cmp_A/fp.vcf.gz -c cmp_B/fp.vcf.gz -o shared_fps ... +``` \ No newline at end of file diff --git a/docs/v4.0.0/Development.md b/docs/v4.0.0/Development.md new file mode 100644 index 00000000..ccb38493 --- /dev/null +++ b/docs/v4.0.0/Development.md @@ -0,0 +1,90 @@ +# Truvari API +Many of the helper methods/objects are documented such that developers can reuse truvari in their own code. To see developer documentation, visit [readthedocs](https://truvari.readthedocs.io/en/latest/). + +Documentation can also be seen using +```python +import truvari +help(truvari) +``` + +# docker + +A Dockerfile exists to build an image of Truvari. To make a Docker image, clone the repository and run +```bash +docker build -t truvari . +``` + +You can then run Truvari through docker using +```bash +docker run -v `pwd`:/data -it truvari +``` +Where `pwd` can be whatever directory you'd like to mount in the docker to the path `/data/`, which is the working directory for the Truvari run. You can provide parameters directly to the entry point. +```bash +docker run -v `pwd`:/data -it truvari anno svinfo -i example.vcf.gz +``` + +If you'd like to interact within the docker container for things like running the CI/CD scripts +```bash +docker run -v `pwd`:/data --entrypoint /bin/bash -it truvari +``` +You'll now be inside the container and can run FuncTests or run Truvari directly +```bash +bash repo_utils/truvari_ssshtests.sh +truvari anno svinfo -i example.vcf.gz +``` + +# CI/CD + +Scripts that help ensure the tool's quality. Extra dependencies need to be installed in order to run Truvari's CI/CD scripts. + +```bash +pip install pylint anybadge coverage +``` + +Check code formatting with +```bash +python repo_utils/pylint_maker.py +``` +We use [autopep8](https://pypi.org/project/autopep8/) (via [vim-autopep8](https://github.com/tell-k/vim-autopep8)) for formatting. + +Test the code and generate a coverage report with +```bash +bash repo_utils/truvari_ssshtests.sh +``` + +Truvari leverages github actions to perform these checks when new code is pushed to the repository. We've noticed that the actions sometimes hangs through no fault of the code. If this happens, cancel and resubmit the job. Once FuncTests are successful, it uploads an artifact of the `coverage html` report which you can download to see a line-by-line accounting of test coverage. + +# git flow + +To organize the commits for the repository, we use [git-flow](https://danielkummer.github.io/git-flow-cheatsheet/). Therefore, `develop` is the default branch, the latest tagged release is on `master`, and new, in-development features are within `feature/` + +When contributing to the code, be sure you're working off of develop and have run `git flow init`. + +# versioning + +Truvari uses [Semantic Versioning](https://semver.org/) and tries to stay compliant to [PEP440](https://peps.python.org/pep-0440/). As of v3.0.0, a single version is kept in the code under `truvari/__init__.__version__`. We try to keep the suffix `-dev` on the version in the develop branch. When cutting a new release, we may replace the suffix with `-rc` if we've built a release candidate that may need more testing/development. Once we've committed to a full release that will be pushed to PyPi, no suffix is placed on the version. If you install Truvari from the develop branch, the git repo hash is appended to the installed version as well as '.uc' if there are un-staged commits in the repo. + +# docs + +The github wiki serves the documentation most relevant to the `develop/` branch. When cutting a new release, we freeze and version the wiki's documentation with the helper utility `docs/freeze_wiki.sh`. + +# Creating a release +Follow these steps to create a release + +0) Bump release version +1) Run tests locally +2) Update API Docs +3) Change Updates Wiki +4) Freeze the Wiki +5) Ensure all code is checked in +6) Do a [git-flow release](https://danielkummer.github.io/git-flow-cheatsheet/) +7) Use github action to make a testpypi release +8) Check test release +```bash +python3 -m venv test_truvari +python3 -m pip install --index-url https://test.pypi.org/simple --extra-index-url https://pypi.org/simple/ truvari +``` +9) Use GitHub action to make a pypi release +10) Download release-tarball.zip from step #9’s action +11) Create release (include #9) from the tag +12) Checkout develop and Bump to dev version and README ‘commits since’ badge \ No newline at end of file diff --git a/docs/v4.0.0/Edit-Distance-Ratio-vs-Sequence-Similarity.md b/docs/v4.0.0/Edit-Distance-Ratio-vs-Sequence-Similarity.md new file mode 100644 index 00000000..eb45ce30 --- /dev/null +++ b/docs/v4.0.0/Edit-Distance-Ratio-vs-Sequence-Similarity.md @@ -0,0 +1,55 @@ +By default, Truvari uses [edlib](https://github.com/Martinsos/edlib) to calculate the edit distance between two SV calls. Optionally, the [Levenshtein edit distance ratio](https://en.wikipedia.org/wiki/Levenshtein_distance) can be used to compute the `--pctsim` between two variants. These measures are different than the sequence similarity calculated by [Smith-Waterman alignment](https://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm). + +To show this difference, consider the following two sequences.: + +``` + AGATACAGGAGTACGAACAGTACAGTACGA + |||||||||||||||*|||||||||||||| +ATCACAGATACAGGAGTACGTACAGTACAGTACGA + +30bp Aligned +1bp Mismatched (96% similarity) +5bp Left-Trimmed (~14% of the bottom sequence) +``` + +The code below runs swalign, Levenshtein, and edlib to compute the `--pctsim` between the two sequences. + + +```python +import swalign +import Levenshtein +import edlib + +seq1 = "AGATACAGGAGTACGAACAGTACAGTACGA" +seq2 = "ATCACAGATACAGGAGTACGTACAGTACAGTACGA" + +scoring = swalign.NucleotideScoringMatrix(2, -1) +alner = swalign.LocalAlignment(scoring, gap_penalty=-2, gap_extension_decay=0.5) +aln = alner.align(seq1, seq2) +mat_tot = aln.matches +mis_tot = aln.mismatches +denom = float(mis_tot + mat_tot) +if denom == 0: + ident = 0 +else: + ident = mat_tot / denom +scr = edlib.align(seq1, seq2) +totlen = len(seq1) + len(seq2) + +print('swalign', ident) +# swalign 0.966666666667 +print('levedit', Levenshtein.ratio(seq1, seq2)) +# levedit 0.892307692308 +print('edlib', (totlen - scr["editDistance"]) / totlen) +# edlib 0.9076923076923077 +``` + +Because the swalign procedure only considers the number of matches and mismatches, the `--pctsim` is higher than the edlib and Levenshtein ratio. + +If we were to account for the 5 'trimmed' bases from the Smith-Waterman alignment when calculating the `--pctsim` by counting each trimmed base as a mismatch, we would see the similarity drop to ~83%. + +[This post](https://stackoverflow.com/questions/14260126/how-python-levenshtein-ratio-is-computed) has a nice response describing exactly how the Levenshtein ratio is computed. + +The Smith-Waterman alignment is much more expensive to compute compared to the Levenshtein ratio, and does not account for 'trimmed' sequence difference. + +However, edlib is the fastest comparison method and is used by default. Levenshtein can be specified with `--use-lev` in `bench` and `collapse`. \ No newline at end of file diff --git a/docs/v4.0.0/Home.md b/docs/v4.0.0/Home.md new file mode 100644 index 00000000..312fa193 --- /dev/null +++ b/docs/v4.0.0/Home.md @@ -0,0 +1,36 @@ +The wiki holds documentation most relevant for develop. For information on a specific version of Truvari, see [`docs/`](https://github.com/spiralgenetics/truvari/tree/develop/docs) + +Citation: +English, A.C., Menon, V.K., Gibbs, R.A. et al. Truvari: refined structural variant comparison preserves allelic diversity. Genome Biol 23, 271 (2022). https://doi.org/10.1186/s13059-022-02840-6 + +# Before you start +VCFs aren't always created with a strong adherence to the format's specification. + +Truvari expects input VCFs to be valid so that it will only output valid VCFs. + +We've developed a separate tool that runs multiple validation programs and standard VCF parsing libraries in order to validate a VCF. + +Run [this program](https://github.com/acenglish/usable_vcf) over any VCFs that are giving Truvari trouble. + +Furthermore, Truvari expects 'resolved' SVs (e.g. DEL/INS) and will not interpret BND signals across SVTYPEs (e.g. combining two BND lines to match a DEL call). A brief description of Truvari bench methodology is linked below. + +Finally, Truvari does not handle multi-allelic VCF entries and as of v4.0 will throw an error if multi-allelics are encountered. Please use `bcftools norm` to split multi-allelic entries. + +# Index + +- [[Updates|Updates]] +- [[Installation|Installation]] +- Truvari Commands: + - [[anno|anno]] + - [[bench|bench]] + - [[collapse|collapse]] + - [[consistency|consistency]] + - [[divide|divide]] + - [[phab|phab]] + - [[refine|refine]] + - [[segment|segment]] + - [[stratify|stratify]] + - [[vcf2df|vcf2df]] +- [[Development|Development]] +- [[Citations|Citations]] +- [[Resources|Resources]] \ No newline at end of file diff --git a/docs/v4.0.0/Installation.md b/docs/v4.0.0/Installation.md new file mode 100644 index 00000000..a929d245 --- /dev/null +++ b/docs/v4.0.0/Installation.md @@ -0,0 +1,56 @@ +Recommended +=========== +For stable versions of Truvari, use pip +``` +python3 -m pip install truvari +``` +Specific versions can be installed via +``` +python3 -m pip install truvari==3.2.0 +``` +See [pypi](https://pypi.org/project/Truvari/#history) for a history of all distributed releases. + +Manual Installation +=================== +To build Truvari directly, clone the repository and switch to a specific tag. +``` +git clone https://github.com/spiralgenetics/truvari.git +git checkout tags/v3.0.0 +python3 -m pip install . +``` + +To see a list of all available tags, run: +``` +git tag -l +``` + +If you have an older clone of the repository and don't see the version you're looking for in tags, make sure to pull the latest changes: +``` +git pull +git fetch --all --tags +``` + +Mamba / Conda +============= +NOTE!! There is a very old version of Truvari on bioconda that - for unknown reasons - supersedes the newer, supported versions. Users may need to specify to conda which release to build. See [this ticket](https://github.com/ACEnglish/truvari/issues/130#issuecomment-1196607866) for details. + +Truvari releases are automatically deployed to bioconda. +Users can follow instructions here (https://mamba.readthedocs.io/en/latest/installation.html) to install mamba. (A faster alternative conda compatible package manager.) + +Creating an environment with Truvari and its dependencies. +``` +mamba create -c conda-forge -c bioconda -n truvari truvari +``` + +Alternatively, see the [conda page](https://anaconda.org/bioconda/truvari) for details +``` +conda install -c bioconda truvari +``` + +Building from develop +===================== +The default branch is `develop`, which holds in-development changes. This is for developers or those wishing to try experimental features and is not recommended for production. Development is versioned higher than the most recent stable release with an added suffix (e.g. Current stable release is `3.0.0`, develop holds `3.1.0-dev`). If you'd like to install develop, repeat the steps above but without `git checkout tags/v3.0.0`. See [wiki](https://github.com/spiralgenetics/truvari/wiki/Development#git-flow) for details on how branching is handled. + +Docker +====== +See [Development](https://github.com/spiralgenetics/truvari/wiki/Development#docker) for details on building a docker container. diff --git a/docs/v4.0.0/MatchIds.md b/docs/v4.0.0/MatchIds.md new file mode 100644 index 00000000..f7bcfd4f --- /dev/null +++ b/docs/v4.0.0/MatchIds.md @@ -0,0 +1,30 @@ +Using MatchId +============= + +MatchIds are used to tie base/comparison calls together in post-processing for debugging or other exploring. MatchIds are in `bench` and `collapse` outputs. In the `collapse` main output, the field is named 'CollapseId'. + +MatchIds have a structure of `{chunkid}.{baseid}.{compid}`. + +Where: + - chunkid - Unique id per-chunk of calls. All calls sharing chunkid were within `--chunksize` distance and were + compared. + - baseid - The number of the base call from this chunk + - compid - The number of the comp call from this chunk + +Doing basic pairing with MatchIds when results didn't use `--pick multi` is straight forward. For example, to tie tp-base.vcf and tp-comp.vcf calls together, they will have identical MatchIds. + +MatchIds with `_` for the baseid or compid are calls that were in a chunk without a counterpart (e.g. `5._.0` is the +first comparison call from the fifth chunk, which had no base calls.) + +When using `--pick multi` there can be instances such as: +``` +VCF MatchId +tp-base 3.0.0 +tp-comp 3.0.0 +tp-comp 3.0.1 +``` +Here, the 0th base/comp call match to one another. Additionally, the 1st comp call `3.0.1` also matches to the 0th base call `tp-base 3.0.0`. + +This makes tieing false positives/negatives to their closest matching counter part a little tricker. +For example, if we have a false negative with MatchId `3.1.0`, we'll need to look in both the `fp.vcf` and `tp-comp.vcf` for +`3.*.0`. This search will find the 0th comp call in the third chunk which may have matched to a different baseid than 1. \ No newline at end of file diff --git a/docs/v4.0.0/Multi-allelic-VCFs.md b/docs/v4.0.0/Multi-allelic-VCFs.md new file mode 100644 index 00000000..fd0eb23e --- /dev/null +++ b/docs/v4.0.0/Multi-allelic-VCFs.md @@ -0,0 +1,11 @@ +Truvari only compares the first alternate allele in VCFs. If a VCF contains multi-allelic sites such as: + +``` +chr2 1948201 . T TACAACACGTACGATCAGTAGAC,TCAACACACAACACGTACGATCAGTAGAC .... +``` + +Then pre-process the VCFs with bcftools: + +```bash +bcftools norm -m-any base_calls.vcf.gz | bgzip > base_calls_split.vcf.gz +``` \ No newline at end of file diff --git a/docs/v4.0.0/Resources.md b/docs/v4.0.0/Resources.md new file mode 100644 index 00000000..25a76ce1 --- /dev/null +++ b/docs/v4.0.0/Resources.md @@ -0,0 +1,3 @@ +*page in progress* + +Use `git-lfs` to pull the resources. Currently only useful for `truvari anno trf` \ No newline at end of file diff --git a/docs/v4.0.0/Updates.md b/docs/v4.0.0/Updates.md new file mode 100644 index 00000000..350dbf01 --- /dev/null +++ b/docs/v4.0.0/Updates.md @@ -0,0 +1,181 @@ +# Truvari 4.0 +*March 13, 2023* + +As part of the GIAB TR effort, we have made many changes to Truvari's tooling to enable comparison of variants in TR regions down to 5bp. Additionally, in order to keep Truvari user friendly we have made changes to the UI. Namely, we've updated some default parameters, some command-line arguments, and some outputs. There are also a few new tools and how a couple of tools work has changed. Therefore, we decided to bump to a new major release. If you're using Truvari in any kind of production capacity, be sure to test your pipeline before moving to v4.0. + +* New `refine` command for refining benchmarking results. [Details](refine) +* `bench` + * [Unroll](bench#unroll) is now the default sequence comparison approach. + * New `--pick` parameter to control the number of matches a variant can participate in [details](bench#controlling-the-number-of-matches) + * The `summary.txt` is now named `summary.json` + * Outputs parameters to `params.json` + * Output VCFs are sorted, compressed, and indexed + * Ambiguous use of 'call' in outputs corrected to 'comp' (e.g. `tp-call.vcf.gz` is now `tp-comp.vcf.gz`) + * Renamed `--pctsim` parameter to `--pctseq` + * Fixed bug where FP/FN weren't getting the correct, highest scoring match reported + * Fixed bug where `INFO/Multi` wasn't being properly applied + * Fixed bug where variants spanning exactly one `--includebed` region were erroneously being counted. + * Removed parameters: `--giabreport`, `--gtcomp`,`--multimatch`, `--use-lev`, `--prog`, `--unroll` +* `collapse` + * Renamed `--pctsim` parameter to `--pctseq` + * Runtime reduction by ~40% with short-circuiting during `Matcher.build_match` + * Better output sorting which may allow pipelines to be a little faster. +* `vcf2df` + * More granular sizebins for `[0,50)` including better handling of SNPs + * `--multisample` is removed. Now automatically add all samples with `--format` + * key index column removed and replaced by chrom, start, end. Makes rows easier to read and easier to work with e.g. pyranges +* `anno` + * Simplified ui. Commands that work on a single VCF and can stream (stdin/stdout) no longer use `--input` but a positional argument. + * Added `addid` +* `consistency` + * Slight speed improvement + * Better json output format +* `segment` + * Added `--passonly` flag + * Changed UI, including writing to stdout by default + * Fixed END and 1bp DEL bugs, now adds N to segmented variants' REF, and info fields SVTYPE/SVLEN +* API + * Began a focused effort on improving re-usability of Truvari code. + * Entry point to run benchmarking programmatically with [Bench object](https://truvari.readthedocs.io/en/latest/truvari.html#bench). + * Better development version tracking. [details](https://github.com/ACEnglish/truvari/commit/4bbf8d9a5be3b6a3f935afbd3a9b323811b676a0) + * Improved developer documentation. See [readthedocs](https://truvari.readthedocs.io/) +* general + * msa2vcf now left-trims and decomposes variants into indels + * Functional tests reorganization + * Fix for off-by-one errors when using pyintervaltree. See [ticket](https://github.com/ACEnglish/truvari/issues/137) + * Removed progressbar and Levenshtein dependencies as they are no longer used. + +# Truvari 3.5 +*August 27, 2022* + +* `bench` + * `--dup-to-ins` flag automatically treats SVTYPE==DUP as INS, which helps compare some programs/benchmarks + * New `--unroll` sequence comparison method for `bench` and `collapse` ([details](bench#unroll)) +* Major `anno trf` refactor (TODO write docs) including: + * annotation of DEL is fixed (was reporting the ALT copy numbers, not the sample's copy numbers after incorporating the ALT + * allow 'denovo' annotation by applying any TRF annotations found, not just those with corresponding annotations +* New `anno grpaf` annotates vcf with allele frequency info for groups of samples +* New `phab` for variant harmonization ([details](../phab)) +* backend + * `truvari.entry_size` returns the length of the event in the cases where len(REF) == len(ALT) (e.g. SNPs entry_size is 1) + * New key utility for `truvari.build_anno_trees` +* general + * Float metrics written to the VCF (e.g. PctSizeSimilarity) are rounded to precision of 4 + * Nice colors in some `--help` with [rich](https://github.com/Textualize/rich/) +* `divide` + * output shards are now more easily sorted (i.e. `ls divide_result/*.vcf.gz` will return the shards in the order they were made) + * compression/indexing of sub-VCFs in separate threads, reducing runtime +* user issues + * Monomorphic reference ALT alleles no longer throw an error in `bench` ([#131](https://github.com/ACEnglish/truvari/issues/131)) + * `SVLEN Number=A` fix ([#132](https://github.com/ACEnglish/truvari/issues/132)) + +# Truvari 3.4 +*July 7, 2022* + +* Improved performance of `consistency` (see [#127](https://github.com/ACEnglish/truvari/pull/127)) +* Added optional json output of `consistency` report +* Allow GT to be missing, which is allowed by VCF format specification +* TRF now uses `truvari.entry_variant_type` instead of trying to use `pysam.VariantRecord.info["SVLEN"]` +directly which allows greater flexibility. +* vcf2df now parses fields with `Number=\d` (e.g. 2+), which is a valid description +* `truvari.seqsim` is now case insensitive (see [#128](https://github.com/ACEnglish/truvari/issues/128)) +* Collapse option to skip consolidation of genotype information so kept alleles are unaltered +* `truvari anno dpcnt --present` will only count the depths of non ./. variants +* New collapse annotation `NumConsolidate` records how many FORMATs were consolidated +* Official [conda](https://anaconda.org/bioconda/truvari) support + +# Truvari 3.3 +*May 25, 2022* + +* New utilities `vcf_ranges` and `make_temp_filename` +* New annotations `dpcnt` and `lcr` +* Fixed a bug in `truvari collapse --keep` that prevented the `maxqual` or `common` options from working +* Increased determinism for `truvari collapse` so that in cases of tied variant position the longer allele is returned. If the alleles also have the same length, they are sorted alphabetically by the REF +* New `truvari bench --extend` functionality. See [discussion](https://github.com/ACEnglish/truvari/discussions/99) for details + +# Truvari 3.2 +*Apr 1, 2022* + +* Removed `truvari.copy_entry` for `pysam.VariantRecord.translate` a 10x faster operation +* Faster `truvari collapse` ([@c8b319b](https://github.com/ACEnglish/truvari/commit/c8b319b0e717a9e342f52e4a5e927f154eeb0e4a)) +* When building `MatchResult` between variants with shared start/end positions, we save processing work by skipping haplotype creation and just compare REFs/ALTs directly. +* Updated documentation to reference the paper https://doi.org/10.1101/2022.02.21.481353 +* New `truvari anno density` for identifying regions with 'sparse' and 'dense' overlapping SVs ([details](https://github.com/spiralgenetics/truvari/wiki/anno#truvari-anno-density)) +* Better `bench` genotype reporting with `summary.txt` having a `gt_matrix` of Base GT x Comp GT for all Base calls' best, TP match. +* New `truvari anno bpovl` for intersecting against tab-delimited files ([details](https://github.com/spiralgenetics/truvari/wiki/anno#truvari-anno-bpovl)) +* New `truvari divide` command to split VCFs into independent parts ([details](https://github.com/ACEnglish/truvari/wiki/divide)) +* Replaced `--buffer` parameter with `--minhaplen` for slightly better matching specificity +* Bugfix - `truvari anno trf` no longer duplicates entries spanning multple parallelization regions +* Bugfix - `collapse` MatchId/CollapseId annotation wasn't working +* Bugfixes - from [wwliao](https://github.com/wwliao) ([@4dd9968](https://github.com/ACEnglish/truvari/commit/4dd99683912236f433166889bb0b5667e9fa936d) [@ef2cfb3](https://github.com/ACEnglish/truvari/commit/ef2cfb366b60a5af4671d65d3ed987b08da72227)) +* Bugfixes - Issues [#107](https://github.com/ACEnglish/truvari/issues/107), [#108](https://github.com/ACEnglish/truvari/issues/108) + +# Truvari 3.1 +*Dec 22, 2021* + +* `bench` now annotates FPs by working a little differently. See [[bench|bench#methodology]] for details. +* Recalibrated TruScore and new reciprocal overlap measurement for sequence resolved `INS` ([details](https://github.com/spiralgenetics/truvari/discussions/92)) +* Match objects are now usable via the SDK. See [#94](https://github.com/spiralgenetics/truvari/discussions/94) for an example of using Truvari programmatically +* `file_zipper` VCF iteration strategy (`GenomeTree` -> `RegionVCFIterator`) that improves speed, particularly when using `--includebed` +* `collapse` refactored to use Match object and for prettier code, cleaner output. +* `anno remap` now optionally adds `INFO` field of the location of the top N hits. +* An experimental tool `truvari segment` added to help SV association analysis. +* `vcf2df` now supports pulling `FORMAT` fields from multiple samples. +* `vcf2df` now adds `('_ref', '_alt')`, or `('_ref', '_het', '_hom')` for `INFO,Number=[R|G]` fields, respectively. +* Improved documentation, including http://truvari.readthedocs.io/ for developers. +* Increasing/diversifying test coverage exposed minor bugs which were fixed. +* `bench --no-ref --cSample` bug fixes. +* Minor usability feature implemented in `help_unknown_cmd`. + +# Truvari 3.0 +*Sep 15, 2021* + +As Truvari's adoption and functionality grows, we decided to spend time working on sustainability and performance of the tool. Multiple [Actions](https://github.com/spiralgenetics/truvari/actions) for CI/CD have been added. Many components have been refactored for speed, and other 'cruft' code has been removed. Some of these changes (particularly the switch to using edlib for sequence similarity) affects the results. Therefore, we've bumped to a new major release version. + +* Working on speed improvements +* Added edlib as the default when calculating pctseq_sim, keeping Levenstein as an option (`--use-lev`). +* `truvari bench` summary's gt_precision/gt_recall are replaced by gt_concordance, which is just the percent of TP-comp calls with a concordant genotype. `--no-ref` has better functionality. `--giabreport` is different. +* Added `—keep common` to `truvari collapse`, which allows one to choose to keep the allele with the highest MAC. +* `truvari collapse --hap` wasn't working correctly. The assumptions about the calls being phased wasn't being +properly used (e.g. don't collapse 1|1) and the NumCollapsed was being populated before the single-best +match was chosen. The latter is a reporting problem, but the former had an effect on the results with +~3% of collapsed calls being mis-collapsed. +* `truvari anno trf` is now faster and simpler in its approach and whats reported.. and hopefully more useful. +* `truvari anno grm` has min_size and regions arguments added. +* truv2df has become `truvari vcf2df` where the default is vcf conversion with options to run on a `truvari bench` output directory. It also allows a specific sample to be parsed with `--format` and better Number=A handling. +* NeighId added to `truvari anno numneigh`, which works like bedtools cluster. +* The method af_calc now makes MAC/AC. +* Added 'partial' to `truvari anno remap`. +* Added `truvari anno svinfo`. +* Removed `truvari stats` as `truvari vcf2df` is better and began building [community-driven summaries](https://github.com/spiralgenetics/truvari/discussions/categories/vcf2df-recipes). +* Ubiquitous single version. +* Added a Dockerfile and instructions for making a Truvari docker container. +* Code and repository cleaning. +* Github actions for automated pylint, testing, and releases to pypi. +* Preserving per-version documentation from the wiki in `docs/`. + + +# Truvari 2.1 +*Jan 27, 2021* + +We've expanded and improved Truvari's [annotations](https://github.com/spiralgenetics/truvari/wiki/anno). We've added an [SV "collapsing" tool](https://github.com/spiralgenetics/truvari/wiki/collapse). And we've added a way to [turn VCFs into pandas DataFrames](https://github.com/spiralgenetics/truvari/wiki/truv2df) easily for downstream analysis/QC. + +# Truvari 2.0 +*May 14, 2020* + +After performing a drastic code refactor, we were able to create several helper methods from Truvari's core functionality around SV comparisons and VCF manipulations. This reusable code gave us an opportunity to create tools relevant for SV analysis. + +Truvari now contains multiple subcommands. In addition to the original benchmarking functionality (`truvari bench`), Truvari can generate SV relevant summary statistics, compute consistency of calls within VCFs, and we've begun to develop annotations for SVs. Details on these tools are on the [WIKI](https://github.com/spiralgenetics/truvari/wiki). + +We are committed to continually improving Truvari with the hopes of advancing the study and analysis of structural variation. + +# Truvari 1.3 +*September 25th, 2019* + +Truvari has some big changes. In order to keep up with the o deement of Python 2.7 https://pythonclock.org/ +We're now only supporting Python 3. + +Additionally, we now package Truvari so it and its dependencies can be installed directly. See Installation +below. This will enable us to refactor the code for easier maintenance and reusability. + +Finally, we now automatically report genotype comparisons in the summary stats. \ No newline at end of file diff --git a/docs/v4.0.0/anno.md b/docs/v4.0.0/anno.md new file mode 100644 index 00000000..beb60812 --- /dev/null +++ b/docs/v4.0.0/anno.md @@ -0,0 +1,468 @@ + +Truvari annotations: +* [gcpct](anno#truvari-anno-gcpct) - GC Percent +* [gtcnt](anno#truvari-anno-gtcnt) - Genotype Counts +* [trf](anno#truvari-anno-trf) - Tandem Repeats +* [grm](anno#truvari-anno-grm) - Mappability +* [repmask](anno#truvari-anno-repmask) - Repeats +* [remap](anno#truvari-anno-remap) - Allele Remapping +* [hompct](anno#truvari-anno-hompct) - Homozygous Percent +* [numneigh](anno#truvari-anno-numneigh) - Number of Neighbors +* [svinfo](anno#truvari-anno-svinfo) - SVINFO Fields +* [bpovl](anno#truvari-anno-bpovl) - Annotation Intersection +* [density](anno#truvari-anno-density) - Call Density +* [dpcnt](anno#truvari-anno-dpcnt) - Depth (DP) and Alt-Depth (AD) Counts +* [lcr](anno#truvari-anno-lcr) - Low-complexity Regions +* [grpaf](anno#truvari-anno-grpaf) - Sample Group Allele-Frequency Annotations + +# truvari anno gcpct + +This will add an INFO tag `GCPCT` to each element in a VCF of the GC percent of the call's sequence. + +For deletions, this is the GC percent of the reference range of the call. For insertions, the ALT sequence is analyzed. +``` +usage: gcpct [-h] [-o OUTPUT] -r REFERENCE [input] + +Annotates GC content of SVs + +positional arguments: + input VCF to annotate (stdin) + +options: + -h, --help show this help message and exit + -o OUTPUT, --output OUTPUT + Output filename (stdout) + -r REFERENCE, --reference REFERENCE + Reference fasta +``` + +# truvari anno gtcnt +This will add an INFO tag `GTCNT` to each element in a VCF with the count of genotypes found across all samples. The value is a list of Counts of genotypes for the allele across all samples (UNK, REF, HET, HOM). This is most useful for pVCFs. + +``` +usage: gtcnt [-h] [-o OUTPUT] [input] + +Annotates GTCounts of alleles + +positional arguments: + input VCF to annotate (stdin) + +options: + -h, --help show this help message and exit + -o OUTPUT, --output OUTPUT + Output filename (stdout) +``` + +# truvari anno trf +Adds a tandem-repeat annotation to each entry in your VCF. + +Recently refactored in v3.5-dev. Documentation in progress +``` +usage: trf [-h] -i INPUT [-o OUTPUT] [-e EXECUTABLE] [-T TRF_PARAMS] -r REPEATS -f REFERENCE [-s MOTIF_SIMILARITY] + [-m MIN_LENGTH] [-R] [--no-estimate] [-C CHUNK_SIZE] [-t THREADS] [--debug] + +Intersect vcf with reference tandem repeats and annotate +variants with the best fitting repeat motif and its copy number +relative to the reference + +options: + -h, --help show this help message and exit + -i INPUT, --input INPUT + VCF to annotate + -o OUTPUT, --output OUTPUT + Output filename (stdout) + -e EXECUTABLE, --executable EXECUTABLE + Path to tandem repeat finder (trf409.linux64) + -T TRF_PARAMS, --trf-params TRF_PARAMS + Default parameters to send to trf (3 7 7 80 5 40 500 -h -ngs) + -r REPEATS, --repeats REPEATS + Reference repeat annotations + -f REFERENCE, --reference REFERENCE + Reference fasta file + -s MOTIF_SIMILARITY, --motif-similarity MOTIF_SIMILARITY + Motif similarity threshold (0.9) + -m MIN_LENGTH, --min-length MIN_LENGTH + Minimum size of entry to annotate (50) + -R, --regions-only Only write variants within --repeats regions (False) + --no-estimate Skip INS estimation procedure and run everything through TRF. (False) + -C CHUNK_SIZE, --chunk-size CHUNK_SIZE + Size (in mbs) of reference chunks for parallelization (5) + -t THREADS, --threads THREADS + Number of threads to use (1) + --debug Verbose logging +``` + +# truvari anno grm + +For every SV, we create a kmer over the the upstream and downstream reference and alternate breakpoints. +We then remap that kmer to the reference genome and report alignment information. +This does not alter the VCF traditional annotations, but instead will create a pandas +DataFrame and save it to a joblib object. + +There are four queries made per-SV. For both reference (r), alternate (a) we create upstream (up) and downstream (dn) kmers. +So the columns are all prefixed with one of "rup_", "rdn_", "aup_", "adn_". + +In the alignment information per-query, there are three 'hit' counts: +- nhits : number of query hits +- dir_hits : direct strand hit count +- com_hits : compliment strand hit count + +The rest of the alignment information is reported by average (avg), maximum (max), and minimum (min) + +The suffixes are: +- q : mapping quality score of the hits +- ed : edit distance of the hits +- mat : number of matches +- mis : number of mismatches + +For example, "aup_avg_q", is the alternate's upstream breakend kmer's average mapping quality score. + +``` +usage: grm [-h] -i INPUT -r REFERENCE [-R REGIONS] [-o OUTPUT] [-k KMERSIZE] [-m MIN_SIZE] [-t THREADS] [--debug] + +Maps graph edge kmers with BWA to assess Graph Reference Mappability + +options: + -h, --help show this help message and exit + -i INPUT, --input INPUT + Input VCF + -r REFERENCE, --reference REFERENCE + BWA indexed reference + -R REGIONS, --regions REGIONS + Bed file of regions to parse (None) + -o OUTPUT, --output OUTPUT + Output dataframe (results.jl) + -k KMERSIZE, --kmersize KMERSIZE + Size of kmer to map (50) + -m MIN_SIZE, --min-size MIN_SIZE + Minimum size of variants to map (25) + -t THREADS, --threads THREADS + Number of threads (1) + --debug Verbose logging +``` + +# truvari anno repmask + +``` +usage: repmask [-h] -i INPUT [-o OUTPUT] [-e EXECUTABLE] [-m MIN_LENGTH] [-M MAX_LENGTH] [-t THRESHOLD] [-p PARAMS] [-T THREADS] + [--debug] + + Wrapper around RepeatMasker to annotate insertion sequences in a VCF + +options: + -h, --help show this help message and exit + -i INPUT, --input INPUT + VCF to annotate (None) + -o OUTPUT, --output OUTPUT + Output filename (/dev/stdout) + -e EXECUTABLE, --executable EXECUTABLE + Path to RepeatMasker (RepeatMasker) + -m MIN_LENGTH, --min-length MIN_LENGTH + Minimum size of entry to annotate (50) + -M MAX_LENGTH, --max-length MAX_LENGTH + Maximum size of entry to annotate (50000) + -t THRESHOLD, --threshold THRESHOLD + Threshold for pct of allele covered (0.8) + -p PARAMS, --params PARAMS + Default parameter string to send to RepeatMasker (-pa {threads} -qq -e hmmer -species human -lcambig + -nocut -div 50 -no_id -s {fasta}) + -T THREADS, --threads THREADS + Number of threads to use (1) + --debug Verbose logging +``` + +# truvari anno remap + +Taking the Allele’s sequence, remap it to the reference and annotate based on the closest alignment. + +![](https://github.com/spiralgenetics/truvari/blob/develop/imgs/remap_example.png) + +``` +usage: remap [-h] -r REFERENCE [-o OUTPUT] [-m MINLENGTH] [-t THRESHOLD] [-d DIST] [-H HITS] [--debug] [input] + +Remap VCF'S alleles sequence to the reference to annotate REMAP + +- novel : Allele has no hits in reference +- tandem : Allele's closest hit is within len(allele) bp of the SV's position +- interspersed : Allele's closest hit is not tandem +- partial : Allele only has partial hit(s) less than --threshold + +Which alleles and alignments to consider can be altered with: +- --minlength : minimum SV length to considred (50) +- --dist : For deletion SVs, do not consider alignments that hit within Nbp of the SV's position +(a.k.a. alignments back to the source sequence) (10) +- --threshold : Minimum percent of allele's sequence used by alignment to be considered (.8) + +positional arguments: + input Input VCF (/dev/stdin) + +options: + -h, --help show this help message and exit + -r REFERENCE, --reference REFERENCE + BWA indexed reference + -o OUTPUT, --output OUTPUT + Output VCF (/dev/stdout) + -m MINLENGTH, --minlength MINLENGTH + Smallest length of allele to remap (50) + -t THRESHOLD, --threshold THRESHOLD + Threshold for pct of allele covered to consider hit (0.8) + -d DIST, --dist DIST Minimum distance an alignment must be from a DEL's position to be considered (10)) + -H HITS, --hits HITS Report top hits as chr:start-end.pct (max 0) + --debug Verbose logging +``` +# truvari anno hompct + +``` +usage: hompct [-h] -i INPUT [-o OUTPUT] [-b BUFFER] [-m MINANNO] [-M MAXGT] [-c MINCOUNT] [--debug] + +Calcluate the the Hom / (Het + Hom) of variants in the region of SVs +Requires the VCF to contain SVs beside SNPs/Indels + +options: + -h, --help show this help message and exit + -i INPUT, --input INPUT + Compressed, indexed VCF to annotate + -o OUTPUT, --output OUTPUT + Output filename (stdout) + -b BUFFER, --buffer BUFFER + Number of base-pairs up/dn-stream to query (5000) + -m MINANNO, --minanno MINANNO + Minimum size of event to annotate (50) + -M MAXGT, --maxgt MAXGT + Largest event size to count for genotyping (1) + -c MINCOUNT, --mincount MINCOUNT + Minimum number of genotyping events to report HOMPCT (0) + --debug Verbose logging +``` + +# truvari anno numneigh + +``` +usage: numneigh [-h] [-o OUTPUT] [-r REFDIST] [-s SIZEMIN] [--passonly] [--debug] [input] + +For every call within size boundaries, +Add NumNeighbors info field of how many calls are within the distance +Add NeighId clustering field in the same chained neighborhood +For example, +:: + -- is a call, refdist is 2 + - - - - - - + nn: 1 2 1 0 1 1 + id: 0 0 0 1 2 2 + +positional arguments: + input VCF to annotate + +options: + -h, --help show this help message and exit + -o OUTPUT, --output OUTPUT + Output vcf (stdout) + -r REFDIST, --refdist REFDIST + Max reference location distance (1000) + -s SIZEMIN, --sizemin SIZEMIN + Minimum variant size to consider for annotation (50) + --passonly Only count calls with FILTER == PASS + --debug Verbose logging +``` + +# truvari anno svinfo + +Uses `truvari.entry_size` and `truvari.entry_variant_type` on entries >= `args.minsize` to add 'SVLEN' and ‘SVTYPE’ annotations to a VCF’s INFO. + +How SVLEN is determined: +- Starts by trying to use INFO/SVLEN +- If SVLEN is unavailable and ALT field is an SV (e.g. \, \, etc), use abs(vcf.start - vcf.end). The INFO/END tag needs to be available, especially for INS. +- Otherwise, return the size difference of the sequence resolved call using abs(len(vcf.REF) - len(str(vcf.ALT[0]))) + +How SVTYPE is determined: +- Starts by trying to use INFO/SVTYPE +- If SVTYPE is unavailable, infer if entry is a insertion or deletion by looking at the REF/ALT sequence size differences +- If REF/ALT sequences are not available, try to parse the \, \, etc from the ALT column. +- Otherwise, assume 'UNK' + +``` +usage: svinfo [-h] [-o OUTPUT] [-m MINSIZE] [input] + +Adds SVTYPE and SVLEN INFO fields + +positional arguments: + input VCF to annotate (stdin) + +options: + -h, --help show this help message and exit + -o OUTPUT, --output OUTPUT + Output filename (stdout) + -m MINSIZE, --minsize MINSIZE + Minimum size of entry to annotate (50) +``` + +# truvari anno bpovl + +After turning a tab-delimited annotation file into an IntervalTree, intersect the start/end and overlap of SVs. +The output is a light-weight pandas DataFrame saved with joblib. The columns in the output are: + +- vcf_key : Variant key from `truvari.entry_to_key` +- intersection : Type of intersection between the SV and the annotation + - start_bnd - SV's start breakpoints hits the annotation + - end_bnd - SV's end breakpoint hits the annotation + - overlaps - Annotation's start/end boundaries are completely within the SV + - contains - Annotation's start/end boundaries span the entire SV +- anno_key : Annotation file's line index + +The idea with this tool is to annotate variants against tab-delimited files, especially when there's a 1-to-N variant to annotations. This tool is useful when used in conjunction with `truvari vcf2df` and pandas DataFrames. + +For example, if we have a VCF of SVs and a GTF of genes/gene features from Ensmbl. Any SV may intersect multiple features, which doesn't lend itself well to directly annotating the VCF's INFO. After using `bpovl`, we'll use Truvari to convert the SVs to a DataFrame. + +```bash +truvari anno bpovl -i variants.vcf.gz -a genes.gtf.gz -o anno.jl -p gff +truvari vcf2df variants.vcf.gz variants.jl +``` + +We can then treat the files similar to a database and do queries and joins to report which variants intersect which annotations. + +```python +import joblib +from gtfparse import read_gtf +variants = joblib.load("variants.jl") +genes = read_gtf("genes.gtf.gz") +annos = joblib.load("anno.jl") +to_check = annos.iloc[0] + +print(to_check) +# vcf_key chr20:958486-958487.A +# intersection start_bnd +# anno_key 11 + +print(variants.loc[to_check['vcf_key']]) +# id None +# svtype INS +# ... etc + +print(annos.loc[to_check['anno_key']]) +# seqname chr20 +# source ensembl_havana +# feature exon +# start 958452 +# ... etc +``` + +Similar to tabix, `bpovl` has presets for known file types like bed and gff. But any tab-delimited file with sequence/chromosome, start position, and end position can be parsed. Just set the "Annotation File Arguments" to the 0-based column indexes. For example, a bed file +has arguments `-s 0 -b 1 -e 2 -c #`. + +``` +usage: bpovl [-h] -a ANNO -o OUTPUT [--sizemin SIZEMIN] [--spanmax SPANMAX] [-p {bed,gff}] [-c COMMENT] [-s SEQUENCE] [-b BEGIN] + [-e END] [-1] + [input] + +Creates intersection of features in an annotation file with SVs' breakpoints and overlap + +positional arguments: + input VCF to annotate (stdin) + +options: + -h, --help show this help message and exit + -a ANNO, --anno ANNO Tab-delimited annotation file + -o OUTPUT, --output OUTPUT + Output joblib DataFrame + --sizemin SIZEMIN Minimum size of variant to annotate (50) + --spanmax SPANMAX Maximum span of SVs to annotate (50000) + +Annotation File Arguments: + -p {bed,gff}, --preset {bed,gff} + Annotation format. This option overwrites -s, -b, -e, -c and -1 (None) + -c COMMENT, --comment COMMENT + Skip lines started with character. (#) + -s SEQUENCE, --sequence SEQUENCE + Column of sequence/chromosome name. (0) + -b BEGIN, --begin BEGIN + Column of start chromosomal position. (1) + -e END, --end END Column of end chromosomal position. (2) + -1, --one-based The position in the anno file is 1-based rather than 0-based. (False) +``` +# truvari anno density +Partitions a `--genome` into `--windowsize` regions and count how many variants overlap. Annotate +regions with no variants as 'sparse' and with greater than or equal to (mean + `--threshold` * standard +deviation) number of variants as 'dense'. Outputs a joblib DataFrame with columns +`chrom, start, end, count, anno`. + +``` +usage: density [-h] -g GENOME -o OUTPUT [-m MASK] [-w WINDOWSIZE] [-t THRESHOLD] [input] + +Identify 'dense' and 'sparse' variant windows of the genome + +positional arguments: + input Input VCF (/dev/stdin) + +options: + -h, --help show this help message and exit + -g GENOME, --genome GENOME + Genome bed file + -o OUTPUT, --output OUTPUT + Output joblib DataFrame + -m MASK, --mask MASK Mask bed file + -w WINDOWSIZE, --windowsize WINDOWSIZE + Window size (10000) + -t THRESHOLD, --threshold THRESHOLD + std for identifying 'dense' regions (3) +``` + +# truvari anno dpcnt + +For multi-sample VCFs, it is often useful to have summarized depth (DP) information across samples per-variant. This adds a `INFO/DPCNT` with counts of how many samples have `FORMAT/DP` for each of the user-defined bins. Bins are incremented using `bisect` e.g. `pos = bisect.bisect(bins, dp); bins[pos] += 1; + +``` +usage: dpcnt [-h] [-b BINS] [--no-ad] [-p] [-o OUTPUT] [input] + +Quick utility to count how many samples have >= Nx coverage per-variant + +positional arguments: + input VCF to annotate (stdin) + +options: + -h, --help show this help message and exit + -b BINS, --bins BINS Coverage bins to bisect left the counts (0,5,10,15) + --no-ad Skip adding ADCNT bins + -p, --present Only count sites with present (non ./.) genotypes + -o OUTPUT, --output OUTPUT + Output filename (stdout) +``` + +# truvari anno lcr + +``` +usage: lcr [-h] [-o OUTPUT] [input] + +Annotate low complexity region entropy score for variants +Credit: https://jszym.com/blog/dna_protein_complexity/ + +positional arguments: + input VCF to annotate (stdin) + +options: + -h, --help show this help message and exit + -o OUTPUT, --output OUTPUT + Output filename (stdout) +``` + +# truvari anno grpaf + +Add INFO tags of allele frequency annotations for groups of samples. For every group in `--labels` tab-delimited file, calculate the AF,MAF,ExcHet,HWE,MAC,AC for the samples in the group. Adds INFO tags with suffix of the group identifier (e.g. `AF_EAS`). `--strict` will hard fail if there are samples in the `--labels` not present in the vcf header. + +``` +usage: grpaf [-h] [-o OUTPUT] -l LABELS [-t TAGS] [--strict] [--debug] [input] + +Add allele frequency annotations for subsets of samples + +positional arguments: + input VCF to annotate + +options: + -h, --help show this help message and exit + -o OUTPUT, --output OUTPUT + Output filename (stdout) + -l LABELS, --labels LABELS + Tab-delimited file of sample and group + -t TAGS, --tags TAGS Comma-separated list of tags to add from AF,MAF,ExcHet,HWE,MAC,AC,AN (all) + --strict Exit if sample listed in labels is not present in VCF (False) + --debug Verbose logging +``` \ No newline at end of file diff --git a/docs/v4.0.0/bench.md b/docs/v4.0.0/bench.md new file mode 100644 index 00000000..d97096a3 --- /dev/null +++ b/docs/v4.0.0/bench.md @@ -0,0 +1,278 @@ + +Quick start +=========== +Run this command where base is your 'truth set' SVs and comp is the comparison set of SVs. +```bash +truvari bench -b base_calls.vcf -c comp_calls.vcf -o output_dir/ +``` + +Matching Parameters +=================== +Picking matching parameters can be more of an art than a science. It really depends on the precision of your callers and the tolerance you wish to allow them such that it is a fair comparison. + +For example, depth of coverage callers (such as CNVnator) will have very 'fuzzy' boundaries, and don't report the exact deleted sequence but only varying regions. So thresholds of `pctseq=0`, `pctsize=.5`, `pctovl=.5`, `refdist=1000` may seem fair. + +[BioGraph](https://github.com/spiralgenetics/biograph) and many long-read callers report precise breakpoints and full alternate allele sequences. When benchmarking those results, we want to ensure our accuracy by using the stricter default thresholds. + +If you're still having trouble picking thresholds, it may be beneficial to do a few runs of Truvari bench over different values. Start with the strict defaults and gradually increase the leniency. From there, you can look at the performance metrics and manually inspect differences between the runs to find out what level you find acceptable. Truvari is meant to be flexible for comparison. More importantly, Truvari helps one clearly report the thresholds used for reproducibility. + +Here is a rundown of each matching parameter. +| Parameter | Default | Definition | +|------------|---------|------------| +| refdist | 500 | Maximum distance comparison calls must be within from base call's start/end | +| pctseq | 0.7 | Edit distance ratio between the REF/ALT haplotype sequences of base and
comparison call. See "Comparing Sequences of Variants" below. | +| pctsize | 0.7 | Ratio of min(base_size, comp_size)/max(base_size, comp_size) | +| pctovl | 0.0 | Ratio of two calls' (overlapping bases)/(longest span) | +| typeignore | False | Types don't need to match to compare calls. | + +Below are matching parameter diagrams to illustrate (approximately) how they work. + +``` + █ = Deletion ^ = Insertion + +--refdist REFDIST (500) + Max reference location distance + + ACTGATCATGAT + |--████--| + █████ + + Calls are within reference distance of 2 + +--pctsize PCTSIZE (0.7) + Min pct allele size similarity + + ACTGATCATGA sizes + █████ -> 5bp + ████ -> 4bp + + variants have 0.8 size similarity + + +--pctovl PCTOVL (0.0) + Min pct reciprocal overlap + + ACTGATCATGA ranges + █████ [2,7) + ████ [4,8) + + variants have 0.6 reciprocial overlap + + +--pctseq PCTSEQ (0.7) + Min percent allele sequence similarity + + A-CTG-ACTG + ^ ^ haplotypes + | └ACTG -> CTGACTGA + └CTGA -> CTGACTGA + + haplotypes have 100% sequence similarity +``` + +Outputs +======= +Truvari bench writes the following files to the `--output` directory. +| File | Description | +|----------------|---------------------------------------------| +| tp-base.vcf.gz | True positive calls form the base VCF | +| tp-comp.vcf.gz | True positive calls from the comparison VCF | +| fp.vcf.gz | False positive calls from comparison | +| fn.vcf.gz | False negative calls from base | +| summary.json | Json output of performance stats | +| params.json | Json output of parameters used | +| log.txt | Run's log | + +summary.json +------------ +Stats generated by benchmarking are written to `summary.json`. + +| Metric | Definition | +|----------------|------------------------------------------------------------| +| TP-base | Number of matching calls from the base vcf | +| TP-comp | Number of matching calls from the comp vcf | +| FP | Number of non-matching calls from the comp vcf | +| FN | Number of non-matching calls from the base vcf | +| precision | TP-comp / (TP-comp + FP) | +| recall | TP-base / (TP-base + FN) | +| f1 | 2 * ((recall * precision) / (recall + precision)) | +| base cnt | Number of calls in the base vcf | +| comp cnt | Number of calls in the comp vcf | +| TP-comp_TP-gt | TP-comp with genotype match | +| TP-comp_FP-gt | TP-comp without genotype match | +| TP-base_TP-gt | TP-base with genotype match | +| TP-base_FP-gt | TP-base without genotype match | +| gt_concordance | TP-comp_TP-gt / (TP-comp_TP-gt + TP-comp_FP-gt) | +| gt_matrix | Base GT x Comp GT Matrix of all Base calls' best, TP match | + +The `gt_matrix` is a table. For example: +```json +"gt_matrix": { + "(0, 1)": { + "(0, 1)": 500, + "(1, 1)": 10 + }, + "(1, 1)": { + "(1, 1)": 800, + "(0, 1)": 20 + } + } +``` +Represents -> +``` +comp (0,1) (1,1) +base +(0,1) 500 10 +(1,1) 20 800 +``` + + +Added annotations +----------------- +The output vcfs are annotated with INFO fields described above and then sorted, compressed, and indexed inside of the output directory. + +| Anno | Definition | +|-------------------|-----------------------------------------------------------------------------------------------------------------| +| TruScore | Truvari score for similarity of match. `((pctseq + pctsize + pctovl) / 3 * 100)` | +| PctSeqSimilarity | Pct sequence similarity between this variant and its closest match | +| PctSizeSimilarity | Pct size similarity between this variant and its closest match | +| PctRecOverlap | Percent reciprocal overlap percent of the two calls | +| StartDistance | Distance of the base call's start from comparison call's start | +| EndDistance | Distance of the base call's end from comparison call's end | +| SizeDiff | Difference in size of base and comp calls | +| GTMatch | Base/comp calls' Genotypes match | +| MatchId | Id to help tie base/comp calls together {chunkid}.{baseid}.{compid} See [[MatchIds wiki\|MatchIds]] for details. | + +Comparing Sequences of Variants +=============================== + +Truvari has implemented two approaches to compare variant sequences. The default comparison is called 'unroll'. Optionally, a `--reference` can be provided and Truvari will use the reference context of a pair of variants for comparison. + +## Reference context +For the reference context method, consider a hypothetical tandem repeat expansion of the reference sequence 'AB'. Here, we'll represent the 'insertion' sequence as lower-case 'ab', though it should be considered equivalent to 'AB'. Three equally valid descriptions of this +variant would be: + +```text +#POS INS Haplotype + 0 ab abAB + 1 ba AbaB + 2 ab ABab +``` + +Therefore, to compare the sequence similarity, Truvari builds the haplotypes over the range of a pair of calls' +`min(starts):max(ends)` before making the the sequence change introduced by the variants. In python, this line +looks like: + +``` python +hap1_seq = ref.get_seq(a1_chrom, start + 1, a1_start).seq + a1_seq + ref.get_seq(a1_chrom, a1_end + 1, end).seq +``` + +Where `a1_seq1` is the longer of the REF or ALT allele. + +## Unroll +The method of giving a pair of calls the same reference context can be achieved using an 'unroll' method. For a formal description, see [this gist](https://gist.github.com/ACEnglish/1e7421c46ee10c71bee4c03982e5df6c). + +The main idea is that in order to move variants upstream/downstream, the reference sequence flanking the variant will need to be moved downstream/upstream respectively. Or, to say this another way, we can think of the alternate sequences as being circular instead of linear. This means that in order to move the variant e.g. 1bp downstream for an INS, we could remove the first base from the ALT and append it to the end. So in our 'ab' example above, we only need to unroll the insertion at a position by the distance between it and another variant e.g. the INS `ab` at POS 2 becomes identical to the INS `ba` at POS 1 by rolling `2-1 = 1` bases from the start to the end. + +This unroll method has a number of benefits and a couple of considerations. +* Unroll does not need a `--reference` for comparison, which saves I/O time. +* In the limited testing performed so far, unroll increase the number of matching SVs +* Unroll seems to decrease the number of 'suspect' matches in smaller size regimes +* The pattern between PctSizeSimilarity and PctSeqSimilarity is simpler + +## SVs without sequences + +If the base or comp vcfs do not have sequence resolved calls (e.g. ``, simply set `--pctseq=0` to turn off +sequence comparison. The `--reference` does not need to be provided when not using sequence comparison. + +Controlling the number of matches +================================= + +How many matches a variant is allowed to participate in is controlled by the `--pick` parameter. The available pickers are `single`, `ac`, and `multi`. + +* `single` (the default option) allows each variant to participate in up to one match. +* `ac` uses the genotype allele count to control how many matches a variant can have. This means a homozygous alternate variant can participate in two matches (its GT is 1/1 so AC=2). A heterozygous variant can only participate in one match (GT 0/1, AC=1). And, a homozygous reference variant cannot be matched. Note that missing genotypes are considered reference alleles and do not add to the AC e.g. (GT ./1, AC=1). +* `multi` variants can participate in all matches available. + +As an example, imagine we have three variants in a pVCF with two samples we want to compare. + +``` +CHROM POS ID REF ALT base comp +chr20 17785968 ID1 A ACGCGCGCGCG 1/1 1/0 +chr20 17785968 ID2 A ACGCGCGCGCGCG 0/0 0/1 +chr20 17785969 ID3 C CGCGCGCGCGCGC 0/0 1/1 +``` + +To compare samples inside the same vcf, we would use the command: +```bash +truvari bench -b input.vcf.gz -c input.vcf.gz -o output/ --bSample base --cSample comp --no-ref a +``` + +This VCF makes different results depending on the `--pick` parameter + +| Parameter | ID1 State | ID2 State | ID3 State | +|-----------|-----------|-----------|-----------| +| single | TP | FP | FP | +| ac | TP | TP | FP | +| multi | TP | TP | TP | + +--dup-to-ins +============ + +Most SV benchmarks only report DEL and INS SVTYPEs. The flag `--dup-to-ins` will interpret SVs with SVTYPE == DUP to SVTYPE == INS. Note that DUPs generally aren't sequence resolved (i.e. the ALT isn't a sequence) like INS. Therefore, `--dup-to-ins` typically should be used without sequence comparison via `--pctseq 0` + +--sizemin and --sizefilt +======================== + +`--sizemin` is the minimum size of a base call to be considered. + +`--sizefilt` is the minimum size of a comparison call that will be matched to base calls. It should +be less than `sizemin` for edge case variants. + +For example: `sizemin` is 50 and `sizefilt` is 30. A 50bp base call is 98% similar to a 49bp comparison +call at the same position. + +These two calls should be considered matching. If we instead removed comparison calls less than `sizemin`, +we'd incorrectly classify the 50bp base call as a false negative. + +This does have the side effect of artificially inflating specificity. If that same 49bp call in the +above were below the similarity threshold, it would not be classified as a FP due to the `sizemin` +threshold. So we're giving the call a better chance to be useful and less chance to be detrimental +to final statistics. + +Include Bed & VCF Header Contigs +================================ + +If an `--includebed` is provided, only base and comp calls contained within the defined regions are used +for comparison. This is similar to pre-filtering your base/comp calls using: + +```bash +(zgrep "#" my_calls.vcf.gz && bedtools intersect -u -a my_calls.vcf.gz -b include.bed) | bgzip > filtered.vcf.gz +``` + +with the exception that Truvari requires the start and the end to be contained in the same includebed region +whereas `bedtools intersect` does not. + +If an `--includebed` is not provided, the comparison is restricted to only the contigs present in the base VCF +header. Therefore, any comparison calls on contigs not in the base calls will not be counted toward summary +statistics and will not be present in any output vcfs. + +Extending an Include Bed +------------------------ +The option `--extend` extends the regions of interest (set in `--includebed` argument) by the given number of bases on each side, allowing base variants to match comparison variants that are just outside of the original region. If a comparison variant is in the extended regions it can potentially match a base variant that is in the original regions turning it to TP. Comparison variants in the extended regions that don't have a match are not counted as FP. This strategy is similar to the one implemented for size matching where only the base variants longer than sizemin (equal to 50 by default) are considered, but they are allowed to match shorter comparison variants sizefilt (30bp by default) or longer. + +See this [discussion](https://github.com/ACEnglish/truvari/discussions/99)for details. + +Methodology +=========== +Here is a high-level pseudocode description of the steps Truvari bench conducts to compare the two VCFs. +``` +* zip the Base and Comp calls together in sorted order +* create chunks of all calls overlapping within ±`--chunksize` basepairs +* make a |BaseCall| x |CompCall| match matrix for each chunk +* build a Match for each call pair in the chunk - annotate as TP if >= all thresholds +* if the chunk has no Base or Comp calls +** return them all as FNs/FPs +* use `--pick` method to sort and annotate variants with their best match +``` +![](https://github.com/spiralgenetics/truvari/blob/develop/imgs/TruvariBenchMethod.png) diff --git a/docs/v4.0.0/collapse.md b/docs/v4.0.0/collapse.md new file mode 100644 index 00000000..aa29a74d --- /dev/null +++ b/docs/v4.0.0/collapse.md @@ -0,0 +1,144 @@ +`collapse` is Truvari's approach to SV merging. After leveraging `bcftools` to merge VCFs, `truvari collapse` can then iterate over the calls and create clusters of SVs that match over the [provided thresholds](https://github.com/spiralgenetics/truvari/wiki/bench#matching-parameters). This is also useful when removing potentially redundant calls within a single sample. + +Example +======= +To start, we merge multiple VCFs (each with their own sample) and ensure there are no multi-allelic entries via: +```bash +bcftools merge -m none one.vcf.gz two.vcf.gz | bgzip > merge.vcf.gz +``` + +This will `paste` SAMPLE information between vcfs when calls have the exact same chrom, pos, ref, and alt. +For example, consider two vcfs: + + >> one.vcf: + chr1 1 ... GT 0/1 + chr1 5 ... GT 1/1 + >> two.vcf: + chr1 1 ... GT 1/1 + chr1 7 ... GT 0/1 + +`bcftools merge` creates: + + >> merge.vcf: + chr1 1 ... GT 0/1 1/1 + chr1 5 ... GT 1/1 ./. + chr1 7 ... GT ./. 0/1 + +This VCF can then be collapsed to allow 'fuzzier' matching than the exact merge just performed. + +```bash +truvari collapse -i merge.vcf.gz -o truvari_merge.vcf -c truvari_collapsed.vcf -f /path/to/reference.fa +``` + +For example, if we collapsed our example merge.vcf by matching any calls within 3bp, we'd create: + + >> truvari_merge.vcf + chr1 1 ... GT 0/1 1/1 + chr1 5 ... GT 1/1 0/1 + >> truvari_collapsed.vcf + chr1 7 ... GT ./. 0/1 + +--choose behavior +================= +When collapsing, the default `--choose` behavior is to take the first variant from a cluster to +be written to the output while the others will be placed in the collapsed output. +Other choosing options are `maxqual` (the call with the highest quality score) or `common` (the call with the highest minor allele count). + +Samples with no genotype information in the kept variant will be filled by the first +collapsed variant containing genotype information. + +--hap mode +========== +When using `--hap`, we assume phased variants from a single individual. Only the +single best matching call from the other haplotype will be collapsed, +and the consolidated genotype will become 1/1 + +For example, if we collapse anything at the same position: + + chr1 1 .. GT 0|1 + chr1 1 .. GT 1|0 + chr1 2 .. GT 1|0 + +will become: + + chr1 1 .. GT 1/1 + chr1 2 .. GT 1|0 + +--chain mode +============ +Normally, every variant in a set of variants that are collapsed together matches every other variant in the set. However, when using `--chain` mode, we allow 'transitive matching'. This means that all variants match to only at least one other variant in the set. In situations where a 'middle' variant has two matches that don't match each other, without `--chain` the locus will produce two variants whereas using `--chain` will produce one. +For example, if we have + + chr1 5 .. + chr1 7 .. + chr1 9 .. + +When we collapse anything within 2bp of each other, without `--chain`, we output: + + chr1 5 .. + chr1 9 .. + +With `--chain`, we would collapse `chr1 9` as well, producing + + chr1 5 .. + +Annotations +=========== +`collapse` produces two files. The output file has kept variants along with unanalyzed (< sizemin) variants. The collapsed file contains the variants that were collapsed into the kept variants. + +The output file has only two annotations added to the `INFO`. +- `CollapseId` - the identifier of the variant when comparing to the collapse outputs. +- `NumCollapsed` - the number of variants collapsed into this variant + +The collapsed file has all of the annotations added by [[bench|bench#definition-of-annotations-added-to-tp-vcfs]]. Note that `MatchId` is tied to the output file's `CollapseId`. See [MatchIds](https://github.com/spiralgenetics/truvari/wiki/MatchIds) for details. + +``` +usage: collapse [-h] -i INPUT [-o OUTPUT] [-c COLLAPSED_OUTPUT] [-f REFERENCE] [-k {first,maxqual,common}] [--debug] + [-r REFDIST] [-p PCTSIM] [-B MINHAPLEN] [-P PCTSIZE] [-O PCTOVL] [-t] [--use-lev] [--hap] [--chain] + [--no-consolidate] [--null-consolidate NULL_CONSOLIDATE] [-s SIZEMIN] [-S SIZEMAX] [--passonly] + +Structural variant collapser + +Will collapse all variants within sizemin/max that match over thresholds + +options: + -h, --help show this help message and exit + -i INPUT, --input INPUT + Comparison set of calls + -o OUTPUT, --output OUTPUT + Output vcf (stdout) + -c COLLAPSED_OUTPUT, --collapsed-output COLLAPSED_OUTPUT + Where collapsed variants are written (collapsed.vcf) + -f REFERENCE, --reference REFERENCE + Indexed fasta used to call variants + -k {first,maxqual,common}, --keep {first,maxqual,common} + When collapsing calls, which one to keep (first) + --debug Verbose logging + --hap Collapsing a single individual's haplotype resolved calls (False) + --chain Chain comparisons to extend possible collapsing (False) + --no-consolidate Skip consolidation of sample genotype fields (True) + --null-consolidate NULL_CONSOLIDATE + Comma separated list of FORMAT fields to consolidate into the kept entry by taking the first non-null + from all neighbors (None) + +Comparison Threshold Arguments: + -r REFDIST, --refdist REFDIST + Max reference location distance (500) + -p PCTSIM, --pctsim PCTSIM + Min percent allele sequence similarity. Set to 0 to ignore. (0.95) + -B MINHAPLEN, --minhaplen MINHAPLEN + Minimum haplotype sequence length to create (50) + -P PCTSIZE, --pctsize PCTSIZE + Min pct allele size similarity (minvarsize/maxvarsize) (0.95) + -O PCTOVL, --pctovl PCTOVL + Min pct reciprocal overlap (0.0) for DEL events + -t, --typeignore Variant types don't need to match to compare (False) + --use-lev Use the Levenshtein distance ratio instead of edlib editDistance ratio (False) + +Filtering Arguments: + -s SIZEMIN, --sizemin SIZEMIN + Minimum variant size to consider for comparison (50) + -S SIZEMAX, --sizemax SIZEMAX + Maximum variant size to consider for comparison (50000) + --passonly Only consider calls with FILTER == PASS +``` \ No newline at end of file diff --git a/docs/v4.0.0/consistency.md b/docs/v4.0.0/consistency.md new file mode 100644 index 00000000..41fd599c --- /dev/null +++ b/docs/v4.0.0/consistency.md @@ -0,0 +1,170 @@ + +In addition to looking at performance of a single set of variation against a baseline, one may wish to measure the consistency between multiple sets of variation. The tool `truvari consistency` can automatically create that result. + +Running +======= + +``` +usage: consistency [-h] [-j] VCFs [VCFs ...] + +Over multiple vcfs, calculate their intersection/consistency. + +Calls will match between VCFs if they have a matching key of: + CHROM:POS ID REF ALT + +positional arguments: + VCFs VCFs to intersect + +optional arguments: + -h, --help show this help message and exit + -j, --json Output report in json format +``` +Example +======= + +```bash +truvari consistency fileA.vcf fileB.vcf fileC.vcf +``` + +Matching Entries +================ + +VCF entries will be considered matching if and only if they have an exact same key of `CHROM:POS ID REF ALT`. Because of this stringency, it is recommend that you compare the tp-base.vcf or fn.vcf results from each individual VCF's Truvari output. + +Output Report +============= + +Below is an example report: + +```text +# +# Total 5534 calls across 3 VCFs +# +#File NumCalls +fileA.vcf 4706 +fileB.vcf 4827 +fileC.vcf 4882 +# +# Summary of consistency +# +#VCFs Calls Pct +3 3973 71.79% +2 935 16.90% +1 626 11.31% +# +# Breakdown of VCFs' consistency +# +#Group Total TotalPct PctOfFileCalls +111 3973 71.79% 84.42% 82.31% 81.38% +011 351 6.34% 7.27% 7.19% +101 308 5.57% 6.54% 6.31% +110 276 4.99% 5.86% 5.72% +001 250 4.52% 5.12% +010 227 4.10% 4.70% +100 149 2.69% 3.17% +``` + +At the top we see that we compared 5,534 unique variants between the 3 files, with fileC.vcf having the most calls at 4,882. + +The "Summary of consistency" shows us that 3,973 (71.79%) of all the calls are shared between the 3 VCFs, while 626 (11.31%) are only found in one of the VCFs. + +Reading the "Breakdown of VCFs' consistency", a `Group` is a unique key for presence (1) or absence (0) of a call within each of the listed `#Files`. For example: `Group 111` is calls present in all VCFs; `Group 011` is calls present in only the 2nd and 3rd VCFs (i.e. fileB.vcf and fileC.vcf). + +We see that `Group 101` has calls belonging to the 1st and 3rd `#Files` (i.e. fileA.vcf and fileC.vcf). This group has a total of 308 calls that intersect, or 5.57% of all calls in all VCFs. This 308 represents 6.54% of calls in fileA.vcf and 6.31% of calls in fileC.vcf. + +Finally, we see that fileA.vcf has the least amount of calls unique to it on the `Group 100` line. + +Json +==== +Below is a consistency report in json format. +```json +{ + "vcfs": [ + "repo_utils/test_files/variants/input1.vcf.gz", + "repo_utils/test_files/variants/input2.vcf.gz", + "repo_utils/test_files/variants/input3.vcf.gz" + ], + "total_calls": 3513, + "num_vcfs": 3, + "vcf_counts": { + "repo_utils/test_files/variants/input1.vcf.gz": 2151, + "repo_utils/test_files/variants/input2.vcf.gz": 1783, + "repo_utils/test_files/variants/input3.vcf.gz": 2065 + }, + "shared": [ + { + "vcf_count": 3, + "num_calls": 701, + "call_pct": 0.1995445488186735 + }, + { + "vcf_count": 2, + "num_calls": 1084, + "call_pct": 0.3085681753487048 + }, + { + "vcf_count": 1, + "num_calls": 1728, + "call_pct": 0.4918872758326217 + } + ], + "detailed": [ + { + "group": "111", + "total": 701, + "total_pct": 0.1995445488186735, + "repo_utils/test_files/variants/input1.vcf.gz": 0.32589493258949326, + "repo_utils/test_files/variants/input2.vcf.gz": 0.393157599551318, + "repo_utils/test_files/variants/input3.vcf.gz": 0.3394673123486683 + }, + { + "group": "001", + "total": 645, + "total_pct": 0.18360375747224594, + "repo_utils/test_files/variants/input1.vcf.gz": 0, + "repo_utils/test_files/variants/input2.vcf.gz": 0, + "repo_utils/test_files/variants/input3.vcf.gz": 0.31234866828087166 + }, + { + "group": "100", + "total": 598, + "total_pct": 0.17022487902077996, + "repo_utils/test_files/variants/input1.vcf.gz": 0.2780102278010228, + "repo_utils/test_files/variants/input2.vcf.gz": 0, + "repo_utils/test_files/variants/input3.vcf.gz": 0 + }, + { + "group": "101", + "total": 487, + "total_pct": 0.1386279533162539, + "repo_utils/test_files/variants/input1.vcf.gz": 0.22640632264063226, + "repo_utils/test_files/variants/input2.vcf.gz": 0, + "repo_utils/test_files/variants/input3.vcf.gz": 0.2358353510895884 + }, + { + "group": "010", + "total": 485, + "total_pct": 0.13805863933959578, + "repo_utils/test_files/variants/input1.vcf.gz": 0, + "repo_utils/test_files/variants/input2.vcf.gz": 0.27201346045989905, + "repo_utils/test_files/variants/input3.vcf.gz": 0 + }, + { + "group": "110", + "total": 365, + "total_pct": 0.10389980074010817, + "repo_utils/test_files/variants/input1.vcf.gz": 0.1696885169688517, + "repo_utils/test_files/variants/input2.vcf.gz": 0.2047111609646663, + "repo_utils/test_files/variants/input3.vcf.gz": 0 + }, + { + "group": "011", + "total": 232, + "total_pct": 0.06604042129234272, + "repo_utils/test_files/variants/input1.vcf.gz": 0, + "repo_utils/test_files/variants/input2.vcf.gz": 0.13011777902411667, + "repo_utils/test_files/variants/input3.vcf.gz": 0.11234866828087167 + } + ] +} +``` \ No newline at end of file diff --git a/docs/v4.0.0/divide.md b/docs/v4.0.0/divide.md new file mode 100644 index 00000000..3bbad3cb --- /dev/null +++ b/docs/v4.0.0/divide.md @@ -0,0 +1,58 @@ +Divide a VCF into independent shards. + +Unfortunately, `pysam.VariantRecord` objects aren't pickle-able. This means that if we wanted to have Truvari leverage python's multiprocessing we'd need to make a custom VCF parser. However, the command `truvari divide` allows us to take an input VCF and divide it into multiple independent parts (or shards) which can the be processed over multiple processes. + +`truvari divide` works by parsing a VCF and splitting it into multiple, smaller sub-VCFs. If any variants are within `--buffer` base-pairs, they're output to the same sub-VCF. This allows variants in the same region which would need to be compared to one-another (see `--refdist`) to stay in the same sub-VCF. The `--min` parameter allows us to control the minimum number of variants per sub-VCF so that we don't make too many tiny VCFs. Once the sub-VCFs are created, we can process each independently through whatever truvari command. + +For example, let's say we want to run `truvari collapse` on a very large VCF with many variants and many samples. First, we divide the VCF: + +```bash +truvari divide big_input.vcf.gz sub_vcfs_directory/ +``` + +Inside of `sub_vcfs_directory/` we'll have multiple VCFs, which we can process with a simple bash script + +```bash +NJOBS=$(nproc) # use all processors by default +mkdir -p output_vcfs/ +mkdir -p collap_vcfs/ +mkdir -p logs/ + +for in_vcf in sub_vcfs_directory/*.vcf.gz +do + # Setup file names + base_name=$(basename $in_vcf) + base_name=${base_name%.vcf.gz} + output_name=output_vcfs/${base_name}.vcf + collap_name=collap_vcfs/${base_name}.vcf + log_name=logs/${base_name}.log + # Run the command and send it to the background + truvari collapse -i $in_vcf -o $output_name -c $collap_name -f reference.fa &> logs/${log_name}.log & + # If too many jobs are running, wait for one to finish + while [ $( jobs | wc -l ) -ge ${NJOBS} ] + do + sleep 5 + done +done +``` + +Obviously the logs and `while` loop are tricks for running on a single machine. If you have access to a cluster, I'm sure you can imagine how to create/submit the commands. + +``` +usage: divide [-h] [-b BUFFER] [-m MIN] [--no-compress] [-T THREADS] VCF DIR + +Divide a VCF into independent parts + +positional arguments: + VCF VCF to split + DIR Output directory to save parts + +options: + -h, --help show this help message and exit + -b BUFFER, --buffer BUFFER + Buffer to make mini-clusters (1000) + -m MIN, --min MIN Minimum number of entries per-vcf (100) + --no-compress Don't attempt to compress/index sub-VCFs + -T THREADS, --threads THREADS + Number of threads for compressing/indexing sub-VCFs (1) +``` \ No newline at end of file diff --git a/docs/v4.0.0/phab.md b/docs/v4.0.0/phab.md new file mode 100644 index 00000000..2fdc57fb --- /dev/null +++ b/docs/v4.0.0/phab.md @@ -0,0 +1,161 @@ +Introduction +------------ + +Truvari's comparison engine can match variants using a wide range of thresholds. However, some alleles can produce radically different variant representations. We could dramatically lower our thresholds to identify the match, but this would cause variants from unidentical alleles to be falsely matched. + +This problem is easiest to conceptualize in the case of 'split' variants: imagine a pipeline calls a single 100bp DEL that can also be represented as two 50bp DELs. To match these variants, we would need to loosen our thresholds to `--pick multi --pctsim 0.50 --pctsize 0.50`. Plus, these thresholds leave no margin for error. If the variant caller erroneously deleted an extra base to make a 101bp DEL we would have to lower our thresholds even further. These thresholds are already too low because there's plenty of distinct alleles with >= 50% homology. + +So how do we deal with inconsistent representations? Perhaps we could build [dynamic-thresholds](https://github.com/ACEnglish/truvari/discussions/94) that would increase or decrease depending on measurements (e.g. variant distance, sequence context); but building a reliable model would require an expansive training dataset. + +In an ideal world, we would simply get rid of inconsistent variant representations. + +`truvari phab` is designed to remove variant representation inconsistencies through harmonization. By reconstructing haplotypes from variants, running multiple-sequence alignment of the haplotypes along with the reference, and then recalling variants, we expect to remove discordance between variant representations and simplify the work required to perform variant comparison. + +`truvari phab` works by wrapping a number of trusted bioinformatics tools. Reference from the region being analyzed is fetched with `samtools`. Haplotypes are reconstructed from VCFs using `bcftools consensus`. The sequences are then aligned using [MAFFT](https://mafft.cbrc.jp/alignment/software/) - a fast multiple-sequence alignment software. Truvari parses the resultant MSA and calls variants to reproduce the region's VCF. + +Requirements +------------ +Since `truvari phab` uses existing tools, it expects them to be found in the environment path. The list of tools `phab` will call are: + +- bcftools 1.10.2 +- vcf-sort 0.1.16 +- tabix / bgzip - 1.10.2-3 +- samtools 1.10 +- mafft v7.505 + +You can install each of these or you can can build a Truvari [Docker container](Development#docker) + +Example +------- +As an example, we'll use Truvari's test files in `repo_utils/test_files/phab*` which were created from real data over a tandem repeat at GRCh38 chr1:26399065-26401053 and translated to a small test genome with coordinates chr1:1-1988. + +* `phab_base.vcf.gz` - an 86 sample squared-off pVCF +* `phab_comp.vcf.gz` - a single sample's VCF +* `phab_ref.fa` - a subset of the GRCh38 reference + +This dataset is interesting because the `HG002` sample in `phab_base.vcf.gz` uses the same sequencing experiment ([HPRC](https://github.com/human-pangenomics/HPP_Year1_Assemblies)) as the sample `syndip` in `phab_comp.vcf.gz`, but processed with a different pipeline. And as we will see, the pipeline can make all the difference. + +To start, let's use `truvari bench` to see how similar the variant calls are in this region. +```bash +truvari bench --base phab_base.vcf.gz \ + --comp phab_comp.vcf.gz \ + --sizemin 1 --sizefilt 1 \ + --bSample HG002 \ + --cSample syndip \ + --no-ref a \ + --output initial_bench +``` +This will compare all variants greater than 1bp ( `-S 1 -s 1` which includes SNPs) from the `HG002` sample to the `syndip` sample. We're also excluding any uncalled or reference homozygous sites with `--no-ref a`. The report in `initial_bench/summary.txt` shows: +```json +{ + "TP-base": 5, + "TP-comp": 5, + "FP": 2, + "FN": 22, + "precision": 0.7142857142857143, + "recall": 0.18518518518518517, + "f1": 0.2941176470588235, +} +``` + +These variants are pretty poorly matched, especially considering the `HG002` and `syndip` samples are using the same sequencing experiment. We can also inspect the `initial_bench/fn.vcf.gz` and see a lot of these discordant calls are concentrated in a 200bp window. Let's use `truvari phab` to harmonize the variants in this region. +```bash +truvari phab --base phab_base.vcf.gz \ + --comp phab_comp.vcf.gz \ + --bSample HG002 \ + --cSample syndip \ + --reference phab_ref.fa \ + --region chr1:700-900 \ + -o phab_result/ +``` + +The main file `phab` produces is the `phab_result/output.vcf.gz` which holds our harmonized variants. In it we can see there are now only 9 variants. Let's run `truvari bench` again on the output to see how well the variants match after running `phab`. + +```bash +truvari bench -b phab_result/output.vcf.gz \ + -c phab_result/output.vcf.gz \ + -S 1 -s 1 \ + --no-ref a \ + --bSample HG002 \ + --cSample syndip \ + -o harmonized_bench/ +``` +Looking at `harmonized_bench/summary.txt` shows: +```json +{ + "TP-base": 8, + "TP-comp": 8, + "FP": 0, + "FN": 0, + "precision": 1.0, + "recall": 1.0, + "f1": 1.0, +} +``` +Now there is no difference between our two sets of variants in this region. + +For this variant call-set, `truvri phab` makes `truvari bench` overkill since the variants create identical haplotypes. In fact, we can benchmark simply by counting the genotypes. +```bash +$ bcftools query -f "[%GT ]\n" phab_result/output.vcf.gz | sort | uniq -c + 1 0/1 1/0 + 1 1/0 0/1 + 6 1/1 1/1 +``` +(We can ignore the phasing differences (`0/1` vs. `1/0`). These pipelines reported the parental alleles in a different order) + +MSA +--- + +If you read the `truvari phab --help` , you may have noticed that the `--comp` VCF is optional. This is by design so that we can also harmonize the variants inside a single VCF. By performing a multiple-sequence alignment across samples, we can better represent variation across a population. To see this in action, let's run `phab` on all 86 samples in the `repo_utils/test_files/phab_base.vcf.gz` +```bash +truvari phab -b phab_base.vcf.gz \ + -f phab_ref.fa \ + -r chr1:700-900 \ + -o msa_example +``` + +As a simple check, we can count the number of variants before/after `phab`: +```bash +bcftools view -r chr1:700-900 phab_base.vcf.gz | grep -vc "#" +bcftools view -r chr1:700-900 msa_example/output.vcf.gz | grep -vc "#" +``` +The `160` original variants given to `phab` became just `60`. + +Better yet, these fewer variants occur on fewer positions: +```bash + +bcftools query -r chr1:700-900 -f "%POS\n" phab_base.vcf.gz | sort | uniq | wc -l +bcftools query -r chr1:700-900 -f "%POS\n" msa_example/output.vcf.gz | sort | uniq | wc -l +``` +This returns that the variants were over `98` positions but now sit at just `16` + +We can also observe changes in the allele frequency after running `phab`: +```bash +bcftools +fill-tags -r chr1:700-900 phab_base.vcf.gz | bcftools query -f "%AC\n" | sort -n | uniq -c +bcftools +fill-tags -r chr1:700-900 msa_example/output.vcf.gz | bcftools query -f "%AC\n" | sort -n | uniq -c +``` +The allele-count (AC) shows a 15% reduction in singletons and removal of all variants with an AF > 0.50 which would have suggested the reference holds a minor allele. +```txt + original phab + # AC # AC + 39 1 33 1 + 18 2 4 2 + 3 3 2 3 + 3 4 2 4 + 2 5 1 5 + ... + 3 69 1 35 + 1 89 1 40 + 8 109 1 53 + 1 132 1 56 + 1 150 1 81 +``` + +(TODO: pull the adotto TR region annotations and run this example through `truvari anno trf`. I bet we'll get a nice spectrum of copy-diff of the same motif in the `phab` calls.) + +Limitations +----------- +* MAFFT, while very fast, is impractical for very long sequences and maybe impossible for entire human chromosomes. Therefore, `truvari phab` is recommended to only be run on sub-regions. +* By giving the variants new representations, it becomes harder to count how many TP/FP calls the original pipeline created. +* Early testing on `phab` is on phased variants. While it can run on unphased variants, we can't yet recommend it. If regions contain unphased Hets or overlapping variants, it becomes more difficult to build a consensus sequence. So you can try unphased variants out, but proceed with caution. + diff --git a/docs/v4.0.0/refine.md b/docs/v4.0.0/refine.md new file mode 100644 index 00000000..6e08c730 --- /dev/null +++ b/docs/v4.0.0/refine.md @@ -0,0 +1,107 @@ +As described in the [[phab|phab]] documentation, a constraint on Truvari `bench` finding matches is that there needs to be some consistency in how the variants are represented. To help automate the process of running Truvari `phab` on a benchmarking result, we present the tool `refine`. + +Quick Start +=========== + +After making a `bench` result: +```bash +truvari bench -b base.vcf.gz -c comp.vcf.gz -o result/ +``` +Use `refine` on the `result/` +```bash +truvari refine -r subset.bed -f ref.fa result/ +``` + +Output +====== +* `refine.variant_summary.json` - result of re-evaluating calls within the specified regions. Same structure as [[summary.json|bench#summaryjson]] +* `refine.regions.txt` - Tab-delimited file with per-region variant counts +* `refine.region_summary.json` - Per-region performance metrics +* `phab/` - Per-region results from variant re-evaluation (optional) +* `phab_bench/` - Bench results on the harmonized variants + +To see an example output, look at [test data](https://github.com/ACEnglish/truvari/tree/develop/answer_key/refine/refine_output_one) + +Using `refine.regions.txt` +========================== +| Column | Description | +| ----------------- | --------------------------------------- | +| chrom | Region's chromosome | +| start | Region's start | +| end | Region's end | +| in_tpbase | Input's True Positive base count | +| in_tp | Input's True Positive comparison count | +| in_fp | Input's false positive count | +| in_fn | Input's false negative count | +| refined | Boolean for if region was re-evaluated | +| out_tpbase | Output's true positive base count | +| out_tp | Output's true positive comparison count | +| out_fn | Outputs false positive count | +| out_fp | Output's false negative count | +| state | True/False state of the region | + + +Performance by Regions +====================== + +Because `truvari phab` can alter variant counts during harmonization, one may wish to assess the performance on a per-region basis rather than the per-variant basis. In the `refine.regions.txt`, a column `state` will have a TP/FN/FP value as defined by the following rules: + +```python +false_pos = (data['out_fp'] != 0) +false_neg = (data['out_fn'] != 0) +any_false = false_pos | false_neg + +true_positives = (data['out_tp'] != 0) & (data['out_tpbase'] != 0) & ~any_false + +true_negatives = (data[['out_tpbase', 'out_tp', 'out_fn', 'out_fp']] == 0).all(axis=1) + +baseP = (data['out_tpbase'] != 0) | (data['out_fn'] != 0) +compP = (data['out_tp'] != 0) | (data['out_fp'] != 0) +``` + +This logic has two edge cases to consider. 1) a region with at least one false-positive and one false-negative will be counted as both a false-positive and a false-negative. 2) Regions within `--refdist` may experience 'variant bleed' where they e.g. have an out_tp, but no other variants because a neighboring region actually contains the the corresponding `out_tpbase`. For the first case, we simply count the region twice and set its state in `refine.regions.txt` to "FP,FN". For the second case, we set the state to 'UNK' and ignore it when calculating the region summary. Future versions may figure out exactly how to handle (prevent?) 'UNK' regions. + +These by-region state counts are summarized and written to `refine.region_summary.json`. The definition of metrics inside this json are: +| Key | Definition | Formula | +|--------|----------------------------------------------|---------------------------------| +| TP | True Positive region count | | +| TN | True Negative region count | | +| FP | False Positive region count | | +| FN | False Negative region count | | +| base P | Regions with base variant(s) | | +| base N | Regions without base variant(s) | | +| comp P | Regions with comparison variant(s) | | +| comp N | Regions without comparison variant(s) | | +| PPV | Positive Predictive Value (a.k.a. precision) | TP / comp P | +| TPR | True Positive Rate (a.k.a. recall) | TP / base P | +| TNR | True Negative Rate (a.k.a. specificity) | TN / base N | +| NPV | Negative Predictive Value | TN / comp N | +| ACC | Accuracy | (TP + TN) / (base P + base N) | +| BA | Balanced Accuracy | (TPR + TNR) / 2 | +| F1 | f1 score | 2 * ((PPV * TPR) / (PPV + TPR)) | +| UND | Regions without an undetermined state | | + +Even though PPV is synonymous with precision, we use these abbreviated names when dealing with per-region performance in order to help users differentiate from the by-variant performance reports. + +`--use-original` +================ + +By default, `refine` will use the base/comparison variants from the `bench` results `tp-base.vcf.gz`, `fn.vcf.gz`, `tp-comp.vcf.gz`, and `fp.vcf.gz` as input for `phab`. However, this typically contains a filtered subset of variants originally provided to `bench` since it does filtering such as `--sizemin` and `--passonly`. With the `--use-original` parameter, all of the original calls from the input vcfs are fetched. + + +`--regions` +=========== + +This parameter specifies which regions to re-evaluate. If this is not provided, the original `bench` result's `--includebed` is used. If both `--regions` and `--includebed` are provided, the `--regions` are subset to only those intersecting `--includebed`. + +Note that the larger these regions are the slower MAFFT (used by `phab`) will run. Also, when performing the intersection as described above, there may be edge effects in the reported `refine.variant_summary.json`. For example, if a `--region` partially overlaps an `--includebed` region, you may not be analyzing a subset of calls looked at during the original `bench` run. Therefore, the `*summary.json` should be compared with caution. + +`--use-includebed` +================== + +When intersecting includebed with regions, use includebed coordinates. This is helpful for when the original bench result's `--includebed` boundaries should be used instead of the `--regions` + +`--reference` +============= + +By default, the reference is pulled from the original `bench` result's `params.json`. If a reference wasn't used with `bench`, it must be specified with `refine` as it's used by `phab` to realign variants. \ No newline at end of file diff --git a/docs/v4.0.0/segment.md b/docs/v4.0.0/segment.md new file mode 100644 index 00000000..953e5822 --- /dev/null +++ b/docs/v4.0.0/segment.md @@ -0,0 +1,18 @@ +Segmentation: Normalization of SVs into disjointed genomic regions + +For SVs with a span in the genome (currently only DELs), split the overlaps into disjointed regions. This is an experimental tool that explores the possibility of assisting SV association analysis. + +This tool adds an INFO field `SEGCNT` which holds the number of original SVs that overlap the newly reported region. It also adds a FORMAT field `SEG`, which is the 'allele coverage' per-sample. For example, if a sample has two overlapping heterozygous deletions, the shared region will have `SEG=2`. If the two deletions were homozygous then `SEG=4`. + +In the below example, we have three deletions found across three samples. + +![](https://github.com/spiralgenetics/truvari/blob/develop/imgs/segment_example.png) + +The `segment` added annotations for the regions would then be: +| Region | INFO/SEGCNT | S1/SEG | S2/SEG | S3/SEG | +|--------|-------------|--------|--------|--------| +| A | 1 | 2 | 0 | 0 | +| B | 2 | 2 | 1 | 0 | +| C | 3 | 2 | 2 | 2 | +| D | 2 | 2 | 1 | 0 | +| E | 1 | 0 | 1 | 0 | \ No newline at end of file diff --git a/docs/v4.0.0/stratify.md b/docs/v4.0.0/stratify.md new file mode 100644 index 00000000..353dcab5 --- /dev/null +++ b/docs/v4.0.0/stratify.md @@ -0,0 +1,58 @@ +`stratify` is a helper utility for counting variants within bed regions which is essentially the same as running `bedtools intersect -c`. When working with benchmarking results, there are are four vcfs to count (tp-base, tp-comp, fn, fp). Instead of running bedtools four times and collating the results, `stratify` can be given a single `bench` result directory to generate the counts. + +For example: +```bash +$ truvari stratify input.bed bench/ +chrom start end tpbase tp fn fp +chr20 280300 280900 0 0 0 0 +chr20 100000 200000 1 1 0 0 +chr20 642000 642350 1 1 2 1 +``` + +The output from this can then be parsed to generate more details: + +```python +import pandas as pd +import truvari + +df = pd.read_csv("stratify.output.txt", sep='\t') + +# If the input.bed didn't have a header and so we couldn't use the `--header` parameter, we need to name columns +df.columns = ['chrom', 'start', 'end', 'tpbase', 'tp', 'fn', 'fp'] + +# Create the precision, recall, and f1 for each row +metrics = df[["tpbase", "tp", "fn", "fp"]].apply((lambda x: truvari.performance_metrics(*x)), axis=1) + +# metrics is now a DataFrame with a single column of tuples, lets separate them into columns +metrics = pd.DataFrame(metrics.to_list(), columns=["precision", "recall", "f1"]) + +# Extend the dataframe's columns +df = df.join(metrics) +df.head() +``` +Which gives the result: +``` + chrom start end tpbase tp fn fp precision recall f1 +0 chr20 135221 239308 1 1 0 0 1.00 1.00 1.000000 +1 chr20 260797 465632 3 3 3 1 0.75 0.50 0.600000 +2 chr20 465866 622410 1 1 0 0 1.00 1.00 1.000000 +3 chr20 623134 655257 1 1 3 1 0.50 0.25 0.333333 +4 chr20 708338 732041 1 1 1 0 1.00 0.50 0.666667 +``` + +``` +usage: stratify [-h] [-o OUT] [--header] [-w] [--debug] BED VCF + +Count variants per-region in vcf + +positional arguments: + BED Regions to process + VCF Truvari bench result directory or a single VCF + +optional arguments: + -h, --help show this help message and exit + -o OUT, --output OUT Output bed-like file + --header Input regions have header to preserve in output + -w, --within Only count variants contained completely within region boundaries + --debug Verbose logging +``` \ No newline at end of file diff --git a/docs/v4.0.0/vcf2df.md b/docs/v4.0.0/vcf2df.md new file mode 100644 index 00000000..14d9f06c --- /dev/null +++ b/docs/v4.0.0/vcf2df.md @@ -0,0 +1,81 @@ +We enjoy using [pandas](https://pandas.pydata.org/)/[seaborn](https://seaborn.pydata.org/) for python plotting, so we've made the command `truvari vcf2df`. This will turn a VCF into a pandas DataFrame and save it to a file using joblib. The resulting DataFrame will always have the columns: +* chrom: variant chromosome +* start: 0-based start from pysam.VariantRecord.start +* end: 0-based end from pysam.VariantRecord.stop +* id : VCF column ID +* svtype : SVTYPE as determined by `truvari.entry_variant_type` +* svlen : SVLEN as determined by `truvari.entry_size` +* szbin : SVLEN's size bin as determined by `truvari.get_sizebin` +* qual : VCF column QUAL +* filter : VCF column FILTER +* is_pass : boolean of if the filter is empty or PASS + +Optionally, `vcf2df` can attempt to pull `INFO` and `FORMAT` fields from the VCF and put each field into the DataFrame as a new column. For FORMAT fields, the VCF header definition's `Number` is considered and multiple columns may be added. For example, the `AD` field, typically holding Allele Depth has `Number=A`, indicating that there will be one value for each allele. Truvari assumes that all VCFs hold one allele per-line, so there are only 2 alleles described per-line, the reference and alternate allele. Therefore, two columns are added to the DataFrame, `AD_ref` and `AD_alt` corresponding to the 0th and 1st values from the AD field's list of values. Similarity, for PL (genotype likelihood) with `Number=G`, there's three values and columns are created named `PL_ref`, `PL_het`, `PL_hom`. + +After you've created your benchmarking results with `truvari bench`, you'll often want to plot different views of your results. `vcf2df --bench-dir` can parse a truvari output directory's multiple VCF files and add a 'state' column +* state : The truvari state assigned to the variant + * tpbase : Parsed from the tp-base.vcf + * tp : Parsed from the tp-comp.vcf + * fp : Parsed from the fp.vcf + * fn : Parsed from the fn.vcf + +The created DataFrame is saved into a joblib file, which can then be plotted as simply as: +```python +import joblib +import seaborn as sb +import matplotlib.pyplot as plt + +data = joblib.load("test.jl") +p = sb.countplot(data=data[data["state"] == 'tp'], x="szbin", hue="svtype", hue_order=["DEL", "INS"]) +plt.xticks(rotation=45, ha='right') +p.set(title="True Positives by svtype and szbin") +``` +![](https://github.com/spiralgenetics/truvari/blob/develop/imgs/truv2df_example.png) + +This enables concatenation of Truvari results across multiple benchmarking experiments for advanced comparison. For example, imagine there's multiple parameters used for SV discovery over multiple samples. After running `truvari bench` on each of the results with the output directories named to `params/sample/` and each converted to DataFrames with `truvari vcf2df`, we can expand/concatenate the saved joblib DataFrames with: + +```python +import glob +import joblib +import pandas as pd + +files = glob.glob("*/*/data.jl") +dfs = [] +for f in files: + params, sample, frame = f.split('/') + d = joblib.load(f) + d["params"] = params + d["sample"] = sample + dfs.append(d) +df = pd.concat(dfs) +joblib.dump(df, "results.jl") +``` + +To facilitate range queries, PyRanges is helpful. `vcf2df` results can be parsed quickly by pyranges with the command: +```python +result = pyranges.PyRanges(df.rename(columns={'chrom':"Chromosome", "start":"Start", "end":"End"})) +``` + +``` +usage: vcf2df [-h] [-b] [-i] [-f] [-s SAMPLE] [-n] [-S] [-c LVL] [--debug] VCF JL + +Takes a vcf and creates a data frame. Can parse a bench output directory + +positional arguments: + VCF VCF to parse + JL Output joblib to save + +optional arguments: + -h, --help show this help message and exit + -b, --bench-dir Input is a truvari bench directory + -i, --info Attempt to put the INFO fields into the dataframe + -f, --format Attempt to put the FORMAT fileds into the dataframe + -s SAMPLE, --sample SAMPLE + SAMPLE name to parse when building columns for --format + -n, --no-prefix Don't prepend sample name to format columns + -S, --skip-compression + Skip the attempt to optimize the dataframe's size + -c LVL, --compress LVL + Compression level for joblib 0-9 (3) + --debug Verbose logging +``` \ No newline at end of file diff --git a/imgs/BoxScale1_DarkBG.png b/imgs/BoxScale1_DarkBG.png new file mode 100644 index 00000000..391de411 Binary files /dev/null and b/imgs/BoxScale1_DarkBG.png differ diff --git a/imgs/BoxScale1_DarkNoBG.png b/imgs/BoxScale1_DarkNoBG.png new file mode 100644 index 00000000..eb17a9f9 Binary files /dev/null and b/imgs/BoxScale1_DarkNoBG.png differ diff --git a/imgs/Horizontal1_DarkBG.png b/imgs/Horizontal1_DarkBG.png new file mode 100644 index 00000000..a34ddad9 Binary files /dev/null and b/imgs/Horizontal1_DarkBG.png differ diff --git a/imgs/Horizontal1_DarkNoBG.png b/imgs/Horizontal1_DarkNoBG.png new file mode 100644 index 00000000..96f0f1e2 Binary files /dev/null and b/imgs/Horizontal1_DarkNoBG.png differ diff --git a/imgs/README.md b/imgs/README.md new file mode 100644 index 00000000..dd2c2119 --- /dev/null +++ b/imgs/README.md @@ -0,0 +1,6 @@ +Logos +----- +![Logo1](BoxScale1_DarkBG.png) +![Logo2](BoxScale1_DarkNoBG.png) +![Logo3](Horizontal1_DarkBG.png) +![Logo4](Horizontal1_DarkNoBG.png) diff --git a/imgs/coverage.svg b/imgs/coverage.svg index 1fa327ea..ea71b13a 100644 --- a/imgs/coverage.svg +++ b/imgs/coverage.svg @@ -17,7 +17,7 @@ coverage - 84% - 84% + 90% + 90% diff --git a/repo_utils/README.md b/repo_utils/README.md index af8568fe..4e643618 100644 --- a/repo_utils/README.md +++ b/repo_utils/README.md @@ -32,5 +32,21 @@ The hardest part of maintaining functional tests is creating/maintaining the inp - `test_files/make_anno.sh` makes a VCF with all INFO fields of the multiple `truvari anno` fields. - `test_files/add_dp.py` was used to add fake depth information in VCFs. +- `repo_utils/test_files/external/` hold fake external programs so that CI/CD doesn't have to download/run them every time When functional tests fail because of files not matching up (e.g. md5sum aren't equal), I usually manually inspect with something like `vimdiff` on the `test_results/` and the `repo_utils/test_files/answer_key/`. If I'm CERTAIN that the `test_results/` is correct, then I copy that into `repo_utils/test_files/answer_key/`. + +Running Individual Tests +======================== + +At the time of writing this, there are ~148 functional tests run by `ssshtest.sh` which take a couple of minutes to run. +Fortunately, we can focus which tests are run by adding parameters to `truvari_ssshtest.sh`. + +We can run an individual test with e.g. +```bash +bash repo_utils/truvari_sshtests.sh test_bench_unroll +``` + +Multiple individual test names can be passed to the script and all will be run. Unfortunately, there's no easy way to +group tests so that they're easy to run (e.g. `bash repo_utils/truvari_sshtests.sh test_bench` can't run all +`repo_utils/sub_tests/bench.sh` tests) diff --git a/repo_utils/answer_key/anno/addid.vcf b/repo_utils/answer_key/anno/addid.vcf new file mode 100644 index 00000000..2cad0e88 --- /dev/null +++ b/repo_utils/answer_key/anno/addid.vcf @@ -0,0 +1,3554 @@ +##fileformat=VCFv4.1 +##FILTER= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##INFO= +##INFO= +##INFO= +##FORMAT= +##bcftools_mergeVersion=1.10.2+htslib-1.10.2 +##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 +##INFO= +##INFO= +##bcftools_viewVersion=1.12+htslib-1.12 +##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 +##bcftools_mergeVersion=1.12+htslib-1.12 +##bcftools_mergeCommand=merge -O z -f x -m none input1.vcf.gz input2.vcf.gz input3.vcf.gz; Date=Mon Aug 16 18:05:13 2021 +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 +chr20 63971 200x0 TTCCATTCCAC T 60 . QNAME=cluster19_000000F;QSTART=25698928;QSTRAND=- GT:DP:AD ./.:17:12,5 1|0:42:24,18 ./.:33:14,19 +chr20 64506 200x1 C CTCCAT 60 . QNAME=cluster19_000000F;QSTART=25698398;QSTRAND=- GT:DP:AD ./.:35:13,22 1|0:30:14,16 ./.:21:12,9 +chr20 66141 200x2 AATTCC A 60 . QNAME=cluster23_scaffold_3;QSTART=25645835;QSTRAND=- GT:DP:AD ./.:18:10,8 ./.:43:18,25 1|1:32:16,16 +chr20 66235 200x3 C CGACTCCACTCCATT 60 . QNAME=HG002-S9-H1-000001F;QSTART=45138;QSTRAND=+ GT:DP:AD 1|1:42:20,22 1|1:27:5,22 1|1:33:22,11 +chr20 66369 200x4 C T 60 . QNAME=cluster19_000000F;QSTART=25696521;QSTRAND=- GT:DP:AD ./.:34:21,13 1|0:30:21,9 ./.:41:16,25 +chr20 67373 200x5 G GAAATGTGAT 60 . QNAME=cluster23_scaffold_2;QSTART=25629267;QSTRAND=- GT:DP:AD ./.:38:18,20 ./.:37:20,17 0|1:29:20,9 +chr20 68303 200x6 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=47219;QSTRAND=+ GT:DP:AD 1|1:41:18,23 0|1:43:18,25 1|1:29:15,14 +chr20 72450 200x7 G A 60 . QNAME=cluster19_000000F;QSTART=25690440;QSTRAND=- GT:DP:AD ./.:16:6,10 1|0:23:10,13 ./.:33:15,18 +chr20 72765 200x8 T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=51682;QSTRAND=+ GT:DP:AD 1|1:14:9,5 0|1:33:10,23 1|0:36:18,18 +chr20 72765 200x9 TA T 60 . QNAME=cluster19_000000F;QSTART=25690125;QSTRAND=- GT:DP:AD ./.:39:16,23 1|0:48:24,24 ./.:24:15,9 +chr20 72765 200xa T TAA 60 . QNAME=cluster23_scaffold_2;QSTART=25623873;QSTRAND=- GT:DP:AD ./.:43:18,25 ./.:15:6,9 0|1:31:13,18 +chr20 72982 200xb A C 60 . QNAME=cluster19_000000F;QSTART=25689909;QSTRAND=- GT:DP:AD ./.:43:18,25 1|0:32:23,9 ./.:17:6,11 +chr20 73765 200xc C A 60 . QNAME=cluster19_000000F;QSTART=25689126;QSTRAND=- GT:DP:AD ./.:26:6,20 1|0:22:9,13 ./.:14:8,6 +chr20 75250 200xd C T 60 . QNAME=cluster23_scaffold_2;QSTART=25621388;QSTRAND=- GT:DP:AD ./.:19:8,11 ./.:16:5,11 0|1:18:11,7 +chr20 76709 200xe C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25635256;QSTRAND=- GT:DP:AD ./.:27:7,20 ./.:37:25,12 1|0:43:25,18 +chr20 77005 200xf A G 60 . QNAME=cluster19_000000F;QSTART=25685886;QSTRAND=- GT:DP:AD ./.:27:7,20 1|0:14:6,8 ./.:32:13,19 +chr20 77736 200x10 CA C 60 . QNAME=cluster19_000000F;QSTART=25685155;QSTRAND=- GT:DP:AD ./.:34:11,23 1|0:30:14,16 ./.:41:25,16 +chr20 77736 200x11 C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25618901;QSTRAND=- GT:DP:AD ./.:47:23,24 ./.:28:13,15 0|1:36:17,19 +chr20 78705 200x12 A T 60 . QNAME=cluster19_000000F;QSTART=25684187;QSTRAND=- GT:DP:AD ./.:38:14,24 1|0:45:22,23 ./.:45:21,24 +chr20 80457 200x13 C T 60 . QNAME=cluster19_000000F;QSTART=25682435;QSTRAND=- GT:DP:AD ./.:30:18,12 1|0:33:12,21 ./.:41:17,24 +chr20 80497 200x14 C CT 60 . QNAME=cluster19_000000F;QSTART=25682394;QSTRAND=- GT:DP:AD ./.:37:13,24 1|0:32:20,12 ./.:26:16,10 +chr20 81154 200x15 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=60071;QSTRAND=+ GT:DP:AD 1|1:11:5,6 0|1:36:16,20 1|1:27:16,11 +chr20 82603 200x16 A C 60 . QNAME=cluster19_000000F;QSTART=25680288;QSTRAND=- GT:DP:AD ./.:19:6,13 1|0:24:11,13 ./.:24:12,12 +chr20 83158 200x17 C T 60 . QNAME=cluster19_000000F;QSTART=25679733;QSTRAND=- GT:DP:AD ./.:25:8,17 1|0:31:11,20 ./.:32:10,22 +chr20 85259 200x18 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=64176;QSTRAND=+ GT:DP:AD 1|1:24:11,13 0|1:38:19,19 1|1:31:19,12 +chr20 85729 200x19 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=64646;QSTRAND=+ GT:DP:AD 1|1:25:17,8 0|1:30:16,14 1|1:31:14,17 +chr20 86079 200x1a C A 60 . QNAME=cluster19_000000F;QSTART=45136;QSTRAND=+ GT:DP:AD ./.:15:7,8 0|1:34:14,20 ./.:29:15,14 +chr20 86859 200x1b T TTGGTATCTAG 60 . QNAME=HG002-S9-H1-000001F;QSTART=65777;QSTRAND=+ GT:DP:AD 1|1:34:25,9 0|1:36:19,17 1|1:38:17,21 +chr20 88108 200x1c T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=67035;QSTRAND=+ GT:DP:AD 1|1:20:7,13 1|1:40:24,16 1|1:33:11,22 +chr20 88453 200x1d G A 60 . QNAME=cluster23_scaffold_3;QSTART=25623502;QSTRAND=- GT:DP:AD ./.:24:12,12 ./.:24:10,14 1|0:33:22,11 +chr20 88865 200x1e G GACACAC 60 . QNAME=cluster19_000000F;QSTART=47933;QSTRAND=+ GT:DP:AD ./.:18:9,9 0|1:30:12,18 1|0:38:17,21 +chr20 88865 200x1f G GACAC 60 . QNAME=cluster19_000000F;QSTART=25674022;QSTRAND=- GT:DP:AD ./.:44:23,21 1|0:32:21,11 ./.:45:23,22 +chr20 89843 200x20 CTCTT C 60 . QNAME=cluster19_000000F;QSTART=25673044;QSTRAND=- GT:DP:AD ./.:28:13,15 1|0:15:6,9 ./.:37:23,14 +chr20 90339 200x21 G A 60 . QNAME=cluster19_000000F;QSTART=25672552;QSTRAND=- GT:DP:AD ./.:32:20,12 1|0:30:15,15 ./.:25:18,7 +chr20 91463 200x22 TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=70391;QSTRAND=+ GT:DP:AD 1|1:38:15,23 1|0:37:25,12 ./.:23:10,13 +chr20 92251 200x23 G A 60 . QNAME=cluster19_000000F;QSTART=25670641;QSTRAND=- GT:DP:AD ./.:37:18,19 1|0:41:25,16 ./.:36:12,24 +chr20 92395 200x24 C CT 60 . QNAME=cluster19_000000F;QSTART=25670496;QSTRAND=- GT:DP:AD ./.:15:8,7 1|0:24:19,5 ./.:35:17,18 +chr20 92969 200x25 CTT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=71896;QSTRAND=+ GT:DP:AD 1|1:43:20,23 ./.:35:17,18 ./.:43:20,23 +chr20 92969 200x26 CT C 60 . QNAME=cluster19_000000F;QSTART=25669922;QSTRAND=- GT:DP:AD ./.:39:16,23 1|1:40:15,25 ./.:23:7,16 +chr20 92969 200x27 C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25618979;QSTRAND=- GT:DP:AD ./.:32:12,20 ./.:28:13,15 1|0:30:17,13 +chr20 93706 200x28 G A 60 . QNAME=cluster19_000000F;QSTART=52778;QSTRAND=+ GT:DP:AD ./.:31:21,10 0|1:31:21,10 ./.:38:18,20 +chr20 94088 200x29 G GT 60 . QNAME=HG002-S9-H1-000001F;QSTART=73013;QSTRAND=+ GT:DP:AD 1|1:27:20,7 1|0:26:8,18 ./.:39:21,18 +chr20 94613 200x2a C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=73538;QSTRAND=+ GT:DP:AD 1|1:27:21,6 ./.:21:15,6 ./.:20:13,7 +chr20 96130 200x2b C T 60 . QNAME=cluster19_000000F;QSTART=25666761;QSTRAND=- GT:DP:AD ./.:39:14,25 1|0:34:22,12 ./.:32:7,25 +chr20 96321 200x2c T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=75246;QSTRAND=+ GT:DP:AD 1|1:35:19,16 1|1:28:12,16 ./.:33:23,10 +chr20 97324 200x2d G GT 60 . QNAME=HG002-S9-H1-000001F;QSTART=76250;QSTRAND=+ GT:DP:AD 1|1:20:15,5 ./.:33:8,25 ./.:24:12,12 +chr20 98593 200x2e T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=77519;QSTRAND=+ GT:DP:AD 1|1:27:14,13 1|0:30:9,21 ./.:26:8,18 +chr20 99430 200x2f G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=78356;QSTRAND=+ GT:DP:AD 1|1:37:17,20 ./.:49:24,25 ./.:31:17,14 +chr20 99840 200x30 G C 60 . QNAME=cluster19_000000F;QSTART=25663051;QSTRAND=- GT:DP:AD ./.:37:19,18 1|0:41:19,22 ./.:24:5,19 +chr20 100014 200x31 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=78940;QSTRAND=+ GT:DP:AD 1|1:21:11,10 1|1:32:10,22 1|1:11:5,6 +chr20 101338 200x32 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=54816;QSTRAND=+ GT:DP:AD 0|1:21:5,16 ./.:16:7,9 ./.:14:6,8 +chr20 101341 200x33 A G 60 . QNAME=cluster23_scaffold_3;QSTART=25610607;QSTRAND=- GT:DP:AD ./.:46:25,21 ./.:48:25,23 1|0:31:6,25 +chr20 101371 200x34 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=80297;QSTRAND=+ GT:DP:AD 1|0:14:6,8 0|1:34:17,17 ./.:28:8,20 +chr20 101433 200x35 A C 60 . QNAME=cluster19_000000F;QSTART=25661458;QSTRAND=- GT:DP:AD ./.:36:14,22 1|1:30:12,18 ./.:24:11,13 +chr20 101438 200x36 G A 60 . QNAME=cluster19_000000F;QSTART=25661453;QSTRAND=- GT:DP:AD ./.:30:22,8 1|1:47:22,25 ./.:27:8,19 +chr20 101498 200x37 A G 60 . QNAME=cluster23_scaffold_3;QSTART=25610450;QSTRAND=- GT:DP:AD ./.:21:6,15 ./.:36:21,15 1|0:25:9,16 +chr20 101505 200x38 A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=54983;QSTRAND=+ GT:DP:AD 0|1:47:25,22 ./.:31:7,24 1|0:36:25,11 +chr20 101576 200x39 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=80502;QSTRAND=+ GT:DP:AD 1|1:19:10,9 1|1:30:10,20 0|1:18:6,12 +chr20 102609 200x3a CTGTGTGTGTGTGTGTGTGTGTG C 60 . QNAME=HG002-S9-H1-000001F;QSTART=81536;QSTRAND=+ GT:DP:AD 1|0:22:16,6 ./.:44:20,24 ./.:28:21,7 +chr20 102609 200x3b CTG C 60 . QNAME=HG002-S9-H2-000001F;QSTART=56088;QSTRAND=+ GT:DP:AD 0|1:45:20,25 ./.:15:6,9 ./.:17:5,12 +chr20 102609 200x3c CTGTGTGTG C 60 . QNAME=cluster19_000000F;QSTART=25660282;QSTRAND=- GT:DP:AD ./.:43:19,24 1|1:26:12,14 1|0:31:23,8 +chr20 102609 200x3d C CTGTG 60 . QNAME=cluster23_scaffold_2;QSTART=25594014;QSTRAND=- GT:DP:AD ./.:19:5,14 ./.:21:6,15 0|1:30:14,16 +chr20 102613 200x3e G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=56089;QSTRAND=+ GT:DP:AD 0|1:25:14,11 ./.:39:20,19 ./.:35:11,24 +chr20 102619 200x3f G C 60 . QNAME=cluster19_000000F;QSTART=25660280;QSTRAND=- GT:DP:AD ./.:41:21,20 1|1:40:16,24 1|0:29:18,11 +chr20 102621 200x40 G C 60 . QNAME=cluster23_scaffold_3;QSTART=25609335;QSTRAND=- GT:DP:AD ./.:49:25,24 ./.:37:22,15 1|0:28:15,13 +chr20 102623 200x41 G C 60 . QNAME=cluster23_scaffold_3;QSTART=25609333;QSTRAND=- GT:DP:AD ./.:30:15,15 ./.:38:23,15 1|0:34:16,18 +chr20 102633 200x42 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=81537;QSTRAND=+ GT:DP:AD 1|0:45:25,20 ./.:14:6,8 ./.:23:12,11 +chr20 102634 200x43 T C 60 . QNAME=cluster19_000000F;QSTART=25660265;QSTRAND=- GT:DP:AD ./.:24:7,17 1|1:31:22,9 ./.:13:7,6 +chr20 105364 200x44 CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=84269;QSTRAND=+ GT:DP:AD 1|1:33:12,21 ./.:31:13,18 ./.:42:24,18 +chr20 105364 200x45 C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25591258;QSTRAND=- GT:DP:AD ./.:39:16,23 ./.:28:16,12 0|1:24:8,16 +chr20 106471 200x46 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=85374;QSTRAND=+ GT:DP:AD 1|1:40:18,22 ./.:31:8,23 ./.:27:5,22 +chr20 106775 200x47 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=85678;QSTRAND=+ GT:DP:AD 1|1:20:7,13 ./.:41:19,22 0|1:20:15,5 +chr20 107149 200x48 C T 60 . QNAME=cluster23_scaffold_2;QSTART=25589473;QSTRAND=- GT:DP:AD ./.:23:11,12 ./.:22:12,10 0|1:28:22,6 +chr20 107514 200x49 T C 60 . QNAME=cluster23_scaffold_2;QSTART=25589108;QSTRAND=- GT:DP:AD ./.:36:19,17 ./.:38:15,23 0|1:15:10,5 +chr20 109367 200x4a C A 60 . QNAME=cluster19_000000F;QSTART=25653532;QSTRAND=- GT:DP:AD ./.:35:11,24 1|1:38:23,15 ./.:12:6,6 +chr20 110447 200x4b C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=89350;QSTRAND=+ GT:DP:AD 1|1:30:5,25 1|1:20:6,14 0|1:31:23,8 +chr20 110867 200x4c G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=89770;QSTRAND=+ GT:DP:AD 1|1:26:18,8 1|1:29:9,20 0|1:24:15,9 +chr20 111066 200x4d C T 60 . QNAME=cluster19_000000F;QSTART=70130;QSTRAND=+ GT:DP:AD ./.:33:11,22 0|1:37:14,23 ./.:43:24,19 +chr20 111725 200x4e A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=90628;QSTRAND=+ GT:DP:AD 1|1:18:6,12 ./.:22:17,5 ./.:32:7,25 +chr20 111886 200x4f A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=90789;QSTRAND=+ GT:DP:AD 1|1:45:24,21 1|1:36:11,25 0|1:32:14,18 +chr20 112799 200x50 A G 60 . QNAME=cluster19_000000F;QSTART=25650100;QSTRAND=- GT:DP:AD ./.:19:5,14 1|0:31:7,24 ./.:47:22,25 +chr20 113005 200x51 C CT 60 . QNAME=cluster19_000000F;QSTART=25649893;QSTRAND=- GT:DP:AD ./.:24:13,11 1|0:19:14,5 ./.:35:11,24 +chr20 113290 200x52 G A 60 . QNAME=cluster19_000000F;QSTART=25649608;QSTRAND=- GT:DP:AD ./.:19:10,9 1|0:27:21,6 ./.:29:9,20 +chr20 115856 200x53 C G 60 . QNAME=cluster23_scaffold_2;QSTART=25580766;QSTRAND=- GT:DP:AD ./.:33:20,13 ./.:25:16,9 0|1:46:21,25 +chr20 120058 200x54 C T 60 . QNAME=cluster19_000000F;QSTART=25642840;QSTRAND=- GT:DP:AD ./.:25:10,15 1|0:32:22,10 ./.:21:16,5 +chr20 120721 200x55 G A 60 . QNAME=cluster19_000000F;QSTART=79785;QSTRAND=+ GT:DP:AD ./.:36:12,24 0|1:15:6,9 ./.:40:24,16 +chr20 121264 200x56 G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=74739;QSTRAND=+ GT:DP:AD 0|1:32:20,12 ./.:19:9,10 ./.:34:16,18 +chr20 121439 200x57 TATTCTTCAGCTGTCAAA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=100343;QSTRAND=+ GT:DP:AD 1|1:36:18,18 ./.:32:8,24 ./.:39:14,25 +chr20 121540 200x58 T C 60 . QNAME=cluster19_000000F;QSTART=25641358;QSTRAND=- GT:DP:AD ./.:26:11,15 1|0:28:5,23 ./.:32:18,14 +chr20 122158 200x59 G A 60 . QNAME=cluster19_000000F;QSTART=25640740;QSTRAND=- GT:DP:AD ./.:20:7,13 1|0:27:20,7 ./.:26:7,19 +chr20 122876 200x5a A T 60 . QNAME=cluster19_000000F;QSTART=25640022;QSTRAND=- GT:DP:AD ./.:26:21,5 1|0:30:19,11 ./.:34:9,25 +chr20 124258 200x5b C T 60 . QNAME=cluster19_000000F;QSTART=25638640;QSTRAND=- GT:DP:AD ./.:37:13,24 1|0:33:21,12 ./.:39:19,20 +chr20 125994 200x5c G A 60 . QNAME=cluster19_000000F;QSTART=25636904;QSTRAND=- GT:DP:AD ./.:47:23,24 1|0:13:8,5 ./.:36:11,25 +chr20 126062 200x5d C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=104949;QSTRAND=+ GT:DP:AD 1|0:41:25,16 0|1:33:20,13 1|1:45:24,21 +chr20 126062 200x5e C CTTT 60 . QNAME=cluster19_000000F;QSTART=25636833;QSTRAND=- GT:DP:AD ./.:45:24,21 1|0:29:9,20 ./.:31:18,13 +chr20 127645 200x5f T G 60 . QNAME=cluster19_000000F;QSTART=25635250;QSTRAND=- GT:DP:AD ./.:28:19,9 1|0:33:15,18 ./.:47:25,22 +chr20 127687 200x60 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=106574;QSTRAND=+ GT:DP:AD 1|1:32:17,15 1|1:31:8,23 0|1:32:11,21 +chr20 128317 200x61 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=107204;QSTRAND=+ GT:DP:AD 1|1:39:15,24 ./.:41:18,23 ./.:13:6,7 +chr20 128517 200x62 C CAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=107405;QSTRAND=+ GT:DP:AD 1|0:18:8,10 ./.:48:25,23 1|0:38:22,16 +chr20 128517 200x63 C CA 60 . QNAME=HG002-S9-H2-000001F;QSTART=81976;QSTRAND=+ GT:DP:AD 0|1:31:12,19 0|1:21:6,15 ./.:41:16,25 +chr20 128517 200x64 CA C 60 . QNAME=cluster19_000000F;QSTART=25634378;QSTRAND=- GT:DP:AD ./.:26:21,5 1|0:19:10,9 ./.:45:20,25 +chr20 129417 200x65 G C 60 . QNAME=cluster19_000000F;QSTART=25633479;QSTRAND=- GT:DP:AD ./.:31:6,25 1|0:38:19,19 ./.:32:13,19 +chr20 129457 200x66 A G 60 . QNAME=cluster19_000000F;QSTART=25633439;QSTRAND=- GT:DP:AD ./.:34:15,19 1|0:41:24,17 ./.:31:10,21 +chr20 130061 200x67 C T 60 . QNAME=cluster19_000000F;QSTART=25632835;QSTRAND=- GT:DP:AD ./.:17:10,7 1|0:36:17,19 ./.:27:13,14 +chr20 130282 200x68 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=83741;QSTRAND=+ GT:DP:AD 0|1:32:14,18 ./.:36:19,17 ./.:24:10,14 +chr20 130329 200x69 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=109218;QSTRAND=+ GT:DP:AD 1|1:27:7,20 ./.:47:24,23 ./.:35:16,19 +chr20 130338 200x6a A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=109227;QSTRAND=+ GT:DP:AD 1|1:21:7,14 0|1:48:23,25 0|1:34:24,10 +chr20 130338 200x6b A G 60 . QNAME=cluster19_000000F;QSTART=25632558;QSTRAND=- GT:DP:AD ./.:35:19,16 1|0:25:17,8 ./.:20:5,15 +chr20 130339 200x6c T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=109228;QSTRAND=+ GT:DP:AD 1|1:34:14,20 0|1:41:22,19 0|1:44:19,25 +chr20 130636 200x6d T C 60 . QNAME=cluster23_scaffold_2;QSTART=25565985;QSTRAND=- GT:DP:AD ./.:39:16,23 ./.:42:20,22 0|1:24:13,11 +chr20 130736 200x6e A C 60 . QNAME=cluster19_000000F;QSTART=25632160;QSTRAND=- GT:DP:AD ./.:20:8,12 1|0:21:10,11 ./.:40:24,16 +chr20 130742 200x6f T C 60 . QNAME=cluster19_000000F;QSTART=25632154;QSTRAND=- GT:DP:AD ./.:38:25,13 1|0:21:12,9 ./.:37:23,14 +chr20 131163 200x70 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=110052;QSTRAND=+ GT:DP:AD 1|1:28:13,15 ./.:39:25,14 ./.:27:22,5 +chr20 131230 200x71 A G 60 . QNAME=cluster19_000000F;QSTART=25631666;QSTRAND=- GT:DP:AD ./.:35:14,21 1|0:30:9,21 ./.:35:21,14 +chr20 131374 200x72 G A 60 . QNAME=cluster19_000000F;QSTART=25631522;QSTRAND=- GT:DP:AD ./.:13:6,7 1|0:38:16,22 ./.:21:6,15 +chr20 132236 200x73 C T 60 . QNAME=cluster19_000000F;QSTART=91302;QSTRAND=+ GT:DP:AD ./.:32:7,25 0|1:29:23,6 ./.:36:20,16 +chr20 133539 200x74 T C 60 . QNAME=cluster19_000000F;QSTART=25629357;QSTRAND=- GT:DP:AD ./.:23:8,15 1|0:35:21,14 ./.:47:25,22 +chr20 133631 200x75 A G 60 . QNAME=cluster23_scaffold_2;QSTART=25562990;QSTRAND=- GT:DP:AD ./.:32:16,16 ./.:37:23,14 0|1:44:19,25 +chr20 133700 200x76 C A 60 . QNAME=cluster19_000000F;QSTART=25629196;QSTRAND=- GT:DP:AD ./.:28:16,12 1|0:35:12,23 ./.:35:17,18 +chr20 134275 200x77 G A 60 . QNAME=cluster23_scaffold_2;QSTART=25562346;QSTRAND=- GT:DP:AD ./.:27:19,8 ./.:29:11,18 0|1:27:20,7 +chr20 134452 200x78 A C 60 . QNAME=cluster19_000000F;QSTART=25628444;QSTRAND=- GT:DP:AD ./.:19:12,7 1|0:25:15,10 ./.:22:10,12 +chr20 134675 200x79 C CA 60 . QNAME=cluster19_000000F;QSTART=25628220;QSTRAND=- GT:DP:AD ./.:16:5,11 1|0:24:6,18 ./.:36:23,13 +chr20 134915 200x7a G A 60 . QNAME=cluster19_000000F;QSTART=25627980;QSTRAND=- GT:DP:AD ./.:17:6,11 1|0:37:15,22 ./.:36:13,23 +chr20 135005 200x7b T C 60 . QNAME=cluster19_000000F;QSTART=25627890;QSTRAND=- GT:DP:AD ./.:43:20,23 1|0:22:17,5 ./.:27:19,8 +chr20 135211 200x7c C CA 60 . QNAME=cluster19_000000F;QSTART=25627683;QSTRAND=- GT:DP:AD ./.:31:23,8 1|0:40:19,21 ./.:23:5,18 +chr20 135293 200x7d C G 60 . QNAME=cluster19_000000F;QSTART=25627601;QSTRAND=- GT:DP:AD ./.:15:5,10 1|0:30:5,25 ./.:35:13,22 +chr20 135387 200x7e G A 60 . QNAME=cluster19_000000F;QSTART=94453;QSTRAND=+ GT:DP:AD ./.:24:16,8 0|1:28:23,5 ./.:30:22,8 +chr20 135595 200x7f A G 60 . QNAME=cluster19_000000F;QSTART=25627299;QSTRAND=- GT:DP:AD ./.:40:25,15 1|0:28:13,15 ./.:29:7,22 +chr20 135764 200x80 G A 60 . QNAME=cluster19_000000F;QSTART=25627130;QSTRAND=- GT:DP:AD ./.:45:24,21 1|0:34:23,11 ./.:28:11,17 +chr20 135904 200x81 G A 60 . QNAME=cluster19_000000F;QSTART=25626990;QSTRAND=- GT:DP:AD ./.:36:25,11 1|0:36:24,12 ./.:17:10,7 +chr20 136146 200x82 A G 60 . QNAME=cluster19_000000F;QSTART=25626748;QSTRAND=- GT:DP:AD ./.:31:13,18 1|0:20:12,8 ./.:30:11,19 +chr20 136216 200x83 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=89675;QSTRAND=+ GT:DP:AD 0|1:42:23,19 ./.:27:20,7 ./.:27:5,22 +chr20 136668 200x84 G GCAGGATTTCAT 60 . QNAME=cluster19_000000F;QSTART=25626215;QSTRAND=- GT:DP:AD ./.:22:7,15 1|0:24:7,17 ./.:32:10,22 +chr20 139004 200x85 G GT 60 . QNAME=cluster19_000000F;QSTART=25623878;QSTRAND=- GT:DP:AD ./.:19:8,11 1|1:41:21,20 ./.:23:7,16 +chr20 139481 200x86 A AAG 60 . QNAME=HG002-S9-H1-000001F;QSTART=118371;QSTRAND=+ GT:DP:AD 1|1:29:23,6 1|1:31:17,14 0|1:28:8,20 +chr20 139830 200x87 A G 60 . QNAME=cluster19_000000F;QSTART=25623050;QSTRAND=- GT:DP:AD ./.:32:12,20 1|0:20:9,11 ./.:33:13,20 +chr20 140109 200x88 C CAATT 60 . QNAME=HG002-S9-H1-000001F;QSTART=119001;QSTRAND=+ GT:DP:AD 1|1:35:15,20 1|1:28:17,11 0|1:31:7,24 +chr20 140669 200x89 A C 60 . QNAME=cluster19_000000F;QSTART=25622207;QSTRAND=- GT:DP:AD ./.:41:20,21 1|0:32:15,17 ./.:31:19,12 +chr20 140837 200x8a C A 60 . QNAME=cluster19_000000F;QSTART=25622039;QSTRAND=- GT:DP:AD ./.:24:16,8 1|0:45:20,25 ./.:36:17,19 +chr20 140838 200x8b G GT 60 . QNAME=cluster23_scaffold_3;QSTART=25571114;QSTRAND=- GT:DP:AD ./.:36:20,16 ./.:38:16,22 1|0:24:16,8 +chr20 140859 200x8c CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=94325;QSTRAND=+ GT:DP:AD 0|1:27:6,21 1|0:23:18,5 ./.:29:11,18 +chr20 140859 200x8d C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25571092;QSTRAND=- GT:DP:AD ./.:44:21,23 ./.:29:6,23 1|1:33:15,18 +chr20 141183 200x8e C T 60 . QNAME=cluster19_000000F;QSTART=25621694;QSTRAND=- GT:DP:AD ./.:40:24,16 1|0:14:9,5 ./.:39:19,20 +chr20 141335 200x8f G A 60 . QNAME=cluster19_000000F;QSTART=25621542;QSTRAND=- GT:DP:AD ./.:21:6,15 1|0:32:14,18 ./.:29:22,7 +chr20 141634 200x90 GA G 60 . QNAME=cluster19_000000F;QSTART=25621243;QSTRAND=- GT:DP:AD ./.:43:22,21 1|0:36:18,18 ./.:30:8,22 +chr20 141867 200x91 G A 60 . QNAME=cluster19_000000F;QSTART=25621011;QSTRAND=- GT:DP:AD ./.:36:12,24 1|0:37:12,25 ./.:34:24,10 +chr20 142165 200x92 T TTA 60 . QNAME=cluster19_000000F;QSTART=25620711;QSTRAND=- GT:DP:AD ./.:20:11,9 1|0:26:15,11 ./.:26:7,19 +chr20 143010 200x93 G GT 60 . QNAME=cluster19_000000F;QSTART=102084;QSTRAND=+ GT:DP:AD ./.:33:21,12 0|1:21:13,8 0|1:28:18,10 +chr20 143661 200x94 A C 60 . QNAME=cluster19_000000F;QSTART=25619215;QSTRAND=- GT:DP:AD ./.:33:22,11 1|0:34:12,22 ./.:28:9,19 +chr20 143771 200x95 C T 60 . QNAME=cluster19_000000F;QSTART=25619105;QSTRAND=- GT:DP:AD ./.:28:5,23 1|0:13:7,6 ./.:23:18,5 +chr20 144480 200x96 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=123375;QSTRAND=+ GT:DP:AD 1|1:33:11,22 ./.:17:10,7 ./.:29:13,16 +chr20 144897 200x97 G C 60 . QNAME=cluster19_000000F;QSTART=25617979;QSTRAND=- GT:DP:AD ./.:27:8,19 1|0:31:7,24 ./.:33:13,20 +chr20 145514 200x98 GCAAA G 60 . QNAME=cluster19_000000F;QSTART=25617362;QSTRAND=- GT:DP:AD ./.:22:13,9 1|0:33:22,11 ./.:40:21,19 +chr20 145669 200x99 ACC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=124565;QSTRAND=+ GT:DP:AD 1|1:31:20,11 1|0:32:17,15 1|0:19:10,9 +chr20 145888 200x9a G A 60 . QNAME=cluster19_000000F;QSTART=25616994;QSTRAND=- GT:DP:AD ./.:22:15,7 1|1:26:5,21 ./.:25:6,19 +chr20 145959 200x9b C A 60 . QNAME=cluster19_000000F;QSTART=25616923;QSTRAND=- GT:DP:AD ./.:35:25,10 1|1:34:10,24 ./.:37:20,17 +chr20 145973 200x9c T C 60 . QNAME=cluster19_000000F;QSTART=25616909;QSTRAND=- GT:DP:AD ./.:32:11,21 1|1:13:7,6 ./.:29:18,11 +chr20 146089 200x9d C T 60 . QNAME=cluster19_000000F;QSTART=25616793;QSTRAND=- GT:DP:AD ./.:22:6,16 1|1:38:18,20 ./.:30:24,6 +chr20 146119 200x9e C T 60 . QNAME=cluster19_000000F;QSTART=25616763;QSTRAND=- GT:DP:AD ./.:25:17,8 1|1:24:19,5 ./.:29:18,11 +chr20 146282 200x9f C A 60 . QNAME=cluster19_000000F;QSTART=25616600;QSTRAND=- GT:DP:AD ./.:28:13,15 1|1:22:6,16 ./.:23:7,16 +chr20 146289 200xa0 A T 60 . QNAME=cluster19_000000F;QSTART=25616593;QSTRAND=- GT:DP:AD ./.:30:17,13 1|1:45:22,23 ./.:39:25,14 +chr20 147079 200xa1 A C 60 . QNAME=cluster19_000000F;QSTART=25615803;QSTRAND=- GT:DP:AD ./.:35:11,24 1|1:24:16,8 ./.:20:14,6 +chr20 147311 200xa2 C T 60 . QNAME=cluster23_scaffold_3;QSTART=25564642;QSTRAND=- GT:DP:AD ./.:45:21,24 ./.:17:7,10 1|1:36:18,18 +chr20 148061 200xa3 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=101523;QSTRAND=+ GT:DP:AD 0|1:33:25,8 ./.:27:19,8 ./.:21:16,5 +chr20 148072 200xa4 C G 60 . QNAME=cluster19_000000F;QSTART=25614810;QSTRAND=- GT:DP:AD ./.:33:24,9 1|1:31:23,8 ./.:24:10,14 +chr20 148222 200xa5 G C 60 . QNAME=cluster23_scaffold_3;QSTART=25563731;QSTRAND=- GT:DP:AD ./.:40:18,22 ./.:41:16,25 1|1:42:22,20 +chr20 148422 200xa6 A G 60 . QNAME=cluster23_scaffold_3;QSTART=25563531;QSTRAND=- GT:DP:AD ./.:42:24,18 ./.:44:19,25 1|1:20:6,14 +chr20 148972 200xa7 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=127865;QSTRAND=+ GT:DP:AD 1|1:23:9,14 1|1:33:15,18 1|1:23:16,7 +chr20 148994 200xa8 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=127887;QSTRAND=+ GT:DP:AD 1|1:20:12,8 ./.:39:24,15 ./.:26:5,21 +chr20 149013 200xa9 A ACCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=127907;QSTRAND=+;SVTYPE=INS;SVLEN=69 GT:DP:AD 1/1:35:19,16 ./.:31:21,10 1/0:17:8,9 +chr20 149073 200xaa G GAATCCTGACCCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCA 60 . QNAME=cluster23_scaffold_2;QSTART=25547471;QSTRAND=-;SVTYPE=INS;SVLEN=69 GT:DP:AD ./.:44:25,19 ./.:36:12,24 0/1:27:20,7 +chr20 149095 200xab G GGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGACCCATATTTGGGAA 60 . QNAME=cluster19_000000F;QSTART=25613718;QSTRAND=-;SVTYPE=INS;SVLEN=69 GT:DP:AD ./.:36:13,23 1/1:14:7,7 ./.:40:19,21 +chr20 149223 200xac C T 60 . QNAME=cluster19_000000F;QSTART=25613590;QSTRAND=- GT:DP:AD ./.:26:5,21 1|1:42:19,23 ./.:38:21,17 +chr20 150418 200xad T A 60 . QNAME=cluster23_scaffold_2;QSTART=25546126;QSTRAND=- GT:DP:AD ./.:22:14,8 ./.:28:18,10 0|1:35:25,10 +chr20 150492 200xae G A 60 . QNAME=cluster23_scaffold_3;QSTART=25561392;QSTRAND=- GT:DP:AD ./.:39:17,22 ./.:37:20,17 1|0:29:9,20 +chr20 150721 200xaf C T 60 . QNAME=cluster19_000000F;QSTART=25612092;QSTRAND=- GT:DP:AD ./.:30:24,6 1|1:14:5,9 ./.:33:17,16 +chr20 150854 200xb0 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=129816;QSTRAND=+ GT:DP:AD 1|1:41:20,21 1|1:31:13,18 1|1:29:16,13 +chr20 150864 200xb1 CTCT C 60 . QNAME=cluster19_000000F;QSTART=25611949;QSTRAND=- GT:DP:AD ./.:30:12,18 1|1:14:5,9 ./.:25:19,6 +chr20 151016 200xb2 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=129978;QSTRAND=+ GT:DP:AD 1|1:25:5,20 1|1:40:18,22 1|1:42:17,25 +chr20 151307 200xb3 C CCA 60 . QNAME=cluster19_000000F;QSTART=25611507;QSTRAND=- GT:DP:AD ./.:21:11,10 1|1:22:17,5 ./.:31:10,21 +chr20 151663 200xb4 TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=130626;QSTRAND=+ GT:DP:AD 1|1:32:14,18 1|1:31:9,22 1|1:29:24,5 +chr20 151898 200xb5 A T 60 . QNAME=cluster23_scaffold_2;QSTART=25544647;QSTRAND=- GT:DP:AD ./.:30:25,5 ./.:25:13,12 0|1:37:20,17 +chr20 152134 200xb6 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=131095;QSTRAND=+ GT:DP:AD 1|1:37:20,17 ./.:34:24,10 ./.:43:18,25 +chr20 152450 200xb7 CAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=131412;QSTRAND=+ GT:DP:AD 1|1:11:5,6 ./.:27:12,15 1|0:43:18,25 +chr20 152450 200xb8 C CA 60 . QNAME=cluster19_000000F;QSTART=25610364;QSTRAND=- GT:DP:AD ./.:50:25,25 1|1:30:23,7 ./.:33:15,18 +chr20 152450 200xb9 CAA C 60 . QNAME=cluster23_scaffold_2;QSTART=25544095;QSTRAND=- GT:DP:AD ./.:40:25,15 ./.:28:7,21 0|1:36:13,23 +chr20 152517 200xba T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=131475;QSTRAND=+ GT:DP:AD 1|1:14:8,6 1|1:33:19,14 1|1:16:7,9 +chr20 152792 200xbb A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=131750;QSTRAND=+ GT:DP:AD 1|0:25:5,20 ./.:32:17,15 1|1:21:11,10 +chr20 153098 200xbc G GT 60 . QNAME=HG002-S9-H1-000001F;QSTART=132057;QSTRAND=+ GT:DP:AD 1|0:49:24,25 ./.:27:21,6 1|1:39:23,16 +chr20 153259 200xbd C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=132218;QSTRAND=+ GT:DP:AD 1|0:31:15,16 ./.:26:12,14 1|1:32:18,14 +chr20 153376 200xbe A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=106903;QSTRAND=+ GT:DP:AD 0|1:23:12,11 1|1:27:6,21 ./.:38:23,15 +chr20 153555 200xbf C T 60 . QNAME=cluster23_scaffold_3;QSTART=25558332;QSTRAND=- GT:DP:AD ./.:35:17,18 ./.:26:5,21 1|1:45:22,23 +chr20 153640 200xc0 C T 60 . QNAME=cluster23_scaffold_3;QSTART=25558247;QSTRAND=- GT:DP:AD ./.:25:20,5 ./.:32:25,7 1|1:49:24,25 +chr20 153643 200xc1 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=132602;QSTRAND=+ GT:DP:AD 1|1:45:20,25 1|1:16:6,10 1|1:25:14,11 +chr20 153725 200xc2 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=132684;QSTRAND=+ GT:DP:AD 1|1:35:11,24 1|1:25:6,19 1|1:15:5,10 +chr20 153759 200xc3 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=132718;QSTRAND=+ GT:DP:AD 1|0:33:17,16 ./.:32:14,18 1|0:36:23,13 +chr20 153780 200xc4 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=132739;QSTRAND=+ GT:DP:AD 1|1:26:19,7 1|1:31:6,25 1|1:29:5,24 +chr20 153787 200xc5 CAAAAAAAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=132747;QSTRAND=+ GT:DP:AD 1|1:36:19,17 1|1:23:11,12 1|1:20:13,7 +chr20 153835 200xc6 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=132785;QSTRAND=+ GT:DP:AD 1|1:21:15,6 1|1:30:9,21 1|1:14:7,7 +chr20 153898 200xc7 A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=132848;QSTRAND=+ GT:DP:AD 1|0:20:13,7 ./.:30:25,5 1|0:36:16,20 +chr20 154002 200xc8 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=132952;QSTRAND=+ GT:DP:AD 1|1:38:17,21 1|1:27:9,18 1|1:40:25,15 +chr20 154128 200xc9 T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=133079;QSTRAND=+ GT:DP:AD 1|0:25:6,19 ./.:33:16,17 1|1:22:17,5 +chr20 154203 200xca T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=133154;QSTRAND=+ GT:DP:AD 1|1:26:12,14 1|1:37:13,24 1|1:27:6,21 +chr20 154290 200xcb T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=133241;QSTRAND=+ GT:DP:AD 1|1:29:6,23 1|1:33:10,23 1|1:37:17,20 +chr20 154474 200xcc G GTTTGCATTCACAGGAAGACTATAAATAAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=133426;QSTRAND=+;SVTYPE=INS;SVLEN=29 GT:DP:AD 1/1:24:18,6 1/1:18:11,7 1/1:19:9,10 +chr20 154475 200xcd TGCTC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=133456;QSTRAND=+ GT:DP:AD 1|1:33:8,25 1|1:36:21,15 1|1:28:20,8 +chr20 154847 200xce C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=133823;QSTRAND=+ GT:DP:AD 1|1:35:14,21 1|1:27:9,18 1|1:22:7,15 +chr20 155384 200xcf C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=134360;QSTRAND=+ GT:DP:AD 1|0:24:13,11 ./.:25:12,13 1|1:17:7,10 +chr20 155733 200xd0 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=134709;QSTRAND=+ GT:DP:AD 1|0:17:10,7 ./.:25:13,12 1|1:36:24,12 +chr20 155813 200xd1 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=134789;QSTRAND=+ GT:DP:AD 1|0:37:15,22 ./.:27:11,16 1|1:23:5,18 +chr20 156080 200xd2 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=135056;QSTRAND=+ GT:DP:AD 1|0:26:12,14 ./.:21:15,6 1|1:28:21,7 +chr20 156287 200xd3 G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=135264;QSTRAND=+ GT:DP:AD 1|0:31:12,19 ./.:49:25,24 1|1:20:8,12 +chr20 156473 200xd4 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=135450;QSTRAND=+ GT:DP:AD 1|0:30:13,17 ./.:41:25,16 1|1:35:10,25 +chr20 156486 200xd5 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=110029;QSTRAND=+ GT:DP:AD 0|1:31:9,22 1|1:31:8,23 ./.:31:19,12 +chr20 156669 200xd6 C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=135646;QSTRAND=+ GT:DP:AD 1|0:37:25,12 ./.:32:17,15 1|1:21:14,7 +chr20 156813 200xd7 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=135790;QSTRAND=+ GT:DP:AD 1|0:19:9,10 ./.:25:14,11 1|1:36:13,23 +chr20 156877 200xd8 GTA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=135855;QSTRAND=+ GT:DP:AD 1|1:35:19,16 1|1:19:8,11 1|1:39:16,23 +chr20 156881 200xd9 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=135856;QSTRAND=+ GT:DP:AD 1|0:50:25,25 ./.:35:14,21 1|1:33:9,24 +chr20 157033 200xda G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=110574;QSTRAND=+ GT:DP:AD 0|1:15:6,9 1|1:34:19,15 ./.:38:17,21 +chr20 157259 200xdb T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=136234;QSTRAND=+ GT:DP:AD 1|0:25:6,19 ./.:25:14,11 1|1:34:21,13 +chr20 157292 200xdc C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=136267;QSTRAND=+ GT:DP:AD 1|1:30:11,19 1|1:21:14,7 1|1:35:25,10 +chr20 157363 200xdd G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=136338;QSTRAND=+ GT:DP:AD 1|1:18:9,9 1|1:20:12,8 1|1:33:24,9 +chr20 157484 200xde G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=136459;QSTRAND=+ GT:DP:AD 1|0:25:19,6 ./.:25:7,18 1|1:21:6,15 +chr20 157507 200xdf C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=136482;QSTRAND=+ GT:DP:AD 1|0:29:17,12 ./.:44:22,22 1|1:27:6,21 +chr20 157537 200xe0 GC G 60 . QNAME=HG002-S9-H2-000001F;QSTART=111079;QSTRAND=+ GT:DP:AD 0|1:39:15,24 1|1:15:7,8 ./.:41:22,19 +chr20 157819 200xe1 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=136794;QSTRAND=+ GT:DP:AD 1|0:32:10,22 ./.:17:10,7 1|1:26:13,13 +chr20 157914 200xe2 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=136889;QSTRAND=+ GT:DP:AD 1|0:31:10,21 ./.:35:23,12 1|1:16:8,8 +chr20 157922 200xe3 AATAT A 60 . QNAME=cluster23_scaffold_2;QSTART=25538608;QSTRAND=- GT:DP:AD ./.:19:12,7 ./.:33:17,16 0|1:27:5,22 +chr20 157927 200xe4 ATATATGTG A 60 . QNAME=HG002-S9-H1-000001F;QSTART=136903;QSTRAND=+ GT:DP:AD 1|0:23:7,16 ./.:26:8,18 ./.:42:24,18 +chr20 157927 200xe5 ATATATG A 60 . QNAME=cluster23_scaffold_3;QSTART=25553944;QSTRAND=- GT:DP:AD ./.:33:10,23 ./.:19:9,10 1|0:36:12,24 +chr20 157929 200xe6 ATATGTGTG A 60 . QNAME=HG002-S9-H2-000001F;QSTART=111470;QSTRAND=+ GT:DP:AD 0|1:41:18,23 1|1:32:16,16 ./.:15:10,5 +chr20 157960 200xe7 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=111492;QSTRAND=+ GT:DP:AD 0|1:26:9,17 1|1:24:10,14 ./.:32:20,12 +chr20 157962 200xe8 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=111494;QSTRAND=+ GT:DP:AD 0|1:32:15,17 1|1:30:18,12 ./.:35:24,11 +chr20 157965 200xe9 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=136932;QSTRAND=+ GT:DP:AD 1|0:13:8,5 ./.:38:21,17 1|1:27:17,10 +chr20 157974 200xea G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=136941;QSTRAND=+ GT:DP:AD 1|0:31:25,6 ./.:33:21,12 1|1:30:14,16 +chr20 157979 200xeb A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=136946;QSTRAND=+ GT:DP:AD 1|0:39:25,14 ./.:46:21,25 1|1:15:7,8 +chr20 158513 200xec A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=137480;QSTRAND=+ GT:DP:AD 1|0:31:8,23 ./.:22:5,17 1|1:44:23,21 +chr20 158532 200xed T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=137499;QSTRAND=+ GT:DP:AD 1|0:27:18,9 ./.:49:24,25 1|0:33:22,11 +chr20 158721 200xee G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=112253;QSTRAND=+ GT:DP:AD 0|1:30:17,13 1|1:14:6,8 ./.:43:20,23 +chr20 158768 200xef G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=137735;QSTRAND=+ GT:DP:AD 1|0:36:24,12 ./.:26:15,11 1|1:31:8,23 +chr20 158815 200xf0 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=137782;QSTRAND=+ GT:DP:AD 1|0:38:17,21 ./.:25:13,12 1|1:39:16,23 +chr20 158935 200xf1 C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=137902;QSTRAND=+ GT:DP:AD 1|0:19:14,5 ./.:36:23,13 1|1:41:25,16 +chr20 159104 200xf2 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=138071;QSTRAND=+ GT:DP:AD 1|1:35:25,10 1|1:24:6,18 1|1:19:6,13 +chr20 159197 200xf3 A T 60 . QNAME=cluster23_scaffold_2;QSTART=25537337;QSTRAND=- GT:DP:AD ./.:24:10,14 ./.:26:17,9 0|1:28:22,6 +chr20 159200 200xf4 A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=112732;QSTRAND=+ GT:DP:AD 0|1:26:6,20 1|1:44:24,20 ./.:31:22,9 +chr20 159274 200xf5 T TAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=138242;QSTRAND=+ GT:DP:AD 1|0:24:13,11 ./.:23:6,17 1|1:19:13,6 +chr20 159274 200xf6 T TAA 60 . QNAME=HG002-S9-H2-000001F;QSTART=112807;QSTRAND=+ GT:DP:AD 0|1:21:6,15 1|1:31:11,20 ./.:31:23,8 +chr20 159286 200xf7 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=138259;QSTRAND=+ GT:DP:AD 1|0:28:13,15 ./.:25:15,10 1|1:29:18,11 +chr20 159445 200xf8 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=112979;QSTRAND=+ GT:DP:AD 0|1:26:5,21 1|1:35:15,20 ./.:31:17,14 +chr20 159495 200xf9 G GAATGGCATAAACT 60 . QNAME=HG002-S9-H1-000001F;QSTART=138469;QSTRAND=+ GT:DP:AD 1|0:25:6,19 ./.:27:14,13 1|1:26:13,13 +chr20 159530 200xfa A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=138516;QSTRAND=+ GT:DP:AD 1|0:39:22,17 ./.:24:15,9 1|1:37:12,25 +chr20 159639 200xfb C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=113173;QSTRAND=+ GT:DP:AD 0|1:44:21,23 1|1:22:6,16 ./.:32:16,16 +chr20 159755 200xfc TTTG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=138742;QSTRAND=+ GT:DP:AD 1|1:29:17,12 1|1:24:7,17 1|1:38:18,20 +chr20 159864 200xfd C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=138847;QSTRAND=+ GT:DP:AD 1|0:21:15,6 ./.:41:18,23 1|1:34:16,18 +chr20 159865 200xfe A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=138848;QSTRAND=+ GT:DP:AD 1|0:21:13,8 ./.:37:16,21 1|1:39:16,23 +chr20 159952 200xff AG A 60 . QNAME=HG002-S9-H1-000001F;QSTART=138936;QSTRAND=+ GT:DP:AD 1|0:44:20,24 ./.:27:6,21 1|1:23:15,8 +chr20 160054 200x100 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=139036;QSTRAND=+ GT:DP:AD 1|0:24:19,5 ./.:48:23,25 1|1:19:11,8 +chr20 160212 200x101 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=139194;QSTRAND=+ GT:DP:AD 1|0:30:9,21 ./.:42:20,22 1|1:25:16,9 +chr20 160282 200x102 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=139264;QSTRAND=+ GT:DP:AD 1|0:32:14,18 ./.:41:17,24 1|1:24:17,7 +chr20 160312 200x103 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=139294;QSTRAND=+ GT:DP:AD 1|0:30:14,16 ./.:33:20,13 1|1:28:10,18 +chr20 160384 200x104 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=139366;QSTRAND=+ GT:DP:AD 1|0:34:19,15 ./.:30:10,20 1|1:22:17,5 +chr20 160388 200x105 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=139370;QSTRAND=+ GT:DP:AD 1|0:29:24,5 ./.:31:20,11 1|1:22:15,7 +chr20 160408 200x106 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=139390;QSTRAND=+ GT:DP:AD 1|0:35:16,19 ./.:20:12,8 1|1:35:10,25 +chr20 160413 200x107 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=139395;QSTRAND=+ GT:DP:AD 1|0:14:8,6 ./.:26:10,16 1|1:20:6,14 +chr20 160433 200x108 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=139415;QSTRAND=+ GT:DP:AD 1|0:37:16,21 ./.:18:9,9 1|1:32:11,21 +chr20 160558 200x109 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=139540;QSTRAND=+ GT:DP:AD 1|0:42:24,18 ./.:29:12,17 1|0:36:25,11 +chr20 160625 200x10a T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=139607;QSTRAND=+ GT:DP:AD 1|0:22:7,15 ./.:35:11,24 1|1:34:10,24 +chr20 160727 200x10b T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=139709;QSTRAND=+ GT:DP:AD 1|0:46:25,21 ./.:24:14,10 1|1:27:21,6 +chr20 160731 200x10c C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=139713;QSTRAND=+ GT:DP:AD 1|0:31:9,22 ./.:40:22,18 1|1:18:8,10 +chr20 160873 200x10d G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=139855;QSTRAND=+ GT:DP:AD 1|0:28:19,9 ./.:29:9,20 1|1:23:5,18 +chr20 160889 200x10e A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=139871;QSTRAND=+ GT:DP:AD 1|0:29:13,16 ./.:20:12,8 1|1:31:10,21 +chr20 160956 200x10f T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=139938;QSTRAND=+ GT:DP:AD 1|0:19:11,8 ./.:28:19,9 1|1:32:18,14 +chr20 160967 200x110 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=139949;QSTRAND=+ GT:DP:AD 1|0:29:20,9 ./.:38:22,16 1|1:17:10,7 +chr20 161128 200x111 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140110;QSTRAND=+ GT:DP:AD 1|0:30:12,18 ./.:28:11,17 1|1:20:10,10 +chr20 161181 200x112 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140163;QSTRAND=+ GT:DP:AD 1|0:17:8,9 ./.:41:24,17 1|1:32:7,25 +chr20 161221 200x113 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140203;QSTRAND=+ GT:DP:AD 1|0:32:16,16 ./.:15:7,8 1|1:19:14,5 +chr20 161380 200x114 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=140362;QSTRAND=+ GT:DP:AD 1|1:15:8,7 1|1:36:17,19 1|1:23:18,5 +chr20 161451 200x115 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=140433;QSTRAND=+ GT:DP:AD 1|0:30:9,21 ./.:25:13,12 1|1:32:16,16 +chr20 161571 200x116 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=140553;QSTRAND=+ GT:DP:AD 1|0:22:12,10 ./.:17:8,9 1|1:26:20,6 +chr20 161588 200x117 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140570;QSTRAND=+ GT:DP:AD 1|1:18:5,13 1|1:45:22,23 1|1:39:19,20 +chr20 161621 200x118 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=140603;QSTRAND=+ GT:DP:AD 1|0:27:6,21 ./.:15:9,6 1|1:29:9,20 +chr20 161638 200x119 C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=140620;QSTRAND=+ GT:DP:AD 1|1:34:12,22 1|1:37:13,24 1|1:33:25,8 +chr20 161698 200x11a T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140680;QSTRAND=+ GT:DP:AD 1|0:43:18,25 ./.:34:18,16 1|1:38:17,21 +chr20 161730 200x11b C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=140712;QSTRAND=+ GT:DP:AD 1|0:32:11,21 ./.:35:15,20 1|1:28:16,12 +chr20 161734 200x11c G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=140716;QSTRAND=+ GT:DP:AD 1|0:45:20,25 ./.:31:21,10 1|1:26:12,14 +chr20 161770 200x11d G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140752;QSTRAND=+ GT:DP:AD 1|0:19:7,12 ./.:39:16,23 1|1:29:12,17 +chr20 161914 200x11e A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=140896;QSTRAND=+ GT:DP:AD 1|0:32:12,20 ./.:25:20,5 1|1:20:7,13 +chr20 161918 200x11f C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=115449;QSTRAND=+ GT:DP:AD 0|1:25:5,20 1|1:27:16,11 ./.:40:17,23 +chr20 161991 200x120 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140973;QSTRAND=+ GT:DP:AD 1|0:28:22,6 ./.:29:16,13 1|1:32:21,11 +chr20 162151 200x121 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=141133;QSTRAND=+ GT:DP:AD 1|1:40:19,21 1|1:25:8,17 1|1:32:8,24 +chr20 162224 200x122 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=141206;QSTRAND=+ GT:DP:AD 1|0:34:15,19 ./.:21:16,5 1|1:30:12,18 +chr20 162225 200x123 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=141207;QSTRAND=+ GT:DP:AD 1|0:42:17,25 ./.:28:13,15 1|1:23:10,13 +chr20 162228 200x124 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=141210;QSTRAND=+ GT:DP:AD 1|0:26:10,16 ./.:27:5,22 1|1:41:21,20 +chr20 162268 200x125 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=141250;QSTRAND=+ GT:DP:AD 1|0:37:19,18 ./.:44:25,19 1|1:42:23,19 +chr20 162455 200x126 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=141437;QSTRAND=+ GT:DP:AD 1|0:15:7,8 ./.:39:20,19 1|1:18:6,12 +chr20 162806 200x127 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=116337;QSTRAND=+ GT:DP:AD 0|1:48:24,24 1|1:31:12,19 ./.:30:24,6 +chr20 162854 200x128 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=141836;QSTRAND=+ GT:DP:AD 1|0:44:25,19 ./.:24:14,10 1|1:23:11,12 +chr20 162932 200x129 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=141914;QSTRAND=+ GT:DP:AD 1|0:19:14,5 ./.:39:25,14 1|1:36:11,25 +chr20 163082 200x12a G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=142064;QSTRAND=+ GT:DP:AD 1|0:45:22,23 ./.:16:8,8 1|1:28:10,18 +chr20 163113 200x12b C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=142095;QSTRAND=+ GT:DP:AD 1|0:14:7,7 ./.:29:11,18 1|1:24:12,12 +chr20 163277 200x12c C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=142259;QSTRAND=+ GT:DP:AD 1|1:15:9,6 1|1:49:25,24 1|1:46:24,22 +chr20 163741 200x12d T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=117272;QSTRAND=+ GT:DP:AD 0|1:23:9,14 1|1:26:7,19 ./.:28:10,18 +chr20 163894 200x12e A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=117425;QSTRAND=+ GT:DP:AD 0|1:30:18,12 1|1:26:18,8 ./.:17:6,11 +chr20 163919 200x12f T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=117450;QSTRAND=+ GT:DP:AD 0|1:45:22,23 1|1:22:14,8 ./.:35:15,20 +chr20 163929 200x130 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=117460;QSTRAND=+ GT:DP:AD 0|1:35:14,21 1|1:34:25,9 ./.:31:21,10 +chr20 164191 200x131 C CT 60 . QNAME=HG002-S9-H2-000001F;QSTART=117723;QSTRAND=+ GT:DP:AD 0|1:35:19,16 1|1:25:18,7 ./.:36:17,19 +chr20 164243 200x132 CCTT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=117776;QSTRAND=+ GT:DP:AD 0|1:30:7,23 1|1:28:9,19 ./.:31:20,11 +chr20 164258 200x133 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=117787;QSTRAND=+ GT:DP:AD 0|1:28:21,7 1|1:26:20,6 ./.:26:5,21 +chr20 164569 200x134 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=143551;QSTRAND=+ GT:DP:AD 1|1:37:22,15 1|1:37:20,17 1|1:30:21,9 +chr20 164616 200x135 G GC 60 . QNAME=HG002-S9-H2-000001F;QSTART=118146;QSTRAND=+ GT:DP:AD 0|1:17:5,12 1|1:25:11,14 ./.:23:11,12 +chr20 164772 200x136 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=118302;QSTRAND=+ GT:DP:AD 0|1:44:21,23 1|1:20:13,7 ./.:40:20,20 +chr20 165108 200x137 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=118638;QSTRAND=+ GT:DP:AD 0|1:30:20,10 1|1:22:12,10 ./.:26:9,17 +chr20 165108 200x138 C CAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=144091;QSTRAND=+ GT:DP:AD 1|0:27:9,18 ./.:26:9,17 ./.:24:9,15 +chr20 165108 200x139 C CACAT 60 . QNAME=cluster23_scaffold_3;QSTART=25546750;QSTRAND=- GT:DP:AD ./.:31:19,12 ./.:39:20,19 1|1:35:16,19 +chr20 165212 200x13a C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=144196;QSTRAND=+ GT:DP:AD 1|0:23:12,11 ./.:43:24,19 1|1:26:16,10 +chr20 166310 200x13b A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=145294;QSTRAND=+ GT:DP:AD 1|0:41:16,25 ./.:45:25,20 1|1:14:6,8 +chr20 166354 200x13c A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=119884;QSTRAND=+ GT:DP:AD 0|1:40:15,25 1|1:29:20,9 ./.:37:13,24 +chr20 166856 200x13d G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=145840;QSTRAND=+ GT:DP:AD 1|0:30:9,21 ./.:33:25,8 1|1:44:23,21 +chr20 166960 200x13e CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=145945;QSTRAND=+ GT:DP:AD 1|0:40:20,20 ./.:30:15,15 1|1:46:21,25 +chr20 167044 200x13f A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=146027;QSTRAND=+ GT:DP:AD 1|0:17:10,7 ./.:33:15,18 1|1:42:23,19 +chr20 167104 200x140 G A 60 . QNAME=cluster23_scaffold_2;QSTART=25529412;QSTRAND=- GT:DP:AD ./.:42:18,24 ./.:33:25,8 0|1:15:10,5 +chr20 167274 200x141 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=146257;QSTRAND=+ GT:DP:AD 1|0:29:16,13 ./.:36:21,15 1|1:36:22,14 +chr20 167276 200x142 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=146259;QSTRAND=+ GT:DP:AD 1|0:35:10,25 ./.:38:15,23 1|1:25:12,13 +chr20 167443 200x143 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=146426;QSTRAND=+ GT:DP:AD 1|1:20:14,6 1|1:15:6,9 1|1:35:12,23 +chr20 167839 200x144 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=146822;QSTRAND=+ GT:DP:AD 1|1:21:7,14 1|1:26:5,21 1|1:23:10,13 +chr20 168062 200x145 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=147045;QSTRAND=+ GT:DP:AD 1|0:30:8,22 ./.:25:14,11 1|1:26:16,10 +chr20 168478 200x146 CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=147462;QSTRAND=+ GT:DP:AD 1|0:31:11,20 ./.:16:8,8 1|1:36:25,11 +chr20 168766 200x147 C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=122296;QSTRAND=+ GT:DP:AD 0|1:29:18,11 1|1:29:19,10 ./.:30:13,17 +chr20 169334 200x148 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=122864;QSTRAND=+ GT:DP:AD 0|1:20:8,12 1|1:36:17,19 ./.:25:15,10 +chr20 170008 200x149 CTACA C 60 . QNAME=cluster23_scaffold_2;QSTART=25526509;QSTRAND=- GT:DP:AD ./.:40:15,25 ./.:31:10,21 0|1:23:12,11 +chr20 170689 200x14a T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=124219;QSTRAND=+ GT:DP:AD 0|1:27:9,18 1|1:25:10,15 ./.:27:18,9 +chr20 171892 200x14b G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=125422;QSTRAND=+ GT:DP:AD 0|1:29:6,23 1|1:22:8,14 ./.:40:17,23 +chr20 171929 200x14c G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=125459;QSTRAND=+ GT:DP:AD 0|1:36:22,14 1|1:39:15,24 0|1:36:11,25 +chr20 172156 200x14d G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=125686;QSTRAND=+ GT:DP:AD 0|1:20:8,12 1|0:28:20,8 ./.:21:8,13 +chr20 172258 200x14e G T 60 . QNAME=cluster23_scaffold_3;QSTART=25539602;QSTRAND=- GT:DP:AD ./.:35:19,16 ./.:31:9,22 1|0:36:23,13 +chr20 172331 200x14f T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=125861;QSTRAND=+ GT:DP:AD 0|1:26:13,13 1|1:42:23,19 0|1:19:13,6 +chr20 172351 200x150 C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=125881;QSTRAND=+ GT:DP:AD 0|1:41:16,25 1|1:32:7,25 0|1:27:19,8 +chr20 172626 200x151 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=126156;QSTRAND=+ GT:DP:AD 0|1:27:22,5 1|1:16:5,11 0|1:34:24,10 +chr20 172657 200x152 T TTC 60 . QNAME=HG002-S9-H2-000001F;QSTART=126188;QSTRAND=+ GT:DP:AD 0|1:40:25,15 1|1:38:16,22 0|1:19:5,14 +chr20 172752 200x153 C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=126284;QSTRAND=+ GT:DP:AD 0|1:37:22,15 1|1:36:11,25 ./.:41:24,17 +chr20 172789 200x154 G T 60 . QNAME=cluster23_scaffold_2;QSTART=25523730;QSTRAND=- GT:DP:AD ./.:29:11,18 ./.:38:20,18 0|1:36:25,11 +chr20 173036 200x155 T C 60 . QNAME=cluster23_scaffold_2;QSTART=25523483;QSTRAND=- GT:DP:AD ./.:46:24,22 ./.:17:12,5 0|1:36:22,14 +chr20 173050 200x156 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=126582;QSTRAND=+ GT:DP:AD 0|1:32:13,19 1|1:16:6,10 ./.:32:12,20 +chr20 173133 200x157 C T 60 . QNAME=cluster23_scaffold_2;QSTART=25523386;QSTRAND=- GT:DP:AD ./.:28:12,16 ./.:40:24,16 0|1:38:14,24 +chr20 173215 200x158 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=152197;QSTRAND=+ GT:DP:AD 1|0:29:12,17 ./.:15:10,5 ./.:34:12,22 +chr20 173791 200x159 CCTT C 60 . QNAME=cluster23_scaffold_2;QSTART=25522728;QSTRAND=- GT:DP:AD ./.:32:23,9 ./.:44:19,25 0|1:44:19,25 +chr20 173973 200x15a T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=127505;QSTRAND=+ GT:DP:AD 0|1:35:24,11 1|1:42:17,25 ./.:35:11,24 +chr20 174069 200x15b G A 60 . QNAME=cluster19_000000F;QSTART=133216;QSTRAND=+ GT:DP:AD ./.:36:16,20 0|1:19:12,7 ./.:49:24,25 +chr20 174270 200x15c TC T 60 . QNAME=cluster23_scaffold_2;QSTART=25522252;QSTRAND=- GT:DP:AD ./.:40:16,24 ./.:15:10,5 0|1:26:6,20 +chr20 174280 200x15d T C 60 . QNAME=cluster23_scaffold_2;QSTART=25522243;QSTRAND=- GT:DP:AD ./.:23:18,5 ./.:31:7,24 0|1:45:24,21 +chr20 174737 200x15e G A 60 . QNAME=cluster23_scaffold_2;QSTART=25521786;QSTRAND=- GT:DP:AD ./.:34:10,24 ./.:18:5,13 0|1:31:7,24 +chr20 174986 200x15f T C 60 . QNAME=cluster23_scaffold_2;QSTART=25521537;QSTRAND=- GT:DP:AD ./.:32:20,12 ./.:48:23,25 0|1:44:24,20 +chr20 175210 200x160 T C 60 . QNAME=cluster23_scaffold_2;QSTART=25521313;QSTRAND=- GT:DP:AD ./.:24:11,13 ./.:38:16,22 0|1:23:11,12 +chr20 175239 200x161 G A 60 . QNAME=cluster23_scaffold_2;QSTART=25521284;QSTRAND=- GT:DP:AD ./.:23:17,6 ./.:25:8,17 0|1:41:16,25 +chr20 175269 200x162 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=128801;QSTRAND=+ GT:DP:AD 0|1:28:8,20 1|1:23:13,10 0|1:36:12,24 +chr20 175314 200x163 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=128846;QSTRAND=+ GT:DP:AD 0|1:28:18,10 1|1:19:13,6 ./.:42:17,25 +chr20 175375 200x164 A G 60 . QNAME=cluster23_scaffold_2;QSTART=25521148;QSTRAND=- GT:DP:AD ./.:30:14,16 ./.:26:15,11 0|1:38:21,17 +chr20 175501 200x165 T C 60 . QNAME=cluster23_scaffold_2;QSTART=25521022;QSTRAND=- GT:DP:AD ./.:27:10,17 ./.:31:19,12 0|1:18:7,11 +chr20 175524 200x166 C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=129056;QSTRAND=+ GT:DP:AD 0|1:30:23,7 1|1:21:13,8 0|1:25:16,9 +chr20 175532 200x167 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=129064;QSTRAND=+ GT:DP:AD 0|1:43:25,18 1|1:36:21,15 0|1:28:17,11 +chr20 175563 200x168 T C 60 . QNAME=cluster23_scaffold_2;QSTART=25520960;QSTRAND=- GT:DP:AD ./.:14:5,9 ./.:29:6,23 0|1:18:5,13 +chr20 175565 200x169 G A 60 . QNAME=cluster23_scaffold_2;QSTART=25520958;QSTRAND=- GT:DP:AD ./.:15:8,7 ./.:29:20,9 0|1:37:24,13 +chr20 175595 200x16a G A 60 . QNAME=cluster23_scaffold_2;QSTART=25520928;QSTRAND=- GT:DP:AD ./.:26:15,11 ./.:35:21,14 0|1:30:17,13 +chr20 175658 200x16b C T 60 . QNAME=cluster23_scaffold_2;QSTART=25520865;QSTRAND=- GT:DP:AD ./.:32:25,7 ./.:16:10,6 0|1:47:25,22 +chr20 175659 200x16c C T 60 . QNAME=cluster23_scaffold_2;QSTART=25520864;QSTRAND=- GT:DP:AD ./.:18:10,8 ./.:33:12,21 0|1:29:19,10 +chr20 175676 200x16d C T 60 . QNAME=cluster23_scaffold_2;QSTART=25520847;QSTRAND=- GT:DP:AD ./.:26:18,8 ./.:38:15,23 0|1:35:14,21 +chr20 175688 200x16e G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=129220;QSTRAND=+ GT:DP:AD 0|1:30:13,17 1|1:38:17,21 0|1:24:18,6 +chr20 175689 200x16f G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=129221;QSTRAND=+ GT:DP:AD 0|1:28:7,21 1|1:31:13,18 0|1:27:5,22 +chr20 175813 200x170 T C 60 . QNAME=cluster23_scaffold_2;QSTART=25520710;QSTRAND=- GT:DP:AD ./.:30:25,5 ./.:35:18,17 0|1:26:17,9 +chr20 175893 200x171 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=129425;QSTRAND=+ GT:DP:AD 0|1:38:19,19 1|1:34:14,20 0|1:23:17,6 +chr20 175897 200x172 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=129429;QSTRAND=+ GT:DP:AD 0|1:20:11,9 1|1:31:11,20 0|1:46:25,21 +chr20 176011 200x173 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=129543;QSTRAND=+ GT:DP:AD 0|1:35:25,10 1|1:40:16,24 ./.:42:21,21 +chr20 176015 200x174 A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=129547;QSTRAND=+ GT:DP:AD 0|1:29:22,7 1|1:26:10,16 ./.:30:18,12 +chr20 176015 200x175 A G 60 . QNAME=cluster23_scaffold_2;QSTART=25520508;QSTRAND=- GT:DP:AD ./.:25:10,15 ./.:36:18,18 0|1:38:19,19 +chr20 176128 200x176 G T 60 . QNAME=cluster23_scaffold_2;QSTART=25520395;QSTRAND=- GT:DP:AD ./.:28:12,16 ./.:18:5,13 0|1:41:17,24 +chr20 176156 200x177 A T 60 . QNAME=cluster23_scaffold_2;QSTART=25520367;QSTRAND=- GT:DP:AD ./.:25:20,5 ./.:31:17,14 0|1:37:24,13 +chr20 176325 200x178 A G 60 . QNAME=cluster23_scaffold_2;QSTART=25520198;QSTRAND=- GT:DP:AD ./.:27:14,13 ./.:29:9,20 0|1:39:23,16 +chr20 176400 200x179 G GCCC 60 . QNAME=cluster23_scaffold_2;QSTART=25520120;QSTRAND=- GT:DP:AD ./.:42:25,17 ./.:19:10,9 0|1:20:7,13 +chr20 176406 200x17a T C 60 . QNAME=cluster23_scaffold_2;QSTART=25520114;QSTRAND=- GT:DP:AD ./.:31:10,21 ./.:21:5,16 0|1:25:9,16 +chr20 176516 200x17b T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=130048;QSTRAND=+ GT:DP:AD 0|1:36:14,22 1|1:35:19,16 0|1:23:12,11 +chr20 176631 200x17c C T 60 . QNAME=cluster19_000000F;QSTART=135778;QSTRAND=+ GT:DP:AD ./.:36:20,16 0|1:29:24,5 ./.:25:8,17 +chr20 176881 200x17d C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=130413;QSTRAND=+ GT:DP:AD 0|1:24:13,11 1|0:31:23,8 ./.:39:14,25 +chr20 177105 200x17e A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=130637;QSTRAND=+ GT:DP:AD 0|1:26:6,20 1|1:17:6,11 0|1:18:9,9 +chr20 177210 200x17f G A 60 . QNAME=cluster23_scaffold_2;QSTART=25519310;QSTRAND=- GT:DP:AD ./.:25:20,5 ./.:23:18,5 0|1:40:19,21 +chr20 177334 200x180 C T 60 . QNAME=cluster23_scaffold_2;QSTART=25519186;QSTRAND=- GT:DP:AD ./.:33:15,18 ./.:47:24,23 0|1:23:5,18 +chr20 177335 200x181 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=130867;QSTRAND=+ GT:DP:AD 0|1:27:16,11 1|1:18:9,9 0|1:18:13,5 +chr20 177343 200x182 C T 60 . QNAME=cluster23_scaffold_2;QSTART=25519177;QSTRAND=- GT:DP:AD ./.:38:22,16 ./.:28:7,21 0|1:29:14,15 +chr20 177473 200x183 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=131005;QSTRAND=+ GT:DP:AD 0|1:37:17,20 1|1:43:18,25 0|1:29:23,6 +chr20 177674 200x184 G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=131206;QSTRAND=+ GT:DP:AD 0|1:37:17,20 1|1:20:9,11 ./.:25:19,6 +chr20 177749 200x185 A G 60 . QNAME=cluster23_scaffold_2;QSTART=25518771;QSTRAND=- GT:DP:AD ./.:26:21,5 ./.:23:7,16 0|1:20:5,15 +chr20 177793 200x186 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=131325;QSTRAND=+ GT:DP:AD 0|1:34:20,14 1|1:25:14,11 ./.:32:7,25 +chr20 177854 200x187 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=131386;QSTRAND=+ GT:DP:AD 0|1:35:12,23 1|1:31:19,12 0|1:20:11,9 +chr20 178043 200x188 C T 60 . QNAME=cluster23_scaffold_2;QSTART=25518477;QSTRAND=- GT:DP:AD ./.:20:15,5 ./.:29:19,10 0|1:27:14,13 +chr20 178049 200x189 G A 60 . QNAME=cluster23_scaffold_2;QSTART=25518471;QSTRAND=- GT:DP:AD ./.:22:5,17 ./.:35:16,19 0|1:28:15,13 +chr20 178343 200x18a C T 60 . QNAME=cluster23_scaffold_2;QSTART=25518177;QSTRAND=- GT:DP:AD ./.:28:15,13 ./.:26:16,10 0|1:43:21,22 +chr20 178456 200x18b T C 60 . QNAME=cluster23_scaffold_2;QSTART=25518064;QSTRAND=- GT:DP:AD ./.:29:7,22 ./.:42:20,22 0|1:28:11,17 +chr20 178604 200x18c T C 60 . QNAME=cluster23_scaffold_2;QSTART=25517916;QSTRAND=- GT:DP:AD ./.:22:7,15 ./.:40:24,16 0|1:40:17,23 +chr20 178648 200x18d C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=132180;QSTRAND=+ GT:DP:AD 0|1:20:5,15 1|1:27:12,15 ./.:27:6,21 +chr20 178883 200x18e G A 60 . QNAME=cluster23_scaffold_2;QSTART=25517637;QSTRAND=- GT:DP:AD ./.:33:19,14 ./.:21:9,12 0|1:22:16,6 +chr20 179104 200x18f A C 60 . QNAME=cluster23_scaffold_2;QSTART=25517416;QSTRAND=- GT:DP:AD ./.:33:11,22 ./.:28:6,22 0|1:37:16,21 +chr20 179470 200x190 A AT 60 . QNAME=HG002-S9-H2-000001F;QSTART=133003;QSTRAND=+ GT:DP:AD 0|1:25:8,17 1|1:27:5,22 0|1:42:25,17 +chr20 179567 200x191 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=133100;QSTRAND=+ GT:DP:AD 0|1:26:8,18 1|1:24:11,13 0|1:27:20,7 +chr20 179575 200x192 T C 60 . QNAME=cluster23_scaffold_2;QSTART=25516944;QSTRAND=- GT:DP:AD ./.:41:16,25 ./.:23:9,14 0|1:38:20,18 +chr20 179892 200x193 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=133425;QSTRAND=+ GT:DP:AD 0|1:33:16,17 1|1:29:21,8 ./.:26:6,20 +chr20 179910 200x194 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=133443;QSTRAND=+ GT:DP:AD 0|1:22:17,5 1|1:30:20,10 0|1:44:20,24 +chr20 180809 200x195 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=134342;QSTRAND=+ GT:DP:AD 0|1:33:25,8 1|1:46:24,22 0|1:49:25,24 +chr20 180861 200x196 C T 60 . QNAME=cluster23_scaffold_2;QSTART=25515658;QSTRAND=- GT:DP:AD ./.:28:7,21 ./.:41:17,24 0|1:33:25,8 +chr20 180945 200x197 G A 60 . QNAME=cluster23_scaffold_2;QSTART=25515574;QSTRAND=- GT:DP:AD ./.:21:16,5 ./.:28:8,20 0|1:23:7,16 +chr20 181095 200x198 C T 60 . QNAME=cluster23_scaffold_2;QSTART=25515424;QSTRAND=- GT:DP:AD ./.:19:12,7 ./.:27:17,10 0|1:12:7,5 +chr20 181461 200x199 C T 60 . QNAME=cluster23_scaffold_2;QSTART=25515058;QSTRAND=- GT:DP:AD ./.:28:7,21 ./.:15:6,9 0|1:31:8,23 +chr20 181576 200x19a C T 60 . QNAME=cluster23_scaffold_2;QSTART=25514943;QSTRAND=- GT:DP:AD ./.:40:15,25 ./.:19:9,10 0|1:35:20,15 +chr20 181650 200x19b C T 60 . QNAME=cluster23_scaffold_2;QSTART=25514869;QSTRAND=- GT:DP:AD ./.:32:15,17 ./.:23:13,10 0|1:17:10,7 +chr20 181651 200x19c A G 60 . QNAME=cluster23_scaffold_2;QSTART=25514868;QSTRAND=- GT:DP:AD ./.:38:16,22 ./.:16:7,9 0|1:28:21,7 +chr20 181704 200x19d AAAAT A 60 . QNAME=cluster23_scaffold_2;QSTART=25514815;QSTRAND=- GT:DP:AD ./.:37:24,13 ./.:38:17,21 0|1:38:25,13 +chr20 182042 200x19e C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=135575;QSTRAND=+ GT:DP:AD 0|1:36:22,14 1|1:38:15,23 ./.:27:11,16 +chr20 182056 200x19f C G 60 . QNAME=cluster23_scaffold_2;QSTART=25514467;QSTRAND=- GT:DP:AD ./.:34:21,13 ./.:36:13,23 0|1:32:13,19 +chr20 182966 200x1a0 A AAT 60 . QNAME=HG002-S9-H2-000001F;QSTART=136500;QSTRAND=+ GT:DP:AD 0|1:22:7,15 1|1:33:25,8 0|1:39:14,25 +chr20 182982 200x1a1 G A 60 . QNAME=cluster23_scaffold_2;QSTART=25513539;QSTRAND=- GT:DP:AD ./.:50:25,25 ./.:31:8,23 0|1:35:18,17 +chr20 183100 200x1a2 T TACACAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=136636;QSTRAND=+ GT:DP:AD 0|1:46:22,24 1|1:24:19,5 ./.:23:14,9 +chr20 183100 200x1a3 T TAC 60 . QNAME=cluster23_scaffold_2;QSTART=25513419;QSTRAND=- GT:DP:AD ./.:43:22,21 ./.:22:6,16 0|1:26:20,6 +chr20 183442 200x1a4 T C 60 . QNAME=cluster23_scaffold_2;QSTART=25513077;QSTRAND=- GT:DP:AD ./.:42:20,22 ./.:26:11,15 0|1:32:22,10 +chr20 183617 200x1a5 G GGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAA 60 . QNAME=cluster23_scaffold_2;QSTART=25512867;QSTRAND=-;SVTYPE=INS;SVLEN=35 GT:DP:AD ./.:35:16,19 ./.:32:20,12 0/1:24:11,13 +chr20 183638 200x1a6 G GAAAAC 60 . QNAME=cluster19_000000F;QSTART=142795;QSTRAND=+ GT:DP:AD ./.:30:6,24 0|1:45:25,20 ./.:40:19,21 +chr20 183643 200x1a7 G C 60 . QNAME=cluster19_000000F;QSTART=142804;QSTRAND=+ GT:DP:AD ./.:37:17,20 0|1:33:24,9 ./.:27:12,15 +chr20 183643 200x1a8 G GAAAAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=137185;QSTRAND=+ GT:DP:AD 0|1:41:22,19 1|0:40:25,15 ./.:30:17,13 +chr20 183699 200x1a9 A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=137245;QSTRAND=+ GT:DP:AD 0|1:31:23,8 1|1:37:21,16 ./.:47:24,23 +chr20 183795 200x1aa C T 60 . QNAME=cluster23_scaffold_2;QSTART=25512689;QSTRAND=- GT:DP:AD ./.:23:18,5 ./.:31:7,24 0|1:49:24,25 +chr20 184483 200x1ab C T 60 . QNAME=cluster23_scaffold_2;QSTART=25512001;QSTRAND=- GT:DP:AD ./.:32:10,22 ./.:43:23,20 0|1:30:19,11 +chr20 184792 200x1ac A G 60 . QNAME=cluster23_scaffold_2;QSTART=25511692;QSTRAND=- GT:DP:AD ./.:18:9,9 ./.:23:7,16 0|1:38:13,25 +chr20 184838 200x1ad T C 60 . QNAME=cluster23_scaffold_2;QSTART=25511646;QSTRAND=- GT:DP:AD ./.:42:25,17 ./.:28:15,13 0|1:17:7,10 +chr20 185161 200x1ae C G 60 . QNAME=cluster23_scaffold_2;QSTART=25511323;QSTRAND=- GT:DP:AD ./.:29:13,16 ./.:21:11,10 0|1:31:11,20 +chr20 185267 200x1af T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=138813;QSTRAND=+ GT:DP:AD 0|1:31:22,9 1|1:49:24,25 0|1:44:19,25 +chr20 185522 200x1b0 T C 60 . QNAME=cluster23_scaffold_2;QSTART=25510962;QSTRAND=- GT:DP:AD ./.:41:24,17 ./.:47:24,23 0|1:23:7,16 +chr20 185547 200x1b1 G A 60 . QNAME=cluster23_scaffold_2;QSTART=25510937;QSTRAND=- GT:DP:AD ./.:23:11,12 ./.:48:24,24 0|1:30:22,8 +chr20 185835 200x1b2 C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25510648;QSTRAND=- GT:DP:AD ./.:33:20,13 ./.:19:6,13 0|1:37:18,19 +chr20 186086 200x1b3 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=139632;QSTRAND=+ GT:DP:AD 0|1:24:18,6 1|1:43:22,21 ./.:30:15,15 +chr20 186099 200x1b4 C CAA 60 . QNAME=cluster23_scaffold_2;QSTART=25510382;QSTRAND=- GT:DP:AD ./.:22:6,16 ./.:21:14,7 0|1:41:25,16 +chr20 186183 200x1b5 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=139729;QSTRAND=+ GT:DP:AD 0|1:34:18,16 1|1:25:7,18 ./.:24:7,17 +chr20 186577 200x1b6 G A 60 . QNAME=cluster23_scaffold_2;QSTART=25509904;QSTRAND=- GT:DP:AD ./.:20:12,8 ./.:18:7,11 0|1:23:7,16 +chr20 186669 200x1b7 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=140215;QSTRAND=+ GT:DP:AD 0|1:40:23,17 1|1:29:21,8 ./.:31:14,17 +chr20 186684 200x1b8 G T 60 . QNAME=cluster23_scaffold_2;QSTART=25509797;QSTRAND=- GT:DP:AD ./.:24:17,7 ./.:28:9,19 0|1:28:15,13 +chr20 186790 200x1b9 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=140336;QSTRAND=+ GT:DP:AD 0|1:28:18,10 1|1:10:5,5 0|1:23:10,13 +chr20 186800 200x1ba G A 60 . QNAME=cluster23_scaffold_2;QSTART=25509681;QSTRAND=- GT:DP:AD ./.:28:19,9 ./.:19:13,6 0|1:31:8,23 +chr20 186814 200x1bb A G 60 . QNAME=cluster23_scaffold_2;QSTART=25509667;QSTRAND=- GT:DP:AD ./.:24:17,7 ./.:46:21,25 0|1:39:21,18 +chr20 187006 200x1bc T A 60 . QNAME=cluster23_scaffold_2;QSTART=25509475;QSTRAND=- GT:DP:AD ./.:41:16,25 ./.:33:25,8 0|1:35:22,13 +chr20 187133 200x1bd G A 60 . QNAME=cluster23_scaffold_2;QSTART=25509348;QSTRAND=- GT:DP:AD ./.:30:17,13 ./.:41:24,17 0|1:46:23,23 +chr20 187259 200x1be C G 60 . QNAME=cluster23_scaffold_2;QSTART=25509222;QSTRAND=- GT:DP:AD ./.:32:18,14 ./.:28:13,15 0|1:34:22,12 +chr20 187379 200x1bf T C 60 . QNAME=cluster23_scaffold_2;QSTART=25509102;QSTRAND=- GT:DP:AD ./.:34:15,19 ./.:28:13,15 0|1:22:9,13 +chr20 187439 200x1c0 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=140985;QSTRAND=+ GT:DP:AD 0|1:33:14,19 1|1:26:15,11 ./.:24:13,11 +chr20 187498 200x1c1 G A 60 . QNAME=cluster23_scaffold_2;QSTART=25508983;QSTRAND=- GT:DP:AD ./.:20:5,15 ./.:18:13,5 0|1:35:21,14 +chr20 187600 200x1c2 G A 60 . QNAME=cluster23_scaffold_2;QSTART=25508881;QSTRAND=- GT:DP:AD ./.:15:7,8 ./.:36:18,18 0|1:23:10,13 +chr20 187825 200x1c3 T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=141371;QSTRAND=+ GT:DP:AD 0|1:31:12,19 1|1:16:8,8 ./.:41:24,17 +chr20 188087 200x1c4 T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=141633;QSTRAND=+ GT:DP:AD 0|1:20:13,7 1|1:41:23,18 0|1:25:15,10 +chr20 188490 200x1c5 C T 60 . QNAME=cluster23_scaffold_2;QSTART=25507991;QSTRAND=- GT:DP:AD ./.:18:7,11 ./.:18:7,11 0|1:26:21,5 +chr20 189060 200x1c6 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=142606;QSTRAND=+ GT:DP:AD 0|1:14:8,6 1|1:42:18,24 ./.:30:6,24 +chr20 189354 200x1c7 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=142900;QSTRAND=+ GT:DP:AD 0|1:24:9,15 1|1:21:11,10 0|1:34:21,13 +chr20 189473 200x1c8 T C 60 . QNAME=cluster23_scaffold_2;QSTART=25507008;QSTRAND=- GT:DP:AD ./.:33:17,16 ./.:34:23,11 0|1:48:25,23 +chr20 189948 200x1c9 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=143494;QSTRAND=+ GT:DP:AD 0|1:23:6,17 1|1:40:19,21 0|1:26:21,5 +chr20 190001 200x1ca G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=143547;QSTRAND=+ GT:DP:AD 0|1:14:6,8 1|1:44:20,24 0|1:29:10,19 +chr20 190548 200x1cb C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=144094;QSTRAND=+ GT:DP:AD 0|1:34:13,21 1|1:41:18,23 ./.:37:19,18 +chr20 190675 200x1cc C CTT 60 . QNAME=HG002-S9-H2-000001F;QSTART=144222;QSTRAND=+ GT:DP:AD 0|1:23:7,16 1|1:36:25,11 ./.:45:20,25 +chr20 190675 200x1cd C CT 60 . QNAME=cluster23_scaffold_2;QSTART=25505805;QSTRAND=- GT:DP:AD ./.:26:6,20 ./.:27:9,18 0|1:24:11,13 +chr20 190950 200x1ce G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=144498;QSTRAND=+ GT:DP:AD 0|1:26:8,18 1|1:28:20,8 ./.:45:24,21 +chr20 190986 200x1cf G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=144534;QSTRAND=+ GT:DP:AD 0|1:37:24,13 1|1:42:21,21 ./.:33:23,10 +chr20 191069 200x1d0 G A 60 . QNAME=cluster23_scaffold_2;QSTART=25505411;QSTRAND=- GT:DP:AD ./.:35:24,11 ./.:24:13,11 0|1:24:5,19 +chr20 191221 200x1d1 A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=170203;QSTRAND=+ GT:DP:AD 1|0:43:20,23 ./.:25:7,18 ./.:44:21,23 +chr20 191726 200x1d2 CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=145275;QSTRAND=+ GT:DP:AD 0|1:33:20,13 1|1:34:19,15 ./.:24:13,11 +chr20 191726 200x1d3 C CTT 60 . QNAME=cluster23_scaffold_3;QSTART=25520132;QSTRAND=- GT:DP:AD ./.:32:18,14 ./.:17:5,12 1|0:23:15,8 +chr20 191726 200x1d4 CTT C 60 . QNAME=cluster23_scaffold_2;QSTART=25504754;QSTRAND=- GT:DP:AD ./.:16:8,8 ./.:41:22,19 0|1:43:24,19 +chr20 191877 200x1d5 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=145424;QSTRAND=+ GT:DP:AD 0|1:38:25,13 1|1:48:25,23 0|1:40:16,24 +chr20 192100 200x1d6 G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=145647;QSTRAND=+ GT:DP:AD 0|1:21:8,13 1|1:23:17,6 0|1:32:16,16 +chr20 193110 200x1d7 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=146657;QSTRAND=+ GT:DP:AD 0|1:30:23,7 1|1:12:5,7 0|1:22:16,6 +chr20 193428 200x1d8 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=146975;QSTRAND=+ GT:DP:AD 0|1:35:16,19 1|1:30:19,11 0|1:27:19,8 +chr20 193735 200x1d9 G A 60 . QNAME=cluster23_scaffold_2;QSTART=25502747;QSTRAND=- GT:DP:AD ./.:17:8,9 ./.:29:23,6 0|1:39:19,20 +chr20 193942 200x1da C G 60 . QNAME=cluster23_scaffold_2;QSTART=25502540;QSTRAND=- GT:DP:AD ./.:26:18,8 ./.:19:10,9 0|1:20:8,12 +chr20 193996 200x1db G A 60 . QNAME=cluster23_scaffold_2;QSTART=25502486;QSTRAND=- GT:DP:AD ./.:37:23,14 ./.:43:22,21 0|1:39:17,22 +chr20 194746 200x1dc G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=148293;QSTRAND=+ GT:DP:AD 0|1:24:11,13 1|1:38:19,19 0|1:27:12,15 +chr20 195745 200x1dd CGTGTGT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=149293;QSTRAND=+ GT:DP:AD 0|1:22:8,14 1|1:25:13,12 ./.:42:24,18 +chr20 195745 200x1de CGTGT C 60 . QNAME=cluster23_scaffold_3;QSTART=25516113;QSTRAND=- GT:DP:AD ./.:39:19,20 ./.:43:19,24 1|0:20:6,14 +chr20 195745 200x1df C CGT 60 . QNAME=cluster23_scaffold_2;QSTART=25500735;QSTRAND=- GT:DP:AD ./.:41:19,22 ./.:25:8,17 0|1:26:12,14 +chr20 195977 200x1e0 C T 60 . QNAME=cluster23_scaffold_2;QSTART=25500503;QSTRAND=- GT:DP:AD ./.:20:8,12 ./.:39:25,14 0|1:45:22,23 +chr20 196106 200x1e1 A T 60 . QNAME=cluster23_scaffold_3;QSTART=25515756;QSTRAND=- GT:DP:AD ./.:18:7,11 ./.:35:23,12 1|0:28:16,12 +chr20 196584 200x1e2 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=175566;QSTRAND=+ GT:DP:AD 1|0:29:19,10 ./.:23:17,6 1|1:20:7,13 +chr20 196609 200x1e3 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=175591;QSTRAND=+ GT:DP:AD 1|0:20:13,7 ./.:20:14,6 1|0:20:15,5 +chr20 198088 200x1e4 G A 60 . QNAME=cluster23_scaffold_3;QSTART=25513774;QSTRAND=- GT:DP:AD ./.:40:24,16 ./.:34:23,11 1|0:45:23,22 +chr20 198171 200x1e5 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=177153;QSTRAND=+ GT:DP:AD 1|0:27:19,8 ./.:38:17,21 1|1:23:18,5 +chr20 198174 200x1e6 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=177156;QSTRAND=+ GT:DP:AD 1|0:34:11,23 ./.:42:22,20 1|0:14:8,6 +chr20 198215 200x1e7 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=177197;QSTRAND=+ GT:DP:AD 1|0:33:20,13 ./.:31:13,18 1|1:33:9,24 +chr20 198433 200x1e8 G A 60 . QNAME=cluster23_scaffold_2;QSTART=25498047;QSTRAND=- GT:DP:AD ./.:31:7,24 ./.:27:20,7 0|1:25:14,11 +chr20 198814 200x1e9 A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=177796;QSTRAND=+ GT:DP:AD 1|0:31:18,13 ./.:17:7,10 1|0:21:9,12 +chr20 198921 200x1ea A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=177903;QSTRAND=+ GT:DP:AD 1|0:15:9,6 ./.:12:5,7 1|1:31:8,23 +chr20 199123 200x1eb T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=178105;QSTRAND=+ GT:DP:AD 1|0:34:18,16 ./.:33:19,14 1|0:36:18,18 +chr20 199139 200x1ec C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=178122;QSTRAND=+ GT:DP:AD 1|0:20:12,8 ./.:48:24,24 ./.:24:9,15 +chr20 199139 200x1ed C CTT 60 . QNAME=cluster23_scaffold_3;QSTART=25512721;QSTRAND=- GT:DP:AD ./.:18:5,13 ./.:33:9,24 1|1:44:19,25 +chr20 199741 200x1ee C T 60 . QNAME=cluster23_scaffold_2;QSTART=25496737;QSTRAND=- GT:DP:AD ./.:44:20,24 ./.:34:9,25 0|1:15:10,5 +chr20 200997 200x1ef C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=179980;QSTRAND=+ GT:DP:AD 1|0:28:10,18 ./.:34:12,22 1|0:26:12,14 +chr20 201076 200x1f0 A G 60 . QNAME=cluster23_scaffold_3;QSTART=25510784;QSTRAND=- GT:DP:AD ./.:27:20,7 ./.:33:18,15 1|0:35:12,23 +chr20 201326 200x1f1 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=180309;QSTRAND=+ GT:DP:AD 1|0:36:14,22 ./.:25:20,5 1|0:36:17,19 +chr20 201372 200x1f2 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=180355;QSTRAND=+ GT:DP:AD 1|0:39:20,19 ./.:20:11,9 1|1:41:23,18 +chr20 201418 200x1f3 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=180401;QSTRAND=+ GT:DP:AD 1|0:28:17,11 ./.:38:18,20 1|0:31:24,7 +chr20 201525 200x1f4 G A 60 . QNAME=cluster23_scaffold_2;QSTART=25494953;QSTRAND=- GT:DP:AD ./.:36:16,20 ./.:15:10,5 0|1:43:21,22 +chr20 201908 200x1f5 A G 60 . QNAME=cluster23_scaffold_2;QSTART=25494570;QSTRAND=- GT:DP:AD ./.:19:6,13 ./.:27:20,7 0|1:17:12,5 +chr20 201932 200x1f6 C CAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=180916;QSTRAND=+ GT:DP:AD 1|0:31:17,14 ./.:28:9,19 1|0:34:16,18 +chr20 201932 200x1f7 CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=155474;QSTRAND=+ GT:DP:AD 0|1:29:21,8 ./.:24:17,7 ./.:30:7,23 +chr20 201932 200x1f8 C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25494545;QSTRAND=- GT:DP:AD ./.:17:10,7 ./.:30:16,14 0|1:21:10,11 +chr20 202581 200x1f9 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=181568;QSTRAND=+ GT:DP:AD 1|0:24:14,10 ./.:39:24,15 1|0:21:8,13 +chr20 203580 200x1fa G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=182567;QSTRAND=+ GT:DP:AD 1|0:34:13,21 ./.:13:7,6 1|0:37:22,15 +chr20 203602 200x1fb G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=182589;QSTRAND=+ GT:DP:AD 1|0:32:18,14 ./.:24:8,16 ./.:36:24,12 +chr20 203620 200x1fc TCCCTCCC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=182608;QSTRAND=+ GT:DP:AD 1|0:32:8,24 ./.:22:5,17 1|0:28:5,23 +chr20 203847 200x1fd T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=182827;QSTRAND=+ GT:DP:AD 1|0:26:18,8 ./.:34:15,19 1|0:48:24,24 +chr20 204090 200x1fe T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=183070;QSTRAND=+ GT:DP:AD 1|0:21:6,15 ./.:15:10,5 1|0:30:13,17 +chr20 205285 200x1ff G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=184265;QSTRAND=+ GT:DP:AD 1|0:44:23,21 ./.:46:23,23 1|0:42:21,21 +chr20 205764 200x200 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=184744;QSTRAND=+ GT:DP:AD 1|0:22:6,16 ./.:38:15,23 1|1:22:17,5 +chr20 206102 200x201 C T 60 . QNAME=cluster23_scaffold_2;QSTART=25490375;QSTRAND=- GT:DP:AD ./.:18:6,12 ./.:49:25,24 0|1:29:18,11 +chr20 206175 200x202 T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=185156;QSTRAND=+ GT:DP:AD 1|0:40:24,16 ./.:13:5,8 ./.:28:10,18 +chr20 206175 200x203 TAAAA T 60 . QNAME=cluster23_scaffold_2;QSTART=25490302;QSTRAND=- GT:DP:AD ./.:39:23,16 ./.:28:19,9 0|1:39:21,18 +chr20 206197 200x204 T C 60 . QNAME=cluster23_scaffold_2;QSTART=25490284;QSTRAND=- GT:DP:AD ./.:37:15,22 ./.:16:9,7 0|1:33:21,12 +chr20 206446 200x205 T C 60 . QNAME=cluster23_scaffold_2;QSTART=25490035;QSTRAND=- GT:DP:AD ./.:12:5,7 ./.:21:7,14 0|1:40:19,21 +chr20 207202 200x206 T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=186184;QSTRAND=+ GT:DP:AD 1|0:36:11,25 ./.:25:17,8 1|1:34:21,13 +chr20 207307 200x207 T C 60 . QNAME=cluster23_scaffold_2;QSTART=25489173;QSTRAND=- GT:DP:AD ./.:25:10,15 ./.:39:22,17 0|1:25:12,13 +chr20 207389 200x208 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=186371;QSTRAND=+ GT:DP:AD 1|0:37:19,18 ./.:33:18,15 1|1:32:19,13 +chr20 207466 200x209 T C 60 . QNAME=cluster23_scaffold_2;QSTART=25489014;QSTRAND=- GT:DP:AD ./.:36:14,22 ./.:31:12,19 0|1:21:14,7 +chr20 208792 200x20a CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=187775;QSTRAND=+ GT:DP:AD 1|0:39:21,18 ./.:39:22,17 1|1:45:20,25 +chr20 209694 200x20b A C 60 . QNAME=cluster23_scaffold_2;QSTART=25486787;QSTRAND=- GT:DP:AD ./.:43:21,22 ./.:25:7,18 0|1:40:21,19 +chr20 210024 200x20c G A 60 . QNAME=cluster23_scaffold_2;QSTART=25486457;QSTRAND=- GT:DP:AD ./.:27:22,5 ./.:29:6,23 0|1:44:22,22 +chr20 211156 200x20d G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=190137;QSTRAND=+ GT:DP:AD 1|0:13:5,8 ./.:24:7,17 1|1:28:19,9 +chr20 211168 200x20e C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=190149;QSTRAND=+ GT:DP:AD 1|0:26:10,16 ./.:25:19,6 1|1:27:12,15 +chr20 211428 200x20f C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=190409;QSTRAND=+ GT:DP:AD 1|0:43:22,21 ./.:22:7,15 1|1:31:7,24 +chr20 212919 200x210 AC A 60 . QNAME=cluster23_scaffold_2;QSTART=25483562;QSTRAND=- GT:DP:AD ./.:34:21,13 ./.:18:10,8 0|1:30:15,15 +chr20 212994 200x211 A AT 60 . QNAME=HG002-S9-H2-000001F;QSTART=166535;QSTRAND=+ GT:DP:AD 0|1:36:16,20 ./.:47:25,22 0|1:24:15,9 +chr20 213120 200x212 T C 60 . QNAME=cluster23_scaffold_2;QSTART=25483361;QSTRAND=- GT:DP:AD ./.:37:15,22 ./.:32:7,25 0|1:38:15,23 +chr20 213126 200x213 A G 60 . QNAME=cluster23_scaffold_2;QSTART=25483355;QSTRAND=- GT:DP:AD ./.:36:25,11 ./.:16:5,11 0|1:35:19,16 +chr20 213223 200x214 G C 60 . QNAME=cluster23_scaffold_2;QSTART=25483258;QSTRAND=- GT:DP:AD ./.:27:7,20 ./.:31:6,25 0|1:20:13,7 +chr20 213244 200x215 A G 60 . QNAME=cluster23_scaffold_2;QSTART=25483237;QSTRAND=- GT:DP:AD ./.:30:17,13 ./.:17:5,12 0|1:21:5,16 +chr20 213641 200x216 C T 60 . QNAME=cluster23_scaffold_3;QSTART=25498222;QSTRAND=- GT:DP:AD ./.:42:22,20 ./.:39:20,19 1|0:43:18,25 +chr20 213649 200x217 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=192630;QSTRAND=+ GT:DP:AD 1|0:35:21,14 ./.:12:6,6 ./.:12:6,6 +chr20 213886 200x218 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=192867;QSTRAND=+ GT:DP:AD 1|0:23:11,12 ./.:26:16,10 ./.:27:20,7 +chr20 214444 200x219 T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=193425;QSTRAND=+ GT:DP:AD 1|0:42:20,22 ./.:25:12,13 ./.:28:15,13 +chr20 214461 200x21a C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=193442;QSTRAND=+ GT:DP:AD 1|0:35:14,21 ./.:40:20,20 ./.:35:16,19 +chr20 214646 200x21b C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=193627;QSTRAND=+ GT:DP:AD 1|0:40:21,19 ./.:17:5,12 ./.:31:24,7 +chr20 214796 200x21c CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=193778;QSTRAND=+ GT:DP:AD 1|0:34:14,20 ./.:30:21,9 ./.:24:10,14 +chr20 214824 200x21d C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=193804;QSTRAND=+ GT:DP:AD 1|0:33:8,25 ./.:34:14,20 ./.:23:16,7 +chr20 214879 200x21e G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=193859;QSTRAND=+ GT:DP:AD 1|0:22:8,14 ./.:40:25,15 ./.:30:21,9 +chr20 214962 200x21f A AT 60 . QNAME=cluster23_scaffold_2;QSTART=25481518;QSTRAND=- GT:DP:AD ./.:30:19,11 ./.:32:20,12 0|1:17:6,11 +chr20 215031 200x220 G A 60 . QNAME=cluster23_scaffold_3;QSTART=25496832;QSTRAND=- GT:DP:AD ./.:30:17,13 ./.:26:18,8 1|0:29:6,23 +chr20 215055 200x221 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=194035;QSTRAND=+ GT:DP:AD 1|0:30:12,18 ./.:42:17,25 1|1:43:20,23 +chr20 215963 200x222 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=194943;QSTRAND=+ GT:DP:AD 1|0:20:13,7 ./.:17:8,9 ./.:27:16,11 +chr20 217163 200x223 C T 60 . QNAME=cluster23_scaffold_2;QSTART=25479317;QSTRAND=- GT:DP:AD ./.:37:13,24 ./.:25:20,5 0|1:44:22,22 +chr20 217714 200x224 ATATG A 60 . QNAME=cluster23_scaffold_2;QSTART=25478766;QSTRAND=- GT:DP:AD ./.:14:8,6 ./.:16:7,9 0|1:24:5,19 +chr20 217754 200x225 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=196734;QSTRAND=+ GT:DP:AD 1|1:37:21,16 1|1:31:18,13 0|1:18:9,9 +chr20 217756 200x226 A G 60 . QNAME=cluster23_scaffold_3;QSTART=25494107;QSTRAND=- GT:DP:AD ./.:25:11,14 ./.:27:7,20 1|0:41:20,21 +chr20 219501 200x227 T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=198481;QSTRAND=+ GT:DP:AD 1|0:26:15,11 ./.:32:20,12 0|1:27:6,21 +chr20 220972 200x228 CTT C 60 . QNAME=cluster23_scaffold_2;QSTART=25475512;QSTRAND=- GT:DP:AD ./.:28:12,16 ./.:14:8,6 0|1:41:17,24 +chr20 221511 200x229 GGGAA G 60 . QNAME=cluster23_scaffold_3;QSTART=25490352;QSTRAND=- GT:DP:AD ./.:19:10,9 ./.:18:5,13 1|1:37:12,25 +chr20 224189 200x22a G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=203169;QSTRAND=+ GT:DP:AD 1|0:32:9,23 ./.:41:16,25 0|1:26:12,14 +chr20 225761 200x22b C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=204741;QSTRAND=+ GT:DP:AD 1|0:22:5,17 ./.:35:16,19 0|1:33:14,19 +chr20 225955 200x22c C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=204935;QSTRAND=+ GT:DP:AD 1|1:28:22,6 1|1:31:19,12 1|1:37:25,12 +chr20 226775 200x22d A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=205755;QSTRAND=+ GT:DP:AD 1|0:25:12,13 ./.:36:22,14 0|1:46:23,23 +chr20 227248 200x22e G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=206228;QSTRAND=+ GT:DP:AD 1|0:14:9,5 ./.:17:11,6 ./.:38:16,22 +chr20 227262 200x22f T C 60 . QNAME=cluster23_scaffold_3;QSTART=25484605;QSTRAND=- GT:DP:AD ./.:33:15,18 ./.:25:9,16 1|0:16:11,5 +chr20 227527 200x230 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=206507;QSTRAND=+ GT:DP:AD 1|0:41:20,21 ./.:44:23,21 1|1:23:17,6 +chr20 227692 200x231 C A 60 . QNAME=cluster23_scaffold_3;QSTART=25484175;QSTRAND=- GT:DP:AD ./.:28:15,13 ./.:38:19,19 1|0:32:14,18 +chr20 227704 200x232 A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=206684;QSTRAND=+ GT:DP:AD 1|0:31:6,25 ./.:29:22,7 1|1:29:7,22 +chr20 227705 200x233 A T 60 . QNAME=cluster23_scaffold_3;QSTART=25484162;QSTRAND=- GT:DP:AD ./.:27:14,13 ./.:26:17,9 1|0:35:23,12 +chr20 227706 200x234 A T 60 . QNAME=cluster23_scaffold_3;QSTART=25484161;QSTRAND=- GT:DP:AD ./.:21:5,16 ./.:27:11,16 1|0:12:5,7 +chr20 227707 200x235 A T 60 . QNAME=cluster23_scaffold_3;QSTART=25484160;QSTRAND=- GT:DP:AD ./.:29:13,16 ./.:25:7,18 1|0:24:5,19 +chr20 227909 200x236 T G 60 . QNAME=cluster23_scaffold_3;QSTART=25483958;QSTRAND=- GT:DP:AD ./.:13:6,7 ./.:32:19,13 1|0:22:8,14 +chr20 228044 200x237 G A 60 . QNAME=cluster23_scaffold_3;QSTART=25483823;QSTRAND=- GT:DP:AD ./.:28:14,14 ./.:20:8,12 1|0:38:17,21 +chr20 228258 200x238 GCTTCTAATGTTTTTAT G 60 . QNAME=cluster23_scaffold_2;QSTART=25468232;QSTRAND=- GT:DP:AD ./.:49:25,24 ./.:19:12,7 0|1:28:5,23 +chr20 228763 200x239 A G 60 . QNAME=cluster23_scaffold_2;QSTART=25467743;QSTRAND=- GT:DP:AD ./.:39:20,19 ./.:38:17,21 0|1:24:7,17 +chr20 229210 200x23a C T 60 . QNAME=cluster23_scaffold_3;QSTART=25482657;QSTRAND=- GT:DP:AD ./.:39:23,16 ./.:27:5,22 1|0:27:10,17 +chr20 229265 200x23b T TCTC 60 . QNAME=cluster23_scaffold_3;QSTART=25482599;QSTRAND=- GT:DP:AD ./.:33:14,19 ./.:29:9,20 1|0:38:25,13 +chr20 229420 200x23c G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=208400;QSTRAND=+ GT:DP:AD 1|0:33:17,16 ./.:24:9,15 ./.:38:24,14 +chr20 229665 200x23d C G 60 . QNAME=cluster23_scaffold_3;QSTART=25482199;QSTRAND=- GT:DP:AD ./.:15:7,8 ./.:37:18,19 1|1:38:17,21 +chr20 229898 200x23e A G 60 . QNAME=cluster23_scaffold_3;QSTART=25481966;QSTRAND=- GT:DP:AD ./.:30:19,11 ./.:36:14,22 1|0:32:13,19 +chr20 229993 200x23f G A 60 . QNAME=cluster23_scaffold_3;QSTART=25481871;QSTRAND=- GT:DP:AD ./.:26:8,18 ./.:31:22,9 1|0:47:24,23 +chr20 230118 200x240 T C 60 . QNAME=cluster23_scaffold_2;QSTART=25466388;QSTRAND=- GT:DP:AD ./.:33:22,11 ./.:18:7,11 0|1:22:8,14 +chr20 230234 200x241 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=209214;QSTRAND=+ GT:DP:AD 1|0:27:9,18 ./.:42:18,24 ./.:29:20,9 +chr20 230273 200x242 T C 60 . QNAME=cluster23_scaffold_3;QSTART=25481591;QSTRAND=- GT:DP:AD ./.:47:22,25 ./.:28:17,11 1|0:32:9,23 +chr20 230354 200x243 C T 60 . QNAME=cluster23_scaffold_3;QSTART=25481510;QSTRAND=- GT:DP:AD ./.:27:21,6 ./.:38:15,23 1|0:38:18,20 +chr20 230514 200x244 G A 60 . QNAME=cluster23_scaffold_3;QSTART=25481350;QSTRAND=- GT:DP:AD ./.:32:18,14 ./.:20:14,6 1|0:31:23,8 +chr20 230790 200x245 T C 60 . QNAME=cluster23_scaffold_3;QSTART=25481074;QSTRAND=- GT:DP:AD ./.:27:9,18 ./.:44:21,23 1|0:18:9,9 +chr20 230868 200x246 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=209848;QSTRAND=+ GT:DP:AD 1|0:31:7,24 ./.:25:20,5 0|1:22:16,6 +chr20 230923 200x247 T C 60 . QNAME=cluster19_000000F;QSTART=190079;QSTRAND=+ GT:DP:AD ./.:33:12,21 0|1:20:13,7 ./.:41:20,21 +chr20 231070 200x248 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=210050;QSTRAND=+ GT:DP:AD 1|0:39:23,16 ./.:27:6,21 0|1:28:10,18 +chr20 231318 200x249 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=210298;QSTRAND=+ GT:DP:AD 1|0:26:9,17 ./.:27:13,14 ./.:28:5,23 +chr20 231710 200x24a T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=210690;QSTRAND=+ GT:DP:AD 1|0:32:10,22 ./.:46:24,22 1|1:22:16,6 +chr20 231898 200x24b C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=185439;QSTRAND=+ GT:DP:AD 0|1:29:6,23 1|1:39:17,22 1|0:44:24,20 +chr20 231900 200x24c G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=185441;QSTRAND=+ GT:DP:AD 0|1:23:10,13 1|1:40:19,21 1|0:34:17,17 +chr20 232009 200x24d G A 60 . QNAME=cluster23_scaffold_3;QSTART=25479855;QSTRAND=- GT:DP:AD ./.:27:10,17 ./.:23:16,7 1|0:42:24,18 +chr20 232033 200x24e A AAAATAAAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=211014;QSTRAND=+ GT:DP:AD 1|1:33:15,18 ./.:22:14,8 ./.:19:12,7 +chr20 232033 200x24f A AAAATAAATAAAT 60 . QNAME=cluster19_000000F;QSTART=25530755;QSTRAND=- GT:DP:AD ./.:26:10,16 1|0:26:11,15 1|0:39:16,23 +chr20 232033 200x250 A AAAAT 60 . QNAME=cluster19_000000F;QSTART=191190;QSTRAND=+ GT:DP:AD ./.:24:12,12 0|1:28:12,16 0|1:39:16,23 +chr20 232468 200x251 C CTT 60 . QNAME=cluster23_scaffold_3;QSTART=25479382;QSTRAND=- GT:DP:AD ./.:36:23,13 ./.:33:19,14 1|0:44:23,21 +chr20 232484 200x252 TG T 60 . QNAME=cluster23_scaffold_3;QSTART=25479366;QSTRAND=- GT:DP:AD ./.:43:25,18 ./.:32:7,25 1|0:26:11,15 +chr20 232614 200x253 G A 60 . QNAME=cluster23_scaffold_3;QSTART=25479237;QSTRAND=- GT:DP:AD ./.:38:14,24 ./.:19:5,14 1|0:34:24,10 +chr20 232882 200x254 A C 60 . QNAME=cluster23_scaffold_3;QSTART=25478969;QSTRAND=- GT:DP:AD ./.:18:6,12 ./.:29:12,17 1|0:32:19,13 +chr20 233198 200x255 TGACGG T 60 . QNAME=cluster23_scaffold_3;QSTART=25478653;QSTRAND=- GT:DP:AD ./.:30:7,23 ./.:31:12,19 1|0:20:7,13 +chr20 233213 200x256 T C 60 . QNAME=cluster23_scaffold_3;QSTART=25478643;QSTRAND=- GT:DP:AD ./.:32:15,17 ./.:28:9,19 1|0:34:23,11 +chr20 233246 200x257 G C 60 . QNAME=cluster23_scaffold_3;QSTART=25478610;QSTRAND=- GT:DP:AD ./.:17:12,5 ./.:36:13,23 1|0:26:14,12 +chr20 233732 200x258 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=212720;QSTRAND=+ GT:DP:AD 1|1:13:8,5 1|0:26:15,11 1|1:31:25,6 +chr20 234020 200x259 A G 60 . QNAME=cluster23_scaffold_3;QSTART=25477836;QSTRAND=- GT:DP:AD ./.:33:22,11 ./.:25:16,9 1|0:26:8,18 +chr20 234023 200x25a C A 60 . QNAME=cluster23_scaffold_3;QSTART=25477833;QSTRAND=- GT:DP:AD ./.:36:24,12 ./.:36:18,18 1|0:26:11,15 +chr20 234144 200x25b CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=213133;QSTRAND=+ GT:DP:AD 1|1:31:9,22 1|1:28:20,8 ./.:18:6,12 +chr20 234144 200x25c CTTTT C 60 . QNAME=cluster23_scaffold_3;QSTART=25477712;QSTRAND=- GT:DP:AD ./.:30:13,17 ./.:24:17,7 1|0:36:15,21 +chr20 234239 200x25d C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=213226;QSTRAND=+ GT:DP:AD 1|0:26:15,11 ./.:27:22,5 ./.:37:16,21 +chr20 234441 200x25e C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=213428;QSTRAND=+ GT:DP:AD 1|1:21:16,5 1|0:20:11,9 ./.:37:22,15 +chr20 234630 200x25f G A 60 . QNAME=cluster23_scaffold_3;QSTART=25477230;QSTRAND=- GT:DP:AD ./.:36:25,11 ./.:22:17,5 1|0:44:23,21 +chr20 234736 200x260 G A 60 . QNAME=cluster23_scaffold_3;QSTART=25477124;QSTRAND=- GT:DP:AD ./.:20:6,14 ./.:17:12,5 1|0:37:19,18 +chr20 234758 200x261 T C 60 . QNAME=cluster23_scaffold_3;QSTART=25477102;QSTRAND=- GT:DP:AD ./.:31:22,9 ./.:26:10,16 1|0:39:15,24 +chr20 234803 200x262 G T 60 . QNAME=cluster23_scaffold_3;QSTART=25477057;QSTRAND=- GT:DP:AD ./.:20:8,12 ./.:32:18,14 1|0:43:22,21 +chr20 234949 200x263 C T 60 . QNAME=cluster23_scaffold_3;QSTART=25476911;QSTRAND=- GT:DP:AD ./.:34:10,24 ./.:23:6,17 1|0:20:7,13 +chr20 235000 200x264 T G 60 . QNAME=cluster23_scaffold_3;QSTART=25476860;QSTRAND=- GT:DP:AD ./.:41:16,25 ./.:25:9,16 1|0:32:14,18 +chr20 235023 200x265 A G 60 . QNAME=cluster23_scaffold_3;QSTART=25476837;QSTRAND=- GT:DP:AD ./.:30:9,21 ./.:30:21,9 1|0:31:14,17 +chr20 235274 200x266 T G 60 . QNAME=cluster23_scaffold_2;QSTART=25461228;QSTRAND=- GT:DP:AD ./.:21:13,8 ./.:27:20,7 0|1:49:25,24 +chr20 235380 200x267 C A 60 . QNAME=cluster23_scaffold_3;QSTART=25476480;QSTRAND=- GT:DP:AD ./.:32:18,14 ./.:20:9,11 1|0:23:10,13 +chr20 235457 200x268 A G 60 . QNAME=cluster23_scaffold_3;QSTART=25476403;QSTRAND=- GT:DP:AD ./.:21:12,9 ./.:34:16,18 1|1:25:18,7 +chr20 235579 200x269 A G 60 . QNAME=cluster23_scaffold_3;QSTART=25476281;QSTRAND=- GT:DP:AD ./.:40:24,16 ./.:21:11,10 1|0:28:16,12 +chr20 235581 200x26a G A 60 . QNAME=cluster23_scaffold_3;QSTART=25476279;QSTRAND=- GT:DP:AD ./.:45:23,22 ./.:16:5,11 1|0:34:9,25 +chr20 235682 200x26b A G 60 . QNAME=cluster23_scaffold_3;QSTART=25476178;QSTRAND=- GT:DP:AD ./.:37:12,25 ./.:29:22,7 1|0:32:12,20 +chr20 236006 200x26c C T 60 . QNAME=cluster23_scaffold_3;QSTART=25475854;QSTRAND=- GT:DP:AD ./.:31:6,25 ./.:29:18,11 1|0:29:15,14 +chr20 236109 200x26d T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=215096;QSTRAND=+ GT:DP:AD 1|1:16:7,9 1|1:38:17,21 1|1:18:11,7 +chr20 236170 200x26e C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=215157;QSTRAND=+ GT:DP:AD 1|1:34:22,12 1|0:23:16,7 1|1:26:8,18 +chr20 236273 200x26f CTAAG C 60 . QNAME=cluster23_scaffold_3;QSTART=25475587;QSTRAND=- GT:DP:AD ./.:37:21,16 ./.:25:11,14 1|0:33:19,14 +chr20 236433 200x270 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=215420;QSTRAND=+ GT:DP:AD 1|1:41:22,19 1|0:29:19,10 0|1:39:25,14 +chr20 236640 200x271 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=215627;QSTRAND=+ GT:DP:AD 1|1:29:7,22 1|0:43:23,20 0|1:28:14,14 +chr20 236959 200x272 C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=215947;QSTRAND=+ GT:DP:AD 1|1:44:19,25 1|0:15:7,8 ./.:31:25,6 +chr20 236959 200x273 CTT C 60 . QNAME=cluster23_scaffold_3;QSTART=25474905;QSTRAND=- GT:DP:AD ./.:23:8,15 ./.:38:15,23 1|0:38:24,14 +chr20 237090 200x274 A C 60 . QNAME=cluster23_scaffold_3;QSTART=25474776;QSTRAND=- GT:DP:AD ./.:33:14,19 ./.:37:12,25 1|0:26:12,14 +chr20 237210 200x275 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=216198;QSTRAND=+ GT:DP:AD 1|1:29:21,8 1|1:25:15,10 1|1:26:19,7 +chr20 237614 200x276 A AG 60 . QNAME=HG002-S9-H1-000001F;QSTART=216603;QSTRAND=+ GT:DP:AD 1|1:23:13,10 1|0:18:5,13 1|0:18:13,5 +chr20 238142 200x277 T C 60 . QNAME=cluster23_scaffold_3;QSTART=25473723;QSTRAND=- GT:DP:AD ./.:31:19,12 ./.:29:8,21 1|1:27:17,10 +chr20 238370 200x278 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=217359;QSTRAND=+ GT:DP:AD 1|1:41:20,21 1|0:19:7,12 1|1:25:9,16 +chr20 238458 200x279 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=217447;QSTRAND=+ GT:DP:AD 1|1:19:14,5 1|0:19:8,11 ./.:20:6,14 +chr20 238622 200x27a ACAAGGT A 60 . QNAME=cluster23_scaffold_3;QSTART=25473243;QSTRAND=- GT:DP:AD ./.:33:24,9 ./.:49:24,25 1|1:41:22,19 +chr20 238634 200x27b G T 60 . QNAME=cluster23_scaffold_3;QSTART=25473237;QSTRAND=- GT:DP:AD ./.:31:19,12 ./.:26:18,8 1|1:37:20,17 +chr20 238645 200x27c G T 60 . QNAME=cluster23_scaffold_3;QSTART=25473226;QSTRAND=- GT:DP:AD ./.:33:20,13 ./.:28:19,9 1|1:29:20,9 +chr20 238721 200x27d G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=217710;QSTRAND=+ GT:DP:AD 1|1:49:25,24 1|0:22:6,16 ./.:38:18,20 +chr20 238845 200x27e G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=217835;QSTRAND=+ GT:DP:AD 1|1:14:5,9 1|0:29:13,16 1|1:49:25,24 +chr20 239021 200x27f T C 60 . QNAME=cluster23_scaffold_3;QSTART=25472849;QSTRAND=- GT:DP:AD ./.:40:22,18 ./.:43:19,24 1|1:36:17,19 +chr20 239041 200x280 G A 60 . QNAME=cluster23_scaffold_2;QSTART=25457466;QSTRAND=- GT:DP:AD ./.:16:8,8 ./.:41:18,23 0|1:30:16,14 +chr20 239418 200x281 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=218408;QSTRAND=+ GT:DP:AD 1|1:41:21,20 1|0:25:6,19 ./.:25:9,16 +chr20 239441 200x282 C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25457065;QSTRAND=- GT:DP:AD ./.:18:10,8 ./.:33:21,12 0|1:33:11,22 +chr20 239444 200x283 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=218434;QSTRAND=+ GT:DP:AD 1|1:10:5,5 1|0:24:16,8 ./.:24:18,6 +chr20 239451 200x284 C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=218441;QSTRAND=+ GT:DP:AD 1|1:18:5,13 1|0:12:6,6 ./.:38:13,25 +chr20 239556 200x285 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=218546;QSTRAND=+ GT:DP:AD 1|1:20:7,13 1|0:29:11,18 1|1:29:15,14 +chr20 239563 200x286 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=218553;QSTRAND=+ GT:DP:AD 1|1:48:24,24 1|0:21:11,10 1|1:33:25,8 +chr20 239613 200x287 A G 60 . QNAME=cluster23_scaffold_2;QSTART=25456893;QSTRAND=- GT:DP:AD ./.:26:19,7 ./.:35:19,16 0|1:15:7,8 +chr20 239649 200x288 C T 60 . QNAME=cluster23_scaffold_3;QSTART=25472221;QSTRAND=- GT:DP:AD ./.:17:12,5 ./.:39:16,23 1|1:31:25,6 +chr20 239662 200x289 A C 60 . QNAME=cluster23_scaffold_3;QSTART=25472208;QSTRAND=- GT:DP:AD ./.:16:6,10 ./.:32:22,10 1|1:20:12,8 +chr20 239803 200x28a G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=218793;QSTRAND=+ GT:DP:AD 1|1:40:23,17 1|0:26:10,16 ./.:29:21,8 +chr20 239945 200x28b A G 60 . QNAME=cluster23_scaffold_3;QSTART=25471925;QSTRAND=- GT:DP:AD ./.:10:5,5 ./.:28:8,20 1|0:38:19,19 +chr20 239951 200x28c C A 60 . QNAME=cluster23_scaffold_3;QSTART=25471919;QSTRAND=- GT:DP:AD ./.:29:21,8 ./.:31:24,7 1|1:24:12,12 +chr20 240008 200x28d A G 60 . QNAME=cluster23_scaffold_3;QSTART=25471862;QSTRAND=- GT:DP:AD ./.:24:10,14 ./.:24:16,8 1|1:39:20,19 +chr20 240075 200x28e C CAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=219066;QSTRAND=+ GT:DP:AD 1|1:34:25,9 1|0:24:8,16 ./.:40:22,18 +chr20 240075 200x28f C CAA 60 . QNAME=cluster23_scaffold_3;QSTART=25471793;QSTRAND=- GT:DP:AD ./.:17:8,9 ./.:32:19,13 1|1:39:22,17 +chr20 240116 200x290 C T 60 . QNAME=cluster23_scaffold_3;QSTART=25471752;QSTRAND=- GT:DP:AD ./.:49:24,25 ./.:33:8,25 1|1:39:18,21 +chr20 240166 200x291 T G 60 . QNAME=cluster23_scaffold_3;QSTART=25471702;QSTRAND=- GT:DP:AD ./.:45:23,22 ./.:15:5,10 1|1:24:18,6 +chr20 240377 200x292 T G 60 . QNAME=cluster23_scaffold_3;QSTART=25471491;QSTRAND=- GT:DP:AD ./.:24:6,18 ./.:32:21,11 1|1:16:8,8 +chr20 240458 200x293 A G 60 . QNAME=cluster23_scaffold_3;QSTART=25471410;QSTRAND=- GT:DP:AD ./.:28:11,17 ./.:39:23,16 1|1:25:7,18 +chr20 240477 200x294 G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=219471;QSTRAND=+ GT:DP:AD 1|1:48:25,23 1|0:25:10,15 ./.:38:21,17 +chr20 240477 200x295 G GAA 60 . QNAME=cluster23_scaffold_3;QSTART=25471389;QSTRAND=- GT:DP:AD ./.:40:18,22 ./.:17:11,6 1|0:37:16,21 +chr20 240477 200x296 G GAAA 60 . QNAME=cluster23_scaffold_2;QSTART=25456024;QSTRAND=- GT:DP:AD ./.:28:8,20 ./.:23:9,14 0|1:30:6,24 +chr20 240872 200x297 G C 60 . QNAME=cluster23_scaffold_3;QSTART=25470994;QSTRAND=- GT:DP:AD ./.:26:12,14 ./.:34:23,11 1|1:36:25,11 +chr20 241191 200x298 G A 60 . QNAME=cluster23_scaffold_3;QSTART=25470675;QSTRAND=- GT:DP:AD ./.:31:13,18 ./.:28:12,16 1|1:35:19,16 +chr20 241301 200x299 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=220295;QSTRAND=+ GT:DP:AD 1|1:23:11,12 1|0:31:17,14 1|1:30:24,6 +chr20 241898 200x29a C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=220893;QSTRAND=+ GT:DP:AD 1|1:22:6,16 1|0:36:18,18 ./.:16:8,8 +chr20 241991 200x29b C T 60 . QNAME=cluster23_scaffold_3;QSTART=25469875;QSTRAND=- GT:DP:AD ./.:39:14,25 ./.:32:17,15 1|1:38:20,18 +chr20 242033 200x29c G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=221028;QSTRAND=+ GT:DP:AD 1|1:26:14,12 1|0:44:23,21 ./.:36:20,16 +chr20 242067 200x29d T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=221062;QSTRAND=+ GT:DP:AD 1|1:40:25,15 1|0:39:21,18 ./.:40:20,20 +chr20 242195 200x29e C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=221190;QSTRAND=+ GT:DP:AD 1|1:37:18,19 1|0:30:12,18 1|1:28:9,19 +chr20 242353 200x29f A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=221348;QSTRAND=+ GT:DP:AD 1|1:23:6,17 1|0:22:9,13 ./.:29:18,11 +chr20 242531 200x2a0 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=221526;QSTRAND=+ GT:DP:AD 1|1:26:13,13 1|0:19:11,8 ./.:27:21,6 +chr20 242614 200x2a1 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=221609;QSTRAND=+ GT:DP:AD 1|1:26:15,11 1|0:39:22,17 ./.:30:13,17 +chr20 242798 200x2a2 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=221793;QSTRAND=+ GT:DP:AD 1|1:25:15,10 1|0:24:13,11 ./.:27:9,18 +chr20 242897 200x2a3 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=221892;QSTRAND=+ GT:DP:AD 1|1:36:25,11 1|0:39:17,22 1|1:33:16,17 +chr20 243066 200x2a4 A G 60 . QNAME=cluster23_scaffold_3;QSTART=25468800;QSTRAND=- GT:DP:AD ./.:21:15,6 ./.:26:6,20 1|1:38:16,22 +chr20 243217 200x2a5 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=222212;QSTRAND=+ GT:DP:AD 1|1:33:15,18 1|0:24:19,5 1|1:41:25,16 +chr20 243487 200x2a6 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=222482;QSTRAND=+ GT:DP:AD 1|1:25:15,10 1|0:33:13,20 ./.:25:8,17 +chr20 243532 200x2a7 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=222527;QSTRAND=+ GT:DP:AD 1|1:29:5,24 1|0:19:11,8 1|1:23:13,10 +chr20 243817 200x2a8 AAG A 60 . QNAME=cluster23_scaffold_3;QSTART=25468049;QSTRAND=- GT:DP:AD ./.:23:5,18 ./.:17:11,6 1|1:14:7,7 +chr20 243818 200x2a9 AG A 60 . QNAME=HG002-S9-H1-000001F;QSTART=222814;QSTRAND=+ GT:DP:AD 1|1:30:7,23 1|0:29:24,5 ./.:31:17,14 +chr20 243960 200x2aa G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=222954;QSTRAND=+ GT:DP:AD 1|1:45:25,20 1|0:25:10,15 ./.:30:11,19 +chr20 244104 200x2ab GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=223099;QSTRAND=+ GT:DP:AD 1|1:17:8,9 1|0:18:6,12 ./.:24:19,5 +chr20 244300 200x2ac T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=223293;QSTRAND=+ GT:DP:AD 1|1:13:5,8 1|0:27:10,17 1|1:32:17,15 +chr20 244330 200x2ad G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=223323;QSTRAND=+ GT:DP:AD 1|1:32:13,19 1|0:41:21,20 1|1:17:9,8 +chr20 244417 200x2ae A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=223410;QSTRAND=+ GT:DP:AD 1|1:31:15,16 1|0:29:19,10 1|1:17:5,12 +chr20 244771 200x2af T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=223764;QSTRAND=+ GT:DP:AD 1|1:43:23,20 1|0:46:22,24 ./.:17:10,7 +chr20 244773 200x2b0 T C 60 . QNAME=cluster23_scaffold_3;QSTART=25467095;QSTRAND=- GT:DP:AD ./.:20:8,12 ./.:20:8,12 1|1:33:14,19 +chr20 244803 200x2b1 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=223796;QSTRAND=+ GT:DP:AD 1|1:27:13,14 1|0:40:21,19 ./.:29:5,24 +chr20 244964 200x2b2 G A 60 . QNAME=cluster23_scaffold_3;QSTART=25466904;QSTRAND=- GT:DP:AD ./.:30:6,24 ./.:21:7,14 1|1:21:15,6 +chr20 244981 200x2b3 T C 60 . QNAME=cluster23_scaffold_3;QSTART=25466887;QSTRAND=- GT:DP:AD ./.:33:12,21 ./.:34:14,20 1|1:30:11,19 +chr20 245127 200x2b4 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=224120;QSTRAND=+ GT:DP:AD 1|1:36:15,21 1|0:17:6,11 ./.:19:8,11 +chr20 245425 200x2b5 G A 60 . QNAME=cluster23_scaffold_3;QSTART=25466443;QSTRAND=- GT:DP:AD ./.:20:13,7 ./.:27:8,19 1|1:36:21,15 +chr20 245437 200x2b6 GTGTATGTATA G 60 . QNAME=cluster23_scaffold_3;QSTART=25466431;QSTRAND=- GT:DP:AD ./.:30:21,9 ./.:22:11,11 1|1:39:17,22 +chr20 245443 200x2b7 GTA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=224437;QSTRAND=+ GT:DP:AD 1|0:47:24,23 ./.:29:19,10 ./.:30:22,8 +chr20 245443 200x2b8 GTATATATA G 60 . QNAME=cluster19_000000F;QSTART=204603;QSTRAND=+ GT:DP:AD ./.:23:13,10 0|1:32:14,18 ./.:42:23,19 +chr20 245470 200x2b9 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=224461;QSTRAND=+ GT:DP:AD 1|0:30:8,22 ./.:26:19,7 ./.:38:23,15 +chr20 245472 200x2ba T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=224463;QSTRAND=+ GT:DP:AD 1|0:35:20,15 ./.:14:6,8 1|0:26:9,17 +chr20 245474 200x2bb G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=199028;QSTRAND=+ GT:DP:AD 0|1:28:9,19 ./.:17:8,9 ./.:16:8,8 +chr20 245512 200x2bc G A 60 . QNAME=cluster23_scaffold_3;QSTART=25466366;QSTRAND=- GT:DP:AD ./.:31:20,11 ./.:30:18,12 1|1:32:25,7 +chr20 245789 200x2bd T C 60 . QNAME=cluster23_scaffold_3;QSTART=25466089;QSTRAND=- GT:DP:AD ./.:31:25,6 ./.:42:20,22 1|1:20:12,8 +chr20 245803 200x2be A G 60 . QNAME=cluster19_000000F;QSTART=204954;QSTRAND=+ GT:DP:AD ./.:45:20,25 0|1:39:23,16 ./.:24:11,13 +chr20 245877 200x2bf G A 60 . QNAME=cluster19_000000F;QSTART=205028;QSTRAND=+ GT:DP:AD ./.:27:5,22 0|1:49:24,25 ./.:31:9,22 +chr20 245928 200x2c0 G A 60 . QNAME=cluster23_scaffold_3;QSTART=25465950;QSTRAND=- GT:DP:AD ./.:34:9,25 ./.:26:17,9 1|1:30:22,8 +chr20 246148 200x2c1 T A 60 . QNAME=cluster19_000000F;QSTART=205299;QSTRAND=+ GT:DP:AD ./.:36:21,15 0|1:24:13,11 1|1:29:20,9 +chr20 246383 200x2c2 G A 60 . QNAME=cluster19_000000F;QSTART=205534;QSTRAND=+ GT:DP:AD ./.:20:10,10 0|1:22:9,13 ./.:33:23,10 +chr20 246501 200x2c3 G T 60 . QNAME=cluster19_000000F;QSTART=205652;QSTRAND=+ GT:DP:AD ./.:36:22,14 0|1:18:9,9 ./.:35:22,13 +chr20 246605 200x2c4 A G 60 . QNAME=cluster19_000000F;QSTART=205756;QSTRAND=+ GT:DP:AD ./.:22:6,16 0|1:48:23,25 1|1:24:9,15 +chr20 246926 200x2c5 T C 60 . QNAME=cluster23_scaffold_2;QSTART=25449587;QSTRAND=- GT:DP:AD ./.:35:25,10 ./.:45:22,23 0|1:24:14,10 +chr20 246986 200x2c6 G GCACA 60 . QNAME=cluster23_scaffold_3;QSTART=25464888;QSTRAND=- GT:DP:AD ./.:25:8,17 ./.:32:13,19 1|1:33:13,20 +chr20 247326 200x2c7 G A 60 . QNAME=cluster19_000000F;QSTART=206477;QSTRAND=+ GT:DP:AD ./.:40:16,24 0|1:26:5,21 1|1:39:16,23 +chr20 247501 200x2c8 AAAAGAAAAAG A 60 . QNAME=cluster23_scaffold_3;QSTART=25464373;QSTRAND=- GT:DP:AD ./.:43:22,21 ./.:49:25,24 1|0:27:19,8 +chr20 247505 200x2c9 GAA G 60 . QNAME=cluster23_scaffold_2;QSTART=25449004;QSTRAND=- GT:DP:AD ./.:24:14,10 ./.:44:19,25 0|1:18:12,6 +chr20 247512 200x2ca A G 60 . QNAME=cluster23_scaffold_2;QSTART=25448999;QSTRAND=- GT:DP:AD ./.:22:16,6 ./.:29:8,21 0|1:14:7,7 +chr20 247516 200x2cb A G 60 . QNAME=cluster23_scaffold_2;QSTART=25448995;QSTRAND=- GT:DP:AD ./.:26:14,12 ./.:27:9,18 0|1:14:9,5 +chr20 247516 200x2cc AAAGG A 60 . QNAME=HG002-S9-H1-000001F;QSTART=226508;QSTRAND=+ GT:DP:AD 1|1:23:15,8 1|0:14:6,8 ./.:23:6,17 +chr20 247516 200x2cd AAAGGAAGG A 60 . QNAME=cluster19_000000F;QSTART=206668;QSTRAND=+ GT:DP:AD ./.:27:15,12 0|1:28:5,23 ./.:36:23,13 +chr20 247565 200x2ce A C 60 . QNAME=cluster19_000000F;QSTART=206708;QSTRAND=+ GT:DP:AD ./.:32:17,15 0|1:27:9,18 1|1:27:15,12 +chr20 247714 200x2cf A T 60 . QNAME=cluster23_scaffold_3;QSTART=25464170;QSTRAND=- GT:DP:AD ./.:29:12,17 ./.:30:25,5 1|1:27:11,16 +chr20 247936 200x2d0 G A 60 . QNAME=cluster19_000000F;QSTART=207079;QSTRAND=+ GT:DP:AD ./.:32:16,16 0|1:13:6,7 1|1:21:10,11 +chr20 248065 200x2d1 G A 60 . QNAME=cluster23_scaffold_3;QSTART=25463819;QSTRAND=- GT:DP:AD ./.:46:22,24 ./.:30:9,21 1|1:19:13,6 +chr20 248099 200x2d2 T A 60 . QNAME=cluster23_scaffold_3;QSTART=25463785;QSTRAND=- GT:DP:AD ./.:33:19,14 ./.:16:11,5 1|1:34:16,18 +chr20 248173 200x2d3 A G 60 . QNAME=cluster23_scaffold_3;QSTART=25463711;QSTRAND=- GT:DP:AD ./.:32:19,13 ./.:29:11,18 1|1:11:5,6 +chr20 248248 200x2d4 C A 60 . QNAME=cluster23_scaffold_3;QSTART=25463636;QSTRAND=- GT:DP:AD ./.:14:7,7 ./.:36:16,20 1|1:18:12,6 +chr20 248357 200x2d5 G A 60 . QNAME=cluster23_scaffold_3;QSTART=25463527;QSTRAND=- GT:DP:AD ./.:31:22,9 ./.:28:15,13 1|1:38:24,14 +chr20 248371 200x2d6 T C 60 . QNAME=cluster23_scaffold_3;QSTART=25463513;QSTRAND=- GT:DP:AD ./.:25:5,20 ./.:20:14,6 1|1:22:11,11 +chr20 248716 200x2d7 G A 60 . QNAME=cluster23_scaffold_2;QSTART=25447795;QSTRAND=- GT:DP:AD ./.:42:21,21 ./.:33:12,21 0|1:48:25,23 +chr20 248740 200x2d8 C CA 60 . QNAME=cluster19_000000F;QSTART=207884;QSTRAND=+ GT:DP:AD ./.:48:24,24 0|1:35:16,19 ./.:21:6,15 +chr20 248740 200x2d9 CA C 60 . QNAME=cluster23_scaffold_3;QSTART=25463144;QSTRAND=- GT:DP:AD ./.:22:8,14 ./.:28:5,23 1|0:22:17,5 +chr20 248815 200x2da G A 60 . QNAME=cluster19_000000F;QSTART=207959;QSTRAND=+ GT:DP:AD ./.:35:13,22 0|1:17:7,10 ./.:35:14,21 +chr20 248838 200x2db C T 60 . QNAME=cluster23_scaffold_3;QSTART=25463047;QSTRAND=- GT:DP:AD ./.:25:15,10 ./.:18:12,6 1|0:45:24,21 +chr20 248854 200x2dc T C 60 . QNAME=cluster19_000000F;QSTART=207998;QSTRAND=+ GT:DP:AD ./.:37:24,13 0|1:47:25,22 1|1:22:17,5 +chr20 249081 200x2dd T C 60 . QNAME=cluster19_000000F;QSTART=208225;QSTRAND=+ GT:DP:AD ./.:23:18,5 0|1:39:18,21 1|1:34:17,17 +chr20 249089 200x2de C CAA 60 . QNAME=cluster19_000000F;QSTART=208234;QSTRAND=+ GT:DP:AD ./.:24:19,5 0|1:48:24,24 0|1:27:11,16 +chr20 249089 200x2df C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25462795;QSTRAND=- GT:DP:AD ./.:36:12,24 ./.:20:7,13 1|0:35:20,15 +chr20 249337 200x2e0 G C 60 . QNAME=cluster19_000000F;QSTART=208483;QSTRAND=+ GT:DP:AD ./.:25:11,14 0|1:25:6,19 ./.:26:12,14 +chr20 249412 200x2e1 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=202962;QSTRAND=+ GT:DP:AD 0|1:24:11,13 1|0:29:9,20 ./.:40:22,18 +chr20 249417 200x2e2 CAT C 60 . QNAME=cluster19_000000F;QSTART=208564;QSTRAND=+ GT:DP:AD ./.:39:24,15 0|1:34:11,23 ./.:24:6,18 +chr20 249417 200x2e3 CATA C 60 . QNAME=cluster23_scaffold_3;QSTART=25462467;QSTRAND=- GT:DP:AD ./.:33:22,11 ./.:15:5,10 1|1:29:20,9 +chr20 249536 200x2e4 A T 60 . QNAME=cluster19_000000F;QSTART=208680;QSTRAND=+ GT:DP:AD ./.:27:20,7 0|1:41:25,16 ./.:20:9,11 +chr20 249875 200x2e5 T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=228862;QSTRAND=+ GT:DP:AD 1|0:21:6,15 0|1:30:7,23 1|1:31:12,19 +chr20 249900 200x2e6 A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=228887;QSTRAND=+ GT:DP:AD 1|0:26:12,14 0|1:32:23,9 1|1:24:18,6 +chr20 250218 200x2e7 C T 60 . QNAME=cluster19_000000F;QSTART=209362;QSTRAND=+ GT:DP:AD ./.:26:9,17 0|1:21:12,9 ./.:19:8,11 +chr20 250342 200x2e8 C T 60 . QNAME=cluster19_000000F;QSTART=209486;QSTRAND=+ GT:DP:AD ./.:25:9,16 0|1:30:8,22 ./.:17:11,6 +chr20 250449 200x2e9 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=229436;QSTRAND=+ GT:DP:AD 1|0:26:7,19 0|1:28:13,15 1|1:33:19,14 +chr20 250472 200x2ea A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=229459;QSTRAND=+ GT:DP:AD 1|0:27:9,18 ./.:26:14,12 1|1:28:13,15 +chr20 250554 200x2eb C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=229541;QSTRAND=+ GT:DP:AD 1|0:35:19,16 ./.:25:20,5 1|1:29:14,15 +chr20 250671 200x2ec A C 60 . QNAME=cluster19_000000F;QSTART=209815;QSTRAND=+ GT:DP:AD ./.:28:8,20 0|1:19:9,10 ./.:40:24,16 +chr20 250864 200x2ed G A 60 . QNAME=cluster19_000000F;QSTART=210008;QSTRAND=+ GT:DP:AD ./.:27:9,18 0|1:38:25,13 ./.:38:19,19 +chr20 251035 200x2ee A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=230022;QSTRAND=+ GT:DP:AD 1|0:40:23,17 ./.:33:23,10 1|1:35:10,25 +chr20 251370 200x2ef C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=230357;QSTRAND=+ GT:DP:AD 1|0:39:20,19 ./.:45:21,24 1|0:36:17,19 +chr20 251466 200x2f0 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=230453;QSTRAND=+ GT:DP:AD 1|0:24:10,14 0|1:16:5,11 1|1:35:10,25 +chr20 251699 200x2f1 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=230686;QSTRAND=+ GT:DP:AD 1|0:37:15,22 ./.:35:15,20 1|1:28:19,9 +chr20 251939 200x2f2 G C 60 . QNAME=cluster19_000000F;QSTART=211083;QSTRAND=+ GT:DP:AD ./.:45:25,20 0|1:18:7,11 ./.:34:24,10 +chr20 251993 200x2f3 T TACACACACACACACAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=230981;QSTRAND=+ GT:DP:AD 1|0:41:17,24 ./.:28:9,19 ./.:23:8,15 +chr20 251993 200x2f4 T TACACAC 60 . QNAME=cluster19_000000F;QSTART=211138;QSTRAND=+ GT:DP:AD ./.:32:12,20 0|1:30:5,25 ./.:42:22,20 +chr20 251993 200x2f5 T TACACACACAC 60 . QNAME=cluster23_scaffold_3;QSTART=25459884;QSTRAND=- GT:DP:AD ./.:16:10,6 ./.:31:10,21 1|0:38:25,13 +chr20 251993 200x2f6 T TACACACACACACAC 60 . QNAME=cluster23_scaffold_2;QSTART=25444505;QSTRAND=- GT:DP:AD ./.:18:6,12 ./.:20:8,12 0|1:28:18,10 +chr20 252833 200x2f7 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=231836;QSTRAND=+ GT:DP:AD 1|0:32:8,24 ./.:40:20,20 1|1:16:10,6 +chr20 252834 200x2f8 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=231837;QSTRAND=+ GT:DP:AD 1|0:42:18,24 ./.:29:12,17 1|1:30:10,20 +chr20 252881 200x2f9 GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=231885;QSTRAND=+ GT:DP:AD 1|0:32:10,22 ./.:21:16,5 1|1:47:24,23 +chr20 252982 200x2fa A T 60 . QNAME=cluster19_000000F;QSTART=212132;QSTRAND=+ GT:DP:AD ./.:36:25,11 0|1:28:12,16 ./.:37:24,13 +chr20 253238 200x2fb C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=232240;QSTRAND=+ GT:DP:AD 1|1:42:18,24 1|1:44:20,24 1|1:36:17,19 +chr20 253538 200x2fc A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=232540;QSTRAND=+ GT:DP:AD 1|0:48:23,25 0|1:35:24,11 1|1:34:22,12 +chr20 253719 200x2fd C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=232721;QSTRAND=+ GT:DP:AD 1|0:15:7,8 0|1:28:15,13 1|1:39:24,15 +chr20 253968 200x2fe A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25457909;QSTRAND=- GT:DP:AD ./.:23:13,10 ./.:45:21,24 1|0:24:14,10 +chr20 254466 200x2ff A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=233468;QSTRAND=+ GT:DP:AD 1|0:16:6,10 0|1:30:21,9 1|1:27:16,11 +chr20 255081 200x300 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=234083;QSTRAND=+ GT:DP:AD 1|0:24:10,14 0|1:27:18,9 1|1:16:10,6 +chr20 255329 200x301 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=234331;QSTRAND=+ GT:DP:AD 1|0:26:17,9 0|1:42:17,25 1|1:30:25,5 +chr20 255356 200x302 C CAAAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=234359;QSTRAND=+ GT:DP:AD 1|0:37:19,18 0|1:36:21,15 ./.:25:11,14 +chr20 255356 200x303 C CAAAAAAAAA 60 . QNAME=cluster23_scaffold_3;QSTART=25456512;QSTRAND=- GT:DP:AD ./.:27:15,12 ./.:13:6,7 1|1:39:21,18 +chr20 255447 200x304 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=234457;QSTRAND=+ GT:DP:AD 1|0:23:12,11 0|1:30:6,24 1|1:34:11,23 +chr20 255527 200x305 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=234537;QSTRAND=+ GT:DP:AD 1|0:33:14,19 0|1:35:23,12 1|1:43:19,24 +chr20 255597 200x306 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=234607;QSTRAND=+ GT:DP:AD 1|0:36:21,15 0|1:22:16,6 1|1:24:12,12 +chr20 255645 200x307 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=234655;QSTRAND=+ GT:DP:AD 1|0:44:22,22 0|1:27:18,9 1|1:17:12,5 +chr20 255687 200x308 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=234697;QSTRAND=+ GT:DP:AD 1|0:38:17,21 0|1:32:11,21 1|1:36:19,17 +chr20 255778 200x309 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=234788;QSTRAND=+ GT:DP:AD 1|0:38:21,17 0|1:36:25,11 1|1:43:18,25 +chr20 255818 200x30a GAT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=234829;QSTRAND=+ GT:DP:AD 1|0:30:6,24 ./.:25:9,16 1|1:26:13,13 +chr20 255818 200x30b G GAT 60 . QNAME=cluster19_000000F;QSTART=25506967;QSTRAND=- GT:DP:AD ./.:32:7,25 1|0:24:15,9 ./.:39:18,21 +chr20 256161 200x30c C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=235169;QSTRAND=+ GT:DP:AD 1|0:46:25,21 0|1:18:7,11 1|1:32:16,16 +chr20 256351 200x30d C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=235359;QSTRAND=+ GT:DP:AD 1|0:21:5,16 0|1:16:7,9 1|1:37:14,23 +chr20 256411 200x30e G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=235419;QSTRAND=+ GT:DP:AD 1|0:45:23,22 0|1:30:12,18 1|1:25:18,7 +chr20 256777 200x30f G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=235785;QSTRAND=+ GT:DP:AD 1|0:28:17,11 0|1:33:15,18 1|1:19:7,12 +chr20 256856 200x310 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=235864;QSTRAND=+ GT:DP:AD 1|0:34:15,19 0|1:27:13,14 1|1:25:8,17 +chr20 256904 200x311 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=235912;QSTRAND=+ GT:DP:AD 1|0:22:10,12 0|1:18:11,7 1|1:36:12,24 +chr20 256928 200x312 C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=235936;QSTRAND=+ GT:DP:AD 1|0:18:6,12 0|1:19:6,13 1|1:22:10,12 +chr20 256977 200x313 A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=235985;QSTRAND=+ GT:DP:AD 1|0:18:7,11 0|1:21:13,8 1|1:12:6,6 +chr20 257008 200x314 CAGAT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=236017;QSTRAND=+ GT:DP:AD 1|1:26:20,6 0|1:36:18,18 1|1:35:15,20 +chr20 257036 200x315 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=236040;QSTRAND=+ GT:DP:AD 1|0:33:20,13 0|1:36:19,17 1|1:35:25,10 +chr20 257175 200x316 A AT 60 . QNAME=HG002-S9-H1-000001F;QSTART=236180;QSTRAND=+ GT:DP:AD 1|0:37:24,13 0|1:23:9,14 1|1:31:22,9 +chr20 257379 200x317 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=236384;QSTRAND=+ GT:DP:AD 1|0:27:22,5 0|1:19:6,13 1|1:39:18,21 +chr20 257794 200x318 CTGGTCT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=236800;QSTRAND=+ GT:DP:AD 1|0:28:21,7 0|1:43:19,24 1|1:36:20,16 +chr20 257866 200x319 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=236865;QSTRAND=+ GT:DP:AD 1|0:20:13,7 0|1:29:14,15 1|1:22:6,16 +chr20 257889 200x31a T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=236888;QSTRAND=+ GT:DP:AD 1|0:36:12,24 0|1:24:7,17 1|1:36:14,22 +chr20 257899 200x31b C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=236898;QSTRAND=+ GT:DP:AD 1|0:28:21,7 0|1:11:5,6 1|1:47:23,24 +chr20 258096 200x31c C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=237095;QSTRAND=+ GT:DP:AD 1|0:33:8,25 0|1:23:18,5 1|1:17:9,8 +chr20 258653 200x31d T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=237652;QSTRAND=+ GT:DP:AD 1|0:28:7,21 0|1:16:10,6 1|1:24:18,6 +chr20 258767 200x31e A ACTGTGAAGACCTGGTCCCCACCCCCGTTTTTAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=237767;QSTRAND=+;SVTYPE=INS;SVLEN=33 GT:DP:AD 1/0:20:13,7 0/1:41:19,22 1/1:25:12,13 +chr20 258770 200x31f G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=237802;QSTRAND=+ GT:DP:AD 1|0:24:12,12 0|1:48:25,23 1|1:32:7,25 +chr20 259023 200x320 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=238055;QSTRAND=+ GT:DP:AD 1|0:39:24,15 0|1:20:5,15 1|1:31:22,9 +chr20 259047 200x321 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=238079;QSTRAND=+ GT:DP:AD 1|0:27:20,7 0|1:15:9,6 1|1:34:10,24 +chr20 259056 200x322 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=238088;QSTRAND=+ GT:DP:AD 1|0:43:20,23 0|1:21:6,15 1|1:29:7,22 +chr20 260063 200x323 T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=239095;QSTRAND=+ GT:DP:AD 1|0:44:21,23 0|1:38:17,21 1|1:42:21,21 +chr20 260065 200x324 T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=239097;QSTRAND=+ GT:DP:AD 1|0:35:20,15 0|1:28:11,17 1|1:31:18,13 +chr20 260593 200x325 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=239625;QSTRAND=+ GT:DP:AD 1|0:42:19,23 0|1:37:15,22 1|1:36:22,14 +chr20 260725 200x326 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=239757;QSTRAND=+ GT:DP:AD 1|0:19:5,14 0|1:18:7,11 1|1:25:19,6 +chr20 260755 200x327 T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=239787;QSTRAND=+ GT:DP:AD 1|0:46:21,25 ./.:14:6,8 1|1:18:7,11 +chr20 260997 200x328 G A 60 . QNAME=cluster19_000000F;QSTART=220179;QSTRAND=+ GT:DP:AD ./.:29:7,22 0|1:38:25,13 ./.:46:21,25 +chr20 261185 200x329 TTTTG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=240218;QSTRAND=+ GT:DP:AD 1|0:20:7,13 ./.:22:17,5 1|1:19:9,10 +chr20 261768 200x32a G A 60 . QNAME=cluster19_000000F;QSTART=220950;QSTRAND=+ GT:DP:AD ./.:34:10,24 0|1:35:14,21 ./.:19:14,5 +chr20 261944 200x32b G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=240972;QSTRAND=+ GT:DP:AD 1|0:20:12,8 ./.:34:19,15 1|1:26:11,15 +chr20 261974 200x32c G T 60 . QNAME=cluster19_000000F;QSTART=221156;QSTRAND=+ GT:DP:AD ./.:16:11,5 0|1:32:22,10 ./.:32:25,7 +chr20 262044 200x32d G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=241072;QSTRAND=+ GT:DP:AD 1|0:31:8,23 0|1:40:19,21 1|1:40:25,15 +chr20 262053 200x32e T C 60 . QNAME=cluster19_000000F;QSTART=221235;QSTRAND=+ GT:DP:AD ./.:39:19,20 0|1:37:12,25 ./.:30:16,14 +chr20 262157 200x32f C T 60 . QNAME=cluster19_000000F;QSTART=221339;QSTRAND=+ GT:DP:AD ./.:48:23,25 0|1:21:11,10 ./.:33:14,19 +chr20 262198 200x330 C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25434273;QSTRAND=- GT:DP:AD ./.:16:6,10 ./.:28:11,17 0|1:29:15,14 +chr20 262582 200x331 C CT 60 . QNAME=cluster19_000000F;QSTART=221765;QSTRAND=+ GT:DP:AD ./.:30:25,5 0|1:27:16,11 ./.:22:10,12 +chr20 262711 200x332 G T 60 . QNAME=cluster19_000000F;QSTART=221894;QSTRAND=+ GT:DP:AD ./.:24:7,17 0|1:29:9,20 ./.:45:22,23 +chr20 262757 200x333 G C 60 . QNAME=cluster19_000000F;QSTART=221940;QSTRAND=+ GT:DP:AD ./.:11:5,6 0|1:39:21,18 ./.:37:13,24 +chr20 263038 200x334 A C 60 . QNAME=cluster19_000000F;QSTART=222221;QSTRAND=+ GT:DP:AD ./.:19:11,8 0|1:28:20,8 ./.:44:19,25 +chr20 263283 200x335 C A 60 . QNAME=cluster19_000000F;QSTART=222466;QSTRAND=+ GT:DP:AD ./.:31:16,15 0|1:30:9,21 ./.:15:7,8 +chr20 263451 200x336 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=242479;QSTRAND=+ GT:DP:AD 1|0:33:13,20 0|1:43:23,20 1|1:31:24,7 +chr20 263479 200x337 G GGT 60 . QNAME=cluster19_000000F;QSTART=222663;QSTRAND=+ GT:DP:AD ./.:24:9,15 0|1:23:6,17 ./.:33:10,23 +chr20 263497 200x338 TGTGTGTGC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=242526;QSTRAND=+ GT:DP:AD 1|0:40:24,16 ./.:31:24,7 1|1:26:7,19 +chr20 263505 200x339 C T 60 . QNAME=cluster19_000000F;QSTART=222690;QSTRAND=+ GT:DP:AD ./.:25:15,10 0|1:22:7,15 ./.:18:13,5 +chr20 263692 200x33a A G 60 . QNAME=cluster19_000000F;QSTART=222877;QSTRAND=+ GT:DP:AD ./.:25:18,7 0|1:18:9,9 ./.:22:8,14 +chr20 263732 200x33b C T 60 . QNAME=cluster19_000000F;QSTART=222917;QSTRAND=+ GT:DP:AD ./.:27:22,5 0|1:26:11,15 ./.:26:21,5 +chr20 263776 200x33c G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=242796;QSTRAND=+ GT:DP:AD 1|0:39:14,25 ./.:12:5,7 1|1:29:7,22 +chr20 264344 200x33d G A 60 . QNAME=cluster19_000000F;QSTART=223529;QSTRAND=+ GT:DP:AD ./.:32:21,11 0|1:30:7,23 ./.:39:14,25 +chr20 264825 200x33e T G 60 . QNAME=cluster19_000000F;QSTART=224010;QSTRAND=+ GT:DP:AD ./.:29:9,20 0|1:41:21,20 ./.:38:16,22 +chr20 265021 200x33f G T 60 . QNAME=cluster19_000000F;QSTART=224206;QSTRAND=+ GT:DP:AD ./.:24:8,16 0|1:41:20,21 ./.:26:17,9 +chr20 265021 200x340 G GT 60 . QNAME=HG002-S9-H2-000001F;QSTART=218568;QSTRAND=+ GT:DP:AD 0|1:18:13,5 1|0:24:9,15 0|1:48:24,24 +chr20 265021 200x341 GT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=244042;QSTRAND=+ GT:DP:AD 1|0:20:9,11 ./.:41:21,20 ./.:23:16,7 +chr20 265024 200x342 T G 60 . QNAME=cluster19_000000F;QSTART=224209;QSTRAND=+ GT:DP:AD ./.:36:13,23 0|1:36:20,16 ./.:47:25,22 +chr20 265028 200x343 T G 60 . QNAME=cluster19_000000F;QSTART=224213;QSTRAND=+ GT:DP:AD ./.:31:20,11 0|1:36:12,24 ./.:12:6,6 +chr20 265032 200x344 T G 60 . QNAME=cluster19_000000F;QSTART=224217;QSTRAND=+ GT:DP:AD ./.:35:25,10 0|1:27:6,21 ./.:22:8,14 +chr20 265049 200x345 C T 60 . QNAME=cluster19_000000F;QSTART=224234;QSTRAND=+ GT:DP:AD ./.:41:24,17 0|1:28:12,16 ./.:19:9,10 +chr20 265294 200x346 G T 60 . QNAME=cluster19_000000F;QSTART=224479;QSTRAND=+ GT:DP:AD ./.:21:15,6 0|1:27:19,8 ./.:39:17,22 +chr20 265390 200x347 AAAG A 60 . QNAME=HG002-S9-H1-000001F;QSTART=244410;QSTRAND=+ GT:DP:AD 1|0:25:15,10 ./.:35:12,23 1|1:26:9,17 +chr20 265614 200x348 C T 60 . QNAME=cluster19_000000F;QSTART=224799;QSTRAND=+ GT:DP:AD ./.:27:22,5 0|1:16:8,8 ./.:31:8,23 +chr20 265842 200x349 T TTAAA 60 . QNAME=cluster19_000000F;QSTART=225028;QSTRAND=+ GT:DP:AD ./.:27:6,21 0|1:20:5,15 1|1:42:20,22 +chr20 266980 200x34a CCT C 60 . QNAME=cluster23_scaffold_3;QSTART=25444877;QSTRAND=- GT:DP:AD ./.:32:23,9 ./.:22:8,14 1|1:29:12,17 +chr20 267423 200x34b G A 60 . QNAME=cluster23_scaffold_2;QSTART=25429056;QSTRAND=- GT:DP:AD ./.:32:20,12 ./.:34:19,15 0|1:35:10,25 +chr20 268285 200x34c C A 60 . QNAME=cluster23_scaffold_2;QSTART=25428194;QSTRAND=- GT:DP:AD ./.:20:5,15 ./.:27:9,18 0|1:37:21,16 +chr20 268294 200x34d A T 60 . QNAME=cluster23_scaffold_2;QSTART=25428185;QSTRAND=- GT:DP:AD ./.:28:17,11 ./.:21:8,13 0|1:23:12,11 +chr20 268599 200x34e T A 60 . QNAME=cluster23_scaffold_3;QSTART=25443260;QSTRAND=- GT:DP:AD ./.:32:9,23 ./.:24:13,11 1|1:29:8,21 +chr20 269435 200x34f G A 60 . QNAME=cluster23_scaffold_3;QSTART=25442424;QSTRAND=- GT:DP:AD ./.:38:25,13 ./.:41:22,19 1|1:28:5,23 +chr20 269686 200x350 CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=223234;QSTRAND=+ GT:DP:AD 0|1:31:10,21 ./.:37:16,21 ./.:27:20,7 +chr20 269844 200x351 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=223390;QSTRAND=+ GT:DP:AD 0|1:34:11,23 ./.:11:6,5 ./.:30:20,10 +chr20 270732 200x352 ACTT A 60 . QNAME=cluster19_000000F;QSTART=229922;QSTRAND=+ GT:DP:AD ./.:24:17,7 0|1:25:19,6 ./.:30:11,19 +chr20 271440 200x353 GCATACACACACA G 60 . QNAME=cluster23_scaffold_3;QSTART=25440419;QSTRAND=- GT:DP:AD ./.:42:22,20 ./.:20:14,6 1|0:24:14,10 +chr20 271443 200x354 TACAC T 60 . QNAME=cluster19_000000F;QSTART=25491341;QSTRAND=- GT:DP:AD ./.:32:22,10 1|0:32:12,20 ./.:47:25,22 +chr20 271443 200x355 T TAC 60 . QNAME=cluster23_scaffold_2;QSTART=25425034;QSTRAND=- GT:DP:AD ./.:31:21,10 ./.:13:6,7 0|1:25:13,12 +chr20 271455 200x356 C A 60 . QNAME=cluster23_scaffold_3;QSTART=25440416;QSTRAND=- GT:DP:AD ./.:49:25,24 ./.:46:21,25 1|0:30:23,7 +chr20 271524 200x357 A G 60 . QNAME=cluster23_scaffold_3;QSTART=25440347;QSTRAND=- GT:DP:AD ./.:21:14,7 ./.:36:19,17 1|0:33:9,24 +chr20 271615 200x358 T C 60 . QNAME=cluster23_scaffold_3;QSTART=25440256;QSTRAND=- GT:DP:AD ./.:34:22,12 ./.:22:13,9 1|0:18:10,8 +chr20 272116 200x359 A AC 60 . QNAME=cluster23_scaffold_3;QSTART=25439754;QSTRAND=- GT:DP:AD ./.:27:21,6 ./.:42:23,19 1|0:36:15,21 +chr20 272200 200x35a TA T 60 . QNAME=cluster23_scaffold_3;QSTART=25439670;QSTRAND=- GT:DP:AD ./.:23:12,11 ./.:27:12,15 1|0:46:21,25 +chr20 272348 200x35b G A 60 . QNAME=cluster23_scaffold_3;QSTART=25439523;QSTRAND=- GT:DP:AD ./.:28:9,19 ./.:21:7,14 1|0:40:16,24 +chr20 272493 200x35c C A 60 . QNAME=cluster23_scaffold_2;QSTART=25423984;QSTRAND=- GT:DP:AD ./.:26:20,6 ./.:15:6,9 0|1:25:13,12 +chr20 273372 200x35d C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=252388;QSTRAND=+ GT:DP:AD 1|0:26:11,15 ./.:35:19,16 1|0:36:16,20 +chr20 273876 200x35e C CAAGAA 60 . QNAME=cluster23_scaffold_3;QSTART=25437990;QSTRAND=- GT:DP:AD ./.:24:12,12 ./.:23:16,7 1|0:31:20,11 +chr20 273894 200x35f A G 60 . QNAME=cluster23_scaffold_3;QSTART=25437972;QSTRAND=- GT:DP:AD ./.:22:13,9 ./.:30:24,6 1|0:47:24,23 +chr20 273903 200x360 A AAGGGAGGG 60 . QNAME=HG002-S9-H2-000001F;QSTART=227450;QSTRAND=+ GT:DP:AD 0|1:41:24,17 1|1:19:5,14 ./.:34:19,15 +chr20 273903 200x361 AAGGGAGGG A 60 . QNAME=cluster23_scaffold_3;QSTART=25437963;QSTRAND=- GT:DP:AD ./.:42:18,24 ./.:36:20,16 1|0:31:13,18 +chr20 273903 200x362 AAGGG A 60 . QNAME=cluster23_scaffold_2;QSTART=25422574;QSTRAND=- GT:DP:AD ./.:32:21,11 ./.:24:10,14 0|1:22:13,9 +chr20 274125 200x363 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=253141;QSTRAND=+ GT:DP:AD 1|0:16:9,7 ./.:12:6,6 ./.:36:20,16 +chr20 274210 200x364 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=253226;QSTRAND=+ GT:DP:AD 1|0:22:7,15 ./.:27:14,13 1|0:18:11,7 +chr20 274599 200x365 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=253615;QSTRAND=+ GT:DP:AD 1|0:17:11,6 ./.:39:16,23 ./.:26:16,10 +chr20 274820 200x366 TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=253837;QSTRAND=+ GT:DP:AD 1|0:17:12,5 ./.:39:14,25 ./.:48:25,23 +chr20 274829 200x367 A T 60 . QNAME=cluster23_scaffold_3;QSTART=25437045;QSTRAND=- GT:DP:AD ./.:47:25,22 ./.:41:22,19 1|0:38:13,25 +chr20 274893 200x368 G C 60 . QNAME=cluster23_scaffold_3;QSTART=25436981;QSTRAND=- GT:DP:AD ./.:24:6,18 ./.:27:7,20 1|0:28:6,22 +chr20 275122 200x369 G T 60 . QNAME=cluster23_scaffold_3;QSTART=25436752;QSTRAND=- GT:DP:AD ./.:33:17,16 ./.:41:20,21 1|0:21:5,16 +chr20 275241 200x36a G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=254256;QSTRAND=+ GT:DP:AD 1|0:35:17,18 ./.:36:13,23 1|0:39:18,21 +chr20 275322 200x36b C CG 60 . QNAME=cluster23_scaffold_3;QSTART=25436551;QSTRAND=- GT:DP:AD ./.:26:19,7 ./.:13:7,6 1|0:35:22,13 +chr20 275361 200x36c C T 60 . QNAME=cluster23_scaffold_3;QSTART=25436512;QSTRAND=- GT:DP:AD ./.:25:16,9 ./.:49:24,25 1|0:28:11,17 +chr20 275466 200x36d T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=254481;QSTRAND=+ GT:DP:AD 1|0:31:7,24 ./.:34:12,22 ./.:32:19,13 +chr20 275606 200x36e G A 60 . QNAME=cluster23_scaffold_3;QSTART=25436267;QSTRAND=- GT:DP:AD ./.:25:12,13 ./.:34:11,23 1|0:32:22,10 +chr20 275918 200x36f G A 60 . QNAME=cluster23_scaffold_3;QSTART=25435955;QSTRAND=- GT:DP:AD ./.:42:22,20 ./.:37:12,25 1|0:30:17,13 +chr20 275932 200x370 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=254947;QSTRAND=+ GT:DP:AD 1|0:25:6,19 ./.:43:23,20 1|0:29:21,8 +chr20 276086 200x371 T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=255101;QSTRAND=+ GT:DP:AD 1|0:21:9,12 ./.:26:10,16 1|0:29:6,23 +chr20 276119 200x372 G GA 60 . QNAME=cluster23_scaffold_3;QSTART=25435753;QSTRAND=- GT:DP:AD ./.:22:6,16 ./.:31:6,25 1|0:33:23,10 +chr20 276122 200x373 G C 60 . QNAME=cluster23_scaffold_3;QSTART=25435750;QSTRAND=- GT:DP:AD ./.:42:24,18 ./.:39:18,21 1|0:39:25,14 +chr20 276225 200x374 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=255240;QSTRAND=+ GT:DP:AD 1|0:34:12,22 ./.:35:17,18 1|0:32:14,18 +chr20 276245 200x375 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=255260;QSTRAND=+ GT:DP:AD 1|0:30:5,25 ./.:14:5,9 ./.:24:18,6 +chr20 276351 200x376 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=255366;QSTRAND=+ GT:DP:AD 1|0:30:13,17 ./.:33:14,19 1|0:41:17,24 +chr20 276391 200x377 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=255406;QSTRAND=+ GT:DP:AD 1|0:25:6,19 ./.:40:15,25 1|0:39:19,20 +chr20 276679 200x378 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=255694;QSTRAND=+ GT:DP:AD 1|0:27:21,6 ./.:32:11,21 1|0:32:15,17 +chr20 277092 200x379 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=256107;QSTRAND=+ GT:DP:AD 1|0:22:9,13 ./.:37:23,14 1|0:32:14,18 +chr20 277162 200x37a G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=256177;QSTRAND=+ GT:DP:AD 1|0:21:15,6 ./.:45:23,22 ./.:30:23,7 +chr20 277171 200x37b T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=256186;QSTRAND=+ GT:DP:AD 1|1:15:7,8 ./.:19:13,6 1|0:28:9,19 +chr20 277550 200x37c C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=256565;QSTRAND=+ GT:DP:AD 1|0:14:5,9 ./.:28:22,6 1|0:31:20,11 +chr20 277574 200x37d G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=256589;QSTRAND=+ GT:DP:AD 1|0:30:21,9 ./.:21:6,15 1|0:35:23,12 +chr20 277654 200x37e G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=256669;QSTRAND=+ GT:DP:AD 1|0:20:13,7 ./.:18:7,11 1|0:24:10,14 +chr20 277664 200x37f G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=256679;QSTRAND=+ GT:DP:AD 1|0:31:7,24 ./.:26:10,16 1|0:43:18,25 +chr20 277800 200x380 C CAG 60 . QNAME=HG002-S9-H1-000001F;QSTART=256816;QSTRAND=+ GT:DP:AD 1|0:29:21,8 ./.:21:11,10 1|0:43:20,23 +chr20 277808 200x381 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=256825;QSTRAND=+ GT:DP:AD 1|0:34:15,19 ./.:21:14,7 1|0:23:13,10 +chr20 277915 200x382 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=256932;QSTRAND=+ GT:DP:AD 1|0:35:16,19 ./.:32:22,10 1|0:33:12,21 +chr20 278070 200x383 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=257087;QSTRAND=+ GT:DP:AD 1|0:19:9,10 ./.:23:10,13 1|0:42:22,20 +chr20 278107 200x384 C T 60 . QNAME=cluster23_scaffold_3;QSTART=25433763;QSTRAND=- GT:DP:AD ./.:31:8,23 ./.:30:25,5 1|0:30:14,16 +chr20 278224 200x385 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=257241;QSTRAND=+ GT:DP:AD 1|0:46:25,21 ./.:30:25,5 1|0:21:6,15 +chr20 278515 200x386 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=257532;QSTRAND=+ GT:DP:AD 1|0:29:16,13 ./.:29:24,5 ./.:33:13,20 +chr20 278561 200x387 G A 60 . QNAME=cluster23_scaffold_3;QSTART=25433309;QSTRAND=- GT:DP:AD ./.:34:18,16 ./.:13:7,6 1|0:39:18,21 +chr20 278930 200x388 C CGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAG 60 . QNAME=HG002-S9-H2-000001F;QSTART=232485;QSTRAND=+;SVTYPE=INS;SVLEN=184 GT:DP:AD 0/1:29:9,20 ./.:22:16,6 ./.:24:5,19 +chr20 278930 200x389 C CGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGCGGGAG 60 . QNAME=cluster23_scaffold_2;QSTART=25417363;QSTRAND=-;SVTYPE=INS;SVLEN=188 GT:DP:AD ./.:19:11,8 ./.:33:12,21 0/1:36:12,24 +chr20 278962 200x38a G GGGAGGGAGGGACGGAGGGAGGAAGGGCGGGAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=257980;QSTRAND=+;SVTYPE=INS;SVLEN=32 GT:DP:AD 1/0:42:17,25 ./.:17:10,7 ./.:20:9,11 +chr20 278966 200x38b C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=258015;QSTRAND=+ GT:DP:AD 1|0:15:5,10 ./.:38:13,25 ./.:42:17,25 +chr20 278977 200x38c A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=258026;QSTRAND=+ GT:DP:AD 1|0:28:5,23 ./.:26:12,14 ./.:12:7,5 +chr20 279062 200x38d G GGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGTGGGAGGGAGGGAGGGAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=258112;QSTRAND=+;SVTYPE=INS;SVLEN=139 GT:DP:AD 1/0:29:6,23 ./.:40:23,17 ./.:32:9,23 +chr20 279069 200x38e A AGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGCGGGACGGAGGGAGGGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=232808;QSTRAND=+;SVTYPE=INS;SVLEN=438 GT:DP:AD 0/1:26:5,21 ./.:30:8,22 ./.:38:15,23 +chr20 279069 200x38f A AGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGC 60 . QNAME=cluster19_000000F;QSTART=25483168;QSTRAND=-;SVTYPE=INS;SVLEN=543 GT:DP:AD ./.:37:13,24 1/1:24:6,18 ./.:42:19,23 +chr20 279069 200x390 A AGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGCGGGACGGAGGGAGGGC 60 . QNAME=cluster23_scaffold_2;QSTART=25416710;QSTRAND=-;SVTYPE=INS;SVLEN=514 GT:DP:AD ./.:39:23,16 ./.:26:5,21 0/1:21:11,10 +chr20 279098 200x391 G GGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGCGGGACGGAGGGAGGGACGGAGGGCGGGACGGAGGGAC 60 . QNAME=cluster23_scaffold_3;QSTART=25432493;QSTRAND=-;SVTYPE=INS;SVLEN=179 GT:DP:AD ./.:25:20,5 ./.:28:17,11 1/0:23:13,10 +chr20 279102 200x392 C G 60 . QNAME=cluster23_scaffold_3;QSTART=25432489;QSTRAND=- GT:DP:AD ./.:40:22,18 ./.:29:22,7 1|0:42:19,23 +chr20 279177 200x393 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=258365;QSTRAND=+ GT:DP:AD 1|1:30:10,20 ./.:29:6,23 0|1:32:15,17 +chr20 279328 200x394 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=258516;QSTRAND=+ GT:DP:AD 1|0:14:6,8 ./.:17:8,9 1|0:12:5,7 +chr20 279759 200x395 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=258947;QSTRAND=+ GT:DP:AD 1|0:33:13,20 ./.:47:25,22 1|0:35:19,16 +chr20 279880 200x396 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=259068;QSTRAND=+ GT:DP:AD 1|0:33:13,20 ./.:37:23,14 1|0:21:9,12 +chr20 280083 200x397 G T 60 . QNAME=cluster23_scaffold_3;QSTART=25431508;QSTRAND=- GT:DP:AD ./.:29:15,14 ./.:30:13,17 1|0:25:18,7 +chr20 280211 200x398 CAACAACAACAATTGTACTTCCCTAAGGTTACACCCAGCAGGTGCATAAAACCTACAGTAACAAT C 60 . QNAME=cluster23_scaffold_3;QSTART=25431380;QSTRAND=-;SVTYPE=DEL;SVLEN=-64 GT:DP:AD ./.:42:24,18 ./.:45:20,25 1/0:39:24,15 +chr20 280230 200x399 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=259418;QSTRAND=+ GT:DP:AD 1|0:28:7,21 ./.:32:11,21 ./.:15:5,10 +chr20 280339 200x39a T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=259527;QSTRAND=+ GT:DP:AD 1|0:47:22,25 ./.:25:17,8 ./.:35:23,12 +chr20 280403 200x39b TAAC T 60 . QNAME=cluster23_scaffold_3;QSTART=25431252;QSTRAND=- GT:DP:AD ./.:20:15,5 ./.:31:23,8 1|0:39:16,23 +chr20 280418 200x39c C T 60 . QNAME=cluster23_scaffold_3;QSTART=25431240;QSTRAND=- GT:DP:AD ./.:41:25,16 ./.:18:5,13 1|0:42:25,17 +chr20 280635 200x39d G A 60 . QNAME=cluster23_scaffold_3;QSTART=25431023;QSTRAND=- GT:DP:AD ./.:41:18,23 ./.:29:21,8 1|0:34:10,24 +chr20 281010 200x39e G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=260198;QSTRAND=+ GT:DP:AD 1|0:45:23,22 ./.:44:20,24 ./.:28:10,18 +chr20 281470 200x39f C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=260658;QSTRAND=+ GT:DP:AD 1|0:27:7,20 ./.:38:23,15 1|0:26:8,18 +chr20 281585 200x3a0 C T 60 . QNAME=cluster23_scaffold_3;QSTART=25430073;QSTRAND=- GT:DP:AD ./.:45:24,21 ./.:31:6,25 1|0:20:15,5 +chr20 281929 200x3a1 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=261117;QSTRAND=+ GT:DP:AD 1|0:29:16,13 ./.:43:20,23 1|0:32:14,18 +chr20 282596 200x3a2 A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=261784;QSTRAND=+ GT:DP:AD 1|0:13:5,8 ./.:44:23,21 ./.:27:22,5 +chr20 282775 200x3a3 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=261963;QSTRAND=+ GT:DP:AD 1|0:35:24,11 ./.:35:12,23 ./.:26:8,18 +chr20 283019 200x3a4 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=262207;QSTRAND=+ GT:DP:AD 1|0:39:19,20 ./.:17:8,9 ./.:20:10,10 +chr20 283328 200x3a5 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=262516;QSTRAND=+ GT:DP:AD 1|0:29:6,23 ./.:19:5,14 ./.:30:20,10 +chr20 283411 200x3a6 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=262599;QSTRAND=+ GT:DP:AD 1|0:14:6,8 ./.:32:18,14 ./.:37:21,16 +chr20 283535 200x3a7 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=262723;QSTRAND=+ GT:DP:AD 1|0:18:7,11 ./.:37:17,20 ./.:28:7,21 +chr20 283694 200x3a8 T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=262883;QSTRAND=+ GT:DP:AD 1|0:31:21,10 ./.:37:20,17 ./.:26:5,21 +chr20 283724 200x3a9 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=262913;QSTRAND=+ GT:DP:AD 1|0:19:13,6 ./.:24:5,19 ./.:26:14,12 +chr20 283802 200x3aa C T 60 . QNAME=cluster23_scaffold_3;QSTART=25427856;QSTRAND=- GT:DP:AD ./.:37:14,23 ./.:27:16,11 1|0:35:18,17 +chr20 283857 200x3ab A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=263046;QSTRAND=+ GT:DP:AD 1|0:30:25,5 ./.:22:14,8 ./.:29:7,22 +chr20 284338 200x3ac A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=263527;QSTRAND=+ GT:DP:AD 1|0:37:12,25 ./.:45:24,21 ./.:22:8,14 +chr20 284356 200x3ad G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=263545;QSTRAND=+ GT:DP:AD 1|0:28:12,16 ./.:29:5,24 ./.:35:11,24 +chr20 284597 200x3ae T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=263786;QSTRAND=+ GT:DP:AD 1|0:17:11,6 ./.:30:17,13 1|0:39:20,19 +chr20 284724 200x3af A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=263913;QSTRAND=+ GT:DP:AD 1|0:32:18,14 ./.:25:13,12 1|0:28:15,13 +chr20 284881 200x3b0 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=264070;QSTRAND=+ GT:DP:AD 1|0:41:16,25 ./.:42:23,19 1|0:17:9,8 +chr20 285327 200x3b1 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=264516;QSTRAND=+ GT:DP:AD 1|0:30:12,18 ./.:43:19,24 1|0:26:15,11 +chr20 285600 200x3b2 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=264789;QSTRAND=+ GT:DP:AD 1|0:35:12,23 ./.:38:17,21 1|0:26:18,8 +chr20 285621 200x3b3 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=264810;QSTRAND=+ GT:DP:AD 1|0:39:21,18 ./.:22:15,7 1|0:39:21,18 +chr20 285738 200x3b4 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=264927;QSTRAND=+ GT:DP:AD 1|0:37:16,21 ./.:40:21,19 ./.:40:24,16 +chr20 286151 200x3b5 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=265340;QSTRAND=+ GT:DP:AD 1|0:11:5,6 ./.:39:23,16 ./.:20:8,12 +chr20 286163 200x3b6 CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=265353;QSTRAND=+ GT:DP:AD 1|0:13:6,7 ./.:19:10,9 ./.:18:12,6 +chr20 286710 200x3b7 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=265898;QSTRAND=+ GT:DP:AD 1|0:14:8,6 ./.:21:12,9 1|0:28:5,23 +chr20 286812 200x3b8 C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=266000;QSTRAND=+ GT:DP:AD 1|0:29:19,10 ./.:28:7,21 1|0:43:21,22 +chr20 287237 200x3b9 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=266425;QSTRAND=+ GT:DP:AD 1|0:25:20,5 ./.:36:17,19 1|0:37:24,13 +chr20 287305 200x3ba G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=266493;QSTRAND=+ GT:DP:AD 1|0:37:19,18 ./.:30:14,16 1|0:33:23,10 +chr20 287629 200x3bb T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=266817;QSTRAND=+ GT:DP:AD 1|0:18:8,10 ./.:36:23,13 1|0:39:14,25 +chr20 287833 200x3bc C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=267021;QSTRAND=+ GT:DP:AD 1|0:14:8,6 ./.:27:6,21 1|0:30:16,14 +chr20 287837 200x3bd A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=267025;QSTRAND=+ GT:DP:AD 1|0:19:6,13 ./.:32:13,19 ./.:31:20,11 +chr20 287876 200x3be C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=267064;QSTRAND=+ GT:DP:AD 1|0:24:15,9 ./.:26:15,11 1|0:20:14,6 +chr20 287908 200x3bf C CAAAAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=267097;QSTRAND=+ GT:DP:AD 1|0:26:10,16 ./.:30:17,13 ./.:44:21,23 +chr20 287908 200x3c0 C CAAAAAAAA 60 . QNAME=cluster23_scaffold_3;QSTART=25423742;QSTRAND=- GT:DP:AD ./.:40:18,22 ./.:38:21,17 1|0:29:24,5 +chr20 287932 200x3c1 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=267129;QSTRAND=+ GT:DP:AD 1|0:32:15,17 ./.:27:14,13 ./.:23:14,9 +chr20 288158 200x3c2 C CTTTCTTTTTCTT 60 . QNAME=HG002-S9-H1-000001F;QSTART=267356;QSTRAND=+ GT:DP:AD 1|0:36:16,20 ./.:34:16,18 ./.:30:5,25 +chr20 288174 200x3c3 C CTTTTTCTTTTTCTT 60 . QNAME=cluster23_scaffold_3;QSTART=25423462;QSTRAND=- GT:DP:AD ./.:27:11,16 ./.:31:8,23 1|0:41:16,25 +chr20 288174 200x3c4 C CT 60 . QNAME=cluster23_scaffold_2;QSTART=25407604;QSTRAND=- GT:DP:AD ./.:23:6,17 ./.:33:11,22 0|1:46:25,21 +chr20 288365 200x3c5 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=267574;QSTRAND=+ GT:DP:AD 1|0:32:7,25 ./.:44:21,23 1|0:39:18,21 +chr20 288516 200x3c6 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=267725;QSTRAND=+ GT:DP:AD 1|0:18:13,5 ./.:25:9,16 1|0:32:16,16 +chr20 289049 200x3c7 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=268258;QSTRAND=+ GT:DP:AD 1|0:22:5,17 ./.:39:16,23 1|0:24:14,10 +chr20 289196 200x3c8 A ACC 60 . QNAME=HG002-S9-H1-000001F;QSTART=268406;QSTRAND=+ GT:DP:AD 1|0:37:12,25 ./.:27:19,8 ./.:28:23,5 +chr20 289196 200x3c9 A ACCC 60 . QNAME=cluster23_scaffold_3;QSTART=25422437;QSTRAND=- GT:DP:AD ./.:28:5,23 ./.:28:15,13 1|0:44:21,23 +chr20 289773 200x3ca TC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=268985;QSTRAND=+ GT:DP:AD 1|0:29:19,10 ./.:35:22,13 1|0:27:6,21 +chr20 289787 200x3cb C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=268997;QSTRAND=+ GT:DP:AD 1|0:34:22,12 ./.:27:17,10 1|0:30:18,12 +chr20 289993 200x3cc G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=269203;QSTRAND=+ GT:DP:AD 1|0:43:25,18 ./.:29:6,23 1|0:41:23,18 +chr20 290134 200x3cd G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=269344;QSTRAND=+ GT:DP:AD 1|0:46:23,23 ./.:48:24,24 1|0:18:13,5 +chr20 290494 200x3ce G GC 60 . QNAME=HG002-S9-H2-000001F;QSTART=244671;QSTRAND=+ GT:DP:AD 0|1:18:12,6 1|1:47:22,25 0|1:30:5,25 +chr20 290563 200x3cf A ATT 60 . QNAME=cluster23_scaffold_2;QSTART=25405212;QSTRAND=- GT:DP:AD ./.:40:20,20 ./.:33:10,23 0|1:27:15,12 +chr20 290584 200x3d0 T TTA 60 . QNAME=HG002-S9-H1-000001F;QSTART=269795;QSTRAND=+ GT:DP:AD 1|0:16:10,6 ./.:32:16,16 ./.:18:10,8 +chr20 290584 200x3d1 T TTTA 60 . QNAME=cluster23_scaffold_3;QSTART=25421047;QSTRAND=- GT:DP:AD ./.:44:24,20 ./.:23:10,13 1|0:27:17,10 +chr20 291169 200x3d2 TTCTC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=270382;QSTRAND=+ GT:DP:AD 1|0:41:25,16 ./.:27:21,6 1|0:30:13,17 +chr20 291796 200x3d3 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=271004;QSTRAND=+ GT:DP:AD 1|0:30:23,7 ./.:11:6,5 1|0:27:14,13 +chr20 291952 200x3d4 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=271160;QSTRAND=+ GT:DP:AD 1|1:25:15,10 1|1:23:5,18 1|1:37:23,14 +chr20 292806 200x3d5 CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=272015;QSTRAND=+ GT:DP:AD 1|0:33:17,16 ./.:28:7,21 1|0:22:12,10 +chr20 293331 200x3d6 T C 60 . QNAME=cluster23_scaffold_3;QSTART=25418305;QSTRAND=- GT:DP:AD ./.:45:25,20 ./.:44:24,20 1|0:20:15,5 +chr20 293433 200x3d7 GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=272641;QSTRAND=+ GT:DP:AD 1|0:36:16,20 ./.:22:17,5 ./.:32:25,7 +chr20 293692 200x3d8 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=272898;QSTRAND=+ GT:DP:AD 1|0:35:25,10 ./.:29:8,21 1|0:17:5,12 +chr20 294073 200x3d9 AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=273280;QSTRAND=+ GT:DP:AD 1|0:32:23,9 ./.:34:20,14 ./.:46:22,24 +chr20 296976 200x3da C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=251153;QSTRAND=+ GT:DP:AD 0|1:33:17,16 1|1:21:16,5 0|1:25:8,17 +chr20 297051 200x3db C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=251228;QSTRAND=+ GT:DP:AD 0|1:24:6,18 1|1:26:10,16 0|1:25:15,10 +chr20 297191 200x3dc C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=251368;QSTRAND=+ GT:DP:AD 0|1:43:24,19 1|1:32:10,22 0|1:30:9,21 +chr20 297482 200x3dd CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=276688;QSTRAND=+ GT:DP:AD 1|0:23:7,16 ./.:29:23,6 1|0:40:16,24 +chr20 297874 200x3de T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=252051;QSTRAND=+ GT:DP:AD 0|1:18:13,5 1|1:44:23,21 0|1:23:6,17 +chr20 298162 200x3df C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=277366;QSTRAND=+ GT:DP:AD 1|0:24:19,5 ./.:25:8,17 0|1:36:25,11 +chr20 298541 200x3e0 C T 60 . QNAME=cluster19_000000F;QSTART=258279;QSTRAND=+ GT:DP:AD ./.:30:6,24 0|1:40:23,17 ./.:21:5,16 +chr20 298839 200x3e1 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=278043;QSTRAND=+ GT:DP:AD 1|0:33:9,24 ./.:44:19,25 1|0:26:15,11 +chr20 299130 200x3e2 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=278334;QSTRAND=+ GT:DP:AD 1|0:36:15,21 ./.:50:25,25 1|0:40:20,20 +chr20 301074 200x3e3 G C 60 . QNAME=cluster23_scaffold_2;QSTART=25394701;QSTRAND=- GT:DP:AD ./.:35:20,15 ./.:19:5,14 0|1:25:5,20 +chr20 301778 200x3e4 A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=280982;QSTRAND=+ GT:DP:AD 1|0:22:17,5 ./.:32:25,7 1|0:32:25,7 +chr20 302639 200x3e5 T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=281844;QSTRAND=+ GT:DP:AD 1|0:26:20,6 ./.:40:21,19 1|0:30:24,6 +chr20 302891 200x3e6 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=282096;QSTRAND=+ GT:DP:AD 1|1:36:12,24 1|1:41:21,20 1|1:20:6,14 +chr20 303233 200x3e7 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=282438;QSTRAND=+ GT:DP:AD 1|1:26:18,8 1|1:47:22,25 1|1:26:12,14 +chr20 303404 200x3e8 C A 60 . QNAME=cluster19_000000F;QSTART=263142;QSTRAND=+ GT:DP:AD ./.:24:17,7 0|1:39:22,17 ./.:28:18,10 +chr20 303430 200x3e9 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=282635;QSTRAND=+ GT:DP:AD 1|1:25:16,9 1|0:22:9,13 1|1:43:18,25 +chr20 304111 200x3ea C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=283316;QSTRAND=+ GT:DP:AD 1|1:27:17,10 1|0:30:7,23 1|1:46:25,21 +chr20 304170 200x3eb T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=283375;QSTRAND=+ GT:DP:AD 1|1:29:6,23 1|1:16:7,9 1|1:26:14,12 +chr20 304190 200x3ec A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=283395;QSTRAND=+ GT:DP:AD 1|1:43:23,20 ./.:25:7,18 1|1:14:7,7 +chr20 304257 200x3ed C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=258434;QSTRAND=+ GT:DP:AD 0|1:37:22,15 1|0:20:5,15 0|1:17:12,5 +chr20 304335 200x3ee G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=258512;QSTRAND=+ GT:DP:AD 0|1:33:12,21 1|0:34:15,19 0|1:28:23,5 +chr20 304365 200x3ef G C 60 . QNAME=cluster19_000000F;QSTART=264103;QSTRAND=+ GT:DP:AD ./.:39:19,20 0|1:32:12,20 ./.:24:7,17 +chr20 304375 200x3f0 C T 60 . QNAME=cluster23_scaffold_2;QSTART=25391400;QSTRAND=- GT:DP:AD ./.:20:6,14 ./.:29:7,22 0|1:40:21,19 +chr20 304376 200x3f1 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=258553;QSTRAND=+ GT:DP:AD 0|1:39:16,23 1|1:33:15,18 ./.:36:24,12 +chr20 304377 200x3f2 G C 60 . QNAME=cluster23_scaffold_2;QSTART=25391398;QSTRAND=- GT:DP:AD ./.:23:10,13 ./.:28:5,23 0|1:28:22,6 +chr20 304450 200x3f3 T C 60 . QNAME=cluster19_000000F;QSTART=264188;QSTRAND=+ GT:DP:AD ./.:37:18,19 0|1:23:14,9 ./.:31:25,6 +chr20 304460 200x3f4 T C 60 . QNAME=cluster19_000000F;QSTART=264198;QSTRAND=+ GT:DP:AD ./.:34:15,19 0|1:33:19,14 ./.:36:13,23 +chr20 304461 200x3f5 T C 60 . QNAME=cluster19_000000F;QSTART=264199;QSTRAND=+ GT:DP:AD ./.:35:22,13 0|1:32:18,14 ./.:24:7,17 +chr20 304463 200x3f6 A T 60 . QNAME=cluster19_000000F;QSTART=264201;QSTRAND=+ GT:DP:AD ./.:29:13,16 0|1:49:24,25 ./.:17:12,5 +chr20 304504 200x3f7 CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=258682;QSTRAND=+ GT:DP:AD 0|1:39:22,17 1|0:41:25,16 0|1:16:8,8 +chr20 304679 200x3f8 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=283884;QSTRAND=+ GT:DP:AD 1|0:32:8,24 ./.:42:23,19 1|0:26:5,21 +chr20 304705 200x3f9 G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=258881;QSTRAND=+ GT:DP:AD 0|1:28:8,20 1|1:31:25,6 0|1:15:9,6 +chr20 305012 200x3fa A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=284217;QSTRAND=+ GT:DP:AD 1|1:35:15,20 1|1:20:6,14 1|1:33:12,21 +chr20 305384 200x3fb G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=284589;QSTRAND=+ GT:DP:AD 1|0:29:19,10 0|1:21:14,7 1|0:35:23,12 +chr20 305403 200x3fc A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=284608;QSTRAND=+ GT:DP:AD 1|1:35:11,24 1|1:21:7,14 1|1:43:23,20 +chr20 305843 200x3fd G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=260019;QSTRAND=+ GT:DP:AD 0|1:29:20,9 1|0:30:17,13 0|1:38:15,23 +chr20 305871 200x3fe T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=260047;QSTRAND=+ GT:DP:AD 0|1:39:20,19 1|1:44:23,21 0|1:24:12,12 +chr20 305882 200x3ff C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=260058;QSTRAND=+ GT:DP:AD 0|1:21:10,11 1|1:48:25,23 0|1:29:19,10 +chr20 305943 200x400 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=285148;QSTRAND=+ GT:DP:AD 1|1:43:19,24 1|1:34:16,18 1|1:22:13,9 +chr20 306004 200x401 TAAATA T 60 . QNAME=cluster19_000000F;QSTART=265743;QSTRAND=+ GT:DP:AD ./.:38:19,19 0|1:14:8,6 ./.:45:24,21 +chr20 306194 200x402 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=285399;QSTRAND=+ GT:DP:AD 1|1:32:18,14 1|1:41:17,24 1|1:39:23,16 +chr20 306232 200x403 C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=285438;QSTRAND=+ GT:DP:AD 1|0:29:12,17 0|1:23:6,17 1|0:23:5,18 +chr20 306268 200x404 A ACCAGGCTGGAGTGCAGTGGCTCACTGCGTGGCTCGCTACAGCCTACAACTCCTGGGCTCCAGCAATCCTGCTGCCCCAGCCTCCTGTGTAACTGAGACTACAGGCACGCACCACCACACCCAGCTAATTTTTTCTTTCTTTTTTTTTTTTTTGAGATGAACTCTCACTCTGTTGC 60 . QNAME=HG002-S9-H1-000001F;QSTART=285475;QSTRAND=+;SVTYPE=INS;SVLEN=175 GT:DP:AD 1/1:34:18,16 ./.:32:19,13 1/1:25:13,12 +chr20 306268 200x405 A ACCAGGCTGGAGTGCAGTGGCTCACTGCGTGGCTCGCTACAGCCTACAACTCCTGGGCTCCAGCAATCCTGCTGCCCCAGCCTCCTGTGTAACTGAGACTACAGGCACGCACCACCACACCCAGCTAATGTTTTCTTTCTTTTTTTTTTTTTTGAGATGAACTCTCACTCTGTTGC 60 . QNAME=cluster19_000000F;QSTART=25455794;QSTRAND=-;SVTYPE=INS;SVLEN=175 GT:DP:AD ./.:33:15,18 1/1:35:11,24 ./.:34:9,25 +chr20 306413 200x406 T TC 60 . QNAME=cluster23_scaffold_2;QSTART=25389187;QSTRAND=- GT:DP:AD ./.:32:25,7 ./.:21:7,14 0|1:26:11,15 +chr20 306414 200x407 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=260765;QSTRAND=+ GT:DP:AD 0|1:37:21,16 1|0:46:25,21 ./.:36:11,25 +chr20 306535 200x408 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=260886;QSTRAND=+ GT:DP:AD 0|1:36:22,14 1|0:37:14,23 0|1:16:11,5 +chr20 306582 200x409 A G 60 . QNAME=cluster19_000000F;QSTART=266491;QSTRAND=+ GT:DP:AD ./.:33:9,24 0|1:22:12,10 ./.:20:11,9 +chr20 306627 200x40a T G 60 . QNAME=cluster19_000000F;QSTART=25455435;QSTRAND=- GT:DP:AD ./.:33:15,18 1|0:30:22,8 ./.:24:13,11 +chr20 306642 200x40b T C 60 . QNAME=cluster19_000000F;QSTART=25455420;QSTRAND=- GT:DP:AD ./.:32:10,22 1|1:27:15,12 ./.:29:12,17 +chr20 306653 200x40c C T 60 . QNAME=cluster19_000000F;QSTART=25455409;QSTRAND=- GT:DP:AD ./.:49:24,25 1|0:33:13,20 ./.:19:6,13 +chr20 306667 200x40d T C 60 . QNAME=cluster19_000000F;QSTART=25455395;QSTRAND=- GT:DP:AD ./.:28:5,23 1|0:45:22,23 ./.:35:21,14 +chr20 306742 200x40e A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=261093;QSTRAND=+ GT:DP:AD 0|1:25:15,10 ./.:32:9,23 0|1:14:6,8 +chr20 306776 200x40f T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=286157;QSTRAND=+ GT:DP:AD 1|0:33:23,10 ./.:21:11,10 1|0:33:13,20 +chr20 306885 200x410 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=286266;QSTRAND=+ GT:DP:AD 1|1:27:9,18 1|1:31:23,8 1|1:31:17,14 +chr20 306993 200x411 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=286374;QSTRAND=+ GT:DP:AD 1|0:30:25,5 1|1:25:18,7 1|0:27:18,9 +chr20 307589 200x412 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=286970;QSTRAND=+ GT:DP:AD 1|1:32:12,20 1|0:31:16,15 1|1:26:16,10 +chr20 307693 200x413 C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=262044;QSTRAND=+ GT:DP:AD 0|1:34:25,9 ./.:19:13,6 ./.:33:10,23 +chr20 307712 200x414 CA C 60 . QNAME=cluster19_000000F;QSTART=25454350;QSTRAND=- GT:DP:AD ./.:36:20,16 1|0:33:9,24 0|1:21:13,8 +chr20 308128 200x415 C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=262479;QSTRAND=+ GT:DP:AD 0|1:18:11,7 0|1:40:25,15 ./.:41:18,23 +chr20 308132 200x416 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=287513;QSTRAND=+ GT:DP:AD 1|1:43:21,22 1|1:24:8,16 1|1:29:13,16 +chr20 308261 200x417 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=262612;QSTRAND=+ GT:DP:AD 0|1:25:9,16 0|1:30:5,25 ./.:37:25,12 +chr20 308278 200x418 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=262629;QSTRAND=+ GT:DP:AD 0|1:24:12,12 1|1:32:10,22 0|1:45:22,23 +chr20 308352 200x419 T C 60 . QNAME=cluster19_000000F;QSTART=25453711;QSTRAND=- GT:DP:AD ./.:16:8,8 1|0:33:13,20 0|1:27:22,5 +chr20 308718 200x41a G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=263069;QSTRAND=+ GT:DP:AD 0|1:23:15,8 1|1:23:17,6 0|1:24:7,17 +chr20 308968 200x41b G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=288349;QSTRAND=+ GT:DP:AD 1|1:23:7,16 1|1:17:6,11 1|1:11:6,5 +chr20 309141 200x41c A G 60 . QNAME=cluster19_000000F;QSTART=25452922;QSTRAND=- GT:DP:AD ./.:27:10,17 1|0:37:12,25 0|1:33:14,19 +chr20 309613 200x41d G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=263964;QSTRAND=+ GT:DP:AD 0|1:38:22,16 ./.:22:16,6 ./.:34:22,12 +chr20 309637 200x41e T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=289018;QSTRAND=+ GT:DP:AD 1|1:29:24,5 ./.:12:7,5 1|0:39:24,15 +chr20 309639 200x41f C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=289020;QSTRAND=+ GT:DP:AD 1|1:36:18,18 ./.:25:9,16 1|0:41:21,20 +chr20 309653 200x420 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=289034;QSTRAND=+ GT:DP:AD 1|1:46:24,22 ./.:15:8,7 1|0:32:23,9 +chr20 309674 200x421 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=289055;QSTRAND=+ GT:DP:AD 1|1:39:16,23 1|1:35:14,21 1|1:37:25,12 +chr20 310521 200x422 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=289902;QSTRAND=+ GT:DP:AD 1|1:21:6,15 1|0:34:20,14 0|1:13:7,6 +chr20 310522 200x423 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=289903;QSTRAND=+ GT:DP:AD 1|1:19:9,10 1|0:29:8,21 0|1:42:21,21 +chr20 310523 200x424 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=289904;QSTRAND=+ GT:DP:AD 1|1:27:20,7 1|0:21:13,8 0|1:23:18,5 +chr20 310719 200x425 A AT 60 . QNAME=HG002-S9-H1-000001F;QSTART=290101;QSTRAND=+ GT:DP:AD 1|1:35:20,15 1|0:31:6,25 0|1:45:24,21 +chr20 311107 200x426 C G 60 . QNAME=cluster19_000000F;QSTART=271016;QSTRAND=+ GT:DP:AD ./.:35:22,13 0|1:32:12,20 1|0:38:25,13 +chr20 311145 200x427 T G 60 . QNAME=cluster19_000000F;QSTART=271054;QSTRAND=+ GT:DP:AD ./.:33:10,23 0|1:32:13,19 1|0:30:7,23 +chr20 311237 200x428 C T 60 . QNAME=cluster19_000000F;QSTART=271146;QSTRAND=+ GT:DP:AD ./.:39:21,18 0|1:28:8,20 1|0:25:8,17 +chr20 311327 200x429 G C 60 . QNAME=cluster19_000000F;QSTART=271236;QSTRAND=+ GT:DP:AD ./.:31:24,7 0|1:30:10,20 1|0:34:21,13 +chr20 311347 200x42a C CATTATT 60 . QNAME=cluster19_000000F;QSTART=271257;QSTRAND=+ GT:DP:AD ./.:21:11,10 0|1:32:12,20 1|0:19:8,11 +chr20 311683 200x42b T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=291065;QSTRAND=+ GT:DP:AD 1|0:39:20,19 1|0:46:22,24 0|1:40:16,24 +chr20 311774 200x42c T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=291156;QSTRAND=+ GT:DP:AD 1|0:29:21,8 1|1:16:7,9 0|1:18:12,6 +chr20 311791 200x42d G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=291173;QSTRAND=+ GT:DP:AD 1|1:32:17,15 1|1:22:14,8 1|1:34:17,17 +chr20 312718 200x42e A AT 60 . QNAME=cluster23_scaffold_2;QSTART=25382881;QSTRAND=- GT:DP:AD ./.:46:21,25 ./.:18:10,8 0|1:25:15,10 +chr20 314417 200x42f C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=293799;QSTRAND=+ GT:DP:AD 1|0:18:7,11 ./.:16:9,7 ./.:43:19,24 +chr20 314431 200x430 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=293813;QSTRAND=+ GT:DP:AD 1|0:48:23,25 ./.:40:23,17 ./.:25:16,9 +chr20 314495 200x431 C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=268847;QSTRAND=+ GT:DP:AD 0|1:31:6,25 ./.:34:24,10 ./.:38:22,16 +chr20 314567 200x432 G A 60 . QNAME=cluster23_scaffold_2;QSTART=25381032;QSTRAND=- GT:DP:AD ./.:21:7,14 ./.:41:18,23 0|1:18:9,9 +chr20 314595 200x433 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=268947;QSTRAND=+ GT:DP:AD 0|1:30:15,15 ./.:36:15,21 1|0:27:12,15 +chr20 314668 200x434 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=269020;QSTRAND=+ GT:DP:AD 0|1:40:19,21 ./.:27:7,20 1|0:33:11,22 +chr20 314877 200x435 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=269229;QSTRAND=+ GT:DP:AD 0|1:21:13,8 ./.:15:6,9 1|0:37:25,12 +chr20 314905 200x436 CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=269258;QSTRAND=+ GT:DP:AD 0|1:34:9,25 ./.:19:6,13 ./.:24:15,9 +chr20 314905 200x437 C CTT 60 . QNAME=cluster23_scaffold_2;QSTART=25380692;QSTRAND=- GT:DP:AD ./.:37:25,12 ./.:21:14,7 0|1:30:22,8 +chr20 315222 200x438 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=269573;QSTRAND=+ GT:DP:AD 0|1:47:25,22 ./.:35:23,12 1|0:26:6,20 +chr20 315528 200x439 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=269879;QSTRAND=+ GT:DP:AD 0|1:30:20,10 ./.:28:14,14 1|0:32:7,25 +chr20 315724 200x43a G GTATTAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=270076;QSTRAND=+ GT:DP:AD 0|1:40:23,17 ./.:35:14,21 1|0:28:16,12 +chr20 316587 200x43b C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=295969;QSTRAND=+ GT:DP:AD 1|0:39:14,25 ./.:23:5,18 ./.:37:17,20 +chr20 316724 200x43c GTT G 60 . QNAME=HG002-S9-H2-000001F;QSTART=271082;QSTRAND=+ GT:DP:AD 0|1:12:5,7 ./.:21:13,8 ./.:44:19,25 +chr20 316724 200x43d GTTT G 60 . QNAME=cluster23_scaffold_3;QSTART=25394724;QSTRAND=- GT:DP:AD ./.:31:19,12 ./.:23:13,10 1|0:31:14,17 +chr20 316724 200x43e G GT 60 . QNAME=cluster23_scaffold_2;QSTART=25378872;QSTRAND=- GT:DP:AD ./.:17:5,12 ./.:34:11,23 0|1:34:12,22 +chr20 317772 200x43f GA G 60 . QNAME=HG002-S9-H2-000001F;QSTART=272128;QSTRAND=+ GT:DP:AD 0|1:28:8,20 ./.:34:13,21 1|0:22:7,15 +chr20 318091 200x440 C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=272445;QSTRAND=+ GT:DP:AD 0|1:35:17,18 ./.:30:16,14 1|0:31:18,13 +chr20 318388 200x441 A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=272742;QSTRAND=+ GT:DP:AD 0|1:26:5,21 ./.:18:11,7 1|0:16:11,5 +chr20 318854 200x442 C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=273208;QSTRAND=+ GT:DP:AD 0|1:17:10,7 1|1:26:10,16 1|1:15:9,6 +chr20 318941 200x443 AC A 60 . QNAME=HG002-S9-H2-000001F;QSTART=273296;QSTRAND=+ GT:DP:AD 0|1:35:15,20 1|1:21:15,6 1|1:31:8,23 +chr20 318943 200x444 C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=273296;QSTRAND=+ GT:DP:AD 0|1:44:23,21 1|1:22:16,6 1|1:29:16,13 +chr20 318971 200x445 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=298353;QSTRAND=+ GT:DP:AD 1|1:43:19,24 1|1:38:21,17 1|0:31:10,21 +chr20 319115 200x446 G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=273468;QSTRAND=+ GT:DP:AD 0|1:41:22,19 1|1:29:12,17 1|0:16:5,11 +chr20 319367 200x447 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=298749;QSTRAND=+ GT:DP:AD 1|0:33:11,22 ./.:28:7,21 ./.:30:17,13 +chr20 319623 200x448 G C 60 . QNAME=cluster19_000000F;QSTART=25442440;QSTRAND=- GT:DP:AD ./.:37:23,14 1|0:24:5,19 ./.:27:5,22 +chr20 319633 200x449 CCA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=299016;QSTRAND=+ GT:DP:AD 1|1:47:22,25 0|1:36:13,23 1|0:37:15,22 +chr20 319838 200x44a G A 60 . QNAME=cluster19_000000F;QSTART=25442225;QSTRAND=- GT:DP:AD ./.:16:9,7 1|0:37:15,22 ./.:29:12,17 +chr20 320255 200x44b CA C 60 . QNAME=cluster23_scaffold_2;QSTART=25375342;QSTRAND=- GT:DP:AD ./.:27:9,18 ./.:37:25,12 0|1:31:9,22 +chr20 321250 200x44c A G 60 . QNAME=cluster19_000000F;QSTART=25440813;QSTRAND=- GT:DP:AD ./.:32:11,21 1|0:31:15,16 ./.:37:23,14 +chr20 326089 200x44d G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=305469;QSTRAND=+ GT:DP:AD 1|0:33:14,19 0|1:44:19,25 ./.:31:20,11 +chr20 328517 200x44e ATT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=307898;QSTRAND=+ GT:DP:AD 1|1:29:22,7 ./.:41:23,18 1|0:33:25,8 +chr20 328517 200x44f AT A 60 . QNAME=cluster19_000000F;QSTART=25433546;QSTRAND=- GT:DP:AD ./.:31:20,11 1|1:29:5,24 0|1:20:5,15 +chr20 328569 200x450 GA G 60 . QNAME=cluster19_000000F;QSTART=25433495;QSTRAND=- GT:DP:AD ./.:17:9,8 1|0:46:25,21 ./.:28:21,7 +chr20 328569 200x451 G GA 60 . QNAME=cluster23_scaffold_3;QSTART=25382887;QSTRAND=- GT:DP:AD ./.:38:15,23 ./.:39:21,18 1|0:31:7,24 +chr20 328717 200x452 G A 60 . QNAME=cluster23_scaffold_3;QSTART=25382739;QSTRAND=- GT:DP:AD ./.:32:24,8 ./.:37:24,13 1|0:37:21,16 +chr20 336200 200x453 C CTCTTCT 60 . QNAME=HG002-S9-H1-000001F;QSTART=315579;QSTRAND=+ GT:DP:AD 1|0:34:11,23 0|1:25:14,11 ./.:46:21,25 +chr20 336200 200x454 CTCTTCTTCT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=290550;QSTRAND=+ GT:DP:AD 0|1:43:21,22 ./.:31:14,17 ./.:34:22,12 +chr20 336200 200x455 C CTCT 60 . QNAME=cluster23_scaffold_3;QSTART=25375253;QSTRAND=- GT:DP:AD ./.:37:25,12 ./.:34:23,11 1|0:26:17,9 +chr20 336200 200x456 CTCT C 60 . QNAME=cluster23_scaffold_2;QSTART=25359399;QSTRAND=- GT:DP:AD ./.:38:17,21 ./.:24:13,11 0|1:26:18,8 +chr20 336263 200x457 TTC T 60 . QNAME=cluster19_000000F;QSTART=25425802;QSTRAND=- GT:DP:AD ./.:27:20,7 1|0:34:18,16 ./.:29:11,18 +chr20 336308 200x458 CTCTTCCTCTTCT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=315693;QSTRAND=+ GT:DP:AD 1|1:30:20,10 0|1:42:25,17 0|1:31:24,7 +chr20 336308 200x459 CTCTTCCTCTTCTTCT C 60 . QNAME=cluster23_scaffold_3;QSTART=25375145;QSTRAND=- GT:DP:AD ./.:28:5,23 ./.:41:24,17 1|0:33:8,25 +chr20 336336 200x45a C T 60 . QNAME=cluster23_scaffold_3;QSTART=25375132;QSTRAND=- GT:DP:AD ./.:31:24,7 ./.:26:16,10 1|0:37:13,24 +chr20 338577 200x45b A ATG 60 . QNAME=HG002-S9-H1-000001F;QSTART=317950;QSTRAND=+ GT:DP:AD 1|0:48:24,24 0|1:33:16,17 1|1:37:17,20 +chr20 340238 200x45c CTTTCT C 60 . QNAME=cluster23_scaffold_2;QSTART=25355374;QSTRAND=- GT:DP:AD ./.:34:24,10 ./.:35:18,17 0|1:16:7,9 +chr20 340763 200x45d C T 60 . QNAME=cluster19_000000F;QSTART=25421304;QSTRAND=- GT:DP:AD ./.:30:11,19 1|0:24:16,8 ./.:34:16,18 +chr20 340858 200x45e T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=295186;QSTRAND=+ GT:DP:AD 0|1:18:11,7 ./.:32:15,17 ./.:16:10,6 +chr20 340865 200x45f C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=295193;QSTRAND=+ GT:DP:AD 0|1:25:7,18 ./.:38:13,25 ./.:36:21,15 +chr20 341112 200x460 T TCACACA 60 . QNAME=HG002-S9-H2-000001F;QSTART=295441;QSTRAND=+ GT:DP:AD 0|1:38:21,17 ./.:29:15,14 ./.:20:11,9 +chr20 341505 200x461 AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=320880;QSTRAND=+ GT:DP:AD 1|0:29:19,10 ./.:16:11,5 ./.:15:10,5 +chr20 341505 200x462 ATTTTT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=295840;QSTRAND=+ GT:DP:AD 0|1:28:23,5 ./.:34:16,18 ./.:37:20,17 +chr20 341968 200x463 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=296297;QSTRAND=+ GT:DP:AD 0|1:15:5,10 1|0:34:19,15 ./.:32:11,21 +chr20 342602 200x464 C CTTT 60 . QNAME=HG002-S9-H1-000001F;QSTART=321976;QSTRAND=+ GT:DP:AD 1|0:26:9,17 ./.:30:5,25 ./.:30:21,9 +chr20 342602 200x465 CTTTTTTTT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=296932;QSTRAND=+ GT:DP:AD 0|1:20:15,5 ./.:39:25,14 ./.:25:12,13 +chr20 342602 200x466 C CTTTTT 60 . QNAME=cluster19_000000F;QSTART=302510;QSTRAND=+ GT:DP:AD ./.:30:9,21 0|1:44:19,25 ./.:46:21,25 +chr20 342602 200x467 C CTTTTTTTT 60 . QNAME=cluster23_scaffold_3;QSTART=25368856;QSTRAND=- GT:DP:AD ./.:22:15,7 ./.:19:10,9 1|0:31:25,6 +chr20 342602 200x468 C CTTTTTTT 60 . QNAME=cluster23_scaffold_2;QSTART=25353008;QSTRAND=- GT:DP:AD ./.:32:14,18 ./.:45:25,20 0|1:26:5,21 +chr20 342621 200x469 T TTTC 60 . QNAME=cluster19_000000F;QSTART=25419443;QSTRAND=- GT:DP:AD ./.:44:19,25 1|0:35:16,19 ./.:24:7,17 +chr20 342641 200x46a A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=296962;QSTRAND=+ GT:DP:AD 0|1:29:8,21 ./.:41:21,20 ./.:32:8,24 +chr20 342664 200x46b G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=296985;QSTRAND=+ GT:DP:AD 0|1:46:24,22 ./.:33:18,15 ./.:29:16,13 +chr20 342939 200x46c C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=297260;QSTRAND=+ GT:DP:AD 0|1:36:22,14 ./.:42:25,17 ./.:39:21,18 +chr20 343326 200x46d G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=297647;QSTRAND=+ GT:DP:AD 0|1:36:16,20 ./.:34:9,25 ./.:46:25,21 +chr20 343479 200x46e A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=297800;QSTRAND=+ GT:DP:AD 0|1:42:23,19 ./.:26:11,15 ./.:26:5,21 +chr20 343825 200x46f A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=298146;QSTRAND=+ GT:DP:AD 0|1:46:23,23 ./.:34:24,10 ./.:45:22,23 +chr20 343865 200x470 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=298186;QSTRAND=+ GT:DP:AD 0|1:17:12,5 ./.:15:8,7 ./.:36:22,14 +chr20 343893 200x471 G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=298214;QSTRAND=+ GT:DP:AD 0|1:36:21,15 ./.:27:15,12 ./.:17:10,7 +chr20 344097 200x472 C CAA 60 . QNAME=HG002-S9-H2-000001F;QSTART=298419;QSTRAND=+ GT:DP:AD 0|1:39:24,15 ./.:29:6,23 ./.:42:17,25 +chr20 344097 200x473 C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25367360;QSTRAND=- GT:DP:AD ./.:37:19,18 ./.:37:23,14 1|0:34:20,14 +chr20 344354 200x474 C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=298677;QSTRAND=+ GT:DP:AD 0|1:33:10,23 ./.:22:6,16 ./.:32:10,22 +chr20 344458 200x475 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=298781;QSTRAND=+ GT:DP:AD 0|1:40:22,18 ./.:30:17,13 ./.:43:22,21 +chr20 344798 200x476 T G 60 . QNAME=cluster23_scaffold_3;QSTART=25366659;QSTRAND=- GT:DP:AD ./.:25:9,16 ./.:32:13,19 1|0:21:14,7 +chr20 345372 200x477 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=299695;QSTRAND=+ GT:DP:AD 0|1:34:15,19 ./.:19:9,10 ./.:31:22,9 +chr20 345506 200x478 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=299829;QSTRAND=+ GT:DP:AD 0|1:23:6,17 ./.:29:23,6 ./.:36:15,21 +chr20 345647 200x479 T TACAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=299971;QSTRAND=+ GT:DP:AD 0|1:22:5,17 ./.:19:14,5 ./.:44:23,21 +chr20 348484 200x47a C CGTGTGTGTGT 60 . QNAME=HG002-S9-H1-000001F;QSTART=327861;QSTRAND=+ GT:DP:AD 1|0:34:21,13 ./.:25:5,20 1|0:26:6,20 +chr20 348484 200x47b CGTGTGT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=302812;QSTRAND=+ GT:DP:AD 0|1:35:15,20 ./.:34:23,11 ./.:17:12,5 +chr20 348484 200x47c C CGTGTGTGTGTGT 60 . QNAME=cluster19_000000F;QSTART=308397;QSTRAND=+ GT:DP:AD ./.:34:21,13 0|1:26:15,11 0|1:16:5,11 +chr20 349198 200x47d T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=303519;QSTRAND=+ GT:DP:AD 0|1:35:14,21 ./.:31:20,11 ./.:17:6,11 +chr20 350477 200x47e TA T 60 . QNAME=HG002-S9-H2-000001F;QSTART=304799;QSTRAND=+ GT:DP:AD 0|1:21:14,7 ./.:34:10,24 ./.:39:14,25 +chr20 350477 200x47f T TA 60 . QNAME=cluster23_scaffold_3;QSTART=25360969;QSTRAND=- GT:DP:AD ./.:30:9,21 ./.:28:11,17 1|0:31:22,9 +chr20 350646 200x480 CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=330033;QSTRAND=+ GT:DP:AD 1|0:32:20,12 1|1:40:22,18 ./.:33:22,11 +chr20 350646 200x481 C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25360799;QSTRAND=- GT:DP:AD ./.:30:15,15 ./.:12:7,5 1|0:27:7,20 +chr20 350660 200x482 AAAAAAAAAAAAAAAAAG A 60 . QNAME=HG002-S9-H2-000001F;QSTART=304981;QSTRAND=+ GT:DP:AD 0|1:17:5,12 ./.:21:9,12 ./.:26:17,9 +chr20 351164 200x483 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=305467;QSTRAND=+ GT:DP:AD 0|1:36:13,23 ./.:43:23,20 ./.:29:21,8 +chr20 352819 200x484 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=332204;QSTRAND=+ GT:DP:AD 1|0:42:19,23 1|1:38:23,15 1|1:22:12,10 +chr20 353673 200x485 TC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=333059;QSTRAND=+ GT:DP:AD 1|0:31:16,15 1|1:40:18,22 1|1:44:19,25 +chr20 354581 200x486 G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=308884;QSTRAND=+ GT:DP:AD 0|1:35:16,19 ./.:14:8,6 ./.:24:18,6 +chr20 355283 200x487 C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=309586;QSTRAND=+ GT:DP:AD 0|1:20:5,15 ./.:41:25,16 ./.:32:19,13 +chr20 356342 200x488 CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=335727;QSTRAND=+ GT:DP:AD 1|0:36:24,12 1|1:21:11,10 1|1:28:13,15 +chr20 356748 200x489 ACC A 60 . QNAME=cluster19_000000F;QSTART=25405319;QSTRAND=- GT:DP:AD ./.:30:18,12 1|0:26:12,14 ./.:44:23,21 +chr20 356924 200x48a C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=336307;QSTRAND=+ GT:DP:AD 1|1:30:8,22 1|1:14:9,5 1|1:18:10,8 +chr20 358579 200x48b CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=337963;QSTRAND=+ GT:DP:AD 1|0:33:17,16 1|0:34:14,20 ./.:41:16,25 +chr20 358579 200x48c CTT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=312883;QSTRAND=+ GT:DP:AD 0|1:27:19,8 ./.:26:10,16 ./.:18:12,6 +chr20 358585 200x48d T C 60 . QNAME=cluster19_000000F;QSTART=25403485;QSTRAND=- GT:DP:AD ./.:11:6,5 1|0:26:10,16 ./.:25:19,6 +chr20 358586 200x48e T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=312887;QSTRAND=+ GT:DP:AD 0|1:35:24,11 ./.:34:9,25 ./.:44:20,24 +chr20 358841 200x48f A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=338223;QSTRAND=+ GT:DP:AD 1|0:16:10,6 0|1:28:8,20 1|1:26:5,21 +chr20 359400 200x490 GCAC G 60 . QNAME=HG002-S9-H1-000001F;QSTART=338783;QSTRAND=+ GT:DP:AD 1|0:25:8,17 0|1:32:14,18 1|1:31:13,18 +chr20 359869 200x491 T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=314170;QSTRAND=+ GT:DP:AD 0|1:24:14,10 1|0:41:16,25 ./.:17:10,7 +chr20 359913 200x492 G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=314214;QSTRAND=+ GT:DP:AD 0|1:43:19,24 1|0:36:23,13 ./.:31:7,24 +chr20 359914 200x493 G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=314215;QSTRAND=+ GT:DP:AD 0|1:21:12,9 1|0:34:19,15 ./.:20:12,8 +chr20 359916 200x494 G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=314217;QSTRAND=+ GT:DP:AD 0|1:22:14,8 1|0:37:21,16 ./.:42:22,20 +chr20 359924 200x495 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=314225;QSTRAND=+ GT:DP:AD 0|1:30:22,8 1|0:28:5,23 ./.:24:11,13 +chr20 359930 200x496 C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=314231;QSTRAND=+ GT:DP:AD 0|1:37:20,17 1|0:37:18,19 ./.:28:17,11 +chr20 359931 200x497 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=314232;QSTRAND=+ GT:DP:AD 0|1:18:10,8 1|0:25:13,12 ./.:34:22,12 +chr20 359947 200x498 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=314248;QSTRAND=+ GT:DP:AD 0|1:22:7,15 1|0:43:23,20 ./.:12:5,7 +chr20 359953 200x499 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=314254;QSTRAND=+ GT:DP:AD 0|1:11:6,5 1|0:26:16,10 ./.:30:20,10 +chr20 359954 200x49a G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=314255;QSTRAND=+ GT:DP:AD 0|1:40:22,18 1|0:44:19,25 ./.:26:19,7 +chr20 359955 200x49b C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=314256;QSTRAND=+ GT:DP:AD 0|1:30:15,15 1|0:26:9,17 ./.:31:16,15 +chr20 359960 200x49c C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=314261;QSTRAND=+ GT:DP:AD 0|1:32:7,25 1|0:31:25,6 ./.:42:22,20 +chr20 359969 200x49d C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=314270;QSTRAND=+ GT:DP:AD 0|1:27:8,19 1|0:31:21,10 ./.:39:15,24 +chr20 359998 200x49e C CA 60 . QNAME=HG002-S9-H2-000001F;QSTART=314300;QSTRAND=+ GT:DP:AD 0|1:40:23,17 ./.:35:17,18 1|0:31:14,17 +chr20 360554 200x49f T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=314856;QSTRAND=+ GT:DP:AD 0|1:26:9,17 1|0:32:13,19 ./.:28:15,13 +chr20 360556 200x4a0 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=314858;QSTRAND=+ GT:DP:AD 0|1:38:20,18 1|0:36:18,18 ./.:24:15,9 +chr20 360622 200x4a1 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=314924;QSTRAND=+ GT:DP:AD 0|1:11:6,5 1|0:32:20,12 ./.:29:15,14 +chr20 361302 200x4a2 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=315604;QSTRAND=+ GT:DP:AD 0|1:48:23,25 1|0:34:25,9 ./.:24:15,9 +chr20 362051 200x4a3 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=316353;QSTRAND=+ GT:DP:AD 0|1:33:11,22 1|0:38:18,20 ./.:29:16,13 +chr20 362052 200x4a4 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=316354;QSTRAND=+ GT:DP:AD 0|1:40:24,16 1|0:34:14,20 ./.:29:8,21 +chr20 362185 200x4a5 G GA 60 . QNAME=cluster23_scaffold_3;QSTART=25349263;QSTRAND=- GT:DP:AD ./.:37:17,20 ./.:31:12,19 1|0:26:12,14 +chr20 362679 200x4a6 A ATG 60 . QNAME=HG002-S9-H2-000001F;QSTART=316982;QSTRAND=+ GT:DP:AD 0|1:19:8,11 1|0:21:15,6 ./.:39:24,15 +chr20 363003 200x4a7 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=317307;QSTRAND=+ GT:DP:AD 0|1:28:10,18 1|0:41:21,20 ./.:15:5,10 +chr20 363114 200x4a8 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=317418;QSTRAND=+ GT:DP:AD 0|1:32:7,25 1|0:32:7,25 ./.:40:16,24 +chr20 363119 200x4a9 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=317423;QSTRAND=+ GT:DP:AD 0|1:34:21,13 1|0:36:22,14 ./.:35:12,23 +chr20 363245 200x4aa C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=342624;QSTRAND=+ GT:DP:AD 1|0:23:15,8 0|1:41:19,22 1|0:23:8,15 +chr20 363435 200x4ab T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=317739;QSTRAND=+ GT:DP:AD 0|1:24:14,10 1|0:22:7,15 ./.:38:17,21 +chr20 363987 200x4ac G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=318291;QSTRAND=+ GT:DP:AD 0|1:38:13,25 1|0:11:6,5 ./.:41:18,23 +chr20 364755 200x4ad T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=319059;QSTRAND=+ GT:DP:AD 0|1:11:5,6 1|0:35:23,12 ./.:34:20,14 +chr20 364763 200x4ae C CAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=344143;QSTRAND=+ GT:DP:AD 1|1:17:11,6 1|1:29:10,19 1|1:35:10,25 +chr20 365042 200x4af G A 60 . QNAME=cluster19_000000F;QSTART=25397024;QSTRAND=- GT:DP:AD ./.:30:12,18 1|0:32:25,7 ./.:21:6,15 +chr20 365220 200x4b0 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=344601;QSTRAND=+ GT:DP:AD 1|1:22:5,17 1|1:33:25,8 1|1:35:17,18 +chr20 365798 200x4b1 CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=345180;QSTRAND=+ GT:DP:AD 1|1:35:14,21 ./.:29:17,12 0|1:21:8,13 +chr20 365798 200x4b2 CTT C 60 . QNAME=cluster19_000000F;QSTART=25396268;QSTRAND=- GT:DP:AD ./.:26:13,13 1|0:29:8,21 ./.:33:9,24 +chr20 366032 200x4b3 C T 60 . QNAME=cluster19_000000F;QSTART=25396036;QSTRAND=- GT:DP:AD ./.:24:5,19 1|0:28:9,19 ./.:13:8,5 +chr20 366058 200x4b4 AGCCTCCCAAAGGAG A 60 . QNAME=cluster19_000000F;QSTART=25396010;QSTRAND=- GT:DP:AD ./.:12:5,7 1|0:13:8,5 ./.:32:23,9 +chr20 366107 200x4b5 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=345487;QSTRAND=+ GT:DP:AD 1|1:12:6,6 1|1:42:23,19 1|1:31:25,6 +chr20 366279 200x4b6 C T 60 . QNAME=cluster19_000000F;QSTART=25395803;QSTRAND=- GT:DP:AD ./.:45:24,21 1|0:43:21,22 ./.:34:14,20 +chr20 366317 200x4b7 A G 60 . QNAME=cluster19_000000F;QSTART=25395765;QSTRAND=- GT:DP:AD ./.:40:22,18 1|0:46:22,24 ./.:33:16,17 +chr20 366341 200x4b8 A G 60 . QNAME=cluster19_000000F;QSTART=25395741;QSTRAND=- GT:DP:AD ./.:40:19,21 1|0:33:14,19 ./.:14:7,7 +chr20 366365 200x4b9 C A 60 . QNAME=cluster19_000000F;QSTART=25395717;QSTRAND=- GT:DP:AD ./.:18:12,6 1|0:30:12,18 ./.:31:13,18 +chr20 366711 200x4ba C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=346091;QSTRAND=+ GT:DP:AD 1|0:25:11,14 ./.:23:8,15 1|1:29:18,11 +chr20 367006 200x4bb A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=346386;QSTRAND=+ GT:DP:AD 1|1:29:17,12 1|0:44:22,22 1|1:37:23,14 +chr20 367079 200x4bc C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=346459;QSTRAND=+ GT:DP:AD 1|0:45:23,22 ./.:26:15,11 1|1:11:5,6 +chr20 367082 200x4bd A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=346462;QSTRAND=+ GT:DP:AD 1|0:44:25,19 ./.:32:16,16 1|1:31:20,11 +chr20 367106 200x4be C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=346486;QSTRAND=+ GT:DP:AD 1|0:36:24,12 ./.:25:9,16 1|1:34:13,21 +chr20 367141 200x4bf A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=346521;QSTRAND=+ GT:DP:AD 1|0:33:16,17 1|0:20:14,6 1|1:48:24,24 +chr20 367164 200x4c0 TCGCA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=346545;QSTRAND=+ GT:DP:AD 1|0:43:21,22 ./.:20:14,6 1|1:18:10,8 +chr20 367176 200x4c1 A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=346552;QSTRAND=+ GT:DP:AD 1|0:26:14,12 ./.:42:17,25 1|1:36:14,22 +chr20 367214 200x4c2 AAAACAAAC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=346591;QSTRAND=+ GT:DP:AD 1|0:23:6,17 ./.:36:24,12 1|1:45:20,25 +chr20 367226 200x4c3 A C 60 . QNAME=cluster19_000000F;QSTART=25394856;QSTRAND=- GT:DP:AD ./.:30:20,10 1|0:43:21,22 ./.:44:20,24 +chr20 367234 200x4c4 A AAAAC 60 . QNAME=cluster19_000000F;QSTART=25394844;QSTRAND=- GT:DP:AD ./.:29:8,21 1|0:36:24,12 ./.:28:17,11 +chr20 367235 200x4c5 C A 60 . QNAME=cluster19_000000F;QSTART=25394843;QSTRAND=- GT:DP:AD ./.:21:12,9 1|0:41:21,20 ./.:29:13,16 +chr20 367244 200x4c6 AAAC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=346613;QSTRAND=+ GT:DP:AD 1|0:43:23,20 ./.:29:23,6 1|1:29:6,23 +chr20 367252 200x4c7 C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=346617;QSTRAND=+ GT:DP:AD 1|0:46:22,24 ./.:31:20,11 1|1:37:20,17 +chr20 367264 200x4c8 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=321569;QSTRAND=+ GT:DP:AD 0|1:36:12,24 1|1:17:7,10 ./.:34:10,24 +chr20 367521 200x4c9 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=346886;QSTRAND=+ GT:DP:AD 1|0:35:25,10 0|1:38:17,21 ./.:11:6,5 +chr20 367522 200x4ca G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=346887;QSTRAND=+ GT:DP:AD 1|0:24:18,6 ./.:15:5,10 ./.:38:16,22 +chr20 367522 200x4cb G C 60 . QNAME=cluster19_000000F;QSTART=327442;QSTRAND=+ GT:DP:AD ./.:23:15,8 0|1:17:9,8 ./.:35:18,17 +chr20 367544 200x4cc T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=321849;QSTRAND=+ GT:DP:AD 0|1:40:23,17 ./.:34:14,20 1|0:20:8,12 +chr20 367675 200x4cd C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=347040;QSTRAND=+ GT:DP:AD 1|0:18:12,6 ./.:45:21,24 0|1:34:19,15 +chr20 367690 200x4ce G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=321995;QSTRAND=+ GT:DP:AD 0|1:20:10,10 ./.:30:10,20 0|1:35:14,21 +chr20 367721 200x4cf G GT 60 . QNAME=HG002-S9-H1-000001F;QSTART=347087;QSTRAND=+ GT:DP:AD 1|0:37:15,22 0|1:34:25,9 1|0:28:19,9 +chr20 367877 200x4d0 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=347243;QSTRAND=+ GT:DP:AD 1|0:22:11,11 ./.:37:17,20 ./.:30:24,6 +chr20 368132 200x4d1 T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=322437;QSTRAND=+ GT:DP:AD 0|1:23:11,12 1|0:19:9,10 ./.:32:14,18 +chr20 368260 200x4d2 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=322565;QSTRAND=+ GT:DP:AD 0|1:13:7,6 1|0:20:11,9 ./.:28:6,22 +chr20 368284 200x4d3 CTT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=322590;QSTRAND=+ GT:DP:AD 0|1:38:17,21 1|0:36:21,15 ./.:20:12,8 +chr20 368410 200x4d4 C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=322713;QSTRAND=+ GT:DP:AD 0|1:18:5,13 1|0:41:23,18 ./.:29:23,6 +chr20 368474 200x4d5 C T 60 . QNAME=cluster19_000000F;QSTART=328395;QSTRAND=+ GT:DP:AD ./.:22:14,8 0|1:40:21,19 1|0:40:17,23 +chr20 368491 200x4d6 G A 60 . QNAME=cluster19_000000F;QSTART=328412;QSTRAND=+ GT:DP:AD ./.:25:7,18 0|1:21:8,13 ./.:26:10,16 +chr20 368580 200x4d7 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=322883;QSTRAND=+ GT:DP:AD 0|1:26:7,19 1|0:29:22,7 ./.:33:13,20 +chr20 368662 200x4d8 G C 60 . QNAME=cluster19_000000F;QSTART=25393418;QSTRAND=- GT:DP:AD ./.:46:21,25 1|0:29:15,14 ./.:36:11,25 +chr20 368677 200x4d9 ACT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=322981;QSTRAND=+ GT:DP:AD 0|1:26:9,17 1|0:39:20,19 ./.:23:15,8 +chr20 369093 200x4da T C 60 . QNAME=cluster19_000000F;QSTART=25392989;QSTRAND=- GT:DP:AD ./.:17:7,10 1|0:32:19,13 ./.:38:25,13 +chr20 369284 200x4db C T 60 . QNAME=cluster23_scaffold_3;QSTART=25342176;QSTRAND=- GT:DP:AD ./.:46:25,21 ./.:19:7,12 1|0:27:16,11 +chr20 369514 200x4dc G A 60 . QNAME=cluster19_000000F;QSTART=25392568;QSTRAND=- GT:DP:AD ./.:37:12,25 1|0:26:11,15 ./.:25:20,5 +chr20 369594 200x4dd T A 60 . QNAME=cluster23_scaffold_3;QSTART=25341866;QSTRAND=- GT:DP:AD ./.:27:6,21 ./.:32:21,11 1|0:37:18,19 +chr20 369657 200x4de CAAAAAA C 60 . QNAME=cluster19_000000F;QSTART=25392425;QSTRAND=- GT:DP:AD ./.:22:14,8 1|0:44:22,22 ./.:40:19,21 +chr20 369657 200x4df C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25341802;QSTRAND=- GT:DP:AD ./.:37:20,17 ./.:13:8,5 1|1:31:11,20 +chr20 369846 200x4e0 T C 60 . QNAME=cluster19_000000F;QSTART=25392242;QSTRAND=- GT:DP:AD ./.:31:11,20 1|0:32:9,23 1|0:33:25,8 +chr20 369998 200x4e1 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=349364;QSTRAND=+ GT:DP:AD 1|0:28:7,21 ./.:31:11,20 ./.:48:25,23 +chr20 370237 200x4e2 C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=349603;QSTRAND=+ GT:DP:AD 1|0:28:18,10 0|1:31:8,23 ./.:38:16,22 +chr20 370371 200x4e3 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=349737;QSTRAND=+ GT:DP:AD 1|0:30:5,25 1|1:20:12,8 ./.:18:13,5 +chr20 371300 200x4e4 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=350666;QSTRAND=+ GT:DP:AD 1|0:31:10,21 0|1:35:22,13 ./.:39:19,20 +chr20 371526 200x4e5 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=350892;QSTRAND=+ GT:DP:AD 1|0:33:8,25 1|1:25:16,9 ./.:16:7,9 +chr20 372007 200x4e6 T C 60 . QNAME=cluster19_000000F;QSTART=25390081;QSTRAND=- GT:DP:AD ./.:25:8,17 1|0:42:18,24 ./.:29:12,17 +chr20 372073 200x4e7 A G 60 . QNAME=cluster19_000000F;QSTART=25390015;QSTRAND=- GT:DP:AD ./.:24:8,16 1|0:28:19,9 ./.:16:8,8 +chr20 372441 200x4e8 A G 60 . QNAME=cluster19_000000F;QSTART=25389647;QSTRAND=- GT:DP:AD ./.:26:12,14 1|0:23:16,7 ./.:20:12,8 +chr20 372564 200x4e9 A C 60 . QNAME=cluster19_000000F;QSTART=25389524;QSTRAND=- GT:DP:AD ./.:48:23,25 1|0:31:17,14 ./.:28:14,14 +chr20 372676 200x4ea C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=352042;QSTRAND=+ GT:DP:AD 1|0:35:19,16 1|1:37:25,12 ./.:12:7,5 +chr20 372735 200x4eb G T 60 . QNAME=cluster19_000000F;QSTART=25389353;QSTRAND=- GT:DP:AD ./.:30:6,24 1|0:31:18,13 ./.:44:20,24 +chr20 373053 200x4ec A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=352419;QSTRAND=+ GT:DP:AD 1|0:23:6,17 1|1:28:10,18 ./.:22:12,10 +chr20 373694 200x4ed C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=353060;QSTRAND=+ GT:DP:AD 1|0:29:20,9 0|1:13:5,8 ./.:22:5,17 +chr20 373749 200x4ee C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=353115;QSTRAND=+ GT:DP:AD 1|0:28:22,6 0|1:38:15,23 ./.:26:11,15 +chr20 374221 200x4ef C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=353587;QSTRAND=+ GT:DP:AD 1|0:27:21,6 0|1:32:13,19 ./.:31:23,8 +chr20 374323 200x4f0 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=353689;QSTRAND=+ GT:DP:AD 1|0:18:11,7 1|1:25:6,19 ./.:27:17,10 +chr20 374523 200x4f1 A G 60 . QNAME=cluster19_000000F;QSTART=25387565;QSTRAND=- GT:DP:AD ./.:35:20,15 1|0:47:23,24 ./.:36:21,15 +chr20 374580 200x4f2 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=353946;QSTRAND=+ GT:DP:AD 1|0:22:6,16 0|1:30:13,17 ./.:20:15,5 +chr20 374601 200x4f3 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=353967;QSTRAND=+ GT:DP:AD 1|0:28:17,11 0|1:29:21,8 ./.:34:20,14 +chr20 374675 200x4f4 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=354041;QSTRAND=+ GT:DP:AD 1|0:31:19,12 1|1:42:17,25 ./.:35:17,18 +chr20 374716 200x4f5 C T 60 . QNAME=cluster19_000000F;QSTART=334637;QSTRAND=+ GT:DP:AD ./.:31:18,13 0|1:23:8,15 ./.:32:23,9 +chr20 374726 200x4f6 C T 60 . QNAME=cluster19_000000F;QSTART=334647;QSTRAND=+ GT:DP:AD ./.:19:10,9 0|1:42:23,19 ./.:39:19,20 +chr20 374740 200x4f7 G GGT 60 . QNAME=HG002-S9-H1-000001F;QSTART=354107;QSTRAND=+ GT:DP:AD 1|0:30:11,19 0|1:36:22,14 ./.:15:8,7 +chr20 374743 200x4f8 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=354111;QSTRAND=+ GT:DP:AD 1|0:17:9,8 0|1:33:14,19 ./.:29:14,15 +chr20 374744 200x4f9 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=354112;QSTRAND=+ GT:DP:AD 1|0:19:11,8 0|1:10:5,5 ./.:27:10,17 +chr20 374747 200x4fa G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=354115;QSTRAND=+ GT:DP:AD 1|0:30:25,5 0|1:34:19,15 ./.:12:7,5 +chr20 374754 200x4fb G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=354122;QSTRAND=+ GT:DP:AD 1|0:36:17,19 0|1:31:19,12 ./.:28:5,23 +chr20 374836 200x4fc T C 60 . QNAME=cluster19_000000F;QSTART=25387252;QSTRAND=- GT:DP:AD ./.:34:22,12 1|0:20:7,13 ./.:24:14,10 +chr20 374900 200x4fd C G 60 . QNAME=cluster19_000000F;QSTART=25387188;QSTRAND=- GT:DP:AD ./.:16:7,9 1|0:24:19,5 ./.:26:17,9 +chr20 374905 200x4fe A AC 60 . QNAME=HG002-S9-H1-000001F;QSTART=354274;QSTRAND=+ GT:DP:AD 1|0:23:10,13 1|1:39:19,20 ./.:27:5,22 +chr20 375120 200x4ff G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=354489;QSTRAND=+ GT:DP:AD 1|0:29:23,6 1|1:41:22,19 ./.:23:13,10 +chr20 375218 200x500 GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=354588;QSTRAND=+ GT:DP:AD 1|0:26:18,8 ./.:43:21,22 ./.:24:10,14 +chr20 375218 200x501 G GA 60 . QNAME=cluster19_000000F;QSTART=335143;QSTRAND=+ GT:DP:AD ./.:29:19,10 0|1:29:12,17 ./.:22:14,8 +chr20 375359 200x502 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=354727;QSTRAND=+ GT:DP:AD 1|0:28:20,8 1|1:34:18,16 ./.:48:23,25 +chr20 375590 200x503 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=354958;QSTRAND=+ GT:DP:AD 1|0:34:14,20 0|1:41:17,24 ./.:36:25,11 +chr20 376026 200x504 T TCAAA 60 . QNAME=cluster19_000000F;QSTART=25386057;QSTRAND=- GT:DP:AD ./.:26:18,8 1|0:32:17,15 ./.:21:14,7 +chr20 376031 200x505 A C 60 . QNAME=cluster19_000000F;QSTART=25386052;QSTRAND=- GT:DP:AD ./.:18:9,9 1|0:44:21,23 ./.:32:19,13 +chr20 376031 200x506 A AAAAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=355400;QSTRAND=+ GT:DP:AD 1|0:42:25,17 0|1:20:7,13 ./.:32:23,9 +chr20 376141 200x507 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=355513;QSTRAND=+ GT:DP:AD 1|0:18:7,11 1|1:36:17,19 ./.:24:9,15 +chr20 376217 200x508 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=355589;QSTRAND=+ GT:DP:AD 1|0:24:7,17 1|1:43:25,18 ./.:29:20,9 +chr20 376406 200x509 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=355778;QSTRAND=+ GT:DP:AD 1|0:47:22,25 1|1:18:7,11 ./.:27:20,7 +chr20 376484 200x50a A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=355856;QSTRAND=+ GT:DP:AD 1|0:38:24,14 1|1:36:14,22 ./.:25:6,19 +chr20 376926 200x50b T C 60 . QNAME=cluster19_000000F;QSTART=25385157;QSTRAND=- GT:DP:AD ./.:28:8,20 1|0:12:7,5 ./.:21:10,11 +chr20 376988 200x50c C T 60 . QNAME=cluster19_000000F;QSTART=25385095;QSTRAND=- GT:DP:AD ./.:41:16,25 1|0:31:14,17 ./.:23:10,13 +chr20 377035 200x50d T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=356407;QSTRAND=+ GT:DP:AD 1|0:27:14,13 1|1:32:23,9 ./.:47:24,23 +chr20 377056 200x50e T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=356428;QSTRAND=+ GT:DP:AD 1|0:16:9,7 1|1:34:17,17 ./.:28:6,22 +chr20 377153 200x50f AT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=331455;QSTRAND=+ GT:DP:AD 0|1:43:20,23 ./.:18:11,7 ./.:36:21,15 +chr20 377153 200x510 ATTTTTT A 60 . QNAME=cluster19_000000F;QSTART=25384930;QSTRAND=- GT:DP:AD ./.:31:20,11 1|0:30:19,11 ./.:39:14,25 +chr20 377184 200x511 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=356556;QSTRAND=+ GT:DP:AD 1|0:24:12,12 1|1:35:11,24 ./.:27:9,18 +chr20 377366 200x512 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=356738;QSTRAND=+ GT:DP:AD 1|0:43:22,21 1|1:25:7,18 ./.:33:24,9 +chr20 377503 200x513 CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=356876;QSTRAND=+ GT:DP:AD 1|0:19:5,14 1|1:24:6,18 ./.:34:25,9 +chr20 377680 200x514 GT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=357052;QSTRAND=+ GT:DP:AD 1|1:42:25,17 1|1:17:7,10 ./.:24:16,8 +chr20 377680 200x515 G GT 60 . QNAME=cluster23_scaffold_2;QSTART=25317935;QSTRAND=- GT:DP:AD ./.:42:19,23 ./.:30:16,14 0|1:19:10,9 +chr20 377737 200x516 T C 60 . QNAME=cluster19_000000F;QSTART=25384354;QSTRAND=- GT:DP:AD ./.:26:9,17 1|1:26:10,16 ./.:48:25,23 +chr20 377922 200x517 G A 60 . QNAME=cluster19_000000F;QSTART=25384169;QSTRAND=- GT:DP:AD ./.:25:6,19 1|1:35:17,18 ./.:31:14,17 +chr20 377975 200x518 A G 60 . QNAME=cluster19_000000F;QSTART=25384116;QSTRAND=- GT:DP:AD ./.:25:13,12 1|1:14:9,5 ./.:37:12,25 +chr20 378291 200x519 C T 60 . QNAME=cluster19_000000F;QSTART=25383800;QSTRAND=- GT:DP:AD ./.:25:8,17 1|1:25:14,11 ./.:31:12,19 +chr20 378708 200x51a CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=333008;QSTRAND=+ GT:DP:AD 0|1:31:24,7 ./.:35:11,24 ./.:15:5,10 +chr20 378907 200x51b T A 60 . QNAME=cluster19_000000F;QSTART=338834;QSTRAND=+ GT:DP:AD ./.:24:18,6 0|1:47:24,23 ./.:44:21,23 +chr20 379030 200x51c C T 60 . QNAME=cluster19_000000F;QSTART=25383061;QSTRAND=- GT:DP:AD ./.:21:7,14 1|1:49:24,25 ./.:27:10,17 +chr20 379398 200x51d G A 60 . QNAME=cluster19_000000F;QSTART=25382693;QSTRAND=- GT:DP:AD ./.:37:15,22 1|1:25:13,12 ./.:32:14,18 +chr20 379418 200x51e T C 60 . QNAME=cluster19_000000F;QSTART=25382673;QSTRAND=- GT:DP:AD ./.:24:13,11 1|0:41:16,25 ./.:41:21,20 +chr20 379468 200x51f G A 60 . QNAME=cluster19_000000F;QSTART=25382623;QSTRAND=- GT:DP:AD ./.:23:5,18 1|1:36:17,19 ./.:43:22,21 +chr20 379581 200x520 A C 60 . QNAME=cluster19_000000F;QSTART=25382510;QSTRAND=- GT:DP:AD ./.:31:9,22 1|0:35:24,11 ./.:32:16,16 +chr20 379662 200x521 T C 60 . QNAME=cluster19_000000F;QSTART=25382429;QSTRAND=- GT:DP:AD ./.:36:12,24 1|1:39:18,21 ./.:29:20,9 +chr20 379675 200x522 G GA 60 . QNAME=cluster19_000000F;QSTART=339603;QSTRAND=+ GT:DP:AD ./.:27:10,17 0|1:21:15,6 ./.:29:5,24 +chr20 379699 200x523 G C 60 . QNAME=cluster19_000000F;QSTART=25382392;QSTRAND=- GT:DP:AD ./.:24:13,11 1|1:16:5,11 ./.:39:22,17 +chr20 379759 200x524 T C 60 . QNAME=cluster19_000000F;QSTART=25382332;QSTRAND=- GT:DP:AD ./.:36:20,16 1|1:45:20,25 ./.:25:13,12 +chr20 379794 200x525 T C 60 . QNAME=cluster19_000000F;QSTART=25382297;QSTRAND=- GT:DP:AD ./.:19:13,6 1|1:16:7,9 ./.:32:19,13 +chr20 379816 200x526 C T 60 . QNAME=cluster19_000000F;QSTART=25382275;QSTRAND=- GT:DP:AD ./.:37:12,25 1|1:31:6,25 ./.:39:16,23 +chr20 379966 200x527 G T 60 . QNAME=cluster19_000000F;QSTART=25382125;QSTRAND=- GT:DP:AD ./.:37:22,15 1|1:40:15,25 ./.:32:18,14 +chr20 380070 200x528 G C 60 . QNAME=cluster19_000000F;QSTART=25382021;QSTRAND=- GT:DP:AD ./.:39:17,22 1|1:34:18,16 ./.:22:16,6 +chr20 380078 200x529 G C 60 . QNAME=cluster19_000000F;QSTART=25382013;QSTRAND=- GT:DP:AD ./.:32:21,11 1|1:38:13,25 ./.:22:8,14 +chr20 380145 200x52a T C 60 . QNAME=cluster19_000000F;QSTART=340073;QSTRAND=+ GT:DP:AD ./.:38:24,14 0|1:25:18,7 ./.:37:19,18 +chr20 380283 200x52b TAA T 60 . QNAME=cluster19_000000F;QSTART=25381808;QSTRAND=- GT:DP:AD ./.:28:9,19 1|1:32:14,18 ./.:33:22,11 +chr20 380289 200x52c A C 60 . QNAME=cluster19_000000F;QSTART=25381804;QSTRAND=- GT:DP:AD ./.:31:20,11 1|1:17:8,9 ./.:28:21,7 +chr20 380548 200x52d T C 60 . QNAME=cluster19_000000F;QSTART=25381545;QSTRAND=- GT:DP:AD ./.:25:13,12 1|1:24:17,7 ./.:23:7,16 +chr20 380662 200x52e G A 60 . QNAME=cluster19_000000F;QSTART=25381431;QSTRAND=- GT:DP:AD ./.:24:8,16 1|1:43:22,21 1|0:15:6,9 +chr20 380663 200x52f C A 60 . QNAME=cluster19_000000F;QSTART=25381430;QSTRAND=- GT:DP:AD ./.:22:9,13 1|1:40:16,24 1|0:23:7,16 +chr20 380672 200x530 A G 60 . QNAME=cluster19_000000F;QSTART=25381421;QSTRAND=- GT:DP:AD ./.:22:8,14 1|1:17:5,12 1|0:27:12,15 +chr20 380679 200x531 T C 60 . QNAME=cluster19_000000F;QSTART=25381414;QSTRAND=- GT:DP:AD ./.:32:10,22 1|1:34:24,10 1|0:23:18,5 +chr20 380684 200x532 CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=360055;QSTRAND=+ GT:DP:AD 1|0:15:10,5 1|1:31:9,22 ./.:24:14,10 +chr20 380684 200x533 C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25330774;QSTRAND=- GT:DP:AD ./.:42:25,17 ./.:28:9,19 1|0:38:25,13 +chr20 380878 200x534 T TGATTAGCTCCGGTTTGCATCACCCGGACCGGGGGATTAGCTCCGGTTTGCATCACCCGGACCGGGG 60 . QNAME=cluster19_000000F;QSTART=25381150;QSTRAND=-;SVTYPE=INS;SVLEN=66 GT:DP:AD ./.:21:9,12 1/0:15:8,7 ./.:25:20,5 +chr20 380878 200x535 TGATTAGCTCCGGTTTGCATCACCCGGACCGGGG T 60 . QNAME=cluster23_scaffold_3;QSTART=25330580;QSTRAND=-;SVTYPE=DEL;SVLEN=-33 GT:DP:AD ./.:13:5,8 ./.:24:18,6 1/0:18:13,5 +chr20 381233 200x536 G A 60 . QNAME=cluster19_000000F;QSTART=25380795;QSTRAND=- GT:DP:AD ./.:43:23,20 1|0:24:7,17 ./.:34:10,24 +chr20 381358 200x537 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=360727;QSTRAND=+ GT:DP:AD 1|0:28:17,11 ./.:23:6,17 ./.:31:23,8 +chr20 381423 200x538 C G 60 . QNAME=cluster23_scaffold_3;QSTART=25330068;QSTRAND=- GT:DP:AD ./.:26:6,20 ./.:36:14,22 1|0:40:19,21 +chr20 381585 200x539 AG A 60 . QNAME=cluster23_scaffold_3;QSTART=25329906;QSTRAND=- GT:DP:AD ./.:24:6,18 ./.:32:17,15 1|0:33:22,11 +chr20 381637 200x53a A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=361006;QSTRAND=+ GT:DP:AD 1|0:41:21,20 1|1:36:16,20 0|1:26:13,13 +chr20 381684 200x53b A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=361053;QSTRAND=+ GT:DP:AD 1|0:29:11,18 0|1:31:10,21 1|0:34:25,9 +chr20 381742 200x53c T TG 60 . QNAME=HG002-S9-H2-000001F;QSTART=336041;QSTRAND=+ GT:DP:AD 0|1:35:16,19 1|0:28:6,22 1|0:20:15,5 +chr20 381797 200x53d C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=336096;QSTRAND=+ GT:DP:AD 0|1:28:23,5 0|1:32:8,24 1|0:33:8,25 +chr20 382099 200x53e C CTG 60 . QNAME=cluster19_000000F;QSTART=25379926;QSTRAND=- GT:DP:AD ./.:39:24,15 1|0:19:12,7 ./.:39:18,21 +chr20 382099 200x53f C CTGTGTGTG 60 . QNAME=cluster23_scaffold_3;QSTART=25329384;QSTRAND=- GT:DP:AD ./.:26:20,6 ./.:26:8,18 1|0:40:16,24 +chr20 382124 200x540 TGTGC T 60 . QNAME=cluster23_scaffold_2;QSTART=25313491;QSTRAND=- GT:DP:AD ./.:22:6,16 ./.:35:12,23 0|1:26:8,18 +chr20 383089 200x541 C T 60 . QNAME=cluster23_scaffold_3;QSTART=25328394;QSTRAND=- GT:DP:AD ./.:31:14,17 ./.:14:7,7 1|0:36:15,21 +chr20 383651 200x542 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=363020;QSTRAND=+ GT:DP:AD 1|0:44:20,24 1|0:34:13,21 0|1:30:16,14 +chr20 384031 200x543 A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25327451;QSTRAND=- GT:DP:AD ./.:14:9,5 ./.:29:15,14 1|0:21:16,5 +chr20 384050 200x544 T C 60 . QNAME=cluster23_scaffold_2;QSTART=25311569;QSTRAND=- GT:DP:AD ./.:42:23,19 ./.:33:12,21 0|1:29:16,13 +chr20 384103 200x545 C A 60 . QNAME=cluster23_scaffold_3;QSTART=25327379;QSTRAND=- GT:DP:AD ./.:38:22,16 ./.:20:11,9 1|0:44:23,21 +chr20 385414 200x546 AT A 60 . QNAME=cluster19_000000F;QSTART=345340;QSTRAND=+ GT:DP:AD ./.:24:13,11 0|1:37:13,24 1|0:39:17,22 +chr20 385860 200x547 A AT 60 . QNAME=cluster23_scaffold_2;QSTART=25309758;QSTRAND=- GT:DP:AD ./.:45:22,23 ./.:43:20,23 0|1:25:10,15 +chr20 385969 200x548 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=365338;QSTRAND=+ GT:DP:AD 1|0:17:7,10 ./.:19:5,14 0|1:41:18,23 +chr20 386036 200x549 T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=365405;QSTRAND=+ GT:DP:AD 1|0:25:16,9 1|1:50:25,25 1|1:48:24,24 +chr20 386320 200x54a T C 60 . QNAME=cluster19_000000F;QSTART=346244;QSTRAND=+ GT:DP:AD ./.:24:5,19 0|1:35:25,10 1|0:25:7,18 +chr20 387554 200x54b GA G 60 . QNAME=cluster19_000000F;QSTART=347479;QSTRAND=+ GT:DP:AD ./.:44:21,23 0|1:24:6,18 ./.:24:13,11 +chr20 391001 200x54c CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=345301;QSTRAND=+ GT:DP:AD 0|1:27:22,5 1|0:15:5,10 0|1:30:25,5 +chr20 391001 200x54d C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25320481;QSTRAND=- GT:DP:AD ./.:29:17,12 ./.:26:19,7 1|0:31:19,12 +chr20 391003 200x54e A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=345301;QSTRAND=+ GT:DP:AD 0|1:46:24,22 1|0:40:19,21 0|1:36:24,12 +chr20 391137 200x54f C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=345435;QSTRAND=+ GT:DP:AD 0|1:39:18,21 1|0:28:23,5 0|1:46:25,21 +chr20 391138 200x550 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=345436;QSTRAND=+ GT:DP:AD 0|1:32:25,7 1|0:42:17,25 0|1:40:24,16 +chr20 391328 200x551 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=345626;QSTRAND=+ GT:DP:AD 0|1:36:24,12 1|0:39:23,16 0|1:18:6,12 +chr20 392021 200x552 CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=346320;QSTRAND=+ GT:DP:AD 0|1:40:17,23 ./.:27:22,5 ./.:17:5,12 +chr20 392557 200x553 A AT 60 . QNAME=HG002-S9-H2-000001F;QSTART=346855;QSTRAND=+ GT:DP:AD 0|1:26:15,11 1|0:29:12,17 1|1:26:21,5 +chr20 393192 200x554 C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=347407;QSTRAND=+ GT:DP:AD 0|1:13:6,7 1|0:35:20,15 0|1:13:8,5 +chr20 393337 200x555 CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=347553;QSTRAND=+ GT:DP:AD 0|1:24:18,6 1|0:23:9,14 1|1:23:7,16 +chr20 393417 200x556 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=347631;QSTRAND=+ GT:DP:AD 0|1:21:12,9 1|0:38:16,22 0|1:28:11,17 +chr20 393740 200x557 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=347954;QSTRAND=+ GT:DP:AD 0|1:13:5,8 1|0:44:21,23 0|1:23:14,9 +chr20 393795 200x558 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=348009;QSTRAND=+ GT:DP:AD 0|1:17:9,8 1|0:40:19,21 0|1:39:17,22 +chr20 394032 200x559 C CT 60 . QNAME=HG002-S9-H2-000001F;QSTART=348247;QSTRAND=+ GT:DP:AD 0|1:39:18,21 1|0:30:12,18 0|1:15:8,7 +chr20 394119 200x55a C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=348334;QSTRAND=+ GT:DP:AD 0|1:33:8,25 1|0:31:15,16 0|1:26:18,8 +chr20 394301 200x55b C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=348516;QSTRAND=+ GT:DP:AD 0|1:11:5,6 ./.:28:17,11 0|1:31:6,25 +chr20 394462 200x55c G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=348677;QSTRAND=+ GT:DP:AD 0|1:14:8,6 1|1:44:21,23 0|1:21:14,7 +chr20 394799 200x55d G GA 60 . QNAME=cluster23_scaffold_3;QSTART=25316682;QSTRAND=- GT:DP:AD ./.:37:17,20 ./.:46:23,23 1|0:35:10,25 +chr20 394955 200x55e A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=349170;QSTRAND=+ GT:DP:AD 0|1:25:11,14 ./.:31:22,9 0|1:24:14,10 +chr20 395162 200x55f CT C 60 . QNAME=cluster19_000000F;QSTART=25366946;QSTRAND=- GT:DP:AD ./.:21:10,11 1|0:22:8,14 ./.:41:22,19 +chr20 396582 200x560 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=350797;QSTRAND=+ GT:DP:AD 0|1:16:10,6 1|0:30:13,17 0|1:50:25,25 +chr20 397598 200x561 G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=351813;QSTRAND=+ GT:DP:AD 0|1:38:24,14 1|0:43:21,22 0|1:21:14,7 +chr20 397600 200x562 T A 60 . QNAME=cluster23_scaffold_2;QSTART=25298101;QSTRAND=- GT:DP:AD ./.:30:25,5 ./.:39:24,15 0|1:14:8,6 +chr20 397886 200x563 A AC 60 . QNAME=cluster23_scaffold_3;QSTART=25313594;QSTRAND=- GT:DP:AD ./.:23:13,10 ./.:41:16,25 1|0:23:10,13 +chr20 398287 200x564 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=352502;QSTRAND=+ GT:DP:AD 0|1:44:20,24 1|0:28:5,23 0|1:33:24,9 +chr20 398312 200x565 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=352527;QSTRAND=+ GT:DP:AD 0|1:46:23,23 1|0:32:13,19 0|1:24:14,10 +chr20 398313 200x566 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=352528;QSTRAND=+ GT:DP:AD 0|1:33:24,9 1|0:32:18,14 0|1:14:6,8 +chr20 398315 200x567 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=352530;QSTRAND=+ GT:DP:AD 0|1:31:21,10 1|0:13:7,6 0|1:28:13,15 +chr20 398320 200x568 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=352535;QSTRAND=+ GT:DP:AD 0|1:41:20,21 1|0:25:20,5 0|1:35:19,16 +chr20 398324 200x569 T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=352539;QSTRAND=+ GT:DP:AD 0|1:35:13,22 1|0:39:16,23 0|1:36:23,13 +chr20 398327 200x56a A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=352542;QSTRAND=+ GT:DP:AD 0|1:29:24,5 1|0:31:21,10 0|1:40:19,21 +chr20 398334 200x56b A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=352549;QSTRAND=+ GT:DP:AD 0|1:36:21,15 1|0:16:11,5 0|1:31:22,9 +chr20 398897 200x56c C T 60 . QNAME=cluster19_000000F;QSTART=25363212;QSTRAND=- GT:DP:AD ./.:22:13,9 1|0:20:8,12 ./.:16:5,11 +chr20 399283 200x56d A G 60 . QNAME=cluster19_000000F;QSTART=25362826;QSTRAND=- GT:DP:AD ./.:29:8,21 1|1:36:14,22 1|1:27:13,14 +chr20 399958 200x56e A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=379327;QSTRAND=+ GT:DP:AD 1|0:30:7,23 1|0:48:25,23 ./.:23:6,17 +chr20 400146 200x56f C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=379516;QSTRAND=+ GT:DP:AD 1|0:18:5,13 1|1:30:7,23 1|0:19:12,7 +chr20 400336 200x570 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=379706;QSTRAND=+ GT:DP:AD 1|0:22:7,15 1|1:41:25,16 1|0:20:12,8 +chr20 400547 200x571 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=379917;QSTRAND=+ GT:DP:AD 1|0:44:25,19 1|1:14:6,8 1|0:36:20,16 +chr20 400677 200x572 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=380047;QSTRAND=+ GT:DP:AD 1|0:31:17,14 1|1:32:25,7 1|0:27:6,21 +chr20 400755 200x573 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=380125;QSTRAND=+ GT:DP:AD 1|0:32:7,25 1|0:24:15,9 ./.:22:17,5 +chr20 400797 200x574 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=380167;QSTRAND=+ GT:DP:AD 1|0:23:10,13 1|1:23:9,14 1|0:34:10,24 +chr20 400887 200x575 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=380257;QSTRAND=+ GT:DP:AD 1|0:32:25,7 1|1:38:16,22 1|0:18:5,13 +chr20 401685 200x576 C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=381056;QSTRAND=+ GT:DP:AD 1|0:34:24,10 1|1:23:18,5 ./.:38:25,13 +chr20 401685 200x577 C CAA 60 . QNAME=cluster23_scaffold_3;QSTART=25309792;QSTRAND=- GT:DP:AD ./.:27:19,8 ./.:28:12,16 1|0:19:11,8 +chr20 401702 200x578 C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=381073;QSTRAND=+ GT:DP:AD 1|0:38:23,15 1|1:26:14,12 1|0:47:25,22 +chr20 401915 200x579 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=381286;QSTRAND=+ GT:DP:AD 1|0:35:20,15 1|1:42:19,23 1|0:44:25,19 +chr20 401983 200x57a A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=381354;QSTRAND=+ GT:DP:AD 1|0:40:22,18 1|1:20:11,9 1|0:25:17,8 +chr20 402232 200x57b T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=381603;QSTRAND=+ GT:DP:AD 1|0:43:19,24 1|1:35:20,15 1|0:39:14,25 +chr20 402478 200x57c CAAAAAAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=381850;QSTRAND=+ GT:DP:AD 1|0:16:8,8 1|0:37:16,21 ./.:34:13,21 +chr20 402478 200x57d C CAA 60 . QNAME=HG002-S9-H2-000001F;QSTART=356694;QSTRAND=+ GT:DP:AD 0|1:28:13,15 ./.:32:12,20 ./.:25:13,12 +chr20 402478 200x57e C CAAA 60 . QNAME=cluster23_scaffold_2;QSTART=25293220;QSTRAND=- GT:DP:AD ./.:41:24,17 ./.:38:17,21 0|1:35:18,17 +chr20 402492 200x57f A AT 60 . QNAME=cluster19_000000F;QSTART=362418;QSTRAND=+ GT:DP:AD ./.:36:15,21 0|1:14:5,9 1|0:16:6,10 +chr20 402498 200x580 A T 60 . QNAME=cluster19_000000F;QSTART=362424;QSTRAND=+ GT:DP:AD ./.:39:20,19 0|1:43:18,25 1|0:23:5,18 +chr20 402504 200x581 A T 60 . QNAME=cluster19_000000F;QSTART=362430;QSTRAND=+ GT:DP:AD ./.:28:12,16 0|1:30:15,15 1|0:34:24,10 +chr20 402509 200x582 A T 60 . QNAME=cluster19_000000F;QSTART=362435;QSTRAND=+ GT:DP:AD ./.:19:14,5 0|1:32:11,21 1|0:28:22,6 +chr20 403076 200x583 C T 60 . QNAME=cluster19_000000F;QSTART=363002;QSTRAND=+ GT:DP:AD ./.:22:16,6 0|1:38:15,23 1|0:38:16,22 +chr20 403697 200x584 A G 60 . QNAME=cluster19_000000F;QSTART=363623;QSTRAND=+ GT:DP:AD ./.:39:17,22 0|1:17:8,9 1|0:13:8,5 +chr20 403859 200x585 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=383222;QSTRAND=+ GT:DP:AD 1|0:38:18,20 1|0:45:24,21 ./.:20:6,14 +chr20 404000 200x586 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=383363;QSTRAND=+ GT:DP:AD 1|0:14:7,7 1|1:30:11,19 1|0:25:19,6 +chr20 404254 200x587 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=383617;QSTRAND=+ GT:DP:AD 1|0:21:7,14 1|0:34:11,23 ./.:25:12,13 +chr20 404408 200x588 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=383771;QSTRAND=+ GT:DP:AD 1|0:35:24,11 1|1:16:10,6 1|0:38:22,16 +chr20 404596 200x589 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=383959;QSTRAND=+ GT:DP:AD 1|1:37:12,25 1|1:40:21,19 1|1:20:15,5 +chr20 405155 200x58a T TCACA 60 . QNAME=cluster19_000000F;QSTART=365082;QSTRAND=+ GT:DP:AD ./.:29:16,13 0|1:33:21,12 1|0:17:11,6 +chr20 405155 200x58b TCA T 60 . QNAME=cluster19_000000F;QSTART=25356960;QSTRAND=- GT:DP:AD ./.:35:23,12 1|0:39:17,22 ./.:28:5,23 +chr20 405220 200x58c C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=384583;QSTRAND=+ GT:DP:AD 1|0:27:14,13 1|1:28:16,12 1|0:33:11,22 +chr20 405345 200x58d T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=384709;QSTRAND=+ GT:DP:AD 1|0:27:11,16 1|0:38:20,18 ./.:23:5,18 +chr20 405478 200x58e C T 60 . QNAME=cluster19_000000F;QSTART=365408;QSTRAND=+ GT:DP:AD ./.:31:13,18 0|1:30:16,14 1|0:22:12,10 +chr20 405820 200x58f A G 60 . QNAME=cluster19_000000F;QSTART=365750;QSTRAND=+ GT:DP:AD ./.:33:17,16 0|1:46:22,24 1|0:31:15,16 +chr20 405931 200x590 GTTCT G 60 . QNAME=cluster19_000000F;QSTART=365862;QSTRAND=+ GT:DP:AD ./.:26:6,20 0|1:31:7,24 1|0:33:14,19 +chr20 405942 200x591 CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=360160;QSTRAND=+ GT:DP:AD 0|1:16:6,10 ./.:30:19,11 ./.:24:19,5 +chr20 406708 200x592 CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=360925;QSTRAND=+ GT:DP:AD 0|1:35:13,22 ./.:39:20,19 ./.:22:10,12 +chr20 406708 200x593 CAAA C 60 . QNAME=cluster19_000000F;QSTART=366635;QSTRAND=+ GT:DP:AD ./.:26:14,12 0|1:41:23,18 1|0:29:11,18 +chr20 406708 200x594 C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25288989;QSTRAND=- GT:DP:AD ./.:21:6,15 ./.:45:21,24 0|1:16:6,10 +chr20 406732 200x595 A AAAAAAAAAAAAG 60 . QNAME=HG002-S9-H1-000001F;QSTART=386097;QSTRAND=+ GT:DP:AD 1|0:14:8,6 ./.:37:20,17 ./.:34:24,10 +chr20 406732 200x596 A AAAAAAAAAAG 60 . QNAME=cluster19_000000F;QSTART=25355374;QSTRAND=- GT:DP:AD ./.:45:21,24 1|0:30:23,7 ./.:36:12,24 +chr20 407013 200x597 G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=386390;QSTRAND=+ GT:DP:AD 1|0:39:24,15 1|1:36:14,22 1|0:29:12,17 +chr20 407083 200x598 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=386460;QSTRAND=+ GT:DP:AD 1|0:24:10,14 1|0:41:17,24 ./.:34:9,25 +chr20 407113 200x599 A G 60 . QNAME=cluster19_000000F;QSTART=367037;QSTRAND=+ GT:DP:AD ./.:41:20,21 0|1:33:8,25 1|0:36:14,22 +chr20 407171 200x59a G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=386548;QSTRAND=+ GT:DP:AD 1|0:33:24,9 1|0:39:20,19 ./.:21:6,15 +chr20 407872 200x59b C T 60 . QNAME=cluster19_000000F;QSTART=367796;QSTRAND=+ GT:DP:AD ./.:33:23,10 0|1:33:8,25 1|0:18:11,7 +chr20 407964 200x59c CG C 60 . QNAME=HG002-S9-H1-000001F;QSTART=387342;QSTRAND=+ GT:DP:AD 1|0:40:24,16 1|0:12:5,7 ./.:30:8,22 +chr20 407977 200x59d CG C 60 . QNAME=HG002-S9-H1-000001F;QSTART=387354;QSTRAND=+ GT:DP:AD 1|0:25:6,19 1|0:21:8,13 ./.:24:9,15 +chr20 408008 200x59e GC G 60 . QNAME=HG002-S9-H1-000001F;QSTART=387384;QSTRAND=+ GT:DP:AD 1|0:30:16,14 ./.:19:6,13 ./.:33:8,25 +chr20 408028 200x59f G GGCCCCGCCC 60 . QNAME=HG002-S9-H2-000001F;QSTART=362274;QSTRAND=+ GT:DP:AD 0|1:18:11,7 ./.:31:18,13 0|1:35:22,13 +chr20 408029 200x5a0 G GCCCCGCCCA 60 . QNAME=cluster19_000000F;QSTART=367992;QSTRAND=+ GT:DP:AD ./.:12:6,6 0|1:20:9,11 1|0:25:9,16 +chr20 408057 200x5a1 T TC 60 . QNAME=HG002-S9-H1-000001F;QSTART=387432;QSTRAND=+ GT:DP:AD 1|1:23:13,10 1|1:34:24,10 1|1:24:15,9 +chr20 408812 200x5a2 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=363067;QSTRAND=+ GT:DP:AD 0|1:33:15,18 0|1:50:25,25 1|1:24:18,6 +chr20 409237 200x5a3 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=363492;QSTRAND=+ GT:DP:AD 0|1:30:22,8 0|1:19:5,14 1|1:42:18,24 +chr20 409291 200x5a4 AT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=363547;QSTRAND=+ GT:DP:AD 0|1:42:22,20 ./.:29:24,5 ./.:19:14,5 +chr20 409340 200x5a5 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=363594;QSTRAND=+ GT:DP:AD 0|1:34:23,11 0|1:27:13,14 1|1:47:24,23 +chr20 409466 200x5a6 CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=363721;QSTRAND=+ GT:DP:AD 0|1:28:10,18 ./.:28:19,9 ./.:26:20,6 +chr20 410526 200x5a7 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=364779;QSTRAND=+ GT:DP:AD 0|1:26:10,16 0|1:39:16,23 1|1:23:5,18 +chr20 412325 200x5a8 CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=366579;QSTRAND=+ GT:DP:AD 0|1:17:11,6 ./.:42:17,25 ./.:31:23,8 +chr20 413334 200x5a9 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=367586;QSTRAND=+ GT:DP:AD 0|1:40:15,25 0|1:17:12,5 1|1:34:19,15 +chr20 413917 200x5aa CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=368170;QSTRAND=+ GT:DP:AD 0|1:41:24,17 0|1:38:24,14 1|1:21:16,5 +chr20 413941 200x5ab A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=368192;QSTRAND=+ GT:DP:AD 0|1:26:12,14 0|1:27:20,7 1|1:22:13,9 +chr20 414091 200x5ac C CA 60 . QNAME=HG002-S9-H2-000001F;QSTART=368343;QSTRAND=+ GT:DP:AD 0|1:31:21,10 0|1:39:21,18 1|1:13:6,7 +chr20 414091 200x5ad CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=393467;QSTRAND=+ GT:DP:AD 1|0:40:15,25 ./.:37:12,25 ./.:37:19,18 +chr20 414317 200x5ae T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=368569;QSTRAND=+ GT:DP:AD 0|1:27:15,12 0|1:19:12,7 1|1:20:12,8 +chr20 415178 200x5af C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=369430;QSTRAND=+ GT:DP:AD 0|1:29:24,5 0|1:29:23,6 1|1:22:14,8 +chr20 415379 200x5b0 A AAAAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=394754;QSTRAND=+ GT:DP:AD 1|1:24:5,19 1|1:32:20,12 1|1:17:6,11 +chr20 415512 200x5b1 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=394890;QSTRAND=+ GT:DP:AD 1|0:15:9,6 1|0:20:8,12 ./.:28:15,13 +chr20 416154 200x5b2 C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25295271;QSTRAND=- GT:DP:AD ./.:40:15,25 ./.:30:21,9 1|0:25:19,6 +chr20 416334 200x5b3 G T 60 . QNAME=cluster19_000000F;QSTART=376310;QSTRAND=+ GT:DP:AD ./.:44:20,24 0|1:22:12,10 1|0:41:21,20 +chr20 417284 200x5b4 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=396662;QSTRAND=+ GT:DP:AD 1|1:43:21,22 1|1:40:18,22 1|1:34:17,17 +chr20 417395 200x5b5 T TTG 60 . QNAME=cluster23_scaffold_3;QSTART=25294028;QSTRAND=- GT:DP:AD ./.:24:16,8 ./.:32:21,11 1|1:38:13,25 +chr20 417634 200x5b6 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=397012;QSTRAND=+ GT:DP:AD 1|0:41:16,25 1|0:40:20,20 ./.:28:18,10 +chr20 418430 200x5b7 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=397808;QSTRAND=+ GT:DP:AD 1|0:36:22,14 1|0:31:9,22 ./.:39:16,23 +chr20 418432 200x5b8 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=397810;QSTRAND=+ GT:DP:AD 1|0:15:6,9 1|0:31:24,7 ./.:28:9,19 +chr20 418579 200x5b9 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=372835;QSTRAND=+ GT:DP:AD 0|1:27:15,12 ./.:18:12,6 1|1:28:14,14 +chr20 418601 200x5ba T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=372857;QSTRAND=+ GT:DP:AD 0|1:37:25,12 ./.:35:24,11 1|1:49:24,25 +chr20 418603 200x5bb T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=372859;QSTRAND=+ GT:DP:AD 0|1:36:17,19 ./.:36:21,15 1|1:16:9,7 +chr20 418658 200x5bc A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=372914;QSTRAND=+ GT:DP:AD 0|1:35:24,11 ./.:40:17,23 1|1:15:9,6 +chr20 419117 200x5bd G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=398495;QSTRAND=+ GT:DP:AD 1|1:25:10,15 1|0:35:25,10 1|1:27:8,19 +chr20 419860 200x5be AGTGACCCTGCACCTGGCT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=374117;QSTRAND=+ GT:DP:AD 0|1:24:19,5 ./.:14:7,7 1|1:27:8,19 +chr20 420228 200x5bf A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=374466;QSTRAND=+ GT:DP:AD 0|1:36:17,19 ./.:25:11,14 1|1:29:10,19 +chr20 420465 200x5c0 A AG 60 . QNAME=HG002-S9-H2-000001F;QSTART=374704;QSTRAND=+ GT:DP:AD 0|1:19:11,8 ./.:22:8,14 1|1:24:5,19 +chr20 420561 200x5c1 A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=399939;QSTRAND=+ GT:DP:AD 1|1:31:17,14 1|0:37:21,16 1|1:47:25,22 +chr20 420665 200x5c2 G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCATCCCCCGTCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 60 . QNAME=HG002-S9-H1-000001F;QSTART=400044;QSTRAND=+;SVTYPE=INS;SVLEN=226 GT:DP:AD 1/0:45:21,24 1/1:27:20,7 ./.:31:15,16 +chr20 420665 200x5c3 G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCCATCCCCCGTCCGCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 61 . QNAME=HG002-S9-H2-000001F;QSTART=374905;QSTRAND=+;SVTYPE=INS;SVLEN=227 GT:DP:AD 0/1:27:19,8 ./.:40:20,20 1/1:23:7,16 +chr20 421409 200x5c4 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=401013;QSTRAND=+ GT:DP:AD 1|1:29:23,6 1|0:33:15,18 1|1:17:6,11 +chr20 421527 200x5c5 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=375993;QSTRAND=+ GT:DP:AD 0|1:29:24,5 ./.:36:17,19 1|1:37:13,24 +chr20 422066 200x5c6 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=401670;QSTRAND=+ GT:DP:AD 1|1:31:24,7 1|0:40:16,24 1|1:30:23,7 +chr20 422277 200x5c7 C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=376743;QSTRAND=+ GT:DP:AD 0|1:44:23,21 ./.:42:22,20 1|1:29:14,15 +chr20 422514 200x5c8 GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=402119;QSTRAND=+ GT:DP:AD 1|0:42:17,25 1|0:50:25,25 ./.:20:5,15 +chr20 422548 200x5c9 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=402151;QSTRAND=+ GT:DP:AD 1|0:26:8,18 1|0:30:22,8 ./.:34:19,15 +chr20 422567 200x5ca C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=402170;QSTRAND=+ GT:DP:AD 1|0:26:11,15 1|0:38:15,23 ./.:32:13,19 +chr20 423009 200x5cb T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=402612;QSTRAND=+ GT:DP:AD 1|1:40:21,19 1|0:26:20,6 1|1:31:20,11 +chr20 423705 200x5cc G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=403308;QSTRAND=+ GT:DP:AD 1|1:22:17,5 1|0:38:15,23 1|1:43:22,21 +chr20 423763 200x5cd T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=403366;QSTRAND=+ GT:DP:AD 1|1:40:20,20 1|0:30:25,5 1|1:17:7,10 +chr20 424272 200x5ce T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=403875;QSTRAND=+ GT:DP:AD 1|1:34:17,17 1|0:47:25,22 1|1:26:17,9 +chr20 424413 200x5cf A AC 60 . QNAME=HG002-S9-H1-000001F;QSTART=404017;QSTRAND=+ GT:DP:AD 1|0:38:17,21 1|0:21:6,15 1|0:31:19,12 +chr20 425626 200x5d0 CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=405231;QSTRAND=+ GT:DP:AD 1|1:14:6,8 1|0:31:21,10 1|1:41:16,25 +chr20 426816 200x5d1 C CT 60 . QNAME=cluster19_000000F;QSTART=25335060;QSTRAND=- GT:DP:AD ./.:16:9,7 1|0:27:22,5 1|0:40:22,18 +chr20 429226 200x5d2 AT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=383692;QSTRAND=+ GT:DP:AD 0|1:31:21,10 ./.:32:16,16 ./.:33:15,18 +chr20 429226 200x5d3 A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25281985;QSTRAND=- GT:DP:AD ./.:31:23,8 ./.:34:24,10 1|1:31:10,21 +chr20 429249 200x5d4 G A 60 . QNAME=cluster19_000000F;QSTART=389451;QSTRAND=+ GT:DP:AD ./.:36:17,19 0|1:30:10,20 ./.:17:9,8 +chr20 431198 200x5d5 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=410801;QSTRAND=+ GT:DP:AD 1|1:33:8,25 1|0:34:24,10 1|1:36:13,23 +chr20 433739 200x5d6 AGGCTACCCACACTTCCTG A 60 . QNAME=HG002-S9-H1-000001F;QSTART=413343;QSTRAND=+ GT:DP:AD 1|1:46:21,25 1|0:32:15,17 1|1:43:23,20 +chr20 433902 200x5d7 T C 60 . QNAME=cluster19_000000F;QSTART=25327992;QSTRAND=- GT:DP:AD ./.:46:25,21 1|0:27:9,18 ./.:15:8,7 +chr20 434000 200x5d8 G GT 60 . QNAME=cluster23_scaffold_3;QSTART=25277228;QSTRAND=- GT:DP:AD ./.:14:5,9 ./.:15:9,6 1|1:20:8,12 +chr20 434001 200x5d9 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=413586;QSTRAND=+ GT:DP:AD 1|1:16:9,7 1|0:36:12,24 1|1:28:12,16 +chr20 434561 200x5da A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=414146;QSTRAND=+ GT:DP:AD 1|1:49:24,25 1|0:39:23,16 1|1:13:8,5 +chr20 435505 200x5db A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=415090;QSTRAND=+ GT:DP:AD 1|1:30:10,20 1|0:25:18,7 1|1:45:20,25 +chr20 436968 200x5dc T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=416553;QSTRAND=+ GT:DP:AD 1|1:25:19,6 1|0:28:19,9 1|1:13:5,8 +chr20 437555 200x5dd T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=417140;QSTRAND=+ GT:DP:AD 1|1:43:21,22 1|0:38:17,21 1|1:26:19,7 +chr20 438423 200x5de C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=418008;QSTRAND=+ GT:DP:AD 1|1:32:25,7 1|0:39:22,17 ./.:38:24,14 +chr20 439461 200x5df G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=419046;QSTRAND=+ GT:DP:AD 1|1:41:22,19 1|0:36:25,11 ./.:30:18,12 +chr20 441161 200x5e0 T TCCA 60 . QNAME=HG002-S9-H1-000001F;QSTART=420747;QSTRAND=+ GT:DP:AD 1|1:32:17,15 1|0:31:18,13 ./.:12:6,6 +chr20 443554 200x5e1 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=423142;QSTRAND=+ GT:DP:AD 1|0:28:18,10 1|0:36:16,20 ./.:38:24,14 +chr20 443921 200x5e2 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=423509;QSTRAND=+ GT:DP:AD 1|0:27:17,10 1|0:19:9,10 ./.:36:11,25 +chr20 444453 200x5e3 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=424041;QSTRAND=+ GT:DP:AD 1|0:48:25,23 1|0:18:13,5 ./.:27:17,10 +chr20 444562 200x5e4 GTTTT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=424151;QSTRAND=+ GT:DP:AD 1|0:39:14,25 1|0:34:13,21 ./.:29:7,22 +chr20 444790 200x5e5 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=424374;QSTRAND=+ GT:DP:AD 1|0:30:20,10 1|0:45:23,22 ./.:29:16,13 +chr20 444962 200x5e6 C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=424546;QSTRAND=+ GT:DP:AD 1|0:40:20,20 1|0:21:11,10 ./.:34:17,17 +chr20 445789 200x5e7 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=425373;QSTRAND=+ GT:DP:AD 1|0:42:22,20 1|0:35:17,18 ./.:20:7,13 +chr20 446426 200x5e8 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=426010;QSTRAND=+ GT:DP:AD 1|0:17:8,9 1|0:39:24,15 ./.:26:17,9 +chr20 446529 200x5e9 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=426113;QSTRAND=+ GT:DP:AD 1|0:21:8,13 1|0:17:6,11 ./.:26:18,8 +chr20 446943 200x5ea AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=426528;QSTRAND=+ GT:DP:AD 1|1:35:19,16 1|0:25:8,17 ./.:16:9,7 +chr20 446943 200x5eb A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25264284;QSTRAND=- GT:DP:AD ./.:17:9,8 ./.:40:20,20 1|1:36:22,14 +chr20 447123 200x5ec A AT 60 . QNAME=cluster23_scaffold_2;QSTART=25248333;QSTRAND=- GT:DP:AD ./.:23:16,7 ./.:40:20,20 0|1:15:8,7 +chr20 447395 200x5ed T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=426978;QSTRAND=+ GT:DP:AD 1|0:28:8,20 1|0:22:17,5 ./.:31:17,14 +chr20 448123 200x5ee A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=427706;QSTRAND=+ GT:DP:AD 1|0:36:13,23 1|0:24:12,12 ./.:39:22,17 +chr20 448284 200x5ef C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=427867;QSTRAND=+ GT:DP:AD 1|0:26:8,18 1|0:29:7,22 ./.:21:11,10 +chr20 448552 200x5f0 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=428135;QSTRAND=+ GT:DP:AD 1|0:22:7,15 1|0:22:11,11 ./.:24:7,17 +chr20 448689 200x5f1 GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=428273;QSTRAND=+ GT:DP:AD 1|0:31:10,21 ./.:44:25,19 ./.:19:12,7 +chr20 448689 200x5f2 G GA 60 . QNAME=cluster19_000000F;QSTART=25313206;QSTRAND=- GT:DP:AD ./.:31:7,24 1|0:47:25,22 1|0:41:17,24 +chr20 448841 200x5f3 C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25262384;QSTRAND=- GT:DP:AD ./.:38:13,25 ./.:28:21,7 1|0:37:18,19 +chr20 449078 200x5f4 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=428660;QSTRAND=+ GT:DP:AD 1|0:36:21,15 1|0:30:15,15 ./.:37:21,16 +chr20 449153 200x5f5 C CTT 60 . QNAME=HG002-S9-H1-000001F;QSTART=428736;QSTRAND=+ GT:DP:AD 1|0:32:25,7 1|0:27:18,9 ./.:31:15,16 +chr20 449266 200x5f6 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=428850;QSTRAND=+ GT:DP:AD 1|0:35:11,24 1|0:25:9,16 ./.:34:25,9 +chr20 449285 200x5f7 T TAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=428870;QSTRAND=+ GT:DP:AD 1|0:26:18,8 1|0:21:7,14 ./.:20:8,12 +chr20 449285 200x5f8 T TA 60 . QNAME=cluster19_000000F;QSTART=409488;QSTRAND=+ GT:DP:AD ./.:21:9,12 0|1:23:7,16 ./.:33:18,15 +chr20 449362 200x5f9 C T 60 . QNAME=cluster23_scaffold_3;QSTART=25261863;QSTRAND=- GT:DP:AD ./.:38:20,18 ./.:28:15,13 1|0:39:21,18 +chr20 449514 200x5fa GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=429105;QSTRAND=+ GT:DP:AD 1|1:30:11,19 1|0:18:5,13 1|1:29:10,19 +chr20 450092 200x5fb C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=429681;QSTRAND=+ GT:DP:AD 1|0:40:24,16 1|0:44:24,20 ./.:24:9,15 +chr20 450315 200x5fc A AT 60 . QNAME=cluster23_scaffold_2;QSTART=25245141;QSTRAND=- GT:DP:AD ./.:29:6,23 ./.:34:25,9 0|1:34:23,11 +chr20 450858 200x5fd T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=430447;QSTRAND=+ GT:DP:AD 1|0:39:18,21 1|0:49:24,25 ./.:28:18,10 +chr20 452042 200x5fe T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=431631;QSTRAND=+ GT:DP:AD 1|0:17:12,5 1|0:33:11,22 ./.:32:7,25 +chr20 452135 200x5ff C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=431724;QSTRAND=+ GT:DP:AD 1|0:20:7,13 1|0:44:25,19 ./.:22:17,5 +chr20 453153 200x600 CAAAAAAAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=432743;QSTRAND=+ GT:DP:AD 1|0:30:17,13 1|0:30:21,9 ./.:30:18,12 +chr20 453153 200x601 C CAA 60 . QNAME=cluster23_scaffold_3;QSTART=25258071;QSTRAND=- GT:DP:AD ./.:29:20,9 ./.:10:5,5 1|0:28:20,8 +chr20 453153 200x602 C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25242302;QSTRAND=- GT:DP:AD ./.:40:24,16 ./.:33:17,16 0|1:39:23,16 +chr20 453460 200x603 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=433040;QSTRAND=+ GT:DP:AD 1|0:44:21,23 1|0:13:6,7 ./.:30:19,11 +chr20 453539 200x604 C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=433120;QSTRAND=+ GT:DP:AD 1|0:50:25,25 1|0:29:19,10 ./.:26:19,7 +chr20 453540 200x605 A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=433121;QSTRAND=+ GT:DP:AD 1|0:36:16,20 1|0:21:12,9 ./.:30:18,12 +chr20 453540 200x606 A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25257683;QSTRAND=- GT:DP:AD ./.:42:17,25 ./.:32:15,17 1|1:32:14,18 +chr20 453995 200x607 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=433576;QSTRAND=+ GT:DP:AD 1|0:35:11,24 1|0:15:6,9 ./.:44:24,20 +chr20 454087 200x608 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=433668;QSTRAND=+ GT:DP:AD 1|0:32:17,15 1|0:21:6,15 ./.:16:9,7 +chr20 454236 200x609 CAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=433818;QSTRAND=+ GT:DP:AD 1|0:21:13,8 ./.:43:19,24 ./.:37:14,23 +chr20 454236 200x60a CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=408684;QSTRAND=+ GT:DP:AD 0|1:21:13,8 ./.:22:11,11 ./.:21:11,10 +chr20 454236 200x60b CAA C 60 . QNAME=cluster19_000000F;QSTART=25307660;QSTRAND=- GT:DP:AD ./.:36:13,23 1|0:38:22,16 ./.:40:23,17 +chr20 454295 200x60c G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=433874;QSTRAND=+ GT:DP:AD 1|0:33:15,18 1|0:24:11,13 ./.:20:12,8 +chr20 454614 200x60d T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=434193;QSTRAND=+ GT:DP:AD 1|0:20:9,11 1|0:37:20,17 ./.:35:22,13 +chr20 454650 200x60e C CATTATT 60 . QNAME=HG002-S9-H1-000001F;QSTART=434230;QSTRAND=+ GT:DP:AD 1|0:29:12,17 1|0:21:7,14 ./.:33:22,11 +chr20 454798 200x60f G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=434383;QSTRAND=+ GT:DP:AD 1|0:14:5,9 1|0:20:10,10 ./.:25:20,5 +chr20 456053 200x610 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=435638;QSTRAND=+ GT:DP:AD 1|0:38:19,19 1|0:25:18,7 ./.:15:10,5 +chr20 456337 200x611 TTTCATCCA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=435923;QSTRAND=+ GT:DP:AD 1|0:45:23,22 1|0:29:10,19 ./.:28:23,5 +chr20 456571 200x612 CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=411018;QSTRAND=+ GT:DP:AD 0|1:28:18,10 ./.:14:7,7 ./.:37:20,17 +chr20 456603 200x613 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=436180;QSTRAND=+ GT:DP:AD 1|0:32:12,20 ./.:20:14,6 ./.:29:6,23 +chr20 456818 200x614 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=436395;QSTRAND=+ GT:DP:AD 1|0:12:5,7 1|0:42:17,25 ./.:24:18,6 +chr20 456933 200x615 AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=436511;QSTRAND=+ GT:DP:AD 1|0:39:21,18 ./.:44:20,24 ./.:25:11,14 +chr20 456933 200x616 ATTTT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=411379;QSTRAND=+ GT:DP:AD 0|1:35:22,13 ./.:11:5,6 ./.:31:15,16 +chr20 456933 200x617 ATTT A 60 . QNAME=cluster19_000000F;QSTART=417137;QSTRAND=+ GT:DP:AD ./.:41:24,17 0|1:40:17,23 1|1:34:16,18 +chr20 458314 200x618 A AT 60 . QNAME=cluster23_scaffold_2;QSTART=25237142;QSTRAND=- GT:DP:AD ./.:41:18,23 ./.:35:25,10 0|1:25:15,10 +chr20 458331 200x619 A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=412772;QSTRAND=+ GT:DP:AD 0|1:38:20,18 0|1:28:5,23 1|1:26:16,10 +chr20 458461 200x61a G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=412902;QSTRAND=+ GT:DP:AD 0|1:46:22,24 0|1:24:13,11 1|1:35:16,19 +chr20 459799 200x61b C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=414240;QSTRAND=+ GT:DP:AD 0|1:33:11,22 0|1:45:21,24 1|1:32:19,13 +chr20 460434 200x61c CAAA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=414876;QSTRAND=+ GT:DP:AD 0|1:43:23,20 0|1:32:16,16 1|1:25:10,15 +chr20 460464 200x61d C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=414902;QSTRAND=+ GT:DP:AD 0|1:33:11,22 0|1:23:11,12 1|1:24:12,12 +chr20 461679 200x61e T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=416117;QSTRAND=+ GT:DP:AD 0|1:28:18,10 0|1:31:18,13 1|1:22:9,13 +chr20 462293 200x61f C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=416731;QSTRAND=+ GT:DP:AD 0|1:42:18,24 0|1:28:7,21 1|1:44:24,20 +chr20 463154 200x620 A G 60 . QNAME=cluster19_000000F;QSTART=423351;QSTRAND=+ GT:DP:AD ./.:21:16,5 0|1:36:13,23 1|1:47:25,22 +chr20 463252 200x621 C G 60 . QNAME=cluster19_000000F;QSTART=423449;QSTRAND=+ GT:DP:AD ./.:41:18,23 0|1:35:13,22 1|1:36:13,23 +chr20 463841 200x622 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=418279;QSTRAND=+ GT:DP:AD 0|1:34:11,23 ./.:37:24,13 ./.:26:12,14 +chr20 465665 200x623 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=445241;QSTRAND=+ GT:DP:AD 1|1:35:18,17 1|1:41:24,17 1|1:38:23,15 +chr20 465676 200x624 GC G 60 . QNAME=HG002-S9-H1-000001F;QSTART=445253;QSTRAND=+ GT:DP:AD 1|1:27:17,10 1|1:27:6,21 1|1:23:6,17 +chr20 466029 200x625 A AAAAT 60 . QNAME=HG002-S9-H2-000001F;QSTART=420467;QSTRAND=+ GT:DP:AD 0|1:22:14,8 ./.:15:10,5 ./.:47:23,24 +chr20 466637 200x626 GTA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=446213;QSTRAND=+ GT:DP:AD 1|0:26:18,8 1|0:29:5,24 ./.:32:19,13 +chr20 466637 200x627 G GTGTATATATA 60 . QNAME=HG002-S9-H2-000001F;QSTART=421079;QSTRAND=+ GT:DP:AD 0|1:47:23,24 ./.:28:22,6 ./.:31:23,8 +chr20 466637 200x628 G GTATA 60 . QNAME=cluster19_000000F;QSTART=426834;QSTRAND=+ GT:DP:AD ./.:28:7,21 0|1:22:14,8 1|0:19:14,5 +chr20 466637 200x629 G GTA 60 . QNAME=cluster23_scaffold_2;QSTART=25228821;QSTRAND=- GT:DP:AD ./.:21:15,6 ./.:16:10,6 0|1:22:15,7 +chr20 467024 200x62a C CT 60 . QNAME=cluster23_scaffold_2;QSTART=25228433;QSTRAND=- GT:DP:AD ./.:36:15,21 ./.:32:23,9 0|1:43:24,19 +chr20 468015 200x62b G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=447588;QSTRAND=+ GT:DP:AD 1|1:28:14,14 1|1:32:19,13 1|1:26:10,16 +chr20 468269 200x62c C A 60 . QNAME=cluster19_000000F;QSTART=428469;QSTRAND=+ GT:DP:AD ./.:25:8,17 0|1:39:14,25 1|1:40:15,25 +chr20 469249 200x62d G A 60 . QNAME=cluster19_000000F;QSTART=429449;QSTRAND=+ GT:DP:AD ./.:26:7,19 0|1:30:21,9 1|1:28:17,11 +chr20 469257 200x62e A T 60 . QNAME=cluster19_000000F;QSTART=429457;QSTRAND=+ GT:DP:AD ./.:27:8,19 0|1:37:25,12 1|1:33:19,14 +chr20 470060 200x62f C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=424511;QSTRAND=+ GT:DP:AD 0|1:18:7,11 ./.:30:24,6 ./.:27:18,9 +chr20 471168 200x630 G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=425619;QSTRAND=+ GT:DP:AD 0|1:22:10,12 ./.:38:23,15 ./.:17:9,8 +chr20 472424 200x631 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=451997;QSTRAND=+ GT:DP:AD 1|0:37:18,19 ./.:17:7,10 ./.:44:25,19 +chr20 472457 200x632 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=452030;QSTRAND=+ GT:DP:AD 1|1:22:8,14 1|1:28:8,20 1|1:22:8,14 +chr20 475460 200x633 CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=429912;QSTRAND=+ GT:DP:AD 0|1:35:25,10 ./.:28:10,18 ./.:31:14,17 +chr20 475460 200x634 CAAAAA C 60 . QNAME=cluster19_000000F;QSTART=435661;QSTRAND=+ GT:DP:AD ./.:34:25,9 0|1:32:15,17 ./.:34:15,19 +chr20 477729 200x635 C T 60 . QNAME=cluster19_000000F;QSTART=25284173;QSTRAND=- GT:DP:AD ./.:35:17,18 1|0:24:14,10 1|1:29:15,14 +chr20 478540 200x636 TC T 60 . QNAME=HG002-S9-H2-000001F;QSTART=432991;QSTRAND=+ GT:DP:AD 0|1:33:10,23 ./.:22:14,8 ./.:31:14,17 +chr20 480234 200x637 T G 60 . QNAME=cluster23_scaffold_3;QSTART=25230992;QSTRAND=- GT:DP:AD ./.:25:15,10 ./.:28:23,5 1|0:25:6,19 +chr20 484694 200x638 T TTG 60 . QNAME=cluster19_000000F;QSTART=25277206;QSTRAND=- GT:DP:AD ./.:41:22,19 1|0:23:12,11 ./.:24:19,5 +chr20 484991 200x639 C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=464564;QSTRAND=+ GT:DP:AD 1|0:25:13,12 ./.:44:20,24 ./.:35:17,18 +chr20 485066 200x63a CAAAA C 60 . QNAME=cluster23_scaffold_3;QSTART=25226160;QSTRAND=- GT:DP:AD ./.:21:10,11 ./.:27:20,7 1|0:22:12,10 +chr20 485088 200x63b AAAAAAAAAAAAAAAAAAAAAAATATATATATAT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=464662;QSTRAND=+;SVTYPE=DEL;SVLEN=-33 GT:DP:AD 1/0:26:11,15 ./.:21:12,9 ./.:20:14,6 +chr20 485103 200x63c A ATATATATATAT 60 . QNAME=cluster23_scaffold_2;QSTART=25210343;QSTRAND=- GT:DP:AD ./.:32:7,25 ./.:26:9,17 0|1:19:7,12 +chr20 485105 200x63d A T 60 . QNAME=cluster23_scaffold_2;QSTART=25210341;QSTRAND=- GT:DP:AD ./.:36:20,16 ./.:44:24,20 0|1:26:18,8 +chr20 485105 200x63e A ATAATATATATATAT 60 . QNAME=HG002-S9-H2-000001F;QSTART=439555;QSTRAND=+ GT:DP:AD 0|1:31:16,15 ./.:16:9,7 ./.:16:5,11 +chr20 485105 200x63f A ATATATATATAT 60 . QNAME=cluster19_000000F;QSTART=25276784;QSTRAND=- GT:DP:AD ./.:32:13,19 1|0:26:11,15 ./.:23:7,16 +chr20 485107 200x640 A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=439570;QSTRAND=+ GT:DP:AD 0|1:15:8,7 1|0:46:23,23 1|1:21:15,6 +chr20 485109 200x641 A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=439572;QSTRAND=+ GT:DP:AD 0|1:23:7,16 1|0:28:19,9 1|1:22:7,15 +chr20 485110 200x642 ATAT A 60 . QNAME=cluster19_000000F;QSTART=445306;QSTRAND=+ GT:DP:AD ./.:33:12,21 0|1:25:15,10 ./.:26:21,5 +chr20 485115 200x643 T A 60 . QNAME=cluster19_000000F;QSTART=445307;QSTRAND=+ GT:DP:AD ./.:16:7,9 0|1:32:13,19 ./.:13:6,7 +chr20 485117 200x644 T A 60 . QNAME=cluster19_000000F;QSTART=445309;QSTRAND=+ GT:DP:AD ./.:49:25,24 0|1:18:10,8 ./.:18:12,6 +chr20 485138 200x645 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=439601;QSTRAND=+ GT:DP:AD 0|1:35:14,21 ./.:40:17,23 ./.:31:21,10 +chr20 485139 200x646 A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=439602;QSTRAND=+ GT:DP:AD 0|1:32:23,9 ./.:31:25,6 ./.:37:15,22 +chr20 487542 200x647 G A 60 . QNAME=cluster19_000000F;QSTART=447734;QSTRAND=+ GT:DP:AD ./.:38:19,19 0|1:33:14,19 ./.:13:5,8 +chr20 488040 200x648 C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25223189;QSTRAND=- GT:DP:AD ./.:41:23,18 ./.:36:17,19 1|1:29:14,15 +chr20 490335 200x649 C CT 60 . QNAME=cluster19_000000F;QSTART=25271553;QSTRAND=- GT:DP:AD ./.:38:19,19 1|0:33:12,21 ./.:29:5,24 +chr20 490909 200x64a A C 60 . QNAME=cluster19_000000F;QSTART=25270979;QSTRAND=- GT:DP:AD ./.:31:18,13 1|0:17:11,6 ./.:32:25,7 +chr20 493202 200x64b A T 60 . QNAME=cluster19_000000F;QSTART=25268686;QSTRAND=- GT:DP:AD ./.:43:20,23 1|0:42:24,18 1|1:36:22,14 +chr20 494543 200x64c T C 60 . QNAME=cluster19_000000F;QSTART=25267345;QSTRAND=- GT:DP:AD ./.:33:16,17 1|0:43:21,22 ./.:37:17,20 +chr20 498335 200x64d CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=452799;QSTRAND=+ GT:DP:AD 0|1:28:6,22 ./.:30:18,12 ./.:46:22,24 +chr20 498335 200x64e C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25212893;QSTRAND=- GT:DP:AD ./.:28:10,18 ./.:30:15,15 1|1:16:7,9 +chr20 498901 200x64f T C 60 . QNAME=cluster19_000000F;QSTART=459093;QSTRAND=+ GT:DP:AD ./.:20:6,14 0|1:31:12,19 ./.:28:19,9 +chr20 499958 200x650 C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25195485;QSTRAND=- GT:DP:AD ./.:31:17,14 ./.:19:5,14 0|1:26:15,11 +chr20 500634 200x651 C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25210593;QSTRAND=- GT:DP:AD ./.:25:17,8 ./.:39:20,19 1|0:41:19,22 +chr20 501285 200x652 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=480825;QSTRAND=+ GT:DP:AD 1|0:19:5,14 ./.:17:11,6 ./.:29:17,12 +chr20 504037 200x653 G GC 60 . QNAME=HG002-S9-H2-000001F;QSTART=458500;QSTRAND=+ GT:DP:AD 0|1:29:17,12 ./.:21:9,12 ./.:31:19,12 +chr20 505351 200x654 G GT 60 . QNAME=cluster19_000000F;QSTART=25256536;QSTRAND=- GT:DP:AD ./.:25:18,7 1|0:29:21,8 1|0:38:19,19 +chr20 505587 200x655 C G 60 . QNAME=cluster19_000000F;QSTART=465779;QSTRAND=+ GT:DP:AD ./.:44:22,22 0|1:11:6,5 ./.:26:15,11 +chr20 505869 200x656 AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=485410;QSTRAND=+ GT:DP:AD 1|0:19:5,14 ./.:20:5,15 ./.:22:12,10 +chr20 505869 200x657 A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25205356;QSTRAND=- GT:DP:AD ./.:37:20,17 ./.:31:25,6 1|0:37:21,16 +chr20 505905 200x658 T C 60 . QNAME=cluster23_scaffold_3;QSTART=25205320;QSTRAND=- GT:DP:AD ./.:32:14,18 ./.:14:8,6 1|0:38:17,21 +chr20 506070 200x659 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=485609;QSTRAND=+ GT:DP:AD 1|0:29:8,21 ./.:33:16,17 0|1:44:25,19 +chr20 506079 200x65a T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=485618;QSTRAND=+ GT:DP:AD 1|0:17:11,6 ./.:32:9,23 0|1:29:14,15 +chr20 506080 200x65b G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=485619;QSTRAND=+ GT:DP:AD 1|0:35:15,20 ./.:18:11,7 0|1:37:18,19 +chr20 506097 200x65c C T 60 . QNAME=cluster19_000000F;QSTART=25255790;QSTRAND=- GT:DP:AD ./.:25:10,15 1|0:45:20,25 1|0:15:9,6 +chr20 506098 200x65d G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=485637;QSTRAND=+ GT:DP:AD 1|0:16:8,8 ./.:20:10,10 0|1:33:13,20 +chr20 506127 200x65e T C 60 . QNAME=cluster23_scaffold_3;QSTART=25205098;QSTRAND=- GT:DP:AD ./.:27:20,7 ./.:26:14,12 1|0:32:12,20 +chr20 507967 200x65f G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=487506;QSTRAND=+ GT:DP:AD 1|1:35:14,21 1|1:29:21,8 1|1:37:13,24 +chr20 508286 200x660 C T 60 . QNAME=cluster19_000000F;QSTART=25253601;QSTRAND=- GT:DP:AD ./.:33:22,11 1|0:33:20,13 1|1:35:21,14 +chr20 508793 200x661 A G 60 . QNAME=cluster23_scaffold_2;QSTART=25186650;QSTRAND=- GT:DP:AD ./.:22:16,6 ./.:39:19,20 0|1:34:24,10 +chr20 511703 200x662 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=466166;QSTRAND=+ GT:DP:AD 0|1:16:8,8 ./.:27:6,21 ./.:45:22,23 +chr20 511705 200x663 C T 60 . QNAME=cluster19_000000F;QSTART=25250182;QSTRAND=- GT:DP:AD ./.:46:24,22 1|0:41:25,16 1|1:15:5,10 +chr20 512561 200x664 G T 60 . QNAME=cluster19_000000F;QSTART=25249326;QSTRAND=- GT:DP:AD ./.:16:7,9 1|0:30:14,16 1|1:18:7,11 +chr20 512965 200x665 T C 60 . QNAME=cluster19_000000F;QSTART=25248922;QSTRAND=- GT:DP:AD ./.:25:18,7 1|0:35:16,19 ./.:37:18,19 +chr20 514164 200x666 C T 60 . QNAME=cluster19_000000F;QSTART=25247723;QSTRAND=- GT:DP:AD ./.:45:24,21 1|0:20:8,12 1|1:24:5,19 +chr20 518713 200x667 ATT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=498253;QSTRAND=+ GT:DP:AD 1|0:22:7,15 1|0:44:24,20 0|1:27:6,21 +chr20 518713 200x668 AT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=473177;QSTRAND=+ GT:DP:AD 0|1:25:10,15 0|1:37:21,16 1|0:20:15,5 +chr20 518933 200x669 CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=473396;QSTRAND=+ GT:DP:AD 0|1:41:19,22 ./.:36:24,12 ./.:17:7,10 +chr20 518933 200x66a C CT 60 . QNAME=cluster23_scaffold_2;QSTART=25176511;QSTRAND=- GT:DP:AD ./.:15:7,8 ./.:28:22,6 0|1:28:18,10 +chr20 522293 200x66b C T 60 . QNAME=cluster19_000000F;QSTART=25239596;QSTRAND=- GT:DP:AD ./.:19:14,5 1|0:31:12,19 1|1:37:18,19 +chr20 523858 200x66c C CA 60 . QNAME=cluster19_000000F;QSTART=25238030;QSTRAND=- GT:DP:AD ./.:37:22,15 1|0:48:24,24 0|1:31:7,24 +chr20 523869 200x66d A C 60 . QNAME=cluster19_000000F;QSTART=484060;QSTRAND=+ GT:DP:AD ./.:19:5,14 0|1:21:15,6 ./.:33:13,20 +chr20 524145 200x66e C T 60 . QNAME=cluster19_000000F;QSTART=25237743;QSTRAND=- GT:DP:AD ./.:32:23,9 1|1:33:8,25 1|1:26:12,14 +chr20 524654 200x66f T C 60 . QNAME=cluster19_000000F;QSTART=25237234;QSTRAND=- GT:DP:AD ./.:31:6,25 1|0:37:23,14 ./.:29:21,8 +chr20 524708 200x670 CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=504246;QSTRAND=+ GT:DP:AD 1|0:36:14,22 1|0:28:16,12 0|1:19:8,11 +chr20 524708 200x671 CAA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=479170;QSTRAND=+ GT:DP:AD 0|1:26:14,12 0|1:26:19,7 ./.:42:21,21 +chr20 525133 200x672 A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=504669;QSTRAND=+ GT:DP:AD 1|0:34:11,23 ./.:32:24,8 ./.:45:21,24 +chr20 525391 200x673 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=504927;QSTRAND=+ GT:DP:AD 1|0:37:12,25 ./.:21:6,15 ./.:20:13,7 +chr20 525650 200x674 CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=505187;QSTRAND=+ GT:DP:AD 1|0:29:13,16 ./.:27:11,16 ./.:35:13,22 +chr20 525836 200x675 TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=505372;QSTRAND=+ GT:DP:AD 1|0:30:25,5 ./.:31:20,11 ./.:34:16,18 +chr20 525836 200x676 T TA 60 . QNAME=cluster23_scaffold_2;QSTART=25169607;QSTRAND=- GT:DP:AD ./.:45:22,23 ./.:40:24,16 0|1:33:21,12 +chr20 526238 200x677 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=505772;QSTRAND=+ GT:DP:AD 1|0:29:23,6 1|0:39:15,24 1|1:36:15,21 +chr20 526685 200x678 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=506219;QSTRAND=+ GT:DP:AD 1|0:34:12,22 ./.:27:14,13 ./.:33:21,12 +chr20 526949 200x679 CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=506484;QSTRAND=+ GT:DP:AD 1|0:37:21,16 ./.:49:25,24 ./.:41:24,17 +chr20 527001 200x67a C CAGAGAGAGAG 60 . QNAME=cluster19_000000F;QSTART=25234878;QSTRAND=- GT:DP:AD ./.:41:17,24 1|0:34:19,15 ./.:23:6,17 +chr20 527001 200x67b C CAGAG 60 . QNAME=cluster23_scaffold_3;QSTART=25184221;QSTRAND=- GT:DP:AD ./.:30:19,11 ./.:23:6,17 1|0:35:20,15 +chr20 527001 200x67c C CAG 60 . QNAME=cluster23_scaffold_2;QSTART=25168440;QSTRAND=- GT:DP:AD ./.:25:13,12 ./.:23:14,9 0|1:26:16,10 +chr20 527003 200x67d G GAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=506537;QSTRAND=+ GT:DP:AD 1|0:33:21,12 ./.:39:14,25 ./.:32:22,10 +chr20 527729 200x67e G A 60 . QNAME=cluster19_000000F;QSTART=487918;QSTRAND=+ GT:DP:AD ./.:47:22,25 0|1:23:14,9 ./.:35:13,22 +chr20 527782 200x67f A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=507317;QSTRAND=+ GT:DP:AD 1|0:21:12,9 ./.:29:12,17 ./.:37:20,17 +chr20 528449 200x680 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=507984;QSTRAND=+ GT:DP:AD 1|0:35:13,22 ./.:26:21,5 ./.:28:6,22 +chr20 528594 200x681 CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=508130;QSTRAND=+ GT:DP:AD 1|0:18:6,12 ./.:28:23,5 ./.:29:18,11 +chr20 529190 200x682 A AT 60 . QNAME=cluster19_000000F;QSTART=25232688;QSTRAND=- GT:DP:AD ./.:43:24,19 1|0:18:5,13 1|1:32:14,18 +chr20 530468 200x683 C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=510003;QSTRAND=+ GT:DP:AD 1|0:33:10,23 ./.:26:13,13 ./.:35:12,23 +chr20 531253 200x684 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=510788;QSTRAND=+ GT:DP:AD 1|0:21:10,11 ./.:32:16,16 ./.:44:21,23 +chr20 532330 200x685 ATT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=511866;QSTRAND=+ GT:DP:AD 1|0:21:10,11 ./.:17:10,7 ./.:17:6,11 +chr20 532352 200x686 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=511885;QSTRAND=+ GT:DP:AD 1|0:25:12,13 ./.:14:9,5 ./.:31:14,17 +chr20 533815 200x687 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=513348;QSTRAND=+ GT:DP:AD 1|0:42:19,23 ./.:36:15,21 ./.:26:5,21 +chr20 535034 200x688 CAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=514568;QSTRAND=+ GT:DP:AD 1|0:12:6,6 ./.:22:13,9 ./.:39:16,23 +chr20 535034 200x689 C CA 60 . QNAME=cluster19_000000F;QSTART=495224;QSTRAND=+ GT:DP:AD ./.:30:7,23 0|1:20:13,7 ./.:24:18,6 +chr20 535629 200x68a A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=515160;QSTRAND=+ GT:DP:AD 1|0:34:16,18 ./.:48:24,24 ./.:29:12,17 +chr20 535685 200x68b G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=515216;QSTRAND=+ GT:DP:AD 1|0:29:19,10 ./.:24:6,18 ./.:33:19,14 +chr20 535739 200x68c CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=515271;QSTRAND=+ GT:DP:AD 1|0:15:8,7 ./.:24:18,6 ./.:26:15,11 +chr20 537243 200x68d C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=516773;QSTRAND=+ GT:DP:AD 1|0:34:21,13 ./.:29:24,5 ./.:17:6,11 +chr20 537496 200x68e G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=517027;QSTRAND=+ GT:DP:AD 1|0:27:8,19 ./.:24:14,10 ./.:29:13,16 +chr20 537963 200x68f C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=517495;QSTRAND=+ GT:DP:AD 1|0:45:20,25 ./.:13:8,5 ./.:34:16,18 +chr20 538108 200x690 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=517640;QSTRAND=+ GT:DP:AD 1|0:47:25,22 1|0:17:5,12 1|1:30:13,17 +chr20 539053 200x691 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=518585;QSTRAND=+ GT:DP:AD 1|0:42:22,20 ./.:21:9,12 ./.:33:8,25 +chr20 539493 200x692 C T 60 . QNAME=cluster23_scaffold_2;QSTART=25155947;QSTRAND=- GT:DP:AD ./.:26:12,14 ./.:16:11,5 0|1:24:9,15 +chr20 541244 200x693 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=520776;QSTRAND=+ GT:DP:AD 1|0:39:16,23 ./.:16:10,6 ./.:16:7,9 +chr20 541502 200x694 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=521034;QSTRAND=+ GT:DP:AD 1|0:37:25,12 ./.:27:12,15 ./.:39:25,14 +chr20 542623 200x695 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=522155;QSTRAND=+ GT:DP:AD 1|0:47:22,25 ./.:24:18,6 ./.:22:11,11 +chr20 544402 200x696 G GT 60 . QNAME=cluster19_000000F;QSTART=25217475;QSTRAND=- GT:DP:AD ./.:42:22,20 1|0:25:12,13 1|1:23:10,13 +chr20 545973 200x697 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=525505;QSTRAND=+ GT:DP:AD 1|0:25:20,5 ./.:40:15,25 ./.:35:19,16 +chr20 546122 200x698 A G 60 . QNAME=cluster23_scaffold_2;QSTART=25149317;QSTRAND=- GT:DP:AD ./.:14:8,6 ./.:29:9,20 0|1:17:11,6 +chr20 546487 200x699 ACT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=526020;QSTRAND=+ GT:DP:AD 1|0:34:13,21 ./.:26:21,5 ./.:19:13,6 +chr20 547548 200x69a T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=527078;QSTRAND=+ GT:DP:AD 1|0:32:15,17 ./.:21:9,12 ./.:30:23,7 +chr20 548222 200x69b C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=527752;QSTRAND=+ GT:DP:AD 1|0:29:16,13 0|1:37:25,12 ./.:19:6,13 +chr20 548575 200x69c ATATTTT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=528106;QSTRAND=+ GT:DP:AD 1|0:20:14,6 ./.:26:19,7 ./.:41:21,20 +chr20 548577 200x69d A AT 60 . QNAME=cluster19_000000F;QSTART=25213299;QSTRAND=- GT:DP:AD ./.:26:9,17 1|0:18:11,7 0|1:16:9,7 +chr20 548577 200x69e A ATT 60 . QNAME=cluster23_scaffold_3;QSTART=25162641;QSTRAND=- GT:DP:AD ./.:27:16,11 ./.:24:18,6 1|0:17:8,9 +chr20 548971 200x69f C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=528495;QSTRAND=+ GT:DP:AD 1|0:27:9,18 ./.:27:8,19 ./.:29:15,14 +chr20 549092 200x6a0 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=528616;QSTRAND=+ GT:DP:AD 1|0:46:23,23 ./.:17:12,5 ./.:31:11,20 +chr20 549227 200x6a1 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=528751;QSTRAND=+ GT:DP:AD 1|0:37:20,17 ./.:14:9,5 ./.:33:12,21 +chr20 549649 200x6a2 GGAAA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=529174;QSTRAND=+ GT:DP:AD 1|0:24:9,15 ./.:33:11,22 ./.:47:22,25 +chr20 549670 200x6a3 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=529190;QSTRAND=+ GT:DP:AD 1|0:39:20,19 ./.:30:20,10 ./.:18:12,6 +chr20 550104 200x6a4 T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=529624;QSTRAND=+ GT:DP:AD 1|0:42:25,17 ./.:19:13,6 ./.:35:12,23 +chr20 550577 200x6a5 C T 60 . QNAME=cluster19_000000F;QSTART=25211299;QSTRAND=- GT:DP:AD ./.:31:8,23 1|0:23:8,15 1|1:35:22,13 +chr20 551334 200x6a6 C A 60 . QNAME=cluster19_000000F;QSTART=25210542;QSTRAND=- GT:DP:AD ./.:13:6,7 1|0:42:18,24 1|1:22:7,15 +chr20 551415 200x6a7 T A 60 . QNAME=cluster19_000000F;QSTART=25210461;QSTRAND=- GT:DP:AD ./.:32:14,18 1|0:32:22,10 1|1:33:25,8 +chr20 551424 200x6a8 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=530944;QSTRAND=+ GT:DP:AD 1|0:30:24,6 1|0:36:11,25 1|1:24:17,7 +chr20 551459 200x6a9 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=530979;QSTRAND=+ GT:DP:AD 1|0:29:5,24 1|0:18:9,9 1|1:23:15,8 +chr20 552161 200x6aa G A 60 . QNAME=cluster19_000000F;QSTART=25209715;QSTRAND=- GT:DP:AD ./.:28:18,10 1|0:26:16,10 1|1:35:14,21 +chr20 552253 200x6ab C T 60 . QNAME=cluster19_000000F;QSTART=25209623;QSTRAND=- GT:DP:AD ./.:39:16,23 1|0:42:18,24 1|1:32:22,10 +chr20 552281 200x6ac A G 60 . QNAME=cluster19_000000F;QSTART=25209595;QSTRAND=- GT:DP:AD ./.:38:19,19 1|0:24:16,8 1|1:29:11,18 +chr20 552720 200x6ad CT C 60 . QNAME=cluster19_000000F;QSTART=25209156;QSTRAND=- GT:DP:AD ./.:38:23,15 1|0:25:12,13 1|1:39:24,15 +chr20 553245 200x6ae C G 60 . QNAME=cluster19_000000F;QSTART=25208632;QSTRAND=- GT:DP:AD ./.:33:24,9 1|0:48:23,25 1|1:25:13,12 +chr20 553335 200x6af C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=532856;QSTRAND=+ GT:DP:AD 1|0:25:15,10 ./.:23:17,6 ./.:40:25,15 +chr20 553335 200x6b0 CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=507795;QSTRAND=+ GT:DP:AD 0|1:48:23,25 ./.:41:16,25 ./.:31:8,23 +chr20 553335 200x6b1 C CAAA 60 . QNAME=cluster19_000000F;QSTART=25208539;QSTRAND=- GT:DP:AD ./.:27:11,16 1|0:25:14,11 1|1:26:5,21 +chr20 553919 200x6b2 C T 60 . QNAME=cluster19_000000F;QSTART=25207955;QSTRAND=- GT:DP:AD ./.:32:15,17 1|0:37:22,15 1|1:23:7,16 +chr20 554853 200x6b3 T A 60 . QNAME=cluster19_000000F;QSTART=25207021;QSTRAND=- GT:DP:AD ./.:33:19,14 1|0:19:14,5 1|1:32:11,21 +chr20 555892 200x6b4 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=535413;QSTRAND=+ GT:DP:AD 1|1:40:17,23 1|1:37:18,19 1|1:22:8,14 +chr20 556119 200x6b5 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=535640;QSTRAND=+ GT:DP:AD 1|0:22:6,16 0|1:17:12,5 1|1:22:15,7 +chr20 556141 200x6b6 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=535662;QSTRAND=+ GT:DP:AD 1|1:22:6,16 1|1:34:21,13 1|1:28:6,22 +chr20 556215 200x6b7 G A 60 . QNAME=cluster19_000000F;QSTART=516405;QSTRAND=+ GT:DP:AD ./.:16:10,6 0|1:41:21,20 1|1:20:9,11 +chr20 556356 200x6b8 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=535877;QSTRAND=+ GT:DP:AD 1|0:22:17,5 ./.:22:15,7 ./.:32:10,22 +chr20 556431 200x6b9 T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=510889;QSTRAND=+ GT:DP:AD 0|1:16:11,5 1|0:34:17,17 ./.:33:9,24 +chr20 556435 200x6ba G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=535956;QSTRAND=+ GT:DP:AD 1|0:34:15,19 0|1:39:20,19 1|1:43:22,21 +chr20 556632 200x6bb T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=536153;QSTRAND=+ GT:DP:AD 1|1:39:17,22 1|1:38:13,25 1|1:20:9,11 +chr20 556794 200x6bc T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=536315;QSTRAND=+ GT:DP:AD 1|1:25:18,7 1|1:32:10,22 1|1:48:25,23 +chr20 556861 200x6bd C A 60 . QNAME=cluster19_000000F;QSTART=517051;QSTRAND=+ GT:DP:AD ./.:20:9,11 0|1:28:19,9 1|1:44:25,19 +chr20 556869 200x6be C CAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=536391;QSTRAND=+ GT:DP:AD 1|1:50:25,25 1|0:27:5,22 ./.:46:25,21 +chr20 556869 200x6bf C CAAAAAA 60 . QNAME=cluster23_scaffold_3;QSTART=25154341;QSTRAND=- GT:DP:AD ./.:35:23,12 ./.:42:25,17 1|0:36:13,23 +chr20 556869 200x6c0 C CAAAAA 60 . QNAME=cluster23_scaffold_2;QSTART=25138562;QSTRAND=- GT:DP:AD ./.:32:15,17 ./.:44:25,19 0|1:15:6,9 +chr20 556881 200x6c1 A AAAAAAT 60 . QNAME=cluster19_000000F;QSTART=517072;QSTRAND=+ GT:DP:AD ./.:28:9,19 0|1:33:16,17 ./.:16:11,5 +chr20 556883 200x6c2 T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=536407;QSTRAND=+ GT:DP:AD 1|1:26:6,20 1|0:29:5,24 ./.:33:17,16 +chr20 556885 200x6c3 T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=536409;QSTRAND=+ GT:DP:AD 1|1:21:14,7 1|0:11:6,5 ./.:17:8,9 +chr20 556887 200x6c4 T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=536411;QSTRAND=+ GT:DP:AD 1|1:29:13,16 1|0:38:25,13 ./.:16:5,11 +chr20 557034 200x6c5 T C 60 . QNAME=cluster19_000000F;QSTART=517230;QSTRAND=+ GT:DP:AD ./.:14:9,5 0|1:28:13,15 1|1:41:22,19 +chr20 557559 200x6c6 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=537083;QSTRAND=+ GT:DP:AD 1|1:37:14,23 1|0:23:14,9 ./.:35:18,17 +chr20 557586 200x6c7 C T 60 . QNAME=cluster19_000000F;QSTART=517782;QSTRAND=+ GT:DP:AD ./.:11:5,6 0|1:18:6,12 1|1:28:21,7 +chr20 557591 200x6c8 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=537115;QSTRAND=+ GT:DP:AD 1|1:47:22,25 1|1:14:8,6 1|1:41:24,17 +chr20 557603 200x6c9 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=537127;QSTRAND=+ GT:DP:AD 1|1:20:14,6 1|0:21:14,7 ./.:24:14,10 +chr20 557995 200x6ca C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=537520;QSTRAND=+ GT:DP:AD 1|1:43:25,18 1|1:45:22,23 1|1:23:18,5 +chr20 558185 200x6cb T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=537710;QSTRAND=+ GT:DP:AD 1|1:46:22,24 1|0:21:8,13 ./.:41:25,16 +chr20 558374 200x6cc T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=537899;QSTRAND=+ GT:DP:AD 1|1:14:8,6 1|0:20:14,6 ./.:28:22,6 +chr20 558479 200x6cd G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=538004;QSTRAND=+ GT:DP:AD 1|1:37:14,23 1|0:31:11,20 ./.:25:12,13 +chr20 558579 200x6ce ATTTT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=538105;QSTRAND=+ GT:DP:AD 1|1:23:18,5 1|0:22:10,12 ./.:42:19,23 +chr20 558719 200x6cf G A 60 . QNAME=cluster19_000000F;QSTART=518916;QSTRAND=+ GT:DP:AD ./.:21:11,10 0|1:16:9,7 1|1:39:15,24 +chr20 558928 200x6d0 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=538449;QSTRAND=+ GT:DP:AD 1|1:42:24,18 1|0:34:24,10 ./.:33:22,11 +chr20 559006 200x6d1 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=538527;QSTRAND=+ GT:DP:AD 1|1:29:16,13 1|1:35:15,20 1|1:35:12,23 +chr20 559112 200x6d2 G GT 60 . QNAME=HG002-S9-H1-000001F;QSTART=538634;QSTRAND=+ GT:DP:AD 1|1:38:25,13 1|0:21:9,12 ./.:39:25,14 +chr20 559189 200x6d3 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=538711;QSTRAND=+ GT:DP:AD 1|1:37:22,15 1|1:34:10,24 1|1:28:21,7 +chr20 559234 200x6d4 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=538756;QSTRAND=+ GT:DP:AD 1|1:36:23,13 1|0:38:20,18 1|0:15:10,5 +chr20 559282 200x6d5 G T 60 . QNAME=cluster19_000000F;QSTART=519479;QSTRAND=+ GT:DP:AD ./.:42:21,21 0|1:34:19,15 0|1:36:16,20 +chr20 559554 200x6d6 T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=539077;QSTRAND=+ GT:DP:AD 1|1:17:10,7 1|1:35:15,20 1|1:30:9,21 +chr20 560062 200x6d7 AC A 60 . QNAME=HG002-S9-H2-000001F;QSTART=514523;QSTRAND=+ GT:DP:AD 0|1:33:18,15 ./.:15:7,8 ./.:37:22,15 +chr20 560063 200x6d8 C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=539586;QSTRAND=+ GT:DP:AD 1|0:33:21,12 1|0:18:12,6 ./.:28:6,22 +chr20 560078 200x6d9 CAA C 60 . QNAME=cluster19_000000F;QSTART=520277;QSTRAND=+ GT:DP:AD ./.:38:25,13 0|1:35:10,25 1|1:18:7,11 +chr20 560086 200x6da C G 60 . QNAME=cluster19_000000F;QSTART=520282;QSTRAND=+ GT:DP:AD ./.:31:10,21 0|1:31:20,11 1|1:29:20,9 +chr20 560086 200x6db CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=539610;QSTRAND=+ GT:DP:AD 1|1:24:8,16 1|0:38:19,19 ./.:35:23,12 +chr20 560087 200x6dc A C 60 . QNAME=cluster19_000000F;QSTART=520283;QSTRAND=+ GT:DP:AD ./.:35:17,18 0|1:29:21,8 1|1:33:25,8 +chr20 560103 200x6dd T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=539625;QSTRAND=+ GT:DP:AD 1|1:39:18,21 1|1:28:10,18 1|1:17:5,12 +chr20 560343 200x6de C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=514801;QSTRAND=+ GT:DP:AD 0|1:25:7,18 1|0:39:25,14 ./.:20:14,6 +chr20 560618 200x6df G T 60 . QNAME=cluster19_000000F;QSTART=520814;QSTRAND=+ GT:DP:AD ./.:39:19,20 0|1:22:7,15 1|1:37:16,21 +chr20 560691 200x6e0 G A 60 . QNAME=cluster19_000000F;QSTART=520887;QSTRAND=+ GT:DP:AD ./.:28:9,19 0|1:32:23,9 1|1:28:22,6 +chr20 560945 200x6e1 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=540467;QSTRAND=+ GT:DP:AD 1|1:28:9,19 1|0:27:16,11 ./.:15:5,10 +chr20 561211 200x6e2 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=540733;QSTRAND=+ GT:DP:AD 1|1:26:14,12 1|1:20:10,10 1|1:21:14,7 +chr20 562030 200x6e3 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=541552;QSTRAND=+ GT:DP:AD 1|1:16:11,5 1|1:38:23,15 1|1:34:22,12 +chr20 562133 200x6e4 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=541655;QSTRAND=+ GT:DP:AD 1|1:22:12,10 1|1:31:23,8 1|1:43:21,22 +chr20 562219 200x6e5 A G 60 . QNAME=cluster19_000000F;QSTART=522415;QSTRAND=+ GT:DP:AD ./.:31:14,17 0|1:33:24,9 1|1:27:11,16 +chr20 562642 200x6e6 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=542164;QSTRAND=+ GT:DP:AD 1|1:23:9,14 1|1:23:11,12 1|1:33:17,16 +chr20 562657 200x6e7 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=542179;QSTRAND=+ GT:DP:AD 1|1:29:22,7 1|1:45:20,25 1|1:36:18,18 +chr20 562994 200x6e8 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=542516;QSTRAND=+ GT:DP:AD 1|1:32:11,21 1|1:26:5,21 1|1:36:17,19 +chr20 563100 200x6e9 C T 60 . QNAME=cluster19_000000F;QSTART=523296;QSTRAND=+ GT:DP:AD ./.:34:23,11 0|1:25:14,11 1|1:33:16,17 +chr20 563396 200x6ea C T 60 . QNAME=cluster19_000000F;QSTART=25198477;QSTRAND=- GT:DP:AD ./.:17:6,11 1|0:25:14,11 ./.:29:13,16 +chr20 563773 200x6eb G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=543295;QSTRAND=+ GT:DP:AD 1|1:32:25,7 1|0:22:10,12 ./.:32:9,23 +chr20 564270 200x6ec G A 60 . QNAME=cluster19_000000F;QSTART=25197603;QSTRAND=- GT:DP:AD ./.:24:19,5 1|1:29:12,17 1|1:28:9,19 +chr20 564271 200x6ed T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=543793;QSTRAND=+ GT:DP:AD 1|1:28:9,19 ./.:27:16,11 ./.:20:14,6 +chr20 564553 200x6ee T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=519011;QSTRAND=+ GT:DP:AD 0|1:30:16,14 1|1:21:6,15 1|1:32:15,17 +chr20 564560 200x6ef GTGTT G 60 . QNAME=cluster23_scaffold_3;QSTART=25146650;QSTRAND=- GT:DP:AD ./.:38:13,25 ./.:30:17,13 1|0:25:14,11 +chr20 564629 200x6f0 A G 60 . QNAME=cluster23_scaffold_2;QSTART=25130802;QSTRAND=- GT:DP:AD ./.:24:19,5 ./.:23:17,6 0|1:25:11,14 +chr20 565205 200x6f1 A AT 60 . QNAME=cluster19_000000F;QSTART=25196667;QSTRAND=- GT:DP:AD ./.:37:14,23 1|1:33:8,25 1|1:30:25,5 +chr20 565232 200x6f2 C T 60 . QNAME=cluster19_000000F;QSTART=25196640;QSTRAND=- GT:DP:AD ./.:27:6,21 1|1:47:22,25 1|0:39:24,15 +chr20 565534 200x6f3 T A 60 . QNAME=cluster19_000000F;QSTART=25196338;QSTRAND=- GT:DP:AD ./.:23:18,5 1|1:23:15,8 1|1:25:5,20 +chr20 565902 200x6f4 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=545424;QSTRAND=+ GT:DP:AD 1|0:29:8,21 ./.:16:5,11 ./.:21:6,15 +chr20 565980 200x6f5 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=545502;QSTRAND=+ GT:DP:AD 1|1:30:24,6 ./.:26:6,20 ./.:33:9,24 +chr20 566018 200x6f6 C T 60 . QNAME=cluster23_scaffold_3;QSTART=25145195;QSTRAND=- GT:DP:AD ./.:21:5,16 ./.:31:21,10 1|0:44:24,20 +chr20 566096 200x6f7 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=545618;QSTRAND=+ GT:DP:AD 1|1:31:25,6 ./.:25:18,7 ./.:34:11,23 +chr20 566178 200x6f8 AAAAAAT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=545701;QSTRAND=+ GT:DP:AD 1|1:22:9,13 ./.:27:14,13 ./.:34:22,12 +chr20 567105 200x6f9 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=546621;QSTRAND=+ GT:DP:AD 1|0:35:15,20 ./.:32:24,8 ./.:23:17,6 +chr20 568286 200x6fa C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=522738;QSTRAND=+ GT:DP:AD 0|1:38:21,17 ./.:18:13,5 ./.:40:22,18 +chr20 568720 200x6fb C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=523172;QSTRAND=+ GT:DP:AD 0|1:35:14,21 ./.:34:17,17 ./.:24:17,7 +chr20 568936 200x6fc A T 60 . QNAME=cluster23_scaffold_3;QSTART=25142277;QSTRAND=- GT:DP:AD ./.:19:6,13 ./.:38:16,22 1|0:40:18,22 +chr20 569261 200x6fd C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=523713;QSTRAND=+ GT:DP:AD 0|1:32:13,19 ./.:36:18,18 ./.:28:17,11 +chr20 569263 200x6fe C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=548779;QSTRAND=+ GT:DP:AD 1|0:24:12,12 ./.:16:6,10 ./.:16:11,5 +chr20 569274 200x6ff G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=523726;QSTRAND=+ GT:DP:AD 0|1:32:21,11 ./.:40:21,19 ./.:35:16,19 +chr20 569446 200x700 T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=523898;QSTRAND=+ GT:DP:AD 0|1:28:6,22 1|0:31:23,8 ./.:31:8,23 +chr20 569520 200x701 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=523972;QSTRAND=+ GT:DP:AD 0|1:36:22,14 1|1:32:21,11 1|1:36:15,21 +chr20 569616 200x702 A C 60 . QNAME=cluster19_000000F;QSTART=25192256;QSTRAND=- GT:DP:AD ./.:25:15,10 1|1:42:24,18 1|1:28:7,21 +chr20 569956 200x703 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=524408;QSTRAND=+ GT:DP:AD 0|1:32:17,15 ./.:26:15,11 ./.:24:11,13 +chr20 570171 200x704 A C 60 . QNAME=cluster19_000000F;QSTART=25191701;QSTRAND=- GT:DP:AD ./.:36:24,12 1|1:15:5,10 1|1:23:11,12 +chr20 570174 200x705 T C 60 . QNAME=cluster19_000000F;QSTART=25191698;QSTRAND=- GT:DP:AD ./.:27:9,18 1|1:37:15,22 1|1:26:21,5 +chr20 570223 200x706 C CT 60 . QNAME=cluster19_000000F;QSTART=25191648;QSTRAND=- GT:DP:AD ./.:44:24,20 1|1:24:11,13 0|1:44:20,24 +chr20 570223 200x707 C CTT 60 . QNAME=cluster23_scaffold_3;QSTART=25140988;QSTRAND=- GT:DP:AD ./.:24:7,17 ./.:28:16,12 1|0:36:12,24 +chr20 570243 200x708 G A 60 . QNAME=cluster19_000000F;QSTART=25191628;QSTRAND=- GT:DP:AD ./.:28:17,11 1|1:41:22,19 1|1:37:19,18 +chr20 570390 200x709 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=524842;QSTRAND=+ GT:DP:AD 0|1:27:19,8 1|1:26:16,10 1|1:29:8,21 +chr20 570410 200x70a T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=524862;QSTRAND=+ GT:DP:AD 0|1:43:18,25 ./.:38:16,22 ./.:28:7,21 +chr20 570752 200x70b C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=525204;QSTRAND=+ GT:DP:AD 0|1:38:18,20 1|1:33:18,15 1|1:38:20,18 +chr20 571051 200x70c C CT 60 . QNAME=HG002-S9-H2-000001F;QSTART=525504;QSTRAND=+ GT:DP:AD 0|1:21:15,6 1|1:31:9,22 1|1:34:15,19 +chr20 571277 200x70d T C 60 . QNAME=cluster19_000000F;QSTART=25190593;QSTRAND=- GT:DP:AD ./.:21:13,8 1|1:19:14,5 1|1:34:23,11 +chr20 571843 200x70e G A 60 . QNAME=cluster19_000000F;QSTART=25190027;QSTRAND=- GT:DP:AD ./.:36:24,12 1|0:36:22,14 ./.:12:6,6 +chr20 571992 200x70f CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=551509;QSTRAND=+ GT:DP:AD 1|0:43:23,20 ./.:48:23,25 ./.:31:17,14 +chr20 573141 200x710 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=552656;QSTRAND=+ GT:DP:AD 1|0:43:21,22 ./.:44:25,19 ./.:29:11,18 +chr20 574599 200x711 C CT 60 . QNAME=cluster19_000000F;QSTART=25187270;QSTRAND=- GT:DP:AD ./.:25:12,13 1|0:29:14,15 ./.:29:19,10 +chr20 574632 200x712 G A 60 . QNAME=cluster19_000000F;QSTART=25187237;QSTRAND=- GT:DP:AD ./.:37:12,25 1|0:30:12,18 ./.:31:7,24 +chr20 574708 200x713 G A 60 . QNAME=cluster19_000000F;QSTART=25187161;QSTRAND=- GT:DP:AD ./.:24:7,17 1|1:38:16,22 ./.:43:19,24 +chr20 577333 200x714 G A 60 . QNAME=cluster19_000000F;QSTART=537532;QSTRAND=+ GT:DP:AD ./.:36:19,17 0|1:30:8,22 ./.:32:19,13 +chr20 577957 200x715 CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=557473;QSTRAND=+ GT:DP:AD 1|1:34:16,18 ./.:40:17,23 0|1:26:20,6 +chr20 577957 200x716 CAA C 60 . QNAME=cluster19_000000F;QSTART=25183912;QSTRAND=- GT:DP:AD ./.:23:7,16 1|1:22:15,7 ./.:34:20,14 +chr20 578654 200x717 T TAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=533107;QSTRAND=+ GT:DP:AD 0|1:31:14,17 ./.:32:23,9 1|1:25:8,17 +chr20 578654 200x718 TAC T 60 . QNAME=cluster19_000000F;QSTART=25183217;QSTRAND=- GT:DP:AD ./.:46:24,22 1|1:30:14,16 ./.:25:13,12 +chr20 578790 200x719 T C 60 . QNAME=cluster19_000000F;QSTART=25183083;QSTRAND=- GT:DP:AD ./.:31:15,16 1|1:32:8,24 ./.:28:22,6 +chr20 580481 200x71a T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=559995;QSTRAND=+ GT:DP:AD 1|1:32:16,16 1|1:36:12,24 0|1:42:24,18 +chr20 580899 200x71b A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=560413;QSTRAND=+ GT:DP:AD 1|0:35:17,18 1|1:25:8,17 ./.:31:20,11 +chr20 581272 200x71c A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=560786;QSTRAND=+ GT:DP:AD 1|0:22:9,13 1|0:28:13,15 ./.:33:14,19 +chr20 581577 200x71d A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=536031;QSTRAND=+ GT:DP:AD 0|1:46:22,24 ./.:40:24,16 ./.:35:21,14 +chr20 581670 200x71e G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=561184;QSTRAND=+ GT:DP:AD 1|1:20:11,9 1|1:36:18,18 ./.:18:5,13 +chr20 581801 200x71f C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=561315;QSTRAND=+ GT:DP:AD 1|1:27:17,10 1|1:28:17,11 1|0:26:9,17 +chr20 581995 200x720 GT G 60 . QNAME=HG002-S9-H2-000001F;QSTART=536450;QSTRAND=+ GT:DP:AD 0|1:29:7,22 ./.:17:6,11 1|1:29:16,13 +chr20 581995 200x721 GTTT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=561510;QSTRAND=+ GT:DP:AD 1|0:17:8,9 ./.:29:11,18 ./.:29:21,8 +chr20 581995 200x722 GTT G 60 . QNAME=cluster19_000000F;QSTART=25179878;QSTRAND=- GT:DP:AD ./.:29:9,20 1|1:29:7,22 ./.:45:23,22 +chr20 582041 200x723 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=536494;QSTRAND=+ GT:DP:AD 0|1:20:12,8 ./.:10:5,5 0|1:46:22,24 +chr20 582389 200x724 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=536842;QSTRAND=+ GT:DP:AD 0|1:38:20,18 ./.:20:10,10 0|1:28:11,17 +chr20 583353 200x725 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=562864;QSTRAND=+ GT:DP:AD 1|0:20:7,13 1|1:26:15,11 ./.:26:21,5 +chr20 583466 200x726 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=537919;QSTRAND=+ GT:DP:AD 0|1:29:14,15 ./.:40:18,22 0|1:39:21,18 +chr20 583895 200x727 G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=538348;QSTRAND=+ GT:DP:AD 0|1:29:9,20 ./.:31:14,17 0|1:36:20,16 +chr20 584249 200x728 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=563760;QSTRAND=+ GT:DP:AD 1|1:17:8,9 1|1:39:22,17 0|1:30:17,13 +chr20 584433 200x729 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=538886;QSTRAND=+ GT:DP:AD 0|1:37:22,15 ./.:19:10,9 0|1:22:6,16 +chr20 584664 200x72a T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=539117;QSTRAND=+ GT:DP:AD 0|1:45:23,22 ./.:33:21,12 0|1:38:19,19 +chr20 584861 200x72b C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=539314;QSTRAND=+ GT:DP:AD 0|1:23:5,18 ./.:30:11,19 0|1:16:9,7 +chr20 585289 200x72c G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=564800;QSTRAND=+ GT:DP:AD 1|1:42:21,21 1|1:21:9,12 0|1:24:13,11 +chr20 585341 200x72d T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=539794;QSTRAND=+ GT:DP:AD 0|1:42:17,25 ./.:11:6,5 0|1:33:14,19 +chr20 585726 200x72e A ATATATGTATATGTACG 60 . QNAME=HG002-S9-H2-000001F;QSTART=540180;QSTRAND=+ GT:DP:AD 0|1:17:11,6 ./.:35:12,23 0|1:15:9,6 +chr20 585739 200x72f C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=540208;QSTRAND=+ GT:DP:AD 0|1:28:16,12 ./.:34:20,14 0|1:27:12,15 +chr20 585749 200x730 T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=540218;QSTRAND=+ GT:DP:AD 0|1:24:18,6 ./.:22:5,17 0|1:38:17,21 +chr20 585766 200x731 GTA G 60 . QNAME=HG002-S9-H2-000001F;QSTART=540236;QSTRAND=+ GT:DP:AD 0|1:34:22,12 ./.:28:13,15 0|1:30:20,10 +chr20 586045 200x732 CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=540513;QSTRAND=+ GT:DP:AD 0|1:26:16,10 ./.:28:13,15 0|1:50:25,25 +chr20 586045 200x733 C CT 60 . QNAME=cluster19_000000F;QSTART=25175829;QSTRAND=- GT:DP:AD ./.:33:13,20 1|1:33:10,23 1|0:11:6,5 +chr20 586124 200x734 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=540590;QSTRAND=+ GT:DP:AD 0|1:30:17,13 ./.:32:18,14 0|1:20:7,13 +chr20 586280 200x735 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=565791;QSTRAND=+ GT:DP:AD 1|0:32:15,17 1|1:41:16,25 ./.:25:18,7 +chr20 586536 200x736 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=541002;QSTRAND=+ GT:DP:AD 0|1:31:8,23 ./.:19:8,11 0|1:38:21,17 +chr20 588052 200x737 G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=542518;QSTRAND=+ GT:DP:AD 0|1:32:7,25 ./.:39:15,24 0|1:15:7,8 +chr20 588077 200x738 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=542543;QSTRAND=+ GT:DP:AD 0|1:32:12,20 ./.:44:19,25 0|1:40:16,24 +chr20 588283 200x739 A ATT 60 . QNAME=HG002-S9-H2-000001F;QSTART=542750;QSTRAND=+ GT:DP:AD 0|1:33:24,9 ./.:24:15,9 0|1:25:7,18 +chr20 588283 200x73a A AT 60 . QNAME=cluster19_000000F;QSTART=25173590;QSTRAND=- GT:DP:AD ./.:28:11,17 1|1:44:20,24 ./.:39:17,22 +chr20 590301 200x73b AAC A 60 . QNAME=HG002-S9-H2-000001F;QSTART=544770;QSTRAND=+ GT:DP:AD 0|1:21:8,13 ./.:13:7,6 0|1:21:13,8 +chr20 590301 200x73c A AAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=569813;QSTRAND=+ GT:DP:AD 1|0:46:21,25 ./.:29:24,5 ./.:34:13,21 +chr20 590301 200x73d A AACAC 60 . QNAME=cluster19_000000F;QSTART=25171568;QSTRAND=- GT:DP:AD ./.:35:12,23 1|1:11:6,5 ./.:21:5,16 +chr20 590927 200x73e G C 60 . QNAME=cluster23_scaffold_2;QSTART=25104488;QSTRAND=- GT:DP:AD ./.:28:23,5 ./.:49:25,24 0|1:31:6,25 +chr20 591644 200x73f CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=546111;QSTRAND=+ GT:DP:AD 0|1:37:17,20 ./.:20:11,9 ./.:33:20,13 +chr20 592228 200x740 G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=546693;QSTRAND=+ GT:DP:AD 0|1:32:10,22 ./.:34:19,15 0|1:33:10,23 +chr20 592392 200x741 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=546857;QSTRAND=+ GT:DP:AD 0|1:27:6,21 ./.:14:6,8 0|1:23:7,16 +chr20 593097 200x742 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=547562;QSTRAND=+ GT:DP:AD 0|1:30:6,24 ./.:18:11,7 0|1:13:7,6 +chr20 593103 200x743 T TTA 60 . QNAME=cluster19_000000F;QSTART=25168764;QSTRAND=- GT:DP:AD ./.:20:6,14 1|0:20:12,8 ./.:34:16,18 +chr20 593121 200x744 A T 60 . QNAME=cluster23_scaffold_3;QSTART=25118087;QSTRAND=- GT:DP:AD ./.:20:8,12 ./.:36:13,23 1|0:31:16,15 +chr20 593121 200x745 A ATATATATTTTT 60 . QNAME=HG002-S9-H2-000001F;QSTART=547587;QSTRAND=+ GT:DP:AD 0|1:34:23,11 ./.:36:22,14 ./.:29:16,13 +chr20 593121 200x746 A ATATATTTTTTT 60 . QNAME=cluster23_scaffold_2;QSTART=25102283;QSTRAND=- GT:DP:AD ./.:13:6,7 ./.:47:22,25 0|1:38:16,22 +chr20 593122 200x747 T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=572636;QSTRAND=+ GT:DP:AD 1|0:31:18,13 0|1:34:22,12 ./.:40:16,24 +chr20 593123 200x748 T A 60 . QNAME=cluster19_000000F;QSTART=25168744;QSTRAND=- GT:DP:AD ./.:27:7,20 1|0:36:21,15 ./.:27:10,17 +chr20 593266 200x749 CTTTTTTT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=572781;QSTRAND=+ GT:DP:AD 1|0:29:24,5 1|1:27:5,22 ./.:46:25,21 +chr20 593638 200x74a A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=548114;QSTRAND=+ GT:DP:AD 0|1:39:18,21 ./.:30:24,6 0|1:21:14,7 +chr20 593664 200x74b G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=548140;QSTRAND=+ GT:DP:AD 0|1:26:9,17 ./.:29:9,20 0|1:11:6,5 +chr20 594618 200x74c CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=549095;QSTRAND=+ GT:DP:AD 0|1:34:25,9 ./.:33:9,24 ./.:25:19,6 +chr20 594618 200x74d C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25100785;QSTRAND=- GT:DP:AD ./.:30:9,21 ./.:24:15,9 0|1:25:8,17 +chr20 595396 200x74e CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=549872;QSTRAND=+ GT:DP:AD 0|1:25:20,5 ./.:43:24,19 ./.:27:22,5 +chr20 595643 200x74f T TTTA 60 . QNAME=HG002-S9-H1-000001F;QSTART=575151;QSTRAND=+ GT:DP:AD 1|0:19:6,13 1|1:30:19,11 ./.:46:22,24 +chr20 596470 200x750 G A 60 . QNAME=cluster23_scaffold_3;QSTART=25114738;QSTRAND=- GT:DP:AD ./.:31:9,22 ./.:43:25,18 1|0:36:13,23 +chr20 596536 200x751 G GAAAACA 60 . QNAME=cluster23_scaffold_3;QSTART=25114666;QSTRAND=- GT:DP:AD ./.:26:8,18 ./.:10:5,5 1|0:46:24,22 +chr20 596656 200x752 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=576166;QSTRAND=+ GT:DP:AD 1|0:30:22,8 1|1:40:15,25 ./.:38:14,24 +chr20 596715 200x753 C T 60 . QNAME=cluster19_000000F;QSTART=556911;QSTRAND=+ GT:DP:AD ./.:10:5,5 0|1:36:22,14 ./.:38:22,16 +chr20 597212 200x754 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=576722;QSTRAND=+ GT:DP:AD 1|0:33:24,9 1|1:24:17,7 ./.:32:8,24 +chr20 597374 200x755 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=576884;QSTRAND=+ GT:DP:AD 1|0:36:19,17 1|1:25:18,7 ./.:23:5,18 +chr20 597779 200x756 C T 60 . QNAME=cluster19_000000F;QSTART=557975;QSTRAND=+ GT:DP:AD ./.:47:22,25 0|1:42:22,20 ./.:29:6,23 +chr20 598186 200x757 G A 60 . QNAME=cluster23_scaffold_3;QSTART=25113016;QSTRAND=- GT:DP:AD ./.:21:14,7 ./.:36:15,21 1|0:17:7,10 +chr20 598263 200x758 C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=552737;QSTRAND=+ GT:DP:AD 0|1:28:22,6 ./.:17:6,11 0|1:24:10,14 +chr20 598702 200x759 C T 60 . QNAME=cluster23_scaffold_3;QSTART=25112500;QSTRAND=- GT:DP:AD ./.:30:7,23 ./.:15:6,9 1|0:24:15,9 +chr20 599013 200x75a A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=578523;QSTRAND=+ GT:DP:AD 1|0:26:14,12 1|1:30:14,16 1|1:30:19,11 +chr20 599169 200x75b AT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=553644;QSTRAND=+ GT:DP:AD 0|1:38:19,19 1|1:24:5,19 1|0:25:18,7 +chr20 599169 200x75c ATT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=578680;QSTRAND=+ GT:DP:AD 1|0:33:8,25 ./.:26:6,20 0|1:39:24,15 +chr20 599421 200x75d C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=578929;QSTRAND=+ GT:DP:AD 1|0:18:8,10 1|1:34:10,24 ./.:22:7,15 +chr20 600604 200x75e A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=580112;QSTRAND=+ GT:DP:AD 1|1:23:15,8 1|1:42:18,24 1|1:34:14,20 +chr20 600839 200x75f G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=580347;QSTRAND=+ GT:DP:AD 1|0:22:17,5 1|1:32:16,16 ./.:15:5,10 +chr20 600991 200x760 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=580499;QSTRAND=+ GT:DP:AD 1|0:44:19,25 1|1:33:14,19 ./.:18:13,5 +chr20 601642 200x761 G A 60 . QNAME=cluster19_000000F;QSTART=25160230;QSTRAND=- GT:DP:AD ./.:23:13,10 1|0:37:15,22 ./.:29:5,24 +chr20 601683 200x762 T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=581192;QSTRAND=+ GT:DP:AD 1|0:44:25,19 1|1:44:22,22 0|1:42:22,20 +chr20 601683 200x763 T TAA 60 . QNAME=cluster23_scaffold_3;QSTART=25109518;QSTRAND=- GT:DP:AD ./.:45:25,20 ./.:40:21,19 1|0:14:9,5 +chr20 601733 200x764 GC G 60 . QNAME=cluster23_scaffold_3;QSTART=25109468;QSTRAND=- GT:DP:AD ./.:24:6,18 ./.:40:25,15 1|1:20:5,15 +chr20 602460 200x765 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=581969;QSTRAND=+ GT:DP:AD 1|0:12:6,6 1|1:33:22,11 ./.:25:5,20 +chr20 602943 200x766 G A 60 . QNAME=cluster23_scaffold_3;QSTART=25108259;QSTRAND=- GT:DP:AD ./.:44:21,23 ./.:30:12,18 1|1:28:15,13 +chr20 606311 200x767 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=585820;QSTRAND=+ GT:DP:AD 1|1:28:13,15 1|1:42:25,17 1|1:23:13,10 +chr20 606780 200x768 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=586289;QSTRAND=+ GT:DP:AD 1|0:25:17,8 ./.:22:9,13 1|1:24:9,15 +chr20 607272 200x769 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=561745;QSTRAND=+ GT:DP:AD 0|1:38:17,21 ./.:14:5,9 ./.:28:10,18 +chr20 607445 200x76a A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=586954;QSTRAND=+ GT:DP:AD 1|1:37:18,19 ./.:31:25,6 1|1:37:19,18 +chr20 607522 200x76b G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=587031;QSTRAND=+ GT:DP:AD 1|0:37:13,24 ./.:40:17,23 1|1:15:5,10 +chr20 607633 200x76c C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=562106;QSTRAND=+ GT:DP:AD 0|1:39:14,25 ./.:29:17,12 ./.:29:22,7 +chr20 607790 200x76d A C 60 . QNAME=cluster19_000000F;QSTART=567986;QSTRAND=+ GT:DP:AD ./.:20:10,10 0|1:23:9,14 ./.:25:12,13 +chr20 608989 200x76e G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=588498;QSTRAND=+ GT:DP:AD 1|0:33:14,19 ./.:33:14,19 1|1:12:5,7 +chr20 609812 200x76f A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=589321;QSTRAND=+ GT:DP:AD 1|1:28:9,19 ./.:26:6,20 1|1:31:10,21 +chr20 609898 200x770 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=589407;QSTRAND=+ GT:DP:AD 1|1:16:11,5 1|1:28:17,11 1|1:39:25,14 +chr20 609899 200x771 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=589408;QSTRAND=+ GT:DP:AD 1|1:19:5,14 1|1:19:8,11 1|1:22:16,6 +chr20 610256 200x772 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=589765;QSTRAND=+ GT:DP:AD 1|1:20:7,13 ./.:38:15,23 1|1:28:6,22 +chr20 610966 200x773 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=590475;QSTRAND=+ GT:DP:AD 1|0:29:20,9 ./.:35:23,12 1|1:18:13,5 +chr20 611394 200x774 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=590903;QSTRAND=+ GT:DP:AD 1|1:42:23,19 ./.:25:13,12 1|1:32:15,17 +chr20 611826 200x775 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=566299;QSTRAND=+ GT:DP:AD 0|1:45:20,25 ./.:31:23,8 ./.:37:17,20 +chr20 611881 200x776 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=591390;QSTRAND=+ GT:DP:AD 1|1:13:6,7 ./.:39:20,19 1|1:35:17,18 +chr20 612157 200x777 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=591666;QSTRAND=+ GT:DP:AD 1|1:24:8,16 ./.:22:6,16 1|1:32:19,13 +chr20 612432 200x778 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=591941;QSTRAND=+ GT:DP:AD 1|1:41:21,20 ./.:27:22,5 1|1:25:20,5 +chr20 612561 200x779 AG A 60 . QNAME=cluster19_000000F;QSTART=25149310;QSTRAND=- GT:DP:AD ./.:33:17,16 1|0:18:13,5 ./.:27:18,9 +chr20 612664 200x77a T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=592173;QSTRAND=+ GT:DP:AD 1|1:31:23,8 ./.:25:19,6 1|1:40:18,22 +chr20 612674 200x77b A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=592183;QSTRAND=+ GT:DP:AD 1|0:20:12,8 ./.:21:12,9 1|1:29:19,10 +chr20 613783 200x77c TGTGTGCTGAGTCCAGCTCAAGTCCCTTGGTTCCCACTGCTGCTAAGCATGCACG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=593293;QSTRAND=+;SVTYPE=DEL;SVLEN=-54 GT:DP:AD 1/1:46:24,22 1/0:29:14,15 1/1:43:19,24 +chr20 614136 200x77d T C 60 . QNAME=cluster19_000000F;QSTART=574332;QSTRAND=+ GT:DP:AD ./.:33:9,24 0|1:39:15,24 ./.:35:23,12 +chr20 614408 200x77e C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=568827;QSTRAND=+ GT:DP:AD 0|1:31:6,25 ./.:27:10,17 ./.:39:18,21 +chr20 614449 200x77f ATCTC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=593905;QSTRAND=+ GT:DP:AD 1|0:30:5,25 ./.:22:8,14 1|1:43:22,21 +chr20 614473 200x780 C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=593924;QSTRAND=+ GT:DP:AD 1|0:18:8,10 ./.:15:5,10 ./.:33:10,23 +chr20 614475 200x781 A C 60 . QNAME=cluster19_000000F;QSTART=574671;QSTRAND=+ GT:DP:AD ./.:16:11,5 0|1:45:21,24 ./.:28:15,13 +chr20 614477 200x782 A C 60 . QNAME=cluster19_000000F;QSTART=574673;QSTRAND=+ GT:DP:AD ./.:25:8,17 0|1:40:17,23 ./.:25:9,16 +chr20 614492 200x783 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=593943;QSTRAND=+ GT:DP:AD 1|0:34:16,18 ./.:47:25,22 1|1:22:15,7 +chr20 614492 200x784 T TAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=568912;QSTRAND=+ GT:DP:AD 0|1:18:10,8 ./.:18:5,13 ./.:29:16,13 +chr20 614494 200x785 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=593945;QSTRAND=+ GT:DP:AD 1|0:29:14,15 ./.:30:16,14 1|1:42:19,23 +chr20 614496 200x786 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=568917;QSTRAND=+ GT:DP:AD 0|1:22:7,15 ./.:16:7,9 ./.:30:23,7 +chr20 614517 200x787 G GTA 60 . QNAME=cluster23_scaffold_3;QSTART=25096741;QSTRAND=- GT:DP:AD ./.:27:12,15 ./.:35:17,18 1|1:41:22,19 +chr20 614555 200x788 A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=594006;QSTRAND=+ GT:DP:AD 1|0:38:23,15 ./.:19:6,13 1|1:23:9,14 +chr20 614561 200x789 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=594012;QSTRAND=+ GT:DP:AD 1|0:44:24,20 ./.:36:21,15 1|1:20:6,14 +chr20 614710 200x78a A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=594161;QSTRAND=+ GT:DP:AD 1|0:45:25,20 ./.:34:18,16 1|1:15:6,9 +chr20 615045 200x78b G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=569466;QSTRAND=+ GT:DP:AD 0|1:39:19,20 ./.:23:5,18 ./.:25:18,7 +chr20 615409 200x78c C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=594860;QSTRAND=+ GT:DP:AD 1|0:18:5,13 ./.:28:6,22 1|1:28:7,21 +chr20 615455 200x78d C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=569876;QSTRAND=+ GT:DP:AD 0|1:31:6,25 ./.:31:13,18 ./.:33:24,9 +chr20 615471 200x78e T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=594922;QSTRAND=+ GT:DP:AD 1|1:16:7,9 ./.:32:7,25 1|1:27:17,10 +chr20 615863 200x78f G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=570284;QSTRAND=+ GT:DP:AD 0|1:29:14,15 ./.:26:20,6 ./.:50:25,25 +chr20 616031 200x790 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=570452;QSTRAND=+ GT:DP:AD 0|1:32:16,16 ./.:44:20,24 ./.:35:19,16 +chr20 616321 200x791 G GT 60 . QNAME=HG002-S9-H1-000001F;QSTART=595773;QSTRAND=+ GT:DP:AD 1|0:26:16,10 ./.:41:20,21 1|1:17:11,6 +chr20 616321 200x792 G GTT 60 . QNAME=HG002-S9-H2-000001F;QSTART=570743;QSTRAND=+ GT:DP:AD 0|1:40:18,22 ./.:34:11,23 ./.:31:23,8 +chr20 616559 200x793 T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=570982;QSTRAND=+ GT:DP:AD 0|1:28:17,11 ./.:36:11,25 ./.:34:24,10 +chr20 616743 200x794 C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=571166;QSTRAND=+ GT:DP:AD 0|1:28:22,6 ./.:35:14,21 ./.:30:5,25 +chr20 617022 200x795 T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=571445;QSTRAND=+ GT:DP:AD 0|1:24:9,15 ./.:31:21,10 ./.:23:10,13 +chr20 617094 200x796 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=596546;QSTRAND=+ GT:DP:AD 1|1:35:14,21 ./.:33:18,15 1|1:25:11,14 +chr20 617427 200x797 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=571850;QSTRAND=+ GT:DP:AD 0|1:34:11,23 ./.:26:6,20 ./.:10:5,5 +chr20 617634 200x798 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=597086;QSTRAND=+ GT:DP:AD 1|0:34:18,16 ./.:37:22,15 1|1:11:5,6 +chr20 617892 200x799 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=597344;QSTRAND=+ GT:DP:AD 1|1:25:13,12 ./.:22:16,6 1|1:27:8,19 +chr20 618050 200x79a C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=597502;QSTRAND=+ GT:DP:AD 1|0:38:21,17 ./.:32:19,13 1|1:35:15,20 +chr20 618051 200x79b G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=572474;QSTRAND=+ GT:DP:AD 0|1:42:20,22 ./.:20:10,10 ./.:39:18,21 +chr20 619223 200x79c C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=573646;QSTRAND=+ GT:DP:AD 0|1:23:13,10 ./.:36:16,20 ./.:43:23,20 +chr20 620320 200x79d C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=599772;QSTRAND=+ GT:DP:AD 1|1:46:24,22 ./.:32:9,23 1|1:33:20,13 +chr20 620391 200x79e C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=599843;QSTRAND=+ GT:DP:AD 1|1:40:24,16 ./.:26:13,13 1|1:31:15,16 +chr20 621742 200x79f A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=576165;QSTRAND=+ GT:DP:AD 0|1:38:25,13 ./.:41:22,19 ./.:29:10,19 +chr20 622380 200x7a0 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=601832;QSTRAND=+ GT:DP:AD 1|0:41:25,16 ./.:29:8,21 1|1:38:21,17 +chr20 622562 200x7a1 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=576985;QSTRAND=+ GT:DP:AD 0|1:26:5,21 ./.:10:5,5 ./.:26:8,18 +chr20 622615 200x7a2 C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=602067;QSTRAND=+ GT:DP:AD 1|1:38:23,15 ./.:28:11,17 1|1:36:17,19 +chr20 622976 200x7a3 G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=577399;QSTRAND=+ GT:DP:AD 0|1:25:18,7 ./.:11:5,6 0|1:23:13,10 +chr20 624131 200x7a4 G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=578554;QSTRAND=+ GT:DP:AD 0|1:17:5,12 ./.:34:24,10 ./.:35:11,24 +chr20 624618 200x7a5 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=579041;QSTRAND=+ GT:DP:AD 0|1:31:23,8 ./.:37:14,23 ./.:41:16,25 +chr20 624679 200x7a6 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=604131;QSTRAND=+ GT:DP:AD 1|1:44:21,23 ./.:25:16,9 1|1:31:9,22 +chr20 625245 200x7a7 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=604697;QSTRAND=+ GT:DP:AD 1|0:39:19,20 ./.:30:16,14 1|1:44:24,20 +chr20 625293 200x7a8 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=604745;QSTRAND=+ GT:DP:AD 1|1:28:12,16 ./.:34:25,9 1|1:29:5,24 +chr20 626070 200x7a9 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=580493;QSTRAND=+ GT:DP:AD 0|1:18:10,8 1|1:36:12,24 ./.:38:20,18 +chr20 626301 200x7aa T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=605753;QSTRAND=+ GT:DP:AD 1|0:29:23,6 ./.:41:25,16 1|1:20:6,14 +chr20 626305 200x7ab G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=605757;QSTRAND=+ GT:DP:AD 1|0:43:22,21 ./.:25:7,18 1|1:28:5,23 +chr20 626441 200x7ac G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=605893;QSTRAND=+ GT:DP:AD 1|0:36:20,16 ./.:34:13,21 1|1:22:10,12 +chr20 626569 200x7ad G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=580992;QSTRAND=+ GT:DP:AD 0|1:34:23,11 ./.:37:16,21 ./.:32:23,9 +chr20 626821 200x7ae A AC 60 . QNAME=HG002-S9-H1-000001F;QSTART=606274;QSTRAND=+ GT:DP:AD 1|0:31:13,18 ./.:33:20,13 1|0:17:12,5 +chr20 626950 200x7af C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=606403;QSTRAND=+ GT:DP:AD 1|0:34:19,15 ./.:44:20,24 1|0:36:13,23 +chr20 627161 200x7b0 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=606614;QSTRAND=+ GT:DP:AD 1|0:24:17,7 ./.:33:14,19 1|1:29:18,11 +chr20 627348 200x7b1 A G 60 . QNAME=cluster19_000000F;QSTART=25134578;QSTRAND=- GT:DP:AD ./.:28:14,14 1|0:31:9,22 ./.:29:17,12 +chr20 628116 200x7b2 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=607569;QSTRAND=+ GT:DP:AD 1|0:32:25,7 ./.:19:7,12 1|0:31:6,25 +chr20 628203 200x7b3 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=607656;QSTRAND=+ GT:DP:AD 1|1:43:19,24 ./.:33:14,19 1|1:43:25,18 +chr20 628339 200x7b4 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=607792;QSTRAND=+ GT:DP:AD 1|1:30:24,6 ./.:40:22,18 1|1:37:22,15 +chr20 628481 200x7b5 G C 60 . QNAME=cluster23_scaffold_2;QSTART=25066979;QSTRAND=- GT:DP:AD ./.:30:16,14 ./.:37:19,18 0|1:41:25,16 +chr20 628698 200x7b6 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=608151;QSTRAND=+ GT:DP:AD 1|0:26:12,14 ./.:31:15,16 1|0:41:17,24 +chr20 628723 200x7b7 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=608176;QSTRAND=+ GT:DP:AD 1|0:10:5,5 ./.:35:19,16 1|0:25:17,8 +chr20 628961 200x7b8 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=608414;QSTRAND=+ GT:DP:AD 1|0:26:11,15 ./.:31:18,13 1|1:17:11,6 +chr20 629302 200x7b9 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=608755;QSTRAND=+ GT:DP:AD 1|0:25:17,8 ./.:38:15,23 1|1:26:11,15 +chr20 629494 200x7ba G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=608947;QSTRAND=+ GT:DP:AD 1|0:25:19,6 ./.:27:19,8 ./.:32:16,16 +chr20 629610 200x7bb A G 60 . QNAME=cluster23_scaffold_2;QSTART=25065850;QSTRAND=- GT:DP:AD ./.:19:8,11 ./.:32:25,7 0|1:31:15,16 +chr20 629678 200x7bc T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=609131;QSTRAND=+ GT:DP:AD 1|0:36:20,16 ./.:23:5,18 1|1:42:19,23 +chr20 629911 200x7bd C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=609364;QSTRAND=+ GT:DP:AD 1|0:31:11,20 ./.:30:14,16 1|1:27:18,9 +chr20 629941 200x7be A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=609394;QSTRAND=+ GT:DP:AD 1|0:34:13,21 ./.:27:15,12 1|1:21:15,6 +chr20 630017 200x7bf T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=609470;QSTRAND=+ GT:DP:AD 1|0:36:12,24 ./.:13:7,6 1|1:32:10,22 +chr20 630420 200x7c0 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=609873;QSTRAND=+ GT:DP:AD 1|0:17:11,6 ./.:37:14,23 ./.:27:21,6 +chr20 630592 200x7c1 CAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=610046;QSTRAND=+ GT:DP:AD 1|0:24:15,9 ./.:24:17,7 1|0:31:6,25 +chr20 630592 200x7c2 CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=585016;QSTRAND=+ GT:DP:AD 0|1:47:22,25 ./.:26:10,16 0|1:45:22,23 +chr20 630708 200x7c3 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=610158;QSTRAND=+ GT:DP:AD 1|0:21:6,15 ./.:25:14,11 1|1:20:5,15 +chr20 631945 200x7c4 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=611395;QSTRAND=+ GT:DP:AD 1|0:40:25,15 ./.:43:19,24 ./.:28:8,20 +chr20 632007 200x7c5 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=611457;QSTRAND=+ GT:DP:AD 1|0:17:6,11 ./.:36:25,11 ./.:23:18,5 +chr20 632024 200x7c6 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=611474;QSTRAND=+ GT:DP:AD 1|0:21:14,7 ./.:23:15,8 ./.:33:11,22 +chr20 632038 200x7c7 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=611488;QSTRAND=+ GT:DP:AD 1|0:24:7,17 ./.:28:8,20 ./.:35:17,18 +chr20 632119 200x7c8 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=611569;QSTRAND=+ GT:DP:AD 1|0:37:19,18 ./.:33:25,8 ./.:31:15,16 +chr20 633319 200x7c9 A G 60 . QNAME=cluster19_000000F;QSTART=25128607;QSTRAND=- GT:DP:AD ./.:24:12,12 1|0:26:14,12 0|1:17:9,8 +chr20 633850 200x7ca T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=613300;QSTRAND=+ GT:DP:AD 1|0:38:13,25 ./.:32:14,18 ./.:17:10,7 +chr20 634306 200x7cb G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=613756;QSTRAND=+ GT:DP:AD 1|0:23:16,7 ./.:33:22,11 ./.:37:13,24 +chr20 634343 200x7cc C T 60 . QNAME=cluster19_000000F;QSTART=25127583;QSTRAND=- GT:DP:AD ./.:24:6,18 1|0:26:16,10 0|1:27:21,6 +chr20 634367 200x7cd T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=613817;QSTRAND=+ GT:DP:AD 1|0:40:15,25 1|0:36:11,25 0|1:35:25,10 +chr20 634490 200x7ce G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=613940;QSTRAND=+ GT:DP:AD 1|0:46:24,22 ./.:44:19,25 ./.:23:18,5 +chr20 634534 200x7cf G A 60 . QNAME=cluster19_000000F;QSTART=25127392;QSTRAND=- GT:DP:AD ./.:25:12,13 1|0:31:15,16 0|1:28:15,13 +chr20 634915 200x7d0 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=614365;QSTRAND=+ GT:DP:AD 1|0:19:9,10 ./.:25:10,15 ./.:30:23,7 +chr20 637164 200x7d1 T C 60 . QNAME=cluster19_000000F;QSTART=25124762;QSTRAND=- GT:DP:AD ./.:13:8,5 1|0:45:22,23 ./.:23:12,11 +chr20 637615 200x7d2 T C 60 . QNAME=cluster19_000000F;QSTART=25124311;QSTRAND=- GT:DP:AD ./.:46:24,22 1|0:27:5,22 ./.:31:19,12 +chr20 638468 200x7d3 TA T 60 . QNAME=cluster19_000000F;QSTART=25123458;QSTRAND=- GT:DP:AD ./.:27:12,15 1|0:35:19,16 ./.:28:9,19 +chr20 638468 200x7d4 T TA 60 . QNAME=cluster23_scaffold_3;QSTART=25072790;QSTRAND=- GT:DP:AD ./.:32:14,18 ./.:35:13,22 1|1:21:5,16 +chr20 638748 200x7d5 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=618198;QSTRAND=+ GT:DP:AD 1|0:26:20,6 1|0:23:10,13 ./.:39:16,23 +chr20 638918 200x7d6 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=618368;QSTRAND=+ GT:DP:AD 1|0:31:11,20 ./.:34:15,19 ./.:16:8,8 +chr20 639104 200x7d7 A AT 60 . QNAME=HG002-S9-H1-000001F;QSTART=618555;QSTRAND=+ GT:DP:AD 1|0:35:12,23 ./.:18:9,9 1|1:35:18,17 +chr20 639255 200x7d8 T C 60 . QNAME=cluster19_000000F;QSTART=25122672;QSTRAND=- GT:DP:AD ./.:39:24,15 1|0:33:16,17 ./.:15:9,6 +chr20 639552 200x7d9 T C 60 . QNAME=cluster19_000000F;QSTART=25122375;QSTRAND=- GT:DP:AD ./.:10:5,5 1|0:28:22,6 0|1:33:13,20 +chr20 639866 200x7da A G 60 . QNAME=cluster23_scaffold_2;QSTART=25055593;QSTRAND=- GT:DP:AD ./.:40:25,15 ./.:22:6,16 0|1:16:5,11 +chr20 640046 200x7db C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=619497;QSTRAND=+ GT:DP:AD 1|0:10:5,5 ./.:33:15,18 ./.:32:22,10 +chr20 640049 200x7dc C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=619500;QSTRAND=+ GT:DP:AD 1|1:28:12,16 ./.:29:5,24 1|0:31:19,12 +chr20 640284 200x7dd T TC 60 . QNAME=cluster23_scaffold_2;QSTART=25055174;QSTRAND=- GT:DP:AD ./.:19:8,11 ./.:48:23,25 0|1:34:25,9 +chr20 641878 200x7de C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621329;QSTRAND=+ GT:DP:AD 1|0:17:11,6 ./.:15:9,6 0|1:33:12,21 +chr20 641905 200x7df T TG 60 . QNAME=cluster23_scaffold_3;QSTART=25069351;QSTRAND=- GT:DP:AD ./.:29:5,24 ./.:18:8,10 1|0:18:7,11 +chr20 641906 200x7e0 G GGCGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCT 60 . QNAME=cluster23_scaffold_2;QSTART=25053389;QSTRAND=-;SVTYPE=INS;SVLEN=163 GT:DP:AD ./.:13:6,7 ./.:34:21,13 0/1:27:16,11 +chr20 641913 200x7e1 G GGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGA 60 . QNAME=HG002-S9-H1-000001F;QSTART=621365;QSTRAND=+;SVTYPE=INS;SVLEN=66 GT:DP:AD 1/0:34:18,16 ./.:32:17,15 ./.:36:16,20 +chr20 641930 200x7e2 A G 60 . QNAME=cluster23_scaffold_2;QSTART=25053365;QSTRAND=- GT:DP:AD ./.:33:16,17 ./.:15:6,9 0|1:27:13,14 +chr20 641944 200x7e3 GGA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621462;QSTRAND=+ GT:DP:AD 1|0:30:16,14 ./.:47:25,22 ./.:32:13,19 +chr20 641970 200x7e4 T TG 60 . QNAME=cluster23_scaffold_2;QSTART=25053324;QSTRAND=- GT:DP:AD ./.:30:14,16 ./.:26:16,10 0|1:31:12,19 +chr20 641977 200x7e5 G T 60 . QNAME=cluster19_000000F;QSTART=25119950;QSTRAND=- GT:DP:AD ./.:34:16,18 1|0:24:7,17 ./.:28:20,8 +chr20 642012 200x7e6 GGT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621528;QSTRAND=+ GT:DP:AD 1|0:20:10,10 ./.:35:18,17 ./.:33:16,17 +chr20 642037 200x7e7 T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=621551;QSTRAND=+ GT:DP:AD 1|0:41:18,23 ./.:44:19,25 ./.:35:18,17 +chr20 642067 200x7e8 T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=621582;QSTRAND=+ GT:DP:AD 1|0:25:9,16 ./.:38:22,16 ./.:27:21,6 +chr20 642068 200x7e9 G GTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCC 60 . QNAME=cluster23_scaffold_2;QSTART=25053097;QSTRAND=-;SVTYPE=INS;SVLEN=129 GT:DP:AD ./.:34:24,10 ./.:30:19,11 0/1:18:11,7 +chr20 642069 200x7ea T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621584;QSTRAND=+ GT:DP:AD 1|0:33:20,13 ./.:15:10,5 ./.:27:19,8 +chr20 642076 200x7eb A G 60 . QNAME=cluster23_scaffold_2;QSTART=25053089;QSTRAND=- GT:DP:AD ./.:31:22,9 ./.:36:21,15 0|1:29:21,8 +chr20 642100 200x7ec T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=621616;QSTRAND=+ GT:DP:AD 1|0:30:22,8 ./.:39:21,18 ./.:45:25,20 +chr20 642123 200x7ed G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=621639;QSTRAND=+ GT:DP:AD 1|0:46:23,23 ./.:21:6,15 0|1:42:20,22 +chr20 642130 200x7ee T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=621647;QSTRAND=+ GT:DP:AD 1|0:34:15,19 ./.:16:8,8 ./.:23:8,15 +chr20 642132 200x7ef G T 60 . QNAME=cluster23_scaffold_2;QSTART=25053033;QSTRAND=- GT:DP:AD ./.:13:6,7 ./.:30:7,23 0|1:35:13,22 +chr20 642171 200x7f0 GGA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621689;QSTRAND=+ GT:DP:AD 1|0:43:23,20 ./.:40:20,20 0|1:40:18,22 +chr20 642205 200x7f1 GGT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621721;QSTRAND=+ GT:DP:AD 1|0:33:11,22 ./.:22:5,17 0|1:30:12,18 +chr20 642207 200x7f2 T TGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGG 60 . QNAME=HG002-S9-H2-000001F;QSTART=596630;QSTRAND=+;SVTYPE=INS;SVLEN=501 GT:DP:AD 0/1:27:12,15 ./.:20:10,10 ./.:22:17,5 +chr20 642207 200x7f3 T TGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGG 60 . QNAME=cluster19_000000F;QSTART=602404;QSTRAND=+;SVTYPE=INS;SVLEN=630 GT:DP:AD ./.:28:16,12 0/1:27:13,14 ./.:24:18,6 +chr20 642230 200x7f4 T TGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTG 60 . QNAME=cluster19_000000F;QSTART=25119065;QSTRAND=-;SVTYPE=INS;SVLEN=632 GT:DP:AD ./.:35:18,17 1/0:33:10,23 ./.:44:25,19 +chr20 642230 200x7f5 T TG 60 . QNAME=cluster23_scaffold_3;QSTART=25069025;QSTRAND=- GT:DP:AD ./.:25:9,16 ./.:21:6,15 1|1:42:23,19 +chr20 642259 200x7f6 CTG C 60 . QNAME=HG002-S9-H1-000001F;QSTART=621773;QSTRAND=+ GT:DP:AD 1|0:19:6,13 ./.:30:7,23 ./.:16:7,9 +chr20 642261 200x7f7 GTGGT G 60 . QNAME=cluster23_scaffold_3;QSTART=25068994;QSTRAND=- GT:DP:AD ./.:34:17,17 ./.:27:20,7 1|0:46:25,21 +chr20 642265 200x7f8 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621776;QSTRAND=+ GT:DP:AD 1|1:37:12,25 0|1:27:9,18 ./.:36:22,14 +chr20 642271 200x7f9 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=621782;QSTRAND=+ GT:DP:AD 1|0:34:25,9 ./.:27:11,16 ./.:40:24,16 +chr20 642271 200x7fa G GC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597195;QSTRAND=+ GT:DP:AD 0|1:17:6,11 1|1:22:17,5 0|1:22:17,5 +chr20 642271 200x7fb G GGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGC 60 . QNAME=cluster23_scaffold_3;QSTART=25068731;QSTRAND=-;SVTYPE=INS;SVLEN=257 GT:DP:AD ./.:36:19,17 ./.:28:5,23 1/0:27:18,9 +chr20 642277 200x7fc G A 60 . QNAME=cluster19_000000F;QSTART=603104;QSTRAND=+ GT:DP:AD ./.:25:6,19 0|1:46:25,21 ./.:25:18,7 +chr20 642284 200x7fd A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621795;QSTRAND=+ GT:DP:AD 1|1:16:5,11 1|1:24:8,16 1|1:25:16,9 +chr20 642300 200x7fe G GGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597225;QSTRAND=+ GT:DP:AD 0|1:27:11,16 0|1:40:18,22 1|1:15:6,9 +chr20 642300 200x7ff G GCCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGC 60 . QNAME=HG002-S9-H1-000001F;QSTART=621812;QSTRAND=+;SVTYPE=INS;SVLEN=408 GT:DP:AD 1/0:44:19,25 ./.:35:12,23 ./.:42:17,25 +chr20 642300 200x800 G GC 60 . QNAME=cluster19_000000F;QSTART=25118993;QSTRAND=- GT:DP:AD ./.:31:7,24 1|0:45:25,20 ./.:37:25,12 +chr20 642330 200x801 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=622249;QSTRAND=+ GT:DP:AD 1|0:34:14,20 ./.:33:15,18 1|0:21:13,8 +chr20 642330 200x802 G GGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597257;QSTRAND=+;SVTYPE=INS;SVLEN=66 GT:DP:AD 0/1:18:11,7 ./.:23:10,13 ./.:25:12,13 +chr20 642330 200x803 G GC 60 . QNAME=cluster19_000000F;QSTART=25118962;QSTRAND=- GT:DP:AD ./.:30:14,16 1|1:45:20,25 ./.:24:18,6 +chr20 642330 200x804 G GCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGGGC 60 . QNAME=cluster23_scaffold_2;QSTART=25052609;QSTRAND=-;SVTYPE=INS;SVLEN=226 GT:DP:AD ./.:41:21,20 ./.:28:9,19 0/1:18:12,6 +chr20 642353 200x805 T G 60 . QNAME=cluster23_scaffold_2;QSTART=25052586;QSTRAND=- GT:DP:AD ./.:23:15,8 ./.:16:6,10 0|1:24:17,7 +chr20 642362 200x806 G C 60 . QNAME=cluster23_scaffold_2;QSTART=25052577;QSTRAND=- GT:DP:AD ./.:48:24,24 ./.:26:12,14 0|1:12:7,5 +chr20 642362 200x807 G GC 60 . QNAME=HG002-S9-H1-000001F;QSTART=622282;QSTRAND=+ GT:DP:AD 1|1:25:14,11 1|1:32:16,16 1|0:30:7,23 +chr20 642391 200x808 G GC 60 . QNAME=HG002-S9-H1-000001F;QSTART=622312;QSTRAND=+ GT:DP:AD 1|1:27:9,18 1|1:16:9,7 0|1:20:15,5 +chr20 642391 200x809 G GGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGGC 60 . QNAME=cluster23_scaffold_3;QSTART=25068286;QSTRAND=-;SVTYPE=INS;SVLEN=322 GT:DP:AD ./.:21:9,12 ./.:41:25,16 1/0:14:6,8 +chr20 642420 200x80a G GC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597415;QSTRAND=+ GT:DP:AD 0|1:14:9,5 1|1:39:25,14 1|0:28:11,17 +chr20 642420 200x80b G GGC 60 . QNAME=HG002-S9-H1-000001F;QSTART=622342;QSTRAND=+ GT:DP:AD 1|0:36:19,17 ./.:30:25,5 ./.:34:25,9 +chr20 642420 200x80c G GGGC 60 . QNAME=cluster23_scaffold_2;QSTART=25052515;QSTRAND=- GT:DP:AD ./.:30:22,8 ./.:36:25,11 0|1:39:16,23 +chr20 642746 200x80d C CGGGGTGCGGGT 60 . QNAME=cluster19_000000F;QSTART=603580;QSTRAND=+ GT:DP:AD ./.:43:22,21 0|1:42:23,19 ./.:20:13,7 +chr20 642746 200x80e C CGGGGGTGCGGGT 60 . QNAME=cluster23_scaffold_2;QSTART=25052177;QSTRAND=- GT:DP:AD ./.:24:12,12 ./.:23:6,17 0|1:23:11,12 +chr20 642861 200x80f G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=622784;QSTRAND=+ GT:DP:AD 1|0:50:25,25 ./.:32:14,18 ./.:33:22,11 +chr20 642893 200x810 GTGA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=622817;QSTRAND=+ GT:DP:AD 1|0:18:8,10 ./.:40:15,25 ./.:39:22,17 +chr20 643742 200x811 G A 60 . QNAME=cluster23_scaffold_2;QSTART=25051181;QSTRAND=- GT:DP:AD ./.:45:22,23 ./.:40:19,21 0|1:32:8,24 +chr20 643827 200x812 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=623747;QSTRAND=+ GT:DP:AD 1|0:30:24,6 ./.:47:23,24 ./.:38:15,23 +chr20 644129 200x813 T A 60 . QNAME=cluster23_scaffold_2;QSTART=25050794;QSTRAND=- GT:DP:AD ./.:16:7,9 ./.:22:14,8 0|1:27:14,13 +chr20 644264 200x814 TA T 60 . QNAME=cluster23_scaffold_2;QSTART=25050659;QSTRAND=- GT:DP:AD ./.:40:21,19 ./.:24:16,8 0|1:26:18,8 +chr20 644423 200x815 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=624343;QSTRAND=+ GT:DP:AD 1|0:33:20,13 ./.:30:25,5 ./.:37:12,25 +chr20 644731 200x816 T TA 60 . QNAME=cluster23_scaffold_2;QSTART=25050192;QSTRAND=- GT:DP:AD ./.:25:13,12 ./.:27:18,9 0|1:26:20,6 +chr20 645244 200x817 C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25049678;QSTRAND=- GT:DP:AD ./.:22:9,13 ./.:27:7,20 0|1:30:25,5 +chr20 645246 200x818 A AT 60 . QNAME=HG002-S9-H1-000001F;QSTART=625167;QSTRAND=+ GT:DP:AD 1|0:41:19,22 ./.:36:22,14 ./.:26:6,20 +chr20 645378 200x819 A AG 60 . QNAME=HG002-S9-H1-000001F;QSTART=625300;QSTRAND=+ GT:DP:AD 1|1:23:13,10 ./.:36:17,19 1|1:13:8,5 +chr20 645437 200x81a G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=625359;QSTRAND=+ GT:DP:AD 1|0:26:12,14 ./.:18:8,10 1|0:12:7,5 +chr20 645520 200x81b T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=625442;QSTRAND=+ GT:DP:AD 1|1:27:18,9 ./.:23:14,9 1|0:36:19,17 +chr20 645645 200x81c G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=625567;QSTRAND=+ GT:DP:AD 1|0:15:9,6 ./.:31:20,11 ./.:33:18,15 +chr20 646133 200x81d T TCTA 60 . QNAME=HG002-S9-H1-000001F;QSTART=626056;QSTRAND=+ GT:DP:AD 1|1:33:11,22 ./.:35:10,25 1|1:43:21,22 +chr20 646134 200x81e T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=626059;QSTRAND=+ GT:DP:AD 1|1:25:13,12 ./.:18:9,9 1|1:22:15,7 +chr20 646331 200x81f G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=626256;QSTRAND=+ GT:DP:AD 1|0:20:8,12 ./.:33:14,19 1|0:44:24,20 +chr20 646515 200x820 C CAAAAAAAAAAAAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=626441;QSTRAND=+ GT:DP:AD 1|0:34:24,10 ./.:40:21,19 ./.:31:20,11 +chr20 646515 200x821 C CAAAAAAAAAAAAAAAA 60 . QNAME=HG002-S9-H2-000001F;QSTART=601515;QSTRAND=+ GT:DP:AD 0|1:30:16,14 ./.:34:14,20 ./.:32:10,22 +chr20 646515 200x822 C CA 60 . QNAME=cluster19_000000F;QSTART=25114773;QSTRAND=- GT:DP:AD ./.:33:21,12 1|0:16:6,10 ./.:35:18,17 +chr20 646515 200x823 C CAAAAAAAAAAAAAAAAAA 60 . QNAME=cluster23_scaffold_3;QSTART=25064139;QSTRAND=- GT:DP:AD ./.:34:14,20 ./.:44:21,23 1|1:31:12,19 +chr20 646526 200x824 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=626468;QSTRAND=+ GT:DP:AD 1|0:30:11,19 ./.:31:6,25 1|0:21:10,11 +chr20 646614 200x825 CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=601630;QSTRAND=+ GT:DP:AD 0|1:10:5,5 ./.:17:7,10 ./.:36:23,13 +chr20 646770 200x826 A G 60 . QNAME=cluster23_scaffold_2;QSTART=25048130;QSTRAND=- GT:DP:AD ./.:29:6,23 ./.:36:18,18 0|1:25:9,16 +chr20 648246 200x827 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=628188;QSTRAND=+ GT:DP:AD 1|1:32:24,8 ./.:18:10,8 1|0:27:14,13 +chr20 648569 200x828 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=628511;QSTRAND=+ GT:DP:AD 1|1:40:22,18 ./.:26:17,9 1|0:29:19,10 +chr20 649005 200x829 T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=628947;QSTRAND=+ GT:DP:AD 1|0:28:12,16 ./.:31:8,23 1|0:25:17,8 +chr20 649182 200x82a T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=604196;QSTRAND=+ GT:DP:AD 0|1:30:10,20 ./.:31:8,23 ./.:28:18,10 +chr20 649701 200x82b CAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=629644;QSTRAND=+ GT:DP:AD 1|0:16:11,5 ./.:49:24,25 ./.:31:19,12 +chr20 649701 200x82c CA C 60 . QNAME=cluster23_scaffold_3;QSTART=25060953;QSTRAND=- GT:DP:AD ./.:50:25,25 ./.:28:6,22 1|0:23:15,8 +chr20 649716 200x82d A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=604730;QSTRAND=+ GT:DP:AD 0|1:38:23,15 ./.:13:8,5 ./.:45:24,21 +chr20 649983 200x82e T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=629923;QSTRAND=+ GT:DP:AD 1|0:39:14,25 ./.:27:19,8 1|0:37:15,22 +chr20 650241 200x82f A G 60 . QNAME=cluster23_scaffold_2;QSTART=25044659;QSTRAND=- GT:DP:AD ./.:28:16,12 ./.:19:9,10 0|1:30:15,15 +chr20 650254 200x830 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=605268;QSTRAND=+ GT:DP:AD 0|1:32:22,10 ./.:34:14,20 0|1:17:5,12 +chr20 650326 200x831 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=630266;QSTRAND=+ GT:DP:AD 1|1:17:8,9 ./.:25:10,15 1|1:29:16,13 +chr20 650473 200x832 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=630413;QSTRAND=+ GT:DP:AD 1|0:17:8,9 ./.:30:11,19 1|0:26:20,6 +chr20 650495 200x833 C T 60 . QNAME=cluster23_scaffold_2;QSTART=25044405;QSTRAND=- GT:DP:AD ./.:41:18,23 ./.:22:9,13 0|1:48:24,24 +chr20 650525 200x834 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=605539;QSTRAND=+ GT:DP:AD 0|1:24:12,12 ./.:27:16,11 ./.:38:15,23 +chr20 650651 200x835 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=605665;QSTRAND=+ GT:DP:AD 0|1:19:8,11 ./.:20:7,13 ./.:30:21,9 +chr20 650723 200x836 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=605737;QSTRAND=+ GT:DP:AD 0|1:36:17,19 ./.:26:9,17 ./.:20:11,9 +chr20 650781 200x837 C A 60 . QNAME=cluster19_000000F;QSTART=25110507;QSTRAND=- GT:DP:AD ./.:12:6,6 1|0:30:7,23 ./.:22:5,17 +chr20 651264 200x838 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=631204;QSTRAND=+ GT:DP:AD 1|1:33:12,21 ./.:27:21,6 1|1:32:15,17 +chr20 651683 200x839 TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=631624;QSTRAND=+ GT:DP:AD 1|0:42:17,25 ./.:48:23,25 ./.:43:25,18 +chr20 651860 200x83a G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=606874;QSTRAND=+ GT:DP:AD 0|1:23:13,10 ./.:38:19,19 0|1:41:18,23 +chr20 651923 200x83b C G 60 . QNAME=cluster23_scaffold_2;QSTART=25042977;QSTRAND=- GT:DP:AD ./.:31:25,6 ./.:11:6,5 0|1:38:14,24 +chr20 652315 200x83c C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=632254;QSTRAND=+ GT:DP:AD 1|0:28:16,12 ./.:31:13,18 1|1:39:25,14 +chr20 652505 200x83d G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=632444;QSTRAND=+ GT:DP:AD 1|0:38:14,24 ./.:32:21,11 1|1:29:23,6 +chr20 652904 200x83e GACCTCCCTCCTCCGGCA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=632844;QSTRAND=+ GT:DP:AD 1|1:34:10,24 ./.:28:5,23 ./.:46:24,22 +chr20 653259 200x83f CG C 60 . QNAME=HG002-S9-H1-000001F;QSTART=633182;QSTRAND=+ GT:DP:AD 1|0:32:19,13 ./.:33:23,10 ./.:28:13,15 +chr20 653265 200x840 G GT 60 . QNAME=cluster23_scaffold_2;QSTART=25041634;QSTRAND=- GT:DP:AD ./.:41:18,23 ./.:26:10,16 0|1:41:21,20 +chr20 653266 200x841 G T 60 . QNAME=cluster23_scaffold_2;QSTART=25041633;QSTRAND=- GT:DP:AD ./.:30:8,22 ./.:21:10,11 0|1:22:8,14 +chr20 653324 200x842 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=633245;QSTRAND=+ GT:DP:AD 1|0:33:10,23 ./.:33:8,25 1|1:32:19,13 +chr20 653378 200x843 C T 60 . QNAME=cluster19_000000F;QSTART=25107910;QSTRAND=- GT:DP:AD ./.:19:6,13 1|0:29:21,8 0|1:25:10,15 +chr20 653790 200x844 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=633711;QSTRAND=+ GT:DP:AD 1|1:37:13,24 ./.:19:12,7 1|0:22:12,10 +chr20 653820 200x845 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=633741;QSTRAND=+ GT:DP:AD 1|1:34:12,22 ./.:25:19,6 ./.:34:25,9 +chr20 653977 200x846 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=608974;QSTRAND=+ GT:DP:AD 0|1:19:14,5 ./.:13:5,8 ./.:24:17,7 +chr20 654666 200x847 T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=609663;QSTRAND=+ GT:DP:AD 0|1:19:12,7 ./.:28:7,21 ./.:42:21,21 +chr20 655173 200x848 C CAGAAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=635095;QSTRAND=+ GT:DP:AD 1|1:26:19,7 1|1:21:7,14 1|1:30:19,11 +chr20 656194 200x849 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=636124;QSTRAND=+ GT:DP:AD 1|0:38:22,16 ./.:37:19,18 ./.:22:15,7 +chr20 658219 200x84a G A 60 . QNAME=cluster19_000000F;QSTART=25103060;QSTRAND=- GT:DP:AD ./.:29:16,13 1|0:42:23,19 1|0:43:23,20 +chr20 658277 200x84b A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=613283;QSTRAND=+ GT:DP:AD 0|1:17:7,10 ./.:32:19,13 ./.:29:10,19 +chr20 659380 200x84c T TGGAG 60 . QNAME=HG002-S9-H2-000001F;QSTART=614387;QSTRAND=+ GT:DP:AD 0|1:18:10,8 ./.:27:19,8 ./.:38:13,25 +chr20 659768 200x84d C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=639698;QSTRAND=+ GT:DP:AD 1|0:40:21,19 ./.:45:20,25 ./.:15:10,5 +chr20 659929 200x84e C T 60 . QNAME=cluster19_000000F;QSTART=25101350;QSTRAND=- GT:DP:AD ./.:19:7,12 1|0:36:17,19 1|0:26:16,10 +chr20 660098 200x84f C A 60 . QNAME=cluster19_000000F;QSTART=620951;QSTRAND=+ GT:DP:AD ./.:47:23,24 0|1:12:6,6 ./.:21:11,10 +chr20 660145 200x850 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=640075;QSTRAND=+ GT:DP:AD 1|1:35:13,22 1|1:22:13,9 1|0:17:11,6 +chr20 660346 200x851 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=640276;QSTRAND=+ GT:DP:AD 1|0:35:15,20 0|1:34:10,24 ./.:20:14,6 +chr20 660450 200x852 C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25050195;QSTRAND=- GT:DP:AD ./.:28:10,18 ./.:35:16,19 1|0:32:13,19 +chr20 660628 200x853 C CAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=640559;QSTRAND=+ GT:DP:AD 1|0:44:20,24 ./.:23:7,16 ./.:21:12,9 +chr20 660628 200x854 C CA 60 . QNAME=cluster19_000000F;QSTART=621482;QSTRAND=+ GT:DP:AD ./.:33:19,14 0|1:29:19,10 ./.:14:6,8 +chr20 660640 200x855 C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=640572;QSTRAND=+ GT:DP:AD 1|1:33:25,8 0|1:21:14,7 ./.:28:20,8 +chr20 660909 200x856 G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=615919;QSTRAND=+ GT:DP:AD 0|1:16:7,9 ./.:33:25,8 ./.:38:16,22 +chr20 661249 200x857 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=641181;QSTRAND=+ GT:DP:AD 1|1:29:11,18 1|1:15:9,6 1|0:49:25,24 +chr20 662494 200x858 C CG 60 . QNAME=cluster23_scaffold_2;QSTART=25032395;QSTRAND=- GT:DP:AD ./.:36:18,18 ./.:32:14,18 0|1:31:10,21 +chr20 663033 200x859 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=642965;QSTRAND=+ GT:DP:AD 1|0:26:20,6 0|1:29:22,7 1|1:31:6,25 +chr20 663218 200x85a G A 60 . QNAME=cluster23_scaffold_3;QSTART=25047427;QSTRAND=- GT:DP:AD ./.:29:20,9 ./.:29:24,5 1|0:42:24,18 +chr20 663275 200x85b T C 60 . QNAME=cluster19_000000F;QSTART=624129;QSTRAND=+ GT:DP:AD ./.:28:6,22 0|1:43:18,25 0|1:36:16,20 +chr20 663449 200x85c G A 60 . QNAME=cluster23_scaffold_3;QSTART=25047196;QSTRAND=- GT:DP:AD ./.:39:17,22 ./.:20:8,12 1|0:47:24,23 +chr20 663558 200x85d A C 60 . QNAME=cluster19_000000F;QSTART=624412;QSTRAND=+ GT:DP:AD ./.:21:16,5 0|1:23:6,17 ./.:11:6,5 +chr20 664220 200x85e G GC 60 . QNAME=cluster23_scaffold_2;QSTART=25030668;QSTRAND=- GT:DP:AD ./.:10:5,5 ./.:42:17,25 0|1:21:10,11 +chr20 665209 200x85f T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=645141;QSTRAND=+ GT:DP:AD 1|1:35:21,14 1|1:26:13,13 1|1:32:8,24 +chr20 665270 200x860 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=645202;QSTRAND=+ GT:DP:AD 1|0:35:17,18 ./.:34:23,11 ./.:33:23,10 +chr20 665483 200x861 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=645415;QSTRAND=+ GT:DP:AD 1|1:12:7,5 1|1:22:12,10 0|1:26:14,12 +chr20 666690 200x862 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=646622;QSTRAND=+ GT:DP:AD 1|0:22:11,11 ./.:38:14,24 ./.:37:25,12 +chr20 667092 200x863 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=647024;QSTRAND=+ GT:DP:AD 1|1:31:15,16 1|1:27:7,20 1|1:29:23,6 +chr20 667181 200x864 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=647113;QSTRAND=+ GT:DP:AD 1|0:29:14,15 ./.:40:21,19 ./.:45:20,25 +chr20 667787 200x865 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=647719;QSTRAND=+ GT:DP:AD 1|0:24:19,5 ./.:29:9,20 ./.:18:7,11 +chr20 668165 200x866 A ATTG 60 . QNAME=HG002-S9-H1-000001F;QSTART=648098;QSTRAND=+ GT:DP:AD 1|0:44:25,19 ./.:22:7,15 1|1:37:13,24 +chr20 668172 200x867 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=648107;QSTRAND=+ GT:DP:AD 1|0:27:12,15 ./.:24:12,12 1|1:30:19,11 +chr20 668176 200x868 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=648111;QSTRAND=+ GT:DP:AD 1|0:18:13,5 ./.:46:22,24 1|1:40:17,23 +chr20 668345 200x869 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=648280;QSTRAND=+ GT:DP:AD 1|0:42:17,25 ./.:25:5,20 1|1:27:22,5 +chr20 669291 200x86a A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=649226;QSTRAND=+ GT:DP:AD 1|0:21:10,11 ./.:18:11,7 1|1:19:14,5 +chr20 670996 200x86b A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=650931;QSTRAND=+ GT:DP:AD 1|0:37:20,17 ./.:37:22,15 1|1:30:19,11 +chr20 671453 200x86c T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=651388;QSTRAND=+ GT:DP:AD 1|0:33:18,15 ./.:14:5,9 1|1:31:9,22 +chr20 671595 200x86d C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=651530;QSTRAND=+ GT:DP:AD 1|0:34:22,12 ./.:36:17,19 1|1:25:9,16 +chr20 672290 200x86e T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=652225;QSTRAND=+ GT:DP:AD 1|0:35:19,16 ./.:50:25,25 1|1:32:25,7 +chr20 672388 200x86f CGT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=652324;QSTRAND=+ GT:DP:AD 1|0:37:15,22 ./.:39:21,18 1|1:42:18,24 +chr20 672422 200x870 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=652355;QSTRAND=+ GT:DP:AD 1|0:48:24,24 ./.:19:10,9 1|1:34:10,24 +chr20 672619 200x871 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=652552;QSTRAND=+ GT:DP:AD 1|0:31:19,12 ./.:27:7,20 1|1:38:18,20 +chr20 673008 200x872 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=652941;QSTRAND=+ GT:DP:AD 1|0:40:21,19 ./.:32:22,10 1|1:20:14,6 +chr20 673547 200x873 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=653480;QSTRAND=+ GT:DP:AD 1|0:24:9,15 ./.:37:20,17 1|1:42:22,20 +chr20 674399 200x874 TCACA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=654333;QSTRAND=+ GT:DP:AD 1|0:28:16,12 ./.:22:11,11 0|1:30:10,20 +chr20 674399 200x875 TCACACA T 60 . QNAME=cluster23_scaffold_3;QSTART=25036245;QSTRAND=- GT:DP:AD ./.:29:12,17 ./.:36:13,23 1|0:30:25,5 +chr20 674405 200x876 A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=654334;QSTRAND=+ GT:DP:AD 1|0:26:12,14 ./.:40:18,22 0|1:28:14,14 +chr20 674407 200x877 A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=654336;QSTRAND=+ GT:DP:AD 1|0:18:9,9 ./.:34:18,16 1|1:26:10,16 +chr20 674409 200x878 A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=654338;QSTRAND=+ GT:DP:AD 1|0:21:14,7 ./.:42:18,24 1|1:39:18,21 +chr20 674411 200x879 A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=654340;QSTRAND=+ GT:DP:AD 1|0:48:24,24 ./.:25:19,6 1|1:34:17,17 +chr20 674413 200x87a A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=654342;QSTRAND=+ GT:DP:AD 1|0:22:12,10 ./.:24:17,7 1|0:38:14,24 +chr20 674688 200x87b A AGT 60 . QNAME=HG002-S9-H2-000001F;QSTART=629699;QSTRAND=+ GT:DP:AD 0|1:37:20,17 1|1:37:23,14 ./.:36:11,25 +chr20 674713 200x87c GTGTGTGTGTGTGTGTGTGTA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=654643;QSTRAND=+ GT:DP:AD 1|0:33:14,19 ./.:36:15,21 1|1:36:14,22 +chr20 675537 200x87d G A 60 . QNAME=cluster23_scaffold_2;QSTART=25019374;QSTRAND=- GT:DP:AD ./.:29:16,13 ./.:20:6,14 0|1:21:7,14 +chr20 675763 200x87e T TGGC 60 . QNAME=cluster19_000000F;QSTART=25085511;QSTRAND=- GT:DP:AD ./.:16:11,5 1|1:40:21,19 ./.:23:15,8 +chr20 676166 200x87f G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=656075;QSTRAND=+ GT:DP:AD 1|0:19:10,9 ./.:39:17,22 1|1:31:23,8 +chr20 676254 200x880 A G 60 . QNAME=cluster23_scaffold_3;QSTART=25034416;QSTRAND=- GT:DP:AD ./.:20:5,15 ./.:35:21,14 1|1:19:11,8 +chr20 677116 200x881 G C 60 . QNAME=cluster23_scaffold_3;QSTART=25033554;QSTRAND=- GT:DP:AD ./.:16:10,6 ./.:34:12,22 1|1:34:13,21 +chr20 677219 200x882 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=632231;QSTRAND=+ GT:DP:AD 0|1:40:20,20 ./.:20:11,9 1|1:27:20,7 +chr20 677414 200x883 TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=657324;QSTRAND=+ GT:DP:AD 1|0:34:16,18 0|1:21:16,5 1|1:26:19,7 +chr20 677414 200x884 TAA T 60 . QNAME=HG002-S9-H2-000001F;QSTART=632427;QSTRAND=+ GT:DP:AD 0|1:49:25,24 ./.:29:8,21 ./.:28:16,12 +chr20 677478 200x885 G A 60 . QNAME=cluster19_000000F;QSTART=638336;QSTRAND=+ GT:DP:AD ./.:33:17,16 0|1:27:6,21 ./.:16:8,8 +chr20 677582 200x886 A AAATAATAAT 60 . QNAME=HG002-S9-H2-000001F;QSTART=632593;QSTRAND=+ GT:DP:AD 0|1:24:14,10 ./.:29:18,11 ./.:20:9,11 +chr20 677689 200x887 G A 60 . QNAME=cluster23_scaffold_3;QSTART=25032982;QSTRAND=- GT:DP:AD ./.:14:9,5 ./.:26:7,19 1|1:35:25,10 +chr20 677734 200x888 G C 60 . QNAME=cluster23_scaffold_3;QSTART=25032937;QSTRAND=- GT:DP:AD ./.:43:20,23 ./.:38:14,24 1|1:28:6,22 +chr20 677799 200x889 C A 60 . QNAME=cluster23_scaffold_3;QSTART=25032872;QSTRAND=- GT:DP:AD ./.:37:17,20 ./.:32:19,13 1|1:43:24,19 +chr20 677892 200x88a AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=657801;QSTRAND=+ GT:DP:AD 1|0:24:17,7 ./.:23:12,11 ./.:14:5,9 +chr20 677892 200x88b A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25032778;QSTRAND=- GT:DP:AD ./.:20:7,13 ./.:27:8,19 1|1:17:12,5 +chr20 678014 200x88c T C 60 . QNAME=cluster23_scaffold_3;QSTART=25032656;QSTRAND=- GT:DP:AD ./.:28:11,17 ./.:45:25,20 1|1:29:14,15 +chr20 678015 200x88d G A 60 . QNAME=cluster23_scaffold_3;QSTART=25032655;QSTRAND=- GT:DP:AD ./.:18:9,9 ./.:28:16,12 1|1:18:10,8 +chr20 678191 200x88e T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=658098;QSTRAND=+ GT:DP:AD 1|1:34:15,19 1|1:47:22,25 1|1:27:11,16 +chr20 678230 200x88f T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=633249;QSTRAND=+ GT:DP:AD 0|1:23:16,7 ./.:26:16,10 1|1:30:6,24 +chr20 678305 200x890 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=633324;QSTRAND=+ GT:DP:AD 0|1:32:8,24 ./.:18:8,10 ./.:18:6,12 +chr20 678433 200x891 C G 60 . QNAME=cluster23_scaffold_3;QSTART=25032237;QSTRAND=- GT:DP:AD ./.:31:11,20 ./.:41:23,18 1|1:39:22,17 +chr20 678642 200x892 G A 60 . QNAME=cluster23_scaffold_3;QSTART=25032028;QSTRAND=- GT:DP:AD ./.:38:13,25 ./.:37:24,13 1|1:23:17,6 +chr20 678678 200x893 G A 60 . QNAME=cluster23_scaffold_3;QSTART=25031992;QSTRAND=- GT:DP:AD ./.:31:16,15 ./.:28:5,23 1|1:12:6,6 +chr20 678706 200x894 T C 60 . QNAME=cluster23_scaffold_3;QSTART=25031964;QSTRAND=- GT:DP:AD ./.:24:18,6 ./.:34:15,19 1|1:19:7,12 +chr20 678778 200x895 T C 60 . QNAME=cluster23_scaffold_3;QSTART=25031892;QSTRAND=- GT:DP:AD ./.:13:6,7 ./.:16:8,8 1|1:23:9,14 +chr20 678797 200x896 G A 60 . QNAME=cluster23_scaffold_3;QSTART=25031873;QSTRAND=- GT:DP:AD ./.:30:22,8 ./.:44:20,24 1|1:31:13,18 +chr20 678839 200x897 A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=633858;QSTRAND=+ GT:DP:AD 0|1:31:23,8 ./.:29:24,5 1|1:27:13,14 +chr20 679151 200x898 G A 60 . QNAME=cluster23_scaffold_3;QSTART=25031519;QSTRAND=- GT:DP:AD ./.:41:20,21 ./.:37:20,17 1|1:48:24,24 +chr20 679482 200x899 T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=634501;QSTRAND=+ GT:DP:AD 0|1:11:6,5 ./.:30:5,25 1|1:31:13,18 +chr20 679483 200x89a T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=634502;QSTRAND=+ GT:DP:AD 0|1:15:5,10 ./.:34:9,25 1|1:34:14,20 +chr20 680009 200x89b A T 60 . QNAME=cluster23_scaffold_3;QSTART=25030661;QSTRAND=- GT:DP:AD ./.:29:7,22 ./.:25:5,20 1|1:24:5,19 +chr20 680029 200x89c A G 60 . QNAME=cluster23_scaffold_3;QSTART=25030641;QSTRAND=- GT:DP:AD ./.:33:8,25 ./.:33:10,23 1|1:21:5,16 +chr20 680047 200x89d A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=635066;QSTRAND=+ GT:DP:AD 0|1:18:13,5 ./.:26:19,7 ./.:26:5,21 +chr20 680149 200x89e A G 60 . QNAME=cluster23_scaffold_3;QSTART=25030521;QSTRAND=- GT:DP:AD ./.:34:12,22 ./.:45:21,24 1|1:28:8,20 +chr20 680216 200x89f G A 60 . QNAME=cluster23_scaffold_2;QSTART=25014695;QSTRAND=- GT:DP:AD ./.:41:25,16 ./.:21:5,16 0|1:27:20,7 +chr20 680257 200x8a0 T C 60 . QNAME=cluster23_scaffold_3;QSTART=25030413;QSTRAND=- GT:DP:AD ./.:28:16,12 ./.:34:20,14 1|1:44:20,24 +chr20 680491 200x8a1 G GA 60 . QNAME=cluster23_scaffold_3;QSTART=25030178;QSTRAND=- GT:DP:AD ./.:38:15,23 ./.:45:24,21 1|1:24:5,19 +chr20 680625 200x8a2 T A 60 . QNAME=cluster23_scaffold_3;QSTART=25030044;QSTRAND=- GT:DP:AD ./.:32:14,18 ./.:27:16,11 1|1:17:10,7 +chr20 680841 200x8a3 A G 60 . QNAME=cluster23_scaffold_3;QSTART=25029828;QSTRAND=- GT:DP:AD ./.:37:24,13 ./.:25:11,14 1|1:44:24,20 +chr20 681789 200x8a4 T C 60 . QNAME=cluster23_scaffold_3;QSTART=25028880;QSTRAND=- GT:DP:AD ./.:24:11,13 ./.:24:6,18 1|1:29:15,14 +chr20 681958 200x8a5 G C 60 . QNAME=cluster23_scaffold_3;QSTART=25028711;QSTRAND=- GT:DP:AD ./.:25:16,9 ./.:26:15,11 1|1:27:15,12 +chr20 682463 200x8a6 C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=637482;QSTRAND=+ GT:DP:AD 0|1:48:24,24 ./.:45:25,20 1|1:34:18,16 +chr20 682684 200x8a7 T C 60 . QNAME=cluster23_scaffold_3;QSTART=25027985;QSTRAND=- GT:DP:AD ./.:15:10,5 ./.:25:16,9 1|1:26:6,20 +chr20 683486 200x8a8 T C 60 . QNAME=cluster23_scaffold_3;QSTART=25027183;QSTRAND=- GT:DP:AD ./.:27:22,5 ./.:37:20,17 1|1:34:15,19 +chr20 683498 200x8a9 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=638517;QSTRAND=+ GT:DP:AD 0|1:38:19,19 0|1:43:18,25 1|1:16:6,10 +chr20 683582 200x8aa C T 60 . QNAME=cluster23_scaffold_3;QSTART=25027087;QSTRAND=- GT:DP:AD ./.:26:12,14 ./.:15:7,8 1|1:41:21,20 +chr20 684734 200x8ab A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=639753;QSTRAND=+ GT:DP:AD 0|1:22:7,15 ./.:24:14,10 1|1:42:22,20 +chr20 684907 200x8ac A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=639926;QSTRAND=+ GT:DP:AD 0|1:22:13,9 ./.:33:20,13 ./.:24:13,11 +chr20 685089 200x8ad A G 60 . QNAME=cluster23_scaffold_3;QSTART=25025580;QSTRAND=- GT:DP:AD ./.:29:23,6 ./.:20:13,7 1|1:34:12,22 +chr20 685645 200x8ae G A 60 . QNAME=cluster23_scaffold_3;QSTART=25025024;QSTRAND=- GT:DP:AD ./.:32:8,24 ./.:26:18,8 1|1:22:13,9 +chr20 685696 200x8af AAATAAT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=665604;QSTRAND=+ GT:DP:AD 1|0:10:5,5 1|0:13:8,5 ./.:26:6,20 +chr20 685696 200x8b0 AAATAATAATAAT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=640716;QSTRAND=+ GT:DP:AD 0|1:36:19,17 0|1:25:17,8 ./.:15:6,9 +chr20 685696 200x8b1 AAATAATAAT A 60 . QNAME=cluster23_scaffold_3;QSTART=25024973;QSTRAND=- GT:DP:AD ./.:21:16,5 ./.:28:8,20 1|1:41:25,16 +chr20 686394 200x8b2 C T 60 . QNAME=cluster19_000000F;QSTART=25074886;QSTRAND=- GT:DP:AD ./.:29:9,20 1|0:36:22,14 ./.:35:19,16 +chr20 686439 200x8b3 C CAAAAAAAAAAAAAA 60 . QNAME=HG002-S9-H2-000001F;QSTART=641447;QSTRAND=+ GT:DP:AD 0|1:25:10,15 ./.:31:18,13 ./.:37:18,19 +chr20 686455 200x8b4 A AAAAAAAAAAAAAAAAAAAAAAAAAAT 60 . QNAME=cluster23_scaffold_3;QSTART=25024197;QSTRAND=-;SVTYPE=INS;SVLEN=26 GT:DP:AD ./.:33:22,11 ./.:29:7,22 1/0:41:25,16 +chr20 686455 200x8b5 A AAAAAAAAAAAAAAAAAAAAAAAAAT 60 . QNAME=cluster23_scaffold_2;QSTART=25008439;QSTRAND=-;SVTYPE=INS;SVLEN=25 GT:DP:AD ./.:31:13,18 ./.:34:16,18 0/1:16:5,11 +chr20 686794 200x8b6 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=641815;QSTRAND=+ GT:DP:AD 0|1:34:23,11 0|1:29:22,7 1|1:34:11,23 +chr20 687380 200x8b7 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=642401;QSTRAND=+ GT:DP:AD 0|1:16:11,5 ./.:23:6,17 ./.:43:19,24 +chr20 687915 200x8b8 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=667816;QSTRAND=+ GT:DP:AD 1|1:14:7,7 1|1:41:20,21 ./.:27:13,14 +chr20 688002 200x8b9 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=667903;QSTRAND=+ GT:DP:AD 1|1:39:20,19 1|1:21:15,6 ./.:37:15,22 +chr20 688657 200x8ba G A 60 . QNAME=cluster23_scaffold_2;QSTART=25006237;QSTRAND=- GT:DP:AD ./.:16:11,5 ./.:22:7,15 0|1:37:16,21 +chr20 688666 200x8bb C G 60 . QNAME=cluster23_scaffold_2;QSTART=25006228;QSTRAND=- GT:DP:AD ./.:33:12,21 ./.:33:24,9 0|1:42:19,23 +chr20 689007 200x8bc A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=668908;QSTRAND=+ GT:DP:AD 1|0:23:13,10 1|1:43:18,25 0|1:37:20,17 +chr20 689613 200x8bd T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=669514;QSTRAND=+ GT:DP:AD 1|0:34:17,17 1|1:45:22,23 0|1:22:7,15 +chr20 689671 200x8be G A 60 . QNAME=cluster19_000000F;QSTART=650517;QSTRAND=+ GT:DP:AD ./.:24:16,8 0|1:31:22,9 ./.:26:10,16 +chr20 690105 200x8bf A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=670006;QSTRAND=+ GT:DP:AD 1|0:27:17,10 1|1:40:18,22 0|1:39:15,24 +chr20 690819 200x8c0 AGTGT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=670721;QSTRAND=+ GT:DP:AD 1|0:17:9,8 1|1:41:23,18 0|1:25:18,7 +chr20 690819 200x8c1 A AGT 60 . QNAME=HG002-S9-H2-000001F;QSTART=645841;QSTRAND=+ GT:DP:AD 0|1:23:7,16 ./.:20:13,7 1|0:30:14,16 +chr20 690853 200x8c2 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=670750;QSTRAND=+ GT:DP:AD 1|0:30:12,18 1|1:35:18,17 ./.:40:19,21 +chr20 690931 200x8c3 C T 60 . QNAME=cluster23_scaffold_2;QSTART=25003967;QSTRAND=- GT:DP:AD ./.:47:25,22 ./.:29:6,23 0|1:26:10,16 +chr20 690947 200x8c4 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=670844;QSTRAND=+ GT:DP:AD 1|0:34:16,18 1|1:21:7,14 ./.:21:6,15 +chr20 691419 200x8c5 T C 60 . QNAME=cluster23_scaffold_2;QSTART=25003479;QSTRAND=- GT:DP:AD ./.:31:7,24 ./.:27:7,20 0|1:42:25,17 +chr20 691923 200x8c6 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=671820;QSTRAND=+ GT:DP:AD 1|0:32:18,14 0|1:41:17,24 ./.:26:17,9 +chr20 692698 200x8c7 C CTT 60 . QNAME=HG002-S9-H1-000001F;QSTART=672596;QSTRAND=+ GT:DP:AD 1|0:26:20,6 0|1:31:22,9 ./.:30:16,14 +chr20 692996 200x8c8 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=672895;QSTRAND=+ GT:DP:AD 1|0:23:15,8 1|1:23:8,15 0|1:33:24,9 +chr20 693104 200x8c9 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=673003;QSTRAND=+ GT:DP:AD 1|0:19:12,7 1|1:28:22,6 0|1:26:6,20 +chr20 693463 200x8ca G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=673362;QSTRAND=+ GT:DP:AD 1|0:18:11,7 1|1:41:22,19 0|1:30:21,9 +chr20 694203 200x8cb C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=649226;QSTRAND=+ GT:DP:AD 0|1:41:16,25 ./.:34:25,9 ./.:31:19,12 +chr20 694318 200x8cc A G 60 . QNAME=cluster19_000000F;QSTART=25066966;QSTRAND=- GT:DP:AD ./.:11:5,6 1|0:48:25,23 0|1:19:7,12 +chr20 694678 200x8cd C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=674577;QSTRAND=+ GT:DP:AD 1|0:37:20,17 0|1:43:19,24 ./.:41:19,22 +chr20 695001 200x8ce G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=674900;QSTRAND=+ GT:DP:AD 1|0:41:21,20 1|1:35:20,15 0|1:21:15,6 +chr20 695004 200x8cf G C 60 . QNAME=cluster19_000000F;QSTART=25066280;QSTRAND=- GT:DP:AD ./.:26:14,12 1|0:33:10,23 0|1:35:19,16 +chr20 695155 200x8d0 G GTA 60 . QNAME=cluster19_000000F;QSTART=656000;QSTRAND=+ GT:DP:AD ./.:37:23,14 0|1:43:24,19 ./.:47:24,23 +chr20 695259 200x8d1 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=675158;QSTRAND=+ GT:DP:AD 1|0:18:12,6 1|1:37:17,20 0|1:35:10,25 +chr20 695798 200x8d2 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=675697;QSTRAND=+ GT:DP:AD 1|0:13:5,8 0|1:24:19,5 ./.:42:23,19 +chr20 695931 200x8d3 A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=675830;QSTRAND=+ GT:DP:AD 1|0:23:16,7 1|1:27:14,13 0|1:35:11,24 +chr20 696160 200x8d4 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=676059;QSTRAND=+ GT:DP:AD 1|0:35:10,25 0|1:29:13,16 ./.:16:6,10 +chr20 697221 200x8d5 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=677120;QSTRAND=+ GT:DP:AD 1|0:29:20,9 0|1:32:17,15 ./.:42:20,22 +chr20 697409 200x8d6 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=677308;QSTRAND=+ GT:DP:AD 1|0:45:24,21 0|1:19:12,7 ./.:18:13,5 +chr20 697409 200x8d7 G T 60 . QNAME=cluster19_000000F;QSTART=25063875;QSTRAND=- GT:DP:AD ./.:21:6,15 1|0:25:12,13 0|1:41:19,22 +chr20 697934 200x8d8 C G 60 . QNAME=cluster19_000000F;QSTART=25063350;QSTRAND=- GT:DP:AD ./.:26:21,5 1|0:22:13,9 0|1:26:10,16 +chr20 698083 200x8d9 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=677982;QSTRAND=+ GT:DP:AD 1|0:15:5,10 ./.:30:5,25 ./.:39:18,21 +chr20 698123 200x8da T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=678022;QSTRAND=+ GT:DP:AD 1|0:20:9,11 1|1:27:8,19 0|1:49:25,24 +chr20 698533 200x8db C T 60 . QNAME=cluster19_000000F;QSTART=659379;QSTRAND=+ GT:DP:AD ./.:35:21,14 0|1:22:13,9 ./.:19:14,5 +chr20 698627 200x8dc A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=653650;QSTRAND=+ GT:DP:AD 0|1:33:11,22 1|0:33:24,9 0|1:32:8,24 +chr20 698723 200x8dd G A 60 . QNAME=cluster19_000000F;QSTART=25062561;QSTRAND=- GT:DP:AD ./.:46:25,21 1|0:28:21,7 0|1:28:16,12 +chr20 699085 200x8de C T 60 . QNAME=cluster19_000000F;QSTART=25062199;QSTRAND=- GT:DP:AD ./.:41:22,19 1|0:30:25,5 0|1:38:21,17 +chr20 699214 200x8df CAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=679114;QSTRAND=+ GT:DP:AD 1|0:37:13,24 ./.:28:7,21 ./.:38:21,17 +chr20 699214 200x8e0 CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=654238;QSTRAND=+ GT:DP:AD 0|1:27:12,15 ./.:45:21,24 ./.:35:20,15 +chr20 699214 200x8e1 C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25011435;QSTRAND=- GT:DP:AD ./.:30:25,5 ./.:30:12,18 1|0:19:12,7 +chr20 700520 200x8e2 C T 60 . QNAME=cluster19_000000F;QSTART=25060764;QSTRAND=- GT:DP:AD ./.:24:10,14 1|0:31:8,23 0|1:23:6,17 +chr20 700649 200x8e3 CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=655672;QSTRAND=+ GT:DP:AD 0|1:14:7,7 ./.:38:20,18 ./.:30:10,20 +chr20 700649 200x8e4 C CT 60 . QNAME=cluster19_000000F;QSTART=25060634;QSTRAND=- GT:DP:AD ./.:23:15,8 1|0:29:14,15 0|1:34:10,24 +chr20 701307 200x8e5 A G 60 . QNAME=cluster19_000000F;QSTART=25059976;QSTRAND=- GT:DP:AD ./.:24:18,6 1|0:20:10,10 0|1:16:6,10 +chr20 701558 200x8e6 C T 60 . QNAME=cluster19_000000F;QSTART=25059725;QSTRAND=- GT:DP:AD ./.:48:23,25 1|0:26:18,8 0|1:17:12,5 +chr20 702627 200x8e7 G A 60 . QNAME=cluster19_000000F;QSTART=25058656;QSTRAND=- GT:DP:AD ./.:45:23,22 1|0:42:22,20 0|1:46:23,23 +chr20 702901 200x8e8 T C 60 . QNAME=cluster19_000000F;QSTART=25058382;QSTRAND=- GT:DP:AD ./.:17:8,9 1|0:28:9,19 0|1:19:6,13 +chr20 702972 200x8e9 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=682868;QSTRAND=+ GT:DP:AD 1|0:33:10,23 0|1:30:7,23 ./.:20:12,8 +chr20 704472 200x8ea A G 60 . QNAME=cluster19_000000F;QSTART=25056811;QSTRAND=- GT:DP:AD ./.:39:17,22 1|0:19:10,9 0|1:24:17,7 +chr20 704662 200x8eb C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=659683;QSTRAND=+ GT:DP:AD 0|1:26:18,8 ./.:35:23,12 ./.:27:10,17 +chr20 704704 200x8ec A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=684600;QSTRAND=+ GT:DP:AD 1|0:32:10,22 1|1:27:9,18 1|0:34:14,20 +chr20 705070 200x8ed C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=684966;QSTRAND=+ GT:DP:AD 1|0:20:12,8 1|1:33:15,18 ./.:39:22,17 +chr20 705212 200x8ee A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=660233;QSTRAND=+ GT:DP:AD 0|1:23:12,11 ./.:39:17,22 1|0:27:9,18 +chr20 705650 200x8ef T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=685546;QSTRAND=+ GT:DP:AD 1|0:40:24,16 1|0:41:21,20 ./.:49:24,25 +chr20 706757 200x8f0 C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=661778;QSTRAND=+ GT:DP:AD 0|1:22:13,9 ./.:45:25,20 1|0:20:10,10 +chr20 707000 200x8f1 T TAA 60 . QNAME=cluster23_scaffold_2;QSTART=24987895;QSTRAND=- GT:DP:AD ./.:44:24,20 ./.:33:8,25 0|1:21:8,13 +chr20 707128 200x8f2 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=687024;QSTRAND=+ GT:DP:AD 1|1:32:10,22 1|0:40:16,24 1|1:19:5,14 +chr20 707704 200x8f3 C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=662725;QSTRAND=+ GT:DP:AD 0|1:33:8,25 ./.:24:12,12 1|0:26:21,5 +chr20 708199 200x8f4 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=688095;QSTRAND=+ GT:DP:AD 1|0:29:22,7 1|0:26:11,15 0|1:48:24,24 +chr20 708250 200x8f5 C CTTTTGT 60 . QNAME=cluster19_000000F;QSTART=669097;QSTRAND=+ GT:DP:AD ./.:38:18,20 0|1:40:21,19 ./.:31:21,10 +chr20 708422 200x8f6 AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=688319;QSTRAND=+ GT:DP:AD 1|0:28:16,12 1|0:27:7,20 ./.:30:6,24 +chr20 708422 200x8f7 A ATT 60 . QNAME=HG002-S9-H2-000001F;QSTART=663444;QSTRAND=+ GT:DP:AD 0|1:31:14,17 ./.:17:11,6 1|0:18:11,7 +chr20 708747 200x8f8 C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=688642;QSTRAND=+ GT:DP:AD 1|0:37:12,25 1|0:21:10,11 ./.:23:13,10 +chr20 708784 200x8f9 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=688679;QSTRAND=+ GT:DP:AD 1|0:37:24,13 1|0:13:5,8 ./.:22:16,6 +chr20 709051 200x8fa TC T 60 . QNAME=cluster23_scaffold_2;QSTART=24985844;QSTRAND=- GT:DP:AD ./.:13:5,8 ./.:19:7,12 0|1:21:8,13 +chr20 709759 200x8fb AGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCC A 60 . QNAME=HG002-S9-H2-000001F;QSTART=664783;QSTRAND=+;SVTYPE=DEL;SVLEN=-93 GT:DP:AD 0/1:16:7,9 1/0:26:21,5 1/1:41:23,18 +chr20 709830 200x8fc G GACACTGCTCGGTCCTCCGCTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCGCTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGAACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGA 60 . QNAME=HG002-S9-H1-000001F;QSTART=689726;QSTRAND=+;SVTYPE=INS;SVLEN=465 GT:DP:AD 1/0:41:16,25 ./.:30:18,12 ./.:21:10,11 +chr20 709916 200x8fd T TG 60 . QNAME=cluster19_000000F;QSTART=670769;QSTRAND=+ GT:DP:AD ./.:37:21,16 0|1:33:16,17 ./.:18:10,8 +chr20 710119 200x8fe C T 60 . QNAME=cluster23_scaffold_2;QSTART=24984870;QSTRAND=- GT:DP:AD ./.:45:23,22 ./.:20:10,10 0|1:21:12,9 +chr20 710584 200x8ff T C 60 . QNAME=cluster23_scaffold_2;QSTART=24984405;QSTRAND=- GT:DP:AD ./.:42:24,18 ./.:15:10,5 0|1:18:6,12 +chr20 710789 200x900 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=691149;QSTRAND=+ GT:DP:AD 1|0:39:24,15 1|1:26:15,11 1|1:30:10,20 +chr20 710948 200x901 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=691308;QSTRAND=+ GT:DP:AD 1|0:29:13,16 0|1:44:25,19 1|0:15:5,10 +chr20 711068 200x902 G A 60 . QNAME=cluster23_scaffold_2;QSTART=24983921;QSTRAND=- GT:DP:AD ./.:37:17,20 ./.:46:22,24 0|1:41:18,23 +chr20 711120 200x903 G GGT 60 . QNAME=HG002-S9-H2-000001F;QSTART=666051;QSTRAND=+ GT:DP:AD 0|1:26:10,16 ./.:32:11,21 ./.:26:18,8 +chr20 711120 200x904 G GGTGT 60 . QNAME=cluster23_scaffold_2;QSTART=24983865;QSTRAND=- GT:DP:AD ./.:41:16,25 ./.:35:19,16 0|1:33:9,24 +chr20 711177 200x905 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=691537;QSTRAND=+ GT:DP:AD 1|0:41:21,20 1|1:38:19,19 1|1:28:19,9 +chr20 711562 200x906 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=691922;QSTRAND=+ GT:DP:AD 1|1:27:12,15 1|1:22:13,9 1|0:34:12,22 +chr20 711631 200x907 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=691991;QSTRAND=+ GT:DP:AD 1|1:27:9,18 1|1:20:11,9 1|1:28:19,9 +chr20 712402 200x908 GT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=692763;QSTRAND=+ GT:DP:AD 1|1:22:15,7 ./.:16:8,8 ./.:21:15,6 +chr20 712536 200x909 C T 60 . QNAME=cluster19_000000F;QSTART=25048841;QSTRAND=- GT:DP:AD ./.:37:14,23 1|0:36:19,17 ./.:42:20,22 +chr20 712711 200x90a CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=693071;QSTRAND=+ GT:DP:AD 1|0:33:13,20 ./.:15:10,5 ./.:22:8,14 +chr20 712711 200x90b C CT 60 . QNAME=cluster19_000000F;QSTART=25048665;QSTRAND=- GT:DP:AD ./.:40:25,15 1|0:45:20,25 ./.:32:7,25 +chr20 712944 200x90c T C 60 . QNAME=cluster19_000000F;QSTART=25048432;QSTRAND=- GT:DP:AD ./.:41:21,20 1|0:35:22,13 ./.:26:6,20 +chr20 712978 200x90d G A 60 . QNAME=cluster19_000000F;QSTART=25048398;QSTRAND=- GT:DP:AD ./.:29:7,22 1|0:32:7,25 ./.:18:13,5 +chr20 713101 200x90e C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=693459;QSTRAND=+ GT:DP:AD 1|1:41:24,17 ./.:32:16,16 ./.:27:16,11 +chr20 713206 200x90f T A 60 . QNAME=cluster19_000000F;QSTART=25048170;QSTRAND=- GT:DP:AD ./.:14:7,7 1|0:35:14,21 ./.:24:12,12 +chr20 713207 200x910 T A 60 . QNAME=cluster19_000000F;QSTART=25048169;QSTRAND=- GT:DP:AD ./.:28:20,8 1|0:20:14,6 ./.:39:19,20 +chr20 713208 200x911 T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=693566;QSTRAND=+ GT:DP:AD 1|1:21:11,10 1|0:30:21,9 ./.:31:17,14 +chr20 713417 200x912 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=693775;QSTRAND=+ GT:DP:AD 1|1:14:6,8 1|1:16:10,6 1|0:26:11,15 +chr20 713874 200x913 C T 60 . QNAME=cluster23_scaffold_2;QSTART=24981111;QSTRAND=- GT:DP:AD ./.:24:15,9 ./.:33:17,16 0|1:16:9,7 +chr20 713943 200x914 T C 60 . QNAME=cluster19_000000F;QSTART=25047433;QSTRAND=- GT:DP:AD ./.:23:7,16 1|0:34:19,15 ./.:25:7,18 +chr20 713965 200x915 G A 60 . QNAME=cluster19_000000F;QSTART=25047411;QSTRAND=- GT:DP:AD ./.:19:5,14 1|0:27:16,11 ./.:35:13,22 +chr20 714250 200x916 T C 60 . QNAME=cluster19_000000F;QSTART=25047126;QSTRAND=- GT:DP:AD ./.:36:25,11 1|0:34:11,23 ./.:29:8,21 +chr20 714816 200x917 A G 60 . QNAME=cluster19_000000F;QSTART=675669;QSTRAND=+ GT:DP:AD ./.:24:15,9 0|1:26:5,21 1|0:28:22,6 +chr20 715026 200x918 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=695384;QSTRAND=+ GT:DP:AD 1|1:25:17,8 0|1:45:23,22 1|0:39:20,19 +chr20 715559 200x919 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=695917;QSTRAND=+ GT:DP:AD 1|1:33:10,23 1|1:42:18,24 1|0:27:14,13 +chr20 715567 200x91a C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=695925;QSTRAND=+ GT:DP:AD 1|1:29:23,6 1|1:37:18,19 1|0:23:15,8 +chr20 715736 200x91b G A 60 . QNAME=cluster23_scaffold_2;QSTART=24979249;QSTRAND=- GT:DP:AD ./.:46:21,25 ./.:27:16,11 0|1:16:11,5 +chr20 715825 200x91c G A 60 . QNAME=cluster23_scaffold_3;QSTART=24994915;QSTRAND=- GT:DP:AD ./.:41:20,21 ./.:49:24,25 1|0:15:5,10 +chr20 715836 200x91d C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=696194;QSTRAND=+ GT:DP:AD 1|1:36:20,16 1|0:25:8,17 1|0:34:24,10 +chr20 716956 200x91e T C 60 . QNAME=cluster19_000000F;QSTART=677809;QSTRAND=+ GT:DP:AD ./.:34:15,19 0|1:30:6,24 1|0:24:8,16 +chr20 717158 200x91f ATT A 60 . QNAME=cluster19_000000F;QSTART=678012;QSTRAND=+ GT:DP:AD ./.:36:18,18 0|1:30:23,7 ./.:47:24,23 +chr20 717272 200x920 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=697630;QSTRAND=+ GT:DP:AD 1|0:28:18,10 ./.:38:20,18 0|1:19:6,13 +chr20 717541 200x921 C T 60 . QNAME=cluster19_000000F;QSTART=678392;QSTRAND=+ GT:DP:AD ./.:19:6,13 0|1:17:9,8 ./.:32:9,23 +chr20 717932 200x922 G C 60 . QNAME=cluster19_000000F;QSTART=25043444;QSTRAND=- GT:DP:AD ./.:34:11,23 1|0:37:16,21 ./.:22:8,14 +chr20 718343 200x923 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=698701;QSTRAND=+ GT:DP:AD 1|0:30:16,14 ./.:37:23,14 0|1:18:6,12 +chr20 718374 200x924 C G 60 . QNAME=cluster19_000000F;QSTART=25043002;QSTRAND=- GT:DP:AD ./.:23:12,11 1|1:28:14,14 ./.:29:16,13 +chr20 718391 200x925 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=698749;QSTRAND=+ GT:DP:AD 1|0:29:21,8 1|1:37:25,12 0|1:44:24,20 +chr20 718820 200x926 T A 60 . QNAME=cluster19_000000F;QSTART=679671;QSTRAND=+ GT:DP:AD ./.:26:7,19 0|1:28:9,19 ./.:39:21,18 +chr20 719274 200x927 C T 60 . QNAME=cluster19_000000F;QSTART=680125;QSTRAND=+ GT:DP:AD ./.:26:15,11 0|1:22:8,14 ./.:37:13,24 +chr20 719464 200x928 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=699822;QSTRAND=+ GT:DP:AD 1|0:24:13,11 1|1:36:15,21 1|1:36:20,16 +chr20 719532 200x929 T C 60 . QNAME=cluster19_000000F;QSTART=25041844;QSTRAND=- GT:DP:AD ./.:19:11,8 1|0:28:7,21 ./.:37:20,17 +chr20 720367 200x92a C G 60 . QNAME=cluster19_000000F;QSTART=681218;QSTRAND=+ GT:DP:AD ./.:23:11,12 0|1:18:8,10 ./.:41:23,18 +chr20 720501 200x92b G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=700859;QSTRAND=+ GT:DP:AD 1|0:39:21,18 1|1:35:17,18 0|1:31:16,15 +chr20 720677 200x92c C G 60 . QNAME=cluster19_000000F;QSTART=25040699;QSTRAND=- GT:DP:AD ./.:24:14,10 1|1:32:11,21 ./.:44:20,24 +chr20 720868 200x92d C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=701226;QSTRAND=+ GT:DP:AD 1|0:35:16,19 0|1:29:6,23 0|1:26:19,7 +chr20 720953 200x92e A G 60 . QNAME=cluster19_000000F;QSTART=25040423;QSTRAND=- GT:DP:AD ./.:35:24,11 1|1:27:13,14 ./.:37:15,22 +chr20 720987 200x92f T C 60 . QNAME=cluster19_000000F;QSTART=25040389;QSTRAND=- GT:DP:AD ./.:34:10,24 1|1:28:11,17 ./.:41:25,16 +chr20 721070 200x930 T C 60 . QNAME=cluster19_000000F;QSTART=25040306;QSTRAND=- GT:DP:AD ./.:28:7,21 1|0:39:22,17 ./.:44:19,25 +chr20 721315 200x931 A T 60 . QNAME=cluster19_000000F;QSTART=25040061;QSTRAND=- GT:DP:AD ./.:36:11,25 1|1:16:10,6 ./.:26:16,10 +chr20 721448 200x932 C T 60 . QNAME=cluster19_000000F;QSTART=25039928;QSTRAND=- GT:DP:AD ./.:33:25,8 1|1:36:17,19 ./.:21:15,6 +chr20 721653 200x933 G A 60 . QNAME=cluster19_000000F;QSTART=25039723;QSTRAND=- GT:DP:AD ./.:22:13,9 1|1:28:12,16 ./.:31:19,12 +chr20 721675 200x934 G C 60 . QNAME=cluster19_000000F;QSTART=25039701;QSTRAND=- GT:DP:AD ./.:33:8,25 1|1:23:10,13 ./.:14:7,7 +chr20 721926 200x935 C T 60 . QNAME=cluster19_000000F;QSTART=25039450;QSTRAND=- GT:DP:AD ./.:35:21,14 1|1:30:15,15 ./.:34:10,24 +chr20 722151 200x936 T C 60 . QNAME=cluster19_000000F;QSTART=683002;QSTRAND=+ GT:DP:AD ./.:25:11,14 0|1:42:23,19 ./.:30:12,18 +chr20 722203 200x937 T C 60 . QNAME=cluster19_000000F;QSTART=25039173;QSTRAND=- GT:DP:AD ./.:21:6,15 1|1:25:7,18 ./.:18:9,9 +chr20 722204 200x938 G A 60 . QNAME=cluster19_000000F;QSTART=683055;QSTRAND=+ GT:DP:AD ./.:30:22,8 0|1:22:9,13 ./.:33:8,25 +chr20 722214 200x939 G T 60 . QNAME=cluster19_000000F;QSTART=25039162;QSTRAND=- GT:DP:AD ./.:22:9,13 1|1:28:7,21 ./.:22:5,17 +chr20 722255 200x93a T C 60 . QNAME=cluster19_000000F;QSTART=25039121;QSTRAND=- GT:DP:AD ./.:41:18,23 1|1:33:14,19 ./.:27:17,10 +chr20 722277 200x93b C T 60 . QNAME=cluster19_000000F;QSTART=25039099;QSTRAND=- GT:DP:AD ./.:41:20,21 1|1:36:24,12 ./.:17:9,8 +chr20 722412 200x93c G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=702770;QSTRAND=+ GT:DP:AD 1|0:23:6,17 ./.:28:22,6 0|1:21:6,15 +chr20 723134 200x93d C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=703492;QSTRAND=+ GT:DP:AD 1|0:22:8,14 ./.:21:16,5 0|1:33:25,8 +chr20 723311 200x93e A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=703669;QSTRAND=+ GT:DP:AD 1|1:33:24,9 1|1:36:18,18 1|1:20:10,10 +chr20 723429 200x93f CTCT C 60 . QNAME=cluster19_000000F;QSTART=684281;QSTRAND=+ GT:DP:AD ./.:41:21,20 0|1:33:17,16 ./.:26:10,16 +chr20 723467 200x940 C CTTTCT 60 . QNAME=cluster19_000000F;QSTART=684316;QSTRAND=+ GT:DP:AD ./.:23:16,7 0|1:33:20,13 ./.:35:11,24 +chr20 723709 200x941 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=704067;QSTRAND=+ GT:DP:AD 1|0:32:22,10 0|1:23:6,17 0|1:17:7,10 +chr20 723727 200x942 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=704085;QSTRAND=+ GT:DP:AD 1|0:27:18,9 ./.:31:10,21 0|1:19:10,9 +chr20 723799 200x943 G A 60 . QNAME=cluster19_000000F;QSTART=25037577;QSTRAND=- GT:DP:AD ./.:20:12,8 1|0:41:20,21 ./.:17:12,5 +chr20 723808 200x944 G A 60 . QNAME=cluster19_000000F;QSTART=684661;QSTRAND=+ GT:DP:AD ./.:44:22,22 0|1:22:13,9 ./.:36:19,17 +chr20 723875 200x945 G A 60 . QNAME=cluster19_000000F;QSTART=684728;QSTRAND=+ GT:DP:AD ./.:26:13,13 0|1:38:20,18 ./.:42:17,25 +chr20 723915 200x946 A G 60 . QNAME=cluster19_000000F;QSTART=25037461;QSTRAND=- GT:DP:AD ./.:19:13,6 1|0:35:25,10 ./.:28:20,8 +chr20 724055 200x947 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=704413;QSTRAND=+ GT:DP:AD 1|0:22:6,16 0|1:13:8,5 0|1:27:18,9 +chr20 724660 200x948 C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=705019;QSTRAND=+ GT:DP:AD 1|0:40:15,25 ./.:31:17,14 0|1:19:12,7 +chr20 725763 200x949 T G 60 . QNAME=cluster19_000000F;QSTART=686616;QSTRAND=+ GT:DP:AD ./.:34:9,25 0|1:31:18,13 ./.:14:7,7 +chr20 726010 200x94a CAAAAAAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=706370;QSTRAND=+ GT:DP:AD 1|0:33:15,18 ./.:36:17,19 0|1:33:8,25 +chr20 726010 200x94b C CA 60 . QNAME=HG002-S9-H2-000001F;QSTART=680942;QSTRAND=+ GT:DP:AD 0|1:12:6,6 1|0:33:12,21 ./.:29:13,16 +chr20 726010 200x94c C CAAAAAAA 60 . QNAME=cluster19_000000F;QSTART=686864;QSTRAND=+ GT:DP:AD ./.:41:18,23 0|1:23:16,7 ./.:29:6,23 +chr20 726075 200x94d G A 60 . QNAME=cluster19_000000F;QSTART=686935;QSTRAND=+ GT:DP:AD ./.:34:16,18 0|1:33:20,13 ./.:19:11,8 +chr20 726115 200x94e A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=706466;QSTRAND=+ GT:DP:AD 1|0:31:23,8 0|1:27:16,11 0|1:44:20,24 +chr20 726166 200x94f T C 60 . QNAME=cluster19_000000F;QSTART=687026;QSTRAND=+ GT:DP:AD ./.:32:11,21 0|1:28:6,22 ./.:26:18,8 +chr20 726847 200x950 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=707198;QSTRAND=+ GT:DP:AD 1|0:25:5,20 ./.:30:5,25 0|1:34:20,14 +chr20 727050 200x951 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=707401;QSTRAND=+ GT:DP:AD 1|0:41:19,22 ./.:18:7,11 0|1:18:11,7 +chr20 727183 200x952 T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=707534;QSTRAND=+ GT:DP:AD 1|0:36:11,25 ./.:48:24,24 0|1:30:14,16 +chr20 727236 200x953 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=707587;QSTRAND=+ GT:DP:AD 1|0:36:23,13 ./.:39:19,20 0|1:34:18,16 +chr20 727293 200x954 G T 60 . QNAME=cluster23_scaffold_3;QSTART=24983447;QSTRAND=- GT:DP:AD ./.:22:13,9 ./.:37:15,22 1|0:35:19,16 +chr20 727295 200x955 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=707646;QSTRAND=+ GT:DP:AD 1|0:30:7,23 ./.:37:17,20 ./.:20:15,5 +chr20 727508 200x956 TATATCTAATATATATAATATCTAATATATATA T 60 . QNAME=cluster19_000000F;QSTART=25033867;QSTRAND=-;SVTYPE=DEL;SVLEN=-32 GT:DP:AD ./.:15:10,5 1/0:29:9,20 ./.:30:15,15 +chr20 727508 200x957 TATATCTAATATATATAATATCTAATATATATAATATCTAATATATATA T 60 . QNAME=cluster19_000000F;QSTART=688369;QSTRAND=+;SVTYPE=DEL;SVLEN=-48 GT:DP:AD ./.:38:18,20 0/1:34:22,12 ./.:28:13,15 +chr20 727556 200x958 AATATCTAATATATATAATATCTAATATATATAAT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=682489;QSTRAND=+;SVTYPE=DEL;SVLEN=-34 GT:DP:AD 0/1:26:8,18 ./.:41:17,24 1/0:30:17,13 +chr20 727600 200x959 G T 60 . QNAME=cluster23_scaffold_3;QSTART=24983174;QSTRAND=- GT:DP:AD ./.:32:21,11 ./.:42:25,17 1|0:33:12,21 +chr20 727602 200x95a G T 60 . QNAME=cluster23_scaffold_3;QSTART=24983172;QSTRAND=- GT:DP:AD ./.:42:23,19 ./.:29:22,7 1|0:32:13,19 +chr20 727613 200x95b A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=707964;QSTRAND=+ GT:DP:AD 1|0:35:21,14 1|1:33:25,8 0|1:14:7,7 +chr20 727615 200x95c C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=707966;QSTRAND=+ GT:DP:AD 1|0:35:11,24 1|1:25:16,9 0|1:38:24,14 +chr20 727615 200x95d C CGA 60 . QNAME=HG002-S9-H2-000001F;QSTART=682514;QSTRAND=+ GT:DP:AD 0|1:35:11,24 ./.:38:16,22 ./.:19:7,12 +chr20 727774 200x95e A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=682674;QSTRAND=+ GT:DP:AD 0|1:13:7,6 1|1:45:21,24 ./.:28:11,17 +chr20 727786 200x95f ATT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=682687;QSTRAND=+ GT:DP:AD 0|1:28:6,22 1|0:37:16,21 ./.:23:15,8 +chr20 727786 200x960 AT A 60 . QNAME=cluster23_scaffold_3;QSTART=24982988;QSTRAND=- GT:DP:AD ./.:19:13,6 ./.:30:10,20 1|0:14:7,7 +chr20 727926 200x961 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=708277;QSTRAND=+ GT:DP:AD 1|0:17:12,5 1|0:35:11,24 ./.:36:15,21 +chr20 727962 200x962 GGC G 60 . QNAME=cluster23_scaffold_3;QSTART=24982813;QSTRAND=- GT:DP:AD ./.:41:24,17 ./.:26:18,8 1|0:42:25,17 +chr20 728062 200x963 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=708413;QSTRAND=+ GT:DP:AD 1|1:37:25,12 1|1:37:21,16 0|1:29:10,19 +chr20 728326 200x964 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=708677;QSTRAND=+ GT:DP:AD 1|0:26:10,16 0|1:24:13,11 ./.:34:25,9 +chr20 728330 200x965 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=708681;QSTRAND=+ GT:DP:AD 1|0:37:13,24 0|1:35:18,17 ./.:36:11,25 +chr20 728371 200x966 G A 60 . QNAME=cluster19_000000F;QSTART=689183;QSTRAND=+ GT:DP:AD ./.:33:16,17 0|1:13:8,5 ./.:20:7,13 +chr20 728488 200x967 T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=683386;QSTRAND=+ GT:DP:AD 0|1:41:17,24 1|0:33:20,13 0|1:31:19,12 +chr20 728626 200x968 A G 60 . QNAME=cluster23_scaffold_2;QSTART=24966366;QSTRAND=- GT:DP:AD ./.:26:21,5 ./.:31:12,19 0|1:38:17,21 +chr20 728679 200x969 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=709030;QSTRAND=+ GT:DP:AD 1|1:37:13,24 1|0:18:8,10 1|1:45:24,21 +chr20 728689 200x96a C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=709040;QSTRAND=+ GT:DP:AD 1|1:34:16,18 1|0:34:19,15 0|1:20:15,5 +chr20 728722 200x96b G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=709073;QSTRAND=+ GT:DP:AD 1|1:37:19,18 1|0:47:24,23 1|1:20:9,11 +chr20 728924 200x96c G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=709275;QSTRAND=+ GT:DP:AD 1|1:33:19,14 1|0:32:12,20 0|1:39:22,17 +chr20 729045 200x96d A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=709396;QSTRAND=+ GT:DP:AD 1|1:18:11,7 1|0:42:23,19 1|1:39:21,18 +chr20 729328 200x96e C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=709679;QSTRAND=+ GT:DP:AD 1|1:34:14,20 1|0:27:8,19 1|1:15:8,7 +chr20 729751 200x96f C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=684649;QSTRAND=+ GT:DP:AD 0|1:32:10,22 1|0:38:21,17 0|1:44:24,20 +chr20 729893 200x970 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=684791;QSTRAND=+ GT:DP:AD 0|1:43:20,23 1|0:25:11,14 0|1:40:24,16 +chr20 730190 200x971 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=710541;QSTRAND=+ GT:DP:AD 1|0:27:14,13 ./.:47:23,24 1|0:50:25,25 +chr20 730755 200x972 A AG 60 . QNAME=HG002-S9-H1-000001F;QSTART=711107;QSTRAND=+ GT:DP:AD 1|1:23:15,8 1|1:40:17,23 1|1:23:12,11 +chr20 731406 200x973 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=686305;QSTRAND=+ GT:DP:AD 0|1:18:6,12 1|0:33:20,13 0|1:30:18,12 +chr20 731541 200x974 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=711893;QSTRAND=+ GT:DP:AD 1|1:41:21,20 1|0:31:6,25 1|1:35:19,16 +chr20 732158 200x975 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=687057;QSTRAND=+ GT:DP:AD 0|1:26:8,18 1|0:30:12,18 0|1:16:10,6 +chr20 732263 200x976 A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=687162;QSTRAND=+ GT:DP:AD 0|1:39:21,18 1|0:27:10,17 0|1:37:15,22 +chr20 732533 200x977 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=712885;QSTRAND=+ GT:DP:AD 1|1:38:16,22 1|0:32:20,12 1|1:33:13,20 +chr20 733181 200x978 T TTATG 60 . QNAME=HG002-S9-H1-000001F;QSTART=713534;QSTRAND=+ GT:DP:AD 1|0:32:13,19 ./.:40:23,17 ./.:30:25,5 +chr20 733364 200x979 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=713720;QSTRAND=+ GT:DP:AD 1|1:34:25,9 1|0:28:5,23 1|1:34:16,18 +chr20 733492 200x97a TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=713849;QSTRAND=+ GT:DP:AD 1|1:27:20,7 1|1:16:8,8 1|1:31:11,20 +chr20 733573 200x97b AAAAAC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=713929;QSTRAND=+ GT:DP:AD 1|0:42:24,18 ./.:17:7,10 ./.:23:18,5 +chr20 733573 200x97c A AAAAACAAAAC 60 . QNAME=cluster23_scaffold_3;QSTART=24977194;QSTRAND=- GT:DP:AD ./.:25:12,13 ./.:47:24,23 1|0:15:8,7 +chr20 733617 200x97d G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=713967;QSTRAND=+ GT:DP:AD 1|0:22:5,17 ./.:22:6,16 1|0:32:7,25 +chr20 733672 200x97e C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=714022;QSTRAND=+ GT:DP:AD 1|0:15:5,10 ./.:26:12,14 ./.:33:24,9 +chr20 733818 200x97f A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=714168;QSTRAND=+ GT:DP:AD 1|1:23:6,17 1|1:29:18,11 1|1:29:20,9 +chr20 733903 200x980 C T 60 . QNAME=cluster23_scaffold_3;QSTART=24976864;QSTRAND=- GT:DP:AD ./.:44:24,20 ./.:22:13,9 1|0:27:7,20 +chr20 734373 200x981 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=714723;QSTRAND=+ GT:DP:AD 1|0:21:6,15 ./.:36:23,13 ./.:35:22,13 +chr20 734383 200x982 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=714733;QSTRAND=+ GT:DP:AD 1|0:14:6,8 ./.:16:11,5 ./.:23:16,7 +chr20 734531 200x983 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=714881;QSTRAND=+ GT:DP:AD 1|1:43:21,22 1|0:28:9,19 1|1:23:14,9 +chr20 734610 200x984 G GGTGTGT 60 . QNAME=HG002-S9-H1-000001F;QSTART=714961;QSTRAND=+ GT:DP:AD 1|0:29:17,12 1|0:36:12,24 1|1:33:15,18 +chr20 734610 200x985 G GGTGTGTGT 60 . QNAME=HG002-S9-H2-000001F;QSTART=689509;QSTRAND=+ GT:DP:AD 0|1:33:14,19 ./.:13:6,7 ./.:25:15,10 +chr20 734610 200x986 G GGT 60 . QNAME=cluster19_000000F;QSTART=695423;QSTRAND=+ GT:DP:AD ./.:49:24,25 0|1:35:13,22 ./.:23:17,6 +chr20 734650 200x987 A G 60 . QNAME=cluster23_scaffold_3;QSTART=24976111;QSTRAND=- GT:DP:AD ./.:28:23,5 ./.:29:16,13 1|0:13:8,5 +chr20 735203 200x988 C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=715560;QSTRAND=+ GT:DP:AD 1|1:33:11,22 1|1:28:19,9 1|1:30:18,12 +chr20 735555 200x989 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=715912;QSTRAND=+ GT:DP:AD 1|1:32:20,12 1|0:33:19,14 1|1:30:23,7 +chr20 735589 200x98a A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=690496;QSTRAND=+ GT:DP:AD 0|1:26:5,21 1|0:26:18,8 1|1:26:7,19 +chr20 736154 200x98b C T 60 . QNAME=cluster23_scaffold_3;QSTART=24974606;QSTRAND=- GT:DP:AD ./.:23:15,8 ./.:47:24,23 1|0:31:11,20 +chr20 736400 200x98c A C 60 . QNAME=cluster23_scaffold_3;QSTART=24974360;QSTRAND=- GT:DP:AD ./.:27:8,19 ./.:34:10,24 1|0:30:21,9 +chr20 736444 200x98d A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=716801;QSTRAND=+ GT:DP:AD 1|1:30:20,10 1|0:47:23,24 1|1:35:10,25 +chr20 736736 200x98e CAA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=691644;QSTRAND=+ GT:DP:AD 0|1:18:13,5 1|0:20:11,9 1|1:42:22,20 +chr20 736736 200x98f CA C 60 . QNAME=cluster19_000000F;QSTART=697552;QSTRAND=+ GT:DP:AD ./.:50:25,25 0|1:36:24,12 ./.:12:7,5 +chr20 736925 200x990 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=691830;QSTRAND=+ GT:DP:AD 0|1:37:17,20 1|0:29:19,10 0|1:40:15,25 +chr20 737005 200x991 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=691910;QSTRAND=+ GT:DP:AD 0|1:34:10,24 1|0:24:13,11 0|1:32:11,21 +chr20 737174 200x992 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=717531;QSTRAND=+ GT:DP:AD 1|1:16:10,6 1|1:46:21,25 1|1:20:14,6 +chr20 737624 200x993 A AAAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=717982;QSTRAND=+ GT:DP:AD 1|0:38:15,23 ./.:20:7,13 ./.:21:8,13 +chr20 737624 200x994 A AAATAAT 60 . QNAME=cluster19_000000F;QSTART=698439;QSTRAND=+ GT:DP:AD ./.:33:21,12 0|1:29:18,11 ./.:36:25,11 +chr20 737624 200x995 AAATAAT A 60 . QNAME=cluster23_scaffold_3;QSTART=24973138;QSTRAND=- GT:DP:AD ./.:36:24,12 ./.:25:13,12 1|0:47:24,23 +chr20 737898 200x996 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=718258;QSTRAND=+ GT:DP:AD 1|0:44:25,19 ./.:32:25,7 ./.:35:10,25 +chr20 738059 200x997 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=718419;QSTRAND=+ GT:DP:AD 1|1:24:11,13 1|1:30:25,5 1|1:26:6,20 +chr20 738091 200x998 C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=718451;QSTRAND=+ GT:DP:AD 1|1:44:23,21 1|1:16:5,11 1|1:30:18,12 +chr20 738584 200x999 C CA 60 . QNAME=cluster19_000000F;QSTART=699405;QSTRAND=+ GT:DP:AD ./.:23:9,14 0|1:32:9,23 ./.:26:16,10 +chr20 738739 200x99a G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=693644;QSTRAND=+ GT:DP:AD 0|1:25:17,8 1|0:32:12,20 0|1:38:22,16 +chr20 739096 200x99b T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=719456;QSTRAND=+ GT:DP:AD 1|1:15:6,9 1|0:38:25,13 1|1:30:6,24 +chr20 739210 200x99c T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=719570;QSTRAND=+ GT:DP:AD 1|1:42:20,22 1|0:22:15,7 1|1:32:18,14 +chr20 739239 200x99d C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=719599;QSTRAND=+ GT:DP:AD 1|1:40:24,16 1|0:35:10,25 1|1:35:16,19 +chr20 740272 200x99e G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=695177;QSTRAND=+ GT:DP:AD 0|1:29:18,11 1|0:33:14,19 0|1:28:11,17 +chr20 740467 200x99f A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=720827;QSTRAND=+ GT:DP:AD 1|1:38:17,21 1|1:29:7,22 1|1:20:9,11 +chr20 741153 200x9a0 T G 60 . QNAME=cluster23_scaffold_3;QSTART=24969615;QSTRAND=- GT:DP:AD ./.:17:12,5 ./.:13:6,7 1|0:44:23,21 +chr20 741453 200x9a1 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=721813;QSTRAND=+ GT:DP:AD 1|0:24:12,12 ./.:39:21,18 ./.:32:22,10 +chr20 741767 200x9a2 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=696672;QSTRAND=+ GT:DP:AD 0|1:20:5,15 1|0:42:18,24 0|1:24:17,7 +chr20 741939 200x9a3 A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=696844;QSTRAND=+ GT:DP:AD 0|1:30:6,24 1|0:15:7,8 1|1:35:23,12 +chr20 742416 200x9a4 T C 60 . QNAME=cluster23_scaffold_3;QSTART=24968352;QSTRAND=- GT:DP:AD ./.:33:17,16 ./.:29:15,14 1|0:32:9,23 +chr20 742511 200x9a5 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=722871;QSTRAND=+ GT:DP:AD 1|0:41:17,24 ./.:34:25,9 ./.:34:9,25 +chr20 742657 200x9a6 G T 60 . QNAME=cluster23_scaffold_3;QSTART=24968111;QSTRAND=- GT:DP:AD ./.:31:14,17 ./.:30:16,14 1|0:42:22,20 +chr20 743121 200x9a7 GTCTCTCTC G 60 . QNAME=HG002-S9-H2-000001F;QSTART=698027;QSTRAND=+ GT:DP:AD 0|1:40:16,24 ./.:29:13,16 ./.:26:20,6 +chr20 743121 200x9a8 GTCTC G 60 . QNAME=cluster19_000000F;QSTART=25018283;QSTRAND=- GT:DP:AD ./.:30:9,21 1|0:40:24,16 ./.:24:14,10 +chr20 743121 200x9a9 G GTCTCTCTCTC 60 . QNAME=cluster19_000000F;QSTART=703943;QSTRAND=+ GT:DP:AD ./.:23:14,9 0|1:47:22,25 ./.:25:13,12 +chr20 743153 200x9aa C CACACACACACACA 60 . QNAME=HG002-S9-H1-000001F;QSTART=723514;QSTRAND=+ GT:DP:AD 1|0:28:18,10 ./.:23:7,16 ./.:12:5,7 +chr20 743153 200x9ab CTCTCTCTCTCT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=723527;QSTRAND=+ GT:DP:AD 1|0:26:20,6 ./.:37:12,25 ./.:38:22,16 +chr20 743160 200x9ac T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=698057;QSTRAND=+ GT:DP:AD 0|1:28:15,13 ./.:31:9,22 ./.:27:12,15 +chr20 743160 200x9ad T TCACACA 60 . QNAME=cluster23_scaffold_3;QSTART=24967602;QSTRAND=- GT:DP:AD ./.:36:24,12 ./.:31:16,15 1|0:31:14,17 +chr20 743162 200x9ae T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=698059;QSTRAND=+ GT:DP:AD 0|1:36:17,19 1|0:22:16,6 1|0:19:5,14 +chr20 743162 200x9af T TCA 60 . QNAME=cluster23_scaffold_2;QSTART=24951823;QSTRAND=- GT:DP:AD ./.:27:6,21 ./.:27:14,13 0|1:35:11,24 +chr20 743164 200x9b0 T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=698061;QSTRAND=+ GT:DP:AD 0|1:30:15,15 1|0:39:25,14 1|1:29:24,5 +chr20 743734 200x9b1 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=724096;QSTRAND=+ GT:DP:AD 1|0:36:18,18 ./.:31:11,20 ./.:29:22,7 +chr20 743803 200x9b2 A AG 60 . QNAME=HG002-S9-H1-000001F;QSTART=724166;QSTRAND=+ GT:DP:AD 1|1:39:14,25 1|0:31:7,24 1|1:47:23,24 +chr20 743934 200x9b3 G A 60 . QNAME=cluster23_scaffold_3;QSTART=24966827;QSTRAND=- GT:DP:AD ./.:34:13,21 ./.:37:15,22 1|0:28:18,10 +chr20 744816 200x9b4 C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=725179;QSTRAND=+ GT:DP:AD 1|1:34:9,25 1|1:25:11,14 1|1:31:9,22 +chr20 745347 200x9b5 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=725710;QSTRAND=+ GT:DP:AD 1|1:16:9,7 1|0:37:14,23 1|1:27:21,6 +chr20 745631 200x9b6 CAGA C 60 . QNAME=cluster19_000000F;QSTART=706463;QSTRAND=+ GT:DP:AD ./.:12:6,6 0|1:29:12,17 ./.:31:7,24 +chr20 745642 200x9b7 C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=726005;QSTRAND=+ GT:DP:AD 1|0:38:22,16 ./.:30:14,16 ./.:33:20,13 +chr20 746583 200x9b8 C T 60 . QNAME=cluster23_scaffold_3;QSTART=24964178;QSTRAND=- GT:DP:AD ./.:17:11,6 ./.:29:7,22 1|0:21:11,10 +chr20 746687 200x9b9 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=701585;QSTRAND=+ GT:DP:AD 0|1:37:19,18 1|1:26:15,11 0|1:27:7,20 +chr20 746832 200x9ba C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=701730;QSTRAND=+ GT:DP:AD 0|1:30:12,18 1|0:29:16,13 0|1:25:14,11 +chr20 746873 200x9bb CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=701772;QSTRAND=+ GT:DP:AD 0|1:30:13,17 1|1:45:20,25 1|1:34:9,25 +chr20 746873 200x9bc C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=727237;QSTRAND=+ GT:DP:AD 1|0:30:14,16 ./.:20:5,15 ./.:30:15,15 +chr20 746937 200x9bd G A 60 . QNAME=cluster23_scaffold_3;QSTART=24963825;QSTRAND=- GT:DP:AD ./.:41:18,23 ./.:13:5,8 1|0:44:25,19 +chr20 747249 200x9be T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=702146;QSTRAND=+ GT:DP:AD 0|1:40:24,16 1|1:33:9,24 0|1:19:8,11 +chr20 747381 200x9bf A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=702278;QSTRAND=+ GT:DP:AD 0|1:27:19,8 1|1:29:16,13 0|1:38:15,23 +chr20 747855 200x9c0 A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=702752;QSTRAND=+ GT:DP:AD 0|1:18:6,12 1|1:29:23,6 0|1:25:15,10 +chr20 748018 200x9c1 G A 60 . QNAME=cluster23_scaffold_3;QSTART=24962744;QSTRAND=- GT:DP:AD ./.:50:25,25 ./.:31:12,19 1|0:37:25,12 +chr20 748207 200x9c2 CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=703105;QSTRAND=+ GT:DP:AD 0|1:39:17,22 1|0:27:14,13 0|1:43:24,19 +chr20 748212 200x9c3 G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=703108;QSTRAND=+ GT:DP:AD 0|1:25:18,7 1|1:31:22,9 0|1:32:15,17 +chr20 748246 200x9c4 CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=728611;QSTRAND=+ GT:DP:AD 1|0:36:13,23 0|1:30:14,16 ./.:14:8,6 +chr20 748431 200x9c5 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=703327;QSTRAND=+ GT:DP:AD 0|1:34:23,11 1|0:26:17,9 0|1:26:7,19 +chr20 748452 200x9c6 AT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=703349;QSTRAND=+ GT:DP:AD 0|1:41:25,16 1|0:30:23,7 1|1:32:8,24 +chr20 748776 200x9c7 G A 60 . QNAME=cluster19_000000F;QSTART=709602;QSTRAND=+ GT:DP:AD ./.:37:24,13 0|1:37:13,24 ./.:11:5,6 +chr20 749061 200x9c8 C T 60 . QNAME=cluster23_scaffold_3;QSTART=24961702;QSTRAND=- GT:DP:AD ./.:38:23,15 ./.:17:6,11 1|0:28:20,8 +chr20 749346 200x9c9 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=704241;QSTRAND=+ GT:DP:AD 0|1:44:19,25 1|0:35:20,15 0|1:24:5,19 +chr20 749546 200x9ca C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=704441;QSTRAND=+ GT:DP:AD 0|1:26:9,17 1|0:23:6,17 0|1:30:10,20 +chr20 749854 200x9cb G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=730217;QSTRAND=+ GT:DP:AD 1|1:39:17,22 1|1:31:15,16 1|1:29:12,17 +chr20 750249 200x9cc C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=705144;QSTRAND=+ GT:DP:AD 0|1:39:21,18 1|0:30:24,6 0|1:30:19,11 +chr20 750361 200x9cd A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=705256;QSTRAND=+ GT:DP:AD 0|1:14:5,9 1|0:29:15,14 0|1:25:13,12 +chr20 750494 200x9ce C CA 60 . QNAME=cluster19_000000F;QSTART=25010915;QSTRAND=- GT:DP:AD ./.:19:6,13 1|0:35:15,20 1|1:16:8,8 +chr20 750546 200x9cf T G 60 . QNAME=cluster23_scaffold_3;QSTART=24960216;QSTRAND=- GT:DP:AD ./.:43:23,20 ./.:37:23,14 1|0:38:19,19 +chr20 750567 200x9d0 C A 60 . QNAME=cluster19_000000F;QSTART=711393;QSTRAND=+ GT:DP:AD ./.:36:16,20 0|1:39:22,17 ./.:31:22,9 +chr20 751100 200x9d1 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=705995;QSTRAND=+ GT:DP:AD 0|1:29:6,23 1|0:32:11,21 0|1:27:10,17 +chr20 751283 200x9d2 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=706178;QSTRAND=+ GT:DP:AD 0|1:25:18,7 1|0:14:5,9 0|1:36:20,16 +chr20 751473 200x9d3 CTTTATTTTATTTTATTTTATTTTAT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=706369;QSTRAND=+;SVTYPE=DEL;SVLEN=-25 GT:DP:AD 0/1:34:11,23 1/0:35:12,23 0/1:35:13,22 +chr20 751473 200x9d4 CTTTATTTTAT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=731837;QSTRAND=+ GT:DP:AD 1|0:27:7,20 0|1:15:10,5 ./.:25:12,13 +chr20 751473 200x9d5 CTTTAT C 60 . QNAME=cluster23_scaffold_3;QSTART=24959289;QSTRAND=- GT:DP:AD ./.:21:12,9 ./.:36:15,21 1|0:27:5,22 +chr20 751519 200x9d6 T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=706389;QSTRAND=+ GT:DP:AD 0|1:39:24,15 1|0:39:20,19 0|1:20:15,5 +chr20 751627 200x9d7 A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=706497;QSTRAND=+ GT:DP:AD 0|1:32:13,19 1|0:35:20,15 0|1:33:19,14 +chr20 751651 200x9d8 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=706521;QSTRAND=+ GT:DP:AD 0|1:43:18,25 1|0:30:6,24 0|1:34:13,21 +chr20 751755 200x9d9 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=706625;QSTRAND=+ GT:DP:AD 0|1:32:15,17 1|0:30:18,12 0|1:48:24,24 +chr20 752069 200x9da ATCTT A 60 . QNAME=cluster23_scaffold_3;QSTART=24958698;QSTRAND=- GT:DP:AD ./.:44:19,25 ./.:29:7,22 1|0:43:21,22 +chr20 752120 200x9db T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=706990;QSTRAND=+ GT:DP:AD 0|1:36:15,21 1|0:18:11,7 0|1:29:13,16 +chr20 752235 200x9dc G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=707105;QSTRAND=+ GT:DP:AD 0|1:32:9,23 1|0:30:21,9 0|1:31:20,11 +chr20 752300 200x9dd C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=707170;QSTRAND=+ GT:DP:AD 0|1:19:14,5 1|0:29:6,23 0|1:14:5,9 +chr20 752450 200x9de T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=732803;QSTRAND=+ GT:DP:AD 1|1:24:11,13 1|1:16:5,11 1|1:21:10,11 +chr20 752821 200x9df T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=707691;QSTRAND=+ GT:DP:AD 0|1:20:8,12 1|0:28:8,20 0|1:44:25,19 +chr20 753097 200x9e0 G GAAGAAAGAAAGAAAGAAAAGA 60 . QNAME=cluster19_000000F;QSTART=25008316;QSTRAND=- GT:DP:AD ./.:34:25,9 1|0:31:7,24 ./.:29:18,11 +chr20 753097 200x9e1 G GAAGA 60 . QNAME=cluster23_scaffold_3;QSTART=24957670;QSTRAND=- GT:DP:AD ./.:34:20,14 ./.:42:24,18 1|0:38:23,15 +chr20 753109 200x9e2 A AAAGAAAAGAAAGAAAGAAAGAAAAGAAAGAAAG 60 . QNAME=HG002-S9-H2-000001F;QSTART=707980;QSTRAND=+;SVTYPE=INS;SVLEN=33 GT:DP:AD 0/1:30:6,24 ./.:29:16,13 ./.:32:20,12 +chr20 753109 200x9e3 A AAAGAAAAGAAAGAAAGAAAGAAAAG 60 . QNAME=cluster23_scaffold_2;QSTART=24941877;QSTRAND=-;SVTYPE=INS;SVLEN=25 GT:DP:AD ./.:45:25,20 ./.:22:10,12 0/1:42:24,18 +chr20 753112 200x9e4 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=733465;QSTRAND=+ GT:DP:AD 1|0:32:21,11 0|1:30:13,17 ./.:34:15,19 +chr20 753113 200x9e5 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=733466;QSTRAND=+ GT:DP:AD 1|0:25:15,10 0|1:28:13,15 ./.:19:7,12 +chr20 753141 200x9e6 GAAAGAAAGAAAGAAAGAA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=733495;QSTRAND=+ GT:DP:AD 1|0:21:10,11 ./.:43:19,24 ./.:28:13,15 +chr20 753148 200x9e7 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=708051;QSTRAND=+ GT:DP:AD 0|1:38:19,19 1|0:22:5,17 0|1:32:9,23 +chr20 753159 200x9e8 A AAG 60 . QNAME=HG002-S9-H2-000001F;QSTART=708063;QSTRAND=+ GT:DP:AD 0|1:30:5,25 1|1:38:21,17 0|1:30:23,7 +chr20 753159 200x9e9 A AAAGAAAG 60 . QNAME=cluster23_scaffold_3;QSTART=24957601;QSTRAND=- GT:DP:AD ./.:37:21,16 ./.:29:6,23 1|0:20:13,7 +chr20 753194 200x9ea G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=708099;QSTRAND=+ GT:DP:AD 0|1:30:16,14 1|0:30:10,20 0|1:40:17,23 +chr20 753319 200x9eb T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=708224;QSTRAND=+ GT:DP:AD 0|1:22:10,12 1|0:27:19,8 0|1:32:16,16 +chr20 753350 200x9ec C T 60 . QNAME=cluster23_scaffold_3;QSTART=24957410;QSTRAND=- GT:DP:AD ./.:36:19,17 ./.:16:5,11 1|0:37:12,25 +chr20 753848 200x9ed C A 60 . QNAME=cluster23_scaffold_3;QSTART=24956912;QSTRAND=- GT:DP:AD ./.:32:7,25 ./.:22:5,17 1|0:48:24,24 +chr20 753849 200x9ee C A 60 . QNAME=cluster23_scaffold_3;QSTART=24956911;QSTRAND=- GT:DP:AD ./.:27:16,11 ./.:34:20,14 1|0:37:20,17 +chr20 753973 200x9ef A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=708878;QSTRAND=+ GT:DP:AD 0|1:44:20,24 1|0:44:24,20 0|1:34:12,22 +chr20 754002 200x9f0 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=734337;QSTRAND=+ GT:DP:AD 1|0:28:16,12 ./.:26:8,18 ./.:17:12,5 +chr20 754073 200x9f1 A G 60 . QNAME=cluster23_scaffold_3;QSTART=24956687;QSTRAND=- GT:DP:AD ./.:48:23,25 ./.:32:9,23 1|0:41:21,20 +chr20 754124 200x9f2 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=734459;QSTRAND=+ GT:DP:AD 1|1:26:5,21 1|0:38:25,13 1|1:34:20,14 +chr20 754553 200x9f3 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=709458;QSTRAND=+ GT:DP:AD 0|1:47:22,25 1|0:36:22,14 0|1:23:15,8 +chr20 755158 200x9f4 G T 60 . QNAME=cluster19_000000F;QSTART=25006253;QSTRAND=- GT:DP:AD ./.:31:6,25 1|0:16:6,10 ./.:24:6,18 +chr20 755213 200x9f5 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=735548;QSTRAND=+ GT:DP:AD 1|1:19:12,7 1|1:25:5,20 1|1:41:24,17 +chr20 755214 200x9f6 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=735549;QSTRAND=+ GT:DP:AD 1|0:12:5,7 ./.:28:12,16 ./.:16:7,9 +chr20 755269 200x9f7 C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=735605;QSTRAND=+ GT:DP:AD 1|1:35:10,25 1|1:36:19,17 1|1:46:25,21 +chr20 755467 200x9f8 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=735803;QSTRAND=+ GT:DP:AD 1|0:28:22,6 ./.:37:21,16 ./.:35:16,19 +chr20 755545 200x9f9 G A 60 . QNAME=cluster23_scaffold_3;QSTART=24955214;QSTRAND=- GT:DP:AD ./.:18:8,10 ./.:37:21,16 1|0:34:25,9 +chr20 755581 200x9fa G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=710487;QSTRAND=+ GT:DP:AD 0|1:37:24,13 1|1:32:12,20 1|1:29:12,17 +chr20 755749 200x9fb T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=736085;QSTRAND=+ GT:DP:AD 1|0:35:10,25 ./.:15:6,9 ./.:33:22,11 +chr20 755803 200x9fc A G 60 . QNAME=cluster19_000000F;QSTART=716622;QSTRAND=+ GT:DP:AD ./.:31:11,20 0|1:25:14,11 ./.:30:22,8 +chr20 756000 200x9fd G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=736336;QSTRAND=+ GT:DP:AD 1|1:31:20,11 1|1:33:11,22 0|1:12:6,6 +chr20 756217 200x9fe C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=736553;QSTRAND=+ GT:DP:AD 1|0:20:15,5 ./.:19:11,8 ./.:46:23,23 +chr20 756388 200x9ff A G 60 . QNAME=cluster23_scaffold_3;QSTART=24954371;QSTRAND=- GT:DP:AD ./.:39:17,22 ./.:36:16,20 1|0:20:14,6 +chr20 756408 200xa00 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=736744;QSTRAND=+ GT:DP:AD 1|0:20:15,5 ./.:24:8,16 ./.:34:12,22 +chr20 756478 200xa01 T C 60 . QNAME=cluster23_scaffold_3;QSTART=24954281;QSTRAND=- GT:DP:AD ./.:34:18,16 ./.:18:10,8 1|0:16:10,6 +chr20 756575 200xa02 CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=736912;QSTRAND=+ GT:DP:AD 1|1:21:16,5 1|1:23:14,9 0|1:35:18,17 +chr20 756637 200xa03 G A 60 . QNAME=cluster23_scaffold_3;QSTART=24954122;QSTRAND=- GT:DP:AD ./.:21:7,14 ./.:34:22,12 1|0:28:5,23 +chr20 756764 200xa04 A G 60 . QNAME=cluster23_scaffold_3;QSTART=24953995;QSTRAND=- GT:DP:AD ./.:28:14,14 ./.:26:11,15 1|0:28:5,23 +chr20 756872 200xa05 CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=737208;QSTRAND=+ GT:DP:AD 1|1:47:22,25 1|1:35:17,18 1|0:31:21,10 +chr20 756909 200xa06 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=737243;QSTRAND=+ GT:DP:AD 1|1:21:11,10 1|1:49:24,25 1|1:15:5,10 +chr20 758241 200xa07 A AT 60 . QNAME=HG002-S9-H1-000001F;QSTART=738576;QSTRAND=+ GT:DP:AD 1|1:28:10,18 1|1:20:8,12 0|1:24:19,5 +chr20 758241 200xa08 A ATTT 60 . QNAME=cluster23_scaffold_3;QSTART=24952516;QSTRAND=- GT:DP:AD ./.:28:19,9 ./.:24:16,8 1|0:21:12,9 +chr20 758268 200xa09 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=738603;QSTRAND=+ GT:DP:AD 1|0:33:14,19 ./.:28:9,19 ./.:20:8,12 +chr20 758339 200xa0a C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=738674;QSTRAND=+ GT:DP:AD 1|0:33:17,16 ./.:16:10,6 ./.:32:21,11 +chr20 758391 200xa0b A C 60 . QNAME=cluster23_scaffold_3;QSTART=24952366;QSTRAND=- GT:DP:AD ./.:14:5,9 ./.:19:12,7 1|0:18:5,13 +chr20 758562 200xa0c T C 60 . QNAME=cluster23_scaffold_3;QSTART=24952195;QSTRAND=- GT:DP:AD ./.:32:21,11 ./.:25:5,20 1|0:27:16,11 +chr20 758620 200xa0d T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=713525;QSTRAND=+ GT:DP:AD 0|1:21:11,10 1|0:39:24,15 0|1:24:12,12 +chr20 758664 200xa0e T C 60 . QNAME=cluster23_scaffold_3;QSTART=24952093;QSTRAND=- GT:DP:AD ./.:31:6,25 ./.:33:24,9 1|0:32:12,20 +chr20 758808 200xa0f G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=739143;QSTRAND=+ GT:DP:AD 1|1:28:14,14 1|1:30:12,18 1|1:19:9,10 +chr20 758874 200xa10 C G 60 . QNAME=cluster19_000000F;QSTART=719692;QSTRAND=+ GT:DP:AD ./.:38:16,22 0|1:34:10,24 ./.:33:18,15 +chr20 758972 200xa11 CGTGTGTGT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=713878;QSTRAND=+ GT:DP:AD 0|1:22:9,13 1|1:33:22,11 0|1:15:7,8 +chr20 758972 200xa12 CGTGTGTGTGT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=739308;QSTRAND=+ GT:DP:AD 1|0:22:14,8 ./.:31:10,21 ./.:17:6,11 +chr20 758972 200xa13 CGTGT C 60 . QNAME=cluster23_scaffold_3;QSTART=24951785;QSTRAND=- GT:DP:AD ./.:45:23,22 ./.:35:25,10 1|0:27:12,15 +chr20 759048 200xa14 AC A 60 . QNAME=cluster23_scaffold_3;QSTART=24951713;QSTRAND=- GT:DP:AD ./.:45:23,22 ./.:29:18,11 1|0:26:21,5 +chr20 759464 200xa15 C CA 60 . QNAME=HG002-S9-H2-000001F;QSTART=714362;QSTRAND=+ GT:DP:AD 0|1:23:14,9 1|1:41:23,18 0|1:25:20,5 +chr20 760189 200xa16 G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=715087;QSTRAND=+ GT:DP:AD 0|1:32:18,14 1|0:26:19,7 0|1:18:8,10 +chr20 760275 200xa17 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=740600;QSTRAND=+ GT:DP:AD 1|1:24:6,18 1|1:32:25,7 1|1:25:6,19 +chr20 761203 200xa18 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=741528;QSTRAND=+ GT:DP:AD 1|1:38:16,22 0|1:24:13,11 1|1:38:19,19 +chr20 761573 200xa19 C G 60 . QNAME=cluster19_000000F;QSTART=24999845;QSTRAND=- GT:DP:AD ./.:43:24,19 1|0:32:17,15 1|0:46:24,22 +chr20 761593 200xa1a G A 60 . QNAME=cluster19_000000F;QSTART=24999825;QSTRAND=- GT:DP:AD ./.:12:6,6 1|1:23:11,12 ./.:25:10,15 +chr20 761595 200xa1b T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=741920;QSTRAND=+ GT:DP:AD 1|1:38:21,17 1|1:22:12,10 1|1:21:15,6 +chr20 761987 200xa1c A G 60 . QNAME=cluster19_000000F;QSTART=24999431;QSTRAND=- GT:DP:AD ./.:31:15,16 1|0:42:18,24 1|1:36:12,24 +chr20 762072 200xa1d A C 60 . QNAME=cluster23_scaffold_3;QSTART=24948690;QSTRAND=- GT:DP:AD ./.:30:22,8 ./.:31:23,8 1|0:26:12,14 +chr20 762187 200xa1e G T 60 . QNAME=cluster19_000000F;QSTART=24999231;QSTRAND=- GT:DP:AD ./.:18:9,9 1|0:34:17,17 1|0:36:11,25 +chr20 762374 200xa1f G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=742699;QSTRAND=+ GT:DP:AD 1|1:22:13,9 1|1:29:13,16 1|0:41:17,24 +chr20 762480 200xa20 C G 60 . QNAME=cluster19_000000F;QSTART=24998938;QSTRAND=- GT:DP:AD ./.:43:21,22 1|0:17:7,10 1|0:17:5,12 +chr20 762486 200xa21 C T 60 . QNAME=cluster19_000000F;QSTART=24998932;QSTRAND=- GT:DP:AD ./.:47:24,23 1|0:14:8,6 1|0:33:25,8 +chr20 762576 200xa22 T C 60 . QNAME=cluster19_000000F;QSTART=24998842;QSTRAND=- GT:DP:AD ./.:25:16,9 1|0:25:6,19 1|0:42:23,19 +chr20 762628 200xa23 C T 60 . QNAME=cluster19_000000F;QSTART=24998790;QSTRAND=- GT:DP:AD ./.:31:20,11 1|0:33:9,24 1|0:27:21,6 +chr20 763183 200xa24 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=743508;QSTRAND=+ GT:DP:AD 1|1:19:12,7 1|1:17:10,7 1|0:16:7,9 +chr20 763406 200xa25 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=743731;QSTRAND=+ GT:DP:AD 1|1:48:24,24 0|1:28:11,17 ./.:30:15,15 +chr20 763806 200xa26 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=744131;QSTRAND=+ GT:DP:AD 1|1:33:23,10 1|1:26:21,5 1|0:36:17,19 +chr20 764018 200xa27 A ACAGGTCAAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=744344;QSTRAND=+ GT:DP:AD 1|1:22:16,6 0|1:27:5,22 ./.:35:10,25 +chr20 764203 200xa28 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=744537;QSTRAND=+ GT:DP:AD 1|1:38:16,22 1|1:38:16,22 1|0:28:23,5 +chr20 764230 200xa29 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=744564;QSTRAND=+ GT:DP:AD 1|1:20:5,15 1|1:36:22,14 1|0:22:14,8 +chr20 764442 200xa2a A AGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGG 60 . QNAME=cluster23_scaffold_3;QSTART=24946242;QSTRAND=-;SVTYPE=INS;SVLEN=78 GT:DP:AD ./.:30:19,11 ./.:35:14,21 1/0:46:22,24 +chr20 764537 200xa2b A AGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=744872;QSTRAND=+;SVTYPE=INS;SVLEN=117 GT:DP:AD 1/1:23:18,5 0/1:14:6,8 ./.:45:20,25 +chr20 764537 200xa2c A AGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAT 60 . QNAME=cluster19_000000F;QSTART=24996803;QSTRAND=-;SVTYPE=INS;SVLEN=78 GT:DP:AD ./.:25:14,11 1/0:43:20,23 ./.:30:22,8 +chr20 764800 200xa2d C A 60 . QNAME=cluster23_scaffold_2;QSTART=24930190;QSTRAND=- GT:DP:AD ./.:34:22,12 ./.:29:16,13 0|1:35:24,11 +chr20 765454 200xa2e G A 60 . QNAME=cluster19_000000F;QSTART=24995886;QSTRAND=- GT:DP:AD ./.:42:17,25 1|0:24:12,12 ./.:41:18,23 +chr20 765937 200xa2f C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=746389;QSTRAND=+ GT:DP:AD 1|1:40:25,15 0|1:13:5,8 ./.:23:11,12 +chr20 766211 200xa30 A AG 60 . QNAME=HG002-S9-H1-000001F;QSTART=746664;QSTRAND=+ GT:DP:AD 1|1:35:10,25 1|1:20:10,10 1|0:47:22,25 +chr20 766216 200xa31 G T 60 . QNAME=cluster19_000000F;QSTART=24995123;QSTRAND=- GT:DP:AD ./.:27:16,11 1|0:28:16,12 ./.:25:7,18 +chr20 766241 200xa32 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=746694;QSTRAND=+ GT:DP:AD 1|1:33:22,11 1|1:24:12,12 1|0:34:22,12 +chr20 766308 200xa33 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=746761;QSTRAND=+ GT:DP:AD 1|1:45:25,20 1|1:42:20,22 1|0:18:10,8 +chr20 766512 200xa34 C A 60 . QNAME=cluster19_000000F;QSTART=24994827;QSTRAND=- GT:DP:AD ./.:40:15,25 1|0:20:10,10 ./.:21:7,14 +chr20 766576 200xa35 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=747029;QSTRAND=+ GT:DP:AD 1|1:22:10,12 1|1:32:11,21 1|1:32:18,14 +chr20 766899 200xa36 T TA 60 . QNAME=cluster23_scaffold_2;QSTART=24928090;QSTRAND=- GT:DP:AD ./.:24:10,14 ./.:26:16,10 0|1:43:21,22 +chr20 767023 200xa37 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=747476;QSTRAND=+ GT:DP:AD 1|1:45:23,22 0|1:40:24,16 ./.:27:16,11 +chr20 767036 200xa38 A ATAG 60 . QNAME=cluster19_000000F;QSTART=24994300;QSTRAND=- GT:DP:AD ./.:27:18,9 1|0:34:19,15 ./.:30:24,6 +chr20 767191 200xa39 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=747644;QSTRAND=+ GT:DP:AD 1|1:31:8,23 1|1:37:17,20 1|0:21:14,7 +chr20 767349 200xa3a C T 60 . QNAME=cluster19_000000F;QSTART=24993987;QSTRAND=- GT:DP:AD ./.:36:22,14 1|0:24:16,8 ./.:25:17,8 +chr20 767359 200xa3b C CT 60 . QNAME=cluster23_scaffold_3;QSTART=24943323;QSTRAND=- GT:DP:AD ./.:21:7,14 ./.:39:25,14 1|0:14:7,7 +chr20 767376 200xa3c T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=747829;QSTRAND=+ GT:DP:AD 1|1:35:12,23 1|1:39:24,15 1|0:19:11,8 +chr20 767966 200xa3d T C 60 . QNAME=cluster19_000000F;QSTART=24993370;QSTRAND=- GT:DP:AD ./.:48:24,24 1|0:32:11,21 ./.:26:12,14 +chr20 768267 200xa3e A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=748720;QSTRAND=+ GT:DP:AD 1|1:21:15,6 0|1:43:22,21 ./.:27:22,5 +chr20 768330 200xa3f T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=748783;QSTRAND=+ GT:DP:AD 1|1:23:14,9 1|1:22:16,6 1|0:27:5,22 +chr20 769651 200xa40 C G 60 . QNAME=cluster23_scaffold_3;QSTART=24941031;QSTRAND=- GT:DP:AD ./.:34:17,17 ./.:15:6,9 1|0:25:14,11 +chr20 769672 200xa41 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=750125;QSTRAND=+ GT:DP:AD 1|1:42:17,25 0|1:22:17,5 ./.:19:14,5 +chr20 769904 200xa42 A C 60 . QNAME=cluster19_000000F;QSTART=730843;QSTRAND=+ GT:DP:AD ./.:23:15,8 0|1:35:14,21 ./.:26:16,10 +chr20 770094 200xa43 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=750547;QSTRAND=+ GT:DP:AD 1|1:43:22,21 1|1:23:16,7 1|0:21:7,14 +chr20 770601 200xa44 C T 60 . QNAME=cluster23_scaffold_3;QSTART=24940081;QSTRAND=- GT:DP:AD ./.:34:15,19 ./.:45:20,25 1|0:36:15,21 +chr20 771027 200xa45 T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=751480;QSTRAND=+ GT:DP:AD 1|1:30:18,12 0|1:37:16,21 ./.:26:10,16 +chr20 771420 200xa46 CTT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=751874;QSTRAND=+ GT:DP:AD 1|1:33:20,13 ./.:32:19,13 ./.:39:22,17 +chr20 771488 200xa47 A G 60 . QNAME=cluster23_scaffold_3;QSTART=24939194;QSTRAND=- GT:DP:AD ./.:27:15,12 ./.:39:19,20 1|0:35:19,16 +chr20 771669 200xa48 G GAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=752121;QSTRAND=+ GT:DP:AD 1|1:28:11,17 ./.:23:6,17 ./.:32:23,9 +chr20 771669 200xa49 GA G 60 . QNAME=cluster19_000000F;QSTART=24989667;QSTRAND=- GT:DP:AD ./.:17:7,10 1|0:34:18,16 ./.:17:5,12 +chr20 771669 200xa4a G GA 60 . QNAME=cluster19_000000F;QSTART=732609;QSTRAND=+ GT:DP:AD ./.:17:7,10 0|1:19:6,13 ./.:44:20,24 +chr20 771669 200xa4b G GAA 60 . QNAME=cluster23_scaffold_3;QSTART=24939011;QSTRAND=- GT:DP:AD ./.:42:17,25 ./.:23:16,7 1|0:34:20,14 +chr20 771724 200xa4c A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=752178;QSTRAND=+ GT:DP:AD 1|1:20:8,12 1|1:22:12,10 1|0:42:20,22 +chr20 771989 200xa4d T G 60 . QNAME=cluster19_000000F;QSTART=24989348;QSTRAND=- GT:DP:AD ./.:23:8,15 1|1:35:12,23 1|0:22:11,11 +chr20 772587 200xa4e GT G 60 . QNAME=cluster19_000000F;QSTART=24988750;QSTRAND=- GT:DP:AD ./.:48:23,25 1|1:26:10,16 ./.:19:5,14 +chr20 772587 200xa4f G GT 60 . QNAME=cluster23_scaffold_3;QSTART=24938092;QSTRAND=- GT:DP:AD ./.:42:22,20 ./.:28:9,19 1|0:32:20,12 +chr20 772587 200xa50 GTT G 60 . QNAME=cluster23_scaffold_2;QSTART=24922402;QSTRAND=- GT:DP:AD ./.:16:8,8 ./.:21:15,6 0|1:27:5,22 +chr20 772599 200xa51 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=753053;QSTRAND=+ GT:DP:AD 1|0:34:10,24 1|1:30:24,6 ./.:27:20,7 +chr20 772666 200xa52 G A 60 . QNAME=cluster23_scaffold_3;QSTART=24938013;QSTRAND=- GT:DP:AD ./.:25:10,15 ./.:23:7,16 1|0:27:16,11 +chr20 772719 200xa53 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=753173;QSTRAND=+ GT:DP:AD 1|1:21:7,14 1|1:33:25,8 1|1:23:14,9 +chr20 772824 200xa54 C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=753278;QSTRAND=+ GT:DP:AD 1|1:40:16,24 1|1:39:15,24 1|0:24:6,18 +chr20 772843 200xa55 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=753297;QSTRAND=+ GT:DP:AD 1|1:33:18,15 1|1:47:23,24 1|1:28:15,13 +chr20 772872 200xa56 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=753326;QSTRAND=+ GT:DP:AD 1|1:41:25,16 0|1:34:16,18 1|0:28:13,15 +chr20 773095 200xa57 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=753549;QSTRAND=+ GT:DP:AD 1|1:37:16,21 0|1:28:5,23 ./.:29:16,13 +chr20 773193 200xa58 C T 60 . QNAME=cluster23_scaffold_2;QSTART=24921798;QSTRAND=- GT:DP:AD ./.:24:11,13 ./.:23:14,9 0|1:36:16,20 +chr20 773273 200xa59 T C 60 . QNAME=cluster23_scaffold_2;QSTART=24921718;QSTRAND=- GT:DP:AD ./.:26:5,21 ./.:37:24,13 0|1:41:19,22 +chr20 773723 200xa5a C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=754177;QSTRAND=+ GT:DP:AD 1|1:42:25,17 1|1:22:11,11 1|1:23:12,11 +chr20 773737 200xa5b A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=754191;QSTRAND=+ GT:DP:AD 1|1:25:14,11 1|1:36:15,21 1|1:18:11,7 +chr20 774159 200xa5c G A 60 . QNAME=cluster19_000000F;QSTART=735098;QSTRAND=+ GT:DP:AD ./.:47:25,22 0|1:29:5,24 ./.:38:24,14 +chr20 774304 200xa5d C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=729331;QSTRAND=+ GT:DP:AD 0|1:38:13,25 ./.:46:23,23 ./.:42:19,23 +chr20 774383 200xa5e T C 60 . QNAME=cluster19_000000F;QSTART=735322;QSTRAND=+ GT:DP:AD ./.:33:14,19 0|1:32:16,16 ./.:38:17,21 +chr20 774574 200xa5f A G 60 . QNAME=cluster19_000000F;QSTART=735513;QSTRAND=+ GT:DP:AD ./.:30:10,20 0|1:33:15,18 ./.:49:25,24 +chr20 775268 200xa60 CTTTTTTTTTTT C 60 . QNAME=cluster19_000000F;QSTART=24986070;QSTRAND=- GT:DP:AD ./.:24:8,16 1|0:27:15,12 1|1:16:10,6 +chr20 775268 200xa61 CTTTTTTTT C 60 . QNAME=cluster19_000000F;QSTART=736208;QSTRAND=+ GT:DP:AD ./.:16:7,9 0|1:30:14,16 ./.:42:21,21 +chr20 775431 200xa62 G A 60 . QNAME=cluster19_000000F;QSTART=24985918;QSTRAND=- GT:DP:AD ./.:16:6,10 1|0:38:20,18 1|1:38:17,21 +chr20 775463 200xa63 T C 60 . QNAME=cluster19_000000F;QSTART=24985886;QSTRAND=- GT:DP:AD ./.:42:19,23 1|1:27:18,9 1|1:36:16,20 +chr20 775534 200xa64 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=755988;QSTRAND=+ GT:DP:AD 1|1:37:15,22 1|1:20:11,9 1|1:38:25,13 +chr20 775539 200xa65 A G 60 . QNAME=cluster19_000000F;QSTART=24985810;QSTRAND=- GT:DP:AD ./.:30:20,10 1|1:27:17,10 1|1:44:24,20 +chr20 775876 200xa66 A G 60 . QNAME=cluster19_000000F;QSTART=24985473;QSTRAND=- GT:DP:AD ./.:25:19,6 1|1:36:24,12 1|1:27:22,5 +chr20 775888 200xa67 A G 60 . QNAME=cluster19_000000F;QSTART=736819;QSTRAND=+ GT:DP:AD ./.:46:22,24 0|1:23:13,10 ./.:22:13,9 +chr20 776848 200xa68 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=757302;QSTRAND=+ GT:DP:AD 1|0:40:25,15 0|1:28:16,12 ./.:32:11,21 +chr20 776855 200xa69 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=757309;QSTRAND=+ GT:DP:AD 1|1:19:7,12 1|1:28:6,22 1|1:38:25,13 +chr20 776856 200xa6a TG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=757311;QSTRAND=+ GT:DP:AD 1|0:28:5,23 1|0:20:11,9 1|1:26:8,18 +chr20 776863 200xa6b G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=731890;QSTRAND=+ GT:DP:AD 0|1:40:23,17 ./.:27:14,13 ./.:21:7,14 +chr20 776921 200xa6c T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=757375;QSTRAND=+ GT:DP:AD 1|1:23:12,11 0|1:42:23,19 ./.:34:13,21 +chr20 777272 200xa6d C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=757727;QSTRAND=+ GT:DP:AD 1|1:22:9,13 1|0:45:20,25 1|1:14:9,5 +chr20 777276 200xa6e A AC 60 . QNAME=cluster19_000000F;QSTART=738209;QSTRAND=+ GT:DP:AD ./.:21:13,8 0|1:23:18,5 ./.:27:5,22 +chr20 777343 200xa6f A G 60 . QNAME=cluster19_000000F;QSTART=738276;QSTRAND=+ GT:DP:AD ./.:46:25,21 0|1:38:21,17 ./.:31:11,20 +chr20 777391 200xa70 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=757846;QSTRAND=+ GT:DP:AD 1|1:36:21,15 ./.:24:19,5 ./.:30:17,13 +chr20 778013 200xa71 CT C 60 . QNAME=cluster19_000000F;QSTART=738947;QSTRAND=+ GT:DP:AD ./.:26:15,11 0|1:28:13,15 ./.:22:16,6 +chr20 778013 200xa72 C CT 60 . QNAME=cluster23_scaffold_2;QSTART=24916988;QSTRAND=- GT:DP:AD ./.:24:8,16 ./.:41:23,18 0|1:44:25,19 +chr20 778339 200xa73 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=758794;QSTRAND=+ GT:DP:AD 1|1:38:25,13 1|1:46:21,25 1|1:32:16,16 +chr20 778729 200xa74 C CT 60 . QNAME=cluster19_000000F;QSTART=24982619;QSTRAND=- GT:DP:AD ./.:30:15,15 1|0:44:20,24 ./.:27:12,15 +chr20 778749 200xa75 C T 60 . QNAME=cluster23_scaffold_2;QSTART=24916252;QSTRAND=- GT:DP:AD ./.:24:18,6 ./.:30:7,23 0|1:29:17,12 +chr20 778880 200xa76 A G 60 . QNAME=cluster19_000000F;QSTART=24982468;QSTRAND=- GT:DP:AD ./.:36:24,12 1|1:18:5,13 1|1:31:7,24 +chr20 779208 200xa77 T C 60 . QNAME=cluster19_000000F;QSTART=24982140;QSTRAND=- GT:DP:AD ./.:26:5,21 1|1:29:6,23 1|1:30:10,20 +chr20 779804 200xa78 T C 60 . QNAME=cluster19_000000F;QSTART=24981544;QSTRAND=- GT:DP:AD ./.:29:15,14 1|0:21:15,6 ./.:20:6,14 +chr20 780086 200xa79 G A 60 . QNAME=cluster19_000000F;QSTART=741018;QSTRAND=+ GT:DP:AD ./.:35:17,18 0|1:27:16,11 ./.:27:14,13 +chr20 780364 200xa7a C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=760819;QSTRAND=+ GT:DP:AD 1|1:30:17,13 ./.:28:21,7 ./.:39:16,23 +chr20 781143 200xa7b G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=761598;QSTRAND=+ GT:DP:AD 1|1:26:6,20 1|1:27:11,16 1|1:31:24,7 +chr20 781912 200xa7c T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=762367;QSTRAND=+ GT:DP:AD 1|1:19:6,13 1|1:19:12,7 1|1:33:22,11 +chr20 782053 200xa7d T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=762508;QSTRAND=+ GT:DP:AD 1|1:34:21,13 1|1:23:13,10 1|1:23:12,11 +chr20 782135 200xa7e C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=762590;QSTRAND=+ GT:DP:AD 1|1:30:11,19 1|1:43:18,25 1|1:33:25,8 +chr20 782243 200xa7f T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=762699;QSTRAND=+ GT:DP:AD 1|0:28:6,22 ./.:30:14,16 ./.:49:24,25 +chr20 782250 200xa80 G GA 60 . QNAME=HG002-S9-H2-000001F;QSTART=737280;QSTRAND=+ GT:DP:AD 0|1:35:25,10 1|1:30:10,20 1|1:19:13,6 +chr20 782334 200xa81 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=762790;QSTRAND=+ GT:DP:AD 1|1:43:22,21 1|1:31:9,22 1|1:18:10,8 +chr20 782552 200xa82 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=763008;QSTRAND=+ GT:DP:AD 1|1:41:21,20 1|1:24:16,8 1|1:19:13,6 +chr20 782748 200xa83 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=763204;QSTRAND=+ GT:DP:AD 1|1:17:10,7 1|1:34:13,21 1|1:32:14,18 +chr20 782898 200xa84 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=763354;QSTRAND=+ GT:DP:AD 1|1:28:21,7 1|1:31:12,19 1|1:33:14,19 +chr20 783008 200xa85 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=763464;QSTRAND=+ GT:DP:AD 1|1:36:21,15 1|1:24:18,6 1|1:43:21,22 +chr20 783188 200xa86 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=763644;QSTRAND=+ GT:DP:AD 1|1:35:20,15 1|1:15:5,10 1|1:21:16,5 +chr20 783194 200xa87 C T 60 . QNAME=cluster19_000000F;QSTART=24978153;QSTRAND=- GT:DP:AD ./.:30:5,25 1|0:45:21,24 1|1:30:22,8 +chr20 783195 200xa88 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=763651;QSTRAND=+ GT:DP:AD 1|1:35:14,21 1|1:48:24,24 1|1:25:12,13 +chr20 783325 200xa89 C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=763781;QSTRAND=+ GT:DP:AD 1|1:27:7,20 1|1:11:6,5 1|1:40:15,25 +chr20 783424 200xa8a T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=763880;QSTRAND=+ GT:DP:AD 1|1:29:10,19 1|1:41:25,16 1|1:23:12,11 +chr20 783447 200xa8b A G 60 . QNAME=cluster19_000000F;QSTART=24977900;QSTRAND=- GT:DP:AD ./.:42:19,23 1|0:19:13,6 1|1:42:17,25 +chr20 783450 200xa8c C T 60 . QNAME=cluster19_000000F;QSTART=744383;QSTRAND=+ GT:DP:AD ./.:27:12,15 0|1:18:6,12 ./.:25:15,10 +chr20 783488 200xa8d T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=763944;QSTRAND=+ GT:DP:AD 1|1:24:15,9 ./.:28:8,20 ./.:25:14,11 +chr20 783520 200xa8e T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=763976;QSTRAND=+ GT:DP:AD 1|1:41:18,23 1|1:23:15,8 1|1:45:25,20 +chr20 783739 200xa8f A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=764195;QSTRAND=+ GT:DP:AD 1|1:36:22,14 1|1:28:23,5 1|1:19:12,7 +chr20 783834 200xa90 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=764290;QSTRAND=+ GT:DP:AD 1|1:14:7,7 1|1:46:23,23 1|1:34:23,11 +chr20 783937 200xa91 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=764393;QSTRAND=+ GT:DP:AD 1|1:39:23,16 1|1:41:22,19 1|1:33:15,18 +chr20 784114 200xa92 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=764570;QSTRAND=+ GT:DP:AD 1|1:31:11,20 1|0:21:16,5 1|1:43:25,18 +chr20 784189 200xa93 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=764645;QSTRAND=+ GT:DP:AD 1|1:18:9,9 1|1:35:23,12 1|1:43:25,18 +chr20 784244 200xa94 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=764700;QSTRAND=+ GT:DP:AD 1|1:39:15,24 1|1:28:13,15 1|1:22:6,16 +chr20 784245 200xa95 C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=764701;QSTRAND=+ GT:DP:AD 1|1:15:5,10 1|1:33:18,15 1|1:35:21,14 +chr20 784337 200xa96 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=764793;QSTRAND=+ GT:DP:AD 1|1:22:6,16 1|1:43:19,24 1|1:21:5,16 +chr20 784347 200xa97 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=764803;QSTRAND=+ GT:DP:AD 1|1:46:23,23 1|1:31:16,15 1|1:29:23,6 +chr20 784686 200xa98 G T 60 . QNAME=cluster19_000000F;QSTART=24976661;QSTRAND=- GT:DP:AD ./.:31:24,7 1|0:19:14,5 1|1:35:21,14 +chr20 784695 200xa99 A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=765151;QSTRAND=+ GT:DP:AD 1|1:26:18,8 1|1:26:15,11 1|1:21:7,14 +chr20 784821 200xa9a A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=765277;QSTRAND=+ GT:DP:AD 1|1:21:7,14 1|1:25:7,18 1|1:24:15,9 +chr20 784842 200xa9b A G 60 . QNAME=cluster19_000000F;QSTART=745775;QSTRAND=+ GT:DP:AD ./.:35:18,17 0|1:20:13,7 ./.:14:9,5 +chr20 785145 200xa9c C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=765601;QSTRAND=+ GT:DP:AD 1|1:20:14,6 0|1:22:17,5 ./.:16:8,8 +chr20 785294 200xa9d C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=765750;QSTRAND=+ GT:DP:AD 1|1:43:23,20 1|1:35:19,16 1|1:41:24,17 +chr20 785303 200xa9e T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=765759;QSTRAND=+ GT:DP:AD 1|1:30:20,10 1|1:32:12,20 1|1:28:23,5 +chr20 785581 200xa9f A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=766037;QSTRAND=+ GT:DP:AD 1|1:13:6,7 1|1:32:18,14 1|1:18:13,5 +chr20 785647 200xaa0 G A 60 . QNAME=cluster19_000000F;QSTART=24975700;QSTRAND=- GT:DP:AD ./.:24:8,16 1|0:27:6,21 1|1:36:17,19 +chr20 785693 200xaa1 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=766149;QSTRAND=+ GT:DP:AD 1|1:27:19,8 1|1:46:22,24 1|1:30:11,19 +chr20 785803 200xaa2 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=766259;QSTRAND=+ GT:DP:AD 1|1:47:24,23 1|1:24:13,11 1|1:15:9,6 +chr20 786660 200xaa3 C T 60 . QNAME=cluster23_scaffold_3;QSTART=24924029;QSTRAND=- GT:DP:AD ./.:34:20,14 ./.:35:18,17 1|0:32:23,9 +chr20 787077 200xaa4 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=767533;QSTRAND=+ GT:DP:AD 1|1:33:15,18 1|1:46:22,24 1|1:23:16,7 +chr20 787239 200xaa5 CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=767696;QSTRAND=+ GT:DP:AD 1|1:30:12,18 ./.:31:21,10 1|0:30:21,9 +chr20 787239 200xaa6 CTT C 60 . QNAME=cluster23_scaffold_2;QSTART=24907761;QSTRAND=- GT:DP:AD ./.:32:18,14 ./.:24:6,18 0|1:26:9,17 +chr20 787512 200xaa7 CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=767968;QSTRAND=+ GT:DP:AD 1|1:24:9,15 1|1:40:22,18 1|0:38:20,18 +chr20 787930 200xaa8 A T 60 . QNAME=cluster19_000000F;QSTART=24973418;QSTRAND=- GT:DP:AD ./.:23:17,6 1|0:46:25,21 1|1:35:10,25 +chr20 788431 200xaa9 T C 60 . QNAME=cluster19_000000F;QSTART=24972917;QSTRAND=- GT:DP:AD ./.:23:5,18 1|0:41:21,20 1|1:33:8,25 +chr20 788945 200xaaa T C 60 . QNAME=cluster19_000000F;QSTART=24972403;QSTRAND=- GT:DP:AD ./.:36:18,18 1|0:45:24,21 1|1:41:21,20 +chr20 789027 200xaab T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=769481;QSTRAND=+ GT:DP:AD 1|1:19:13,6 1|0:27:17,10 1|1:34:20,14 +chr20 789716 200xaac G A 60 . QNAME=cluster19_000000F;QSTART=750648;QSTRAND=+ GT:DP:AD ./.:28:21,7 0|1:32:24,8 ./.:40:18,22 +chr20 789908 200xaad C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=770362;QSTRAND=+ GT:DP:AD 1|1:22:14,8 1|1:39:24,15 1|1:39:18,21 +chr20 789995 200xaae G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=770449;QSTRAND=+ GT:DP:AD 1|1:39:20,19 ./.:18:9,9 ./.:18:11,7 +chr20 790219 200xaaf T C 60 . QNAME=cluster19_000000F;QSTART=24971129;QSTRAND=- GT:DP:AD ./.:36:21,15 1|0:40:24,16 1|1:29:14,15 +chr20 790252 200xab0 G A 60 . QNAME=cluster19_000000F;QSTART=24971096;QSTRAND=- GT:DP:AD ./.:32:11,21 1|0:22:17,5 1|1:15:5,10 +chr20 790270 200xab1 C G 60 . QNAME=cluster19_000000F;QSTART=24971078;QSTRAND=- GT:DP:AD ./.:23:5,18 1|0:44:19,25 1|1:39:23,16 +chr20 790371 200xab2 CAAAAAAA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=745400;QSTRAND=+ GT:DP:AD 0|1:35:25,10 1|0:38:19,19 0|1:35:17,18 +chr20 790371 200xab3 CAAAAAAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=770826;QSTRAND=+ GT:DP:AD 1|0:36:20,16 ./.:15:10,5 1|0:17:6,11 +chr20 790371 200xab4 C CAAAAAAAAAAAA 60 . QNAME=cluster19_000000F;QSTART=751304;QSTRAND=+ GT:DP:AD ./.:23:11,12 0|1:23:12,11 ./.:41:17,24 +chr20 790626 200xab5 T G 60 . QNAME=cluster19_000000F;QSTART=24970729;QSTRAND=- GT:DP:AD ./.:36:13,23 1|0:22:8,14 1|1:40:24,16 +chr20 790639 200xab6 C T 60 . QNAME=cluster19_000000F;QSTART=24970716;QSTRAND=- GT:DP:AD ./.:28:20,8 1|0:31:22,9 1|1:16:8,8 +chr20 791233 200xab7 A G 60 . QNAME=cluster19_000000F;QSTART=24970122;QSTRAND=- GT:DP:AD ./.:14:5,9 1|0:24:14,10 1|1:33:22,11 +chr20 791888 200xab8 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=772334;QSTRAND=+ GT:DP:AD 1|1:34:13,21 ./.:30:10,20 ./.:29:6,23 +chr20 791971 200xab9 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=772417;QSTRAND=+ GT:DP:AD 1|1:30:21,9 1|1:19:12,7 1|1:14:5,9 +chr20 792261 200xaba T C 60 . QNAME=cluster19_000000F;QSTART=753205;QSTRAND=+ GT:DP:AD ./.:27:21,6 0|1:29:11,18 ./.:24:17,7 +chr20 792795 200xabb T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=773241;QSTRAND=+ GT:DP:AD 1|1:30:20,10 1|1:42:17,25 1|1:29:19,10 +chr20 792866 200xabc A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=773312;QSTRAND=+ GT:DP:AD 1|1:43:19,24 1|1:31:22,9 1|1:17:10,7 +chr20 792873 200xabd T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=773319;QSTRAND=+ GT:DP:AD 1|1:40:24,16 1|1:23:6,17 1|1:20:11,9 +chr20 792876 200xabe A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=773322;QSTRAND=+ GT:DP:AD 1|1:20:6,14 1|1:47:23,24 1|1:42:23,19 +chr20 792903 200xabf A G 60 . QNAME=cluster19_000000F;QSTART=24968452;QSTRAND=- GT:DP:AD ./.:19:8,11 1|1:26:5,21 ./.:35:25,10 +chr20 793346 200xac0 C T 60 . QNAME=cluster23_scaffold_3;QSTART=24917353;QSTRAND=- GT:DP:AD ./.:25:19,6 ./.:32:21,11 1|0:15:8,7 +chr20 793395 200xac1 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=773841;QSTRAND=+ GT:DP:AD 1|1:23:6,17 1|1:36:25,11 1|1:14:7,7 +chr20 793450 200xac2 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=748471;QSTRAND=+ GT:DP:AD 0|1:27:13,14 ./.:33:23,10 ./.:17:7,10 +chr20 793500 200xac3 C T 60 . QNAME=cluster19_000000F;QSTART=24967855;QSTRAND=- GT:DP:AD ./.:34:21,13 1|0:21:14,7 ./.:11:5,6 +chr20 793560 200xac4 C CG 60 . QNAME=HG002-S9-H2-000001F;QSTART=748582;QSTRAND=+ GT:DP:AD 0|1:17:12,5 ./.:33:15,18 ./.:29:18,11 +chr20 793560 200xac5 CGG C 60 . QNAME=cluster19_000000F;QSTART=24967795;QSTRAND=- GT:DP:AD ./.:29:5,24 1|0:41:19,22 1|1:39:15,24 +chr20 793560 200xac6 CG C 60 . QNAME=cluster19_000000F;QSTART=754505;QSTRAND=+ GT:DP:AD ./.:28:13,15 0|1:25:7,18 ./.:39:17,22 +chr20 793678 200xac7 C G 60 . QNAME=cluster19_000000F;QSTART=754621;QSTRAND=+ GT:DP:AD ./.:30:8,22 0|1:44:20,24 ./.:29:20,9 +chr20 793771 200xac8 T G 60 . QNAME=cluster19_000000F;QSTART=24967586;QSTRAND=- GT:DP:AD ./.:27:20,7 1|0:18:13,5 1|1:26:18,8 +chr20 794325 200xac9 T C 60 . QNAME=cluster19_000000F;QSTART=24967032;QSTRAND=- GT:DP:AD ./.:33:22,11 1|0:27:18,9 0|1:24:16,8 +chr20 794444 200xaca A G 60 . QNAME=cluster19_000000F;QSTART=24966913;QSTRAND=- GT:DP:AD ./.:41:21,20 1|0:30:7,23 1|1:28:7,21 +chr20 794733 200xacb T G 60 . QNAME=cluster19_000000F;QSTART=24966624;QSTRAND=- GT:DP:AD ./.:27:7,20 1|0:31:19,12 1|1:40:21,19 +chr20 795199 200xacc C T 60 . QNAME=cluster23_scaffold_3;QSTART=24915502;QSTRAND=- GT:DP:AD ./.:30:9,21 ./.:26:6,20 1|0:17:6,11 +chr20 795434 200xacd C A 60 . QNAME=cluster19_000000F;QSTART=24965923;QSTRAND=- GT:DP:AD ./.:30:9,21 1|0:32:17,15 1|1:35:19,16 +chr20 795539 200xace C T 60 . QNAME=cluster23_scaffold_3;QSTART=24915162;QSTRAND=- GT:DP:AD ./.:28:18,10 ./.:22:13,9 1|0:29:8,21 +chr20 795540 200xacf C G 60 . QNAME=cluster23_scaffold_3;QSTART=24915161;QSTRAND=- GT:DP:AD ./.:24:18,6 ./.:14:9,5 1|0:34:25,9 +chr20 795731 200xad0 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=750753;QSTRAND=+ GT:DP:AD 0|1:38:16,22 ./.:32:13,19 ./.:23:15,8 +chr20 795805 200xad1 G A 60 . QNAME=cluster19_000000F;QSTART=24965552;QSTRAND=- GT:DP:AD ./.:33:16,17 1|0:32:13,19 ./.:18:7,11 +chr20 795876 200xad2 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=776322;QSTRAND=+ GT:DP:AD 1|1:33:18,15 ./.:22:5,17 1|0:15:9,6 +chr20 795985 200xad3 T C 60 . QNAME=cluster23_scaffold_2;QSTART=24899026;QSTRAND=- GT:DP:AD ./.:35:18,17 ./.:38:21,17 0|1:24:13,11 +chr20 796225 200xad4 T G 60 . QNAME=cluster19_000000F;QSTART=24965132;QSTRAND=- GT:DP:AD ./.:32:19,13 1|0:20:10,10 ./.:27:10,17 +chr20 796289 200xad5 A G 60 . QNAME=cluster23_scaffold_2;QSTART=24898722;QSTRAND=- GT:DP:AD ./.:34:16,18 ./.:33:15,18 0|1:30:25,5 +chr20 796344 200xad6 C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=751366;QSTRAND=+ GT:DP:AD 0|1:42:25,17 1|1:35:19,16 ./.:17:7,10 +chr20 796564 200xad7 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=751586;QSTRAND=+ GT:DP:AD 0|1:36:20,16 ./.:37:14,23 ./.:35:21,14 +chr20 797048 200xad8 A G 60 . QNAME=cluster19_000000F;QSTART=757991;QSTRAND=+ GT:DP:AD ./.:42:18,24 0|1:39:17,22 ./.:31:9,22 +chr20 797400 200xad9 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=777846;QSTRAND=+ GT:DP:AD 1|0:20:8,12 ./.:34:10,24 ./.:17:10,7 +chr20 797739 200xada A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=778185;QSTRAND=+ GT:DP:AD 1|0:24:18,6 ./.:36:12,24 ./.:34:11,23 +chr20 797871 200xadb G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=752893;QSTRAND=+ GT:DP:AD 0|1:34:16,18 0|1:31:6,25 ./.:43:22,21 +chr20 798053 200xadc T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=753075;QSTRAND=+ GT:DP:AD 0|1:47:23,24 0|1:28:11,17 ./.:27:15,12 +chr20 798278 200xadd G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=753300;QSTRAND=+ GT:DP:AD 0|1:19:12,7 0|1:26:8,18 ./.:24:5,19 +chr20 798467 200xade T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=753489;QSTRAND=+ GT:DP:AD 0|1:40:20,20 0|1:36:17,19 ./.:28:17,11 +chr20 798479 200xadf C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=778925;QSTRAND=+ GT:DP:AD 1|1:22:11,11 0|1:31:16,15 ./.:19:9,10 +chr20 798594 200xae0 T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=753616;QSTRAND=+ GT:DP:AD 0|1:38:22,16 0|1:39:21,18 ./.:27:5,22 +chr20 798717 200xae1 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=753739;QSTRAND=+ GT:DP:AD 0|1:36:15,21 ./.:34:22,12 ./.:22:6,16 +chr20 798853 200xae2 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=779299;QSTRAND=+ GT:DP:AD 1|0:46:25,21 ./.:24:5,19 ./.:35:16,19 +chr20 799277 200xae3 C CAAAA 60 . QNAME=HG002-S9-H2-000001F;QSTART=754300;QSTRAND=+ GT:DP:AD 0|1:26:18,8 ./.:27:19,8 ./.:26:12,14 +chr20 799277 200xae4 C CAA 60 . QNAME=cluster19_000000F;QSTART=24962078;QSTRAND=- GT:DP:AD ./.:18:6,12 1|0:25:15,10 1|1:33:10,23 +chr20 799300 200xae5 C T 60 . QNAME=cluster19_000000F;QSTART=24962055;QSTRAND=- GT:DP:AD ./.:39:17,22 1|0:26:21,5 1|1:24:7,17 +chr20 799510 200xae6 A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=779956;QSTRAND=+ GT:DP:AD 1|1:31:16,15 1|0:30:25,5 1|1:28:6,22 +chr20 799644 200xae7 G A 60 . QNAME=cluster19_000000F;QSTART=24961711;QSTRAND=- GT:DP:AD ./.:26:19,7 1|0:33:9,24 1|1:43:20,23 +chr20 799744 200xae8 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=780190;QSTRAND=+ GT:DP:AD 1|0:27:5,22 ./.:14:8,6 ./.:18:6,12 +chr20 800427 200xae9 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=780873;QSTRAND=+ GT:DP:AD 1|0:29:23,6 ./.:24:11,13 ./.:13:5,8 +chr20 800494 200xaea TCGATTACCTGCTCCACCCTGACTCACTC T 60 . QNAME=HG002-S9-H2-000001F;QSTART=755521;QSTRAND=+;SVTYPE=DEL;SVLEN=-28 GT:DP:AD 0/1:22:7,15 1/0:22:13,9 1/1:29:24,5 +chr20 800604 200xaeb T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781050;QSTRAND=+ GT:DP:AD 1|0:39:25,14 ./.:32:25,7 ./.:34:19,15 +chr20 800640 200xaec T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781086;QSTRAND=+ GT:DP:AD 1|0:27:17,10 ./.:32:20,12 ./.:39:16,23 +chr20 800671 200xaed GCACTCACCCCAT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=781118;QSTRAND=+ GT:DP:AD 1|0:25:17,8 ./.:39:24,15 ./.:15:7,8 +chr20 800707 200xaee G A 60 . QNAME=cluster19_000000F;QSTART=24960676;QSTRAND=- GT:DP:AD ./.:31:15,16 1|0:35:10,25 1|1:12:7,5 +chr20 800818 200xaef T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781252;QSTRAND=+ GT:DP:AD 1|1:19:14,5 1|0:30:21,9 1|1:17:7,10 +chr20 800884 200xaf0 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=781318;QSTRAND=+ GT:DP:AD 1|0:27:15,12 ./.:28:17,11 ./.:31:23,8 +chr20 800927 200xaf1 A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=781361;QSTRAND=+ GT:DP:AD 1|0:22:12,10 ./.:32:12,20 ./.:22:13,9 +chr20 800955 200xaf2 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=781389;QSTRAND=+ GT:DP:AD 1|0:24:19,5 ./.:43:24,19 ./.:36:21,15 +chr20 800960 200xaf3 CCTT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781395;QSTRAND=+ GT:DP:AD 1|0:37:25,12 ./.:25:17,8 ./.:34:22,12 +chr20 801002 200xaf4 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781433;QSTRAND=+ GT:DP:AD 1|0:17:10,7 ./.:29:18,11 ./.:30:18,12 +chr20 801097 200xaf5 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781528;QSTRAND=+ GT:DP:AD 1|0:41:18,23 ./.:36:15,21 ./.:37:15,22 +chr20 801205 200xaf6 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781636;QSTRAND=+ GT:DP:AD 1|0:35:15,20 ./.:27:6,21 ./.:32:18,14 +chr20 801403 200xaf7 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=781834;QSTRAND=+ GT:DP:AD 1|0:23:7,16 ./.:41:22,19 ./.:21:13,8 +chr20 801427 200xaf8 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781858;QSTRAND=+ GT:DP:AD 1|0:21:7,14 ./.:27:8,19 ./.:23:7,16 +chr20 801488 200xaf9 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781919;QSTRAND=+ GT:DP:AD 1|0:18:13,5 1|0:35:13,22 1|1:23:7,16 +chr20 801793 200xafa G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=782224;QSTRAND=+ GT:DP:AD 1|0:36:13,23 ./.:32:14,18 ./.:29:16,13 +chr20 801807 200xafb C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=782238;QSTRAND=+ GT:DP:AD 1|0:35:20,15 ./.:46:22,24 ./.:36:25,11 +chr20 801853 200xafc CAAATAAAT C 60 . QNAME=cluster19_000000F;QSTART=24959530;QSTRAND=- GT:DP:AD ./.:37:13,24 1|0:30:13,17 0|1:39:16,23 +chr20 801853 200xafd CAAAT C 60 . QNAME=cluster23_scaffold_3;QSTART=24908874;QSTRAND=- GT:DP:AD ./.:23:16,7 ./.:29:24,5 1|0:25:16,9 +chr20 801854 200xafe AAATAAAT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=782286;QSTRAND=+ GT:DP:AD 1|0:33:14,19 ./.:40:15,25 ./.:41:23,18 +chr20 801893 200xaff T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=782317;QSTRAND=+ GT:DP:AD 1|0:42:21,21 ./.:36:24,12 ./.:30:19,11 +chr20 802063 200xb00 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=782487;QSTRAND=+ GT:DP:AD 1|0:20:6,14 ./.:23:7,16 ./.:23:7,16 +chr20 802155 200xb01 C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=757153;QSTRAND=+ GT:DP:AD 0|1:33:20,13 1|0:37:18,19 1|1:30:11,19 +chr20 802331 200xb02 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=782755;QSTRAND=+ GT:DP:AD 1|1:26:15,11 1|0:29:8,21 ./.:46:21,25 +chr20 802369 200xb03 G A 60 . QNAME=cluster19_000000F;QSTART=763312;QSTRAND=+ GT:DP:AD ./.:22:6,16 0|1:37:18,19 ./.:23:9,14 +chr20 802531 200xb04 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=757529;QSTRAND=+ GT:DP:AD 0|1:39:16,23 ./.:28:5,23 ./.:24:19,5 +chr20 802606 200xb05 C CA 60 . QNAME=HG002-S9-H2-000001F;QSTART=757605;QSTRAND=+ GT:DP:AD 0|1:43:24,19 ./.:38:20,18 0|1:24:12,12 +chr20 802739 200xb06 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=757738;QSTRAND=+ GT:DP:AD 0|1:38:14,24 0|1:33:24,9 1|0:43:21,22 +chr20 803221 200xb07 C T 60 . QNAME=cluster19_000000F;QSTART=24958170;QSTRAND=- GT:DP:AD ./.:14:6,8 1|1:26:10,16 1|1:48:25,23 +chr20 803367 200xb08 C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=783791;QSTRAND=+ GT:DP:AD 1|1:30:14,16 1|1:28:10,18 1|1:17:9,8 +chr20 803419 200xb09 C T 60 . QNAME=cluster19_000000F;QSTART=24957972;QSTRAND=- GT:DP:AD ./.:21:13,8 1|1:29:5,24 1|1:34:22,12 +chr20 803499 200xb0a A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=783923;QSTRAND=+ GT:DP:AD 1|0:36:17,19 ./.:15:6,9 ./.:23:10,13 +chr20 803703 200xb0b T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=784127;QSTRAND=+ GT:DP:AD 1|1:27:13,14 1|1:25:5,20 1|1:16:11,5 +chr20 803760 200xb0c C T 60 . QNAME=cluster19_000000F;QSTART=24957631;QSTRAND=- GT:DP:AD ./.:37:15,22 1|1:34:15,19 1|1:21:13,8 +chr20 804087 200xb0d G A 60 . QNAME=cluster19_000000F;QSTART=24957304;QSTRAND=- GT:DP:AD ./.:30:15,15 1|1:16:6,10 1|1:41:20,21 +chr20 804255 200xb0e C T 60 . QNAME=cluster19_000000F;QSTART=24957136;QSTRAND=- GT:DP:AD ./.:29:6,23 1|1:30:9,21 1|1:29:21,8 +chr20 804315 200xb0f C G 60 . QNAME=cluster19_000000F;QSTART=24957076;QSTRAND=- GT:DP:AD ./.:47:22,25 1|1:29:10,19 1|1:33:25,8 +chr20 804381 200xb10 C T 60 . QNAME=cluster19_000000F;QSTART=24957010;QSTRAND=- GT:DP:AD ./.:43:20,23 1|1:48:24,24 1|1:39:16,23 +chr20 804444 200xb11 G A 60 . QNAME=cluster19_000000F;QSTART=24956947;QSTRAND=- GT:DP:AD ./.:22:9,13 1|1:37:12,25 1|1:33:25,8 +chr20 804465 200xb12 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=784889;QSTRAND=+ GT:DP:AD 1|1:25:8,17 ./.:27:7,20 ./.:40:21,19 +chr20 804804 200xb13 A AT 60 . QNAME=HG002-S9-H1-000001F;QSTART=785229;QSTRAND=+ GT:DP:AD 1|0:27:22,5 ./.:33:17,16 ./.:23:11,12 +chr20 804804 200xb14 AT A 60 . QNAME=cluster19_000000F;QSTART=24956587;QSTRAND=- GT:DP:AD ./.:34:19,15 1|1:27:16,11 1|1:34:19,15 +chr20 805255 200xb15 T C 60 . QNAME=cluster19_000000F;QSTART=24956137;QSTRAND=- GT:DP:AD ./.:46:25,21 1|1:30:19,11 1|1:23:5,18 +chr20 805274 200xb16 T C 60 . QNAME=cluster19_000000F;QSTART=24956118;QSTRAND=- GT:DP:AD ./.:27:13,14 1|1:16:7,9 1|1:43:23,20 +chr20 805356 200xb17 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=785781;QSTRAND=+ GT:DP:AD 1|1:27:22,5 1|1:27:16,11 1|1:40:24,16 +chr20 805464 200xb18 C G 60 . QNAME=cluster19_000000F;QSTART=24955928;QSTRAND=- GT:DP:AD ./.:28:11,17 1|1:41:24,17 1|1:46:25,21 +chr20 805609 200xb19 AAG A 60 . QNAME=cluster19_000000F;QSTART=24955783;QSTRAND=- GT:DP:AD ./.:48:25,23 1|1:29:21,8 1|1:17:10,7 +chr20 805627 200xb1a AT A 60 . QNAME=cluster23_scaffold_2;QSTART=24889420;QSTRAND=- GT:DP:AD ./.:21:12,9 ./.:26:14,12 0|1:18:11,7 +chr20 805812 200xb1b C T 60 . QNAME=cluster19_000000F;QSTART=24955582;QSTRAND=- GT:DP:AD ./.:36:25,11 1|1:34:17,17 1|1:37:12,25 +chr20 806032 200xb1c T TA 60 . QNAME=cluster23_scaffold_2;QSTART=24889015;QSTRAND=- GT:DP:AD ./.:28:20,8 ./.:31:21,10 0|1:15:9,6 +chr20 806060 200xb1d A G 60 . QNAME=cluster19_000000F;QSTART=24955334;QSTRAND=- GT:DP:AD ./.:30:25,5 1|1:30:8,22 1|1:31:18,13 +chr20 806121 200xb1e T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=786547;QSTRAND=+ GT:DP:AD 1|1:35:11,24 1|1:30:6,24 1|1:35:21,14 +chr20 806416 200xb1f G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=786842;QSTRAND=+ GT:DP:AD 1|1:29:18,11 1|1:42:20,22 1|1:36:18,18 +chr20 806539 200xb20 CT C 60 . QNAME=cluster23_scaffold_2;QSTART=24888507;QSTRAND=- GT:DP:AD ./.:41:18,23 ./.:23:7,16 0|1:20:15,5 +chr20 806698 200xb21 A G 60 . QNAME=cluster19_000000F;QSTART=24954695;QSTRAND=- GT:DP:AD ./.:33:22,11 1|1:29:20,9 1|1:19:8,11 +chr20 806714 200xb22 C T 60 . QNAME=cluster23_scaffold_3;QSTART=24904019;QSTRAND=- GT:DP:AD ./.:32:21,11 ./.:29:10,19 1|0:19:8,11 +chr20 807227 200xb23 T TTTTATTTATTTATTTATTTA 60 . QNAME=cluster19_000000F;QSTART=24954146;QSTRAND=- GT:DP:AD ./.:36:21,15 1|1:40:20,20 1|1:27:12,15 +chr20 807315 200xb24 A G 60 . QNAME=cluster19_000000F;QSTART=24954058;QSTRAND=- GT:DP:AD ./.:40:18,22 1|1:38:16,22 1|1:24:11,13 +chr20 807395 200xb25 C T 60 . QNAME=cluster19_000000F;QSTART=24953978;QSTRAND=- GT:DP:AD ./.:28:6,22 1|1:42:23,19 1|1:46:23,23 +chr20 807886 200xb26 CT C 60 . QNAME=cluster23_scaffold_2;QSTART=24887141;QSTRAND=- GT:DP:AD ./.:34:14,20 ./.:16:8,8 0|1:25:15,10 +chr20 808070 200xb27 G A 60 . QNAME=cluster19_000000F;QSTART=24953303;QSTRAND=- GT:DP:AD ./.:46:25,21 1|1:34:24,10 1|1:15:6,9 +chr20 808486 200xb28 C T 60 . QNAME=cluster19_000000F;QSTART=24952887;QSTRAND=- GT:DP:AD ./.:25:10,15 1|1:39:16,23 1|1:41:21,20 +chr20 808580 200xb29 CT C 60 . QNAME=cluster23_scaffold_2;QSTART=24886448;QSTRAND=- GT:DP:AD ./.:33:20,13 ./.:29:24,5 0|1:35:23,12 +chr20 808747 200xb2a T C 60 . QNAME=cluster19_000000F;QSTART=24952626;QSTRAND=- GT:DP:AD ./.:50:25,25 1|1:35:19,16 1|1:46:23,23 +chr20 808798 200xb2b T TG 60 . QNAME=cluster23_scaffold_2;QSTART=24886230;QSTRAND=- GT:DP:AD ./.:40:20,20 ./.:29:15,14 0|1:20:14,6 +chr20 808973 200xb2c G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=789399;QSTRAND=+ GT:DP:AD 1|1:35:24,11 1|1:28:5,23 1|1:16:8,8 +chr20 809124 200xb2d T TA 60 . QNAME=cluster19_000000F;QSTART=24952248;QSTRAND=- GT:DP:AD ./.:31:11,20 1|1:31:9,22 1|0:26:5,21 +chr20 809124 200xb2e T TAA 60 . QNAME=cluster23_scaffold_2;QSTART=24885902;QSTRAND=- GT:DP:AD ./.:28:18,10 ./.:30:6,24 0|1:32:17,15 +chr20 809392 200xb2f C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=789818;QSTRAND=+ GT:DP:AD 1|1:14:8,6 1|1:45:25,20 1|1:34:22,12 +chr20 809449 200xb30 C A 60 . QNAME=cluster19_000000F;QSTART=24951923;QSTRAND=- GT:DP:AD ./.:22:8,14 1|1:13:6,7 1|1:18:5,13 +chr20 809476 200xb31 C T 60 . QNAME=cluster19_000000F;QSTART=24951896;QSTRAND=- GT:DP:AD ./.:26:15,11 1|1:31:12,19 1|1:23:13,10 +chr20 809653 200xb32 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=790079;QSTRAND=+ GT:DP:AD 1|1:48:23,25 ./.:29:16,13 ./.:21:5,16 +chr20 809775 200xb33 T G 60 . QNAME=cluster19_000000F;QSTART=24951597;QSTRAND=- GT:DP:AD ./.:20:14,6 1|0:35:21,14 ./.:37:21,16 +chr20 810079 200xb34 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=790505;QSTRAND=+ GT:DP:AD 1|1:25:16,9 1|1:33:8,25 1|1:43:21,22 +chr20 810083 200xb35 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=790509;QSTRAND=+ GT:DP:AD 1|1:31:25,6 ./.:38:19,19 ./.:20:9,11 +chr20 810565 200xb36 A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=790991;QSTRAND=+ GT:DP:AD 1|1:42:22,20 1|1:27:11,16 1|1:33:17,16 +chr20 810659 200xb37 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=791085;QSTRAND=+ GT:DP:AD 1|1:24:13,11 1|1:28:23,5 1|1:20:7,13 +chr20 810742 200xb38 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=791168;QSTRAND=+ GT:DP:AD 1|1:20:14,6 ./.:28:23,5 ./.:24:7,17 +chr20 811032 200xb39 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=791458;QSTRAND=+ GT:DP:AD 1|1:22:16,6 ./.:34:22,12 ./.:32:18,14 +chr20 811102 200xb3a G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=791528;QSTRAND=+ GT:DP:AD 1|1:20:12,8 ./.:30:9,21 ./.:42:25,17 +chr20 811314 200xb3b A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=791740;QSTRAND=+ GT:DP:AD 1|1:14:8,6 1|1:30:5,25 1|1:27:8,19 +chr20 811539 200xb3c G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=791965;QSTRAND=+ GT:DP:AD 1|1:37:14,23 ./.:26:19,7 ./.:25:6,19 +chr20 811587 200xb3d G A 60 . QNAME=cluster19_000000F;QSTART=24949785;QSTRAND=- GT:DP:AD ./.:12:5,7 1|1:36:12,24 1|1:46:22,24 +chr20 811839 200xb3e A AG 60 . QNAME=cluster23_scaffold_2;QSTART=24883186;QSTRAND=- GT:DP:AD ./.:34:12,22 ./.:11:6,5 0|1:30:6,24 +chr20 812140 200xb3f C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=792566;QSTRAND=+ GT:DP:AD 1|1:35:22,13 ./.:36:18,18 ./.:31:13,18 +chr20 812429 200xb40 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=792855;QSTRAND=+ GT:DP:AD 1|1:25:8,17 ./.:28:15,13 ./.:37:23,14 +chr20 812492 200xb41 A C 60 . QNAME=cluster19_000000F;QSTART=24948880;QSTRAND=- GT:DP:AD ./.:30:20,10 1|1:14:9,5 1|1:50:25,25 +chr20 813255 200xb42 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=793681;QSTRAND=+ GT:DP:AD 1|1:40:21,19 ./.:38:15,23 1|0:35:23,12 +chr20 813573 200xb43 C T 60 . QNAME=cluster19_000000F;QSTART=24947799;QSTRAND=- GT:DP:AD ./.:37:19,18 1|1:42:18,24 0|1:35:11,24 +chr20 813792 200xb44 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=794218;QSTRAND=+ GT:DP:AD 1|1:22:13,9 ./.:20:14,6 1|0:25:20,5 +chr20 813863 200xb45 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=794289;QSTRAND=+ GT:DP:AD 1|1:33:16,17 1|1:39:14,25 1|1:44:22,22 +chr20 814342 200xb46 T TG 60 . QNAME=cluster23_scaffold_2;QSTART=24880682;QSTRAND=- GT:DP:AD ./.:36:17,19 ./.:27:18,9 0|1:38:15,23 +chr20 814479 200xb47 AT A 60 . QNAME=cluster23_scaffold_2;QSTART=24880545;QSTRAND=- GT:DP:AD ./.:37:23,14 ./.:23:13,10 0|1:28:12,16 +chr20 814505 200xb48 T TTTTATTTA 60 . QNAME=HG002-S9-H1-000001F;QSTART=794932;QSTRAND=+ GT:DP:AD 1|1:40:15,25 ./.:25:12,13 1|0:33:24,9 +chr20 814505 200xb49 T TTTTA 60 . QNAME=cluster19_000000F;QSTART=24946863;QSTRAND=- GT:DP:AD ./.:24:15,9 1|1:15:10,5 0|1:42:23,19 +chr20 815073 200xb4a A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=795507;QSTRAND=+ GT:DP:AD 1|1:34:23,11 ./.:30:13,17 1|0:17:5,12 +chr20 815387 200xb4b A T 60 . QNAME=cluster19_000000F;QSTART=24945981;QSTRAND=- GT:DP:AD ./.:26:10,16 1|1:14:6,8 0|1:39:14,25 +chr20 815789 200xb4c C A 60 . QNAME=cluster19_000000F;QSTART=24945579;QSTRAND=- GT:DP:AD ./.:36:23,13 1|1:27:9,18 ./.:37:23,14 +chr20 816179 200xb4d C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=796613;QSTRAND=+ GT:DP:AD 1|1:38:19,19 ./.:17:11,6 1|0:27:14,13 +chr20 816272 200xb4e CT C 60 . QNAME=cluster23_scaffold_2;QSTART=24878749;QSTRAND=- GT:DP:AD ./.:19:11,8 ./.:24:19,5 0|1:22:9,13 +chr20 816693 200xb4f GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=797128;QSTRAND=+ GT:DP:AD 1|0:17:7,10 1|1:23:15,8 1|0:28:17,11 +chr20 816723 200xb50 TTGTGCG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=797157;QSTRAND=+ GT:DP:AD 1|0:42:21,21 ./.:44:24,20 1|0:30:8,22 +chr20 816728 200xb51 CGT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=771737;QSTRAND=+ GT:DP:AD 0|1:15:10,5 ./.:14:7,7 ./.:30:14,16 +chr20 816728 200xb52 C CGTGT 60 . QNAME=cluster23_scaffold_2;QSTART=24878290;QSTRAND=- GT:DP:AD ./.:27:18,9 ./.:26:7,19 0|1:36:16,20 +chr20 816757 200xb53 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=797184;QSTRAND=+ GT:DP:AD 1|0:33:16,17 ./.:19:5,14 1|0:14:8,6 +chr20 817397 200xb54 G A 60 . QNAME=cluster23_scaffold_2;QSTART=24877621;QSTRAND=- GT:DP:AD ./.:40:20,20 ./.:20:15,5 0|1:33:16,17 +chr20 817512 200xb55 A G 60 . QNAME=cluster19_000000F;QSTART=24943857;QSTRAND=- GT:DP:AD ./.:32:8,24 1|0:10:5,5 ./.:17:8,9 +chr20 817544 200xb56 G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=797972;QSTRAND=+ GT:DP:AD 1|0:35:25,10 ./.:27:12,15 1|0:27:6,21 +chr20 817544 200xb57 GA G 60 . QNAME=HG002-S9-H2-000001F;QSTART=772551;QSTRAND=+ GT:DP:AD 0|1:28:12,16 0|1:35:21,14 ./.:23:10,13 +chr20 817544 200xb58 GAA G 60 . QNAME=cluster19_000000F;QSTART=24943825;QSTRAND=- GT:DP:AD ./.:24:12,12 1|0:24:7,17 0|1:30:23,7 +chr20 817584 200xb59 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=798012;QSTRAND=+ GT:DP:AD 1|0:27:7,20 ./.:35:15,20 1|0:18:13,5 +chr20 817587 200xb5a A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=798015;QSTRAND=+ GT:DP:AD 1|0:34:13,21 ./.:37:15,22 1|0:19:8,11 +chr20 817664 200xb5b C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=798092;QSTRAND=+ GT:DP:AD 1|0:23:8,15 ./.:20:12,8 1|0:33:21,12 +chr20 817690 200xb5c G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=798118;QSTRAND=+ GT:DP:AD 1|0:27:12,15 1|1:32:21,11 1|1:26:8,18 +chr20 817718 200xb5d G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=798146;QSTRAND=+ GT:DP:AD 1|0:31:15,16 ./.:11:5,6 1|0:37:23,14 +chr20 817808 200xb5e T C 60 . QNAME=cluster19_000000F;QSTART=24943563;QSTRAND=- GT:DP:AD ./.:27:21,6 1|1:38:25,13 ./.:41:25,16 +chr20 817809 200xb5f T A 60 . QNAME=cluster19_000000F;QSTART=24943562;QSTRAND=- GT:DP:AD ./.:35:23,12 1|1:13:5,8 ./.:26:19,7 +chr20 817850 200xb60 G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=798279;QSTRAND=+ GT:DP:AD 1|0:41:22,19 ./.:17:8,9 ./.:41:22,19 +chr20 817871 200xb61 G GA 60 . QNAME=cluster23_scaffold_2;QSTART=24877148;QSTRAND=- GT:DP:AD ./.:24:18,6 ./.:37:14,23 0|1:26:13,13 +chr20 818023 200xb62 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=798452;QSTRAND=+ GT:DP:AD 1|0:36:24,12 ./.:21:7,14 1|0:29:18,11 +chr20 818055 200xb63 T TG 60 . QNAME=cluster23_scaffold_2;QSTART=24876963;QSTRAND=- GT:DP:AD ./.:21:9,12 ./.:43:19,24 0|1:29:19,10 +chr20 818068 200xb64 T TG 60 . QNAME=cluster23_scaffold_2;QSTART=24876949;QSTRAND=- GT:DP:AD ./.:30:8,22 ./.:27:11,16 0|1:26:20,6 +chr20 818085 200xb65 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=798514;QSTRAND=+ GT:DP:AD 1|0:31:14,17 ./.:17:11,6 1|0:28:9,19 +chr20 818112 200xb66 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=798541;QSTRAND=+ GT:DP:AD 1|0:21:12,9 1|1:24:5,19 1|1:35:14,21 +chr20 818177 200xb67 T C 60 . QNAME=cluster23_scaffold_2;QSTART=24876840;QSTRAND=- GT:DP:AD ./.:25:12,13 ./.:18:13,5 0|1:40:24,16 +chr20 818388 200xb68 A AG 60 . QNAME=cluster23_scaffold_3;QSTART=24892321;QSTRAND=- GT:DP:AD ./.:48:24,24 ./.:36:14,22 1|0:48:23,25 +chr20 818488 200xb69 A ATT 60 . QNAME=HG002-S9-H1-000001F;QSTART=798918;QSTRAND=+ GT:DP:AD 1|0:14:9,5 ./.:27:21,6 ./.:28:10,18 +chr20 818488 200xb6a A AT 60 . QNAME=HG002-S9-H2-000001F;QSTART=773494;QSTRAND=+ GT:DP:AD 0|1:33:24,9 ./.:14:5,9 ./.:33:15,18 +chr20 818644 200xb6b T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=799075;QSTRAND=+ GT:DP:AD 1|1:23:11,12 ./.:32:16,16 1|0:45:25,20 +chr20 818794 200xb6c C CTT 60 . QNAME=HG002-S9-H1-000001F;QSTART=799226;QSTRAND=+ GT:DP:AD 1|1:21:11,10 ./.:30:10,20 1|0:19:9,10 +chr20 818794 200xb6d CT C 60 . QNAME=cluster23_scaffold_2;QSTART=24876223;QSTRAND=- GT:DP:AD ./.:17:10,7 ./.:31:13,18 0|1:34:14,20 +chr20 818839 200xb6e C G 60 . QNAME=cluster23_scaffold_2;QSTART=24876179;QSTRAND=- GT:DP:AD ./.:19:13,6 ./.:44:20,24 0|1:36:14,22 +chr20 818891 200xb6f A G 60 . QNAME=cluster19_000000F;QSTART=24942480;QSTRAND=- GT:DP:AD ./.:34:9,25 1|1:26:20,6 ./.:20:7,13 +chr20 818898 200xb70 T TC 60 . QNAME=cluster23_scaffold_2;QSTART=24876119;QSTRAND=- GT:DP:AD ./.:21:9,12 ./.:44:21,23 0|1:33:10,23 +chr20 818940 200xb71 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=799373;QSTRAND=+ GT:DP:AD 1|1:35:13,22 ./.:42:18,24 1|1:32:15,17 +chr20 818970 200xb72 G C 60 . QNAME=cluster19_000000F;QSTART=24942401;QSTRAND=- GT:DP:AD ./.:27:13,14 1|1:28:21,7 ./.:21:5,16 +chr20 819017 200xb73 C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=774025;QSTRAND=+ GT:DP:AD 0|1:29:14,15 ./.:31:25,6 ./.:27:15,12 +chr20 819249 200xb74 T C 60 . QNAME=cluster19_000000F;QSTART=780213;QSTRAND=+ GT:DP:AD ./.:24:7,17 0|1:25:5,20 ./.:28:5,23 +chr20 819251 200xb75 C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=774259;QSTRAND=+ GT:DP:AD 0|1:34:21,13 ./.:27:17,10 ./.:27:20,7 +chr20 820514 200xb76 T TTTC 60 . QNAME=HG002-S9-H1-000001F;QSTART=802126;QSTRAND=+ GT:DP:AD 1|1:23:14,9 1|1:36:23,13 1|1:25:9,16 +chr20 820545 200xb77 T TTC 60 . QNAME=cluster19_000000F;QSTART=24937541;QSTRAND=- GT:DP:AD ./.:17:10,7 1|1:29:10,19 ./.:23:15,8 +chr20 820587 200xb78 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=802201;QSTRAND=+ GT:DP:AD 1|1:31:16,15 ./.:31:16,15 1|0:27:18,9 +chr20 820752 200xb79 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=802366;QSTRAND=+ GT:DP:AD 1|1:39:24,15 ./.:40:24,16 1|0:37:20,17 +chr20 821376 200xb7a G T 60 . QNAME=cluster23_scaffold_2;QSTART=24871732;QSTRAND=- GT:DP:AD ./.:28:20,8 ./.:16:5,11 0|1:22:17,5 +chr20 821480 200xb7b G T 60 . QNAME=cluster19_000000F;QSTART=24936606;QSTRAND=- GT:DP:AD ./.:35:17,18 1|1:41:18,23 0|1:17:10,7 +chr20 822153 200xb7c ATTTT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=803768;QSTRAND=+ GT:DP:AD 1|1:27:11,16 ./.:34:18,16 1|0:29:8,21 +chr20 822153 200xb7d ATTT A 60 . QNAME=cluster19_000000F;QSTART=24935933;QSTRAND=- GT:DP:AD ./.:47:23,24 1|1:26:15,11 ./.:48:23,25 +chr20 822153 200xb7e A AT 60 . QNAME=cluster23_scaffold_2;QSTART=24870954;QSTRAND=- GT:DP:AD ./.:41:23,18 ./.:36:23,13 0|1:23:12,11 +chr20 822622 200xb7f G A 60 . QNAME=cluster23_scaffold_2;QSTART=24870485;QSTRAND=- GT:DP:AD ./.:36:12,24 ./.:36:17,19 0|1:25:6,19 +chr20 823109 200xb80 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=804719;QSTRAND=+ GT:DP:AD 1|1:38:15,23 1|1:39:16,23 1|1:28:9,19 +chr20 824454 200xb81 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=806064;QSTRAND=+ GT:DP:AD 1|1:40:22,18 1|1:18:9,9 1|1:38:24,14 +chr20 825318 200xb82 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=806928;QSTRAND=+ GT:DP:AD 1|1:16:10,6 ./.:33:23,10 1|0:24:17,7 +chr20 825338 200xb83 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=806948;QSTRAND=+ GT:DP:AD 1|1:40:19,21 ./.:21:12,9 1|0:32:21,11 +chr20 825828 200xb84 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=807438;QSTRAND=+ GT:DP:AD 1|1:34:23,11 1|1:27:5,22 1|1:39:14,25 +chr20 826034 200xb85 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=807644;QSTRAND=+ GT:DP:AD 1|1:46:25,21 1|1:20:8,12 1|1:47:24,23 +chr20 826235 200xb86 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=807845;QSTRAND=+ GT:DP:AD 1|1:35:15,20 1|1:48:23,25 1|1:40:17,23 +chr20 826944 200xb87 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=808554;QSTRAND=+ GT:DP:AD 1|1:36:23,13 ./.:35:20,15 1|0:23:12,11 +chr20 827056 200xb88 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=808666;QSTRAND=+ GT:DP:AD 1|1:41:22,19 ./.:19:11,8 1|0:29:24,5 +chr20 827617 200xb89 C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=809228;QSTRAND=+ GT:DP:AD 1|1:25:12,13 ./.:20:5,15 1|0:24:11,13 +chr20 827617 200xb8a C CAA 60 . QNAME=cluster19_000000F;QSTART=24930470;QSTRAND=- GT:DP:AD ./.:39:24,15 1|1:45:24,21 0|1:44:23,21 +chr20 827787 200xb8b G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=809398;QSTRAND=+ GT:DP:AD 1|1:40:16,24 1|1:48:23,25 1|1:34:20,14 +chr20 827840 200xb8c G A 60 . QNAME=cluster23_scaffold_2;QSTART=24865265;QSTRAND=- GT:DP:AD ./.:40:25,15 ./.:33:14,19 0|1:40:19,21 +chr20 827959 200xb8d G A 60 . QNAME=cluster19_000000F;QSTART=24930128;QSTRAND=- GT:DP:AD ./.:24:9,15 1|1:32:25,7 ./.:27:11,16 +chr20 828060 200xb8e G GAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=809672;QSTRAND=+ GT:DP:AD 1|1:25:6,19 1|1:39:17,22 0|1:32:19,13 +chr20 828060 200xb8f G GAAAAA 60 . QNAME=cluster23_scaffold_3;QSTART=24881385;QSTRAND=- GT:DP:AD ./.:26:11,15 ./.:31:16,15 1|0:24:9,15 +chr20 828725 200xb90 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=810340;QSTRAND=+ GT:DP:AD 1|1:18:5,13 1|1:39:23,16 1|1:39:18,21 +chr20 828856 200xb91 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=810471;QSTRAND=+ GT:DP:AD 1|1:33:21,12 1|1:28:13,15 1|1:37:23,14 +chr20 828857 200xb92 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=810472;QSTRAND=+ GT:DP:AD 1|1:49:25,24 1|1:42:23,19 1|1:43:21,22 +chr20 828946 200xb93 C T 60 . QNAME=cluster19_000000F;QSTART=24929137;QSTRAND=- GT:DP:AD ./.:29:15,14 1|1:27:9,18 ./.:34:20,14 +chr20 829194 200xb94 G A 60 . QNAME=cluster23_scaffold_2;QSTART=24863907;QSTRAND=- GT:DP:AD ./.:29:13,16 ./.:26:15,11 0|1:49:24,25 +chr20 829287 200xb95 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=810902;QSTRAND=+ GT:DP:AD 1|1:23:6,17 1|1:33:11,22 1|1:38:23,15 +chr20 830064 200xb96 A G 60 . QNAME=cluster19_000000F;QSTART=24928019;QSTRAND=- GT:DP:AD ./.:21:7,14 1|1:43:24,19 0|1:14:6,8 +chr20 830268 200xb97 C CTT 60 . QNAME=cluster23_scaffold_2;QSTART=24862831;QSTRAND=- GT:DP:AD ./.:37:12,25 ./.:29:21,8 0|1:38:15,23 +chr20 830270 200xb98 T C 60 . QNAME=cluster19_000000F;QSTART=24927813;QSTRAND=- GT:DP:AD ./.:33:12,21 1|1:36:20,16 ./.:16:8,8 +chr20 830311 200xb99 A G 60 . QNAME=cluster19_000000F;QSTART=24927772;QSTRAND=- GT:DP:AD ./.:24:13,11 1|1:48:25,23 0|1:17:12,5 +chr20 830449 200xb9a CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=812065;QSTRAND=+ GT:DP:AD 1|0:30:7,23 ./.:36:16,20 ./.:21:10,11 +chr20 830449 200xb9b C CTT 60 . QNAME=cluster19_000000F;QSTART=24927632;QSTRAND=- GT:DP:AD ./.:37:23,14 1|1:28:6,22 0|1:33:13,20 +chr20 830787 200xb9c A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=812401;QSTRAND=+ GT:DP:AD 1|1:17:7,10 1|1:29:8,21 1|1:37:18,19 +chr20 830864 200xb9d G A 60 . QNAME=cluster19_000000F;QSTART=24927217;QSTRAND=- GT:DP:AD ./.:30:10,20 1|1:29:23,6 0|1:49:24,25 +chr20 831203 200xb9e G C 60 . QNAME=cluster19_000000F;QSTART=24926878;QSTRAND=- GT:DP:AD ./.:26:14,12 1|1:28:9,19 ./.:30:7,23 +chr20 831231 200xb9f T C 60 . QNAME=cluster19_000000F;QSTART=24926850;QSTRAND=- GT:DP:AD ./.:28:23,5 1|1:29:5,24 0|1:31:10,21 +chr20 831257 200xba0 C CA 60 . QNAME=cluster19_000000F;QSTART=795540;QSTRAND=+ GT:DP:AD ./.:24:12,12 0|1:45:22,23 1|1:45:22,23 +chr20 831332 200xba1 T C 60 . QNAME=cluster19_000000F;QSTART=24926749;QSTRAND=- GT:DP:AD ./.:20:7,13 1|1:31:25,6 0|1:29:9,20 +chr20 831358 200xba2 A T 60 . QNAME=cluster19_000000F;QSTART=24926723;QSTRAND=- GT:DP:AD ./.:33:13,20 1|1:33:22,11 0|1:39:14,25 +chr20 831366 200xba3 G A 60 . QNAME=cluster23_scaffold_2;QSTART=24861730;QSTRAND=- GT:DP:AD ./.:38:14,24 ./.:38:18,20 0|1:22:17,5 +chr20 832087 200xba4 A C 60 . QNAME=cluster19_000000F;QSTART=24925994;QSTRAND=- GT:DP:AD ./.:28:13,15 1|1:28:13,15 0|1:41:21,20 +chr20 833024 200xba5 A G 60 . QNAME=cluster19_000000F;QSTART=24925057;QSTRAND=- GT:DP:AD ./.:29:13,16 1|0:34:14,20 ./.:29:6,23 +chr20 833025 200xba6 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=814639;QSTRAND=+ GT:DP:AD 1|1:29:14,15 0|1:23:7,16 0|1:24:9,15 +chr20 833025 200xba7 AG A 60 . QNAME=cluster19_000000F;QSTART=24925056;QSTRAND=- GT:DP:AD ./.:29:14,15 1|0:28:6,22 ./.:17:8,9 +chr20 833026 200xba8 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=814640;QSTRAND=+ GT:DP:AD 1|1:26:11,15 0|1:28:11,17 0|1:23:11,12 +chr20 833026 200xba9 G GA 60 . QNAME=cluster23_scaffold_3;QSTART=24876417;QSTRAND=- GT:DP:AD ./.:36:20,16 ./.:21:8,13 1|0:24:9,15 +chr20 833108 200xbaa C G 60 . QNAME=cluster19_000000F;QSTART=24924974;QSTRAND=- GT:DP:AD ./.:39:15,24 1|1:33:15,18 0|1:38:22,16 +chr20 835141 200xbab C T 60 . QNAME=cluster23_scaffold_2;QSTART=24857955;QSTRAND=- GT:DP:AD ./.:23:10,13 ./.:29:19,10 0|1:34:14,20 +chr20 835164 200xbac A ATC 60 . QNAME=HG002-S9-H1-000001F;QSTART=816779;QSTRAND=+ GT:DP:AD 1|1:37:21,16 ./.:41:17,24 ./.:24:7,17 +chr20 835200 200xbad C A 60 . QNAME=cluster23_scaffold_3;QSTART=24874243;QSTRAND=- GT:DP:AD ./.:36:12,24 ./.:37:22,15 1|0:37:19,18 +chr20 835200 200xbae C CTCTATA 60 . QNAME=cluster23_scaffold_2;QSTART=24857890;QSTRAND=- GT:DP:AD ./.:19:6,13 ./.:38:18,20 0|1:33:24,9 +chr20 835202 200xbaf A C 60 . QNAME=cluster19_000000F;QSTART=24922880;QSTRAND=- GT:DP:AD ./.:21:7,14 1|1:21:5,16 ./.:40:18,22 +chr20 836246 200xbb0 TG T 60 . QNAME=cluster19_000000F;QSTART=24921836;QSTRAND=- GT:DP:AD ./.:36:12,24 1|1:31:12,19 0|1:32:20,12 +chr20 837045 200xbb1 G GTT 60 . QNAME=cluster23_scaffold_2;QSTART=24856044;QSTRAND=- GT:DP:AD ./.:44:25,19 ./.:41:16,25 0|1:19:5,14 +chr20 838387 200xbb2 G C 60 . QNAME=cluster23_scaffold_2;QSTART=24854702;QSTRAND=- GT:DP:AD ./.:25:19,6 ./.:21:9,12 0|1:29:24,5 +chr20 841266 200xbb3 C T 60 . QNAME=cluster19_000000F;QSTART=805548;QSTRAND=+ GT:DP:AD ./.:30:19,11 0|1:21:11,10 0|1:21:6,15 +chr20 842793 200xbb4 T C 60 . QNAME=cluster23_scaffold_2;QSTART=24850296;QSTRAND=- GT:DP:AD ./.:29:21,8 ./.:38:17,21 0|1:43:22,21 +chr20 842861 200xbb5 T G 60 . QNAME=cluster23_scaffold_2;QSTART=24850228;QSTRAND=- GT:DP:AD ./.:36:17,19 ./.:19:6,13 0|1:12:6,6 +chr20 843131 200xbb6 T C 60 . QNAME=cluster23_scaffold_2;QSTART=24849958;QSTRAND=- GT:DP:AD ./.:27:18,9 ./.:30:13,17 0|1:41:25,16 +chr20 843133 200xbb7 C T 60 . QNAME=cluster23_scaffold_2;QSTART=24849956;QSTRAND=- GT:DP:AD ./.:35:22,13 ./.:29:17,12 0|1:44:22,22 +chr20 843148 200xbb8 A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=824764;QSTRAND=+ GT:DP:AD 1|0:36:13,23 ./.:35:22,13 ./.:17:6,11 +chr20 843149 200xbb9 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=824765;QSTRAND=+ GT:DP:AD 1|0:32:12,20 ./.:38:22,16 ./.:38:21,17 +chr20 843779 200xbba C A 60 . QNAME=cluster23_scaffold_2;QSTART=24849310;QSTRAND=- GT:DP:AD ./.:31:11,20 ./.:35:23,12 0|1:30:17,13 +chr20 843805 200xbbb T C 60 . QNAME=cluster19_000000F;QSTART=808087;QSTRAND=+ GT:DP:AD ./.:36:18,18 0|1:28:17,11 ./.:24:12,12 +chr20 843879 200xbbc G T 60 . QNAME=cluster23_scaffold_2;QSTART=24849210;QSTRAND=- GT:DP:AD ./.:35:23,12 ./.:19:7,12 0|1:16:8,8 +chr20 844439 200xbbd TGCCCAGGTC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=826056;QSTRAND=+ GT:DP:AD 1|1:26:11,15 1|1:28:12,16 1|1:29:14,15 +chr20 844675 200xbbe C CT 60 . QNAME=HG002-S9-H2-000001F;QSTART=800823;QSTRAND=+ GT:DP:AD 0|1:39:22,17 0|1:26:5,21 1|1:35:15,20 +chr20 845035 200xbbf T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=826642;QSTRAND=+ GT:DP:AD 1|1:32:21,11 1|1:28:21,7 1|1:29:7,22 +chr20 845849 200xbc0 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=827456;QSTRAND=+ GT:DP:AD 1|1:36:24,12 ./.:21:10,11 1|1:42:19,23 +chr20 845870 200xbc1 C G 60 . QNAME=cluster19_000000F;QSTART=810144;QSTRAND=+ GT:DP:AD ./.:13:7,6 0|1:34:12,22 ./.:36:17,19 +chr20 846023 200xbc2 G T 60 . QNAME=cluster19_000000F;QSTART=24912069;QSTRAND=- GT:DP:AD ./.:41:19,22 1|0:25:13,12 ./.:19:12,7 +chr20 846067 200xbc3 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=827674;QSTRAND=+ GT:DP:AD 1|1:22:17,5 ./.:30:10,20 1|1:44:23,21 +chr20 846626 200xbc4 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=828233;QSTRAND=+ GT:DP:AD 1|1:26:21,5 ./.:28:6,22 1|1:26:18,8 +chr20 847610 200xbc5 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=829217;QSTRAND=+ GT:DP:AD 1|1:17:6,11 ./.:30:7,23 1|1:21:7,14 +chr20 847932 200xbc6 C T 60 . QNAME=cluster19_000000F;QSTART=812206;QSTRAND=+ GT:DP:AD ./.:23:10,13 0|1:37:16,21 ./.:37:22,15 +chr20 847948 200xbc7 C T 60 . QNAME=cluster19_000000F;QSTART=812222;QSTRAND=+ GT:DP:AD ./.:36:21,15 0|1:20:7,13 ./.:32:14,18 +chr20 848007 200xbc8 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=829614;QSTRAND=+ GT:DP:AD 1|1:43:22,21 ./.:11:5,6 1|1:34:13,21 +chr20 848148 200xbc9 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=829755;QSTRAND=+ GT:DP:AD 1|1:27:6,21 0|1:27:17,10 0|1:20:14,6 +chr20 848655 200xbca G GCCC 60 . QNAME=cluster19_000000F;QSTART=812930;QSTRAND=+ GT:DP:AD ./.:21:7,14 0|1:20:15,5 ./.:13:6,7 +chr20 848655 200xbcb G GC 60 . QNAME=cluster23_scaffold_2;QSTART=24844441;QSTRAND=- GT:DP:AD ./.:31:15,16 ./.:29:24,5 0|1:45:24,21 +chr20 848966 200xbcc C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=830573;QSTRAND=+ GT:DP:AD 1|1:16:5,11 ./.:20:6,14 1|1:15:7,8 +chr20 849159 200xbcd T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=830766;QSTRAND=+ GT:DP:AD 1|1:29:18,11 ./.:22:17,5 1|1:21:11,10 +chr20 849210 200xbce T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=830817;QSTRAND=+ GT:DP:AD 1|1:40:22,18 1|1:40:25,15 1|1:26:14,12 +chr20 849245 200xbcf A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=830852;QSTRAND=+ GT:DP:AD 1|1:40:17,23 ./.:47:23,24 1|1:13:8,5 +chr20 849258 200xbd0 CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=830866;QSTRAND=+ GT:DP:AD 1|1:31:18,13 0|1:43:24,19 1|1:21:16,5 +chr20 849509 200xbd1 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=831115;QSTRAND=+ GT:DP:AD 1|1:28:14,14 ./.:40:25,15 1|1:45:23,22 +chr20 849655 200xbd2 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=831261;QSTRAND=+ GT:DP:AD 1|1:37:24,13 ./.:29:21,8 1|1:16:10,6 +chr20 849665 200xbd3 T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=831271;QSTRAND=+ GT:DP:AD 1|1:24:13,11 ./.:31:22,9 1|1:27:5,22 +chr20 849770 200xbd4 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=831376;QSTRAND=+ GT:DP:AD 1|1:25:17,8 ./.:28:19,9 1|1:17:8,9 +chr20 849895 200xbd5 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=831501;QSTRAND=+ GT:DP:AD 1|1:17:5,12 ./.:32:19,13 1|1:28:8,20 +chr20 850094 200xbd6 T TACACAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=831701;QSTRAND=+ GT:DP:AD 1|0:34:11,23 ./.:35:14,21 0|1:30:5,25 +chr20 850094 200xbd7 T TACACACACAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=806242;QSTRAND=+ GT:DP:AD 0|1:16:10,6 ./.:26:13,13 ./.:21:12,9 +chr20 850134 200xbd8 C CACACAT 60 . QNAME=cluster19_000000F;QSTART=24907952;QSTRAND=- GT:DP:AD ./.:41:17,24 1|0:22:9,13 1|0:16:5,11 +chr20 850134 200xbd9 C CACACACACACAT 60 . QNAME=cluster19_000000F;QSTART=814411;QSTRAND=+ GT:DP:AD ./.:43:25,18 0|1:34:24,10 ./.:33:16,17 +chr20 850182 200xbda G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=831794;QSTRAND=+ GT:DP:AD 1|1:30:23,7 ./.:27:12,15 1|1:33:11,22 +chr20 850404 200xbdb C T 60 . QNAME=cluster19_000000F;QSTART=814692;QSTRAND=+ GT:DP:AD ./.:31:8,23 0|1:38:25,13 ./.:34:15,19 +chr20 850450 200xbdc A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=832062;QSTRAND=+ GT:DP:AD 1|1:40:20,20 0|1:28:14,14 1|1:26:6,20 +chr20 850608 200xbdd A G 60 . QNAME=cluster19_000000F;QSTART=814896;QSTRAND=+ GT:DP:AD ./.:31:17,14 0|1:33:18,15 ./.:30:8,22 +chr20 850762 200xbde G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=832374;QSTRAND=+ GT:DP:AD 1|1:32:16,16 ./.:39:23,16 1|1:21:12,9 +chr20 850818 200xbdf G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=832430;QSTRAND=+ GT:DP:AD 1|1:30:12,18 0|1:37:19,18 1|1:43:22,21 +chr20 851565 200xbe0 G A 60 . QNAME=cluster19_000000F;QSTART=815853;QSTRAND=+ GT:DP:AD ./.:31:7,24 0|1:22:9,13 ./.:30:22,8 +chr20 851698 200xbe1 C T 60 . QNAME=cluster19_000000F;QSTART=24906388;QSTRAND=- GT:DP:AD ./.:32:18,14 1|0:42:17,25 ./.:38:24,14 +chr20 852010 200xbe2 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=833622;QSTRAND=+ GT:DP:AD 1|1:43:24,19 ./.:33:21,12 1|1:29:20,9 +chr20 852120 200xbe3 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=833732;QSTRAND=+ GT:DP:AD 1|1:44:23,21 ./.:29:7,22 1|1:39:14,25 +chr20 852153 200xbe4 C T 60 . QNAME=cluster19_000000F;QSTART=816441;QSTRAND=+ GT:DP:AD ./.:42:19,23 0|1:44:20,24 ./.:40:22,18 +chr20 852155 200xbe5 T C 60 . QNAME=cluster19_000000F;QSTART=816443;QSTRAND=+ GT:DP:AD ./.:32:25,7 0|1:16:10,6 ./.:37:15,22 +chr20 852165 200xbe6 G A 60 . QNAME=cluster19_000000F;QSTART=816453;QSTRAND=+ GT:DP:AD ./.:33:11,22 0|1:34:11,23 ./.:29:14,15 +chr20 852596 200xbe7 ACT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=834209;QSTRAND=+ GT:DP:AD 1|1:20:11,9 0|1:28:5,23 1|1:42:20,22 +chr20 852714 200xbe8 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=834324;QSTRAND=+ GT:DP:AD 1|1:41:22,19 0|1:13:5,8 1|1:33:10,23 +chr20 852722 200xbe9 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=834332;QSTRAND=+ GT:DP:AD 1|1:30:17,13 ./.:42:19,23 1|1:37:12,25 +chr20 853509 200xbea C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=835119;QSTRAND=+ GT:DP:AD 1|1:22:10,12 ./.:34:25,9 1|1:31:11,20 +chr20 853837 200xbeb C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=835447;QSTRAND=+ GT:DP:AD 1|1:41:24,17 ./.:35:14,21 1|1:27:6,21 +chr20 854857 200xbec TTGTG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=836468;QSTRAND=+ GT:DP:AD 1|0:17:7,10 1|1:19:5,14 ./.:29:13,16 +chr20 854857 200xbed TTGTGTG T 60 . QNAME=HG002-S9-H2-000001F;QSTART=811013;QSTRAND=+ GT:DP:AD 0|1:26:12,14 ./.:24:13,11 1|1:26:5,21 +chr20 855703 200xbee C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=837309;QSTRAND=+ GT:DP:AD 1|0:34:11,23 1|1:32:20,12 1|1:36:21,15 +chr20 855883 200xbef G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=812032;QSTRAND=+ GT:DP:AD 0|1:42:18,24 ./.:46:24,22 ./.:16:7,9 +chr20 856057 200xbf0 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=837663;QSTRAND=+ GT:DP:AD 1|1:33:9,24 1|1:49:24,25 1|1:26:21,5 +chr20 856168 200xbf1 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=837774;QSTRAND=+ GT:DP:AD 1|0:24:10,14 0|1:31:7,24 ./.:23:11,12 +chr20 856433 200xbf2 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=838039;QSTRAND=+ GT:DP:AD 1|1:34:15,19 1|1:29:18,11 1|1:43:18,25 +chr20 856781 200xbf3 G A 60 . QNAME=cluster19_000000F;QSTART=821063;QSTRAND=+ GT:DP:AD ./.:46:25,21 0|1:13:7,6 ./.:39:17,22 +chr20 857157 200xbf4 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=838763;QSTRAND=+ GT:DP:AD 1|1:17:6,11 1|1:25:13,12 1|1:27:21,6 +chr20 857179 200xbf5 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=838785;QSTRAND=+ GT:DP:AD 1|1:16:10,6 1|1:29:7,22 1|1:24:17,7 +chr20 857617 200xbf6 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=839223;QSTRAND=+ GT:DP:AD 1|1:40:17,23 1|1:22:11,11 1|1:33:22,11 +chr20 858872 200xbf7 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=840478;QSTRAND=+ GT:DP:AD 1|1:32:12,20 1|1:41:23,18 1|1:28:9,19 +chr20 858925 200xbf8 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=840531;QSTRAND=+ GT:DP:AD 1|1:26:13,13 1|1:29:22,7 1|1:35:15,20 +chr20 859762 200xbf9 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=841368;QSTRAND=+ GT:DP:AD 1|1:33:11,22 1|1:16:8,8 1|1:41:25,16 +chr20 860453 200xbfa G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=842059;QSTRAND=+ GT:DP:AD 1|0:23:10,13 0|1:30:22,8 ./.:18:5,13 +chr20 860488 200xbfb T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=816637;QSTRAND=+ GT:DP:AD 0|1:19:6,13 1|0:21:5,16 1|1:21:13,8 +chr20 861973 200xbfc G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=843579;QSTRAND=+ GT:DP:AD 1|1:42:23,19 1|1:35:15,20 1|1:32:19,13 +chr20 861975 200xbfd G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=843581;QSTRAND=+ GT:DP:AD 1|1:39:18,21 1|1:25:9,16 1|1:14:7,7 +chr20 862051 200xbfe A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=843657;QSTRAND=+ GT:DP:AD 1|1:15:10,5 1|1:29:8,21 1|1:37:20,17 +chr20 862053 200xbff A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=843659;QSTRAND=+ GT:DP:AD 1|1:16:7,9 1|1:19:11,8 1|1:30:25,5 +chr20 862244 200xc00 CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=818394;QSTRAND=+ GT:DP:AD 0|1:24:15,9 1|0:35:10,25 1|0:13:6,7 +chr20 862244 200xc01 CTT C 60 . QNAME=cluster23_scaffold_2;QSTART=24830855;QSTRAND=- GT:DP:AD ./.:39:25,14 ./.:31:14,17 0|1:15:10,5 +chr20 862270 200xc02 T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=843876;QSTRAND=+ GT:DP:AD 1|1:42:24,18 1|0:45:24,21 1|1:44:19,25 +chr20 862270 200xc03 T TA 60 . QNAME=cluster19_000000F;QSTART=826553;QSTRAND=+ GT:DP:AD ./.:21:11,10 0|1:37:15,22 ./.:37:23,14 +chr20 862295 200xc04 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=843901;QSTRAND=+ GT:DP:AD 1|1:31:6,25 1|1:32:15,17 1|1:27:5,22 +chr20 862400 200xc05 A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=818548;QSTRAND=+ GT:DP:AD 0|1:34:19,15 1|0:15:9,6 1|1:45:23,22 +chr20 863200 200xc06 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=844806;QSTRAND=+ GT:DP:AD 1|0:31:8,23 0|1:35:22,13 ./.:37:15,22 +chr20 863302 200xc07 A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=819450;QSTRAND=+ GT:DP:AD 0|1:15:6,9 1|0:29:16,13 1|1:28:12,16 +chr20 863798 200xc08 CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=845405;QSTRAND=+ GT:DP:AD 1|1:45:23,22 1|1:28:21,7 1|1:30:12,18 +chr20 864029 200xc09 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=820176;QSTRAND=+ GT:DP:AD 0|1:31:17,14 1|0:39:21,18 1|1:24:8,16 +chr20 864049 200xc0a T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=820196;QSTRAND=+ GT:DP:AD 0|1:40:22,18 1|0:47:22,25 1|1:44:22,22 +chr20 864080 200xc0b T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=845685;QSTRAND=+ GT:DP:AD 1|1:30:9,21 1|1:13:6,7 1|1:24:12,12 +chr20 865132 200xc0c AAGCAGAAAAGC A 60 . QNAME=cluster23_scaffold_2;QSTART=24827970;QSTRAND=- GT:DP:AD ./.:15:7,8 ./.:37:20,17 0|1:30:8,22 +chr20 865868 200xc0d C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=847474;QSTRAND=+ GT:DP:AD 1|0:46:24,22 0|1:43:23,20 ./.:22:6,16 +chr20 866330 200xc0e A AC 60 . QNAME=HG002-S9-H1-000001F;QSTART=847937;QSTRAND=+ GT:DP:AD 1|0:26:10,16 0|1:32:13,19 ./.:40:18,22 +chr20 866340 200xc0f A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=847947;QSTRAND=+ GT:DP:AD 1|0:35:15,20 0|1:15:5,10 ./.:28:19,9 +chr20 866636 200xc10 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=848243;QSTRAND=+ GT:DP:AD 1|0:28:10,18 0|1:42:22,20 ./.:39:23,16 +chr20 866712 200xc11 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=848319;QSTRAND=+ GT:DP:AD 1|0:33:10,23 0|1:38:25,13 ./.:42:23,19 +chr20 866777 200xc12 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=848384;QSTRAND=+ GT:DP:AD 1|0:34:11,23 0|1:45:24,21 ./.:24:15,9 +chr20 866852 200xc13 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=848459;QSTRAND=+ GT:DP:AD 1|0:28:20,8 0|1:18:10,8 ./.:26:12,14 +chr20 867420 200xc14 GTA G 60 . QNAME=cluster19_000000F;QSTART=24890672;QSTRAND=- GT:DP:AD ./.:23:6,17 1|0:33:19,14 ./.:40:22,18 +chr20 867422 200xc15 ATATG A 60 . QNAME=cluster23_scaffold_2;QSTART=24825691;QSTRAND=- GT:DP:AD ./.:24:8,16 ./.:37:23,14 0|1:25:13,12 +chr20 867424 200xc16 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=823571;QSTRAND=+ GT:DP:AD 0|1:37:14,23 ./.:27:5,22 1|0:41:18,23 +chr20 867424 200xc17 ATG A 60 . QNAME=cluster19_000000F;QSTART=831709;QSTRAND=+ GT:DP:AD ./.:14:9,5 0|1:36:25,11 ./.:24:9,15 +chr20 867469 200xc18 T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=849076;QSTRAND=+ GT:DP:AD 1|0:27:19,8 1|1:24:11,13 0|1:13:6,7 +chr20 867469 200xc19 T TGA 60 . QNAME=HG002-S9-H2-000001F;QSTART=823617;QSTRAND=+ GT:DP:AD 0|1:31:18,13 ./.:31:6,25 1|0:16:8,8 +chr20 867728 200xc1a C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=849335;QSTRAND=+ GT:DP:AD 1|0:19:12,7 0|1:41:23,18 ./.:37:24,13 +chr20 867974 200xc1b T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=824123;QSTRAND=+ GT:DP:AD 0|1:19:7,12 1|0:30:18,12 1|1:39:22,17 +chr20 868254 200xc1c T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=849861;QSTRAND=+ GT:DP:AD 1|1:10:5,5 1|1:44:22,22 1|1:42:21,21 +chr20 868526 200xc1d C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=850133;QSTRAND=+ GT:DP:AD 1|0:37:15,22 0|1:45:23,22 ./.:25:16,9 +chr20 868606 200xc1e C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=850213;QSTRAND=+ GT:DP:AD 1|0:30:14,16 0|1:48:23,25 ./.:40:22,18 +chr20 868745 200xc1f G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=824894;QSTRAND=+ GT:DP:AD 0|1:24:9,15 1|0:44:19,25 1|1:29:23,6 +chr20 868950 200xc20 C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=850558;QSTRAND=+ GT:DP:AD 1|0:30:5,25 0|1:28:12,16 ./.:24:19,5 +chr20 868955 200xc21 TC T 60 . QNAME=HG002-S9-H2-000001F;QSTART=825105;QSTRAND=+ GT:DP:AD 0|1:37:21,16 ./.:31:17,14 ./.:28:18,10 +chr20 868956 200xc22 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=850564;QSTRAND=+ GT:DP:AD 1|0:32:24,8 1|1:34:21,13 1|1:13:7,6 +chr20 869010 200xc23 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=850618;QSTRAND=+ GT:DP:AD 1|1:24:15,9 1|1:37:12,25 1|1:42:18,24 +chr20 869733 200xc24 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=851341;QSTRAND=+ GT:DP:AD 1|1:35:13,22 1|1:19:6,13 1|1:31:17,14 +chr20 869777 200xc25 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=851385;QSTRAND=+ GT:DP:AD 1|1:29:24,5 1|1:29:17,12 1|1:33:12,21 +chr20 871966 200xc26 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=828114;QSTRAND=+ GT:DP:AD 0|1:27:6,21 1|0:27:19,8 1|1:21:7,14 +chr20 871969 200xc27 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=828117;QSTRAND=+ GT:DP:AD 0|1:31:23,8 1|0:28:6,22 1|1:38:23,15 +chr20 872450 200xc28 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=828598;QSTRAND=+ GT:DP:AD 0|1:32:19,13 1|0:24:15,9 1|1:17:10,7 +chr20 872792 200xc29 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=854400;QSTRAND=+ GT:DP:AD 1|1:39:19,20 1|1:24:13,11 1|1:32:17,15 +chr20 873491 200xc2a G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=855099;QSTRAND=+ GT:DP:AD 1|0:27:19,8 0|1:31:25,6 ./.:40:15,25 +chr20 873608 200xc2b G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=855216;QSTRAND=+ GT:DP:AD 1|0:41:22,19 0|1:25:19,6 ./.:35:25,10 +chr20 873920 200xc2c T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=855528;QSTRAND=+ GT:DP:AD 1|0:17:7,10 0|1:29:19,10 0|1:18:13,5 +chr20 873956 200xc2d C A 60 . QNAME=cluster19_000000F;QSTART=24884138;QSTRAND=- GT:DP:AD ./.:37:17,20 1|0:31:24,7 ./.:38:18,20 +chr20 874038 200xc2e C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=855646;QSTRAND=+ GT:DP:AD 1|0:36:22,14 0|1:33:12,21 0|1:18:6,12 +chr20 874111 200xc2f A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=855719;QSTRAND=+ GT:DP:AD 1|0:25:16,9 0|1:25:13,12 0|1:25:20,5 +chr20 874297 200xc30 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=855905;QSTRAND=+ GT:DP:AD 1|0:22:15,7 0|1:34:13,21 0|1:32:11,21 +chr20 874696 200xc31 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=856304;QSTRAND=+ GT:DP:AD 1|0:21:15,6 0|1:32:25,7 0|1:23:13,10 +chr20 875035 200xc32 TC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=856644;QSTRAND=+ GT:DP:AD 1|0:40:24,16 0|1:42:17,25 0|1:29:6,23 +chr20 875568 200xc33 C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=857175;QSTRAND=+ GT:DP:AD 1|0:46:22,24 0|1:14:9,5 ./.:24:5,19 +chr20 875568 200xc34 C G 60 . QNAME=cluster23_scaffold_2;QSTART=24817550;QSTRAND=- GT:DP:AD ./.:24:13,11 ./.:19:14,5 0|1:27:17,10 +chr20 875920 200xc35 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=857527;QSTRAND=+ GT:DP:AD 1|0:39:20,19 0|1:19:11,8 0|1:17:7,10 +chr20 876104 200xc36 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=857711;QSTRAND=+ GT:DP:AD 1|0:23:12,11 0|1:38:24,14 0|1:45:21,24 +chr20 876144 200xc37 CAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=857752;QSTRAND=+ GT:DP:AD 1|0:32:13,19 0|1:22:14,8 0|1:24:8,16 +chr20 876144 200xc38 C CA 60 . QNAME=cluster23_scaffold_3;QSTART=24833309;QSTRAND=- GT:DP:AD ./.:30:9,21 ./.:28:19,9 1|0:16:7,9 +chr20 876194 200xc39 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=857799;QSTRAND=+ GT:DP:AD 1|0:37:24,13 0|1:36:25,11 0|1:42:22,20 +chr20 876734 200xc3a T C 60 . QNAME=cluster23_scaffold_2;QSTART=24816386;QSTRAND=- GT:DP:AD ./.:46:24,22 ./.:24:14,10 0|1:24:18,6 +chr20 878979 200xc3b C T 60 . QNAME=cluster23_scaffold_2;QSTART=24814141;QSTRAND=- GT:DP:AD ./.:21:13,8 ./.:18:5,13 0|1:34:17,17 +chr20 879508 200xc3c A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=861113;QSTRAND=+ GT:DP:AD 1|0:15:7,8 0|1:27:17,10 ./.:21:10,11 +chr20 880111 200xc3d T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=861716;QSTRAND=+ GT:DP:AD 1|0:18:9,9 0|1:44:20,24 ./.:37:17,20 +chr20 880159 200xc3e G A 60 . QNAME=cluster19_000000F;QSTART=24877935;QSTRAND=- GT:DP:AD ./.:41:23,18 1|0:33:20,13 ./.:37:24,13 +chr20 880302 200xc3f A AG 60 . QNAME=HG002-S9-H1-000001F;QSTART=861908;QSTRAND=+ GT:DP:AD 1|0:30:8,22 0|1:35:10,25 ./.:28:18,10 +chr20 880463 200xc40 C T 60 . QNAME=cluster23_scaffold_2;QSTART=24812657;QSTRAND=- GT:DP:AD ./.:29:14,15 ./.:34:23,11 0|1:19:11,8 +chr20 880587 200xc41 CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=862194;QSTRAND=+ GT:DP:AD 1|0:26:16,10 ./.:25:17,8 ./.:25:9,16 +chr20 880587 200xc42 C CA 60 . QNAME=cluster19_000000F;QSTART=24877506;QSTRAND=- GT:DP:AD ./.:19:13,6 1|0:23:17,6 ./.:14:5,9 +chr20 880743 200xc43 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=862348;QSTRAND=+ GT:DP:AD 1|0:16:9,7 0|1:13:8,5 0|1:33:10,23 +chr20 881100 200xc44 C G 60 . QNAME=cluster23_scaffold_2;QSTART=24812020;QSTRAND=- GT:DP:AD ./.:46:21,25 ./.:18:5,13 0|1:28:9,19 +chr20 881114 200xc45 G GGGAA 60 . QNAME=cluster23_scaffold_2;QSTART=24812002;QSTRAND=- GT:DP:AD ./.:25:20,5 ./.:32:11,21 0|1:27:5,22 +chr20 881524 200xc46 T C 60 . QNAME=cluster23_scaffold_2;QSTART=24811592;QSTRAND=- GT:DP:AD ./.:31:16,15 ./.:35:20,15 0|1:30:11,19 +chr20 881561 200xc47 C T 60 . QNAME=cluster23_scaffold_2;QSTART=24811555;QSTRAND=- GT:DP:AD ./.:29:17,12 ./.:30:15,15 0|1:40:17,23 +chr20 882074 200xc48 T G 60 . QNAME=cluster23_scaffold_2;QSTART=24811042;QSTRAND=- GT:DP:AD ./.:35:24,11 ./.:39:20,19 0|1:47:22,25 +chr20 882180 200xc49 G A 60 . QNAME=cluster23_scaffold_2;QSTART=24810936;QSTRAND=- GT:DP:AD ./.:11:5,6 ./.:24:14,10 0|1:40:22,18 +chr20 882348 200xc4a C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=863953;QSTRAND=+ GT:DP:AD 1|0:39:15,24 0|1:19:10,9 ./.:31:9,22 +chr20 882505 200xc4b C CTAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=864111;QSTRAND=+ GT:DP:AD 1|0:37:22,15 0|1:39:15,24 ./.:18:5,13 +chr20 882628 200xc4c A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=864236;QSTRAND=+ GT:DP:AD 1|0:45:25,20 0|1:36:17,19 ./.:28:8,20 +chr20 882865 200xc4d A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=864473;QSTRAND=+ GT:DP:AD 1|0:32:23,9 0|1:32:10,22 ./.:30:6,24 +chr20 883063 200xc4e C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=864671;QSTRAND=+ GT:DP:AD 1|0:39:20,19 0|1:31:23,8 0|1:28:20,8 +chr20 883101 200xc4f C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=864709;QSTRAND=+ GT:DP:AD 1|0:39:18,21 0|1:29:17,12 ./.:31:17,14 +chr20 883203 200xc50 C T 60 . QNAME=cluster23_scaffold_2;QSTART=24809913;QSTRAND=- GT:DP:AD ./.:24:19,5 ./.:23:16,7 0|1:26:21,5 +chr20 883230 200xc51 C T 60 . QNAME=cluster19_000000F;QSTART=24874863;QSTRAND=- GT:DP:AD ./.:27:13,14 1|0:30:25,5 ./.:13:5,8 +chr20 883431 200xc52 T C 60 . QNAME=cluster23_scaffold_2;QSTART=24809685;QSTRAND=- GT:DP:AD ./.:39:23,16 ./.:20:8,12 0|1:19:7,12 +chr20 883556 200xc53 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=865164;QSTRAND=+ GT:DP:AD 1|0:15:10,5 0|1:42:21,21 ./.:32:13,19 +chr20 883658 200xc54 G T 60 . QNAME=cluster23_scaffold_2;QSTART=24809458;QSTRAND=- GT:DP:AD ./.:37:25,12 ./.:33:10,23 0|1:41:18,23 +chr20 883812 200xc55 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=865420;QSTRAND=+ GT:DP:AD 1|0:42:17,25 0|1:16:7,9 0|1:28:23,5 +chr20 883869 200xc56 A G 60 . QNAME=cluster23_scaffold_2;QSTART=24809247;QSTRAND=- GT:DP:AD ./.:31:19,12 ./.:11:5,6 0|1:28:23,5 +chr20 883997 200xc57 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=865605;QSTRAND=+ GT:DP:AD 1|0:19:14,5 0|1:41:21,20 0|1:28:11,17 +chr20 884017 200xc58 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=865625;QSTRAND=+ GT:DP:AD 1|0:34:10,24 0|1:25:6,19 0|1:34:17,17 +chr20 884411 200xc59 G C 60 . QNAME=cluster23_scaffold_2;QSTART=24808705;QSTRAND=- GT:DP:AD ./.:17:8,9 ./.:18:5,13 0|1:46:25,21 +chr20 884723 200xc5a G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=866331;QSTRAND=+ GT:DP:AD 1|0:42:24,18 0|1:26:9,17 0|1:37:19,18 +chr20 884894 200xc5b C T 60 . QNAME=cluster23_scaffold_2;QSTART=24808222;QSTRAND=- GT:DP:AD ./.:26:21,5 ./.:37:19,18 0|1:37:21,16 +chr20 885021 200xc5c TC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=866630;QSTRAND=+ GT:DP:AD 1|0:34:22,12 0|1:38:21,17 ./.:20:11,9 +chr20 885587 200xc5d C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=867194;QSTRAND=+ GT:DP:AD 1|0:25:12,13 0|1:18:8,10 ./.:17:9,8 +chr20 885689 200xc5e T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=867296;QSTRAND=+ GT:DP:AD 1|0:32:16,16 0|1:23:9,14 ./.:36:16,20 +chr20 885707 200xc5f A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=867314;QSTRAND=+ GT:DP:AD 1|0:27:19,8 0|1:31:7,24 ./.:28:16,12 +chr20 885722 200xc60 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=867329;QSTRAND=+ GT:DP:AD 1|0:18:6,12 0|1:15:8,7 ./.:16:11,5 +chr20 886137 200xc61 AG A 60 . QNAME=cluster23_scaffold_2;QSTART=24806979;QSTRAND=- GT:DP:AD ./.:24:14,10 ./.:36:13,23 0|1:43:18,25 +chr20 886620 200xc62 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=868227;QSTRAND=+ GT:DP:AD 1|0:27:5,22 0|1:36:19,17 ./.:33:19,14 +chr20 886681 200xc63 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=868288;QSTRAND=+ GT:DP:AD 1|0:36:23,13 0|1:41:19,22 0|1:42:21,21 +chr20 886694 200xc64 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=868301;QSTRAND=+ GT:DP:AD 1|0:44:23,21 0|1:19:10,9 ./.:15:6,9 +chr20 887636 200xc65 CTTTT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=869244;QSTRAND=+ GT:DP:AD 1|0:29:19,10 0|1:31:20,11 ./.:15:10,5 +chr20 887636 200xc66 CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=843785;QSTRAND=+ GT:DP:AD 0|1:15:8,7 1|0:47:23,24 ./.:35:11,24 +chr20 887636 200xc67 CTTT C 60 . QNAME=cluster23_scaffold_2;QSTART=24805481;QSTRAND=- GT:DP:AD ./.:11:6,5 ./.:32:21,11 0|1:23:8,15 +chr20 887887 200xc68 G GAGGA 60 . QNAME=cluster23_scaffold_2;QSTART=24805229;QSTRAND=- GT:DP:AD ./.:42:22,20 ./.:32:10,22 0|1:22:11,11 +chr20 887996 200xc69 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=869599;QSTRAND=+ GT:DP:AD 1|0:35:16,19 0|1:29:24,5 0|1:37:12,25 +chr20 888753 200xc6a C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=870356;QSTRAND=+ GT:DP:AD 1|0:23:14,9 0|1:39:21,18 ./.:34:22,12 +chr20 889503 200xc6b C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=871106;QSTRAND=+ GT:DP:AD 1|0:20:7,13 0|1:34:10,24 0|1:42:17,25 +chr20 889671 200xc6c C G 60 . QNAME=cluster23_scaffold_3;QSTART=24819782;QSTRAND=- GT:DP:AD ./.:32:10,22 ./.:39:14,25 1|0:22:9,13 +chr20 890514 200xc6d G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=872117;QSTRAND=+ GT:DP:AD 1|0:32:19,13 0|1:29:18,11 ./.:35:18,17 +chr20 890614 200xc6e C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=872217;QSTRAND=+ GT:DP:AD 1|0:46:23,23 ./.:40:15,25 ./.:30:18,12 +chr20 891187 200xc6f A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=872790;QSTRAND=+ GT:DP:AD 1|0:34:9,25 ./.:28:16,12 ./.:32:21,11 +chr20 891480 200xc70 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=873083;QSTRAND=+ GT:DP:AD 1|0:39:15,24 ./.:27:22,5 ./.:35:24,11 +chr20 891653 200xc71 G A 60 . QNAME=cluster23_scaffold_2;QSTART=24801463;QSTRAND=- GT:DP:AD ./.:18:9,9 ./.:31:13,18 0|1:36:11,25 +chr20 892108 200xc72 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=873711;QSTRAND=+ GT:DP:AD 1|0:31:15,16 ./.:48:24,24 ./.:44:24,20 +chr20 892511 200xc73 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=874114;QSTRAND=+ GT:DP:AD 1|0:32:21,11 ./.:28:15,13 ./.:26:11,15 +chr20 892634 200xc74 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=874237;QSTRAND=+ GT:DP:AD 1|0:25:20,5 ./.:29:10,19 ./.:33:12,21 +chr20 892840 200xc75 C T 60 . QNAME=cluster19_000000F;QSTART=24865254;QSTRAND=- GT:DP:AD ./.:42:19,23 1|0:35:10,25 ./.:32:8,24 +chr20 893106 200xc76 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=874709;QSTRAND=+ GT:DP:AD 1|0:13:8,5 ./.:32:21,11 ./.:24:9,15 +chr20 893464 200xc77 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=875067;QSTRAND=+ GT:DP:AD 1|0:40:15,25 ./.:28:23,5 ./.:13:7,6 +chr20 893483 200xc78 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=875086;QSTRAND=+ GT:DP:AD 1|0:36:25,11 ./.:28:18,10 ./.:35:25,10 +chr20 894385 200xc79 C T 60 . QNAME=cluster19_000000F;QSTART=24863709;QSTRAND=- GT:DP:AD ./.:37:22,15 1|0:28:11,17 ./.:40:24,16 +chr20 895490 200xc7a C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=877093;QSTRAND=+ GT:DP:AD 1|0:42:25,17 ./.:39:25,14 ./.:39:24,15 +chr20 895600 200xc7b G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=877203;QSTRAND=+ GT:DP:AD 1|0:27:15,12 ./.:12:6,6 ./.:40:20,20 +chr20 896059 200xc7c G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=877662;QSTRAND=+ GT:DP:AD 1|0:18:6,12 ./.:19:10,9 ./.:29:14,15 +chr20 896562 200xc7d G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=878165;QSTRAND=+ GT:DP:AD 1|0:43:23,20 ./.:20:12,8 ./.:47:22,25 +chr20 896997 200xc7e A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=878600;QSTRAND=+ GT:DP:AD 1|0:37:13,24 ./.:29:11,18 ./.:32:18,14 +chr20 899093 200xc7f T C 60 . QNAME=cluster19_000000F;QSTART=24859001;QSTRAND=- GT:DP:AD ./.:32:23,9 1|0:28:6,22 ./.:34:9,25 +chr20 899180 200xc80 T A 60 . QNAME=cluster19_000000F;QSTART=24858914;QSTRAND=- GT:DP:AD ./.:25:6,19 1|0:32:23,9 ./.:20:11,9 +chr20 899195 200xc81 C G 60 . QNAME=cluster19_000000F;QSTART=24858899;QSTRAND=- GT:DP:AD ./.:19:11,8 1|0:29:10,19 ./.:32:19,13 +chr20 899251 200xc82 AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=880855;QSTRAND=+ GT:DP:AD 1|1:36:11,25 ./.:13:5,8 ./.:35:24,11 +chr20 899252 200xc83 T A 60 . QNAME=cluster19_000000F;QSTART=24858842;QSTRAND=- GT:DP:AD ./.:35:16,19 1|0:28:8,20 ./.:39:22,17 +chr20 899447 200xc84 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=881049;QSTRAND=+ GT:DP:AD 1|1:31:22,9 1|1:30:25,5 1|1:16:8,8 +chr20 899533 200xc85 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=855679;QSTRAND=+ GT:DP:AD 0|1:32:23,9 ./.:16:8,8 ./.:40:17,23 +chr20 900321 200xc86 A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=856467;QSTRAND=+ GT:DP:AD 0|1:36:19,17 ./.:13:5,8 ./.:35:13,22 +chr20 900721 200xc87 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=856867;QSTRAND=+ GT:DP:AD 0|1:31:25,6 ./.:36:25,11 ./.:36:25,11 +chr20 900932 200xc88 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=857078;QSTRAND=+ GT:DP:AD 0|1:22:7,15 ./.:37:13,24 ./.:32:10,22 +chr20 900977 200xc89 T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=857123;QSTRAND=+ GT:DP:AD 0|1:29:13,16 ./.:22:5,17 ./.:21:8,13 +chr20 901001 200xc8a G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=857147;QSTRAND=+ GT:DP:AD 0|1:24:7,17 ./.:46:21,25 ./.:37:25,12 +chr20 901060 200xc8b T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=857206;QSTRAND=+ GT:DP:AD 0|1:48:25,23 ./.:33:24,9 ./.:18:12,6 +chr20 901437 200xc8c C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=857583;QSTRAND=+ GT:DP:AD 0|1:32:13,19 ./.:45:21,24 ./.:37:13,24 +chr20 901786 200xc8d A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=857932;QSTRAND=+ GT:DP:AD 0|1:41:16,25 0|1:19:9,10 ./.:38:24,14 +chr20 902160 200xc8e G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=858306;QSTRAND=+ GT:DP:AD 0|1:31:10,21 ./.:19:7,12 ./.:17:10,7 +chr20 902357 200xc8f G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=858503;QSTRAND=+ GT:DP:AD 0|1:33:16,17 ./.:33:21,12 ./.:32:25,7 +chr20 902728 200xc90 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=858874;QSTRAND=+ GT:DP:AD 0|1:11:5,6 ./.:32:19,13 ./.:32:12,20 +chr20 903001 200xc91 T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=859147;QSTRAND=+ GT:DP:AD 0|1:33:12,21 ./.:15:10,5 ./.:25:16,9 +chr20 903427 200xc92 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=859573;QSTRAND=+ GT:DP:AD 0|1:22:17,5 ./.:28:15,13 ./.:27:20,7 +chr20 903489 200xc93 C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=859635;QSTRAND=+ GT:DP:AD 0|1:34:12,22 ./.:38:14,24 ./.:31:18,13 +chr20 904502 200xc94 A AC 60 . QNAME=HG002-S9-H2-000001F;QSTART=860649;QSTRAND=+ GT:DP:AD 0|1:27:6,21 ./.:26:19,7 ./.:30:12,18 +chr20 905359 200xc95 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=861506;QSTRAND=+ GT:DP:AD 0|1:25:14,11 ./.:32:8,24 ./.:15:5,10 +chr20 905407 200xc96 G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=861554;QSTRAND=+ GT:DP:AD 0|1:42:17,25 ./.:30:17,13 ./.:29:18,11 +chr20 905736 200xc97 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=861883;QSTRAND=+ GT:DP:AD 0|1:24:8,16 ./.:29:22,7 ./.:23:6,17 +chr20 906213 200xc98 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=862360;QSTRAND=+ GT:DP:AD 0|1:31:14,17 ./.:43:20,23 ./.:36:23,13 +chr20 906268 200xc99 G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=862415;QSTRAND=+ GT:DP:AD 0|1:17:7,10 ./.:25:17,8 ./.:21:7,14 +chr20 906812 200xc9a T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=862959;QSTRAND=+ GT:DP:AD 0|1:33:11,22 ./.:30:9,21 ./.:21:6,15 +chr20 906878 200xc9b C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=863025;QSTRAND=+ GT:DP:AD 0|1:28:23,5 ./.:24:7,17 ./.:22:17,5 +chr20 907157 200xc9c A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=863304;QSTRAND=+ GT:DP:AD 0|1:42:25,17 ./.:40:15,25 ./.:29:18,11 +chr20 907880 200xc9d G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=864027;QSTRAND=+ GT:DP:AD 0|1:37:17,20 ./.:37:15,22 0|1:26:15,11 +chr20 908674 200xc9e C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=864821;QSTRAND=+ GT:DP:AD 0|1:40:19,21 ./.:23:12,11 0|1:36:13,23 +chr20 909226 200xc9f C T 60 . QNAME=cluster23_scaffold_2;QSTART=24783890;QSTRAND=- GT:DP:AD ./.:25:14,11 ./.:13:5,8 0|1:35:20,15 +chr20 909261 200xca0 C A 60 . QNAME=cluster19_000000F;QSTART=873540;QSTRAND=+ GT:DP:AD ./.:32:9,23 0|1:24:11,13 ./.:36:11,25 +chr20 909371 200xca1 G A 60 . QNAME=cluster23_scaffold_2;QSTART=24783745;QSTRAND=- GT:DP:AD ./.:22:16,6 ./.:29:15,14 0|1:44:22,22 +chr20 909453 200xca2 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=891055;QSTRAND=+ GT:DP:AD 1|0:37:14,23 ./.:33:23,10 ./.:39:14,25 +chr20 909635 200xca3 A G 60 . QNAME=cluster23_scaffold_2;QSTART=24783481;QSTRAND=- GT:DP:AD ./.:36:23,13 ./.:30:6,24 0|1:39:23,16 +chr20 909706 200xca4 G C 60 . QNAME=cluster19_000000F;QSTART=873985;QSTRAND=+ GT:DP:AD ./.:21:5,16 0|1:46:21,25 ./.:38:21,17 +chr20 911795 200xca5 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=893397;QSTRAND=+ GT:DP:AD 1|0:23:17,6 ./.:27:5,22 ./.:36:24,12 +chr20 911823 200xca6 AGACAGAGAGAGGGAGAGAGG A 60 . QNAME=HG002-S9-H1-000001F;QSTART=893426;QSTRAND=+ GT:DP:AD 1|0:26:6,20 ./.:21:13,8 ./.:30:18,12 +chr20 912080 200xca7 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=893662;QSTRAND=+ GT:DP:AD 1|0:19:8,11 ./.:25:5,20 ./.:41:23,18 +chr20 912305 200xca8 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=893887;QSTRAND=+ GT:DP:AD 1|0:13:8,5 ./.:28:13,15 ./.:29:13,16 +chr20 913482 200xca9 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=895064;QSTRAND=+ GT:DP:AD 1|0:32:20,12 ./.:31:8,23 ./.:25:12,13 +chr20 914079 200xcaa G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=895661;QSTRAND=+ GT:DP:AD 1|0:16:10,6 1|0:24:7,17 ./.:25:11,14 +chr20 914238 200xcab A G 60 . QNAME=cluster19_000000F;QSTART=24843856;QSTRAND=- GT:DP:AD ./.:45:23,22 1|0:23:13,10 ./.:25:13,12 +chr20 914324 200xcac G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=895906;QSTRAND=+ GT:DP:AD 1|1:37:14,23 1|1:32:18,14 1|0:24:14,10 +chr20 914682 200xcad A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=896264;QSTRAND=+ GT:DP:AD 1|1:35:20,15 1|0:34:14,20 1|1:27:15,12 +chr20 914775 200xcae A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=870922;QSTRAND=+ GT:DP:AD 0|1:25:16,9 ./.:27:10,17 1|0:17:9,8 +chr20 914780 200xcaf C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=896362;QSTRAND=+ GT:DP:AD 1|0:36:18,18 1|0:38:24,14 0|1:32:20,12 +chr20 914814 200xcb0 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=870961;QSTRAND=+ GT:DP:AD 0|1:26:15,11 ./.:16:6,10 1|0:29:19,10 +chr20 915350 200xcb1 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=896932;QSTRAND=+ GT:DP:AD 1|0:33:10,23 ./.:36:22,14 ./.:28:14,14 +chr20 915369 200xcb2 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=896951;QSTRAND=+ GT:DP:AD 1|1:37:14,23 1|0:14:8,6 1|0:18:5,13 +chr20 915656 200xcb3 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=897238;QSTRAND=+ GT:DP:AD 1|1:12:6,6 1|0:30:22,8 1|1:26:12,14 +chr20 916110 200xcb4 T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=872257;QSTRAND=+ GT:DP:AD 0|1:23:8,15 ./.:40:15,25 ./.:35:15,20 +chr20 916419 200xcb5 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=898001;QSTRAND=+ GT:DP:AD 1|1:37:17,20 1|1:20:5,15 1|1:28:5,23 +chr20 916452 200xcb6 A C 60 . QNAME=cluster19_000000F;QSTART=880731;QSTRAND=+ GT:DP:AD ./.:34:21,13 0|1:34:19,15 ./.:38:22,16 +chr20 916852 200xcb7 C T 60 . QNAME=cluster19_000000F;QSTART=881131;QSTRAND=+ GT:DP:AD ./.:29:23,6 0|1:28:5,23 ./.:29:18,11 +chr20 916971 200xcb8 C T 60 . QNAME=cluster19_000000F;QSTART=881250;QSTRAND=+ GT:DP:AD ./.:37:17,20 0|1:30:20,10 ./.:23:6,17 +chr20 917534 200xcb9 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=873681;QSTRAND=+ GT:DP:AD 0|1:22:11,11 ./.:23:8,15 ./.:27:14,13 +chr20 917575 200xcba T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=899157;QSTRAND=+ GT:DP:AD 1|1:39:21,18 1|1:24:7,17 1|1:33:16,17 +chr20 917906 200xcbb T G 60 . QNAME=cluster19_000000F;QSTART=882185;QSTRAND=+ GT:DP:AD ./.:20:9,11 0|1:27:14,13 ./.:19:9,10 +chr20 918736 200xcbc G A 60 . QNAME=cluster19_000000F;QSTART=883015;QSTRAND=+ GT:DP:AD ./.:41:25,16 0|1:24:8,16 ./.:28:14,14 +chr20 919146 200xcbd CTCTT C 60 . QNAME=cluster19_000000F;QSTART=883426;QSTRAND=+ GT:DP:AD ./.:46:22,24 0|1:34:25,9 ./.:21:9,12 +chr20 919167 200xcbe C CTT 60 . QNAME=cluster23_scaffold_2;QSTART=24773947;QSTRAND=- GT:DP:AD ./.:33:9,24 ./.:13:7,6 0|1:28:13,15 +chr20 919371 200xcbf G C 60 . QNAME=cluster19_000000F;QSTART=883646;QSTRAND=+ GT:DP:AD ./.:38:18,20 0|1:32:8,24 ./.:31:9,22 +chr20 919990 200xcc0 TG T 60 . QNAME=cluster19_000000F;QSTART=24838104;QSTRAND=- GT:DP:AD ./.:32:19,13 1|0:35:22,13 ./.:32:24,8 +chr20 919994 200xcc1 T C 60 . QNAME=cluster19_000000F;QSTART=24838101;QSTRAND=- GT:DP:AD ./.:39:25,14 1|0:35:12,23 ./.:46:24,22 +chr20 920055 200xcc2 T TC 60 . QNAME=HG002-S9-H1-000001F;QSTART=901638;QSTRAND=+ GT:DP:AD 1|1:13:7,6 1|1:23:8,15 1|1:29:18,11 +chr20 920188 200xcc3 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=901771;QSTRAND=+ GT:DP:AD 1|0:32:11,21 1|0:41:25,16 ./.:24:8,16 +chr20 920292 200xcc4 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=901875;QSTRAND=+ GT:DP:AD 1|0:23:17,6 1|0:20:9,11 ./.:22:13,9 +chr20 920391 200xcc5 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=901974;QSTRAND=+ GT:DP:AD 1|0:16:10,6 ./.:25:12,13 ./.:21:11,10 +chr20 921033 200xcc6 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=902616;QSTRAND=+ GT:DP:AD 1|1:27:10,17 1|1:38:16,22 1|1:37:15,22 +chr20 921239 200xcc7 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=902822;QSTRAND=+ GT:DP:AD 1|1:38:20,18 1|1:16:6,10 1|1:11:6,5 +chr20 921288 200xcc8 G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=902871;QSTRAND=+ GT:DP:AD 1|1:20:5,15 1|0:38:17,21 1|1:42:21,21 +chr20 921359 200xcc9 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=877507;QSTRAND=+ GT:DP:AD 0|1:17:8,9 ./.:21:14,7 ./.:35:10,25 +chr20 921417 200xcca T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=877565;QSTRAND=+ GT:DP:AD 0|1:18:10,8 1|0:32:23,9 0|1:32:13,19 +chr20 921417 200xccb T TG 60 . QNAME=cluster19_000000F;QSTART=885694;QSTRAND=+ GT:DP:AD ./.:38:17,21 0|1:28:7,21 ./.:31:23,8 +chr20 921667 200xccc G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=903250;QSTRAND=+ GT:DP:AD 1|0:31:18,13 0|1:29:23,6 0|1:38:21,17 +chr20 922254 200xccd C G 60 . QNAME=cluster19_000000F;QSTART=886531;QSTRAND=+ GT:DP:AD ./.:34:13,21 0|1:18:6,12 0|1:39:24,15 +chr20 922377 200xcce G A 60 . QNAME=cluster19_000000F;QSTART=886654;QSTRAND=+ GT:DP:AD ./.:31:8,23 0|1:19:8,11 0|1:34:19,15 +chr20 923331 200xccf C CA 60 . QNAME=cluster23_scaffold_2;QSTART=24769781;QSTRAND=- GT:DP:AD ./.:25:18,7 ./.:13:6,7 0|1:47:22,25 +chr20 923875 200xcd0 C CA 60 . QNAME=cluster23_scaffold_2;QSTART=24769236;QSTRAND=- GT:DP:AD ./.:33:23,10 ./.:45:20,25 0|1:24:16,8 +chr20 924499 200xcd1 C T 60 . QNAME=cluster19_000000F;QSTART=888776;QSTRAND=+ GT:DP:AD ./.:23:12,11 0|1:38:17,21 0|1:19:12,7 +chr20 925913 200xcd2 CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=882062;QSTRAND=+ GT:DP:AD 0|1:47:22,25 ./.:31:16,15 ./.:32:24,8 +chr20 928807 200xcd3 G C 60 . QNAME=cluster19_000000F;QSTART=893084;QSTRAND=+ GT:DP:AD ./.:27:21,6 0|1:34:22,12 0|1:26:19,7 +chr20 929128 200xcd4 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=885275;QSTRAND=+ GT:DP:AD 0|1:48:24,24 1|1:19:11,8 0|1:38:13,25 +chr20 929177 200xcd5 T C 60 . QNAME=cluster19_000000F;QSTART=893454;QSTRAND=+ GT:DP:AD ./.:41:19,22 0|1:37:18,19 ./.:44:20,24 +chr20 929220 200xcd6 A T 60 . QNAME=cluster19_000000F;QSTART=893497;QSTRAND=+ GT:DP:AD ./.:38:18,20 0|1:18:13,5 ./.:25:6,19 +chr20 929302 200xcd7 TTA T 60 . QNAME=cluster19_000000F;QSTART=24828792;QSTRAND=- GT:DP:AD ./.:34:24,10 1|0:49:25,24 ./.:12:6,6 +chr20 929302 200xcd8 TTATGG T 60 . QNAME=cluster19_000000F;QSTART=893580;QSTRAND=+ GT:DP:AD ./.:36:17,19 0|1:19:14,5 ./.:20:15,5 +chr20 929491 200xcd9 A C 60 . QNAME=cluster19_000000F;QSTART=24828605;QSTRAND=- GT:DP:AD ./.:22:9,13 1|1:29:17,12 ./.:24:9,15 +chr20 929623 200xcda T C 60 . QNAME=cluster19_000000F;QSTART=24828473;QSTRAND=- GT:DP:AD ./.:25:14,11 1|1:38:18,20 ./.:44:24,20 +chr20 929701 200xcdb T G 60 . QNAME=cluster19_000000F;QSTART=24828395;QSTRAND=- GT:DP:AD ./.:36:11,25 1|1:25:6,19 ./.:36:11,25 +chr20 931616 200xcdc C T 60 . QNAME=cluster19_000000F;QSTART=24826480;QSTRAND=- GT:DP:AD ./.:40:22,18 1|1:18:10,8 ./.:33:11,22 +chr20 931983 200xcdd A G 60 . QNAME=cluster19_000000F;QSTART=24826113;QSTRAND=- GT:DP:AD ./.:39:21,18 1|1:16:8,8 ./.:26:14,12 +chr20 932022 200xcde T C 60 . QNAME=cluster19_000000F;QSTART=24826074;QSTRAND=- GT:DP:AD ./.:30:21,9 1|1:36:17,19 ./.:45:24,21 +chr20 932357 200xcdf T C 60 . QNAME=cluster19_000000F;QSTART=24825739;QSTRAND=- GT:DP:AD ./.:27:7,20 1|1:42:18,24 ./.:20:11,9 +chr20 932610 200xce0 G A 60 . QNAME=cluster19_000000F;QSTART=24825486;QSTRAND=- GT:DP:AD ./.:29:10,19 1|1:30:21,9 ./.:21:15,6 +chr20 932660 200xce1 A AT 60 . QNAME=cluster19_000000F;QSTART=24825435;QSTRAND=- GT:DP:AD ./.:31:19,12 1|1:47:24,23 ./.:18:9,9 +chr20 932698 200xce2 G A 60 . QNAME=cluster19_000000F;QSTART=24825397;QSTRAND=- GT:DP:AD ./.:38:17,21 1|1:33:10,23 ./.:34:13,21 +chr20 932824 200xce3 G A 60 . QNAME=cluster19_000000F;QSTART=24825271;QSTRAND=- GT:DP:AD ./.:37:13,24 1|1:26:6,20 ./.:30:16,14 +chr20 933093 200xce4 C T 60 . QNAME=cluster19_000000F;QSTART=24825002;QSTRAND=- GT:DP:AD ./.:33:10,23 1|1:31:6,25 ./.:21:16,5 +chr20 933764 200xce5 G T 60 . QNAME=cluster19_000000F;QSTART=24824331;QSTRAND=- GT:DP:AD ./.:43:25,18 1|1:42:19,23 ./.:23:5,18 +chr20 933777 200xce6 T G 60 . QNAME=cluster19_000000F;QSTART=24824318;QSTRAND=- GT:DP:AD ./.:28:13,15 1|1:38:15,23 ./.:29:18,11 +chr20 934006 200xce7 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=890153;QSTRAND=+ GT:DP:AD 0|1:31:22,9 ./.:43:25,18 ./.:43:18,25 +chr20 934616 200xce8 G A 60 . QNAME=cluster19_000000F;QSTART=24823479;QSTRAND=- GT:DP:AD ./.:23:17,6 1|1:33:11,22 ./.:24:8,16 +chr20 935220 200xce9 C A 60 . QNAME=cluster19_000000F;QSTART=24822875;QSTRAND=- GT:DP:AD ./.:29:24,5 1|1:20:14,6 ./.:23:7,16 +chr20 935920 200xcea C T 60 . QNAME=cluster23_scaffold_2;QSTART=24757191;QSTRAND=- GT:DP:AD ./.:35:24,11 ./.:30:18,12 0|1:40:18,22 +chr20 936160 200xceb A C 60 . QNAME=cluster19_000000F;QSTART=24821935;QSTRAND=- GT:DP:AD ./.:41:24,17 1|0:39:16,23 ./.:41:21,20 +chr20 937152 200xcec A T 60 . QNAME=cluster19_000000F;QSTART=24820943;QSTRAND=- GT:DP:AD ./.:31:7,24 1|0:46:22,24 ./.:40:25,15 +chr20 937174 200xced C T 60 . QNAME=cluster19_000000F;QSTART=24820921;QSTRAND=- GT:DP:AD ./.:33:11,22 1|0:17:6,11 ./.:27:16,11 +chr20 937837 200xcee T A 60 . QNAME=cluster19_000000F;QSTART=24820258;QSTRAND=- GT:DP:AD ./.:23:10,13 1|0:33:23,10 ./.:43:18,25 +chr20 937941 200xcef A G 60 . QNAME=cluster19_000000F;QSTART=24820154;QSTRAND=- GT:DP:AD ./.:31:11,20 1|0:25:19,6 ./.:28:19,9 +chr20 938380 200xcf0 G A 60 . QNAME=cluster19_000000F;QSTART=24819715;QSTRAND=- GT:DP:AD ./.:34:16,18 1|0:34:20,14 ./.:32:9,23 +chr20 940109 200xcf1 A G 60 . QNAME=cluster19_000000F;QSTART=24817986;QSTRAND=- GT:DP:AD ./.:40:20,20 1|1:31:16,15 ./.:25:13,12 +chr20 940207 200xcf2 G A 60 . QNAME=cluster19_000000F;QSTART=24817888;QSTRAND=- GT:DP:AD ./.:31:12,19 1|1:15:10,5 ./.:23:8,15 +chr20 941328 200xcf3 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=897475;QSTRAND=+ GT:DP:AD 0|1:27:9,18 1|1:22:16,6 0|1:31:10,21 +chr20 942095 200xcf4 C CA 60 . QNAME=cluster19_000000F;QSTART=906369;QSTRAND=+ GT:DP:AD ./.:26:11,15 0|1:34:20,14 ./.:30:11,19 +chr20 942273 200xcf5 A AT 60 . QNAME=HG002-S9-H2-000001F;QSTART=898421;QSTRAND=+ GT:DP:AD 0|1:33:8,25 1|1:34:12,22 0|1:21:11,10 +chr20 942277 200xcf6 A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=898425;QSTRAND=+ GT:DP:AD 0|1:17:8,9 1|1:37:22,15 0|1:31:20,11 +chr20 942358 200xcf7 C T 60 . QNAME=cluster19_000000F;QSTART=24815736;QSTRAND=- GT:DP:AD ./.:34:10,24 1|1:47:22,25 0|1:26:14,12 +chr20 942424 200xcf8 C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=898572;QSTRAND=+ GT:DP:AD 0|1:25:9,16 ./.:26:13,13 ./.:20:9,11 +chr20 942563 200xcf9 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=898711;QSTRAND=+ GT:DP:AD 0|1:32:18,14 ./.:28:20,8 ./.:21:14,7 +chr20 942659 200xcfa G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=898807;QSTRAND=+ GT:DP:AD 0|1:21:12,9 1|1:37:24,13 0|1:32:13,19 +chr20 943015 200xcfb G A 60 . QNAME=cluster19_000000F;QSTART=24815079;QSTRAND=- GT:DP:AD ./.:36:11,25 1|1:39:16,23 0|1:31:16,15 +chr20 943016 200xcfc C A 60 . QNAME=cluster19_000000F;QSTART=24815078;QSTRAND=- GT:DP:AD ./.:28:16,12 1|1:14:8,6 0|1:46:24,22 +chr20 943950 200xcfd T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=900098;QSTRAND=+ GT:DP:AD 0|1:42:23,19 ./.:33:14,19 ./.:27:8,19 +chr20 943984 200xcfe T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=900132;QSTRAND=+ GT:DP:AD 0|1:34:25,9 1|1:32:17,15 0|1:41:18,23 +chr20 944018 200xcff GCT G 60 . QNAME=cluster19_000000F;QSTART=24814076;QSTRAND=- GT:DP:AD ./.:14:8,6 1|1:21:10,11 0|1:21:13,8 +chr20 944028 200xd00 TC T 60 . QNAME=HG002-S9-H2-000001F;QSTART=900177;QSTRAND=+ GT:DP:AD 0|1:27:18,9 ./.:11:6,5 ./.:21:8,13 +chr20 944029 200xd01 C CTT 60 . QNAME=cluster23_scaffold_3;QSTART=24765421;QSTRAND=- GT:DP:AD ./.:39:18,21 ./.:40:25,15 1|0:42:25,17 +chr20 944093 200xd02 C T 60 . QNAME=cluster23_scaffold_3;QSTART=24765357;QSTRAND=- GT:DP:AD ./.:27:18,9 ./.:36:21,15 1|0:25:16,9 +chr20 944094 200xd03 A G 60 . QNAME=cluster23_scaffold_3;QSTART=24765356;QSTRAND=- GT:DP:AD ./.:13:6,7 ./.:19:10,9 1|0:26:15,11 +chr20 945682 200xd04 T C 60 . QNAME=cluster19_000000F;QSTART=909955;QSTRAND=+ GT:DP:AD ./.:25:7,18 0|1:45:20,25 0|1:22:5,17 +chr20 945711 200xd05 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=901858;QSTRAND=+ GT:DP:AD 0|1:40:19,21 0|1:27:13,14 0|1:41:22,19 +chr20 945754 200xd06 G A 60 . QNAME=cluster19_000000F;QSTART=910027;QSTRAND=+ GT:DP:AD ./.:34:17,17 0|1:33:25,8 0|1:34:10,24 +chr20 945942 200xd07 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=902089;QSTRAND=+ GT:DP:AD 0|1:31:8,23 0|1:15:8,7 0|1:27:13,14 +chr20 946505 200xd08 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=928088;QSTRAND=+ GT:DP:AD 1|0:25:10,15 0|1:27:16,11 0|1:30:10,20 +chr20 946814 200xd09 A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=902961;QSTRAND=+ GT:DP:AD 0|1:18:13,5 ./.:44:22,22 1|0:32:24,8 +chr20 946899 200xd0a C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=903046;QSTRAND=+ GT:DP:AD 0|1:35:16,19 ./.:30:7,23 1|0:22:6,16 +chr20 947202 200xd0b A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=903349;QSTRAND=+ GT:DP:AD 0|1:36:21,15 ./.:18:7,11 1|0:26:17,9 +chr20 947218 200xd0c G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=903365;QSTRAND=+ GT:DP:AD 0|1:20:12,8 ./.:31:14,17 1|0:38:18,20 +chr20 947585 200xd0d T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=903732;QSTRAND=+ GT:DP:AD 0|1:23:16,7 ./.:18:7,11 1|0:30:23,7 +chr20 947624 200xd0e G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=903771;QSTRAND=+ GT:DP:AD 0|1:30:20,10 ./.:32:25,7 1|0:47:25,22 +chr20 947782 200xd0f T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=903929;QSTRAND=+ GT:DP:AD 0|1:35:15,20 ./.:26:7,19 1|0:28:23,5 +chr20 947795 200xd10 A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=903942;QSTRAND=+ GT:DP:AD 0|1:38:20,18 ./.:14:9,5 1|0:26:7,19 +chr20 947914 200xd11 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=904061;QSTRAND=+ GT:DP:AD 0|1:22:8,14 ./.:36:16,20 1|0:20:5,15 +chr20 948357 200xd12 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=904504;QSTRAND=+ GT:DP:AD 0|1:27:13,14 ./.:29:22,7 1|0:34:10,24 +chr20 948492 200xd13 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=904639;QSTRAND=+ GT:DP:AD 0|1:16:8,8 ./.:33:24,9 1|0:19:9,10 +chr20 948493 200xd14 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=904640;QSTRAND=+ GT:DP:AD 0|1:29:19,10 ./.:31:17,14 1|0:13:8,5 +chr20 948861 200xd15 G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=905008;QSTRAND=+ GT:DP:AD 0|1:36:19,17 ./.:37:19,18 1|0:33:23,10 +chr20 949016 200xd16 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=905163;QSTRAND=+ GT:DP:AD 0|1:27:20,7 ./.:32:13,19 1|0:24:18,6 +chr20 949377 200xd17 GA G 60 . QNAME=HG002-S9-H2-000001F;QSTART=905525;QSTRAND=+ GT:DP:AD 0|1:45:20,25 ./.:20:15,5 1|0:15:7,8 +chr20 949516 200xd18 CTCTGAAGAGGTAACATTTGAACTGAGATGTAGAGGGAGAGAAGGAACTAGCCATGTGGAGATCTGGGGGAGGAGCATTCCAGGCAGAGGGGATAGCAAGTGCA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=905663;QSTRAND=+;SVTYPE=DEL;SVLEN=-103 GT:DP:AD 0/1:29:9,20 ./.:28:7,21 1/0:34:12,22 +chr20 949837 200xd19 C T 60 . QNAME=cluster19_000000F;QSTART=914110;QSTRAND=+ GT:DP:AD ./.:12:6,6 0|1:41:23,18 0|1:24:15,9 +chr20 949917 200xd1a T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=905960;QSTRAND=+ GT:DP:AD 0|1:40:25,15 ./.:31:9,22 1|0:38:18,20 +chr20 950840 200xd1b G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=906883;QSTRAND=+ GT:DP:AD 0|1:40:18,22 ./.:15:5,10 1|0:25:5,20 +chr20 950981 200xd1c A AAAATAAAT 60 . QNAME=HG002-S9-H2-000001F;QSTART=907025;QSTRAND=+ GT:DP:AD 0|1:40:25,15 ./.:30:22,8 1|0:32:9,23 +chr20 951023 200xd1d A AAAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=907075;QSTRAND=+ GT:DP:AD 0|1:25:7,18 ./.:29:16,13 1|0:40:19,21 +chr20 951100 200xd1e G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=907154;QSTRAND=+ GT:DP:AD 0|1:42:17,25 ./.:24:10,14 1|0:19:11,8 +chr20 951130 200xd1f A ATT 60 . QNAME=HG002-S9-H1-000001F;QSTART=932714;QSTRAND=+ GT:DP:AD 1|0:37:24,13 ./.:38:13,25 ./.:20:6,14 +chr20 951130 200xd20 ATTTTTTTTTTTTT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=907185;QSTRAND=+ GT:DP:AD 0|1:32:18,14 ./.:34:12,22 ./.:38:18,20 +chr20 951130 200xd21 ATTTTTTTTTTTT A 60 . QNAME=cluster19_000000F;QSTART=24806966;QSTRAND=- GT:DP:AD ./.:47:24,23 1|0:48:24,24 1|0:24:7,17 +chr20 951130 200xd22 A ATTT 60 . QNAME=cluster19_000000F;QSTART=915404;QSTRAND=+ GT:DP:AD ./.:39:17,22 0|1:40:15,25 ./.:36:18,18 +chr20 951130 200xd23 A ATTTTT 60 . QNAME=cluster23_scaffold_2;QSTART=24741977;QSTRAND=- GT:DP:AD ./.:15:9,6 ./.:31:25,6 0|1:24:9,15 +chr20 951172 200xd24 A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=907213;QSTRAND=+ GT:DP:AD 0|1:36:21,15 ./.:31:9,22 1|0:32:8,24 +chr20 951188 200xd25 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=907229;QSTRAND=+ GT:DP:AD 0|1:20:13,7 ./.:27:6,21 1|0:24:7,17 +chr20 951376 200xd26 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=932961;QSTRAND=+ GT:DP:AD 1|1:29:20,9 0|1:42:23,19 1|1:31:6,25 +chr20 951397 200xd27 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=932982;QSTRAND=+ GT:DP:AD 1|0:39:21,18 ./.:37:18,19 ./.:28:22,6 +chr20 951428 200xd28 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=933013;QSTRAND=+ GT:DP:AD 1|0:32:10,22 ./.:31:8,23 ./.:41:25,16 +chr20 951612 200xd29 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=933197;QSTRAND=+ GT:DP:AD 1|0:34:15,19 ./.:32:10,22 ./.:31:11,20 +chr20 951687 200xd2a A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=933272;QSTRAND=+ GT:DP:AD 1|0:39:18,21 ./.:29:15,14 ./.:28:8,20 +chr20 951756 200xd2b A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=933341;QSTRAND=+ GT:DP:AD 1|0:30:25,5 ./.:28:13,15 ./.:36:25,11 +chr20 951868 200xd2c C T 60 . QNAME=cluster19_000000F;QSTART=916144;QSTRAND=+ GT:DP:AD ./.:15:6,9 0|1:25:11,14 1|1:27:19,8 +chr20 951868 200xd2d CGT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=907910;QSTRAND=+ GT:DP:AD 0|1:30:13,17 ./.:24:14,10 ./.:37:18,19 +chr20 951870 200xd2e T C 60 . QNAME=cluster19_000000F;QSTART=916146;QSTRAND=+ GT:DP:AD ./.:19:12,7 0|1:15:8,7 1|1:34:25,9 +chr20 951975 200xd2f T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=908014;QSTRAND=+ GT:DP:AD 0|1:20:8,12 0|1:29:24,5 1|1:34:23,11 +chr20 952317 200xd30 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=933902;QSTRAND=+ GT:DP:AD 1|0:22:12,10 ./.:42:23,19 ./.:27:5,22 +chr20 952372 200xd31 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=933957;QSTRAND=+ GT:DP:AD 1|0:34:13,21 ./.:30:11,19 ./.:38:15,23 +chr20 952391 200xd32 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=908430;QSTRAND=+ GT:DP:AD 0|1:17:9,8 0|1:22:8,14 1|1:16:7,9 +chr20 952475 200xd33 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=934060;QSTRAND=+ GT:DP:AD 1|0:30:10,20 ./.:26:18,8 ./.:27:8,19 +chr20 952558 200xd34 T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=908597;QSTRAND=+ GT:DP:AD 0|1:21:16,5 0|1:40:25,15 1|1:47:24,23 +chr20 952594 200xd35 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=934179;QSTRAND=+ GT:DP:AD 1|0:41:25,16 ./.:17:8,9 ./.:38:13,25 +chr20 952909 200xd36 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=934494;QSTRAND=+ GT:DP:AD 1|0:35:14,21 ./.:33:24,9 ./.:12:7,5 +chr20 953115 200xd37 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=909154;QSTRAND=+ GT:DP:AD 0|1:20:6,14 1|1:37:14,23 1|1:40:23,17 +chr20 953327 200xd38 GTTAT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=934913;QSTRAND=+ GT:DP:AD 1|1:35:16,19 1|1:22:6,16 1|1:34:11,23 +chr20 953360 200xd39 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=934941;QSTRAND=+ GT:DP:AD 1|0:31:24,7 ./.:31:6,25 ./.:20:12,8 +chr20 953456 200xd3a T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=935037;QSTRAND=+ GT:DP:AD 1|0:37:17,20 ./.:29:8,21 ./.:39:20,19 +chr20 953490 200xd3b T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=935071;QSTRAND=+ GT:DP:AD 1|1:32:19,13 1|1:30:21,9 1|1:30:7,23 +chr20 953507 200xd3c T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=935088;QSTRAND=+ GT:DP:AD 1|0:30:15,15 ./.:35:10,25 ./.:41:22,19 +chr20 953510 200xd3d A AT 60 . QNAME=HG002-S9-H2-000001F;QSTART=909546;QSTRAND=+ GT:DP:AD 0|1:30:8,22 1|1:32:11,21 1|1:35:17,18 +chr20 953670 200xd3e G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=909706;QSTRAND=+ GT:DP:AD 0|1:37:24,13 1|1:17:5,12 0|1:31:21,10 +chr20 953787 200xd3f AC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=935369;QSTRAND=+ GT:DP:AD 1|0:10:5,5 ./.:39:21,18 ./.:23:8,15 +chr20 953831 200xd40 T TC 60 . QNAME=HG002-S9-H1-000001F;QSTART=935412;QSTRAND=+ GT:DP:AD 1|0:26:15,11 ./.:23:13,10 ./.:32:21,11 +chr20 953857 200xd41 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=935438;QSTRAND=+ GT:DP:AD 1|0:29:12,17 ./.:33:15,18 ./.:36:16,20 +chr20 953954 200xd42 CG C 60 . QNAME=HG002-S9-H1-000001F;QSTART=935536;QSTRAND=+ GT:DP:AD 1|0:29:23,6 ./.:16:9,7 ./.:25:13,12 +chr20 953974 200xd43 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=935554;QSTRAND=+ GT:DP:AD 1|0:43:20,23 ./.:21:16,5 ./.:38:22,16 +chr20 954305 200xd44 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=935885;QSTRAND=+ GT:DP:AD 1|1:30:8,22 1|1:25:7,18 0|1:17:12,5 +chr20 954418 200xd45 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=910454;QSTRAND=+ GT:DP:AD 0|1:27:12,15 1|1:37:16,21 0|1:44:20,24 +chr20 954610 200xd46 A G 60 . QNAME=cluster23_scaffold_2;QSTART=24738500;QSTRAND=- GT:DP:AD ./.:24:6,18 ./.:32:12,20 0|1:39:25,14 +chr20 954684 200xd47 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=936264;QSTRAND=+ GT:DP:AD 1|1:35:19,16 1|1:26:21,5 1|1:25:6,19 +chr20 954686 200xd48 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=936266;QSTRAND=+ GT:DP:AD 1|1:17:5,12 1|1:45:25,20 0|1:46:22,24 +chr20 954688 200xd49 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=936268;QSTRAND=+ GT:DP:AD 1|0:24:11,13 ./.:44:23,21 ./.:47:22,25 +chr20 954692 200xd4a CAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=936273;QSTRAND=+ GT:DP:AD 1|1:41:22,19 1|1:33:19,14 1|1:39:20,19 +chr20 955001 200xd4b C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=936579;QSTRAND=+ GT:DP:AD 1|0:44:22,22 ./.:28:12,16 ./.:42:21,21 +chr20 956302 200xd4c T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=937880;QSTRAND=+ GT:DP:AD 1|0:24:8,16 ./.:35:13,22 ./.:41:20,21 +chr20 956624 200xd4d T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=938202;QSTRAND=+ GT:DP:AD 1|1:24:8,16 1|1:42:21,21 1|1:31:12,19 +chr20 956630 200xd4e G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=938208;QSTRAND=+ GT:DP:AD 1|0:43:23,20 ./.:12:7,5 ./.:23:10,13 +chr20 957046 200xd4f C T 60 . QNAME=cluster19_000000F;QSTART=24801067;QSTRAND=- GT:DP:AD ./.:32:14,18 1|0:13:5,8 ./.:27:13,14 +chr20 957302 200xd50 G GTA 60 . QNAME=HG002-S9-H1-000001F;QSTART=938881;QSTRAND=+ GT:DP:AD 1|0:46:22,24 ./.:37:25,12 ./.:35:12,23 +chr20 957320 200xd51 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=938900;QSTRAND=+ GT:DP:AD 1|0:26:6,20 ./.:46:22,24 ./.:38:14,24 +chr20 957322 200xd52 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=938902;QSTRAND=+ GT:DP:AD 1|0:30:14,16 ./.:35:18,17 ./.:20:9,11 +chr20 957387 200xd53 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=938967;QSTRAND=+ GT:DP:AD 1|1:24:19,5 1|1:39:19,20 0|1:43:21,22 +chr20 957642 200xd54 C CAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=939223;QSTRAND=+ GT:DP:AD 1|0:24:6,18 ./.:42:17,25 ./.:39:15,24 +chr20 957677 200xd55 T TAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=939264;QSTRAND=+ GT:DP:AD 1|0:28:8,20 ./.:13:5,8 ./.:45:22,23 +chr20 958217 200xd56 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=939805;QSTRAND=+ GT:DP:AD 1|0:26:21,5 ./.:39:21,18 ./.:21:12,9 +chr20 958300 200xd57 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=939888;QSTRAND=+ GT:DP:AD 1|0:32:14,18 ./.:34:11,23 ./.:27:15,12 +chr20 958487 200xd58 T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=940075;QSTRAND=+ GT:DP:AD 1|0:24:9,15 ./.:30:11,19 ./.:36:11,25 +chr20 958518 200xd59 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=940106;QSTRAND=+ GT:DP:AD 1|0:42:17,25 ./.:21:11,10 ./.:30:6,24 +chr20 958523 200xd5a A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=940111;QSTRAND=+ GT:DP:AD 1|0:27:21,6 ./.:25:19,6 ./.:27:17,10 +chr20 958650 200xd5b G A 60 . QNAME=cluster23_scaffold_2;QSTART=24734462;QSTRAND=- GT:DP:AD ./.:46:24,22 ./.:23:7,16 0|1:28:5,23 +chr20 958880 200xd5c C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=940468;QSTRAND=+ GT:DP:AD 1|0:32:24,8 ./.:29:17,12 ./.:13:7,6 +chr20 959105 200xd5d GAGTGTGGTGGTGGGTGTGGGGC G 60 . QNAME=HG002-S9-H1-000001F;QSTART=940694;QSTRAND=+ GT:DP:AD 1|0:27:14,13 ./.:47:22,25 ./.:39:22,17 +chr20 959171 200xd5e A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=940737;QSTRAND=+ GT:DP:AD 1|0:16:11,5 ./.:35:22,13 ./.:44:22,22 +chr20 959315 200xd5f A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=940881;QSTRAND=+ GT:DP:AD 1|0:36:19,17 ./.:35:22,13 ./.:27:8,19 +chr20 959563 200xd60 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=941129;QSTRAND=+ GT:DP:AD 1|0:21:11,10 ./.:27:7,20 ./.:34:15,19 +chr20 959871 200xd61 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=941437;QSTRAND=+ GT:DP:AD 1|0:48:23,25 ./.:23:14,9 ./.:18:9,9 +chr20 960669 200xd62 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=942235;QSTRAND=+ GT:DP:AD 1|0:20:5,15 ./.:30:20,10 ./.:50:25,25 +chr20 960776 200xd63 C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=942342;QSTRAND=+ GT:DP:AD 1|0:33:18,15 ./.:22:5,17 ./.:41:17,24 +chr20 960856 200xd64 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=942422;QSTRAND=+ GT:DP:AD 1|0:39:22,17 ./.:42:21,21 ./.:25:5,20 +chr20 961022 200xd65 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=942588;QSTRAND=+ GT:DP:AD 1|0:27:9,18 ./.:33:11,22 ./.:31:20,11 +chr20 961081 200xd66 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=942647;QSTRAND=+ GT:DP:AD 1|1:31:21,10 1|1:32:14,18 1|1:37:17,20 +chr20 961455 200xd67 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=943021;QSTRAND=+ GT:DP:AD 1|0:29:16,13 ./.:37:15,22 ./.:18:7,11 +chr20 961789 200xd68 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=943355;QSTRAND=+ GT:DP:AD 1|0:40:19,21 ./.:30:15,15 ./.:36:20,16 +chr20 961809 200xd69 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=943375;QSTRAND=+ GT:DP:AD 1|0:30:18,12 ./.:22:7,15 ./.:15:6,9 +chr20 962027 200xd6a T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=943593;QSTRAND=+ GT:DP:AD 1|0:10:5,5 ./.:17:7,10 ./.:16:5,11 +chr20 962140 200xd6b G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=943706;QSTRAND=+ GT:DP:AD 1|0:22:8,14 ./.:20:9,11 ./.:37:20,17 +chr20 962739 200xd6c G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=944305;QSTRAND=+ GT:DP:AD 1|0:32:8,24 ./.:21:5,16 ./.:24:14,10 +chr20 962818 200xd6d C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=944384;QSTRAND=+ GT:DP:AD 1|0:41:18,23 ./.:32:25,7 ./.:28:13,15 +chr20 964006 200xd6e T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=945572;QSTRAND=+ GT:DP:AD 1|0:31:19,12 ./.:35:25,10 ./.:35:19,16 +chr20 964368 200xd6f G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=945934;QSTRAND=+ GT:DP:AD 1|0:45:23,22 ./.:32:14,18 ./.:43:24,19 +chr20 964461 200xd70 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=946027;QSTRAND=+ GT:DP:AD 1|0:28:8,20 ./.:32:17,15 ./.:27:8,19 +chr20 964587 200xd71 T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=946153;QSTRAND=+ GT:DP:AD 1|0:29:24,5 ./.:21:10,11 ./.:37:13,24 +chr20 964681 200xd72 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=946247;QSTRAND=+ GT:DP:AD 1|0:26:12,14 ./.:20:11,9 ./.:35:13,22 +chr20 964763 200xd73 T TAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=946330;QSTRAND=+ GT:DP:AD 1|0:24:11,13 ./.:34:13,21 ./.:22:13,9 +chr20 964805 200xd74 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=946373;QSTRAND=+ GT:DP:AD 1|0:25:18,7 ./.:30:16,14 ./.:30:10,20 +chr20 964823 200xd75 CACACACACATAT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=946392;QSTRAND=+ GT:DP:AD 1|0:23:8,15 ./.:24:13,11 ./.:34:9,25 +chr20 964827 200xd76 CACACAT C 60 . QNAME=cluster23_scaffold_3;QSTART=24744733;QSTRAND=- GT:DP:AD ./.:26:19,7 ./.:23:12,11 1|0:42:24,18 +chr20 964831 200xd77 CAT C 60 . QNAME=cluster19_000000F;QSTART=24793282;QSTRAND=- GT:DP:AD ./.:23:17,6 1|1:25:14,11 0|1:25:16,9 +chr20 965654 200xd78 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=947210;QSTRAND=+ GT:DP:AD 1|0:38:13,25 ./.:38:15,23 ./.:12:5,7 +chr20 965660 200xd79 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=947216;QSTRAND=+ GT:DP:AD 1|0:19:6,13 ./.:37:22,15 ./.:45:20,25 +chr20 965819 200xd7a T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=947375;QSTRAND=+ GT:DP:AD 1|0:29:11,18 ./.:18:6,12 ./.:35:14,21 +chr20 965855 200xd7b G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=947411;QSTRAND=+ GT:DP:AD 1|0:31:15,16 ./.:31:24,7 ./.:40:22,18 +chr20 966123 200xd7c A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=947679;QSTRAND=+ GT:DP:AD 1|0:17:11,6 ./.:19:7,12 ./.:22:14,8 +chr20 966156 200xd7d G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=947712;QSTRAND=+ GT:DP:AD 1|0:26:5,21 ./.:34:14,20 ./.:43:22,21 +chr20 966449 200xd7e G GTC 60 . QNAME=HG002-S9-H1-000001F;QSTART=948006;QSTRAND=+ GT:DP:AD 1|0:30:13,17 ./.:33:21,12 ./.:24:5,19 +chr20 966451 200xd7f CT C 60 . QNAME=cluster23_scaffold_2;QSTART=24726663;QSTRAND=- GT:DP:AD ./.:45:23,22 ./.:16:6,10 0|1:23:15,8 +chr20 966507 200xd80 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=948065;QSTRAND=+ GT:DP:AD 1|0:19:12,7 ./.:12:6,6 ./.:35:12,23 +chr20 966840 200xd81 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=948398;QSTRAND=+ GT:DP:AD 1|0:28:10,18 ./.:19:9,10 ./.:47:24,23 +chr20 966858 200xd82 AAAACAAGC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=948417;QSTRAND=+ GT:DP:AD 1|0:29:9,20 ./.:27:21,6 ./.:30:11,19 +chr20 970054 200xd83 TC T 60 . QNAME=cluster23_scaffold_2;QSTART=24723061;QSTRAND=- GT:DP:AD ./.:29:17,12 ./.:24:15,9 0|1:29:16,13 +chr20 971192 200xd84 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=952742;QSTRAND=+ GT:DP:AD 1|0:14:8,6 ./.:19:10,9 ./.:38:23,15 +chr20 971309 200xd85 A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=927343;QSTRAND=+ GT:DP:AD 0|1:34:15,19 ./.:18:7,11 ./.:30:9,21 +chr20 971575 200xd86 C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=927609;QSTRAND=+ GT:DP:AD 0|1:31:12,19 ./.:22:14,8 ./.:39:23,16 +chr20 972263 200xd87 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=953813;QSTRAND=+ GT:DP:AD 1|1:28:11,17 ./.:40:18,22 ./.:40:24,16 +chr20 972407 200xd88 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=953957;QSTRAND=+ GT:DP:AD 1|1:34:24,10 ./.:13:7,6 ./.:33:23,10 +chr20 972507 200xd89 G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=928541;QSTRAND=+ GT:DP:AD 0|1:21:10,11 ./.:14:8,6 ./.:24:5,19 +chr20 972633 200xd8a G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=954183;QSTRAND=+ GT:DP:AD 1|1:28:7,21 ./.:35:15,20 ./.:35:20,15 +chr20 972877 200xd8b T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=954427;QSTRAND=+ GT:DP:AD 1|1:13:8,5 ./.:29:22,7 ./.:44:22,22 +chr20 972959 200xd8c A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=954509;QSTRAND=+ GT:DP:AD 1|1:22:13,9 ./.:27:10,17 ./.:21:14,7 +chr20 973165 200xd8d TGG T 60 . QNAME=cluster23_scaffold_3;QSTART=24736401;QSTRAND=- GT:DP:AD ./.:28:11,17 ./.:22:17,5 1|0:32:23,9 +chr20 973459 200xd8e ATTGT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=955010;QSTRAND=+ GT:DP:AD 1|1:22:11,11 ./.:35:17,18 ./.:31:15,16 +chr20 973459 200xd8f A ATTGT 60 . QNAME=cluster19_000000F;QSTART=24784652;QSTRAND=- GT:DP:AD ./.:30:8,22 1|0:34:22,12 1|0:40:20,20 +chr20 973633 200xd90 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=955179;QSTRAND=+ GT:DP:AD 1|1:33:13,20 ./.:27:8,19 ./.:22:8,14 +chr20 974110 200xd91 G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=930140;QSTRAND=+ GT:DP:AD 0|1:32:11,21 ./.:30:17,13 ./.:43:23,20 +chr20 974769 200xd92 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=956315;QSTRAND=+ GT:DP:AD 1|1:31:18,13 ./.:35:20,15 ./.:36:14,22 +chr20 975693 200xd93 C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=957239;QSTRAND=+ GT:DP:AD 1|0:29:11,18 ./.:20:13,7 ./.:45:24,21 +chr20 976042 200xd94 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=957588;QSTRAND=+ GT:DP:AD 1|1:47:24,23 ./.:30:12,18 1|0:34:15,19 +chr20 976694 200xd95 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=958240;QSTRAND=+ GT:DP:AD 1|0:47:23,24 ./.:20:13,7 ./.:38:14,24 +chr20 977237 200xd96 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=958783;QSTRAND=+ GT:DP:AD 1|0:16:9,7 ./.:22:11,11 ./.:22:12,10 +chr20 977764 200xd97 A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=959310;QSTRAND=+ GT:DP:AD 1|0:20:8,12 ./.:34:24,10 ./.:28:23,5 +chr20 978561 200xd98 G T 60 . QNAME=cluster23_scaffold_2;QSTART=24714555;QSTRAND=- GT:DP:AD ./.:23:18,5 ./.:17:5,12 0|1:32:25,7 +chr20 978696 200xd99 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=960242;QSTRAND=+ GT:DP:AD 1|0:33:18,15 ./.:42:18,24 ./.:32:7,25 +chr20 979248 200xd9a C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=960794;QSTRAND=+ GT:DP:AD 1|0:24:11,13 ./.:31:24,7 ./.:14:6,8 +chr20 980145 200xd9b A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=961691;QSTRAND=+ GT:DP:AD 1|0:39:16,23 ./.:29:17,12 ./.:36:18,18 +chr20 980577 200xd9c T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=936607;QSTRAND=+ GT:DP:AD 0|1:16:9,7 1|0:26:15,11 ./.:37:19,18 +chr20 980652 200xd9d G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=962198;QSTRAND=+ GT:DP:AD 1|0:27:14,13 ./.:46:21,25 ./.:26:6,20 +chr20 980884 200xd9e A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=962430;QSTRAND=+ GT:DP:AD 1|0:20:9,11 ./.:32:19,13 ./.:30:10,20 +chr20 981108 200xd9f G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=962654;QSTRAND=+ GT:DP:AD 1|0:38:17,21 ./.:25:13,12 ./.:23:7,16 +chr20 981138 200xda0 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=962684;QSTRAND=+ GT:DP:AD 1|0:16:7,9 ./.:34:20,14 ./.:26:20,6 +chr20 984922 200xda1 C CCCAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=966469;QSTRAND=+ GT:DP:AD 1|0:33:12,21 ./.:18:5,13 0|1:34:25,9 +chr20 990421 200xda2 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=971971;QSTRAND=+ GT:DP:AD 1|0:32:22,10 ./.:31:15,16 ./.:40:24,16 +chr20 991150 200xda3 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=972700;QSTRAND=+ GT:DP:AD 1|0:29:19,10 ./.:30:13,17 ./.:29:7,22 +chr20 991319 200xda4 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=972869;QSTRAND=+ GT:DP:AD 1|0:26:17,9 ./.:13:7,6 ./.:42:20,22 +chr20 991428 200xda5 A AT 60 . QNAME=cluster19_000000F;QSTART=955698;QSTRAND=+ GT:DP:AD ./.:24:18,6 0|1:32:21,11 ./.:33:10,23 +chr20 992032 200xda6 G GGGAC 60 . QNAME=cluster23_scaffold_3;QSTART=24717528;QSTRAND=- GT:DP:AD ./.:40:15,25 ./.:24:17,7 1|1:10:5,5 +chr20 992091 200xda7 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=973641;QSTRAND=+ GT:DP:AD 1|0:39:14,25 ./.:26:21,5 ./.:31:8,23 +chr20 992263 200xda8 C CT 60 . QNAME=cluster23_scaffold_3;QSTART=24717296;QSTRAND=- GT:DP:AD ./.:44:21,23 ./.:22:11,11 1|0:34:9,25 +chr20 992288 200xda9 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=973838;QSTRAND=+ GT:DP:AD 1|0:29:6,23 ./.:34:15,19 ./.:35:14,21 +chr20 992532 200xdaa T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=974082;QSTRAND=+ GT:DP:AD 1|0:26:20,6 ./.:31:15,16 ./.:40:21,19 +chr20 992797 200xdab T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=974347;QSTRAND=+ GT:DP:AD 1|0:18:8,10 ./.:32:22,10 ./.:25:19,6 +chr20 993026 200xdac A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=974576;QSTRAND=+ GT:DP:AD 1|0:26:16,10 ./.:30:22,8 ./.:36:18,18 +chr20 993059 200xdad T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=974609;QSTRAND=+ GT:DP:AD 1|0:29:9,20 ./.:29:12,17 ./.:34:14,20 +chr20 993443 200xdae G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=974993;QSTRAND=+ GT:DP:AD 1|0:26:17,9 ./.:31:16,15 ./.:27:21,6 +chr20 993795 200xdaf T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=975345;QSTRAND=+ GT:DP:AD 1|0:41:24,17 ./.:36:19,17 ./.:40:20,20 +chr20 993846 200xdb0 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=975396;QSTRAND=+ GT:DP:AD 1|0:41:16,25 ./.:40:19,21 ./.:32:25,7 +chr20 993854 200xdb1 G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=975404;QSTRAND=+ GT:DP:AD 1|0:29:13,16 ./.:32:15,17 ./.:41:24,17 +chr20 993856 200xdb2 G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=975406;QSTRAND=+ GT:DP:AD 1|0:22:6,16 ./.:20:14,6 ./.:24:5,19 +chr20 994379 200xdb3 C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=975929;QSTRAND=+ GT:DP:AD 1|1:48:23,25 1|0:31:21,10 1|1:19:8,11 +chr20 994584 200xdb4 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=976134;QSTRAND=+ GT:DP:AD 1|0:32:25,7 ./.:19:6,13 ./.:30:7,23 +chr20 994605 200xdb5 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=976155;QSTRAND=+ GT:DP:AD 1|0:40:16,24 ./.:35:22,13 ./.:17:5,12 +chr20 995547 200xdb6 GA G 60 . QNAME=cluster23_scaffold_2;QSTART=24697561;QSTRAND=- GT:DP:AD ./.:31:20,11 ./.:21:9,12 0|1:37:22,15 +chr20 996521 200xdb7 A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=978071;QSTRAND=+ GT:DP:AD 1|0:17:10,7 ./.:39:24,15 ./.:26:14,12 +chr20 999077 200xdb8 T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=980627;QSTRAND=+ GT:DP:AD 1|0:19:8,11 ./.:27:14,13 ./.:40:16,24 diff --git a/repo_utils/answer_key/anno/anno_bpovl.jl b/repo_utils/answer_key/anno/anno_bpovl.jl new file mode 100644 index 00000000..00328b57 Binary files /dev/null and b/repo_utils/answer_key/anno/anno_bpovl.jl differ diff --git a/repo_utils/test_files/answer_key/anno_density.jl b/repo_utils/answer_key/anno/anno_density.jl similarity index 100% rename from repo_utils/test_files/answer_key/anno_density.jl rename to repo_utils/answer_key/anno/anno_density.jl diff --git a/repo_utils/test_files/answer_key/anno_grpaf.subtags.vcf b/repo_utils/answer_key/anno/anno_grpaf.subtags.vcf similarity index 100% rename from repo_utils/test_files/answer_key/anno_grpaf.subtags.vcf rename to repo_utils/answer_key/anno/anno_grpaf.subtags.vcf diff --git a/repo_utils/test_files/answer_key/anno_grpaf.vcf b/repo_utils/answer_key/anno/anno_grpaf.vcf similarity index 100% rename from repo_utils/test_files/answer_key/anno_grpaf.vcf rename to repo_utils/answer_key/anno/anno_grpaf.vcf diff --git a/repo_utils/test_files/answer_key/grm.jl b/repo_utils/answer_key/anno/grm.jl similarity index 100% rename from repo_utils/test_files/answer_key/grm.jl rename to repo_utils/answer_key/anno/grm.jl diff --git a/repo_utils/test_files/answer_key/repmask.vcf b/repo_utils/answer_key/anno/repmask.vcf similarity index 100% rename from repo_utils/test_files/answer_key/repmask.vcf rename to repo_utils/answer_key/anno/repmask.vcf diff --git a/repo_utils/test_files/answer_key/trf.vcf b/repo_utils/answer_key/anno/trf.vcf similarity index 100% rename from repo_utils/test_files/answer_key/trf.vcf rename to repo_utils/answer_key/anno/trf.vcf diff --git a/repo_utils/test_files/answer_key/anno_answers.vcf.gz b/repo_utils/answer_key/anno_answers.vcf.gz similarity index 100% rename from repo_utils/test_files/answer_key/anno_answers.vcf.gz rename to repo_utils/answer_key/anno_answers.vcf.gz diff --git a/repo_utils/test_files/answer_key/anno_answers.vcf.gz.tbi b/repo_utils/answer_key/anno_answers.vcf.gz.tbi similarity index 100% rename from repo_utils/test_files/answer_key/anno_answers.vcf.gz.tbi rename to repo_utils/answer_key/anno_answers.vcf.gz.tbi diff --git a/repo_utils/answer_key/bench/bench12/fn.vcf.gz b/repo_utils/answer_key/bench/bench12/fn.vcf.gz new file mode 100644 index 00000000..ff464113 Binary files /dev/null and b/repo_utils/answer_key/bench/bench12/fn.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench12/fn.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12/fn.vcf.gz.tbi new file mode 100644 index 00000000..2505cf3d Binary files /dev/null and b/repo_utils/answer_key/bench/bench12/fn.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench12/fp.vcf.gz b/repo_utils/answer_key/bench/bench12/fp.vcf.gz new file mode 100644 index 00000000..dd3f57e8 Binary files /dev/null and b/repo_utils/answer_key/bench/bench12/fp.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench12/fp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12/fp.vcf.gz.tbi new file mode 100644 index 00000000..3091b335 Binary files /dev/null and b/repo_utils/answer_key/bench/bench12/fp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench12/log.txt b/repo_utils/answer_key/bench/bench12/log.txt new file mode 100644 index 00000000..4b44637a --- /dev/null +++ b/repo_utils/answer_key/bench/bench12/log.txt @@ -0,0 +1,65 @@ +2022-12-01 18:25:54,715 [INFO] Truvari v4.0.0.dev0+detached +2022-12-01 18:25:54,716 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input2.vcf.gz -f repo_utils/test_files/references/reference.fa -o test_results/bench12/ +2022-12-01 18:25:54,717 [INFO] Params: +{ + "base": "/data/repo_utils/test_files/variants/input1.vcf.gz", + "comp": "/data/repo_utils/test_files/variants/input2.vcf.gz", + "output": "test_results/bench12/", + "reference": "/data/repo_utils/test_files/references/reference.fa", + "debug": false, + "prog": false, + "refdist": 500, + "pctsim": 0.7, + "minhaplen": 50, + "pctsize": 0.7, + "pctovl": 0.0, + "typeignore": false, + "dup_to_ins": false, + "use_lev": false, + "chunksize": 1000, + "gtcomp": false, + "bSample": "NA24385", + "cSample": "NA12878", + "sizemin": 50, + "sizefilt": 30, + "sizemax": 50000, + "passonly": false, + "no_ref": false, + "includebed": null, + "extend": 0, + "multimatch": false +} +2022-12-01 18:25:54,891 [INFO] Zipped 3934 variants Counter({'base': 2151, 'comp': 1783}) +2022-12-01 18:25:54,892 [INFO] 13 chunks of 3934 variants Counter({'__filtered': 3904, 'base': 16, 'comp': 14}) +2022-12-01 18:25:54,897 [INFO] Stats: { + "TP-base": 8, + "TP-call": 8, + "FP": 3, + "FN": 8, + "precision": 0.7272727272727273, + "recall": 0.5, + "f1": 0.5925925925925926, + "base cnt": 16, + "call cnt": 11, + "TP-call_TP-gt": 4, + "TP-call_FP-gt": 4, + "TP-base_TP-gt": 4, + "TP-base_FP-gt": 4, + "gt_concordance": 0.5, + "gt_matrix": { + "(1, 1)": { + "(1, 1)": 2, + "(1, 0)": 1, + "(0, 1)": 1 + }, + "(0, 1)": { + "(1, 1)": 1, + "(0, 1)": 1, + "(1, 0)": 1 + }, + "(1, 0)": { + "(1, 1)": 1 + } + } +} +2022-12-01 18:25:54,987 [INFO] Finished bench diff --git a/repo_utils/answer_key/bench/bench12/params.json b/repo_utils/answer_key/bench/bench12/params.json new file mode 100644 index 00000000..a1620f23 --- /dev/null +++ b/repo_utils/answer_key/bench/bench12/params.json @@ -0,0 +1 @@ +{"base": "/data/repo_utils/test_files/variants/input1.vcf.gz", "comp": "/data/repo_utils/test_files/variants/input2.vcf.gz", "output": "test_results/bench12/", "reference": "/data/repo_utils/test_files/references/reference.fa", "debug": false, "prog": false, "refdist": 500, "pctsim": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "dup_to_ins": false, "use_lev": false, "chunksize": 1000, "gtcomp": false, "bSample": "NA24385", "cSample": "NA12878", "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "includebed": null, "extend": 0, "multimatch": false} \ No newline at end of file diff --git a/repo_utils/answer_key/bench/bench12/summary.json b/repo_utils/answer_key/bench/bench12/summary.json new file mode 100644 index 00000000..6546f1c1 --- /dev/null +++ b/repo_utils/answer_key/bench/bench12/summary.json @@ -0,0 +1,31 @@ +{ + "TP-base": 8, + "TP-comp": 8, + "FP": 3, + "FN": 8, + "precision": 0.7272727272727273, + "recall": 0.5, + "f1": 0.5925925925925926, + "base cnt": 16, + "comp cnt": 11, + "TP-comp_TP-gt": 4, + "TP-comp_FP-gt": 4, + "TP-base_TP-gt": 4, + "TP-base_FP-gt": 4, + "gt_concordance": 0.5, + "gt_matrix": { + "(1, 1)": { + "(1, 1)": 2, + "(1, 0)": 1, + "(0, 1)": 1 + }, + "(0, 1)": { + "(1, 1)": 1, + "(0, 1)": 1, + "(1, 0)": 1 + }, + "(1, 0)": { + "(1, 1)": 1 + } + } +} diff --git a/repo_utils/answer_key/bench/bench12/tp-base.vcf.gz b/repo_utils/answer_key/bench/bench12/tp-base.vcf.gz new file mode 100644 index 00000000..13cfa415 Binary files /dev/null and b/repo_utils/answer_key/bench/bench12/tp-base.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench12/tp-base.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12/tp-base.vcf.gz.tbi new file mode 100644 index 00000000..408db72a Binary files /dev/null and b/repo_utils/answer_key/bench/bench12/tp-base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench12/tp-comp.vcf.gz b/repo_utils/answer_key/bench/bench12/tp-comp.vcf.gz new file mode 100644 index 00000000..1c092feb Binary files /dev/null and b/repo_utils/answer_key/bench/bench12/tp-comp.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench12/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12/tp-comp.vcf.gz.tbi new file mode 100644 index 00000000..3bdab97d Binary files /dev/null and b/repo_utils/answer_key/bench/bench12/tp-comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/fn.vcf.gz b/repo_utils/answer_key/bench/bench12_gtcomp/fn.vcf.gz new file mode 100644 index 00000000..78fbf653 Binary files /dev/null and b/repo_utils/answer_key/bench/bench12_gtcomp/fn.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/fn.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12_gtcomp/fn.vcf.gz.tbi new file mode 100644 index 00000000..159f2fa1 Binary files /dev/null and b/repo_utils/answer_key/bench/bench12_gtcomp/fn.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/fp.vcf.gz b/repo_utils/answer_key/bench/bench12_gtcomp/fp.vcf.gz new file mode 100644 index 00000000..dd3f57e8 Binary files /dev/null and b/repo_utils/answer_key/bench/bench12_gtcomp/fp.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/fp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12_gtcomp/fp.vcf.gz.tbi new file mode 100644 index 00000000..3091b335 Binary files /dev/null and b/repo_utils/answer_key/bench/bench12_gtcomp/fp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/log.txt b/repo_utils/answer_key/bench/bench12_gtcomp/log.txt new file mode 100644 index 00000000..79c1d51c --- /dev/null +++ b/repo_utils/answer_key/bench/bench12_gtcomp/log.txt @@ -0,0 +1,65 @@ +2022-12-01 18:26:08,784 [INFO] Truvari v4.0.0.dev0+detached +2022-12-01 18:26:08,785 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input2.vcf.gz -f repo_utils/test_files/references/reference.fa -o test_results/bench12_gtcomp/ --gtcomp +2022-12-01 18:26:08,786 [INFO] Params: +{ + "base": "/data/repo_utils/test_files/variants/input1.vcf.gz", + "comp": "/data/repo_utils/test_files/variants/input2.vcf.gz", + "output": "test_results/bench12_gtcomp/", + "reference": "/data/repo_utils/test_files/references/reference.fa", + "debug": false, + "prog": false, + "refdist": 500, + "pctsim": 0.7, + "minhaplen": 50, + "pctsize": 0.7, + "pctovl": 0.0, + "typeignore": false, + "dup_to_ins": false, + "use_lev": false, + "chunksize": 1000, + "gtcomp": true, + "bSample": "NA24385", + "cSample": "NA12878", + "sizemin": 50, + "sizefilt": 30, + "sizemax": 50000, + "passonly": false, + "no_ref": false, + "includebed": null, + "extend": 0, + "multimatch": false +} +2022-12-01 18:26:08,975 [INFO] Zipped 3934 variants Counter({'base': 2151, 'comp': 1783}) +2022-12-01 18:26:08,976 [INFO] 13 chunks of 3934 variants Counter({'__filtered': 3904, 'base': 16, 'comp': 14}) +2022-12-01 18:26:08,981 [INFO] Stats: { + "TP-base": 9, + "TP-call": 8, + "FP": 3, + "FN": 7, + "precision": 0.7272727272727273, + "recall": 0.5625, + "f1": 0.6343612334801763, + "base cnt": 16, + "call cnt": 11, + "TP-call_TP-gt": 4, + "TP-call_FP-gt": 4, + "TP-base_TP-gt": 4, + "TP-base_FP-gt": 5, + "gt_concordance": 0.5, + "gt_matrix": { + "(1, 1)": { + "(1, 1)": 2, + "(1, 0)": 1, + "(0, 1)": 1 + }, + "(0, 1)": { + "(1, 1)": 2, + "(0, 1)": 1, + "(1, 0)": 1 + }, + "(1, 0)": { + "(1, 1)": 1 + } + } +} +2022-12-01 18:26:09,088 [INFO] Finished bench diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/params.json b/repo_utils/answer_key/bench/bench12_gtcomp/params.json new file mode 100644 index 00000000..70674a5b --- /dev/null +++ b/repo_utils/answer_key/bench/bench12_gtcomp/params.json @@ -0,0 +1 @@ +{"base": "/data/repo_utils/test_files/variants/input1.vcf.gz", "comp": "/data/repo_utils/test_files/variants/input2.vcf.gz", "output": "test_results/bench12_gtcomp/", "reference": "/data/repo_utils/test_files/references/reference.fa", "debug": false, "prog": false, "refdist": 500, "pctsim": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "dup_to_ins": false, "use_lev": false, "chunksize": 1000, "gtcomp": true, "bSample": "NA24385", "cSample": "NA12878", "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "includebed": null, "extend": 0, "multimatch": false} \ No newline at end of file diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/summary.json b/repo_utils/answer_key/bench/bench12_gtcomp/summary.json new file mode 100644 index 00000000..93baa78f --- /dev/null +++ b/repo_utils/answer_key/bench/bench12_gtcomp/summary.json @@ -0,0 +1,31 @@ +{ + "TP-base": 9, + "TP-comp": 8, + "FP": 3, + "FN": 7, + "precision": 0.7272727272727273, + "recall": 0.5625, + "f1": 0.6343612334801763, + "base cnt": 16, + "comp cnt": 11, + "TP-comp_TP-gt": 4, + "TP-comp_FP-gt": 4, + "TP-base_TP-gt": 4, + "TP-base_FP-gt": 5, + "gt_concordance": 0.5, + "gt_matrix": { + "(1, 1)": { + "(1, 1)": 2, + "(1, 0)": 1, + "(0, 1)": 1 + }, + "(0, 1)": { + "(1, 1)": 2, + "(0, 1)": 1, + "(1, 0)": 1 + }, + "(1, 0)": { + "(1, 1)": 1 + } + } +} diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/tp-base.vcf.gz b/repo_utils/answer_key/bench/bench12_gtcomp/tp-base.vcf.gz new file mode 100644 index 00000000..274bc211 Binary files /dev/null and b/repo_utils/answer_key/bench/bench12_gtcomp/tp-base.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/tp-base.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12_gtcomp/tp-base.vcf.gz.tbi new file mode 100644 index 00000000..7f02f80a Binary files /dev/null and b/repo_utils/answer_key/bench/bench12_gtcomp/tp-base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/tp-comp.vcf.gz b/repo_utils/answer_key/bench/bench12_gtcomp/tp-comp.vcf.gz new file mode 100644 index 00000000..1c092feb Binary files /dev/null and b/repo_utils/answer_key/bench/bench12_gtcomp/tp-comp.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12_gtcomp/tp-comp.vcf.gz.tbi new file mode 100644 index 00000000..3bdab97d Binary files /dev/null and b/repo_utils/answer_key/bench/bench12_gtcomp/tp-comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench13/fn.vcf.gz b/repo_utils/answer_key/bench/bench13/fn.vcf.gz new file mode 100644 index 00000000..07df3b40 Binary files /dev/null and b/repo_utils/answer_key/bench/bench13/fn.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench13/fn.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13/fn.vcf.gz.tbi new file mode 100644 index 00000000..a886873a Binary files /dev/null and b/repo_utils/answer_key/bench/bench13/fn.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench13/fp.vcf.gz b/repo_utils/answer_key/bench/bench13/fp.vcf.gz new file mode 100644 index 00000000..f01cfa99 Binary files /dev/null and b/repo_utils/answer_key/bench/bench13/fp.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench13/fp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13/fp.vcf.gz.tbi new file mode 100644 index 00000000..64c64126 Binary files /dev/null and b/repo_utils/answer_key/bench/bench13/fp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench13/log.txt b/repo_utils/answer_key/bench/bench13/log.txt new file mode 100644 index 00000000..4a62a1be --- /dev/null +++ b/repo_utils/answer_key/bench/bench13/log.txt @@ -0,0 +1,64 @@ +2022-12-01 18:25:56,985 [INFO] Truvari v4.0.0.dev0+detached +2022-12-01 18:25:56,987 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input3.vcf.gz -f repo_utils/test_files/references/reference.fa -o test_results/bench13/ +2022-12-01 18:25:56,989 [INFO] Params: +{ + "base": "/data/repo_utils/test_files/variants/input1.vcf.gz", + "comp": "/data/repo_utils/test_files/variants/input3.vcf.gz", + "output": "test_results/bench13/", + "reference": "/data/repo_utils/test_files/references/reference.fa", + "debug": false, + "prog": false, + "refdist": 500, + "pctsim": 0.7, + "minhaplen": 50, + "pctsize": 0.7, + "pctovl": 0.0, + "typeignore": false, + "dup_to_ins": false, + "use_lev": false, + "chunksize": 1000, + "gtcomp": false, + "bSample": "NA24385", + "cSample": "HG00733", + "sizemin": 50, + "sizefilt": 30, + "sizemax": 50000, + "passonly": false, + "no_ref": false, + "includebed": null, + "extend": 0, + "multimatch": false +} +2022-12-01 18:25:57,189 [INFO] Zipped 4216 variants Counter({'base': 2151, 'comp': 2065}) +2022-12-01 18:25:57,191 [INFO] 15 chunks of 4216 variants Counter({'__filtered': 4179, 'comp': 21, 'base': 16}) +2022-12-01 18:25:57,194 [INFO] Stats: { + "TP-base": 10, + "TP-call": 10, + "FP": 7, + "FN": 6, + "precision": 0.5882352941176471, + "recall": 0.625, + "f1": 0.6060606060606061, + "base cnt": 16, + "call cnt": 17, + "TP-call_TP-gt": 7, + "TP-call_FP-gt": 3, + "TP-base_TP-gt": 7, + "TP-base_FP-gt": 3, + "gt_concordance": 0.7, + "gt_matrix": { + "(1, 1)": { + "(1, 0)": 1, + "(1, 1)": 2 + }, + "(0, 1)": { + "(0, 1)": 2, + "(1, 1)": 2, + "(1, 0)": 1 + }, + "(1, 0)": { + "(1, 0)": 2 + } + } +} +2022-12-01 18:25:57,291 [INFO] Finished bench diff --git a/repo_utils/answer_key/bench/bench13/params.json b/repo_utils/answer_key/bench/bench13/params.json new file mode 100644 index 00000000..d91887b6 --- /dev/null +++ b/repo_utils/answer_key/bench/bench13/params.json @@ -0,0 +1 @@ +{"base": "/data/repo_utils/test_files/variants/input1.vcf.gz", "comp": "/data/repo_utils/test_files/variants/input3.vcf.gz", "output": "test_results/bench13/", "reference": "/data/repo_utils/test_files/references/reference.fa", "debug": false, "prog": false, "refdist": 500, "pctsim": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "dup_to_ins": false, "use_lev": false, "chunksize": 1000, "gtcomp": false, "bSample": "NA24385", "cSample": "HG00733", "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "includebed": null, "extend": 0, "multimatch": false} \ No newline at end of file diff --git a/repo_utils/answer_key/bench/bench13/summary.json b/repo_utils/answer_key/bench/bench13/summary.json new file mode 100644 index 00000000..8bc23896 --- /dev/null +++ b/repo_utils/answer_key/bench/bench13/summary.json @@ -0,0 +1,30 @@ +{ + "TP-base": 10, + "TP-comp": 10, + "FP": 7, + "FN": 6, + "precision": 0.5882352941176471, + "recall": 0.625, + "f1": 0.6060606060606061, + "base cnt": 16, + "comp cnt": 17, + "TP-comp_TP-gt": 7, + "TP-comp_FP-gt": 3, + "TP-base_TP-gt": 7, + "TP-base_FP-gt": 3, + "gt_concordance": 0.7, + "gt_matrix": { + "(1, 1)": { + "(1, 0)": 1, + "(1, 1)": 2 + }, + "(0, 1)": { + "(0, 1)": 2, + "(1, 1)": 2, + "(1, 0)": 1 + }, + "(1, 0)": { + "(1, 0)": 2 + } + } +} diff --git a/repo_utils/answer_key/bench/bench13/tp-base.vcf.gz b/repo_utils/answer_key/bench/bench13/tp-base.vcf.gz new file mode 100644 index 00000000..d2a9ef65 Binary files /dev/null and b/repo_utils/answer_key/bench/bench13/tp-base.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench13/tp-base.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13/tp-base.vcf.gz.tbi new file mode 100644 index 00000000..c5566815 Binary files /dev/null and b/repo_utils/answer_key/bench/bench13/tp-base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench13/tp-comp.vcf.gz b/repo_utils/answer_key/bench/bench13/tp-comp.vcf.gz new file mode 100644 index 00000000..5c4a5fb7 Binary files /dev/null and b/repo_utils/answer_key/bench/bench13/tp-comp.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench13/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13/tp-comp.vcf.gz.tbi new file mode 100644 index 00000000..36661005 Binary files /dev/null and b/repo_utils/answer_key/bench/bench13/tp-comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench13_extend/fn.vcf.gz b/repo_utils/answer_key/bench/bench13_extend/fn.vcf.gz new file mode 100644 index 00000000..d4667d7d Binary files /dev/null and b/repo_utils/answer_key/bench/bench13_extend/fn.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench13_extend/fn.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13_extend/fn.vcf.gz.tbi new file mode 100644 index 00000000..fe1a11ee Binary files /dev/null and b/repo_utils/answer_key/bench/bench13_extend/fn.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench13_extend/fp.vcf.gz b/repo_utils/answer_key/bench/bench13_extend/fp.vcf.gz new file mode 100644 index 00000000..925b6e25 Binary files /dev/null and b/repo_utils/answer_key/bench/bench13_extend/fp.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench13_extend/fp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13_extend/fp.vcf.gz.tbi new file mode 100644 index 00000000..989d2497 Binary files /dev/null and b/repo_utils/answer_key/bench/bench13_extend/fp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench13_extend/log.txt b/repo_utils/answer_key/bench/bench13_extend/log.txt new file mode 100644 index 00000000..d32590fd --- /dev/null +++ b/repo_utils/answer_key/bench/bench13_extend/log.txt @@ -0,0 +1,67 @@ +2022-12-01 18:26:04,018 [INFO] Truvari v4.0.0.dev0+detached +2022-12-01 18:26:04,019 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input3.vcf.gz -f repo_utils/test_files/references/reference.fa -o test_results/bench13_extend/ --includebed repo_utils/test_files/beds/include.bed --extend 500 +2022-12-01 18:26:04,021 [INFO] Params: +{ + "base": "/data/repo_utils/test_files/variants/input1.vcf.gz", + "comp": "/data/repo_utils/test_files/variants/input3.vcf.gz", + "output": "test_results/bench13_extend/", + "reference": "/data/repo_utils/test_files/references/reference.fa", + "debug": false, + "prog": false, + "refdist": 500, + "pctsim": 0.7, + "minhaplen": 50, + "pctsize": 0.7, + "pctovl": 0.0, + "typeignore": false, + "dup_to_ins": false, + "use_lev": false, + "chunksize": 1000, + "gtcomp": false, + "bSample": "NA24385", + "cSample": "HG00733", + "sizemin": 50, + "sizefilt": 30, + "sizemax": 50000, + "passonly": false, + "no_ref": false, + "includebed": "/data/repo_utils/test_files/beds/include.bed", + "extend": 500, + "multimatch": false +} +2022-12-01 18:26:04,070 [INFO] Including 11 bed regions +2022-12-01 18:26:04,072 [INFO] Found 1 chromosomes with overlapping regions +2022-12-01 18:26:04,072 [INFO] Extending the regions by 500 bases +2022-12-01 18:26:04,075 [INFO] Found 1 chromosomes with overlapping regions +2022-12-01 18:26:04,200 [INFO] Zipped 2050 variants Counter({'base': 1130, 'comp': 920}) +2022-12-01 18:26:04,201 [INFO] 11 chunks of 2050 variants Counter({'__filtered': 2025, 'comp': 15, 'base': 10}) +2022-12-01 18:26:04,206 [INFO] Stats: { + "TP-base": 6, + "TP-call": 6, + "FP": 4, + "FN": 4, + "precision": 0.6, + "recall": 0.6, + "f1": 0.6, + "base cnt": 10, + "call cnt": 10, + "TP-call_TP-gt": 4, + "TP-call_FP-gt": 2, + "TP-base_TP-gt": 4, + "TP-base_FP-gt": 2, + "gt_concordance": 0.6666666666666666, + "gt_matrix": { + "(1, 1)": { + "(1, 0)": 1, + "(1, 1)": 2 + }, + "(0, 1)": { + "(1, 1)": 1, + "(1, 0)": 1 + }, + "(1, 0)": { + "(1, 0)": 1 + } + } +} +2022-12-01 18:26:04,309 [INFO] Finished bench diff --git a/repo_utils/answer_key/bench/bench13_extend/params.json b/repo_utils/answer_key/bench/bench13_extend/params.json new file mode 100644 index 00000000..3fd7da8a --- /dev/null +++ b/repo_utils/answer_key/bench/bench13_extend/params.json @@ -0,0 +1 @@ +{"base": "/data/repo_utils/test_files/variants/input1.vcf.gz", "comp": "/data/repo_utils/test_files/variants/input3.vcf.gz", "output": "test_results/bench13_extend/", "reference": "/data/repo_utils/test_files/references/reference.fa", "debug": false, "prog": false, "refdist": 500, "pctsim": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "dup_to_ins": false, "use_lev": false, "chunksize": 1000, "gtcomp": false, "bSample": "NA24385", "cSample": "HG00733", "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "includebed": "/data/repo_utils/test_files/beds/include.bed", "extend": 500, "multimatch": false} \ No newline at end of file diff --git a/repo_utils/answer_key/bench/bench13_extend/summary.json b/repo_utils/answer_key/bench/bench13_extend/summary.json new file mode 100644 index 00000000..35e94aed --- /dev/null +++ b/repo_utils/answer_key/bench/bench13_extend/summary.json @@ -0,0 +1,29 @@ +{ + "TP-base": 6, + "TP-comp": 6, + "FP": 4, + "FN": 4, + "precision": 0.6, + "recall": 0.6, + "f1": 0.6, + "base cnt": 10, + "comp cnt": 10, + "TP-comp_TP-gt": 4, + "TP-comp_FP-gt": 2, + "TP-base_TP-gt": 4, + "TP-base_FP-gt": 2, + "gt_concordance": 0.6666666666666666, + "gt_matrix": { + "(1, 1)": { + "(1, 0)": 1, + "(1, 1)": 2 + }, + "(0, 1)": { + "(1, 1)": 1, + "(1, 0)": 1 + }, + "(1, 0)": { + "(1, 0)": 1 + } + } +} diff --git a/repo_utils/answer_key/bench/bench13_extend/tp-base.vcf.gz b/repo_utils/answer_key/bench/bench13_extend/tp-base.vcf.gz new file mode 100644 index 00000000..5ab6f227 Binary files /dev/null and b/repo_utils/answer_key/bench/bench13_extend/tp-base.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench13_extend/tp-base.vcf.gz.tbi 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b/repo_utils/answer_key/bench/bench13_includebed/log.txt new file mode 100644 index 00000000..04f9a8b0 --- /dev/null +++ b/repo_utils/answer_key/bench/bench13_includebed/log.txt @@ -0,0 +1,62 @@ +2022-12-01 18:26:01,597 [INFO] Truvari v4.0.0.dev0+detached +2022-12-01 18:26:01,598 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input3.vcf.gz -f repo_utils/test_files/references/reference.fa -o test_results/bench13_includebed/ --includebed repo_utils/test_files/beds/include.bed +2022-12-01 18:26:01,600 [INFO] Params: +{ + "base": "/data/repo_utils/test_files/variants/input1.vcf.gz", + "comp": "/data/repo_utils/test_files/variants/input3.vcf.gz", + "output": "test_results/bench13_includebed/", + "reference": "/data/repo_utils/test_files/references/reference.fa", + "debug": false, + "prog": false, + "refdist": 500, + "pctsim": 0.7, + "minhaplen": 50, + "pctsize": 0.7, + "pctovl": 0.0, + "typeignore": false, + "dup_to_ins": false, + "use_lev": false, + "chunksize": 1000, + "gtcomp": false, + "bSample": "NA24385", + "cSample": "HG00733", + "sizemin": 50, + "sizefilt": 30, + "sizemax": 50000, + "passonly": false, + "no_ref": false, + "includebed": "/data/repo_utils/test_files/beds/include.bed", + "extend": 0, + "multimatch": false +} +2022-12-01 18:26:01,638 [INFO] Including 11 bed regions +2022-12-01 18:26:01,640 [INFO] Found 1 chromosomes with overlapping regions +2022-12-01 18:26:01,759 [INFO] Zipped 2030 variants Counter({'base': 1130, 'comp': 900}) +2022-12-01 18:26:01,760 [INFO] 10 chunks of 2030 variants Counter({'__filtered': 2009, 'comp': 11, 'base': 10}) +2022-12-01 18:26:01,764 [INFO] Stats: { + "TP-base": 5, + "TP-call": 5, + "FP": 4, + "FN": 5, + "precision": 0.5555555555555556, + "recall": 0.5, + "f1": 0.5263157894736842, + "base cnt": 10, + "call cnt": 9, + "TP-call_TP-gt": 3, + "TP-call_FP-gt": 2, + "TP-base_TP-gt": 3, + "TP-base_FP-gt": 2, + "gt_concordance": 0.6, + "gt_matrix": { + "(1, 1)": { + "(1, 0)": 1, + "(1, 1)": 2 + }, + "(0, 1)": { + "(1, 1)": 1, + "(1, 0)": 1 + } + } +} +2022-12-01 18:26:01,878 [INFO] Finished bench diff --git a/repo_utils/answer_key/bench/bench13_includebed/params.json b/repo_utils/answer_key/bench/bench13_includebed/params.json new file mode 100644 index 00000000..78a73fe1 --- /dev/null +++ b/repo_utils/answer_key/bench/bench13_includebed/params.json @@ -0,0 +1 @@ +{"base": "/data/repo_utils/test_files/variants/input1.vcf.gz", "comp": "/data/repo_utils/test_files/variants/input3.vcf.gz", "output": "test_results/bench13_includebed/", "reference": "/data/repo_utils/test_files/references/reference.fa", "debug": false, "prog": false, "refdist": 500, "pctsim": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "dup_to_ins": false, "use_lev": false, "chunksize": 1000, "gtcomp": false, "bSample": "NA24385", "cSample": "HG00733", "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "includebed": "/data/repo_utils/test_files/beds/include.bed", "extend": 0, "multimatch": false} \ No newline at end of file diff --git a/repo_utils/answer_key/bench/bench13_includebed/summary.json b/repo_utils/answer_key/bench/bench13_includebed/summary.json new file mode 100644 index 00000000..a9e771aa --- /dev/null +++ b/repo_utils/answer_key/bench/bench13_includebed/summary.json @@ -0,0 +1,26 @@ +{ + "TP-base": 5, + "TP-comp": 5, + "FP": 4, + "FN": 5, + "precision": 0.5555555555555556, + "recall": 0.5, + "f1": 0.5263157894736842, + "base cnt": 10, + "comp cnt": 9, + "TP-comp_TP-gt": 3, + "TP-comp_FP-gt": 2, + "TP-base_TP-gt": 3, + "TP-base_FP-gt": 2, + "gt_concordance": 0.6, + "gt_matrix": { + "(1, 1)": { + "(1, 0)": 1, + "(1, 1)": 2 + }, + "(0, 1)": { + "(1, 1)": 1, + "(1, 0)": 1 + } + } +} diff --git a/repo_utils/answer_key/bench/bench13_includebed/tp-base.vcf.gz b/repo_utils/answer_key/bench/bench13_includebed/tp-base.vcf.gz new file mode 100644 index 00000000..d4f1d591 Binary files /dev/null and b/repo_utils/answer_key/bench/bench13_includebed/tp-base.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench13_includebed/tp-base.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13_includebed/tp-base.vcf.gz.tbi new file mode 100644 index 00000000..765eacef Binary files /dev/null and b/repo_utils/answer_key/bench/bench13_includebed/tp-base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench13_includebed/tp-comp.vcf.gz b/repo_utils/answer_key/bench/bench13_includebed/tp-comp.vcf.gz new file mode 100644 index 00000000..de5d0fce Binary files /dev/null and b/repo_utils/answer_key/bench/bench13_includebed/tp-comp.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench13_includebed/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13_includebed/tp-comp.vcf.gz.tbi new file mode 100644 index 00000000..c8da7221 Binary files /dev/null and b/repo_utils/answer_key/bench/bench13_includebed/tp-comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench23/fn.vcf.gz b/repo_utils/answer_key/bench/bench23/fn.vcf.gz new file mode 100644 index 00000000..a8eba071 Binary files /dev/null and b/repo_utils/answer_key/bench/bench23/fn.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench23/fn.vcf.gz.tbi b/repo_utils/answer_key/bench/bench23/fn.vcf.gz.tbi new file mode 100644 index 00000000..c59089b7 Binary files /dev/null and b/repo_utils/answer_key/bench/bench23/fn.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench23/fp.vcf.gz b/repo_utils/answer_key/bench/bench23/fp.vcf.gz new file mode 100644 index 00000000..04ccd288 Binary files /dev/null and b/repo_utils/answer_key/bench/bench23/fp.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench23/fp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench23/fp.vcf.gz.tbi new file mode 100644 index 00000000..beb1b288 Binary files /dev/null and b/repo_utils/answer_key/bench/bench23/fp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench23/log.txt b/repo_utils/answer_key/bench/bench23/log.txt new file mode 100644 index 00000000..675064d9 --- /dev/null +++ b/repo_utils/answer_key/bench/bench23/log.txt @@ -0,0 +1,60 @@ +2022-12-01 18:25:59,280 [INFO] Truvari v4.0.0.dev0+detached +2022-12-01 18:25:59,281 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input2.vcf.gz -c repo_utils/test_files/variants/input3.vcf.gz -f repo_utils/test_files/references/reference.fa -o test_results/bench23/ --multimatch +2022-12-01 18:25:59,282 [INFO] Params: +{ + "base": "/data/repo_utils/test_files/variants/input2.vcf.gz", + "comp": "/data/repo_utils/test_files/variants/input3.vcf.gz", + "output": "test_results/bench23/", + "reference": "/data/repo_utils/test_files/references/reference.fa", + "debug": false, + "prog": false, + "refdist": 500, + "pctsim": 0.7, + "minhaplen": 50, + "pctsize": 0.7, + "pctovl": 0.0, + "typeignore": false, + "dup_to_ins": false, + "use_lev": false, + "chunksize": 1000, + "gtcomp": false, + "bSample": "NA12878", + "cSample": "HG00733", + "sizemin": 50, + "sizefilt": 30, + "sizemax": 50000, + "passonly": false, + "no_ref": false, + "includebed": null, + "extend": 0, + "multimatch": true +} +2022-12-01 18:25:59,454 [INFO] Zipped 3848 variants Counter({'comp': 2065, 'base': 1783}) +2022-12-01 18:25:59,455 [INFO] 15 chunks of 3848 variants Counter({'__filtered': 3816, 'comp': 21, 'base': 11}) +2022-12-01 18:25:59,460 [INFO] Stats: { + "TP-base": 7, + "TP-call": 8, + "FP": 9, + "FN": 4, + "precision": 0.47058823529411764, + "recall": 0.6363636363636364, + "f1": 0.5410628019323671, + "base cnt": 11, + "call cnt": 17, + "TP-call_TP-gt": 3, + "TP-call_FP-gt": 5, + "TP-base_TP-gt": 3, + "TP-base_FP-gt": 4, + "gt_concordance": 0.375, + "gt_matrix": { + "(1, 1)": { + "(0, 1)": 2, + "(1, 1)": 2 + }, + "(1, 0)": { + "(1, 1)": 2, + "(1, 0)": 1 + } + } +} +2022-12-01 18:25:59,556 [INFO] Finished bench diff --git a/repo_utils/answer_key/bench/bench23/params.json b/repo_utils/answer_key/bench/bench23/params.json new file mode 100644 index 00000000..fad5131b --- /dev/null +++ b/repo_utils/answer_key/bench/bench23/params.json @@ -0,0 +1 @@ +{"base": "/data/repo_utils/test_files/variants/input2.vcf.gz", "comp": "/data/repo_utils/test_files/variants/input3.vcf.gz", "output": "test_results/bench23/", "reference": "/data/repo_utils/test_files/references/reference.fa", "debug": false, "prog": false, "refdist": 500, "pctsim": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "dup_to_ins": false, "use_lev": false, "chunksize": 1000, "gtcomp": false, "bSample": "NA12878", "cSample": "HG00733", "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "includebed": null, "extend": 0, "multimatch": true} \ No newline at end of file diff --git a/repo_utils/answer_key/bench/bench23/summary.json b/repo_utils/answer_key/bench/bench23/summary.json new file mode 100644 index 00000000..16be5a31 --- /dev/null +++ b/repo_utils/answer_key/bench/bench23/summary.json @@ -0,0 +1,26 @@ +{ + "TP-base": 7, + "TP-comp": 8, + "FP": 9, + "FN": 4, + "precision": 0.47058823529411764, + "recall": 0.6363636363636364, + "f1": 0.5410628019323671, + "base cnt": 11, + "comp cnt": 17, + "TP-comp_TP-gt": 3, + "TP-comp_FP-gt": 5, + "TP-base_TP-gt": 3, + "TP-base_FP-gt": 4, + "gt_concordance": 0.375, + "gt_matrix": { + "(1, 1)": { + "(0, 1)": 2, + "(1, 1)": 2 + }, + "(1, 0)": { + "(1, 1)": 2, + "(1, 0)": 1 + } + } +} diff --git a/repo_utils/answer_key/bench/bench23/tp-base.vcf.gz b/repo_utils/answer_key/bench/bench23/tp-base.vcf.gz new file mode 100644 index 00000000..b96a8150 Binary files /dev/null and b/repo_utils/answer_key/bench/bench23/tp-base.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench23/tp-base.vcf.gz.tbi b/repo_utils/answer_key/bench/bench23/tp-base.vcf.gz.tbi new file mode 100644 index 00000000..17b08206 Binary files /dev/null and b/repo_utils/answer_key/bench/bench23/tp-base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench23/tp-comp.vcf.gz b/repo_utils/answer_key/bench/bench23/tp-comp.vcf.gz new file mode 100644 index 00000000..45c34827 Binary files /dev/null and b/repo_utils/answer_key/bench/bench23/tp-comp.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench23/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench23/tp-comp.vcf.gz.tbi new file mode 100644 index 00000000..11b31481 Binary files /dev/null and b/repo_utils/answer_key/bench/bench23/tp-comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/fn.vcf.gz b/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/fn.vcf.gz new file mode 100644 index 00000000..0fdfaa3f Binary files /dev/null and b/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/fn.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/fn.vcf.gz.tbi b/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/fn.vcf.gz.tbi new file mode 100644 index 00000000..0063092d Binary files /dev/null and b/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/fn.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/fp.vcf.gz b/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/fp.vcf.gz new file mode 100644 index 00000000..95adafae Binary files /dev/null and b/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/fp.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/fp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/fp.vcf.gz.tbi new file mode 100644 index 00000000..022dc599 Binary files /dev/null and b/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/fp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/log.txt b/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/log.txt new file mode 100644 index 00000000..1956852c --- /dev/null +++ b/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/log.txt @@ -0,0 +1,56 @@ +2022-12-02 00:27:35,835 [INFO] Truvari v4.0.0.dev0+detached +2022-12-02 00:27:35,836 [INFO] Command /usr/local/bin/truvari bench -b problem1_base.vcf.gz -c problem1_comp.vcf.gz --gtcomp -o bench/ +2022-12-02 00:27:35,837 [INFO] Params: +{ + "base": "/data/temp/problem1_base.vcf.gz", + "comp": "/data/temp/problem1_comp.vcf.gz", + "output": "bench/", + "reference": null, + "debug": false, + "prog": false, + "refdist": 500, + "pctsim": 0.7, + "minhaplen": 50, + "pctsize": 0.7, + "pctovl": 0.0, + "typeignore": false, + "dup_to_ins": false, + "use_lev": false, + "chunksize": 1000, + "gtcomp": true, + "bSample": "HG002", + "cSample": "HG002_30x.GRCh38.deepvariant.haplotagged", + "sizemin": 50, + "sizefilt": 30, + "sizemax": 50000, + "passonly": false, + "no_ref": false, + "includebed": null, + "extend": 0, + "multimatch": false +} +2022-12-02 00:27:35,879 [WARNING] Excluding 171 contigs present in comparison calls header but not base calls. +2022-12-02 00:27:35,920 [INFO] Zipped 4 variants Counter({'base': 2, 'comp': 2}) +2022-12-02 00:27:35,921 [INFO] 1 chunks of 4 variants Counter({'base': 2, 'comp': 2}) +2022-12-02 00:27:35,930 [INFO] Stats: { + "TP-base": 1, + "TP-call": 1, + "FP": 1, + "FN": 1, + "precision": 0.5, + "recall": 0.5, + "f1": 0.5, + "base cnt": 2, + "call cnt": 2, + "TP-call_TP-gt": 0, + "TP-call_FP-gt": 1, + "TP-base_TP-gt": 0, + "TP-base_FP-gt": 1, + "gt_concordance": 0.0, + "gt_matrix": { + "(1, 1)": { + "(1, 0)": 1 + } + } +} +2022-12-02 00:27:36,039 [INFO] Finished bench diff --git a/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/params.json b/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/params.json new file mode 100644 index 00000000..f631d1a1 --- /dev/null +++ b/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/params.json @@ -0,0 +1 @@ +{"base": "/data/temp/problem1_base.vcf.gz", "comp": "/data/temp/problem1_comp.vcf.gz", "output": "bench/", "reference": null, "debug": false, "prog": false, "refdist": 500, "pctsim": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "dup_to_ins": false, "use_lev": false, "chunksize": 1000, "gtcomp": true, "bSample": "HG002", "cSample": "HG002_30x.GRCh38.deepvariant.haplotagged", "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "includebed": null, "extend": 0, "multimatch": false} \ No newline at end of file diff --git a/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/summary.json b/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/summary.json new file mode 100644 index 00000000..cf334f07 --- /dev/null +++ b/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/summary.json @@ -0,0 +1,21 @@ +{ + "TP-base": 1, + "TP-comp": 1, + "FP": 1, + "FN": 1, + "precision": 0.5, + "recall": 0.5, + "f1": 0.5, + "base cnt": 2, + "comp cnt": 2, + "TP-comp_TP-gt": 0, + "TP-comp_FP-gt": 1, + "TP-base_TP-gt": 0, + "TP-base_FP-gt": 1, + "gt_concordance": 0.0, + "gt_matrix": { + "(1, 1)": { + "(1, 0)": 1 + } + } +} diff --git a/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/tp-base.vcf.gz b/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/tp-base.vcf.gz new file mode 100644 index 00000000..dfa476f8 Binary files /dev/null and b/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/tp-base.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/tp-base.vcf.gz.tbi b/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/tp-base.vcf.gz.tbi new file mode 100644 index 00000000..f855dccd Binary files /dev/null and b/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/tp-base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/tp-comp.vcf.gz b/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/tp-comp.vcf.gz new file mode 100644 index 00000000..699ed789 Binary files /dev/null and b/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/tp-comp.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/tp-comp.vcf.gz.tbi new file mode 100644 index 00000000..83c933b4 Binary files /dev/null and b/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/tp-comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench_unroll/fn.vcf.gz b/repo_utils/answer_key/bench/bench_unroll/fn.vcf.gz new file mode 100644 index 00000000..ab1b1c77 Binary files /dev/null and b/repo_utils/answer_key/bench/bench_unroll/fn.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench_unroll/fn.vcf.gz.tbi b/repo_utils/answer_key/bench/bench_unroll/fn.vcf.gz.tbi new file mode 100644 index 00000000..dbcb21c6 Binary files /dev/null and b/repo_utils/answer_key/bench/bench_unroll/fn.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench_unroll/fp.vcf.gz b/repo_utils/answer_key/bench/bench_unroll/fp.vcf.gz new file mode 100644 index 00000000..a3c15b75 Binary files /dev/null and b/repo_utils/answer_key/bench/bench_unroll/fp.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench_unroll/fp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench_unroll/fp.vcf.gz.tbi new file mode 100644 index 00000000..139dc734 Binary files /dev/null and b/repo_utils/answer_key/bench/bench_unroll/fp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench_unroll/log.txt b/repo_utils/answer_key/bench/bench_unroll/log.txt new file mode 100644 index 00000000..1153e6d2 --- /dev/null +++ b/repo_utils/answer_key/bench/bench_unroll/log.txt @@ -0,0 +1,61 @@ +2022-12-01 18:26:06,498 [INFO] Truvari v4.0.0.dev0+detached +2022-12-01 18:26:06,499 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/real_small_base.vcf.gz -c repo_utils/test_files/variants/real_small_comp.vcf.gz -o test_results/bench_unroll/ +2022-12-01 18:26:06,500 [INFO] Params: +{ + "base": "/data/repo_utils/test_files/variants/real_small_base.vcf.gz", + "comp": "/data/repo_utils/test_files/variants/real_small_comp.vcf.gz", + "output": "test_results/bench_unroll/", + "reference": null, + "debug": false, + "prog": false, + "refdist": 500, + "pctsim": 0.7, + "minhaplen": 50, + "pctsize": 0.7, + "pctovl": 0.0, + "typeignore": false, + "dup_to_ins": false, + "use_lev": false, + "chunksize": 1000, + "gtcomp": false, + "bSample": "NA12878", + "cSample": "NULL", + "sizemin": 50, + "sizefilt": 30, + "sizemax": 50000, + "passonly": false, + "no_ref": false, + "includebed": null, + "extend": 0, + "multimatch": false +} +2022-12-01 18:26:06,562 [INFO] Zipped 71 variants Counter({'base': 43, 'comp': 28}) +2022-12-01 18:26:06,563 [INFO] 45 chunks of 71 variants Counter({'base': 43, 'comp': 28}) +2022-12-01 18:26:06,567 [INFO] Stats: { + "TP-base": 18, + "TP-call": 18, + "FP": 1, + "FN": 25, + "precision": 0.9473684210526315, + "recall": 0.4186046511627907, + "f1": 0.5806451612903226, + "base cnt": 43, + "call cnt": 19, + "TP-call_TP-gt": 0, + "TP-call_FP-gt": 18, + "TP-base_TP-gt": 0, + "TP-base_FP-gt": 18, + "gt_concordance": 0.0, + "gt_matrix": { + "(0, 1)": { + "(None, None)": 9 + }, + "(1, 0)": { + "(None, None)": 3 + }, + "(1, 1)": { + "(None, None)": 6 + } + } +} +2022-12-01 18:26:06,694 [INFO] Finished bench diff --git a/repo_utils/answer_key/bench/bench_unroll/params.json b/repo_utils/answer_key/bench/bench_unroll/params.json new file mode 100644 index 00000000..e9241ab6 --- /dev/null +++ b/repo_utils/answer_key/bench/bench_unroll/params.json @@ -0,0 +1 @@ +{"base": "/data/repo_utils/test_files/variants/real_small_base.vcf.gz", "comp": "/data/repo_utils/test_files/variants/real_small_comp.vcf.gz", "output": "test_results/bench_unroll/", "reference": null, "debug": false, "prog": false, "refdist": 500, "pctsim": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "dup_to_ins": false, "use_lev": false, "chunksize": 1000, "gtcomp": false, "bSample": "NA12878", "cSample": "NULL", "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "includebed": null, "extend": 0, "multimatch": false} \ No newline at end of file diff --git a/repo_utils/answer_key/bench/bench_unroll/summary.json b/repo_utils/answer_key/bench/bench_unroll/summary.json new file mode 100644 index 00000000..75b26315 --- /dev/null +++ b/repo_utils/answer_key/bench/bench_unroll/summary.json @@ -0,0 +1,27 @@ +{ + "TP-base": 18, + "TP-comp": 18, + "FP": 1, + "FN": 25, + "precision": 0.9473684210526315, + "recall": 0.4186046511627907, + "f1": 0.5806451612903226, + "base cnt": 43, + "comp cnt": 19, + "TP-comp_TP-gt": 0, + "TP-comp_FP-gt": 18, + "TP-base_TP-gt": 0, + "TP-base_FP-gt": 18, + "gt_concordance": 0.0, + "gt_matrix": { + "(0, 1)": { + "(None, None)": 9 + }, + "(1, 0)": { + "(None, None)": 3 + }, + "(1, 1)": { + "(None, None)": 6 + } + } +} diff --git a/repo_utils/answer_key/bench/bench_unroll/tp-base.vcf.gz b/repo_utils/answer_key/bench/bench_unroll/tp-base.vcf.gz new file mode 100644 index 00000000..60c73293 Binary files /dev/null and b/repo_utils/answer_key/bench/bench_unroll/tp-base.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench_unroll/tp-base.vcf.gz.tbi b/repo_utils/answer_key/bench/bench_unroll/tp-base.vcf.gz.tbi new file mode 100644 index 00000000..b0e3d9ef Binary files /dev/null and b/repo_utils/answer_key/bench/bench_unroll/tp-base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench_unroll/tp-comp.vcf.gz b/repo_utils/answer_key/bench/bench_unroll/tp-comp.vcf.gz new file mode 100644 index 00000000..3aa1b93b Binary files /dev/null and b/repo_utils/answer_key/bench/bench_unroll/tp-comp.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench_unroll/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench_unroll/tp-comp.vcf.gz.tbi new file mode 100644 index 00000000..6107cb81 Binary files /dev/null and b/repo_utils/answer_key/bench/bench_unroll/tp-comp.vcf.gz.tbi differ diff --git a/repo_utils/test_files/answer_key/input1_collapsed.vcf b/repo_utils/answer_key/collapse/input1_collapsed.vcf similarity index 100% rename from repo_utils/test_files/answer_key/input1_collapsed.vcf rename to repo_utils/answer_key/collapse/input1_collapsed.vcf diff --git a/repo_utils/test_files/answer_key/input1_removed.vcf b/repo_utils/answer_key/collapse/input1_removed.vcf similarity index 93% rename from repo_utils/test_files/answer_key/input1_removed.vcf rename to repo_utils/answer_key/collapse/input1_removed.vcf index 36bbfe0a..4fd3a8d6 100644 --- a/repo_utils/test_files/answer_key/input1_removed.vcf +++ b/repo_utils/answer_key/collapse/input1_removed.vcf @@ -43,9 +43,9 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 -chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCATCCCCCGTCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 60 . QNAME=HG002-S9-H1-000001F;QSTART=400044;QSTRAND=+;SVTYPE=INS;SVLEN=226;PctSeqSimilarity=0.9956;PctSizeSimilarity=0.9956;PctRecOverlap=1;SizeDiff=1;StartDistance=0;EndDistance=0;TruScore=99;MatchId=4.0 GT:PL:DP 1/0:4,8,6:32,9 -chr20 642330 . G GGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597257;QSTRAND=+;SVTYPE=INS;SVLEN=66;PctSeqSimilarity=0.9576;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=-417;EndDistance=-417;TruScore=65;MatchId=6.0 GT:PL:DP 0/1:6,1,9:20,25 +chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCATCCCCCGTCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 60 . QNAME=HG002-S9-H1-000001F;QSTART=400044;QSTRAND=+;SVTYPE=INS;SVLEN=226;PctSeqSimilarity=0.9956;PctSizeSimilarity=0.9956;PctRecOverlap=1;SizeDiff=1;StartDistance=0;EndDistance=0;GTMatch=.;TruScore=99;MatchId=4.0 GT:PL:DP 1/0:4,8,6:32,9 +chr20 642330 . G GGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597257;QSTRAND=+;SVTYPE=INS;SVLEN=66;PctSeqSimilarity=0.9576;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=-417;EndDistance=-417;GTMatch=.;TruScore=65;MatchId=6.0 GT:PL:DP 0/1:6,1,9:20,25 diff --git a/repo_utils/test_files/answer_key/input2_collapsed.vcf b/repo_utils/answer_key/collapse/input2_collapsed.vcf similarity index 100% rename from repo_utils/test_files/answer_key/input2_collapsed.vcf rename to repo_utils/answer_key/collapse/input2_collapsed.vcf diff --git a/repo_utils/test_files/answer_key/input2_removed.vcf b/repo_utils/answer_key/collapse/input2_removed.vcf similarity index 96% rename from repo_utils/test_files/answer_key/input2_removed.vcf rename to repo_utils/answer_key/collapse/input2_removed.vcf index 621ca79e..6a7f3f47 100644 --- a/repo_utils/test_files/answer_key/input2_removed.vcf +++ b/repo_utils/answer_key/collapse/input2_removed.vcf @@ -43,8 +43,8 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 -chr20 642230 . T TGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTG 60 . QNAME=cluster19_000000F;QSTART=25119065;QSTRAND=-;SVTYPE=INS;SVLEN=632;PctSeqSimilarity=0.9985;PctSizeSimilarity=0.9968;PctRecOverlap=0.9621;SizeDiff=-2;StartDistance=-23;EndDistance=-23;TruScore=98;MatchId=7.0 GT:PL:AD 1/0:7,5,6:16,7 +chr20 642230 . T TGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTG 60 . QNAME=cluster19_000000F;QSTART=25119065;QSTRAND=-;SVTYPE=INS;SVLEN=632;PctSeqSimilarity=0.9985;PctSizeSimilarity=0.9968;PctRecOverlap=0.9621;SizeDiff=-2;StartDistance=-23;EndDistance=-23;GTMatch=.;TruScore=98;MatchId=7.0 GT:PL:AD 1/0:7,5,6:16,7 diff --git a/repo_utils/test_files/answer_key/input3_collapsed.vcf b/repo_utils/answer_key/collapse/input3_collapsed.vcf similarity index 100% rename from repo_utils/test_files/answer_key/input3_collapsed.vcf rename to repo_utils/answer_key/collapse/input3_collapsed.vcf diff --git a/repo_utils/test_files/answer_key/input3_removed.vcf b/repo_utils/answer_key/collapse/input3_removed.vcf similarity index 95% rename from repo_utils/test_files/answer_key/input3_removed.vcf rename to repo_utils/answer_key/collapse/input3_removed.vcf index 9c7a739d..10e14475 100644 --- a/repo_utils/test_files/answer_key/input3_removed.vcf +++ b/repo_utils/answer_key/collapse/input3_removed.vcf @@ -42,8 +42,8 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00733 -chr20 149073 . G GAATCCTGACCCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCA 60 . QNAME=cluster23_scaffold_2;QSTART=25547471;QSTRAND=-;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=0.9962;PctSizeSimilarity=1;PctRecOverlap=0.1304;SizeDiff=0;StartDistance=-60;EndDistance=-60;TruScore=70;MatchId=1.0 GT 0/1 +chr20 149073 . G GAATCCTGACCCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCA 60 . QNAME=cluster23_scaffold_2;QSTART=25547471;QSTRAND=-;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=0.9962;PctSizeSimilarity=1;PctRecOverlap=0.1304;SizeDiff=0;StartDistance=-60;EndDistance=-60;GTMatch=.;TruScore=70;MatchId=1.0 GT 0/1 diff --git a/repo_utils/test_files/answer_key/multi_collapsed_common.vcf b/repo_utils/answer_key/collapse/multi_collapsed_common.vcf similarity index 100% rename from repo_utils/test_files/answer_key/multi_collapsed_common.vcf rename to repo_utils/answer_key/collapse/multi_collapsed_common.vcf diff --git a/repo_utils/test_files/answer_key/multi_collapsed_first.vcf b/repo_utils/answer_key/collapse/multi_collapsed_first.vcf similarity index 100% rename from repo_utils/test_files/answer_key/multi_collapsed_first.vcf rename to repo_utils/answer_key/collapse/multi_collapsed_first.vcf diff --git a/repo_utils/test_files/answer_key/multi_collapsed_maxqual.vcf b/repo_utils/answer_key/collapse/multi_collapsed_maxqual.vcf similarity index 100% rename from repo_utils/test_files/answer_key/multi_collapsed_maxqual.vcf rename to repo_utils/answer_key/collapse/multi_collapsed_maxqual.vcf diff --git a/repo_utils/test_files/answer_key/multi_removed_common.vcf b/repo_utils/answer_key/collapse/multi_removed_common.vcf similarity index 87% rename from repo_utils/test_files/answer_key/multi_removed_common.vcf rename to repo_utils/answer_key/collapse/multi_removed_common.vcf index 6d3c7507..2b39d322 100644 --- a/repo_utils/test_files/answer_key/multi_removed_common.vcf +++ b/repo_utils/answer_key/collapse/multi_removed_common.vcf @@ -45,15 +45,15 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 149013 . A ACCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=127907;QSTRAND=+;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=0.9967;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=82;EndDistance=82;TruScore=66;MatchId=1.0 GT:DP:AD 1/1:35:19,16 ./.:31:21,10 1/0:17:8,9 -chr20 149073 . G GAATCCTGACCCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCA 60 . QNAME=cluster23_scaffold_2;QSTART=25547471;QSTRAND=-;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=0.9891;PctSizeSimilarity=1;PctRecOverlap=0.6812;SizeDiff=0;StartDistance=22;EndDistance=22;TruScore=89;MatchId=1.0 GT:DP:AD ./.:44:25,19 ./.:36:12,24 0/1:27:20,7 -chr20 278930 . C CGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAG 60 . QNAME=HG002-S9-H2-000001F;QSTART=232485;QSTRAND=+;SVTYPE=INS;SVLEN=184;PctSeqSimilarity=0.9866;PctSizeSimilarity=0.9787;PctRecOverlap=0.9788;SizeDiff=4;StartDistance=0;EndDistance=0;TruScore=98;MatchId=2.1 GT:DP:AD 0/1:29:9,20 ./.:22:16,6 ./.:24:5,19 -chr20 306268 . A ACCAGGCTGGAGTGCAGTGGCTCACTGCGTGGCTCGCTACAGCCTACAACTCCTGGGCTCCAGCAATCCTGCTGCCCCAGCCTCCTGTGTAACTGAGACTACAGGCACGCACCACCACACCCAGCTAATGTTTTCTTTCTTTTTTTTTTTTTTGAGATGAACTCTCACTCTGTTGC 60 . QNAME=cluster19_000000F;QSTART=25455794;QSTRAND=-;SVTYPE=INS;SVLEN=175;PctSeqSimilarity=0.9972;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=99;MatchId=4.0 GT:DP:AD ./.:33:15,18 1/1:35:11,24 ./.:34:9,25 -chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCATCCCCCGTCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 60 . QNAME=HG002-S9-H1-000001F;QSTART=400044;QSTRAND=+;SVTYPE=INS;SVLEN=226;PctSeqSimilarity=0.9956;PctSizeSimilarity=0.9956;PctRecOverlap=1;SizeDiff=1;StartDistance=0;EndDistance=0;TruScore=99;MatchId=6.0 GT:DP:AD 1/0:45:21,24 1/1:27:20,7 ./.:31:15,16 -chr20 642230 . T TGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTG 60 . QNAME=cluster19_000000F;QSTART=25119065;QSTRAND=-;SVTYPE=INS;SVLEN=632;PctSeqSimilarity=0.9985;PctSizeSimilarity=0.9968;PctRecOverlap=0.9621;SizeDiff=-2;StartDistance=-23;EndDistance=-23;TruScore=98;MatchId=8.3 GT:DP:AD ./.:35:18,17 1/0:33:10,23 ./.:44:25,19 -chr20 642330 . G GGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597257;QSTRAND=+;SVTYPE=INS;SVLEN=66;PctSeqSimilarity=0.9576;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=-417;EndDistance=-417;TruScore=65;MatchId=8.1 GT:DP:AD 0/1:18:11,7 ./.:23:10,13 ./.:25:12,13 -chr20 764537 . A AGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAT 60 . QNAME=cluster19_000000F;QSTART=24996803;QSTRAND=-;SVTYPE=INS;SVLEN=78;PctSeqSimilarity=0.9971;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=-95;EndDistance=-95;TruScore=66;MatchId=10.0 GT:DP:AD ./.:25:14,11 1/0:43:20,23 ./.:30:22,8 +chr20 149013 . A ACCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=127907;QSTRAND=+;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=0.9967;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=82;EndDistance=82;GTMatch=.;TruScore=66;MatchId=1.0 GT:DP:AD 1/1:35:19,16 ./.:31:21,10 1/0:17:8,9 +chr20 149073 . G GAATCCTGACCCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCA 60 . QNAME=cluster23_scaffold_2;QSTART=25547471;QSTRAND=-;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=0.9891;PctSizeSimilarity=1;PctRecOverlap=0.6812;SizeDiff=0;StartDistance=22;EndDistance=22;GTMatch=.;TruScore=89;MatchId=1.0 GT:DP:AD ./.:44:25,19 ./.:36:12,24 0/1:27:20,7 +chr20 278930 . C CGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAG 60 . QNAME=HG002-S9-H2-000001F;QSTART=232485;QSTRAND=+;SVTYPE=INS;SVLEN=184;PctSeqSimilarity=0.9866;PctSizeSimilarity=0.9787;PctRecOverlap=0.9788;SizeDiff=4;StartDistance=0;EndDistance=0;GTMatch=.;TruScore=98;MatchId=2.1 GT:DP:AD 0/1:29:9,20 ./.:22:16,6 ./.:24:5,19 +chr20 306268 . A ACCAGGCTGGAGTGCAGTGGCTCACTGCGTGGCTCGCTACAGCCTACAACTCCTGGGCTCCAGCAATCCTGCTGCCCCAGCCTCCTGTGTAACTGAGACTACAGGCACGCACCACCACACCCAGCTAATGTTTTCTTTCTTTTTTTTTTTTTTGAGATGAACTCTCACTCTGTTGC 60 . QNAME=cluster19_000000F;QSTART=25455794;QSTRAND=-;SVTYPE=INS;SVLEN=175;PctSeqSimilarity=0.9972;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch=.;TruScore=99;MatchId=4.0 GT:DP:AD ./.:33:15,18 1/1:35:11,24 ./.:34:9,25 +chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCATCCCCCGTCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 60 . QNAME=HG002-S9-H1-000001F;QSTART=400044;QSTRAND=+;SVTYPE=INS;SVLEN=226;PctSeqSimilarity=0.9956;PctSizeSimilarity=0.9956;PctRecOverlap=1;SizeDiff=1;StartDistance=0;EndDistance=0;GTMatch=.;TruScore=99;MatchId=6.0 GT:DP:AD 1/0:45:21,24 1/1:27:20,7 ./.:31:15,16 +chr20 642230 . T TGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTG 60 . QNAME=cluster19_000000F;QSTART=25119065;QSTRAND=-;SVTYPE=INS;SVLEN=632;PctSeqSimilarity=0.9985;PctSizeSimilarity=0.9968;PctRecOverlap=0.9621;SizeDiff=-2;StartDistance=-23;EndDistance=-23;GTMatch=.;TruScore=98;MatchId=8.3 GT:DP:AD ./.:35:18,17 1/0:33:10,23 ./.:44:25,19 +chr20 642330 . G GGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597257;QSTRAND=+;SVTYPE=INS;SVLEN=66;PctSeqSimilarity=0.9576;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=-417;EndDistance=-417;GTMatch=.;TruScore=65;MatchId=8.1 GT:DP:AD 0/1:18:11,7 ./.:23:10,13 ./.:25:12,13 +chr20 764537 . A AGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAT 60 . QNAME=cluster19_000000F;QSTART=24996803;QSTRAND=-;SVTYPE=INS;SVLEN=78;PctSeqSimilarity=0.9971;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=-95;EndDistance=-95;GTMatch=.;TruScore=66;MatchId=10.0 GT:DP:AD ./.:25:14,11 1/0:43:20,23 ./.:30:22,8 diff --git a/repo_utils/test_files/answer_key/multi_removed_first.vcf b/repo_utils/answer_key/collapse/multi_removed_first.vcf similarity index 87% rename from repo_utils/test_files/answer_key/multi_removed_first.vcf rename to repo_utils/answer_key/collapse/multi_removed_first.vcf index 01d561ca..cfccd81f 100644 --- a/repo_utils/test_files/answer_key/multi_removed_first.vcf +++ b/repo_utils/answer_key/collapse/multi_removed_first.vcf @@ -45,15 +45,15 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 149073 . G GAATCCTGACCCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCA 60 . QNAME=cluster23_scaffold_2;QSTART=25547471;QSTRAND=-;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=0.9962;PctSizeSimilarity=1;PctRecOverlap=0.1304;SizeDiff=0;StartDistance=-60;EndDistance=-60;TruScore=70;MatchId=1.0 GT:DP:AD ./.:44:25,19 ./.:36:12,24 0/1:27:20,7 -chr20 149095 . G GGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGACCCATATTTGGGAA 60 . QNAME=cluster19_000000F;QSTART=25613718;QSTRAND=-;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=0.9967;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=-82;EndDistance=-82;TruScore=66;MatchId=1.0 GT:DP:AD ./.:36:13,23 1/1:14:7,7 ./.:40:19,21 -chr20 278930 . C CGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAG 60 . QNAME=HG002-S9-H2-000001F;QSTART=232485;QSTRAND=+;SVTYPE=INS;SVLEN=184;PctSeqSimilarity=0.9866;PctSizeSimilarity=0.9787;PctRecOverlap=0.9788;SizeDiff=4;StartDistance=0;EndDistance=0;TruScore=98;MatchId=2.0 GT:DP:AD 0/1:29:9,20 ./.:22:16,6 ./.:24:5,19 -chr20 306268 . A ACCAGGCTGGAGTGCAGTGGCTCACTGCGTGGCTCGCTACAGCCTACAACTCCTGGGCTCCAGCAATCCTGCTGCCCCAGCCTCCTGTGTAACTGAGACTACAGGCACGCACCACCACACCCAGCTAATGTTTTCTTTCTTTTTTTTTTTTTTGAGATGAACTCTCACTCTGTTGC 60 . QNAME=cluster19_000000F;QSTART=25455794;QSTRAND=-;SVTYPE=INS;SVLEN=175;PctSeqSimilarity=0.9972;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=99;MatchId=4.0 GT:DP:AD ./.:33:15,18 1/1:35:11,24 ./.:34:9,25 -chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCATCCCCCGTCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 60 . QNAME=HG002-S9-H1-000001F;QSTART=400044;QSTRAND=+;SVTYPE=INS;SVLEN=226;PctSeqSimilarity=0.9956;PctSizeSimilarity=0.9956;PctRecOverlap=1;SizeDiff=1;StartDistance=0;EndDistance=0;TruScore=99;MatchId=6.0 GT:DP:AD 1/0:45:21,24 1/1:27:20,7 ./.:31:15,16 -chr20 642230 . T TGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTG 60 . QNAME=cluster19_000000F;QSTART=25119065;QSTRAND=-;SVTYPE=INS;SVLEN=632;PctSeqSimilarity=0.9985;PctSizeSimilarity=0.9968;PctRecOverlap=0.9621;SizeDiff=-2;StartDistance=-23;EndDistance=-23;TruScore=98;MatchId=8.3 GT:DP:AD ./.:35:18,17 1/0:33:10,23 ./.:44:25,19 -chr20 642330 . G GGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597257;QSTRAND=+;SVTYPE=INS;SVLEN=66;PctSeqSimilarity=0.9576;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=-417;EndDistance=-417;TruScore=65;MatchId=8.1 GT:DP:AD 0/1:18:11,7 ./.:23:10,13 ./.:25:12,13 -chr20 764537 . A AGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAT 60 . QNAME=cluster19_000000F;QSTART=24996803;QSTRAND=-;SVTYPE=INS;SVLEN=78;PctSeqSimilarity=0.9971;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=-95;EndDistance=-95;TruScore=66;MatchId=10.0 GT:DP:AD ./.:25:14,11 1/0:43:20,23 ./.:30:22,8 +chr20 149073 . G GAATCCTGACCCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCA 60 . QNAME=cluster23_scaffold_2;QSTART=25547471;QSTRAND=-;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=0.9962;PctSizeSimilarity=1;PctRecOverlap=0.1304;SizeDiff=0;StartDistance=-60;EndDistance=-60;GTMatch=.;TruScore=70;MatchId=1.0 GT:DP:AD ./.:44:25,19 ./.:36:12,24 0/1:27:20,7 +chr20 149095 . G GGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGACCCATATTTGGGAA 60 . QNAME=cluster19_000000F;QSTART=25613718;QSTRAND=-;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=0.9967;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=-82;EndDistance=-82;GTMatch=.;TruScore=66;MatchId=1.0 GT:DP:AD ./.:36:13,23 1/1:14:7,7 ./.:40:19,21 +chr20 278930 . C CGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAG 60 . QNAME=HG002-S9-H2-000001F;QSTART=232485;QSTRAND=+;SVTYPE=INS;SVLEN=184;PctSeqSimilarity=0.9866;PctSizeSimilarity=0.9787;PctRecOverlap=0.9788;SizeDiff=4;StartDistance=0;EndDistance=0;GTMatch=.;TruScore=98;MatchId=2.0 GT:DP:AD 0/1:29:9,20 ./.:22:16,6 ./.:24:5,19 +chr20 306268 . A ACCAGGCTGGAGTGCAGTGGCTCACTGCGTGGCTCGCTACAGCCTACAACTCCTGGGCTCCAGCAATCCTGCTGCCCCAGCCTCCTGTGTAACTGAGACTACAGGCACGCACCACCACACCCAGCTAATGTTTTCTTTCTTTTTTTTTTTTTTGAGATGAACTCTCACTCTGTTGC 60 . QNAME=cluster19_000000F;QSTART=25455794;QSTRAND=-;SVTYPE=INS;SVLEN=175;PctSeqSimilarity=0.9972;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch=.;TruScore=99;MatchId=4.0 GT:DP:AD ./.:33:15,18 1/1:35:11,24 ./.:34:9,25 +chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCATCCCCCGTCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 60 . QNAME=HG002-S9-H1-000001F;QSTART=400044;QSTRAND=+;SVTYPE=INS;SVLEN=226;PctSeqSimilarity=0.9956;PctSizeSimilarity=0.9956;PctRecOverlap=1;SizeDiff=1;StartDistance=0;EndDistance=0;GTMatch=.;TruScore=99;MatchId=6.0 GT:DP:AD 1/0:45:21,24 1/1:27:20,7 ./.:31:15,16 +chr20 642230 . T TGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTG 60 . QNAME=cluster19_000000F;QSTART=25119065;QSTRAND=-;SVTYPE=INS;SVLEN=632;PctSeqSimilarity=0.9985;PctSizeSimilarity=0.9968;PctRecOverlap=0.9621;SizeDiff=-2;StartDistance=-23;EndDistance=-23;GTMatch=.;TruScore=98;MatchId=8.3 GT:DP:AD ./.:35:18,17 1/0:33:10,23 ./.:44:25,19 +chr20 642330 . G GGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597257;QSTRAND=+;SVTYPE=INS;SVLEN=66;PctSeqSimilarity=0.9576;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=-417;EndDistance=-417;GTMatch=.;TruScore=65;MatchId=8.1 GT:DP:AD 0/1:18:11,7 ./.:23:10,13 ./.:25:12,13 +chr20 764537 . A AGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAT 60 . QNAME=cluster19_000000F;QSTART=24996803;QSTRAND=-;SVTYPE=INS;SVLEN=78;PctSeqSimilarity=0.9971;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=-95;EndDistance=-95;GTMatch=.;TruScore=66;MatchId=10.0 GT:DP:AD ./.:25:14,11 1/0:43:20,23 ./.:30:22,8 diff --git a/repo_utils/test_files/answer_key/multi_removed_maxqual.vcf b/repo_utils/answer_key/collapse/multi_removed_maxqual.vcf similarity index 87% rename from repo_utils/test_files/answer_key/multi_removed_maxqual.vcf rename to repo_utils/answer_key/collapse/multi_removed_maxqual.vcf index 01d561ca..cfccd81f 100644 --- a/repo_utils/test_files/answer_key/multi_removed_maxqual.vcf +++ b/repo_utils/answer_key/collapse/multi_removed_maxqual.vcf @@ -45,15 +45,15 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 149073 . G GAATCCTGACCCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCA 60 . QNAME=cluster23_scaffold_2;QSTART=25547471;QSTRAND=-;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=0.9962;PctSizeSimilarity=1;PctRecOverlap=0.1304;SizeDiff=0;StartDistance=-60;EndDistance=-60;TruScore=70;MatchId=1.0 GT:DP:AD ./.:44:25,19 ./.:36:12,24 0/1:27:20,7 -chr20 149095 . G GGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGACCCATATTTGGGAA 60 . QNAME=cluster19_000000F;QSTART=25613718;QSTRAND=-;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=0.9967;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=-82;EndDistance=-82;TruScore=66;MatchId=1.0 GT:DP:AD ./.:36:13,23 1/1:14:7,7 ./.:40:19,21 -chr20 278930 . C CGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAG 60 . QNAME=HG002-S9-H2-000001F;QSTART=232485;QSTRAND=+;SVTYPE=INS;SVLEN=184;PctSeqSimilarity=0.9866;PctSizeSimilarity=0.9787;PctRecOverlap=0.9788;SizeDiff=4;StartDistance=0;EndDistance=0;TruScore=98;MatchId=2.0 GT:DP:AD 0/1:29:9,20 ./.:22:16,6 ./.:24:5,19 -chr20 306268 . A ACCAGGCTGGAGTGCAGTGGCTCACTGCGTGGCTCGCTACAGCCTACAACTCCTGGGCTCCAGCAATCCTGCTGCCCCAGCCTCCTGTGTAACTGAGACTACAGGCACGCACCACCACACCCAGCTAATGTTTTCTTTCTTTTTTTTTTTTTTGAGATGAACTCTCACTCTGTTGC 60 . QNAME=cluster19_000000F;QSTART=25455794;QSTRAND=-;SVTYPE=INS;SVLEN=175;PctSeqSimilarity=0.9972;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=99;MatchId=4.0 GT:DP:AD ./.:33:15,18 1/1:35:11,24 ./.:34:9,25 -chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCATCCCCCGTCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 60 . QNAME=HG002-S9-H1-000001F;QSTART=400044;QSTRAND=+;SVTYPE=INS;SVLEN=226;PctSeqSimilarity=0.9956;PctSizeSimilarity=0.9956;PctRecOverlap=1;SizeDiff=1;StartDistance=0;EndDistance=0;TruScore=99;MatchId=6.0 GT:DP:AD 1/0:45:21,24 1/1:27:20,7 ./.:31:15,16 -chr20 642230 . T TGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTG 60 . QNAME=cluster19_000000F;QSTART=25119065;QSTRAND=-;SVTYPE=INS;SVLEN=632;PctSeqSimilarity=0.9985;PctSizeSimilarity=0.9968;PctRecOverlap=0.9621;SizeDiff=-2;StartDistance=-23;EndDistance=-23;TruScore=98;MatchId=8.3 GT:DP:AD ./.:35:18,17 1/0:33:10,23 ./.:44:25,19 -chr20 642330 . G GGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597257;QSTRAND=+;SVTYPE=INS;SVLEN=66;PctSeqSimilarity=0.9576;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=-417;EndDistance=-417;TruScore=65;MatchId=8.1 GT:DP:AD 0/1:18:11,7 ./.:23:10,13 ./.:25:12,13 -chr20 764537 . A AGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAT 60 . QNAME=cluster19_000000F;QSTART=24996803;QSTRAND=-;SVTYPE=INS;SVLEN=78;PctSeqSimilarity=0.9971;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=-95;EndDistance=-95;TruScore=66;MatchId=10.0 GT:DP:AD ./.:25:14,11 1/0:43:20,23 ./.:30:22,8 +chr20 149073 . G GAATCCTGACCCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCA 60 . QNAME=cluster23_scaffold_2;QSTART=25547471;QSTRAND=-;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=0.9962;PctSizeSimilarity=1;PctRecOverlap=0.1304;SizeDiff=0;StartDistance=-60;EndDistance=-60;GTMatch=.;TruScore=70;MatchId=1.0 GT:DP:AD ./.:44:25,19 ./.:36:12,24 0/1:27:20,7 +chr20 149095 . G GGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGACCCATATTTGGGAA 60 . QNAME=cluster19_000000F;QSTART=25613718;QSTRAND=-;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=0.9967;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=-82;EndDistance=-82;GTMatch=.;TruScore=66;MatchId=1.0 GT:DP:AD ./.:36:13,23 1/1:14:7,7 ./.:40:19,21 +chr20 278930 . C CGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAG 60 . QNAME=HG002-S9-H2-000001F;QSTART=232485;QSTRAND=+;SVTYPE=INS;SVLEN=184;PctSeqSimilarity=0.9866;PctSizeSimilarity=0.9787;PctRecOverlap=0.9788;SizeDiff=4;StartDistance=0;EndDistance=0;GTMatch=.;TruScore=98;MatchId=2.0 GT:DP:AD 0/1:29:9,20 ./.:22:16,6 ./.:24:5,19 +chr20 306268 . A ACCAGGCTGGAGTGCAGTGGCTCACTGCGTGGCTCGCTACAGCCTACAACTCCTGGGCTCCAGCAATCCTGCTGCCCCAGCCTCCTGTGTAACTGAGACTACAGGCACGCACCACCACACCCAGCTAATGTTTTCTTTCTTTTTTTTTTTTTTGAGATGAACTCTCACTCTGTTGC 60 . QNAME=cluster19_000000F;QSTART=25455794;QSTRAND=-;SVTYPE=INS;SVLEN=175;PctSeqSimilarity=0.9972;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch=.;TruScore=99;MatchId=4.0 GT:DP:AD ./.:33:15,18 1/1:35:11,24 ./.:34:9,25 +chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCATCCCCCGTCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 60 . QNAME=HG002-S9-H1-000001F;QSTART=400044;QSTRAND=+;SVTYPE=INS;SVLEN=226;PctSeqSimilarity=0.9956;PctSizeSimilarity=0.9956;PctRecOverlap=1;SizeDiff=1;StartDistance=0;EndDistance=0;GTMatch=.;TruScore=99;MatchId=6.0 GT:DP:AD 1/0:45:21,24 1/1:27:20,7 ./.:31:15,16 +chr20 642230 . T TGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTG 60 . QNAME=cluster19_000000F;QSTART=25119065;QSTRAND=-;SVTYPE=INS;SVLEN=632;PctSeqSimilarity=0.9985;PctSizeSimilarity=0.9968;PctRecOverlap=0.9621;SizeDiff=-2;StartDistance=-23;EndDistance=-23;GTMatch=.;TruScore=98;MatchId=8.3 GT:DP:AD ./.:35:18,17 1/0:33:10,23 ./.:44:25,19 +chr20 642330 . G GGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597257;QSTRAND=+;SVTYPE=INS;SVLEN=66;PctSeqSimilarity=0.9576;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=-417;EndDistance=-417;GTMatch=.;TruScore=65;MatchId=8.1 GT:DP:AD 0/1:18:11,7 ./.:23:10,13 ./.:25:12,13 +chr20 764537 . A AGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAT 60 . QNAME=cluster19_000000F;QSTART=24996803;QSTRAND=-;SVTYPE=INS;SVLEN=78;PctSeqSimilarity=0.9971;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=-95;EndDistance=-95;GTMatch=.;TruScore=66;MatchId=10.0 GT:DP:AD ./.:25:14,11 1/0:43:20,23 ./.:30:22,8 diff --git a/repo_utils/answer_key/consistency/consistency.json b/repo_utils/answer_key/consistency/consistency.json new file mode 100644 index 00000000..80fd27ba --- /dev/null +++ b/repo_utils/answer_key/consistency/consistency.json @@ -0,0 +1,89 @@ +{ + "vcfs": [ + "repo_utils/test_files/variants/input1.vcf.gz", + "repo_utils/test_files/variants/input2.vcf.gz", + "repo_utils/test_files/variants/input3.vcf.gz" + ], + "total_calls": 3513, + "num_vcfs": 3, + "vcf_counts": { + "repo_utils/test_files/variants/input1.vcf.gz": 2151, + "repo_utils/test_files/variants/input2.vcf.gz": 1783, + "repo_utils/test_files/variants/input3.vcf.gz": 2065 + }, + "shared": [ + { + "vcf_count": 3, + "num_calls": 701, + "call_pct": 0.1995445488186735 + }, + { + "vcf_count": 2, + "num_calls": 1084, + "call_pct": 0.3085681753487048 + }, + { + "vcf_count": 1, + "num_calls": 1728, + "call_pct": 0.4918872758326217 + } + ], + "detailed": [ + { + "group": "111", + "total": 701, + "total_pct": 0.1995445488186735, + "repo_utils/test_files/variants/input1.vcf.gz": 0.32589493258949326, + "repo_utils/test_files/variants/input2.vcf.gz": 0.393157599551318, + "repo_utils/test_files/variants/input3.vcf.gz": 0.3394673123486683 + }, + { + "group": "001", + "total": 645, + "total_pct": 0.18360375747224594, + "repo_utils/test_files/variants/input1.vcf.gz": 0, + "repo_utils/test_files/variants/input2.vcf.gz": 0, + "repo_utils/test_files/variants/input3.vcf.gz": 0.31234866828087166 + }, + { + "group": "100", + "total": 598, + "total_pct": 0.17022487902077996, + "repo_utils/test_files/variants/input1.vcf.gz": 0.2780102278010228, + "repo_utils/test_files/variants/input2.vcf.gz": 0, + "repo_utils/test_files/variants/input3.vcf.gz": 0 + }, + { + "group": "101", + "total": 487, + "total_pct": 0.1386279533162539, + "repo_utils/test_files/variants/input1.vcf.gz": 0.22640632264063226, + "repo_utils/test_files/variants/input2.vcf.gz": 0, + "repo_utils/test_files/variants/input3.vcf.gz": 0.2358353510895884 + }, + { + "group": "010", + "total": 485, + "total_pct": 0.13805863933959578, + "repo_utils/test_files/variants/input1.vcf.gz": 0, + "repo_utils/test_files/variants/input2.vcf.gz": 0.27201346045989905, + "repo_utils/test_files/variants/input3.vcf.gz": 0 + }, + { + "group": "110", + "total": 365, + "total_pct": 0.10389980074010817, + "repo_utils/test_files/variants/input1.vcf.gz": 0.1696885169688517, + "repo_utils/test_files/variants/input2.vcf.gz": 0.2047111609646663, + "repo_utils/test_files/variants/input3.vcf.gz": 0 + }, + { + "group": "011", + "total": 232, + "total_pct": 0.06604042129234272, + "repo_utils/test_files/variants/input1.vcf.gz": 0, + "repo_utils/test_files/variants/input2.vcf.gz": 0.13011777902411667, + "repo_utils/test_files/variants/input3.vcf.gz": 0.11234866828087167 + } + ] +} diff --git a/repo_utils/answer_key/consistency/consistency.txt b/repo_utils/answer_key/consistency/consistency.txt new file mode 100644 index 00000000..b7a25946 --- /dev/null +++ b/repo_utils/answer_key/consistency/consistency.txt @@ -0,0 +1,25 @@ +# +# Total 3513 calls across 3 VCFs +# +#File NumCalls +repo_utils/test_files/variants/input1.vcf.gz 2151 +repo_utils/test_files/variants/input2.vcf.gz 1783 +repo_utils/test_files/variants/input3.vcf.gz 2065 +# +# Summary of consistency +# +#VCFs Calls Pct +3 701 19.95% +2 1084 30.86% +1 1728 49.19% +# +# Breakdown of VCFs' consistency +# +#Group Total TotalPct PctOfFileCalls +111 701 19.95% 32.59% 39.32% 33.95% +001 645 18.36% 0% 0% 31.23% +100 598 17.02% 27.80% 0% 0% +101 487 13.86% 22.64% 0% 23.58% +010 485 13.81% 0% 27.20% 0% +110 365 10.39% 16.97% 20.47% 0% +011 232 6.60% 0% 13.01% 11.23% diff --git a/repo_utils/answer_key/divide/divided/multi_00000000.vcf.gz 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b/repo_utils/answer_key/divide/divided/multi_00000022.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/help.txt b/repo_utils/answer_key/help.txt new file mode 100644 index 00000000..b236ac8f --- /dev/null +++ b/repo_utils/answer_key/help.txt @@ -0,0 +1,24 @@ +usage: truvari [-h] CMD ... + +Truvari v4.0.0 Structural Variant Benchmarking and Annotation + +Available commands: + bench Performance metrics from comparison of two VCFs + collapse Collapse possibly redundant VCF entries + anno Annotate a VCF + consistency Consistency report between multiple VCFs + vcf2df Turn a VCF into a pandas DataFrame + segment Normalization of SVs into disjointed genomic regions + stratify Count variants per-region in vcf + divide Divide a VCF into independent shards + phab Variant harmonization using MSA + refine Automated bench result refinement with phab + version Print the Truvari version and exit + +positional arguments: + CMD Command to execute + OPTIONS Options to pass to the command + +options: + -h, --help show this help message and exit + diff --git a/repo_utils/test_files/answer_key/help_error.txt b/repo_utils/answer_key/help_error.txt similarity index 100% rename from repo_utils/test_files/answer_key/help_error.txt rename to repo_utils/answer_key/help_error.txt diff --git a/repo_utils/answer_key/phab/phab_result.vcf.gz b/repo_utils/answer_key/phab/phab_result.vcf.gz new file mode 100644 index 00000000..c6f9e508 Binary files /dev/null and b/repo_utils/answer_key/phab/phab_result.vcf.gz differ diff --git a/repo_utils/answer_key/phab/phab_result.vcf.gz.tbi b/repo_utils/answer_key/phab/phab_result.vcf.gz.tbi new file mode 100644 index 00000000..a912db09 Binary files /dev/null and b/repo_utils/answer_key/phab/phab_result.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/phab/phab_result/base.vcf.gz b/repo_utils/answer_key/phab/phab_result/base.vcf.gz new file mode 100644 index 00000000..c514c58a Binary files /dev/null and b/repo_utils/answer_key/phab/phab_result/base.vcf.gz differ diff --git a/repo_utils/answer_key/phab/phab_result/base.vcf.gz.tbi b/repo_utils/answer_key/phab/phab_result/base.vcf.gz.tbi new file mode 100644 index 00000000..55e85aa6 Binary files /dev/null and b/repo_utils/answer_key/phab/phab_result/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/phab/phab_result/comp.vcf.gz b/repo_utils/answer_key/phab/phab_result/comp.vcf.gz new file mode 100644 index 00000000..b282d4d4 Binary files /dev/null and b/repo_utils/answer_key/phab/phab_result/comp.vcf.gz differ diff --git a/repo_utils/answer_key/phab/phab_result/comp.vcf.gz.tbi b/repo_utils/answer_key/phab/phab_result/comp.vcf.gz.tbi new file mode 100644 index 00000000..bce32528 Binary files /dev/null and b/repo_utils/answer_key/phab/phab_result/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/phab/phab_result/haps.fa b/repo_utils/answer_key/phab/phab_result/haps.fa new file mode 100644 index 00000000..97961a9e --- /dev/null +++ b/repo_utils/answer_key/phab/phab_result/haps.fa @@ -0,0 +1,2568 @@ +>ref_chr1_600_1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG002_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG002_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG005_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG005_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATGCATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATTATATATATTATATATATTATATATTATATAATATA +TAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAATA +TATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTATA +TATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATA +ATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATAT +ATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCG +GCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG00096_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG00096_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG00171_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG00171_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG00438_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATATTATAATA +TATAATTATATAATATATAATTATATATTATAATATATAATTATATATAATTATATATAT +AATTAATTATAATTAATTATATTTATATATTATATATATAATTATATGTAAATATAATTA +TATATATTATATATAATATATATAATAAATATAATTATATATATAATATATATTATATAT +ATTATATATATTATATATATTATATATTATATAATATACATAATTTATATATATTGTATA +TTATATAATATATAATATATAATATATATAATATATATAATTATAATATATAATTGTATA +TTATAATTATATAATATATAATTATAATATACAATTATATATTATATAATATATAATTAT +ATATAATAAAATTATATATAATTATATATAATTATATATAATATAATTATATATAATTGT +ATATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATAT +AATTATATATATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATT +GTATATATAATTATATATATAATATATACATATATATTTTTTCGAGAAAGAGTCTTTCTC +TGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCACCTCCCAG +GTTCATGCCATTCTCCTGCCTC +>HG00438_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG00512_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATATTATAATA +TATAATTATATAATATATAATTATATATTATAATATATAATTATATATAATTATATATAT +AATTAATTATAATTAATTATATTTATATATTATATATATAATTATATGTAAATATAATTA +TATATATTATATATAATATATATAATAAATATAATTATATATATAATATATATTATATAT +ATTATATATATTATATATATTATATATTATATAATATATAATATACATAATTTATATATA +TTGTATATTATATAATATATAATATATAATATATATAATATATATAATTATAATATATAA +TTGTATATTATAATTATATAATATATAATTATAATATACAATTATATATTATATAATATA +TAATTATATATAATAAAATTATATATAATTATATATAATTATATATAATATAATTATATA +TAATTGTATATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTG +TATATATAATTATATATATATTAATATATAATTGTATATATAATTATATATATATTAATA +TATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCGAGAAAGAGT +CTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCAC +CTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG00512_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATTATTATATATATATTATATATATTATATATATTATATATTATATAAT +ATATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATA +ATATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATT +ATATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG00513_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG00513_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG00514_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG00514_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG00621_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG00621_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +AAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATATAATTATATATATAATT +AATTATAATTAATTATATTTATATATTATATATAATTATATGTAAATATAATTATATATA +TTATATATAATATATAATAAATATAATTATATATATAATATATATTATATATATATTATA +TATATTATATATATTATATATTATATAATATATAATATACATAATTTATATATAGTATAT +TATATAATATATAATATATAATATATATAATATATATAATTATAATATATAATTATATAT +AATAAAATTATATATAATTATATATAATTATATATATTATATATAATATAATTATATATA +ATTGTATATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTA +TATATAATTATATATATAATATATACATATATATTTTTTCGAGAAAGAGTCTTTCTCTGT +CACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCACCTCCCAGGTT +CATGCCATTCTCCTGCCTC +>HG00673_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG00673_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATATTATAATA +TATAATTATATAATATATAATTATATATTATAATATATAATTATATATAATTATATATAT +AATTAATTATAATTAATTATATTTATATATTATATATATAATTATATGTAAATATAATTA +TATATATTATATATAATATATATAATAAATATAATTATATATATAATATATATTATATAT +ATTATATATATTATATATATTATATATTATATAATATACATAATTTATATATATTGTATA +TTATATAATATATAATATATAATATATATAATATATATAATTATAATATATAATTGTATA +TTATAATTATATAATATATAATTATAATATACAATTATATATTATATAATATATAATTAT +ATATAATAAAATTATATATAATTATATATAATTATATATAATATAATTATATATAATTGT +ATATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATAT +AATTATATATATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATT +GTATATATAATTATATATATAATATATACATATATATTTTTTCGAGAAAGAGTCTTTCTC +TGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCACCTCCCAG +GTTCATGCCATTCTCCTGCCTC +>HG00731_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG00731_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +AAATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG00732_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG00732_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +AAATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG00733_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +AAATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG00733_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG00735_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAAATAATTATATATATATTAAT +ATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATAT +ATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAA +TTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATA +TTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGG +CTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG00735_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATATATAATATATAATTATAT +TATATATTATATATAAATATATAATGTATTATACATATATAATTATATAAATTATGTATG +TATTATATAATTTTATATATGTATATATATGTTTATATATGTATATATAATTATATATGT +ATTATAATGTATTATATAATTGTATAATATAATATATAATAATATAATATATAATTATTT +ATTATAATATATAATTATATAATATATAATTATATTATTATAATATATAATTATATATAA +TTATATATAATTAATTATAATTAACTATATTTATATATTATATATAATTATATGTAAATA +TATATATATATAATTATATATTATATAATATATAATATATAATATATAATATATATAATT +ATAATATATAATTGTATATTATATATTATATAATATATAATTGTATATTATATATTATAT +AATATATAATATATATAATTATAATATATAATTGTATATTATAATTATATAATATATAAT +TATAATATACAATTATATATTATATAATATATAATTGTATATTATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATATTAATATATAATTGTAT +ATATAATTTTATATATATTAATATATAATTGTATATATAATTATATATATATTAATATAT +AATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAT +TAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTAT +ATATATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATAT +ATAATTATATATATAATATATACATATATATTTTTTCGAGAAAGAGTCTTTCTCTGTCAC +CCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCACCTCCCAGGTTCAT +GCCATTCTCCTGCCTC +>HG00741_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +AAATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG00741_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG00864_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATATATAATATATAATTATAT +TATATATTATATATAAATATATAATGTATTATACATATATAATTATATAAATTATGTATG +TATTATATAATTTTATATATGTATATATATGTTTATATATGTATATATAATTATATATGT +ATTATAATGTATTATATAATTGTATAATATAATATATAATAATATAATATATAATTATTT +ATTATAATATATAATTATATAATATATAATTATATTATTATAATATATAATTATATATAA +TTATATATAATTAATTATAATTAACTATATTTATATATTATATATAATTATATGTAAATA +TATATATATATAATTATATATTATATAATATATAATATATAATATATAATATATATAATT +ATAATATATAATTGTATATTATATATTATATAATATATAATATATATAATTATAATATAT +AATTGTATATTATAATTATATAATATATAATTATAATATACAATTATATATTATATAATA +TATAATTGTATATTATAATTATATATAATTATATATAATTATATATAATATAATTATATA +TAATTATATATAATATAATTATATATAATTGTATATATATTAATATATAATTGTATATAT +AATTATATATATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATT +GTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATATATATTAAT +ATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG00864_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01071_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATATT +ATAATAATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01071_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01106_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01106_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATATT +ATAATAATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01109_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATATTATAATA +TATAATTATATAATATATAATTATATATTATAATATATAATTATATATAATTATATATAT +AATTAATTATAATTAATTATATTTATATATTATATATATAATTATATGTAAATATAATTA +TATATATTATATATAATATATATAATAAATATAATTATATATATAATATATATTATATAT +ATTATATATATTATATATATTATATATTATATAATATATAATATACATAATTTATATATA +TTGTATATTATATAATATATAATATATAATATATATAATATATATAATTATAATATATAA +TTGTATATTATAATTATATAATATATAATTATAATATACAATTATATATTATATAATATA +TAATTATATATAATAAAATTATATATAATTATATATAATTATATATAATATAATTATATA +TAATTGTATATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTG +TATATATAATTATATATATATTAATATATAATTGTATATATAATTATATATATATTAATA +TATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATATA +TAATATATACATATATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTG +CAGTGGCACAATCTCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGC +CTC +>HG01109_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATATATTATATATTATATATA +ATATATAATTATATTATATATTATATATAATATATAATTATATTATATATTATATATAAT +ATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTTATAT +ATGTATATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATA +ATAATATAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATATT +ATAATATATAATTATATATAATTATATATATAATTATATATATAATTAATTATAATTAAT +TATATTTATATATTATATATAATTATATGTAAATATAATTATATATATTATATATTATAT +ATAATATATTATATATATAATATATATATATTATATAATATATATAAATTATATATATTA +TATATTATATAATATATAATATATAATATATATAATTATAATATATAATTGTATATTATA +TATTATATAATATATAATTATAATATACAATTATATATTATATAATATATAATTATATAT +TATATAATATATAATTATATATAATATAATTATATATAATTGTATATATATTAATATATA +ATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATATATATT +AATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCGAGAAA +GAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCT +CCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01114_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01114_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAAATAATATATAATTATAATAT +ACAATTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATA +ATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATT +ATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATT +TTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCT +CACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01123_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01123_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01175_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATATTATAATA +TATAATTATATAATATATAATTATATATTATAATATATAATTATATATAATTATATATAT +AATTAATTATAATTAATTATATTTATATATTATATATATAATTATATGTAAATATAATTA +TATATATTATATATAATATATATAATAAATATAATTATATATATAATATATATTATATAT +ATTATATATATTATATATTATATAATATATAATATACATAATTTATATATATTGTATATT +ATATAATATATAATATATAATATATATAATATATATAATTATAATATATAATTGTATATT +ATAATTATATAATATATAATTATAATATACAATTATATATTATATAATATATAATTATAT +ATAATAAAATTATATATAATTATATATAATTATATATAATATAATTATATATAATTGTAT +ATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAA +TTATATATATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGT +ATATATAATTATATATATAATATATACATATATATTTTTTCGAGAAAGAGTCTTTCTCTG +TCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCACCTCCCAGGT +TCATGCCATTCTCCTGCCTC +>HG01175_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAAATAATTATATATATATTAAT +ATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATAT +ATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAA +TTATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATT +TTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCT +CACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01243_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATTAT +TATAATATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01243_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATTAT +TATAATATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01258_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01258_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATATATAATATATAATTATAT +TATATATTATATATAAATATATAATGTATTATACATATATAATTATATAAATTATGTATG +TATTATATAATTTTATATATGTATATATATGTTTATATATGTATATATAATTATATATGT +ATTATAATGTATTATATAATTGTATAATATAATATATAATAATATAATATATAATTATTT +ATTATAATATATAATTATATAATATATAATTATATTATTATAATATATAATTATATATAA +TTATATATATAATTAATTATAATTAATTATATTTATATATTATATATAATTATATGTAAA +TATATATATATATAATTATATATTATATAATATATAATATATAATATATAATATATAATA +TATATAATTATAATATATAATTGTATATTATATATTATATAATATATAATATATATAATT +ATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAATTATATAT +TATATAATATATAATTGTATATTATAATTATATATAATTATATATAATTATATATAATAT +AATTATATATAATTGTATATATATTAATATATAATTGTATATATAATTATATATATATTA +ATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATAT +ATATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATAT +AATTATATATATAATATATACATATATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCC +ACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGC +CATTCTCCTGCCTC +>HG01358_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATATATAATATATAATTATAT +TATATATTATATATAAATATATAATGTATTATACATATATAATTATATAAATTATGTATG +TATTATATAATTTTATATATGTATATATATGTTTATATATGTATATATAATTATATATGT +ATTATAATGTATTATATAATTGTATAATATAATATATAATAATATAATATATAATTATTT +ATTATAATATATAATTATATAATATATAATTATATTATTATAATATATAATTATATATAA +TTATATATATAATTAATTATAATTAATTATATTTATATATTATATATAATTATATGTAAA +TATATATATATATAATTATATATTATATAATATATAATATATAATATATAATATATAATA +TATATAATTATAATATATAATTGTATATTATATATTATATAATATATAATATATATAATT +ATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAATTATATAT +TATATAATATATAATTGTATATTATAATTATATATAATTATATATAATTATATATAATAT +AATTATATATAATTGTATATATATTAATATATAATTGTATATATAATTATATATATATTA +ATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATAT +ATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTT +CGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACT +GCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01358_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAAATAATTATATATATATTAAT +ATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATAT +ATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAA +TTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATA +TTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGG +CTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01361_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +AAATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01361_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01505_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAAATAATTATATATATATTAAT +ATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATAT +ATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAA +TTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATA +TTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGG +CTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01505_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01596_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01596_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01891_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATTAT +TATAATATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01891_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATTTATTATAATA +TATAATTATATAATATATAATTATATTATATAATATATAATTATATATAATTATATATAT +AATTAATTATAATTAATTATATTTATATATTATATATATAATTATATGTAAATATAATTA +TATATATTATATATAATATATATAATAAATATAATTATATATATAATATATATTATATAT +ATATTATATATATTATATATATTATATATTATATAATATATAATATACATAATTTATATA +TATTGTATATTATATAATATATAATATATAATATATATAATATATATAATTATAATATAT +AATTGTATATTATAATTATATAATATATAATTATAATATACAATTATATATTATATAATA +TATAATTATATATAATAAAATTATATATAATTATATATAATTATATATAATATAATTATA +TATAATTGTATATATTAATATATAATTGTATATATAATTATATATATATTAATATATAAT +TGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATAT +ATACATATATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGG +CACAATCTCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01928_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01928_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAAATAATTATATATATATTAAT +ATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATAT +ATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAA +TTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATA +TTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGG +CTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01952_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAAATAATTATATATATATTAAT +ATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATAT +ATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAA +TTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATA +TTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGG +CTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01952_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01978_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG01978_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATATATAATATATAATTATAT +TATATATTATATATAAATATATAATGTATTATACATATATAATTATATAAATTATGTATG +TATTATATAATTTTATATATGTATATATATGTTTATATATGTATATATAATTATATATGT +ATTATAATGTATTATATAATTGTATAATATAATATATAATAATATAATATATAATTATTT +ATTATAATATATAATTATATAATATATAATTATATAATTATAATATATAATTATATATAA +TTATATATATAATTAATTATAATTAATTATATTTATATATTATATATAATTATATGTAAA +TATATATATATATAATTATATATTATATAATATATAATATATAATATATAATATATAATA +TATATAATTATAATATATAATTGTATATTATATATTATATAATATATAATATATATAATT +ATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAATTATATAT +TATATAATATATAATTGTATATTATAATTATATATAATTATATATAATTATATATAATAT +AATTATATATAATTGTATATATATTAATATATAATTGTATATATAATTATATATATATTA +ATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATAT +ATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTT +CGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACT +GCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02011_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATTAT +TATAATATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02011_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAAATAATTATATATATATTAAT +ATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATAT +ATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAA +TTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATA +TTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGG +CTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02055_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATTAT +TATAATATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02055_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATTAT +TATAATATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02080_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAAATAATTATATATATATTAAT +ATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATAT +ATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAA +TTATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATT +TTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCT +CACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02080_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02109_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATTAT +TATAATATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02109_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +AAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATA +TAATATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATAT +TATATATATAATTATATGTAAATATAATTATATATATTATATATAATATATATAATAAAT +ATAATTATATATATAATATATATTATATATATATTATATATATTATATATATTATATATT +ATATAATATATAATATACATAATTTATATATATTGTATATTATATAATATATAATATATA +ATATATATAATATATATAATTATAATATATAATTGTATATTATAATTATAATTATAATAT +ACAATTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATA +ATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATT +ATATATATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTAT +ATATAATTATATATATAATATATACATATATATTTTTTCGAGAAAGAGTCTTTCTCTGTC +ACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCACCTCCCAGGTTC +ATGCCATTCTCCTGCCTC +>HG02145_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATAAAATTATATATAATTATATATAATTATATATAATTATATATAATATAATTA +TATATAATTGTATATATTAATATATAATTGTATATATAATTATATATATATTAATATATA +ATTGTATATATAATTATATATATAATATATACATATATATTTTTTCGAGAAAGAGTCTTT +CTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCACCTCC +CAGGTTCATGCCATTCTCCTGCCTC +>HG02145_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02148_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02148_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAAATAATTATATATATATTAAT +ATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATAT +ATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAA +TTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATA +TTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGG +CTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02257_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAAATAATTATATATATATTAAT +ATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATAT +ATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAA +TTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATA +TTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGG +CTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02257_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATTAT +TATAATATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02486_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATATATAATATATAATTATAT +TATATATTATATATAAATATATAATGTATTATACATATATAATTATATAAATTATGTATG +TATTATATAATTTTATATATGTATATATATGTTTATATATGTATATATAATTATATATGT +ATTATAATGTATTATATAATTGTATAATATAATATATAATAATATAATATATAATTATTT +ATTATAATATATAATTATATAATATATAATTATATTATTATAATATATAATTATATATAA +TTATATATATAATTAATTATAATTAATTATATTTATATATTATATATAATTATATGTAAA +TATATATATATAAAATTATATATTATATAATATATAATATATAATATATAATATATAATA +TATATAATTATAATATATAATTGTATATTATATATTATATAATATATAATATATATAATT +ATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAATTATATAT +TATATAATATATAATTGTATATTATAATTATATATAATTATATATAATTATATATAATAT +AATTATATATAATTGTATATATATTAATATATAATTGTATATATAATTATATATATATTA +ATATATAATTGTATATATAATTATATATATTAATATATAATTGTATATATAATTATATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02486_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATATAATTATATATAA +TATAATTATATATAATTGTATATATATTAATATATAATTGTATATATAATTATATATATA +TTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTA +TATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTT +TTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTC +ACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02492_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATAATATATTATATATTATATAATATATA +ATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAATATA +TATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTATATA +TAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAA +TTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATA +TTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGG +CTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02492_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02559_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATATT +ATAATAATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02559_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATATTATAATA +TATAATTATATAATATATAATTATATATTATAATATATAATTATATATAATTATATATAT +AATTAATTATAATTAATTATATTTATATATTATATATATAATTATATGTAAATATAATTA +TATATATTATATATAATATATATAATAAATATAATTATATATATAATATATATTATATAT +ATTATATATATTATATATTATATAATATATAATATACATAATTTATATATATTGTATATT +ATATAATATATAATATATAATATATATAATATATATAATTATAATATATAATTGTATATT +ATAATTATATAATATATAATTATAATATACAATTATATATTATATAATATATAATTATAT +ATAATAAAATTATATATAATTATATATAATTATATATAATATAATTATATATAATTGTAT +ATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAA +TTATATATATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGT +ATATATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATA +CATATATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCAC +AATCTCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02572_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATATATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATATAATTATATATATAATT +AATTATAATTAATTATATTTATATATTATATATAATTATATGTAAATATAATTATATATA +TTATATATAATATATAATAAATATAATTATATATATAATATATATTATATATATTATATA +TTATATATTATATATTATATAATATACATAATTTATATATATTGTATATTATATAATATA +TAATATATAATATATAATATATATAATTATAATATATAATTGTATATTATAATTATATAA +TATATAATTATAATATACAATTATATATTATATAATATATAATTATATATAATAAAATTA +TATATAATTATATATAATTATATATAATATAATTATATATAATTGTATATATTAATATAT +AATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAA +TATATACATATATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAG +TGGCACAATCTCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02572_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATTTATTATAATA +TATAATTATATAATATATAATTATATTATATAATATATAATTATATATAATTATATATAT +AATTAATTATAATTAATTATATTTATATATTATATATATAATTATATGTAAATATAATTA +TATATATTATATATAATATATATAATAAATATAATTATATATATAATATATATTATATAT +ATATTATATATATTATATATATTATATATTATATAATATATAATATACATAATTTATATA +TATTGTATATTATATAATATATAATATATAATATATATAATATATATAATTATAATATAT +AATTGTATATTATAATTATATAATATATAATTATAATATACAATTATATATTATATAATA +TATAATTATATATAATAAAATTATATATAATTATATATAATTATATATAATATAATTATA +TATAATTGTATATATTAATATATAATTGTATATATAATTATATATATATTAATATATAAT +TGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATAT +ATACATATATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGG +CACAATCTCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02587_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATTAT +TATAATATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02587_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATTAT +TATAATATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02622_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATTAT +TATAATATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02622_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATATATTATATATTATTATAT +AATATATAATTATATTATATATTATATATAATATATAATTATATTATATATTATATATAA +TATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTTATA +TATGTATATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATAT +AATAATATAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATAT +TATAATATATAATTATATATAATTATATATATAATTATATATATAATTAATTATAATTAA +TTATATTTATATATTATATATAATTATATGTAAATATAATTATATATATTATATATTATA +TATAATATATTATATATATAATATATATATATTATATAATATATATAAATTATATATATT +ATATATTATATAATATATAATATATAATATATATAATTATAATATATAATTGTATATTAT +ATATTATATAATATATAATTATAATATACAATTATATATTATATAATATATAATTATATA +TTATATAATATATAATTATATATAATATAATTATATATAATTGTATATATATTAATATAT +AATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAT +TAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCGAGAA +AGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGC +TCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02630_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAATATACA +TAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATATATATAA +TTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAATTATAT +ATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTATATATA +ATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATATATATTA +ATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCGAGAAAG +AGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTC +CACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02630_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATATT +ATAATAATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02717_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATATATAATTATAT +ATATAATATATATTATATATATATTATATATATTATATATTATATAATATATAATATACA +TAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATTATAATAT +ATAATTGTATATTATAATTATATAATATATAATTATAATATACAATTATATATTATATAA +TATATAATTATATATAATAAAATTATATATAATTATATATAATTATATATAATATAATTA +TATATAATTGTATATATTAATATATAATTGTATATATAATTATATATATATTAATATATA +ATTGTATATATAATTATATATATTAATATATAATTGTATATATAATTATATATATAATAT +ATACATATATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGG +CACAATCTCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02717_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATATATAATTATAT +ATATAATATATATTATATATATATTATATATATTATATATTATATAATATATAATATACA +TAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATTATAATAT +ATAATTGTATATTATAATTATATAATATATAATTATAATATACAATTATATATTATATAA +TATATAATTATATATAATAAAATTATATATAATTATATATAATTATATATAATATAATTA +TATATAATTGTATATATTAATATATAATTGTATATATAATTATATATATATTAATATATA +ATTGTATATATAATTATATATATTAATATATAATTGTATATATAATTATATATATAATAT +ATACATATATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGG +CACAATCTCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02723_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTGTATATATATTAATATAT +AATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAT +TAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTAT +ATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTT +TTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCA +CTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02723_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +AAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTATA +TAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAATT +ATATAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATATA +ATATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTA +TATATATAATTATATGTAAATATAATTATATATATTATATATAATATATATAATAAATAT +AATTATATATATAATATATATTATATATATATTATATATATTATATATATTATATATTAT +ATAATATATAATATACATAATTTATATATATTGTATATTATATAATATATAATATATAAT +ATATATAATATATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATT +ATAATATACAATTATATATTATATAATATATAATTATATATAATAAAATTATATATAATT +ATATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATA +TATAATTATATATATATTAATATATAATTGTATATATAATTATATATATATTAATATATA +ATTGTATATATAATTATATATATAATATATACATATATATTTTTTCGAGAAAGAGTCTTT +CTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCACCTCC +CAGGTTCATGCCATTCTCCTGCCTC +>HG02818_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTTAT +ATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTA +TATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAAT +ATATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATA +ATATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATT +ATATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATA +TATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACAT +ATATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAAT +CTCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02818_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAAATAATTATATATATATTAAT +ATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATAT +ATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAA +TTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATA +TTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGG +CTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02886_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAAATAATTATATATATATTAAT +ATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATAT +ATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAA +TTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATA +TTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGG +CTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG02886_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATATATAATATATAATTATAT +TATATATTATATATAAATATATAATGTATTATACATATATAATTATATAAATTATGTATG +TATTATATAATTTTATATATGTATATATATGTTTATATATGTATATATAATTATATATGT +ATTATAATGTATTATATAATTGTATAATATAATATATAATAATATAATATATAATTATTT +ATTATAATATATAATTATATAATATATAATTATATTATTATAATATATAATTATATATAA +TTATATATATAATTAATTATAATTAATTATATTTATATATTATATATAATTATATGTAAA +TATATATATATAATTATATATTATATAATATATAATATATAATATATAATATATAATATA +TATAATTATAATATATAATTGTATATTATATATTATATAATATATAATATATATAATTAT +AATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAATTATATATTA +TATAATATATAATTGTATATTATAATTATATATAATTATATATAATTATATATAATATAA +TTATATATAATTGTATATATATTAATATATAATTGTATATATAATTATATATATATTAAT +ATATAATTGTATATATAATTATATATATTAATATATAATTGTATATATAATTATATATAT +ATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCGAG +AAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAA +GCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG03009_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATATTATAATA +TATAATTATATAATATATAATTATATATTATAATATATAATTATATATAATTATATATAT +AATTAATTATAATTAATTATATTTATATATTATATATATAATTATATGTAAATATAATTA +TATATATTATATATAATATATATAATAAATATAATTATATATATAATATATATTATATAT +ATTATATATATTATATATATTATATATTATATAATATATAATATACATAATTTATATATA +TTGTATATTATATAATATATAATATATAATATATATAATATATATAATTATAATATATAA +TTGTATATTATAATTATATAATATATAATTATAATATACAATTATATATTATATAATATA +TAATTATATATAATAAAATTATATATAATTATATATAATTATATATAATATAATTATATA +TAATTGTATATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTG +TATATATAATTATATATATATTAATATATAATTGTATATATAATTATATATATATTAATA +TATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCGAGAAAGAGT +CTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCAC +CTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG03009_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAAATAATTATATATATATTAAT +ATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATAT +ATATTAATATATAATTGTATATATAATTATATATATATATTAATATATAATTGTATATAT +AATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATA +TATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTC +GGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG03065_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATATT +ATAATAATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG03065_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATATATTATATATTATATATA +ATATATAATTATATTATATATTATATATAATATATAATTATATTATATATTATATATAAT +ATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTTATAT +ATGTATATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATA +ATAATATAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATATT +ATAATATATAATTATATATAATTATATATATAATTATATATATAATTAATTATAATTAAT +TATATTTATATATTATATATAATTATATGTAAATATAATTATATATATTATATATTATAT +ATAATATATTATATATATAATATATATATATTATATAATATATATAAATTATATATATTA +TATATTATATAATATATAATATATAATATATATAATTATAATATATAATTGTATATTATA +TATTATATAATATATAATTATAATATACAATTATATATTATATAATATATAATTATATAT +TATATAATATATAATTATATATAATATAATTATATATAATTGTATATATATTAATATATA +ATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATATATATT +AATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCGAGAAA +GAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCT +CCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG03098_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATATATTATATATTATATATA +ATATATAATTATATTATATATTATATATAATATATAATTATATTATATATTATATATAAT +ATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTTATAT +ATGTATATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATA +ATAATATAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATATT +ATAATATATAATTATATATAATTATATATATAATTATATATATAATTAATTATAATTAAT +TATATTTATATATTATATATAATTATATGTAAATATAATTATATATATTATATATTATAT +ATAATATATTATATATATAATATATATATATTATATAATATATATAAATTATATATATTA +TATATTATATAATATATAATATATAATATATATAATTATAATATATAATTGTATATTATA +TATTATATAATATATAATTATAATATACAATTATATATTATATAATATATAATTATATAT +TATATAATATATAATTATATATAATATAATTATATATAATTGTATATATATTAATATATA +ATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATATATATT +AATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCGAGAAA +GAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCT +CCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG03098_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATATATAAATATATAATGTAT +TATACATATATAATTATATAAATTATGTATGTATTATATAATTTTATATATGTATATATA +TGTTTATATATGTATATATAATTATATATGTATTATAATGTATTATATAATTGTATAATA +TAATATATAATAATATAATATATAATTATTTATTATAATATAATTATATAATATATAATT +ATATTATTATAATATATAATTATATATAATTATATATATAATTAATTATAATTAATTATA +TTTATATATTATATATAATTATATGTAAATATATATATATATATAATTATATATTATATA +ATATATAATATATAATATATAATATATAATATATATAATTATAATATATAATTGTATATT +ATATATTATATAATATATAATATATATAATTATAATATATAATTGTATATTATAATTATA +TAATATATAATTATAATATACAATTATATATTATATAATATATAATTGTATATTATAATT +ATATATAATTATATATAATTATATATAATATAATTATATATAATTGTATATATATTAATA +TATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATATA +TATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAAT +TATATATATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTA +TATATAATTATATATATAATATATACATATATATTTTTTCGAGAAAGAGTCTTTCTCTGT +CACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCACCTCCCAGGTT +CATGCCATTCTCCTGCCTC +>HG03125_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATATATTATATATTATATATA +ATATATAATTATATTATATATTATATATAATATATAATTATATTATATATTATATATAAT +ATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTTATAT +ATGTATATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATA +ATAATATAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATATT +ATAATATATAATTATATATAATTATATATATAATTATATATATAATTAATTATAATTAAT +TATATTTATATATTATATATAATTATATGTAAATATAATTATATATATTATATATTATAT +ATAATATATTATATATATAATATATATATATTATATAATATATATAAATTATATATATTA +TATATTATATAATATATAATATATAATATATATAATTATAATATATAATTGTATATTATA +TATTATATAATATATAATTATAATATACAATTATATATTATATAATATATAATTATATAT +TATATAATATATAATTATATATAATATAATTATATATAATTGTATATATATTAATATATA +ATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATATATATT +AATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCGAGAAA +GAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCT +CCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG03125_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATATATTATATATTATATATA +ATATATAATTATATTATATATTATATATAATATATAATTATATTATATATTATATATAAT +ATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTTATAT +ATGTATATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATA +ATAATATAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATATT +ATAATATATAATTATATATAATTATATATATAATTATATATATAATTAATTATAATTAAT +TATATTTATATATTATATATAATTATATGTAAATATAATTATATATATTATATATTATAT +ATAATATATTATATATATAATATATATATATTATATAATATATATAAATTATATATATTA +TATATTATATAATATATAATATATAATATATATAATTATAATATATAATTGTATATTATA +TATTATATAATATATAATTATAATATACAATTATATATTATATAATATATAATTATATAT +TATATAATATATAATTATATATAATATAATTATATATAATTGTATATATATTAATATATA +ATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATATATATT +AATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCGAGAAA +GAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCT +CCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG03371_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATATATAATTATAT +ATATAATATATATTATATATATATTATATATATTATATATTATATAATATATAATATACA +TAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATTATAATAT +ATAATTGTATATTATAATTATATAATATATAATTATAATATACAATTATATATTATATAA +TATATAATTATATATAATAAAATTATATATAATTATATATAATTATATATAATATAATTA +TATATAATTGTATATATTAATATATAATTGTATATATAATTATATATATATTAATATATA +ATTGTATATATAATTATATATATTAATATATAATTGTATATATAATTATATATATAATAT +ATACATATATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGG +CACAATCTCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG03371_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG03453_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATTTATTATAATA +TATAATTATATAATATATAATTATATTATATAATATATAATTATATATAATTATATATAT +AATTAATTATAATTAATTATATTTATATATTATATATATAATTATATGTAAATATAATTA +TATATATTATATATAATATATATAATAAATATAATTATATATATAATATATATTATATAT +ATATTATATATATTATATATATTATATATTATATAATATATAATATACATAATTTATATA +TATTGTATATTATATAATATATAATATATAATATATATAATATATATAATTATAATATAT +AATTGTATATTATAATTATATAATATATAATTATAATATACAATTATATATTATATAATA +TATAATTATATATAATAAAATTATATATAATTATATATAATTATATATAATATAATTATA +TATAATTGTATATATTAATATATAATTGTATATATAATTATATATATATTAATATATAAT +TGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATAT +ATACATATATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGG +CACAATCTCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG03453_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATTAT +TATAATATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG03486_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATTTATTATAATA +TATAATTATATAATATATAATTATATTATATAATATATAATTATATATAATTATATATAT +AATTAATTATAATTAATTATATTTATATATTATATATATAATTATATGTAAATATAATTA +TATATATTATATATAATATATATAATAAATATAATTATATATATAATATATATTATATAT +ATATTATATATATTATATATATTATATATTATATAATATATAATATACATAATTTATATA +TATTGTATATTATATAATATATAATATATAATATATATAATATATATAATTATAATATAT +AATTGTATATTATAATTATATAATATATAATTATAATATACAATTATATATTATATAATA +TATAATTATATATAATAAAATTATATATAATTATATATAATTATATATAATATAATTATA +TATAATTGTATATATTAATATATAATTGTATATATAATTATATATATATTAATATATAAT +TGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATAT +ATACATATATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGG +CACAATCTCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG03486_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATATATAATTATAT +ATATAATATATATTATATATATATTATATATATTATATATTATATAATATATAATATACA +TAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATTATAATAT +ATAATTGTATATTATAATTATATAATATATAATTATAATATACAATTATATATTATATAA +TATATAATTATATATAATAAAATTATATATAATTATATATAATTATATATAATATAATTA +TATATAATTGTATATATTAATATATAATTGTATATATAATTATATATATATTAATATATA +ATTGTATATATAATTATATATATTAATATATAATTGTATATATAATTATATATATAATAT +ATACATATATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGG +CACAATCTCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG03492_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAAATAATTATATATATATTAAT +ATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATAT +ATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAA +TTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATA +TTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGG +CTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG03492_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG03516_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATTAT +TATAATATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG03516_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG03540_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATATT +ATAATAATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG03540_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATTAT +TATAATATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG03579_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATATT +ATAATAATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG03579_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG03683_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAAATAATTATATATATATTAAT +ATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATAT +ATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAA +TTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATA +TTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGG +CTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG03683_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATATAATATATATAATATATA +TAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTATATATA +TTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTA +TATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTT +TTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTC +ACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG03732_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATATATAATTATAT +ATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATATA +TAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAATA +TATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTATA +TATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATA +ATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATAT +ATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCG +GCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>HG03732_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATATTATAATA +TATAATTATATAATATATAATTATATATTATAATATATAATTATATATAATTATATATAT +AATTAATTATAATTAATTATATTTATATATTATATATATAATTATATGTAAATATAATTA +TATATATTATATATAATATATATAATAAATATAATTATATATATAATATATATTATATAT +ATTATATATATTATATATATTATATATTATATAATATACATAATTTATATATATTGTATA +TTATATAATATATAATATATAATATATATAATATATATAATTATAATATATAATTGTATA +TTATAATTATATAATATATAATTATAATATACAATTATATATTATATAATATATAATTAT +ATATAATAAAATTATATATAATTATATATAATTATATATAATATAATTATATATAATTGT +ATATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATAT +AATTATATATATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATT +GTATATATAATTATATATATAATATATACATATATATTTTTTCGAGAAAGAGTCTTTCTC +TGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCACCTCCCAG +GTTCATGCCATTCTCCTGCCTC +>NA12329_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAAATAATTATATATATATTAAT +ATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATAT +ATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAA +TTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATA +TTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGG +CTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA12329_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAAATAATTATATATATATTAAT +ATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATAT +ATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAA +TTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATA +TTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGG +CTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA12878_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATATATAATATATAATTATAT +TATATATTATATATAAATATATAATGTATTATACATATATAATTATATAAATTATGTATG +TATTATATAATTTTATATATGTATATATATGTTTATATATGTATATATAATTATATATGT +ATTATAATGTATTATATAATTGTATAATATAATATATAATAATATAATATATAATTATTT +ATTATAATATATAATTATATAATATATAATTATATTATTATAATATATAATTATATATAA +TTATATATATAATTAATTATAATTAATTATATTTATATATTATATATAATTATATGTAAA +TATATATATATATAATTATATATTATATAATATATAATATATAATATATAATATATAATA +TATATAATTATAATATATAATTGTATATTATATATTATATAATATATAATATATATAATT +ATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAATTATATAT +TATATAATATATAATTGTATATTATAATTATATATAATTATATATAATTATATATAATAT +AATTATATATAATTGTATATATATTAATATATAATTGTATATATAATTATATATATATTA +ATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATAT +ATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTT +CGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACT +GCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA12878_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA18534_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA18534_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +AAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATATAATTATATATATAATT +AATTATAATTAATTATATTTATATATTATATATAATTATATGTAAATATAATTATATATA +TTATATATAATATATAATAAATATAATTATATATATAATATATATTATATATATATTATA +TATATTATATATATTATATATTATATAATATATAATATACATAATTTATATATAGTATAT +TATATAATATATAATATATAATATATATAATATATATAATTATAATATATAATTATATAT +AATAAAATTATATATAATTATATATAATTATATATATTATATATAATATAATTATATATA +ATTGTATATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTA +TATATAATTATATATATAATATATACATATATATTTTTTCGAGAAAGAGTCTTTCTCTGT +CACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCACCTCCCAGGTT +CATGCCATTCTCCTGCCTC +>NA18906_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATATATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATATAATTATATATATAATT +AATTATAATTAATTATATTTATATATTATATATAATTATATGTAAATATAATTATATATA +TTATATATAATATATAATAAATATAATTATATATATAATATATATTATATATATTATATA +TTATATATTATATAATATACATAATTTATATATATTGTATATTATATAATATATAATATA +TAATATATAATATATATAATTATAATATATAATTGTATATTATAATTATATAATATATAA +TTATAATATACAATTATATATTATATAATATATAATTATATATAATAAAATTATATATAA +TTATATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTA +TATATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATAC +ATATATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACA +ATCTCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA18906_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAAATAATTATATATATATTAAT +ATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATAT +ATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAA +TTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATA +TTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGG +CTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA18939_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA18939_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA19238_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATTAT +TATAATATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA19238_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATTAT +TATAATATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA19239_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAAATAATATATAATTATAATAT +ACAATTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATA +ATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATT +ATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATT +TTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCT +CACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA19239_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATATATAATTATAT +ATATAATATATATTATATATATATTATATATATTATATATTATATAATATATAATATACA +TAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATTATAATAT +ATAATTGTATATTATAATTATATAATATATAATTATAATATACAATTATATATTATATAA +TATATAATTATATATAATAAAATTATATATAATTATATATAATTATATATAATATAATTA +TATATAATTGTATATATTAATATATAATTGTATATATAATTATATATATATTAATATATA +ATTGTATATATAATTATATATATTAATATATAATTGTATATATAATTATATATATAATAT +ATACATATATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGG +CACAATCTCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA19240_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATATATAATTATAT +ATATAATATATATTATATATATATTATATATATTATATATTATATAATATATAATATACA +TAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATTATAATAT +ATAATTGTATATTATAATTATATAATATATAATTATAATATACAATTATATATTATATAA +TATATAATTATATATAATAAAATTATATATAATTATATATAATTATATATAATATAATTA +TATATAATTGTATATATTAATATATAATTGTATATATAATTATATATATATTAATATATA +ATTGTATATATAATTATATATATTAATATATAATTGTATATATAATTATATATATAATAT +ATACATATATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGG +CACAATCTCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA19240_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATTAT +TATAATATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA19650_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATTATGTTTATATATGTATA +TATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATAT +AATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAATA +TATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATAT +ATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTATA +TATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATAT +ATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAAT +ATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTAT +ATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATAT +AATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATA +TATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTC +GGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA19650_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTTATATATGTTTATATATGTATA +TATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATAT +AATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAATA +TATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATAT +ATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTATA +TATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATAT +ATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAAT +ATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTAT +ATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA19983_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATTAT +TATAATATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA19983_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAAATAATATATAATTATAATAT +ACAATTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATA +ATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATT +ATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATT +TTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCT +CACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA20129_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAATATACA +TAATTTATATATATTGTATAATATATAATATATAATATATAATATATATAATATATATAA +TTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAATTATAT +ATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTATATATA +ATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATATATATAT +TAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTAT +ATATATAATATATACATATATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTG +GAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCT +CCTGCCTC +>NA20129_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATTAT +TATAATATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA20509_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATATATATATATTATATATAATATATAATAAATATAATTA +TATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAAT +ATATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATA +ATATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATT +ATATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATA +TATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACAT +ATATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAAT +CTCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA20509_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAAATAATTATATATATATTAAT +ATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATAT +ATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAA +TTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATA +TTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGG +CTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA20847_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA20847_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAAATAATTATATATATATTAAT +ATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATAT +ATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAA +TTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATA +TTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGG +CTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA21309_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAAATAATATATAATTATAATAT +ACAATTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATA +ATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATT +ATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATT +TTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCT +CACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA21309_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA24385_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>NA24385_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>PGP1_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATTTATTATAATA +AATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATAT +ATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTATA +TATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATAT +ATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAAT +ATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTAT +ATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>PGP1_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>ei:HG00733_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +AAATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>ei:HG00733_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>ei:HG02818_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTTAT +ATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTA +TATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAAT +ATATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATA +ATATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATT +ATATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATA +TATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACAT +ATATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAAT +CTCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>ei:HG02818_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAAATAATTATATATATATTAAT +ATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATAT +ATATTAATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAA +TTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATA +TTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGG +CTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>ei:HG03486_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATTTATTATAATA +TATAATTATATAATATATAATTATATTATATAATATATAATTATATATAATTATATATAT +AATTAATTATAATTAATTATATTTATATATTATATATATAATTATATGTAAATATAATTA +TATATATTATATATAATATATATAATAAATATAATTATATATATAATATATATTATATAT +ATATTATATATATTATATATATTATATATTATATAATATATAATATACATAATTTATATA +TATTGTATATTATATAATATATAATATATAATATATATAATATATATAATTATAATATAT +AATTGTATATTATAATTATATAATATATAATTATAATATACAATTATATATTATATAATA +TATAATTATATATAATAAAATTATATATAATTATATATAATTATATATAATATAATTATA +TATAATTGTATATATTAATATATAATTGTATATATAATTATATATATATTAATATATAAT +TGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATAT +ATACATATATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGG +CACAATCTCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>ei:HG03486_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATATATAATTATAT +ATATAATATATATTATATATATATTATATATATTATATATTATATAATATATAATATACA +TAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATTATAATAT +ATAATTGTATATTATAATTATATAATATATAATTATAATATACAATTATATATTATATAA +TATATAATTATATATAATAAAATTATATATAATTATATATAATTATATATAATATAATTA +TATATAATTGTATATATTAATATATAATTGTATATATAATTATATATATATTAATATATA +ATTGTATATATAATTATATATATTAATATATAATTGTATATATAATTATATATATAATAT +ATACATATATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGG +CACAATCTCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>ei:NA19240_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATTATATTATATATTATATAT +TAATATATAATGTATTATACATATATAATTATATAAATTATGTATGTATTATATAATTTT +ATATATGTATATATATGTTTATATATGTATATATAATTATATATGTATTATAATGTATTA +TATAATTGTATAATATAATATATAATAATATAATATATAATTATTTATTATAATATATAA +TTATATAATATATAATTATATTATTATAATATATAATTATATAATATATAATTATATTAT +TATAATATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATAT +ATTATATATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATAT +AATTATATATATAATATATATTATATATATTATATATATTATATATTATATAATATATAA +TATACATAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATAT +ATATAATTATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAA +TTATATATTATATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATATAATTATAT +ATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTTCG +AGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGC +AAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>ei:NA19240_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATATATAATTATAT +ATATAATATATATTATATATATATTATATATATTATATATTATATAATATATAATATACA +TAATTTATATATATTGTATATTATATAATATATAATATATAATATATATAATTATAATAT +ATAATTGTATATTATAATTATATAATATATAATTATAATATACAATTATATATTATATAA +TATATAATTATATATAATAAAATTATATATAATTATATATAATTATATATAATATAATTA +TATATAATTGTATATATTAATATATAATTGTATATATAATTATATATATATTAATATATA +ATTGTATATATAATTATATATATTAATATATAATTGTATATATAATTATATATATAATAT +ATACATATATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGG +CACAATCTCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>li:HG00733_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>li:HG00733_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +AAATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>li:NA12878_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>li:NA12878_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATATATAATATATAATTATAT +TATATATTATATATAAATATATAATGTATTATACATATATAATTATATAAATTATGTATG +TATTATATAATTTTATATATGTATATATATGTTTATATATGTATATATAATTATATATGT +ATTATAATGTATTATATAATTGTATAATATAATATATAATAATATAATATATAATTATTT +ATTATAATATATAATTATATAATATATAATTATATTATTATAATATATAATTATATATAA +TTATATATATAATTAATTATAATTAATTATATTTATATATTATATATAATTATATGTAAA +TATATATATATATAATTATATATTATATAATATATAATATATAATATATAATATATAATA +TATATAATTATAATATATAATTGTATATTATATATTATATAATATATAATATATATAATT +ATAATATATAATTGTATATTATAATTATATAATATATAATTATAATATACAATTATATAT +TATATAATATATAATTGTATATTATAATTATATATAATTATATATAATTATATATAATAT +AATTATATATAATTGTATATATATTAATATATAATTGTATATATAATTATATATATATTA +ATATATAATTGTATATATAATTATATATATATTAATATATAATTGTATATATAATTATAT +ATATATTAATATATAATTGTATATATAATTATATATATAATATATACATATATATTTTTT +CGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCTCGGCTCACT +GCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>li:NA24385_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>li:NA24385_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>syndip_1_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATAATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATAT +ATAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATA +TATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATC +TCGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC +>syndip_2_chr1:600-1000 +CTCCCAGCTAATTTATATATATAATATATATAATATATAATTATATTATATATTATATAT +TAATATATAATTATATTATATATTATATATTAATATATAATGTATTATACATATATAATT +ATATAAATTATGTATGTATTATATAATTTTATATATGTATATATATGTTTATATATGTAT +ATATAATTATATATGTATTATAATGTATTATATAATTGTATAATATAATATATAATAATA +TAATATATAATTATTTATTATAATATATAATTATATAATATATAATTATATTATTATAAT +ATATAATTATATATAATTATATATATAATTAATTATAATTAATTATATTTATATATTATA +TATAATTATATGTAAATATAATTATATATATTATATATAATATATAATAAATATAATTAT +ATATATAATATATATTATATATATATTATATATATTATATATATTATATATTATATAATA +TATAATATACATAATTTATATATAGTATATTATATAATATATAATATATAATATATATAA +TATATATAATTATAATATATAATTATATATAATAAAATTATATATAATTATATATAATTA +TATATATTATATATAATATAATTATATATAATTGTATATATTAATATATAATTGTATATA +TAATTATATATATATTAATATATAATTGTATATATAATTATATATATAATATATACATAT +ATATTTTTTCGAGAAAGAGTCTTTCTCTGTCACCCACGCTGGAGTGCAGTGGCACAATCT +CGGCTCACTGCAAGCTCCACCTCCCAGGTTCATGCCATTCTCCTGCCTC diff --git a/repo_utils/answer_key/phab/phab_result/msa.fa b/repo_utils/answer_key/phab/phab_result/msa.fa new file mode 100644 index 00000000..99eda18a --- /dev/null +++ b/repo_utils/answer_key/phab/phab_result/msa.fa @@ -0,0 +1,4200 @@ +>ref_chr1_600_1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtat------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------tatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aat--tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG002_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG002_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG005_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG005_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatgcatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00096_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00096_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00171_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00171_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00438_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatat-attataatatataattatataatatataattata-tatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-ttatatatataattatatgtaaatataat-tatatatattatatataatatatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatatatta +tatat-------tatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtatatatta------------------ +----------------atatataattgtatatataattatatatatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00438_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00512_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatat-attataatatataattatataatatataattata-tatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-ttatatatataattatatgtaaatataat-tatatatattatatataatatatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +-----------tattaatatataattgtatatataattatatatatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00512_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatatattattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00513_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00513_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00514_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00514_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00621_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00621_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatataa +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00673_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00673_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatat-attataatatataattatataatatataattata-tatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-ttatatatataattatatgtaaatataat-tatatatattatatataatatatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatatatta +tatat-------tatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtatatatta------------------ +----------------atatataattgtatatataattatatatatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00731_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00731_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----aaataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00732_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00732_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----aaataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00733_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----aaataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00733_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00735_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataa-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------ataattatatatatatta------------ +------------------------------------------------------------ +------------------------------------------------------------ +--at-atataattgtatatataattatatatata-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------ttaatatataattg------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------tatatataattatata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00735_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataata------------------ +--------------------------tataatatataattatattatatattatatataa +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataat--tatatataattaattataattaactatatttata +ta-t--tatatataattatatgtaa------------------atatata-tatatataa +t-----------tatatattatata---------atatataatatataatatataatata +tataa-ttataatatataattgtatattatatattatataatatata---attgtatatt +atatattatata---------atatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattgta +tattat------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------tatattaatatataattgtatatataattttatatatattaatatataatt +gtatatataattatatatatattaatatataattgtatatataattatatatatattaat +atataattgtatatataattatatatatattaatatataattgtatatataattatatat +atattaatatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00741_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----aaataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00741_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00864_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataata------------------ +--------------------------tataatatataattatattatatattatatataa +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataat--tatatataattaattataattaactatatttata +ta-t--tatatataattatatgtaa------------------atatata-tatatataa +t-----------tatatattatata---------atatataatatataatatataatata +--------------tataat----------------tataatatata---attgtatatt +atatattatata---------atatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattgta +tattat------------aattatatataattatatataattatatataatataattata +tataattatatataatataattatatataattgtata----------------------- +---------tatattaatatataattgtatatataattatatatatattaa--------- +-------------------------tatataattgtatatataattatatatatattaat +atataattgtatatataattatatatatattaatatataattgtatatataattatatat +atattaatatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG00864_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01071_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattata-tatta +taataatataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01071_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01106_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01106_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattata-tatta +taataatataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01109_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatat-attataatatataattatataatatataattata-tatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-ttatatatataattatatgtaaatataat-tatatatattatatataatatatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01109_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataatatattatatatta-tatat +aatatataattatattatatattatatataatatataattatattatatattatatat-a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatg--------------------tatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatat-attataata--------------------------tataa +ttat-atataattatatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatatt--atatataa +ta-----tattatatatataatata-----------------tatatattatataatata +------------------------------------tataaattatatatattatatatt +atataatatata---------atatataatatatataattataatatataattgtatatt +atatattatataatatataattataatatacaattatatattatataatatataattata +tattat-----------------------ataatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01114_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01114_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataa-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------ataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01123_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01123_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01175_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatat-attataatatataattatataatatataattata-tatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-ttatatatataattatatgtaaatataat-tatatatattatatataatatatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtatatattaatat-------------- +--------------------ataattgtatatataattatatatatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01175_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataa-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------ataattatatatatatta------------ +------------------------------------------------------------ +------------------------------------------------------------ +--at-atataattgtatatataattatatatata-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------ttaatatataattg------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------tatatataattatata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aat--tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01243_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattatattatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01243_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattatattatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01258_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01258_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataata------------------ +--------------------------tataatatataattatattatatattatatataa +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaa------------------atatata-tatatataa +t-----------tatatattatata---------atatataatatataatatataatata +-------taatatatataat----------------tataatatata---attgtatatt +atatattatata---------atatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattgta +tattat------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------tatattaatatataattgtatatataattatatatatattaat-------- +------------------------------------------------------------ +----------------------------------atataattgtatatataattatatat +atattaatatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01358_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataata------------------ +--------------------------tataatatataattatattatatattatatataa +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaa------------------atatata-tatatataa +t-----------tatatattatata---------atatataatatataatatataatata +-------taatatatataat----------------tataatatata---attgtatatt +atatattatata---------atatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattgta +tattat------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------tatattaatatataattgtatatataattatatatatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01358_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataa-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------ataattatatatatatta------------ +------------------------------------------------------------ +------------------------------------------------------------ +--at-atataattgtatatataattatatatata-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------ttaatatataattg------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------tatatataattatata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01361_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----aaataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01361_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01505_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataa-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------ataattatatatatatta------------ +------------------------------------------------------------ +------------------------------------------------------------ +--at-atataattgtatatataattatatatata-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------ttaatatataattg------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------tatatataattatata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01505_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01596_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01596_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01891_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattatattatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01891_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattattt-attataatatataattatataatatataattata-ttata +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-ttatatatataattatatgtaaatataat-tatatatattatatataatatatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01928_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01928_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataa-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------ataattatatatatatta------------ +------------------------------------------------------------ +------------------------------------------------------------ +--at-atataattgtatatataattatatatata-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------ttaatatataattg------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------tatatataattatata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01952_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataa-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------ataattatatatatatta------------ +------------------------------------------------------------ +------------------------------------------------------------ +--at-atataattgtatatataattatatatata-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------ttaatatataattg------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------tatatataattatata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01952_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01978_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG01978_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataata------------------ +--------------------------tataatatataattatattatatattatatataa +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatataattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaa------------------atatata-tatatataa +t-----------tatatattatata---------atatataatatataatatataatata +-------taatatatataat----------------tataatatata---attgtatatt +atatattatata---------atatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattgta +tattat------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------tatattaatatataattgtatatataattatatatatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02011_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattatattatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02011_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataa-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------ataattatatatatatta------------ +------------------------------------------------------------ +------------------------------------------------------------ +--at-atataattgtatatataattatatatata-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------ttaatatataattg------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------tatatataattatata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02055_1_chr1:600-1000 +ctcccagctaatttatatatataatatatataatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattatattatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02055_2_chr1:600-1000 +ctcccagctaatttatatatataatatatataatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattatattatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02080_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataa-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------ataattatatatatatta------------ +------------------------------------------------------------ +------------------------------------------------------------ +--at-atataattgtatatataattatatatata-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------ttaatatataattg------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------tatatataattatata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aat--tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02080_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02109_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattatattatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02109_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatataa +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattattt-attataatatataattatataatatataattata-ttata +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-ttatatatataattatatgtaaatataat-tatatatattatatataatatatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-at---------tataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02145_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatata--attatatataattata +tataataaaattatatataattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02145_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02148_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02148_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataa-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------ataattatatatatatta------------ +------------------------------------------------------------ +------------------------------------------------------------ +--at-atataattgtatatataattatatatata-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------ttaatatataattg------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------tatatataattatata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02257_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataa-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------ataattatatatatatta------------ +------------------------------------------------------------ +------------------------------------------------------------ +--at-atataattgtatatataattatatatata-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------ttaatatataattg------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------tatatataattatata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02257_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattatattatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02486_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataata------------------ +--------------------------tataatatataattatattatatattatatataa +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaa------------------atatata-tatataaaa +t-----------tatatattatata---------atatataatatataatatataatata +-------taatatatataat----------------tataatatata---attgtatatt +atatattatata---------atatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattgta +tattat------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------tatattaatatataattgtatatataattatatatatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat----tatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02486_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatta---------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------atatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------tatattaatatataattgtatatataattatatatatat------------ +------------------------------------------------------------ +------------------------------------------------------------ +----taatatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02492_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatata----atatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02492_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02559_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattata-tatta +taataatataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02559_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatat-attataatatataattatataatatataattata-tatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-ttatatatataattatatgtaaatataat-tatatatattatatataatatatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02572_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatatattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatat--tatatattatatattata +ta---------ttatataat----------ata---cataatttatatatattgtatatt +atataatatataatatata--atatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02572_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattattt-attataatatataattatataatatataattata-ttata +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-ttatatatataattatatgtaaatataat-tatatatattatatataatatatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02587_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattatattatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02587_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattatattatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02622_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattatattatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02622_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataatatattatatattattatat +aatatataattatattatatattatatataatatataattatattatatattatatat-a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatg--------------------tatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatat-attataata--------------------------tataa +ttat-atataattatatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatatt--atatataa +ta-----tattatatatataatata-----------------tatatattatataatata +------------------------------------tataaattatatatattatatatt +atataatatata---------atatataatatatataattataatatataattgtatatt +atatattatataatatataattataatatacaattatatattatataatatataattata +tattat-----------------------ataatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02630_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------------------------------------ +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02630_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattata-tatta +taataatataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02717_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatat------------------------------------tatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +t--atataattatatatataatata-tattatatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatata---------atatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aat--tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02717_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatat------------------------------------tatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +t--atataattatatatataatata-tattatatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatata---------atatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aat--tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02723_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------tg--------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +---------------------tatatatattaatatataattg----------------- +---------------------tatatataattatata----------------------- +---------tatattaatatataattgtatatataattatatatatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02723_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatataa +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatg--tatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattattt-attataatatataattatataatatataattata-ttata +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-ttatatatataattatatgtaaatataat-tatatatattatatataatatatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02818_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +tatt--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02818_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataa-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------ataattatatatatatta------------ +------------------------------------------------------------ +------------------------------------------------------------ +--at-atataattgtatatataattatatatata-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------ttaatatataattg------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------tatatataattatata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02886_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataa-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------ataattatatatatatta------------ +------------------------------------------------------------ +------------------------------------------------------------ +--at-atataattgtatatataattatatatata-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------ttaatatataattg------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------tatatataattatata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG02886_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataata------------------ +--------------------------tataatatataattatattatatattatatataa +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaa--------------------atata-tatatataa +t-----------tatatattatata---------atatataatatataatatataatata +-------taatatatataat----------------tataatatata---attgtatatt +atatattatata---------atatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattgta +tattat------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------tatattaatatataattgtatatataattatatatatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat----tatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG03009_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatat-attataatatataattatataatatataattata-tatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-ttatatatataattatatgtaaatataat-tatatatattatatataatatatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +-----------tattaatatataattgtatatataattatatatatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG03009_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataa-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------ataattatatatatatta------------ +------------------------------------------------------------ +------------------------------------------------------------ +--at-atataattgtatatataattatatatata-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------ttaatatataattg------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------tatatataattatata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataattatatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG03065_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattata-tatta +taataatataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG03065_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataatatattatatatta-tatat +aatatataattatattatatattatatataatatataattatattatatattatatat-a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatg--------------------tatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatat-attataata--------------------------tataa +ttat-atataattatatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatatt--atatataa +ta-----tattatatatataatata-----------------tatatattatataatata +------------------------------------tataaattatatatattatatatt +atataatatata---------atatataatatatataattataatatataattgtatatt +atatattatataatatataattataatatacaattatatattatataatatataattata +tattat-----------------------ataatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG03098_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataatatattatatatta-tatat +aatatataattatattatatattatatataatatataattatattatatattatatat-a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatg--------------------tatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatat-attataata--------------------------tataa +ttat-atataattatatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatatt--atatataa +ta-----tattatatatataatata-----------------tatatattatataatata +------------------------------------tataaattatatatattatatatt +atataatatata---------atatataatatatataattataatatataattgtatatt +atatattatataatatataattataatatacaattatatattatataatatataattata +tattat-----------------------ataatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG03098_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatata--------------------- +----------------------------------------------------atatataa +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattata--atataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaa----------------tatatata-tatatataa +t-----------tatatattatata---------atatataatatataatatataatata +-------taatatatataat----------------tataatatata---attgtatatt +atatattatata---------atatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattgta +tattat------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------tatattaatatataattgtatatataattatatatatatt----------- +---------------------------------------------------------aat +atataattgtatatataattatatatatattaatatataattgtatatataattatatat +atattaatatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG03125_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataatatattatatatta-tatat +aatatataattatattatatattatatataatatataattatattatatattatatat-a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatg--------------------tatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatat-attataata--------------------------tataa +ttat-atataattatatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatatt--atatataa +ta-----tattatatatataatata-----------------tatatattatataatata +------------------------------------tataaattatatatattatatatt +atataatatata---------atatataatatatataattataatatataattgtatatt +atatattatataatatataattataatatacaattatatattatataatatataattata +tattat-----------------------ataatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG03125_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataatatattatatatta-tatat +aatatataattatattatatattatatataatatataattatattatatattatatat-a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatg--------------------tatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatat-attataata--------------------------tataa +ttat-atataattatatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatatt--atatataa +ta-----tattatatatataatata-----------------tatatattatataatata +------------------------------------tataaattatatatattatatatt +atataatatata---------atatataatatatataattataatatataattgtatatt +atatattatataatatataattataatatacaattatatattatataatatataattata +tattat-----------------------ataatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG03371_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatat------------------------------------tatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +t--atataattatatatataatata-tattatatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatata---------atatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aat--tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG03371_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG03453_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattattt-attataatatataattatataatatataattata-ttata +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-ttatatatataattatatgtaaatataat-tatatatattatatataatatatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG03453_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattatattatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG03486_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattattt-attataatatataattatataatatataattata-ttata +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-ttatatatataattatatgtaaatataat-tatatatattatatataatatatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG03486_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatat------------------------------------tatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +t--atataattatatatataatata-tattatatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatata---------atatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aat--tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG03492_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataa-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------ataattatatatatatta------------ +------------------------------------------------------------ +------------------------------------------------------------ +--at-atataattgtatatataattatatatata-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------ttaatatataattg------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------tatatataattatata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG03492_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG03516_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattatattatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG03516_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG03540_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattata-tatta +taataatataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG03540_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattatattatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG03579_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattata-tatta +taataatataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG03579_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG03683_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataa-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------ataattatatatatatta------------ +------------------------------------------------------------ +------------------------------------------------------------ +--at-atataattgtatatataattatatatata-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------ttaatatataattg------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------tatatataattatata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG03683_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatata----------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------atataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG03732_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +t--atataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>HG03732_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatat-attataatatataattatataatatataattata-tatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-ttatatatataattatatgtaaatataat-tatatatattatatataatatatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatatatta +tatat-------tatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtatatatta------------------ +----------------atatataattgtatatataattatatatatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA12329_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataa-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------ataattatatatatatta------------ +------------------------------------------------------------ +------------------------------------------------------------ +--at-atataattgtatatataattatatatata-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------ttaatatataattg------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------tatatataattatata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA12329_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataa-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------ataattatatatatatta------------ +------------------------------------------------------------ +------------------------------------------------------------ +--at-atataattgtatatataattatatatata-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------ttaatatataattg------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------tatatataattatata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA12878_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataata------------------ +--------------------------tataatatataattatattatatattatatataa +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaa------------------atatata-tatatataa +t-----------tatatattatata---------atatataatatataatatataatata +-------taatatatataat----------------tataatatata---attgtatatt +atatattatata---------atatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattgta +tattat------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------tatattaatatataattgtatatataattatatatatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA12878_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA18534_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA18534_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatataa +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA18906_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatatattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--ta---------tatatattatatattata +ta---------ttatataat----------ata---cataatttatatatattgtatatt +atataatatataatatata--atatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA18906_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataa-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------ataattatatatatatta------------ +------------------------------------------------------------ +------------------------------------------------------------ +--at-atataattgtatatataattatatatata-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------ttaatatataattg------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------tatatataattatata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA18939_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA18939_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA19238_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattatattatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA19238_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattatattatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA19239_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataa-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------ataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA19239_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatat------------------------------------tatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +t--atataattatatatataatata-tattatatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatata---------atatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aat--tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA19240_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatat------------------------------------tatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +t--atataattatatatataatata-tattatatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatata---------atatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aat--tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA19240_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattatattatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA19650_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatat-tatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA19650_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgt-tatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA19983_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattatattatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA19983_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataa-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------ataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA20129_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatat------------------------------------tatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtataat +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA20129_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattatattatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA20509_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataatatatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA20509_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataa-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------ataattatatatatatta------------ +------------------------------------------------------------ +------------------------------------------------------------ +--at-atataattgtatatataattatatatata-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------ttaatatataattg------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------tatatataattatata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA20847_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA20847_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataa-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------ataattatatatatatta------------ +------------------------------------------------------------ +------------------------------------------------------------ +--at-atataattgtatatataattatatatata-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------ttaatatataattg------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------tatatataattatata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA21309_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataa-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------ataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA21309_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA24385_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>NA24385_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>PGP1_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattat-ttattataat-------------------------------- +-----aaataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>PGP1_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>ei:HG00733_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----aaataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>ei:HG00733_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>ei:HG02818_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +tatt--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>ei:HG02818_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataa-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------ataattatatatatatta------------ +------------------------------------------------------------ +------------------------------------------------------------ +--at-atataattgtatatataattatatatata-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------ttaatatataattg------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------tatatataattatata----------------------- +-------------------------------------------tatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>ei:HG03486_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattattt-attataatatataattatataatatataattata-ttata +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-ttatatatataattatatgtaaatataat-tatatatattatatataatatatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>ei:HG03486_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatat------------------------------------tatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +t--atataattatatatataatata-tattatatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatata---------atatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aat--tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>ei:NA19240_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataat------------------- +---------------------------------------tatattatatattatatatta +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataatatataattatataatatataattatattatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tat--tatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatataatatataatatatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--------------------------------- +-----tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>ei:NA19240_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatat------------------------------------tatta +taat-atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +t--atataattatatatataatata-tattatatatatattatatatattatatattata +ta---------atatataat----------ata---cataatttatatatattgtatatt +atataatatata---------atatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattata +tataataa----------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aat--tatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>li:HG00733_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata 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+------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----aaataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>li:NA12878_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata 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+------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatattaatatataata------------------ +--------------------------tataatatataattatattatatattatatataa +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaa------------------atatata-tatatataa +t-----------tatatattatata---------atatataatatataatatataatata +-------taatatatataat----------------tataatatata---attgtatatt +atatattatata---------atatataatatatataattataatatataattgtatatt +ata-attatataatatataattataatatacaattatatattatataatatataattgta +tattat------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------tatattaatatataattgtatatataattatatatatattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--tatatatatattaatatataattgtatatat +aattatatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>li:NA24385_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>li:NA24385_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>syndip_1_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatataattat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc +>syndip_2_chr1:600-1000 +ctcccagctaatttatatatataatatata------------------------------ +------------------------------taatatataattatattatatattatatat +taatatataattatattatatattatatatt----------------------------- +-----------------------------------------------------------a +atatataatgtattatacatatataattatataaattatgtatgtattatataattttat +atatgtatatatatgtttatatatgtatatataattatatatgtattataatgtattata +taattgtataatataatatataataatataatatataattatttattataatatataatt +atataatatataattatattattataat-------------------------------- +-----atataat--tatatataattatatatataattaattataattaattatatttata +ta-t--tatatataattatatgtaaatataat-tatatatattatatata--atatataa +taaatataattatatatataatata-tattatatatatattatatatattatatatatta +tatattatataatatataat----------ata---cataatttatatata--gtatatt +atataatatataatatataatatatataatatatataattataatatataattatatata +ata-a--------------------------aattatatat------------------- +------------------aattatatataattatatat-attat---------------- +---------atataatataattatatataattgtata----------------------- +---------------------------------------------tattaa--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatataattgtatatataat--t------------------------------ +----atatatatattaatatataattgtatatataattatatatataatatatacatata +tattttttcgagaaagagtctttctctgtcacccacgctggagtgcagtggcacaatctc +ggctcactgcaagctccacctcccaggttcatgccattctcctgcctc diff --git a/repo_utils/answer_key/phab/phab_result/msa.fa.fai b/repo_utils/answer_key/phab/phab_result/msa.fa.fai new file mode 100644 index 00000000..c2c44fbf --- /dev/null +++ b/repo_utils/answer_key/phab/phab_result/msa.fa.fai @@ -0,0 +1,175 @@ +ref_chr1_600_1000 1368 19 60 61 +HG002_1_chr1:600-1000 1368 1433 60 61 +HG002_2_chr1:600-1000 1368 2847 60 61 +HG005_1_chr1:600-1000 1368 4261 60 61 +HG005_2_chr1:600-1000 1368 5675 60 61 +HG00096_1_chr1:600-1000 1368 7091 60 61 +HG00096_2_chr1:600-1000 1368 8507 60 61 +HG00171_1_chr1:600-1000 1368 9923 60 61 +HG00171_2_chr1:600-1000 1368 11339 60 61 +HG00438_1_chr1:600-1000 1368 12755 60 61 +HG00438_2_chr1:600-1000 1368 14171 60 61 +HG00512_1_chr1:600-1000 1368 15587 60 61 +HG00512_2_chr1:600-1000 1368 17003 60 61 +HG00513_1_chr1:600-1000 1368 18419 60 61 +HG00513_2_chr1:600-1000 1368 19835 60 61 +HG00514_1_chr1:600-1000 1368 21251 60 61 +HG00514_2_chr1:600-1000 1368 22667 60 61 +HG00621_1_chr1:600-1000 1368 24083 60 61 +HG00621_2_chr1:600-1000 1368 25499 60 61 +HG00673_1_chr1:600-1000 1368 26915 60 61 +HG00673_2_chr1:600-1000 1368 28331 60 61 +HG00731_1_chr1:600-1000 1368 29747 60 61 +HG00731_2_chr1:600-1000 1368 31163 60 61 +HG00732_1_chr1:600-1000 1368 32579 60 61 +HG00732_2_chr1:600-1000 1368 33995 60 61 +HG00733_1_chr1:600-1000 1368 35411 60 61 +HG00733_2_chr1:600-1000 1368 36827 60 61 +HG00735_1_chr1:600-1000 1368 38243 60 61 +HG00735_2_chr1:600-1000 1368 39659 60 61 +HG00741_1_chr1:600-1000 1368 41075 60 61 +HG00741_2_chr1:600-1000 1368 42491 60 61 +HG00864_1_chr1:600-1000 1368 43907 60 61 +HG00864_2_chr1:600-1000 1368 45323 60 61 +HG01071_1_chr1:600-1000 1368 46739 60 61 +HG01071_2_chr1:600-1000 1368 48155 60 61 +HG01106_1_chr1:600-1000 1368 49571 60 61 +HG01106_2_chr1:600-1000 1368 50987 60 61 +HG01109_1_chr1:600-1000 1368 52403 60 61 +HG01109_2_chr1:600-1000 1368 53819 60 61 +HG01114_1_chr1:600-1000 1368 55235 60 61 +HG01114_2_chr1:600-1000 1368 56651 60 61 +HG01123_1_chr1:600-1000 1368 58067 60 61 +HG01123_2_chr1:600-1000 1368 59483 60 61 +HG01175_1_chr1:600-1000 1368 60899 60 61 +HG01175_2_chr1:600-1000 1368 62315 60 61 +HG01243_1_chr1:600-1000 1368 63731 60 61 +HG01243_2_chr1:600-1000 1368 65147 60 61 +HG01258_1_chr1:600-1000 1368 66563 60 61 +HG01258_2_chr1:600-1000 1368 67979 60 61 +HG01358_1_chr1:600-1000 1368 69395 60 61 +HG01358_2_chr1:600-1000 1368 70811 60 61 +HG01361_1_chr1:600-1000 1368 72227 60 61 +HG01361_2_chr1:600-1000 1368 73643 60 61 +HG01505_1_chr1:600-1000 1368 75059 60 61 +HG01505_2_chr1:600-1000 1368 76475 60 61 +HG01596_1_chr1:600-1000 1368 77891 60 61 +HG01596_2_chr1:600-1000 1368 79307 60 61 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1368 113291 60 61 +HG02492_1_chr1:600-1000 1368 114707 60 61 +HG02492_2_chr1:600-1000 1368 116123 60 61 +HG02559_1_chr1:600-1000 1368 117539 60 61 +HG02559_2_chr1:600-1000 1368 118955 60 61 +HG02572_1_chr1:600-1000 1368 120371 60 61 +HG02572_2_chr1:600-1000 1368 121787 60 61 +HG02587_1_chr1:600-1000 1368 123203 60 61 +HG02587_2_chr1:600-1000 1368 124619 60 61 +HG02622_1_chr1:600-1000 1368 126035 60 61 +HG02622_2_chr1:600-1000 1368 127451 60 61 +HG02630_1_chr1:600-1000 1368 128867 60 61 +HG02630_2_chr1:600-1000 1368 130283 60 61 +HG02717_1_chr1:600-1000 1368 131699 60 61 +HG02717_2_chr1:600-1000 1368 133115 60 61 +HG02723_1_chr1:600-1000 1368 134531 60 61 +HG02723_2_chr1:600-1000 1368 135947 60 61 +HG02818_1_chr1:600-1000 1368 137363 60 61 +HG02818_2_chr1:600-1000 1368 138779 60 61 +HG02886_1_chr1:600-1000 1368 140195 60 61 +HG02886_2_chr1:600-1000 1368 141611 60 61 +HG03009_1_chr1:600-1000 1368 143027 60 61 +HG03009_2_chr1:600-1000 1368 144443 60 61 +HG03065_1_chr1:600-1000 1368 145859 60 61 +HG03065_2_chr1:600-1000 1368 147275 60 61 +HG03098_1_chr1:600-1000 1368 148691 60 61 +HG03098_2_chr1:600-1000 1368 150107 60 61 +HG03125_1_chr1:600-1000 1368 151523 60 61 +HG03125_2_chr1:600-1000 1368 152939 60 61 +HG03371_1_chr1:600-1000 1368 154355 60 61 +HG03371_2_chr1:600-1000 1368 155771 60 61 +HG03453_1_chr1:600-1000 1368 157187 60 61 +HG03453_2_chr1:600-1000 1368 158603 60 61 +HG03486_1_chr1:600-1000 1368 160019 60 61 +HG03486_2_chr1:600-1000 1368 161435 60 61 +HG03492_1_chr1:600-1000 1368 162851 60 61 +HG03492_2_chr1:600-1000 1368 164267 60 61 +HG03516_1_chr1:600-1000 1368 165683 60 61 +HG03516_2_chr1:600-1000 1368 167099 60 61 +HG03540_1_chr1:600-1000 1368 168515 60 61 +HG03540_2_chr1:600-1000 1368 169931 60 61 +HG03579_1_chr1:600-1000 1368 171347 60 61 +HG03579_2_chr1:600-1000 1368 172763 60 61 +HG03683_1_chr1:600-1000 1368 174179 60 61 +HG03683_2_chr1:600-1000 1368 175595 60 61 +HG03732_1_chr1:600-1000 1368 177011 60 61 +HG03732_2_chr1:600-1000 1368 178427 60 61 +NA12329_1_chr1:600-1000 1368 179843 60 61 +NA12329_2_chr1:600-1000 1368 181259 60 61 +NA12878_1_chr1:600-1000 1368 182675 60 61 +NA12878_2_chr1:600-1000 1368 184091 60 61 +NA18534_1_chr1:600-1000 1368 185507 60 61 +NA18534_2_chr1:600-1000 1368 186923 60 61 +NA18906_1_chr1:600-1000 1368 188339 60 61 +NA18906_2_chr1:600-1000 1368 189755 60 61 +NA18939_1_chr1:600-1000 1368 191171 60 61 +NA18939_2_chr1:600-1000 1368 192587 60 61 +NA19238_1_chr1:600-1000 1368 194003 60 61 +NA19238_2_chr1:600-1000 1368 195419 60 61 +NA19239_1_chr1:600-1000 1368 196835 60 61 +NA19239_2_chr1:600-1000 1368 198251 60 61 +NA19240_1_chr1:600-1000 1368 199667 60 61 +NA19240_2_chr1:600-1000 1368 201083 60 61 +NA19650_1_chr1:600-1000 1368 202499 60 61 +NA19650_2_chr1:600-1000 1368 203915 60 61 +NA19983_1_chr1:600-1000 1368 205331 60 61 +NA19983_2_chr1:600-1000 1368 206747 60 61 +NA20129_1_chr1:600-1000 1368 208163 60 61 +NA20129_2_chr1:600-1000 1368 209579 60 61 +NA20509_1_chr1:600-1000 1368 210995 60 61 +NA20509_2_chr1:600-1000 1368 212411 60 61 +NA20847_1_chr1:600-1000 1368 213827 60 61 +NA20847_2_chr1:600-1000 1368 215243 60 61 +NA21309_1_chr1:600-1000 1368 216659 60 61 +NA21309_2_chr1:600-1000 1368 218075 60 61 +NA24385_1_chr1:600-1000 1368 219491 60 61 +NA24385_2_chr1:600-1000 1368 220907 60 61 +PGP1_1_chr1:600-1000 1368 222320 60 61 +PGP1_2_chr1:600-1000 1368 223733 60 61 +ei:HG00733_1_chr1:600-1000 1368 225152 60 61 +ei:HG00733_2_chr1:600-1000 1368 226571 60 61 +ei:HG02818_1_chr1:600-1000 1368 227990 60 61 +ei:HG02818_2_chr1:600-1000 1368 229409 60 61 +ei:HG03486_1_chr1:600-1000 1368 230828 60 61 +ei:HG03486_2_chr1:600-1000 1368 232247 60 61 +ei:NA19240_1_chr1:600-1000 1368 233666 60 61 +ei:NA19240_2_chr1:600-1000 1368 235085 60 61 +li:HG00733_1_chr1:600-1000 1368 236504 60 61 +li:HG00733_2_chr1:600-1000 1368 237923 60 61 +li:NA12878_1_chr1:600-1000 1368 239342 60 61 +li:NA12878_2_chr1:600-1000 1368 240761 60 61 +li:NA24385_1_chr1:600-1000 1368 242180 60 61 +li:NA24385_2_chr1:600-1000 1368 243599 60 61 +syndip_1_chr1:600-1000 1368 245014 60 61 +syndip_2_chr1:600-1000 1368 246429 60 61 diff --git a/repo_utils/answer_key/phab/phab_result/output.vcf.gz b/repo_utils/answer_key/phab/phab_result/output.vcf.gz new file mode 100644 index 00000000..70ebca6c Binary files /dev/null and b/repo_utils/answer_key/phab/phab_result/output.vcf.gz differ diff --git a/repo_utils/answer_key/phab/phab_result/output.vcf.gz.tbi b/repo_utils/answer_key/phab/phab_result/output.vcf.gz.tbi new file mode 100644 index 00000000..8281bbc7 Binary files /dev/null and b/repo_utils/answer_key/phab/phab_result/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/fn.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/fn.vcf.gz new file mode 100644 index 00000000..d3385bcf Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/fn.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/fn.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/fn.vcf.gz.tbi new file mode 100644 index 00000000..e7b65a6a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/fn.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/fp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/fp.vcf.gz new file mode 100644 index 00000000..1fc24349 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/fp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/fp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/fp.vcf.gz.tbi new file mode 100644 index 00000000..eea428cf Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/fp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/log.txt b/repo_utils/answer_key/refine/refine_output_one/log.txt new file mode 100644 index 00000000..451e40ac --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/log.txt @@ -0,0 +1,64 @@ +2023-03-03 23:07:24,705 [INFO] Truvari v4.0.0.dev0+detached +2023-03-03 23:07:24,706 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/refine_data/hg002_base.vcf.gz -c repo_utils/test_files/refine_data/hg002_comp.vcf.gz --includebed repo_utils/test_files/refine_data/h1_hc_tr_hg002.bed -s 5 -o test_results/refine_output_one +2023-03-03 23:07:24,707 [INFO] Params: +{ + "base": "/data/repo_utils/test_files/refine_data/hg002_base.vcf.gz", + "comp": "/data/repo_utils/test_files/refine_data/hg002_comp.vcf.gz", + "output": "test_results/refine_output_one", + "includebed": "/data/repo_utils/test_files/refine_data/h1_hc_tr_hg002.bed", + "extend": 0, + "debug": false, + "reference": null, + "refdist": 500, + "pctseq": 0.7, + "minhaplen": 50, + "pctsize": 0.7, + "pctovl": 0.0, + "typeignore": false, + "chunksize": 1000, + "bSample": "syndip", + "cSample": "HG002", + "dup_to_ins": false, + "sizemin": 5, + "sizefilt": 5, + "sizemax": 50000, + "passonly": false, + "no_ref": false, + "pick": "single" +} +2023-03-03 23:07:24,778 [INFO] Including 225 bed regions +2023-03-03 23:07:26,131 [INFO] Zipped 7158 variants Counter({'comp': 5303, 'base': 1855}) +2023-03-03 23:07:26,132 [INFO] 212 chunks of 7158 variants Counter({'__filtered': 6120, 'base': 587, 'comp': 451}) +2023-03-03 23:07:26,293 [INFO] Stats: { + "TP-base": 386, + "TP-comp": 386, + "FP": 65, + "FN": 201, + "precision": 0.8558758314855875, + "recall": 0.6575809199318569, + "f1": 0.7437379576107899, + "base cnt": 587, + "comp cnt": 451, + "TP-comp_TP-gt": 381, + "TP-comp_FP-gt": 5, + "TP-base_TP-gt": 381, + "TP-base_FP-gt": 5, + "gt_concordance": 0.9870466321243523, + "gt_matrix": { + "(1, 0)": { + "(0, 1)": 202, + "(1, 0)": 14, + "(1, 1)": 1 + }, + "(0, 1)": { + "(1, 0)": 144, + "(0, 1)": 12 + }, + "(1, 1)": { + "(1, 1)": 9, + "(1, 0)": 2, + "(0, 1)": 2 + } + } +} +2023-03-03 23:07:26,294 [INFO] Finished bench diff --git a/repo_utils/answer_key/refine/refine_output_one/params.json b/repo_utils/answer_key/refine/refine_output_one/params.json new file mode 100644 index 00000000..249be78b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/params.json @@ -0,0 +1 @@ +{"base": "/data/repo_utils/test_files/refine_data/hg002_base.vcf.gz", "comp": "/data/repo_utils/test_files/refine_data/hg002_comp.vcf.gz", "output": "test_results/refine_output_one", "includebed": "/data/repo_utils/test_files/refine_data/h1_hc_tr_hg002.bed", "extend": 0, "debug": false, "reference": null, "refdist": 500, "pctseq": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "chunksize": 1000, "bSample": "syndip", "cSample": "HG002", "dup_to_ins": false, "sizemin": 5, "sizefilt": 5, "sizemax": 50000, "passonly": false, "no_ref": false, "pick": "single"} \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_one/phab.output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab.output.vcf.gz new file mode 100644 index 00000000..9dd8a9bc Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab.output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab.output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab.output.vcf.gz.tbi new file mode 100644 index 00000000..7b70bce6 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab.output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/base.vcf.gz new file mode 100644 index 00000000..208a5f0e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/base.vcf.gz.tbi new file mode 100644 index 00000000..adeaae6d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/comp.vcf.gz new file mode 100644 index 00000000..1cc6a041 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/comp.vcf.gz.tbi new file mode 100644 index 00000000..b1616779 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/haps.fa new file mode 100644 index 00000000..baa65001 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/haps.fa @@ -0,0 +1,38 @@ +>ref_chr20_10802576_10803059 +GCCCAACTTAATCCAGTGTGACTCCATTTTAAATCAATTATATCTGCAAAGATCTAATTTTCAAATGAGGTCACAGTCACAAGTATTGGGGGTTAGGACTTTTGGGGGACATAACCCACAATGTCCTCTGAATATATATATATATATCCTCCCATATATATATATATATATATATATCCTCCCATATATATATATATATATATATATATCCTCCCATATATATATATATATATATATCCTCCCATATATATATATATATATGTCCTCCCATATATATATATATATCCTCCCATATATATATATATCCTCCCATATATATATCTATCCTCCCATATATATATATATATATATATTTTCAATGTATCCCTTTATTCAAGTGATTTTAAGCAATGAAAGCAAGACAGCTGTTATAGGATTTACCTTTCTAGATGGAAAAGGACAAGTAAATAAGGTCTTAAGCTCCATGTCAAGAAAGGGGCACAAC +>syndip_1_chr20:10802576-10803059 +GCCCAACTTAATCCAGTGTGACTCCATTTTAAATCAATTATATCTGCAAAGATCTAATTT +TCAAATGAGGTCACAGTCACAAGTATTGGGGGTTAGGACTTTTGGGGGACATAACCCACA +ATGTCCTCTGAATATATATATATATATCCTCCCATATATATATATATCCTCCCATATATA +TATATATATATATATATATATATGTCCTCCCATATATATATATATCCTCCCATATATATA +TCTATCCTCCCATATATATATATATATATTTTCAATGTATCCCTTTATTCAAGTGATTTT +AAGCAATGAAAGCAAGACAGCTGTTATAGGATTTACCTTTCTAGATGGAAAAGGACAAGT +AAATAAGGTCTTAAGCTCCATGTCAAGAAAGGGGCACAAC +>syndip_2_chr20:10802576-10803059 +GCCCAACTTAATCCAGTGTGACTCCATTTTAAATCAATTATATCTGCAAAGATCTAATTT +TCAAATGAGGTCACAGTCACAAGTATTGGGGGTTAGGACTTTTGGGGGACATAACCCACA +ATGTCCTCTGAATATATATATATATATCCTCCCATATATATATATATATATATATATCCT +CCCATATATATATATATATATATATATCCTCCCATATATATATATATATATATATCCTCC +CATATATATATATATATATGTCCTCCCATATATATATATATATCCTCCCATATATATATA +TATCCTCCCATATATATATCTATCCTCCCATATATATATATATATATATATTTTCAATGT +ATCCCTTTATTCAAGTGATTTTAAGCAATGAAAGCAAGACAGCTGTTATAGGATTTACCT +TTCTAGATGGAAAAGGACAAGTAAATAAGGTCTTAAGCTCCATGTCAAGAAAGGGGCACA +AC +>p:HG002_1_chr20:10802576-10803059 +GCCCAACTTAATCCAGTGTGACTCCATTTTAAATCAATTATATCTGCAAAGATCTAATTT +TCAAATGAGGTCACAGTCACAAGTATTGGGGGTTAGGACTTTTGGGGGACATAACCCACA +ATGTCCTCTGAATATATATATATATATCCTCCCATATATATATATATATATATATATCCT +CCCATATATATATATATATATATATATCCTCCCATATATATATATATATATATATCCTCC +CATATATATATATATATATGTCCTCCCATATATATATATATATCCTCCCATATATATATA +TATCCTCCCATATATATATCTATCCTCCCATATATATATATATATATATATTTTCAATGT +ATCCCTTTATTCAAGTGATTTTAAGCAATGAAAGCAAGACAGCTGTTATAGGATTTACCT +TTCTAGATGGAAAAGGACAAGTAAATAAGGTCTTAAGCTCCATGTCAAGAAAGGGGCACA +AC +>p:HG002_2_chr20:10802576-10803059 +GCCCAACTTAATCCAGTGTGACTCCATTTTAAATCAATTATATCTGCAAAGATCTAATTT +TCAAATGAGGTCACAGTCACAAGTATTGGGGGTTAGGACTTTTGGGGGACATAACCCACA +ATGTCCTCTGAATATATATATATATATCCTCCCATATATATATATATCCTCCCATATATA +TATATATATATATATATATATATGTCCTCCCATATATATATATATCCTCCCATATATATA +TCTATCCTCCCATATATATATATATATATTTTCAATGTATCCCTTTATTCAAGTGATTTT +AAGCAATGAAAGCAAGACAGCTGTTATAGGATTTACCTTTCTAGATGGAAAAGGACAAGT +AAATAAGGTCTTAAGCTCCATGTCAAGAAAGGGGCACAAC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/haps.fa.ref.fa new file mode 100644 index 00000000..3c7e80df --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:10802576-10803059 +GCCCAACTTAATCCAGTGTGACTCCATTTTAAATCAATTATATCTGCAAAGATCTAATTTTCAAATGAGGTCACAGTCACAAGTATTGGGGGTTAGGACTTTTGGGGGACATAACCCACAATGTCCTCTGAATATATATATATATATCCTCCCATATATATATATATATATATATATCCTCCCATATATATATATATATATATATATATCCTCCCATATATATATATATATATATATCCTCCCATATATATATATATATATGTCCTCCCATATATATATATATATCCTCCCATATATATATATATCCTCCCATATATATATCTATCCTCCCATATATATATATATATATATATTTTCAATGTATCCCTTTATTCAAGTGATTTTAAGCAATGAAAGCAAGACAGCTGTTATAGGATTTACCTTTCTAGATGGAAAAGGACAAGTAAATAAGGTCTTAAGCTCCATGTCAAGAAAGGGGCACAAC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/msa.fa new file mode 100644 index 00000000..92110931 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/msa.fa @@ -0,0 +1,50 @@ +>ref_chr20_10802576_10803059 +gcccaacttaatccagtgtgactccattttaaatcaattatatctgcaaagatctaattt +tcaaatgaggtcacagtcacaagtattgggggttaggacttttgggggacataacccaca +atgtcctctgaatatatatatatatatcctcccatatatatatatatatatatatatcct +cccatatatatatatatatatatatatatcctcccatatatatatatatatatatatcct +cccatatatatatatatatatgtcctcccatatatatatatatatcctcccatatatata +tatatcctcccatatatatatctatcctcccatatatatatatatatatatattttcaat +gtatccctttattcaagtgattttaagcaatgaaagcaagacagctgttataggatttac +ctttctagatggaaaaggacaagtaaataaggtcttaagctccatgtcaagaaaggggca +caac +>syndip_1_chr20:10802576-10803059 +gcccaacttaatccagtgtgactccattttaaatcaattatatctgcaaagatctaattt +tcaaatgaggtcacagtcacaagtattgggggttaggacttttgggggacataacccaca +atgtcctctgaatatatatatatatatcctccc----------atatatatatatatcct +ccc--atatatatatatatat--------------------------------------- +-----------------------------atatatatatatatgtcctcccatatatata +tatatcctcccatatatatatctatcctccc----atatatatatatatatattttcaat +gtatccctttattcaagtgattttaagcaatgaaagcaagacagctgttataggatttac +ctttctagatggaaaaggacaagtaaataaggtcttaagctccatgtcaagaaaggggca +caac +>syndip_2_chr20:10802576-10803059 +gcccaacttaatccagtgtgactccattttaaatcaattatatctgcaaagatctaattt +tcaaatgaggtcacagtcacaagtattgggggttaggacttttgggggacataacccaca +atgtcctctgaatatatatatatatatcctcccatatatatatatatatatatatatcct +ccc--atatatatatatatatatatatatcctcccatatatatatatatatatatatcct +cccatatatatatatatatatgtcctcccatatatatatatatatcctcccatatatata +tatatcctcccatatatatatctatcctcccatatatatatatatatatatattttcaat +gtatccctttattcaagtgattttaagcaatgaaagcaagacagctgttataggatttac +ctttctagatggaaaaggacaagtaaataaggtcttaagctccatgtcaagaaaggggca +caac +>p:HG002_1_chr20:10802576-10803059 +gcccaacttaatccagtgtgactccattttaaatcaattatatctgcaaagatctaattt +tcaaatgaggtcacagtcacaagtattgggggttaggacttttgggggacataacccaca +atgtcctctgaatatatatatatatatcctcccatatatatatatatatatatatatcct +ccc--atatatatatatatatatatatatcctcccatatatatatatatatatatatcct +cccatatatatatatatatatgtcctcccatatatatatatatatcctcccatatatata +tatatcctcccatatatatatctatcctcccatatatatatatatatatatattttcaat +gtatccctttattcaagtgattttaagcaatgaaagcaagacagctgttataggatttac +ctttctagatggaaaaggacaagtaaataaggtcttaagctccatgtcaagaaaggggca +caac +>p:HG002_2_chr20:10802576-10803059 +gcccaacttaatccagtgtgactccattttaaatcaattatatctgcaaagatctaattt +tcaaatgaggtcacagtcacaagtattgggggttaggacttttgggggacataacccaca +atgtcctctgaatatatatatatatatcctccc----------atatatatatatatcct +ccc--atatatatatatatat--------------------------------------- +-----------------------------atatatatatatatgtcctcccatatatata +tatatcctcccatatatatatctatcctccc----atatatatatatatatattttcaat +gtatccctttattcaagtgattttaagcaatgaaagcaagacagctgttataggatttac +ctttctagatggaaaaggacaagtaaataaggtcttaagctccatgtcaagaaaggggca +caac diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/msa.fa.fai new file mode 100644 index 00000000..27d080c2 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_10802576_10803059 484 29 60 61 +syndip_1_chr20:10802576-10803059 484 556 60 61 +syndip_2_chr20:10802576-10803059 484 1083 60 61 +p:HG002_1_chr20:10802576-10803059 484 1611 60 61 +p:HG002_2_chr20:10802576-10803059 484 2139 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/output.vcf.gz new file mode 100644 index 00000000..c4e24f7b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/output.vcf.gz.tbi new file mode 100644 index 00000000..0886bda6 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:10802676-10802959/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/base.vcf.gz new file mode 100644 index 00000000..bce613ae Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/base.vcf.gz.tbi new file mode 100644 index 00000000..8f332421 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/comp.vcf.gz new file mode 100644 index 00000000..e0900fb7 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/comp.vcf.gz.tbi new file mode 100644 index 00000000..2e7385c3 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/haps.fa new file mode 100644 index 00000000..f1b19697 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/haps.fa @@ -0,0 +1,60 @@ +>ref_chr20_13848064_13848750 +TCTGTAATCCCAGTTATTCAGGAGGCTGAGGCAGGAGAATCACCTGAACCCGGGAGGCAGAGGTTCCAGTGAGTCGAGATCTTGCCACTGCACTCCAGCCTGGGGGACAGAGGGAAATTGCGTCTCAAAAAAAAAAAAGAAGAAGAAAAGTAGAAGACGAAGATGAAGAAGAATAAGAAGAGAGAAAAGAAGAAGAGAAGGTTAGAGAAAAGAAGAGAAGAGAAGGAGAAGGAGAAGGAGGAGGAGAAGGAGAAGGAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGTCAAATATCTGGAGAAGAAGAAGAAGAGGAAGAAGAAGAAAAGGAAGAAGAAGAAGAAGAGGAAGAGGAAGAAAGAAGAAGAACAAGAAGAAGAAGAAGTCAAATATCTGGAGAAGAAGAAGAAGAAGAGGAAGAAGAAGAAGAAGAGGAGGAGGAAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAAATACAAATATCTGGAGCCGGGATTTGAGCCTGGCCCTTGACATATGTCCTAGGCCTCTTACACTCTCCTTACCAGCCCCTGTCCCTTAGGCCTGGGCCCCTGATTTGCCTGTCAGAGAAGCCAGAGAATC +>syndip_1_chr20:13848064-13848750 +TCTGTAATCCCAGTTATTCAGGAGGCTGAGGCAGGAGAATCACCTGAACCCGGGAGGCAG +AGGTTCCAGTGAGTCGAGATCTTGCCACTGCACTCCAGCCTGGGGGACAGAGGGAAATTG +CGTCTCAAAAAAAAAAAAGAAAAGAAAAGTAGAAGACGAAGATGAAGAAGAATAAGAAGA +GAGAAAAGAAGAAGAGAAGGTTAGAGAAAAGAAGAGAAGGAGAAGGAGAAGGAGGAGGAG +AAGGAGAAGGAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG +AAGAAGAAGAAGAAGAAGTCAAATATCTGGAGAAGAAGAAGAAGAAGAGGAAGAAGAAGA +AGAGGAAGAAGAAGAAGAAGAGGAAGAGGAAGAAAGAAGAAGAACAAGAAGAAGAAGAAG +TCAAATATCTGGAGAAGAAGAAGAAGAAGAGGAGGAAGAAGAAGAAGAAGAGGAGGAGGA +AGAAGAAGAAGAAGAAGAAGAAGAAGAAGCAGGAGCAGGAGAAGAAGAAGAAGAAGAAGA +AGAAGAGGAAGAGGAAGAGGAAGAGGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA +AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAGAAGAC +AAATATCTGGAGCCGGGATTTGAGCCTGGCCCTTGACATATGTCCTAGGCCTCTTACACT +CTCCTTACCAGCCCCTGTCCCTTAGGCCTGGGCCCCTGATTTGCCTGTCAGAGAAGCCAG +AGAATC +>syndip_2_chr20:13848064-13848750 +TCTGTAATCCCAGTTATTCAGGAGGCTGAGGCAGGAGAATCACCTGAACCCGGGAGGCAG +AGGTTCCAGTGAGTCGAGATCTTGCCACTGCACTCCAGCCTGGGGGACAGAGGGAAATTG +CGTCTCAAAAAAAAAAAAGAAAAGAAAAGTAGAAGACGAAGATGAAGAAGAATAAGAAGA +GAGAAAAGAAGAAGAGAAGGTTAGAGAAAAGAAGAGAAGGAGAAGGAGAAGGAGGAGGAG +AAGGAGAAGGAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG +AAGAAGAAGAAGAAGAAGTCAAATATCTGGAGAAGAAGAAGAAGAAGAGGAAGAAGAAGA +AGAGGAAGAAGAAGAAGAAGAGGAAGAGGAAGAAAGAAGAAGAACAAGAAGAAGAAGAAG +TCAAATATCTGGAGAAGAAGAAGAAGAAGAGGAGGAAGAAGAAGAAGAAGAGGAGGAGGA +AGAAGAAGAAGAAGAAGAAGAAGAAGAAGCAGGAGCAGGAGAAGAAGAAGAAGAAGAAGA +AGAAGAGGAAGAGGAAGAGGAAGAGGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA +AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAGAAGACAAATATCTGGAGCCG +GGATTTGAGCCTGGCCCTTGACATATGTCCTAGGCCTCTTACACTCTCCTTACCAGCCCC +TGTCCCTTAGGCCTGGGCCCCTGATTTGCCTGTCAGAGAAGCCAGAGAATC +>p:HG002_1_chr20:13848064-13848750 +TCTGTAATCCCAGTTATTCAGGAGGCTGAGGCAGGAGAATCACCTGAACCCGGGAGGCAG +AGGTTCCAGTGAGTCGAGATCTTGCCACTGCACTCCAGCCTGGGGGACAGAGGGAAATTG +CGTCTCAAAAAAAAAAAAGAAAAGAAAAGTAGAAGACGAAGATGAAGAAGAATAAGAAGA +GAGAAAAGAAGAAGAGAAGGTTAGAGAAAAGAAGAGAAGGAGAAGGAGAAGGAGGAGGAG +AAGGAGAAGGAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG +AAGAAGAAGAAGAAGAAGTCAAATATCTGGAGAAGAAGAAGAAGAAGAGGAAGAAGAAGA +AGAGGAAGAAGAAGAAGAAGAGGAAGAGGAAGAAAGAAGAAGAACAAGAAGAAGAAGAAG +TCAAATATCTGGAGAAGAAGAAGAAGAAGAGGAGGAAGAAGAAGAAGAAGAGGAGGAGGA +AGAAGAAGAAGAAGAAGAAGAAGAAGAAGCAGGAGCAGGAGAAGAAGAAGAAGAAGAAGA +AGAAGAGGAAGAGGAAGAGGAAGAGGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA +AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAGAAGACAAATATCTGGAGCCG +GGATTTGAGCCTGGCCCTTGACATATGTCCTAGGCCTCTTACACTCTCCTTACCAGCCCC +TGTCCCTTAGGCCTGGGCCCCTGATTTGCCTGTCAGAGAAGCCAGAGAATC +>p:HG002_2_chr20:13848064-13848750 +TCTGTAATCCCAGTTATTCAGGAGGCTGAGGCAGGAGAATCACCTGAACCCGGGAGGCAG +AGGTTCCAGTGAGTCGAGATCTTGCCACTGCACTCCAGCCTGGGGGACAGAGGGAAATTG +CGTCTCAAAAAAAAAAAAGAAAAGAAAAGTAGAAGACGAAGATGAAGAAGAATAAGAAGA +GAGAAAAGAAGAAGAGAAGGTTAGAGAAAAGAAGAGAAGGAGAAGGAGAAGGAGGAGGAG +AAGGAGAAGGAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG +AAGAAGAAGAAGAAGAAGTCAAATATCTGGAGAAGAAGAAGAAGAAGAGGAAGAAGAAGA +AGAGGAAGAAGAAGAAGAAGAGGAAGAGGAAGAAAGAAGAAGAACAAGAAGAAGAAGAAG +TCAAATATCTGGAGAAGAAGAAGAAGAAGAGGAGGAAGAAGAAGAAGAAGAGGAGGAGGA +AGAAGAAGAAGAAGAAGAAGAAGAAGAAGCAGGAGCAGGAGAAGAAGAAGAAGAAGAAGA +AGAAGAGGAAGAGGAAGAGGAAGAGGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA +AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAGAAGAC +AAATATCTGGAGCCGGGATTTGAGCCTGGCCCTTGACATATGTCCTAGGCCTCTTACACT +CTCCTTACCAGCCCCTGTCCCTTAGGCCTGGGCCCCTGATTTGCCTGTCAGAGAAGCCAG +AGAATC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/haps.fa.ref.fa new file mode 100644 index 00000000..660d9a4e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:13848064-13848750 +TCTGTAATCCCAGTTATTCAGGAGGCTGAGGCAGGAGAATCACCTGAACCCGGGAGGCAGAGGTTCCAGTGAGTCGAGATCTTGCCACTGCACTCCAGCCTGGGGGACAGAGGGAAATTGCGTCTCAAAAAAAAAAAAGAAGAAGAAAAGTAGAAGACGAAGATGAAGAAGAATAAGAAGAGAGAAAAGAAGAAGAGAAGGTTAGAGAAAAGAAGAGAAGAGAAGGAGAAGGAGAAGGAGGAGGAGAAGGAGAAGGAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGTCAAATATCTGGAGAAGAAGAAGAAGAGGAAGAAGAAGAAAAGGAAGAAGAAGAAGAAGAGGAAGAGGAAGAAAGAAGAAGAACAAGAAGAAGAAGAAGTCAAATATCTGGAGAAGAAGAAGAAGAAGAGGAAGAAGAAGAAGAAGAGGAGGAGGAAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAAATACAAATATCTGGAGCCGGGATTTGAGCCTGGCCCTTGACATATGTCCTAGGCCTCTTACACTCTCCTTACCAGCCCCTGTCCCTTAGGCCTGGGCCCCTGATTTGCCTGTCAGAGAAGCCAGAGAATC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/msa.fa new file mode 100644 index 00000000..19d9b767 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/msa.fa @@ -0,0 +1,75 @@ +>ref_chr20_13848064_13848750 +tctgtaatcccagttattcaggaggctgaggcaggagaatcacctgaacccgggaggcag +aggttccagtgagtcgagatcttgccactgcactccagcctgggggacagagggaaattg +cgtctcaaaaaaaaaaaagaagaagaaaagtagaagacgaagatgaagaagaataagaag +agagaaaagaagaagagaaggttagagaaaagaagagaa--------------------- +----gagaaggagaaggagaaggaggaggagaaggagaaggagaagaagaagaagaagaa +gaagaagaagaagaagaagtcaaatatctgg---agaagaagaagaagaggaagaagaag +aaaaggaagaagaagaagaagaggaagaggaagaaagaagaagaacaagaagaagaagaa +gtcaaatatctggagaagaagaagaagaagaggaagaagaagaagaagaggaggaggaag +aaggagaaggagaaggagaaggagaagga------------------------------- +-----------------------------------------gaaggagaaggagaagaag +aagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaaaata +caaatatctggagccgggatttgagcctggcccttgacatatgtcctaggcctcttacac +tctccttaccagcccctgtcccttaggcctgggcccctgatttgcctgtcagagaagcca +gagaatc +>syndip_1_chr20:13848064-13848750 +tctgtaatcccagttattcaggaggctgaggcaggagaatcacctgaacccgggaggcag +aggttccagtgagtcgagatcttgccactgcactccagcctgggggacagagggaaattg +cgtctcaaaaaaaaaaaagaa-aagaaaagtagaagacgaagatgaagaagaataagaag +agagaaaagaagaagagaaggttagagaaaagaagagaaggagaaggagaaggaggagga +gaaggagaaggagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaa +gaagaagaagaagaagaagtcaaatatctggagaagaagaagaagaagaggaagaagaag +aagaggaagaagaagaagaagaggaagaggaagaaagaagaagaacaagaagaagaagaa +gtcaaatatctggagaagaagaagaagaagaggaggaagaagaagaagaagaggaggagg +aagaagaagaagaagaagaagaagaagaagcaggagcaggagaagaagaagaagaagaag +aagaagaggaagaggaagaggaagaggaagaagaagaagaagaagaagaagaagaagaag +aagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagagaaga +caaatatctggagccgggatttgagcctggcccttgacatatgtcctaggcctcttacac +tctccttaccagcccctgtcccttaggcctgggcccctgatttgcctgtcagagaagcca +gagaatc +>syndip_2_chr20:13848064-13848750 +tctgtaatcccagttattcaggaggctgaggcaggagaatcacctgaacccgggaggcag +aggttccagtgagtcgagatcttgccactgcactccagcctgggggacagagggaaattg +cgtctcaaaaaaaaaaaagaa-aagaaaagtagaagacgaagatgaagaagaataagaag +agagaaaagaagaagagaaggttagagaaaagaagagaaggagaaggagaaggaggagga +gaaggagaaggagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaa +gaagaagaagaagaagaagtcaaatatctggagaagaagaagaagaagaggaagaagaag +aagaggaagaagaagaagaagaggaagaggaagaaagaagaagaacaagaagaagaagaa +gtcaaatatctggagaagaagaagaagaagaggaggaagaagaagaagaagaggaggagg +aagaagaagaagaagaagaagaagaagaagcaggagcaggagaagaagaagaagaagaag +aagaagaggaagaggaagaggaagag---------------gaagaagaagaagaagaag +aagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagagaaga +caaatatctggagccgggatttgagcctggcccttgacatatgtcctaggcctcttacac +tctccttaccagcccctgtcccttaggcctgggcccctgatttgcctgtcagagaagcca +gagaatc +>p:HG002_1_chr20:13848064-13848750 +tctgtaatcccagttattcaggaggctgaggcaggagaatcacctgaacccgggaggcag +aggttccagtgagtcgagatcttgccactgcactccagcctgggggacagagggaaattg +cgtctcaaaaaaaaaaaagaa-aagaaaagtagaagacgaagatgaagaagaataagaag +agagaaaagaagaagagaaggttagagaaaagaagagaaggagaaggagaaggaggagga +gaaggagaaggagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaa +gaagaagaagaagaagaagtcaaatatctggagaagaagaagaagaagaggaagaagaag +aagaggaagaagaagaagaagaggaagaggaagaaagaagaagaacaagaagaagaagaa +gtcaaatatctggagaagaagaagaagaagaggaggaagaagaagaagaagaggaggagg +aagaagaagaagaagaagaagaagaagaagcaggagcaggagaagaagaagaagaagaag +aagaagaggaagaggaagaggaagag---------------gaagaagaagaagaagaag +aagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagagaaga +caaatatctggagccgggatttgagcctggcccttgacatatgtcctaggcctcttacac +tctccttaccagcccctgtcccttaggcctgggcccctgatttgcctgtcagagaagcca +gagaatc +>p:HG002_2_chr20:13848064-13848750 +tctgtaatcccagttattcaggaggctgaggcaggagaatcacctgaacccgggaggcag +aggttccagtgagtcgagatcttgccactgcactccagcctgggggacagagggaaattg +cgtctcaaaaaaaaaaaagaa-aagaaaagtagaagacgaagatgaagaagaataagaag +agagaaaagaagaagagaaggttagagaaaagaagagaaggagaaggagaaggaggagga +gaaggagaaggagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaa +gaagaagaagaagaagaagtcaaatatctggagaagaagaagaagaagaggaagaagaag +aagaggaagaagaagaagaagaggaagaggaagaaagaagaagaacaagaagaagaagaa +gtcaaatatctggagaagaagaagaagaagaggaggaagaagaagaagaagaggaggagg +aagaagaagaagaagaagaagaagaagaagcaggagcaggagaagaagaagaagaagaag +aagaagaggaagaggaagaggaagaggaagaagaagaagaagaagaagaagaagaagaag +aagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagagaaga +caaatatctggagccgggatttgagcctggcccttgacatatgtcctaggcctcttacac +tctccttaccagcccctgtcccttaggcctgggcccctgatttgcctgtcagagaagcca +gagaatc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/msa.fa.fai new file mode 100644 index 00000000..9811e691 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_13848064_13848750 787 29 60 61 +syndip_1_chr20:13848064-13848750 787 864 60 61 +syndip_2_chr20:13848064-13848750 787 1699 60 61 +p:HG002_1_chr20:13848064-13848750 787 2535 60 61 +p:HG002_2_chr20:13848064-13848750 787 3371 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/output.vcf.gz new file mode 100644 index 00000000..0bcc04ec Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/output.vcf.gz.tbi new file mode 100644 index 00000000..d0497bfb Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:13848164-13848650/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/base.vcf.gz new file mode 100644 index 00000000..55275dbf Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/base.vcf.gz.tbi new file mode 100644 index 00000000..6977c129 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/comp.vcf.gz new file mode 100644 index 00000000..d406f1d5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/comp.vcf.gz.tbi new file mode 100644 index 00000000..942eacde Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/haps.fa new file mode 100644 index 00000000..d9ff76c5 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/haps.fa @@ -0,0 +1,110 @@ +>ref_chr20_14861837_14862842 +GCTCTCCTGCTGCTGGCCAAGCAGGACCCCAAGGTCCACTGGGATGTACATACTTATGGTATTATGCTCTGCAATACTTGTGGGGGCTGTGGAATGCACACTTCCAAAGTGAAATAGGACATTGGAGGTTTTATATATAAATATATATATATATATTTATATATATATTTATATATATATATTTATATATATTTATATATATTTATATATATATTTATATATATATAAATATATATAAATATATAAATATATATAAATATATATTTATACATAAATATATAAATATATAATATATATAAATATATATTATACATAAATATATAAATATATATAAATATATATAAATATATATTTATACATAAATATATAAATATATATATATATAAATATATATAAATATATATTTATATATTAATATATATAAATATATTACTATGTATATTTATATATATTTATATAAATATATATAAATATATGTAAATATATATATAAAAATATATATTAATATATAAAAATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATAAATATAAATATATATAAATATATAAAAATATATATATAAATATAAATATATATAAATATATATGTATAAATATATATATAAATATAAATATATATAAATATATATATATAAATATATATATAAATATATATATATAAATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATATATTTTTTTTTAATAGAGAGGATGAAGACCAAAGCAGTGAGTTCCACCTAAGCTGGCCCTTGCCTTTTGTCTAACAGGAAACCCAGTCCTTCCTAATGGGCACAGAATTTTCAGAGAAGAGAGCAGAAG +>syndip_1_chr20:14861837-14862842 +GCTCTCCTGCTGCTGGCCAAGCAGGACCCCAAGGTCCACTGGGATGTACATACTTATGGT +ATTATGCTCTGCAATACTTGTGGGGGCTGTGGAATGCACACTTCCAAAGTGAAATAGGAC +ATTGGAGGTTTTATATATAAATATATATATATATTTATATATATATTTATATATATATAT +ATTTATATATATTTATATATATATTTATATATATATTTATATATATATTTATATATATAT +TTATATATATATTTATATATATATTTATATATATATTTATATATATATTTATATATATTT +ATATATATTTATATATATTTTTATATATTTTTATATATATAAATATATAAAAATATATAT +AAATATATAAAAATATATAAAAATATATAAATATATATAAATATATAAATATATATAAAT +ATATATAAATATATATTTATATATAAATATATATAAATATATATTTATACATAAATATAT +ATAAATATATATTTATACATAAATATATAAATATATATAATATATATAAATATATATTAT +ACATAAATATATAAATATATATTATACATAAATATATAAATATATATAAATATATATAAA +TATATATTTATACATAAATATATAAATATATATATAAATATATATAAATATATATAAATA +TATATATAAATATATATATAAATATATATAAATATATATATAAATATATATATAAATATA +TATAAATATATATAAATATATATATAAATATATATAAATATATATAAATATATATTTATA +TATTAATATATAAATATATATAAATATATATTTATATATTAATATATAAATATATATATA +TTAATATATATAAATATATATAAATATATATTTATATATTAATATATATATATTAATATA +TATATATTTATATATTAATATATATATTTATATATTAATATATATAAATATATTACTATG +TATATTTATATATATTTATATAAATATATATAAATATATGTAAATATATATATAAAAATA +TATATTAATATATAAAATATATATATAAATATAAATAAATATATATATAAATATATATAA +ATAAATATATATATAAATATATATAAATAAATATATAAATATATATAAATATATATATAA +ATATATATAAATATATATAAATATATATAAAAATATATATAAATATATATATAAATATAT +ATAAATATATATATAAATATATATATAAATATATATATAAATATATATAAATATATATAT +AAATATATATAAATATATATATAATTATATATAAATATATATAAATATATATAAATATAT +ATATAAATATATATAAATATATATAAATATATATAAATATATATATAAATATATATAAAT +ATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATAAAT +ATATATAAATATATATATAAATATATATAAATATATATATAAATATAAATATATATGTAT +AAATATATATATAAATATAAATATATATGTATAAATATATATATAAATATATATATATAA +ATATATATATACATATATAAATATATATATAAATATATATAAAAATATATATATATATAT +TTTTTTAATAGAGAGGATGAAGACCAAAGCAGTGAGTTCCACCTAAGCTGGCCCTTGCCT +TTTGTCTAACAGGAAACCCAGTCCTTCCTAATGGGCACAGAATTTTCAGAGAAGAGAGCA +GAAG +>syndip_2_chr20:14861837-14862842 +GCTCTCCTGCTGCTGGCCAAGCAGGACCCCAAGGTCCACTGGGATGTACATACTTATGGT +ATTATGCTCTGCAATACTTGTGGGGGCTGTGGAATGCACACTTCCAAAGTGAAATAGGAC +ATTGGAGGTTTTATATATAAATATATATATATATATTTATATATATATTTATATATATAT +ATTTATATATATTTATATATATTTATATATATATTTTTATATATATTTATATATATTTAT +ATATTTATATATATTTATATATATTTTTATATATATAAATATATAAAAATATATAAATAT +ATATAAATATATAAATATATATAAATATATATTTATACATAAATATATAAATATATATAA +TATATATAAATATATATTATACATAAATATATAAATATATATTATACATAAATATATAAA +TATATATAAATATATATAAATATATATTTATACATAAATATATAAATATATATATATATA +AATATATATAAATATATATTTATATATTAATATATATAAATATATTACTATGTATATTTA +TATATATTTATATAAATATATAAATATATGTAAATATATATATAAAAATATATATTAATA +TATAAAAATATATATATAAATATATATATAAATATATATAAATAAATATATATAAATATA +TATATAAATATATATAAATATATATAAATATATATATAAATATATATAAATATATATAAA +TATATATATAAATATATATATAAATATATATAAATATATATAAATAAATATATAAATATA +TATATAAATATATATAAATATATATATAAATATATATAAATATATATATAAATATATATA +AATATATATATAAATATATATAAATATATATATAAATATATATATAAATATATATAAATA +TATATAAATATATATATATAAATATATATAAATATATATATAAATATAAATATATATAAA +TATATAAAAATATATATATAAATATAAATATATATAAATATATATGTATAAATATATATA +TAAATATAAATATATATAAATATATATATATAAATATATATATAAATATATATAAATATA +TATAAAAATATATATAAATATATATATAAATATATATATAAATATATATAAATATATATA +TAAATATATATAAAAATATATATATATTTTTTTTTTTAATAGAGAGGATGAAGACCAAAG +CAGTGAGTTCCACCTAAGCTGGCCCTTGCCTTTTGTCTAACAGGAAACCCAGTCCTTCCT +AATGGGCACAGAATTTTCAGAGAAGAGAGCAGAAG +>p:HG002_1_chr20:14861837-14862842 +GCTCTCCTGCTGCTGGCCAAGCAGGACCCCAAGGTCCACTGGGATGTACATACTTATGGT +ATTATGCTCTGCAATACTTGTGGGGGCTGTGGAATGCACACTTCCAAAGTGAAATAGGAC +ATTGGAGGTTTTATATATAAATATATATATATATATTTATATATATATTTATATATATAT +ATTTATATATATTTATATATATTTATATATATATTTTTATATATATTTATATATATTTAT +ATATTTATATATATTTATATATATTTTTATATATATAAATATATAAAAATATATAAATAT +ATATAAATATATAAATATATATAAATATATATTTATACATAAATATATAAATATATATAA +TATATATAAATATATATTATACATAAATATATAAATATATATTATACATAAATATATAAA +TATATATAAATATATATAAATATATATTTATACATAAATATATAAATATATATATATATA +AATATATATAAATATATATTTATATATTAATATATATAAATATATTACTATGTATATTTA +TATATATTTATATAAATATATAAATATATGTAAATATATATATAAAAATATATATTAATA +TATAAAAATATATATATAAATATATATATAAATATATATAAATAAATATATATAAATATA +TATATAAATATATATAAATATATATAAATATATATATAAATATATATAAATATATATAAA +TATATATATAAATATATATATAAATATATATAAATATATATAAATAAATATATAAATATA +TATATAAATATATATAAATATATATATAAATATATATAAATATATATATAAATATATATA +AATATATATATAAATATATATAAATATATATATAAATATATATATAAATATATATAAATA +TATATAAATATATATATATAAATATATATAAATATATATATAAATATAAATATATATAAA +TATATAAAAATATATATATAAATATAAATATATATAAATATATATGTATAAATATATATA +TAAATATAAATATATATAAATATATATATATAAATATATATATAAATATATATAAATATA +TATAAAAATATATATAAATATATATATAAATATATATATAAATATATATAAATATATATA +TAAATATATATAAAAATATATATATATTTTTTTTTTTAATAGAGAGGATGAAGACCAAAG +CAGTGAGTTCCACCTAAGCTGGCCCTTGCCTTTTGTCTAACAGGAAACCCAGTCCTTCCT +AATGGGCACAGAATTTTCAGAGAAGAGAGCAGAAG +>p:HG002_2_chr20:14861837-14862842 +GCTCTCCTGCTGCTGGCCAAGCAGGACCCCAAGGTCCACTGGGATGTACATACTTATGGT +ATTATGCTCTGCAATACTTGTGGGGGCTGTGGAATGCACACTTCCAAAGTGAAATAGGAC +ATTGGAGGTTTTATATATAAATATATATATATATTTATATATATATTTATATATATATAT +ATTTATATATATTTATATATATATTTATATATATATTTATATATATATTTATATATATAT +TTATATATATATTTATATATATATTTATATATATATTTATATATATATTTATATATATTT +ATATATATTTATATATATTTTTATATATTTTTATATATATAAATATATAAAAATATATAT +AAATATATAAAAATATATAAAAATATATAAATATATATAAATATATAAATATATATAAAT +ATATATAAATATATATTTATATATAAATATATATAAATATATATTTATACATAAATATAT +ATAAATATATATTTATACATAAATATATAAATATATATAATATATATAAATATATATTAT +ACATAAATATATAAATATATATTATACATAAATATATAAATATATATAAATATATATAAA +TATATATTTATACATAAATATATAAATATATATATAAATATATATAAATATATATAAATA +TATATATAAATATATATATAAATATATATAAATATATATATAAATATATATATAAATATA +TATAAATATATATAAATATATATATAAATATATATAAATATATATAAATATATATTTATA +TATTAATATATAAATATATATAAATATATATTTATATATTAATATATAAATATATATATA +TTAATATATATAAATATATATAAATATATATTTATATATTAATATATATATATTAATATA +TATATATTTATATATTAATATATATATTTATATATTAATATATATAAATATATTACTATG +TATATTTATATATATTTATATAAATATATATAAATATATGTAAATATATATATAAAAATA +TATATTAATATATAAAATATATATATAAATATAAATAAATATATATATAAATATATATAA +ATAAATATATATATAAATATATATAAATAAATATATAAATATATATAAATATATATATAA +ATATATATAAATATATATAAATATATATAAAAATATATATAAATATATATATAAATATAT +ATAAATATATATATAAATATATATATAAATATATATATAAATATATATAAATATATATAT +AAATATATATAAATATATATATAATTATATATAAATATATATAAATATATATAAATATAT +ATATAAATATATATAAATATATATAAATATATATAAATATATATATAAATATATATAAAT +ATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATAAAT +ATATATAAATATATATATAAATATATATAAATATATATATAAATATAAATATATATGTAT +AAATATATATATAAATATAAATATATATGTATAAATATATATATAAATATATATATATAA +ATATATATATACATATATAAATATATATATAAATATATATAAAAATATATATATATATAT +TTTTTTAATAGAGAGGATGAAGACCAAAGCAGTGAGTTCCACCTAAGCTGGCCCTTGCCT +TTTGTCTAACAGGAAACCCAGTCCTTCCTAATGGGCACAGAATTTTCAGAGAAGAGAGCA +GAAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/haps.fa.ref.fa new file mode 100644 index 00000000..235ee6a4 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:14861837-14862842 +GCTCTCCTGCTGCTGGCCAAGCAGGACCCCAAGGTCCACTGGGATGTACATACTTATGGTATTATGCTCTGCAATACTTGTGGGGGCTGTGGAATGCACACTTCCAAAGTGAAATAGGACATTGGAGGTTTTATATATAAATATATATATATATATTTATATATATATTTATATATATATATTTATATATATTTATATATATTTATATATATATTTATATATATATAAATATATATAAATATATAAATATATATAAATATATATTTATACATAAATATATAAATATATAATATATATAAATATATATTATACATAAATATATAAATATATATAAATATATATAAATATATATTTATACATAAATATATAAATATATATATATATAAATATATATAAATATATATTTATATATTAATATATATAAATATATTACTATGTATATTTATATATATTTATATAAATATATATAAATATATGTAAATATATATATAAAAATATATATTAATATATAAAAATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATAAATATAAATATATATAAATATATAAAAATATATATATAAATATAAATATATATAAATATATATGTATAAATATATATATAAATATAAATATATATAAATATATATATATAAATATATATATAAATATATATATATAAATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATATATTTTTTTTTAATAGAGAGGATGAAGACCAAAGCAGTGAGTTCCACCTAAGCTGGCCCTTGCCTTTTGTCTAACAGGAAACCCAGTCCTTCCTAATGGGCACAGAATTTTCAGAGAAGAGAGCAGAAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/msa.fa new file mode 100644 index 00000000..35fac4e0 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/msa.fa @@ -0,0 +1,155 @@ +>ref_chr20_14861837_14862842 +gctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggt +attatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggac +attggaggttttatatataaatatatatatatatatttatatatatatttatatatatat +atttatatatatt----------------------------------------------- +---------------tatatatatttatatatatatttatat------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------atatataaatatatataaatatataaatatat +ataaatatatatttatacataaatatataaatatata----------------------- +----atatatataaatatatattatacataaatatataaatatatataaatatatataaa +tatatatttatacataaatatataaatatat------atatatataaatatatataa--- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------atatatatttatatattaatatatataaatatattactatg +tatatttatatatatttatataaatatatataaatatatgtaaatatatatataaaaata +tatattaatatataaaa---------atatatat-------------------------- +ataaatatatataaatatatatataaat--atatataaat-------------------- +------------------------------------------------------------ +--------------------------------------atatatatataaatatatataa +atatatatataaatatatataaatatatatataaatatatataaat--------atatat +atataaatatatataa----------------------atatatatataaatatatataa +atatatatataaatataaatatatataaatatataaaaatatatatataaatataaatat +atataaatatatatgtataaatatatatataaatataaatatatataaatatatatatat +aaatatatatataaat------------------------------atatatatataaat +atatatataaatatatataaatatatatataaatatatataaatatatatatatatattt +ttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcccttgcct +tttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaagagagca +gaag +>syndip_1_chr20:14861837-14862842 +gctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggt +attatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggac +attggaggttttatatataaatatatatatatatttatatatatatttatatatatatat +atttatatatatttatatatatatttatatatatatttatatatatatttatatatatat +ttatatatatatttatatatatatttatatatatatttatatatatatttatatatattt +atatatatttatatatatttttatatatttttatatatataaatatataaaaatatatat +aaatatataaaaatatataaaaatatataaatatatataaatatataaatatatataaat +atatataaatatatatttatatataaatatatataaatatatatttatacataaatatat +ataaatatatatttatacataaatatataaatatatataatatatataaatatatattat +acataaatatataaatatatattatacataaatatataaatatatataaatatatataaa +tatatatttatacataaatatataaatatatatataaatatatataaatatatataaata +tatatataaatatatatataaatatatataaatatatatataaatatatatataaatata +tataaatatatataaatatatatataaatatatataaatatatataaatatatatttata +tattaatatataaatatatataaatatatatttatatattaatatataaatatatatata +ttaatatatataaatatatataaatatatatttatatattaatatatatatattaatata +tatatatttatatattaatatatatatttatatattaatatatataaatatattactatg +tatatttatatatatttatataaatatatataaatatatgtaaatatatatataaaaata +tatattaatatataaaatatatatataaatataaataaatatatatataaatatatataa +ataaatatatatataaatatatataaataaatatataaatatatataaatatatatataa +atatatataaatatatataaatatatataaaaatatatataaatatatatataaatatat +ataaatatatatataaatatatatataaatatatatataaatatatataaatatatatat +aaatatatataaatatatatataattatatataaatatatataaatatatataaatatat +atataaatatatataaatatatataaatatatataaatatatatataaatatatataaat +atatatatataaatatatataaatatatatataaatatatataaatatatatatataaat +atatataaatatatatataaatatatataaatatatatataaatataaatatatatgtat +aaatatatatataaatataaatatatatgtataaatatatatataaatatatatatataa +atatatatatacatatataaatatatatataaatatatataaaaatatatatatatatat +ttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcccttgcct +tttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaagagagca +gaag +>syndip_2_chr20:14861837-14862842 +gctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggt +attatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggac +attggaggttttatatataaatatatatatatatatttatatatatatttatatatatat +atttatatatatt----------------------------------------------- +---------------tatatatatttatatatatatttttatatatatttatatatatt- +-tatatatttatatatatttatatatatttttatatatataaatatataaaa-------- +------------------------------------------------------------ +----------------------------atatataaatatatataaatatataaatatat +ataaatatatatttatacataaatatataaatatatataatatatataaatatatattat +acataaatatataaatatatattatacataaatatataaatatatataaatatatataaa +tatatatttatacataaatatataaatatat------atatatataaatatatataa--- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------atatatatttatatattaatatatataaatatattactatg +tatatttatatatatttatataa--atatataaatatatgtaaatatatatataaaaata +tatattaatatataaaa---------atatatatataaatatatatataaatatatataa +ataaatatatataaatatatatataaat--atatataaatatatataaatatatatataa +atatatataaatatatataaatatatatataaatatatatataaatatatataaatatat +ataaataaatatataaatatatatataaatatatataaatatatatataaatatatataa +atatatatataaatatatataaatatatatataaatatatataaat--------atatat +ataaatatatatataaatatatataaatatatataaatatatatatataaatatatataa +atatatatataaatataaatatatataaatatataaaaatatatatataaatataaatat +atataaatatatatgtataaatatatatataaatataaatatatataaatatatatatat +aaatatatatataaatatatataaatatatataaaaatatatataaatatatatataaat +atatatataaatatatataaatatatatataaatatatataaaaatatatatatattttt +ttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcccttgcct +tttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaagagagca +gaag +>p:HG002_1_chr20:14861837-14862842 +gctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggt +attatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggac +attggaggttttatatataaatatatatatatatatttatatatatatttatatatatat +atttatatatatt----------------------------------------------- +---------------tatatatatttatatatatatttttatatatatttatatatatt- +-tatatatttatatatatttatatatatttttatatatataaatatataaaa-------- +------------------------------------------------------------ +----------------------------atatataaatatatataaatatataaatatat +ataaatatatatttatacataaatatataaatatatataatatatataaatatatattat +acataaatatataaatatatattatacataaatatataaatatatataaatatatataaa +tatatatttatacataaatatataaatatat------atatatataaatatatataa--- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------atatatatttatatattaatatatataaatatattactatg +tatatttatatatatttatataa--atatataaatatatgtaaatatatatataaaaata +tatattaatatataaaa---------atatatatataaatatatatataaatatatataa +ataaatatatataaatatatatataaat--atatataaatatatataaatatatatataa +atatatataaatatatataaatatatatataaatatatatataaatatatataaatatat +ataaataaatatataaatatatatataaatatatataaatatatatataaatatatataa +atatatatataaatatatataaatatatatataaatatatataaat--------atatat +ataaatatatatataaatatatataaatatatataaatatatatatataaatatatataa +atatatatataaatataaatatatataaatatataaaaatatatatataaatataaatat +atataaatatatatgtataaatatatatataaatataaatatatataaatatatatatat +aaatatatatataaatatatataaatatatataaaaatatatataaatatatatataaat +atatatataaatatatataaatatatatataaatatatataaaaatatatatatattttt +ttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcccttgcct +tttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaagagagca +gaag +>p:HG002_2_chr20:14861837-14862842 +gctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggt +attatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggac +attggaggttttatatataaatatatatatatatttatatatatatttatatatatatat +atttatatatatttatatatatatttatatatatatttatatatatatttatatatatat +ttatatatatatttatatatatatttatatatatatttatatatatatttatatatattt +atatatatttatatatatttttatatatttttatatatataaatatataaaaatatatat +aaatatataaaaatatataaaaatatataaatatatataaatatataaatatatataaat +atatataaatatatatttatatataaatatatataaatatatatttatacataaatatat +ataaatatatatttatacataaatatataaatatatataatatatataaatatatattat +acataaatatataaatatatattatacataaatatataaatatatataaatatatataaa +tatatatttatacataaatatataaatatatatataaatatatataaatatatataaata +tatatataaatatatatataaatatatataaatatatatataaatatatatataaatata +tataaatatatataaatatatatataaatatatataaatatatataaatatatatttata +tattaatatataaatatatataaatatatatttatatattaatatataaatatatatata +ttaatatatataaatatatataaatatatatttatatattaatatatatatattaatata +tatatatttatatattaatatatatatttatatattaatatatataaatatattactatg +tatatttatatatatttatataaatatatataaatatatgtaaatatatatataaaaata +tatattaatatataaaatatatatataaatataaataaatatatatataaatatatataa +ataaatatatatataaatatatataaataaatatataaatatatataaatatatatataa +atatatataaatatatataaatatatataaaaatatatataaatatatatataaatatat +ataaatatatatataaatatatatataaatatatatataaatatatataaatatatatat +aaatatatataaatatatatataattatatataaatatatataaatatatataaatatat +atataaatatatataaatatatataaatatatataaatatatatataaatatatataaat +atatatatataaatatatataaatatatatataaatatatataaatatatatatataaat +atatataaatatatatataaatatatataaatatatatataaatataaatatatatgtat +aaatatatatataaatataaatatatatgtataaatatatatataaatatatatatataa +atatatatatacatatataaatatatatataaatatatataaaaatatatatatatatat +ttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcccttgcct +tttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaagagagca +gaag diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/msa.fa.fai new file mode 100644 index 00000000..95952e07 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_14861837_14862842 1744 29 60 61 +syndip_1_chr20:14861837-14862842 1744 1837 60 61 +syndip_2_chr20:14861837-14862842 1744 3645 60 61 +p:HG002_1_chr20:14861837-14862842 1744 5454 60 61 +p:HG002_2_chr20:14861837-14862842 1744 7263 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/output.vcf.gz new file mode 100644 index 00000000..8600c256 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:14861937-14862742/output.vcf.gz.tbi new file mode 100644 index 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--- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16257741-16259346/haps.fa @@ -0,0 +1,161 @@ +>ref_chr20_16257641_16259446 +CTGAGATTCCTGCCACCTTTGCCCCTTACTTTTCTCACCCCGTTCACTGAGGGCCCTCAAGTCTGTTTCTAAGCAGCAGCCTGAGGGATCCATTTTTATAATCTGAAATCAGATATCATACCCACACCCCAAAACACACACACTCCTTCCCCATCCCAAAGAGACACACCCCTTCCCCATCCCAAAGAGACACACCCCTTCCCCATCCCAAAGAGACACACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCATCCCAAACACACACACCCCTTTCCCATCCCAAACACACACACCCATTGCCCATCCTAAACACACACACACCTTGCCTTCGCAAACACACACACCCCTTCCCCATCACAAACACACACACCCTTTCCCTATCCCATGCACACACACCTTCCACTTCCCAAACACACACACCCCTTCCCCATGCCAAACACACACAACCCTTCCCCAATTCTAAACACACACACCTCTTCCCCATCCCAAACACAAACACCCCTTCCCCATCCCAAACACACCCACCCTTTCCTGCATGCCAAACACCCACACCCCTTCCCCATCCCAAACACACACCCCATCCCCAATTCCAAACACACACACCCCTTCCCCATCCCAAACACACACACCCCTTCCACATGAGAAACACACACACCCCTTCTCATCCCAAACACAAACACACCCATTCCCCATCACAAACACACGCACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCAATTGTAAACACACACACCCCTTCTCCAATTCCAAACACACACACCCCTTCCCATCACAAACACACACACACCTTCCACATCCCAAATACACACACCCCTTCCCATCTCAAACACACACATCCCTTCCCCAATTCCAAAAACACACACCCCTTCCCCATCCCAAACACCCCCACCCCTTCCCATCCCCAAACACACACCCCTTTCCCATCCCAAATACACAAACCCCTTCCCTAATTCCACACACACACACCCCTTCCCCATCCCAAACACACATACCCCTTCCCATCCCAAAGACACACACTCATTCTGCATCCCAAACACACACACCCCTTCCCATCCCAAACACACACACTACCTCCGCATCCCAAACACATATACCCCTTCCCCATCCCAAACACATACACCCCTTCCCCATCGCCAACACACACACCCCTTCCCCATCCCAAACACACACACCCCTTTCCATCCCAAACACACACCCATTCCCCATCCCAGACACACCCACCCGTTCCCCATCCCAGACACACACAACCCTTCCCCAATTCCAAACACACACCCCTTCCCATCCCAAACACACACACCCATTTCCCATCCCAGACACATCCACCCCTTCCACAACTCTGAACACCCACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCATCCCAAACACACACACCCATTCCCCATCCCAAACACACACACCCATTCCCCATCCCAAACACAACCACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCATCCCAAACACACACACACCTTCCCCATCCCAAACACACCCACCCTTACTCCATCTCAAACATGTACACCCCTTCCCCTATCCCAAAATACACACATCCATCCCTACACACCCTCACCCATTTCCCCATCCCAGAACCTATGCACCAACTCAGTTTATTTGAACATGCCAGGCACTGAACTAAGAGAACCAAAGTAGCAGGAGGAATACGGTGTTGTCCTCCCAGAACTTACCCCCTGCACGGGAGTCAGCCAGGGAAG +>syndip_1_chr20:16257641-16259446 +CTGAGATTCCTGCCACCTTTGCCCCTTACTTTTCTCACCCCGTTCACTGAGGGCCCTCAA +GTCTGTTTCTAAGCAGCAGCCTGAGGGATCCATTTTTATAATCTGAAATCAGATATCATA +CCCACACCCCAAAACACACACACTCCTTCCCCATCCCAAAGAGACACACCCCTTCCCCAT +CCCAAAGAGACACACCCCTTCCCCATCCCAAAGAGACACACCCCTTCCCCATCCCAAACA +CACACACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCATCCCAAACACACACACC +CCTTTCCCATCCCAAACACACACACCCATTGCCCATCCTAAACACACACACACCTTCCCT +TCGCAAACACACACACCCCTTCCCCATCACAAACACACACACCCTTTCCCTATCCCATGC +ACACACACCTTCCACTTCCCAAACACACACACCCCTTCCCCATCCCAAACACACACAACC +CTTCCCCAATTCTAAACACACACACCTCTTCCCCATCCCAAACACAAACACCCCTTCCCC +ATCCCAAACACACCCACCCTTTCCTGCATCCCAAACACCCACACCCCTTCCCCATCCCAA +ACACACACCCCATCCCCAATTCCAAACACACACACCCCTTCCCCATCCCAAACACACACA +CCCCTTCCACATCAGAAACACACACACCCCTTCTCATCCCAAACACAAACACACCCATTC +CCCATCACAAACACACGCACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCAATTC +TAAACACACACACCCCTTCCCCATCCCAAACACACACCCCCCTTCCCCATCCCAAACACA +CACCCCCCTTCCCCATCCCAAACACACCCACCCCTTCCCACATCCCAAACACACACACCC +CTTCCCTATCCCAAACACACACTCCATCCCCAATTCCAAACACACACACCCCTTCCCCAT +CCCAAACACACACACCCCTTCCCCCATCCCAAACGCACACACCCCTTCCCTATCCCAAAC +ACACACCCCTTCCCTTTCCAAAACACACCCATCCCTTCCCCATCCCAAACACACACAACC +CTTCCCATCCCAGACACACCCACCCCTTCCCATCTCAAATACACGCAACCCTTCCCCATC +CCAAACACACACACCTATTCCCCATCCGAAACACACACACCCCTTCCTCATCCCACACAC +ACCCATTCCCCATCCCAGACACACCCATCCCTTCCCCATACTAAACACAACCACCCCTTC +CCCATCCCACACACACACACCCCTTCCCCAATTCCAAACACACACACCCCTTCCCCATTC +AAAACACACGCACCCCTTCCCATCTGAAACACACCCACTCCTTCCCATCTGAAACACACC +CACTCCTTCCCATCCCAAACACACCCACTCCTTCCCATCCCAAACACACACACCCCTTCC +CCATCCCAAAAACACACACCCTTTCGCAATCCCAAATACACAAGCCCCTTCCCAAATTCC +ACACACACACACCTCTTCCCCATCCCAAACAAACCCACCCTTTCCCCATTCGAAACACAC +ACACCCCTTCTCCAATTCCAAACACACACACCCCTTCCCATCTCAAACACACGGACACCT +TCCACATCCCAAATACACACACCCCTTCCCATCCCAAACACACACATCCCTTCCCCAATT +CCAAAAACACACACCCCTTCCCCATCCCAAACACCCCCACCCCTTCCCATCCCCAAAACA +CACACCCCTTTCCCATCCCAAATACACAAACCCCTTCCCTAATTCCACACACACACACCC +CTTCCCCATCCCAAACACACATACCCCTTCCCATCCCAAAGACACACACTCATTCTGCAT +CCCAAACACACACACCCCTTCCCATCCCAAACACACACACTACCTCCGCATCCCAAACAC +ATATACCCCTTCCCCATCCCAAACACATACACCCCTTCCCCATCGCCAACACACACACCC +CTTCCCCATCCCAAACACACACACCCCTTTCCATCCCAAACACACACCCATTCCCCATCC +CAGACACACCCACCCGTTCCCCATCCCAGACACACACAACCCTTCCCCAATTCCAAACAC +ACACCCCTTCCCATCCCAAACACACACACCCATTTCCCATCCCAGACACATCCACCCCTT +CCACAACTCTGAACACCCACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCATCCC +AAACACACACACCCATTCCCCATCCCAAACACACACACCCATTCCCCATCCCAAACACAA +CCACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCATCCCAAACACACACACACCT +TCCCCATCCCAAACACACCCACCCTTACTCCATCTCAAACATGTACACCCCTTCCCCTAT +CCCAAAATACACACATCCATCCCTACACACCCTCACCCATTTCCCCATCCCAGAACCTAT +GCACCAACTCAGTTTATTTGAACATGCCAGGCACTGAACTAAGAGAACCAAAGTAGCAGG +AGGAATACGGTGTTGTCCTCCCAGAACTTACCCCCTGCACGGGAGTCAGCCAGGGAAG +>syndip_2_chr20:16257641-16259446 +CTGAGATTCCTGCCACCTTTGCCCCTTACTTTTCTCACCCCGTTCACTGAGGGCCCTCAA +GTCTGTTTCTAAGCAGCAGCCTGAGGGATCCATTTTTATAATCTGAAATCAGATATCATA +CCCACACCCCAAAACACACACACTCCTTCCCCATCCCAAAGAGACACACCCCTTCCCCAT +CCCAAAGAGACACACCCCTTCCCCATCCCAAAGAGACACACCCCTTCCCCATCCCAAACA +CACACACCCCTTCCCCATCCCAAACACACACACCCCTTTCCCATCCCAAACACACACACC +CATTGCCCATCCTAAACACACACACACCTTCCCTTCGCAAACACACACACCCCTTCCCCA +TCACAAACACACACACCCTTTCCCTATCCCATGCACACACACCTTCCACTTCCCAAACAC +ACACACCCCTTCCCCATCCCAAACACACACAACCCTTCCCCAATTCTAAACACACACACC +TCTTCCCCATCCCAAACACAAACACCCCTTCCCCATCCCAAACACACCCACCCTTTCCTG +CATCCCAAACACACACACCCCTTCCCCATCCCAAACACACACCCCATCCCCAATTCCAAA +CACACACACCCCTTCCCCATCCCAAACACACACACCCCTTCCACATCAGAAACACACACA +CCCCTTCTCATCCCAAACACAAACACACCCATTCCCCATCACAAACACACGCACCCCTTC +CCCATCCCAAACATACACACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCAATTC +TAAACACACACACCCCTTCCCCATCCCAAACACACACCCCCCTTCCCCATCCCAAACACA +CACCCCCCTTCCCCATCCCAAACACACCCACCCCTTCCCACATCCCAAACACACACACCC +CTTCCCTATCCCAAACACACACTCCATCCCCAATTCCAAACACACACACCCCTTCCCCAT +CCCAAACACACACACCCCTTCCCCCATCCCAAACGCACACACCCCTTCCCTATCCCAAAC +ACACACCCCTTCCCTTTCCAAAACACACCCATCCCTTCCCCATCCCAAACACACACAACC +CTTCCCATCCCAGACACACCCACCCCTTCCCATCTCAAATACACGCAACCCTTCCCCATC +CCAAACACACACACCCCTTCCCCATCCCAAAAACACACACCCTTTCGCAATCCCAAATAC +ACAAGCCCCTTCCCAAATTCCACACACACACACCTCTTCCCCATCCCAAACAAACCCACC +CTTTCCCCATTCGAAACACACACACCCCTTCTCCAATTCCAAACACACACACCCCTTCCC +ATCTCAAACACACGGACACCTTCCACATCCCAAATACACACACCCCTTCCCATCCCAAAC +ACACACATCCCTTCCCCAATTCCAAAAACACACACCCCTTCCCCATCCCAAACACCCCCA +CCCCTTCCCATCCCCAAAACACACACCCCTTTCCCATCCCAAATACACAAACCCCTTCCC +TAATTCCACACACACACACCCCTTCCCCATCCCAAACACACATACCCCTTCCCATCCCAA +AGACACACACTCATTCTGCATCCCAAACACACACACCCCTTCCCATCCCAAACACACACA +CTACCTCCGCATCCCAAACACATATACCCCTTCCCCATCCCAAACACATACACCCCTTCC +CCATCGCCAACACACACACCCCTTCCCCATCCCAAACACACACACCCCTTTCCATCCCAA +ACACACACCCATTCCCCATCCCAGACACACCCACCCGTTCCCCATCCCAGACACACACAA +CCCTTCCCCAATTCCAAACACACACCCCTTCCCATCCCAAACACACACACCCATTTCCCA +TCCCAGACACATCCACCCCTTCCACAACTCCGAACACCCACCCCTTCCCCATCCCAAACA +CACACACCCCTTCCCCATCCCAAACACACACACCCATTCCCCATCCCAAACACACACACC +CATTCCCCATCCCAAACACAACCACCCCTTCCCCATCCCAAACACACACACCCCTTCCCC +ATCCCAAACACACACACACCTTCCCATCCCAAACACACACACCCCTTCCCCATCCCAAAC +ACACCCACCCTTACTCCATCTCAAACATGTACACCCCTTCCCCTATCCCAAAATACACAC +ATCCATCCCTACACACCCTCACCCATTTCCCCATCCCAGAACCTATGCACCAACTCAGTT +TATTTGAACATGCCAGGCACTGAACTAAGAGAACCAAAGTAGCAGGAGGAATACGGTGTT +GTCCTCCCAGAACTTACCCCCTGCACGGGAGTCAGCCAGGGAAG +>p:HG002_1_chr20:16257641-16259446 +CTGAGATTCCTGCCACCTTTGCCCCTTACTTTTCTCACCCCGTTCACTGAGGGCCCTCAA +GTCTGTTTCTAAGCAGCAGCCTGAGGGATCCATTTTTATAATCTGAAATCAGATATCATA +CCCACACCCCAAAACACACACACTCCTTCCCCATCCCAAAGAGACACACCCCTTCCCCAT +CCCAAAGAGACACACCCCTTCCCCATCCCAAAGAGACACACCCCTTCCCCATCCCAAACA +CACACACCCCTTCCCCATCCCAAACACACACACCCCTTTCCCATCCCAAACACACACACC +CATTGCCCATCCTAAACACACACACACCTTCCCTTCGCAAACACACACACCCCTTCCCCA +TCACAAACACACACACCCTTTCCCTATCCCATGCACACACACCTTCCACTTCCCAAACAC +ACACACCCCTTCCCCATCCCAAACACACACAACCCTTCCCCAATTCTAAACACACACACC +TCTTCCCCATCCCAAACACAAACACCCCTTCCCCATCCCAAACACACCCACCCTTTCCTG +CATCCCAAACACACACACCCCTTCCCCATCCCAAACACACACCCCATCCCCAATTCCAAA +CACACACACCCCTTCCCCATCCCAAACACACACACCCCTTCCACATCAGAAACACACACA +CCCCTTCTCATCCCAAACACAAACACACCCATTCCCCATCACAAACACACGCACCCCTTC +CCCATCCCAAACATACACACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCAATTC +TAAACACACACACCCCTTCCCCATCCCAAACACACACCCCCCTTCCCCATCCCAAACACA +CACCCCCCTTCCCCATCCCAAACACACCCACCCCTTCCCACATCCCAAACACACACACCC +CTTCCCTATCCCAAACACACACTCCATCCCCAATTCCAAACACACACACCCCTTCCCCAT +CCCAAACACACACACCCCTTCCCCCATCCCAAACGCACACACCCCTTCCCTATCCCAAAC +ACACACCCCTTCCCTTTCCAAAACACACCCATCCCTTCCCCATCCCAAACACACACAACC +CTTCCCATCCCAGACACACCCACCCCTTCCCATCTCAAATACACGCAACCCTTCCCCATC +CCAAACACACACACCCCTTCCCCATCCCAAAAACACACACCCTTTCGCAATCCCAAATAC +ACAAGCCCCTTCCCAAATTCCACACACACACACCTCTTCCCCATCCCAAACAAACCCACC +CTTTCCCCATTCGAAACACACACACCCCTTCTCCAATTCCAAACACACACACCCCTTCCC +ATCTCAAACACACGGACACCTTCCACATCCCAAATACACACACCCCTTCCCATCCCAAAC +ACACACATCCCTTCCCCAATTCCAAAAACACACACCCCTTCCCCATCCCAAACACCCCCA +CCCCTTCCCATCCCCAAAACACACACCCCTTTCCCATCCCAAATACACAAACCCCTTCCC +TAATTCCACACACACACACCCCTTCCCCATCCCAAACACACATACCCCTTCCCATCCCAA +AGACACACACTCATTCTGCATCCCAAACACACACACCCCTTCCCATCCCAAACACACACA +CTACCTCCGCATCCCAAACACATATACCCCTTCCCCATCCCAAACACATACACCCCTTCC +CCATCGCTGAACATGCCAGGCACTGAACTAAGAGAACCAAAGTAGCAGGAGGAATACGGT +GTTGTCCTCCCAGAACTTACCCCCTGCACGGGAGTCAGCCAGGGAAG +>p:HG002_2_chr20:16257641-16259446 +CTGAGATTCCTGCCACCTTTGCCCCTTACTTTTCTCACCCCGTTCACTGAGGGCCCTCAA +GTCTGTTTCTAAGCAGCAGCCTGAGGGATCCATTTTTATAATCTGAAATCAGATATCATA +CCCACACCCCAAAACACACACACTCCTTCCCCATCCCAAAGAGACACACCCCTTCCCCAT +CCCAAAGAGACACACCCCTTCCCCATCCCAAAGAGACACACCCCTTCCCCATCCCAAACA +CACACACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCATCCCAAACACACACACC +CCTTTCCCATCCCAAACACACACACCCATTGCCCATCCTAAACACACACACACCTTCCCT +TCGCAAACACACACACCCCTTCCCCATCACAAACACACACACCCTTTCCCTATCCCATGC +ACACACACCTTCCACTTCCCAAACACACACACCCCTTCCCCATCCCAAACACACACAACC +CTTCCCCAATTCTAAACACACACACCTCTTCCCCATCCCAAACACAAACACCCCTTCCCC +ATCCCAAACACACCCACCCTTTCCTGCATCCCAAACACCCACACCCCTTCCCCATCCCAA +ACACACACCCCATCCCCAATTCCAAACACACACACCCCTTCCCCATCCCAAACACACACA +CCCCTTCCACATCAGAAACACACACACCCCTTCTCATCCCAAACACAAACACACCCATTC 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+CCAAAAACACACACCCCTTCCCCATCCCAAACACCCCCACCCCTTCCCATCCCCAAAACA +CACACCCCTTTCCCATCCCAAATACACAAACCCCTTCCCTAATTCCACACACACACACCC +CTTCCCCATCCCAAACACACATACCCCTTCCCATCCCAAAGACACACACTCATTCTGCAT +CCCAAACACACACACCCCTTCCCATCCCAAACACACACACTACCTCCGCATCCCAAACAC +ATATACCCCTTCCCCATCCCAAACACATACACCCCTTCCCCATCGCCAACACACACACCC +CTTCCCCATCCCAAACACACACACCCCTTTCCATCCCAAACACACACCCATTCCCCATCC +CAGACACACCCACCCGTTCCCCATCCCAGACACACACAACCCTTCCCCAATTCCAAACAC +ACACCCCTTCCCATCCCAAACACACACACCCATTTCCCATCCCAGACACATCCACCCCTT +CCACAACTCTGAACACCCACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCATCCC +AAACACACACACCCATTCCCCATCCCAAACACACACACCCATTCCCCATCCCAAACACAA +CCACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCATCCCAAACACACACACACCT +TCCCCATCCCAAACACACCCACCCTTACTCCATCTCAAACATGTACACCCCTTCCCCTAT +CCCAAAATACACACATCCATCCCTACACACCCTCACCCATTTCCCCATCCCAGAACCTAT +GCACCAACTCAGTTTATTTGAACATGCCAGGCACTGAACTAAGAGAACCAAAGTAGCAGG +AGGAATACGGTGTTGTCCTCCCAGAACTTACCCCCTGCACGGGAGTCAGCCAGGGAAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16257741-16259346/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16257741-16259346/haps.fa.ref.fa new file mode 100644 index 00000000..4e854eb5 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16257741-16259346/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:16257641-16259446 +CTGAGATTCCTGCCACCTTTGCCCCTTACTTTTCTCACCCCGTTCACTGAGGGCCCTCAAGTCTGTTTCTAAGCAGCAGCCTGAGGGATCCATTTTTATAATCTGAAATCAGATATCATACCCACACCCCAAAACACACACACTCCTTCCCCATCCCAAAGAGACACACCCCTTCCCCATCCCAAAGAGACACACCCCTTCCCCATCCCAAAGAGACACACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCATCCCAAACACACACACCCCTTTCCCATCCCAAACACACACACCCATTGCCCATCCTAAACACACACACACCTTGCCTTCGCAAACACACACACCCCTTCCCCATCACAAACACACACACCCTTTCCCTATCCCATGCACACACACCTTCCACTTCCCAAACACACACACCCCTTCCCCATGCCAAACACACACAACCCTTCCCCAATTCTAAACACACACACCTCTTCCCCATCCCAAACACAAACACCCCTTCCCCATCCCAAACACACCCACCCTTTCCTGCATGCCAAACACCCACACCCCTTCCCCATCCCAAACACACACCCCATCCCCAATTCCAAACACACACACCCCTTCCCCATCCCAAACACACACACCCCTTCCACATGAGAAACACACACACCCCTTCTCATCCCAAACACAAACACACCCATTCCCCATCACAAACACACGCACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCAATTGTAAACACACACACCCCTTCTCCAATTCCAAACACACACACCCCTTCCCATCACAAACACACACACACCTTCCACATCCCAAATACACACACCCCTTCCCATCTCAAACACACACATCCCTTCCCCAATTCCAAAAACACACACCCCTTCCCCATCCCAAACACCCCCACCCCTTCCCATCCCCAAACACACACCCCTTTCCCATCCCAAATACACAAACCCCTTCCCTAATTCCACACACACACACCCCTTCCCCATCCCAAACACACATACCCCTTCCCATCCCAAAGACACACACTCATTCTGCATCCCAAACACACACACCCCTTCCCATCCCAAACACACACACTACCTCCGCATCCCAAACACATATACCCCTTCCCCATCCCAAACACATACACCCCTTCCCCATCGCCAACACACACACCCCTTCCCCATCCCAAACACACACACCCCTTTCCATCCCAAACACACACCCATTCCCCATCCCAGACACACCCACCCGTTCCCCATCCCAGACACACACAACCCTTCCCCAATTCCAAACACACACCCCTTCCCATCCCAAACACACACACCCATTTCCCATCCCAGACACATCCACCCCTTCCACAACTCTGAACACCCACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCATCCCAAACACACACACCCATTCCCCATCCCAAACACACACACCCATTCCCCATCCCAAACACAACCACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCATCCCAAACACACACACACCTTCCCCATCCCAAACACACCCACCCTTACTCCATCTCAAACATGTACACCCCTTCCCCTATCCCAAAATACACACATCCATCCCTACACACCCTCACCCATTTCCCCATCCCAGAACCTATGCACCAACTCAGTTTATTTGAACATGCCAGGCACTGAACTAAGAGAACCAAAGTAGCAGGAGGAATACGGTGTTGTCCTCCCAGAACTTACCCCCTGCACGGGAGTCAGCCAGGGAAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16257741-16259346/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16257741-16259346/msa.fa new file mode 100644 index 00000000..25d9d886 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16257741-16259346/msa.fa @@ -0,0 +1,225 @@ +>ref_chr20_16257641_16259446 +ctgagattcctgccacctttgccccttacttttctcaccccgttcactgagggccctcaa +gtctgtttctaagcagcagcctgagggatccatttttataatctgaaatcagatatcata +cccacaccccaaaacacacacactccttccccatcccaaagagacacaccccttccccat +cccaaagagacacaccccttccccatcccaaagagacacaccccttccccatcccaaaca +cacacaccccttccccatcccaaacacacacaccccttccccatcccaaacacacacacc +cctttcccatcccaaacacacacacccattgcccatcctaaacacacacacaccttgcct +tcgcaaacacacacaccccttccccatcacaaacacacacaccctttccctatcccatgc +acacacaccttccacttcccaaacacacacaccccttccccatgccaaacacacacaacc +cttccccaattctaaacacacacacctcttccccatcccaaacacaaacaccccttcccc +atcccaaacacacccaccctttcctgcatgccaaacacccacaccccttccccatcccaa +acacacaccccatccccaattccaaacacacacaccccttccccatcccaaacacacaca +ccccttccacatgagaaacacacacaccccttctcatcccaaacacaaacacacccattc +cccatcacaaacacacg--------------------------caccccttccccatccc +aaacacacacaccccttccccaattgt--------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------aaacacacacaccccttctccaattccaaacacacacacccc +ttcccatcacaaacacacacacaccttccacatcccaaatacacacaccccttcccatct +caaacacacacatcccttccccaattccaaaaacacacaccccttccccatcccaaacac +ccccaccccttcccatcccc-aaacacacacccctttcccatcccaaatacacaaacccc +ttccctaattccacacacacacaccccttccccatcccaaacacacataccccttcccat +cccaaagacacacactcattctgcatcccaaacacacacaccccttcccatcccaaacac +acacactacctccgcatcccaaacacatataccccttccccatcccaaacacatacaccc +cttccccatcgccaacacacacaccccttccccatcccaaacacacacacccctttccat +cccaaacacacacccattccccatcccagacacacccacccgttccccatcccagacaca +cacaacccttccccaattccaaacacacaccccttcccatcccaaacacacacacccatt +tcccatcccagacacatccaccccttccacaactctgaacacccaccccttccccatccc +aaacacacacaccccttccccatcccaaacacacacacccattccccatcccaaacacac +acacccattccccatcccaaacacaaccaccccttccccatcccaaacacacacacccct +tccccatcccaaacacacacaca-------------------------ccttccccatcc +caaacacacccacccttactccatctcaaacatgtacaccccttcccctatcccaaaata +cacacatccatccctacacaccctcacccatttccccatcccagaacctatgcaccaact +cagtttatttgaacatgccaggcactgaactaagagaaccaaagtagcaggaggaatacg +gtgttgtcctcccagaacttaccccctgcacgggagtcagccagggaag +>syndip_1_chr20:16257641-16259446 +ctgagattcctgccacctttgccccttacttttctcaccccgttcactgagggccctcaa +gtctgtttctaagcagcagcctgagggatccatttttataatctgaaatcagatatcata +cccacaccccaaaacacacacactccttccccatcccaaagagacacaccccttccccat +cccaaagagacacaccccttccccatcccaaagagacacaccccttccccatcccaaaca +cacacaccccttccccatcccaaacacacacaccccttccccatcccaaacacacacacc +cctttcccatcccaaacacacacacccattgcccatcctaaacacacacacaccttccct +tcgcaaacacacacaccccttccccatcacaaacacacacaccctttccctatcccatgc +acacacaccttccacttcccaaacacacacaccccttccccatcccaaacacacacaacc +cttccccaattctaaacacacacacctcttccccatcccaaacacaaacaccccttcccc +atcccaaacacacccaccctttcctgcatcccaaacacccacaccccttccccatcccaa +acacacaccccatccccaattccaaacacacacaccccttccccatcccaaacacacaca +ccccttccacatcagaaacacacacaccccttctcatcccaaacacaaacacacccattc +cccatcacaaacacacg--------------------------caccccttccccatccc +aaacacacacaccccttccccaattctaaacacacacaccccttccccatcccaaacaca +caccccccttccccatcccaaacacacaccccccttccccatcccaaacacacccacccc +ttcccacatcccaaacacacacaccccttccctatcccaaacacacactccatccccaat +tccaaacacacacaccccttccccatcccaaacacacacaccccttcccccatcccaaac +gcacacaccccttccctatcccaaacacacaccccttccctttccaaaacacacccatcc +cttccccatcccaaacacacacaacccttcccatcccagacacacccaccccttcccatc +tcaaatacacgcaacccttccccatcccaaacacacacacctattccccatccgaaacac +acacaccccttcctcatcccacacacacccattccccatcccagacacacccatcccttc +cccatactaaacacaaccaccccttccccatcccacacacacacaccccttccccaattc +caaacacacacaccccttccccattcaaaacacacgcaccccttcccatctgaaacacac +ccactccttcccatctgaaacacacccactccttcccatcccaaacacacccactccttc +ccatcccaaacacacacaccccttccccatcccaaaaacacacaccctttcgcaatccca +aatacacaagccccttcccaaattccacacacacacacctcttccccatcccaaacaaac +ccaccctttccccattcgaaacacacacaccccttctccaattccaaacacacacacccc +ttcccatctcaaacacacggacaccttccacatcccaaatacacacaccccttcccatcc +caaacacacacatcccttccccaattccaaaaacacacaccccttccccatcccaaacac +ccccaccccttcccatccccaaaacacacacccctttcccatcccaaatacacaaacccc +ttccctaattccacacacacacaccccttccccatcccaaacacacataccccttcccat +cccaaagacacacactcattctgcatcccaaacacacacaccccttcccatcccaaacac +acacactacctccgcatcccaaacacatataccccttccccatcccaaacacatacaccc +cttccccatcgccaacacacacaccccttccccatcccaaacacacacacccctttccat +cccaaacacacacccattccccatcccagacacacccacccgttccccatcccagacaca +cacaacccttccccaattccaaacacacaccccttcccatcccaaacacacacacccatt +tcccatcccagacacatccaccccttccacaactctgaacacccaccccttccccatccc +aaacacacacaccccttccccatcccaaacacacacacccattccccatcccaaacacac +acacccattccccatcccaaacacaaccaccccttccccatcccaaacacacacacccct +tccccatcccaaacacacacaca-------------------------ccttccccatcc +caaacacacccacccttactccatctcaaacatgtacaccccttcccctatcccaaaata +cacacatccatccctacacaccctcacccatttccccatcccagaacctatgcaccaact +cagtttatttgaacatgccaggcactgaactaagagaaccaaagtagcaggaggaatacg +gtgttgtcctcccagaacttaccccctgcacgggagtcagccagggaag +>syndip_2_chr20:16257641-16259446 +ctgagattcctgccacctttgccccttacttttctcaccccgttcactgagggccctcaa +gtctgtttctaagcagcagcctgagggatccatttttataatctgaaatcagatatcata +cccacaccccaaaacacacacactccttccccatcccaaagagacacaccccttccccat +cccaaagagacacaccccttccccatcccaaagag------------------------- +-acacaccccttccccatcccaaacacacacaccccttccccatcccaaacacacacacc +cctttcccatcccaaacacacacacccattgcccatcctaaacacacacacaccttccct +tcgcaaacacacacaccccttccccatcacaaacacacacaccctttccctatcccatgc +acacacaccttccacttcccaaacacacacaccccttccccatcccaaacacacacaacc +cttccccaattctaaacacacacacctcttccccatcccaaacacaaacaccccttcccc +atcccaaacacacccaccctttcctgcatcccaaacacacacaccccttccccatcccaa +acacacaccccatccccaattccaaacacacacaccccttccccatcccaaacacacaca +ccccttccacatcagaaacacacacaccccttctcatcccaaacacaaacacacccattc +cccatcacaaacacacgcaccccttccccatcccaaacatacacaccccttccccatccc +aaacacacacaccccttccccaattctaaacacacacaccccttccccatcccaaacaca +caccccccttccccatcccaaacacacaccccccttccccatcccaaacacacccacccc +ttcccacatcccaaacacacacaccccttccctatcccaaacacacactccatccccaat +tccaaacacacacaccccttccccatcccaaacacacacaccccttcccccatcccaaac +gcacacaccccttccctatcccaaacacacaccccttccctttccaaaacacacccatcc +cttccccatcccaaacacacacaacccttcccatcccagacacacccaccccttcccatc +tcaaatacacgcaacccttc---------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------------------------------c +ccatcccaaacacacacaccccttccccatcccaaaaacacacaccctttcgcaatccca +aatacacaagccccttcccaaattccacacacacacacctcttccccatcccaaacaaac +ccaccctttccccattcgaaacacacacaccccttctccaattccaaacacacacacccc +ttcccatctcaaacacacggacaccttccacatcccaaatacacacaccccttcccatcc +caaacacacacatcccttccccaattccaaaaacacacaccccttccccatcccaaacac +ccccaccccttcccatccccaaaacacacacccctttcccatcccaaatacacaaacccc +ttccctaattccacacacacacaccccttccccatcccaaacacacataccccttcccat +cccaaagacacacactcattctgcatcccaaacacacacaccccttcccatcccaaacac +acacactacctccgcatcccaaacacatataccccttccccatcccaaacacatacaccc +cttccccatcgccaacacacacaccccttccccatcccaaacacacacacccctttccat +cccaaacacacacccattccccatcccagacacacccacccgttccccatcccagacaca +cacaacccttccccaattccaaacacacaccccttcccatcccaaacacacacacccatt +tcccatcccagacacatccaccccttccacaactccgaacacccaccccttccccatccc +aaacacacacaccccttccccatcccaaacacacacacccattccccatcccaaacacac +acacccattccccatcccaaacacaaccaccccttccccatcccaaacacacacacccct +tccccatcccaaacacacacacaccttcccatcccaaacacacacaccccttccccatcc +caaacacacccacccttactccatctcaaacatgtacaccccttcccctatcccaaaata +cacacatccatccctacacaccctcacccatttccccatcccagaacctatgcaccaact +cagtttatttgaacatgccaggcactgaactaagagaaccaaagtagcaggaggaatacg +gtgttgtcctcccagaacttaccccctgcacgggagtcagccagggaag +>p:HG002_1_chr20:16257641-16259446 +ctgagattcctgccacctttgccccttacttttctcaccccgttcactgagggccctcaa +gtctgtttctaagcagcagcctgagggatccatttttataatctgaaatcagatatcata +cccacaccccaaaacacacacactccttccccatcccaaagagacacaccccttccccat +cccaaagagacacaccccttccccatcccaaagag------------------------- +-acacaccccttccccatcccaaacacacacaccccttccccatcccaaacacacacacc +cctttcccatcccaaacacacacacccattgcccatcctaaacacacacacaccttccct +tcgcaaacacacacaccccttccccatcacaaacacacacaccctttccctatcccatgc +acacacaccttccacttcccaaacacacacaccccttccccatcccaaacacacacaacc +cttccccaattctaaacacacacacctcttccccatcccaaacacaaacaccccttcccc +atcccaaacacacccaccctttcctgcatcccaaacacacacaccccttccccatcccaa +acacacaccccatccccaattccaaacacacacaccccttccccatcccaaacacacaca +ccccttccacatcagaaacacacacaccccttctcatcccaaacacaaacacacccattc +cccatcacaaacacacgcaccccttccccatcccaaacatacacaccccttccccatccc +aaacacacacaccccttccccaattctaaacacacacaccccttccccatcccaaacaca +caccccccttccccatcccaaacacacaccccccttccccatcccaaacacacccacccc +ttcccacatcccaaacacacacaccccttccctatcccaaacacacactccatccccaat +tccaaacacacacaccccttccccatcccaaacacacacaccccttcccccatcccaaac +gcacacaccccttccctatcccaaacacacaccccttccctttccaaaacacacccatcc +cttccccatcccaaacacacacaacccttcccatcccagacacacccaccccttcccatc +tcaaatacacgcaacccttc---------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------------------------------c +ccatcccaaacacacacaccccttccccatcccaaaaacacacaccctttcgcaatccca +aatacacaagccccttcccaaattccacacacacacacctcttccccatcccaaacaaac +ccaccctttccccattcgaaacacacacaccccttctccaattccaaacacacacacccc +ttcccatctcaaacacacggacaccttccacatcccaaatacacacaccccttcccatcc +caaacacacacatcccttccccaattccaaaaacacacaccccttccccatcccaaacac +ccccaccccttcccatccccaaaacacacacccctttcccatcccaaatacacaaacccc +ttccctaattccacacacacacaccccttccccatcccaaacacacataccccttcccat +cccaaagacacacactcattctgcatcccaaacacacacaccccttcccatcccaaacac +acacactacctccgcatcccaaacacatataccccttccccatcccaaacacatacaccc +cttccccatcgctga--------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------acatgccaggcactgaactaagagaaccaaagtagcaggaggaatacg +gtgttgtcctcccagaacttaccccctgcacgggagtcagccagggaag +>p:HG002_2_chr20:16257641-16259446 +ctgagattcctgccacctttgccccttacttttctcaccccgttcactgagggccctcaa +gtctgtttctaagcagcagcctgagggatccatttttataatctgaaatcagatatcata +cccacaccccaaaacacacacactccttccccatcccaaagagacacaccccttccccat +cccaaagagacacaccccttccccatcccaaagagacacaccccttccccatcccaaaca +cacacaccccttccccatcccaaacacacacaccccttccccatcccaaacacacacacc +cctttcccatcccaaacacacacacccattgcccatcctaaacacacacacaccttccct +tcgcaaacacacacaccccttccccatcacaaacacacacaccctttccctatcccatgc +acacacaccttccacttcccaaacacacacaccccttccccatcccaaacacacacaacc +cttccccaattctaaacacacacacctcttccccatcccaaacacaaacaccccttcccc +atcccaaacacacccaccctttcctgcatcccaaacacccacaccccttccccatcccaa +acacacaccccatccccaattccaaacacacacaccccttccccatcccaaacacacaca +ccccttccacatcagaaacacacacaccccttctcatcccaaacacaaacacacccattc +cccatcacaaacacacg--------------------------caccccttccccatccc +aaacacacacaccccttccccaattctaaacacacacaccccttccccatcccaaacaca +caccccccttccccatcccaaacacacaccccccttccccatcccaaacacacccacccc +ttcccacatcccaaacacacacaccccttccctatcccaaacacacactccatccccaat +tccaaacacacacaccccttccccatcccaaacacacacaccccttcccccatcccaaac +gcacacaccccttccctatcccaaacacacaccccttccctttccaaaacacacccatcc +cttccccatcccaaacacacacaacccttcccatcccagacacacccaccccttcccatc +tcaaatacacgcaacccttccccatcccaaacacacacacctattccccatccgaaacac +acacaccccttcctcatcccacacacacccattccccatcccagacacacccatcccttc +cccatactaaacacaaccaccccttccccatcccacacacacacaccccttccccaattc +caaacacacacaccccttccccattcaaaacacacgcaccccttcccatctgaaacacac +ccactccttcccatctgaaacacacccactccttcccatcccaaacacacccactccttc +ccatcccaaacacacacaccccttccccatcccaaaaacacacaccctttcgcaatccca +aatacacaagccccttcccaaattccacacacacacacctcttccccatcccaaacaaac +ccaccctttccccattcgaaacacacacaccccttctccaattccaaacacacacacccc +ttcccatctcaaacacacggacaccttccacatcccaaatacacacaccccttcccatcc +caaacacacacatcccttccccaattccaaaaacacacaccccttccccatcccaaacac +ccccaccccttcccatccccaaaacacacacccctttcccatcccaaatacacaaacccc +ttccctaattccacacacacacaccccttccccatcccaaacacacataccccttcccat +cccaaagacacacactcattctgcatcccaaacacacacaccccttcccatcccaaacac +acacactacctccgcatcccaaacacatataccccttccccatcccaaacacatacaccc +cttccccatcgccaacacacacaccccttccccatcccaaacacacacacccctttccat +cccaaacacacacccattccccatcccagacacacccacccgttccccatcccagacaca +cacaacccttccccaattccaaacacacaccccttcccatcccaaacacacacacccatt +tcccatcccagacacatccaccccttccacaactctgaacacccaccccttccccatccc +aaacacacacaccccttccccatcccaaacacacacacccattccccatcccaaacacac +acacccattccccatcccaaacacaaccaccccttccccatcccaaacacacacacccct +tccccatcccaaacacacacaca-------------------------ccttccccatcc +caaacacacccacccttactccatctcaaacatgtacaccccttcccctatcccaaaata +cacacatccatccctacacaccctcacccatttccccatcccagaacctatgcaccaact +cagtttatttgaacatgccaggcactgaactaagagaaccaaagtagcaggaggaatacg +gtgttgtcctcccagaacttaccccctgcacgggagtcagccagggaag diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16257741-16259346/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16257741-16259346/msa.fa.fai new file mode 100644 index 00000000..4f0fd497 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16257741-16259346/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_16257641_16259446 2629 29 60 61 +syndip_1_chr20:16257641-16259446 2629 2736 60 61 +syndip_2_chr20:16257641-16259446 2629 5443 60 61 +p:HG002_1_chr20:16257641-16259446 2629 8151 60 61 +p:HG002_2_chr20:16257641-16259446 2629 10859 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16257741-16259346/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16257741-16259346/output.vcf.gz new file mode 100644 index 00000000..538ffe66 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16257741-16259346/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16257741-16259346/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16257741-16259346/output.vcf.gz.tbi new file mode 100644 index 00000000..fd4e7146 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16257741-16259346/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/base.vcf.gz new file mode 100644 index 00000000..a1fe8ee0 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/base.vcf.gz.tbi new file mode 100644 index 00000000..36dde587 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/comp.vcf.gz new file mode 100644 index 00000000..671d4050 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/comp.vcf.gz.tbi new file mode 100644 index 00000000..aa2383e1 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/haps.fa new file mode 100644 index 00000000..019f88b3 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/haps.fa @@ -0,0 +1,38 @@ +>ref_chr20_16395049_16395522 +ACAGTCGTGGACAGCAAAGCTAAGGCTCAGTACAACAAAGGGCATACCCCTGTCATCGGTGTCTTCTTACTCTCTCCCTAATGTGATGTATTCATCCTCCCAGTTTAGTCAAGGCAGAAAGGAGATGAGGAAGGGGAGAGGAGGGGAGAGGAGGGAAGAGGAGGGGAGGGGAGGGGAGAGGAGGAGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGAAGATATGAAAGAAATAGGGAAGGAGTGGGACACAGGGAGGAAAACAAAACTATTTCCTTTCATATAAATGTTGTCATCTGGGGAGAAGCCCTCACTATCTCCTTGGTGCCTTTGGCTTTTGGTATTCAAA +>syndip_1_chr20:16395049-16395522 +ACAGTCGTGGACAGCAAAGCTAAGGCTCAGTACAACAAAGGGCATACCCCTGTCATCGGT +GTCTTCTTACTCTCTCCCTAATGTGATGTATTCATCCTCCCAGTTTAGTCAAGGCAGAAA +GGAGATGAGGAAGGGGAGAGGAGGGGAGAGGAGGGAAGAGGAGGGGAGGGGAGGGGAGAG +GAGGAGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGGGAGGAGAGGGGAGGC +CAAGGGAGGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGGGAGGA +GAGGGGAGGCCAAGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGG +GAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGAA +GATATGAAAGAAATAGGGAAGGAGTGGGACACAGGGAGGAAAACAAAACTATTTCCTTTC +ATATAAATGTTGTCATCTGGGGAGAAGCCCTCACTATCTCCTTGGTGCCTTTGGCTTTTG +GTATTCAAA +>syndip_2_chr20:16395049-16395522 +ACAGTCGTGGACAGCAAAGCTAAGGCTCAGTACAACAAAGGGCATACCCCTGTCATCGGT +GTCTTCTTACTCTCTCCCTAATGTGATGTATTCATCCTCCCAGTTTAGTCCAGGCAGAAA +GGAGATGAGGAAGGGGAGAGGAGGGGAGAGGAGGGGAGGGGAGGGGAGGGGAGAGGAGGG +GAGGCCAAGGGAGAAGATATGAAAGAAATAGGGAAGGAGTGGGACACAGGGAGGAAAACA +AAACTATTTCCTTTCATATAAATGTTGTCATCTGGGGAGAAGCCCTCACTATCTCCTTGG +TGCCTTTGGCTTTTGGTATTCAAA +>p:HG002_1_chr20:16395049-16395522 +ACAGTCGTGGACAGCAAAGCTAAGGCTCAGTACAACAAAGGGCATACCCCTGTCATCGGT +GTCTTCTTACTCTCTCCCTAATGTGATGTATTCATCCTCCCAGTTTAGTCCAGGCAGAAA +GGAGATGAGGAAGGGGAGAGGAGGGGAGAGGAGGGGAGGGGAGGGGAGGGGAGAGGAGGG +GAGGCCAAGGGAGAAGATATGAAAGAAATAGGGAAGGAGTGGGACACAGGGAGGAAAACA +AAACTATTTCCTTTCATATAAATGTTGTCATCTGGGGAGAAGCCCTCACTATCTCCTTGG +TGCCTTTGGCTTTTGGTATTCAAA +>p:HG002_2_chr20:16395049-16395522 +ACAGTCGTGGACAGCAAAGCTAAGGCTCAGTACAACAAAGGGCATACCCCTGTCATCGGT +GTCTTCTTACTCTCTCCCTAATGTGATGTATTCATCCTCCCAGTTTAGTCAAGGCAGAAA +GGAGATGAGGAAGGGGAGAGGAGGGGAGAGGAGGGAAGAGGAGGGGAGGGGAGGGGAGAG +GAGGAGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGGGAGGAGAGGGGAGGC +CAAGGGAGGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGGGAGGA +GAGGGGAGGCCAAGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGG +GAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGAA +GATATGAAAGAAATAGGGAAGGAGTGGGACACAGGGAGGAAAACAAAACTATTTCCTTTC +ATATAAATGTTGTCATCTGGGGAGAAGCCCTCACTATCTCCTTGGTGCCTTTGGCTTTTG +GTATTCAAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/haps.fa.ref.fa new file mode 100644 index 00000000..d48bb2c9 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:16395049-16395522 +ACAGTCGTGGACAGCAAAGCTAAGGCTCAGTACAACAAAGGGCATACCCCTGTCATCGGTGTCTTCTTACTCTCTCCCTAATGTGATGTATTCATCCTCCCAGTTTAGTCAAGGCAGAAAGGAGATGAGGAAGGGGAGAGGAGGGGAGAGGAGGGAAGAGGAGGGGAGGGGAGGGGAGAGGAGGAGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGAAGATATGAAAGAAATAGGGAAGGAGTGGGACACAGGGAGGAAAACAAAACTATTTCCTTTCATATAAATGTTGTCATCTGGGGAGAAGCCCTCACTATCTCCTTGGTGCCTTTGGCTTTTGGTATTCAAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/msa.fa new file mode 100644 index 00000000..8efb459b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/msa.fa @@ -0,0 +1,55 @@ +>ref_chr20_16395049_16395522 +acagtcgtggacagcaaagctaaggctcagtacaacaaagggcatacccctgtcatcggt +gtcttcttactctctccctaatgtgatgtattcatcctcccagtttagtcaaggcagaaa +ggagatgaggaaggggagaggaggggagaggagggaagaggaggggaggggaggggagag +gaggagaggggaggagaggggaggccaagggaggggaggggaggggaggagaggggaggc +caa-----gggaggggaggggaggagaggggaggccaagggaggggaggggaggggagga +gaggggaggccaa----------------------------------------------- +-----------------------gggaggggaggggaggagaggggaggccaagggagaa +gatatgaaagaaatagggaaggagtgggacacagggaggaaaacaaaactatttcctttc +atataaatgttgtcatctggggagaagccctcactatctccttggtgcctttggcttttg +gtattcaaa +>syndip_1_chr20:16395049-16395522 +acagtcgtggacagcaaagctaaggctcagtacaacaaagggcatacccctgtcatcggt +gtcttcttactctctccctaatgtgatgtattcatcctcccagtttagtcaaggcagaaa +ggagatgaggaaggggagaggaggggagaggagggaagaggaggggaggggaggggagag +gaggagaggggaggagaggggaggccaagggaggggaggggaggggaggagaggggaggc +caagggaggggaggggaggggaggagaggggaggccaagggaggggaggggaggggagga +gaggggaggccaagggaggggaggggaggagaggggaggccaagggaggggaggggaggg +gaggagaggggaggccaagggaggggaggggaggggaggagaggggaggccaagggagaa +gatatgaaagaaatagggaaggagtgggacacagggaggaaaacaaaactatttcctttc +atataaatgttgtcatctggggagaagccctcactatctccttggtgcctttggcttttg +gtattcaaa +>syndip_2_chr20:16395049-16395522 +acagtcgtggacagcaaagctaaggctcagtacaacaaagggcatacccctgtcatcggt +gtcttcttactctctccctaatgtgatgtattcatcctcccagtttagtccaggcagaaa +ggagatgaggaaggggagaggaggggagaggaggggag---------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------gggaggggaggggagaggaggggaggccaagggagaa +gatatgaaagaaatagggaaggagtgggacacagggaggaaaacaaaactatttcctttc +atataaatgttgtcatctggggagaagccctcactatctccttggtgcctttggcttttg +gtattcaaa +>p:HG002_1_chr20:16395049-16395522 +acagtcgtggacagcaaagctaaggctcagtacaacaaagggcatacccctgtcatcggt +gtcttcttactctctccctaatgtgatgtattcatcctcccagtttagtccaggcagaaa +ggagatgaggaaggggagaggaggggagaggaggggag---------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------gggaggggaggggagaggaggggaggccaagggagaa +gatatgaaagaaatagggaaggagtgggacacagggaggaaaacaaaactatttcctttc +atataaatgttgtcatctggggagaagccctcactatctccttggtgcctttggcttttg +gtattcaaa +>p:HG002_2_chr20:16395049-16395522 +acagtcgtggacagcaaagctaaggctcagtacaacaaagggcatacccctgtcatcggt +gtcttcttactctctccctaatgtgatgtattcatcctcccagtttagtcaaggcagaaa +ggagatgaggaaggggagaggaggggagaggagggaagaggaggggaggggaggggagag +gaggagaggggaggagaggggaggccaagggaggggaggggaggggaggagaggggaggc +caagggaggggaggggaggggaggagaggggaggccaagggaggggaggggaggggagga +gaggggaggccaagggaggggaggggaggagaggggaggccaagggaggggaggggaggg +gaggagaggggaggccaagggaggggaggggaggggaggagaggggaggccaagggagaa +gatatgaaagaaatagggaaggagtgggacacagggaggaaaacaaaactatttcctttc +atataaatgttgtcatctggggagaagccctcactatctccttggtgcctttggcttttg +gtattcaaa diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/msa.fa.fai new file mode 100644 index 00000000..45035466 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_16395049_16395522 549 29 60 61 +syndip_1_chr20:16395049-16395522 549 622 60 61 +syndip_2_chr20:16395049-16395522 549 1215 60 61 +p:HG002_1_chr20:16395049-16395522 549 1809 60 61 +p:HG002_2_chr20:16395049-16395522 549 2403 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/output.vcf.gz new file mode 100644 index 00000000..955ac1ee Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/output.vcf.gz.tbi new file mode 100644 index 00000000..a7cf6819 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:16395149-16395422/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:17081216-17081411/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:17081216-17081411/base.vcf.gz new file mode 100644 index 00000000..53bd471b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:17081216-17081411/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:17081216-17081411/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:17081216-17081411/base.vcf.gz.tbi new file mode 100644 index 00000000..9fa6ac23 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:17081216-17081411/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:17081216-17081411/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:17081216-17081411/comp.vcf.gz new file mode 100644 index 00000000..3e284465 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:17081216-17081411/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:17081216-17081411/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:17081216-17081411/comp.vcf.gz.tbi new file mode 100644 index 00000000..5369892d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:17081216-17081411/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:17081216-17081411/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:17081216-17081411/haps.fa new file mode 100644 index 00000000..01d063b5 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:17081216-17081411/haps.fa @@ -0,0 +1,30 @@ +>ref_chr20_17081116_17081511 +TGAATATTCTTTTATGTAGTAAAAGTATAAAACTATGGCTGGTAAAAATGCATGCCACATTGTGGATCATGACTACCTCTGGGTCAGAAGGAAATGTGATGGGTAAAGGAATCAACTCCATGTGGAATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTATTTTATTTTATTACGACAAGGTCTGGCTCTGTCGCCTAGGCTGGAGTGCATTGTGGTAATCTTGGCTTACTGCAACCTCTGCCTCCCAGACTCAACCAGTCCTCCCACCTCAGCCTCCCAAGTAGCTGGGACTACAAGTACGT +>syndip_1_chr20:17081116-17081511 +TGAATATTCTTTTATGTAGTAAAAGTATAAAACTATGGCTGGTAAAAATGCATGCCACAT +TGTGGATCATGACTACCTCTGGGTCAGAAGGAAATGTGATGGGTAAAGGAATCAACTCCA +TGTGGAATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTT +TATTTTATTTTATTTTATTACGACAAGGTCTGGCTCTGTCGCCTAGGCTGGAGTGCATTG +TGGTAATCTTGGCTTACTGCAACCTCTGCCTCCCAGACTCAACCAGTCCTCCCACCTCAG +CCTCCCAAGTAGCTGGGACTACAAGTACGT +>syndip_2_chr20:17081116-17081511 +TGAATATTCTTTTATGTAGTAAAAGTATAAAACTATGGCTGGTAAAAATGCATGCCACAT +TGTGGATCATGACTACCTCTGGGTCAGAAGGAAATGTGATGGGTAAAGGAATCAACTCCA +TGTGGAATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTT +TATTTTATTTTATTACGACAAGGTCTGGCTCTGTCGCCTAGGCTGGAGTGCATTGTGGTA +ATCTTGGCTTACTGCAACCTCTGCCTCCCAGACTCAACCAGTCCTCCCACCTCAGCCTCC +CAAGTAGCTGGGACTACAAGTACGT +>p:HG002_1_chr20:17081116-17081511 +TGAATATTCTTTTATGTAGTAAAAGTATAAAACTATGGCTGGTAAAAATGCATGCCACAT +TGTGGATCATGACTACCTCTGGGTCAGAAGGAAATGTGATGGGTAAAGGAATCAACTCCA +TGTGGAATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTT +TATTTTATTTTATTACGACAAGGTCTGGCTCTGTCGCCTAGGCTGGAGTGCATTGTGGTA +ATCTTGGCTTACTGCAACCTCTGCCTCCCAGACTCAACCAGTCCTCCCACCTCAGCCTCC +CAAGTAGCTGGGACTACAAGTACGT +>p:HG002_2_chr20:17081116-17081511 +TGAATATTCTTTTATGTAGTAAAAGTATAAAACTATGGCTGGTAAAAATGCATGCCACAT +TGTGGATCATGACTACCTCTGGGTCAGAAGGAAATGTGATGGGTAAAGGAATCAACTCCA +TGTGGAATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTT +TATTTTATTTTATTTTATTACGACAAGGTCTGGCTCTGTCGCCTAGGCTGGAGTGCATTG +TGGTAATCTTGGCTTACTGCAACCTCTGCCTCCCAGACTCAACCAGTCCTCCCACCTCAG +CCTCCCAAGTAGCTGGGACTACAAGTACGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:17081216-17081411/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:17081216-17081411/haps.fa.ref.fa new file mode 100644 index 00000000..0c5f103e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:17081216-17081411/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:17081116-17081511 +TGAATATTCTTTTATGTAGTAAAAGTATAAAACTATGGCTGGTAAAAATGCATGCCACATTGTGGATCATGACTACCTCTGGGTCAGAAGGAAATGTGATGGGTAAAGGAATCAACTCCATGTGGAATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTATTTTATTTTATTACGACAAGGTCTGGCTCTGTCGCCTAGGCTGGAGTGCATTGTGGTAATCTTGGCTTACTGCAACCTCTGCCTCCCAGACTCAACCAGTCCTCCCACCTCAGCCTCCCAAGTAGCTGGGACTACAAGTACGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:17081216-17081411/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:17081216-17081411/msa.fa new file mode 100644 index 00000000..07ae1836 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:17081216-17081411/msa.fa @@ -0,0 +1,40 @@ +>ref_chr20_17081116_17081511 +tgaatattcttttatgtagtaaaagtataaaactatggctggtaaaaatgcatgccacat +tgtggatcatgactacctctgggtcagaaggaaatgtgatgggtaaaggaatcaactcca +tgtggaattttattttattttattttattttattttattttattttattttattttattt +tattattttattttattttattttattttattttattttattttattttattttatttta +ttttattttattattttattttattacgacaaggtctggctctgtcgcctaggctggagt +gcattgtggtaatcttggcttactgcaacctctgcctcccagactcaaccagtcctccca +cctcagcctcccaagtagctgggactacaagtacgt +>syndip_1_chr20:17081116-17081511 +tgaatattcttttatgtagtaaaagtataaaactatggctggtaaaaatgcatgccacat +tgtggatcatgactacctctgggtcagaaggaaatgtgatgggtaaaggaatcaactcca +tgtggaattttattttattttattttattttattttattttattttattttattttattt +tatt-------------------------------------------------------- +----------ttattttattttattacgacaaggtctggctctgtcgcctaggctggagt +gcattgtggtaatcttggcttactgcaacctctgcctcccagactcaaccagtcctccca +cctcagcctcccaagtagctgggactacaagtacgt +>syndip_2_chr20:17081116-17081511 +tgaatattcttttatgtagtaaaagtataaaactatggctggtaaaaatgcatgccacat +tgtggatcatgactacctctgggtcagaaggaaatgtgatgggtaaaggaatcaactcca +tgtgga-----attttattttattttattttattttattttattttattttattttattt +tatt-------------------------------------------------------- +----------ttattttattttattacgacaaggtctggctctgtcgcctaggctggagt +gcattgtggtaatcttggcttactgcaacctctgcctcccagactcaaccagtcctccca +cctcagcctcccaagtagctgggactacaagtacgt +>p:HG002_1_chr20:17081116-17081511 +tgaatattcttttatgtagtaaaagtataaaactatggctggtaaaaatgcatgccacat +tgtggatcatgactacctctgggtcagaaggaaatgtgatgggtaaaggaatcaactcca +tgtgga-----attttattttattttattttattttattttattttattttattttattt +tatt-------------------------------------------------------- +----------ttattttattttattacgacaaggtctggctctgtcgcctaggctggagt +gcattgtggtaatcttggcttactgcaacctctgcctcccagactcaaccagtcctccca +cctcagcctcccaagtagctgggactacaagtacgt +>p:HG002_2_chr20:17081116-17081511 +tgaatattcttttatgtagtaaaagtataaaactatggctggtaaaaatgcatgccacat +tgtggatcatgactacctctgggtcagaaggaaatgtgatgggtaaaggaatcaactcca +tgtggaattttattttattttattttattttattttattttattttattttattttattt +tatt-------------------------------------------------------- +----------ttattttattttattacgacaaggtctggctctgtcgcctaggctggagt +gcattgtggtaatcttggcttactgcaacctctgcctcccagactcaaccagtcctccca +cctcagcctcccaagtagctgggactacaagtacgt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/base.vcf.gz new file mode 100644 index 00000000..4e9a396f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/base.vcf.gz.tbi new file mode 100644 index 00000000..b39161b8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/comp.vcf.gz new file mode 100644 index 00000000..1bf6bc3a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/comp.vcf.gz.tbi new file mode 100644 index 00000000..ca61ae92 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/haps.fa new file mode 100644 index 00000000..063bc2fe --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/haps.fa @@ -0,0 +1,148 @@ +>ref_chr20_18208997_18210828 +GTATTCTTTGTACTGTTTTTATTTTTGCAACTTTTCTGTGTTTACAGTTATTTCCAAATAAAAAATAAGCAGAAAGGAAAAGCTAATCATCTCCCCCTATTCCAGTCCCCCAGGCATGTATCCTTCCGTAGCTTCTCCACACCTACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCATTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTCCACACCCACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCTAGACGATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCAGACCTTCTCCACACCCACACAGACCTAGACGATTCCTTCCACACCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTGTGCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTGCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAAACGATTCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGACAATTCCTTGCACACCTTCTCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGACAATTCCTTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGATGATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCCTAACACCCACACGAACCTAGAGAATTCCTTCCACACCTTCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAAATTCTTATACACTTAAAATGGGATTTTGTTGTTTTATTAAAATGCAGTCATTCTCTATGCATTAATTATTGTGCAGCTTGATTTTTCTCCTTTTTTTTTGTTAAATCTTCCTCCGTCATCCAGGCTGGAGTGCAG +>syndip_1_chr20:18208997-18210828 +GTATTCTTTGTACTGTTTTTATTTTTGCAACTTTTCTGTGTTTACAGTTATTTCCAAATA +AAAAATAAGCAGAAAGGAAAAGCTAATCATCTCCCCCTATTCCAGTCCCCCAGGCATGTA +TCCTTCCGTAGCTTCTCCACACCTACACGAACCTAGACGATTCCTTCCACACCTTCCCCA +CACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGAT +GAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTC +CCCACACCCATTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTCCACACCC +ACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCTAGACGATT +CCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCAGACCTTCTCCA +CACCCACACAGACCTAGACGATTCCTTCCACACCTCCACACCCACACGAACCTAGACGAA +TTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTC +CACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTA +GACGATTCCTTCCACACTTTCCCCACACCCACACGAACCTAGACGATTCCTTCCACACCT +CCACACCCACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCT +AGACGATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAATTCCTTCCACACA +CACATGAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACATGAACCTAGACGAT +TCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCACACCTTCCCC +ACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAG +ACGATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTCCACACCTT +CTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACGAACC +TAAACGATTCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCACA +CCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACAC +GAACCTAGACGATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTC +CACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCA +CACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACAATTC +CTTCCACACCTTCTCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCTCCACA +CCCACACAAACCTAGATGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGACG +ATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCT +CCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTA +GACAATTCCTTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCT +TCTCCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAA +CCTAGACGATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCA +CACCTTCCTAACACCCACACGAACCTAGAGAATTCCTTCCACACCTTCACACCCACACAA +ACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAAATTCTTAT +ACACTTAAAATGGGATTTTGTTGTTTTATTAAAATGCAGTCATTCTCTATGCATTAATTA +TTGTGCAGCTTGATTTTTCTCCTTTTTTTTTGTTAAATCTTCCTCCGTCATCCAGGCTGG +AGTGCAG +>syndip_2_chr20:18208997-18210828 +GTATTCTTTGTACTGTTTTTATTTTTGCAACTTTTCTGTGTTTACAGTTATTTCCAAATA +AAAAATAAGCAGAAAGGAAAAGCTAATCATCTCCCCCTATTCCAGTCCCCCAGGCATGTA +TCCTTCCGTAGCTTCTCCACACCTACACGAACCTAGACGATTCCTTCCACACCTTCCCCA +CACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGAT +GAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTC +CCCACACCCATTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTCCACACCC +ACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCTAGACGATT +CCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCAGACCTTCTCCA +CACCCACACAGACCTAGACGATTCCTTCCACACCTCCACACCCACACGAACCTAGACGAA +TTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTC +CACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTA +GACGATTCCTTCCACACTTTCCCCACACCCACAAGAACCTAGACGATTCCTTCCACACCT +CCACACCCACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCT +AGACGATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAATTCCTTCCACACA +CACATGAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACATGAACCTAGACGAT +TCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCACACCTTCCCC +ACACCCACACAGACCTAGACGAATTCCTTCCACACATTCTCCACACCCACACGAACCTAG +ACGATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTCCACACCTT +CTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACGAACC +TAAACGATTCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCACA +CCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACAC +GAACCTAGACGATTCCTTCCACACCACACGAACCTAGACAATTCCTTCCACACCTTCTCA +CACCCACACAAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGA +CGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACAATTCCTTCCACACCTT +CTCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACAAACC +TAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGACGATTCCTTCCACA +CCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACAC +GAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGACAATTCCTTC +CACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCA +CACAAACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGACGATTC +CTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCCTAAC +ACCCACACGAACCTAGAGAATTCCTTCCACACCTTCACACCCACACAAACCTAGACGAAT +TCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAAATTCTTATACACTTAAAATG +GGATTTTGTTGTTTTATTAAAATGCAGTCATTCTCTATGCATTAATTATTGTGCAGCTTG +ATTTTTCTCCTTTTTTTTTGTTAAATCTTCCTCCGTCATCCAGGCTGGAGTGCAG +>p:HG002_1_chr20:18208997-18210828 +GTATTCTTTGTACTGTTTTTATTTTTGCAACTTTTCTGTGTTTACAGTTATTTCCAAATA +AAAAATAAGCAGAAAGGAAAAGCTAATCATCTCCCCCTATTCCAGTCCCCCAGGCATGTA +TCCTTCCGTAGCTTCTCCACACCTACACGAACCTAGACGATTCCTTCCACACCTTCCCCA +CACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGAT +GAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTC +CCCACACCCATTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTCCACACCC +ACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCTAGACGATT +CCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCAGACCTTCTCCA +CACCCACACAGACCTAGACGATTCCTTCCACACCTCCACACCCACACGAACCTAGACGAA +TTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTC +CACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTA +GACGATTCCTTCCACACTTTCCCCACACCCACAAGAACCTAGACGATTCCTTCCACACCT +CCACACCCACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCT +AGACGATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAATTCCTTCCACACA +CACATGAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACATGAACCTAGACGAT +TCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCACACCTTCCCC +ACACCCACACAGACCTAGACGAATTCCTTCCACACATTCTCCACACCCACACGAACCTAG +ACGATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTCCACACCTT +CTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACGAACC +TAAACGATTCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCACA +CCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACAC +GAACCTAGACGATTCCTTCCACACCACACGAACCTAGACAATTCCTTCCACACCTTCTCA +CACCCACACAAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGA +CGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACAATTCCTTCCACACCTT +CTCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACAAACC +TAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGACGATTCCTTCCACA +CCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACAC +GAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGACAATTCCTTC +CACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCA +CACAAACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGACGATTC +CTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCCTAAC +ACCCACACGAACCTAGAGAATTCCTTCCACACCTTCACACCCACACAAACCTAGACGAAT +TCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAAATTCTTATACACTTAAAATG +GGATTTTGTTGTTTTATTAAAATGCAGTCATTCTCTATGCATTAATTATTGTGCAGCTTG +ATTTTTCTCCTTTTTTTTTGTTAAATCTTCCTCCGTCATCCAGGCTGGAGTGCAG +>p:HG002_2_chr20:18208997-18210828 +GTATTCTTTGTACTGTTTTTATTTTTGCAACTTTTCTGTGTTTACAGTTATTTCCAAATA +AAAAATAAGCAGAAAGGAAAAGCTAATCATCTCCCCCTATTCCAGTCCCCCAGGCATGTA +TCCTTCCGTAGCTTCTCCACACCTACACGAACCTAGACGATTCCTTCCACACCTTCCCCA +CACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGAT +GAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTC +CCCACACCCATTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTCCACACCC +ACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCTAGACGATT +CCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCAGACCTTCTCCA +CACCCACACAGACCTAGACGATTCCTTCCACACCTCCACACCCACACGAACCTAGACGAA +TTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTC +CACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTA +GACGATTCCTTCCACACTTTCCCCACACCCACACGAACCTAGACGATTCCTTCCACACCT +CCACACCCACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCT +AGACGATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAATTCCTTCCACACA +CACATGAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACATGAACCTAGACGAT +TCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCACACCTTCCCC +ACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAG +ACGATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTCCACACCTT +CTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACGAACC +TAAACGATTCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCACA +CCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACAC +GAACCTAGACGATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTC +CACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCA +CACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACAATTC +CTTCCACACCTTCTCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCTCCACA +CCCACACAAACCTAGATGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGACG +ATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCT +CCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTA +GACAATTCCTTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCT +TCTCCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAA +CCTAGACGATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCA +CACCTTCCTAACACCCACACGAACCTAGAGAATTCCTTCCACACCTTCACACCCACACAA +ACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAAATTCTTAT +ACACTTAAAATGGGATTTTGTTGTTTTATTAAAATGCAGTCATTCTCTATGCATTAATTA +TTGTGCAGCTTGATTTTTCTCCTTTTTTTTTGTTAAATCTTCCTCCGTCATCCAGGCTGG +AGTGCAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/haps.fa.ref.fa new file mode 100644 index 00000000..48f827cd --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:18208997-18210828 +GTATTCTTTGTACTGTTTTTATTTTTGCAACTTTTCTGTGTTTACAGTTATTTCCAAATAAAAAATAAGCAGAAAGGAAAAGCTAATCATCTCCCCCTATTCCAGTCCCCCAGGCATGTATCCTTCCGTAGCTTCTCCACACCTACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCATTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTCCACACCCACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCTAGACGATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCAGACCTTCTCCACACCCACACAGACCTAGACGATTCCTTCCACACCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTGTGCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTGCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAAACGATTCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGACAATTCCTTGCACACCTTCTCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGACAATTCCTTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGATGATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCCTAACACCCACACGAACCTAGAGAATTCCTTCCACACCTTCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAAATTCTTATACACTTAAAATGGGATTTTGTTGTTTTATTAAAATGCAGTCATTCTCTATGCATTAATTATTGTGCAGCTTGATTTTTCTCCTTTTTTTTTGTTAAATCTTCCTCCGTCATCCAGGCTGGAGTGCAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/msa.fa new file mode 100644 index 00000000..34f19f48 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/msa.fa @@ -0,0 +1,185 @@ +>ref_chr20_18208997_18210828 +gtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatttccaaata +aaaaataagcagaaaggaaaagctaatcatctccccctattccagtcccccaggcatgta +tccttccgtagcttctccacacct------------------------------------ +-----acacgaacctagacgattccttccacaccttccccacacccacacgaacctagat +gaattccttccacaccttctccacacccacacgaacctagacgattccttccacaccttc +cccacacccattctccacacccacacgaacctagacgattccttccacacctccacaccc +acacgaacctagatgaattccttccacaccttccccacacccacacaaacctagacgatt +ccttccacaccttctccacacccacacgaacctagacgaattccttccagaccttctcca +cacccacacagacctagacgattccttccacacctccacacccacacgaacctagacgaa +ttccttccacaccttgtgcacacccacacgaacctagacgaattccttccacaccttctc +cacacccacacgaacctagacgaattccttccacaccttctccacacccacacgaaccta +gacgattccttccacaccttccccacacccacacagacctagacgaattccttgcacacc +ttctccacacccacacgaacctagacgaattccttccacaccttctccatacccacacga +acctagacaattccttccacaccttct-------------------------------ca +cacccacacaaacctagatgaattccttccacaccttctccacacccacacgaacctaaa +cgattccttccacaccttctccacacccacacacacctagatgaattccttccacacctt +ccccacacccacacagacctagacgaattccttccacaccttctccacacccacacgaac +ctagacgattccttccacaccttctccatacccacacgaacctagacaattccttccaca +ccttctcacacccacacaa----------------------------------------- +------------------------------------------acctagatgaattccttc +cacaccttccccacacccacacagacctagacgaattccttccacaccttctccacaccc +acacgaacctagacg--------------------------------------------- +------------------------------------------------------------ +-------------------attccttccacaccttccccacacccacacgaacctagaca +attccttgcacaccttctcacacccacacaaacctagacgaattccttccacaccttctc +cacacccacacaaacctagacgaattccttccacaccttcctcacacccacacgaaccta +gacgattccttccacaccttccccacacccacacagacctagacgaattccttccacacc +ttctccacacccacacgaacctagacgattccttccacaccttccccacacccacacgaa +cctagacaattccttccacaccttctcacacccacacaaacctagatgaattccttccac +accttctccacacccacacaaacctagacgaattccttccacaccttcctcacacccaca +cgaacctagatgattccttccacaccttccccacacccacacagacctagacgaattcct +tccacaccttcctaacacccacacgaacctagagaattccttccacaccttcacacccac +acaaacctagacgaattccttccacaccttctccacacccacacaaacctagacaaattc +ttatacacttaaaatgggattttgttgttttattaaaatgcagtcattctctatgcatta +attattgtgcagcttgatttttctcctttttttttgttaaatcttcctccgtcatccagg +ctggagtgcag +>syndip_1_chr20:18208997-18210828 +gtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatttccaaata +aaaaataagcagaaaggaaaagctaatcatctccccctattccagtcccccaggcatgta +tccttccgtagcttctccacacctacacgaacctagacgattccttccacaccttcccca +cacccacacgaacctagacgattccttccacaccttccccacacccacacgaacctagat +gaattccttccacaccttctccacacccacacgaacctagacgattccttccacaccttc +cccacacccattctccacacccacacgaacctagacgattccttccacacctccacaccc +acacgaacctagatgaattccttccacaccttccccacacccacacaaacctagacgatt +ccttccacaccttctccacacccacacgaacctagacgaattccttccagaccttctcca +cacccacacagacctagacgattccttccacacctccacacccacacgaacctagacgaa +ttccttccacaccttctccacacccacacgaacctagacgaattccttccacaccttctc +cacacccacacgaacctagacgaattccttccacaccttctccacacccacacgaaccta +gacgattccttccacactttccccacacccacacgaacctagacg-attccttccacac- +--ctccacacccacacgaacctagatgaattccttccacaccttccccacacccacacaa +acctagacgattccttccacaccttctccacacccacacaaacctagacaattccttcca +cacacacatgaacctagatgaattccttccacaccttctccacacccacatgaacctaga +cgattccttccacaccttctccacacccacacacacctagatgaattccttccacacctt +ccccacacccacacagacctagacgaattccttccacaccttctccacacccacacgaac +ctagacgattccttccacaccttctccatacccacacgaacctagacaattccttccaca +ccttctcacacccacacaaacctagatgaattccttccacaccttctccacacccacacg +aacctaaacgattccttccacaccttctccacacccacacacacctagatgaattccttc +cacaccttccccacacccacacagacctagacgaattccttccacaccttctccacaccc 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+1,5 @@ +ref_chr20_18208997_18210828 2111 29 60 61 +syndip_1_chr20:18208997-18210828 2111 2210 60 61 +syndip_2_chr20:18208997-18210828 2111 4391 60 61 +p:HG002_1_chr20:18208997-18210828 2111 6573 60 61 +p:HG002_2_chr20:18208997-18210828 2111 8755 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/output.vcf.gz new file mode 100644 index 00000000..3eada7e4 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/output.vcf.gz.tbi new file mode 100644 index 00000000..34e82b29 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:18209097-18210728/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/base.vcf.gz new file mode 100644 index 00000000..3f1f23d2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/base.vcf.gz.tbi new file mode 100644 index 00000000..57b1f071 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/comp.vcf.gz new file mode 100644 index 00000000..a1c8e163 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/comp.vcf.gz.tbi new file mode 100644 index 00000000..5358a000 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/haps.fa new file mode 100644 index 00000000..5112703e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/haps.fa @@ -0,0 +1,84 @@ +>ref_chr20_20295855_20296666 +GATGCCTGTGGCAGGAGCTGAGGGCAAGGGATGAGCAGAGGAGACCAGGCCCCTGCAGCCAGAGGCTCAGTCCTGGCTTTTTCCAAACTCTTCTCCAGAGGAGCCCGCCCTTGCACACCAACGCCTGCATGCTTCCCTCCTTCCTTCCTTCCTTCCCTCCTTTCCTTCCTTCTTTCTTTTCTTCCTCCCTCCCTTCCTTCCCTTCCTTCCCTTCCTTCCCTCCTTTTCTTCCTTCTTTCCTTCCTTCCTTCCCTCCCTCCTTCCCTTCCTTCCTTCCTTCCTCCCTCCCTCCCTCCTTCCCTCCTTCATTCCTTCCTTCCCTCCTTTCCTTCCTTCACCTCCTTCCCTTCTCTCCTCCCTTCATCCCTTCCTTCCTTTCTTCCTTCCCTCCCTCTTCCTTCCTTTCTTCACCCCTCCCCCTTCCCTCATCCCTTCCCTCCTTCCCTTCCTTCCTTCCTTCCCTCCTTCCTTCCCTTCCTTCCTTCCTTGCTTCCTTCCTTCTTTCCTTTCTTCATCCCTCCTTCCCTCCCTCCCTCCTTCCTGCCTTCCTTCTTTCTTTCTTTTCTTTCTTCCTCCCTCCCTCCTTCCTTCCCTCCTTCCTGCCTTCCTTCCTTCCTTTCTTTTTCCTCCCTCCCTCCTTCCTTCTTTACTCCCTTCCTTCCTTCCTTCCTCCCCTCACTCAATTTGTTCATCAAAAAATCTAGTTCCTTGCCATGCCACAGCCTGAGTATTTAAAAATAACTTTTCCTCATTTTAGAAGTAATGATCATTTTTTAAAAATTAGAAGCTGCAGATAGTCAAATAACTGTAAG +>syndip_1_chr20:20295855-20296666 +GATGCCTGTGGCAGGAGCTGAGGGCAAGGGATGAGCAGAGGAGACCAGGCCCCTGCAGCC +AGAGGCTCAGTCCTGGCTTTTTCCAAACTCTTCTCCAGAGGAGCCCGCCCTTGCACACCA +ACGCCTGCATGCTTCCCTCCTTCCTTCCTTCCTTCCCTCCTTTCCTTCCTTCTTTCTTTT +CTTCCTCCCTCCCTTCCTTCCCTTCCTTCCCTTCCTTCCCTCCTTTTCTTCCTTCTTTCC +TTCCTTCCTTCCCTCCCTCCTTCCCTTCCTTCCTTCCTTCCCTTCCTTCCTTCTCTCCTT +CCTTCCTTCCCTCCCTCCTTCCCTTCCTTCCTTCTCTCCTTCCTTCCCTTCCTTCCTTCT +CTCCTTCCTTCCCTTCCTTCCTTCTCTCCTTCCTTCCCTTCCTTCCTTCTCTCCTTCCTT +CCCTTCCTTCCTTCTCTCCTTCCTTCCCTTGCTTCCTTTCTTCCTTCCTTTGCTTCCTTG +CTTCCTTCTTTCCTTTCTTCATCCCTCCCTCCCTCCTTCCTTCCTTTCCTTCCTTCCCTC +TATCCTTCCTTCCTTCCTTTCTTTCTCCCTCCCTTCCTTCCCTTCCTTCCTTCCCTCTTT +TCCTTCCATCTTTCCTTTCTTCCTCCCTCCCTCCCTCCTTCCCTCCTTCATTACTTCCTT +CCCTCCTTTCCTTCCTTCACCTCCTTCCCTTCTCTCCTCCCTTCATCCCTTCCTTCCTTT +CTTCCTTCCCTCCCTCTTCCTTCCTTTCTTCACCCCTCCCCCTTCCCTCATCCCTTCCCT +CCTTCCCTTCCTTCCTTCCTTCCCTCCTTCCTTCCCTTCCTTCCTTCCTTGCTTCCTTCC +TTCTTTCCTTTCTTCATCCCTCCTTCCCTCCCTCCCTCCTTCCTGCCTTCCTTCTTTCTT +TCTTTTCTTTCTTCCTCCCTCCCTCCTTCCTTCCCTCCTTCCTGCCTTCCTTCCTTCCTT +TCTTTTTCCTCCCTCCCTCCTTCCTTCTTTACTCCCTTCCTTCCTTCCTTCCTCCCCTCA +CTCAATTTGTTCATCAAAAAATCTAGTTCCTTGCCATGCCACAGCCTGAGTATTTAAAAA +TAACTTTTCCTCATTTTAGAAGTAATGATCATTTTTTAAAAATTAGAAGCTGCAGATAGT +CAAATAACTGTAAG +>syndip_2_chr20:20295855-20296666 +GATGCCTGTGGCAGGAGCTGAGGGCAAGGGATGAGCAGAGGAGACCAGGCCCCTGCAGCC +AGAGGCTCAGTCCTGGCTTTTTCCAAACTCTTCTCCAGAGGAGCCCGCCCTTGCACACCA +ACGCCTGCATGCTTCCCTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC +TTCCTGCCTGCCTGCCTGCCTTCCTGCCTTCCCTTCCTCCCTCCCTCCCTACCTCCCTCC +CTCCTTCCTTCCCTTCCTCCCTCCCTCCCTTCTTTACTTCCTTCCTCCTTCCCTCCTCCT +TTCCTCCATCCTTCCCTCCCTTCTTTCCTTTCTTCCTCCTGCCCTCCCTCCTTCTTTCCC +TTCCTCCCTCCCTTCCTTCCCATCCTCCTTCCCTCCCTCCTTCCTTCCTGCCTTCCTTCC +TTCCCTCCATCCTTCCTTCCTTCCTTTCTTCCTCCCTCCCTTCCTTCCTCCCTTCCTTCC +CTTCCTTCCTTCCCTCTTTTCCTTCCATCTTTCCTTTCTTCCTCCCTCCCTCCCTCCTTC +CCTCCTTCATTCCTTTCTTCCCTCCTTTCCTTCCTTCACCTCCTTCCCTTCTCTCCTCCC +TTCATCCCTTCCTTCCTTTCTTCCTTCCCTCCCTCTTCCTTCCTTTCTTCACCCCTCCCC +CTTCCCTCATCCCTTCCCTCCTTCCCTTCCTTCCTTCCTTCCCTCCTTCCTTCCCTTCCT +TCCTTCCTTCCCTCCTTCCTTCCCTTCCTTCCTTGCTTCCTTCCTTCCTTCCCTTCCTTC +CTTGCTTCCTTCCTTCCTTCCCTTCCTTCCTTGCTTCCTTCCTTCTTTCCTTTCTTCATC +CCTCCTTCCCTCCCTCCCTCCTTCCTGCCTTCCTTCTTTCTTTCTTTTCTTTCTTCCTCC +CTCCCTCCTTCCTTCCCTCCTTCCTGCCTTCCTTCCTTCCTTTCTTTTTCCTCCCTCCCT +CCTTCCTTCTTTACTCCCTTCCTTCCTTCCTTCCTCCCCTCACTCAATTTGTTCATCAAA +AAATCTAGTTCCTTGCCATGCCACAGCCTGAGTATTTAAAAATAACTTTTCCTCATTTTA +GAAGTAATGATCATTTTTTAAAAATTAGAAGCTGCAGATAGTCAAATAACTGTAAG +>p:HG002_1_chr20:20295855-20296666 +GATGCCTGTGGCAGGAGCTGAGGGCAAGGGATGAGCAGAGGAGACCAGGCCCCTGCAGCC +AGAGGCTCAGTCCTGGCTTTTTCCAAACTCTTCTCCAGAGGAGCCCGCCCTTGCACACCA +ACGCCTGCATGCTTCCCTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC +TTCCTGCCTGCCTGCCTGCCTTCCTGCCTTCCCTTCCTCCCTCCCTCCCTACCTCCCTCC +CTCCTTCCTTCCCTTCCTCCCTCCCTCCCTTCTTTACTTCCTTCCTCCTTCCCTCCTCCT +TTCCTCCATCCTTCCCTCCCTTCTTTCCTTTCTTCCTCCTGCCCTCCCTCCTTCTTTCCC +TTCCTCCCTCCCTTCCTTCCCATCCTCCTTCCCTCCCTCCTTCCTTCCTGCCTTCCTTCC +TTCCCTCCATCCTTCCTTCCTTCCTTTCTTCCTCCCTCCCTTCCTTCCTCCCTTCCTTCC +CTTCCTTCCTTCCCTCTTTTCCTTCCATCTTTCCTTTCTTCCTCCCTCCCTCCCTCCTTC +CCTCCTTCATTCCTTTCTTCCCTCCTTTCCTTCCTTCACCTCCTTCCCTTCTCTCCTCCC +TTCATCCCTTCCTTCCTTTCTTCCTTCCCTCCCTCTTCCTTCCTTTCTTCACCCCTCCCC +CTTCCCTCATCCCTTCCCTCCTTCCCTTCCTTCCTTCCTTCCCTCCTTCCTTCCCTTCCT +TCCTTCCTTCCCTCCTTCCTTCCCTTCCTTCCTTGCTTCCTTCCTTCCTTCCCTTCCTTC +CTTGCTTCCTTCCTTCCTTCCCTTCCTTCCTTGCTTCCTTCCTTCTTTCCTTTCTTCATC +CCTCCTTCCCTCCCTCCCTCCTTCCTGCCTTCCTTCTTTCTTTCTTTTCTTTCTTCCTCC +CTCCCTCCTTCCTTCCCTCCTTCCTGCCTTCCTTCCTTCCTTTCTTTTTCCTCCCTCCCT +CCTTCCTTCTTTACTCCCTTCCTTCCTTCCTTCCTCCCCTCACTCAATTTGTTCATCAAA +AAATCTAGTTCCTTGCCATGCCACAGCCTGAGTATTTAAAAATAACTTTTCCTCATTTTA +GAAGTAATGATCATTTTTTAAAAATTAGAAGCTGCAGATAGTCAAATAACTGTAAG +>p:HG002_2_chr20:20295855-20296666 +GATGCCTGTGGCAGGAGCTGAGGGCAAGGGATGAGCAGAGGAGACCAGGCCCCTGCAGCC +AGAGGCTCAGTCCTGGCTTTTTCCAAACTCTTCTCCAGAGGAGCCCGCCCTTGCACACCA +ACGCCTGCATGCTTCCCTCCTTCCTTCCTTCCTTCCCTCCTTTCCTTCCTTCTTTCTTTT +CTTCCTCCCTCCCTTCCTTCCCTTCCTTCCCTTCCTTCCCTCCTTTTCTTCCTTCTTTCC +TTCCTTCCTTCCCTCCCTCCTTCCCTTCCTTCCTTCCTTCCCTTCCTTCCTTCTCTCCTT +CCTTCCTTCCCTCCCTCCTTCCCTTCCTTCCTTCTCTCCTTCCTTCCCTTCCTTCCTTCT +CTCCTTCCTTCCCTTCCTTCCTTCTCTCCTTCCTTCCCTTCCTTCCTTCTCTCCTTCCTT +CCCTTCCTTCCTTCTCTCCTTCCTTCCCTTGCTTCCTTTCTTCCTTCCTTTGCTTCCTTG +CTTCCTTCTTTCCTTTCTTCATCCCTCCCTCCCTCCTTCCTTCCTTTCCTTCCTTCCCTC +TATCCTTCCTTCCTTCCTTTCTTTCTCCCTCCCTTCCTTCCCTTCCTTCCTTCCCTCTTT +TCCTTCCATCTTTCCTTTCTTCCTCCCTCCCTCCCTCCTTCCCTCCTTCATTACTTCCTT +CCCTCCTTTCCTTCCTTCACCTCCTTCCCTTCTCTCCTCCCTTCATCCCTTCCTTCCTTT +CTTCCTTCCCTCCCTCTTCCTTCCTTTCTTCACCCCTCCCCCTTCCCTCATCCCTTCCCT +CCTTCCCTTCCTTCCTTCCTTCCCTCCTTCCTTCCCTTCCTTCCTTCCTTGCTTCCTTCC +TTCTTTCCTTTCTTCATCCCTCCTTCCCTCCCTCCCTCCTTCCTGCCTTCCTTCTTTCTT +TCTTTTCTTTCTTCCTCCCTCCCTCCTTCCTTCCCTCCTTCCTGCCTTCCTTCCTTCCTT +TCTTTTTCCTCCCTCCCTCCTTCCTTCTTTACTCCCTTCCTTCCTTCCTTCCTCCCCTCA +CTCAATTTGTTCATCAAAAAATCTAGTTCCTTGCCATGCCACAGCCTGAGTATTTAAAAA +TAACTTTTCCTCATTTTAGAAGTAATGATCATTTTTTAAAAATTAGAAGCTGCAGATAGT +CAAATAACTGTAAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/haps.fa.ref.fa new file mode 100644 index 00000000..5c189ea8 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:20295855-20296666 +GATGCCTGTGGCAGGAGCTGAGGGCAAGGGATGAGCAGAGGAGACCAGGCCCCTGCAGCCAGAGGCTCAGTCCTGGCTTTTTCCAAACTCTTCTCCAGAGGAGCCCGCCCTTGCACACCAACGCCTGCATGCTTCCCTCCTTCCTTCCTTCCTTCCCTCCTTTCCTTCCTTCTTTCTTTTCTTCCTCCCTCCCTTCCTTCCCTTCCTTCCCTTCCTTCCCTCCTTTTCTTCCTTCTTTCCTTCCTTCCTTCCCTCCCTCCTTCCCTTCCTTCCTTCCTTCCTCCCTCCCTCCCTCCTTCCCTCCTTCATTCCTTCCTTCCCTCCTTTCCTTCCTTCACCTCCTTCCCTTCTCTCCTCCCTTCATCCCTTCCTTCCTTTCTTCCTTCCCTCCCTCTTCCTTCCTTTCTTCACCCCTCCCCCTTCCCTCATCCCTTCCCTCCTTCCCTTCCTTCCTTCCTTCCCTCCTTCCTTCCCTTCCTTCCTTCCTTGCTTCCTTCCTTCTTTCCTTTCTTCATCCCTCCTTCCCTCCCTCCCTCCTTCCTGCCTTCCTTCTTTCTTTCTTTTCTTTCTTCCTCCCTCCCTCCTTCCTTCCCTCCTTCCTGCCTTCCTTCCTTCCTTTCTTTTTCCTCCCTCCCTCCTTCCTTCTTTACTCCCTTCCTTCCTTCCTTCCTCCCCTCACTCAATTTGTTCATCAAAAAATCTAGTTCCTTGCCATGCCACAGCCTGAGTATTTAAAAATAACTTTTCCTCATTTTAGAAGTAATGATCATTTTTTAAAAATTAGAAGCTGCAGATAGTCAAATAACTGTAAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/msa.fa new file mode 100644 index 00000000..5636b463 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/msa.fa @@ -0,0 +1,105 @@ +>ref_chr20_20295855_20296666 +gatgcctgtggcaggagctgagggcaagggatgagcagaggagaccaggcccctgcagcc +agaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacca +acgcctgcatgcttccctccttccttccttccttccctcctttccttccttctttctttt +cttcctccctcccttcct---tcccttccttcccttccttccctcctttt--cttccttc +tttccttccttccttccctccctccttcccttccttccttc------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------cttcctccctccctccctccttccctccttcattcc +ttccttccctcctttccttccttcacctccttcccttctctcctcccttcatcccttcct +tcctttcttccttccctccctcttccttcctttcttcacccctcccccttccctcatccc +ttccctccttcccttccttccttccttccctccttccttcccttccttccttccttgctt +ccttccttctttcctttcttcatccctccttccctccctccctccttcctgccttccttc +tttctttcttttctttcttcctccctccctccttccttccctccttcctgccttccttcc +ttcctttctttttcctccctccctccttccttctttactcccttccttccttccttcctc +ccctcactcaatttgttcatcaaaaaatctagttccttgccatgccacagcctgagtatt +taaaaataacttttcctcattttagaagtaatgatcattttttaaaaattagaagctgca +gatagtcaaataactgtaag +>syndip_1_chr20:20295855-20296666 +gatgcctgtggcaggagctgagggcaagggatgagcagaggagaccaggcccctgcagcc +agaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacca +acgcctgcatgcttccctccttccttccttccttccctcctttccttccttctttctttt +cttcctccctcccttcct---tcccttccttcccttccttccctcctttt--cttccttc +tttccttccttccttccctccctccttcccttccttccttccttcc-cttccttccttct +ctccttccttccttccctccctccttcccttccttccttctctccttccttcccttcctt +ccttctctccttccttcccttccttccttctctccttccttcccttccttccttctctcc +ttccttcccttccttccttctctccttccttcccttgcttcctttcttccttcctttgct +tccttgcttccttctttcctttcttcatccctccctccctccttccttcctttccttcct +tccctctatccttccttccttcctttctttctccctcccttccttcccttccttccttcc +ctcttttccttccatctttcctttcttcctccctccctccctccttccctccttcattac +ttccttccctcctttccttccttcacctccttcccttctctcctcccttcatcccttcct +tcctttcttccttccctccctcttccttcctttcttcacccctcccccttccctcatccc +ttccctccttcccttccttccttccttccctccttccttcccttccttccttccttgctt +ccttccttctttcctttcttcatccctccttccctccctccctccttcctgccttccttc +tttctttcttttctttcttcctccctccctccttccttccctccttcctgccttccttcc +ttcctttctttttcctccctccctccttccttctttactcccttccttccttccttcctc +ccctcactcaatttgttcatcaaaaaatctagttccttgccatgccacagcctgagtatt +taaaaataacttttcctcattttagaagtaatgatcattttttaaaaattagaagctgca +gatagtcaaataactgtaag +>syndip_2_chr20:20295855-20296666 +gatgcctgtggcaggagctgagggcaagggatgagcagaggagaccaggcccctgcagcc +agaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacca +acgcctgcatgcttccctccttccttccttccttccttcctt-ccttccttccttccttc +cttcctgcctgcctgcctgccttcctgccttcccttcctccctccctccctacctccctc +cctccttccttcccttcctccctccctcccttctttacttccttcctccttccctcctcc +tttcctccatccttccctcccttctttcctttcttcctcctgccct------ccctcctt +ctttcccttcctccctcccttccttcccatcctccttccctccct--ccttccttcctgc +cttccttccttccctccatccttccttccttccttt-cttcctccctcccttccttcctc +ccttccttcccttccttccttccctcttttccttccatctttcctttcttcctccctccc +tccctccttccctccttcattcctttct---tccctcctttccttccttcacctccttcc +cttctctcctcccttcatcccttccttcctttcttccttccctccctcttccttcctttc +ttcacccctcccccttccctcatcccttccctccttcccttccttccttccttccctcct +tccttcccttccttccttc--cttccctccttcctt---------cccttccttccttgc +ttccttccttccttcccttccttccttgcttccttccttccttcccttccttccttgctt +ccttccttctttcctttcttcatccctccttccctccctccctccttcctgccttccttc +tttctttcttttctttcttcctccctccctccttccttccctccttcctgccttccttcc +ttcctttctttttcctccctccctccttccttctttactcccttccttccttccttcctc +ccctcactcaatttgttcatcaaaaaatctagttccttgccatgccacagcctgagtatt +taaaaataacttttcctcattttagaagtaatgatcattttttaaaaattagaagctgca +gatagtcaaataactgtaag +>p:HG002_1_chr20:20295855-20296666 +gatgcctgtggcaggagctgagggcaagggatgagcagaggagaccaggcccctgcagcc +agaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacca +acgcctgcatgcttccctccttccttccttccttccttcctt-ccttccttccttccttc +cttcctgcctgcctgcctgccttcctgccttcccttcctccctccctccctacctccctc +cctccttccttcccttcctccctccctcccttctttacttccttcctccttccctcctcc +tttcctccatccttccctcccttctttcctttcttcctcctgccct------ccctcctt +ctttcccttcctccctcccttccttcccatcctccttccctccct--ccttccttcctgc +cttccttccttccctccatccttccttccttccttt-cttcctccctcccttccttcctc +ccttccttcccttccttccttccctcttttccttccatctttcctttcttcctccctccc +tccctccttccctccttcattcctttct---tccctcctttccttccttcacctccttcc +cttctctcctcccttcatcccttccttcctttcttccttccctccctcttccttcctttc +ttcacccctcccccttccctcatcccttccctccttcccttccttccttccttccctcct +tccttcccttccttccttc--cttccctccttcctt---------cccttccttccttgc +ttccttccttccttcccttccttccttgcttccttccttccttcccttccttccttgctt +ccttccttctttcctttcttcatccctccttccctccctccctccttcctgccttccttc +tttctttcttttctttcttcctccctccctccttccttccctccttcctgccttccttcc +ttcctttctttttcctccctccctccttccttctttactcccttccttccttccttcctc +ccctcactcaatttgttcatcaaaaaatctagttccttgccatgccacagcctgagtatt +taaaaataacttttcctcattttagaagtaatgatcattttttaaaaattagaagctgca +gatagtcaaataactgtaag +>p:HG002_2_chr20:20295855-20296666 +gatgcctgtggcaggagctgagggcaagggatgagcagaggagaccaggcccctgcagcc +agaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacca +acgcctgcatgcttccctccttccttccttccttccctcctttccttccttctttctttt +cttcctccctcccttcct---tcccttccttcccttccttccctcctttt--cttccttc +tttccttccttccttccctccctccttcccttccttccttccttcc-cttccttccttct +ctccttccttccttccctccctccttcccttccttccttctctccttccttcccttcctt +ccttctctccttccttcccttccttccttctctccttccttcccttccttccttctctcc +ttccttcccttccttccttctctccttccttcccttgcttcctttcttccttcctttgct +tccttgcttccttctttcctttcttcatccctccctccctccttccttcctttccttcct +tccctctatccttccttccttcctttctttctccctcccttccttcccttccttccttcc +ctcttttccttccatctttcctttcttcctccctccctccctccttccctccttcattac +ttccttccctcctttccttccttcacctccttcccttctctcctcccttcatcccttcct +tcctttcttccttccctccctcttccttcctttcttcacccctcccccttccctcatccc +ttccctccttcccttccttccttccttccctccttccttcccttccttccttccttgctt +ccttccttctttcctttcttcatccctccttccctccctccctccttcctgccttccttc +tttctttcttttctttcttcctccctccctccttccttccctccttcctgccttccttcc +ttcctttctttttcctccctccctccttccttctttactcccttccttccttccttcctc +ccctcactcaatttgttcatcaaaaaatctagttccttgccatgccacagcctgagtatt +taaaaataacttttcctcattttagaagtaatgatcattttttaaaaattagaagctgca +gatagtcaaataactgtaag diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/msa.fa.fai new file mode 100644 index 00000000..e5ba32e9 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_20295855_20296666 1160 29 60 61 +syndip_1_chr20:20295855-20296666 1160 1243 60 61 +syndip_2_chr20:20295855-20296666 1160 2457 60 61 +p:HG002_1_chr20:20295855-20296666 1160 3672 60 61 +p:HG002_2_chr20:20295855-20296666 1160 4887 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/output.vcf.gz new file mode 100644 index 00000000..9c15bfd8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/output.vcf.gz.tbi new file mode 100644 index 00000000..0b302534 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20295955-20296566/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/base.vcf.gz new file mode 100644 index 00000000..8d9dd543 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/base.vcf.gz.tbi new file mode 100644 index 00000000..2a49b68e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/comp.vcf.gz new file mode 100644 index 00000000..9aa33647 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/comp.vcf.gz.tbi new file mode 100644 index 00000000..1bef0580 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/haps.fa new file mode 100644 index 00000000..4fef927d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/haps.fa @@ -0,0 +1,84 @@ +>ref_chr20_20320185_20320680 +ATCCTGATTCAGATAAACTGTTAAACAAAAATCTGTGCCATTTATGAGGTGATTGGAAATTTGAAACCTGGAGAGTTAATGATGATAAGCAATTATGATTAATTTTTTTAGCAGTAAAGATGGTATTTCAGATATATAGATATATATATATTATATATATGTAATATATATAATATATGTAATATATATTATATATATGTAATATATATAATATATGTAATATATGTAATATATATTATATATGTAATATAATATATGTAATATATATTATATATGTAATATATAATATATGTAATATATAATATATGTAATATATATTATATATGTAATATATAATATATATTATATATGTAATATATATATATTTAAAAACAGAACCATTATCTTTTAGAGATACATACTGAAGTGTCTGGAGACATGCTTCAAGATAACCCAGGAGGGAGAATGGTAGAAGGAACTAGAGATGACCCAAGACTGCCCTTGAGCTAATAACTGT +>syndip_1_chr20:20320185-20320680 +ATCCTGATTCAGATAAACTGTTAAACAAAAATCTGTGCCATTTATGAGGTGATTGGAAAT +TTGAAACCTGGAGAGTTAATGATGATAAGCAATTATGATTAATTTTTTTAGCAGTAAAGA +TGGTATTTCAGATATATAGATATATATATTATATATATGTAATATATATAATATATGTAA +TATATTATATATATGTAATATATATAATATATGTAATATATTATATATATGTAATATATA +TAATATATGTAATATATATTATATATGTAATATATATAATATATGTAATATATATTATAT +ATGTAATATATATAATATATGTAATATATATTATATATGTAATATATAATATATGTAATA +TATATTATATATGTAATATAATATATGTAATATATATTATATATGTAATATATATTACAT +ATATTATATATGCAATATATATTATATATATTATATATGCAATATATATTATATATATTA +TATATGCAATATATATTATATATGCAATATATATTATATATATTATATATGCAATATATA +TTATATATATTACATATGTAATATATATTACATATGTAATATATAATATATTATATATTA +CATATGTAATATATAATATATTATATATTACATATGTAATATATAATATATATTACATAT +GTAATATATAATATATATTACATATGTAATATATTATATATTACATATGTAATATATTAT +ATATTACATATGTAATATATTATATATTACATATGTAATATATTATATATTACATATGTA +ATATATTATATATTACATATGTAATATATATAATATATTACATATGTAATATATAATATA +TTATATATGTAATATATATTACATATATAATATATATAATATATATGTAATATATTATAT +ATATTATATATGTAATATATATTACATATATAATATATATTATATATATTACATATATTA +TATATGTAATATATATTACATATGTAATATATGTAATATATATTACATATGTAATATATA +TTATATATGTAATATATATTACATATATTATATATGTAATATATATTATATATATTATAT +ATGTAATGTATAATATATATATTATATATGTAATATATATTATATATAATATATGTAATA +TATATTATATATGTAATGTATATTATATATATTATATATGTAATGTATATTATATATAAT +ATATGTAATGTATATTATATATGTAATATATATTATGTATATTATATATGTAATATATAT +TATATATATTATATATGTAATATATATTATATATATTATATATGTAATATATATTATATA +TATTATATATGTAATATATATTATATATATTATATATGTAATATATATTATATATATTAT +ATATGTAATATATATTATATATATTATATATGTAATATATATTATATATATTATATATGT +AATATATATTATATATATTATATATGTAATATATATTATATATATTATATATGTAATATA +TATTATATATATTATATATGTAATATATATTATATATATTATATATGTAATATATATTAT +ATATATTATATATGTAATATATATTATATATATTATATATGTAATATATATTATATATAT +TATATATGTAATATATATATATTTAAAAACAGAACCATTATCTTTTAGAGATACATACTG +AAGTGTCTGGAGACATGCTTCAAGATAACCCAGGAGGGAGAATGGTAGAAGGAACTAGAG +ATGACCCAAGACTGCCCTTGAGCTAATAACTGT +>syndip_2_chr20:20320185-20320680 +ATCCTGATTCAGATAAACTGTTAAACAAAAATCTGTGCCATTTATGAGGTGATTGGAAAT +TTGAAACCTGGAGAGTTAATGATGATAAGCAATTATGATTAATTTTTTTAGCAGTAAAGA +TGGTATTTCAGATATATAGATATATATATATTATATATATGTAATATATATAATATATGT +AATATATATTATATATATGTAATATATATAATATATGTAATATATGTAATATATATTATA +TATGTAATATAATATATGTAATATATATTATATATGTAATATATAATATATGTAATATAT +AATATATGTAATATATATTATATATGTAATATATAATATATATTATATATGTAATATATA +TATATTTAAAAACAGAACCATTATCTTTTAGAGATACATACTGAAGTGTCTGGAGACATG +CTTCAAGATAACCCAGGAGGGAGAATGGTAGAAGGAACTAGAGATGACCCAAGACTGCCC +TTGAGCTAATAACTGT +>p:HG002_1_chr20:20320185-20320680 +ATCCTGATTCAGATAAACTGTTAAACAAAAATCTGTGCCATTTATGAGGTGATTGGAAAT +TTGAAACCTGGAGAGTTAATGATGATAAGCAATTATGATTAATTTTTTTAGCAGTAAAGA +TGGTATTTCAGATATATAGATATATATATATTATATATATGTAATATATATAATATATGT +AATATATATTATATATATGTAATATATATAATATATGTAATATATGTAATATATATTATA +TATGTAATATAATATATGTAATATATATTATATATGTAATATATAATATATGTAATATAT +AATATATGTAATATATATTATATATGTAATATATAATATATATTATATATGTAATATATA +TATATTTAAAAACAGAACCATTATCTTTTAGAGATACATACTGAAGTGTCTGGAGACATG +CTTCAAGATAACCCAGGAGGGAGAATGGTAGAAGGAACTAGAGATGACCCAAGACTGCCC +TTGAGCTAATAACTGT +>p:HG002_2_chr20:20320185-20320680 +ATCCTGATTCAGATAAACTGTTAAACAAAAATCTGTGCCATTTATGAGGTGATTGGAAAT +TTGAAACCTGGAGAGTTAATGATGATAAGCAATTATGATTAATTTTTTTAGCAGTAAAGA +TGGTATTTCAGATATATAGATATATATATTATATATATGTAATATATATAATATATGTAA +TATATTATATATATGTAATATATATAATATATGTAATATATTATATATATGTAATATATA +TAATATATGTAATATATATTATATATGTAATATATATAATATATGTAATATATATTATAT +ATGTAATATATATAATATATGTAATATATATTATATATGTAATATATAATATATGTAATA +TATATTATATATGTAATATAATATATGTAATATATATTATATATGTAATATATATTACAT +ATATTATATATGCAATATATATTATATATATTATATATGCAATATATATTATATATATTA +TATATGCAATATATATTATATATGCAATATATATTATATATATTATATATGCAATATATA +TTATATATATTACATATGTAATATATATTACATATGTAATATATAATATATTATATATTA +CATATGTAATATATAATATATTATATATTACATATGTAATATATAATATATATTACATAT +GTAATATATAATATATATTACATATGTAATATATTATATATTACATATGTAATATATTAT +ATATTACATATGTAATATATTATATATTACATATGTAATATATTATATATTACATATGTA +ATATATTATATATTACATATGTAATATATATAATATATTACATATGTAATATATAATATA +TTATATATGTAATATATATTACATATATAATATATATAATATATATGTAATATATTATAT +ATATTATATATGTAATATATATTACATATATAATATATATTATATATATTACATATATTA +TATATGTAATATATATTACATATGTAATATATGTAATATATATTACATATGTAATATATA +TTATATATGTAATATATATTACATATATTATATATGTAATATATATTATATATATTATAT +ATGTAATGTATAATATATATATTATATATGTAATATATATTATATATAATATATGTAATA +TATATTATATATGTAATGTATATTATATATATTATATATGTAATGTATATTATATATAAT +ATATGTAATGTATATTATATATGTAATATATATTATGTATATTATATATGTAATATATAT +TATATATATTATATATGTAATATATATTATATATATTATATATGTAATATATATTATATA +TATTATATATGTAATATATATTATATATATTATATATGTAATATATATTATATATATTAT +ATATGTAATATATATTATATATATTATATATGTAATATATATTATATATATTATATATGT +AATATATATTATATATATTATATATGTAATATATATTATATATATTATATATGTAATATA +TATTATATATATTATATATGTAATATATATTATATATATTATATATGTAATATATATTAT +ATATATTATATATGTAATATATATTATATATATTATATATGTAATATATATTATATATAT +TATATATGTAATATATATATATTTAAAAACAGAACCATTATCTTTTAGAGATACATACTG +AAGTGTCTGGAGACATGCTTCAAGATAACCCAGGAGGGAGAATGGTAGAAGGAACTAGAG +ATGACCCAAGACTGCCCTTGAGCTAATAACTGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/haps.fa.ref.fa new file mode 100644 index 00000000..b9b227e4 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:20320185-20320680 +ATCCTGATTCAGATAAACTGTTAAACAAAAATCTGTGCCATTTATGAGGTGATTGGAAATTTGAAACCTGGAGAGTTAATGATGATAAGCAATTATGATTAATTTTTTTAGCAGTAAAGATGGTATTTCAGATATATAGATATATATATATTATATATATGTAATATATATAATATATGTAATATATATTATATATATGTAATATATATAATATATGTAATATATGTAATATATATTATATATGTAATATAATATATGTAATATATATTATATATGTAATATATAATATATGTAATATATAATATATGTAATATATATTATATATGTAATATATAATATATATTATATATGTAATATATATATATTTAAAAACAGAACCATTATCTTTTAGAGATACATACTGAAGTGTCTGGAGACATGCTTCAAGATAACCCAGGAGGGAGAATGGTAGAAGGAACTAGAGATGACCCAAGACTGCCCTTGAGCTAATAACTGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/msa.fa new file mode 100644 index 00000000..4c5e2abd --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/msa.fa @@ -0,0 +1,155 @@ +>ref_chr20_20320185_20320680 +atcctgattcagataaactgttaaacaaaaatctgtgccatttatgaggtgattggaaat +ttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcagtaaaga +tggtatttcagatatatagatatatatatattatatatatgtaatatatataatatatgt +aatatatattatatatatgtaatatatataatatatgta---------atatatgtaata +tatattatatatgtaatata----atatatgtaatatatattatatatgtaatatataat +atatgta----atatataatatatgtaatatatattatatatgtaatatataatatatat +tatatatgtaatatatatatatttaaaaacagaaccattatctttta-gagatacatact +gaagtgtctggagacatgcttcaagata-------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------acccaggagggagaatggtagaaggaact +agagatgacccaagactgcccttgagctaataactgt +>syndip_1_chr20:20320185-20320680 +atcctgattcagataaactgttaaacaaaaatctgtgccatttatgaggtgattggaaat +ttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcagtaaaga +tggtatttcagatatatag--atatatatattatatatatgtaatatatataatatatgt +a--atatattatatatatgtaatatatataatatatgtaatatattatatatatgtaata +tatataatatatgtaatatatattatatatgtaatatatataatatatgtaatatatatt +atatatgtaatatatataatatatgtaatatatattatatatgtaatatataatatatgt +aatatatattatatatgtaatataatatatgtaatatatattatatatgtaatatatatt +acatatattatatatgcaatatatattatatatattatatatgcaatatatattatatat +attatatatgcaatatatattatatatgcaatatatattatatatattatatatgcaata +tatattatatatattacatatgtaatatatattacatatgtaatatataatatattatat +attacatatgtaatatataatatattatatattacatatgtaatatataatatatattac +atatgtaatatataatatatattacatatgtaatatattatatattacatatgtaatata +ttatatattacatatgtaatatattatatattacatatgtaatatattatatattacata +tgtaatatattatatattacatatgtaatatatataatatattacatatgtaatatataa +tatattatatatgtaatatatattacatatataatatatataatatatatgtaatatatt +atatatattatatatgtaatatatattacatatataatatatattatatatattacatat +attatatatgtaatatatattacatatgtaatatatgtaatatatattacatatgtaata +tatattatatatgtaatatatattacatatattatatatgtaatatatattatatatatt +atatatgtaatgtataatatatatattatatatgtaatatatattatatataatatatgt +aatatatattatatatgtaatgtatattatatatattatatatgtaatgtatattatata +taatatatgtaatgtatattatatatgtaatatatattatgtatattatatatgtaatat +atattatatatattatatatgtaatatatattatatatattatatatgtaatatatatta +tatatattatatatgtaatatatattatatatattatatatgtaatatatattatatata +ttatatatgtaatatatattatatatattatatatgtaatatatattatatatattatat +atgtaatatatattatatatattatatatgtaatatatattatatatattatatatgtaa +tatatattatatatattatatatgtaatatatattatatatattatatatgtaatatata +ttatatatattatatatgtaatatatattatatatattatatatgtaatatatattatat +atattatatatgtaatatatatatatttaaaaacagaaccattatcttttagagatacat +actgaagtgtctggagacatgcttcaagataacccaggagggagaatggtagaaggaact +agagatgacccaagactgcccttgagctaataactgt +>syndip_2_chr20:20320185-20320680 +atcctgattcagataaactgttaaacaaaaatctgtgccatttatgaggtgattggaaat +ttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcagtaaaga +tggtatttcagatatatagatatatatatattatatatatgtaatatatataatatatgt +aatatatattatatatatgtaatatatataatatatgta---------atatatgtaata +tatattatatatgtaatata----atatatgtaatatatattatatatgtaatatataat +atatgta----atatataatatatgtaatatatattatatatgtaatatataatatatat +tatatatgtaatatatatatatttaaaaacagaaccattatctttta-gagatacatact +gaagtgtctggagacatgcttcaagata-------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------acccaggagggagaatggtagaaggaact +agagatgacccaagactgcccttgagctaataactgt +>p:HG002_1_chr20:20320185-20320680 +atcctgattcagataaactgttaaacaaaaatctgtgccatttatgaggtgattggaaat +ttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcagtaaaga +tggtatttcagatatatagatatatatatattatatatatgtaatatatataatatatgt +aatatatattatatatatgtaatatatataatatatgta---------atatatgtaata +tatattatatatgtaatata----atatatgtaatatatattatatatgtaatatataat +atatgta----atatataatatatgtaatatatattatatatgtaatatataatatatat +tatatatgtaatatatatatatttaaaaacagaaccattatctttta-gagatacatact +gaagtgtctggagacatgcttcaagata-------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------acccaggagggagaatggtagaaggaact +agagatgacccaagactgcccttgagctaataactgt +>p:HG002_2_chr20:20320185-20320680 +atcctgattcagataaactgttaaacaaaaatctgtgccatttatgaggtgattggaaat +ttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcagtaaaga +tggtatttcagatatatag--atatatatattatatatatgtaatatatataatatatgt +a--atatattatatatatgtaatatatataatatatgtaatatattatatatatgtaata +tatataatatatgtaatatatattatatatgtaatatatataatatatgtaatatatatt +atatatgtaatatatataatatatgtaatatatattatatatgtaatatataatatatgt +aatatatattatatatgtaatataatatatgtaatatatattatatatgtaatatatatt +acatatattatatatgcaatatatattatatatattatatatgcaatatatattatatat +attatatatgcaatatatattatatatgcaatatatattatatatattatatatgcaata +tatattatatatattacatatgtaatatatattacatatgtaatatataatatattatat +attacatatgtaatatataatatattatatattacatatgtaatatataatatatattac +atatgtaatatataatatatattacatatgtaatatattatatattacatatgtaatata +ttatatattacatatgtaatatattatatattacatatgtaatatattatatattacata +tgtaatatattatatattacatatgtaatatatataatatattacatatgtaatatataa +tatattatatatgtaatatatattacatatataatatatataatatatatgtaatatatt +atatatattatatatgtaatatatattacatatataatatatattatatatattacatat +attatatatgtaatatatattacatatgtaatatatgtaatatatattacatatgtaata +tatattatatatgtaatatatattacatatattatatatgtaatatatattatatatatt +atatatgtaatgtataatatatatattatatatgtaatatatattatatataatatatgt +aatatatattatatatgtaatgtatattatatatattatatatgtaatgtatattatata +taatatatgtaatgtatattatatatgtaatatatattatgtatattatatatgtaatat +atattatatatattatatatgtaatatatattatatatattatatatgtaatatatatta +tatatattatatatgtaatatatattatatatattatatatgtaatatatattatatata +ttatatatgtaatatatattatatatattatatatgtaatatatattatatatattatat +atgtaatatatattatatatattatatatgtaatatatattatatatattatatatgtaa +tatatattatatatattatatatgtaatatatattatatatattatatatgtaatatata +ttatatatattatatatgtaatatatattatatatattatatatgtaatatatattatat +atattatatatgtaatatatatatatttaaaaacagaaccattatcttttagagatacat +actgaagtgtctggagacatgcttcaagataacccaggagggagaatggtagaaggaact +agagatgacccaagactgcccttgagctaataactgt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/msa.fa.fai new file mode 100644 index 00000000..97aee165 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_20320185_20320680 1777 29 60 61 +syndip_1_chr20:20320185-20320680 1777 1870 60 61 +syndip_2_chr20:20320185-20320680 1777 3711 60 61 +p:HG002_1_chr20:20320185-20320680 1777 5553 60 61 +p:HG002_2_chr20:20320185-20320680 1777 7395 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/output.vcf.gz new file mode 100644 index 00000000..674d5565 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/output.vcf.gz.tbi new file mode 100644 index 00000000..4007d642 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20320285-20320580/output.vcf.gz.tbi differ diff --git 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00000000..c72f9af5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20337200-20337708/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20337200-20337708/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20337200-20337708/comp.vcf.gz.tbi new file mode 100644 index 00000000..b9e2175c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20337200-20337708/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20337200-20337708/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20337200-20337708/haps.fa new file mode 100644 index 00000000..5bc69989 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20337200-20337708/haps.fa @@ -0,0 +1,144 @@ +>ref_chr20_20337100_20337808 +TACGTGGAAGCATAGGGAAGGAAGGGATGTTTGTTGAGGGGTGGTGTGATGCAGCAGAGGAAGAGGACCAGAGGAAAGCAGCCACTGGAAATAAGGAAACAGGGTTTAGGAAGGCCTCACTAGACCTGTTAGGATGGATGCATGGATGGATGGATGGATGGACAGAATGGGTGGGTGGATGGATGGATGGATAGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGATGGATAAATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGGTGGATGGATGGATGGATGGATAGATGGGTGGGTGGGTGGATGGATGGATGGATGGATAGAATAAAAAAGAAAGCTAGGACATGGTTCTAGTGTTCTTAGCAGACGTCCCACCATGGAAGAGGTCATGGAGCACAGGGGCTTTGGGAAAGGTGTTTACAATCCTGCCTGCCTCTCACCCAGACCTCTTG +>syndip_1_chr20:20337100-20337808 +TACGTGGAAGCATAGGGAAGGAAGGGATGTTTGTTGAGGGGTGGTGTGATGCAGCAGAGG +AAGAGGACCAGAGGAAAGCAGCCACTGGAAATAAGGAAACAGGGTTTAGGAAGGCCTCAC +TAGACCTGTTAGGATGGATGCATGGATGGATGGATGGATGGACAGAATGGGTGGGTGGAT +GGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGAT +GGGTGGATGGATAGATGGGTGGATGGATAAATGGATGGATGGATGGATGGATAGATGGGT +GGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGATAGATGGGT +GGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGT +GGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATAGATGGGTGGATGGATAAATGGATGGATGGATGGAT +GGATAGATGTGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGAT +GGGTGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGT +GGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGAT +GGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGT +GGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATAGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +GGATGGATGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGT +GGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGGT +GGATGGATGGATGGATGGATGGATAGAATAAAAAGAAAGCTAGGACATGGTTCTAGTGTT +CTTAGCAGACGTCCCACCATGGAAGAGGTCATGGAGCACAGGGGCTTTGGGAAAGGTGTT +TACAATCCTGCCTGCCTCTCACCCAGACCTCTTG +>syndip_2_chr20:20337100-20337808 +TACGTGGAAGCATAGGGAAGGAAGGGATGTTTGTTGAGGGGTGGTGTGATGCAGCAGAGG +AAGAGGACCAGAGGAAAGCAGCCACTGGAAATAAGGAAACAGGGTTTAGGAAGGCCTCAC +TAGACCTGTTAGGATGGATGCATGGATGGATGGATGGATGGACAGAATGGGTGGGTGGAT +GGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGATGGATAAATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATGGATGGATGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGT +GGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGGTGGATGGATAAATGGATGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATAGATGGATAGATGGGTGGGT +GGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGATGGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGGTGGGTGGGTGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGGTGGATGGATGGAT +GGATGGATGGATAGAATAAAAAGAAAGCTAGGACATGGTTCTAGTGTTCTTAGCAGACGT +CCCACCATGGAAGAGGTCATGGAGCACAGGGGCTTTGGGAAAGGTGTTTACAATCCTGCC +TGCCTCTCACCCAGACCTCTTG +>p:HG002_1_chr20:20337100-20337808 +TACGTGGAAGCATAGGGAAGGAAGGGATGTTTGTTGAGGGGTGGTGTGATGCAGCAGAGG +AAGAGGACCAGAGGAAAGCAGCCACTGGAAATAAGGAAACAGGGTTTAGGAAGGCCTCAC +TAGACCTGTTAGGATGGATGCATGGATGGATGGATGGATGGACAGAATGGGTGGGTGGAT +GGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGATGGATAAATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATGGATGGATGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGT +GGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGGTGGATGGATAAATGGATGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATAGATGGATAGATGGGTGGGT +GGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGATGGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGGTGGGTGGGTGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGGTGGATGGATGGAT +GGATGGATGGATAGAATAAAAAGAAAGCTAGGACATGGTTCTAGTGTTCTTAGCAGACGT +CCCACCATGGAAGAGGTCATGGAGCACAGGGGCTTTGGGAAAGGTGTTTACAATCCTGCC +TGCCTCTCACCCAGACCTCTTG +>p:HG002_2_chr20:20337100-20337808 +TACGTGGAAGCATAGGGAAGGAAGGGATGTTTGTTGAGGGGTGGTGTGATGCAGCAGAGG +AAGAGGACCAGAGGAAAGCAGCCACTGGAAATAAGGAAACAGGGTTTAGGAAGGCCTCAC +TAGACCTGTTAGGATGGATGCATGGATGGATGGATGGATGGACAGAATGGGTGGGTGGAT +GGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGAT +GGGTGGATGGATAGATGGGTGGATGGATAAATGGATGGATGGATGGATGGATAGATGGGT +GGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGATAGATGGGT +GGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGT +GGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATAGATGGGTGGATGGATAAATGGATGGATGGATGGAT +GGATAGATGTGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGAT +GGGTGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGT +GGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGAT +GGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGT +GGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATAGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +GGATGGATGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGT +GGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGGT +GGATGGATGGATGGATGGATGGATAGAATAAAAAGAAAGCTAGGACATGGTTCTAGTGTT +CTTAGCAGACGTCCCACCATGGAAGAGGTCATGGAGCACAGGGGCTTTGGGAAAGGTGTT +TACAATCCTGCCTGCCTCTCACCCAGACCTCTTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20337200-20337708/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20337200-20337708/haps.fa.ref.fa new file mode 100644 index 00000000..5bb631b5 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20337200-20337708/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:20337100-20337808 +TACGTGGAAGCATAGGGAAGGAAGGGATGTTTGTTGAGGGGTGGTGTGATGCAGCAGAGGAAGAGGACCAGAGGAAAGCAGCCACTGGAAATAAGGAAACAGGGTTTAGGAAGGCCTCACTAGACCTGTTAGGATGGATGCATGGATGGATGGATGGATGGACAGAATGGGTGGGTGGATGGATGGATGGATAGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGATGGATAAATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGGTGGATGGATGGATGGATGGATAGATGGGTGGGTGGGTGGATGGATGGATGGATGGATAGAATAAAAAAGAAAGCTAGGACATGGTTCTAGTGTTCTTAGCAGACGTCCCACCATGGAAGAGGTCATGGAGCACAGGGGCTTTGGGAAAGGTGTTTACAATCCTGCCTGCCTCTCACCCAGACCTCTTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20337200-20337708/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20337200-20337708/msa.fa new file mode 100644 index 00000000..11fabdd5 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20337200-20337708/msa.fa @@ -0,0 +1,190 @@ +>ref_chr20_20337100_20337808 +tacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagagg +aagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctcac +tagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtggat +ggatggatggatagatggatggatggatggatggatggatggatggatggatggatggat +agatgggtgggtgg----gtggatgg----atggatggatggatggatggatggatggat +ggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtggat +ggatggatggatagatgggtgggtggatggatggatggatagatgggtggatggataaat +ggatggatggatggatggatagatgggtgggtggatggatggatggatggatggatggat +ggatggatagat------------------gtgggtggatggatggatggatagatgggt +gggtgggtggatggatggatggatggatagatgggtgggtgggtggatggatggatggat +ggatagaataaaaaagaaa----------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------gctaggacatggttctagtgtt +cttagcagacgtcccaccatggaagaggtcatggagcacaggggctttgggaaaggtgtt +tacaatcctgcctgcctctcacccagacctcttg +>syndip_1_chr20:20337100-20337808 +tacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagagg +aagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctcac +tagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtggat +ggatggatggatggatggatggatggatagatgggtgggtggatggatggatggatagat +gggtggatggatagatgggtggatggataaatggatggatggatggatggatagatgggt +gggtggatggatggatggatggatggatggatggatggatggatagatggatagatgggt +gggtggatggatggatggatggatggatggatggatggatggatagatgggtgggtggat +ggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggt +ggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggt +gggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat +gggtgggtggatggatggatggatagatgggtggatggataaatggatggatggatggat +ggatagatgtgtgggtggatggatggatggatggatggatggatggatggatggatagat +ggatagatgggtgggtggatggatggatggatggatggatggatggatggatggatagat +gggtggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt +gggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat +gggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggat +agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat +ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat +agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat +ggatagatgggtgggtggatggatggatggatggatggatggatggatagatgggtgggt +ggatggatggatggatagatgggtgggtggatggatggatggatggatggatggatggat +ggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggat +ggatggatggatagatggatagatgggtgggtggatggatggatggatagatggatagat +gggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggt +gggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggt +ggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt +gggtggatggatggatggatagatgggtgggtggatggatggatggatggatggatagat +ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat +ggatggatggatggatggatggatagatggatagatgggtgggtggatggatggatggat +agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat +ggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggat +ggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtggat +ggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggt +ggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtgggt +ggatggatggatggatggatggatagaataaaaagaaagctaggacatggttctagtgtt +cttagcagacgtcccaccatggaagaggtcatggagcacaggggctttgggaaaggtgtt +tacaatcctgcctgcctctcacccagacctcttg +>syndip_2_chr20:20337100-20337808 +tacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagagg +aagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctcac +tagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtggat +ggatggatggatggatggatggatggatggatagatgggtgggtggatggatggatggat +agatgggtggatggataaatggatgg----atggatggatggatagatgggtgggtggat +ggatggatggatggatggatggatggatggatggatagatggatagatgggtgggtggat +ggatggatggatggatggatggatggatggatggatggatggatagatgggtgggtggat +ggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggt +ggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggt +gggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat +gggtgggtggatggatggatggatagatgggtggatggataaatggatggatggatggat +ggatagatgggtgggtggatggatggatggatggatggatggatagatggataga----- +-----------tgggtgggtggatggatggatggatggatggatggatggatggatagat +gggtggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt +gggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat +gggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggat +agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat +ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat +agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat +ggatagatgggtgggtggatggatggatggatggatggatagatggatagatgggtgggt +ggatggatggatggatagatgggtggg----tggatggatggatggatggatggatggat +ggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggat +ggatggatggatagatggatagatgggtgggtggatggatggatggatagatggatagat +gggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggt +gggtggatggatggatggata--------------------gatggatagatgggtgggt +ggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt +gggtggatggatggatggatagatgggtgggtggatggatggatggataga--------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------tgggtgggtgggtggatggatggatagatgggtgggtggat +ggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggt +ggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtgggt +ggatggatggatggatggatggatagaataaaaagaaagctaggacatggttctagtgtt +cttagcagacgtcccaccatggaagaggtcatggagcacaggggctttgggaaaggtgtt +tacaatcctgcctgcctctcacccagacctcttg +>p:HG002_1_chr20:20337100-20337808 +tacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagagg +aagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctcac +tagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtggat +ggatggatggatggatggatggatggatggatagatgggtgggtggatggatggatggat +agatgggtggatggataaatggatgg----atggatggatggatagatgggtgggtggat +ggatggatggatggatggatggatggatggatggatagatggatagatgggtgggtggat +ggatggatggatggatggatggatggatggatggatggatggatagatgggtgggtggat +ggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggt +ggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggt +gggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat +gggtgggtggatggatggatggatagatgggtggatggataaatggatggatggatggat +ggatagatgggtgggtggatggatggatggatggatggatggatagatggataga----- +-----------tgggtgggtggatggatggatggatggatggatggatggatggatagat +gggtggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt +gggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat +gggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggat +agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat +ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat +agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat +ggatagatgggtgggtggatggatggatggatggatggatagatggatagatgggtgggt +ggatggatggatggatagatgggtggg----tggatggatggatggatggatggatggat +ggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggat +ggatggatggatagatggatagatgggtgggtggatggatggatggatagatggatagat +gggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggt +gggtggatggatggatggata--------------------gatggatagatgggtgggt +ggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt +gggtggatggatggatggatagatgggtgggtggatggatggatggataga--------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------tgggtgggtgggtggatggatggatagatgggtgggtggat +ggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggt +ggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtgggt +ggatggatggatggatggatggatagaataaaaagaaagctaggacatggttctagtgtt +cttagcagacgtcccaccatggaagaggtcatggagcacaggggctttgggaaaggtgtt +tacaatcctgcctgcctctcacccagacctcttg +>p:HG002_2_chr20:20337100-20337808 +tacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagagg +aagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctcac +tagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtggat +ggatggatggatggatggatggatggatagatgggtgggtggatggatggatggatagat +gggtggatggatagatgggtggatggataaatggatggatggatggatggatagatgggt +gggtggatggatggatggatggatggatggatggatggatggatagatggatagatgggt +gggtggatggatggatggatggatggatggatggatggatggatagatgggtgggtggat +ggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggt +ggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggt +gggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat +gggtgggtggatggatggatggatagatgggtggatggataaatggatggatggatggat +ggatagatgtgtgggtggatggatggatggatggatggatggatggatggatggatagat +ggatagatgggtgggtggatggatggatggatggatggatggatggatggatggatagat +gggtggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt +gggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat +gggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggat +agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat +ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat +agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat +ggatagatgggtgggtggatggatggatggatggatggatggatggatagatgggtgggt +ggatggatggatggatagatgggtgggtggatggatggatggatggatggatggatggat +ggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggat +ggatggatggatagatggatagatgggtgggtggatggatggatggatagatggatagat +gggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggt +gggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggt +ggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt +gggtggatggatggatggatagatgggtgggtggatggatggatggatggatggatagat +ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat +ggatggatggatggatggatggatagatggatagatgggtgggtggatggatggatggat +agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat +ggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggat +ggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtggat +ggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggt +ggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtgggt +ggatggatggatggatggatggatagaataaaaagaaagctaggacatggttctagtgtt +cttagcagacgtcccaccatggaagaggtcatggagcacaggggctttgggaaaggtgtt +tacaatcctgcctgcctctcacccagacctcttg diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20337200-20337708/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20337200-20337708/msa.fa.fai new file mode 100644 index 00000000..217590d1 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20337200-20337708/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_20337100_20337808 2194 29 60 61 +syndip_1_chr20:20337100-20337808 2194 2294 60 61 +syndip_2_chr20:20337100-20337808 2194 4559 60 61 +p:HG002_1_chr20:20337100-20337808 2194 6825 60 61 +p:HG002_2_chr20:20337100-20337808 2194 9091 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20337200-20337708/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20337200-20337708/output.vcf.gz new file mode 100644 index 00000000..a2f0a001 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20337200-20337708/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20337200-20337708/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20337200-20337708/output.vcf.gz.tbi new file mode 100644 index 00000000..d7110e5e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20337200-20337708/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/base.vcf.gz new file mode 100644 index 00000000..aa76d26c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/base.vcf.gz.tbi new file mode 100644 index 00000000..b91d893c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/comp.vcf.gz new file mode 100644 index 00000000..7e593bcf Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/comp.vcf.gz.tbi new file mode 100644 index 00000000..4fb0da50 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/haps.fa new file mode 100644 index 00000000..fd8e3a0a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/haps.fa @@ -0,0 +1,356 @@ +>ref_chr20_20354470_20358424 +TCCAGTCTGGGTGACAGAGAGAGACCTTGTCTCAAAAAAAAAAAAAAAAAATCAGGTACAGAAAGGTAAATACTGCACGATCTCACTTACATGTGGAATCTAAAGAAGTTGAATTCATAAGGGTAATGAGGGGAGGAAGGGGTGGTCATACTGTGTGAAGGGAGATAGTCACACTGAGGGAAGGTGGTCACACTGTGAGAAGGGAGGTAGTCACATTGTGAGAGAAAAAGTGATCACACTGTGTGAGGGGAGGTGGTCACACTGTGAGAGAAAAAGTAATCATACTGTGAAAGGGAGGTGGTCACGCTGAGAGGGGAGGTGGTCACACTGTGTCAGGGGAGGTGGTCACACTGTGAGAGAAAAAGTAATCACACTGTGAGGGGATGTGGTCACACTGAGAGGGGAGGTGGTCAGACTGTGTCAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAGATGGTCACACTGCAAGAGGGGAGGTGATCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACATTGTGAGAGGGAAGGGGGTCACTGTGAGAGGGGAGAAGGTCACACTAAGGGGAGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAGGAGGTGGTCACACTGTGAGGGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACTATGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGGGGTCACACTGTGAGGGGGAAGGTGGTCACACTGTGAGAGGGGAGAAGGTCACACTAAGGGGAGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAGGAGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACTATGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTAAGGGGAGGTGATCACACTGTGAGGGGACGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGACCACACAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGGGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGCTAGTCACACTGAGGGGAGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGCGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGCGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGAAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGGCACACTGTGAGGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTCACACTGTGAAAGAAGATGATCACAGTATGAGAGGTCATCCTTCAAGAGGCAAGTGCCCAAAAATCTGTTTATAATCTAGAGCAATATTTGCCTGAAATAAACTTTAAAAGTGGTTTTACGCTATTTAACCCAGTGTCAGA +>syndip_1_chr20:20354470-20358424 +TCCAGTCTGGGTGACAGAGAGAGACCTTGTCTCAAAAAAAAAAAAAAAAAATCAGGTACA +GAAAGGTAAATACTGCACGATCTCACTTACATGTGGAATCTAAAGAAGTTGAATTCATAA +GGGTAATGAGGGGAGGAAGGGGTGGTCATACTGTGTGAAGGGAGATGGTCACACTGAGGG +AAGGTGGTCACACTGTGAGAAGGGAGGTAGTCACATTGTGAGAGAAAAAGTGATCACACT +GTGTGAGGGGAGGTGGTCACACTGTGAGAGAAAAAGTAATCATACTGTGAAAGGGAGGTG +GTCACGCTGAGAGGGGAGGTGGTCACACTGTGTCAGGGGAGGTGGTCACACTGTGAGAGA +AAAAGTAATCACACTGTGAGGGGATGTGGTCACACTGAGAGGGGAGGTGGTCAGACTGTG +TCAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCAGA +CTCTGTCAGAGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAAGTGG +TCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAGATGGTCACACTGCAAGAGGGGA +GGTGATCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGAGA +GGGAAGGTGGTCACACTGTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACAT +TGTGAGAGGGAAGGGGGTCACTGTGAGAGGGGAGAAGGTCACACTAAGGGGAGGTAGTCA +CACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAGGAGGTGGTC +ACACTGTGAGGGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACT +ATGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACAC +TGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTACTCACA +CTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGAC +ACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGGGGTCACACTGTGAGGGGGAAGGTG +GTCACACTGTGAGAGGGGAGAAGGTCACACTAAGGGGAGGTAGTCACACTGTGAGGGGAG +GTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAGGAGGTGGTCACACTGTGAGGGGA +GGTCACACTGAGGGGAGGTAGTGACACTATGAGCAGAGATGGTCACACTGTGAGGGGAGG +TGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAG +GTGGTCACACTGAGGGGAGGTAGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGA +GGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGG +AGGGGGTCACACTGTGAGGGGGAAGGTGGTCACACTGTGAGAGGGGAGAAGGTCACACTA +AGGGGAGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGT +GAGAGGAGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACTATGA +GCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTG +AGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTCACACTGT +GAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTG +TGAGCAGAGATGGTCACACTGTAAGGGGAGGTGATCACACTGTGAGGGGACGTGGTCACA +CTGTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGACCACACAGGGGAGGTGGTCAC +ACTGAGGGGAGGTAGTGACACTGTGAGCAGAGGTGGTCACACTGTGAGGGGAGGTGGTCA +CACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCAC +ACTGAGGGGGGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCA +CACTGAGGGGAGGGGTCATACTGCGAGTGGAGGTGGTCACACTGTGAAGGGTGGTAGTCA +CACTGAGAGGAGGTGTTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAC +TGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACA +CTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACAC +TGAGGGGAGGTGGTCACAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGT +GTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACAC +TGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGA +GGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAG +GGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGG +GGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGG +GAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGG +AGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGG +TGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCATACTGTGAGTGAGG +AGGTAGTCACACTGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGG +GTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAG +GTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGA +GGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAG +GTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGAGGAGGTGGTCACACTGAGGGGAGG +TGGTCACAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAG +GTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGG +TGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGT +GGTCACAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGG +TGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGT +GGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGG +TAGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGGGG +TCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTG +GTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGG +TCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGT +CACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTC +ACAGTGTACGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGT +CACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTC +ACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCA +TAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCAT +AGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATA +GTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCAC +ACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACA +GTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCAC +ACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACA +CTGTGAGGGGAGGTGGTCACATTGAGGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCAC +ACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACA +CTGAGGAGAGGTGGTCATAGTGTGCGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAC +TGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACA +CTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAC +TGAGGGAAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCATAGT +GTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAG +TGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGGCACA +CTGTGAGGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACAC +TGAGGGGAGGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTCACACTG +AGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTCACACTGTG +AAAGAAGATGATCACAGTATGAGAGGTCATCCTTCAAGAGGCAAGTGCCCAAAAATCTGT +TTATAATCTAGAGCAATATTTGCCTGAAATAAACTTTAAAAGTGGTTTTACGCTATTTAA +CCCAGTGTCAGA +>syndip_2_chr20:20354470-20358424 +TCCAGTCTGGGTGACAGAGAGAGACCTTGTCTCAAAAAAAAAAAAAAAAAATCAGGTACA +GAAAGGTAAATACTGCACGATCTCACTTACATGTGGAATCTAAAGAAGTTGAATTCATAA +GGGTAATGAGGGGAGGAAGGGGTGGTCATACTGTGTGAAGGGAGATGGTCACACTGAGGG +AAGGTGGTCACACTGTGAGAAGGGAGGTAGTCACATTGTGAGAGAAAAAGTGATCACACT +GTGTGAGGGGAGGTGGTCACACTGTGAGAGAAAAAGTAATCATACTGTGAAAGGGAGGTG +GTCACGCTGAGAGGGGAGGTGGTCACACTGTGTCAGGGGAGGTGGTCACACTGTGAGAGA +AAAAGTAATCACACTGTGAGGGGATGTGGTCACACTGAGAGGGGAGGTGGTCAGACTGTG +TCAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCAGA +CTCTGTCAGAGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAAGTGG +TCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAGATGGTCACACTGCAAGAGGGGA +GGTGATCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGAGA +GGGAAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGTGAGGGGAGGTGGTCAC +ACTGTGAGGGGAGGTGGTCACATTGTGAGAGGGAAGGGGGTCACTGTGAGAGGGGAGAAG +GTCACACTAAGGGGAGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGG +TCACACTGTGAGAGGAGGTGGTCACACTGTGAGGGGTGGTCACACTGTGAGGGGAGGTCA +CACTGAGGGGAGGTAGTGACACTATGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTC +ACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGT +CACACTGAGGGGAGGTACTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGG +TCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGGG +GTCACACTGTGAGGGGGAAGGTGGTCACACTGTGAGAGGGGAGAAGGTCACACTAAGGGG +AGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAG +GAGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACTATGAGCAGA +GATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAG +AGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTCACACTGTGAGGG +GAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGC +AGAGATGGTCACACTGTAAGGGGAGGTGATCACACTGTGAGGGGACGTGGTCACACTGTG +AGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGACCACACAGGGGAGGTGGTCACACTGA +GGGGAGGTAGTGACACTGTGAGCAGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTG +TGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGA +GGGGGGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTG +AGGGGAGGGGTCATACTGCGAGTGGAGGTGGTCACACTGTGAAGGGTGGTAGTCACACTG +AGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGA +GGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAG +GGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGG +GGAGGTGGTCACAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGTGTGAG +GGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGG +GGAGGTGGTCACACTGTGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGA +GGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAG +GTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTG +GTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTC +ACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCA +CACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCAC +ACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACA +CTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTG +AGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAAGTGGTCACACT +GAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACAC +TGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACA +CTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTG +TGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACT +GAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTG +AGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGT +GAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTG +AGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGA +GGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAG +TGAGGAAGTAGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGG +GGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAGGGGGTCATACTGCG +AGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGA +GGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAG +GGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGA +GAGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTG +AGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGA +GTGAGGAGGTAGTCACACTGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTG +TGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGA +GGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTG +AGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGA +GGGGAGGTGGTCACAGTGTGCGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACAGTGTG +AGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGCGGGGAGGTGGTCACACTGA +GGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACACTGTG +AGGGGAGGTGGTCACACTGAGGAGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGA +GGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAG +GGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGTGA +GGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAG +GGGAGGTGGTGACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGG +GGAGGTGGTCACACTGTGAGGGGAGGTGGTCACATTGAGGAGAGGTGGTCATAGTGTGAG +GGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGG +GGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGG +GAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACAGTGTGAGG +GGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGG +GAGGTGGTCACACTGAGGGAAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGG +AGGTGGTCATAGTGTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGA +GAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGG +GGAGGTGGGCACACTGTGAGGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGG +GAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGA +GGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGG +TGGTCACACTGTGAAAGAAGATGATCACAGTATGAGAGGTCATCCTTCAAGAGGCAAGTG +CCCAAAAATCTGTTTATAATCTAGAGCAATATTTGCCTGAAATAAACTTTAAAAGTGGTT +TTACGCTATTTAACCCAGTGTCAGA +>p:HG002_1_chr20:20354470-20358424 +TCCAGTCTGGGTGACAGAGAGAGACCTTGTCTCAAAAAAAAAAAAAAAAAATCAGGTACA +GAAAGGTAAATACTGCACGATCTCACTTACATGTGGAATCTAAAGAAGTTGAATTCATAA +GGGTAATGAGGGGAGGAAGGGGTGGTCATACTGTGTGAAGGGAGATGGTCACACTGAGGG +AAGGTGGTCACACTGTGAGAAGGGAGGTAGTCACATTGTGAGAGAAAAAGTGATCACACT +GTGTGAGGGGAGGTGGTCACACTGTGAGAGAAAAAGTAATCATACTGTGAAAGGGAGGTG +GTCACGCTGAGAGGGGAGGTGGTCACACTGTGTCAGGGGAGGTGGTCACACTGTGAGAGA +AAAAGTAATCACACTGTGAGGGGATGTGGTCACACTGAGAGGGGAGGTGGTCAGACTGTG +TCAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCAGA +CTCTGTCAGAGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAAGTGG +TCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAGATGGTCACACTGCAAGAGGGGA +GGTGATCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGAGA +GGGAAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGTGAGGGGAGGTGGTCAC +ACTGTGAGGGGAGGTGGTCACATTGTGAGAGGGAAGGGGGTCACTGTGAGAGGGGAGAAG +GTCACACTAAGGGGAGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGG +TCACACTGTGAGAGGAGGTGGTCACACTGTGAGGGGTGGTCACACTGTGAGGGGAGGTCA +CACTGAGGGGAGGTAGTGACACTATGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTC +ACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGT +CACACTGAGGGGAGGTACTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGG +TCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGGG +GTCACACTGTGAGGGGGAAGGTGGTCACACTGTGAGAGGGGAGAAGGTCACACTAAGGGG +AGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAG +GAGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACTATGAGCAGA +GATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAG +AGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTCACACTGTGAGGG +GAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGC +AGAGATGGTCACACTGTAAGGGGAGGTGATCACACTGTGAGGGGACGTGGTCACACTGTG +AGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGACCACACAGGGGAGGTGGTCACACTGA +GGGGAGGTAGTGACACTGTGAGCAGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTG +TGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGA +GGGGGGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTG +AGGGGAGGGGTCATACTGCGAGTGGAGGTGGTCACACTGTGAAGGGTGGTAGTCACACTG +AGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGA +GGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAG +GGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGG +GGAGGTGGTCACAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGTGTGAG +GGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGG +GGAGGTGGTCACACTGTGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGA +GGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAG +GTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTG +GTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTC +ACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCA +CACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCAC +ACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACA +CTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTG +AGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAAGTGGTCACACT +GAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACAC +TGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACA +CTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTG +TGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACT +GAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTG +AGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGT +GAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTG +AGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGA +GGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAG +TGAGGAAGTAGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGG +GGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAGGGGGTCATACTGCG +AGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGA +GGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAG +GGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGA +GAGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTG +AGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGA +GTGAGGAGGTAGTCACACTGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTG +TGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGA +GGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTG +AGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGA +GGGGAGGTGGTCACAGTGTGCGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACAGTGTG +AGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGCGGGGAGGTGGTCACACTGA +GGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACACTGTG +AGGGGAGGTGGTCACACTGAGGAGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGA +GGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAG +GGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGTGA +GGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAG +GGGAGGTGGTGACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGG +GGAGGTGGTCACACTGTGAGGGGAGGTGGTCACATTGAGGAGAGGTGGTCATAGTGTGAG +GGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGG +GGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGG +GAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACAGTGTGAGG +GGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGG +GAGGTGGTCACACTGAGGGAAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGG +AGGTGGTCATAGTGTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGA +GAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGG +GGAGGTGGGCACACTGTGAGGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGG +GAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGA +GGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGG +TGGTCACACTGTGAAAGAAGATGATCACAGTATGAGAGGTCATCCTTCAAGAGGCAAGTG +CCCAAAAATCTGTTTATAATCTAGAGCAATATTTGCCTGAAATAAACTTTAAAAGTGGTT +TTACGCTATTTAACCCAGTGTCAGA +>p:HG002_2_chr20:20354470-20358424 +TCCAGTCTGGGTGACAGAGAGAGACCTTGTCTCAAAAAAAAAAAAAAAAAATCAGGTACA +GAAAGGTAAATACTGCACGATCTCACTTACATGTGGAATCTAAAGAAGTTGAATTCATAA +GGGTAATGAGGGGAGGAAGGGGTGGTCATACTGTGTGAAGGGAGATGGTCACACTGAGGG +AAGGTGGTCACACTGTGAGAAGGGAGGTAGTCACATTGTGAGAGAAAAAGTGATCACACT +GTGTGAGGGGAGGTGGTCACACTGTGAGAGAAAAAGTAATCATACTGTGAAAGGGAGGTG +GTCACGCTGAGAGGGGAGGTGGTCACACTGTGTCAGGGGAGGTGGTCACACTGTGAGAGA +AAAAGTAATCACACTGTGAGGGGATGTGGTCACACTGAGAGGGGAGGTGGTCAGACTGTG +TCAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCAGA +CTCTGTCAGAGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAAGTGG +TCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAGATGGTCACACTGCAAGAGGGGA +GGTGATCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGAGA +GGGAAGGTGGTCACACTGTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACAT +TGTGAGAGGGAAGGGGGTCACTGTGAGAGGGGAGAAGGTCACACTAAGGGGAGGTAGTCA +CACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAGGAGGTGGTC +ACACTGTGAGGGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACT +ATGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACAC +TGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTACTCACA +CTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGAC +ACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGGGGTCACACTGTGAGGGGGAAGGTG +GTCACACTGTGAGAGGGGAGAAGGTCACACTAAGGGGAGGTAGTCACACTGTGAGGGGAG +GTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAGGAGGTGGTCACACTGTGAGGGGA +GGTCACACTGAGGGGAGGTAGTGACACTATGAGCAGAGATGGTCACACTGTGAGGGGAGG +TGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAG +GTGGTCACACTGAGGGGAGGTAGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGA +GGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGG +AGGGGGTCACACTGTGAGGGGGAAGGTGGTCACACTGTGAGAGGGGAGAAGGTCACACTA +AGGGGAGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGT +GAGAGGAGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACTATGA +GCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTG +AGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTCACACTGT +GAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTG +TGAGCAGAGATGGTCACACTGTAAGGGGAGGTGATCACACTGTGAGGGGACGTGGTCACA +CTGTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGACCACACAGGGGAGGTGGTCAC +ACTGAGGGGAGGTAGTGACACTGTGAGCAGAGGTGGTCACACTGTGAGGGGAGGTGGTCA +CACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCAC +ACTGAGGGGGGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCA +CACTGAGGGGAGGGGTCATACTGCGAGTGGAGGTGGTCACACTGTGAAGGGTGGTAGTCA +CACTGAGAGGAGGTGTTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAC +TGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACA +CTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACAC +TGAGGGGAGGTGGTCACAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGT +GTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACAC +TGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGA +GGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAG +GGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGG +GGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGG +GAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGG +AGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGG +TGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCATACTGTGAGTGAGG +AGGTAGTCACACTGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGG +GTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAG +GTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGA +GGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAG +GTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGAGGAGGTGGTCACACTGAGGGGAGG +TGGTCACAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAG +GTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGG +TGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGT +GGTCACAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGG +TGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGT +GGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGG +TAGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGGGG +TCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTG +GTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGG +TCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGT +CACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTC +ACAGTGTACGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGT +CACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTC +ACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCA +TAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCAT +AGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATA +GTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCAC +ACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACA +GTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCAC +ACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACA +CTGTGAGGGGAGGTGGTCACATTGAGGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCAC +ACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACA +CTGAGGAGAGGTGGTCATAGTGTGCGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAC +TGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACA +CTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAC +TGAGGGAAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCATAGT +GTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAG +TGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGGCACA +CTGTGAGGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACAC +TGAGGGGAGGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTCACACTG +AGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTCACACTGTG +AAAGAAGATGATCACAGTATGAGAGGTCATCCTTCAAGAGGCAAGTGCCCAAAAATCTGT +TTATAATCTAGAGCAATATTTGCCTGAAATAAACTTTAAAAGTGGTTTTACGCTATTTAA +CCCAGTGTCAGA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/haps.fa.ref.fa new file mode 100644 index 00000000..53b76a9d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:20354470-20358424 +TCCAGTCTGGGTGACAGAGAGAGACCTTGTCTCAAAAAAAAAAAAAAAAAATCAGGTACAGAAAGGTAAATACTGCACGATCTCACTTACATGTGGAATCTAAAGAAGTTGAATTCATAAGGGTAATGAGGGGAGGAAGGGGTGGTCATACTGTGTGAAGGGAGATAGTCACACTGAGGGAAGGTGGTCACACTGTGAGAAGGGAGGTAGTCACATTGTGAGAGAAAAAGTGATCACACTGTGTGAGGGGAGGTGGTCACACTGTGAGAGAAAAAGTAATCATACTGTGAAAGGGAGGTGGTCACGCTGAGAGGGGAGGTGGTCACACTGTGTCAGGGGAGGTGGTCACACTGTGAGAGAAAAAGTAATCACACTGTGAGGGGATGTGGTCACACTGAGAGGGGAGGTGGTCAGACTGTGTCAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAGATGGTCACACTGCAAGAGGGGAGGTGATCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACATTGTGAGAGGGAAGGGGGTCACTGTGAGAGGGGAGAAGGTCACACTAAGGGGAGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAGGAGGTGGTCACACTGTGAGGGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACTATGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGGGGTCACACTGTGAGGGGGAAGGTGGTCACACTGTGAGAGGGGAGAAGGTCACACTAAGGGGAGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAGGAGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACTATGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTAAGGGGAGGTGATCACACTGTGAGGGGACGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGACCACACAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGGGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGCTAGTCACACTGAGGGGAGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGCGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGCGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGAAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGGCACACTGTGAGGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTCACACTGTGAAAGAAGATGATCACAGTATGAGAGGTCATCCTTCAAGAGGCAAGTGCCCAAAAATCTGTTTATAATCTAGAGCAATATTTGCCTGAAATAAACTTTAAAAGTGGTTTTACGCTATTTAACCCAGTGTCAGA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/msa.fa new file mode 100644 index 00000000..3f977e3f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/msa.fa @@ -0,0 +1,475 @@ +>ref_chr20_20354470_20358424 +tccagtctgggtgacagagagagaccttgtctcaaaaaaaaaaaaaaaaaatcaggtaca +gaaaggtaaatactgcacgatctcacttacatgtggaatctaaagaagttgaattcataa +gggtaatgaggggaggaaggggtggtcatactgtgtgaagggagatagtcacactgaggg +aaggtggtcacactgtgagaagggaggtagtcacattgtgagagaaaaagtgatcacact +gtgtgaggggaggtggtcacactgtgagagaaaaagtaatcatactgtgaaagggaggtg +gtcacgctgagaggggaggtggtcacactgtgtcaggggaggtggtcacactgtgagaga +aaaagtaatcacactgtgaggggatgtggtcacactgagaggggaggtggtcagactgtg +tcagaggaggtggtcacactgagg------------------------------------ +----------ggaggtggtcacactgtgagaggggaggtggtcacactgaggggaagtgg +tcacactgtgagaggggaggtggtcacactgaggggagatggtcacactgcaagagggga +ggtgatcacactgagggg-----------------------aggtggtcacactgtgaga +gggaaggtggtcacactgtgagagggaaggtggtcacactgtgtgaggggaggtggtcac +actgtgaggggaggtggtcacattgtgagagggaagggggtcactgtgagaggggagaag +gtcacactaaggggaggtagtcacactgtgaggggaggtgatcacactaaggggaggtgg +tcacactgtgagaggaggtggtcacactgtgaggggtggtcacactgtgaggggaggtca +cactgaggggaggtagtgacactatgagcagagatggtcacactgtgaggggaggtggtc +acactgaggggaggtagtgacactgtgagcagagatggtcacactgtgaggggaggtggt +cacactgaggggagg--------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---tggtcacactgtgaggggaggtggtcacactgaggggaggtggtcacactgtgaggg +gaggtggtcacactgtgaggggaggtggtcacactgaggggaggtagtgacactgtgagc 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+ctgaaataaactttaaaagtggttttacgctatttaacccagtgtcaga diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/msa.fa.fai new file mode 100644 index 00000000..5edf4419 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_20354470_20358424 5629 29 60 61 +syndip_1_chr20:20354470-20358424 5629 5786 60 61 +syndip_2_chr20:20354470-20358424 5629 11543 60 61 +p:HG002_1_chr20:20354470-20358424 5629 17301 60 61 +p:HG002_2_chr20:20354470-20358424 5629 23059 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/output.vcf.gz new file mode 100644 index 00000000..1e4d9841 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/output.vcf.gz.tbi new file mode 100644 index 00000000..aa7f7317 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:20354570-20358324/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/base.vcf.gz new file mode 100644 index 00000000..7bcfaf0f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/base.vcf.gz.tbi new file mode 100644 index 00000000..42a8c32a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/comp.vcf.gz new file mode 100644 index 00000000..9c5b7121 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/comp.vcf.gz.tbi new file mode 100644 index 00000000..3c4efbee Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/haps.fa new file mode 100644 index 00000000..02d0d23a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/haps.fa @@ -0,0 +1,34 @@ +>ref_chr20_21120112_21120640 +ACAGACTGAGACTTTGTCTTAAAATCAAATTAATTTAATTTAAAAAACAAATGCCTTTGAGCAAAGTGCTGTTAGTAACCTCATGTCTTCCTGTATTCATCAGGGTTCTTCAGAGAAACAGAACCAGTAGGACACACACACACGCACACACACACACGTGTGTGTATATATATGTGTGTATGTATATATATATATATATTTATATATATATATATTTATATATATATATTTATATATATATATTTATATATATATATATTTATATATATATATTTATATATATATATTTATATATATATATATTTATATATATATATATTTATATATATATATTTATATATATATATATTTATATATATATATTTATATATATATATATTTATATGGAGAGAGAGAGATTTATTTTTAGGAAGTGGTTCATGAGATTGTGAGGGACTTCATTCTTTTCTCCTAAGGCCTTCAACTGACTGGATGAGGCCCATCCACATTTTGGAGAGCAGTCTACTTTCCTCAAAGCCTACTGCTTCAA +>syndip_1_chr20:21120112-21120640 +ACAGACTGAGACTTTGTCTTAAAATCAAATTAATTTAATTTAAAAAACAAATGCCTTTGA +GCAAAGTGCTGTTAGTAACCTCATGTCTTCCTGTATTCATCAGGGTTCTTCAGAGAAACA +GAACCAGTAGGACACACACACACGCACACACACACACGTGTGTGTATATATATGTGTGTA +TGTATATATATATATATATATTTATATATATATATATATTTATATATATATATATTTATA +TATATATATATATATATGGAGAGAGAGAGATTTATTTTTAGGAAGTGGTTCATGAGATTG +TGAGGGACTTCATTCTTTTCTCCTAAGGCCTTCAACTGACTGGATGAGGCCCATCCACAT +TTTGGAGAGCAGTCTACTTTCCTCAAAGCCTACTGCTTCAA +>syndip_2_chr20:21120112-21120640 +ACAGACTGAGACTTTGTCTTAAAATCAAATTAATTTAATTTAAAAAACAAATGCCTTTGA +GCAAAGTGCTGTTAGTAACCTCATGTCTTCCTGTATTCATCAGGGTTCTTCAGAGAAACA +GAACCAGTAGGACACACACACACGCACACACACACACGTGTGTGTATATATATGTGTGTA +TGTATATATATATATATATATTTATATATATATATATATTTATATATATATATATATATT +TATATATATATATATATATATGGAGAGAGAGAGATTTATTTTTAGGAAGTGGTTCATGAG +ATTGTGAGGGACTTCATTCTTTTCTCCTAAGGCCTTCAACTGACTGGATGAGGCCCATCC +ACATTTTGGAGAGCAGTCTACTTTCCTCAAAGCCTACTGCTTCAA +>p:HG002_1_chr20:21120112-21120640 +ACAGACTGAGACTTTGTCTTAAAATCAAATTAATTTAATTTAAAAAACAAATGCCTTTGA +GCAAAGTGCTGTTAGTAACCTCATGTCTTCCTGTATTCATCAGGGTTCTTCAGAGAAACA +GAACCAGTAGGACACACACACACGCACACACACACACGTGTGTGTATATATATGTGTGTA +TGTATATATATATATATATATTTATATATATATATATATTTATATATATATATATATATT +TATATATATATATATATATATGGAGAGAGAGAGATTTATTTTTAGGAAGTGGTTCATGAG +ATTGTGAGGGACTTCATTCTTTTCTCCTAAGGCCTTCAACTGACTGGATGAGGCCCATCC +ACATTTTGGAGAGCAGTCTACTTTCCTCAAAGCCTACTGCTTCAA +>p:HG002_2_chr20:21120112-21120640 +ACAGACTGAGACTTTGTCTTAAAATCAAATTAATTTAATTTAAAAAACAAATGCCTTTGA +GCAAAGTGCTGTTAGTAACCTCATGTCTTCCTGTATTCATCAGGGTTCTTCAGAGAAACA +GAACCAGTAGGACACACACACACGCACACACACACACGTGTGTGTATATATATGTGTGTA +TGTATATATATATATATATATTTATATATATATATATATTTATATATATATATATTTATA +TATATATATATATATATGGAGAGAGAGAGATTTATTTTTAGGAAGTGGTTCATGAGATTG +TGAGGGACTTCATTCTTTTCTCCTAAGGCCTTCAACTGACTGGATGAGGCCCATCCACAT +TTTGGAGAGCAGTCTACTTTCCTCAAAGCCTACTGCTTCAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/haps.fa.ref.fa new file mode 100644 index 00000000..eb28f31d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:21120112-21120640 +ACAGACTGAGACTTTGTCTTAAAATCAAATTAATTTAATTTAAAAAACAAATGCCTTTGAGCAAAGTGCTGTTAGTAACCTCATGTCTTCCTGTATTCATCAGGGTTCTTCAGAGAAACAGAACCAGTAGGACACACACACACGCACACACACACACGTGTGTGTATATATATGTGTGTATGTATATATATATATATATTTATATATATATATATTTATATATATATATTTATATATATATATTTATATATATATATATTTATATATATATATTTATATATATATATTTATATATATATATATTTATATATATATATATTTATATATATATATTTATATATATATATATTTATATATATATATTTATATATATATATATTTATATGGAGAGAGAGAGATTTATTTTTAGGAAGTGGTTCATGAGATTGTGAGGGACTTCATTCTTTTCTCCTAAGGCCTTCAACTGACTGGATGAGGCCCATCCACATTTTGGAGAGCAGTCTACTTTCCTCAAAGCCTACTGCTTCAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/msa.fa new file mode 100644 index 00000000..52ea3338 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/msa.fa @@ -0,0 +1,50 @@ +>ref_chr20_21120112_21120640 +acagactgagactttgtcttaaaatcaaattaatttaatttaaaaaacaaatgcctttga +gcaaagtgctgttagtaacctcatgtcttcctgtattcatcagggttcttcagagaaaca +gaaccagtaggacacacacacacgcacacacacacacgtgtgtgtatatatatgtgtgta +tgtatatatatatatatatttatatatatatatatttatatatatatatttatatatata +tatttatatatatatatatttatatatatatatttatatatatatatttatatatatata +tatttatatatatatatatttatatatatatatttatatatatatatatttatatatata +tatttatatatatatatatttatatggagagagagagatttatttttaggaagtggttca +tgagattgtgagggacttcattcttttctcctaaggccttcaactgactggatgaggccc +atccacattttggagagcagtctactttcctcaaagcctactgcttcaa +>syndip_1_chr20:21120112-21120640 +acagactgagactttgtcttaaaatcaaattaatttaatttaaaaaacaaatgcctttga +gcaaagtgctgttagtaacctcatgtcttcctgtattcatcagggttcttcagagaaaca +gaaccagtaggacacacacacacgcacacacacacacgtgtgtgtatatatatgtgtgta +tgtatatatatatata-------------------------------------------- +------------------------------------------------------------ +--------------------tatatttatatatatatatatatt----tatatatatata +tatttatatatatatatatatatatggagagagagagatttatttttaggaagtggttca +tgagattgtgagggacttcattcttttctcctaaggccttcaactgactggatgaggccc +atccacattttggagagcagtctactttcctcaaagcctactgcttcaa +>syndip_2_chr20:21120112-21120640 +acagactgagactttgtcttaaaatcaaattaatttaatttaaaaaacaaatgcctttga +gcaaagtgctgttagtaacctcatgtcttcctgtattcatcagggttcttcagagaaaca +gaaccagtaggacacacacacacgcacacacacacacgtgtgtgtatatatatgtgtgta +tgtatatatatatata-------------------------------------------- +------------------------------------------------------------ +--------------------tatatttatatatatatatatatttatatatatatatata +tatttatatatatatatatatatatggagagagagagatttatttttaggaagtggttca +tgagattgtgagggacttcattcttttctcctaaggccttcaactgactggatgaggccc +atccacattttggagagcagtctactttcctcaaagcctactgcttcaa +>p:HG002_1_chr20:21120112-21120640 +acagactgagactttgtcttaaaatcaaattaatttaatttaaaaaacaaatgcctttga +gcaaagtgctgttagtaacctcatgtcttcctgtattcatcagggttcttcagagaaaca +gaaccagtaggacacacacacacgcacacacacacacgtgtgtgtatatatatgtgtgta +tgtatatatatatata-------------------------------------------- +------------------------------------------------------------ +--------------------tatatttatatatatatatatatttatatatatatatata +tatttatatatatatatatatatatggagagagagagatttatttttaggaagtggttca +tgagattgtgagggacttcattcttttctcctaaggccttcaactgactggatgaggccc +atccacattttggagagcagtctactttcctcaaagcctactgcttcaa +>p:HG002_2_chr20:21120112-21120640 +acagactgagactttgtcttaaaatcaaattaatttaatttaaaaaacaaatgcctttga +gcaaagtgctgttagtaacctcatgtcttcctgtattcatcagggttcttcagagaaaca +gaaccagtaggacacacacacacgcacacacacacacgtgtgtgtatatatatgtgtgta +tgtatatatatatata-------------------------------------------- +------------------------------------------------------------ +--------------------tatatttatatatatatatatatt----tatatatatata +tatttatatatatatatatatatatggagagagagagatttatttttaggaagtggttca +tgagattgtgagggacttcattcttttctcctaaggccttcaactgactggatgaggccc +atccacattttggagagcagtctactttcctcaaagcctactgcttcaa diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/msa.fa.fai new file mode 100644 index 00000000..1d0b7fc1 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_21120112_21120640 529 29 60 61 +syndip_1_chr20:21120112-21120640 529 601 60 61 +syndip_2_chr20:21120112-21120640 529 1173 60 61 +p:HG002_1_chr20:21120112-21120640 529 1746 60 61 +p:HG002_2_chr20:21120112-21120640 529 2319 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/output.vcf.gz new file mode 100644 index 00000000..8228a935 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/output.vcf.gz.tbi new file mode 100644 index 00000000..c5e5ec93 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21120212-21120540/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/base.vcf.gz new file mode 100644 index 00000000..84a93694 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/base.vcf.gz.tbi new file mode 100644 index 00000000..2a820957 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/comp.vcf.gz new file mode 100644 index 00000000..f4732b1e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/comp.vcf.gz.tbi new file mode 100644 index 00000000..ca13d660 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/haps.fa new file mode 100644 index 00000000..412dd99e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/haps.fa @@ -0,0 +1,92 @@ +>ref_chr20_21721074_21721836 +AGTAGGGACTTGCTTTGGGTCACAGTCAGCTTTTATTAGTGTTATTATTGTTGCTGTTTTCTTCTTTTTCTTTGTACATCAACGTTTTATGGTGAATTAAATCGTGTTTTAACCTTGTAGACCACATTGGCTATTACATATATATATATAATATATATGTAATATATATATGTAATGTATATTATATATGTAATGTATATAATATATGTAATGTATATAATATATATGTAATACATATATATTATATATGTATATAATACATATATATGTATATATATGTATGTATATATATATGTATATATGTATATATATATGTATATAATACATATATATACATATATATTATATATGTAATACATATATAATATATATGTAATGTATATATATGTAATGTATATAATATATATGTAATACATATATAATATATATGTAATGTATATTATATATGTAATGTATATAATATGTATGTAATACATATATTATATATGTAATGTATATTATATATGTATTACATATATGTATTACATATATAACATATATGTATTACATATATGTATTACATATATAACATATATGTATTACATATATGTAATACACATATAATATATATGTTATATATATATATATATATAAAATTTTTTAAAAAATTGTTTCTTGAGATAGGGTCTCACTCTGTCACCCAGGCTGGAGTATAATGGTTTGATCATAGTTCACTGCAGCCTTGAACTTCTAGACTCAGGTGATCCTCCCACCTCAACCTCCT +>syndip_1_chr20:21721074-21721836 +AGTAGGGACTTGCTTTGGGTCACAGTCAGCTTTTATTAGTGTTATTATTGTTGCTGTTTT +CTTCTTTTTCTTTGTACATCAACGTTTTATGGTGAATTAAATCGTGTTTTAACCTTGTAG +ACCACATTGGCTATTACATATATATATATAATATATATGTAATATATATATGTAATGTAT +ATTATATATGTAATGTATATAATATATGTAATGTATATAATATATATGTAATACATATAT +ATTATATATGTATATAATACATATATATGTATATATATGTATGTATATATATATGTATAT +ATGTATATATATATGTATATAATACATATATATACATATATATTATATATGTAATACATA +TATAATATATATGTAATGTATATATATGTAATGTATATAATATATATGTAATACATATAT +AATATATATGTAATGTATATAATATATATGTAATACATATATAATATATATGTAATGTAT +ATTATATATGTAATGTATATAATATGTATGTAATACATATATTATATATGTAATGTATAT +TATATATGTATTACATATATGTATTACATATATAACATATATGTATTACATATATGTATT +ACATATATAACATATATGTATTACATATATGTATTACATATATAACATATATGTATTACA +TATATGTATTACATATATAACATATATGTAATACATATATGTATTACATATATAACATAT +ATGTATTACATATATGTATTACATATATAACATATATGTATTACATATATGTATTACATA +TATAACATATATGTATTACATATATGTATTACATATATAACATATATGTATTACATATAT +GTATTACATATATAACATATATGTATTACATATATGTAATACATATATAACATATATGTA +TTACATATATGTAATACATATATAACATATATGTATTACATATATGTAATACATATATAA +CATATATGTATTACATATATGTAATACATATATAACATGTATTACATATATGTAATACAT +ATATAACATGTATTACATATATGTAATACATATATAACATGTATTACATATATGTAATAC +ACATATAATATATATGTTATATATATATATATATATAAAATTTTTTAAAAAATTGTTTCT +TGAGATAGGGTCTCACTCTGTCACCCAGGCTGGAGTATAATGGTTTGATCATAGTTCACT +GCAGCCTTGAACTTCTAGACTCAGGTGATCCTCCCACCTCAACCTCCT +>syndip_2_chr20:21721074-21721836 +AGTAGGGACTTGCTTTGGGTCACAGTCAGCTTTTATTAGTGTTATTATTGTTGCTGTTTT +CTTCTTTTTCTTTGTACATCAACGTTTTATGGTGAATTAAATCGTGTTTTAACCTTGTAG +ACCACATTGGCTATTACATATATATATATAATATATATGTAATATATATATGTAATGTAT +ATTATATATGTAATGTATATAATATATGTAATGTATATAATACATATGTAATACATATAT +ATTATATATGTATATAATACATATATATGTATATATATGTATGTATATATATATGTATAT +ATGTATATATATATGTATATAATACATATATATACATATATATTATATATGTAATACATA +TATAATATATATGTAATGTATATATATGTAATGTATATAATATATATGTAATACATATAT +AATATATATGTAATGTATATAATATATATGTAATACATATATAATATATATGTAATGTAT +ATTATATATGTAATGTATATAATATGTATGTAATACATATATTATATATGTAATGTATAT +TATATATGTATTACATATATGTATTACATATATAACATATATGTATTACATATATGTATT +ACATATATAACATATATGTATTACATATATGTATTACATATATAACATATATGTATTACA +TATATGTATTACATATATAACATATATGTATTACATATATGTATTACATATATAACATAT +ATGTATTACATATATGTATTACATATATAACATATATGTATTACATATATGTATTACATA +TATAACATATATGTATTACATATATGTATTACATATATAACATATATGTATTACATATAT +GTATTACATATATAACATATATGTATTACATATATGTATTACATATATAACATATATGTA +TTACATATATGTATTACATATATAACATATATGTATTACATATATGTATTACATATATAA +CATATATGTATTACATATATGTAATACATATATAACATATATGTATTACATATATGTAAT +ACATATATAACATATATGTAATACATATATAACATATATGTATTACATATATGTAATACA +TATATAACATGTATTACATATATGTAATACACATATAATATATATGTTATATATATATAT +ATATATAAAATTTTTTAAAAAATTGTTTCTTGAGATAGGGTCTCACTCTGTCACCCAGGC +TGGAGTATAATGGTTTGATCATAGTTCACTGCAGCCTTGAACTTCTAGACTCAGGTGATC +CTCCCACCTCAACCTCCT +>p:HG002_1_chr20:21721074-21721836 +AGTAGGGACTTGCTTTGGGTCACAGTCAGCTTTTATTAGTGTTATTATTGTTGCTGTTTT +CTTCTTTTTCTTTGTACATCAACGTTTTATGGTGAATTAAATCGTGTTTTAACCTTGTAG +ACCACATTGGCTATTACATATATATATATAATATATATGTAATATATATATGTAATGTAT +ATTATATATGTAATGTATATAATATATGTAATGTATATAATACATATGTAATACATATAT +ATTATATATGTATATAATACATATATATGTATATATATGTATGTATATATATATGTATAT +ATGTATATATATATGTATATAATACATATATATACATATATATTATATATGTAATACATA +TATAATATATATGTAATGTATATATATGTAATGTATATAATATATATGTAATACATATAT +AATATATATGTAATGTATATAATATATATGTAATACATATATAATATATATGTAATGTAT +ATTATATATGTAATGTATATAATATGTATGTAATACATATATTATATATGTAATGTATAT +TATATATGTATTACATATATGTATTACATATATAACATATATGTATTACATATATGTATT +ACATATATAACATATATGTATTACATATATGTATTACATATATAACATATATGTATTACA +TATATGTATTACATATATAACATATATGTATTACATATATGTATTACATATATAACATAT +ATGTATTACATATATGTATTACATATATAACATATATGTATTACATATATGTATTACATA +TATAACATATATGTATTACATATATGTATTACATATATAACATATATGTATTACATATAT +GTATTACATATATAACATATATGTATTACATATATGTATTACATATATAACATATATGTA +TTACATATATGTATTACATATATAACATATATGTATTACATATATGTATTACATATATAA +CATATATGTATTACATATATGTAATACATATATAACATATATGTATTACATATATGTAAT +ACATATATAACATATATGTAATACATATATAACATATATGTATTACATATATGTAATACA +TATATAACATGTATTACATATATGTAATACACATATAATATATATGTTATATATATATAT +ATATATAAAATTTTTTAAAAAATTGTTTCTTGAGATAGGGTCTCACTCTGTCACCCAGGC +TGGAGTATAATGGTTTGATCATAGTTCACTGCAGCCTTGAACTTCTAGACTCAGGTGATC +CTCCCACCTCAACCTCCT +>p:HG002_2_chr20:21721074-21721836 +AGTAGGGACTTGCTTTGGGTCACAGTCAGCTTTTATTAGTGTTATTATTGTTGCTGTTTT +CTTCTTTTTCTTTGTACATCAACGTTTTATGGTGAATTAAATCGTGTTTTAACCTTGTAG +ACCACATTGGCTATTACATATATATATATAATATATATGTAATATATATATGTAATGTAT +ATTATATATGTAATGTATATAATATATGTAATGTATATAATATATATGTAATACATATAT +ATTATATATGTATATAATACATATATATGTATATATATGTATGTATATATATATGTATAT +ATGTATATATATATGTATATAATACATATATATACATATATATTATATATGTAATACATA +TATAATATATATGTAATGTATATATATGTAATGTATATAATATATATGTAATACATATAT +AATATATATGTAATGTATATAATATATATGTAATACATATATAATATATATGTAATGTAT +ATTATATATGTAATGTATATAATATGTATGTAATACATATATTATATATGTAATGTATAT +TATATATGTATTACATATATGTATTACATATATAACATATATGTATTACATATATGTATT +ACATATATAACATATATGTATTACATATATGTATTACATATATAACATATATGTATTACA +TATATGTATTACATATATAACATATATGTAATACATATATGTATTACATATATAACATAT +ATGTATTACATATATGTATTACATATATAACATATATGTATTACATATATGTATTACATA +TATAACATATATGTATTACATATATGTATTACATATATAACATATATGTATTACATATAT +GTATTACATATATAACATATATGTATTACATATATGTAATACATATATAACATATATGTA +TTACATATATGTAATACATATATAACATATATGTATTACATATATGTAATACATATATAA +CATATATGTATTACATATATGTAATACATATATAACATGTATTACATATATGTAATACAT +ATATAACATGTATTACATATATGTAATACATATATAACATGTATTACATATATGTAATAC +ACATATAATATATATGTTATATATATATATATATATAAAATTTTTTAAAAAATTGTTTCT +TGAGATAGGGTCTCACTCTGTCACCCAGGCTGGAGTATAATGGTTTGATCATAGTTCACT +GCAGCCTTGAACTTCTAGACTCAGGTGATCCTCCCACCTCAACCTCCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/haps.fa.ref.fa new file mode 100644 index 00000000..75bcdd02 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:21721074-21721836 +AGTAGGGACTTGCTTTGGGTCACAGTCAGCTTTTATTAGTGTTATTATTGTTGCTGTTTTCTTCTTTTTCTTTGTACATCAACGTTTTATGGTGAATTAAATCGTGTTTTAACCTTGTAGACCACATTGGCTATTACATATATATATATAATATATATGTAATATATATATGTAATGTATATTATATATGTAATGTATATAATATATGTAATGTATATAATATATATGTAATACATATATATTATATATGTATATAATACATATATATGTATATATATGTATGTATATATATATGTATATATGTATATATATATGTATATAATACATATATATACATATATATTATATATGTAATACATATATAATATATATGTAATGTATATATATGTAATGTATATAATATATATGTAATACATATATAATATATATGTAATGTATATTATATATGTAATGTATATAATATGTATGTAATACATATATTATATATGTAATGTATATTATATATGTATTACATATATGTATTACATATATAACATATATGTATTACATATATGTATTACATATATAACATATATGTATTACATATATGTAATACACATATAATATATATGTTATATATATATATATATATAAAATTTTTTAAAAAATTGTTTCTTGAGATAGGGTCTCACTCTGTCACCCAGGCTGGAGTATAATGGTTTGATCATAGTTCACTGCAGCCTTGAACTTCTAGACTCAGGTGATCCTCCCACCTCAACCTCCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/msa.fa new file mode 100644 index 00000000..7b4e4e00 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/msa.fa @@ -0,0 +1,115 @@ +>ref_chr20_21721074_21721836 +agtagggacttgctttgggtcacagtcagcttttattagtgttattattgttgctgtttt +cttctttttctttgtacatcaacgttttatggtgaattaaatcgtgttttaaccttgtag +accacattggctattacatatatatatataatatatatgtaatatatatatgtaatgtat +attatatatgtaatgtatataatatatgtaatgtatataatatatatgtaatacatatat +attatatatgtatataatacatatatatgtatatatatgtatgtatatatatatgtatat +atgtatatatatatgtatataatacatatatatacatatatattatatatgtaatacata +tataatatatatgtaatgt----------------------------------------- +-atatatatgtaatgtatataatatatatgtaatacatatataatatatatgtaatgtat +attatatatgtaatgtatataatatgtatgtaatacatatattatatatgtaatgtatat +tatatatgtattacatatatgtattacatatataacatatatgtattacatatatgtatt +acatatataacatatatgtattacatatatgtaatacacatataatatatatgttatata +tatatatat--------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--atataaaattttttaaaaaattgtttcttgagatagggtctcactctgtcacccaggc +tggagtataatggtttgatcatagttcactgcagccttgaacttctagactcaggtgatc +ctcccacctcaacctcct +>syndip_1_chr20:21721074-21721836 +agtagggacttgctttgggtcacagtcagcttttattagtgttattattgttgctgtttt +cttctttttctttgtacatcaacgttttatggtgaattaaatcgtgttttaaccttgtag +accacattggctattacatatatatatataatatatatgtaatatatatatgtaatgtat +attatatatgtaatgtatataatatatgtaatgtatataatatatatgtaatacatatat +attatatatgtatataatacatatatatgtatatatatgtatgtatatatatatgtatat +atgtatatatatatgtatataatacatatatatacatatatattatatatgtaatacata +tataatatatatgtaatgtatatatatgtaatgtatataatatatatgtaatacatatat +aatatatatgtaatgtatataatatatatgtaatacatatataatatatatgtaatgtat +attatatatgtaatgtatataatatgtatgtaatacatatattatatatgtaatgtatat +tatatatgtattacatatatgtattacatatataacatatatgtattacatatatgtatt +acatatataacatatatgtattacatatatgtattacatatataacatatatgtattaca +tatatgtattacatatataacatatatgtaatacatatatgtattacatatataacatat +atgtattacatatatgtattacatatataacatatatgtattacatatatgtattacata +tataacatatatgtattacatatatgtattacatatataacatatatgtattacatatat +gtattacatatataacatatatgtattacatatatgtaatacatatataacatatatgta +ttacatatatgtaatacatatataacatatatgtattacatatatgtaatacatatataa +catatatgtattacatatatgtaatacatatataac----atgtattacatatatgtaat +acatatataac--------------------------atgtattacatatatgtaataca +tatataacatgtattacatatatgtaatacacatataatatatatgttatatatatatat +atatataaaattttttaaaaaattgtttcttgagatagggtctcactctgtcacccaggc +tggagtataatggtttgatcatagttcactgcagccttgaacttctagactcaggtgatc +ctcccacctcaacctcct +>syndip_2_chr20:21721074-21721836 +agtagggacttgctttgggtcacagtcagcttttattagtgttattattgttgctgtttt +cttctttttctttgtacatcaacgttttatggtgaattaaatcgtgttttaaccttgtag +accacattggctattacatatatatatataatatatatgtaatatatatatgtaatgtat +attatatatgtaatgtatataatatatgtaatgtatataatacatatgtaatacatatat +attatatatgtatataatacatatatatgtatatatatgtatgtatatatatatgtatat +atgtatatatatatgtatataatacatatatatacatatatattatatatgtaatacata +tataatatatatgtaatgtatatatatgtaatgtatataatatatatgtaatacatatat +aatatatatgtaatgtatataatatatatgtaatacatatataatatatatgtaatgtat +attatatatgtaatgtatataatatgtatgtaatacatatattatatatgtaatgtatat +tatatatgtattacatatatgtattacatatataacatatatgtattacatatatgtatt +acatatataacatatatgtattacatatatgtattacatatataacatatatgtattaca +tatatgtattacatatataacatatatgtattacatatatgtattacatatataacatat +atgtattacatatatgtattacatatataacatatatgtattacatatatgtattacata +tataacatatatgtattacatatatgtattacatatataacatatatgtattacatatat +gtattacatatataacatatatgtattacatatatgtattacatatataacatatatgta +ttacatatatgtattacatatataacatatatgtattacatatatgtattacatatataa +catatatgtattacatatatgtaatacatatataacatatatgtattacatatatgtaat +acatatataacatatatgtaatacatatataacatatatgtattacatatatgtaataca +tatataacatgtattacatatatgtaatacacatataatatatatgttatatatatatat +atatataaaattttttaaaaaattgtttcttgagatagggtctcactctgtcacccaggc +tggagtataatggtttgatcatagttcactgcagccttgaacttctagactcaggtgatc +ctcccacctcaacctcct +>p:HG002_1_chr20:21721074-21721836 +agtagggacttgctttgggtcacagtcagcttttattagtgttattattgttgctgtttt +cttctttttctttgtacatcaacgttttatggtgaattaaatcgtgttttaaccttgtag +accacattggctattacatatatatatataatatatatgtaatatatatatgtaatgtat +attatatatgtaatgtatataatatatgtaatgtatataatacatatgtaatacatatat +attatatatgtatataatacatatatatgtatatatatgtatgtatatatatatgtatat +atgtatatatatatgtatataatacatatatatacatatatattatatatgtaatacata +tataatatatatgtaatgtatatatatgtaatgtatataatatatatgtaatacatatat +aatatatatgtaatgtatataatatatatgtaatacatatataatatatatgtaatgtat +attatatatgtaatgtatataatatgtatgtaatacatatattatatatgtaatgtatat +tatatatgtattacatatatgtattacatatataacatatatgtattacatatatgtatt +acatatataacatatatgtattacatatatgtattacatatataacatatatgtattaca +tatatgtattacatatataacatatatgtattacatatatgtattacatatataacatat +atgtattacatatatgtattacatatataacatatatgtattacatatatgtattacata +tataacatatatgtattacatatatgtattacatatataacatatatgtattacatatat +gtattacatatataacatatatgtattacatatatgtattacatatataacatatatgta +ttacatatatgtattacatatataacatatatgtattacatatatgtattacatatataa +catatatgtattacatatatgtaatacatatataacatatatgtattacatatatgtaat +acatatataacatatatgtaatacatatataacatatatgtattacatatatgtaataca +tatataacatgtattacatatatgtaatacacatataatatatatgttatatatatatat +atatataaaattttttaaaaaattgtttcttgagatagggtctcactctgtcacccaggc +tggagtataatggtttgatcatagttcactgcagccttgaacttctagactcaggtgatc +ctcccacctcaacctcct +>p:HG002_2_chr20:21721074-21721836 +agtagggacttgctttgggtcacagtcagcttttattagtgttattattgttgctgtttt +cttctttttctttgtacatcaacgttttatggtgaattaaatcgtgttttaaccttgtag +accacattggctattacatatatatatataatatatatgtaatatatatatgtaatgtat +attatatatgtaatgtatataatatatgtaatgtatataatatatatgtaatacatatat +attatatatgtatataatacatatatatgtatatatatgtatgtatatatatatgtatat +atgtatatatatatgtatataatacatatatatacatatatattatatatgtaatacata +tataatatatatgtaatgtatatatatgtaatgtatataatatatatgtaatacatatat +aatatatatgtaatgtatataatatatatgtaatacatatataatatatatgtaatgtat +attatatatgtaatgtatataatatgtatgtaatacatatattatatatgtaatgtatat +tatatatgtattacatatatgtattacatatataacatatatgtattacatatatgtatt +acatatataacatatatgtattacatatatgtattacatatataacatatatgtattaca +tatatgtattacatatataacatatatgtaatacatatatgtattacatatataacatat +atgtattacatatatgtattacatatataacatatatgtattacatatatgtattacata +tataacatatatgtattacatatatgtattacatatataacatatatgtattacatatat +gtattacatatataacatatatgtattacatatatgtaatacatatataacatatatgta +ttacatatatgtaatacatatataacatatatgtattacatatatgtaatacatatataa +catatatgtattacatatatgtaatacatatataac----atgtattacatatatgtaat +acatatataac--------------------------atgtattacatatatgtaataca +tatataacatgtattacatatatgtaatacacatataatatatatgttatatatatatat +atatataaaattttttaaaaaattgtttcttgagatagggtctcactctgtcacccaggc +tggagtataatggtttgatcatagttcactgcagccttgaacttctagactcaggtgatc +ctcccacctcaacctcct diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/msa.fa.fai new file mode 100644 index 00000000..1546e6f4 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_21721074_21721836 1278 29 60 61 +syndip_1_chr20:21721074-21721836 1278 1363 60 61 +syndip_2_chr20:21721074-21721836 1278 2697 60 61 +p:HG002_1_chr20:21721074-21721836 1278 4032 60 61 +p:HG002_2_chr20:21721074-21721836 1278 5367 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/output.vcf.gz new file mode 100644 index 00000000..80ae4bfc Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/output.vcf.gz.tbi new file mode 100644 index 00000000..0556ada8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:21721174-21721736/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/base.vcf.gz new file mode 100644 index 00000000..360dd943 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/base.vcf.gz.tbi new file mode 100644 index 00000000..4b87cdb0 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/comp.vcf.gz new file mode 100644 index 00000000..a0d1f765 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/comp.vcf.gz.tbi new file mode 100644 index 00000000..d3b7e3d9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/haps.fa new file mode 100644 index 00000000..dcf26ec0 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/haps.fa @@ -0,0 +1,176 @@ +>ref_chr20_22081861_22084223 +GGATGGTTCCATATTTTTGCAGTTGTGTATTTTGCTGCTATAAACATGTGTGTGCAGGTGTCTTTTTCATATAACAACTTCTTTTCCTTTGGGTAGGTTTACAAAAACTATCTTTTTCCCGTTCTTTTACTTATATATGCTTATTTATATATATTATATATACACTTTTAATATATACTTATTACTATATATTAATATAATATAATAATAATACAATATAATATATGTATATATGTAGGTATATAATAATATACCTACATATATACATATATTATATATACTATCTGTATATTATATGTATAATATATGTATATATAATATATGTATATACTATACATGTATATATTATATTATACATGTATATATTATAAGTATATACTATACATGCATGTATTATATGTATATACTATACATGCATGTATTATATGTATATATTATACATGCATGTATTATATGTATATATTATACATGCATGTATTATATGTATATATTATACATGCATGTATTATATGTATATATTATACATGTATGTATTATATGTATAGATTATACATGTATATATTATATATGTATATATTACACATGTACATATATGTATATATTAAACACGTTTATATTATTTATTATACATGTAGGTATATATGACATATGCATATATCATATAGGTATATATGACATATGCATATATCATATAGGTATATATGATATATGCGCATATATCATATAGGTATATATGATATATGCGCATATATCATACAGGTATATGCGCATATATCATATAGGTATAGGTATAGGTAGATATATGATATATGCACACATATCATATAGGTATATATGATATATGCGCATATATCATATAGGTATATATGATATATGATAGGTATATATGATATATGATAGGTATATATGATATATATCATATCGGTATATATGATATATATCATATCGGTATATATAGGTATATATCATAGGTATATATAGGTATATATCACATAGGTATATATAGGTATATATCATATAGGTATATATAATATATGCATTTATATTATATAGGTATATATATTACATAGGTATATGTAATATGTGCATATATATTATATAGGTATATATATTATACAGGCATATATAATACGTATATATATTATATGGGCATATATATGTGTATATATTATATAGGTATATATAATATATGTGTATATATTATGTGGGTATATATAATATATGTGTATATATTATGTGGGTATATATAATATATGTGTACATATTATGTGGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATATATGTAATAGGAAGCAGGAATGAATGCACAGAAGACCTTAGAGTTTAAGGCATTATTTGTGTAATGAGAAATATTATATATACGTATATTAATATAGACGTATATATAATATATACATATATTAATATAGACGTATATATAATATATACATATATACATATATAGTATATACTATGTATACATATATACTATACATACGTATATTATATACATGTGTATTATATACATGTGTATTATATATATGTGTATACATATATACTATATATACATACATTATATACATACATTATATATGTGTATTATATATGTATATATTATGTATGTATATATTATATATACGTATATATTAATATACATATATATGTGTCTCATTATACCAATAATGCCTTAAACTCTAAGGTCTTCTGTGCATTCATTCCTGCTTCCTATTACATATATATTATATAGATACATATATAATATATACATATATACTACATAATATATGCATATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTGTATATGTATTATATGTATATATTACATATTATATATACTTATGTATGTATAATATATATATAATATATATATATCTTAGGCAACTTTTCATTGCTCATTTTTATTAAACCCTGAAAACTTTCACTTTACTCCATTTCTAAGTTTGATATTCTGGTAGAATTAAAGTAAGAGTTTTCTTTCTTTCATCTCCTTTTTATCTCTCTCA +>syndip_1_chr20:22081861-22084223 +GGATGGTTCCATATTTTTGCAGTTGTGTATTTTGCTGCTATAAACATGTGTGTGCAGGTG +TCTTTTTCATATAACAACTTCTTTTCCTTTGGGTAGGTTTACAAAAACTATCTTTTTCCC +GTTCTTTTACTTATATATGCTTATTTATATATATTATATATACACTTTTAATATATACTT +ATTAATATATATTAATATAATATAATAATAATACAATATAATATATGTATATATGTAGGT +ATATAATAATATACCTACATATATACATATATTATATATACTATCTGTATATTATATGTA +TAATATATGTATATATAATATATGTATATACTATACATGTATATATTATATTATACATGT +ATATATTATAAGTATATACTATACATGCATGTATTATATGTATATACTATACATGCATGT +ATTATATGTATATATTATACATGCATGTATTATATGTATATATTATACATGCATGTATTA +TATGTATATATTATACATGTATGTATTATATGTATAGATTATACATGTATATATTATATA +TGTATATATTACACATGTACATATATGTATATATTAAACACGTTTATATTATTTATTATA +CATGACTATATTATATAGGTATATATGATATATGCATATATGTCATATAGGTATATATGA +CATATATGCATATATCATGTAGGTATATATGACATATGCATATATCATATAGGTATATAT +GACATATGCATATATCATATAGGTATATATGATATATGCGCATATATCATATAGGTATAT +ATGATATATGCGCATATATCATATAGGTATATATGATATATGCGCATATATCATATAGGT +ATATATGATATATGCGCATATATCATATAGGTATATATGATATATGCGCATATATCATAT +AGGTATATATGATATATGCGCATATATCATATAGGTATATATGATATATGCGCATATATC +ATACAGGTATATGTGCATATATCATATAGGTATAGGTATAGGTAGATATATGATATATGC +ACACATATCATATAGGTATATATGATATATGATAGGTATATATGATATATGATAGGTATA +TATGATATATATCATATTGGTATATATGATATATATCATATCGGTATATATGATATATAT +CATATCGGTATATATAGGTATATATCATAGGTATATATAGGTATATATCACATAGGTATA +TATAGGTATATATCATATAGGTATATATAATATATGCATTTATATTATATAGGTATATAT +ATTACATAGGTATATGTAATATGTGCATATATATTATATAGGTATATATATTATACAGGC +ATATATAATACGTATATATATTATATGGGCATATATATGTATATATATTATATAGGTATA +TATAATATATGTGTATATATTATGTGGGTATATATAATATATGTGTACATATTATGTGGG +TATATATAATATATGTGTACATATTATGTGGGTATATATAATATATGTGTACATATTATG +TGGGTATATATAATATATGTGTATATATTATGTGGGTATATATAATATATGTGTATATAT +TATGTGGGTATATATAATATATGTGTATATATTATGTGGGTATATATAATATATGTGTAT +ATATTATGTGGGTATATATAATATATGTGTATATATTATGTGGGTATATATAATATATGT +GTATATATTATGTGGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATAT +ATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATA +ATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATA +TATAATATATGTGTATATATTATATATGTAATAGGAAGCAGGAATGAATGCACAGAAGAC +CTTAGAGTTTAAGGCATTATTTGTGTAATGAGAAATATTATATATACGTATATTAATATA +GACGTATATATAATATATACATATATACATATATAGTATATACTATGTATACATATATAC +TATACATACGTATATTATATACATGTGTATTATATACATGTGTATTATATATATGTGTAT +ACATATATACTATATATACATACATTATATACATACATTATATATGTGTATTATATATGT +ATATATTATGTATGTATATATTATATATACGTATATATTAATATGCATATATATGTGTCT +CTTTATACCAATAATGCCTTAAACTCTAAGGTCTTCTGTGCATTCATTCCTGCTTCCTAT +TACATATATATTATATAGATACATATATAATATATACATATATACTACATAATATATGCA +TATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTGTATATGTA +TATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTGTATATGTA +TATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTGTATATGTA +TATATAATATATACATATGTTGTATATGTATTATATGTATATATTACATATTATATATAC +TTATGTATGTATAATATATATATAATATATATATATCTTAGGCAACTTTTCATTGCTCAT +TTTTATTAAACCCTGAAAACTTTCACTTTACTCCATTTCTAAGTTTGATATTCTGGTAGA +ATTAAAGTAAGAGTTTTCTTTCTTTCATCTCCTTTTTATCTCTCTCA +>syndip_2_chr20:22081861-22084223 +GGATGGTTCCATATTTTTGCAGTTGTGTATTTTGCTGCTATAAACATGTGTGTGCAGGTG +TCTTTTTCATATAACAACTTCTTTTCCTTTGGGTAGGTTTACAAAAACTATCTTTTTCCC +GTTCTTTTACTTATATATGCTTATTTATATATATTATATATACACTTTTAATATATACTT +ATTACTATATATTAATATAATATAATAATAATACAATATAATATATGTATATATGTAGGT +ATATAATAATATACCTACATATATACATATATTATATATACTATCTGTATATTATATGTA +TAATATATGTATATATAATATATGTATATACTATACATGTATATATTATATTATACATGT +ATATATTATAAGTATATACTATACATGCATGTATTATATGTATATACTATACATGCATGT +ATTATATGTATATATTATACATGCATGTATTATATGTATATATTATACATGCATGTATTA +TATGTATATATTATACATGTATGTATTATATGTATAGATTATACATGTATATATTATATA +TGTATATATTACACATGTACATATATGTATATATTAAACACGTTTATATTATTTATTATA +CATGTAGGTATATATGACATATGCATATATCATATAGGTATATATGACATATGCATATAT +CATATAGGTATATATGATATATGCGCATATATCATATAGGTATATATGATATATGCGCAT +ATATCATACAGGTATATGCGCATATATCATATAGGTATAGGTATAGGTAGATATATGATA +TATGCACACATATCATATAGGTATATATGATATATGCGCATATATCATATAGGTATATAT +GATATATGATAGGTATATATGATATATGATAGGTATATATGATATATATCATATCGGTAT +ATATGATATATATCATATCGGTATATATAGGTATATATCATAGGTATATATAGGTATATA +TCACATAGGTATATATAGGTATATATCATATAGGTATATATAATATATGCATTTATATTA +TATAGGTATATATATTACATAGGTATATGTAATATGTGCATATATATTATATAGGTATAT +ATATTATACAGGCATATATAATACGTATATATATTATATGGGCATATATATGTGTATATA +TTATATAGGTATATATAATATATGTGTATATATTATGTGGGTATATATAATATATGTGTA +TATATTATGTGGGTATATATAATATATGTGTACATATTATGTGGGTATATATAATATATG +TGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATA +TATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATAT +AATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTAT +ATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAG +GTATATATAATATATGTGTATATATTATATATGTAATAGGAAGCAGGAATGAATGCACAG +AAGACCTTAGAGTTTAAGGCATTATTTGTGTAATGAGAAATATTATATATACGTATATTA +ATATAGACGTATATATAATATATACATATATTAATATAGACGTATATATAATATATACAT +ATATACATATATAGTATATACTATGTATACATATATACTATACATACGTATATTATATAC +ATGTGTATTATATACATGTGTATTATATATATGTGTATACATATATACTATATATACATA +CATTATATACATACATTATATATGTGTATTATATATGTATATATTATGTATGTATATATT +ATATATACGTATATATTAATATACATATATATGTGTCTCATTATACCAATAATGCCTTAA +ACTCTAAGGTCTTCTGTGCATTCATTCCTGCTTCCTATTACATATATATTATATAGATAC +ATATATAATATATACATATATACTACATAATATATGCATATATAATATATACATATGTTG +TATATGTATATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTG +TATATGTATATATAATATATACATATGTTGTATATGTATTATATGTATATATTACATATT +ATATATACTTATGTATGTATAATATATATATAATATATATATATCTTAGGCAACTTTTCA +TTGCTCATTTTTATTAAACCCTGAAAACTTTCACTTTACTCCATTTCTAAGTTTGATATT +CTGGTAGAATTAAAGTAAGAGTTTTCTTTCTTTCATCTCCTTTTTATCTCTCTCA +>p:HG002_1_chr20:22081861-22084223 +GGATGGTTCCATATTTTTGCAGTTGTGTATTTTGCTGCTATAAACATGTGTGTGCAGGTG +TCTTTTTCATATAACAACTTCTTTTCCTTTGGGTAGGTTTACAAAAACTATCTTTTTCCC +GTTCTTTTACTTATATATGCTTATTTATATATATTATATATACACTTTTAATATATACTT +ATTACTATATATTAATATAATATAATAATAATACAATATAATATATGTATATATGTAGGT +ATATAATAATATACCTACATATATACATATATTATATATACTATCTGTATATTATATGTA +TAATATATGTATATATAATATATGTATATACTATACATGTATATATTATATTATACATGT +ATATATTATAAGTATATACTATACATGCATGTATTATATGTATATACTATACATGCATGT +ATTATATGTATATATTATACATGCATGTATTATATGTATATATTATACATGCATGTATTA +TATGTATATATTATACATGTATGTATTATATGTATAGATTATACATGTATATATTATATA +TGTATATATTACACATGTACATATATGTATATATTAAACACGTTTATATTATTTATTATA +CATGTAGGTATATATGACATATGCATATATCATATAGGTATATATGACATATGCATATAT +CATATAGGTATATATGATATATGCGCATATATCATATAGGTATATATGATATATGCGCAT +ATATCATACAGGTATATGCGCATATATCATATAGGTATAGGTATAGGTAGATATATGATA +TATGCACACATATCATATAGGTATATATGATATATGCGCATATATCATATAGGTATATAT +GATATATGATAGGTATATATGATATATGATAGGTATATATGATATATATCATATCGGTAT +ATATGATATATATCATATCGGTATATATAGGTATATATCATAGGTATATATAGGTATATA +TCACATAGGTATATATAGGTATATATCATATAGGTATATATAATATATGCATTTATATTA +TATAGGTATATATATTACATAGGTATATGTAATATGTGCATATATATTATATAGGTATAT +ATATTATACAGGCATATATAATACGTATATATATTATATGGGCATATATATGTGTATATA +TTATATAGGTATATATAATATATGTGTATATATTATGTGGGTATATATAATATATGTGTA +TATATTATGTGGGTATATATAATATATGTGTACATATTATGTGGGTATATATAATATATG +TGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATA +TATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATAT +AATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTAT +ATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAG +GTATATATAATATATGTGTATATATTATATATGTAATAGGAAGCAGGAATGAATGCACAG +AAGACCTTAGAGTTTAAGGCATTATTTGTGTAATGAGAAATATTATATATACGTATATTA +ATATAGACGTATATATAATATATACATATATTAATATAGACGTATATATAATATATACAT +ATATACATATATAGTATATACTATGTATACATATATACTATACATACGTATATTATATAC +ATGTGTATTATATACATGTGTATTATATATATGTGTATACATATATACTATATATACATA +CATTATATACATACATTATATATGTGTATTATATATGTATATATTATGTATGTATATATT +ATATATACGTATATATTAATATACATATATATGTGTCTCATTATACCAATAATGCCTTAA +ACTCTAAGGTCTTCTGTGCATTCATTCCTGCTTCCTATTACATATATATTATATAGATAC +ATATATAATATATACATATATACTACATAATATATGCATATATAATATATACATATGTTG +TATATGTATATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTG +TATATGTATATATAATATATACATATGTTGTATATGTATTATATGTATATATTACATATT +ATATATACTTATGTATGTATAATATATATATAATATATATATATCTTAGGCAACTTTTCA +TTGCTCATTTTTATTAAACCCTGAAAACTTTCACTTTACTCCATTTCTAAGTTTGATATT +CTGGTAGAATTAAAGTAAGAGTTTTCTTTCTTTCATCTCCTTTTTATCTCTCTCA +>p:HG002_2_chr20:22081861-22084223 +GGATGGTTCCATATTTTTGCAGTTGTGTATTTTGCTGCTATAAACATGTGTGTGCAGGTG +TCTTTTTCATATAACAACTTCTTTTCCTTTGGGTAGGTTTACAAAAACTATCTTTTTCCC +GTTCTTTTACTTATATATGCTTATTTATATATATTATATATACACTTTTAATATATACTT +ATTAATATATATTAATATAATATAATAATAATACAATATAATATATGTATATATGTAGGT +ATATAATAATATACCTACATATATACATATATTATATATACTATCTGTATATTATATGTA +TAATATATGTATATATAATATATGTATATACTATACATGTATATATTATATTATACATGT +ATATATTATAAGTATATACTATACATGCATGTATTATATGTATATACTATACATGCATGT +ATTATATGTATATATTATACATGCATGTATTATATGTATATATTATACATGCATGTATTA +TATGTATATATTATACATGTATGTATTATATGTATAGATTATACATGTATATATTATATA +TGTATATATTACACATGTACATATATGTATATATTAAACACGTTTATATTATTTATTATA +CATGACTATATTATATAGGTATATATGATATATGCATATATGTCATATAGGTATATATGA +CATATATGCATATATCATGTAGGTATATATGACATATGCATATATCATATAGGTATATAT +GACATATGCATATATCATATAGGTATATATGATATATGCGCATATATCATATAGGTATAT +ATGATATATGCGCATATATCATATAGGTATATATGATATATGCGCATATATCATATAGGT +ATATATGATATATGCGCATATATCATATAGGTATATATGATATATGCGCATATATCATAT +AGGTATATATGATATATGCGCATATATCATATAGGTATATATGATATATGCGCATATATC +ATACAGGTATATGTGCATATATCATATAGGTATAGGTATAGGTAGATATATGATATATGC +ACACATATCATATAGGTATATATGATATATGATAGGTATATATGATATATGATAGGTATA +TATGATATATATCATATTGGTATATATGATATATATCATATCGGTATATATGATATATAT +CATATCGGTATATATAGGTATATATCATAGGTATATATAGGTATATATCACATAGGTATA +TATAGGTATATATCATATAGGTATATATAATATATGCATTTATATTATATAGGTATATAT +ATTACATAGGTATATGTAATATGTGCATATATATTATATAGGTATATATATTATACAGGC +ATATATAATACGTATATATATTATATGGGCATATATATGTATATATATTATATAGGTATA +TATAATATATGTGTATATATTATGTGGGTATATATAATATATGTGTACATATTATGTGGG +TATATATAATATATGTGTACATATTATGTGGGTATATATAATATATGTGTACATATTATG +TGGGTATATATAATATATGTGTATATATTATGTGGGTATATATAATATATGTGTATATAT +TATGTGGGTATATATAATATATGTGTATATATTATGTGGGTATATATAATATATGTGTAT +ATATTATGTGGGTATATATAATATATGTGTATATATTATGTGGGTATATATAATATATGT +GTATATATTATGTGGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATAT +ATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATA +ATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATA +TATAATATATGTGTATATATTATATATGTAATAGGAAGCAGGAATGAATGCACAGAAGAC +CTTAGAGTTTAAGGCATTATTTGTGTAATGAGAAATATTATATATACGTATATTAATATA +GACGTATATATAATATATACATATATACATATATAGTATATACTATGTATACATATATAC +TATACATACGTATATTATATACATGTGTATTATATACATGTGTATTATATATATGTGTAT +ACATATATACTATATATACATACATTATATACATACATTATATATGTGTATTATATATGT +ATATATTATGTATGTATATATTATATATACGTATATATTAATATGCATATATATGTGTCT +CTTTATACCAATAATGCCTTAAACTCTAAGGTCTTCTGTGCATTCATTCCTGCTTCCTAT +TACATATATATTATATAGATACATATATAATATATACATATATACTACATAATATATGCA +TATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTGTATATGTA +TATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTGTATATGTA +TATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTGTATATGTA +TATATAATATATACATATGTTGTATATGTATTATATGTATATATTACATATTATATATAC +TTATGTATGTATAATATATATATAATATATATATATCTTAGGCAACTTTTCATTGCTCAT +TTTTATTAAACCCTGAAAACTTTCACTTTACTCCATTTCTAAGTTTGATATTCTGGTAGA +ATTAAAGTAAGAGTTTTCTTTCTTTCATCTCCTTTTTATCTCTCTCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/haps.fa.ref.fa new file mode 100644 index 00000000..c53a131c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:22081861-22084223 +GGATGGTTCCATATTTTTGCAGTTGTGTATTTTGCTGCTATAAACATGTGTGTGCAGGTGTCTTTTTCATATAACAACTTCTTTTCCTTTGGGTAGGTTTACAAAAACTATCTTTTTCCCGTTCTTTTACTTATATATGCTTATTTATATATATTATATATACACTTTTAATATATACTTATTACTATATATTAATATAATATAATAATAATACAATATAATATATGTATATATGTAGGTATATAATAATATACCTACATATATACATATATTATATATACTATCTGTATATTATATGTATAATATATGTATATATAATATATGTATATACTATACATGTATATATTATATTATACATGTATATATTATAAGTATATACTATACATGCATGTATTATATGTATATACTATACATGCATGTATTATATGTATATATTATACATGCATGTATTATATGTATATATTATACATGCATGTATTATATGTATATATTATACATGCATGTATTATATGTATATATTATACATGTATGTATTATATGTATAGATTATACATGTATATATTATATATGTATATATTACACATGTACATATATGTATATATTAAACACGTTTATATTATTTATTATACATGTAGGTATATATGACATATGCATATATCATATAGGTATATATGACATATGCATATATCATATAGGTATATATGATATATGCGCATATATCATATAGGTATATATGATATATGCGCATATATCATACAGGTATATGCGCATATATCATATAGGTATAGGTATAGGTAGATATATGATATATGCACACATATCATATAGGTATATATGATATATGCGCATATATCATATAGGTATATATGATATATGATAGGTATATATGATATATGATAGGTATATATGATATATATCATATCGGTATATATGATATATATCATATCGGTATATATAGGTATATATCATAGGTATATATAGGTATATATCACATAGGTATATATAGGTATATATCATATAGGTATATATAATATATGCATTTATATTATATAGGTATATATATTACATAGGTATATGTAATATGTGCATATATATTATATAGGTATATATATTATACAGGCATATATAATACGTATATATATTATATGGGCATATATATGTGTATATATTATATAGGTATATATAATATATGTGTATATATTATGTGGGTATATATAATATATGTGTATATATTATGTGGGTATATATAATATATGTGTACATATTATGTGGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATATATGTAATAGGAAGCAGGAATGAATGCACAGAAGACCTTAGAGTTTAAGGCATTATTTGTGTAATGAGAAATATTATATATACGTATATTAATATAGACGTATATATAATATATACATATATTAATATAGACGTATATATAATATATACATATATACATATATAGTATATACTATGTATACATATATACTATACATACGTATATTATATACATGTGTATTATATACATGTGTATTATATATATGTGTATACATATATACTATATATACATACATTATATACATACATTATATATGTGTATTATATATGTATATATTATGTATGTATATATTATATATACGTATATATTAATATACATATATATGTGTCTCATTATACCAATAATGCCTTAAACTCTAAGGTCTTCTGTGCATTCATTCCTGCTTCCTATTACATATATATTATATAGATACATATATAATATATACATATATACTACATAATATATGCATATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTGTATATGTATTATATGTATATATTACATATTATATATACTTATGTATGTATAATATATATATAATATATATATATCTTAGGCAACTTTTCATTGCTCATTTTTATTAAACCCTGAAAACTTTCACTTTACTCCATTTCTAAGTTTGATATTCTGGTAGAATTAAAGTAAGAGTTTTCTTTCTTTCATCTCCTTTTTATCTCTCTCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/msa.fa new file mode 100644 index 00000000..72dfc312 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/msa.fa @@ -0,0 +1,240 @@ +>ref_chr20_22081861_22084223 +ggatggttccatatttttgcagttgtgtattttgctgctataaacatgtgtgtgcaggtg +tctttttcatataacaacttcttttcctttgggtaggtttacaaaaactatctttttccc +gttcttttacttatatatgcttatttatatatattatatatacacttttaatatatactt +attactatatattaatataatataataataatacaatataatatatgtatatatgtaggt +atataataatatacctacatatatacatatattatatatactatctgtatattatatgta +taatatatgtatatataatatatgtatatactatacatgtatatattatattatacatgt +atatattataagtatatactatacatgcatgtattatatgtatatactatacatgcatgt +attatatgtatatattatacatgcatgtattatatgtatatattatacatgcatgtatta +tatgtatatattatacatgcatgtattatatgtatatattatacatgtatgtattatatg +tatagattatacatgtatatattatatatgtatatattacacatgtacatatatgtatat +attaaacacgtttatattatttattata-------------------------------- +-------------------------------------------catgtaggtatatatga +catatgcatatatcatataggtatatatgacatatgcatatatcatataggtatatatga +tatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatacagg----- +----tatatgcgcatatatcatataggtataggt------------------ataggtag +atatatgatatatgcacacatatcatataggtatatatgatatatgcgcatatatcatat +aggtatatatgatatatg------------------------------------------ +---------------------------------------ataggtatatatgatatatga +ta--------------------------------------------ggtatatatgatat +atatcatatcggtatatatgatatatatcatatcggtatatataggtatatatcataggt +atatataggtatatatcacataggtatatataggtatatatcatataggtatatataata +tatgcatttatattatataggtatatatattacataggtatatgtaatatgtgcatatat +attatataggtatatatattatacaggcatatataatacgtatatatattatatgggcat +atatatgtgtatatattatata-------------------------------------- +------------------------------------------------------------ +------------------------------ggtatatataatatatgtgtatatattatg +tgggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtacatat +tatgtgggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtat +atattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgt +gtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatat +atgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatata +atatatgtgtatatattatgtaggtatatataatatatgtgtatatattatatatgtaat +aggaagcaggaatgaatgcacagaagaccttagagtttaaggcattatttgtgtaatgag +aaatattatatatacgtatattaatatagacgtatatataatatatacatatattaatat +agacgtatatataatatatacatatatacatatatagtatatactatgtatacatatata +ctatacatacgtatattatatacatgtgtattatatacatgtgtattatatatatgtgta +tacatatatactatatatacatacattatatacatacattatatatgtgtattatatatg +tatatattatgtatgtatatattatatatacgtatatattaatatacatatatatgtgtc +tcattataccaataatgccttaaactctaaggtcttctgtgcattcattcctgcttccta +ttacatatatattatatagatacatatataatatatacatatatactacataatatatgc +------------------------------------------------------------ +------------------------------atatataatatatacatatgttgtatatgt +atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt +atatataatatatacatatgttgtatatgtattatatgtatatattacatattatatata +cttatgtatgtataatatatatataatatatatatatcttaggcaacttttcattgctca +tttttattaaaccctgaaaactttcactttactccatttctaagtttgatattctggtag +aattaaagtaagagttttctttctttcatctcctttttatctctctca +>syndip_1_chr20:22081861-22084223 +ggatggttccatatttttgcagttgtgtattttgctgctataaacatgtgtgtgcaggtg +tctttttcatataacaacttcttttcctttgggtaggtttacaaaaactatctttttccc +gttcttttacttatatatgcttatttatatatattatatatacacttttaatatatactt +attaatatatattaatataatataataataatacaatataatatatgtatatatgtaggt +atataataatatacctacatatatacatatattatatatactatctgtatattatatgta +taatatatgtatatataatatatgtatatactatacatgtatatattatattatacatgt +atatattataagtatatactatacatgcatgtattatatgtatatac------------- +---------------tatacatgcatgtattatatgtatatattatacatgcatgtatta +tatgtatatattatacatgcatgtattatatgtatatattatacatgtatgtattatatg +tatagattatacatgtatatattatatatgtatatattacacatgtacatatatgtatat +attaaacacgtttatattatttattatacatgactatattatataggtatatatgatata +tgcatatatgtcatataggtatatatgacatatatgcatatatcatgtaggtatatatga +catatgcatatatcatataggtatatatgacatatgcatatatcatataggtatatatga +tatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatataggtatat +atgatatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatataggt +atatatgatatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatat +aggtatatatgatatatgcgcatatatcatacaggtatatgtgcatatatcatataggta +taggtataggtagatatatgatatatgcacacatatcatataggtatatatgatatatga +taggtatatatgatatatgataggtatatatgatatatatcatattggtatatatgatat +atatcatatcggtatatatgatatatatcatatcggtatatataggtatatatcataggt +atatataggtatatatcacataggtatatataggtatatatcatataggtatatataata +tatgcatttatattatataggtatatatattacataggtatatgtaatatgtgcatatat +attatataggtatatatattatacaggcatatataatacgtatatatattatatgggcat +atatatgtatatatattatataggtatatataatatatgtgtatatattatgtgggtata +tataatatatgtgtacatattatgtgggtatatataatatatgtgtacatattatgtggg +tatatataatatatgtgtacatattatgtgggtatatataatatatgtgtatatattatg +tgggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtatatat +tatgtgggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtat +atattatgtgggtatatataatatatgtgtatatattatgtgggtatatataatatatgt +gtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatat +atgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatata +atatatgtgtatatattatgtaggtatatataatatatgtgtatatattatatatgtaat +aggaagcaggaatgaatgcacagaagaccttagagtttaaggcattatttgtgtaatgag +aaatattatatatacg---------------------------------tatattaatat +agacgtatatataatatatacatatatacatatatagtatatactatgtatacatatata +ctatacatacgtatattatatacatgtgtattatatacatgtgtattatatatatgtgta +tacatatatactatatatacatacattatatacatacattatatatgtgtattatatatg +tatatattatgtatgtatatattatatatacgtatatattaatatgcatatatatgtgtc +tctttataccaataatgccttaaactctaaggtcttctgtgcattcattcctgcttccta +ttacatatatattatatagatacatatataatatatacatatatactacataatatatgc +atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt +atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt +atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt +atatataatatatacatatgttgtatatgtattatatgtatatattacatattatatata +cttatgtatgtataatatatatataatatatatatatcttaggcaacttttcattgctca +tttttattaaaccctgaaaactttcactttactccatttctaagtttgatattctggtag +aattaaagtaagagttttctttctttcatctcctttttatctctctca +>syndip_2_chr20:22081861-22084223 +ggatggttccatatttttgcagttgtgtattttgctgctataaacatgtgtgtgcaggtg +tctttttcatataacaacttcttttcctttgggtaggtttacaaaaactatctttttccc +gttcttttacttatatatgcttatttatatatattatatatacacttttaatatatactt +attactatatattaatataatataataataatacaatataatatatgtatatatgtaggt +atataataatatacctacatatatacatatattatatatactatctgtatattatatgta +taatatatgtatatataatatatgtatatactatacatgtatatattatattatacatgt +atatattataagtatatactatacatgcatgtattatatgtatatac------------- +---------------tatacatgcatgtattatatgtatatattatacatgcatgtatta +tatgtatatattatacatgcatgtattatatgtatatattatacatgtatgtattatatg +tatagattatacatgtatatattatatatgtatatattacacatgtacatatatgtatat +attaaacacgtttatattatttattata-------------------------------- +-------------------------------------------catgtaggtatatatga +catatgcatatatcatataggtatatatgacatatgcatatatcatataggtatatatga +tatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatacagg----- +----tatatgcgcatatatcatataggtataggt------------------ataggtag +atatatgatatatgcacacatatcatataggtatatatgatatatgcgcatatatcatat +aggtatatatgatatatg------------------------------------------ +---------------------------------------ataggtatatatgatatatga +ta--------------------------------------------ggtatatatgatat +atatcatatcggtatatatgatatatatcatatcggtatatataggtatatatcataggt +atatataggtatatatcacataggtatatataggtatatatcatataggtatatataata +tatgcatttatattatataggtatatatattacataggtatatgtaatatgtgcatatat +attatataggtatatatattatacaggcatatataatacgtatatatattatatgggcat +atatatgtgtatatattatata-------------------------------------- +------------------------------------------------------------ +------------------------------ggtatatataatatatgtgtatatattatg +tgggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtacatat +tatgtgggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtat +atattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgt +gtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatat +atgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatata +atatatgtgtatatattatgtaggtatatataatatatgtgtatatattatatatgtaat +aggaagcaggaatgaatgcacagaagaccttagagtttaaggcattatttgtgtaatgag +aaatattatatatacgtatattaatatagacgtatatataatatatacatatattaatat +agacgtatatataatatatacatatatacatatatagtatatactatgtatacatatata +ctatacatacgtatattatatacatgtgtattatatacatgtgtattatatatatgtgta +tacatatatactatatatacatacattatatacatacattatatatgtgtattatatatg +tatatattatgtatgtatatattatatatacgtatatattaatatacatatatatgtgtc +tcattataccaataatgccttaaactctaaggtcttctgtgcattcattcctgcttccta +ttacatatatattatatagatacatatataatatatacatatatactacataatatatgc +------------------------------------------------------------ +------------------------------atatataatatatacatatgttgtatatgt +atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt +atatataatatatacatatgttgtatatgtattatatgtatatattacatattatatata +cttatgtatgtataatatatatataatatatatatatcttaggcaacttttcattgctca +tttttattaaaccctgaaaactttcactttactccatttctaagtttgatattctggtag +aattaaagtaagagttttctttctttcatctcctttttatctctctca +>p:HG002_1_chr20:22081861-22084223 +ggatggttccatatttttgcagttgtgtattttgctgctataaacatgtgtgtgcaggtg +tctttttcatataacaacttcttttcctttgggtaggtttacaaaaactatctttttccc +gttcttttacttatatatgcttatttatatatattatatatacacttttaatatatactt +attactatatattaatataatataataataatacaatataatatatgtatatatgtaggt +atataataatatacctacatatatacatatattatatatactatctgtatattatatgta +taatatatgtatatataatatatgtatatactatacatgtatatattatattatacatgt +atatattataagtatatactatacatgcatgtattatatgtatatac------------- +---------------tatacatgcatgtattatatgtatatattatacatgcatgtatta +tatgtatatattatacatgcatgtattatatgtatatattatacatgtatgtattatatg +tatagattatacatgtatatattatatatgtatatattacacatgtacatatatgtatat +attaaacacgtttatattatttattata-------------------------------- +-------------------------------------------catgtaggtatatatga +catatgcatatatcatataggtatatatgacatatgcatatatcatataggtatatatga +tatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatacagg----- +----tatatgcgcatatatcatataggtataggt------------------ataggtag +atatatgatatatgcacacatatcatataggtatatatgatatatgcgcatatatcatat +aggtatatatgatatatg------------------------------------------ +---------------------------------------ataggtatatatgatatatga +ta--------------------------------------------ggtatatatgatat +atatcatatcggtatatatgatatatatcatatcggtatatataggtatatatcataggt +atatataggtatatatcacataggtatatataggtatatatcatataggtatatataata +tatgcatttatattatataggtatatatattacataggtatatgtaatatgtgcatatat +attatataggtatatatattatacaggcatatataatacgtatatatattatatgggcat +atatatgtgtatatattatata-------------------------------------- +------------------------------------------------------------ +------------------------------ggtatatataatatatgtgtatatattatg +tgggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtacatat +tatgtgggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtat +atattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgt +gtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatat +atgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatata +atatatgtgtatatattatgtaggtatatataatatatgtgtatatattatatatgtaat +aggaagcaggaatgaatgcacagaagaccttagagtttaaggcattatttgtgtaatgag +aaatattatatatacgtatattaatatagacgtatatataatatatacatatattaatat +agacgtatatataatatatacatatatacatatatagtatatactatgtatacatatata +ctatacatacgtatattatatacatgtgtattatatacatgtgtattatatatatgtgta +tacatatatactatatatacatacattatatacatacattatatatgtgtattatatatg +tatatattatgtatgtatatattatatatacgtatatattaatatacatatatatgtgtc +tcattataccaataatgccttaaactctaaggtcttctgtgcattcattcctgcttccta +ttacatatatattatatagatacatatataatatatacatatatactacataatatatgc +------------------------------------------------------------ +------------------------------atatataatatatacatatgttgtatatgt +atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt +atatataatatatacatatgttgtatatgtattatatgtatatattacatattatatata +cttatgtatgtataatatatatataatatatatatatcttaggcaacttttcattgctca +tttttattaaaccctgaaaactttcactttactccatttctaagtttgatattctggtag +aattaaagtaagagttttctttctttcatctcctttttatctctctca +>p:HG002_2_chr20:22081861-22084223 +ggatggttccatatttttgcagttgtgtattttgctgctataaacatgtgtgtgcaggtg +tctttttcatataacaacttcttttcctttgggtaggtttacaaaaactatctttttccc +gttcttttacttatatatgcttatttatatatattatatatacacttttaatatatactt +attaatatatattaatataatataataataatacaatataatatatgtatatatgtaggt +atataataatatacctacatatatacatatattatatatactatctgtatattatatgta +taatatatgtatatataatatatgtatatactatacatgtatatattatattatacatgt +atatattataagtatatactatacatgcatgtattatatgtatatac------------- +---------------tatacatgcatgtattatatgtatatattatacatgcatgtatta +tatgtatatattatacatgcatgtattatatgtatatattatacatgtatgtattatatg +tatagattatacatgtatatattatatatgtatatattacacatgtacatatatgtatat +attaaacacgtttatattatttattatacatgactatattatataggtatatatgatata +tgcatatatgtcatataggtatatatgacatatatgcatatatcatgtaggtatatatga +catatgcatatatcatataggtatatatgacatatgcatatatcatataggtatatatga +tatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatataggtatat +atgatatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatataggt +atatatgatatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatat +aggtatatatgatatatgcgcatatatcatacaggtatatgtgcatatatcatataggta +taggtataggtagatatatgatatatgcacacatatcatataggtatatatgatatatga +taggtatatatgatatatgataggtatatatgatatatatcatattggtatatatgatat +atatcatatcggtatatatgatatatatcatatcggtatatataggtatatatcataggt +atatataggtatatatcacataggtatatataggtatatatcatataggtatatataata +tatgcatttatattatataggtatatatattacataggtatatgtaatatgtgcatatat +attatataggtatatatattatacaggcatatataatacgtatatatattatatgggcat +atatatgtatatatattatataggtatatataatatatgtgtatatattatgtgggtata +tataatatatgtgtacatattatgtgggtatatataatatatgtgtacatattatgtggg +tatatataatatatgtgtacatattatgtgggtatatataatatatgtgtatatattatg +tgggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtatatat +tatgtgggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtat +atattatgtgggtatatataatatatgtgtatatattatgtgggtatatataatatatgt +gtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatat +atgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatata +atatatgtgtatatattatgtaggtatatataatatatgtgtatatattatatatgtaat +aggaagcaggaatgaatgcacagaagaccttagagtttaaggcattatttgtgtaatgag +aaatattatatatacg---------------------------------tatattaatat +agacgtatatataatatatacatatatacatatatagtatatactatgtatacatatata +ctatacatacgtatattatatacatgtgtattatatacatgtgtattatatatatgtgta +tacatatatactatatatacatacattatatacatacattatatatgtgtattatatatg +tatatattatgtatgtatatattatatatacgtatatattaatatgcatatatatgtgtc +tctttataccaataatgccttaaactctaaggtcttctgtgcattcattcctgcttccta +ttacatatatattatatagatacatatataatatatacatatatactacataatatatgc +atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt +atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt +atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt +atatataatatatacatatgttgtatatgtattatatgtatatattacatattatatata +cttatgtatgtataatatatatataatatatatatatcttaggcaacttttcattgctca +tttttattaaaccctgaaaactttcactttactccatttctaagtttgatattctggtag +aattaaagtaagagttttctttctttcatctcctttttatctctctca diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/msa.fa.fai new file mode 100644 index 00000000..460d3d7e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_22081861_22084223 2808 29 60 61 +syndip_1_chr20:22081861-22084223 2808 2918 60 61 +syndip_2_chr20:22081861-22084223 2808 5807 60 61 +p:HG002_1_chr20:22081861-22084223 2808 8697 60 61 +p:HG002_2_chr20:22081861-22084223 2808 11587 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/output.vcf.gz new file mode 100644 index 00000000..2a67b2a4 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/output.vcf.gz.tbi new file mode 100644 index 00000000..f75dff19 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:22081961-22084123/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/base.vcf.gz new file mode 100644 index 00000000..0d353036 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/base.vcf.gz.tbi new file mode 100644 index 00000000..11ac9498 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/comp.vcf.gz new file mode 100644 index 00000000..ab45cc1f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/comp.vcf.gz.tbi new file mode 100644 index 00000000..9a84a476 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/haps.fa new file mode 100644 index 00000000..87aa5032 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/haps.fa @@ -0,0 +1,74 @@ +>ref_chr20_2240825_2241827 +GTGACCCTTAGGTAAATCGTTCCAACTCTCTGAGCCTCAGTGTTGTTATCTACAAATGGGAGAATCAAGGCACCCTCCTACAAGCGGCGGCTCATCAGCTCACTTGGAAAATGTAGTCATCTTCTCAAAGTTTTCTTTTTCTTTCTTTCTTTTTCCTTTCTTTCTTTCTTTTTCTTTCTTTCTCTCTCTCTCCTTCCTTCCTTCTTTCCTTCCCTCCCTCCCTTCCTTTTTTCTTCTTTCTTTCATTTTCTTTCTTTCTCTCTTTCTTCTTTCTCTTCCTTTCTTTCCTTCCGTCCCTCCCTTCCTTCCTTTTTTCTTCTTCCTTTCATTTTCTTTCTTTCTCTCTTTCTTCTTTCTCTTCCTTTCTTCTTTCTTTTCCTCCTTCCTCCCTTCTTTCCTTCCCTTCCTTCTTCCCTCCCTCCCTCTTTGTTTCTTTCTTTCTCTCCCTCCTTCCCTCCCTCCCTTTCTGTCTCCCTCTTTCTTTCTCTTTTTTCTTTTCCTTCCTTCCGTCTTTTTCCTCCCTTCTTTCCTCCCTCCTCCCTCCCTCCCTCCTCCCTCTTTTTCTTTCTTTCTTTCTTTTTTCTTTCTCTCTTCTTTTTTTTTTTTTTTTTTTAAGAGATAGGGTCTGTTGCCCAGGCTGGAGTGCAGTGGCATGATCATGGTTCACTGCAGCCTTGAACTCCTGGGCTCAGGTGATCCTCCTACCTCAGCCTCCTAAGTAGCTGGGACTATAGGTGCATGCCATCACACCCAGCTAATTTTTTAAAAGAAATTTTGTAAAGACAGGGGTCTTGCTATGTTCCCCAGGCTGGTCTCAAACTCCTGGGCTCAAGTGATCCTCCAGCCTCAGTATCCCAAAGTGCTGGGATTATAGGTGTGAGTCACTGCAGCCAGCTCAAATATTTTCTTAAATGAATGTAAGGTTGAGGATGCATTATTATAATGGCTAATTTAGATCTAAAAAATGCTTTGCAGTTTACCAGATTCACTTATGTACATTCTC +>syndip_1_chr20:2240825-2241827 +GTGACCCTTAGGTAAATCGTTCCAACTCTCTGAGCCTCAGTGTTGTTATCTACAAATGGG +AGAATCAAGGCACCCTCCTACAAGCGGCGGCTCATCAGCTCACTTGGAAAATGTAGTCAT +CTTCTCAAAGTTTTCTTTTTCTTTCTTTCTTTTTCCTTTCTTTCTTTCTTTTTCTTTCTT +TCTCTCTCTCTCCTTCCTTCCTTCTTTCCTTCCCTCCCTCCCTTCCTTTTTTCTTCTTTC +TTTCATTTTCTTTCTTTCTCTCTTTCTTCTTTCTCTTCCTTTCTTCTTTCTTTTCCTCCT +TCCTCCCTTCTTTCCTTCCCTTCCTTCTTCCCTCCCTCCCTCTTTGTTTCTTTCTTTCTC +TCCCTCCTTCCCTCCCTCCCTTTCTTTCTCCTTTTCTTCCTTCCCTCCCTGCCTGTCTCC +CTCTTTCTTTCTCTTTTTTCTTTTCCTTCCTTCCGTCTTTTTCCTCCCTTCTTTCCTCCC +TCCTCCCTCCCTCCCTCCTCCCTCTTTTTCTTTCTTTCTTTCTTTTTTCTTTCTCTCTTC +TTTTTTTTTTTTTTTTTTAAGAGATAGGGTCTGTTGCCCAGGCTGGAGTGCAGTGGCATG +ATCATGGTTCACTGCAGCCTTGAACTCCTGGGCTCAGGTGATCCTCCTACCTCAGCCTCC +TAAGTAGCTGGGACTATAGGTGCATGCCATCACACCCAGCTAATTTTTTAAAAGAAATTT +TGTAAAGACAGGGGTCTTGCTATGTTCCCCAGGCTGGTCTCAAACTCCTGGGCTCAAGTG +ATCCTCCAGCCTCAGTATCCCAAAGTGCTGGGATTATAGGTGTGAGTCACTGCAGCCAGC +TCAAATATTTTCTTAAATGAATGTAAGGTTGAGGATGCATTATTATAATGGCTAATTTAG +ATCTAAAAAATGCTTTGCAGTTTACCAGATTCACTTATGTACATTCTC +>syndip_2_chr20:2240825-2241827 +GTGACCCTTAGGTAAATCGTTCCAACTCTCTGAGCCTCAGTGTTGTTATCTACAAATGGG +AGAATCAAGGCACCCTCCTACAAGCGGCGGCTCATCAGCTCACTTGGAAAATGTAGTCAT +CTTCTCAAAGTTTTCTTTTTCTTTCTTTCTTTTTCTTTCTTTCTCTCTCTCTCCTTCCTT +CCTTCTTTCCTTCCCTCCCTCCCTTCCTTTTTTCTTCTTCCTTTCATTTTCTTTCTTTCT +CTCTTTCTTCTTTCTCTTCCTTTCTTCTTTCTTTTCCTCCTTCCTCCCTTCTTTCCTTCC +CTTCCTTCTTCCCTCCCTCCCTCTTTGTTTCTTTCTTTCTCTCCCTCCTTCCCTCCCTCC +CTTTCTTCCTTCTTTCCTTATCCCTCCCTTCTTTCCTTCCTTCCCTTTGTTTCTCTTTCT +TTCTTTCTTTCTCTCTCTCTTCCTTCCTTCCCTCCCTCCCTCCCTCCTTCCTCCCTTCTT +TCCTTCCCTCCCTGCCTCTCTGTCTCCCTCTTTCTTTCTCTTTTTTCTTTTCCTTCCTTC +CGTCTTTTTCCTCCCTTCTTTCCTCCCTCCTCCCTCCCTCCCTCCTCCCTCTTTTTCTTT +CTTTCTTTCTTTTTTCTCTCTCTCTTCTTTTTTTTTTTTTTTTTTTAAGAGATAGGGTCT +GTTGCCCAGGCTGGAGTGCAGTGGCATGATCATGGTTCACTGCAGCCTTGAACTCCTGGG +CTCAGGTGATCCTCCTACCTCAGCCTCCTAAGTAGCTGGGACTATAGGTGCATGCCATCA +CACCCAGCTAATTTTTTAAAAGAAATTTTGTAAAGACAGGGGTCTTGCTATGTTCCCCAG +GCTGGTCTCAAACTCCTGGGCTCAAGTGATCCTCCAGCCTCAGTATCCCAAAGTGCTGGG +ATTATAGGTGTGAGTCACTGCAGCCAGCTCAAATATTTTCTTAAATGAATGTAAGGTTGA +GGATGCATTATTATAATGGCTAATTTAGATCTAAAAAATGCTTTGCAGTTTACCAGATTC +ACTTATGTACATTCTC +>p:HG002_1_chr20:2240825-2241827 +GTGACCCTTAGGTAAATCGTTCCAACTCTCTGAGCCTCAGTGTTGTTATCTACAAATGGG +AGAATCAAGGCACCCTCCTACAAGCGGCGGCTCATCAGCTCACTTGGAAAATGTAGTCAT +CTTCTCAAAGTTTTCTTTTTCTTTCTTTCTTTTTCTTTCTTTCTCTCTCTCTCCTTCCTT +CCTTCTTTCCTTCCCTCCCTCCCTTCCTTTTTTCTTCTTCCTTTCATTTTCTTTCTTTCT +CTCTTTCTTCTTTCTCTTCCTTTCTTCTTTCTTTTCCTCCTTCCTCCCTTCTTTCCTTCC +CTTCCTTCTTCCCTCCCTCCCTCTTTGTTTCTTTCTTTCTCTCCCTCCTTCCCTCCCTCC +CTTTCTTCCTTCTTTCCTTATCCCTCCCTTCTTTCCTTCCTTCCCTTTGTTTCTCTTTCT +TTCTTTCTTTCTCTCTCTCTTCCTTCCTTCCCTCCCTCCCTCCCTCCTTCCTCCCTTCTT +TCCTTCCCTCCCTGCCTCTCTGTCTCCCTCTTTCTTTCTCTTTTTTCTTTTCCTTCCTTC +CGTCTTTTTCCTCCCTTCTTTCCTCCCTCCTCCCTCCCTCCCTCCTCCCTCTTTTTCTTT +CTTTCTTTCTTTTTTCTCTCTCTCTTCTTTTTTTTTTTTTTTTTTTAAGAGATAGGGTCT +GTTGCCCAGGCTGGAGTGCAGTGGCATGATCATGGTTCACTGCAGCCTTGAACTCCTGGG +CTCAGGTGATCCTCCTACCTCAGCCTCCTAAGTAGCTGGGACTATAGGTGCATGCCATCA +CACCCAGCTAATTTTTTAAAAGAAATTTTGTAAAGACAGGGGTCTTGCTATGTTCCCCAG +GCTAGTCTCAAACTCCTGGGCTCAAGTGATCCTCCAGCCTCAGTATCCCAAAGTGCTGGG +ATTATAGGTGTGAGTCACTGCAGCCAGCTCAAATATTTTCTTAAATGAATGTAAGGTTGA +GGATGCATTATTATAATGGCTAATTTAGATCTAAAAAATGCTTTGCAGTTTACCAGATTC +ACTTATGTACATTCTC +>p:HG002_2_chr20:2240825-2241827 +GTGACCCTTAGGTAAATCGTTCCAACTCTCTGAGCCTCAGTGTTGTTATCTACAAATGGG +AGAATCAAGGCACCCTCCTACAAGCGGCGGCTCATCAGCTCACTTGGAAAATGTAGTCAT +CTTCTCAAAGTTTTCTTTTTCTTTCTTTCTTTTTCCTTTCTTTCTTTCTTTTTCTTTCTT +TCTCTCTCTCTCCTTCCTTCCTTCTTTCCTTCCCTCCCTCCCTTCCTTTTTTCTTCTTTC +TTTCATTTTCTTTCTTTCTCTCTTTCTTCTTTCTCTTCCTTTCTTCTTTCTTTTCCTCCT +TCCTCCCTTCTTTCCTTCCCTTCCTTCTTCCCTCCCTCCCTCTTTGTTTCTTTCTTTCTC +TCCCTCCTTCCCTCCCTCCCTTTCTTTCTCCTTTTCTTCCTTCCCTCCCTGCCTGTCTCC +CTCTTTCTTTCTCTTTTTTCTTTTCCTTCCTTCCGTCTTTTTCCTCCCTTCTTTCCTCCC +TCCTCCCTCCCTCCCTCCTCCCTCTTTTTCTTTCTTTCTTTCTTTTTTCTTTCTCTCTTC +TTTTTTTTTTTTTTTTTTAAGAGATAGGGTCTGTTGCCCAGGCTGGAGTGCAGTGGCATG +ATCATGGTTCACTGCAGCCTTGAACTCCTGGGCTCAGGTGATCCTCCTACCTCAGCCTCC +TAAGTAGCTGGGACTATAGGTGCATGCCATCACACCCAGCTAATTTTTTAAAAGAAATTT +TGTAAAGACAGGGGTCTTGCTATGTTCCCCAGGCTGGTCTCAAACTCCTGGGCTCAAGTG +ATCCTCCAGCCTCAGTATCCCAAAGTGCTGGGATTATAGGTGTGAGTCACTGCAGCCAGC +TCAAATATTTTCTTAAATGAATGTAAGGTTGAGGATGCATTATTATAATGGCTAATTTAG +ATCTAAAAAATGCTTTGCAGTTTACCAGATTCACTTATGTACATTCTC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/haps.fa.ref.fa new file mode 100644 index 00000000..10349967 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:2240825-2241827 +GTGACCCTTAGGTAAATCGTTCCAACTCTCTGAGCCTCAGTGTTGTTATCTACAAATGGGAGAATCAAGGCACCCTCCTACAAGCGGCGGCTCATCAGCTCACTTGGAAAATGTAGTCATCTTCTCAAAGTTTTCTTTTTCTTTCTTTCTTTTTCCTTTCTTTCTTTCTTTTTCTTTCTTTCTCTCTCTCTCCTTCCTTCCTTCTTTCCTTCCCTCCCTCCCTTCCTTTTTTCTTCTTTCTTTCATTTTCTTTCTTTCTCTCTTTCTTCTTTCTCTTCCTTTCTTTCCTTCCGTCCCTCCCTTCCTTCCTTTTTTCTTCTTCCTTTCATTTTCTTTCTTTCTCTCTTTCTTCTTTCTCTTCCTTTCTTCTTTCTTTTCCTCCTTCCTCCCTTCTTTCCTTCCCTTCCTTCTTCCCTCCCTCCCTCTTTGTTTCTTTCTTTCTCTCCCTCCTTCCCTCCCTCCCTTTCTGTCTCCCTCTTTCTTTCTCTTTTTTCTTTTCCTTCCTTCCGTCTTTTTCCTCCCTTCTTTCCTCCCTCCTCCCTCCCTCCCTCCTCCCTCTTTTTCTTTCTTTCTTTCTTTTTTCTTTCTCTCTTCTTTTTTTTTTTTTTTTTTTAAGAGATAGGGTCTGTTGCCCAGGCTGGAGTGCAGTGGCATGATCATGGTTCACTGCAGCCTTGAACTCCTGGGCTCAGGTGATCCTCCTACCTCAGCCTCCTAAGTAGCTGGGACTATAGGTGCATGCCATCACACCCAGCTAATTTTTTAAAAGAAATTTTGTAAAGACAGGGGTCTTGCTATGTTCCCCAGGCTGGTCTCAAACTCCTGGGCTCAAGTGATCCTCCAGCCTCAGTATCCCAAAGTGCTGGGATTATAGGTGTGAGTCACTGCAGCCAGCTCAAATATTTTCTTAAATGAATGTAAGGTTGAGGATGCATTATTATAATGGCTAATTTAGATCTAAAAAATGCTTTGCAGTTTACCAGATTCACTTATGTACATTCTC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/msa.fa new file mode 100644 index 00000000..59b6ae59 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/msa.fa @@ -0,0 +1,95 @@ +>ref_chr20_2240825_2241827 +gtgacccttaggtaaatcgttccaactctctgagcctcagtgttgttatctacaaatggg +agaatcaaggcaccctcctacaagcggcggctcatcagctcacttggaaaatgtagtcat +cttctcaaagttttctttttctttctttctttttcctttctttctttctttttctttctt +tctctctctctccttccttccttctttccttccctccctcccttccttttttcttctttc +tttcattttctttctttctctctttcttctttctcttcctttctt--------------- +tccttccgtccctcccttccttccttttttcttcttcctttcat--tttctttctttctc +tctttcttctttctcttcctttcttctttcttttcctccttcctcccttctttccttccc +ttcctt-----------------------------------cttccctccctccctcttt +gtttctttctttctctccctccttccctccctccctttctgtctccctctttctttctct +tttttcttttccttccttccgtctttttcctcccttctttcctccctcctccctccctcc +ctcctccctctttttctttctttctttcttttttctttctctcttctttttttttttttt +tttttaagagatagggtctgttgcccaggctggagtgcagtggcatgatcatggttcact +gcagccttgaactcctgggctcaggtgatcctcctacctcagcctcctaagtagctggga +ctataggtgcatgccatcacacccagctaattttttaaaagaaattttgtaaagacaggg +gtcttgctatgttccccaggctggtctcaaactcctgggctcaagtgatcctccagcctc +agtatcccaaagtgctgggattataggtgtgagtcactgcagccagctcaaatattttct +taaatgaatgtaaggttgaggatgcattattataatggctaatttagatctaaaaaatgc +tttgcagtttaccagattcacttatgtacattctc +>syndip_1_chr20:2240825-2241827 +gtgacccttaggtaaatcgttccaactctctgagcctcagtgttgttatctacaaatggg +agaatcaaggcaccctcctacaagcggcggctcatcagctcacttggaaaatgtagtcat +cttctcaaagttttctttttctttctttctttttcctttctttctttctttttctttctt +tctctctctctccttccttccttctttccttccctccctcccttccttttttcttctttc +tttcattttctttctttctctctttcttctttctcttcctttctt--------------- +-------------------------------------------c--tttcttttcctcct +tcctcccttctttccttcccttccttcttccctccctccctctttgtttctttctttctc +tccctc-----------------------------------cttccctccctccctttct +ttctcctt-----------ttcttccttccctccctgcctgtctccctctttctttctct +tttttcttttccttccttccgtctttttcctcccttctttcctccctcctccctccctcc +ctcctccctctttttctttctttctttcttttttctttctctcttc-ttttttttttttt +tttttaagagatagggtctgttgcccaggctggagtgcagtggcatgatcatggttcact +gcagccttgaactcctgggctcaggtgatcctcctacctcagcctcctaagtagctggga +ctataggtgcatgccatcacacccagctaattttttaaaagaaattttgtaaagacaggg +gtcttgctatgttccccaggctggtctcaaactcctgggctcaagtgatcctccagcctc +agtatcccaaagtgctgggattataggtgtgagtcactgcagccagctcaaatattttct +taaatgaatgtaaggttgaggatgcattattataatggctaatttagatctaaaaaatgc +tttgcagtttaccagattcacttatgtacattctc +>syndip_2_chr20:2240825-2241827 +gtgacccttaggtaaatcgttccaactctctgagcctcagtgttgttatctacaaatggg +agaatcaaggcaccctcctacaagcggcggctcatcagctcacttggaaaatgtagtcat +cttctcaaagttttctt-------------------tttctttctttctttttctttctt +tctctctctctccttccttccttctttccttccctccctcccttccttttttcttcttcc +tttcattttctttctttctctctttcttctttctcttcctttcttctttcttttcctcct +tcctcccttctttccttcccttccttcttccctccctccctctttgtttctttctttctc +tccctccttccctccctccctttcttccttctttccttatccctcccttctttccttcct +tccctttgtttctctttctttctttctttctctctctcttccttccttccctccctccct +ccctccttcctcccttctttccttccctccctgcctctctgtctccctctttctttctct +tttttcttttccttccttccgtctttttcctcccttctttcctccctcctccctccctcc +ctcctccctctttttctttctttctttcttttttctctctctcttctttttttttttttt +tttttaagagatagggtctgttgcccaggctggagtgcagtggcatgatcatggttcact +gcagccttgaactcctgggctcaggtgatcctcctacctcagcctcctaagtagctggga +ctataggtgcatgccatcacacccagctaattttttaaaagaaattttgtaaagacaggg +gtcttgctatgttccccaggctggtctcaaactcctgggctcaagtgatcctccagcctc +agtatcccaaagtgctgggattataggtgtgagtcactgcagccagctcaaatattttct +taaatgaatgtaaggttgaggatgcattattataatggctaatttagatctaaaaaatgc +tttgcagtttaccagattcacttatgtacattctc +>p:HG002_1_chr20:2240825-2241827 +gtgacccttaggtaaatcgttccaactctctgagcctcagtgttgttatctacaaatggg +agaatcaaggcaccctcctacaagcggcggctcatcagctcacttggaaaatgtagtcat +cttctcaaagttttctt-------------------tttctttctttctttttctttctt +tctctctctctccttccttccttctttccttccctccctcccttccttttttcttcttcc +tttcattttctttctttctctctttcttctttctcttcctttcttctttcttttcctcct +tcctcccttctttccttcccttccttcttccctccctccctctttgtttctttctttctc +tccctccttccctccctccctttcttccttctttccttatccctcccttctttccttcct +tccctttgtttctctttctttctttctttctctctctcttccttccttccctccctccct +ccctccttcctcccttctttccttccctccctgcctctctgtctccctctttctttctct +tttttcttttccttccttccgtctttttcctcccttctttcctccctcctccctccctcc +ctcctccctctttttctttctttctttcttttttctctctctcttctttttttttttttt +tttttaagagatagggtctgttgcccaggctggagtgcagtggcatgatcatggttcact +gcagccttgaactcctgggctcaggtgatcctcctacctcagcctcctaagtagctggga +ctataggtgcatgccatcacacccagctaattttttaaaagaaattttgtaaagacaggg +gtcttgctatgttccccaggctagtctcaaactcctgggctcaagtgatcctccagcctc +agtatcccaaagtgctgggattataggtgtgagtcactgcagccagctcaaatattttct +taaatgaatgtaaggttgaggatgcattattataatggctaatttagatctaaaaaatgc +tttgcagtttaccagattcacttatgtacattctc +>p:HG002_2_chr20:2240825-2241827 +gtgacccttaggtaaatcgttccaactctctgagcctcagtgttgttatctacaaatggg +agaatcaaggcaccctcctacaagcggcggctcatcagctcacttggaaaatgtagtcat +cttctcaaagttttctttttctttctttctttttcctttctttctttctttttctttctt +tctctctctctccttccttccttctttccttccctccctcccttccttttttcttctttc +tttcattttctttctttctctctttcttctttctcttcctttctt--------------- +-------------------------------------------c--tttcttttcctcct +tcctcccttctttccttcccttccttcttccctccctccctctttgtttctttctttctc +tccctc-----------------------------------cttccctccctccctttct +ttctcctt-----------ttcttccttccctccctgcctgtctccctctttctttctct +tttttcttttccttccttccgtctttttcctcccttctttcctccctcctccctccctcc +ctcctccctctttttctttctttctttcttttttctttctctcttc-ttttttttttttt +tttttaagagatagggtctgttgcccaggctggagtgcagtggcatgatcatggttcact +gcagccttgaactcctgggctcaggtgatcctcctacctcagcctcctaagtagctggga +ctataggtgcatgccatcacacccagctaattttttaaaagaaattttgtaaagacaggg +gtcttgctatgttccccaggctggtctcaaactcctgggctcaagtgatcctccagcctc +agtatcccaaagtgctgggattataggtgtgagtcactgcagccagctcaaatattttct +taaatgaatgtaaggttgaggatgcattattataatggctaatttagatctaaaaaatgc +tttgcagtttaccagattcacttatgtacattctc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/msa.fa.fai new file mode 100644 index 00000000..216b9d85 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_2240825_2241827 1055 27 60 61 +syndip_1_chr20:2240825-2241827 1055 1132 60 61 +syndip_2_chr20:2240825-2241827 1055 2237 60 61 +p:HG002_1_chr20:2240825-2241827 1055 3343 60 61 +p:HG002_2_chr20:2240825-2241827 1055 4449 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/output.vcf.gz new file mode 100644 index 00000000..3f32f4f0 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/output.vcf.gz.tbi new file mode 100644 index 00000000..8c55bac8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:2240925-2241727/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/base.vcf.gz new file mode 100644 index 00000000..7c98d94a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/base.vcf.gz.tbi new file mode 100644 index 00000000..2eb9fbe1 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/comp.vcf.gz new file mode 100644 index 00000000..749edde3 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/comp.vcf.gz.tbi new file mode 100644 index 00000000..dcb9c8cc Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/haps.fa new file mode 100644 index 00000000..5e387a1b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/haps.fa @@ -0,0 +1,68 @@ +>ref_chr20_23155404_23156076 +GGGAAAGACACAGAGGTAGAATCTGCGTTAGGAATAAAAACCGCTACTCTCCGTTGTTCTGTGTGCTTTTGCAGTCATGATTGATGCAGGCAGCACCCTTCTGCAGAAGTAAATTTTGCCCTGCAGCACAAAAGAGGAAGGAAAGCAAGGGAAGGGAAGGGGAGGGGAGGAAGGGAAGGAAAAGAGAGAGAAAGAGAAAGAGAGAAAGAGAGGAAGGAAGGAAGGAAGGAGAGAGAGAAAGAAAGAAGGAAAGAGGAAGGAAGGAAGAAAGAAAAGAAAGAAAGAAAAAAGAAAGAAAGGAAGGAGAGAAAGAAATGAAAGAGAAAGAAAGAAAGAAAGAAAGAAAGGAGAGAAAAAGGAAAAACAAAGAAAGAGAAAAGAAGGAGAGAAGGAAAGGAAAAAGAAAGAAAGAAGGAAAGAAAGAAAAAAGAAGGAAAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAAAGAGAAAGGAAGGAAGGAAGGAAGGTCTTAACACCTTGGTAATTTTTGTGCTCTTCCCTGGACTTTGGACTTTGCAGCCTTAGGGAGACAGAGCTCTTTAATGTACACTTTCCCATCAGGCACTGCATGGCCAAGAACCTGCCTGCAAAGCCCCCA +>syndip_1_chr20:23155404-23156076 +GGGAAAGACACAGAGGTAGAATCTGCGTTAGGAATAAAAACCGCTACTCTCCGTTGTTCT +GTGTGCTTTTGCAGTCATGATTGATGCAGGCAGCACCCTTCTGCAGAAGTAAATTTTGCC +CTGCAGCACAAAAGAGGAAGGAAAGCAAGGGAAGGGAAGGGGAGGGGAGGAAGGGAAGGG +GAGGGGAGGAAGGGAAGGGGAGGGGAGGAAGGCGAGGTGAGGGGAGGAGAGGTGAGGGGA +GGGGGGGAGGGGAGGGGAGGGAGAGTGAGGAAGAGAGAGAGAAAGGGAGAGAGGAAGGAA +AGAAGAAAGGAAGGAAGGAAAGAAGGAAGGAAGGGAGGGAGGGAGGGAGGAAAGAAGGAA +GGAAAGGAGGGAGGAAGGGAGGGAAAGAGAGAGAGAGGAAAAGAGAGAGAAAGAGAAAGA +GAGAAAGAGAGGAAGGAAGGAAGGAAGGAGAGAGAGAAAGAAAGAAGGAAAGAGGAAGGA +AGGAAGAAAGAAAAGAAAGAAAGAAAAAAGAAAGAAAGGAAGGAGAGAAAGAAATGAAAG +AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGGAGAGAAAAAGGAAAAACAAAGAAAG +AGAAAAGAAGGAGAGAAGGAAAGGAAAAAGAAAGAAAGAAGGAAAGAAAGAAAAAAGAAG +GAAAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG +AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAAAGAGAAAGGAAGGAAGGAAGGAAG +GTCTTAACACCTTGGTAATTTTTGTGCTCTTCCCTGGACTTTGGACTTTGCAGCCTTAGG +GAGACAGAGCTCTTTAATGTACACTTTCCCATCAGGCACTGCATGGCCAAGAACCTGCCT +GCAAAGCCCCCA +>syndip_2_chr20:23155404-23156076 +GGGAAAGACACAGAGGTAGAATCTGCGTTAGGAATAAAAACCGCTACTCTCCGTTGTTCT +GTGTGCTTTTGCAGTCATGATTGATGCAGGCAGCACCCTTCTGCAGAAGTAAATTTTGCC +CTGCAGCACAAAAGAGGAAGGAAAGCAAGGGAAGGGAAGGGGAGGGGAGGAAGGGAAGGG +GAGGGGAGGAAGGCGAGGTGAGGGGAGGAGAGGTGAGGGGAGGGGGGGAGGGGAGGGGAG +GGAGAGTGAGGAAGAGAGAGAGAAAGGGAGAGAGGAAGGAAAGAAGAAAGGAAGGAAGGA +AAGAAGGAAGGAAGGGAGGGAGGGAGGGAGGAAAGAAGGAAGGAAAGGAGGGAGGAAGGG +AGGGAAAGAGAGAGAGAGGAAAAGAGAGAGAAAGAGAAAGAGAGAAAGAGAGGAAGGAAG +GAAGGAAGGAGAGAGAGAAAGAAAGAAGGAAAGAGGAAGGAAGGAAGAAAGAAAAGAAAG +AAAGAAAAAAGAAAGAAAGGAAGGAGAGAAAGAAATGAAAGAGAAAGAAAGAAAGAAAGA +AAGAAAGAAAGGAGAGAAAAAGGAAAAACAAAGAAAGAGAAAAGAAGGAGAGAAGGAAAG +GAAAAAGAAAGAAAGAAGGAAAGAAAGAAAAAAGAAGGAAAGAAAGAAGAAAGAAAGAAA +GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAAAGAGAAAGGAA +GGAAGGAAGGAAGGTCTTAACACCTTGGTAATTTTTGTGCTCTTCCCTGGACTTTGGACT +TTGCAGCCTTAGGGAGACAGAGCTCTTTAATGTACACTTTCCCATCAGGCACTGCATGGC +CAAGAACCTGCCTGCAAAGCCCCCA +>p:HG002_1_chr20:23155404-23156076 +GGGAAAGACACAGAGGTAGAATCTGCGTTAGGAATAAAAACCGCTACTCTCCGTTGTTCT +GTGTGCTTTTGCAGTCATGATTGATGCAGGCAGCACCCTTCTGCAGAAGTAAATTTTGCC +CTGCAGCACAAAAGAGGAAGGAAAGCAAGGGAAGGGAAGGGGAGGGGAGGAAGGGAAGGG +GAGGGGAGGAAGGCGAGGTGAGGGGAGGAGAGGTGAGGGGAGGGGGGGAGGGGAGGGGAG +GGAGAGTGAGGAAGAGAGAGAGAAAGGGAGAGAGGAAGGAAAGAAGAAAGGAAGGAAGGA +AAGAAGGAAGGAAGGGAGGGAGGGAGGGAGGAAAGAAGGAAGGAAAGGAGGGAGGAAGGG +AGGGAAAGAGAGAGAGAGGAAAAGAGAGAGAAAGAGAAAGAGAGAAAGAGAGGAAGGAAG +GAAGGAAGGAGAGAGAGAAAGAAAGAAGGAAAGAGGAAGGAAGGAAGAAAGAAAAGAAAG +AAAGAAAAAAGAAAGAAAGGAAGGAGAGAAAGAAATGAAAGAGAAAGAAAGAAAGAAAGA +AAGAAAGAAAGGAGAGAAAAAGGAAAAACAAAGAAAGAGAAAAGAAGGAGAGAAGGAAAG +GAAAAAGAAAGAAAGAAGGAAAGAAAGAAAAAAGAAGGAAAGAAAGAAGAAAGAAAGAAA +GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAAAGAGAAAGGAA +GGAAGGAAGGAAGGTCTTAACACCTTGGTAATTTTTGTGCTCTTCCCTGGACTTTGGACT +TTGCAGCCTTAGGGAGACAGAGCTCTTTAATGTACACTTTCCCATCAGGCACTGCATGGC +CAAGAACCTGCCTGCAAAGCCCCCA +>p:HG002_2_chr20:23155404-23156076 +GGGAAAGACACAGAGGTAGAATCTGCGTTAGGAATAAAAACCGCTACTCTCCGTTGTTCT +GTGTGCTTTTGCAGTCATGATTGATGCAGGCAGCACCCTTCTGCAGAAGTAAATTTTGCC +CTGCAGCACAAAAGAGGAAGGAAAGCAAGGGAAGGGAAGGGGAGGGGAGGAAGGGAAGGG +GAGGGGAGGAAGGGAAGGGGAGGGGAGGAAGGCGAGGTGAGGGGAGGAGAGGTGAGGGGA +GGGGGGGAGGGGAGGGGAGGGAGAGTGAGGAAGAGAGAGAGAAAGGGAGAGAGGAAGGAA +AGAAGAAAGGAAGGAAGGAAAGAAGGAAGGAAGGGAGGGAGGGAGGGAGGAAAGAAGGAA +GGAAAGGAGGGAGGAAGGGAGGGAAAGAGAGAGAGAGGAAAAGAGAGAGAAAGAGAAAGA +GAGAAAGAGAGGAAGGAAGGAAGGAAGGAGAGAGAGAAAGAAAGAAGGAAAGAGGAAGGA +AGGAAGAAAGAAAAGAAAGAAAGAAAAAAGAAAGAAAGGAAGGAGAGAAAGAAATGAAAG +AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGGAGAGAAAAAGGAAAAACAAAGAAAG +AGAAAAGAAGGAGAGAAGGAAAGGAAAAAGAAAGAAAGAAGGAAAGAAAGAAAAAAGAAG +GAAAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG +AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAAAGAGAAAGGAAGGAAGGAAGGAAG +GTCTTAACACCTTGGTAATTTTTGTGCTCTTCCCTGGACTTTGGACTTTGCAGCCTTAGG +GAGACAGAGCTCTTTAATGTACACTTTCCCATCAGGCACTGCATGGCCAAGAACCTGCCT +GCAAAGCCCCCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/haps.fa.ref.fa new file mode 100644 index 00000000..74c4f4f3 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:23155404-23156076 +GGGAAAGACACAGAGGTAGAATCTGCGTTAGGAATAAAAACCGCTACTCTCCGTTGTTCTGTGTGCTTTTGCAGTCATGATTGATGCAGGCAGCACCCTTCTGCAGAAGTAAATTTTGCCCTGCAGCACAAAAGAGGAAGGAAAGCAAGGGAAGGGAAGGGGAGGGGAGGAAGGGAAGGAAAAGAGAGAGAAAGAGAAAGAGAGAAAGAGAGGAAGGAAGGAAGGAAGGAGAGAGAGAAAGAAAGAAGGAAAGAGGAAGGAAGGAAGAAAGAAAAGAAAGAAAGAAAAAAGAAAGAAAGGAAGGAGAGAAAGAAATGAAAGAGAAAGAAAGAAAGAAAGAAAGAAAGGAGAGAAAAAGGAAAAACAAAGAAAGAGAAAAGAAGGAGAGAAGGAAAGGAAAAAGAAAGAAAGAAGGAAAGAAAGAAAAAAGAAGGAAAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAAAGAGAAAGGAAGGAAGGAAGGAAGGTCTTAACACCTTGGTAATTTTTGTGCTCTTCCCTGGACTTTGGACTTTGCAGCCTTAGGGAGACAGAGCTCTTTAATGTACACTTTCCCATCAGGCACTGCATGGCCAAGAACCTGCCTGCAAAGCCCCCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/msa.fa new file mode 100644 index 00000000..c61ccc31 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/msa.fa @@ -0,0 +1,85 @@ +>ref_chr20_23155404_23156076 +gggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttct +gtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgcc +ctgcagcacaaaagaggaaggaaagcaag-------------------ggaagggaaggg +gaggggaggaaggga--------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------aggaaaagagagagaaagagaaaga +gagaaagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaagga +aggaagaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag +--------agaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaag +agaaaagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaag +gaaagaaag------------aagaaagaaagaaagaaagaaagaaagaaagaaagaaag +aaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaag +gtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttagg +gagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcct +gcaaagccccca +>syndip_1_chr20:23155404-23156076 +gggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttct +gtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgcc +ctgcagcacaaaagaggaaggaaagcaagggaagggaaggggaggggaggaagggaaggg +gaggggaggaagggaaggggaggggaggaaggcgaggtgaggggaggagaggtgagggga +gggggggaggggaggggagggagagtgaggaagagagagagaaagggagagaggaaggaa +agaagaaaggaaggaaggaaagaaggaaggaagggagggagggagggaggaaagaaggaa +ggaaaggagggaggaagggagggaaagagagagagaggaaaagagagagaaagagaaaga +gagaaagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaagga +aggaagaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag +agaaagaaagaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaag +agaaaagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaag +gaaagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag +aaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaag +gtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttagg +gagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcct +gcaaagccccca +>syndip_2_chr20:23155404-23156076 +gggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttct +gtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgcc +ctgcagcacaaaagaggaaggaaagcaag-------------------ggaagggaaggg +gaggggaggaagggaaggggaggggaggaaggcgaggtgaggggaggagaggtgagggga +gggggggaggggaggggagggagagtgaggaagagagagagaaagggagagaggaaggaa +agaagaaaggaaggaaggaaagaaggaaggaagggagggagggagggaggaaagaaggaa +ggaaaggagggaggaagggagggaaagagagagagaggaaaagagagagaaagagaaaga +gagaaagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaagga +aggaagaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag +----agaaagaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaag +agaaaagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaag +gaaagaaag------------------------aagaaagaaagaaagaaagaaagaaag +aaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaag +gtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttagg +gagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcct +gcaaagccccca +>p:HG002_1_chr20:23155404-23156076 +gggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttct +gtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgcc +ctgcagcacaaaagaggaaggaaagcaag-------------------ggaagggaaggg +gaggggaggaagggaaggggaggggaggaaggcgaggtgaggggaggagaggtgagggga +gggggggaggggaggggagggagagtgaggaagagagagagaaagggagagaggaaggaa +agaagaaaggaaggaaggaaagaaggaaggaagggagggagggagggaggaaagaaggaa +ggaaaggagggaggaagggagggaaagagagagagaggaaaagagagagaaagagaaaga +gagaaagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaagga +aggaagaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag +----agaaagaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaag +agaaaagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaag +gaaagaaag------------------------aagaaagaaagaaagaaagaaagaaag +aaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaag +gtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttagg +gagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcct +gcaaagccccca +>p:HG002_2_chr20:23155404-23156076 +gggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttct +gtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgcc +ctgcagcacaaaagaggaaggaaagcaagggaagggaaggggaggggaggaagggaaggg +gaggggaggaagggaaggggaggggaggaaggcgaggtgaggggaggagaggtgagggga +gggggggaggggaggggagggagagtgaggaagagagagagaaagggagagaggaaggaa +agaagaaaggaaggaaggaaagaaggaaggaagggagggagggagggaggaaagaaggaa +ggaaaggagggaggaagggagggaaagagagagagaggaaaagagagagaaagagaaaga +gagaaagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaagga +aggaagaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag +agaaagaaagaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaag +agaaaagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaag +gaaagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag +aaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaag +gtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttagg +gagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcct +gcaaagccccca diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/msa.fa.fai new file mode 100644 index 00000000..bc806fd7 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_23155404_23156076 912 29 60 61 +syndip_1_chr20:23155404-23156076 912 991 60 61 +syndip_2_chr20:23155404-23156076 912 1953 60 61 +p:HG002_1_chr20:23155404-23156076 912 2916 60 61 +p:HG002_2_chr20:23155404-23156076 912 3879 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/output.vcf.gz new file mode 100644 index 00000000..cac67760 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/output.vcf.gz.tbi new file mode 100644 index 00000000..153058e9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23155504-23155976/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/base.vcf.gz new file mode 100644 index 00000000..038ee1bf Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/base.vcf.gz.tbi new file mode 100644 index 00000000..5f7ff992 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/comp.vcf.gz new file mode 100644 index 00000000..6a24eab2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/comp.vcf.gz.tbi new file mode 100644 index 00000000..18786028 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/haps.fa new file mode 100644 index 00000000..7395e813 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/haps.fa @@ -0,0 +1,38 @@ +>ref_chr20_23560783_23561292 +TAAAATCTTCATACAGAAGATATAAGAGATTTGCAAATTACCGTTATAGTATTAGAGTATTCTGAATGTCAGTATGTACTTAGTTTCACTAGGGAGATTTTTATTCCCTAATGTTCTTCAGCATTCCTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCCTTCTTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTCTTTCTTTCTTTTTCTTTTACAGAGTCTTACTCTTGTTGCCCAGGCTGTAGTGCAGTGGTGTGATCTCGGCTCACTGCAACCTCCACCTCTGCCTCCTGCATTCAAGAAATTCTCCTGCCTCAGCCTCCAGAGTAGCTGGGAT +>syndip_1_chr20:23560783-23561292 +TAAAATCTTCATACAGAAGATATAAGAGATTTGCAAATTACCGTTATAGTATTAGAGTAT +TCTGAATGTCAGTATGTACTTAGTTTCACTAGGGAGATTTTTATTCCCTAATGTTCTTCA +GCATTCCTTTCTCTCTCTTTCTTTCTTTCTTTCTTTCTTTCCTTCCTTCCTTCCTTCCTT +CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT +TCTTTCTTTTTTTCTTTCTTTCTTTCTTTCTTTTTCTTTTACAGAGTCTTACTCTTGTTG +CCCAGGCTGTAGTGCAGTGGTGTGATCTCGGCTCACTGCAACCTCCACCTCTGCCTCCTG +CATTCAAGAAATTCTCCTGCCTCAGCCTCCAGAGTAGCTGGGAT +>syndip_2_chr20:23560783-23561292 +TAAAATCTTCATACAGAAGATATAAGAGATTTGCAAATTACCGTTATAGTATTAGAGTAT +TCTGAATGTCAGTATGTACTTAGTTTCACTAGGGAGATTTTTATTCCCTAATGTTCTTCA +GCATTCCTTTCTCTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT +CTTTCTTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCTTTCCTT +CTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTT +CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT +CTTTCTTTCTTTCTTTCTTCTTTCTTTCTTTTTCTTTTACAGAGTCTTACTCTTGTTGCC +CAGGCTGTAGTGCAGTGGTGTGATCTCGGCTCACTGCAACCTCCACCTCTGCCTCCTGCA +TTCAAGAAATTCTCCTGCCTCAGCCTCCAGAGTAGCTGGGAT +>p:HG002_1_chr20:23560783-23561292 +TAAAATCTTCATACAGAAGATATAAGAGATTTGCAAATTACCGTTATAGTATTAGAGTAT +TCTGAATGTCAGTATGTACTTAGTTTCACTAGGGAGATTTTTATTCCCTAATGTTCTTCA +GCATTCCTTTCTCTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT +CTTTCTTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCTTTCCTT +CTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTT +CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT +CTTTCTTTCTTTCTTTCTTCTTTCTTTCTTTTTCTTTTACAGAGTCTTACTCTTGTTGCC +CAGGCTGTAGTGCAGTGGTGTGATCTCGGCTCACTGCAACCTCCACCTCTGCCTCCTGCA +TTCAAGAAATTCTCCTGCCTCAGCCTCCAGAGTAGCTGGGAT +>p:HG002_2_chr20:23560783-23561292 +TAAAATCTTCATACAGAAGATATAAGAGATTTGCAAATTACCGTTATAGTATTAGAGTAT +TCTGAATGTCAGTATGTACTTAGTTTCACTAGGGAGATTTTTATTCCCTAATGTTCTTCA +GCATTCCTTTCTCTCTCTTTCTTTCTTTCTTTCTTTCTTTCCTTCCTTCCTTCCTTCCTT +CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT +TCTTTCTTTTTTTCTTTCTTTCTTTCTTTCTTTTTCTTTTACAGAGTCTTACTCTTGTTG +CCCAGGCTGTAGTGCAGTGGTGTGATCTCGGCTCACTGCAACCTCCACCTCTGCCTCCTG +CATTCAAGAAATTCTCCTGCCTCAGCCTCCAGAGTAGCTGGGAT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/haps.fa.ref.fa new file mode 100644 index 00000000..2375f67a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:23560783-23561292 +TAAAATCTTCATACAGAAGATATAAGAGATTTGCAAATTACCGTTATAGTATTAGAGTATTCTGAATGTCAGTATGTACTTAGTTTCACTAGGGAGATTTTTATTCCCTAATGTTCTTCAGCATTCCTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCCTTCTTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTCTTTCTTTCTTTTTCTTTTACAGAGTCTTACTCTTGTTGCCCAGGCTGTAGTGCAGTGGTGTGATCTCGGCTCACTGCAACCTCCACCTCTGCCTCCTGCATTCAAGAAATTCTCCTGCCTCAGCCTCCAGAGTAGCTGGGAT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/msa.fa new file mode 100644 index 00000000..360a2abb --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/msa.fa @@ -0,0 +1,50 @@ +>ref_chr20_23560783_23561292 +taaaatcttcatacagaagatataagagatttgcaaattaccgttatagtattagagtat +tctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttcttca +gcattcctttctctttctttctttctttctttctttctttctttctttctttctttcctt +ctttccttccttccttccttccttccttccttccttccttccttccttccttccttcctt +ctttccttctttccttctttccttctttccttctttccttctttccttctttcc------ +------ttctttccttctttccttctttctttctttctttctttctttctttctttcttt +ctttctttctttctttcttctttctttctttttcttttacagagtcttactcttgttgcc +caggctgtagtgcagtggtgtgatctcggctcactgcaacctccacctctgcctcctgca +ttcaagaaattctcctgcctcagcctccagagtagctgggat +>syndip_1_chr20:23560783-23561292 +taaaatcttcatacagaagatataagagatttgcaaattaccgttatagtattagagtat +tctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttcttca +gcattcctttctctctctttctttctttctttctttctttccttccttccttccttcctt +ccttccttccttccttccttccttccttcct----------------------------- +------------------------------------------------------------ +----------------------ttctttctttctttctttctttctttctttctttcttt +ttttctttct-------ttctttctttctttttcttttacagagtcttactcttgttgcc +caggctgtagtgcagtggtgtgatctcggctcactgcaacctccacctctgcctcctgca +ttcaagaaattctcctgcctcagcctccagagtagctgggat +>syndip_2_chr20:23560783-23561292 +taaaatcttcatacagaagatataagagatttgcaaattaccgttatagtattagagtat +tctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttcttca +gcattcctttctctctctttctttctttctttctttctttctttctttctttctttcttt +ctttctttccttccttccttccttccttccttccttccttccttccttccttctttcctt +ctttccttctttccttctttccttctttccttctttccttctttccttctttccttcttt +ctttctttctttctttctttctttctttctttctttctttctttctttctttctttcttt +ctttctttctttctttcttctttctttctttttcttttacagagtcttactcttgttgcc +caggctgtagtgcagtggtgtgatctcggctcactgcaacctccacctctgcctcctgca +ttcaagaaattctcctgcctcagcctccagagtagctgggat +>p:HG002_1_chr20:23560783-23561292 +taaaatcttcatacagaagatataagagatttgcaaattaccgttatagtattagagtat +tctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttcttca +gcattcctttctctctctttctttctttctttctttctttctttctttctttctttcttt +ctttctttccttccttccttccttccttccttccttccttccttccttccttctttcctt +ctttccttctttccttctttccttctttccttctttccttctttccttctttccttcttt +ctttctttctttctttctttctttctttctttctttctttctttctttctttctttcttt +ctttctttctttctttcttctttctttctttttcttttacagagtcttactcttgttgcc +caggctgtagtgcagtggtgtgatctcggctcactgcaacctccacctctgcctcctgca +ttcaagaaattctcctgcctcagcctccagagtagctgggat +>p:HG002_2_chr20:23560783-23561292 +taaaatcttcatacagaagatataagagatttgcaaattaccgttatagtattagagtat +tctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttcttca +gcattcctttctctctctttctttctttctttctttctttccttccttccttccttcctt +ccttccttccttccttccttccttccttcct----------------------------- +------------------------------------------------------------ +----------------------ttctttctttctttctttctttctttctttctttcttt +ttttctttct-------ttctttctttctttttcttttacagagtcttactcttgttgcc +caggctgtagtgcagtggtgtgatctcggctcactgcaacctccacctctgcctcctgca +ttcaagaaattctcctgcctcagcctccagagtagctgggat diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/msa.fa.fai new file mode 100644 index 00000000..efb04c69 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_23560783_23561292 522 29 60 61 +syndip_1_chr20:23560783-23561292 522 594 60 61 +syndip_2_chr20:23560783-23561292 522 1159 60 61 +p:HG002_1_chr20:23560783-23561292 522 1725 60 61 +p:HG002_2_chr20:23560783-23561292 522 2291 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/output.vcf.gz new file mode 100644 index 00000000..04efc8e2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/output.vcf.gz.tbi new file mode 100644 index 00000000..78661e86 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:23560883-23561192/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/base.vcf.gz new file mode 100644 index 00000000..d8f012d8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/base.vcf.gz.tbi new file mode 100644 index 00000000..05b5a483 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/comp.vcf.gz new file mode 100644 index 00000000..f2a63224 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/comp.vcf.gz.tbi new file mode 100644 index 00000000..ffb781c4 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/haps.fa new file mode 100644 index 00000000..9450c866 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/haps.fa @@ -0,0 +1,78 @@ +>ref_chr20_24407883_24409098 +CTCAGTTTATTCATCTATAAAACAGATGTGGCAGTGGTAGTGCCACAATTCACAGCCCAGTTCCACCTTCCTCACAGGCTCGTGATAAAGCTCCATTTCCTACCCTTCCTCTCAGTTATGTTGGAGCCACAGGAGGTGATATAGGGTGCTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGAGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGTTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGAGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTAGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCTTGGCCATCTCCTCTCCTTTAAGATACCTACACTTGTTCTTTCCCACCCACAACTGTATCAGTCAGCTTTTACTGAATAACAAAGCACCCCTAACCTCAGTGCATGATGAAACCCTGTCTCTACTAAAAGCACAAAAAT +>syndip_1_chr20:24407883-24409098 +CTCAGTTTATTCATCTATAAAACAGATGTGGCAGTGGTAGTGCCACAATTCACAGCCCAG +TTCCACCTTCCTCACAGGCTCGTGATAAAGCTCCATTTCCTACCCTTCCTCTCAGTTATG +TTGGAGCCACAGGAGGTGATATAGGGTGCTTCCGGCCCTGGCCATAGGGTACTTCTGGGA +GGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTA +TTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCTTGGC +CATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCT +GGGAGGAGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAG +GGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCT +TGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCCTGGCCATAGGGTAC +TTCTAGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGAT +ATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCA +GCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGG +TACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGT +GATATAGGATACTTCCAGCCTTGGCCATCTCCTCTCCTTTAAGATACCTACACTTGTTCT +TTCCCACCCACAACTGTATCAGTCAGCTTTTACTGAATAACAAAGCACCCCTAACCTCAG +TGCATGATGAAACCCTGTCTCTACTAAAAGCACAAAAAT +>syndip_2_chr20:24407883-24409098 +CTCAGTTTATTCATCTATAAAACAGATGTGGCAGTGGTAGTGCCACAATTCACAGCCCAG +TTCCACCTTCCTCACAGGCTCGTGATAAAGCTCCATTTCCTACCCTTCCTCTCAGTTATG +TTGGAGCCACAGGAGGTGATATAGGGTGCTTCCAGCCCTGGCCATAGGGTACTTCTGGGA +GGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTA +TTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCTTGGC +CATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCT +GGGAGGAGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAG +GGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCT +TGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCTTGGCCATAGGGTAC +TTCTGGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGAGAT +ATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCA +GCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGG +GTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTAGGAGG +TGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACT +TCCAGCCCTGGCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCAT +AGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGG +AGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGAT +ACTTCCAGCCTTGGCCATCTCCTCTCCTTTAAGATACCTACACTTGTTCTTTCCCACCCA +CAACTGTATCAGTCAGCTTTTACTGAATAACAAAGCACCCCTAACCTCAGTGCATGATGA +AACCCTGTCTCTACTAAAAGCACAAAAAT +>p:HG002_1_chr20:24407883-24409098 +CTCAGTTTATTCATCTATAAAACAGATGTGGCAGTGGTAGTGCCACAATTCACAGCCCAG +TTCCACCTTCCTCACAGGCTCGTGATAAAGCTCCATTTCCTACCCTTCCTCTCAGTTATG +TTGGAGCCACAGGAGGTGATATAGGGTGCTTCCAGCCCTGGCCATAGGGTACTTCTGGGA +GGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTA +TTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCTTGGC +CATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCT +GGGAGGAGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAG +GGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCT +TGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCTTGGCCATAGGGTAC +TTCTGGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGAGAT +ATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCA +GCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGG +GTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTAGGAGG +TGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACT +TCCAGCCCTGGCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCAT +AGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGG +AGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGAT +ACTTCCAGCCTTGGCCATCTCCTCTCCTTTAAGATACCTACACTTGTTCTTTCCCACCCA +CAACTGTATCAGTCAGCTTTTACTGAATAACAAAGCACCCCTAACCTCAGTGCATGATGA +AACCCTGTCTCTACTAAAAGCACAAAAAT +>p:HG002_2_chr20:24407883-24409098 +CTCAGTTTATTCATCTATAAAACAGATGTGGCAGTGGTAGTGCCACAATTCACAGCCCAG +TTCCACCTTCCTCACAGGCTCGTGATAAAGCTCCATTTCCTACCCTTCCTCTCAGTTATG +TTGGAGCCACAGGAGGTGATATAGGGTGCTTCCGGCCCTGGCCATAGGGTACTTCTGGGA +GGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTA +TTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCTTGGC +CATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCT +GGGAGGAGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAG +GGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCT +TGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCCTGGCCATAGGGTAC +TTCTAGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGAT +ATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCA +GCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGG +TACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGT +GATATAGGATACTTCCAGCCTTGGCCATCTCCTCTCCTTTAAGATACCTACACTTGTTCT +TTCCCACCCACAACTGTATCAGTCAGCTTTTACTGAATAACAAAGCACCCCTAACCTCAG +TGCATGATGAAACCCTGTCTCTACTAAAAGCACAAAAAT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/haps.fa.ref.fa new file mode 100644 index 00000000..382d8a68 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:24407883-24409098 +CTCAGTTTATTCATCTATAAAACAGATGTGGCAGTGGTAGTGCCACAATTCACAGCCCAGTTCCACCTTCCTCACAGGCTCGTGATAAAGCTCCATTTCCTACCCTTCCTCTCAGTTATGTTGGAGCCACAGGAGGTGATATAGGGTGCTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGAGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGTTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGAGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTAGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCTTGGCCATCTCCTCTCCTTTAAGATACCTACACTTGTTCTTTCCCACCCACAACTGTATCAGTCAGCTTTTACTGAATAACAAAGCACCCCTAACCTCAGTGCATGATGAAACCCTGTCTCTACTAAAAGCACAAAAAT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/msa.fa new file mode 100644 index 00000000..5cf5e356 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/msa.fa @@ -0,0 +1,110 @@ +>ref_chr20_24407883_24409098 +ctcagtttattcatctataaaacagatgtggcagtggtagtgccacaattcacagcccag +ttccaccttcctcacaggctcgtgataaagctccatttcctacccttcctctcagttatg +ttggagccacaggaggtgatatagggtgcttccagccctggccatagggtacttctggga +ggtgatatagggtatttccagccttggccatagggtacttctgggaggtgatatagggta +cttccagccttggccatagggtacttctgggaggtgatatagggtacttccagccttggc +catagggtacttctgggaggtgatatagggtacttccagccctggccatagggtacttct +gggaggagatatagggtatttccagccttggccatagggtacttctgggaggtgatatag +gttatttccagccttggccatagggtacttctgggaggtgatatagggtatttccagcct +tggccatagggtacttctgggaggtgatatagggtacttccagccctggccatagggtac +ttctgggaggtgatatagggtacttccagccctggccatagggtacttctgggaggagat +atagggtatttccagccttggccatagggtacttctgggaggtgatatagggtatttcca +gccttggccatagggtacttctgggaggtgatatagggtatttccagccttggccatagg +gtacttctgggaggtgatatagggtatttccagccttggccatagggtacttctaggagg +tgatatagggtacttccagccctggccatagggtacttctgggaggtgatataggatact +tccagccctggccatagggtacttctgggaggtgatataggatacttccagccctggcca +tagggtacttctgggaggtgatataggatacttccagccctggccatagggtacttctgg +gaggtgatataggatacttccagccctggccatagggtacttctgggaggtgatatagga +tacttccagccctggccatagggtacttctgggaggtgatataggatacttccagccttg +gccatctcctctcctttaagatacctacacttgttctttcccacccacaactgtatcagt +cagcttttactgaataacaaagcacccctaacctcagtgcatgatgaaaccctgtctcta +ctaaaagcacaaaaat +>syndip_1_chr20:24407883-24409098 +ctcagtttattcatctataaaacagatgtggcagtggtagtgccacaattcacagcccag +ttccaccttcctcacaggctcgtgataaagctccatttcctacccttcctctcagttatg +ttggagccacaggaggtgatatagggtgcttccggccctggccatagggtacttctggga +ggtgatatagggtatttccagccttggccatagggtacttctgggaggtgatatagggta +tttccagccttggccatagggtacttctgggaggtgatatagggtacttccagccttggc +catagggtacttctgggaggtgatatagggtacttccagccctggccatagggtacttct +gggaggagatatagggtatttccagccttggccatagggtacttctgggaggtgatatag +ggtatttccagccttggccatagggtacttctgggaggtgatatagggtatttccagcct +tggccatagggtacttctgggaggtgatatagggtatttccagccctggccatagggtac +ttctaggaggtgatatagggtacttccagccctggccatagggtacttctgggaggtgat +ataggatacttccagccctggccatagggtacttctgggaggtgatataggatacttcca +g----------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------cctggccatagggtacttctgg +gaggtgatataggatacttccagccctggccatagggtacttctgggaggtgatatagga +tacttccagccctggccatagggtacttctgggaggtgatataggatacttccagccttg +gccatctcctctcctttaagatacctacacttgttctttcccacccacaactgtatcagt +cagcttttactgaataacaaagcacccctaacctcagtgcatgatgaaaccctgtctcta +ctaaaagcacaaaaat +>syndip_2_chr20:24407883-24409098 +ctcagtttattcatctataaaacagatgtggcagtggtagtgccacaattcacagcccag +ttccaccttcctcacaggctcgtgataaagctccatttcctacccttcctctcagttatg +ttggagccacaggaggtgatatagggtgcttccagccctggccatagggtacttctggga +ggtgatatagggtatttccagccttggccatagggtacttctgggaggtgatatagggta +tttccagccttggccatagggtacttctgggaggtgatatagggtacttccagccttggc +catagggtacttctgggaggtgatatagggtacttccagccctggccatagggtacttct +gggaggagatatagggtatttccagccttggccatagggtacttctgggaggtgatatag +ggtatttccagccttggccatagggtacttctgggaggtgatatagggtatttccagcct +tggccatagggtacttctgggaggtgatatagggtacttccagccttggccatagggtac +ttctgggaggtgatatagggtacttccagccctggccatagggtacttctgggaggagat +atagggtatttccagccttggccatagggtacttctgggaggtgatatagggtatttcca +gccttggccatagggtacttctgggaggtgatatagggtatttccagccttggccatagg +gtacttctgggaggtgatatagggtatttccagccttggccatagggtacttctaggagg +tgatatagggtacttccagccctggccatagggtacttctgggaggtgatataggatact +tccagccctgg-----------------------------------------------ca +tagggtacttctgggaggtgatataggatacttccagccctggccatagggtacttctgg +gaggtgatataggatacttccagccctggccatagggtacttctgggaggtgatatagga +tacttccagccctggccatagggtacttctgggaggtgatataggatacttccagccttg +gccatctcctctcctttaagatacctacacttgttctttcccacccacaactgtatcagt +cagcttttactgaataacaaagcacccctaacctcagtgcatgatgaaaccctgtctcta +ctaaaagcacaaaaat +>p:HG002_1_chr20:24407883-24409098 +ctcagtttattcatctataaaacagatgtggcagtggtagtgccacaattcacagcccag +ttccaccttcctcacaggctcgtgataaagctccatttcctacccttcctctcagttatg +ttggagccacaggaggtgatatagggtgcttccagccctggccatagggtacttctggga +ggtgatatagggtatttccagccttggccatagggtacttctgggaggtgatatagggta +tttccagccttggccatagggtacttctgggaggtgatatagggtacttccagccttggc +catagggtacttctgggaggtgatatagggtacttccagccctggccatagggtacttct +gggaggagatatagggtatttccagccttggccatagggtacttctgggaggtgatatag +ggtatttccagccttggccatagggtacttctgggaggtgatatagggtatttccagcct +tggccatagggtacttctgggaggtgatatagggtacttccagccttggccatagggtac +ttctgggaggtgatatagggtacttccagccctggccatagggtacttctgggaggagat +atagggtatttccagccttggccatagggtacttctgggaggtgatatagggtatttcca +gccttggccatagggtacttctgggaggtgatatagggtatttccagccttggccatagg +gtacttctgggaggtgatatagggtatttccagccttggccatagggtacttctaggagg +tgatatagggtacttccagccctggccatagggtacttctgggaggtgatataggatact +tccagccctgg-----------------------------------------------ca +tagggtacttctgggaggtgatataggatacttccagccctggccatagggtacttctgg +gaggtgatataggatacttccagccctggccatagggtacttctgggaggtgatatagga +tacttccagccctggccatagggtacttctgggaggtgatataggatacttccagccttg +gccatctcctctcctttaagatacctacacttgttctttcccacccacaactgtatcagt +cagcttttactgaataacaaagcacccctaacctcagtgcatgatgaaaccctgtctcta +ctaaaagcacaaaaat +>p:HG002_2_chr20:24407883-24409098 +ctcagtttattcatctataaaacagatgtggcagtggtagtgccacaattcacagcccag +ttccaccttcctcacaggctcgtgataaagctccatttcctacccttcctctcagttatg +ttggagccacaggaggtgatatagggtgcttccggccctggccatagggtacttctggga +ggtgatatagggtatttccagccttggccatagggtacttctgggaggtgatatagggta +tttccagccttggccatagggtacttctgggaggtgatatagggtacttccagccttggc +catagggtacttctgggaggtgatatagggtacttccagccctggccatagggtacttct +gggaggagatatagggtatttccagccttggccatagggtacttctgggaggtgatatag +ggtatttccagccttggccatagggtacttctgggaggtgatatagggtatttccagcct +tggccatagggtacttctgggaggtgatatagggtatttccagccctggccatagggtac +ttctaggaggtgatatagggtacttccagccctggccatagggtacttctgggaggtgat +ataggatacttccagccctggccatagggtacttctgggaggtgatataggatacttcca +g----------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------cctggccatagggtacttctgg +gaggtgatataggatacttccagccctggccatagggtacttctgggaggtgatatagga +tacttccagccctggccatagggtacttctgggaggtgatataggatacttccagccttg +gccatctcctctcctttaagatacctacacttgttctttcccacccacaactgtatcagt +cagcttttactgaataacaaagcacccctaacctcagtgcatgatgaaaccctgtctcta +ctaaaagcacaaaaat diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/msa.fa.fai new file mode 100644 index 00000000..9e3f4479 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_24407883_24409098 1216 29 60 61 +syndip_1_chr20:24407883-24409098 1216 1300 60 61 +syndip_2_chr20:24407883-24409098 1216 2571 60 61 +p:HG002_1_chr20:24407883-24409098 1216 3843 60 61 +p:HG002_2_chr20:24407883-24409098 1216 5115 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/output.vcf.gz new file mode 100644 index 00000000..faa13b1d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/output.vcf.gz.tbi new file mode 100644 index 00000000..03a7950b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24407983-24408998/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/base.vcf.gz new file mode 100644 index 00000000..a73ca10a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/base.vcf.gz.tbi new file mode 100644 index 00000000..f574d09d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/comp.vcf.gz new file mode 100644 index 00000000..025fb70b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/comp.vcf.gz.tbi new file mode 100644 index 00000000..86244bcf Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/haps.fa new file mode 100644 index 00000000..474a081b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/haps.fa @@ -0,0 +1,41 @@ +>ref_chr20_24681888_24682378 +CTCTGCTGCTGGGGTGTACTCGATGTCCTGGCTCGACTGACACAGTCCTGATCTTGCCAGTTGGTGTCTGTGGACCTGTGTTTTGGCATGGACAGGCACAAGGCTAAGGAGGTCAGCATGCAGCAGGAGGCAAACTGTGAAGTACCTCTCTGGCCTGGCCTTTGTGAATTACCACAGTGCGGGGTCCACCCAGGAAACTGTGAAGTACCTCTGTGGCCTTTGTGAATTACCACAGTCAGGGGTCCACCCAGGAAACTGTGAAGTACCTCTCTGGGCGTTGTGAATTACCACAGTTAGGGGTTTACCCAGGAAACTGTGAAGTATCTCTCTGGCCTTTGTGAATCACCACAGTTAGGGGTCTATGCAGGAGTACTGGTCATTCACAGACTCAGCTCATTCCAGGCCTTAGCAGTGTGCACCTCAGAGTGAAGCAGAGAGGCCCCAGGAGAAGCCATGGCCACGCCCTCAACCTCCTGCTCCGAGGAGGAGAC +>syndip_1_chr20:24681888-24682378 +CTCTGCTGCTGGGGTGTACTCGATGTCCTGGCTCGACTGACACAGTCCTGATCTTGCCAG +TTGGTGTCTGTGGACCTGTGTTTTGGCATGGACAGGCACAAGGCTAAGGAGGTCAGCATG +CAGCAGGAGGCAAACTGTGAAGTACCTCTCTGGCCTGGCCTTTGTGAATTACCACAGTGC +GGGGTCCACCCAGGAAACTGTGAAGTACCTCTCTGGGCGTTGTGAATTACCACAGTTAGG +GGTTTACCCAGGAAACTGTGAAGTATCTCTCTGGCCTTTGTGAATCACCACAGTTAGGGG +TCTATGCAGGAGTACTGGTCATTCACAGACTCAGCTCATTCCAGGCCTTAGCAGTGTGCA +CCTCAGAGTGAAGCAGAGAGGCCCCAGGAGAAGCCATGGCCACGCCCTCAACCTCCTGCT +CCGAGGAGGAGAC +>syndip_2_chr20:24681888-24682378 +CTCTGCTGCTGGGGTGTACTCGATGTCCTGGCTCGACTGACACAGTCCTGATCTTGCCAG +TTGGTGTCTGTGGACCTGTGTTTTGGCATGGACAGGCACAAGGCTAAGGAGGTCAGCATG +CAGCAGGAGGCAAACTGTGAAGTACCTCTCTGGCCTGGCCTTTGTGAATTACCACAGTCA +GGGGTCCACCCAGGAAACTGTGAAGTACCTCTGTGGCCTTTGTGAATTACCACAGTCAGG +GGTCCACCCAGGAAACTGTGAAGTACCTCTCTGGGCGTTGTGAATTACCACAGTTAGGGG +TTTACCCAGGAAACTGTGAAGTATCTCTCTGGCCTTTGTGAATCACCACAGTTAGGGGTC +TATGCAGGAGTACTGGTCATTCACAGACTCAGCTCATTCCAGGCCTTAGCAGTGTGCACC +TCAGAGTGAAGCAGAGAGGCCCCAGGAGAAGCCATGGCCACGCCCTCAACCTCCTGCTCC +GAGGAGGAGAC +>p:HG002_1_chr20:24681888-24682378 +CTCTGCTGCTGGGGTGTACTCGATGTCCTGGCTCGACTGACACAGTCCTGATCTTGCCAG +TTGGTGTCTGTGGACCTGTGTTTTGGCATGGACAGGCACAAGGCTAAGGAGGTCAGCATG +CAGCAGGAGGCAAACTGTGAAGTACCTCTCTGGCCTGGCCTTTGTGAATTACCACAGTCA +GGGGTCTACCCAGGAAACTGTGAAGTACCTCTCTGGCCTTTGTGAATTACCACAGTCAGG +GGTCCACCCAGGAAACTGTGAAGTACCTCTCTGGCCTTTGTGAATTACCACAGTCAGGGG +TCCACCCAGGAAACTGTGAAGTACCTCTCTGGGCGTTGTGAATTACCACAGTTAGGGGTT +TACCCAGGAAACTGTGAAGTATCTCTCTGGCCTTTGTGAATCACCACAGTTAGGGGTCTA +TGCAGGAGTACTGGTCATTCACAGACTCAGCTCATTCCAGGCCTTAGCAGTGTGCACCTC +AGAGTGAAGCAGAGAGGCCCCAGGAGAAGCCATGGCCACGCCCTCAACCTCCTGCTCCGA +GGAGGAGAC +>p:HG002_2_chr20:24681888-24682378 +CTCTGCTGCTGGGGTGTACTCGATGTCCTGGCTCGACTGACACAGTCCTGATCTTGCCAG +TTGGTGTCTGTGGACCTGTGTTTTGGCATGGACAGGCACAAGGCTAAGGAGGTCAGCATG +CAGCAGGAGGCAAACTGTGAAGTACCTCTCTGGCCTGGCCTTTGTGAATTACCACAGTGC +GGGGTCCACCCAGGAAACTGTGAAGTACCTCTCTGGGCGTTGTGAATTACCACAGTTAGG +GGTTTACCCAGGAAACTGTGAAGTATCTCTCTGGCCTTTGTGAATCACCACAGTTAGGGG +TCTATGCAGGAGTACTGGTCATTCACAGACTCAGCTCATTCCAGGCCTTAGCAGTGTGCA +CCTCAGAGTGAAGCAGAGAGGCCCCAGGAGAAGCCATGGCCACGCCCTCAACCTCCTGCT +CCGAGGAGGAGAC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/haps.fa.ref.fa new file mode 100644 index 00000000..4e044ed6 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:24681888-24682378 +CTCTGCTGCTGGGGTGTACTCGATGTCCTGGCTCGACTGACACAGTCCTGATCTTGCCAGTTGGTGTCTGTGGACCTGTGTTTTGGCATGGACAGGCACAAGGCTAAGGAGGTCAGCATGCAGCAGGAGGCAAACTGTGAAGTACCTCTCTGGCCTGGCCTTTGTGAATTACCACAGTGCGGGGTCCACCCAGGAAACTGTGAAGTACCTCTGTGGCCTTTGTGAATTACCACAGTCAGGGGTCCACCCAGGAAACTGTGAAGTACCTCTCTGGGCGTTGTGAATTACCACAGTTAGGGGTTTACCCAGGAAACTGTGAAGTATCTCTCTGGCCTTTGTGAATCACCACAGTTAGGGGTCTATGCAGGAGTACTGGTCATTCACAGACTCAGCTCATTCCAGGCCTTAGCAGTGTGCACCTCAGAGTGAAGCAGAGAGGCCCCAGGAGAAGCCATGGCCACGCCCTCAACCTCCTGCTCCGAGGAGGAGAC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/msa.fa new file mode 100644 index 00000000..ad3d1e33 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/msa.fa @@ -0,0 +1,55 @@ +>ref_chr20_24681888_24682378 +ctctgctgctggggtgtactcgatgtcctggctcgactgacacagtcctgatcttgccag +ttggtgtctgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcatg +cagcaggaggcaaactgtgaagtacctctctggc-------------------------- +--------------------------------ctggcctttgtgaattaccacagtgcgg +ggtccacccaggaaactgtgaagtacctctgtggcctttgtgaattaccacagtcagggg +tccacccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggtt +tacccaggaaactgtgaagtatctctctggcctttgtgaatcaccacagttaggggtcta +tgcaggagtactggtcattcacagactcagctcattccaggccttagcagtgtgcacctc +agagtgaagcagagaggccccaggagaagccatggccacgccctcaacctcctgctccga +ggaggagac +>syndip_1_chr20:24681888-24682378 +ctctgctgctggggtgtactcgatgtcctggctcgactgacacagtcctgatcttgccag +ttggtgtctgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcatg +cagcaggaggcaaactgtgaagtacctctctggc-------------------------- +------------------------------------------------------------ +------------------------------ctggcctttgtgaattaccacagtgcgggg +tccacccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggtt +tacccaggaaactgtgaagtatctctctggcctttgtgaatcaccacagttaggggtcta +tgcaggagtactggtcattcacagactcagctcattccaggccttagcagtgtgcacctc +agagtgaagcagagaggccccaggagaagccatggccacgccctcaacctcctgctccga +ggaggagac +>syndip_2_chr20:24681888-24682378 +ctctgctgctggggtgtactcgatgtcctggctcgactgacacagtcctgatcttgccag +ttggtgtctgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcatg +cagcaggaggcaaactgtgaagtacctctctggc-------------------------- +--------------------------------ctggcctttgtgaattaccacagtcagg +ggtccacccaggaaactgtgaagtacctctgtggcctttgtgaattaccacagtcagggg +tccacccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggtt +tacccaggaaactgtgaagtatctctctggcctttgtgaatcaccacagttaggggtcta +tgcaggagtactggtcattcacagactcagctcattccaggccttagcagtgtgcacctc +agagtgaagcagagaggccccaggagaagccatggccacgccctcaacctcctgctccga +ggaggagac +>p:HG002_1_chr20:24681888-24682378 +ctctgctgctggggtgtactcgatgtcctggctcgactgacacagtcctgatcttgccag +ttggtgtctgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcatg +cagcaggaggcaaactgtgaagtacctctctggcctggcctttgtgaattaccacagtca +ggggtctacccaggaaactgtgaagtacctctctggcctttgtgaattaccacagtcagg +ggtccacccaggaaactgtgaagtacctctctggcctttgtgaattaccacagtcagggg +tccacccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggtt +tacccaggaaactgtgaagtatctctctggcctttgtgaatcaccacagttaggggtcta +tgcaggagtactggtcattcacagactcagctcattccaggccttagcagtgtgcacctc +agagtgaagcagagaggccccaggagaagccatggccacgccctcaacctcctgctccga +ggaggagac +>p:HG002_2_chr20:24681888-24682378 +ctctgctgctggggtgtactcgatgtcctggctcgactgacacagtcctgatcttgccag +ttggtgtctgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcatg +cagcaggaggcaaactgtgaagtacctctctggc-------------------------- +------------------------------------------------------------ +------------------------------ctggcctttgtgaattaccacagtgcgggg +tccacccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggtt +tacccaggaaactgtgaagtatctctctggcctttgtgaatcaccacagttaggggtcta +tgcaggagtactggtcattcacagactcagctcattccaggccttagcagtgtgcacctc +agagtgaagcagagaggccccaggagaagccatggccacgccctcaacctcctgctccga +ggaggagac diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/msa.fa.fai new file mode 100644 index 00000000..5141810c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_24681888_24682378 549 29 60 61 +syndip_1_chr20:24681888-24682378 549 622 60 61 +syndip_2_chr20:24681888-24682378 549 1215 60 61 +p:HG002_1_chr20:24681888-24682378 549 1809 60 61 +p:HG002_2_chr20:24681888-24682378 549 2403 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/output.vcf.gz new file mode 100644 index 00000000..b44bd9ea Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/output.vcf.gz.tbi new file mode 100644 index 00000000..4870886b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:24681988-24682278/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/base.vcf.gz new file mode 100644 index 00000000..5cbe0238 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/base.vcf.gz.tbi new file mode 100644 index 00000000..bb297398 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/comp.vcf.gz new file mode 100644 index 00000000..bea7a4c2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/comp.vcf.gz.tbi new file mode 100644 index 00000000..47d388e9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/haps.fa new file mode 100644 index 00000000..25da5c0a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/haps.fa @@ -0,0 +1,44 @@ +>ref_chr20_25781536_25782027 +ACAAGAATCAGTTACTTCACCAACTGTGAGACCCTGAGGGGCTGGGTTTCTATCCTACAAGATGTGTTAGAAGCCCTGACCCAAGAGCCCTGCTACCCAGAATGCATGGTTTCATGTAGCAAGGATCCTTGTGATGGTGGTGATGATGATGGTGAGGATGGTGATGGTGAAGGTGGAGGTGGTGATAATGAAGTGATAGTTATGTTGAGGATGATGAAGGTGATGATGATGGTGAGAATGGTAAAGGTGAACAAGGTGATGGTGAGAATGGCGAGGGTAAGAATGGTGATGGCGATGATGATAGTGTTGGTGATTGTAAGGATGGTGATGGCGATCATGGTGATGAAGATAATGGTGCTGACAGGGCTATGAGGTAATGGAGGCAGAAAAGTGGCAGTTTCCAGGAAGTATAGAGCCAGCTGGGAACTGCAAGGTAACCTTAGTGGGGGTGGAAGATGTAGGGTCCCTGCCTCATTTCTAGACATCTGGAGA +>syndip_1_chr20:25781536-25782027 +ACAAGAATCAGTTACTTCACCAACTGTGAGACCCTGAGGGGCTGGGTTTCTATCCTACAA +GATGTGTTAGAAGCCCTGACCCAAGAGCCCTGCTACCCAGAATGCATGGTTTCATGTAGC +AAGGATCCTTGTGATGGTGGTGATGATGATGGTGAGGATGGTGATGGTGAAGGTGGAGGT +GGTGATAATGAAGTGATAGTTATGTTGAGGATGATGAAGGTGATGATGATGGTGAGAATG +GTAAAGGTGAACAAGGTGATGGTGAGAATGGCGAGGGTAAGAATGGTGATGGCGATGATG +ATAGTGTTGGTGATTGTAAGGATGGTGATGGCGATCATGGTGATGAAGATAATGGTGCTG +ACAGGGCTATGAGGTAATGGAGGCAGAAAAGTGGCAGTTTCCAGGAAGTATAGAGCCAGC +TGGGAACTGCAAGGTAACCTTAGTGGGGGTGGAAGATGTAGGGTCCCTGCCTCATTTCTA +GACATCTGGAGA +>syndip_2_chr20:25781536-25782027 +ACAAGAATCAGTTACTTCACCAACTGTGAGACCCTGAGGGGCTGGGTTTCTATCCTACAA +GATGTGTTAGAAGCCCTGACCCAAGAGCCCTGCTACCCAGAATGCATGGTTTCATGTAGC +AAGGATCCTTGTGATGGTGGTGATGATGATGGTGAGGATGGTGATGGTGAAGGTGGAGGT +GGTGATAATGAAGTGATAGTTATGTTGAGGATGATGAAGGTGATGATGATGGTGAGAATG +GTAAAGGTGAACAAGGTGATGGTGAGAATGGCGAGGGTAAGAATGGTGATGGCGATGATG +ATAGTGTTGGTGATTGTAAGGATGGTGATGGCGATCATGGTGATGAAGATAATGGTGCTG +ACAGGGCTATGAGGTAATGGAGGCAGAAAAGTGGCAGTTTCCAGGAAGTATAGAGCCAGC +TGGGAACTGCAAGGTAACCTTAGTGGGGGTGGAAGATGTAGGGTCCCTGCCTCATTTCTA +GACATCTGGAGA +>p:HG002_1_chr20:25781536-25782027 +ACAAGAATCAGTTACTTCACCAACTGTGAGACCCTGAGGGGCTGGGTTTCTATCCTACAA +GATGTGTTAGAAGCCCTGACCCAAGAGCCCTGCTACCCAGAATGCATGGTTTCATGTAGC +AAGGATCCTTGTGATGGTGGTGATAATGATGGTGAGGATGGTGATGGTGAAGGTGGAGGT +GGTGATAATGAAGTGATAGTTATGTTGAGGATGATGAAGGTGATGATGATGGTGAGAATG +GTAAAGGTGAACAAGGTGATGGTGAGAATGGTGATGGTGGTGATTGTGATGGTGATGATA +AGGATGGTGATGGCGAAGGTGGTGATGATAGTAGTGATAGTTATGGTAAGGATAATGGTG +ATGATGATGAGGATGATGATGGTGAGAATGGTGATAGTGACGATGATAGTGATGGTAATG +ATAATGATGGTGAGAATGGCGAGGGTAAGAATGGTGATGGCGATGATGATAGTGTTGGTG +ATTGTAAGGATGGTGATGGCAATCATGGTGATGATGATAATGGTGCTGACTGGGCTATGA +GGTAATGGAGGCAGAAAAGTGGCAGTTTCCAGGAAGTATAGAGCCAGCTGGGAACTGCAA +GGTAACCTTAGTGGGGGTGGAAGATGTAGGGTCCCTGCCTCATTTCTAGACATCTGGAGA +>p:HG002_2_chr20:25781536-25782027 +ACAAGAATCAGTTACTTCACCAACTGTGAGACCCTGAGGGGCTGGGTTTCTATCCTACAA +GATGTGTTAGAAGCCCTGACCCAAGAGCCCTGCTACCCAGAATGCATGGTTTCATGTAGC +AAGGATCCTTGTGATGGTGGTGATGATGATGGTGAGGATGGTGATGGTGAAGGTGGAGGT +GGTGATAATGAAGTGATAGTTATGTTGAGGATGATGAAGGTGATGATGATGGTGAGAATG +GTAAAGGTGAACAAGGTGATGGTGAGAATGGCGAGGGTAAGAATGGTGATGGCGATGATG +ATAGTGTTGGTGATTGTAAGGATGGTGATGGCGATCATGGTGATGAAGATAATGGTGCTG +ACAGGGCTATGAGGTAATGGAGGCAGAAAAGTGGCAGTTTCCAGGAAGTATAGAGCCAGC +TGGGAACTGCAAGGTAACCTTAGTGGGGGTGGAAGATGTAGGGTCCCTGCCTCATTTCTA +GACATCTGGAGA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/haps.fa.ref.fa new file mode 100644 index 00000000..6fbf1469 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:25781536-25782027 +ACAAGAATCAGTTACTTCACCAACTGTGAGACCCTGAGGGGCTGGGTTTCTATCCTACAAGATGTGTTAGAAGCCCTGACCCAAGAGCCCTGCTACCCAGAATGCATGGTTTCATGTAGCAAGGATCCTTGTGATGGTGGTGATGATGATGGTGAGGATGGTGATGGTGAAGGTGGAGGTGGTGATAATGAAGTGATAGTTATGTTGAGGATGATGAAGGTGATGATGATGGTGAGAATGGTAAAGGTGAACAAGGTGATGGTGAGAATGGCGAGGGTAAGAATGGTGATGGCGATGATGATAGTGTTGGTGATTGTAAGGATGGTGATGGCGATCATGGTGATGAAGATAATGGTGCTGACAGGGCTATGAGGTAATGGAGGCAGAAAAGTGGCAGTTTCCAGGAAGTATAGAGCCAGCTGGGAACTGCAAGGTAACCTTAGTGGGGGTGGAAGATGTAGGGTCCCTGCCTCATTTCTAGACATCTGGAGA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/msa.fa new file mode 100644 index 00000000..e61c1bf1 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/msa.fa @@ -0,0 +1,60 @@ +>ref_chr20_25781536_25782027 +acaagaatcagttacttcaccaactgtgagaccctgaggggctgggtttctatcctacaa +gatgtgttagaagccctgacccaagagccctgctacccagaatgcatggtttcatgtagc +aaggatccttgtgatggtggtgatgatgatggtgaggatggtgatggtgaaggtggaggt +ggtgataatgaagtgatagttatgttgaggatgatgaaggtgatgatgatggtgagaatg +gtaaaggtgaacaagg-------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----tgatggtgagaatggcgagggtaagaatggtgatggcgatgatgatagtgttggtg +attgtaaggatggtgatggcgatcatggtgatgaagataatggtgctgacagggctatga +ggtaatggaggcagaaaagtggcagtttccaggaagtatagagccagctgggaactgcaa +ggtaaccttagtgggggtggaagatgtagggtccctgcctcatttctagacatctggaga +>syndip_1_chr20:25781536-25782027 +acaagaatcagttacttcaccaactgtgagaccctgaggggctgggtttctatcctacaa +gatgtgttagaagccctgacccaagagccctgctacccagaatgcatggtttcatgtagc +aaggatccttgtgatggtggtgatgatgatggtgaggatggtgatggtgaaggtggaggt +ggtgataatgaagtgatagttatgttgaggatgatgaaggtgatgatgatggtgagaatg +gtaaaggtgaacaagg-------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----tgatggtgagaatggcgagggtaagaatggtgatggcgatgatgatagtgttggtg +attgtaaggatggtgatggcgatcatggtgatgaagataatggtgctgacagggctatga +ggtaatggaggcagaaaagtggcagtttccaggaagtatagagccagctgggaactgcaa +ggtaaccttagtgggggtggaagatgtagggtccctgcctcatttctagacatctggaga +>syndip_2_chr20:25781536-25782027 +acaagaatcagttacttcaccaactgtgagaccctgaggggctgggtttctatcctacaa +gatgtgttagaagccctgacccaagagccctgctacccagaatgcatggtttcatgtagc +aaggatccttgtgatggtggtgatgatgatggtgaggatggtgatggtgaaggtggaggt +ggtgataatgaagtgatagttatgttgaggatgatgaaggtgatgatgatggtgagaatg +gtaaaggtgaacaagg-------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----tgatggtgagaatggcgagggtaagaatggtgatggcgatgatgatagtgttggtg +attgtaaggatggtgatggcgatcatggtgatgaagataatggtgctgacagggctatga +ggtaatggaggcagaaaagtggcagtttccaggaagtatagagccagctgggaactgcaa +ggtaaccttagtgggggtggaagatgtagggtccctgcctcatttctagacatctggaga +>p:HG002_1_chr20:25781536-25782027 +acaagaatcagttacttcaccaactgtgagaccctgaggggctgggtttctatcctacaa +gatgtgttagaagccctgacccaagagccctgctacccagaatgcatggtttcatgtagc +aaggatccttgtgatggtggtgataatgatggtgaggatggtgatggtgaaggtggaggt +ggtgataatgaagtgatagttatgttgaggatgatgaaggtgatgatgatggtgagaatg +gtaaaggtgaacaaggtgatggtgagaatggtgatggtggtgattgtgatggtgatgata +aggatggtgatggcgaaggtggtgatgatagtagtgatagttatggtaaggataatggtg +atgatgatgaggatgatgatggtgagaatggtgatagtgacgatgatagtgatggtaatg +ataatgatggtgagaatggcgagggtaagaatggtgatggcgatgatgatagtgttggtg +attgtaaggatggtgatggcaatcatggtgatgatgataatggtgctgactgggctatga +ggtaatggaggcagaaaagtggcagtttccaggaagtatagagccagctgggaactgcaa +ggtaaccttagtgggggtggaagatgtagggtccctgcctcatttctagacatctggaga +>p:HG002_2_chr20:25781536-25782027 +acaagaatcagttacttcaccaactgtgagaccctgaggggctgggtttctatcctacaa +gatgtgttagaagccctgacccaagagccctgctacccagaatgcatggtttcatgtagc +aaggatccttgtgatggtggtgatgatgatggtgaggatggtgatggtgaaggtggaggt +ggtgataatgaagtgatagttatgttgaggatgatgaaggtgatgatgatggtgagaatg +gtaaaggtgaacaagg-------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----tgatggtgagaatggcgagggtaagaatggtgatggcgatgatgatagtgttggtg +attgtaaggatggtgatggcgatcatggtgatgaagataatggtgctgacagggctatga +ggtaatggaggcagaaaagtggcagtttccaggaagtatagagccagctgggaactgcaa +ggtaaccttagtgggggtggaagatgtagggtccctgcctcatttctagacatctggaga diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/msa.fa.fai new file mode 100644 index 00000000..d3cc744c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_25781536_25782027 660 29 60 61 +syndip_1_chr20:25781536-25782027 660 734 60 61 +syndip_2_chr20:25781536-25782027 660 1439 60 61 +p:HG002_1_chr20:25781536-25782027 660 2145 60 61 +p:HG002_2_chr20:25781536-25782027 660 2851 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/output.vcf.gz new file mode 100644 index 00000000..433618d1 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/output.vcf.gz.tbi new file mode 100644 index 00000000..62df16c2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:25781636-25781927/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/base.vcf.gz new file mode 100644 index 00000000..9d0870ca Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/base.vcf.gz.tbi new file mode 100644 index 00000000..344ecd0e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/comp.vcf.gz new file mode 100644 index 00000000..965f2939 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/comp.vcf.gz.tbi new file mode 100644 index 00000000..9ba1cb80 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/haps.fa new file mode 100644 index 00000000..bc114cfe --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/haps.fa @@ -0,0 +1,66 @@ +>ref_chr20_278800_279287 +GATGAAACCCATCTCGGTCCTCTTGCAAAGCCCAGGTGAGGGGAGTGAAGGGTGAAGAAATGCGTCTTCCAGGTGGAGGAAGCACCACGTGCAGTGGGCGGGGAAAGGCAGGAGAGGGCGCGCGAGTGCGCGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGAGGGACGGAGGTTGGGACGGAGGGACGGAGGGCGGGCGGATGCCGCGGGTCTCACCGCCAGGGTGTCCTGCTGCTGCAGCAGGGCCCGCACGTGCAGGGTCGTGCTGTTCTCCATCTCCTGGATGGTCTCGATCAGCTCCCGGTTGAGCTTGCTGAGGAAGTTCTCACGGC +>syndip_1_chr20:278800-279287 +GATGAAACCCATCTCGGTCCTCTTGCAAAGCCCAGGTGAGGGGAGTGAAGGGTGAAGAAA +TGCGTCTTCCAGGTGGAGGAAGCACCACGTGCAGTGGGCGGGGAAAGGCAGGAGAGGGCG +CGCGAGTGCGCGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGAGGGACGGAGG +GAGGAAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGACGGAGGGCGGGACGGCGGGAGG +GCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGG +GAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGG +GAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGTGGG +AGGGAGGGAGGGATGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGACGGAGGG +AGGGAGGGAGGGACGGAGGTTGGGACGGAGGGACGGAGGGCGGGCGGATGCCGCGGGTCT +CACCGCCAAGGTGTCCTGCTGCTGCAGCAGGGCCCGCACGTGCAGGGTCGTGCTGTTCTC +CATCTCCTGGATGGTCTCGATCAGCTCCCGGTTGAGCTTGCTGAGGAAGTTCTCACGGC +>syndip_2_chr20:278800-279287 +GATGAAACCCATCTCGGTCCTCTTGCAAAGCCCAGGTGAGGGGAGTGAAGGGTGAAGAAA +TGCGTCTTCCAGGTGGAGGAAGCACCACGTGCAGTGGGCGGGGAAAGGCAGGAGAGGGCG +CGCGAGTGCGCGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGG +GAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGG +GACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGG +GACGGAGGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGG +GAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGG +GACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGG +GAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACG +GAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGG +GAGGGCGGGACGGAGGGCGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGG +GCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGACGGAGGGAGGGAGGGAGGGAGG +GACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGG +AGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGA +GGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGCGGGACGGAGGGAGGGCGGGAGGGA +GGGACGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGAGGGACGGAGGTTGGGACGGA +GGGACGGAGGGCGGGCGGATGCCGCGGGTCTCACCGCCAAGGTGTCCTGCTGCTGCAGCA +GGGCCCGCACGTGCAGGGTCGTGCTGTTCTCCATCTCCTGGATGGTCTCGATCAGCTCCC +GGTTGAGCTTGCTGAGGAAGTTCTCACGGC +>p:HG002_1_chr20:278800-279287 +GATGAAACCCATCTCGGTCCTCTTGCAAAGCCCAGGTGAGGGGAGTGAAGGGTGAAGAAA +TGCGTCTTCCAGGTGGAGGAAGCACCACGTGCAGTGGGCGGGGAAAGGCAGGAGAGGGCG +CGCGAGTGCGCGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGG +GAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGG +GACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGG +GACGGAGGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGG +GAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGG +GACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGG +GAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACG +GAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGG +GAGGGCGGGACGGAGGGCGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGG +GCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGACGGAGGGAGGGAGGGAGGGAGG +GACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGG +AGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGA +GGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGCGGGACGGAGGGAGGGCGGGAGGGA +GGGACGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGAGGGACGGAGGTTGGGACGGA +GGGACGGAGGGCGGGCGGATGCCGCGGGTCTCACCGCCAAGGTGTCCTGCTGCTGCAGCA +GGGCCCGCACGTGCAGGGTCGTGCTGTTCTCCATCTCCTGGATGGTCTCGATCAGCTCCC +GGTTGAGCTTGCTGAGGAAGTTCTCACGGC +>p:HG002_2_chr20:278800-279287 +GATGAAACCCATCTCGGTCCTCTTGCAAAGCCCAGGTGAGGGGAGTGAAGGGTGAAGAAA +TGCGTCTTCCAGGTGGAGGAAGCACCACGTGCAGTGGGCGGGGAAAGGCAGGAGAGGGCG +CGCGAGTGCGCGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGAGGGACGGAGG +GAGGAAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGACGGAGGGCGGGACGGCGGGAGG +GCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGG +GAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGG +GAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGTGGG +AGGGAGGGAGGGATGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGACGGAGGG +AGGGAGGGAGGGACGGAGGTTGGGACGGAGGGACGGAGGGCGGGCGGATGCCGCGGGTCT +CACCGCCAAGGTGTCCTGCTGCTGCAGCAGGGCCCGCACGTGCAGGGTCGTGCTGTTCTC +CATCTCCTGGATGGTCTCGATCAGCTCCCGGTTGAGCTTGCTGAGGAAGTTCTCACGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/haps.fa.ref.fa new file mode 100644 index 00000000..601396f1 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:278800-279287 +GATGAAACCCATCTCGGTCCTCTTGCAAAGCCCAGGTGAGGGGAGTGAAGGGTGAAGAAATGCGTCTTCCAGGTGGAGGAAGCACCACGTGCAGTGGGCGGGGAAAGGCAGGAGAGGGCGCGCGAGTGCGCGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGAGGGACGGAGGTTGGGACGGAGGGACGGAGGGCGGGCGGATGCCGCGGGTCTCACCGCCAGGGTGTCCTGCTGCTGCAGCAGGGCCCGCACGTGCAGGGTCGTGCTGTTCTCCATCTCCTGGATGGTCTCGATCAGCTCCCGGTTGAGCTTGCTGAGGAAGTTCTCACGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/msa.fa new file mode 100644 index 00000000..68240cf0 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/msa.fa @@ -0,0 +1,100 @@ +>ref_chr20_278800_279287 +gatgaaacccatctcggtcctcttgcaaagcccaggtgaggggagtgaagggtgaagaaa +tgcgtcttccaggtggaggaagcaccacgtgcagt------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------------------gggcg +gggaaaggcaggagagggcgcgcgagtgcgcggagggagggcgggacggag----ggagg +gagggcg--------------------------------ggacggagggagggagggagg +gacggagggcgggacggcgggagggcgggacggagggacggagggagggcgggacggagg +gcgggagggcgggacggag----------------------------------------- +------------------------------------------------------------ +-----------------------------------------ggaggga----gggaggga +gggacggagggcgggacggagggacggagggagggagggagggacggaggttgggacgga +gggacggagggcgggcggatgccgcgggtctcaccgccagggtgtcctgctgctgcagca +gggcccgcacgtgcagggtcgtgctgttctccatctcctggatggtctcgatcagctccc +ggttgagcttgctgaggaagttctcacggc +>syndip_1_chr20:278800-279287 +gatgaaacccatctcggtcctcttgcaaagcccaggtgaggggagtgaagggtgaagaaa +tgcgtcttccaggtggaggaagcaccacgtgcagt------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------------------gggcg +gggaaaggcaggagagggcgcgcgagtgcgcggagggagggcgggacggag----ggagg +gagggcgggagggagggacggagggaggaagggcgggacggagggagggagggcgggagg +gacggagggcgggacggcgggagggcgggacggagggacggagggagggcgggacggagg +gcgggagggcgggacggagggagggag---ggagggagggcgggacggagggagggaggg +agggagggacggagggcgggacggagggagggagggcggagggagggagggcgggacgga +gggagggagggcgggacggagggtgggagggagggagggatggaggga----gggaggga +gggacggagggcgggacggagggacggagggagggagggagggacggaggttgggacgga +gggacggagggcgggcggatgccgcgggtctcaccgccaaggtgtcctgctgctgcagca +gggcccgcacgtgcagggtcgtgctgttctccatctcctggatggtctcgatcagctccc +ggttgagcttgctgaggaagttctcacggc +>syndip_2_chr20:278800-279287 +gatgaaacccatctcggtcctcttgcaaagcccaggtgaggggagtgaagggtgaagaaa +tgcgtcttccaggtggaggaagcaccacgtgcagtgggcggggaaaggcaggagagggcg +cgcgagtgcgcggagggagggcgggacggagggagggagggcgggacggagggagggagg +gagggcgggacggagggagggagggcgggacggagggagggagggagggacggagggcgg +gacggcgggagggcgggacggagggacggagggagggcgggacggagggcgggagggcgg +gacggagggagggagggagggagggcgggacggagggagggagggcgggacggagggagg +gagggagggacggagggcgggacggcgggagggcgggacggagggacggagggagggcgg +gacggagggcgggagggcgggacggagggagggagggcgggacggagggacggagggagg +gagggcgggacggagggagggagggcgggacggagggacggagggagggagggcgggacg +gagggagggagggagggacggagggcgggacggcgggagggcgggacggagggacggagg +gagggcgggacggagggcgggagggagggagggcgggacggagggagggagggagggagg +gcgggacggagggagggagggagggagggacggagggacggagggagggagggagggagg +gacggagggcgggacggagggagggagggcggagggagggagggcgggacggagggaggg +agggagggacggagggcgggacggagggagggagggcggagggagggagggcgggacgga +gggagggagggcgggagggatggagggagggagggcgggacggagggagggcgggaggga +gggacggagggcgggacggagggacggagggagggagggagggacggaggttgggacgga +gggacggagggcgggcggatgccgcgggtctcaccgccaaggtgtcctgctgctgcagca +gggcccgcacgtgcagggtcgtgctgttctccatctcctggatggtctcgatcagctccc +ggttgagcttgctgaggaagttctcacggc +>p:HG002_1_chr20:278800-279287 +gatgaaacccatctcggtcctcttgcaaagcccaggtgaggggagtgaagggtgaagaaa +tgcgtcttccaggtggaggaagcaccacgtgcagtgggcggggaaaggcaggagagggcg +cgcgagtgcgcggagggagggcgggacggagggagggagggcgggacggagggagggagg +gagggcgggacggagggagggagggcgggacggagggagggagggagggacggagggcgg +gacggcgggagggcgggacggagggacggagggagggcgggacggagggcgggagggcgg +gacggagggagggagggagggagggcgggacggagggagggagggcgggacggagggagg +gagggagggacggagggcgggacggcgggagggcgggacggagggacggagggagggcgg +gacggagggcgggagggcgggacggagggagggagggcgggacggagggacggagggagg +gagggcgggacggagggagggagggcgggacggagggacggagggagggagggcgggacg +gagggagggagggagggacggagggcgggacggcgggagggcgggacggagggacggagg +gagggcgggacggagggcgggagggagggagggcgggacggagggagggagggagggagg +gcgggacggagggagggagggagggagggacggagggacggagggagggagggagggagg +gacggagggcgggacggagggagggagggcggagggagggagggcgggacggagggaggg +agggagggacggagggcgggacggagggagggagggcggagggagggagggcgggacgga +gggagggagggcgggagggatggagggagggagggcgggacggagggagggcgggaggga +gggacggagggcgggacggagggacggagggagggagggagggacggaggttgggacgga +gggacggagggcgggcggatgccgcgggtctcaccgccaaggtgtcctgctgctgcagca +gggcccgcacgtgcagggtcgtgctgttctccatctcctggatggtctcgatcagctccc +ggttgagcttgctgaggaagttctcacggc +>p:HG002_2_chr20:278800-279287 +gatgaaacccatctcggtcctcttgcaaagcccaggtgaggggagtgaagggtgaagaaa +tgcgtcttccaggtggaggaagcaccacgtgcagt------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------------------gggcg +gggaaaggcaggagagggcgcgcgagtgcgcggagggagggcgggacggag----ggagg +gagggcgggagggagggacggagggaggaagggcgggacggagggagggagggcgggagg +gacggagggcgggacggcgggagggcgggacggagggacggagggagggcgggacggagg +gcgggagggcgggacggagggagggag---ggagggagggcgggacggagggagggaggg +agggagggacggagggcgggacggagggagggagggcggagggagggagggcgggacgga +gggagggagggcgggacggagggtgggagggagggagggatggaggga----gggaggga +gggacggagggcgggacggagggacggagggagggagggagggacggaggttgggacgga +gggacggagggcgggcggatgccgcgggtctcaccgccaaggtgtcctgctgctgcagca +gggcccgcacgtgcagggtcgtgctgttctccatctcctggatggtctcgatcagctccc +ggttgagcttgctgaggaagttctcacggc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/msa.fa.fai new file mode 100644 index 00000000..8f87f334 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_278800_279287 1110 25 60 61 +syndip_1_chr20:278800-279287 1110 1184 60 61 +syndip_2_chr20:278800-279287 1110 2343 60 61 +p:HG002_1_chr20:278800-279287 1110 3503 60 61 +p:HG002_2_chr20:278800-279287 1110 4663 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/output.vcf.gz new file mode 100644 index 00000000..6ba4a143 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/output.vcf.gz.tbi new file mode 100644 index 00000000..8cd49ebf Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:278900-279187/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/base.vcf.gz new file mode 100644 index 00000000..065d47e6 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/base.vcf.gz.tbi new file mode 100644 index 00000000..5b885e41 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/comp.vcf.gz new file mode 100644 index 00000000..f3c99c24 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/comp.vcf.gz.tbi new file mode 100644 index 00000000..4f301c91 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/haps.fa new file mode 100644 index 00000000..90f0631d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/haps.fa @@ -0,0 +1,58 @@ +>ref_chr20_32722324_32723313 +ACAGAGGTCTCCTGAAAATTAGTGCCCATAACAGGTGTTTGGTAGACAGGTCTCAGCCCTCAGACAAACCCATTTCCAAAGATGAAGGCCAGAGAATGAGAATAATGATTTATCGTTCTGGCCGGGTGTGATGGCTCATGCCTGTAATCCCAGCGCTGTGGGAGGCGTGGCCGGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACTTGGTCTCTACTAAAAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGCAATCCCAGCTACCCAGAAGGCTGAGTCAGAAGAATCACTTGAACCCGGGAGGTGGAGGTTGCAGTGAGCCGAGATCGTGCCACTGCACTCCAGCCTGGGTGACAGAGTGAGACTCAGGAAAAAAAAAAAAAAGACTTGGCCGAGCCCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGTGGATCACGAGGTCAAGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCATCTCTACTAAAAAATACAAAAAATTAGCCGGGCGTGGTGGTGGGCACCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGAATGGCGTGAACCTGGTAGGCAGAGCTTGCAGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGTGACAGAGCAAGACTCCATCTCAAAAATAAATAAATAAATAAATAAATAAATAATAATAATAATAATAAAGACTTGTGATCCTCTCCCTCTCCCTCTCCCTCTCCGTCTCCCTCTCCCTCTCCCTCTCCCTCCCTCTCCGTCTCCGTCTCCGTCTCCGTCTCCCTCTCCCTCTCCCCACGGTCTCCCTCTCATGCGGAGCCGAAGCTGGACTGTACTGCTGCCATCTCGGCTCACTGCAACCTCCCTGCCTGATTCTCCTGCCTCAGCCTGCCGAGTGCCTGCGATTGCAGGCACGCGCCGCCACGCCTGACTGGTT +>syndip_1_chr20:32722324-32723313 +ACAGAGGTCTCCTGAAAATTAGTGCCCATAACAGGTGTTTGGTAGACAGGTCTCAGCCCT +CAGACAAACCCATTTCCAAAGATGAAGGCCAGAGAATGAGAATAATGATTTATCGTTCTG +GCCGGGTGTGATGGCTCATGCCTGTAATCCCAGCGCTGTGGGAGGCGTGGCCGGCAGATC +ACCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACTTGGTCTCTACTAA +AAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGCAATCCCAGCTACCCAGAAGGC +TGAGTCAGAAGAATCACTTGAACCCGGGAGGTGGAGGTTGCAGTGAGCCGAGATCGTGCC +ACTGCACTCCAGCCTGGGTGACAGAGTGAGACTCAGGAAAAAAAAAAAAAAGACTTGGCC +GAGCCCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGTGGATCAC +GAGGTCAAGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCATCTCTACTAAAAAA +TACAAAAAATTAGCCGGGCGTGGTGGTGGGCACCTGTAGTCCCAGCTACTCGGGAGGCTG +AGGCAGAATGGCGTGAACCTGGTAGGCAGAGCTTGCAGTGAGCTGAGATCACGCCACTGC +ACTCCAGCCTGGGTGACAGAGCAAGACTCCATCTCAAAAATAAATAAATAAATAAATAAA +TAAATAATAATAATAATAATAAAAAA +>syndip_2_chr20:32722324-32723313 +ACAGAGGTCTCCTGAAAATTAGTGCCCATAACAGGTGTTTGGTAGACAGGTCTCAGCCCT +CAGACAAACCCATTTCCAAAGATGAAGGCCAGAGAATGAGAATAATGATTTATCGTTCTG +GCCGGGTGTGATGGCTCATGCCTGTAATCCCAGCGCTGTGGGAGGCGTGGCCGGCAGATC +ACCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACTTGGTCTCTACTAA +AAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGCAATCCCAGCTACCCAGAAGGC +TGAGTCAGAAGAATCACTTGAACCCGGGAGGTGGAGGTTGCAGTGAGCCGAGATCGTGCC +ACTGCACTCCAGCCTGGGTGACAGAGTGAGACTCAGGAAAAAAAAAAAAAAGACTTGGCC +GAGCCCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGTGGATCAC +GAGGTCAAGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCATCTCTACTAAAAAA +TACAAAAAATTAGCCGGGCGTGGTGGTGGGCACCTGTAGTCCCAGCTACTCGGGAGGCTG +AGGCAGAATGGCGTGAACCTGGTAGGCAGAGCTTGCAGTGAGCTGAGATCACACCACTGC +ACTCCAGCCTGGGTGACAGAGCAAGACTCCATCTCAAAAATAAATAAATAAATAAATAAA +TAAATAAATAATAATAATAATAATAAT +>p:HG002_1_chr20:32722324-32723313 +ACAGAGGTCTCCTGAAAATTAGTGCCCATAACAGGTGTTTGGTAGACAGGTCTCAGCCCT +CAGACAAACCCATTTCCAAAGATGAAGGCCAGAGAATGAGAATAATGATTTATCGTTCTG +GCCGGGTGTGATGGCTCATGCCTGTAATCCCAGCGCTGTGGGAGGCGTGGCCGGCAGATC +ACCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACTTGGTCTCTACTAA +AAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGCAATCCCAGCTACCCAGAAGGC +TGAGTCAGAAGAATCACTTGAACCCGGGAGGTGGAGGTTGCAGTGAGCCGAGATCGTGCC +ACTGCACTCCAGCCTGGGTGACAGAGTGAGACTCAGGAAAAAAAAAAAAAAGACTTGGCC +GAGCCCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGTGGATCAC +GAGGTCAAGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCATCTCTACTAAAAAA +TACAAAAAATTAGCCGGGCGTGGTGGTGGGCACCTGTAGTCCCAGCTACTCGGGAGGCTG +AGGCAGAATGGCGTGAACCTGGTAGGCAGAGCTTGCAGTGAGCTGAGATCACACCACTGC +ACTCCAGCCTGGGTGACAGAGCAAGACTCCATCTCAAAAATAAATAAATAAATAAATAAA +TAAATAA +>p:HG002_2_chr20:32722324-32723313 +ACAGAGGTCTCCTGAAAATTAGTGCCCATAACAGGTGTTTGGTAGACAGGTCTCAGCCCT +CAGACAAACCCATTTCCAAAGATGAAGGCCAGAGAATGAGAATAATGATTTATCGTTCTG +GCCGGGTGTGATGGCTCATGCCTGTAATCCCAGCGCTGTGGGAGGCGTGGCCGGCAGATC +ACCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACTTGGTCTCTACTAA +AAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGCAATCCCAGCTACCCAGAAGGC +TGAGTCAGAAGAATCACTTGAACCCGGGAGGTGGAGGTTGCAGTGAGCCGAGATCGTGCC +ACTGCACTCCAGCCTGGGTGACAGAGTGAGACTCAGGAAAAAAAAAAAAAAGACTTGGCC +GAGCCCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGTGGATCAC +GAGGTCAAGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCATCTCTACTAAAAAA +TACAAAAAATTAGCCGGGCGTGGTGGTGGGCACCTGTAGTCCCAGCTACTCGGGAGGCTG +AGGCAGAATGGCGTGAACCTGGTAGGCAGAGCTTGCAGTGAGCTGAGATCACGCCACTGC +ACTCCAGCCTGGGTGACAGAGCAAGACTCCATCTCAAAAATAAATAAATAAATAAATAAA +TAAATAATAATAATAATAAT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/haps.fa.ref.fa new file mode 100644 index 00000000..d05be16a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:32722324-32723313 +ACAGAGGTCTCCTGAAAATTAGTGCCCATAACAGGTGTTTGGTAGACAGGTCTCAGCCCTCAGACAAACCCATTTCCAAAGATGAAGGCCAGAGAATGAGAATAATGATTTATCGTTCTGGCCGGGTGTGATGGCTCATGCCTGTAATCCCAGCGCTGTGGGAGGCGTGGCCGGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACTTGGTCTCTACTAAAAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGCAATCCCAGCTACCCAGAAGGCTGAGTCAGAAGAATCACTTGAACCCGGGAGGTGGAGGTTGCAGTGAGCCGAGATCGTGCCACTGCACTCCAGCCTGGGTGACAGAGTGAGACTCAGGAAAAAAAAAAAAAAGACTTGGCCGAGCCCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGTGGATCACGAGGTCAAGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCATCTCTACTAAAAAATACAAAAAATTAGCCGGGCGTGGTGGTGGGCACCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGAATGGCGTGAACCTGGTAGGCAGAGCTTGCAGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGTGACAGAGCAAGACTCCATCTCAAAAATAAATAAATAAATAAATAAATAAATAATAATAATAATAATAAAGACTTGTGATCCTCTCCCTCTCCCTCTCCCTCTCCGTCTCCCTCTCCCTCTCCCTCTCCCTCCCTCTCCGTCTCCGTCTCCGTCTCCGTCTCCCTCTCCCTCTCCCCACGGTCTCCCTCTCATGCGGAGCCGAAGCTGGACTGTACTGCTGCCATCTCGGCTCACTGCAACCTCCCTGCCTGATTCTCCTGCCTCAGCCTGCCGAGTGCCTGCGATTGCAGGCACGCGCCGCCACGCCTGACTGGTT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/msa.fa new file mode 100644 index 00000000..19c97710 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/msa.fa @@ -0,0 +1,90 @@ +>ref_chr20_32722324_32723313 +acagaggtctcctgaaaattagtgcccataacaggtgtttggtagacaggtctcagccct +cagacaaacccatttccaaagatgaaggccagagaatgagaataatgatttatcgttctg +gccgggtgtgatggctcatgcctgtaatcccagcgctgtgggaggcgtggccggcagatc +acctgaggtcaggagttcaagaccagcctggccaacatggtgaaacttggtctctactaa +aaatacaaaaattagccaggcatggtggtgggcgcctgcaatcccagctacccagaaggc +tgagtcagaagaatcacttgaacccgggaggtggaggttgcagtgagccgagatcgtgcc +actgcactccagcctgggtgacagagtgagactcaggaaaaaaaaaaaaaagacttggcc +gagcccagtggctcacacctgtaatcccagcactttgggaggctgaggcgggtggatcac +gaggtcaagagatcgagaccatcctggctaacacggtgaaaccccatctctactaaaaaa +tacaaaaaattagccgggcgtggtggtgggcacctgtagtcccagctactcgggaggctg +aggcagaatggcgtgaacctggtaggcagagcttgcagtgagctgagatcacgccactgc +actccagcctgggtgacagagcaagactccatctcaaaaataaataaataaataaataaa +taaataa-taataataataataaagacttgtgatcctctccctctccctctccctctccg +tctccctctccctctccctctccctccctctccgtctccgtctccgtctccgtctccctc +tccctctccccacggtctccctctcatgcggagccgaagctggactgtactgctgccatc +tcggctcactgcaacctccctgcctgattctcctgcctcagcctgccgagtgcctgcgat +tgcaggcacgcgccgccacgcctgactggtt +>syndip_1_chr20:32722324-32723313 +acagaggtctcctgaaaattagtgcccataacaggtgtttggtagacaggtctcagccct +cagacaaacccatttccaaagatgaaggccagagaatgagaataatgatttatcgttctg +gccgggtgtgatggctcatgcctgtaatcccagcgctgtgggaggcgtggccggcagatc +acctgaggtcaggagttcaagaccagcctggccaacatggtgaaacttggtctctactaa +aaatacaaaaattagccaggcatggtggtgggcgcctgcaatcccagctacccagaaggc +tgagtcagaagaatcacttgaacccgggaggtggaggttgcagtgagccgagatcgtgcc +actgcactccagcctgggtgacagagtgagactcaggaaaaaaaaaaaaaagacttggcc +gagcccagtggctcacacctgtaatcccagcactttgggaggctgaggcgggtggatcac +gaggtcaagagatcgagaccatcctggctaacacggtgaaaccccatctctactaaaaaa +tacaaaaaattagccgggcgtggtggtgggcacctgtagtcccagctactcgggaggctg +aggcagaatggcgtgaacctggtaggcagagcttgcagtgagctgagatcacgccactgc +actccagcctgggtgacagagcaagactccatctcaaaaataaataaataaataaataaa +taaataa-taataataataataaaaaa--------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------- +>syndip_2_chr20:32722324-32723313 +acagaggtctcctgaaaattagtgcccataacaggtgtttggtagacaggtctcagccct +cagacaaacccatttccaaagatgaaggccagagaatgagaataatgatttatcgttctg +gccgggtgtgatggctcatgcctgtaatcccagcgctgtgggaggcgtggccggcagatc +acctgaggtcaggagttcaagaccagcctggccaacatggtgaaacttggtctctactaa +aaatacaaaaattagccaggcatggtggtgggcgcctgcaatcccagctacccagaaggc +tgagtcagaagaatcacttgaacccgggaggtggaggttgcagtgagccgagatcgtgcc +actgcactccagcctgggtgacagagtgagactcaggaaaaaaaaaaaaaagacttggcc +gagcccagtggctcacacctgtaatcccagcactttgggaggctgaggcgggtggatcac +gaggtcaagagatcgagaccatcctggctaacacggtgaaaccccatctctactaaaaaa +tacaaaaaattagccgggcgtggtggtgggcacctgtagtcccagctactcgggaggctg +aggcagaatggcgtgaacctggtaggcagagcttgcagtgagctgagatcacaccactgc +actccagcctgggtgacagagcaagactccatctcaaaaataaataaataaataaataaa +taaataaataataataataataataat--------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------- +>p:HG002_1_chr20:32722324-32723313 +acagaggtctcctgaaaattagtgcccataacaggtgtttggtagacaggtctcagccct +cagacaaacccatttccaaagatgaaggccagagaatgagaataatgatttatcgttctg +gccgggtgtgatggctcatgcctgtaatcccagcgctgtgggaggcgtggccggcagatc +acctgaggtcaggagttcaagaccagcctggccaacatggtgaaacttggtctctactaa +aaatacaaaaattagccaggcatggtggtgggcgcctgcaatcccagctacccagaaggc +tgagtcagaagaatcacttgaacccgggaggtggaggttgcagtgagccgagatcgtgcc +actgcactccagcctgggtgacagagtgagactcaggaaaaaaaaaaaaaagacttggcc +gagcccagtggctcacacctgtaatcccagcactttgggaggctgaggcgggtggatcac +gaggtcaagagatcgagaccatcctggctaacacggtgaaaccccatctctactaaaaaa +tacaaaaaattagccgggcgtggtggtgggcacctgtagtcccagctactcgggaggctg +aggcagaatggcgtgaacctggtaggcagagcttgcagtgagctgagatcacaccactgc +actccagcctgggtgacagagcaagactccatctcaaaaataaataaataaataaataaa +taaataa----------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------- +>p:HG002_2_chr20:32722324-32723313 +acagaggtctcctgaaaattagtgcccataacaggtgtttggtagacaggtctcagccct +cagacaaacccatttccaaagatgaaggccagagaatgagaataatgatttatcgttctg +gccgggtgtgatggctcatgcctgtaatcccagcgctgtgggaggcgtggccggcagatc +acctgaggtcaggagttcaagaccagcctggccaacatggtgaaacttggtctctactaa +aaatacaaaaattagccaggcatggtggtgggcgcctgcaatcccagctacccagaaggc +tgagtcagaagaatcacttgaacccgggaggtggaggttgcagtgagccgagatcgtgcc +actgcactccagcctgggtgacagagtgagactcaggaaaaaaaaaaaaaagacttggcc +gagcccagtggctcacacctgtaatcccagcactttgggaggctgaggcgggtggatcac +gaggtcaagagatcgagaccatcctggctaacacggtgaaaccccatctctactaaaaaa +tacaaaaaattagccgggcgtggtggtgggcacctgtagtcccagctactcgggaggctg +aggcagaatggcgtgaacctggtaggcagagcttgcagtgagctgagatcacgccactgc +actccagcctgggtgacagagcaagactccatctcaaaaataaataaataaataaataaa +taaataa-taataataataat--------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------- diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/msa.fa.fai new file mode 100644 index 00000000..de0608cb --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_32722324_32723313 991 29 60 61 +syndip_1_chr20:32722324-32723313 991 1071 60 61 +syndip_2_chr20:32722324-32723313 991 2113 60 61 +p:HG002_1_chr20:32722324-32723313 991 3156 60 61 +p:HG002_2_chr20:32722324-32723313 991 4199 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/output.vcf.gz new file mode 100644 index 00000000..1da4c32c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/output.vcf.gz.tbi new file mode 100644 index 00000000..c7636e7e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:32722424-32723213/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/base.vcf.gz new file mode 100644 index 00000000..e88e305a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/base.vcf.gz.tbi new file mode 100644 index 00000000..f587d03d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/comp.vcf.gz new file mode 100644 index 00000000..83c00fd4 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/comp.vcf.gz.tbi new file mode 100644 index 00000000..a6b69791 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/haps.fa new file mode 100644 index 00000000..e9e8c8d2 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/haps.fa @@ -0,0 +1,58 @@ +>ref_chr20_34235650_34236314 +AGCGCATGCCTGTGGCCCCTACTACTCAGGAGGCAGGGGTGGGAGGATTGCTAGAGCCCAGGAAGTCGTGGCTGAAGTGGGCTCATGATAATGCCACTGCACTCCAGCCTGTGTGACAGAGTGAGACTCTGAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAGGAAGGAAGGAAGGAAGGAAGGAAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGAAGGAAGGAAGGAGGGAGGGAGGGAAGAAGGAAAGAAGGAAGGAAGGAGAAAGAGAGAAAGAGAGAGAGAAGAAGAAAGAGAAAGAAACAGAAAAGGAAGGAAGGAGAGAGAGAAAGAAAGAGAAAGAGAAGGAAGGAAGGAAGGAGAAAGAAAGGAAAGGAAAGGAGTGGAAAGGAAAGGAGAGGAAAGGAGAAAGGAGGGAGGGAGGGAAAAGAAAGAAAGAAAGAAAAGGCTAAACCTGACTATGATATTGAATTTACTGCTAGCTCTAGGTGGTTTAAATGATTCAAGAATCATGGCCATGGCTGGGCGCAGTGGCTCACGCCTATAATCCCAGCACTTTGGGAGGCCGAAGCGGGC +>syndip_1_chr20:34235650-34236314 +AGCGCATGCCTGTGGCCCCTACTACTCAGGAGGCAGGGGTGGGAGGATTGCTAGAGCCCA +GGAAGTCGTGGCTGAAGTGGGCTCATGATAATGCCACTGCACTCCAGCCTGTGTGACAGA +GTGAGACTCTGAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG +AAAGAAAGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGGAAGGAAG +GAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGAAGGAGGAGGGAGGGAAGAAT +GAAGGAAGGAAGGAAGGAGGGAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGA +AGGAAGGAAGGAGGGAGGGAGGGAAGAAGGAAGGAGGAGGGAGGGAGGGAAGCAGGAAAG +AAGGAAGGAAGGAGAAAGAGAGAAAGAGAGAGAAGAAGAAAGAGAAAGAAACAGAAAAGG +AAGGAAGGAGAGAGAGAAAGAAAGAGAAAGAGAAGGAAGGAAGGAGAAAGAAAGGAAAAG +GAAAGGAAAGGAGTGGAAAGGAAAGGAGAGGAAAGGAGAAAGGAGGGAGGGAGGGAAAAG +AAAGAAAGAAAGAAAAGGCTAAACCTGACTATGATATTGAATTTACTGCTAGCTCTAGGT +GGTTTAAATGATTCAAGAATCATGGCCATGGCTGGGCGCAGTGGCTCACGCCTATAATCC +CAGCACTTTGGGAGGCCGAAGCGGGC +>syndip_2_chr20:34235650-34236314 +AGCGCATGCCTGTGGCCCCTACTACTCAGGAGGCAGGGGTGGGAGGATTGCTAGAGCCCA +GGAAGTCGTGGCTGAAGTGGGCTCATGATAATGCCACTGCACTCCAGCCTGTGTGACAGA +GTGAGACTCTGAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG +AAAGAAAGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGGAAGGAAG +GAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGAAGGAGGAGGGAGGGAAGAAT +GAAGGAAGGAAGGAAGGAGGGAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGA +AGGAAGGAAGGAGGGAGGGAGGGAAGAAGGAAGGAGGAGGGAGGGAGGGAAGCAGGAAAG +AAGGAAGGAAGGAGAAAGAGAGAAAGAGAGAGAAGAAGAAAGAGAAAGAAACAGAAAAGG +AAGGAAGGAGAGAGAGAAAGAAAGAGAAAGAGAAGGAAGGAAGGAGAAAGAAAGGAAAAG +GAAAGGAAAGGAGTGGAAAGGAAAGGAGAGGAAAGGAGAAAGGAGGGAGGGAGGGAAAAG +AAAGAAAGAAAGAAAAGGCTAAACCTGACTATGATATTGAATTTACTGCTAGCTCTAGGT +GGTTTAAATGATTCAAGAATCATGGCCATGGCTGGGCGCAGTGGCTCACGCCTATAATCC +CAGCACTTTGGGAGGCCGAAGCGGGC +>p:HG002_1_chr20:34235650-34236314 +AGCGCATGCCTGTGGCCCCTACTACTCAGGAGGCAGGGGTGGGAGGATTGCTAGAGCCCA +GGAAGTCGTGGCTGAAGTGGGCTCATGATAATGCCACTGCACTCCAGCCTGTGTGACAGA +GTGAGACTCTGAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG +AAAGAAAGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGGAAGGAAG +GAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGAAGGAGGAGGGAGGGAAGAAT +GAAGGAAGGAAGGAAGGAGGGAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGA +AGGAAGGAAGGAGGGAGGGAGGGAAGAAGGAAGGAGGAGGGAGGGAGGGAAGCAGGAAAG +AAGGAAGGAAGGAGAAAGAGAGAAAGAGAGAGAAGAAGAAAGAGAAAGAAACAGAAAAGG +AAGGAAGGAGAGAGAGAAAGAAAGAGAAAGAGAAGGAAGGAAGGAGAAAGAAAGGAAAAG +GAAAGGAAAGGAGTGGAAAGGAAAGGAGAGGAAAGGAGAAAGGAGGGAGGGAGGGAAAAG +AAAGAAAGAAAGAAAAGGCTAAACCTGACTATGATATTGAATTTACTGCTAGCTCTAGGT +GGTTTAAATGATTCAAGAATCATGGCCATGGCTGGGCGCAGTGGCTCACGCCTATAATCC +CAGCACTTTGGGAGGCCGAAGCGGGC +>p:HG002_2_chr20:34235650-34236314 +AGCGCATGCCTGTGGCCCCTACTACTCAGGAGGCAGGGGTGGGAGGATTGCTAGAGCCCA +GGAAGTCGTGGCTGAAGTGGGCTCATGATAATGCCACTGCACTCCAGCCTGTGTGACAGA +GTGAGACTCTGAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG +AAAGAAAGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGGAAGGAAG +GAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGAAGGAGGAGGGAGGGAAGAAT +GAAGGAAGGAAGGAAGGAGGGAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGA +AGGAAGGAAGGAGGGAGGGAGGGAAGAAGGAAGGAGGAGGGAGGGAGGGAAGCAGGAAAG +AAGGAAGGAAGGAGAAAGAGAGAAAGAGAGAGAAGAAGAAAGAGAAAGAAACAGAAAAGG +AAGGAAGGAGAGAGAGAAAGAAAGAGAAAGAGAAGGAAGGAAGGAGAAAGAAAGGAAAAG +GAAAGGAAAGGAGTGGAAAGGAAAGGAGAGGAAAGGAGAAAGGAGGGAGGGAGGGAAAAG +AAAGAAAGAAAGAAAAGGCTAAACCTGACTATGATATTGAATTTACTGCTAGCTCTAGGT +GGTTTAAATGATTCAAGAATCATGGCCATGGCTGGGCGCAGTGGCTCACGCCTATAATCC +CAGCACTTTGGGAGGCCGAAGCGGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/haps.fa.ref.fa new file mode 100644 index 00000000..83fe6093 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:34235650-34236314 +AGCGCATGCCTGTGGCCCCTACTACTCAGGAGGCAGGGGTGGGAGGATTGCTAGAGCCCAGGAAGTCGTGGCTGAAGTGGGCTCATGATAATGCCACTGCACTCCAGCCTGTGTGACAGAGTGAGACTCTGAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAGGAAGGAAGGAAGGAAGGAAGGAAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGAAGGAAGGAAGGAGGGAGGGAGGGAAGAAGGAAAGAAGGAAGGAAGGAGAAAGAGAGAAAGAGAGAGAGAAGAAGAAAGAGAAAGAAACAGAAAAGGAAGGAAGGAGAGAGAGAAAGAAAGAGAAAGAGAAGGAAGGAAGGAAGGAGAAAGAAAGGAAAGGAAAGGAGTGGAAAGGAAAGGAGAGGAAAGGAGAAAGGAGGGAGGGAGGGAAAAGAAAGAAAGAAAGAAAAGGCTAAACCTGACTATGATATTGAATTTACTGCTAGCTCTAGGTGGTTTAAATGATTCAAGAATCATGGCCATGGCTGGGCGCAGTGGCTCACGCCTATAATCCCAGCACTTTGGGAGGCCGAAGCGGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/msa.fa new file mode 100644 index 00000000..6d5785e2 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/msa.fa @@ -0,0 +1,70 @@ +>ref_chr20_34235650_34236314 +agcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccca +ggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacaga +gtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag +aaagaaagaaagaaggaaggaaggaaggaaggaaggaaaggaaggaaggaaggaaggaag +gaaggaagga-------------------------------------------------- +-----aaggaaggaaggaaggaaggaaggaaggaagcgggagggagggaagaaggaagga +aggaaggaaggagggagggagggaaga--------------------------aggaaag +aaggaaggaaggagaaagagagaaagagagagagaagaagaaagagaaagaaacagaaaa +ggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggaaggagaaag--aa +aggaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaaa +agaaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctctag +gtggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataat +cccagcactttgggaggccgaagcgggc +>syndip_1_chr20:34235650-34236314 +agcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccca +ggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacaga +gtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag +aaagaaagaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaagggaaggaag +gaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaggagggagggaagaat +gaaggaaggaaggaaggagggaaggaaggaaggaagcgggagggagggaagaaggaagga +aggaaggaaggagggagggagggaagaaggaaggaggagggagggagggaagcaggaaag +aaggaaggaaggagaaagagagaa--agagagagaagaagaaagagaaagaaacagaaaa +ggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggagaaagaaaggaaa +aggaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaaa +agaaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctctag +gtggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataat +cccagcactttgggaggccgaagcgggc +>syndip_2_chr20:34235650-34236314 +agcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccca +ggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacaga +gtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag +aaagaaagaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaagggaaggaag +gaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaggagggagggaagaat +gaaggaaggaaggaaggagggaaggaaggaaggaagcgggagggagggaagaaggaagga +aggaaggaaggagggagggagggaagaaggaaggaggagggagggagggaagcaggaaag +aaggaaggaaggagaaagagagaa--agagagagaagaagaaagagaaagaaacagaaaa +ggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggagaaagaaaggaaa +aggaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaaa +agaaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctctag +gtggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataat +cccagcactttgggaggccgaagcgggc +>p:HG002_1_chr20:34235650-34236314 +agcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccca +ggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacaga +gtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag +aaagaaagaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaagggaaggaag +gaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaggagggagggaagaat +gaaggaaggaaggaaggagggaaggaaggaaggaagcgggagggagggaagaaggaagga +aggaaggaaggagggagggagggaagaaggaaggaggagggagggagggaagcaggaaag +aaggaaggaaggagaaagagagaa--agagagagaagaagaaagagaaagaaacagaaaa +ggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggagaaagaaaggaaa +aggaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaaa +agaaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctctag +gtggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataat +cccagcactttgggaggccgaagcgggc +>p:HG002_2_chr20:34235650-34236314 +agcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccca +ggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacaga +gtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag +aaagaaagaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaagggaaggaag +gaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaggagggagggaagaat +gaaggaaggaaggaaggagggaaggaaggaaggaagcgggagggagggaagaaggaagga +aggaaggaaggagggagggagggaagaaggaaggaggagggagggagggaagcaggaaag +aaggaaggaaggagaaagagagaa--agagagagaagaagaaagagaaagaaacagaaaa +ggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggagaaagaaaggaaa +aggaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaaa +agaaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctctag +gtggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataat +cccagcactttgggaggccgaagcgggc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/msa.fa.fai new file mode 100644 index 00000000..f5d2be63 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_34235650_34236314 748 29 60 61 +syndip_1_chr20:34235650-34236314 748 824 60 61 +syndip_2_chr20:34235650-34236314 748 1619 60 61 +p:HG002_1_chr20:34235650-34236314 748 2415 60 61 +p:HG002_2_chr20:34235650-34236314 748 3211 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/output.vcf.gz new file mode 100644 index 00000000..34b6effc Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/output.vcf.gz.tbi new file mode 100644 index 00000000..1e60e2ed Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:34235750-34236214/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/base.vcf.gz new file mode 100644 index 00000000..825b9675 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/base.vcf.gz.tbi new file mode 100644 index 00000000..2634fdcb Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/comp.vcf.gz new file mode 100644 index 00000000..5ea31fc7 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/comp.vcf.gz.tbi new file mode 100644 index 00000000..5d82c139 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/haps.fa new file mode 100644 index 00000000..50a2ab03 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/haps.fa @@ -0,0 +1,56 @@ +>ref_chr20_35539020_35539825 +TTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTAGCCAGGATGGTCTTGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACAGCGCCCGGCCTATGTTTTACATATATAACAATTTATATATAACTACATATATAATATATATAACAGTTTATATATATATATAACAGTTTATATATATAATATATATAACAGTTTATATATATATATATAACAGTTTATATATATAATATATATAACAGTTTATATATATAATATATATAACAGTTTATATATATAATATATAAGTTTATATATTATATATAACAGTTTATATATAACAGTTTATATATAATATATATAAGTTTATATATAACAGTTTATATATATAATATATATAAGTTTATATATAATATATATAAGTTTATATATATGTTTATATATAATATATATAACAGTTTATATATATAATATATATAACAGTTTATATATATAATATATATAACAGTTTATATATATAATATATATAACAGTTTATATATATAAAATATATAACAGTTTATATATATAATATATATAAGTTTATATATATAATATATATAACAGTTTATATATATTATATATATATATATGCACACACACAAAGAGAGAGAGAGAGACTCGCTCTGTCGCCCAGGCTGTAGTGCAGTGGTGTAATCACAGCTCACTATGAGGCAGGAGAACAGGGAATCAGGGTAACCGGGGGTTAAGACATAAGCAAATGAAGGGGTGCAGCCAGTTCTAGGCAGCA +>syndip_1_chr20:35539020-35539825 +TTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTAGCCAGGATGGTCTTGATCTCC +TGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCAC +AGCGCCCGGCCTATGTTTTACATATATAACAATTTATATATAACTACATATATAATATAT +ATAACAGTTTATATATATATATAACAGTTTATATATATATTATATATAACAGTTTATATA +TATAATATATATGTTTATATATTATATATAACAGTTTATATATAACAGTTTATATATAAT +ATATATAAGTTTATATATAACAGTTTATATATATAATATATATAAGTTTATATATAATAT +ATATAAGTTTATATATGTTTATATATAATATATATAACAGTTTATATATATAATATATAT +AACAGTTTATATATATAATATATATAACAGTTTATATATATAATATATATAAGTTTATAT +ATATAATATATATAACAGTTTATATATATTATATATATATATATGCACACACACAAAGAG +AGAGAGAGAGACTCGCTCTGTCGCCCAGGCTGTAGTGCAGTGGTGTAATCACAGCTCACT +ATGAGGCAGGAGAACAGGGAATCAGGGTAACCGGGGGTTAAGACATAAGCAAATGAAGGG +GTGCAGCCAGTTCTAGGCAGCA +>syndip_2_chr20:35539020-35539825 +TTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTAGCCAGGATGGTCTTGATCTCC +TGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCAC +AGCGCCCGGCCTATGTTTTACATATATAACAATTTATATATAACTACATATATAATATAT +ATAACAGTTTATATATATATATAACAGTTTATATATATAATATATATAACAGTTTATATA +TATATATAACAGTTTATATATATAATATATATAAGTTTATATATTATATATAACAGTTTA +TATATAACAGTTTATATATAATATATATAAGTTTATATATAACAGTTTATATATATAATA +TATATAAGTTTATATATAATATATATAAGTTTATATATATGTTTATATATAATATATATA +ACAGTTTATATATATAATATATATAACAGTTTATATATATAATATATATAACAGTTTATA +TATATAATATATATAACAGTTTATATATATAATATATATAAGTTTATATATATAATATAT +ATAACAGTTTATATATATTATATATATATATATGCACACACACAAAGAGAGAGAGAGAGA +CTCGCTCTGTCGCCCAGGCTGTAGTGCAGTGGTGTAATCACAGCTCACTATGAGGCAGGA +GAACAGGGAATCAGGGTAACCGGGGGTTAAGACATAAGCAAATGAAGGGGTGCAGCCAGT +TCTAGGCAGCA +>p:HG002_1_chr20:35539020-35539825 +TTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTAGCCAGGATGGTCTTGATCTCC +TGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCAC +AGCGCCCGGCCTATGTTTTACATATATAACAATTTATATATAACTACATATATAATATAT +ATAACAGTTTATATATATATATAACAGTTTATATATATAATATATATAACAGTTTATATA +TATATATAACAGTTTATATATATAATATATATAAGTTTATATATTATATATAACAGTTTA +TATATAACAGTTTATATATAATATATATAAGTTTATATATAACAGTTTATATATATAATA +TATATAAGTTTATATATAATATATATAAGTTTATATATATGTTTATATATAATATATATA +ACAGTTTATATATATAATATATATAACAGTTTATATATATAATATATATAACAGTTTATA +TATATAATATATATAACAGTTTATATATATAATATATATAAGTTTATATATATAATATAT +ATAACAGTTTATATATATTATATATATATATATGCACACACACAAAGAGAGAGAGAGAGA +CTCGCTCTGTCGCCCAGGCTGTAGTGCAGTGGTGTAATCACAGCTCACTATGAGGCAGGA +GAACAGGGAATCAGGGTAACCGGGGGTTAAGACATAAGCAAATGAAGGGGTGCAGCCAGT +TCTAGGCAGCA +>p:HG002_2_chr20:35539020-35539825 +TTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTAGCCAGGATGGTCTTGATCTCC +TGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCAC +AGCGCCCGGCCTATGTTTTACATATATAACAATTTATATATAACTACATATATAATATAT +ATAACAGTTTATATATATATATAACAGTTTATATATATATTATATATAACAGTTTATATA +TATAATATATATGTTTATATATTATATATAACAGTTTATATATAACAGTTTATATATAAT +ATATATAAGTTTATATATAACAGTTTATATATATAATATATATAAGTTTATATATAATAT +ATATAAGTTTATATATGTTTATATATAATATATATAACAGTTTATATATATAATATATAT +AACAGTTTATATATATAATATATATAACAGTTTATATATATAATATATATAAGTTTATAT +ATATAATATATATAACAGTTTATATATATTATATATATATATATGCACACACACAAAGAG +AGAGAGAGAGACTCGCTCTGTCGCCCAGGCTGTAGTGCAGTGGTGTAATCACAGCTCACT +ATGAGGCAGGAGAACAGGGAATCAGGGTAACCGGGGGTTAAGACATAAGCAAATGAAGGG +GTGCAGCCAGTTCTAGGCAGCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/haps.fa.ref.fa new file mode 100644 index 00000000..74f390c8 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:35539020-35539825 +TTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTAGCCAGGATGGTCTTGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACAGCGCCCGGCCTATGTTTTACATATATAACAATTTATATATAACTACATATATAATATATATAACAGTTTATATATATATATAACAGTTTATATATATAATATATATAACAGTTTATATATATATATATAACAGTTTATATATATAATATATATAACAGTTTATATATATAATATATATAACAGTTTATATATATAATATATAAGTTTATATATTATATATAACAGTTTATATATAACAGTTTATATATAATATATATAAGTTTATATATAACAGTTTATATATATAATATATATAAGTTTATATATAATATATATAAGTTTATATATATGTTTATATATAATATATATAACAGTTTATATATATAATATATATAACAGTTTATATATATAATATATATAACAGTTTATATATATAATATATATAACAGTTTATATATATAAAATATATAACAGTTTATATATATAATATATATAAGTTTATATATATAATATATATAACAGTTTATATATATTATATATATATATATGCACACACACAAAGAGAGAGAGAGAGACTCGCTCTGTCGCCCAGGCTGTAGTGCAGTGGTGTAATCACAGCTCACTATGAGGCAGGAGAACAGGGAATCAGGGTAACCGGGGGTTAAGACATAAGCAAATGAAGGGGTGCAGCCAGTTCTAGGCAGCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/msa.fa new file mode 100644 index 00000000..d5e3bc13 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/msa.fa @@ -0,0 +1,75 @@ +>ref_chr20_35539020_35539825 +tttttgtatttttagtagagacagggtttcaccatgttagccaggatggtcttgatctcc +tgacctcgtgatccgcccgcctcggcctcccaaagtgctgggattacaggcgtgagccac +agcgcccggcctatgttttacatatataacaatttatatataactacatatataatatat +ataacagtttatatatatatataacagtttatatatataatatatataacagtttatata +tatatatataacagtttatatatataatatatataacagtttatatatataatatatata +acagtttatatatataatatataagtttatatattatatataacagtttatatataacag +tttatatataatatatataagtttatatataacagtttatatatataatatatataagtt +tatatataatatatataagtttatatatatgtttatatataatatatataacagtttata +tatataatatatataacagtttatatatataatatatataacagtttatatatataatat +atataacagtttatatatataaaatatataacagtttatatatataatatatataagttt +atatatataatatatataacagtttatatatattatatatatatatatgcacacacacaa +agagagagagagagactcgctctgtcgcccaggctgtagtgcagtggtgtaatcacagct +cactatgaggcaggagaacagggaatcagggtaaccgggggttaagacataagcaaatga +aggggtgcagccagttctaggcagca +>syndip_1_chr20:35539020-35539825 +tttttgtatttttagtagagacagggtttcaccatgttagccaggatggtcttgatctcc +tgacctcgtgatccgcccgcctcggcctcccaaagtgctgggattacaggcgtgagccac +agcgcccggcctatgttttacatatataacaatttatatataactacatatataatatat +ataacagtttatatatatatataacagtttatatatatattatatataacagtt--tata +tatata------------------------------------------------------ +----------------atatatatgtttatatattatatataacagtttatatataacag +tttatatataatatatataagtttatatataacagtttatatatataatatatataagtt +tatatataatatatataagtttatatatg------------------------------- +---------------------tttatatataatatatataacagtttatatatataatat +atataacagtttatatatataatatatataacagtttatatatataatatatataagttt +atatatataatatatataacagtttatatatattatatatatatatatgcacacacacaa +agagagagagagagactcgctctgtcgcccaggctgtagtgcagtggtgtaatcacagct +cactatgaggcaggagaacagggaatcagggtaaccgggggttaagacataagcaaatga +aggggtgcagccagttctaggcagca +>syndip_2_chr20:35539020-35539825 +tttttgtatttttagtagagacagggtttcaccatgttagccaggatggtcttgatctcc +tgacctcgtgatccgcccgcctcggcctcccaaagtgctgggattacaggcgtgagccac +agcgcccggcctatgttttacatatataacaatttatatataactacatatataatatat +ataacagtttatatatatatataacagtttatatatataatatatataacagtt--tata +tatatatataacagtttatatatataat-------------------------------- +----------------atatataagtttatatattatatataacagtttatatataacag +tttatatataatatatataagtttatatataacagtttatatatataatatatataagtt +tatatataatatatataagtttatatatatgtttatatataatatatataacagtt---- +---------------------tatatatataatatatataacagtttatatatataatat +atataacagtttatatatataatatatataacagtttatatatataatatatataagttt +atatatataatatatataacagtttatatatattatatatatatatatgcacacacacaa +agagagagagagagactcgctctgtcgcccaggctgtagtgcagtggtgtaatcacagct +cactatgaggcaggagaacagggaatcagggtaaccgggggttaagacataagcaaatga +aggggtgcagccagttctaggcagca +>p:HG002_1_chr20:35539020-35539825 +tttttgtatttttagtagagacagggtttcaccatgttagccaggatggtcttgatctcc +tgacctcgtgatccgcccgcctcggcctcccaaagtgctgggattacaggcgtgagccac +agcgcccggcctatgttttacatatataacaatttatatataactacatatataatatat +ataacagtttatatatatatataacagtttatatatataatatatataacagtt--tata +tatatatataacagtttatatatataat-------------------------------- +----------------atatataagtttatatattatatataacagtttatatataacag +tttatatataatatatataagtttatatataacagtttatatatataatatatataagtt +tatatataatatatataagtttatatatatgtttatatataatatatataacagtt---- +---------------------tatatatataatatatataacagtttatatatataatat +atataacagtttatatatataatatatataacagtttatatatataatatatataagttt +atatatataatatatataacagtttatatatattatatatatatatatgcacacacacaa +agagagagagagagactcgctctgtcgcccaggctgtagtgcagtggtgtaatcacagct +cactatgaggcaggagaacagggaatcagggtaaccgggggttaagacataagcaaatga +aggggtgcagccagttctaggcagca +>p:HG002_2_chr20:35539020-35539825 +tttttgtatttttagtagagacagggtttcaccatgttagccaggatggtcttgatctcc +tgacctcgtgatccgcccgcctcggcctcccaaagtgctgggattacaggcgtgagccac +agcgcccggcctatgttttacatatataacaatttatatataactacatatataatatat +ataacagtttatatatatatataacagtttatatatatattatatataacagtt--tata +tatata------------------------------------------------------ +----------------atatatatgtttatatattatatataacagtttatatataacag +tttatatataatatatataagtttatatataacagtttatatatataatatatataagtt +tatatataatatatataagtttatatatg------------------------------- +---------------------tttatatataatatatataacagtttatatatataatat +atataacagtttatatatataatatatataacagtttatatatataatatatataagttt +atatatataatatatataacagtttatatatattatatatatatatatgcacacacacaa +agagagagagagagactcgctctgtcgcccaggctgtagtgcagtggtgtaatcacagct +cactatgaggcaggagaacagggaatcagggtaaccgggggttaagacataagcaaatga +aggggtgcagccagttctaggcagca diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/msa.fa.fai new file mode 100644 index 00000000..4954776a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_35539020_35539825 806 29 60 61 +syndip_1_chr20:35539020-35539825 806 883 60 61 +syndip_2_chr20:35539020-35539825 806 1737 60 61 +p:HG002_1_chr20:35539020-35539825 806 2592 60 61 +p:HG002_2_chr20:35539020-35539825 806 3447 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/output.vcf.gz new file mode 100644 index 00000000..7003cc01 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/output.vcf.gz.tbi new file mode 100644 index 00000000..8ed81d9e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35539120-35539725/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/base.vcf.gz new file mode 100644 index 00000000..651477d0 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/base.vcf.gz.tbi new file mode 100644 index 00000000..f54b5b24 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/comp.vcf.gz new file mode 100644 index 00000000..63e8428d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/comp.vcf.gz.tbi new file mode 100644 index 00000000..364db081 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/haps.fa new file mode 100644 index 00000000..51e65823 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/haps.fa @@ -0,0 +1,88 @@ +>ref_chr20_35579913_35580987 +AAAACTCCATCTCAAAAAAAAAAAAAAAAAAAAAGGGACACAATCCTGGATTCAAAAGACTGTTGTAAATATCAAATGACATAATAGAAACATAAGTACTTTGGAGCCTACAAAGTGCTGTCAGAAGCTGGGCATGGTGGCTCATGCCTGTAACCCCAGCACTTTGGGAGGCTGAGGCAGGCAGACTGCTCAAACTCAGGAGTTCGAGACCAGCCTGGGCAACATGGCAAGACACCATCTGTACCAAAAATACAAAAAAATAGCCGGGCATAGTGGTGCGCACCTGTGGTCCCAGCTACTCAGGAGGTTGAGGTGGGAGGATCACTTGAGCCCAGGGGGCGGAGGTTACAGTGAGCCAAGATTTGCACTCCAGCCTTGGTGACAGAGCAAGAGACCCTGTCTAAAATATATATGTGTATATACACACACACACACACAAATATATTTTTTGGCTGGGCATGGTGGCTGACACCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGCAGATCACTTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAAGATGATGAAATCCTGTCTCTACTAAAAATACAAAAAAATTAGCTGGGTGTGGTAACGGGTGGCTGTAATCCCAGCTACTTGGGAAGCTGAGGCAGAAGAATAGCTTGAACCTGGGAGGCACAGGTTGCAGTGAGCCGAGATCGCGCCACTGCAGCCTAGGCAGCAGAGTGAGACTCTGTCTTAAAATATATATTATGGTTTATTTTATTTTATGGTTAAAGGCCATATATATATATATATAAAATATATATATATAAAATATATATAAAATATATATATATAAAATATATATATAATATATATATATAAAATATATATATATAATATATATATATAAAATATATATATATAAAATATATATATATATAAAATATATATATATATAAAATATATATATGGAATTCCATATCTATCAATGGATCCTAAGGGAAACAATTTTACTACTGTATTGGTGGGTTTATTTTATGTATTTGTAGATATATACATATATACACATATATATGACAATTTTAGCACAAAAGAGAGGAA +>syndip_1_chr20:35579913-35580987 +AAAACTCCATCTCAAAAAAAAAAAAAAAAAAAAAGGGACACAATCCTGGATTCAAAAGAC +TGTTGTAAATATCAAATGACATAATAGAAACATAAGTACTTTGGAGCCTACAAAGTGCTG +TCAGAAGCTGGGCATGGTGGCTCATGCCTGTAACCCCAGCACTTTGGGAGGCTGAGGCAG +GCAGACTGCTCAAACTCAGGAGTTCGAGACCAGCCTGGGCAACATGGCAAGACACCATCT +GTACCAAAAATACAAAAAAATAGCCGGGCATAGTGGTGCGCACCTGTGGTCCCAGCTACT +CAGGAGGTTGAGGTGGGAGGATCACTTGAGCCCAGGGGGCGGAGGTTACAGTGAGCCAAG +ATTTGCACTCCAGCCTTGGTGACAGAGCAAGAGACCCTGTCTAAAATATATATGTGTATA +TACACACACACACACACAAATATATTTTTTGGCTGGGCATGGTGGCTGACACCTGTAATC +CCAGCACTTTGGGAGGCCAAGGCAGGCAGATCACTTGAGGTCAGGAGTTTGAGACCAGCC +TGGCCAAGATGATGAAATCCTGTCTCTACTAAAAATACAAAAAAATTAGCTGGGTGTGGT +AACGGGTGGCTGTAATCCCAGCTACTTGGGAAGCTGAGGCAGAAGAATAGCTTGAACCTG +GGAGGCACAGGTTGCAGTGAGCCGAGATCGCGCCACTGCAGCCTAGGCAGCAGAGTGAGA +CTCTGTCTTAAAATATATATTATGGTTTATTTTATTTTATGGTTAAAGGCCATATATATA +TATATATATATATATATAATATATATATATATAAAATATATATATATAAAATATATATAT +ATATAAAATATATATATATAAAATATATATATATATATAAAATATATATATATAAAATAT +ATATATATAAAATATATATATATATAAAATATATATATATATAAAATATATATATATAAA +ATATATATATATATAAAATATATATATATAAAATATATATATATAAAATATATATATATA +TAAAATATATATATATAAAATATATATATATAAAATATATATATATATAATATATATATA +TAAAATATATATATATAAAATATATATATAAAATATATATATATAAAATATATATATATA +AAATATATATATATAAAATATATATATATAAAATATATATATAAAATATATATATATAAA +ATATATATATATAAAATATATATATATAAAATATATATATGGAATTCCATATCTATCAAT +GGATCCTAAGGGAAACAATTTTACTACTGTATTGGTGGGTTTATTTTATGTATTTGTAGA +TATATACATATATACACATATATATGACAATTTTAGCACAAAAGAGAGGAA +>syndip_2_chr20:35579913-35580987 +AAAACTCCATCTCAAAAAAAAAAAAAAAAAAAAAGGGACACAATCCTGGATTCAAAAGAC +TGTTGTAAATATCAAATGACATAATAGAAACATAAGTACTTTGGAGCCTACAAAGTGCTG +TCAGAAGCTGGGCATGGTGGCTCATGCCTGTAACCCCAGCACTTTGGGAGGCTGAGGCAG +GCAGACTGCTCAAACTCAGGAGTTCGAGACCAGCCTGGGCAACATGGCAAGACACCATCT +GTACCAAAAATACAAAAAAATAGCCGGGCATAGTGGTGCGCACCTGTGGTCCCAGCTACT +CAGGAGGTTGAGGTGGGAGGATCACTTGAGCCCAGGGGGCGGAGGTTACAGTGAGCCAAG +ATTTGCACTCCAGCCTTGGTGACAGAGCAAGAGACCCTGTCTAAAATATATATGTGTATA +TACACACACACACACACAAATATATTTTTTGGCTGGGCATGGTGGCTGACACCTGTAATC +CCAGCACTTTGGGAGGCCAAGGCAGGCAGATCACTTGAGGTCAGGAGTTTGAGACCAGCC +TGGCCAAGATGATGAAATCCTGTCTCTACTAAAAATACAAAAAAATTAGCTGGGTGTGGT +AACGGGTGGCTGTAATCCCAGCTACTTGGGAAGCTGAGGCAGAAGAATAGCTTGAACCTG +GGAGGCACAGGTTGCAGTGAGCCGAGATCGCGCCACTGCAGCCTAGGCAGCAGAGTGAGA +CTCTGTCTTAAAATATATATTATGGTTTATTTTATTTTATGGTTAAAGGCCATATATATA +TATATATATATATAAAATATATATAATATATATATATATAATATATATATAAAATATATA +TAAAATATATATATATAAAATATATATATATAAAATATATATATATAAAATATATATATA +TATATAAAATATATATATGGAATTCCATATCTATCAATGGATCCTAAGGGAAACAATTTT +ACTACTGTATTGGTGGGTTTATTTTATGTATTTGTAGATATATACATATATACACATATA +TATGACAATTTTAGCACAAAAGAGAGGAA +>p:HG002_1_chr20:35579913-35580987 +AAAACTCCATCTCAAAAAAAAAAAAAAAAAAAAAGGGACACAATCCTGGATTCAAAAGAC +TGTTGTAAATATCAAATGACATAATAGAAACATAAGTACTTTGGAGCCTACAAAGTGCTG +TCAGAAGCTGGGCATGGTGGCTCATGCCTGTAACCCCAGCACTTTGGGAGGCTGAGGCAG +GCAGACTGCTCAAACTCAGGAGTTCGAGACCAGCCTGGGCAACATGGCAAGACACCATCT +GTACCAAAAATACAAAAAAATAGCCGGGCATAGTGGTGCGCACCTGTGGTCCCAGCTACT +CAGGAGGTTGAGGTGGGAGGATCACTTGAGCCCAGGGGGCGGAGGTTACAGTGAGCCAAG +ATTTGCACTCCAGCCTTGGTGACAGAGCAAGAGACCCTGTCTAAAATATATATGTGTATA +TACACACACACACACACAAATATATTTTTTGGCTGGGCATGGTGGCTGACACCTGTAATC +CCAGCACTTTGGGAGGCCAAGGCAGGCAGATCACTTGAGGTCAGGAGTTTGAGACCAGCC +TGGCCAAGATGATGAAATCCTGTCTCTACTAAAAATACAAAAAAATTAGCTGGGTGTGGT +AACGGGTGGCTGTAATCCCAGCTACTTGGGAAGCTGAGGCAGAAGAATAGCTTGAACCTG +GGAGGCACAGGTTGCAGTGAGCCGAGATCGCGCCACTGCAGCCTAGGCAGCAGAGTGAGA +CTCTGTCTTAAAATATATATTATGGTTTATTTTATTTTATGGTTAAAGGCCATATATATA +TATATATATATATAAAATATATATAATATATATATATATAATATATATATAAAATATATA +TAAAATATATATATATAAAATATATATATATAAAATATATATATATAAAATATATATATA +TATATAAAATATATATATGGAATTCCATATCTATCAATGGATCCTAAGGGAAACAATTTT +ACTACTGTATTGGTGGGTTTATTTTATGTATTTGTAGATATATACATATATACACATATA +TATGACAATTTTAGCACAAAAGAGAGGAA +>p:HG002_2_chr20:35579913-35580987 +AAAACTCCATCTCAAAAAAAAAAAAAAAAAAAAAGGGACACAATCCTGGATTCAAAAGAC +TGTTGTAAATATCAAATGACATAATAGAAACATAAGTACTTTGGAGCCTACAAAGTGCTG +TCAGAAGCTGGGCATGGTGGCTCATGCCTGTAACCCCAGCACTTTGGGAGGCTGAGGCAG +GCAGACTGCTCAAACTCAGGAGTTCGAGACCAGCCTGGGCAACATGGCAAGACACCATCT +GTACCAAAAATACAAAAAAATAGCCGGGCATAGTGGTGCGCACCTGTGGTCCCAGCTACT +CAGGAGGTTGAGGTGGGAGGATCACTTGAGCCCAGGGGGCGGAGGTTACAGTGAGCCAAG +ATTTGCACTCCAGCCTTGGTGACAGAGCAAGAGACCCTGTCTAAAATATATATGTGTATA +TACACACACACACACACAAATATATTTTTTGGCTGGGCATGGTGGCTGACACCTGTAATC +CCAGCACTTTGGGAGGCCAAGGCAGGCAGATCACTTGAGGTCAGGAGTTTGAGACCAGCC +TGGCCAAGATGATGAAATCCTGTCTCTACTAAAAATACAAAAAAATTAGCTGGGTGTGGT +AACGGGTGGCTGTAATCCCAGCTACTTGGGAAGCTGAGGCAGAAGAATAGCTTGAACCTG +GGAGGCACAGGTTGCAGTGAGCCGAGATCGTGCCACTGCAGCCTAGGCAGCAGAGTGAGA +CTCTGTCTTAAAATATATATTATGGTTTATTTTATTTTATGGTTAAAGGCCATATATATA +TATATATATATATATATAATATATATATATATAAAATATATATATATAAAATATATATAT +ATATAAAATATATATATATAAAATATATATATATATATAAAATATATATATATAAAATAT +ATATATATAAAATATATATATATATAAAATATATATATATATAAAATATATATATATAAA +ATATATATATATATAAAATATATATATATAAAATATATATATATAAAATATATATATATA +TAAAATATATATATATAAAATATATATATATAAAATATATATATATATAATATATATATA +TAAAATATATATATATAAAATATATATATAAAATATATATATATAAAATATATATATATA +AAATATATATATATAAAATATATATATATAAAATATATATATAAAATATATATATATAAA +ATATATATATATAAAATATATATATATAAAATATATATATGGAATTCCATATCTATCAAT +GGATCCTAAGGGAAACAATTTTACTACTGTATTGGTGGGTTTATTTTATGTATTTGTAGA +TATATACATATATACACATATATATGACAATTTTAGCACAAAAGAGAGGAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/haps.fa.ref.fa new file mode 100644 index 00000000..358aa93e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:35579913-35580987 +AAAACTCCATCTCAAAAAAAAAAAAAAAAAAAAAGGGACACAATCCTGGATTCAAAAGACTGTTGTAAATATCAAATGACATAATAGAAACATAAGTACTTTGGAGCCTACAAAGTGCTGTCAGAAGCTGGGCATGGTGGCTCATGCCTGTAACCCCAGCACTTTGGGAGGCTGAGGCAGGCAGACTGCTCAAACTCAGGAGTTCGAGACCAGCCTGGGCAACATGGCAAGACACCATCTGTACCAAAAATACAAAAAAATAGCCGGGCATAGTGGTGCGCACCTGTGGTCCCAGCTACTCAGGAGGTTGAGGTGGGAGGATCACTTGAGCCCAGGGGGCGGAGGTTACAGTGAGCCAAGATTTGCACTCCAGCCTTGGTGACAGAGCAAGAGACCCTGTCTAAAATATATATGTGTATATACACACACACACACACAAATATATTTTTTGGCTGGGCATGGTGGCTGACACCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGCAGATCACTTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAAGATGATGAAATCCTGTCTCTACTAAAAATACAAAAAAATTAGCTGGGTGTGGTAACGGGTGGCTGTAATCCCAGCTACTTGGGAAGCTGAGGCAGAAGAATAGCTTGAACCTGGGAGGCACAGGTTGCAGTGAGCCGAGATCGCGCCACTGCAGCCTAGGCAGCAGAGTGAGACTCTGTCTTAAAATATATATTATGGTTTATTTTATTTTATGGTTAAAGGCCATATATATATATATATAAAATATATATATATAAAATATATATAAAATATATATATATAAAATATATATATAATATATATATATAAAATATATATATATAATATATATATATAAAATATATATATATAAAATATATATATATATAAAATATATATATATATAAAATATATATATGGAATTCCATATCTATCAATGGATCCTAAGGGAAACAATTTTACTACTGTATTGGTGGGTTTATTTTATGTATTTGTAGATATATACATATATACACATATATATGACAATTTTAGCACAAAAGAGAGGAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/msa.fa new file mode 100644 index 00000000..a92e0ef2 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/msa.fa @@ -0,0 +1,120 @@ +>ref_chr20_35579913_35580987 +aaaactccatctcaaaaaaaaaaaaaaaaaaaaagggacacaatcctggattcaaaagac +tgttgtaaatatcaaatgacataatagaaacataagtactttggagcctacaaagtgctg +tcagaagctgggcatggtggctcatgcctgtaaccccagcactttgggaggctgaggcag +gcagactgctcaaactcaggagttcgagaccagcctgggcaacatggcaagacaccatct +gtaccaaaaatacaaaaaaatagccgggcatagtggtgcgcacctgtggtcccagctact +caggaggttgaggtgggaggatcacttgagcccagggggcggaggttacagtgagccaag +atttgcactccagccttggtgacagagcaagagaccctgtctaaaatatatatgtgtata +tacacacacacacacacaaatatattttttggctgggcatggtggctgacacctgtaatc +ccagcactttgggaggccaaggcaggcagatcacttgaggtcaggagtttgagaccagcc +tggccaagatgatgaaatcctgtctctactaaaaatacaaaaaaattagctgggtgtggt +aacgggtggctgtaatcccagctacttgggaagctgaggcagaagaatagcttgaacctg +ggaggcacaggttgcagtgagccgagatcgcgccactgcagcctaggcagcagagtgaga +ctctgtcttaaaatatatattatggtttattttattttatggttaaaggccatatatata +t-------------------------atatataaaatatatatatataaa------atat +atataaaatatatatatataaa-------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------atatatatataatatatatata +taa---------------aatatatatatataatatatatatataaaatatatatatata +aaatatatatatatataaaat--------------------------------------- +---------------atatatatatataaaatatatatatggaattccatatctatcaat +ggatcctaagggaaacaattttactactgtattggtgggtttattttatgtatttgtaga +tatatacatatatacacatatatatgacaattttagcacaaaagagaggaa +>syndip_1_chr20:35579913-35580987 +aaaactccatctcaaaaaaaaaaaaaaaaaaaaagggacacaatcctggattcaaaagac +tgttgtaaatatcaaatgacataatagaaacataagtactttggagcctacaaagtgctg +tcagaagctgggcatggtggctcatgcctgtaaccccagcactttgggaggctgaggcag +gcagactgctcaaactcaggagttcgagaccagcctgggcaacatggcaagacaccatct +gtaccaaaaatacaaaaaaatagccgggcatagtggtgcgcacctgtggtcccagctact +caggaggttgaggtgggaggatcacttgagcccagggggcggaggttacagtgagccaag +atttgcactccagccttggtgacagagcaagagaccctgtctaaaatatatatgtgtata +tacacacacacacacacaaatatattttttggctgggcatggtggctgacacctgtaatc +ccagcactttgggaggccaaggcaggcagatcacttgaggtcaggagtttgagaccagcc +tggccaagatgatgaaatcctgtctctactaaaaatacaaaaaaattagctgggtgtggt +aacgggtggctgtaatcccagctacttgggaagctgaggcagaagaatagcttgaacctg +ggaggcacaggttgcagtgagccgagatcgcgccactgcagcctaggcagcagagtgaga +ctctgtcttaaaatatatattatggtttattttattttatggttaaaggccatatatata +tatatatatatatatataatatatatatatataaaatatatatatataaaatatatatat +atataaaatatatatatataaaatatatatatatatataaaatatatatatataaaatat +atatatataaaatatatatatatataaaatatatatatatataaaatatatatatataaa +atatatatatatataaaatatatatatataaaatatatatatataaaatatatatatata 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+tggccaagatgatgaaatcctgtctctactaaaaatacaaaaaaattagctgggtgtggt +aacgggtggctgtaatcccagctacttgggaagctgaggcagaagaatagcttgaacctg +ggaggcacaggttgcagtgagccgagatcgcgccactgcagcctaggcagcagagtgaga +ctctgtcttaaaatatatattatggtttattttattttatggttaaaggccatatatata +t----------------------------------atatatatatataaa------atat +atataatatatatatatata---------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------------------------atatata +tat---------------aaaatatatataaaatatatatatataaaatatatatatata +aaatatatatatataaaatat--------------------------------------- +---------------atatatatatataaaatatatatatggaattccatatctatcaat +ggatcctaagggaaacaattttactactgtattggtgggtttattttatgtatttgtaga +tatatacatatatacacatatatatgacaattttagcacaaaagagaggaa +>p:HG002_1_chr20:35579913-35580987 +aaaactccatctcaaaaaaaaaaaaaaaaaaaaagggacacaatcctggattcaaaagac +tgttgtaaatatcaaatgacataatagaaacataagtactttggagcctacaaagtgctg +tcagaagctgggcatggtggctcatgcctgtaaccccagcactttgggaggctgaggcag +gcagactgctcaaactcaggagttcgagaccagcctgggcaacatggcaagacaccatct +gtaccaaaaatacaaaaaaatagccgggcatagtggtgcgcacctgtggtcccagctact +caggaggttgaggtgggaggatcacttgagcccagggggcggaggttacagtgagccaag +atttgcactccagccttggtgacagagcaagagaccctgtctaaaatatatatgtgtata +tacacacacacacacacaaatatattttttggctgggcatggtggctgacacctgtaatc +ccagcactttgggaggccaaggcaggcagatcacttgaggtcaggagtttgagaccagcc +tggccaagatgatgaaatcctgtctctactaaaaatacaaaaaaattagctgggtgtggt +aacgggtggctgtaatcccagctacttgggaagctgaggcagaagaatagcttgaacctg +ggaggcacaggttgcagtgagccgagatcgcgccactgcagcctaggcagcagagtgaga +ctctgtcttaaaatatatattatggtttattttattttatggttaaaggccatatatata +t----------------------------------atatatatatataaa------atat +atataatatatatatatata---------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------------------------atatata +tat---------------aaaatatatataaaatatatatatataaaatatatatatata +aaatatatatatataaaatat--------------------------------------- +---------------atatatatatataaaatatatatatggaattccatatctatcaat +ggatcctaagggaaacaattttactactgtattggtgggtttattttatgtatttgtaga +tatatacatatatacacatatatatgacaattttagcacaaaagagaggaa +>p:HG002_2_chr20:35579913-35580987 +aaaactccatctcaaaaaaaaaaaaaaaaaaaaagggacacaatcctggattcaaaagac +tgttgtaaatatcaaatgacataatagaaacataagtactttggagcctacaaagtgctg +tcagaagctgggcatggtggctcatgcctgtaaccccagcactttgggaggctgaggcag +gcagactgctcaaactcaggagttcgagaccagcctgggcaacatggcaagacaccatct +gtaccaaaaatacaaaaaaatagccgggcatagtggtgcgcacctgtggtcccagctact +caggaggttgaggtgggaggatcacttgagcccagggggcggaggttacagtgagccaag +atttgcactccagccttggtgacagagcaagagaccctgtctaaaatatatatgtgtata +tacacacacacacacacaaatatattttttggctgggcatggtggctgacacctgtaatc +ccagcactttgggaggccaaggcaggcagatcacttgaggtcaggagtttgagaccagcc +tggccaagatgatgaaatcctgtctctactaaaaatacaaaaaaattagctgggtgtggt +aacgggtggctgtaatcccagctacttgggaagctgaggcagaagaatagcttgaacctg +ggaggcacaggttgcagtgagccgagatcgtgccactgcagcctaggcagcagagtgaga +ctctgtcttaaaatatatattatggtttattttattttatggttaaaggccatatatata +tatatatatatatatataatatatatatatataaaatatatatatataaaatatatatat +atataaaatatatatatataaaatatatatatatatataaaatatatatatataaaatat +atatatataaaatatatatatatataaaatatatatatatataaaatatatatatataaa +atatatatatatataaaatatatatatataaaatatatatatataaaatatatatatata +taaaatatatatatataaaatatatatatataaaatatatatatatataatatatatata +taaaatatatatatataaaatatatatataaaatatatatatataaaatatatatatata +aaatatatatatataaaatatatatatataaaatatatatataaaatatatatatataaa +atatatatatataaaatatatatatataaaatatatatatggaattccatatctatcaat +ggatcctaagggaaacaattttactactgtattggtgggtttattttatgtatttgtaga +tatatacatatatacacatatatatgacaattttagcacaaaagagaggaa diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/msa.fa.fai new file mode 100644 index 00000000..da71203f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_35579913_35580987 1371 29 60 61 +syndip_1_chr20:35579913-35580987 1371 1457 60 61 +syndip_2_chr20:35579913-35580987 1371 2885 60 61 +p:HG002_1_chr20:35579913-35580987 1371 4314 60 61 +p:HG002_2_chr20:35579913-35580987 1371 5743 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/output.vcf.gz new file mode 100644 index 00000000..bb5a8099 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/output.vcf.gz.tbi new file mode 100644 index 00000000..19d62830 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:35580013-35580887/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/base.vcf.gz new file mode 100644 index 00000000..75ce34b0 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/base.vcf.gz.tbi new file mode 100644 index 00000000..a601d88f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/comp.vcf.gz new file mode 100644 index 00000000..1034aa8b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/comp.vcf.gz.tbi new file mode 100644 index 00000000..e8557b69 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/haps.fa new file mode 100644 index 00000000..e0e8ba49 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/haps.fa @@ -0,0 +1,36 @@ +>ref_chr20_37361652_37362159 +CATCAGGGGTGGGGCAGCTGGGGGCTCTCGGAAAGATGACCTACGGCTGGGAGAGAGCAAAACTTGCCACCTCAGTGTTCTCTGTGATCCTCTCCTGACACTGAGCAGGGGCAGGGCAGGAGTGCTGCTGAGGGCCTCTGTGTGCAGGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGAGATGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGAGATGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGAGATGTAGAGATGCTGGGGTCTCTGTGTGCAGGTAGAGATGCTGGGGTCTCTGTGTGCAGGCAGAGATGCTGAAGCCCAGGTTAGCTCTTATTTATGTCTTTATTTATTTTTTTGAGACAAGGTCTCACTCTGTTGCCCAGGCTGGAGTGCAGTGGTGTAATCATAGCTCACTGCAGCCTCAAACTCCTGGGTGCAAGCAA +>syndip_1_chr20:37361652-37362159 +CATCAGGGGTGGGGCAGCTGGGGGCTCTCGGAAAGATGACCTACGGCTGGGAGAGAGCAA +AACTTGCCACCTCAGTGTTCTCTGTGATCCTCTCCTGACACTGAGCAGGGGCAGGGCAGG +AGTGCTGCTGAGGGCCTCTGTGTGCAGGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGA +GATGCCGGGGTCTCTGTGTGCAGGTAGAGATGTAGAGATGCTGGGGTCTCTGTGTGCAGG +TAGAGATGCTGGGGTCTCTGTGTGCAGGCAGAGATGCTGAAGCCCAGGTTAGCTCTTATT +TATGTCTTTATTTATTTTTTTGAGACAAGGTCTCACTCTGTTGCCCAGGCTGGAGTGCAG +TGGTGTAATCATAGCTCACTGCAGCCTCAAACTCCTGGGTGCAAGCAA +>syndip_2_chr20:37361652-37362159 +CATCAGGGGTGGGGCAGCTGGGGGCTCTCGGAAAGATGACCTACGGCTGGGAGAGAGCAA +AACTTGCCACCTCAGTGTTCTCTGTGATCCTCTCCTGACACTGAGCAGGGGCAGGGCAGG +AGTGCTGCTGAGGGCCTCTGTGTGCAGGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGA +GATGCCGGGGTCTCTGTGTGCAGGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGAGATG +CCGGGGTCTCTGTGTGCAGGTAGAGATGTAGAGATGCTGGGGTCTCTGTGTGCAGGTAGA +GATGCTGGGGTCTCTGTGTGCAGGCAGAGATGCTGAAGCCCAGGTTAGCTCTTATTTATG +TCTTTATTTATTTTTTTGAGACAAGGTCTCACTCTGTTGCCCAGGCTGGAGTGCAGTGGT +GTAATCATAGCTCACTGCAGCCTCAAACTCCTGGGTGCAAGCAA +>p:HG002_1_chr20:37361652-37362159 +CATCAGGGGTGGGGCAGCTGGGGGCTCTCGGAAAGATGACCTACGGCTGGGAGAGAGCAA +AACTTGCCACCTCAGTGTTCTCTGTGATCCTCTCCTGACACTGAGCAGGGGCAGGGCAGG +AGTGCTGCTGAGGGCCTCTGTGTGCAGGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGA +GATGCCGGGGTCTCTGTGTGCAGGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGAGATG +CCGGGGTCTCTGTGTGCAGGTAGAGATGTAGAGATGCTGGGGTCTCTGTGTGCAGGTAGA +GATGCTGGGGTCTCTGTGTGCAGGCAGAGATGCTGAAGCCCAGGTTAGCTCTTATTTATG +TCTTTATTTATTTTTTTGAGACAAGGTCTCACTCTGTTGCCCAGGCTGGAGTGCAGTGGT +GTAATCATAGCTCACTGCAGCCTCAAACTCCTGGGTGCAAGCAA +>p:HG002_2_chr20:37361652-37362159 +CATCAGGGGTGGGGCAGCTGGGGGCTCTCGGAAAGATGACCTACGGCTGGGAGAGAGCAA +AACTTGCCACCTCAGTGTTCTCTGTGATCCTCTCCTGACACTGAGCAGGGGCAGGGCAGG +AGTGCTGCTGAGGGCCTCTGTGTGCAGGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGA +GATGCCGGGGTCTCTGTGTGCAGGTAGAGATGTAGAGATGCTGGGGTCTCTGTGTGCAGG +TAGAGATGCTGGGGTCTCTGTGTGCAGGCAGAGATGCTGAAGCCCAGGTTAGCTCTTATT +TATGTCTTTATTTATTTTTTTGAGACAAGGTCTCACTCTGTTGCCCAGGCTGGAGTGCAG +TGGTGTAATCATAGCTCACTGCAGCCTCAAACTCCTGGGTGCAAGCAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/haps.fa.ref.fa new file mode 100644 index 00000000..0b1a5aca --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:37361652-37362159 +CATCAGGGGTGGGGCAGCTGGGGGCTCTCGGAAAGATGACCTACGGCTGGGAGAGAGCAAAACTTGCCACCTCAGTGTTCTCTGTGATCCTCTCCTGACACTGAGCAGGGGCAGGGCAGGAGTGCTGCTGAGGGCCTCTGTGTGCAGGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGAGATGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGAGATGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGAGATGTAGAGATGCTGGGGTCTCTGTGTGCAGGTAGAGATGCTGGGGTCTCTGTGTGCAGGCAGAGATGCTGAAGCCCAGGTTAGCTCTTATTTATGTCTTTATTTATTTTTTTGAGACAAGGTCTCACTCTGTTGCCCAGGCTGGAGTGCAGTGGTGTAATCATAGCTCACTGCAGCCTCAAACTCCTGGGTGCAAGCAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/msa.fa new file mode 100644 index 00000000..c62559de --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/msa.fa @@ -0,0 +1,50 @@ +>ref_chr20_37361652_37362159 +catcaggggtggggcagctgggggctctcggaaagatgacctacggctgggagagagcaa +aacttgccacctcagtgttctctgtgatcctctcctgacactgagcaggggcagggcagg +agtgctgctgagggcctctgtgtgcaggtagagatgccggggtctctgtgtgcaggtaga +gatgtagagatgccggggtctctgtgtgcaggtagagatgtagagatgccggggtctctg +tgtgcaggtagagatgccggggtctctgtgtgcaggtagagatgccggggtctctgtgtg +caggtagagatgtagagatgctggggtctctgtgtgcaggtagagatgctggggtctctg +tgtgcaggcagagatgctgaagcccaggttagctcttatttatgtctttatttatttttt +tgagacaaggtctcactctgttgcccaggctggagtgcagtggtgtaatcatagctcact +gcagcctcaaactcctgggtgcaagcaa +>syndip_1_chr20:37361652-37362159 +catcaggggtggggcagctgggggctctcggaaagatgacctacggctgggagagagcaa +aacttgccacctcagtgttctctgtgatcctctcctgacactgagcaggggcagggcagg +agtgctgctgagggc--------------------------------------------- +-------------------------------------------------------ctctg +tgtgcaggtagagatgccggggtctctgtgtgcaggtagagatgccggggtctctgtgtg +caggtagagatgtagagatgctggggtctctgtgtgcaggtagagatgctggggtctctg +tgtgcaggcagagatgctgaagcccaggttagctcttatttatgtctttatttatttttt +tgagacaaggtctcactctgttgcccaggctggagtgcagtggtgtaatcatagctcact +gcagcctcaaactcctgggtgcaagcaa +>syndip_2_chr20:37361652-37362159 +catcaggggtggggcagctgggggctctcggaaagatgacctacggctgggagagagcaa +aacttgccacctcagtgttctctgtgatcctctcctgacactgagcaggggcagggcagg +agtgctgctgagggcctctgtgtgcaggtagagatgccggggtctctgtgtgcag----- +---------------------------------------gtagagatgccggggtctctg +tgtgcaggtagagatgccggggtctctgtgtgcaggtagagatgccggggtctctgtgtg +caggtagagatgtagagatgctggggtctctgtgtgcaggtagagatgctggggtctctg +tgtgcaggcagagatgctgaagcccaggttagctcttatttatgtctttatttatttttt +tgagacaaggtctcactctgttgcccaggctggagtgcagtggtgtaatcatagctcact +gcagcctcaaactcctgggtgcaagcaa +>p:HG002_1_chr20:37361652-37362159 +catcaggggtggggcagctgggggctctcggaaagatgacctacggctgggagagagcaa +aacttgccacctcagtgttctctgtgatcctctcctgacactgagcaggggcagggcagg +agtgctgctgagggcctctgtgtgcaggtagagatgccggggtctctgtgtgcag----- +---------------------------------------gtagagatgccggggtctctg +tgtgcaggtagagatgccggggtctctgtgtgcaggtagagatgccggggtctctgtgtg +caggtagagatgtagagatgctggggtctctgtgtgcaggtagagatgctggggtctctg +tgtgcaggcagagatgctgaagcccaggttagctcttatttatgtctttatttatttttt +tgagacaaggtctcactctgttgcccaggctggagtgcagtggtgtaatcatagctcact +gcagcctcaaactcctgggtgcaagcaa +>p:HG002_2_chr20:37361652-37362159 +catcaggggtggggcagctgggggctctcggaaagatgacctacggctgggagagagcaa +aacttgccacctcagtgttctctgtgatcctctcctgacactgagcaggggcagggcagg +agtgctgctgagggc--------------------------------------------- +-------------------------------------------------------ctctg +tgtgcaggtagagatgccggggtctctgtgtgcaggtagagatgccggggtctctgtgtg +caggtagagatgtagagatgctggggtctctgtgtgcaggtagagatgctggggtctctg +tgtgcaggcagagatgctgaagcccaggttagctcttatttatgtctttatttatttttt +tgagacaaggtctcactctgttgcccaggctggagtgcagtggtgtaatcatagctcact +gcagcctcaaactcctgggtgcaagcaa diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/msa.fa.fai new file mode 100644 index 00000000..91cfe1c6 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_37361652_37362159 508 29 60 61 +syndip_1_chr20:37361652-37362159 508 580 60 61 +syndip_2_chr20:37361652-37362159 508 1131 60 61 +p:HG002_1_chr20:37361652-37362159 508 1683 60 61 +p:HG002_2_chr20:37361652-37362159 508 2235 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/output.vcf.gz new file mode 100644 index 00000000..59a5092b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/output.vcf.gz.tbi new file mode 100644 index 00000000..7953f413 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:37361752-37362059/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/base.vcf.gz new file mode 100644 index 00000000..e5697875 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/base.vcf.gz.tbi new file mode 100644 index 00000000..71032ffa Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/comp.vcf.gz new file mode 100644 index 00000000..d0b96108 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/comp.vcf.gz.tbi new file mode 100644 index 00000000..200e655a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/haps.fa new file mode 100644 index 00000000..44efa372 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/haps.fa @@ -0,0 +1,146 @@ +>ref_chr20_38123490_38124806 +TTTTAAGTCCACAGCCTGTGACCAATGGCAACAGAGCAGAAGGTTAGAGCAATTACTGTGGATGGAGCTTGCCCAGTAGGCCTCCTAGCTCCATTTTCTAGCTTTGTGATCTCAGGCCTGTCCTGTAACCTCTCTGGGCCTCAGAAACCTCTCTCTCTCTCTATATATATATATATATAATAATATATAATAATAATATATAATATGTATAATAATAATATATAATATTTATAATAATAATATATATAATATGTATATATAATATACATATACCTATTATATATAATATACCTATTATATATAATATACATAAACCTATTATATATAATATACCTATTATATATAAGATACCTATTATATATAATATACCTATTATATATAAGATACCTATTATATATAATATACATATACCTATTATATATATAATATACCTATTATATATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTATATATAATACACATTATATATAATATATAACACACATTATATATAATATATAACACACATTATATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACACATTATATATTATATATAATACACATTATATATAATATATAATACACATTATATATAATACTTATTATATATTATACATAATATACATATTATATATAATACATAATATACGTATATTATATAATATACATATTATATATAATACATAATATACGTATATTATATAATATACATATTATATATATTATACTATATATAATACTCATATATATACATATTATATATACATATTATATATAATACTCATATTATATGTACATATTATACATACATATTATATATAATACACATATATACATATTATATATAATACACACACACATTATATATGTCTTATATATAATATACATATTATATATGTATTATATTATTATAGATATAATATACATATTATATCTATATATAAAATATATATGTAGAGAGAGAGAGACAGGGTCTCATTTTGTCTCCCAGGCTGGAGTGCAGTGGTGCAATCTTGGCTCACTACAACCTCCACCTCCCAGGCTCAAGGGATCCTCCAGCTTCAGCCCCCCGAGTACCTGGGACTACAGGAACGCGTCACCATGCCTGGCTAATTTTTTTTTATTTTTTGTAGAGATGGGGTTTCGCCATGTTGCCGAGGCTGGTGTCAA +>syndip_1_chr20:38123490-38124806 +TTTTAAGTCCACAGCCTGTGACCAATGGCAACAGAGCAGAAGGTTAGAGCAATTACTGTG +GATGGAGCTTGCCCAGTAGGCCTCCTAGCTCCATTTTCTAGCTTTGTGATCTCAGGCCTG +TCCTGTAACCTCTCTGGGCCTCAGAAACCTCTCTCTCTCTCTATATATATATATATAATA +ATATATAATAATAATATATAATATGTATAATAATAATATATAATATTTATAATAATAATA +TATATAATATGTATATATAATATACATATACCTATTATATATAATATACCTATTATATAT +AATATACATATACCTATTATATATAATATACCTATTATATATAAGATACCTATTATATAT +AATATACATATACCTATTATATATATAATATACCTATTATATATATATAATATACCTATT +ATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTAT +ATATATAATATACCTATTATATATAATATACCTATTATATATAAAATATACCTATTATAT +ATAATATACCTATTATATACATTATATATAATATACCTATTATATGCATTATATATAATA +TACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATACCTA +TTATATGCATTATATATAATATACCTATTATATGCATTATATAATATATTATATATAATA +TGCATATTATATGTATTATATATTATATATTATATATATAATATACATATTATATGTATT +ATATATTATATATTATATATATAATATACATATTATATGTATTATATATTATATATAATA +TACATATTATATATTATATATTATATACATATTATATATTATATATTATATACATATTAT +ATATTATATACATATTATATATTATATATTATATACATATTATACATTATATATATCTAA +AATATATAATACACATTATATATTATATAATACACATTATATATAATATATAATACACAT +TATATATTATATATAATACACATTATATATTATATATAATACACATTATATATTATATAA +TACACATTATATATTATATATAATACACATTATATATTATATATAATACACATTATATAT +TATATATAATACACATTATATATTATATAATACACATTATATATTATATATAATACACAT +TATATATATAATACACATTATATATTATATATAATACATAATACACATTATATATTATAT +ATAATACACATTATATATAATATATAACACACATTATATATAATATATAACACACATTAT +ATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACA +CATTATATATTATATATAATACACATATATTATATATAATACACATTATATATTATATAT +AATACACATTATATATAATATATAATACACATTATATATAATACTTATTATATATTATAC +ATAATATACATATTATATATAATACATAATATACGTATATTATATAATATACATATTATA +TATAATACATAATATACGTATATTATATAATATACATATTATATATATTATACTATATAT +AATACTCATATATATACATATTATATATACATATTATATATAATACTCATATTATATGTA +CATATTATACATACATATTATATATAATACACATATATACATATTATATATAATACACAC +ACACATTATATATGTCTTATATATAATATACATATTATATATGTATTATATTATTATAGA +TATAATATACATATTATATCTATATATAAAATATATATGTAGAGAGAGAGAGACAGGGTC +TCATTTTGTCTCCCAGGCTGGAGTGCAGTGGTGCAATCTTGGCTCACTACAACCTCCACC +TCCCAGGCTCAAGGGATCCTCCAGCTTCAGCCCCCCGAGTACCTGGGACTACAGGAACGC +GTCACCATGCCTGGCTAATTTTTTTTTATTTTTTGTAGAGATGGGGTTTCGCCATGTTGC +CGAGGCTGGTGTCAA +>syndip_2_chr20:38123490-38124806 +TTTTAAGTCCACAGCCTGTGACCAATGGCAACAGAGCAGAAGGTTAGAGCAATTACTGTG +GATGGAGCTTGCCCAGTAGGCCTCCTAGCTCCATTTTCTAGCTTTGTGATCTCAGGCCTG +TCCTGTAACCTCTCTGGGCCTCAGAAACCTCTCTCTCTCTCTATATATATATATATAATA +ATATATAATAATAATATATAATATGTATAATAATAATATATAATATTTATAATAATAATA +TATATAATATGTATATATAATATACATATACCTATTATATATAATATACCTATTATATAT +AATATACATATACCTATTATATATAATATACCTATTATATATAAGATACCTATTATATAT +AATATACATATACCTATTATATATATAATATACCTATTATATATATATAATATACCTATT +ATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTAT +ATATATAATATACCTATTATATATAATATACCTATTATATATAAAATATACCTATTATAT +ATAATATACCTATTATATACATTATATATAATATACCTATTATATGCATTATATATAATA +TACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATACCTA +TTATATGCATTATATAATATATTATATATAATATGCATATTATATGTATTATATATTATA +TATTATATATATAATATACATATTATATGTATTATATATTATATATTATATATATAATAT +ACATATTATATGTATTATATATTATATATAATATACATATTATATATTATATATTATATA +CATATTATATATTATATATTATATACATATTATATATTATATACATATTATATATTATAT +ATTATATACATATTATACATTATATATATCTAAAATATATAATACACATTATATATTATA +TAATACACATTATATATAATATATAATACACATTATATATTATATATAATACACATTATA +TATTATATATAATACACATTATATATTATATAATACACATTATATATTATATATAATACA +CATTATATATTATATATAATACACATTATATATTATATATAATACACATTATATATTATA +TATAATACACATTATATATTATATAATACACATTATATATTATATATAATACACATTATA +TATATAATACACATTATATATTATATATAATACATAATACACATTATATATTATATATAA +TACACATTATATATAATATATAACACACATTATATATAATATATAACACACATTATATAT +TATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACACATT +ATATATTATATATAATACACATATATTATATATAATACACATTATATATTATATATAATA +CACATTATATATAATATATAATACACATTATATATAATACTTATTATATATTATACATAA +TATACATATTATATATAATACATAATATACGTATATTATATAATATACATATTATATATA +ATACATAATATACGTATATTATATAATATACATATTATATATATTATACTATATATAATA +CTCATATATATACATATTATATATACATATTATATATAATACTCATATTATATGTACATA +TTATACATACATATTATATATAATACACATATATACATATTATATATAATACACACACAC +ATTATATATGTCTTATATATAATATACATATTATATATGTATTATATTATTATAGATATA +ATATACATATTATATCTATATATAAAATATATATGTAGAGAGAGAGAGACAGGGTCTCAT +TTTGTCTCCCAGGCTGGAGTGCAGTGGTGCAATCTTGGCTCACTACAACCTCCACCTCCC +AGGCTCAAGGGATCCTCCAGCTTCAGCCCCCCGAGTACCTGGGACTACAGGAACGCGTCA +CCATGCCTGGCTAATTTTTTTTTATTTTTTGTAGAGATGGGGTTTCGCCATGTTGCCGAG +GCTGGTGTCAA +>p:HG002_1_chr20:38123490-38124806 +TTTTAAGTCCACAGCCTGTGACCAATGGCAACAGAGCAGAAGGTTAGAGCAATTACTGTG +GATGGAGCTTGCCCAGTAGGCCTCCTAGCTCCATTTTCTAGCTTTGTGATCTCAGGCCTG +TCCTGTAACCTCTCTGGGCCTCAGAAACCTCTCTCTCTCTCTATATATATATATATAATA +ATATATAATAATAATATATAATATGTATAATAATAATATATAATATTTATAATAATAATA +TATATAATATGTATATATAATATACATATACCTATTATATATAATATACCTATTATATAT +AATATACATATACCTATTATATATAATATACCTATTATATATAAGATACCTATTATATAT +AATATACATATACCTATTATATATATAATATACCTATTATATATATATAATATACCTATT +ATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTAT +ATATATAATATACCTATTATATATAATATACCTATTATATATAAAATATACCTATTATAT +ATAATATACCTATTATATACATTATATATAATATACCTATTATATGCATTATATATAATA +TACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATACCTA +TTATATGCATTATATAATATATTATATATAATATGCATATTATATGTATTATATATTATA +TATTATATATATAATATACATATTATATGTATTATATATTATATATTATATATATAATAT +ACATATTATATGTATTATATATTATATATAATATACATATTATATATTATATATTATATA +CATATTATATATTATATATTATATACATATTATATATTATATACATATTATATATTATAT +ATTATATACATATTATACATTATATATATCTAAAATATATAATACACATTATATATTATA +TAATACACATTATATATAATATATAATACACATTATATATTATATATAATACACATTATA +TATTATATATAATACACATTATATATTATATAATACACATTATATATTATATATAATACA +CATTATATATTATATATAATACACATTATATATTATATATAATACACATTATATATTATA +TATAATACACATTATATATTATATAATACACATTATATATTATATATAATACACATTATA +TATATAATACACATTATATATTATATATAATACATAATACACATTATATATTATATATAA +TACACATTATATATAATATATAACACACATTATATATAATATATAACACACATTATATAT +TATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACACATT +ATATATTATATATAATACACATATATTATATATAATACACATTATATATTATATATAATA +CACATTATATATAATATATAATACACATTATATATAATACTTATTATATATTATACATAA +TATACATATTATATATAATACATAATATACGTATATTATATAATATACATATTATATATA +ATACATAATATACGTATATTATATAATATACATATTATATATATTATACTATATATAATA +CTCATATATATACATATTATATATACATATTATATATAATACTCATATTATATGTACATA +TTATACATACATATTATATATAATACACATATATACATATTATATATAATACACACACAC +ATTATATATGTCTTATATATAATATACATATTATATATGTATTATATTATTATAGATATA +ATATACATATTATATCTATATATAAAATATATATGTAGAGAGAGAGAGACAGGGTCTCAT +TTTGTCTCCCAGGCTGGAGTGCAGTGGTGCAATCTTGGCTCACTACAACCTCCACCTCCC +AGGCTCAAGGGATCCTCCAGCTTCAGCCCCCCGAGTACCTGGGACTACAGGAACGCGTCA +CCATGCCTGGCTAATTTTTTTTTATTTTTTGTAGAGATGGGGTTTCGCCATGTTGCCGAG +GCTGGTGTCAA +>p:HG002_2_chr20:38123490-38124806 +TTTTAAGTCCACAGCCTGTGACCAATGGCAACAGAGCAGAAGGTTAGAGCAATTACTGTG +GATGGAGCTTGCCCAGTAGGCCTCCTAGCTCCATTTTCTAGCTTTGTGATCTCAGGCCTG +TCCTGTAACCTCTCTGGGCCTCAGAAACCTCTCTCTCTCTCTATATATATATATATAATA +ATATATAATAATAATATATAATATGTATAATAATAATATATAATATTTATAATAATAATA +TATATAATATGTATATATAATATACATATACCTATTATATATAATATACCTATTATATAT +AATATACATATACCTATTATATATAATATACCTATTATATATAAGATACCTATTATATAT +AATATACATATACCTATTATATATATAATATACCTATTATATATATATAATATACCTATT +ATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTAT +ATATATAATATACCTATTATATATAATATACCTATTATATATAAAATATACCTATTATAT +ATAATATACCTATTATATACATTATATATAATATACCTATTATATGCATTATATATAATA +TACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATACCTA +TTATATGCATTATATATAATATACCTATTATATGCATTATATAATATATTATATATAATA +TGCATATTATATGTATTATATATTATATATTATATATATAATATACATATTATATGTATT +ATATATTATATATTATATATATAATATACATATTATATGTATTATATATTATATATAATA +TACATATTATATATTATATATTATATACATATTATATATTATATATTATATACATATTAT +ATATTATATACATATTATATATTATATATTATATACATATTATACATTATATATATCTAA +AATATATAATACACATTATATATTATATAATACACATTATATATAATATATAATACACAT +TATATATTATATATAATACACATTATATATTATATATAATACACATTATATATTATATAA +TACACATTATATATTATATATAATACACATTATATATTATATATAATACACATTATATAT +TATATATAATACACATTATATATTATATAATACACATTATATATTATATATAATACACAT +TATATATATAATACACATTATATATTATATATAATACATAATACACATTATATATTATAT +ATAATACACATTATATATAATATATAACACACATTATATATAATATATAACACACATTAT +ATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACA +CATTATATATTATATATAATACACATATATTATATATAATACACATTATATATTATATAT +AATACACATTATATATAATATATAATACACATTATATATAATACTTATTATATATTATAC +ATAATATACATATTATATATAATACATAATATACGTATATTATATAATATACATATTATA +TATAATACATAATATACGTATATTATATAATATACATATTATATATATTATACTATATAT +AATACTCATATATATACATATTATATATACATATTATATATAATACTCATATTATATGTA +CATATTATACATACATATTATATATAATACACATATATACATATTATATATAATACACAC +ACACATTATATATGTCTTATATATAATATACATATTATATATGTATTATATTATTATAGA +TATAATATACATATTATATCTATATATAAAATATATATGTAGAGAGAGAGAGACAGGGTC +TCATTTTGTCTCCCAGGCTGGAGTGCAGTGGTGCAATCTTGGCTCACTACAACCTCCACC +TCCCAGGCTCAAGGGATCCTCCAGCTTCAGCCCCCCGAGTACCTGGGACTACAGGAACGC +GTCACCATGCCTGGCTAATTTTTTTTTATTTTTTGTAGAGATGGGGTTTCGCCATGTTGC +CGAGGCTGGTGTCAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/haps.fa.ref.fa new file mode 100644 index 00000000..5cab64c6 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:38123490-38124806 +TTTTAAGTCCACAGCCTGTGACCAATGGCAACAGAGCAGAAGGTTAGAGCAATTACTGTGGATGGAGCTTGCCCAGTAGGCCTCCTAGCTCCATTTTCTAGCTTTGTGATCTCAGGCCTGTCCTGTAACCTCTCTGGGCCTCAGAAACCTCTCTCTCTCTCTATATATATATATATATAATAATATATAATAATAATATATAATATGTATAATAATAATATATAATATTTATAATAATAATATATATAATATGTATATATAATATACATATACCTATTATATATAATATACCTATTATATATAATATACATAAACCTATTATATATAATATACCTATTATATATAAGATACCTATTATATATAATATACCTATTATATATAAGATACCTATTATATATAATATACATATACCTATTATATATATAATATACCTATTATATATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTATATATAATACACATTATATATAATATATAACACACATTATATATAATATATAACACACATTATATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACACATTATATATTATATATAATACACATTATATATAATATATAATACACATTATATATAATACTTATTATATATTATACATAATATACATATTATATATAATACATAATATACGTATATTATATAATATACATATTATATATAATACATAATATACGTATATTATATAATATACATATTATATATATTATACTATATATAATACTCATATATATACATATTATATATACATATTATATATAATACTCATATTATATGTACATATTATACATACATATTATATATAATACACATATATACATATTATATATAATACACACACACATTATATATGTCTTATATATAATATACATATTATATATGTATTATATTATTATAGATATAATATACATATTATATCTATATATAAAATATATATGTAGAGAGAGAGAGACAGGGTCTCATTTTGTCTCCCAGGCTGGAGTGCAGTGGTGCAATCTTGGCTCACTACAACCTCCACCTCCCAGGCTCAAGGGATCCTCCAGCTTCAGCCCCCCGAGTACCTGGGACTACAGGAACGCGTCACCATGCCTGGCTAATTTTTTTTTATTTTTTGTAGAGATGGGGTTTCGCCATGTTGCCGAGGCTGGTGTCAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/msa.fa new file mode 100644 index 00000000..c856c61f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/msa.fa @@ -0,0 +1,180 @@ +>ref_chr20_38123490_38124806 +ttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgtg +gatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcctg +tcctgtaacctctctgggcctcagaaacctctctctctctctatatatatatatatataa +taatatataataataatatataatatgtataataataatatataatatttataataataa +tatatataatatgtatatataatatacatatacctattatatataatatacctattatat +ataatatacataaacctattatatataatatacctattatatataagatacctattatat +ataatatacctat------------------------------tatatataagataccta +ttatatataatatac--------------atatacctattatatatataatatacctatt +ata----------------tatatataatatacctattatatatataatatacctatta- +---------------------------------------------------tatatataa +tatacctattatatatataata-------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------tacctattatatataatacacattatatataatatataacacacatt +atatataatatataacacacattatatattatatataatacacattatatattatatata +atacacatatattatatataatacacattatatattatatataatacacatatattatat +ataatacacattatatattatatataatacacattatatataatatataatacacattat +atataatacttattatatattatacataatatacatattatatataatacataatatacg +tatattatataatatacatattatatataatacataatatacgtatattatataatatac +atattatatatattatactatatataatactcatatatatacatattatatatacatatt +atatataatactcatattatatgtacatattatacatacatattatatataatacacata +tatacatattatatataatacacacacacattatatatgtcttatatataatatacatat +tatatatgtattatattattatagatataatatacatattatatctatatataaaatata +tatgtagagagagagagacagggtctcattttgtctcccaggctggagtgcagtggtgca +atcttggctcactacaacctccacctcccaggctcaagggatcctccagcttcagccccc +cgagtacctgggactacaggaacgcgtcaccatgcctggctaatttttttttattttttg +tagagatggggtttcgccatgttgccgaggctggtgtcaa +>syndip_1_chr20:38123490-38124806 +ttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgtg +gatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcctg +tcctgtaacctctctgggcctcagaaacctctctctctctc--tatatatatatatataa +taatatataataataatatataatatgtataataataatatataatatttataataataa +tatatataatatgtatatataatatacatatacctattatatataatatacctattatat +ataatatacatatacctattatatataatatacctattatatataagatacctattatat +ataatatacatatacctattatatatataatatacctattatatatatataatataccta +ttatatataatatacctattatatatataatatacctattatatatataatatacctatt +atatatataatatacctattatatataatatacctattatatataaaatatacctattat +atataatatacctattatatacattatatataatatacctattatatgcattatatataa +tatacctattatatgcattatatataatatacctattatatgcattatatataatatacc +tattatatgcattatatataatatacctattatatgcattatataatatattatatataa +tatgcatattatatgtattatatattatatattatatatataatatacatattatatgta +ttatatattatatattatatatataatatacatattatatgtattatatattatatataa +tatacatattatatattatatattatatacatattatatattatatattatatacatatt +atatattatatacatattatatattatatattatatacatattatacattatatatatct +aaaatatataatacacattatatattatataatacacattatatataatatataatacac +attatatattatatataatacacattatatattatatataatacacattatatat----- +------------------tatataatacacattatatattatatataatacacattatat +attatatataatacacattatatattatatataatacacattatatattatataatacac +attatatattatatataatacacattatatatataatacacattatatattatatataat +acataatacacattatatattatatataatacacattatatataatatataacacacatt +atatataatatataacacacattatatattatatataatacacattatatattatatata +atacacatatattatatataatacacattatatattatatataatacacatatattatat +ataatacacattatatattatatataatacacattatatataatatataatacacattat +atataatacttattatatattatacataatatacatattatatataatacataatatacg +tatattatataatatacatattatatataatacataatatacgtatattatataatatac +atattatatatattatactatatataatactcatatatatacatattatatatacatatt +atatataatactcatattatatgtacatattatacatacatattatatataatacacata +tatacatattatatataatacacacacacattatatatgtcttatatataatatacatat +tatatatgtattatattattatagatataatatacatattatatctatatataaaatata +tatgtagagagagagagacagggtctcattttgtctcccaggctggagtgcagtggtgca +atcttggctcactacaacctccacctcccaggctcaagggatcctccagcttcagccccc +cgagtacctgggactacaggaacgcgtcaccatgcctggctaatttttttttattttttg +tagagatggggtttcgccatgttgccgaggctggtgtcaa +>syndip_2_chr20:38123490-38124806 +ttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgtg +gatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcctg +tcctgtaacctctctgggcctcagaaacctctctctctctc--tatatatatatatataa +taatatataataataatatataatatgtataataataatatataatatttataataataa +tatatataatatgtatatataatatacatatacctattatatataatatacctattatat +ataatatacatatacctattatatataatatacctattatatataagatacctattatat +ataatatacatatacctattatatatataatatacctattatatatatataatataccta +ttatatataatatacctattatatatataatatacctattatatatataatatacctatt +atatatataatatacctattatatataatatacctattatatataaaatatacctattat +atataatatacctattatata---------------------------cattatatataa +tatacctattatatgcattatatataatatacctattatatgcattatatataatatacc +tattatatgcattatatataatatacctattatatgcattatataatatattatatataa +tatgcatattatatgtattatatattatatattatatatataatatacatattatatgta +ttatatattatatattatatatataatatacatattatatgtattatatattatatataa +tatacatattatatattatatattatatacatattatatattatatattatatacatatt +atatattatatacatattatatattatatattatatacatattatacattatatatatct +aaaatatataatacacattatatattatataatacacattatatataatatataatacac +attatatattatatataatacacattatatattatatataatacacattatatattatat +aatacacattatatattatatataatacacattatatattatatataatacacattatat +attatatataatacacattatatattatatataatacacattatatattatataatacac +attatatattatatataatacacattatatatataatacacattatatattatatataat +acataatacacattatatattatatataatacacattatatataatatataacacacatt +atatataatatataacacacattatatattatatataatacacattatatattatatata +atacacatatattatatataatacacattatatattatatataatacacatatattatat +ataatacacattatatattatatataatacacattatatataatatataatacacattat +atataatacttattatatattatacataatatacatattatatataatacataatatacg +tatattatataatatacatattatatataatacataatatacgtatattatataatatac +atattatatatattatactatatataatactcatatatatacatattatatatacatatt +atatataatactcatattatatgtacatattatacatacatattatatataatacacata +tatacatattatatataatacacacacacattatatatgtcttatatataatatacatat +tatatatgtattatattattatagatataatatacatattatatctatatataaaatata +tatgtagagagagagagacagggtctcattttgtctcccaggctggagtgcagtggtgca +atcttggctcactacaacctccacctcccaggctcaagggatcctccagcttcagccccc +cgagtacctgggactacaggaacgcgtcaccatgcctggctaatttttttttattttttg +tagagatggggtttcgccatgttgccgaggctggtgtcaa +>p:HG002_1_chr20:38123490-38124806 +ttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgtg +gatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcctg +tcctgtaacctctctgggcctcagaaacctctctctctctc--tatatatatatatataa +taatatataataataatatataatatgtataataataatatataatatttataataataa +tatatataatatgtatatataatatacatatacctattatatataatatacctattatat +ataatatacatatacctattatatataatatacctattatatataagatacctattatat +ataatatacatatacctattatatatataatatacctattatatatatataatataccta +ttatatataatatacctattatatatataatatacctattatatatataatatacctatt +atatatataatatacctattatatataatatacctattatatataaaatatacctattat +atataatatacctattatata---------------------------cattatatataa +tatacctattatatgcattatatataatatacctattatatgcattatatataatatacc +tattatatgcattatatataatatacctattatatgcattatataatatattatatataa +tatgcatattatatgtattatatattatatattatatatataatatacatattatatgta +ttatatattatatattatatatataatatacatattatatgtattatatattatatataa +tatacatattatatattatatattatatacatattatatattatatattatatacatatt +atatattatatacatattatatattatatattatatacatattatacattatatatatct +aaaatatataatacacattatatattatataatacacattatatataatatataatacac +attatatattatatataatacacattatatattatatataatacacattatatattatat +aatacacattatatattatatataatacacattatatattatatataatacacattatat +attatatataatacacattatatattatatataatacacattatatattatataatacac +attatatattatatataatacacattatatatataatacacattatatattatatataat +acataatacacattatatattatatataatacacattatatataatatataacacacatt +atatataatatataacacacattatatattatatataatacacattatatattatatata +atacacatatattatatataatacacattatatattatatataatacacatatattatat +ataatacacattatatattatatataatacacattatatataatatataatacacattat +atataatacttattatatattatacataatatacatattatatataatacataatatacg +tatattatataatatacatattatatataatacataatatacgtatattatataatatac +atattatatatattatactatatataatactcatatatatacatattatatatacatatt +atatataatactcatattatatgtacatattatacatacatattatatataatacacata +tatacatattatatataatacacacacacattatatatgtcttatatataatatacatat +tatatatgtattatattattatagatataatatacatattatatctatatataaaatata +tatgtagagagagagagacagggtctcattttgtctcccaggctggagtgcagtggtgca +atcttggctcactacaacctccacctcccaggctcaagggatcctccagcttcagccccc +cgagtacctgggactacaggaacgcgtcaccatgcctggctaatttttttttattttttg +tagagatggggtttcgccatgttgccgaggctggtgtcaa +>p:HG002_2_chr20:38123490-38124806 +ttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgtg +gatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcctg +tcctgtaacctctctgggcctcagaaacctctctctctctc--tatatatatatatataa +taatatataataataatatataatatgtataataataatatataatatttataataataa +tatatataatatgtatatataatatacatatacctattatatataatatacctattatat +ataatatacatatacctattatatataatatacctattatatataagatacctattatat +ataatatacatatacctattatatatataatatacctattatatatatataatataccta +ttatatataatatacctattatatatataatatacctattatatatataatatacctatt +atatatataatatacctattatatataatatacctattatatataaaatatacctattat +atataatatacctattatatacattatatataatatacctattatatgcattatatataa +tatacctattatatgcattatatataatatacctattatatgcattatatataatatacc +tattatatgcattatatataatatacctattatatgcattatataatatattatatataa +tatgcatattatatgtattatatattatatattatatatataatatacatattatatgta +ttatatattatatattatatatataatatacatattatatgtattatatattatatataa +tatacatattatatattatatattatatacatattatatattatatattatatacatatt +atatattatatacatattatatattatatattatatacatattatacattatatatatct +aaaatatataatacacattatatattatataatacacattatatataatatataatacac +attatatattatatataatacacattatatattatatataatacacattatatat----- +------------------tatataatacacattatatattatatataatacacattatat +attatatataatacacattatatattatatataatacacattatatattatataatacac +attatatattatatataatacacattatatatataatacacattatatattatatataat +acataatacacattatatattatatataatacacattatatataatatataacacacatt +atatataatatataacacacattatatattatatataatacacattatatattatatata +atacacatatattatatataatacacattatatattatatataatacacatatattatat +ataatacacattatatattatatataatacacattatatataatatataatacacattat +atataatacttattatatattatacataatatacatattatatataatacataatatacg +tatattatataatatacatattatatataatacataatatacgtatattatataatatac +atattatatatattatactatatataatactcatatatatacatattatatatacatatt +atatataatactcatattatatgtacatattatacatacatattatatataatacacata +tatacatattatatataatacacacacacattatatatgtcttatatataatatacatat +tatatatgtattatattattatagatataatatacatattatatctatatataaaatata +tatgtagagagagagagacagggtctcattttgtctcccaggctggagtgcagtggtgca +atcttggctcactacaacctccacctcccaggctcaagggatcctccagcttcagccccc +cgagtacctgggactacaggaacgcgtcaccatgcctggctaatttttttttattttttg +tagagatggggtttcgccatgttgccgaggctggtgtcaa diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/msa.fa.fai new file mode 100644 index 00000000..0a510d7d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_38123490_38124806 2080 29 60 61 +syndip_1_chr20:38123490-38124806 2080 2178 60 61 +syndip_2_chr20:38123490-38124806 2080 4327 60 61 +p:HG002_1_chr20:38123490-38124806 2080 6477 60 61 +p:HG002_2_chr20:38123490-38124806 2080 8627 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/output.vcf.gz new file mode 100644 index 00000000..b130afae Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/output.vcf.gz.tbi new file mode 100644 index 00000000..d047264d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38123590-38124706/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/base.vcf.gz new file mode 100644 index 00000000..cedbde12 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/base.vcf.gz.tbi new file mode 100644 index 00000000..d66102d1 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/comp.vcf.gz new file mode 100644 index 00000000..96733b52 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/comp.vcf.gz.tbi new file mode 100644 index 00000000..0fa328f4 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/haps.fa new file mode 100644 index 00000000..0f61fff2 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/haps.fa @@ -0,0 +1,280 @@ +>ref_chr20_38462831_38464884 +CACCATGTTACCTAGGCTGATCTTGAATTCCTGGGCTCAAGTGTTAGACTCACTTCGGCCTCCCAAAGTGTTGGGATTACAGGCGTGAGCCACTGCACCCAGCCTGTTTTGTTTGGGGCAAGGGTTTTAACATTTATATATATATAAATATATATATATTTTATATATACAAATATATATATAAATATATATTTATATATATTTATATATAATATATTATATATAAATATATTTATATATAATATATTATATATAAATATATTATATATAAAATATTATATATAAATATATATATTTATATATATAAATATATATAAATATATATATATATAAAAATACCAGCACATCAGTATCAGGAATAAATGGGCTGGGCAGTATATATATATATATATATGTATATATATATACTGTTTTTCATATATATATACTGTCTTATATATATATATACTGTTTTACATATATATACTGTTTCATATATATAATGTTTTATATATATACTGTTATATATATTATATGTACTGTTATATATTTTTTATATATATACTGTTATATATATTTTTTATATATACTGTTATATATTATATATATACTGTTATATATATATTTTACATATATACTGTTATATATATATTTTATATATATATACTGTTATATATATATATTTTATATATGTATACTGTTATATATTTATATTTTTTATATGTATACTGTTATATATATATTATATGTATACTGTTATATATATATTTTATATGTATACTGTTATATATATATATTTCATATATATATACTGTTATATATATTTTATATATATATACTGTCATATATATATTTTATATATATACTGTCATATATATATTTTATATATATATACTGTCATATATATATTTTATATATATATATACTGTCATATATATATTTTATATATATATACTGTCATATATATTTTATATATATACTGTCATATATATATTTTATATATATACTGTCATATATATATTTTATATATATACTGTCATATATATATTTTATATATATACTGTCATATATATATTTTATATATATATACTGTCATATATATATTTTATATATATATACTGTCATATATATATTTTATATATATACTGTCATATGTATATTTTATATATATACTGTCATATGTATATTTTATATATATACTGTTATATGTATATTTTATATATATATACTGTTATATATATATTTTTATATATATACTGTTATATATATTTTTTTATATATATACTGTTATATATATTTTTATATATATACTGTTATATATATATTTTATATATATACTGTTATATATATATTTTATATATACTGTTATATAGATACTGTTATATATATACTGATATATATACTGTTATATATATACTGATATATATATACTGTTATATATATACTGTTATATATATATACTGTTACATATACATATATATACTGTTATATATATACTGTTATATATATTGTTATATATATACACATATATATATACATATATATATACATATATATATACATATATATATACATATATATATACACGTATATATATACATATATATATACACATATATATATATACACACACATATATATATATATATATACTGGCTGTGTGTGGTGGTGCACACCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGCTGATGGCTTGAGCTCAGGAGTTCAAGACCAGCTAAGCAACATACTGAGATCCCATCTCTAAAAAAAATACAAAAAGGCCAGGCACAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGTGGGCAGATCACGAGGTCAGCAGTTCGAGACCAGCCTGGCCAGCATGGTGAAACCCCATCTCTACTAAAAATACAAAACATTAGCCGGACATGGTGGCACACACCTGTAATTCCAGCTACTCAGGAAGCTGAGGCAGGAGAATAGCTTGAACCCAGGAGGCGAAAGTTTCAGTCAGCCAAAATCACACCACTGCACTCCAGCCTGGGCAACAGAGCAAGACTCTGTCTCCAAAAAAA +>syndip_1_chr20:38462831-38464884 +CACCATGTTACCTAGGCTGATCTTGAATTCCTGGGCTCAAGTGTTAGACTCACTTCGGCC +TCCCAAAGTGTTGGGATTACAGGCGTGAGCCACTGCACCCAGCCTGTTTTGTTTGGGGCA +AGGGTTTTAACATTTATATATATATAAATATATATATATTTTATATATACAAATATATAT +ATAAATATATATTTATATATATTTATATATAATATATTATATATAAATATATTTATATAT +AATATATTATATATAAATATATTATATATAAAATATTATATATAAATATATATATTTATA +TATATAAATATATATAAATATATATATATATAAAAATACCAGCACATCAGTATCAGGAAT +AAATGGGCTGGGCAGTATATATATATATATATATGTATATATATATACTGTTTTTCATAT +ATATATACTGTCTTATATATATATATACTGTTTTACATATATATACTGTTTCATATATAT +AATGTTTTATATATATACTGTTATATATATTATATGTACTGTTATATATTTTTTATATAT +ATACTGTTATATATATTTTTTATATATACTGTTATATATTATATATATACTGTTATATAT +ATATTTTACATATATACTGTTATATATATATTTTATATATATATACTGTTATATATATAT +ATTTTATATATGTATACTGTTATATATTTATATTTTTTATATGTATACTGTTATATATAT +ATTATATGTATACTGTTATATATATATTTTATATGTATACTGTTATATATATATATTTCA +TATATATATACTGTTATATATATTTTATATATATATACTGTCATATATATATTTTATATA +TATACTGTCATATATATATTTTATATATATATACTGTCATATATATATTTTATATATATA +TATACTGTCATATATATATTTTATATATATATACTGTCATATATATTTTATATATATACT +GTCATATATATATTTTATATATATACTGTCATATATATATTTTATATATATACTGTCATA +TATATATTTTATATATATACTGTCATATATATATTTTATATATATATACTGTCATATATA +TATTTTATATATATATACTGTCATATATATATTTTATATATATACTGTCATATGTATATT +TTATATATATACTGTCATATGTATATTTTATATATATACTGTTATATGTATATTTTATAT +ATATATACTGTTATATATATATTTTTATATATATACTGTTATATATATTTTTTTATATAT +ATACTGTTATATATATTTTTATATATATACTGTTATATATATATTTTATATATATACTGT +TATATATATATTTTATATATACTGTTATATATATATATTTTATATATATACTGTTATATA +TAATTTTTTTCATATATATACTGTTATATATATATTTTATATATATATACTGTTATATAT +ATATTTTATATATATACTGTTATATATATATATTTTATATATATACTGTTATTTTTTATA +TATATACTGTTATATATATATTTTATATATATACTGTTATATATATATTATCTATATACT +GTTATGTGTATATTTTATCTATATACTGTTATGTGTATATTTTATCTATATACTGTTATG +TGTATATTTTACCTATATACTTTTATGTGTATATTTTATATATATACTGTTATGTGTATA +TTTTATATATATACTGTTATGTGTATATTTTTTATATATACTGTTATGTGTATATTTTAT +ATATATATACTGTTATGTGTATATTTTATATATATATACTGTTATGTGTATATTTTATAT +ATATACTGTTATGTGTATATTTTATATATATACTGTTATATATAGTTCATATATATACTG +TTATATGTATAGTTCATATATATACTGTTATATATATAGTTCATATGTATACTGTTATAT +ATATAGTTCATATATATACTGTTATATATATAGTTCATATATATACTGTTATATATATAT +AGTTCATATATATACTGTTATATATAGTTCATATATATACTGTTATATATATAGTTCATA +TATATACTGTTATATATATAGTTCATATATATACTGTTATATATAGTTCATATATATATA +CTGTTCTATATATAGTTCATATATATATACTGTTATATATATAGTTCATATATATATACT +GTTATATATAGTTCATATATATATAGTTCATATATATACTGTTATATATATAGTTCATAT +ATATACTGTTATATACATAGTTCATATATATACTGTTATATATATAGTTCATATATATAT +ACTGTTATATATATAGTTCATATATATACTGTTGTATATAGTTCATATATATACTGTTAT +ATATATAGTTCATATATTACTGTTATATATATAGTTCATATATATACTGTTATATATATA +TAGTTCATATATATACTGTTATATATAGTTTATATATATATACTGTTATATATATAGTTT +ATATATATATACTGTTATATATATAGTTTATATATATATACTGTTATATATATATAGTTT +ATATATATATACTGTTATATATATAGTTTATATATATATACTGTTATATATATATAGTTT +ATATATACTGTTATATATATAGTTTATATATATACTGTTATATATATAGTTTATATATAT +ACTGTTATATATATAGTTTATATATATACTGTTATATATATAGTTTATATATATACTGTT +ATATATATAGTTTATATATATACTGTTATATATATAGTTTATATATATACTGTTATATAT +ATAGTTTATATATATATACTGTTATATATAGTTTATATATACTGTTATATATATAGTTTA +TATACTGTTATATATAGTTTATATATATATACTGTTATATATAGTTTATATATATATACT +GTTATATATATATAGTTTATATATATATACTGTTATATATATATAGTTTATATATATACT +GTTATATATATATAGTTTATATATATACTGTTGTATATATAGTTTATATATATACTGTTA +TATATATATTTGTGTATATATACTGTTATATAAATATATTTGTGTATATATACTGTTATA +TATATATTTTATGTATATATACTGTTATATATATATTTTATGTATATATACTGTTATATA +TATATTTTATGTATATATACTGTTATATATATATTTTATGTATATATACTGTTATATATA +TATTTTATGTATATATACTGTTATATATATTTTATGTATATATACTGTTATATATATTTT +ATGTATATATACTGTTATATATATATTTTATGTATATATACTGTTATATCTGTATATTTT +ATGTTTATATACTGTTATATCTGTATATTTTATGTATATATACTGTTATATCTGTATATT +TTATGTATATACTGTTATATATATACTGTTATATATATACTGATATATATACTGTTATAT +ATATACTGATATATATATACTGTTATATATATACTGTTATATATATATACTGTTACATAT +ACATATATATACTGTTATATATATACTGTTATATATATTGTTATATATATACACATATAT +ATATACATATATATACATATATATATACATATATATATACATATATATATACACGTATAT +ATATACATATATATATACACATATATATATATACACACACATATATATATATATATATAC +TGGCTGTGTGTGGTGGTGCACACCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGCTG +ATGGCTTGAGCTCAGGAGTTCAAGACCAGCTAAGCAACATACTGAGATCCCATCTCTAAA +AAAAATACAAAAAGGCCAGGCACAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGC +TGAGGTGGGCAGATCACGAGGTCAGCAGTTCGAGACCAGCCTGGCCAGCATGGTGAAACC +CCATCTCTACTAAAAATACAAAACATTAGCCGGACATGGTGGCACACACCTGTAATTCCA +GCTACTCAGGAAGCTGAGGCAGGAGAATAGCTTGAACCCAGGAGGCGAAAGTTTCAGTCA +GCCAAAATCACACCACTGCACTCCAGCCTGGGCAACAGAGCAAGACTCTGTCTCCAAAAA +AA +>syndip_2_chr20:38462831-38464884 +CACCATGTTACCTAGGCTGATCTTGAATTCCTGGGCTCAAGTGTTAGACTCACTTCGGCC +TCCCAAAGTGTTGGGATTACAGGCGTGAGCCACTGCACCCAGCCTGTTTTGTTTGGGGCA +AGGGTTTTAACATTTATATATATATAAATATATATATATTTTATATATACAAATATATAT +ATAAATATATATTTATATATATTTATATATAATATATTATATATAATATATTTATATATA +ATATATTATATATAAATATATTATATATAAAATATTATATATAAATATATATATTTATAT +ATATAAATATATATAAATATATATATATATAAAAATACCAGCACATCAGTATCAGGAATA +AATGGGCTGGGCAGTATATATATATATATATGTATATATATATACTGTTTTTCATATATA +TATACTGTCTTATATATATATATACTGTTTTACATATATATACTGTTTCATATATATAAT +GTTTTATATATATACTGTTATATATATTATATGTACTGTTATATATTTTTTATATATATA +CTGTTATATATATTTTTTATATATACTGTTATATATTATATATATACTGTTATATATATA +TTTTACATATATACTGTTATATATATATTTTATATATATATACTGTTATATATATATATT +TTATATATGTATACTGTTATATATTTATATTTTTTATATGTATACTGTTATATATATATT +ATATGTATACTGTTATATATATATTTTATATGTATACTGTTATATATATATATTTCATAT +ATATATACTGTTATATATATTTTATATATATATACTGTCATATATATATTTTATATATAT +ACTGTCATATATATATTTTATATATATATACTGTCATATATATATTTTATATATATATAC +TGTCATATATATATTTTATATATATATACTGTCATATATATTTTATATATATACTGTCAT +ATATATATTTTATATATATACTGTCATATATATATTTTATATATATACTGTCATATATAT +ATTTTATATATATATACTGTCATATATATATTTTATATATATATACTGTCATATATATAT +TTTATATATATACTGTCATATGTATATTTTATATATATACTGTCATATGTATATTTTATA +TATATACTGTTATATGTATATTTTATATATATATACTGTTATATATATATTTTATATATA +TATACTGTTATATATATATTTTATATATATATACTGTTATATATATATTTTTATATATAT +ACTGTTATATATATTTTTTTATATATATACTGTTATATATATTTTTATATATATACTGTT +ATATATATATTTTATATATATACTGTTATATATATATTTTATATATACTGTTATATATAT +ATATTTTATATATATACTGTTATATATAATTTTTTTCATATATATACTGTTATATATATA +TTTTATATATATATACTGTTATATATATATTTTATATATATACTGTTATATATATATATT +TTATATATATACTGTTATTTTTTATATATATACTGTTATATATATATTTTATATATATAC +TGTTATATATATATTATCTATATACTGTTATGTGTATATTTTATCTATATACTGTTATGT +GTATATTTTATCTATATACTGTTATGTGTATATTTTACCTATATACTTTTATGTGTATAT +TTTATATATATACTGTTATGTGTATATTTTATATATATACTGTTATGTGTATATTTTTTA +TATATACTGTTATGTGTATATTTTATATATATATACTGTTATGTGTATATTTTATATATA +TATACTGTTATGTGTATATTTTATATATATACTGTTATGTGTATATTTTATATATATACT +GTTATATATAGTTCATATATATACTGTTATATGTATAGTTCATATATATACTGTTATATA +TATAGTTCATATGTATACTGTTATATATATAGTTCATATATATACTGTTATATATATAGT +TCATATATATACTGTTATATATATATAGTTCATATATATACTGTTATATATAGTTCATAT +ATATACTGTTATATATATAGTTCATATATATACTGTTATATATATAGTTCATATATATAC +TGTTATATATAGTTCATATATATATACTGTTCTATATATAGTTCATATATATATACTGTT +ATATATATAGTTCATATATATATACTGTTATATATAGTTCATATATATATAGTTCATATA +TATACTGTTATATATATAGTTCATATATATACTGTTATATACATAGTTCATATATATACT +GTTATATATATAGTTCATATATATATACTGTTATATATATAGTTCATATATATACTGTTG +TATATAGTTCATATATATACTGTTATATATATAGTTCATATATTACTGTTATATATATAG +TTCATATATATACTGTTATATATATATAGTTCATATATATACTGTTATATATAGTTTATA +TATATATACTGTTATATATATAGTTTATATATATATACTGTTATATATATAGTTTATATA +TATATACTGTTATATATATATAGTTTATATATATATACTGTTATATATATAGTTTATATA +TATATACTGTTATATATATAGTTTATATATACTGTTATATATATATAGTTTATATATATA +CTGTTATATATATAGTTTATATATATACTGTTATATATATAGTTTATATATATACTGTTA +TATATATAGTTTATATATATACTGTTATATATATAGTTTATATATATACTGTTATATATA +TAGTTTATATATATATACTGTTATATATATAGTTTATAAATACTGTTATATATATAGTTT +ATATACTGTTATATATAGTTTATATATATATACTGTTATATATAGTTTATATATATATAC +TGTTATATATATATAGTTTATATATATATACTGTTATATATATATAGTTTATATATATAC +TGTTATATATATATAGTTTATATATATACTGTTGTATATATAGTTTATATATATACTGTT +ATATATATATTTGTGTATATATACTGTTATATAAATATATTTGTGTATATATACTGTTAT +ATATATATTTTATGTATATATACTGTTATATATATATTTTATGTATATATACTGTTATAT +ATATATTTTATGTATATATACTGTTATATATATATTTTATGTATATATACTGTTATATAT +ATATTTTATGTATATATACTGTTATATATATTTTATGTATATATACTGTTATATATATAT +TTTATGTATATATACTGTTATATCTGTATATTTTATGTTTATATACTGTTATATCTGTAT +ATTTTATGTATATATACTGTTATATCTGTATATTTTATGTATATACTGTTATATATATAC +TGTTATATATATACTGATATATATACTGTTATATATATACTGATATATATATACTGTTAT +ATATATACTGTTATATATATATACTGTTACATATACATATATATACTGTTATATATATAC +TGTTATATATATTGTTATATATATACACATATATATATACATATATATATACATATATAT +ATACATATATATATACACGTATATATATACATATATATATACACATATATATATATACAC +ACACATATATATATATATATATACTGGCTGTGTGTGGTGGTGCACACCTGTAATCCCAGC +ACTTTGGGAGGCCAAGGCAGGCTGATGGCTTGAGCTCAGGAGTTCAAGACCAGCTAAGCA +ACATACTGAGATCCCATCTCTAAAAAAAATACAAAAAGGCCAGGCACAGTGGCTCACACC +TGTAATCCCAGCACTTTGGGAGGCTGAGGTGGGCAGATCACGAGGTCAGCAGTTCGAGAC +CAGCCTGGCCAGCATGGTGAAACCCCATCTCTACTAAAAATACAAAACATTAGCCGGACA +TGGTGGCACACACCTGTAATTCCAGCTACTCAGGAAGCTGAGGCAGGAGAATAGCTTGAA +CCCAGGAGGCGAAAGTTTCAGTCAGCCAAAATCACACCACTGCACTCCAGCCTGGGCAAC +AGAGCAAGACTCTGTCTCCAAAAAAA +>p:HG002_1_chr20:38462831-38464884 +CACCATGTTACCTAGGCTGATCTTGAATTCCTGGGCTCAAGTGTTAGACTCACTTCGGCC +TCCCAAAGTGTTGGGATTACAGGCGTGAGCCACTGCACCCAGCCTGTTTTGTTTGGGGCA +AGGGTTTTAACATTTATATATATATAAATATATATATATTTTATATATACAAATATATAT +ATAAATATATATTTATATATATTTATATATAATATATTATATATAATATATTTATATATA +ATATATTATATATAAATATATTATATATAAAATATTATATATAAATATATATATTTATAT +ATATAAATATATATAAATATATATATATATAAAAATACCAGCACATCAGTATCAGGAATA +AATGGGCTGGGCAGTATATATATATATATATGTATATATATATACTGTTTTTCATATATA +TATACTGTCTTATATATATATATACTGTTTTACATATATATACTGTTTCATATATATAAT +GTTTTATATATATACTGTTATATATATTATATGTACTGTTATATATTTTTTATATATATA +CTGTTATATATATTTTTTATATATACTGTTATATATTATATATATACTGTTATATATATA +TTTTACATATATACTGTTATATATATATTTTATATATATATACTGTTATATATATATATT +TTATATATGTATACTGTTATATATTTATATTTTTTATATGTATACTGTTATATATATATT +ATATGTATACTGTTATATATATATTTTATATGTATACTGTTATATATATATATTTCATAT +ATATATACTGTTATATATATTTTATATATATATACTGTCATATATATATTTTATATATAT +ACTGTCATATATATATTTTATATATATATACTGTCATATATATATTTTATATATATATAC +TGTCATATATATATTTTATATATATATACTGTCATATATATTTTATATATATACTGTCAT +ATATATATTTTATATATATACTGTCATATATATATTTTATATATATACTGTCATATATAT +ATTTTATATATATATACTGTCATATATATATTTTATATATATATACTGTCATATATATAT +TTTATATATATACTGTCATATGTATATTTTATATATATACTGTCATATGTATATTTTATA +TATATACTGTTATATGTATATTTTATATATATATACTGTTATATATATATTTTATATATA +TATACTGTTATATATATATTTTATATATATATACTGTTATATATATATTTTTATATATAT +ACTGTTATATATATTTTTTTATATATATACTGTTATATATATTTTTATATATATACTGTT +ATATATATATTTTATATATATACTGTTATATATATATTTTATATATACTGTTATATATAT +ATATTTTATATATATACTGTTATATATAATTTTTTTCATATATATACTGTTATATATATA +TTTTATATATATATACTGTTATATATATATTTTATATATATACTGTTATATATATATATT +TTATATATATACTGTTATTTTTTATATATATACTGTTATATATATATTTTATATATATAC +TGTTATATATATATTATCTATATACTGTTATGTGTATATTTTATCTATATACTGTTATGT +GTATATTTTATCTATATACTGTTATGTGTATATTTTACCTATATACTTTTATGTGTATAT +TTTATATATATACTGTTATGTGTATATTTTATATATATACTGTTATGTGTATATTTTTTA +TATATACTGTTATGTGTATATTTTATATATATATACTGTTATGTGTATATTTTATATATA +TATACTGTTATGTGTATATTTTATATATATACTGTTATGTGTATATTTTATATATATACT +GTTATATATAGTTCATATATATACTGTTATATGTATAGTTCATATATATACTGTTATATA +TATAGTTCATATGTATACTGTTATATATATAGTTCATATATATACTGTTATATATATAGT +TCATATATATACTGTTATATATATATAGTTCATATATATACTGTTATATATAGTTCATAT +ATATACTGTTATATATATAGTTCATATATATACTGTTATATATATAGTTCATATATATAC +TGTTATATATAGTTCATATATATATACTGTTCTATATATAGTTCATATATATATACTGTT +ATATATATAGTTCATATATATATACTGTTATATATAGTTCATATATATATAGTTCATATA +TATACTGTTATATATATAGTTCATATATATACTGTTATATACATAGTTCATATATATACT +GTTATATATATAGTTCATATATATATACTGTTATATATATAGTTCATATATATACTGTTG +TATATAGTTCATATATATACTGTTATATATATAGTTCATATATTACTGTTATATATATAG +TTCATATATATACTGTTATATATATATAGTTCATATATATACTGTTATATATAGTTTATA +TATATATACTGTTATATATATAGTTTATATATATATACTGTTATATATATAGTTTATATA +TATATACTGTTATATATATATAGTTTATATATATATACTGTTATATATATAGTTTATATA +TATATACTGTTATATATATAGTTTATATATACTGTTATATATATATAGTTTATATATATA +CTGTTATATATATAGTTTATATATATACTGTTATATATATAGTTTATATATATACTGTTA +TATATATAGTTTATATATATACTGTTATATATATAGTTTATATATATACTGTTATATATA +TAGTTTATATATATATACTGTTATATATATAGTTTATAAATACTGTTATATATATAGTTT +ATATACTGTTATATATAGTTTATATATATATACTGTTATATATAGTTTATATATATATAC +TGTTATATATATATAGTTTATATATATATACTGTTATATATATATAGTTTATATATATAC +TGTTATATATATATAGTTTATATATATACTGTTGTATATATAGTTTATATATATACTGTT +ATATATATATTTGTGTATATATACTGTTATATAAATATATTTGTGTATATATACTGTTAT +ATATATATTTTATGTATATATACTGTTATATATATATTTTATGTATATATACTGTTATAT +ATATATTTTATGTATATATACTGTTATATATATATTTTATGTATATATACTGTTATATAT +ATATTTTATGTATATATACTGTTATATATATTTTATGTATATATACTGTTATATATATAT +TTTATGTATATATACTGTTATATCTGTATATTTTATGTTTATATACTGTTATATCTGTAT +ATTTTATGTATATATACTGTTATATCTGTATATTTTATGTATATACTGTTATATATATAC +TGTTATATATATACTGATATATATACTGTTATATATATACTGATATATATATACTGTTAT +ATATATACTGTTATATATATATACTGTTACATATACATATATATACTGTTATATATATAC +TGTTATATATATTGTTATATATATACACATATATATATACATATATATATACATATATAT +ATACATATATATATACACGTATATATATACATATATATATACACATATATATATATACAC +ACACATATATATATATATATATACTGGCTGTGTGTGGTGGTGCACACCTGTAATCCCAGC +ACTTTGGGAGGCCAAGGCAGGCTGATGGCTTGAGCTCAGGAGTTCAAGACCAGCTAAGCA +ACATACTGAGATCCCATCTCTAAAAAAAATACAAAAAGGCCAGGCACAGTGGCTCACACC +TGTAATCCCAGCACTTTGGGAGGCTGAGGTGGGCAGATCACGAGGTCAGCAGTTCGAGAC +CAGCCTGGCCAGCATGGTGAAACCCCATCTCTACTAAAAATACAAAACATTAGCCGGACA +TGGTGGCACACACCTGTAATTCCAGCTACTCAGGAAGCTGAGGCAGGAGAATAGCTTGAA +CCCAGGAGGCGAAAGTTTCAGTCAGCCAAAATCACACCACTGCACTCCAGCCTGGGCAAC +AGAGCAAGACTCTGTCTCCAAAAAAA +>p:HG002_2_chr20:38462831-38464884 +CACCATGTTACCTAGGCTGATCTTGAATTCCTGGGCTCAAGTGTTAGACTCACTTCGGCC +TCCCAAAGTGTTGGGATTACAGGCGTGAGCCACTGCACCCAGCCTGTTTTGTTTGGGGCA +AGGGTTTTAACATTTATATATATATAAATATATATATATTTTATATATACAAATATATAT +ATAAATATATATTTATATATATTTATATATAATATATTATATATAAATATATTTATATAT +AATATATTATATATAAATATATTATATATAAAATATTATATATAAATATATATATTTATA +TATATAAATATATATAAATATATATATATATAAAAATACCAGCACATCAGTATCAGGAAT +AAATGGGCTGGGCAGTATATATATATATATATATGTATATATATATACTGTTTTTCATAT +ATATATACTGTCTTATATATATATATACTGTTTTACATATATATACTGTTTCATATATAT +AATGTTTTATATATATACTGTTATATATATTATATGTACTGTTATATATTTTTTATATAT +ATACTGTTATATATATTTTTTATATATACTGTTATATATTATATATATACTGTTATATAT +ATATTTTACATATATACTGTTATATATATATTTTATATATATATACTGTTATATATATAT +ATTTTATATATGTATACTGTTATATATTTATATTTTTTATATGTATACTGTTATATATAT +ATTATATGTATACTGTTATATATATATTTTATATGTATACTGTTATATATATATATTTCA +TATATATATACTGTTATATATATTTTATATATATATACTGTCATATATATATTTTATATA +TATACTGTCATATATATATTTTATATATATATACTGTCATATATATATTTTATATATATA +TATACTGTCATATATATATTTTATATATATATACTGTCATATATATTTTATATATATACT +GTCATATATATATTTTATATATATACTGTCATATATATATTTTATATATATACTGTCATA +TATATATTTTATATATATACTGTCATATATATATTTTATATATATATACTGTCATATATA +TATTTTATATATATATACTGTCATATATATATTTTATATATATACTGTCATATGTATATT +TTATATATATACTGTCATATGTATATTTTATATATATACTGTTATATGTATATTTTATAT +ATATATACTGTTATATATATATTTTTATATATATACTGTTATATATATTTTTTTATATAT +ATACTGTTATATATATTTTTATATATATACTGTTATATATATATTTTATATATATACTGT +TATATATATATTTTATATATACTGTTATATATATATATTTTATATATATACTGTTATATA +TAATTTTTTTCATATATATACTGTTATATATATATTTTATATATATATACTGTTATATAT +ATATTTTATATATATACTGTTATATATATATATTTTATATATATACTGTTATTTTTTATA +TATATACTGTTATATATATATTTTATATATATACTGTTATATATATATTATCTATATACT +GTTATGTGTATATTTTATCTATATACTGTTATGTGTATATTTTATCTATATACTGTTATG +TGTATATTTTACCTATATACTTTTATGTGTATATTTTATATATATACTGTTATGTGTATA +TTTTATATATATACTGTTATGTGTATATTTTTTATATATACTGTTATGTGTATATTTTAT +ATATATATACTGTTATGTGTATATTTTATATATATATACTGTTATGTGTATATTTTATAT +ATATACTGTTATGTGTATATTTTATATATATACTGTTATATATAGTTCATATATATACTG +TTATATGTATAGTTCATATATATACTGTTATATATATAGTTCATATGTATACTGTTATAT +ATATAGTTCATATATATACTGTTATATATATAGTTCATATATATACTGTTATATATATAT +AGTTCATATATATACTGTTATATATAGTTCATATATATACTGTTATATATATAGTTCATA +TATATACTGTTATATATATAGTTCATATATATACTGTTATATATAGTTCATATATATATA +CTGTTCTATATATAGTTCATATATATATACTGTTATATATATAGTTCATATATATATACT +GTTATATATAGTTCATATATATATAGTTCATATATATACTGTTATATATATAGTTCATAT +ATATACTGTTATATACATAGTTCATATATATACTGTTATATATATAGTTCATATATATAT +ACTGTTATATATATAGTTCATATATATACTGTTGTATATAGTTCATATATATACTGTTAT +ATATATAGTTCATATATTACTGTTATATATATAGTTCATATATATACTGTTATATATATA +TAGTTCATATATATACTGTTATATATAGTTTATATATATATACTGTTATATATATAGTTT +ATATATATATACTGTTATATATATAGTTTATATATATATACTGTTATATATATATAGTTT +ATATATATATACTGTTATATATATAGTTTATATATATATACTGTTATATATATATAGTTT +ATATATACTGTTATATATATAGTTTATATATATACTGTTATATATATAGTTTATATATAT +ACTGTTATATATATAGTTTATATATATACTGTTATATATATAGTTTATATATATACTGTT +ATATATATAGTTTATATATATACTGTTATATATATAGTTTATATATATACTGTTATATAT +ATAGTTTATATATATATACTGTTATATATAGTTTATATATACTGTTATATATATAGTTTA +TATACTGTTATATATAGTTTATATATATATACTGTTATATATAGTTTATATATATATACT +GTTATATATATATAGTTTATATATATATACTGTTATATATATATAGTTTATATATATACT +GTTATATATATATAGTTTATATATATACTGTTGTATATATAGTTTATATATATACTGTTA +TATATATATTTGTGTATATATACTGTTATATAAATATATTTGTGTATATATACTGTTATA +TATATATTTTATGTATATATACTGTTATATATATATTTTATGTATATATACTGTTATATA +TATATTTTATGTATATATACTGTTATATATATATTTTATGTATATATACTGTTATATATA +TATTTTATGTATATATACTGTTATATATATTTTATGTATATATACTGTTATATATATTTT +ATGTATATATACTGTTATATATATATTTTATGTATATATACTGTTATATCTGTATATTTT +ATGTTTATATACTGTTATATCTGTATATTTTATGTATATATACTGTTATATCTGTATATT +TTATGTATATACTGTTATATATATACTGTTATATATATACTGATATATATACTGTTATAT +ATATACTGATATATATATACTGTTATATATATACTGTTATATATATATACTGTTACATAT +ACATATATATACTGTTATATATATACTGTTATATATATTGTTATATATATACACATATAT +ATATACATATATATACATATATATATACATATATATATACATATATATATACACGTATAT +ATATACATATATATATACACATATATATATATACACACACATATATATATATATATATAC +TGGCTGTGTGTGGTGGTGCACACCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGCTG +ATGGCTTGAGCTCAGGAGTTCAAGACCAGCTAAGCAACATACTGAGATCCCATCTCTAAA +AAAAATACAAAAAGGCCAGGCACAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGC +TGAGGTGGGCAGATCACGAGGTCAGCAGTTCGAGACCAGCCTGGCCAGCATGGTGAAACC +CCATCTCTACTAAAAATACAAAACATTAGCCGGACATGGTGGCACACACCTGTAATTCCA +GCTACTCAGGAAGCTGAGGCAGGAGAATAGCTTGAACCCAGGAGGCGAAAGTTTCAGTCA +GCCAAAATCACACCACTGCACTCCAGCCTGGGCAACAGAGCAAGACTCTGTCTCCAAAAA +AA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/haps.fa.ref.fa new file mode 100644 index 00000000..c0fd3940 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:38462831-38464884 +CACCATGTTACCTAGGCTGATCTTGAATTCCTGGGCTCAAGTGTTAGACTCACTTCGGCCTCCCAAAGTGTTGGGATTACAGGCGTGAGCCACTGCACCCAGCCTGTTTTGTTTGGGGCAAGGGTTTTAACATTTATATATATATAAATATATATATATTTTATATATACAAATATATATATAAATATATATTTATATATATTTATATATAATATATTATATATAAATATATTTATATATAATATATTATATATAAATATATTATATATAAAATATTATATATAAATATATATATTTATATATATAAATATATATAAATATATATATATATAAAAATACCAGCACATCAGTATCAGGAATAAATGGGCTGGGCAGTATATATATATATATATATGTATATATATATACTGTTTTTCATATATATATACTGTCTTATATATATATATACTGTTTTACATATATATACTGTTTCATATATATAATGTTTTATATATATACTGTTATATATATTATATGTACTGTTATATATTTTTTATATATATACTGTTATATATATTTTTTATATATACTGTTATATATTATATATATACTGTTATATATATATTTTACATATATACTGTTATATATATATTTTATATATATATACTGTTATATATATATATTTTATATATGTATACTGTTATATATTTATATTTTTTATATGTATACTGTTATATATATATTATATGTATACTGTTATATATATATTTTATATGTATACTGTTATATATATATATTTCATATATATATACTGTTATATATATTTTATATATATATACTGTCATATATATATTTTATATATATACTGTCATATATATATTTTATATATATATACTGTCATATATATATTTTATATATATATATACTGTCATATATATATTTTATATATATATACTGTCATATATATTTTATATATATACTGTCATATATATATTTTATATATATACTGTCATATATATATTTTATATATATACTGTCATATATATATTTTATATATATACTGTCATATATATATTTTATATATATATACTGTCATATATATATTTTATATATATATACTGTCATATATATATTTTATATATATACTGTCATATGTATATTTTATATATATACTGTCATATGTATATTTTATATATATACTGTTATATGTATATTTTATATATATATACTGTTATATATATATTTTTATATATATACTGTTATATATATTTTTTTATATATATACTGTTATATATATTTTTATATATATACTGTTATATATATATTTTATATATATACTGTTATATATATATTTTATATATACTGTTATATAGATACTGTTATATATATACTGATATATATACTGTTATATATATACTGATATATATATACTGTTATATATATACTGTTATATATATATACTGTTACATATACATATATATACTGTTATATATATACTGTTATATATATTGTTATATATATACACATATATATATACATATATATATACATATATATATACATATATATATACATATATATATACACGTATATATATACATATATATATACACATATATATATATACACACACATATATATATATATATATACTGGCTGTGTGTGGTGGTGCACACCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGCTGATGGCTTGAGCTCAGGAGTTCAAGACCAGCTAAGCAACATACTGAGATCCCATCTCTAAAAAAAATACAAAAAGGCCAGGCACAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGTGGGCAGATCACGAGGTCAGCAGTTCGAGACCAGCCTGGCCAGCATGGTGAAACCCCATCTCTACTAAAAATACAAAACATTAGCCGGACATGGTGGCACACACCTGTAATTCCAGCTACTCAGGAAGCTGAGGCAGGAGAATAGCTTGAACCCAGGAGGCGAAAGTTTCAGTCAGCCAAAATCACACCACTGCACTCCAGCCTGGGCAACAGAGCAAGACTCTGTCTCCAAAAAAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/msa.fa new file mode 100644 index 00000000..f9c8425d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/msa.fa @@ -0,0 +1,350 @@ +>ref_chr20_38462831_38464884 +caccatgttacctaggctgatcttgaattcctgggctcaagtgttagactcacttcggcc +tcccaaagtgttgggattacaggcgtgagccactgcacccagcctgttttgtttggggca +agggttttaacatttatatatatataaatatatatatattttatatatacaaatatatat +ataaatatatatttatatatatttatatataatatattatatataaatatatttatatat +aatatattatatataaatatattatatataaaatattatatataaatatatatatttata +tatataaatatatataaatatatatatatataaaaataccagcacatcagtatcaggaat +aaatgggctgggcagtatatatatatatatatatgtatatatatatactgtttttcatat +atatatactgtcttatatatatatatactgttttacatatatatactgtttcatatatat +aatgttttatatatatactgttatatatattatatgtactgttatatattttttatatat +atactgttatatatattttttatatatactgttatatattatatatatactgttatatat +atattttacatatatactgttatatatatattttatatatatatactgttatatatatat +attttatatatgtatactgttatatatttatattttttatatgtatactgttatatatat +attatatgtatactgttatatatatattttatatgtatactgttatatatatatatttca +tatatatatactgttatatatattttatatatatatactgtcatatatatattttatata +tatactgtcatatatatattttatatatatatactgtcatatatatattttatatatata +tatactgtcatatatatattttatatatatatactgtcatatatattttatatatatact +gtcatatatatattttatatatatactgtcatatatatattttatatatatactgtcata +tatatattt--tatatatatactgtcatatatatattttatatatatatactgtcatata +tatattttatatatatatactgtcatatatatattttatatatatactgtcatatgtata +ttttatatatatactgtcatatgtatattt------------------------------ +-tatatatatactgttatatgtatattttatatatatatactgttatatatatattttta +tatatatactgttatatatatttttttatatatatactgttatatatatttttatatata +tactgttatatatatattttatatatatactgttatatatatatttta------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------tatatactgttatatagata +ctgttatatatatactgatatatatactgttatatatatactgatatatatatactgtta +tatatatactgttatatatatatactgttacatatacatatatatactgttatatatata +ctgttatatatattgttatatatatacacatatatatatacatatatatatacatatata +tatacatatatatatacatatatatatacacgtatatatatacatatatatatacacata +tatatatatacacacacatatatatatatatatatactggctgtgtgtggtggtgcacac +ctgtaatcccagcactttgggaggccaaggcaggctgatggcttgagctcaggagttcaa +gaccagctaagcaacatactgagatcccatctctaaaaaaaatacaaaaaggccaggcac +agtggctcacacctgtaatcccagcactttgggaggctgaggtgggcagatcacgaggtc +agcagttcgagaccagcctggccagcatggtgaaaccccatctctactaaaaatacaaaa +cattagccggacatggtggcacacacctgtaattccagctactcaggaagctgaggcagg +agaatagcttgaacccaggaggcgaaagtttcagtcagccaaaatcacaccactgcactc +cagcctgggcaacagagcaagactctgtctccaaaaaaa +>syndip_1_chr20:38462831-38464884 +caccatgttacctaggctgatcttgaattcctgggctcaagtgttagactcacttcggcc +tcccaaagtgttgggattacaggcgtgagccactgcacccagcctgttttgtttggggca +agggttttaacatttatatatatataaatatatatatattttatatatacaaatatatat +ataaatatatatttatatatatttatatataatatattatatataaatatatttatatat +aatatattatatataaatatattatatataaaatattatatataaatatatatatttata +tatataaatatatataaatatatatatatataaaaataccagcacatcagtatcaggaat +aaatgggctgggcagtatatatatatatatatatgtatatatatatactgtttttcatat +atatatactgtcttatatatatatatactgttttacatatatatactgtttcatatatat +aatgttttatatatatactgttatatatattatatgtactgttatatattttttatatat +atactgttatatatattttttatatatactgttatatattatatatatactgttatatat +atattttacatatatactgttatatatatattttatatatatatactgttatatatatat +attttatatatgtatactgttatatatttatattttttatatgtatactgttatatatat +attatatgtatactgttatatatatattttatatgtatactgttatatatatatatttca +tatatatatactgttatatatattttatatatatatactgtcatatatatattttatata +tatactgtcatatatatattttatatatatatactgtcatatatatattttatatatata +tatactgtcatatatatattttatatatatatactgtcatatatattttatatatatact +gtcatatatatattttatatatatactgtcatatatatattttatatatatactgtcata +tatatattt--tatatatatactgtcatatatatattttatatatatatactgtcatata +tatattttatatatatatactgtcatatatatattttatatatatactgtcatatgtata +ttttatatatatactgtcatatgtatattt------------------------------ +-tatatatatactgttatatgtatattttatatatatatactgttatatatatattttta +tatatatactgttatatatatttttttatatatatactgttatatatatttttatatata +tactgttatatatatattttatatatatactgttatatatatattttatatatactgtta +tatatatatattttatatatatactgttatatataatttttttcatatatatactgttat +atatatattttatatatatatactgttatatatatattttatatatatactgttatatat +atatattttatatatatactgttattttttatatatatactgttatatatatattttata +tatatactgttatatatatattatctatatactgttatgtgtatattttatctatatact +gttatgtgtatattttatctatatactgttatgtgtatattttacctatatacttttatg +tgtatattttatatatatactgttatgtgtatattttatatatatactgttatgtgtata +ttttttatatatactgttatgtgtatattttatatatatatactgttatgtgtatatttt +atatatatatactgttatgtgtatattttatatatatactgttatgtgtatattttatat +atatactgttatatatagttcatatatatactgttatatgtatagttcatatatatactg +ttatatatatagttcatatgtatactgttatatatatagttcatatatatactgttatat +atatagttcatatatatactgttatatatatatagttcatatatatactgttatatatag +ttcatatatatactgttatatatatagttcatatatatactgttatatatatagttcata +tatatactgttatatatagttcatatatatatactgttctatatatagttcatatatata +tactgttatatatatagttcatatatatatactgttatatatagttcatatatatatagt +tcatatatatactgttatatatatagttcatatatatactgttatatacatagttcatat +atatactgttatatatatagttcatatatatatactgttatatatatagttcatatatat +actgttgtatatagttcatatatatactgttatatatatagttcatatattactgttata +tatatagttcatatatatactgttatatatatatagttcatatatatactgttatatata +gtttatatatatatactgttatatatatagtttatatatatatactgttatatatatagt +ttatatatatatactgttatatatatatagtttatatatatatactgttatatatatagt +ttatatatatatactgttatatatatatagtttatatatactgttatatatatagtttat +atatatactgttatatatatagtttatatatatactgttatatatatagtttatatatat +actgttatatatatagtttatatatatactgttatatatatagtttatatatatactgtt +atatatatagtttatatatatactgttatatatatagtttatatatatatactgt--tat +atatagtttatatatactgttatatatatagtttatatactgttatatatagtttatata +tatatactgttatatatagtttatatatatatactgttatatatatatagtttatatata +tatactgttatatatatatagtttatatatatactgttatatatatatagtttatatata +tactgttgtatatatagtttatatatatactgttatatatatatttgtgtatatatactg +ttatataaatatatttgtgtatatatactgttatatatatattttatgtatatatactgt +tatatatatattttatgtatatatactgttatatatatattttatgtatatatactgtta +tatatatattttatgtatatatactgttatatatatattttatgtatatatactgttata +tatattttatgtatatatactgttatatatattttatgtatatatactgttatatatata +ttttatgtatatatactgttatatctgtatattttatgtttatatactgttatatctgta +tattttatgtatatatactgttatatctgtatattttatgtatatactgttatatatata +ctgttatatatatactgatatatatactgttatatatatactgatatatatatactgtta +tatatatactgttatatatatatactgttacatatacatatatatactgttatatatata +ctgttatatatattgttatatatatacacatatatatatac--atatatatacatatata +tatacatatatatatacatatatatatacacgtatatatatacatatatatatacacata +tatatatatacacacacatatatatatatatatatactggctgtgtgtggtggtgcacac +ctgtaatcccagcactttgggaggccaaggcaggctgatggcttgagctcaggagttcaa +gaccagctaagcaacatactgagatcccatctctaaaaaaaatacaaaaaggccaggcac +agtggctcacacctgtaatcccagcactttgggaggctgaggtgggcagatcacgaggtc +agcagttcgagaccagcctggccagcatggtgaaaccccatctctactaaaaatacaaaa +cattagccggacatggtggcacacacctgtaattccagctactcaggaagctgaggcagg +agaatagcttgaacccaggaggcgaaagtttcagtcagccaaaatcacaccactgcactc +cagcctgggcaacagagcaagactctgtctccaaaaaaa +>syndip_2_chr20:38462831-38464884 +caccatgttacctaggctgatcttgaattcctgggctcaagtgttagactcacttcggcc +tcccaaagtgttgggattacaggcgtgagccactgcacccagcctgttttgtttggggca +agggttttaacatttatatatatataaatatatatatattttatatatacaaatatatat +ataaatatatatttatatatatttatatataatatattatatat-aatatatttatatat +aatatattatatataaatatattatatataaaatattatatataaatatatatatttata +tatataaatatatataaatatatatatatataaaaataccagcacatcagtatcaggaat +aaatgggctgggcag--tatatatatatatatatgtatatatatatactgtttttcatat +atatatactgtcttatatatatatatactgttttacatatatatactgtttcatatatat +aatgttttatatatatactgttatatatattatatgtactgttatatattttttatatat +atactgttatatatattttttatatatactgttatatattatatatatactgttatatat +atattttacatatatactgttatatatatattttatatatatatactgttatatatatat +attttatatatgtatactgttatatatttatattttttatatgtatactgttatatatat +attatatgtatactgttatatatatattttatatgtatactgttatatatatatatttca +tatatatatactgttatatatattttatatatatatactgtcatatatatattttatata +tatactgtcatatatatattttatatatatatactgtcatatatatattt--tatatata +tatactgtcatatatatattttatatatatatactgtcatatatattttatatatatact +gtcatatatatattttatatatatactgtcatatatatattttatatatatactgtcata +tatatattttatatatatatactgtcatatatatattttatatatatatactgtcatata +tatattt--tatatatatactgtcatatgtatattttatatatatactgtcatatgtata +ttttatatatatactgttatatgtatattttatatatatatactgttatatatatatttt +atatatatatactgttatatatatattttatatatatatactgttatatatatattttta +tatatatactgttatatatatttttttatatatatactgttatatatatttttatatata +tactgttatatatatattttatatatatactgttatatatatattttatatatactgtta +tatatatatattttatatatatactgttatatataatttttttcatatatatactgttat +atatatattttatatatatatactgttatatatatattttatatatatactgttatatat +atatattttatatatatactgttattttttatatatatactgttatatatatattttata +tatatactgttatatatatattatctatatactgttatgtgtatattttatctatatact +gttatgtgtatattttatctatatactgttatgtgtatattttacctatatacttttatg +tgtatattttatatatatactgttatgtgtatattttatatatatactgttatgtgtata +ttttttatatatactgttatgtgtatattttatatatatatactgttatgtgtatatttt +atatatatatactgttatgtgtatattttatatatatactgttatgtgtatattttatat +atatactgttatatatagttcatatatatactgttatatgtatagttcatatatatactg +ttatatatatagttcatatgtatactgttatatatatagttcatatatatactgttatat +atatagttcatatatatactgttatatatatatagttcatatatatactgttatatatag +ttcatatatatactgttatatatatagttcatatatatactgttatatatatagttcata +tatatactgttatatatagttcatatatatatactgttctatatatagttcatatatata +tactgttatatatatagttcatatatatatactgttatatatagttcatatatatatagt +tcatatatatactgttatatatatagttcatatatatactgttatatacatagttcatat +atatactgttatatatatagttcatatatatatactgttatatatatagttcatatatat +actgttgtatatagttcatatatatactgttatatatatagttcatatattactgttata +tatatagttcatatatatactgttatatatatatagttcatatatatactgttatatata +gtttatatatatatactgttatatatatagtttatatatatatactgttatatatatagt +ttatatatatatactgttatatatatatagtttatatatatatactgttatatatatagt +ttatatatatatactgt--tatatatatagtttatatatactgtta-------------- +-----------tatatatatagtttatatatatactgttatatatatagtttatatatat +actgttatatatatagtttatatatatactgttatatatatagtttatatatatactgtt +atatatatagtttatatatatactgttatatatatagtttatatatatatactgttatat +atatagtttataaatactgttatatatatagtttatatactgttatatatagtttatata +tatatactgttatatatagtttatatatatatactgttatatatatatagtttatatata +tatactgttatatatatatagtttatatatatactgttatatatatatagtttatatata +tactgttgtatatatagtttatatatatactgttatatatatatttgtgtatatatactg +ttatataaatatatttgtgtatatatactgttatatatatattttatgtatatatactgt +tatatatatattttatgtatatatactgttatatatatattttatgtatatatactgtta +tatatatattttatgtatatatactgtta---------------------------tata +tatattttatgtatatatactgttatatatattttatgtatatatactgttatatatata +ttttatgtatatatactgttatatctgtatattttatgtttatatactgttatatctgta +tattttatgtatatatactgttatatctgtatattttatgtatatactgttatatatata +ctgttatatatatactgatatatatactgttatatatatactgatatatatatactgtta +tatatatactgttatatatatatactgttacatatacatatatatactgttatatatata +ctgttatatatattgttatatatatacacat------------atatatatacatatata +tatacatatatatatacatatatatatacacgtatatatatacatatatatatacacata 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+tatactgttatatatatatagtttatatatatactgttatatatatatagtttatatata +tactgttgtatatatagtttatatatatactgttatatatatatttgtgtatatatactg +ttatataaatatatttgtgtatatatactgttatatatatattttatgtatatatactgt +tatatatatattttatgtatatatactgttatatatatattttatgtatatatactgtta +tatatatattttatgtatatatactgttatatatatattttatgtatatatactgttata +tatattttatgtatatatactgttatatatattttatgtatatatactgttatatatata +ttttatgtatatatactgttatatctgtatattttatgtttatatactgttatatctgta +tattttatgtatatatactgttatatctgtatattttatgtatatactgttatatatata +ctgttatatatatactgatatatatactgttatatatatactgatatatatatactgtta +tatatatactgttatatatatatactgttacatatacatatatatactgttatatatata +ctgttatatatattgttatatatatacacatatatatatac--atatatatacatatata +tatacatatatatatacatatatatatacacgtatatatatacatatatatatacacata +tatatatatacacacacatatatatatatatatatactggctgtgtgtggtggtgcacac +ctgtaatcccagcactttgggaggccaaggcaggctgatggcttgagctcaggagttcaa +gaccagctaagcaacatactgagatcccatctctaaaaaaaatacaaaaaggccaggcac +agtggctcacacctgtaatcccagcactttgggaggctgaggtgggcagatcacgaggtc +agcagttcgagaccagcctggccagcatggtgaaaccccatctctactaaaaatacaaaa +cattagccggacatggtggcacacacctgtaattccagctactcaggaagctgaggcagg +agaatagcttgaacccaggaggcgaaagtttcagtcagccaaaatcacaccactgcactc +cagcctgggcaacagagcaagactctgtctccaaaaaaa diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/msa.fa.fai new file mode 100644 index 00000000..0fbd95dc --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_38462831_38464884 4119 29 60 61 +syndip_1_chr20:38462831-38464884 4119 4251 60 61 +syndip_2_chr20:38462831-38464884 4119 8473 60 61 +p:HG002_1_chr20:38462831-38464884 4119 12696 60 61 +p:HG002_2_chr20:38462831-38464884 4119 16919 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/output.vcf.gz new file mode 100644 index 00000000..d2d11b7f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/output.vcf.gz.tbi new file mode 100644 index 00000000..2eb56f31 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:38462931-38464784/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/base.vcf.gz new file mode 100644 index 00000000..d8858ad8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/base.vcf.gz.tbi new file mode 100644 index 00000000..55d29663 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/comp.vcf.gz new file mode 100644 index 00000000..c403f9a0 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/comp.vcf.gz.tbi new file mode 100644 index 00000000..e7cebfea Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/haps.fa new file mode 100644 index 00000000..5c0c9583 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/haps.fa @@ -0,0 +1,132 @@ +>ref_chr20_4032119_4033702 +CGGGATTGCAGATGAAGTCTCGTTCACTCAGTGCTCAGTGGTGTCCAGGCTGGAGTGCAGCGGCGTGATCTCGGCTCGCTACAACCACCTCCCAGCCGCCTGCCTTGGCCTCCCAAAGAGCCGAGATTGCAGCCTCTGCCCGGCCGCCACCCCGTCTGGGAAGTGAGGAGCGTCTCTGCTTGGCCACCCATCGTCTGGGATATGAGGAGCCCCTCTGCCTGGCTGCCCAGTCTGGAAAGTGAGGAGCGTCTCTGCCCGGCCGCCATCCCATCTAGGAAGCGAGGAGCGTCTCTGCCCGGCCGCCATCCCATCTAGGAAGCGAGGAGCGCCTCTTCCCGGCTGCCATCCCATCTAGGAACTGAGGAGCGTCTCTGCCCGGCCGCCCATCGTCTGAGATGTGGGGAGCACCTCTGCCCCACCGCCCTGTCTGGGATGTGAGGAGCGCCTCTGCTGGGCCGCAACCCTGTCTGGGAGGTGAGGAGCGTCTCTGCCCCGCCGCTCCGTCTGAGAAGTGAGGAAACCCTCTGCCTGGCAACCGCCCCGTCTGAGAAGTGAGGAGCCCCTCCGTCCGGCAACCACCCCGTCTGGGAAGTGAGGAGCGTCTCCGCCCGGCAGCCACCCCGTCCGGGAGGGAGGTGGGGGGGGGGGTCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCGGCCGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCGGCTGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCTGCCCCGCCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCTGGCCAGCCGCCCCATCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGGGGGAGGGGGGGTCAGCCCCCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGGGGTCAGCCCCCTTTCCGGCCGCCGCCTGTCCGGGAGGTGAGGGGCGCCTCTGCCTGGCCGCCCCTACTGGGAAGTGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGACAGCCCCCCGCCCGGCCAGCCGCCCTATCCAGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCTGGCCAGCCGCCCCGTCCGGGAGGGTAGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCATCCGGGAGGTGAGGGGCGCTTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCACGACCCCGTCTGGGAGGTGTGCCCAGCGGCTCATTGGGGATGGGCCATGATGACAATGGCGGTTTTGTGGAATAGAAAGGCGGGAAGGGTGGGGAAAAAATTGAGAAATCGGATGGTTGCCGGGTCTGTGTGGATGGAAGTAGACATG +>syndip_1_chr20:4032119-4033702 +CGGGATTGCAGATGAAGTCTCGTTCACTCAGTGCTCAGTGGTGTCCAGGCTGGAGTGCAG +CGGCGTGATCTCGGCTCGCTACAACCACCTCCCAGCCGCCTGCCTTGGCCTCCCAAAGAG +CCGAGATTGCAGCCTCTGCCCGGCCGCCACCCCGTCTGGGAAGTGAGGAGCGTCTCTGCT +TGGCCACCCATCGTCTGGGATATGAGGAGCCCCTCTGCCTGGCTGCCCAGTCTGGAAAGT +GAGGAGCGTCTCTGCCCGGCCGCCATCCCATCTAGGAAGCGAGGAGCGCCTCTTCCCGGC +TGCCATCCCATCTAGGAAGTGAGGAGCGTCTCTGCCCGGCCGCCCATCGTCTGAGATGTG +GGGAGCACCTCTGCCCCACCGCCCTGTCTGGGATGTGAGGAGCGCCTCTGCTGGGCCGCA +ACCCTGTCTGGGAGGTGAGGAGCGTCTCTGCCCCGCCGCTCCGTCTGAGAAGTGAGGAAA +CCCTCTGCCTGGCAACCGCCCCGTCTGAGAAGTGAGGAGCCCCTCCGTCCGGCAACCACC +CCGTCTGGGAAGTGAGGAGCGTCTCCGCCCGGCAGCCACCCCGTCCGGGAGGGAGGTGGG +GGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGTGAGGGGCTCCTCTGCCC +GGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGG +GAGGCGGGGGGGGGGGTCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCC +CCCGCCCGGCCGGCCGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTAC +TGGGAAGTGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGT +CAGTCCCCCGCCCGGCCGGCTGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGC +CCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCTGCCCCGCCCGGGAGGGAGGTG +GGGGGGTCAGCCCCCCGCCTGGCCAGCCGCCCCATCCGGGAGGGAGGTGGGGGGGTCAGC +CCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGGGGGAGGGGGGGTCAGCCCCCTGCCCGG +CCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCC +CCGTCCGGGAGGGAGGTGGGGGGATCAGCCCCCCGCCTGGCCAGCCGCCCCGTCCGGGAG +GTGAGGGGCGCCTCTGCCCGGCCACCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCC +AGCCGCCCCGTCCGGGAGGGAGGCGGGGGGGGGGGTCGGCCAGCCGCCCCGTCCGGGAGG +GAGGTGGGGGGGTCAGCCCCCCTTCCGGCCGGCCGCCCTGTCCGGGAGGTGAGGGGCGCC +TCTGCCTGGCCGCCCCTACTGGGAAGTGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCC +GGGAGGGAGGTGGGGGGGACAGCCCCCCGCCCGGCCAGCCGCCCTATCCAGGAGGTGAGG +GGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCCGC +CCCGTCCGGGAGGGTAGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCATCCGGGA +GGTGAGGGGCGCTTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGC +CACGACCCCGTCTGGGAGGTGTGCCCAGCGGCTCATTGGGGATGGGCCATGATGACAATG +GCGGTTTTGTGGAATAGAAAGGCGGGAAGGGTGGGGAAAAAATTGAGAAATCGGATGGTT +GCCGGGTCTGTGTGGATGGAAGTAGACATG +>syndip_2_chr20:4032119-4033702 +CGGGATTGCAGATGAAGTCTCGTTCACTCAGTGCTCAGTGGTGTCCAGGCTGGAGTGCAG +CGGCGTGATCTCGGCTCGCTACAACCACCTCCCAGCCGCCTGCCTTGGCCTCCCAAAGAG +CCGAGATTGCAGCCTCTGCCCGGCCGCCACCCCGTCTGGGAAGTGAGGAGCGTCTCTGCT +TGGCCACCCATCGTCTGGGATATGAGGAGCCCCTCTGCCTGGCTGCCCAGTCTGGAAAGT +GAGGAGCGTCTCTGCCCGGCCGCCATCCCATCTAGGAAGCGAGGAGCGTCTCTGCCCGGC +CGCCATCCCATCTAGGAAGCGAGGAGCGCCTCTTCCCGGCTGCCATCCCATCTAGGAACT +GAGGAGCGTCTCTGCCCGGCCGCCCATCGTCTGAGATGTGGGGAGCACCTCTGCCCCACC +GCCCTGTCTGGGATGTGAGGAGCGCCTCTGCTGGGCCGCAACCCTGTCTGGGAGGTGAGG +AGCGTCTCTGCCCCGCCGCTCCGTCTGAGAAGTGAGGAAACCCTCTGCCTGGCAACCGCC +CCGTCTGAGAAGTGAGGAGCCCCTCCGTCCGGCAACCACCCCGTCTGGGAAGTGAGGAGC +GTCTCCGCCCGGCAGCCACCCCGTCCGGGAGGGAGGTGGGGGGGGGGGTCGGCCAGCCGC +CCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCGGCCGCCCCGTCCGGGA +GGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGACCCCTCTGCCCGGCC +AGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCGGCTGCCCCGT +CCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTG +CCCGGCCAGCTGCCCCGCCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCTGGCCAGCC +GCCCCATCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGG +GAGGGGGGAGGGGGGGTCAGCCCCCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGG +GGGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGATC +AGCCCCCCGCCTGGCCAGCCGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCACC +CCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGCGG +GGGGGGGGGTCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCTTCC +GGCCGGCCGCCCTGTCCGGGAGGTGAGGGGCGCCTCTGCCTGGCCGCCCCTACTGGGAAG +TGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGACAGCCCC +CCGCCCGGCCAGCCGCCCTATCCAGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACT +GGGAAGTGAGGAGCCCCTCTGCCTGGCCAGCCGCCCCGTCCGGGAGGGTAGTGGGGGGGT +CAGCCCCCCGCCCGGCCAGCCGCCCCATCCGGGAGGTGAGGGGCGCTTCTGCCCGGCCGC +CCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCACGACCCCGTCTGGGAGGTGTGCCC +AGCGGCTCATTGGGGATGGGCCATGATGACAATGGCGGTTTTGTGGAATAGAAAGGCGGG +AAGGGTGGGGAAAAAATTGAGAAATCGGATGGTTGCCGGGTCTGTGTGGATGGAAGTAGA +CATG +>p:HG002_1_chr20:4032119-4033702 +CGGGATTGCAGATGAAGTCTCGTTCACTCAGTGCTCAGTGGTGTCCAGGCTGGAGTGCAG +CGGCGTGATCTCGGCTCGCTACAACCACCTCCCAGCCGCCTGCCTTGGCCTCCCAAAGAG +CCGAGATTGCAGCCTCTGCCCGGCCGCCACCCCGTCTGGGAAGTGAGGAGCGTCTCTGCT +TGGCCACCCATCGTCTGGGATATGAGGAGCCCCTCTGCCTGGCTGCCCAGTCTGGAAAGT +GAGGAGCGTCTCTGCCCGGCCGCCATCCCATCTAGGAAGCGAGGAGCGTCTCTGCCCGGC +CGCCATCCCATCTAGGAAGCGAGGAGCGCCTCTTCCCGGCTGCCATCCCATCTAGGAACT +GAGGAGCGTCTCTGCCCGGCCGCCCATCGTCTGAGATGTGGGGAGCACCTCTGCCCCACC +GCCCTGTCTGGGATGTGAGGAGCGCCTCTGCTGGGCCGCAACCCTGTCTGGGAGGTGAGG +AGCGTCTCTGCCCCGCCGCTCCGTCTGAGAAGTGAGGAAACCCTCTGCCTGGCAACCGCC +CCGTCTGAGAAGTGAGGAGCCCCTCCGTCCGGCAACCACCCCGTCTGGGAAGTGAGGAGC +GTCTCCGCCCGGCAGCCACCCCGTCCGGGAGGGAGGTGGGGGGGGGGGTCGGCCAGCCGC +CCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCGGCCGCCCCGTCCGGGA +GGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGACCCCTCTGCCCGGCC +AGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCGGCTGCCCCGT +CCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTG +CCCGGCCAGCTGCCCCGCCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCTGGCCAGCC +GCCCCATCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGG +GAGGGGGGAGGGGGGGTCAGCCCCCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGG +GGGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGATC +AGCCCCCCGCCTGGCCAGCCGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCACC +CCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGCGG +GGGGGGGGGTCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCTTCC +GGCCGGCCGCCCTGTCCGGGAGGTGAGGGGCGCCTCTGCCTGGCCGCCCCTACTGGGAAG +TGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGACAGCCCC +CCGCCCGGCCAGCCGCCCTATCCAGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACT +GGGAAGTGAGGAGCCCCTCTGCCTGGCCAGCCGCCCCGTCCGGGAGGGTAGTGGGGGGGT +CAGCCCCCCGCCCGGCCAGCCGCCCCATCCGGGAGGTGAGGGGCGCTTCTGCCCGGCCGC +CCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCACGACCCCGTCTGGGAGGTGTGCCC +AGCGGCTCATTGGGGATGGGCCATGATGACAATGGCGGTTTTGTGGAATAGAAAGGCGGG +AAGGGTGGGGAAAAAATTGAGAAATCGGATGGTTGCCGGGTCTGTGTGGATGGAAGTAGA +CATG +>p:HG002_2_chr20:4032119-4033702 +CGGGATTGCAGATGAAGTCTCGTTCACTCAGTGCTCAGTGGTGTCCAGGCTGGAGTGCAG +CGGCGTGATCTCGGCTCGCTACAACCACCTCCCAGCCGCCTGCCTTGGCCTCCCAAAGAG +CCGAGATTGCAGCCTCTGCCCGGCCGCCACCCCGTCTGGGAAGTGAGGAGCGTCTCTGCT +TGGCCACCCATCGTCTGGGATATGAGGAGCCCCTCTGCCTGGCTGCCCAGTCTGGAAAGT +GAGGAGCGTCTCTGCCCGGCCGCCATCCCATCTAGGAAGCGAGGAGCGCCTCTTCCCGGC +TGCCATCCCATCTAGGAAGTGAGGAGCGTCTCTGCCCGGCCGCCCATCGTCTGAGATGTG +GGGAGCACCTCTGCCCCACCGCCCTGTCTGGGATGTGAGGAGCGCCTCTGCTGGGCCGCA +ACCCTGTCTGGGAGGTGAGGAGCGTCTCTGCCCCGCCGCTCCGTCTGAGAAGTGAGGAAA +CCCTCTGCCTGGCAACCGCCCCGTCTGAGAAGTGAGGAGCCCCTCCGTCCGGCAACCACC +CCGTCTGGGAAGTGAGGAGCGTCTCCGCCCGGCAGCCACCCCGTCCGGGAGGGAGGTGGG +GGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGTGAGGGGCTCCTCTGCCC +GGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGG +GAGGCGGGGGGGGGGGTCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCC +CCCGCCCGGCCGGCCGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTAC +TGGGAAGTGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGT +CAGTCCCCCGCCCGGCCGGCTGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGC +CCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCTGCCCCGCCCGGGAGGGAGGTG +GGGGGGTCAGCCCCCCGCCTGGCCAGCCGCCCCATCCGGGAGGGAGGTGGGGGGGTCAGC +CCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGGGGGAGGGGGGGTCAGCCCCCTGCCCGG +CCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCC +CCGTCCGGGAGGGAGGTGGGGGGATCAGCCCCCCGCCTGGCCAGCCGCCCCGTCCGGGAG +GTGAGGGGCGCCTCTGCCCGGCCACCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCC +AGCCGCCCCGTCCGGGAGGGAGGCGGGGGGGGGGGTCGGCCAGCCGCCCCGTCCGGGAGG +GAGGTGGGGGGGTCAGCCCCCCTTCCGGCCGGCCGCCCTGTCCGGGAGGTGAGGGGCGCC +TCTGCCTGGCCGCCCCTACTGGGAAGTGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCC +GGGAGGGAGGTGGGGGGGACAGCCCCCCGCCCGGCCAGCCGCCCTATCCAGGAGGTGAGG +GGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCCGC +CCCGTCCGGGAGGGTAGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCATCCGGGA +GGTGAGGGGCGCTTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGC +CACGACCCCGTCTGGGAGGTGTGCCCAGCGGCTCATTGGGGATGGGCCATGATGACAATG +GCGGTTTTGTGGAATAGAAAGGCGGGAAGGGTGGGGAAAAAATTGAGAAATCGGATGGTT +GCCGGGTCTGTGTGGATGGAAGTAGACATG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/haps.fa.ref.fa new file mode 100644 index 00000000..5d92d772 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:4032119-4033702 +CGGGATTGCAGATGAAGTCTCGTTCACTCAGTGCTCAGTGGTGTCCAGGCTGGAGTGCAGCGGCGTGATCTCGGCTCGCTACAACCACCTCCCAGCCGCCTGCCTTGGCCTCCCAAAGAGCCGAGATTGCAGCCTCTGCCCGGCCGCCACCCCGTCTGGGAAGTGAGGAGCGTCTCTGCTTGGCCACCCATCGTCTGGGATATGAGGAGCCCCTCTGCCTGGCTGCCCAGTCTGGAAAGTGAGGAGCGTCTCTGCCCGGCCGCCATCCCATCTAGGAAGCGAGGAGCGTCTCTGCCCGGCCGCCATCCCATCTAGGAAGCGAGGAGCGCCTCTTCCCGGCTGCCATCCCATCTAGGAACTGAGGAGCGTCTCTGCCCGGCCGCCCATCGTCTGAGATGTGGGGAGCACCTCTGCCCCACCGCCCTGTCTGGGATGTGAGGAGCGCCTCTGCTGGGCCGCAACCCTGTCTGGGAGGTGAGGAGCGTCTCTGCCCCGCCGCTCCGTCTGAGAAGTGAGGAAACCCTCTGCCTGGCAACCGCCCCGTCTGAGAAGTGAGGAGCCCCTCCGTCCGGCAACCACCCCGTCTGGGAAGTGAGGAGCGTCTCCGCCCGGCAGCCACCCCGTCCGGGAGGGAGGTGGGGGGGGGGGTCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCGGCCGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCGGCTGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCTGCCCCGCCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCTGGCCAGCCGCCCCATCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGGGGGAGGGGGGGTCAGCCCCCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGGGGTCAGCCCCCTTTCCGGCCGCCGCCTGTCCGGGAGGTGAGGGGCGCCTCTGCCTGGCCGCCCCTACTGGGAAGTGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGACAGCCCCCCGCCCGGCCAGCCGCCCTATCCAGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCTGGCCAGCCGCCCCGTCCGGGAGGGTAGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCATCCGGGAGGTGAGGGGCGCTTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCACGACCCCGTCTGGGAGGTGTGCCCAGCGGCTCATTGGGGATGGGCCATGATGACAATGGCGGTTTTGTGGAATAGAAAGGCGGGAAGGGTGGGGAAAAAATTGAGAAATCGGATGGTTGCCGGGTCTGTGTGGATGGAAGTAGACATG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/msa.fa new file mode 100644 index 00000000..8f3d46af --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/msa.fa @@ -0,0 +1,170 @@ +>ref_chr20_4032119_4033702 +cgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgcag +cggcgtgatctcggctcgctacaaccacctcccagccgcctgccttggcctcccaaagag +ccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctctgct +tggccacccatcgtctgggatatgaggagcccctctgcctggctgcccagtctggaaagt +gaggagcgtctctgcccggccgccatcccatctaggaagcgaggagcgtctctgcccggc +cgccatcccatctaggaagcgaggagcgcctcttcccggctgccatcccatctaggaact +gaggagcgtctctgcccggccgcccatcgtctgagatgtggggagcacctctgccccacc +gccctgtctgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggtgagg +agcgtctctgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaaccgcc +ccgtctgagaagtgaggagcccctccgtccggcaaccaccccgtctgggaagtgaggagc +gtctccgcccggcagccaccccgtccgggagggaggt----------------------- +------------------------------------------------------------ +---------------------------------------------gggggggggggtcgg +ccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggccgcccc +gtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggacccctct +gcccggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggc +tgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggag +cccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagccccccgcct +ggccagccgccccatccgggagggaggtgggggggtcagccccccgcccggccagccgcc +ccgtccgggaggggggagggggggtcagccccctgcccggccagccgccccgtccgggag +ggaggtggg--------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------------------gggggggtcagcc +ccctttccggccg--ccgcctgtccgggaggtgaggggcgcctctgcctggccgccccta +ctgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtggggggg +acagccccccgcccggccagccgccctatccaggaggtgaggggcgcctctgcccggccg +cccctactgggaagtgaggagcccctctgcctggccagccgccccgtccgggagggtagt +gggggggtcagccccccgcccggccagccgccccatccgggaggtgaggggcgcttctgc +ccggccgcccctactgggaagtgaggagcccctctgcccggccacgaccccgtctgggag +gtgtgcccagcggctcattggggatgggccatgatgacaatggcggttttgtggaataga +aaggcgggaagggtggggaaaaaattgagaaatcggatggttgccgggtctgtgtggatg +gaagtagacatg +>syndip_1_chr20:4032119-4033702 +cgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgcag +cggcgtgatctcggctcgctacaaccacctcccagccgcctgccttggcctcccaaagag +ccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctctgct +tggccacccatcgtctgggatatgaggagcccctctgcctggctgcccagtctggaaagt +----------------------------------------gaggagcgtctctgcccggc +cgccatcccatctaggaagcgaggagcgcctcttcccggctgccatcccatctaggaagt +gaggagcgtctctgcccggccgcccatcgtctgagatgtggggagcacctctgccccacc +gccctgtctgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggtgagg +agcgtctctgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaaccgcc +ccgtctgagaagtgaggagcccctccgtccggcaaccaccccgtctgggaagtgaggagc +gtctccgcccggcagccaccccgtccgggagggaggtggggggggtcagccccccgcccg +gccagccgccccgtccgggaggtgaggggctcctctgcccggccgcccctactgggaagt +gaggagcccctctgcccggccagccgccccgtccgggagggaggcgggggggggggtcgg +ccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggccgcccc +gtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggacccctct +gcccggccagccgccccgtccgggagggaggtgggggggtcagtcccccgcccggccggc +tgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggag +cccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagccccccgcct +ggccagccgccccatccgggagggaggtgggggggtcagccccccgcccggccagccgcc +ccgtccgggaggggggagggggggtcagccccctgcccggccagccgccccgtccgggag +ggaggtggg--ggggggtcagccccccgcccggccagccgccccgtccgggagggaggtg +gggggatcagccccccgcctggccagccgccccgtccgggaggtgaggggcgcctctgcc +cggccacccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgggag +ggaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggggggtcagcc +ccccttccggccggccgccctgtccgggaggtgaggggcgcctctgcctggccgccccta +ctgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtggggggg +acagccccccgcccggccagccgccctatccaggaggtgaggggcgcctctgcccggccg +cccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgggagggtagt +gggggggtcagccccccgcccggccagccgccccatccgggaggtgaggggcgcttctgc +ccggccgcccctactgggaagtgaggagcccctctgcccggccacgaccccgtctgggag +gtgtgcccagcggctcattggggatgggccatgatgacaatggcggttttgtggaataga +aaggcgggaagggtggggaaaaaattgagaaatcggatggttgccgggtctgtgtggatg +gaagtagacatg +>syndip_2_chr20:4032119-4033702 +cgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgcag +cggcgtgatctcggctcgctacaaccacctcccagccgcctgccttggcctcccaaagag +ccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctctgct +tggccacccatcgtctgggatatgaggagcccctctgcctggctgcccagtctggaaagt +gaggagcgtctctgcccggccgccatcccatctaggaagcgaggagcgtctctgcccggc +cgccatcccatctaggaagcgaggagcgcctcttcccggctgccatcccatctaggaact +gaggagcgtctctgcccggccgcccatcgtctgagatgtggggagcacctctgccccacc +gccctgtctgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggtgagg +agcgtctctgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaaccgcc +ccgtctgagaagtgaggagcccctccgtccggcaaccaccccgtctgggaagtgaggagc +gtctccgcccggcagccaccccgtccgggagggaggt----------------------- +------------------------------------------------------------ +---------------------------------------------gggggggggggtcgg +ccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggccgcccc +gtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggacccctct +gcccggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggc +tgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggag +cccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagccccccgcct +ggccagccgccccatccgggagggaggtgggggggtcagccccccgcccggccagccgcc +ccgtccgggaggggggagggggggtcagccccctgcccggccagccgccccgtccgggag +ggaggtgggggggggggtcagccccccgcccggccagccgccccgtccgggagggaggtg +gggggatcagccccccgcctggccagccgccccgtccgggaggtgaggggcgcctctgcc +cggccacccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgggag +ggaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggggggtcagcc +ccccttccggccggccgccctgtccgggaggtgaggggcgcctctgcctggccgccccta +ctgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtggggggg +acagccccccgcccggccagccgccctatccaggaggtgaggggcgcctctgcccggccg +cccctactgggaagtgaggagcccctctgcctggccagccgccccgtccgggagggtagt +gggggggtcagccccccgcccggccagccgccccatccgggaggtgaggggcgcttctgc +ccggccgcccctactgggaagtgaggagcccctctgcccggccacgaccccgtctgggag +gtgtgcccagcggctcattggggatgggccatgatgacaatggcggttttgtggaataga +aaggcgggaagggtggggaaaaaattgagaaatcggatggttgccgggtctgtgtggatg +gaagtagacatg +>p:HG002_1_chr20:4032119-4033702 +cgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgcag +cggcgtgatctcggctcgctacaaccacctcccagccgcctgccttggcctcccaaagag +ccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctctgct +tggccacccatcgtctgggatatgaggagcccctctgcctggctgcccagtctggaaagt +gaggagcgtctctgcccggccgccatcccatctaggaagcgaggagcgtctctgcccggc +cgccatcccatctaggaagcgaggagcgcctcttcccggctgccatcccatctaggaact +gaggagcgtctctgcccggccgcccatcgtctgagatgtggggagcacctctgccccacc +gccctgtctgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggtgagg +agcgtctctgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaaccgcc +ccgtctgagaagtgaggagcccctccgtccggcaaccaccccgtctgggaagtgaggagc +gtctccgcccggcagccaccccgtccgggagggaggt----------------------- +------------------------------------------------------------ +---------------------------------------------gggggggggggtcgg +ccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggccgcccc +gtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggacccctct +gcccggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggc +tgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggag +cccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagccccccgcct +ggccagccgccccatccgggagggaggtgggggggtcagccccccgcccggccagccgcc +ccgtccgggaggggggagggggggtcagccccctgcccggccagccgccccgtccgggag +ggaggtgggggggggggtcagccccccgcccggccagccgccccgtccgggagggaggtg +gggggatcagccccccgcctggccagccgccccgtccgggaggtgaggggcgcctctgcc +cggccacccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgggag +ggaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggggggtcagcc +ccccttccggccggccgccctgtccgggaggtgaggggcgcctctgcctggccgccccta +ctgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtggggggg +acagccccccgcccggccagccgccctatccaggaggtgaggggcgcctctgcccggccg +cccctactgggaagtgaggagcccctctgcctggccagccgccccgtccgggagggtagt +gggggggtcagccccccgcccggccagccgccccatccgggaggtgaggggcgcttctgc +ccggccgcccctactgggaagtgaggagcccctctgcccggccacgaccccgtctgggag +gtgtgcccagcggctcattggggatgggccatgatgacaatggcggttttgtggaataga +aaggcgggaagggtggggaaaaaattgagaaatcggatggttgccgggtctgtgtggatg +gaagtagacatg +>p:HG002_2_chr20:4032119-4033702 +cgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgcag +cggcgtgatctcggctcgctacaaccacctcccagccgcctgccttggcctcccaaagag +ccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctctgct +tggccacccatcgtctgggatatgaggagcccctctgcctggctgcccagtctggaaagt +----------------------------------------gaggagcgtctctgcccggc +cgccatcccatctaggaagcgaggagcgcctcttcccggctgccatcccatctaggaagt +gaggagcgtctctgcccggccgcccatcgtctgagatgtggggagcacctctgccccacc +gccctgtctgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggtgagg +agcgtctctgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaaccgcc +ccgtctgagaagtgaggagcccctccgtccggcaaccaccccgtctgggaagtgaggagc +gtctccgcccggcagccaccccgtccgggagggaggtggggggggtcagccccccgcccg +gccagccgccccgtccgggaggtgaggggctcctctgcccggccgcccctactgggaagt +gaggagcccctctgcccggccagccgccccgtccgggagggaggcgggggggggggtcgg +ccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggccgcccc +gtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggacccctct +gcccggccagccgccccgtccgggagggaggtgggggggtcagtcccccgcccggccggc +tgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggag +cccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagccccccgcct +ggccagccgccccatccgggagggaggtgggggggtcagccccccgcccggccagccgcc +ccgtccgggaggggggagggggggtcagccccctgcccggccagccgccccgtccgggag +ggaggtggg--ggggggtcagccccccgcccggccagccgccccgtccgggagggaggtg +gggggatcagccccccgcctggccagccgccccgtccgggaggtgaggggcgcctctgcc +cggccacccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgggag +ggaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggggggtcagcc +ccccttccggccggccgccctgtccgggaggtgaggggcgcctctgcctggccgccccta +ctgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtggggggg +acagccccccgcccggccagccgccctatccaggaggtgaggggcgcctctgcccggccg +cccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgggagggtagt +gggggggtcagccccccgcccggccagccgccccatccgggaggtgaggggcgcttctgc +ccggccgcccctactgggaagtgaggagcccctctgcccggccacgaccccgtctgggag +gtgtgcccagcggctcattggggatgggccatgatgacaatggcggttttgtggaataga +aaggcgggaagggtggggaaaaaattgagaaatcggatggttgccgggtctgtgtggatg +gaagtagacatg diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/msa.fa.fai new file mode 100644 index 00000000..3af87227 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_4032119_4033702 1932 27 60 61 +syndip_1_chr20:4032119-4033702 1932 2024 60 61 +syndip_2_chr20:4032119-4033702 1932 4021 60 61 +p:HG002_1_chr20:4032119-4033702 1932 6019 60 61 +p:HG002_2_chr20:4032119-4033702 1932 8017 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/output.vcf.gz new file mode 100644 index 00000000..36590681 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/output.vcf.gz.tbi new file mode 100644 index 00000000..bcb3dab9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:4032219-4033602/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/base.vcf.gz new file mode 100644 index 00000000..3995c13d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/base.vcf.gz.tbi new file mode 100644 index 00000000..72ae8d00 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/comp.vcf.gz new file mode 100644 index 00000000..b9a71903 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/comp.vcf.gz.tbi new file mode 100644 index 00000000..4005291f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/haps.fa new file mode 100644 index 00000000..465bb058 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/haps.fa @@ -0,0 +1,58 @@ +>ref_chr20_41196110_41196749 +AGAGTGTTGTTGAAATCCTCTATTTCCTGATTGATCTTCTGTCTGGTTTCTATATCCATTATCGGACATGGAATATTAAAGTCTCCAACTATTTTTGTCTTTCTCCCTTTAATTCTGTCATTTCTGTTTCATATGTTTTGGAGCTCTGTTAGGGGTATATATATATATAATATATATAAATAAATATATAAAAATAAATATATATTTATAATAAATATATTTTTATTTCATATATAAATATATATCTTATAAATATATATATTTATATAACATAAATATATATTTATATATATTATATATTATATATAATATATATTTATATAAATATATATATTATATATAATATATTTATATATAATATATATTTATATATTATAAATATATATTATATATTATAAATATATATTATATATTATATATTATATAAATATTATATATAATATATATTATATATAATATATATAAAAATATATATATTTATATATATAAATATTTTATCAATATAATATCCTTGTCTCTTGTAACCTTTCTTGATTTAACATTTATTTTGTGTGCCTTTTTCAAAAGAGGACACTGGAGGTGAAGAAGGAAGCTCTTGACTCTCCTAAAGCTGATCCCAAAGTGAAGGCTTTGAAGGCCA +>syndip_1_chr20:41196110-41196749 +AGAGTGTTGTTGAAATCCTCTATTTCCTGATTGATCTTCTGTCTGGTTTCTATATCCATT +ATCGGACATGGAATATTAAAGTCTCCAACTATTTTTGTCTTTCTCCCTTTAATTCTGTCA +TTTCTGTTTCATATGTTTTGGAGCTCTGTTAGGGGTATATATATATATAATATATATAAA +TAAATATATAAAAATAAATATATATTTATAATAAATATATTTTTATTTCATATATAAATA +TATATCTTATAAATATATATATTTATATAACATAAATATATATTTATATATATTATAAAT +ATATATTATATATAATATATATTTATATAAATATATATATTATATATAATATATTTATAT +ATAATATATATTTATATATTATAAATATATATTATATATAATATATATTTATATAAATAT +ATATTATATATAAATATATATTATATATAATATATATTTATATAAATATATATTATATAT +TATATAAATATTATATATAATATATATTTATATAAATATATATTATATATTATAAATATA +TATTATATATTATATATTATATAAATATTATATATAATATATATTATATATAATATATAT +AAAAATATATATATTTATATATATAAATATTTTATCAATATAATATCCTTGTCTCTTGTA +ACCTTTCTTGATTTAACATTTATTTTGTGTGCCTTTTTCAAAAGAGGACACTGGAGGTGA +AGAAGGAAGCTCTTGACTCTCCTAAAGCTGATCCCAAAGTGAAGGCTTTGAAGGCCA +>syndip_2_chr20:41196110-41196749 +AGAGTGTTGTTGAAATCCTCTATTTCCTGATTGATCTTCTGTCTGGTTTCTATATCCATT +ATCGGACATGGAATATTAAAGTCTCCAACTATTTTTGTCTTTCTCCCTTTAATTCTGTCA +TTTCTGTTTCATATGTTTTGGAGCTCTGTTAGGGGTATATATATATATAATATATATAAA +TAAATATATAAAAATAAATATATATTTATAATAAATATATTTTTATTTCATATATAAATA +TATATCTTATAAATATATATATTTATATAACATAAATATATATTTATATATATTATATAA +CATAAATATATATTTATATATATTATATATTATATATAATATATATTTATATAAATATAT +ATATTATATATAATATATTTATATATAATATATATTTATATATTATAAATATATATTATA +TATAATATATATTTATATAAATATATATTATATATTATAAATATATATTATATATTATAT +AAATATTATATATAATATATATTTATATAAATATATAATATATATTATAAATATATATTA +TATATTATATATTATATAAATATTATATATAATATATATTATATATAATATATATAAAAA +TATATATATTTATATATATAAATATTTTATCAATATAATATCCTTGTCTCTTGTAACCTT +TCTTGATTTAACATTTATTTTGTGTGCCTTTTTCAAAAGAGGACACTGGAGGTGAAGAAG +GAAGCTCTTGACTCTCCTAAAGCTGATCCCAAAGTGAAGGCTTTGAAGGCCA +>p:HG002_1_chr20:41196110-41196749 +AGAGTGTTGTTGAAATCCTCTATTTCCTGATTGATCTTCTGTCTGGTTTCTATATCCATT +ATCGGACATGGAATATTAAAGTCTCCAACTATTTTTGTCTTTCTCCCTTTAATTCTGTCA +TTTCTGTTTCATATGTTTTGGAGCTCTGTTAGGGGTATATATATATATAATATATATAAA +TAAATATATAAAAATAAATATATATTTATAATAAATATATTTTTATTTCATATATAAATA +TATATCTTATAAATATATATATTTATATAACATAAATATATATTTATATATATTATATAA +CATAAATATATATTTATATATATTATATATTATATATAATATATATTTATATAAATATAT +ATATTATATATAATATATTTATATATAATATATATTTATATATTATAAATATATATTATA +TATAATATATATTTATATAAATATATATTATATATTATAAATATATATTATATATTATAT +AAATATTATATATAATATATATTTATATAAATATATAATATATATTATAAATATATATTA +TATATTATATATTATATAAATATTATATATAATATATATTATATATAATATATATAAAAA +TATATATATTTATATATATAAATATTTTATCAATATAATATCCTTGTCTCTTGTAACCTT +TCTTGATTTAACATTTATTTTGTGTGCCTTTTTCAAAAGAGGACACTGGAGGTGAAGAAG +GAAGCTCTTGACTCTCCTAAAGCTGATCCCAAAGTGAAGGCTTTGAAGGCCA +>p:HG002_2_chr20:41196110-41196749 +AGAGTGTTGTTGAAATCCTCTATTTCCTGATTGATCTTCTGTCTGGTTTCTATATCCATT +ATCGGACATGGAATATTAAAGTCTCCAACTATTTTTGTCTTTCTCCCTTTAATTCTGTCA +TTTCTGTTTCATATGTTTTGGAGCTCTGTTAGGGGTATATATATATATAATATATATAAA +TAAATATATAAAAATAAATATATATTTATAATAAATATATTTTTATTTCATATATAAATA +TATATCTTATAAATATATATATTTATATAACATAAATATATATTTATATATATTATAAAT +ATATATTATATATAATATATATTTATATAAATATATATATTATATATAATATATTTATAT +ATAATATATATTTATATATTATAAATATATATTATATATAATATATATTTATATAAATAT +ATATTATATATAAATATATATTATATATAATATATATTTATATAAATATATATTATATAT +TATATAAATATTATATATAATATATATTTATATAAATATATATTATATATTATAAATATA +TATTATATATTATATATTATATAAATATTATATATAATATATATTATATATAATATATAT +AAAAATATATATATTTATATATATAAATATTTTATCAATATAATATCCTTGTCTCTTGTA +ACCTTTCTTGATTTAACATTTATTTTGTGTGCCTTTTTCAAAAGAGGACACTGGAGGTGA +AGAAGGAAGCTCTTGACTCTCCTAAAGCTGATCCCAAAGTGAAGGCTTTGAAGGCCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/haps.fa.ref.fa new file mode 100644 index 00000000..e75d2a9f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:41196110-41196749 +AGAGTGTTGTTGAAATCCTCTATTTCCTGATTGATCTTCTGTCTGGTTTCTATATCCATTATCGGACATGGAATATTAAAGTCTCCAACTATTTTTGTCTTTCTCCCTTTAATTCTGTCATTTCTGTTTCATATGTTTTGGAGCTCTGTTAGGGGTATATATATATATAATATATATAAATAAATATATAAAAATAAATATATATTTATAATAAATATATTTTTATTTCATATATAAATATATATCTTATAAATATATATATTTATATAACATAAATATATATTTATATATATTATATATTATATATAATATATATTTATATAAATATATATATTATATATAATATATTTATATATAATATATATTTATATATTATAAATATATATTATATATTATAAATATATATTATATATTATATATTATATAAATATTATATATAATATATATTATATATAATATATATAAAAATATATATATTTATATATATAAATATTTTATCAATATAATATCCTTGTCTCTTGTAACCTTTCTTGATTTAACATTTATTTTGTGTGCCTTTTTCAAAAGAGGACACTGGAGGTGAAGAAGGAAGCTCTTGACTCTCCTAAAGCTGATCCCAAAGTGAAGGCTTTGAAGGCCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/msa.fa new file mode 100644 index 00000000..116ad3ca --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/msa.fa @@ -0,0 +1,75 @@ +>ref_chr20_41196110_41196749 +agagtgttgttgaaatcctctatttcctgattgatcttctgtctggtttctatatccatt +atcggacatggaatattaaagtctccaactatttttgtctttctccctttaattctgtca +tttctgtttcatatgttttggagctctgttaggggtatatatatatataatatatataaa +taaatatataaaaataaatatatatttataataaatatatttttatttcatatataaata +tatatcttataaatatatatatttatataacataaatatatatttatatat--------- +---------------------attatatattatatataatatatatttatataaatatat +atattatatataatatatttatatataatatatatttatatattataaatatatat---- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatatattataaatatatattatatattatatattatataaatattatatata +atatatattatatataatatatataaaaatatatatatttatatatataaatattttatc +aatataatatccttgtctcttgtaacctttcttgatttaacatttattttgtgtgccttt +ttcaaaagaggacactggaggtgaagaaggaagctcttgactctcctaaagctgatccca +aagtgaaggctttgaaggcca +>syndip_1_chr20:41196110-41196749 +agagtgttgttgaaatcctctatttcctgattgatcttctgtctggtttctatatccatt +atcggacatggaatattaaagtctccaactatttttgtctttctccctttaattctgtca +tttctgtttcatatgttttggagctctgttaggggtatatatatatataatatatataaa +taaatatataaaaataaatatatatttataataaatatatttttatttcatatataaata +tatatcttataaatatatatatttatataacataaatatatatttatatatattata--- +---------------------aatatatattatatataatatatatttatataaatatat +atattatatataatatatttatatataatatatatttatatattataaatatatattata +tataatatatatttatataaatatatattatatataaatatatattatatataatatata +tttatataaatatatattatatattatataaatattatatataatatatatttatataaa +tatatattatatattataaatatatattatatattatatattatataaatattatatata +atatatattatatataatatatataaaaatatatatatttatatatataaatattttatc +aatataatatccttgtctcttgtaacctttcttgatttaacatttattttgtgtgccttt +ttcaaaagaggacactggaggtgaagaaggaagctcttgactctcctaaagctgatccca +aagtgaaggctttgaaggcca +>syndip_2_chr20:41196110-41196749 +agagtgttgttgaaatcctctatttcctgattgatcttctgtctggtttctatatccatt +atcggacatggaatattaaagtctccaactatttttgtctttctccctttaattctgtca +tttctgtttcatatgttttggagctctgttaggggtatatatatatataatatatataaa +taaatatataaaaataaatatatatttataataaatatatttttatttcatatataaata +tatatcttataaatatatatatttatataacataaatatatatttatatatattatataa +cataaatatatatttatatatattatatattatatataatatatatttatataaatatat +atattatatataatatatttatatataatatatatttatatattataaatatatattata +tataatatatatttatataaatatatattatatat------------------------- +----tataaatatatattatatattatataaatattatatataatatatatttatataaa +tatataatatatattataaatatatattatatattatatattatataaatattatatata +atatatattatatataatatatataaaaatatatatatttatatatataaatattttatc +aatataatatccttgtctcttgtaacctttcttgatttaacatttattttgtgtgccttt +ttcaaaagaggacactggaggtgaagaaggaagctcttgactctcctaaagctgatccca +aagtgaaggctttgaaggcca +>p:HG002_1_chr20:41196110-41196749 +agagtgttgttgaaatcctctatttcctgattgatcttctgtctggtttctatatccatt +atcggacatggaatattaaagtctccaactatttttgtctttctccctttaattctgtca +tttctgtttcatatgttttggagctctgttaggggtatatatatatataatatatataaa +taaatatataaaaataaatatatatttataataaatatatttttatttcatatataaata +tatatcttataaatatatatatttatataacataaatatatatttatatatattatataa +cataaatatatatttatatatattatatattatatataatatatatttatataaatatat +atattatatataatatatttatatataatatatatttatatattataaatatatattata +tataatatatatttatataaatatatattatatat------------------------- +----tataaatatatattatatattatataaatattatatataatatatatttatataaa +tatataatatatattataaatatatattatatattatatattatataaatattatatata +atatatattatatataatatatataaaaatatatatatttatatatataaatattttatc +aatataatatccttgtctcttgtaacctttcttgatttaacatttattttgtgtgccttt +ttcaaaagaggacactggaggtgaagaaggaagctcttgactctcctaaagctgatccca +aagtgaaggctttgaaggcca +>p:HG002_2_chr20:41196110-41196749 +agagtgttgttgaaatcctctatttcctgattgatcttctgtctggtttctatatccatt +atcggacatggaatattaaagtctccaactatttttgtctttctccctttaattctgtca +tttctgtttcatatgttttggagctctgttaggggtatatatatatataatatatataaa +taaatatataaaaataaatatatatttataataaatatatttttatttcatatataaata +tatatcttataaatatatatatttatataacataaatatatatttatatatattata--- +---------------------aatatatattatatataatatatatttatataaatatat +atattatatataatatatttatatataatatatatttatatattataaatatatattata +tataatatatatttatataaatatatattatatataaatatatattatatataatatata +tttatataaatatatattatatattatataaatattatatataatatatatttatataaa +tatatattatatattataaatatatattatatattatatattatataaatattatatata +atatatattatatataatatatataaaaatatatatatttatatatataaatattttatc +aatataatatccttgtctcttgtaacctttcttgatttaacatttattttgtgtgccttt +ttcaaaagaggacactggaggtgaagaaggaagctcttgactctcctaaagctgatccca +aagtgaaggctttgaaggcca diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/msa.fa.fai new file mode 100644 index 00000000..2d712f88 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_41196110_41196749 801 29 60 61 +syndip_1_chr20:41196110-41196749 801 878 60 61 +syndip_2_chr20:41196110-41196749 801 1727 60 61 +p:HG002_1_chr20:41196110-41196749 801 2577 60 61 +p:HG002_2_chr20:41196110-41196749 801 3427 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/output.vcf.gz new file mode 100644 index 00000000..bc9698db Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/output.vcf.gz.tbi new file mode 100644 index 00000000..1aa6f389 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41196210-41196649/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/base.vcf.gz new file mode 100644 index 00000000..8531d286 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/base.vcf.gz.tbi new file mode 100644 index 00000000..bb297398 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/comp.vcf.gz new file mode 100644 index 00000000..1053a57d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/comp.vcf.gz.tbi new file mode 100644 index 00000000..9d492f77 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/haps.fa new file mode 100644 index 00000000..ef4a7718 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/haps.fa @@ -0,0 +1,58 @@ +>ref_chr20_41257474_41258304 +AGGGGATTTAACCCTAAGCTTTCTTTCATATTCTTAATCCAGTTTCTACTCAGGTCCAAATTCATTCTCTAACTCCACAATGACTCTTAAAAGTGAGATAGAAAATAAGATCTTGTCAGGATTTGTTTTCTTTTCTTTCTTTTTTTTTTTTTTTTTGAGACAGAGTCTCACTCTGTTGCCCAGGCTGCAGTGCAGTGGCGTGATCTCAGCTCACTGCAACCTCCGCCTGCCAGCTTCAAGCAATTCTCCTGCCTCAGCCTCCTTAGTAGCTGGGACTACAGGCACACGCCACCATGCCTGGCTAAGTTTTCGTATTTTTAGTAGAGACGGGGTTTCACCATGCTAGCCAGGCTGGTCTCGAACTCCTGACCTTGTGATCTGCCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGTGTTAGCCACCACGCCCAACCCTTTTTTTTTTTGAGACGGAGTTTTGCTCTTGTCAGCCAGGCTGGGGTACAGTGGCACAGCTCACTGCAACCTCCACCTCCCAGGTTCAAGTGATTCTCCTGTCTCAGCCACCTGAGTAGCTGGGTTTACAGGCACCCGCCACCATGCCCAGATAATTTTTGTATTTTTAGTAGAGATGAGGTTTCACCAAGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGAGTGAGCCACTGCACCTAGCCAAGATTTCTTTTAAAAAATCATTTTGAGCTAATTTTAGAGTTACAGAAAAGTTGCAAAAATCGTACAGAGTTTCCATATATCCTGGCCCCAGCTTCCCCAGTGTT +>syndip_1_chr20:41257474-41258304 +AGGGGATTTAACCCTAAGCTTTCTTTCATATTCTTAATCCAGTTTCTACTCAGGTCCAAA +TTCATTCTCTAACTCCACAATGACTCTTAAAAGTGAGATAGAAAATAAGATCTTGTCAGG +ATTTGTTTTCTTTTCTTTCTTTTTTTTTTTTTTTTTGAGACAGAGTCTCACTCTGTTGCC +CAGGCTGCAGTGCAGTGGCGTGATCTCAGCTCACTGCAACCTCCGCCTGCCAGCTTCAAG +CAATTCTCCTGCCTCAGCCTCCTTAGTAGCTGGGACTACAGGCACACGCCACCATGCCTG +GCTAAGTTTTCGTATTTTTAGTAGAGACGGGGTTTCACCATGCTAGCCAGGCTGGTCTCG +AACTCCTGACCTTGTGATCTGCCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGTGTT +AGCCACCACGCCCAACCCTTTTTTTTTTTGAGACGGAGTTTTGCTCTTGTCAGCCAGGCT +GGGGTACAGTGGCACAGCTCACTGCAACCTCCACCTCCCAGGTTCAAGTGATTCTCCTGT +CTCAGCCACCTGAGTAGCTGGGTTTACAGGCACCCGCCACCATGCCCAGATAATTTTTGT +ATTTTTAGTAGAGATGAGGTTTCACCAAGTTGGCCAGGCTGGTCTCAAACTCCTGACCTC +AGGTGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGAGTGAGCCACTGCAC +CTAGCCAAGATTTCTTTTAAAAAATCATTTTGAGCTAATTTTAGAGTTACAGAAAAGTTG +CAAAAATCGTACAGAGTTTCCATATATCCTGGCCCCAGCTTCCCCAGTGTT +>syndip_2_chr20:41257474-41258304 +AGGGGATTTAACCCTAAGCTTTCTTTCATATTCTTAATCCAGTTTCTACTCAGGTCCAAA +TTCATTCTCTAACTCCACAATGACTCTTAAAAGTGAGATAGAAAATAAGATCTTGTCAGG +ATTTGTTTTCTTTTCTTTCTTTTTTTTTTTTTTTTTGAGACAGAGTCTCACTCTGTTGCC +CAGGCTGCAGTGCAGTGGCGTGATCTCAGCTCACTGCAACCTCCGCCTGCCAGCTTCAAG +CAATTCTCCTGCCTCAGCCTCCTTAGTAGCTGGGACTACAGGCACACGCCACCATGCCTG +GCTAAGTTTTCGTATTTTTAGTAGAGACGGGGTTTCACCATGCTAGCCAGGCTGGTCTCG +AACTCCTGACCTTGTGATCTGCCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGTGTT +AGCCACCACGCCCAACCCTTTTTTTTTTTGAGACGGAGTTTTGCTCTTGTCAGCCAGGCT +GGGGTACAGTGGCACAGCTCACTGCAACCTCCACCTCCCAGGTTCAAGTGATTCTCCTGT +CTCAGCCACCTGAGTAGCTGGGTTTACAGGCACCCGCCACCATGCCCAGATAATTTTTGT +ATTTTTAGTAGAGATGAGGTTTCACCAAGTTGGCCAGGCTGGTCTCAAACTCCTGACCTC +AGGTGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGAGTGAGCCACTGCAC +CTAGCCAAGATTTCTTTTAAAAAATCATTTTGAGCTAATTTTAGAGTTACAGAAAAGTTG +CAAAAATCGTACAGAGTTTCCATATATCCTGGCCCCAGCTTCCCCAGTGTT +>p:HG002_1_chr20:41257474-41258304 +AGGGGATTTAACCCTAAGCTTTCTTTCATATTCTTAATCCAGTTTCTACTCAGGTCCAAA +TTCATTCTCTAACTCCACAATGACTCTTAAAAGTGAGATAGAAAATAAGATCTTGTCAGG +ATTTGTTTTCTTTTCTTTCTTTTTTTTTTTTTTTTTGAGACAGAGTCTCACTCTGTTGCC +CAGGCTGCAGTGCAGTGGCGTGATCTCAGCTCACTGCAACCTCCGCCTGCCAGCTTCAAG +CAATTCTCCTGCCTCAGCCTCCTTAGTAGCTGGGACTACAGGCACACGCCACCATGCCTG +GCTAAGTTTTCGTATTTTTAGTAGAGACGGGGTTTCACCATGCTAGCCAGGCTGGTCTCG +AACTCCTGACCTTGTGATCTGCCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGTGTT +AGCCACCACGCCCAACCCTTTTTTTTTTTGAGACGGAGTTTTGCTCTTGTCAGCCAGGCT +GGGGTACAGTGGCACAGCTCACTGCAACCTCCACCTCCCAGGTTCAAGTGATTCTCCTGT +CTCAGCCACCTGAGTAGCTGGGTTTACAGGCACCCGCCACCATGCCCAGATAATTTTTGT +ATTTTTAGTAGAGATGAGGTTTCACCAAGTTGGCCAGGCTGGTCTCAAACTCCTGACCTC +AGGTGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGAGTGAGCCACTGCAC +CTAGCCAAGATTTCTTTTAAAAAATCATTTTGAGCTAATTTTAGAGTTACAGAAAAGTTG +CAAAAATCGTACAGAGTTTCCATATATCCTGGCCCCAGCTTCCCCAGTGTT +>p:HG002_2_chr20:41257474-41258304 +AGGGGATTTAACCCTAAGCTTTCTTTCATATTCTTAATCCAGTTTCTACTCAGGTCCAAA +TTCATTCTCTAACTCCACAATGACTCTTAAAAGTGAGATAGAAAATAAGATCTTGTCAGG +ATTTGTTTTCTTTTCTTTCTTTTTTTTTTTTTTTTTGAGACAGAGTCTCACTCTGTTGCC +CAGGCTGCAGTGCAGTGGCGTGATCTCAGCTCACTGCAACCTCCGCCTGCCAGCTTCAAG +CAATTCTCCTGTCTCAGCCACCTGAGTAGCTGGGTTTACAGGCACCCGCCACCATGCCCA +GATAATTTTTGTATTTTTAGTAGAGATGAGGTTTCACCAAGTTGGCCAGGCTGGTCTCAA +ACTCCTGACCTCAGGTGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGAGT +GAGCCACTGCACCTAGCCAAGATTTCTTTTAAAAAATCATTTTGAGCTAATTTTAGAGTT +ACAGAAAAGTTGCAAAAATCGTACAGAGTTTCCATATATCCTGGCCCCAGCTTCCCCAGT +GTT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/haps.fa.ref.fa new file mode 100644 index 00000000..dacfd787 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:41257474-41258304 +AGGGGATTTAACCCTAAGCTTTCTTTCATATTCTTAATCCAGTTTCTACTCAGGTCCAAATTCATTCTCTAACTCCACAATGACTCTTAAAAGTGAGATAGAAAATAAGATCTTGTCAGGATTTGTTTTCTTTTCTTTCTTTTTTTTTTTTTTTTTGAGACAGAGTCTCACTCTGTTGCCCAGGCTGCAGTGCAGTGGCGTGATCTCAGCTCACTGCAACCTCCGCCTGCCAGCTTCAAGCAATTCTCCTGCCTCAGCCTCCTTAGTAGCTGGGACTACAGGCACACGCCACCATGCCTGGCTAAGTTTTCGTATTTTTAGTAGAGACGGGGTTTCACCATGCTAGCCAGGCTGGTCTCGAACTCCTGACCTTGTGATCTGCCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGTGTTAGCCACCACGCCCAACCCTTTTTTTTTTTGAGACGGAGTTTTGCTCTTGTCAGCCAGGCTGGGGTACAGTGGCACAGCTCACTGCAACCTCCACCTCCCAGGTTCAAGTGATTCTCCTGTCTCAGCCACCTGAGTAGCTGGGTTTACAGGCACCCGCCACCATGCCCAGATAATTTTTGTATTTTTAGTAGAGATGAGGTTTCACCAAGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGAGTGAGCCACTGCACCTAGCCAAGATTTCTTTTAAAAAATCATTTTGAGCTAATTTTAGAGTTACAGAAAAGTTGCAAAAATCGTACAGAGTTTCCATATATCCTGGCCCCAGCTTCCCCAGTGTT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/msa.fa new file mode 100644 index 00000000..915fefe7 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/msa.fa @@ -0,0 +1,75 @@ +>ref_chr20_41257474_41258304 +aggggatttaaccctaagctttctttcatattcttaatccagtttctactcaggtccaaa +ttcattctctaactccacaatgactcttaaaagtgagatagaaaataagatcttgtcagg +atttgttttcttttctttctttttttttttttttttgagacagagtctcactctgttgcc +caggctgcagtgcagtggcgtgatctcagctcactgcaacctccgcctgccagcttcaag +caattctcctgcctcagcctccttagtagctgggactacaggcacacgccaccatgcctg +gctaagttttcgtatttttagtagagacggggtttcaccatgctagccaggctggtctcg +aactcctgaccttgtgatctgcccaccttggcctcccaaagtgctgggattacaggtgtt +agccaccacgcccaaccctttttttttttgagacggagttttgctcttgtcagccaggct +ggggtacagtggcacagctcactgcaacctccacctcccaggttcaagtgattctcctgt +ctcagccacctgagtagctgggtttacaggcacccgccaccatgcccagataatttttgt +atttttagtagagatgaggtttcaccaagttggccaggctggtctcaaactcctgacctc +aggtgatccacccgcctcggcctcccaaagtgctgggattacaggagtgagccactgcac +ctagccaagatttcttttaaaaaatcattttgagctaattttagagttacagaaaagttg +caaaaatcgtacagagtttccatatatcctggccccagcttccccagtgtt +>syndip_1_chr20:41257474-41258304 +aggggatttaaccctaagctttctttcatattcttaatccagtttctactcaggtccaaa +ttcattctctaactccacaatgactcttaaaagtgagatagaaaataagatcttgtcagg +atttgttttcttttctttctttttttttttttttttgagacagagtctcactctgttgcc +caggctgcagtgcagtggcgtgatctcagctcactgcaacctccgcctgccagcttcaag +caattctcctgcctcagcctccttagtagctgggactacaggcacacgccaccatgcctg +gctaagttttcgtatttttagtagagacggggtttcaccatgctagccaggctggtctcg +aactcctgaccttgtgatctgcccaccttggcctcccaaagtgctgggattacaggtgtt +agccaccacgcccaaccctttttttttttgagacggagttttgctcttgtcagccaggct +ggggtacagtggcacagctcactgcaacctccacctcccaggttcaagtgattctcctgt +ctcagccacctgagtagctgggtttacaggcacccgccaccatgcccagataatttttgt +atttttagtagagatgaggtttcaccaagttggccaggctggtctcaaactcctgacctc +aggtgatccacccgcctcggcctcccaaagtgctgggattacaggagtgagccactgcac +ctagccaagatttcttttaaaaaatcattttgagctaattttagagttacagaaaagttg +caaaaatcgtacagagtttccatatatcctggccccagcttccccagtgtt +>syndip_2_chr20:41257474-41258304 +aggggatttaaccctaagctttctttcatattcttaatccagtttctactcaggtccaaa +ttcattctctaactccacaatgactcttaaaagtgagatagaaaataagatcttgtcagg +atttgttttcttttctttctttttttttttttttttgagacagagtctcactctgttgcc +caggctgcagtgcagtggcgtgatctcagctcactgcaacctccgcctgccagcttcaag +caattctcctgcctcagcctccttagtagctgggactacaggcacacgccaccatgcctg +gctaagttttcgtatttttagtagagacggggtttcaccatgctagccaggctggtctcg +aactcctgaccttgtgatctgcccaccttggcctcccaaagtgctgggattacaggtgtt +agccaccacgcccaaccctttttttttttgagacggagttttgctcttgtcagccaggct +ggggtacagtggcacagctcactgcaacctccacctcccaggttcaagtgattctcctgt +ctcagccacctgagtagctgggtttacaggcacccgccaccatgcccagataatttttgt +atttttagtagagatgaggtttcaccaagttggccaggctggtctcaaactcctgacctc +aggtgatccacccgcctcggcctcccaaagtgctgggattacaggagtgagccactgcac +ctagccaagatttcttttaaaaaatcattttgagctaattttagagttacagaaaagttg +caaaaatcgtacagagtttccatatatcctggccccagcttccccagtgtt +>p:HG002_1_chr20:41257474-41258304 +aggggatttaaccctaagctttctttcatattcttaatccagtttctactcaggtccaaa +ttcattctctaactccacaatgactcttaaaagtgagatagaaaataagatcttgtcagg +atttgttttcttttctttctttttttttttttttttgagacagagtctcactctgttgcc +caggctgcagtgcagtggcgtgatctcagctcactgcaacctccgcctgccagcttcaag +caattctcctgcctcagcctccttagtagctgggactacaggcacacgccaccatgcctg +gctaagttttcgtatttttagtagagacggggtttcaccatgctagccaggctggtctcg +aactcctgaccttgtgatctgcccaccttggcctcccaaagtgctgggattacaggtgtt +agccaccacgcccaaccctttttttttttgagacggagttttgctcttgtcagccaggct +ggggtacagtggcacagctcactgcaacctccacctcccaggttcaagtgattctcctgt +ctcagccacctgagtagctgggtttacaggcacccgccaccatgcccagataatttttgt +atttttagtagagatgaggtttcaccaagttggccaggctggtctcaaactcctgacctc +aggtgatccacccgcctcggcctcccaaagtgctgggattacaggagtgagccactgcac +ctagccaagatttcttttaaaaaatcattttgagctaattttagagttacagaaaagttg +caaaaatcgtacagagtttccatatatcctggccccagcttccccagtgtt +>p:HG002_2_chr20:41257474-41258304 +aggggatttaaccctaagctttctttcatattcttaatccagtttctactcaggtccaaa +ttcattctctaactccacaatgactcttaaaagtgagatagaaaataagatcttgtcagg +atttgttttcttttctttctttttttttttttttttgagacagagtctcactctgttgcc +caggctgcagtgcagtggcgtgatctcagctcactgcaacctccgcctgccagcttcaag +ca---------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------------------attctcctgt +ctcagccacctgagtagctgggtttacaggcacccgccaccatgcccagataatttttgt +atttttagtagagatgaggtttcaccaagttggccaggctggtctcaaactcctgacctc +aggtgatccacccgcctcggcctcccaaagtgctgggattacaggagtgagccactgcac +ctagccaagatttcttttaaaaaatcattttgagctaattttagagttacagaaaagttg +caaaaatcgtacagagtttccatatatcctggccccagcttccccagtgtt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/msa.fa.fai new file mode 100644 index 00000000..a72a3a52 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_41257474_41258304 831 29 60 61 +syndip_1_chr20:41257474-41258304 831 908 60 61 +syndip_2_chr20:41257474-41258304 831 1787 60 61 +p:HG002_1_chr20:41257474-41258304 831 2667 60 61 +p:HG002_2_chr20:41257474-41258304 831 3547 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/output.vcf.gz new file mode 100644 index 00000000..bd57ec69 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/output.vcf.gz.tbi new file mode 100644 index 00000000..6297178a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:41257574-41258204/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/base.vcf.gz new file mode 100644 index 00000000..ec0ad7ff Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/base.vcf.gz.tbi new file mode 100644 index 00000000..600550d4 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/comp.vcf.gz new file mode 100644 index 00000000..6aca81fb Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/comp.vcf.gz.tbi new file mode 100644 index 00000000..2f0233a8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/haps.fa new file mode 100644 index 00000000..f1d4eec9 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/haps.fa @@ -0,0 +1,58 @@ +>ref_chr20_44763796_44764386 +GACTCCATTCTCTTTTCCAGATGGATCACTCGTCTCAACAGCATCAGAAATTAAAAGGTTGCACAGCCCTTGTGGTGATTATAGGTTATGTGATTCTCAAAGGTTTAGGAGTTTACGGGTTCCCTGTCCATCCATTCACTACATGCTCACCTATCCATCCATCCATCCATTTATCCATCCATCCATCCACCTATCACTTCATCCATCCATCCATTTATCCATCCATCCATTTATCCATCCATCCATCCATTTATCCATCCATCCATCCATTTATCCATCCATCCATCCATCCATCCACCCATCCATCCGTCCATCCATTTATCCATCCATCCATCCATCCATTTATGCATCCATTTATCCATCCATCCATCCATCCATCCATCCATCCATCCATTTATCCATCCATCCATCCATCCACCCATCCATCCATCCGTCCATCCATTCATCCATCCATCCATCCTCCCACAAACTCACCAAGCCTACAATGCAATCAATTCTGCTGTAACATGAAATATACATTTCTAAAAATTACTGTGCAACGCAAAATCTTGCTATAAAAATCACACAGCTTATGGGAAAATGGGGTCAGTG +>syndip_1_chr20:44763796-44764386 +GACTCCATTCTCTTTTCCAGATGGATCACTCGTCTCAACAGCATCAGAAATTAAAAGGTT +GCACAGCCCTTGTGGTGATTATAGGTTATGTGATTCTCAAAGGTTTAGGAGTTTACGGGT +TCCCTGTCCATCCATTCACTACATGCTCACCTATCCATCCATCCATCCATTTATCCATCC +ATCCATCCACCTATCACTTCATCCATCCATCCATTTATCCATCCATCCATTTATCCATCC +ATCCATCCATTTATCCATCCATCCATCCATTTATCCATCCATCCATCCATCCATCCACCC +ATCCATCCGTCCATCCATTTATCCATCCATCCATCCATCCATTTATCCATCCATTTATCC +ATCCATCCATCCATCCATCCATCCATCCATCCATTTATCCATCCATCCATCCATCCACCC +ATCCATCCATCCGTCCATCCATTTATCCATCCATCCATCCATCCATCCATCCATCCATCC +ATTTATCCATCCGTCCATTTATCCATCCATCCATCCACCCACCCATCCATCCATCCATCC +ACTTATCCATCCACCCATCCATCCATCCGTCCATCCATTCATCCATCCATCCATCCTCCC +ACAAACTCACCAAGCCTACAATACAATCAATTCTGCTGTAACATGAAATATACATTTCTA +AAAATTACTGTGCAACGCAAAATCTTGCTATAAAAATCACACAGCTTATGGGAAAATGGG +GTCAGTG +>syndip_2_chr20:44763796-44764386 +GACTCCATTCTCTTTTCCAGATGGATCACTCGTCTCAACAGCATCAGAAATTAAAAGGTT +GCACAGCCCTTGTGGTGATTATAGGTTATGTGATTCTCAAAGGTTTAGGAGTTTACGGGT +TCCCTGTCCATCCATTCACTACATGCTCACCTATCCATCCATCCATCCATTTATCCATCC +ATCCATCCACCTATCACTTCATCCATCCATCCATTTATCCATCCATCCATTTATCCATCC +ATCCATCCATTTATCCATCCATCCATCCATTTATCCATCCATCCATCCATCCATCCACCC +ATCCATCCGTCCATCCATTTATCCATCCATCCATCCATCCATTTATCCATCCATTTATCC +ATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATTTATCCATCCATCCATCC +ATCCACCCATCCATCCATCCGTCCATCCATTTATCCATCCATCCATCCATCCATCCATCC +ATCCATTTATCCATCCGTCCATTTATCCATCCATCCATCCACCCACCCATCCATCCATCC +ATCCATTTATCCATCCACCCATCCATCCATCCGTCCATCCATTCATCCATCCATCCATCC +TCCCACAAACTCACCAAGCCTACAATACAATCAATTCTGCTGTAACATGAAATATACATT +TCTAAAAATTACTGTGCAACGCAAAATCTTGCTATAAAAATCACACAGCTTATGGGAAAA +TGGGGTCAGTG +>p:HG002_1_chr20:44763796-44764386 +GACTCCATTCTCTTTTCCAGATGGATCACTCGTCTCAACAGCATCAGAAATTAAAAGGTT +GCACAGCCCTTGTGGTGATTATAGGTTATGTGATTCTCAAAGGTTTAGGAGTTTACGGGT +TCCCTGTCCATCCATTCACTACATGCTCACCTATCCATCCATCCATCCATTTATCCATCC +ATCCATCCACCTATCACTTCATCCATCCATCCATTTATCCATCCATCCATTTATCCATCC +ATCCATCCATTTATCCATCCATCCATCCATTTATCCATCCATCCATCCATCCATCCACCC +ATCCATCCGTCCATCCATTTATCCATCCATCCATCCATCCATTTATCCATCCATTTATCC +ATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATTTATCCATCCATCCATCC +ATCCACCCATCCATCCATCCGTCCATCCATTTATCCATCCATCCATCCATCCATCCATCC +ATCCATTTATCCATCCGTCCATTTATCCATCCATCCATCCACCCACCCATCCATCCATCC +ATCCATTTATCCATCCACCCATCCATCCATCCGTCCATCCATTCATCCATCCATCCATCC +TCCCACAAACTCACCAAGCCTACAATACAATCAATTCTGCTGTAACATGAAATATACATT +TCTAAAAATTACTGTGCAACGCAAAATCTTGCTATAAAAATCACACAGCTTATGGGAAAA +TGGGGTCAGTG +>p:HG002_2_chr20:44763796-44764386 +GACTCCATTCTCTTTTCCAGATGGATCACTCGTCTCAACAGCATCAGAAATTAAAAGGTT +GCACAGCCCTTGTGGTGATTATAGGTTATGTGATTCTCAAAGGTTTAGGAGTTTACGGGT +TCCCTGTCCATCCATTCACTACATGCTCACCTATCCATCCATCCATCCATTTATCCATCC +ATCCATCCACCTATCACTTCATCCATCCATCCATTTATCCATCCATCCATTTATCCATCC +ATCCATCCATTTATCCATCCATCCATCCATTTATCCATCCATCCATCCATCCATCCACCC +ATCCATCCGTCCATCCATTTATCCATCCATCCATCCATCCATTTATCCATCCATTTATCC +ATCCATCCATCCATCCATCCATCCATCCATCCATTTATCCATCCATCCATCCATCCACCC +ATCCATCCATCCGTCCATCCATTTATCCATCCATCCATCCATCCATCCATCCATCCATCC +ATTTATCCATCCGTCCATTTATCCATCCATCCATCCACCCACCCATCCATCCATCCATCC +ACTTATCCATCCACCCATCCATCCATCCGTCCATCCATTCATCCATCCATCCATCCTCCC +ACAAACTCACCAAGCCTACAATACAATCAATTCTGCTGTAACATGAAATATACATTTCTA +AAAATTACTGTGCAACGCAAAATCTTGCTATAAAAATCACACAGCTTATGGGAAAATGGG +GTCAGTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/haps.fa.ref.fa new file mode 100644 index 00000000..bb372205 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:44763796-44764386 +GACTCCATTCTCTTTTCCAGATGGATCACTCGTCTCAACAGCATCAGAAATTAAAAGGTTGCACAGCCCTTGTGGTGATTATAGGTTATGTGATTCTCAAAGGTTTAGGAGTTTACGGGTTCCCTGTCCATCCATTCACTACATGCTCACCTATCCATCCATCCATCCATTTATCCATCCATCCATCCACCTATCACTTCATCCATCCATCCATTTATCCATCCATCCATTTATCCATCCATCCATCCATTTATCCATCCATCCATCCATTTATCCATCCATCCATCCATCCATCCACCCATCCATCCGTCCATCCATTTATCCATCCATCCATCCATCCATTTATGCATCCATTTATCCATCCATCCATCCATCCATCCATCCATCCATCCATTTATCCATCCATCCATCCATCCACCCATCCATCCATCCGTCCATCCATTCATCCATCCATCCATCCTCCCACAAACTCACCAAGCCTACAATGCAATCAATTCTGCTGTAACATGAAATATACATTTCTAAAAATTACTGTGCAACGCAAAATCTTGCTATAAAAATCACACAGCTTATGGGAAAATGGGGTCAGTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/msa.fa new file mode 100644 index 00000000..aad2c957 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/msa.fa @@ -0,0 +1,70 @@ +>ref_chr20_44763796_44764386 +gactccattctcttttccagatggatcactcgtctcaacagcatcagaaattaaaaggtt +gcacagcccttgtggtgattataggttatgtgattctcaaaggtttaggagtttacgggt +tccctgtccatccattcactacatgctcacctatccatccatccatccatttatccatcc +atccatccacctatcacttcatccatccatccatttatccatccatccatttatccatcc +atccatccatttatccatccatccatccatttatccatccatccatccatccatccaccc +atccatccgtccatccatttatccatccatccatccatccatttatgcatccatttatcc +atccatccatccatccatccatccatccatccatttatcc-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +atccatccatccatccacccatccatccatccgtccatccattcatccatccatccatcc +tcccacaaactcaccaagcctacaatgcaatcaattctgctgtaacatgaaatatacatt +tctaaaaattactgtgcaacgcaaaatcttgctataaaaatcacacagcttatgggaaaa +tggggtcagtg +>syndip_1_chr20:44763796-44764386 +gactccattctcttttccagatggatcactcgtctcaacagcatcagaaattaaaaggtt +gcacagcccttgtggtgattataggttatgtgattctcaaaggtttaggagtttacgggt +tccctgtccatccattcactacatgctcacctatccatccatccatccatttatccatcc +atccatccacctatcacttcatccatccatccatttatccatccatccatttatccatcc +atccatccatttatccatccatccatccatttatccatccatccatccatccatccaccc +atccatccgtccatccatttatccatccatccatccatccatttatccatccatttatcc +atccatccatccatccatccatccatccatccatttatcc----atccatccatccatcc +acccatccatccatccgtccatccatttatccatccatccatccatccatccatccatcc +atccatttatccatccgtccatttatccatccatccatccacccacccatccatccatcc +atccacttatccatccacccatccatccatccgtccatccattcatccatccatccatcc +tcccacaaactcaccaagcctacaatacaatcaattctgctgtaacatgaaatatacatt +tctaaaaattactgtgcaacgcaaaatcttgctataaaaatcacacagcttatgggaaaa +tggggtcagtg +>syndip_2_chr20:44763796-44764386 +gactccattctcttttccagatggatcactcgtctcaacagcatcagaaattaaaaggtt +gcacagcccttgtggtgattataggttatgtgattctcaaaggtttaggagtttacgggt +tccctgtccatccattcactacatgctcacctatccatccatccatccatttatccatcc +atccatccacctatcacttcatccatccatccatttatccatccatccatttatccatcc +atccatccatttatccatccatccatccatttatccatccatccatccatccatccaccc +atccatccgtccatccatttatccatccatccatccatccatttatccatccatttatcc +atccatccatccatccatccatccatccatccatccatccatttatccatccatccatcc +atccacccatccatccatccgtccatccatttatccatccatccatccatccatccatcc +atccatttatccatccgtccatttatccatccatccatccacccacccatccatccatcc +atccatttatccatccacccatccatccatccgtccatccattcatccatccatccatcc +tcccacaaactcaccaagcctacaatacaatcaattctgctgtaacatgaaatatacatt +tctaaaaattactgtgcaacgcaaaatcttgctataaaaatcacacagcttatgggaaaa +tggggtcagtg +>p:HG002_1_chr20:44763796-44764386 +gactccattctcttttccagatggatcactcgtctcaacagcatcagaaattaaaaggtt +gcacagcccttgtggtgattataggttatgtgattctcaaaggtttaggagtttacgggt +tccctgtccatccattcactacatgctcacctatccatccatccatccatttatccatcc +atccatccacctatcacttcatccatccatccatttatccatccatccatttatccatcc +atccatccatttatccatccatccatccatttatccatccatccatccatccatccaccc +atccatccgtccatccatttatccatccatccatccatccatttatccatccatttatcc +atccatccatccatccatccatccatccatccatccatccatttatccatccatccatcc +atccacccatccatccatccgtccatccatttatccatccatccatccatccatccatcc +atccatttatccatccgtccatttatccatccatccatccacccacccatccatccatcc +atccatttatccatccacccatccatccatccgtccatccattcatccatccatccatcc +tcccacaaactcaccaagcctacaatacaatcaattctgctgtaacatgaaatatacatt +tctaaaaattactgtgcaacgcaaaatcttgctataaaaatcacacagcttatgggaaaa +tggggtcagtg +>p:HG002_2_chr20:44763796-44764386 +gactccattctcttttccagatggatcactcgtctcaacagcatcagaaattaaaaggtt +gcacagcccttgtggtgattataggttatgtgattctcaaaggtttaggagtttacgggt +tccctgtccatccattcactacatgctcacctatccatccatccatccatttatccatcc +atccatccacctatcacttcatccatccatccatttatccatccatccatttatccatcc +atccatccatttatccatccatccatccatttatccatccatccatccatccatccaccc +atccatccgtccatccatttatccatccatccatccatccatttatccatccatttatcc +atccatccatccatccatccatccatccatccatttatcc----atccatccatccatcc +acccatccatccatccgtccatccatttatccatccatccatccatccatccatccatcc +atccatttatccatccgtccatttatccatccatccatccacccacccatccatccatcc +atccacttatccatccacccatccatccatccgtccatccattcatccatccatccatcc +tcccacaaactcaccaagcctacaatacaatcaattctgctgtaacatgaaatatacatt +tctaaaaattactgtgcaacgcaaaatcttgctataaaaatcacacagcttatgggaaaa +tggggtcagtg diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/msa.fa.fai new file mode 100644 index 00000000..0cd24afe --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_44763796_44764386 731 29 60 61 +syndip_1_chr20:44763796-44764386 731 807 60 61 +syndip_2_chr20:44763796-44764386 731 1585 60 61 +p:HG002_1_chr20:44763796-44764386 731 2364 60 61 +p:HG002_2_chr20:44763796-44764386 731 3143 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/output.vcf.gz new file mode 100644 index 00000000..da817201 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/output.vcf.gz.tbi new file mode 100644 index 00000000..c956a508 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:44763896-44764286/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/base.vcf.gz new file mode 100644 index 00000000..61953262 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/base.vcf.gz.tbi new file mode 100644 index 00000000..38e1fc51 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/comp.vcf.gz new file mode 100644 index 00000000..ee0726a2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/comp.vcf.gz.tbi new file mode 100644 index 00000000..d5c89e52 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/haps.fa new file mode 100644 index 00000000..d9002f1f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/haps.fa @@ -0,0 +1,44 @@ +>ref_chr20_45600469_45600847 +AATATTGGGAATTTTACTGATGGTAAAATTAAAATAGGAGGAGGAGGTTACATCACTATCATATGGTAACATTCCCTTAAAAATCATCTCTTTATCTTTCCTAAATATTCCACTGTCTTTGACTGCTATACCTCTCTCTCTTTTCTTTCACCAAGCCTCTCTCTTTGCTTTCCTTCTGGTAAAAGCAGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATCCCCCCCTCTCCCTCTCTCTCTACCCCTGAATCTGGCCTTTCTAAACACCCTCAACTTGTGTACCTGTATACTATACTGAGCTACACTAAAGTTTCTATATTTAGCCAAATCCAGCCCATCATACCAGCTCTTCCCCTGGTATATTCCTAGGAGTGGA +>syndip_1_chr20:45600469-45600847 +AATATTGGGAATTTTACTGATGGTAAAATTAAAATAGGAGGAGGAGGTTACATCACTATC +ATATGGTAACATTCCCTTAAAAATCATCTCTTTATCTTTCCTAAATATTCCACTGTCTTT +GACTGCTATACCTCTCTCTCTTTTCTTTCACCAAGCCTCTCTCTTTGCTTTCCTTCTGGT +AAAAGCAGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATCCCCCCCTCCC +TCCCTCCTTCCCTCCCTCCCTCTCTCTCTCTCTCTCCCTTTCTCTGTCTCTCCCTCTCTC +TCTCTCTCTCTCCCTCTCTCTCTCTTTCTCCCTCTCTCTCCCTCTCTCTCTCTCTCTCTC +CCTCTCTCTCTCTTTCTCCCTCTCTCTCCCTCTCTCCCCCTCTCTCTCCCTCTCTCCCTC +TCTCCCTCTCTCTCCCTCTCTCTCTACCCCTGAATCTGGCCTTTCTAAACACCCTCAACT +TGTGTACCTGTATACTATACTGAGCTACACTAAAGTTTCTATATTTAGCCAAATCCAGCC +CATCATACCAGCTCTTCCCCTGGTATATTCCTAGGAGTGGA +>syndip_2_chr20:45600469-45600847 +AATATTGGGAATTTTACTGATGGTAAAATTAAAATAGGAGGAGGAGGTTACATCACTATC +ATATGGTAACATTCCCTTAAAAATCATCTCTTTATCTTTCCTAAATATTCCACTGTCTTT +GACTGCTATACCTCTCTCTCTTTTCTTTCACCAAGCCTCTCTCTTTGCTTTCCTTCTGGT +AAAAGCAGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATCCCCCCCTCCCTC +CCTCCTTCCCTCCCTCCCTCTCTCTCTCTCTCTCCCTTTCTCTGTCTCTCCCTCTCTCTC +TCTCTCTCTCCCTCTCTCTCCCTCTCTCCCCCTCTCTCTCCCTCTCTCCCTCTCTCCCTC +TCTCTCTACCCCTGAATCTGGCCTTTCTAAACACCCTCAACTTGTGTACCTGTATACTAT +ACTGAGCTACACTAAAGTTTCTATATTTAGCCAAATCCAGCCCATCATACCAGCTCTTCC +CCTGGTATATTCCTAGGAGTGGA +>p:HG002_1_chr20:45600469-45600847 +AATATTGGGAATTTTACTGATGGTAAAATTAAAATAGGAGGAGGAGGTTACATCACTATC +ATATGGTAACATTCCCTTAAAAATCATCTCTTTATCTTTCCTAAATATTCCACTGTCTTT +GACTGCTATACCTCTCTCTCTTTTCTTTCACCAAGCCTCTCTCTTTGCTTTCCTTCTGGT +AAAAGCAGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATCCCCCCCTCCCTC +CCTCCTTCCCTCCCTCCCTCTCTCTCTCTCTCTCCCTTTCTCTGTCTCTCCCTCTCTCTC +TCTCTCTCTCCCTCTCTCTCCCTCTCTCCCCCTCTCTCTCCCTCTCTCCCTCTCTCCCTC +TCTCTCTACCCCTGAATCTGGCCTTTCTAAACACCCTCAACTTGTGTACCTGTATACTAT +ACTGAGCTACACTAAAGTTTCTATATTTAGCCAAATCCAGCCCATCATACCAGCTCTTCC +CCTGGTATATTCCTAGGAGTGGA +>p:HG002_2_chr20:45600469-45600847 +AATATTGGGAATTTTACTGATGGTAAAATTAAAATAGGAGGAGGAGGTTACATCACTATC +ATATGGTAACATTCCCTTAAAAATCATCTCTTTATCTTTCCTAAATATTCCACTGTCTTT +GACTGCTATACCTCTCTCTCTTTTCTTTCACCAAGCCTCTCTCTTTGCTTTCCTTCTGGT +AAAAGCAGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATCCCCCCCTCCC +TCCCTCCTTCCCTCCCTCCCTCTCTCTCTCTCTCTCCCTTTCTCTGTCTCTCCCTCTCTC +TCTCTCTCTCTCCCTCTCTCTCTCTTTCTCCCTCTCTCTCCCTCTCTCTCTCTCTCTCTC +CCTCTCTCTCTCTTTCTCCCTCTCTCTCCCTCTCTCCCCCTCTCTCTCCCTCTCTCCCTC +TCTCCCTCTCTCTCCCTCTCTCTCTACCCCTGAATCTGGCCTTTCTAAACACCCTCAACT +TGTGTACCTGTATACTATACTGAGCTACACTAAAGTTTCTATATTTAGCCAAATCCAGCC +CATCATACCAGCTCTTCCCCTGGTATATTCCTAGGAGTGGA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/haps.fa.ref.fa new file mode 100644 index 00000000..ae82eca8 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:45600469-45600847 +AATATTGGGAATTTTACTGATGGTAAAATTAAAATAGGAGGAGGAGGTTACATCACTATCATATGGTAACATTCCCTTAAAAATCATCTCTTTATCTTTCCTAAATATTCCACTGTCTTTGACTGCTATACCTCTCTCTCTTTTCTTTCACCAAGCCTCTCTCTTTGCTTTCCTTCTGGTAAAAGCAGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATCCCCCCCTCTCCCTCTCTCTCTACCCCTGAATCTGGCCTTTCTAAACACCCTCAACTTGTGTACCTGTATACTATACTGAGCTACACTAAAGTTTCTATATTTAGCCAAATCCAGCCCATCATACCAGCTCTTCCCCTGGTATATTCCTAGGAGTGGA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/msa.fa new file mode 100644 index 00000000..f8425911 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/msa.fa @@ -0,0 +1,55 @@ +>ref_chr20_45600469_45600847 +aatattgggaattttactgatggtaaaattaaaataggaggaggaggttacatcactatc +atatggtaacattcccttaaaaatcatctctttatctttcctaaatattccactgtcttt +gactgctatacctctctctcttttctttcaccaagcctctctctttgctttccttctggt +aaaagcagtctctctctctctctctctctctctct------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------------------------ctc +tatccccccctctccctctctctctacccctgaatctggcctttctaaacaccctcaact +tgtgtacctgtatactatactgagctacactaaagtttctatatttagccaaatccagcc +catcataccagctcttcccctggtatattcctaggagtgga +>syndip_1_chr20:45600469-45600847 +aatattgggaattttactgatggtaaaattaaaataggaggaggaggttacatcactatc +atatggtaacattcccttaaaaatcatctctttatctttcctaaatattccactgtcttt +gactgctatacctctctctcttttctttcaccaagcctctctctttgctttccttctggt +aaaagcagtctctctctctctctctctctctctctctctctctctctatccccccctccc +tccctccttccctccctccctctctctctctctctccctttctctgtctctccctctctc +tctctctctctccctctctctctctttctccctctctctccctctctctctctctctctc +cctctctctctctttctccctctctctccctctctccccctctctctccctctctccctc +tctccctctctctccctctctctctacccctgaatctggcctttctaaacaccctcaact +tgtgtacctgtatactatactgagctacactaaagtttctatatttagccaaatccagcc +catcataccagctcttcccctggtatattcctaggagtgga +>syndip_2_chr20:45600469-45600847 +aatattgggaattttactgatggtaaaattaaaataggaggaggaggttacatcactatc +atatggtaacattcccttaaaaatcatctctttatctttcctaaatattccactgtcttt +gactgctatacctctctctcttttctttcaccaagcctctctctttgctttccttctggt +aaaagcagtctctctctctctctctctctctctct--ctctctctctatccccccctccc +tccctccttccctccctccctctctctctctctctccctttctctgtctctccctctctc +tctctctctctccctctctct--------------------------------------- +-------------------------------------ccctctctccccctctctctccc +tctctccctctctccctctctctctacccctgaatctggcctttctaaacaccctcaact +tgtgtacctgtatactatactgagctacactaaagtttctatatttagccaaatccagcc +catcataccagctcttcccctggtatattcctaggagtgga +>p:HG002_1_chr20:45600469-45600847 +aatattgggaattttactgatggtaaaattaaaataggaggaggaggttacatcactatc +atatggtaacattcccttaaaaatcatctctttatctttcctaaatattccactgtcttt +gactgctatacctctctctcttttctttcaccaagcctctctctttgctttccttctggt +aaaagcagtctctctctctctctctctctctctct--ctctctctctatccccccctccc +tccctccttccctccctccctctctctctctctctccctttctctgtctctccctctctc +tctctctctctccctctctct--------------------------------------- +-------------------------------------ccctctctccccctctctctccc +tctctccctctctccctctctctctacccctgaatctggcctttctaaacaccctcaact +tgtgtacctgtatactatactgagctacactaaagtttctatatttagccaaatccagcc +catcataccagctcttcccctggtatattcctaggagtgga +>p:HG002_2_chr20:45600469-45600847 +aatattgggaattttactgatggtaaaattaaaataggaggaggaggttacatcactatc +atatggtaacattcccttaaaaatcatctctttatctttcctaaatattccactgtcttt +gactgctatacctctctctcttttctttcaccaagcctctctctttgctttccttctggt +aaaagcagtctctctctctctctctctctctctctctctctctctctatccccccctccc +tccctccttccctccctccctctctctctctctctccctttctctgtctctccctctctc +tctctctctctccctctctctctctttctccctctctctccctctctctctctctctctc +cctctctctctctttctccctctctctccctctctccccctctctctccctctctccctc +tctccctctctctccctctctctctacccctgaatctggcctttctaaacaccctcaact +tgtgtacctgtatactatactgagctacactaaagtttctatatttagccaaatccagcc +catcataccagctcttcccctggtatattcctaggagtgga diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/msa.fa.fai new file mode 100644 index 00000000..f49d0b16 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_45600469_45600847 581 29 60 61 +syndip_1_chr20:45600469-45600847 581 654 60 61 +syndip_2_chr20:45600469-45600847 581 1279 60 61 +p:HG002_1_chr20:45600469-45600847 581 1905 60 61 +p:HG002_2_chr20:45600469-45600847 581 2531 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/output.vcf.gz new file mode 100644 index 00000000..ab827dd3 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/output.vcf.gz.tbi new file mode 100644 index 00000000..ecd78c68 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:45600569-45600747/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/base.vcf.gz new file mode 100644 index 00000000..b8403352 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/base.vcf.gz.tbi new file mode 100644 index 00000000..ba53ed30 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/comp.vcf.gz new file mode 100644 index 00000000..4236ee0e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/comp.vcf.gz.tbi new file mode 100644 index 00000000..203839b6 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/haps.fa new file mode 100644 index 00000000..42ff1e4e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/haps.fa @@ -0,0 +1,104 @@ +>ref_chr20_48449605_48450562 +CATGAGAATATGCTCAGTGATAAGGCAGTGGCGTTAAATCTGCAGGCAGTGGGCTATCTGTGGGTCCTTAAATCTATTTAGTGCATCTTGAACAGTATTTTTAAGCTGGGATAAGTGGAATAGGAAGGAGTGGAGTGGAGCATGATGGTATGGGATGGGATGGATGGGATGGGATGGATGGATGGATGGGGTGGGATGGGATGGGATGGGATGGGATGGATGGATGGGATGGATGGATGGGATGGGATAGGATGGATGGGGTGAGATGGGATGGAATGGATGGGATGGGATGGATGGATGGGATGGGATGGATGGGATGGGATGGATGGGATGGGATGGATGGGATGGATGGGATGGAATGGGATGGATGGGATGGGATGGGATTGGATGGGGTGGGATGGGATGGATGGATGGGATGGATGGATGGGATGGAATGGATGGATGGGATGGGATGGATGGGATGGGATGGATGGATGGGATGGGATGGATGCAATGGATGGATGGGATGGGATGGGATGGGATGGATGGAATGGATGGATGGGATGGGATGGGATGGATGGGGTGGGATGAGATGGATGGGATGGATGGGATGGGATGGATGGATGGATGGGATGGGATGGATGGATGGGATGGGATGGGATGGGGTGGATGGGATGGATGGATGGATGGGATGGGATGGATGGATGGGATGGGATGGATGGGATGGGATGGGGTGGGGTGGGGTGGGATGGGATGGGATGGGGTGGGGTGGGATGGGATTGGATGGGGTGGGATGCGATGGGATGAGATGAGATGGATGGCATGGGATGGGTGGGAGGGGATGGGATATTATCAGATGGCAAAAGTAAGAAGTGTTCATATTTTGTCTTCAAAATATAAATATGAGTGCATAATGGCTTGTGATGCAAAATACATTTCTTACTAAAGATCATGGACAAAGCACTTAAAACCACACAGT +>syndip_1_chr20:48449605-48450562 +CATGAGAATATGCTCAGTGATAAGGCAGTGGCGTTAAATCTGCAGGCAGTGGGCTATCTG +TGGGTCCTTAAATCTATTTAGTGCATCTTGAACAGTATTTTTAAGCTGGGATAAGTGGAA +TAGGAAGGAGTGGAGTGGAGCATGATGGTATGGGATGGGATGGATGGGATGGGATGGATG +GATGGATGGGGTGGGATGGGATGGGATGGGATGGATGGATGGGATGGATGGATGGGATGG +GATAGGATGGATGGGGTGAGATGGGATGGAATGGATGGGATGGGATGGATGGATGGGATG +GGATGGATGGGATGGGATGGATGGGATGGGATGGATGGGATGGATGGGATGGAATGGGAT +GGATGGGATGGGATGGGATTGGATGGGGTGGGATGGGATGGATGGATGGGATGGATGGAT +GGGATGGAATGGATGGATGGGATGGGATGGATGGGATGGGATGGATGGATGGGATGGGAT +GGATGCAATGGATGGATGGGATGGGATGGGATGGGATGGATGGAATGGATGGATGGGATG +GGATGGGATGGATGGGGTGGGATGAGATGGATGGGATGGATGGGATGGGATGGATGGATG +GATGGGATGGGATGGATGGATGGGATGGGATGGGATGGGGTGGATGGGATGGATGGATGG +ATGGGATGGGATGGATGGATGGGATGGAATGGATGAATGGGATGTGATGGATGGGATGGA +ATGGGATAGATGGGATGGGATTGGATGGGATGGGGTGGGATGGGGTAAGATGGGGTGGGA +TGGGATGGTATGGGATGGATGGATGAGATGGGATGGGATGAGATGGGATTGGATGGGGTG +GGATGCAATGGGATGAGATGAGATGAGATGAGATGGGATGGATGGCATGGGATGGGATGG +GATTGGATGGGGTGGGATGGGATGGGGTAGGATGGGATGGGATGGGATGGGATGGGATGG +GATGGGATGGGATGGGATGGGGTGGGATGGGTTGGGATGGGATGGGGTGGGTTGGGATGG +GGTGGGGTGGGATGGGATGGGATGGGATGGGGTGGGGTGGGGTGGGGTGGGATGGGGTGG +GATGGGGTGGGATGGGATGGGGTGGGATGGGATGGGATGGGGTGGGATGGGATGGGGTGG +GGTGGGGTGGGGTGGGATGAGGTGGGGTGGGATGGGATGGGATGGGGTGGGGTGGGGTGG +GATGGGATGGGATGGGGTGGGGTGGGATGGGATTGGATGGGGTGGGATGCGATGGGATGA +GATGAGATGGATGGCATGGGATGGGTGGGAGGGGATGGGATATTATCAGATGGCAAAAGT +AAGAAGTGTTCATATTTTGTCTTCAAAATATAAATATGAGTGCATAATGGCTTGTGATGC +AAAATACATTTCTTACTAAAGATCATGGACAAAGCACTTAAAACCACACAGT +>syndip_2_chr20:48449605-48450562 +CATGAGAATATGCTCAGTGATAAGGCAGTGGCGTTAAATCTGCAGGCAGTGGGCTATCTG +TGGGTCCTTAAATCTATTTAGTGCATCTTGAACAGTATTTTTAAGCTGGGATAAGTGGAA +TAGGAAGGAGTGGAGTGGAGCATGATGGTATGGGATGGGATGGATGGGATGGGATGGATG +GATGGATGGGGTGGGATGGGATGGGATGGGATGGGGTGGATGGATGGGATGGGATAGGAT +GGATGGGGTGAGATGGGATGGAATGGATGGAATGGGATGGATGGATGGGATGGGATGGAT +GGGATGGGATGGATGGGATGGATGGGATGGGATGGATGGGATGGAATGGGATGGATGGGA +TGGGATGGGATTGGATGGGGTGGGATGGGATGGATGGATGGGATGGATGGATGGGATGGA +ATGGATGGATGGGATGGGATGGATGGGATGGGATGGATGGATGGGATGGGATGGATGCAA +TGGATGGATGGGATGGGATGGGATGGGATGGATGGAATGGATGGATGGGATGGGATGGGA +TGGATGGGGTGGGATGAGATGGATGGGATGGATGGGATGGGATGGATGGATGGATGGGAT +GGGATGGATGGATGGGATGGGATGGGATGGATGGATGGGATGGGATGGGATGGGGTGGAT +GGGATGGATGGATGGATGGGATGGGATGGATGGATGGGATGGAATGGATGAATGGGATGT +GATGGATGGGATGGAATGGGATAGATGGGATGGGATTGGATGGGATGGGGTGGGATGGGG +TAAGATGGGGTGGGATGGGATGGTATGGGATGGATGGATGAGATGGGATGGGATGAGATG +GGATTGGATGGGGTGGGATGCAATGGGATGAGATGAGATGAGATGAGATGGGATGGATGG +CATGGGATGGAATGGGATTGGATGGGGTGGGATGGGATGGGGTAGGATGGGATGGGATGG +GATGGGATGGGATGGGATGGGGTGGGATGGGTTGGGATGGGATGGGGTGGGTTGGGATGG +GGTGGGGTGGGATGGGATGGGATGGGGTGGGATGGGGTGGGATGGGGTGGGATGGGGTGG +GATGGGATGGGGTGGGATGGGATGGGATGGGATGGGGTGGGATGGGGTGGGATGGGATGG +GGTGGGGTGGGGTGGGGTGGGATGAGGTGGGGTGGGATGGGATGGGATGGGGTGGGGTGG +GGTGGGATGGGATGGGATGGGGTGGGGTGGGATGGGATTGGATGGGGTGGGATGCGATGG +GATGAGATGAGATGAGATGAATGGCATGGGATGGGTGGGAGGGGATGGGATATTATCAGA +TGGCAAAAGTAAGAAGTGTTCATATTTTGTCTTCAAAATATAAATATGAGTGCATAATGG +CTTGTGATGCAAAATACATTTCTTACTAAAGATCATGGACAAAGCACTTAAAACCACACA +GT +>p:HG002_1_chr20:48449605-48450562 +CATGAGAATATGCTCAGTGATAAGGCAGTGGCGTTAAATCTGCAGGCAGTGGGCTATCTG +TGGGTCCTTAAATCTATTTAGTGCATCTTGAACAGTATTTTTAAGCTGGGATAAGTGGAA +TAGGAAGGAGTGGAGTGGAGCATGATGGTATGGGATGGGATGGATGGGATGGGATGGATG +GATGGATGGGGTGGGATGGGATGGGATGGGATGGGGTGGATGGATGGGATGGGATAGGAT +GGATGGGGTGAGATGGGATGGAATGGATGGAATGGGATGGATGGATGGGATGGGATGGAT +GGGATGGGATGGATGGGATGGATGGGATGGGATGGATGGGATGGAATGGGATGGATGGGA +TGGGATGGGATTGGATGGGGTGGGATGGGATGGATGGATGGGATGGATGGATGGGATGGA +ATGGATGGATGGGATGGGATGGATGGGATGGGATGGATGGATGGGATGGGATGGATGCAA +TGGATGGATGGGATGGGATGGGATGGGATGGATGGAATGGATGGATGGGATGGGATGGGA +TGGATGGGGTGGGATGAGATGGATGGGATGGATGGGATGGGATGGATGGATGGATGGGAT +GGGATGGATGGATGGGATGGGATGGGATGGATGGATGGGATGGGATGGGATGGGGTGGAT +GGGATGGATGGATGGATGGGATGGGATGGATGGATGGGATGGAATGGATGAATGGGATGT +GATGGATGGGATGGAATGGGATAGATGGGATGGGATTGGATGGGATGGGGTGGGATGGGG +TAAGATGGGGTGGGATGGGATGGTATGGGATGGATGGATGAGATGGGATGGGATGAGATG +GGATTGGATGGGGTGGGATGCAATGGGATGAGATGAGATGAGATGAGATGGGATGGATGG +CATGGGATGGAATGGGATTGGATGGGGTGGGATGGGATGGGGTAGGATGGGATGGGATGG +GATGGGATGGGATGGGATGGGGTGGGATGGGTTGGGATGGGATGGGGTGGGTTGGGATGG +GGTGGGGTGGGATGGGATGGGATGGGGTGGGATGGGGTGGGATGGGGTGGGATGGGGTGG +GATGGGATGGGGTGGGATGGGATGGGATGGGATGGGGTGGGATGGGGTGGGATGGGATGG +GGTGGGGTGGGGTGGGGTGGGATGAGGTGGGGTGGGATGGGATGGGATGGGGTGGGGTGG +GGTGGGATGGGATGGGATGGGGTGGGGTGGGATGGGATTGGATGGGGTGGGATGCGATGG +GATGAGATGAGATGAGATGAATGGCATGGGATGGGTGGGAGGGGATGGGATATTATCAGA +TGGCAAAAGTAAGAAGTGTTCATATTTTGTCTTCAAAATATAAATATGAGTGCATAATGG +CTTGTGATGCAAAATACATTTCTTACTAAAGATCATGGACAAAGCACTTAAAACCACACA +GT +>p:HG002_2_chr20:48449605-48450562 +CATGAGAATATGCTCAGTGATAAGGCAGTGGCGTTAAATCTGCAGGCAGTGGGCTATCTG +TGGGTCCTTAAATCTATTTAGTGCATCTTGAACAGTATTTTTAAGCTGGGATAAGTGGAA +TAGGAAGGAGTGGAGTGGAGCATGATGGTATGGGATGGGATGGATGGGATGGGATGGATG +GATGGATGGGGTGGGATGGGATGGGATGGGATGGATGGATGGGATGGATGGATGGGATGG +GATAGGATGGATGGGGTGAGATGGGATGGAATGGATGGGATGGGATGGATGGATGGGATG +GGATGGATGGGATGGGATGGATGGGATGGGATGGATGGGATGGATGGGATGGAATGGGAT +GGATGGGATGGGATGGGATTGGATGGGGTGGGATGGGATGGATGGATGGGATGGATGGAT +GGGATGGAATGGATGGATGGGATGGGATGGATGGGATGGGATGGATGGATGGGATGGGAT +GGATGCAATGGATGGATGGGATGGGATGGGATGGGATGGATGGAATGGATGGATGGGATG +GGATGGGATGGATGGGGTGGGATGAGATGGATGGGATGGATGGGATGGGATGGATGGATG +GATGGGATGGGATGGATGGATGGGATGGGATGGGATGGGGTGGATGGGATGGATGGATGG +ATGGGATGGGATGGATGGATGGGATGGAATGGATGAATGGGATGTGATGGATGGGATGGA +ATGGGATAGATGGGATGGGATTGGATGGGATGGGGTGGGATGGGGTAAGATGGGGTGGGA +TGGGATGGTATGGGATGGATGGATGAGATGGGATGGGATGAGATGGGATTGGATGGGGTG +GGATGCAATGGGATGAGATGAGATGAGATGAGATGGGATGGATGGCATGGGATGGGATGG +GATTGGATGGGGTGGGATGGGATGGGGTAGGATGGGATGGGATGGGATGGGATGGGATGG +GATGGGATGGGATGGGATGGGGTGGGATGGGTTGGGATGGGATGGGGTGGGTTGGGATGG +GGTGGGGTGGGATGGGATGGGATGGGATGGGGTGGGGTGGGGTGGGGTGGGATGGGGTGG +GATGGGGTGGGATGGGATGGGGTGGGATGGGATGGGATGGGGTGGGATGGGATGGGGTGG +GGTGGGGTGGGGTGGGATGAGGTGGGGTGGGATGGGATGGGATGGGGTGGGGTGGGGTGG +GATGGGATGGGATGGGGTGGGGTGGGATGGGATTGGATGGGGTGGGATGCGATGGGATGA +GATGAGATGGATGGCATGGGATGGGTGGGAGGGGATGGGATATTATCAGATGGCAAAAGT +AAGAAGTGTTCATATTTTGTCTTCAAAATATAAATATGAGTGCATAATGGCTTGTGATGC +AAAATACATTTCTTACTAAAGATCATGGACAAAGCACTTAAAACCACACAGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/haps.fa.ref.fa new file mode 100644 index 00000000..173876c8 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:48449605-48450562 +CATGAGAATATGCTCAGTGATAAGGCAGTGGCGTTAAATCTGCAGGCAGTGGGCTATCTGTGGGTCCTTAAATCTATTTAGTGCATCTTGAACAGTATTTTTAAGCTGGGATAAGTGGAATAGGAAGGAGTGGAGTGGAGCATGATGGTATGGGATGGGATGGATGGGATGGGATGGATGGATGGATGGGGTGGGATGGGATGGGATGGGATGGGATGGATGGATGGGATGGATGGATGGGATGGGATAGGATGGATGGGGTGAGATGGGATGGAATGGATGGGATGGGATGGATGGATGGGATGGGATGGATGGGATGGGATGGATGGGATGGGATGGATGGGATGGATGGGATGGAATGGGATGGATGGGATGGGATGGGATTGGATGGGGTGGGATGGGATGGATGGATGGGATGGATGGATGGGATGGAATGGATGGATGGGATGGGATGGATGGGATGGGATGGATGGATGGGATGGGATGGATGCAATGGATGGATGGGATGGGATGGGATGGGATGGATGGAATGGATGGATGGGATGGGATGGGATGGATGGGGTGGGATGAGATGGATGGGATGGATGGGATGGGATGGATGGATGGATGGGATGGGATGGATGGATGGGATGGGATGGGATGGGGTGGATGGGATGGATGGATGGATGGGATGGGATGGATGGATGGGATGGGATGGATGGGATGGGATGGGGTGGGGTGGGGTGGGATGGGATGGGATGGGGTGGGGTGGGATGGGATTGGATGGGGTGGGATGCGATGGGATGAGATGAGATGGATGGCATGGGATGGGTGGGAGGGGATGGGATATTATCAGATGGCAAAAGTAAGAAGTGTTCATATTTTGTCTTCAAAATATAAATATGAGTGCATAATGGCTTGTGATGCAAAATACATTTCTTACTAAAGATCATGGACAAAGCACTTAAAACCACACAGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/msa.fa new file mode 100644 index 00000000..2696ae99 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/msa.fa @@ -0,0 +1,130 @@ +>ref_chr20_48449605_48450562 +catgagaatatgctcagtgataaggcagtggcgttaaatctgcaggcagtgggctatctg +tgggtccttaaatctatttagtgcatcttgaacagtatttttaagctgggataagtggaa +taggaaggagtggagtggagcatgatggtatgggatgggatggatgggatgggatggatg +gatggatggggtgggatgggatgggatgggatgggatggatggatgggatggatggatgg +gatgggataggatggatggggtgagatgggatggaatggatgggatgggatggatggatg +ggatgggatggatgggatgggatggatgggatgggatggatgggatggatgggatggaat +gggatggatgggatgggatgggattggatggggtgggatgggatggatggatgggatgga +tggatgggatggaatggatggatgggatgggatggatgggatgggatggatggatgggat +gggatggatgcaatggatggatgggatgggatgggatgggatggatggaatggatggatg +ggatgggatgggatggatggggtgggatgagatggatgggatggatgggatgggatggat +ggat-----------------------ggatgggatgggatggatggatgggatgggatg +ggatggggtggatgggatggatggatggatgggatgggatggatggatgggatgggat-- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------------------------gga +tgggatgggatggggtggggtggggtgggatgggatgggatggggtggggtgggatggga +ttggatggggtgggatgcgatgg-----gatgagatgagatggatggcatgggatgggtg +ggaggggatgggatattatcagatggcaaaagtaagaagtgttcatattttgtcttcaaa +atataaatatgagtgcataatggcttgtgatgcaaaatacatttcttactaaagatcatg +gacaaagcacttaaaaccacacagt +>syndip_1_chr20:48449605-48450562 +catgagaatatgctcagtgataaggcagtggcgttaaatctgcaggcagtgggctatctg +tgggtccttaaatctatttagtgcatcttgaacagtatttttaagctgggataagtggaa +taggaaggagtggagtggagcatgatggtatgggatgggatggatgggatgggatggatg +gatggatggggtgggatgggatgggatg-----ggatggatggatgggatggatggatgg +gatgggataggatggatggggtgagatgggatggaatggatgggatgggatggatggatg +ggatgggatggatgggatgggatggatgggatgggatggatgggatggatgggatggaat +gggatggatgggatgggatgggattggatggggtgggatgggatggatggatgggatgga +tggatgggatggaatggatggatgggatgggatggatgggatgggatggatggatgggat +gggatggatgcaatggatggatgggatgggatgggatgggatggatggaatggatggatg +ggatgggatgggatggatggggtgggatgagatggatgggatggatgggatgggatggat +ggat-----------------------ggatgggatgggatggatggatgggatgggatg +ggatggggtggatgggatggatggatggatgggatgggatggatggatgggatggaatgg +atgaatgggatgtgatggatgggatggaatgggatagatgggatgggattggatgggatg +gggtgggatggggtaagatggggtgggatgggatggtatgggatggatggatgagatggg +atgggatgagatgggattggatggggtgggatgcaatgggatgagatgagatgagatgag +atgggatggatggcatgggatgggatgggattggatggggtgggatgggatggggtagga +tgggatgggatgggatgggatgggatgggatgggatgggatgggatggggtgggatgggt +tgggatgggatggggtgggttgggatggggtggggtgggatgggatgggatgggatgggg +tggggtggggtggggtgggatggggtgggatggggtgggatgggatggggtgggatggga +tgggatggggtgggatgggatggggtggggtggggtggggtgggatgaggtggggtggga +tgggatgggatggggtggggtggggtgggatgggatgggatggggtggggtgggatggga +ttggatggggtgggatgcgatgg-----gatgagatgagatggatggcatgggatgggtg +ggaggggatgggatattatcagatggcaaaagtaagaagtgttcatattttgtcttcaaa +atataaatatgagtgcataatggcttgtgatgcaaaatacatttcttactaaagatcatg +gacaaagcacttaaaaccacacagt +>syndip_2_chr20:48449605-48450562 +catgagaatatgctcagtgataaggcagtggcgttaaatctgcaggcagtgggctatctg +tgggtccttaaatctatttagtgcatcttgaacagtatttttaagctgggataagtggaa +taggaaggagtggagtggagcatgatggtatgggatgggatggatgggatgggatggatg +gatggatggggtgggatgggatgggatg-------------ggatggggtggatggatgg +gatgggataggatggatggggtgagatgggatggaatggatggaatgggatggatggatg +ggatgggatggatgggatgggatggatgggatggatgggatgggatggatgggatggaat +gggatggatgggatgggatgggattggatggggtgggatgggatggatggatgggatgga +tggatgggatggaatggatggatgggatgggatggatgggatgggatggatggatgggat +gggatggatgcaatggatggatgggatgggatgggatgggatggatggaatggatggatg +ggatgggatgggatggatggggtgggatgagatggatgggatggatgggatgggatggat +ggatggatgggatgggatggatggatgggatgggatgggatggatggatgggatgggatg +ggatggggtggatgggatggatggatggatgggatgggatggatggatgggatggaatgg +atgaatgggatgtgatggatgggatggaatgggatagatgggatgggattggatgggatg +gggtgggatggggtaagatggggtgggatgggatggtatgggatggatggatgagatggg +atgggatgagatgggattggatggggtgggatgcaatgggatgagatgagatgagatgag +atgggatggatggcatgggatggaatgggattggatggggtgggatgggatggggtagga +tgggatgggatgggatgggatgggatgggatggggtgggatgggttgggatgggatgggg +tgggttgggatgggg----------tggggtgggatgggatgggatggggtgggatgggg +tgggatggggtgggatggggtgggatgggatggggtgggatgggatgggatgggatgggg +tgggatggggtgggatgggatggggtggggtggggtggggtgggatgaggtggggtggga +tgggatgggatggggtggggtggggtgggatgggatgggatggggtggggtgggatggga +ttggatggggtgggatgcgatgggatgagatgagatgagatgaatggcatgggatgggtg +ggaggggatgggatattatcagatggcaaaagtaagaagtgttcatattttgtcttcaaa +atataaatatgagtgcataatggcttgtgatgcaaaatacatttcttactaaagatcatg +gacaaagcacttaaaaccacacagt +>p:HG002_1_chr20:48449605-48450562 +catgagaatatgctcagtgataaggcagtggcgttaaatctgcaggcagtgggctatctg +tgggtccttaaatctatttagtgcatcttgaacagtatttttaagctgggataagtggaa +taggaaggagtggagtggagcatgatggtatgggatgggatggatgggatgggatggatg +gatggatggggtgggatgggatgggatg-------------ggatggggtggatggatgg +gatgggataggatggatggggtgagatgggatggaatggatggaatgggatggatggatg +ggatgggatggatgggatgggatggatgggatggatgggatgggatggatgggatggaat +gggatggatgggatgggatgggattggatggggtgggatgggatggatggatgggatgga +tggatgggatggaatggatggatgggatgggatggatgggatgggatggatggatgggat +gggatggatgcaatggatggatgggatgggatgggatgggatggatggaatggatggatg +ggatgggatgggatggatggggtgggatgagatggatgggatggatgggatgggatggat +ggatggatgggatgggatggatggatgggatgggatgggatggatggatgggatgggatg +ggatggggtggatgggatggatggatggatgggatgggatggatggatgggatggaatgg +atgaatgggatgtgatggatgggatggaatgggatagatgggatgggattggatgggatg +gggtgggatggggtaagatggggtgggatgggatggtatgggatggatggatgagatggg +atgggatgagatgggattggatggggtgggatgcaatgggatgagatgagatgagatgag +atgggatggatggcatgggatggaatgggattggatggggtgggatgggatggggtagga +tgggatgggatgggatgggatgggatgggatggggtgggatgggttgggatgggatgggg +tgggttgggatgggg----------tggggtgggatgggatgggatggggtgggatgggg +tgggatggggtgggatggggtgggatgggatggggtgggatgggatgggatgggatgggg +tgggatggggtgggatgggatggggtggggtggggtggggtgggatgaggtggggtggga +tgggatgggatggggtggggtggggtgggatgggatgggatggggtggggtgggatggga +ttggatggggtgggatgcgatgggatgagatgagatgagatgaatggcatgggatgggtg +ggaggggatgggatattatcagatggcaaaagtaagaagtgttcatattttgtcttcaaa +atataaatatgagtgcataatggcttgtgatgcaaaatacatttcttactaaagatcatg +gacaaagcacttaaaaccacacagt +>p:HG002_2_chr20:48449605-48450562 +catgagaatatgctcagtgataaggcagtggcgttaaatctgcaggcagtgggctatctg +tgggtccttaaatctatttagtgcatcttgaacagtatttttaagctgggataagtggaa +taggaaggagtggagtggagcatgatggtatgggatgggatggatgggatgggatggatg +gatggatggggtgggatgggatgggatg-----ggatggatggatgggatggatggatgg +gatgggataggatggatggggtgagatgggatggaatggatgggatgggatggatggatg +ggatgggatggatgggatgggatggatgggatgggatggatgggatggatgggatggaat +gggatggatgggatgggatgggattggatggggtgggatgggatggatggatgggatgga +tggatgggatggaatggatggatgggatgggatggatgggatgggatggatggatgggat +gggatggatgcaatggatggatgggatgggatgggatgggatggatggaatggatggatg +ggatgggatgggatggatggggtgggatgagatggatgggatggatgggatgggatggat +ggat-----------------------ggatgggatgggatggatggatgggatgggatg +ggatggggtggatgggatggatggatggatgggatgggatggatggatgggatggaatgg +atgaatgggatgtgatggatgggatggaatgggatagatgggatgggattggatgggatg +gggtgggatggggtaagatggggtgggatgggatggtatgggatggatggatgagatggg +atgggatgagatgggattggatggggtgggatgcaatgggatgagatgagatgagatgag +atgggatggatggcatgggatgggatgggattggatggggtgggatgggatggggtagga +tgggatgggatgggatgggatgggatgggatgggatgggatgggatggggtgggatgggt +tgggatgggatggggtgggttgggatggggtggggtgggatgggatgggatgggatgggg +tggggtggggtggggtgggatggggtgggatggggtgggatgggatggggtgggatggga +tgggatggggtgggatgggatggggtggggtggggtggggtgggatgaggtggggtggga +tgggatgggatggggtggggtggggtgggatgggatgggatggggtggggtgggatggga +ttggatggggtgggatgcgatgg-----gatgagatgagatggatggcatgggatgggtg +ggaggggatgggatattatcagatggcaaaagtaagaagtgttcatattttgtcttcaaa +atataaatatgagtgcataatggcttgtgatgcaaaatacatttcttactaaagatcatg +gacaaagcacttaaaaccacacagt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/msa.fa.fai new file mode 100644 index 00000000..c39a55fc --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_48449605_48450562 1465 29 60 61 +syndip_1_chr20:48449605-48450562 1465 1553 60 61 +syndip_2_chr20:48449605-48450562 1465 3077 60 61 +p:HG002_1_chr20:48449605-48450562 1465 4602 60 61 +p:HG002_2_chr20:48449605-48450562 1465 6127 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/output.vcf.gz new file mode 100644 index 00000000..87694cef Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/output.vcf.gz.tbi new file mode 100644 index 00000000..326524bd Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:48449705-48450462/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/base.vcf.gz new file mode 100644 index 00000000..3ca1aa94 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/base.vcf.gz.tbi new file mode 100644 index 00000000..2d3d9e75 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/comp.vcf.gz new file mode 100644 index 00000000..9e64991b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/comp.vcf.gz.tbi new file mode 100644 index 00000000..02f24231 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/haps.fa new file mode 100644 index 00000000..749b06cb --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/haps.fa @@ -0,0 +1,48 @@ +>ref_chr20_49834009_49834659 +GAGGCTGAGACAGGCGGATCACCTGAGGTTGGGAGTTCAAGACCAGCTTGGCCAACATGGTGAAACTCTGTCTCTGCTAAAAATACAAAAATTAGCCGGGCGTGGTGGTGCACGCTTGTAATATTAGCTTGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATATATATATATATATATATATATATATACACACACACACTATGTATATACACACACTGTATATACGCACTATATGCACTATATATACACACAGTATATGTATATACACACACTATATATACAGTGTGTATATATATATATACTGTGTATATATATATATACTGTATATATATATATACTGTGTATATATATATATACTGTGTATATATATATACTGTGTATATATATATACTGTATATATATACTGTATATATATATATATACTGTATATATATATACTGTGTATATATATATATACTGTATATATACACACACACACTATATATATGCCATATATAATATCTGGTGGCCAGTTGTGTGAAATACATTCATTTTCTCTGTTGGGTAGATTGATTTGACCTAACTATGAGCCTCAATCTCAAGAGGTAAAGTGGTAGTTTGCCAATTTAATGCTGCACAAAGGATTATTTAAG +>syndip_1_chr20:49834009-49834659 +GAGGCTGAGACAGGCGGATCACCTGAGGTTGGGAGTTCAAGACCAGCTTGGCCAACATGG +TGAAACTCTGTCTCTGCTAAAAATACAAAAATTAGCCGGGCGTGGTGGTGCACGCTTGTA +ATATTAGCTTGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATAT +ATATATATATATACACACACACACACACTATGTATATACACACACTGTATATACGCACTA +TATGCACTATATATACACACAGTATATGTATATACACACACTATATATACAGTGTGTATA +TATATATATACTGTGTGTATATATATATATACTGTATATATATATATATATACTGTGTAT +ATATATATACTGTGTATATATATATATATACTGTATATATACACACACACACTATATATA +TGCCATATATAATATCTGGTGGCCAGTTGTGTGAAATACATTCATTTTCTCTGTTGGGTA +GATTGATTTGACCTAACTATGAGCCTCAATCTCAAGAGGTAAAGTGGTAGTTTGCCAATT +TAATGCTGCACAAAGGATTATTTAAG +>syndip_2_chr20:49834009-49834659 +GAGGCTGAGACAGGCGGATCACCTGAGGTTGGGAGTTCAAGACCAGCTTGGCCAACATGG +TGAAACTCTGTCTCTGCTAAAAATACAAAAATTAGCCGGGCGTGGTGGTGCACGCTTGTA +ATATTAGCTTGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT +CTCTATATATATATATATATATATATATACACACACACACTATGTATATACACACACTGT +ATATACGCACTATATGCACTATATATACACACAGTATATGTATATACACACACTATATAT +ACAGTGTGTATATATATATATACTGTGTATATATATATATACTGTATATATATATATACT +GTGTATATATATATATACTGTATATATATATATACTGTGTATATATATATACTGTATATA +TATACTGTATATATATATATATACTGTATATATATATACTGTGTATATATATATATACTG +TATATATACACACACACACTATATATATGCCATATATAATATCTGGTGGCCAGTTGTGTG +AAATACATTCATTTTCTCTGTTGGGTAGATTGATTTGACCTAACTATGAGCCTCAATCTC +AAGAGGTAAAGTGGTAGTTTGCCAATTTAATGCTGCACAAAGGATTATTTAAG +>p:HG002_1_chr20:49834009-49834659 +GAGGCTGAGACAGGCGGATCACCTGAGGTTGGGAGTTCAAGACCAGCTTGGCCAACATGG +TGAAACTCTGTCTCTGCTAAAAATACAAAAATTAGCCGGGCGTGGTGGTGCACGCTTGTA +ATATTAGCTTGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT +CTCTATATATATATATATATATATATATACACACACACACTATGTATATACACACACTGT +ATATACGCACTATATGCACTATATATACACACAGTATATGTATATACACACACTATATAT +ACAGTGTGTATATATATATATACTGTGTATATATATATATACTGTATATATATATATACT +GTGTATATATATATATACTGTATATATATATATACTGTGTATATATATATACTGTATATA +TATACTGTATATATATATATATACTGTATATATATATACTGTGTATATATATATATACTG +TATATATACACACACACACTATATATATGCCATATATAATATCTGGTGGCCAGTTGTGTG +AAATACATTCATTTTCTCTGTTGGGTAGATTGATTTGACCTAACTATGAGCCTCAATCTC +AAGAGGTAAAGTGGTAGTTTGCCAATTTAATGCTGCACAAAGGATTATTTAAG +>p:HG002_2_chr20:49834009-49834659 +GAGGCTGAGACAGGCGGATCACCTGAGGTTGGGAGTTCAAGACCAGCTTGGCCAACATGG +TGAAACTCTGTCTCTGCTAAAAATACAAAAATTAGCCGGGCGTGGTGGTGCACGCTTGTA +ATATTAGCTTGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATAT +ATATATATATATACACACACACACACACTATGTATATACACACACTGTATATACGCACTA +TATGCACTATATATACACACAGTATATGTATATACACACACTATATATACAGTGTGTATA +TATATATATACTGTGTGTATATATATATATACTGTATATATATATATATATACTGTGTAT +ATATATATACTGTGTATATATATATATATACTGTATATATACACACACACACTATATATA +TGCCATATATAATATCTGGTGGCCAGTTGTGTGAAATACATTCATTTTCTCTGTTGGGTA +GATTGATTTGACCTAACTATGAGCCTCAATCTCAAGAGGTAAAGTGGTAGTTTGCCAATT +TAATGCTGCACAAAGGATTATTTAAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/haps.fa.ref.fa new file mode 100644 index 00000000..015f1db9 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:49834009-49834659 +GAGGCTGAGACAGGCGGATCACCTGAGGTTGGGAGTTCAAGACCAGCTTGGCCAACATGGTGAAACTCTGTCTCTGCTAAAAATACAAAAATTAGCCGGGCGTGGTGGTGCACGCTTGTAATATTAGCTTGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATATATATATATATATATATATATATATACACACACACACTATGTATATACACACACTGTATATACGCACTATATGCACTATATATACACACAGTATATGTATATACACACACTATATATACAGTGTGTATATATATATATACTGTGTATATATATATATACTGTATATATATATATACTGTGTATATATATATATACTGTGTATATATATATACTGTGTATATATATATACTGTATATATATACTGTATATATATATATATACTGTATATATATATACTGTGTATATATATATATACTGTATATATACACACACACACTATATATATGCCATATATAATATCTGGTGGCCAGTTGTGTGAAATACATTCATTTTCTCTGTTGGGTAGATTGATTTGACCTAACTATGAGCCTCAATCTCAAGAGGTAAAGTGGTAGTTTGCCAATTTAATGCTGCACAAAGGATTATTTAAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/msa.fa new file mode 100644 index 00000000..4d260dc3 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/msa.fa @@ -0,0 +1,60 @@ +>ref_chr20_49834009_49834659 +gaggctgagacaggcggatcacctgaggttgggagttcaagaccagcttggccaacatgg +tgaaactctgtctctgctaaaaatacaaaaattagccgggcgtggtggtgcacgcttgta +atattagcttg--tctctctctctctctctctctctctctctctctctctctctctctct +atatatatatatatatatatatatatatacacacacacactatgtatatacacacactgt +atatacgcactatatgcactatatatacacacagtatatgtatatacacacactatatat +acagtgtgtatatatatatatactgtgtatatatatatatactgtatatatatatatact +gtgtatatatatatatactgtgtatatatatatactgtgtatatatatatactgtatata +tatactgtatatatatatatatactgtatatatatatactgtgtatatatatatatactg +tatatatacacacacacactatatatatgccatatataatatctggtggccagttgtgtg +aaatacattcattttctctgttgggtagattgatttgacctaactatgagcctcaatctc +aagaggtaaagtggtagtttgccaatttaatgctgcacaaaggattatttaag +>syndip_1_chr20:49834009-49834659 +gaggctgagacaggcggatcacctgaggttgggagttcaagaccagcttggccaacatgg +tgaaactctgtctctgctaaaaatacaaaaattagccgggcgtggtggtgcacgcttgta +atattagcttgtctctctctctctctctctctctctctctctctctctctctctc----- +-------tatatatatatatatatacacacacacacacactatgtatatacacacactgt +atatacgcactatatgcactatatatacacacagtatatgtatatacacacactatatat +acagtgtgtatatatatatatactgtgtgtatatatatatatactgtata---------- +--------------------tatatatatatatactgtgtatatatatatactg------ +---------------------------------------tgtatatatatatatatactg +tatatatacacacacacactatatatatgccatatataatatctggtggccagttgtgtg +aaatacattcattttctctgttgggtagattgatttgacctaactatgagcctcaatctc +aagaggtaaagtggtagtttgccaatttaatgctgcacaaaggattatttaag +>syndip_2_chr20:49834009-49834659 +gaggctgagacaggcggatcacctgaggttgggagttcaagaccagcttggccaacatgg +tgaaactctgtctctgctaaaaatacaaaaattagccgggcgtggtggtgcacgcttgta +atattagcttgtctctctctctctctctctctctctctctctctctctctctctctctct +ctctatatatatatatatatatatatatacacacacacactatgtatatacacacactgt +atatacgcactatatgcactatatatacacacagtatatgtatatacacacactatatat +acagtgtgtatatatatatatactgtgtatatatatatatactgtatatatatatatact +gtgtatatatatatatactgtatatatatatatactgtgtatatatatatactgtatata +tatactgtatatatatatatatactgtatatatatatactgtgtatatatatatatactg +tatatatacacacacacactatatatatgccatatataatatctggtggccagttgtgtg +aaatacattcattttctctgttgggtagattgatttgacctaactatgagcctcaatctc +aagaggtaaagtggtagtttgccaatttaatgctgcacaaaggattatttaag +>p:HG002_1_chr20:49834009-49834659 +gaggctgagacaggcggatcacctgaggttgggagttcaagaccagcttggccaacatgg +tgaaactctgtctctgctaaaaatacaaaaattagccgggcgtggtggtgcacgcttgta +atattagcttgtctctctctctctctctctctctctctctctctctctctctctctctct +ctctatatatatatatatatatatatatacacacacacactatgtatatacacacactgt +atatacgcactatatgcactatatatacacacagtatatgtatatacacacactatatat +acagtgtgtatatatatatatactgtgtatatatatatatactgtatatatatatatact +gtgtatatatatatatactgtatatatatatatactgtgtatatatatatactgtatata +tatactgtatatatatatatatactgtatatatatatactgtgtatatatatatatactg +tatatatacacacacacactatatatatgccatatataatatctggtggccagttgtgtg +aaatacattcattttctctgttgggtagattgatttgacctaactatgagcctcaatctc +aagaggtaaagtggtagtttgccaatttaatgctgcacaaaggattatttaag +>p:HG002_2_chr20:49834009-49834659 +gaggctgagacaggcggatcacctgaggttgggagttcaagaccagcttggccaacatgg +tgaaactctgtctctgctaaaaatacaaaaattagccgggcgtggtggtgcacgcttgta +atattagcttgtctctctctctctctctctctctctctctctctctctctctctc----- +-------tatatatatatatatatacacacacacacacactatgtatatacacacactgt +atatacgcactatatgcactatatatacacacagtatatgtatatacacacactatatat +acagtgtgtatatatatatatactgtgtgtatatatatatatactgtata---------- +--------------------tatatatatatatactgtgtatatatatatactg------ +---------------------------------------tgtatatatatatatatactg +tatatatacacacacacactatatatatgccatatataatatctggtggccagttgtgtg +aaatacattcattttctctgttgggtagattgatttgacctaactatgagcctcaatctc +aagaggtaaagtggtagtttgccaatttaatgctgcacaaaggattatttaag diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/msa.fa.fai new file mode 100644 index 00000000..06e6a233 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_49834009_49834659 653 29 60 61 +syndip_1_chr20:49834009-49834659 653 727 60 61 +syndip_2_chr20:49834009-49834659 653 1425 60 61 +p:HG002_1_chr20:49834009-49834659 653 2124 60 61 +p:HG002_2_chr20:49834009-49834659 653 2823 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/output.vcf.gz new file mode 100644 index 00000000..4470ed14 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/output.vcf.gz.tbi new file mode 100644 index 00000000..41f379ab Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:49834109-49834559/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/base.vcf.gz new file mode 100644 index 00000000..a2d71d1e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/base.vcf.gz.tbi new file mode 100644 index 00000000..89b11eee Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/comp.vcf.gz new file mode 100644 index 00000000..cecad0b5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/comp.vcf.gz.tbi new file mode 100644 index 00000000..095ad15c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/haps.fa new file mode 100644 index 00000000..15325c04 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/haps.fa @@ -0,0 +1,68 @@ +>ref_chr20_5039849_5040600 +AGACACAGTGTCCAGGATTGCATTATGTGGCCACCCCAGATGAAGGGGAGATGAGAATGTGAGTGTTCCGTTTTCTAATATGTATAATACAGGTAGGCTGGGCAGAAAGAGTTAGACAGGTATTGGGTTAGCCAGCCTACAGTGTCTAACACACCAACAAAATCAAGCATTGGAGAGCATTTGGATATGGAAGAGTGCTGAGAAGGTGTGGTGGCTCATGCCTATAATCCTAGTACTTTGGGAGGCTGAGGCAGGAGGATCACTTAAGTCCAGGAGTTTGAGAGCAGCCTGGGCAACAAAGTGAGACCTTGTCTCTACAAAAAATAAACAAAATTAGCTGGTGGTGGCACCTGCCTGTTGTCCCAGCTACTCAGGGGGCTGAGGTGGGAGGATGGCTTGAGCCTGGGAGATTGAAGCTTCAGTTAGCCATGATCATGCCACTGCGCTCCAGCCTGGGTGACAGAGAGAGATCCTGCCTCAAAAAAAAAATAAAAATAAAAAAGAGGGGCCGGGTGTGGTGGCTCAGGCCTGTAATCTTAGCACTCTTTGGGAGGCTGAGACTGGAGGATCCTTTGAGCCCAGGGGTTTGAGACCAGCCTGGGCAACATAGGGAGAACTTGTCTCTATTTAAAAAAAAAAATGCTCATACGTGGTTGGCAGGAGTGTAAATAGCCTCAACCAATTTGGAAAGCAATTTGCCAATACTAGTTAATATAACGATCTAGATAGTGGGCAACCCGGATTAGCCTTTT +>syndip_1_chr20:5039849-5040600 +AGACACAGTGTCCAGGATTGCATTATGTGGCCACCCCAGATGAAGGGGAGATGAGAATGT +GAGTGTTCCGTTTTCTAATATGTATAATACAGGTAGGCTGGGCAGAAAGAGTTAGACAGG +TATTGGGTTAGCCAGCCTACAGTGTCTAACACACCAACAAAATCAAGCATTGGAGAGCAT +TTGGATATGGAAGAGTGCTGAGAAGGTGTGGTGGCTCATGCCTATAATCCTAGTACTTTG +GGAGGCTGAGGCAGGAGGATCACTTAAGTCCAGGAGTTTGAGAGCAGCCTGGGCAACAAA +GTGAGACCTTGTCTCTACAAAAAATAAACAAAATTAGCTGGTGGTGGCACCTGCCTGTTG +TCCCAGCTACTCAGGGGGCTGAGGTGGGAGGATGGCTTGAGCCTGGGAGATTGAAGCTTC +AGTTAGCCATGATCATGCCACTGCGCTCCAGCCTGGGTGACAGAGAGAGATCCTGCCTCA +AAAAAAAAAATAAAAATAAAAAAGAGGGGCCGGGTGTGGTGGCTCAGGCCTGTAATCTTA +GCACTCTTTGGGAGGCTGAGACTGGAGGATCCTTTGAGCCCAGGGGTTTGAGACCAGCCT +GGGCAACATAGGGAGAACTTGTCTCTATTTAAAAAAAAAAATGCTCATACGTGGTTGGCA +GGAGTGTAAATAGCCTCAACCAATTTGGAAAGCAATTTGCCAATACTAGTTAATATAACG +ATCTAGATAGTGGGCAACCCGGATTAGCCTTTT +>syndip_2_chr20:5039849-5040600 +AGACACAGTGTCCAGGATTGCATTATGTGGCCACCCCAGATGAAGGGGAGATGAGAATGT +GAGTGTTCCGTTTTCTAATATGTATAATACAGGTAGGCTGGGCAGAAAGAGTTAGACAGG +TATTGGGTTAGCCAGCCTACAGTGTCTAACACACCAACAAAATCAAGCATTGGAGAGCAT +TTGGATATGGAAGAGTGCTGAGAAGGTGTGGTGGCTCATGCCTATAATCCTAGTACTTTG +GGAGGCTGAGGCAGGAGGATCACTTAAGTCCAGGAGTTTGAGAGCAGCCTGGGCAACAAA +GTGAGACCTTGTCTCTACAAAAAATAAACAAAATTAGCTGGTGGTGGCACCTGCCTGTTG +TCCCAGCTACTCAGGGGGCTGAGGTGGGAGGATGGCTTGAGCCTGGGAGATTGAAGCTTC +AGTTAGCCATGATCATGCCACTGCGCTCCAGCCTGGGTGACAGAGAGAGATCCTGCCTCA +AAAAAAAAATAAAAATAAAAAAGAGGGGCCGGGTGTGGTGGCTCAGGCCTGTAATCTTAG +CACTCTTTGGGAGGCTGAGACTGGAGGATCCTTTGAGCCCAGGGGTTTGAGACCAGCCTG +GGCAACATAGGGAGAACTTGTCTCTATTTAAAAAAAAAAATGCTCATACGTGGTTGGCAG +GAGTGTAAATAGCCTCAACCAATTTGGAAAGCAATTTGCCAATACTAGTTAATATAACGA +TCTAGATAGTGGGCAACCCGGATTAGCCTTTT +>p:HG002_1_chr20:5039849-5040600 +AGACACAGTGTCCAGGATTGCATTATGTGGCCACCCCAGATGAAGGGGAGATGAGAATGT +GAGTGTTCCGTTTTCTAATATGTATAATACAGGTAGGCTGGGCAGAAAGAGTTAGACAGG +TATTGGGTTAGCCAGCCTACAGTGTCTAACACACCAACAAAATCAAGCATTGGAGAGCAT +TTGGATATGGAAGAGTGCTGAGAAGGTGTGGTGGCTCATGCCTATAATCCTAGTACTTTG +GGAGGCTGAGGCAGGAGGATCACTTAAGTCCAGGAGTTTGAGAGCAGCCTGGGCAACAAA +GTGAGACCTTGTCTCTACAAAAAATAAACAAAATTAGCTGGTGGTGGCACCTGCCTGTTG +TCCCAGCTACTCAGGGGGCTGAGGTGGGAGGATGGCTTGAGCCTGGGAGATTGAAGCTTC +AGTTAGCCATGATCATGCCACTGCGCTCCAGCCTGGGTGACAGAGAGAGATCCTGCCTCA +AAAAAAAAATAAAAATAAAAAAGAGGGGCCGGGTGTGGTGGCTCAGGCCTGTAATCTTAG +CACTCTTTGGGAGGCTGAGACTGGAGGATCTTTTGAGCCCAGGGGTTTGAGACCAGCCTG +GGCAACATAGGGAGAACTTGTCTCTATTTAAAAAAAAAGGCCGGGCGCGGTGGCTCACGC +CTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCATGAGGTCAGGAGATCGAGA +CCATCCTGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGC +GCGGTGGCGGGCGCCTAGGCAGGAGAATGGCGTGAACCCGGGAAGCGGAGCTTGCAGTGA +GCCGAGATTGCGCCACTGCAGTCCGCAGTCCGACCTGGGCGACAGAGAGAGACTCCGTCT +CAAAAAAAAAAAAAAAAAAAAAAATGCTCATACGTGGTTGGCAGGAGTGTAAATAGCCTC +AACCAATTTGGAAAGCAATTTGCCAATACTAGTTAATATAACGATCTAGATAGTGGGCAA +CCCGGATTAGCCTTTT +>p:HG002_2_chr20:5039849-5040600 +AGACACAGTGTCCAGGATTGCATTATGTGGCCACCCCAGATGAAGGGGAGATGAGAATGT +GAGTGTTCCGTTTTCTAATATGTATAATACAGGTAGGCTGGGCAGAAAGAGTTAGACAGG +TATTGGGTTAGCCAGCCTACAGTGTCTAACACACCAACAAAATCAAGCATTGGAGAGCAT +TTGGATATGGAAGAGTGCTGAGAAGGTGTGGTGGCTCATGCCTATAATCCTAGTACTTTG +GGAGGCTGAGGCAGGAGGATCACTTAAGTCCAGGAGTTTGAGAGCAGCCTGGGCAACAAA +GTGAGACCTTGTCTCTACAAAAAATAAACAAAATTAGCTGGTGGTGGCACCTGCCTGTTG +TCCCAGCTACTCAGGGGGCTGAGGTGGGAGGATGGCTTGAGCCTGGGAGATTGAAGCTTC +AGTTAGCCATGATCATGCCACTGCGCTCCAGCCTGGGTGACAGAGAGAGATCCTGCCTCA +AAAAAAAAAATAAAAATAAAAAAGAGGGGCCGGGTGTGGTGGCTCAGGCCTGTAATCTTA +GCACTCTTTGGGAGGCTGAGACTGGAGGATCTTTTGAGCCCAGGGGTTTGAGACCAGCCT +GGGCAACATAGGGAGAACTTGTCTCTATTTTAAAAAAAAGGCCGGGCGCGGTGGCTCACG +CCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCATGAGGTCAGGAGATCGAG +ACCATCCTGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGG +CGCGGTGGCGGGCGCCTAGGCAGGAGAATGGCGTGAACCCGGGAAGCGGAGCTTGCAGTG +AGCCGAGATTGCGCCACTGCAGTCCGCAGTCCGACCTGGGCGACAGAGAGAGACTCCGTC +TCAAAAAAAAAAAAAAAAAAAATGCTCATACGTGGTTGGCAGGAGTGTAAATAGCCTCAA +CCAATTTGGAAAGCAATTTGCCAATACTAGTTAATATAACGATCTAGATAGTGGGCAACC +CGGATTAGCCTTTT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/haps.fa.ref.fa new file mode 100644 index 00000000..4310f49e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:5039849-5040600 +AGACACAGTGTCCAGGATTGCATTATGTGGCCACCCCAGATGAAGGGGAGATGAGAATGTGAGTGTTCCGTTTTCTAATATGTATAATACAGGTAGGCTGGGCAGAAAGAGTTAGACAGGTATTGGGTTAGCCAGCCTACAGTGTCTAACACACCAACAAAATCAAGCATTGGAGAGCATTTGGATATGGAAGAGTGCTGAGAAGGTGTGGTGGCTCATGCCTATAATCCTAGTACTTTGGGAGGCTGAGGCAGGAGGATCACTTAAGTCCAGGAGTTTGAGAGCAGCCTGGGCAACAAAGTGAGACCTTGTCTCTACAAAAAATAAACAAAATTAGCTGGTGGTGGCACCTGCCTGTTGTCCCAGCTACTCAGGGGGCTGAGGTGGGAGGATGGCTTGAGCCTGGGAGATTGAAGCTTCAGTTAGCCATGATCATGCCACTGCGCTCCAGCCTGGGTGACAGAGAGAGATCCTGCCTCAAAAAAAAAATAAAAATAAAAAAGAGGGGCCGGGTGTGGTGGCTCAGGCCTGTAATCTTAGCACTCTTTGGGAGGCTGAGACTGGAGGATCCTTTGAGCCCAGGGGTTTGAGACCAGCCTGGGCAACATAGGGAGAACTTGTCTCTATTTAAAAAAAAAAATGCTCATACGTGGTTGGCAGGAGTGTAAATAGCCTCAACCAATTTGGAAAGCAATTTGCCAATACTAGTTAATATAACGATCTAGATAGTGGGCAACCCGGATTAGCCTTTT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/msa.fa new file mode 100644 index 00000000..38363f4f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/msa.fa @@ -0,0 +1,95 @@ +>ref_chr20_5039849_5040600 +agacacagtgtccaggattgcattatgtggccaccccagatgaaggggagatgagaatgt +gagtgttccgttttctaatatgtataatacaggtaggctgggcagaaagagttagacagg +tattgggttagccagcctacagtgtctaacacaccaacaaaatcaagcattggagagcat +ttggatatggaagagtgctgagaaggtgtggtggctcatgcctataatcctagtactttg +ggaggctgaggcaggaggatcacttaagtccaggagtttgagagcagcctgggcaacaaa +gtgagaccttgtctctacaaaaaataaacaaaattagctggtggtggcacctgcctgttg +tcccagctactcagggggctgaggtgggaggatggcttgagcctgggagattgaagcttc +agttagccatgatcatgccactgcgctccagcctgggtgacagagagagatcctgcctc- +aaaaaaaaaataaaaataaaaaagaggggccgggtgtggtggctcaggcctgtaatctta +gcactctttgggaggctgagactggaggatcctttgagcccaggggtttgagaccagcct +gggcaacatagggagaacttgtctctattt------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------aaaaaaaaaaatgctcatacgtggttggcaggagtgtaaatagcct +caaccaatttggaaagcaatttgccaatactagttaatataacgatctagatagtgggca +acccggattagcctttt +>syndip_1_chr20:5039849-5040600 +agacacagtgtccaggattgcattatgtggccaccccagatgaaggggagatgagaatgt +gagtgttccgttttctaatatgtataatacaggtaggctgggcagaaagagttagacagg +tattgggttagccagcctacagtgtctaacacaccaacaaaatcaagcattggagagcat +ttggatatggaagagtgctgagaaggtgtggtggctcatgcctataatcctagtactttg +ggaggctgaggcaggaggatcacttaagtccaggagtttgagagcagcctgggcaacaaa +gtgagaccttgtctctacaaaaaataaacaaaattagctggtggtggcacctgcctgttg +tcccagctactcagggggctgaggtgggaggatggcttgagcctgggagattgaagcttc +agttagccatgatcatgccactgcgctccagcctgggtgacagagagagatcctgcctca +aaaaaaaaaataaaaataaaaaagaggggccgggtgtggtggctcaggcctgtaatctta +gcactctttgggaggctgagactggaggatcctttgagcccaggggtttgagaccagcct +gggcaacatagggagaacttgtctctattt------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------aaaaaaaaaaatgctcatacgtggttggcaggagtgtaaatagcct +caaccaatttggaaagcaatttgccaatactagttaatataacgatctagatagtgggca +acccggattagcctttt +>syndip_2_chr20:5039849-5040600 +agacacagtgtccaggattgcattatgtggccaccccagatgaaggggagatgagaatgt +gagtgttccgttttctaatatgtataatacaggtaggctgggcagaaagagttagacagg +tattgggttagccagcctacagtgtctaacacaccaacaaaatcaagcattggagagcat +ttggatatggaagagtgctgagaaggtgtggtggctcatgcctataatcctagtactttg +ggaggctgaggcaggaggatcacttaagtccaggagtttgagagcagcctgggcaacaaa +gtgagaccttgtctctacaaaaaataaacaaaattagctggtggtggcacctgcctgttg +tcccagctactcagggggctgaggtgggaggatggcttgagcctgggagattgaagcttc +agttagccatgatcatgccactgcgctccagcctgggtgacagagagagatcctgcctc- +aaaaaaaaaataaaaataaaaaagaggggccgggtgtggtggctcaggcctgtaatctta +gcactctttgggaggctgagactggaggatcctttgagcccaggggtttgagaccagcct +gggcaacatagggagaacttgtctctattt------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------aaaaaaaaaaatgctcatacgtggttggcaggagtgtaaatagcct +caaccaatttggaaagcaatttgccaatactagttaatataacgatctagatagtgggca +acccggattagcctttt +>p:HG002_1_chr20:5039849-5040600 +agacacagtgtccaggattgcattatgtggccaccccagatgaaggggagatgagaatgt +gagtgttccgttttctaatatgtataatacaggtaggctgggcagaaagagttagacagg +tattgggttagccagcctacagtgtctaacacaccaacaaaatcaagcattggagagcat +ttggatatggaagagtgctgagaaggtgtggtggctcatgcctataatcctagtactttg +ggaggctgaggcaggaggatcacttaagtccaggagtttgagagcagcctgggcaacaaa +gtgagaccttgtctctacaaaaaataaacaaaattagctggtggtggcacctgcctgttg +tcccagctactcagggggctgaggtgggaggatggcttgagcctgggagattgaagcttc +agttagccatgatcatgccactgcgctccagcctgggtgacagagagagatcctgcctc- +aaaaaaaaaataaaaataaaaaagaggggccgggtgtggtggctcaggcctgtaatctta +gcactctttgggaggctgagactggaggatcttttgagcccaggggtttgagaccagcct +gggcaacatagggagaacttgtctctatttaaaaaaaaaggccgggcgcggtggctcacg +cctgtaatcccagcactttgggaggccgaggcgggtggatcatgaggtcaggagatcgag +accatcctggctaaaacggtgaaaccccgtctctactaaaaatacaaaaaattagccggg +cgcggtggcgggcgcctaggcaggagaatggcgtgaacccgggaagcggagcttgcagtg +agccgagattgcgccactgcagtccgcagtccgacctgggcgacagagagagactccgtc +tcaaaaaaaaaaaaaaaaaaaaaaatgctcatacgtggttggcaggagtgtaaatagcct +caaccaatttggaaagcaatttgccaatactagttaatataacgatctagatagtgggca +acccggattagcctttt +>p:HG002_2_chr20:5039849-5040600 +agacacagtgtccaggattgcattatgtggccaccccagatgaaggggagatgagaatgt +gagtgttccgttttctaatatgtataatacaggtaggctgggcagaaagagttagacagg +tattgggttagccagcctacagtgtctaacacaccaacaaaatcaagcattggagagcat +ttggatatggaagagtgctgagaaggtgtggtggctcatgcctataatcctagtactttg +ggaggctgaggcaggaggatcacttaagtccaggagtttgagagcagcctgggcaacaaa +gtgagaccttgtctctacaaaaaataaacaaaattagctggtggtggcacctgcctgttg +tcccagctactcagggggctgaggtgggaggatggcttgagcctgggagattgaagcttc +agttagccatgatcatgccactgcgctccagcctgggtgacagagagagatcctgcctca +aaaaaaaaaataaaaataaaaaagaggggccgggtgtggtggctcaggcctgtaatctta +gcactctttgggaggctgagactggaggatcttttgagcccaggggtttgagaccagcct +gggcaacatagggagaacttgtctctattttaaaaaaaaggccgggcgcggtggctcacg +cctgtaatcccagcactttgggaggccgaggcgggtggatcatgaggtcaggagatcgag +accatcctggctaaaacggtgaaaccccgtctctactaaaaatacaaaaaattagccggg +cgcggtggcgggcgcctaggcaggagaatggcgtgaacccgggaagcggagcttgcagtg +agccgagattgcgccactgcagtccgcagtccgacctgggcgacagagagagactccgtc +tc---aaaaaaaaaaaaaaaaaaaatgctcatacgtggttggcaggagtgtaaatagcct +caaccaatttggaaagcaatttgccaatactagttaatataacgatctagatagtgggca +acccggattagcctttt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/msa.fa.fai new file mode 100644 index 00000000..1ff4220c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_5039849_5040600 1037 27 60 61 +syndip_1_chr20:5039849-5040600 1037 1114 60 61 +syndip_2_chr20:5039849-5040600 1037 2201 60 61 +p:HG002_1_chr20:5039849-5040600 1037 3289 60 61 +p:HG002_2_chr20:5039849-5040600 1037 4377 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/output.vcf.gz new file mode 100644 index 00000000..f0030816 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/output.vcf.gz.tbi new file mode 100644 index 00000000..3500121a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5039949-5040500/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/base.vcf.gz new file mode 100644 index 00000000..7b4e5c84 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/base.vcf.gz.tbi new file mode 100644 index 00000000..bb622a4a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/comp.vcf.gz new file mode 100644 index 00000000..a72abeae Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/comp.vcf.gz.tbi new file mode 100644 index 00000000..1f40d72c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/haps.fa new file mode 100644 index 00000000..73c30929 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/haps.fa @@ -0,0 +1,82 @@ +>ref_chr20_5041757_5042810 +CAGTGTTGGAGCCTGCAGATGCTGACAGTGCCTGCAGCTTTCCTGCCTATTTTAGGACTTGCTAGAAGCTTGGCATGTCCTAAAAACCCTTTTTCAAGAGTCTCTCCCCAGCTGCTGCTAGCGGGATTTTTTTTTTAACTCTCTATCCTATTTAACCTCCTCACTGATGACCTTTTAATGCGTAACTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTCCCAGGCTGGAGTGCAGTGGTGTGATCTCGGCTCACTGCAACCTGTGCCTCCCAGGTTCAAGCGATCTCCTGCCTCAGCCTCCCCAGTACCTAGGATTACAGGTGCGCGCCTCCAGCATAGCTAATGTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTTATGCATAACTTTTTATCACAGATGTTTGATCTCAGTTTTAATCTTTTCAACATTTGTAAACCCTTGGTTCATTGTGCTTCTCCCTTTATTACTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTTTCGCTCTTGTTGCCCAGGCTGGAGTGCAGTGGCGCACTCTCGGTTCACTGCAATCTCCACCTCATAGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGCACACGCCACCATGCCTGGCTAATTTTTCTTTTTCTTTTTTGTATTTTTAGTAGAGATGGGGTTTCACTATGTTGGCCAGACTGGTCTTGAACTCCTGACCTCGTGATCTGCCCACCTCAGACTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCGTGCCTGGCCTAATTTTGTATTTTTAGTAGAGACGGGGTTTCTCCATGTTGGTCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCTGCTCGTCTTGGCCTCCCAAAGTGTTGGGATTATAGGCATAAGCCACCACAACCGACCTGACTGCTCATTTTTAAACTCTTGATCTGACACTGGGGGACTTTAAGCTATAATCTTGTTCTGTTTTTTTTCTTTTTCTCTTGCCTTCTATGCTTTCCATT +>syndip_1_chr20:5041757-5042810 +CAGTGTTGGAGCCTGCAGATGCTGACAGTGCCTGCAGCTTTCCTGCCTATTTTAGGACTT +GCTAGAAGCTTGGCATGTCCTAAAAACCCTTTTTCAAGAGTCTCTCCCCAGCTGCTGCTA +GCGGGATTTTTTTTTTAACTCTCTATCCTATTTAACCTCCTCACTGATGACCTTTTAATG +CATAACTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTCCCAGGCTGGAGTGCA +GTGGTGTGATCTCGGCTCACTGCAACCTGTGCCTCCCAGGTTCAAGCGATCTCCTGCCTC +AGCCTCCCCAGTACCTAGGATTACAGGTGCGCGCCTCCAGCATAGCTAATGTTTGTATTT +TTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTTATGCATAACTTTTTATCACA +GATGTTTGATCTCAGTTTTAATCTTTTCAACATTTGTAAACCCTTGGTTCATTGTGCTTC +TCCCTTTATTACTCTTTTTTTTTTTTTTTTGAGACGGAGTTTCGCTCTTGTTGCCCAGGC +TGGAGTGCAGTGGCGCACTCTCGGTTCACTGCAATCTCCACCTCATAGGTTCAAGCGATT +CTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGCACACGCCACCATGCCTGGCTAA +TTTTTCTTTTTCTTTTTTGTATTTTTAGTAGAGATGGGGTTTCACTATGTTGGCCAGACT +GGTCTTGAACTCCTGACCTCGTGATCTGCCCACCTCAGACTCCCAAAGTGCTGGGATTAC +AGGTGTGAGCCACCGTGCCTGGCCTAATTTTGTATTTTTAGTAGAGACGGGGTTTCTCCA +TGTTGGTCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCTGCTCGTCTTGGCCTCCCA +AAGTGTTGGGATTATAGGCATAAGCCACCACAACCGACCTGACTGCTCATTTTTAAACTC +TTGATCTGACACTGGGGGACTTTAAGCTATAATCTTGTTCTGTTTTTTTTCTTTTTCTCT +TGCCTTCTATGCTTTCCATT +>syndip_2_chr20:5041757-5042810 +CAGTGTTGGAGCCTGCAGATGCTGACAGTGCCTGCAGCTTTCCTGCCTATTTTAGGACTT +GCTAGAAGCTTGGCATGTCCTAAAAACCCTTTTTCAAGAGTCTCTCCCCAGCTGCTGCTA +GCGGGATTTTTTTTTTAACTCTCTATCCTATTTAACCTCCTCACTGATGACCTTTTAATG +CGTAACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGA +CGGAGTCTCGCTCTCCCAGGCTGGAGTGCAGTGGTGTGATCTCGGCTCACTGCAACCTGT +GCCTCCCAGGTTCAAGCGATCTCCTGCCTCAGCCTCCCCAGTACCTAGGATTACAGGTGC +GCGCCTCCAGCATAGCTAATGTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGC +CAGGCTGGTTATGCATAACTTTTTATCACAGATGTTTGATCTCAGTTTTAATCTTTTCAA +CATTTGTAAACCCTTGGTTCATTGTGCTTCTCCCTTTATTACTCTTTTTTTTTTTTTTTT +TTTTTTTTTTTTTTTTGAGACGGAGTTTCGCTCTTGTTGCCCAGGCTGGAGTGCAGTGGC +GCACTCTCGGTTCACTGCAATCTCCACCTCATAGGTTCAAGCGATTCTCCTGCCTCAGCC +TCCTGAGTAGCTGGGATTACAGGCACACGCCACCATGCCTGGCTAATTTTTCTTTTTCTT +TTTTGTATTTTTAGTAGAGATGGGGTTTCACTATGTTGGCCAGACTGGTCTTGAACTCCT +GACCTCGTGATCTGCCCACCTCAGACTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACC +GTGCCTGGCCTAATTTTGTATTTTTAGTAGAGACGGGGTTTCTCCATGTTGGTCAGGCTG +GTCTCGAACTCCTGACCTCAGGTGATCTGCTCGTCTTGGCCTCCCAAAGTGTTGGGATTA +TAGGCATAAGCCACCACAACCGACCTGACTGCTCATTTTTAAACTCTTGATCTGACACTG +GGGGACTTTAAGCTATAATCTTGTTCTGTTTTTTTTCTTTTTCTCTTGCCTTCTATGCTT +TCCATT +>p:HG002_1_chr20:5041757-5042810 +CAGTGTTGGAGCCTGCAGATGCTGACAGTGCCTGCAGCTTTCCTGCCTATTTTAGGACTT +GCTAGAAGCTTGGCATGTCCTAAAAACCCTTTTTCAAGAGTCTCTCCCCAGCTGCTGCTA +GCGGGATTTTTTTTTTTAACTCTCTATCCTATTTAACCTCCTCACTGATGACCTTTTAAT +GCGTAACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAG +ACGGAGTCTCGCTCTCCCAGGCTGGAGTGCAGTGGTGTGATCTCGGCTCACTGCAACCTG +TGCCTCCCAGGTTCAAGCGATCTCCTGCCTCAGCCTCCCCAGTACCTAGGATTACAGGTG +CGCGCCTCCAGCATAGCTAATGTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGG +CCAGGCTGGTTATGCATAACTTTTTATCACAGATGTTTGATCTCAGTTTTAATCTTTTCA +ACATTTGTAAACCCTTGGTTCATTGTGCTTCTCCCTTTATTACTCTTTTTTTTTTTTTTT +TTTTTTTTTTTTTTTTTGAGACGGAGTTTCGCTCTTGTTGCCCAGGCTGGAGTGCAGTGG +CGCACTCTCGGTTCACTGCAATCTCCACCTCATAGGTTCAAGCGATTCTCCTGCCTCAGC +CTCCTGAGTAGCTGGGATTACAGGCACACGCCACCATGCCTGGCTAATTTTTCTTTTTCT +TTTTTGTATTTTTAGTAGAGATGGGGTTTCACTATGTTGGCCAGACTGGTCTTGAACTCC +TGACCTCGTGATCTGCCCACCTCAGACTCCCAAAGTGCTGGGATTACAGGTGTGAGCCAC +CGTGCCTGGCCTAATTTTGTATTTTTAGTAGAGACGGGGTTTCTCCATGTTGGTCAGGCT +GGTCTCGAACTCCTGACCTCAGGTGATCTGCTCGTCTTGGCCTCCCAAAGTGTTGGGATT +ATAGGCATGAGCCACCACAACCGACCTGACTGCTCATTTTTAAACTCTTGATCTGACACT +GGGGGACTTTAAGCTATAATCTTGTTCTGTTTTTTTTCTTTTTCTCTTGCCTTCTATGCT +TTCCATT +>p:HG002_2_chr20:5041757-5042810 +CAGTGTTGGAGCCTGCAGATGCTGACAGTGCCTGCAGCTTTCCTGCCTATTTTAGGACTT +GCTAGAAGCTTGGCATGTCCTAAAAACCCTTTTTCAAGAGTCTCTCCCCAGCTGCTGCTA +GCGGGATTTTTTTTTTAACTCTCTATCCTATTTAACCTCCTCACTGATGACCTTTTAATG +CATAACTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTCCCAGGCTGGAGTGCA +GTGGTGTGATCTCGGCTCACCGCAACCTGTGCCTCCCAGGTTCAAGTGATCTCCTGCCTC +AGCCTCCCCAGTACCTAGGATTACAGGTGCGCGCCTCCAGCATAGCTAATGTTTGTATTT +TTAGTAGAAACGGGGTTTCACCATGTTGGCCAGGATGGTTATGCATAACTTTTTATCACA +GATGTTTGATCTCAGTTTTAATCTTTTCAACATTTGTAAACCCTTGGTTCATTGTGCTTC +TCCCTTTATTACTCTTTTTTTTTTTTTTTTGAGACGGAGTTTCGCTCTTGTTGCCCAGGC +TGGAGTGCAGTGGAGCACTCTCGGTTCACTGCAACCTCCACCTCATAGGTTCAAGCGATT +CTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGTGCCCACCACCATGCCCAGCTAA +TTTTTTTTTTTGAGAGTCTCACACTGTCGCCCAGGCTGGAGTGCAATGGCACTATCTTGA +CTCACTGCAACCTCCTCCTGTGTTCACGTGATTCTCCTGCCTCAGCCTCCTGAGTAGCTG +GGATTACAGGCACATGCCACCATGCCCGGCTAATTTTTCTTTTTTTTTTTTTTTGTATTT +TTAGTAGAGATGGGGTTTCACTATGTTGGCCAGACTGGTCTTGAACTCCTGACCTCGTGA +TCTGCCCGCCTCGGACTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCGTGCCCGGCC +TAATTTTGTATTTTTAGTAGAGACGGGGTTTCTCCATGTTGGTCAGGCTGGTCTCGAACT +CCCGATCTCAGGTGATCCGCTCGTCTTGGCCTCCCAAAGTGTTGGGATTACAGGCATGAG +CCACCACACCCAGCCTGACTGCTCATTTTTAAACTCTTGATCTGACACTGGGGGACTTTA +AGCTATAATCTTGTTCTGTTTTTTTTCTTTTTCTCTTGCCTTCTATGCTTTCCATT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/haps.fa.ref.fa new file mode 100644 index 00000000..bdb60847 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:5041757-5042810 +CAGTGTTGGAGCCTGCAGATGCTGACAGTGCCTGCAGCTTTCCTGCCTATTTTAGGACTTGCTAGAAGCTTGGCATGTCCTAAAAACCCTTTTTCAAGAGTCTCTCCCCAGCTGCTGCTAGCGGGATTTTTTTTTTAACTCTCTATCCTATTTAACCTCCTCACTGATGACCTTTTAATGCGTAACTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTCCCAGGCTGGAGTGCAGTGGTGTGATCTCGGCTCACTGCAACCTGTGCCTCCCAGGTTCAAGCGATCTCCTGCCTCAGCCTCCCCAGTACCTAGGATTACAGGTGCGCGCCTCCAGCATAGCTAATGTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTTATGCATAACTTTTTATCACAGATGTTTGATCTCAGTTTTAATCTTTTCAACATTTGTAAACCCTTGGTTCATTGTGCTTCTCCCTTTATTACTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTTTCGCTCTTGTTGCCCAGGCTGGAGTGCAGTGGCGCACTCTCGGTTCACTGCAATCTCCACCTCATAGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGCACACGCCACCATGCCTGGCTAATTTTTCTTTTTCTTTTTTGTATTTTTAGTAGAGATGGGGTTTCACTATGTTGGCCAGACTGGTCTTGAACTCCTGACCTCGTGATCTGCCCACCTCAGACTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCGTGCCTGGCCTAATTTTGTATTTTTAGTAGAGACGGGGTTTCTCCATGTTGGTCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCTGCTCGTCTTGGCCTCCCAAAGTGTTGGGATTATAGGCATAAGCCACCACAACCGACCTGACTGCTCATTTTTAAACTCTTGATCTGACACTGGGGGACTTTAAGCTATAATCTTGTTCTGTTTTTTTTCTTTTTCTCTTGCCTTCTATGCTTTCCATT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/msa.fa new file mode 100644 index 00000000..ca1646fc --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/msa.fa @@ -0,0 +1,110 @@ +>ref_chr20_5041757_5042810 +cagtgttggagcctgcagatgctgacagtgcctgcagctttcctgcctattttaggactt +gctagaagcttggcatgtcctaaaaaccctttttcaagagtctctccccagctgctgcta +gcggga-ttttttttttaactctctatcctatttaacctcctcactgatgaccttttaat +gcgtaac----------------------------ttttttttttttttttttttttgag +acggagtctcgctctcccaggctggagtgcagtggtgtgatctcggctcactgcaacctg +tgcctcccaggttcaagcgatctcctgcctcagcctccccagtacctaggattacaggtg +cgcgcctccagcatagctaatgtttgtatttttagtagagacggggtttcaccatgttgg +ccaggctggttatgcataactttttatcacagatgtttgatctcagttttaatcttttca +acatttgtaaacccttggttcattgtgcttctccctttattactc----ttttttttttt +tttttttttttttttttgagacggagtttcgctcttgttgcccaggctggagtgcagtgg +cgcactctcggttcactgcaatctccacctcataggttcaagcgattctcctgcctcagc +ctcctgagtagctgggattacaggcacacgccaccatgcctggctaattt---------- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------ttctttttcttttttgtatttttagtagagatgg +ggtttcactatgttggccagactggtcttgaactcctgacctcgtgatctgcccacctca +gactcccaaagtgctgggattacaggtgtgagccaccgtgcctggcctaattttgtattt +ttagtagagacggggtttctccatgttggtcaggctggtctcgaactcctgacctcaggt +gatctgctcgtcttggcctcccaaagtgttgggattataggcataagccaccacaaccga +cctgactgctcatttttaaactcttgatctgacactgggggactttaagctataatcttg +ttctgttttttttctttttctcttgccttctatgctttccatt +>syndip_1_chr20:5041757-5042810 +cagtgttggagcctgcagatgctgacagtgcctgcagctttcctgcctattttaggactt +gctagaagcttggcatgtcctaaaaaccctttttcaagagtctctccccagctgctgcta +gcggga-ttttttttttaactctctatcctatttaacctcctcactgatgaccttttaat +gcataac------------------------------ttttttttttttttttttttgag +acggagtctcgctctcccaggctggagtgcagtggtgtgatctcggctcactgcaacctg +tgcctcccaggttcaagcgatctcctgcctcagcctccccagtacctaggattacaggtg +cgcgcctccagcatagctaatgtttgtatttttagtagagacggggtttcaccatgttgg +ccaggctggttatgcataactttttatcacagatgtttgatctcagttttaatcttttca +acatttgtaaacccttggttcattgtgcttctccctttattactc--------------- +-ttttttttttttttttgagacggagtttcgctcttgttgcccaggctggagtgcagtgg +cgcactctcggttcactgcaatctccacctcataggttcaagcgattctcctgcctcagc +ctcctgagtagctgggattacaggcacacgccaccatgcctggctaattt---------- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------ttctttttcttttttgtatttttagtagagatgg +ggtttcactatgttggccagactggtcttgaactcctgacctcgtgatctgcccacctca +gactcccaaagtgctgggattacaggtgtgagccaccgtgcctggcctaattttgtattt +ttagtagagacggggtttctccatgttggtcaggctggtctcgaactcctgacctcaggt +gatctgctcgtcttggcctcccaaagtgttgggattataggcataagccaccacaaccga +cctgactgctcatttttaaactcttgatctgacactgggggactttaagctataatcttg +ttctgttttttttctttttctcttgccttctatgctttccatt +>syndip_2_chr20:5041757-5042810 +cagtgttggagcctgcagatgctgacagtgcctgcagctttcctgcctattttaggactt +gctagaagcttggcatgtcctaaaaaccctttttcaagagtctctccccagctgctgcta +gcggga-ttttttttttaactctctatcctatttaacctcctcactgatgaccttttaat +gcgtaacttttttttttttttttttttttttttttttttttttttttttttttttttgag +acggagtctcgctctcccaggctggagtgcagtggtgtgatctcggctcactgcaacctg +tgcctcccaggttcaagcgatctcctgcctcagcctccccagtacctaggattacaggtg +cgcgcctccagcatagctaatgtttgtatttttagtagagacggggtttcaccatgttgg +ccaggctggttatgcataactttttatcacagatgtttgatctcagttttaatcttttca +acatttgtaaacccttggttcattgtgcttctccctttattactcttttttttttttttt +tttttttttttttttttgagacggagtttcgctcttgttgcccaggctggagtgcagtgg +cgcactctcggttcactgcaatctccacctcataggttcaagcgattctcctgcctcagc +ctcctgagtagctgggattacaggcacacgccaccatgcctggctaattt---------- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------ttctttttcttttttgtatttttagtagagatgg +ggtttcactatgttggccagactggtcttgaactcctgacctcgtgatctgcccacctca +gactcccaaagtgctgggattacaggtgtgagccaccgtgcctggcctaattttgtattt +ttagtagagacggggtttctccatgttggtcaggctggtctcgaactcctgacctcaggt +gatctgctcgtcttggcctcccaaagtgttgggattataggcataagccaccacaaccga +cctgactgctcatttttaaactcttgatctgacactgggggactttaagctataatcttg +ttctgttttttttctttttctcttgccttctatgctttccatt +>p:HG002_1_chr20:5041757-5042810 +cagtgttggagcctgcagatgctgacagtgcctgcagctttcctgcctattttaggactt +gctagaagcttggcatgtcctaaaaaccctttttcaagagtctctccccagctgctgcta +gcgggatttttttttttaactctctatcctatttaacctcctcactgatgaccttttaat +gcgtaacttttttttttttttttttttttttttttttttttttttttttttttttttgag +acggagtctcgctctcccaggctggagtgcagtggtgtgatctcggctcactgcaacctg +tgcctcccaggttcaagcgatctcctgcctcagcctccccagtacctaggattacaggtg +cgcgcctccagcatagctaatgtttgtatttttagtagagacggggtttcaccatgttgg +ccaggctggttatgcataactttttatcacagatgtttgatctcagttttaatcttttca +acatttgtaaacccttggttcattgtgcttctccctttattactcttttttttttttttt +tttttttttttttttttgagacggagtttcgctcttgttgcccaggctggagtgcagtgg +cgcactctcggttcactgcaatctccacctcataggttcaagcgattctcctgcctcagc +ctcctgagtagctgggattacaggcacacgccaccatgcctggctaattt---------- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------ttctttttcttttttgtatttttagtagagatgg +ggtttcactatgttggccagactggtcttgaactcctgacctcgtgatctgcccacctca +gactcccaaagtgctgggattacaggtgtgagccaccgtgcctggcctaattttgtattt +ttagtagagacggggtttctccatgttggtcaggctggtctcgaactcctgacctcaggt +gatctgctcgtcttggcctcccaaagtgttgggattataggcatgagccaccacaaccga +cctgactgctcatttttaaactcttgatctgacactgggggactttaagctataatcttg +ttctgttttttttctttttctcttgccttctatgctttccatt +>p:HG002_2_chr20:5041757-5042810 +cagtgttggagcctgcagatgctgacagtgcctgcagctttcctgcctattttaggactt +gctagaagcttggcatgtcctaaaaaccctttttcaagagtctctccccagctgctgcta +gcggga-ttttttttttaactctctatcctatttaacctcctcactgatgaccttttaat +gcataac------------------------------ttttttttttttttttttttgag +acggagtctcgctctcccaggctggagtgcagtggtgtgatctcggctcaccgcaacctg +tgcctcccaggttcaagtgatctcctgcctcagcctccccagtacctaggattacaggtg +cgcgcctccagcatagctaatgtttgtatttttagtagaaacggggtttcaccatgttgg +ccaggatggttatgcataactttttatcacagatgtttgatctcagttttaatcttttca +acatttgtaaacccttggttcattgtgcttctccctttattactc--------------- +-ttttttttttttttttgagacggagtttcgctcttgttgcccaggctggagtgcagtgg +agcactctcggttcactgcaacctccacctcataggttcaagcgattctcctgcctcagc +ctcctgagtagctgggattacaggtgcccaccaccatgcccagctaatttttttttttga +gagtctcacactgtcgcccaggctggagtgcaatggcactatcttgactcactgcaacct +cctcctgtgttcacgtgattctcctgcctcagcctcctgagtagctgggattacaggcac +atgccaccatgcccggctaatttttctttttttttttttttgtatttttagtagagatgg +ggtttcactatgttggccagactggtcttgaactcctgacctcgtgatctgcccgcctcg +gactcccaaagtgctgggattacaggtgtgagccaccgtgcccggcctaattttgtattt +ttagtagagacggggtttctccatgttggtcaggctggtctcgaactcccgatctcaggt +gatccgctcgtcttggcctcccaaagtgttgggattacaggcatgagccaccacacccag +cctgactgctcatttttaaactcttgatctgacactgggggactttaagctataatcttg +ttctgttttttttctttttctcttgccttctatgctttccatt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/msa.fa.fai new file mode 100644 index 00000000..5bdcc190 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_5041757_5042810 1243 27 60 61 +syndip_1_chr20:5041757-5042810 1243 1323 60 61 +syndip_2_chr20:5041757-5042810 1243 2619 60 61 +p:HG002_1_chr20:5041757-5042810 1243 3916 60 61 +p:HG002_2_chr20:5041757-5042810 1243 5213 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/output.vcf.gz new file mode 100644 index 00000000..333611d1 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/output.vcf.gz.tbi new file mode 100644 index 00000000..7d878697 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:5041857-5042710/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/base.vcf.gz new file mode 100644 index 00000000..c9abfd82 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/base.vcf.gz.tbi new file mode 100644 index 00000000..3b2d7b29 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/comp.vcf.gz new file mode 100644 index 00000000..f624ee86 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/comp.vcf.gz.tbi new file mode 100644 index 00000000..4b70fb9f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/haps.fa new file mode 100644 index 00000000..19770031 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/haps.fa @@ -0,0 +1,58 @@ +>ref_chr20_50775444_50776124 +TGAACAAAGTGAACTAATAGTAGTTCACGAAATCTACTGGTTTATAATGTCACATACCAAAGGCTTGTGTCTTTAAATCTATCTCTAGACTTGGTATTCTGCTTTCTCATTCTGTCTCTCCAAAGATTTCCATATATATATATATATATATATATATATATATATATATATATAAATATAAATATATTCTATATATTCATATATATATATTCTATATATTCATATATATAAATATATTCTATATATTCATATATAAATATATTCCATATATATAAATATATTCCATATATTTATATATAAATATATATCATATATTTATATATAAATATATATCATATATTTATATATAAATATATATCATATATTTATATATAATATATATCATATATTTATATATAAATATATATCATATATTTATATATAAATATATATCATATATTAATATATATCATATATTTATATATTAATATATATCATATATTTATATATTAATATATATCATATATTTATATATAAATATATATCATATATTTATATATAAATATATATCTACATTTTTTGAGACAGAGTCTGGCTCTGTCACCCCAGCTGGAGTGCAGTGGTACGATCTCAGCTCATTGCAACCTCCACCTCCCAGGTTCAAGCGATTCTCGTGCCTCAGCCTCCATAGTAGCTGGAATT +>syndip_1_chr20:50775444-50776124 +TGAACAAAGTGAACTAATAGTAGTTCACGAAATCTACTGGTTTATAATGTCACATACCAA +AGGCTTGTGTCTTTAAATCTATCTCTAGACTTGGTATTCTGCTTTCTCATTCTGTCTCTC +CAAAGATTTCCATATATATATATATATATATATAAATATAAATATATTCTATATATTCAT +ATATATATATTCTATATATTCATATATATAAATATATTCTATATATTCATATATATAAAT +ATATTCTATATATTCATATATAAATATATTCCATATATATAAATATATTCCATATATTTA +TATATAAATATATATCATATATTTATATATAAATATATATCATATATTTATATATAAATA +TATATCATATATTTATATATAAATATATATCATATATTTATATATAAATATATATCATAT +ATTTATATATAAATATATATCATATATTTATATATAATATATATCATATATTATATATAA +ATATATATCATATATTTATATATAAATATATATCATATATTAATATATATCATATATTTA +TATATTAATATATATCATATATTTATATATTAATATATATCATATATTTATATATAAATA +TATATCATATATTTATATATAAATATATATCTACATTTTTTGAGACAGAGTCTGGCTCTG +TCACCCCAGCTGGAGTGCAGTGGTACGATCTCAGCTCATTGCAACCTCCACCTCCCAGGT +TCAAGCGATTCTCGTGCCTCAGCCTCCATAGTAGCTGGAATT +>syndip_2_chr20:50775444-50776124 +TGAACAAAGTGAACTAATAGTAGTTCACGAAATCTACTGGTTTATAATGTCACATACCAA +AGGCTTGTGTCTTTAAATCTATCTCTAGACTTGGTATTCTGCTTTCTCATTCTGTCTCTC +CAAAGATTTCCATATATATATATATATATATATATATATATATATATATATATAAATATA +AATATATTCTATATATTCATATATATATATTCTATATATTCATATATATAAATATATTCT +ATATATTCATATATATAAATATATTCTATATATTCATATATAAATATATTCCATATATAT +AAATATATTCCATATATTTATATATAAATATATATCATATATTTATATATAAATATATAT +CATATATTTATATATAAATATATATCATATATTTATATATAAATATATATCATATATTTA +TATATAAATATATATCATATATTTATATATAATATATATCATATATTATATATAAATATA +TATCATATATTTATATATAAATATATATCATATATTAATATATATCATATATTTATATAT +TAATATATATCATATATTTATATATTAATATATATCATATATTTATATATAAATATATAT +CATATATTTATATATAAATATATATCTACATTTTTTGAGACAGAGTCTGGCTCTGTCACC +CCAGCTGGAGTGCAGTGGTACGATCTCAGCTCATTGCAACCTCCACCTCCCAGGTTCAAG +CGATTCTCGTGCCTCAGCCTCCATAGTAGCTGGAATT +>p:HG002_1_chr20:50775444-50776124 +TGAACAAAGTGAACTAATAGTAGTTCACGAAATCTACTGGTTTATAATGTCACATACCAA +AGGCTTGTGTCTTTAAATCTATCTCTAGACTTGGTATTCTGCTTTCTCATTCTGTCTCTC +CAAAGATTTCCATATATATATATATATATATATATATATATATATATATATATAAATATA +AATATATTCTATATATTCATATATATATATTCTATATATTCATATATATAAATATATTCT +ATATATTCATATATATAAATATATTCTATATATTCATATATAAATATATTCCATATATAT +AAATATATTCCATATATTTATATATAAATATATATCATATATTTATATATAAATATATAT +CATATATTTATATATAAATATATATCATATATTTATATATAAATATATATCATATATTTA +TATATAAATATATATCATATATTTATATATAATATATATCATATATTATATATAAATATA +TATCATATATTTATATATAAATATATATCATATATTAATATATATCATATATTTATATAT +TAATATATATCATATATTTATATATTAATATATATCATATATTTATATATAAATATATAT +CATATATTTATATATAAATATATATCTACATTTTTTGAGACAGAGTCTGGCTCTGTCACC +CCAGCTGGAGTGCAGTGGTACGATCTCAGCTCATTGCAACCTCCACCTCCCAGGTTCAAG +CGATTCTCGTGCCTCAGCCTCCATAGTAGCTGGAATT +>p:HG002_2_chr20:50775444-50776124 +TGAACAAAGTGAACTAATAGTAGTTCACGAAATCTACTGGTTTATAATGTCACATACCAA +AGGCTTGTGTCTTTAAATCTATCTCTAGACTTGGTATTCTGCTTTCTCATTCTGTCTCTC +CAAAGATTTCCATATATATATATATATATATATAAATATAAATATATTCTATATATTCAT +ATATATATATTCTATATATTCATATATATAAATATATTCTATATATTCATATATATAAAT +ATATTCTATATATTCATATATAAATATATTCCATATATATAAATATATTCCATATATTTA +TATATAAATATATATCATATATTTATATATAAATATATATCATATATTTATATATAAATA +TATATCATATATTTATATATAAATATATATCATATATTTATATATAAATATATATCATAT +ATTTATATATAAATATATATCATATATTTATATATAATATATATCATATATTATATATAA +ATATATATCATATATTTATATATAAATATATATCATATATTAATATATATCATATATTTA +TATATTAATATATATCATATATTTATATATTAATATATATCATATATTTATATATAAATA +TATATCATATATTTATATATAAATATATATCTACATTTTTTGAGACAGAGTCTGGCTCTG +TCACCCCAGCTGGAGTGCAGTGGTACGATCTCAGCTCATTGCAACCTCCACCTCCCAGGT +TCAAGCGATTCTCGTGCCTCAGCCTCCATAGTAGCTGGAATT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/haps.fa.ref.fa new file mode 100644 index 00000000..434fbfbe --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:50775444-50776124 +TGAACAAAGTGAACTAATAGTAGTTCACGAAATCTACTGGTTTATAATGTCACATACCAAAGGCTTGTGTCTTTAAATCTATCTCTAGACTTGGTATTCTGCTTTCTCATTCTGTCTCTCCAAAGATTTCCATATATATATATATATATATATATATATATATATATATATATAAATATAAATATATTCTATATATTCATATATATATATTCTATATATTCATATATATAAATATATTCTATATATTCATATATAAATATATTCCATATATATAAATATATTCCATATATTTATATATAAATATATATCATATATTTATATATAAATATATATCATATATTTATATATAAATATATATCATATATTTATATATAATATATATCATATATTTATATATAAATATATATCATATATTTATATATAAATATATATCATATATTAATATATATCATATATTTATATATTAATATATATCATATATTTATATATTAATATATATCATATATTTATATATAAATATATATCATATATTTATATATAAATATATATCTACATTTTTTGAGACAGAGTCTGGCTCTGTCACCCCAGCTGGAGTGCAGTGGTACGATCTCAGCTCATTGCAACCTCCACCTCCCAGGTTCAAGCGATTCTCGTGCCTCAGCCTCCATAGTAGCTGGAATT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/msa.fa new file mode 100644 index 00000000..bc7feb72 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/msa.fa @@ -0,0 +1,75 @@ +>ref_chr20_50775444_50776124 +tgaacaaagtgaactaatagtagttcacgaaatctactggtttataatgtcacataccaa +aggcttgtgtctttaaatctatctctagacttggtattctgctttctcattctgtctctc +caaagatttccatatatatatatatatatatatatatatatatatatatatataaatata +aatatattctatatattcatatat---------------------------atatattct +atatattcatatatataaatatattctatatattcatatataaatatattccatatatat +aaatatattc-------------------------catatatttatatataaatatatat +catatatttatatataaatatatatcatatatttatatataaatatatatcatatattta +tatat-aatatatatcatatat-------------------------------------- +----------ttatatataaatatatatcatatatttatatataaatatatatcatatat +taatatatatcatatatttatatattaatatatatcatatatttatatattaatatatat +catatatttatatataaatatatatcatatatttatatataaatatatatctacattttt +tgagacagagtctggctctgtcaccccagctggagtgcagtggtacgatctcagctcatt +gcaacctccacctcccaggttcaagcgattctcgtgcctcagcctccatagtagctggaa +tt +>syndip_1_chr20:50775444-50776124 +tgaacaaagtgaactaatagtagttcacgaaatctactggtttataatgtcacataccaa +aggcttgtgtctttaaatctatctctagacttggtattctgctttctcattctgtctctc +caaagatttcc--------------------atatatatatatatatatatataaatata +aatatattctatatattcatatatatatattctatatattcatatatataaatatattct +atatattcatatatataaatatattctatatattcatatataaatatattccatatatat +aaatatattccatatatttatatataaatatatatcatatatttatatataaatatatat +catatatttatatataaatatatatcatatatttatatataaatatatatcatatattta +tatataaatatatatcatatatttatatataaatatatatcatatatttatatataatat +atatcatatattatatataaatatatatcatatatttatatataaatatatatcatatat +taatatatatcatatatttatatattaatatatatcatatatttatatattaatatatat +catatatttatatataaatatatatcatatatttatatataaatatatatctacattttt +tgagacagagtctggctctgtcaccccagctggagtgcagtggtacgatctcagctcatt +gcaacctccacctcccaggttcaagcgattctcgtgcctcagcctccatagtagctggaa +tt +>syndip_2_chr20:50775444-50776124 +tgaacaaagtgaactaatagtagttcacgaaatctactggtttataatgtcacataccaa +aggcttgtgtctttaaatctatctctagacttggtattctgctttctcattctgtctctc +caaagatttccatatatatatatatatatatatatatatatatatatatatataaatata +aatatattctatatattcatatatatatattctatatattcatatatataaatatattct +atatattcatatatataaatatattctatatattcatatataaatatattccatatatat +aaatatattc-------------------------catatatttatatataaatatatat +catatatttatatataaatatatatcatatatttatatataaatatatatcatatattta +tatataaatatatatcatatatttatatataaatatatatcatatatttatatataatat +atatcatatattatatataaatatatatcatatatttatatataaatatatatcatatat +taatatatatcatatatttatatattaatatatatcatatatttatatattaatatatat +catatatttatatataaatatatatcatatatttatatataaatatatatctacattttt +tgagacagagtctggctctgtcaccccagctggagtgcagtggtacgatctcagctcatt +gcaacctccacctcccaggttcaagcgattctcgtgcctcagcctccatagtagctggaa +tt +>p:HG002_1_chr20:50775444-50776124 +tgaacaaagtgaactaatagtagttcacgaaatctactggtttataatgtcacataccaa +aggcttgtgtctttaaatctatctctagacttggtattctgctttctcattctgtctctc +caaagatttccatatatatatatatatatatatatatatatatatatatatataaatata +aatatattctatatattcatatatatatattctatatattcatatatataaatatattct +atatattcatatatataaatatattctatatattcatatataaatatattccatatatat +aaatatattc-------------------------catatatttatatataaatatatat +catatatttatatataaatatatatcatatatttatatataaatatatatcatatattta +tatataaatatatatcatatatttatatataaatatatatcatatatttatatataatat +atatcatatattatatataaatatatatcatatatttatatataaatatatatcatatat +taatatatatcatatatttatatattaatatatatcatatatttatatattaatatatat +catatatttatatataaatatatatcatatatttatatataaatatatatctacattttt +tgagacagagtctggctctgtcaccccagctggagtgcagtggtacgatctcagctcatt +gcaacctccacctcccaggttcaagcgattctcgtgcctcagcctccatagtagctggaa +tt +>p:HG002_2_chr20:50775444-50776124 +tgaacaaagtgaactaatagtagttcacgaaatctactggtttataatgtcacataccaa +aggcttgtgtctttaaatctatctctagacttggtattctgctttctcattctgtctctc +caaagatttcc--------------------atatatatatatatatatatataaatata +aatatattctatatattcatatatatatattctatatattcatatatataaatatattct +atatattcatatatataaatatattctatatattcatatataaatatattccatatatat +aaatatattccatatatttatatataaatatatatcatatatttatatataaatatatat +catatatttatatataaatatatatcatatatttatatataaatatatatcatatattta +tatataaatatatatcatatatttatatataaatatatatcatatatttatatataatat +atatcatatattatatataaatatatatcatatatttatatataaatatatatcatatat +taatatatatcatatatttatatattaatatatatcatatatttatatattaatatatat +catatatttatatataaatatatatcatatatttatatataaatatatatctacattttt +tgagacagagtctggctctgtcaccccagctggagtgcagtggtacgatctcagctcatt +gcaacctccacctcccaggttcaagcgattctcgtgcctcagcctccatagtagctggaa +tt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/msa.fa.fai new file mode 100644 index 00000000..1c7328a9 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_50775444_50776124 782 29 60 61 +syndip_1_chr20:50775444-50776124 782 859 60 61 +syndip_2_chr20:50775444-50776124 782 1689 60 61 +p:HG002_1_chr20:50775444-50776124 782 2520 60 61 +p:HG002_2_chr20:50775444-50776124 782 3351 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/output.vcf.gz new file mode 100644 index 00000000..cc54bd88 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/output.vcf.gz.tbi new file mode 100644 index 00000000..d28f75ff Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:50775544-50776024/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/base.vcf.gz new file mode 100644 index 00000000..c1d6568b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/base.vcf.gz.tbi new file mode 100644 index 00000000..7c6ae579 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/comp.vcf.gz new file mode 100644 index 00000000..da6a3f75 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/comp.vcf.gz.tbi new file mode 100644 index 00000000..cb248694 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/haps.fa new file mode 100644 index 00000000..55d46e01 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/haps.fa @@ -0,0 +1,187 @@ +>ref_chr20_51952383_51954993 +CTCTGTCTCAAAAAAAAAAAAGTCATTGATTGATCTCTTTCTGGTTTAACTGCTATTATTTAGTTTTATAGCATTACATTCAAGTTTTTATAGCATTACAATTCCTAGATTCTATTTTCAAATATTGATTTGCTTAATTTTTTTTTTTTTTTTGAGATGGGGTTTTGCTCTGTCGCCCAGGCTGGAGTGCAATGGCATGATCTTGGCTCACTGCAACCTCTGCCTCCTGGGTTCAGCCATTCTCCTGCCTCAGCCTCCCGAGTGGCTGGGACTACAGGTGCCCGCCACCACGCCTGGCTAATTTTTTTTTTTTATATTTTTAGTAGAGACGGGGTTTCACCATGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTAGGATTACAGGCTTGAGCCACCGCGCCTGGCCTTTAATATAATTTTTATGAAGACATTATTTCCACTTCATTGGGCTCTCTAGAATTAGATTGCATAAATACTGTAGTTTTATTTCAATAAAAAGTCAACTGTTATTTAAACCATGACTAAAGCTTGACATGAATAGAGACTTTAAAACAATAAACATTGCCAGACATGGTGGCACATGCCTGTAGTCTCAGCTACTCAAGAAACTGAGACAGGAGGATCTCCTGAGCCAAGGAGTTCCAGCCCAGCCTGGACAACATAGTGAGATCCCATCTCTTAAAAAAAAAAAAAAAAAGATTTGCTTAATTTTACTTTTACAATTTTTTCTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGATGGAGTCTTGCTCTGTTACCAGGCTGGAGTGCAGTGGTGTGATATCGGCTCCCTGCAACCTCTGCCTCCTGGGTTAAAGCAATTTTCCTGCCCCAGCCTCCCGAGTAGCTGGGACTACAGGCGCGCGTCACCACACCCAGCTAATTTTTGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGATGGTCTCAATCTCTTGATCTCGTGATCCGCCCACCTTGGCCTCCCAAAGTGCTGGAATTACAGGCGTGATCCGCCATAACCTGGCCTTCCTTCTTTTCTTTAAAAATTTTTTTCTGAGACAGAGTCTCACTCTGTTGCCCAGCCTGGAGTGCAGTGGCACAATCTCGGCTCACTGTAGCCTCCACCTTCTGGGTTCAAGTGATTCTCGTGCCTCAGCCTCCCGAGTAGCTGTGACTACAGGTGTGTGCCCTCATGCCTGGCTAATTTTTGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACCCTGGGCTCAAGTGTTCTGTCTGCCTCAGCCCCCCAAAGTGCTGGGATTACAGGCATGAGCCAAAGTGCCTGGCTAGAAAATTGTAAAAGTAACTTAATATCTGCCTCATATACTTTTGTTTTATTTAAAAATGCAAATCCTCAACCACAAATCGAAACAAGAACAACCCTCTGATGACTTCCCTCCCTCTCTCTTTGTACAAAGAAGACTTTCTGCTGTCTGACTCTGACCACCTTGGTCTATTTTATGGAGCTCCAACCCTGCCTTGTTTCCTTCTCAGGCCATCTGTCCTGGTTGGCCTCACTGTTGGAAATGCTCTTCTCAAGATGTTCACGTGGCTGGTTCTTTGTCATTCAGTCTCAGTTCAAATACTCCCTCCTCCAGGAAGCCTTCCCTAACTTCCTAGGTGAAAGTGGTTCCCTTCCCCTGAGTCACGATTATGGTTTCTTCAGTGTACTTATTAATGGCCAACACTGTCTCCTTTATTGTTTGCTTATGAATTTAAAGTCTGTTAGCAGCACCTGCAGCTTTTAAAAGCCTCCTTGTCTCTCTCTCTTTTTTTTTTTTTTTTTTTTTTTGAGGCGGAGTTTCGCTCTTGTTGGCCAGGCTGGAACGCAGTGATGCGATCTCGGCTCAGTGCAACCTCCACCTCTTGGGTTCAAGTGATTCTCCTGCCTCAGCCTCCTTAGTAGCTGAGACTACAGGCATGTGCCACCATGCTGGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCGTCATATTGGCCAAGCTGGTCTCGAACCCCTGACCTCAGGTGATCCACCCATCTTGGCCTCCCAGATGCTGGGATTACAGGCGTGAGCCACTGCGCCTGGCCTAATTGTCATTTTCGTTTTTTTGTTGAGACAGAGTTTCTGTCACCCAGGCTGGAATGCAGTGGCACGATCTCAGCTCACTGCAGCCTCTGCCTCTTGGGTTCAATTGATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGTGTGTGCCACCACACCCAGCTAATTTTTTCATTTTTAGTAGAGACGGGGTTTCACCATGTTGGTCAGGCTTGTCTCGAACTCCTGACCTCAGGTGATCCGTCCAACTTGGCCTCCCAAAGTGCTGAGATTACAGGCATGAGCTACCGTGCCCAGCTCTCAATTGTCACTTTTAGTGCATATTTTCTGGTTGTATAAAAGCTCTCCCATGCAAGAGGGCTGATGTTATAACAGTCGATTATTATACTGTCCTGCATTTTCATCAGGTAAAGAAAGCTTTTCATGTTTCACTGAG +>syndip_1_chr20:51952383-51954993 +CTCTGTCTCAAAAAAAAAAAAGTCATTGATTGATCTCTTTCTGGTTTAACTGCTATTATT +TAGTTTTATAGCATTACATTCAAGTTTTTATAGCATTACAATTCCTAGATTCTATTTTCA +AATATTGATTTGCTTAATTTTTTTTTTTTTTGAGATGGGGTTTTGCTCTGTCGCCCAGGC +TGGAGTGCAATGGCATGATCTTGGCTCACTGCAACCTCTGCCTCCTGGGTTCAGCCATTC +TCCTGCCTCAGCCTCCCGAGTGGCTGGGACTACAGGTGCCCGCCACCACGCCTGGCTAAT +TTTTTTTTTTTATATTTTTAGTAGAGACGGGGTTTCACCATGTTAGCCAGGATGGTCTCG +ATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTAGGATTACAGGCTTG +AGCCACCGCGCCTGGCCTTTAATATAATTTTTATGAAGACATTATTTCCACTTCATTGGG +CTCTCTAGAATTAGATTGCATAAATACTGTAGTTTTATTTCAATAAAAAGTCAACTGTTA +TTTAAACCATGACTAAAGCTTGACATGAATAGAGACTTTAAAACAATAAACATTGCCAGA +CATGGTGGCACATGCCTGTAGTCTCAGCTACTCAAGAAACTGAGACAGGAGGATCTCCTG +AGCCAAGGAGTTCCAGCCCAGCCTGGACAACATAGTGAGATCCCATCTCTTAAAAAAAAA +AAAAAAAGATTTGCTTAATTTTACTTTTACAATTTTTTCTTTTCTTTTTTTTTTTTTTTT +TTTTTTTTTTTTTGAGATGGAGTCTTGCTCTGTTACCAGGCTGGAGTGCAGTGGTGTGAT +ATCGGCTCCCTGCAACCTCTGCCTCCTGGGTTAAAGCAATTTTCCTGCCCCAGCCTCCCG +AGTAGCTGGGACTACAGGCGCGCGTCACCACACCCAGCTAATTTTTGTATTTTTAGTAGA +GATGGGGTTTCACCATGTTGGCCAGGATGGTCTCAATCTCTTGATCTCGTGATCCGCCCA +CCTTGGCCTCCCAAAGTGCTGGAATTACAGGCGTGATCCGCCATAACCTGGCCTTCCTTC +TTTTCTTTAAAAATTTTTTTCTGAGACAGAGTCTCACTCTGTTGCCCAGCCTGGAGTGCA +GTGGCACAATCTCGGCTCACTGTAGCCTCCACCTTCTGGGTTCAAGTGATTCTCGTGCCT +CAGCCTCCCGAGTAGCTGTGACTACAGGTGTGTGCCCTCATGCCTGGCTAATTTTTGTAT +TTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACCCTGGGCTCAAG +TGTTCTGTCTGCCTCAGCCCCCCAAAGTGCTGGGATTACAGGCATGAGCCAAAGTGCCTG +GCTAGAAAATTGTAAAAGTAACTTAATATCTGCCTCATATACTTTTGTTTTATTTAAAAA +TGCAAATCCTCAACCACAAATCGAAACAAGAACAACCCTCTGATGACTTCCCTCCCTCTC +TCTTTGTACAAAGAAGACTTTCTGCTGTCTGACTCTGACCACCTTGGTCTATTTTATGGA +GCTCCAACCCTGCCTTGTTTCCTTCTCAGGCCATCTGTCCTGGTTGGCCTCACTGTTGGA +AATGCTCTTCTCAAGATGTTCACGTGGCTGGTTCTTTGTCATTCAGTCTCAGTTCAAATA +CTCCCTCCTCCAGGAAGCCTTCCCTAACTTCCTAGGTGAAAGTGGTTCCCTTCCCCTGAG +TCACGATTATGGTTTCTTCAGTGTACTTATTAATGGCCAACACTGTCTCCTTTATTGTTT +GCTTATGAATTTAAAGTCTGTTAGCAGCACCTGCAGCTTTTAAAAGCCTCCTTGTCTCTC +TCTATTTTTTTTTTTTTTTTTTTGAGGCGGAGTTTCGCTCTTGTTGGCCAGGCTGGAACG +CAGTGATGCGATCTCGGCTCAGTGCAACCTCCACCTCTTGGGTTCAAGTGATTCTCCTGC +CTCAGCCTCCTTAGTAGCTGAGACTACAGGCATGTGCCACCATGCTGGCTAATTTTTGTA +TTTTTAGTAGAGACAGGGTTTCGTCATATTGGCCAAGCTGGTCTCGAACCCCTGACCTCA +GGTGATCCACCCATCTTGGCCTCCCAGATGCTGGGATTACAGGCGTGAGCCACTGCGCCT +GGCCTAATTGTCATTTTCGTTTTTTTGTTGAGACAGAGTTTCTGTCACCCAGGCTGGAAT +GCAGTGGCACGATCTCAGCTCACTGCAGCCTCTGCCTCTTGGGTTCAATTGATTCTCCTG +CCTCAGCCTCCCAAGTAGCTGGGACTACAGGTGTGTGCCACCACACCCAGCTAATTTTTT +CATTTTTAGTAGAGACGGGGTTTCACCATGTTGGTCAGGCTTGTCTCGAACTCCTGACCT +CAGGTGATCCGTCCAACTTGGCCTCCCAAAGTGCTGAGATTACAGGCATGAGCTACCGTG +CCCAGCTCTCAATTGTCACTTTTAGTGCATATTTTCTGGTTGTATAAAAGCTCTCCCATG +CAAGAGGGCTGATGTTATAACAGTCGATTATTATACTGTCCTGCATTTTCATCAGGTAAA +GAAAGCTTTTCATGTTTCACTGAG +>syndip_2_chr20:51952383-51954993 +CTCTGTCTCAAAAAAAAAAAAGTCATTGATTGATCTCTTTCTGGTTTAACTGCTATTATT +TAGTTTTATAGCATTACATTCAAGTTTTTATAGCATTACAATTCCTAGATTCTATTTTCA +AATATTGATTTGCTTAATTTTTTTTTTTTTTTGAGATGGGGTTTTGCTCTGTCGCCCAGG +CTGGAGTGCAATGGCATGATCTTGGCTCACTGCAACCTCTGCCTCCTGGGTTCAGCCATT +CTCCTGCCTCAGCCTCCCGAGTGGCTGGGACTACAGGTGCCCGCCACCACGCCTGGCTAA +TTTTTTTTTTTTATATTTTTAGTAGAGACGGGGTTTCACCATGTTAGCCAGGATGGTCTC +GATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTAGGATTACAGGCTT +GAGCCACCGCGCCTGGCCTTTAATATAATTTTTATGAAGACATTATTTCCACTTCATTGG +GCTCTCTAGAATTAGATTGCATAAATACTGTAGTTTTATTTCAATAAAAAGTCAACTGTT +ATTTAAACCATGACTAAAGCTTGACATGAATAGAGACTTTAAAACAATAAACATTGCCAG +ACATGGTGGCACATGCCTGTAGTCTCAGCTACTCAAGAAACTGAGACAGGAGGATCTCCT +GAGCCAAGGAGTTCCAGCCCAGCCTGGACAACATAGTGAGATCCCATCTCTTAAAAAAAA +AAAAAAAAAAAGATTTGCTTAATTTTACTTTTACAATTTTTTCTTTTCTTTTTTTTTTTT +TTTTTTTTTTTTTTTGAGATGGAGTCTTGCTCTGTTACCAGGCTGGAGTGCAGTGGTGTG +ATATCGGCTCCCTGCAACCTCTGCCTCCTGGGTTAAAGCAATTTTCCTGCCCCAGCCTCC +CGAGTAGCTGGGACTACAGGCGCGCGTCACCACACCCAGCTAATTTTTGTATTTTTAGTA +GAGATGGGGTTTCACCATGTTGGCCAGGATGGTCTCAATCTCTTGATCTCGTGATCCGCC +CACCTTGGCCTCCCAAAGTGCTGGAATTACAGGCGTGATCCGCCATAACCTGGCCTTCCT +TCTTTTCTTTAAAAATTTTTTTCTGAGACAGAGTCTCACTCTGTTGCCCAGCCTGGAGTG +CAGTGGCACAATCTCGGCTCACTGTAGCCTCCACCTTCTGGGTTCAAGTGATTCTCGTGC +CTCAGCCTCCCGAGTAGCTGTGACTACAGGTGTGTGCCCTCATGCCTGGCTAATTTTTGT +ATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACCCTGGGCTCA +AGTGTTCTGTCTGCCTCAGCCCCCCAAAGTGCTGGGATTACAGGCATGAGCCAAAGTGCC +TGGCTAGAAAATTGTAAAAGTAACTTAATATCTGCCTCATATACTTTTGTTTTATTTAAA +AATGCAAATCCTCAACCACAAATCGAAACAAGAACAACCCTCTGATGACTTCCCTCCCTC +TCTCTTTGTACAAAGAAGACTTTCTGCTGTCTGACTCTGACCACCTTGGTCTATTTTATG +GAGCTCCAACCCTGCCTTGTTTCCTTCTCAGGCCATCTGTCCTGGTTGGCCTCACTGTTG +GAAATGCTCTTCTCAAGATGTTCACGTGGCTGGTTCTTTGTCATTCAGTCTCAGTTCAAA +TACTCCCTCCTCCAGGAAGCCTTCCCTAACTTCCTAGGTGAAAGTGGTTCCCTTCCCCTG +AGTCACGATTATGGTTTCTTCAGTGTACTTATTAATGGCCAACACTGTCTCCTTTATTGT +TTGCTTATGAATTTAAAGTCTGTTAGCAGCACCTGCAGCTTTTAAAAGCCTCCTTGTCTC +TCTCTATTTTTTTTTTTTTTTTTTTTTGAGGCGGAGTTTCGCTCTTGTTGGCCAGGCTGG +AACGCAGTGATGCGATCTCGGCTCAGTGCAACCTCCACCTCTTGGGTTCAAGTGATTCTC +CTGCCTCAGCCTCCTTAGTAGCTGAGACTACAGGCATGTGCCACCATGCTGGCTAATTTT +TGTATTTTTAGTAGAGACAGGGTTTCGTCATATTGGCCAAGCTGGTCTCGAACCCCTGAC +CTCAGGTGATCCACCCATCTTGGCCTCCCAGATGCTGGGATTACAGGCGTGAGCCACTGC +GCCTGGCCTAATTGTCATTTTCGTTTTTTTGTTGAGACAGAGTTTCTGTCACCCAGGCTG +GAATGCAGTGGCACGATCTCAGCTCACTGCAGCCTCTGCCTCTTGGGTTCAATTGATTCT +CCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGTGTGTGCCACCACACCCAGCTAATT +TTTTCATTTTTAGTAGAGACGGGGTTTCACCATGTTGGTCAGGCTTGTCTCGAACTCCTG +ACCTCAGGTGATCCGTCCAACTTGGCCTCCCAAAGTGCTGAGATTACAGGCATGAGCTAC +CGTGCCCAGCTCTCAATTGTCACTTTTAGTGCATATTTTCTGGTTGTATAAAAGCTCTCC +CATGCAAGAGGGCTGATGTTATAACAGTCGATTATTATACTGTCCTGCATTTTCATCAGG +TAAAGAAAGCTTTTCATGTTTCACTGAG +>p:HG002_1_chr20:51952383-51954993 +CTCTGTCTCAAAAAAAAAAAAGTCATTGATTGATCTCTTTCTGGTTTAACTGCTATTATT +TAGTTTTATAGCATTACATTCAAGTTTTTATAGCATTACAATTCCTAGATTCTATTTTCA +AATATTGATTTGCTTAATTTTTTTTTTTTTTTGAGATGGGGTTTTGCTCTGTCGCCCAGG +CTGGAGTGCAATGGCATGATCTTGGCTCACTGCAACCTCCGCCTCCTGGGTTCAGCCATT +CTCCTGCCTCAGCCTCCCGAGTGGCTGGGACTACAGGTGCCCGCCACCACGCCTGGCTAA +TTTTTTTTTTTTATATTTTTAGTAGAGACGGGGTTTCACCATGTTAGCCAGGATGGTCTC +GATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTAGGATTACAGGCTT +GAGCCACCGCGCCTGGCCTTTAATATAATTTTTATGAAGACATTATTTCCACTTCATTGG +GCTCTCTAGAATTAGATTGCATAAATACTGTAGTTTTATTTCAATAAAAAGTCAACTGTT +ATTTAAACCATGACTAAAGCTTGACATGAATAGAGACTTTAAAACAATAAACATTGCCAG +ACATGGTGGCACATGCCTGTAGTCTCAGCTACTCAAGAAACTGAGACAGGAGGATCTCCT +GAGCCAAGGAGTTCCAGCCCAGCCTGGACAACATAGTGAGATCCCATCTCTTAAAAAAAA +AAAAAAAAAAAGATTTGCTTAATTTTACTTTTACAATTTTTTCTTTTCTTTTTTTTTTTT +TTTTTTTTTTTTTTTGAGATGGAGTCTTGCTCTGTTACCAGGCTGGAGTGCAGTGGTGTG +ATATCAGCTCCCTGCAACCTCTGCCTCCTGGGTTAAAGCAATTTTCCTGCCCCAGCCTCC +CGAGTAGCTGGGACTACAGGCGCGCGTCACCACACCCAGCTAATTTTTGTATTTTTAGTA +GAGATGGGGTTTCACCATGTTGGCCAGGATGGTCTCAATCTCTTGATCTCGTGATCCGCC +CACCTTGGCCTCCCAAAGTGCTGGAATTACAGGCGTGATCCGCCATAACCTGGCCTTCCT +TCTTTCCTTTAAAAATTTTTTTCTGAGACAGAGTCTCACTCTGTTGCCCAGCCTGGAGTG +CAGTGGCACAATCTCGGCTCACTGTAGCCTCCACCTTCTGGGTTCAAGTGATTCTCGTGC +CTCAGCCTCCCGAGTAGCTGTGACTACAGGTGTGTGCCCTCATGCCTGGCTAATTTTTGT +ATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACCCTGGGCTCA +AGTGTTCTGTCTGCCTCAGCCCCCCAAAGTGCTGGGATTACAGGCATGAGCCAAAGTGCC +TGGCTAGAAAATTGTAAAAGTAACTTAATATCTGCCTCATATACTTTTGTTTTATTTAAA +AATGCAAATCCTCAACCACAAATCGAAACAAGAACAACCCTCTGATGACTTCCCTCCCTC +TCTCTTTGTACAAAGAAGACTTTCTGCTGTCTGACTCTGACCACCTTGGTCTATTTTATG +GAGCTCCAACCCTGCCTTGTTTCCTTCTCAGGCCATCTGTCCTGGTTGGCCTCACTGTTG +GAAATGCTCTTCTCAAGATGTTCACGTGGCTGGTTCTTTGTCATTCAGTCTCAGTTCAAA +TACTCCCTCCTCCAGGAAGCCTTCCCTAACTTCCTAGGTGAAAGTGGTTCCCTTCCCCTG +AGTCACGATTATGGTTTCTTCAGTGTACTTATTAATGGCCAACACTGTCTCCTTTATTGT +TTGCTTATGAATTTAAAGTCTGTTAGCAGCACCTGCAGCTTTTAAAAGCCTCCTTGTCTC +TCTCTATTTTTTTTTTTTTTTTTTTTTGAGGCGGAGTTTCGCTCTTGTTGGCCAGGCTGG +AACGCAGTGATGCGATCTCGGCTCAGTGCAACCTCCACCTCTTGGGTTCAAGTGATTCTC +CTGCCTCAGCCTCCTTAGTAGCTGAGACTACAGGCATGTGCCACCATGCTGGCTAATTTT +TGTATTTTTAGTAGAGACAGGGTTTCGTCATATTGGCCAAGCTGGTCTCGAACCCCTGAC +CTCAGGTGATCCACCCATCTTGGCCTCCCAGATGCTGGGATTACAGGCGTGAGCCACTGC +GCCTGGCCTAATTGTCATTTTCGTTTTTTTGTTGAGACAGAGTTTCTGTCACCCAGGCTG +GAATGCAGTGGCACGATCTCAGCTCACTGCAGCCTCTGCCTCTTGGGTTCAATTGATTCT +CCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGTGTGTGCCACCACACCCAGCTAATT +TTTTCATTTTTAGTAGAGACGGGGTTTCACCATGTTGGTCAGGCTTGTCTCGAACTCCTG +ACCTCAGGTGATCCGTCCAACTTGGCCTCCCAAAGTGCTGAGATTACAGGCATGAGCTAC +CGTGCCCAGCTCTCAATTGTCACTTTTAGTGCATATTTTCTGGTTGTATAAAAGCTCTCC +CATGCAAGAGGGCTGATGTTATAACAGTCGATTATTATACTGTCCTGCATTTTCATCAGG +TAAAGAAAGCTTTTCATGTTTCACTGAG +>p:HG002_2_chr20:51952383-51954993 +CTCTGTCTCAAAAAAAAAAAAGTCATTGATTGATCTCTTTCTGGTTTAACTGCTATTATT +TAGTTTTATAGCATTACATTCAAGTTTTTATAGCATTACAATTCCTAGATTCTATTTTCA +AATATTGATTTGCTTAATTTTTTTTTTTTTTGAGATGGGGTTTTGCTCTGTCGCCCAGGC +TGGAGTGCAATGGCATGATCTTGGCTCACTGCAACCTCCGCCTCCTGGGTTCAGCCATTC +TCCTGCCTCAGCCTCCCGAGTGGCTGGGACTACAGGTGCCCGCCACCACGCCTGGCTAAT +TTTTTTTTTTTATATTTTTAGTAGAGACGGGGTTTCACCATGTTAGCCAGGATGGTCTCG +ATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTAGGATTACAGGCTTG +AGCCACCGCGCCTGGCCTTTAATATAATTTTTATGAAGACATTATTTCCACTTCATTGGG +CTCTCTAGAATTAGATTGCATAAATACTGTAGTTTTATTTCAATAAAAAGTCAACTGTTA +TTTAAACCATGACTAAAGCTTGACATGAATAGAGACTTTAAAACAATAAACATTGCCAGA +CATGGTGGCACATGCCTGTAGTCTCAGCTACTCAAGAAACTGAGACAGGAGGATCTCCTG +AGCCAAGGAGTTCCAGCCCAGCCTGGACAACATAGTGAGATCCCATCTCTTAAAAAAAAA +AAAAAAAGATTTGCTTAATTTTACTTTTACAATTTTTTCTTTTCTTTTTTTTTTTTTTTT +TTTTTTTTTTTTTGAGATGGAGTCTTGCTCTGTTACCAGGCTGGAGTGCAGTGGTGTGAT +ATCGGCTCCCTGCAACCTCTGCCTCCTGGGTTAAAGCAATTTTCCTGCCCCAGCCTCCCG +AGTAGCTGGGACTACAGGCGCGCGTCACCACACCCAGCTAATTTTTGTATTTTCAGTAGA +GATGGGGTTTCACCATGTTGGCCAGGATGGTCTCAATCTCTTGATCTCGTGATCCGCCCA +CCTTGGCCTCCCAAAGTGCTGGAATTACAGGCGTGATCCGCCATAACCTGGCCTTCCTTC +TTTTCTTTAAAAATTTTTTTCTGAGACAGAGTCTCACTCTGTTGCCCAGCCTGGAGTGCA +GTGGCACAATCTCGGCTCACTGTAGCCTCCACCTTCTGGGTTCAAGTGATTCTCGTGCCT +CAGCCTCCCGAGTAGCTGTGACTACAGGTGTGTGCCCTCATGCCTGGCTAATTTTTGTAT +TTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACCCTGGGCTCAAG +TGTTCTGTCTGCCTCAGCCCCCCAAAGTGCTGGGATTACAGGCATGAGCCAAAGTGCCTG +GCTAGAAAATTGTAAAAGTAACTTAATATCTGCCTCATATACTTTTGTTTTATTTAAAAA +TGCAAATCCGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAG +GCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGT +CTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTA +CTTGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCG +AGATCCCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAA +AAAAAAAAAATGCAAATCCTCAACCACAAATCGAAACAAGAACAACCCTCTGATGACTTC +CCTCCCTCTCTCTTTGTACAAAGAAGACTTTCTGCTGTCTGACTCTGACCACCTTGGTCT +ATTTTATGGAGCTCCAACCCTGCCTTGTTTCCTTCTCAGGCCATCTGTCCTGGTTGGCCT +CACTGTTGGAAATGCTCTTCTCAAGATGTTCACGTGGCTGGTTCTTTGTCATTCAGTCTC +AGTTCAAATACTCCCTCCTCCAGGAAGCCTTCCCTAACTTCCTAGGTGAAAGTGGTTCCC +TTCCCCTGAGTCACGATTATGGTTTCTTCAGTGTACTTATTAATGGCCAACACTGTCTCC +TTTATTGTTTGCTTATGAATTTAAAGTCTGTTAGCAGCACCTGCAGCTTTTAAAAGCCTC +CTTGTCTCTCTCTATTTTTTTTTTTTTTTTTTTGAGGCGGAGTTTCGCTCTTGTTGGCCA +GGCTGGAATGCAGTGATGCGATCTCGGCTCAGTGCAACCTCCACCTCTTGGGTTCAAGTG +ATTCTCCTGCCTCAGCCTCCTTAGTAGCTGAGACTACAGGCATGTGCCACCATGCTGGCT +AATTTTTGTATTTTTAGTAGAGACAGGGTTTCGTCATATTGGCCAAGCTGGTCTCGAACC +CCTGACCTCAGGTGATCCACCCATCTTGGCCTCCCAGATGCTGGGATTACAGGCGTGAGC +CACTGCGCCTGGCCTAATTGTCATTTTCGTTTTTTTGTTGAGACAGAGTTTCTGTCACCC +AGGCTGGAATGCAGTGGCACGATCTCAGCTCACTGCAGCCTCTGCCTCTTGGGTTCAATT +GATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGTGTGTGCCACCACACCCAG +CTAATTTTTTCATTTTTAGTAGAGACGGGGTTTCACCATGTTGGTCAGGCTTGTCTCGAA +CTCCTGACCTCAGGTGATCCGTCCAACTTGGCCTCCCAAAGTGCTGAGATTACAGGCATG +AGCTACCGTGCCCAGCTCTCAATTGTCACTTTTAGTGCATATTTTCTGGTTGTATAAAAG +CTCTCCCATGCAAGAGGGCTGATGTTATAACAGTCGATTATTATACTGTCCTGCATTTTC +ATCAGGTAAAGAAAGCTTTTCATGTTTCACTGAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/haps.fa.ref.fa new file mode 100644 index 00000000..0b99d97b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:51952383-51954993 +CTCTGTCTCAAAAAAAAAAAAGTCATTGATTGATCTCTTTCTGGTTTAACTGCTATTATTTAGTTTTATAGCATTACATTCAAGTTTTTATAGCATTACAATTCCTAGATTCTATTTTCAAATATTGATTTGCTTAATTTTTTTTTTTTTTTTGAGATGGGGTTTTGCTCTGTCGCCCAGGCTGGAGTGCAATGGCATGATCTTGGCTCACTGCAACCTCTGCCTCCTGGGTTCAGCCATTCTCCTGCCTCAGCCTCCCGAGTGGCTGGGACTACAGGTGCCCGCCACCACGCCTGGCTAATTTTTTTTTTTTATATTTTTAGTAGAGACGGGGTTTCACCATGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTAGGATTACAGGCTTGAGCCACCGCGCCTGGCCTTTAATATAATTTTTATGAAGACATTATTTCCACTTCATTGGGCTCTCTAGAATTAGATTGCATAAATACTGTAGTTTTATTTCAATAAAAAGTCAACTGTTATTTAAACCATGACTAAAGCTTGACATGAATAGAGACTTTAAAACAATAAACATTGCCAGACATGGTGGCACATGCCTGTAGTCTCAGCTACTCAAGAAACTGAGACAGGAGGATCTCCTGAGCCAAGGAGTTCCAGCCCAGCCTGGACAACATAGTGAGATCCCATCTCTTAAAAAAAAAAAAAAAAAGATTTGCTTAATTTTACTTTTACAATTTTTTCTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGATGGAGTCTTGCTCTGTTACCAGGCTGGAGTGCAGTGGTGTGATATCGGCTCCCTGCAACCTCTGCCTCCTGGGTTAAAGCAATTTTCCTGCCCCAGCCTCCCGAGTAGCTGGGACTACAGGCGCGCGTCACCACACCCAGCTAATTTTTGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGATGGTCTCAATCTCTTGATCTCGTGATCCGCCCACCTTGGCCTCCCAAAGTGCTGGAATTACAGGCGTGATCCGCCATAACCTGGCCTTCCTTCTTTTCTTTAAAAATTTTTTTCTGAGACAGAGTCTCACTCTGTTGCCCAGCCTGGAGTGCAGTGGCACAATCTCGGCTCACTGTAGCCTCCACCTTCTGGGTTCAAGTGATTCTCGTGCCTCAGCCTCCCGAGTAGCTGTGACTACAGGTGTGTGCCCTCATGCCTGGCTAATTTTTGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACCCTGGGCTCAAGTGTTCTGTCTGCCTCAGCCCCCCAAAGTGCTGGGATTACAGGCATGAGCCAAAGTGCCTGGCTAGAAAATTGTAAAAGTAACTTAATATCTGCCTCATATACTTTTGTTTTATTTAAAAATGCAAATCCTCAACCACAAATCGAAACAAGAACAACCCTCTGATGACTTCCCTCCCTCTCTCTTTGTACAAAGAAGACTTTCTGCTGTCTGACTCTGACCACCTTGGTCTATTTTATGGAGCTCCAACCCTGCCTTGTTTCCTTCTCAGGCCATCTGTCCTGGTTGGCCTCACTGTTGGAAATGCTCTTCTCAAGATGTTCACGTGGCTGGTTCTTTGTCATTCAGTCTCAGTTCAAATACTCCCTCCTCCAGGAAGCCTTCCCTAACTTCCTAGGTGAAAGTGGTTCCCTTCCCCTGAGTCACGATTATGGTTTCTTCAGTGTACTTATTAATGGCCAACACTGTCTCCTTTATTGTTTGCTTATGAATTTAAAGTCTGTTAGCAGCACCTGCAGCTTTTAAAAGCCTCCTTGTCTCTCTCTCTTTTTTTTTTTTTTTTTTTTTTTGAGGCGGAGTTTCGCTCTTGTTGGCCAGGCTGGAACGCAGTGATGCGATCTCGGCTCAGTGCAACCTCCACCTCTTGGGTTCAAGTGATTCTCCTGCCTCAGCCTCCTTAGTAGCTGAGACTACAGGCATGTGCCACCATGCTGGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCGTCATATTGGCCAAGCTGGTCTCGAACCCCTGACCTCAGGTGATCCACCCATCTTGGCCTCCCAGATGCTGGGATTACAGGCGTGAGCCACTGCGCCTGGCCTAATTGTCATTTTCGTTTTTTTGTTGAGACAGAGTTTCTGTCACCCAGGCTGGAATGCAGTGGCACGATCTCAGCTCACTGCAGCCTCTGCCTCTTGGGTTCAATTGATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGTGTGTGCCACCACACCCAGCTAATTTTTTCATTTTTAGTAGAGACGGGGTTTCACCATGTTGGTCAGGCTTGTCTCGAACTCCTGACCTCAGGTGATCCGTCCAACTTGGCCTCCCAAAGTGCTGAGATTACAGGCATGAGCTACCGTGCCCAGCTCTCAATTGTCACTTTTAGTGCATATTTTCTGGTTGTATAAAAGCTCTCCCATGCAAGAGGGCTGATGTTATAACAGTCGATTATTATACTGTCCTGCATTTTCATCAGGTAAAGAAAGCTTTTCATGTTTCACTGAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/msa.fa new file mode 100644 index 00000000..980a08bc --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/msa.fa @@ -0,0 +1,250 @@ +>ref_chr20_51952383_51954993 +ctctgtctcaaaaaaaaaaaagtcattgattgatctctttctggtttaactgctattatt +tagttttatagcattacattcaagtttttatagcattacaattcctagattctattttca +aatattgatttgcttaattttttttttttttttgagatggggttttgctctgtcgcccag +gctggagtgcaatggcatgatcttggctcactgcaacctctgcctcctgggttcagccat +tctcctgcctcagcctcccgagtggctgggactacaggtgcccgccaccacgcctggcta +attttttttttttatatttttagtagagacggggtttcaccatgttagccaggatggtct +cgatctcctgacctcgtgatccgcccgcctcggcctcccaaagtgctaggattacaggct +tgagccaccgcgcctggcctttaatataatttttatgaagacattatttccacttcattg +ggctctctagaattagattgcataaatactgtagttttatttcaataaaaagtcaactgt +tatttaaaccatgactaaagcttgacatgaatagagactttaaaacaataaacattgcca +gacatggtggcacatgcctgtagtctcagctactcaagaaactgagacaggaggatctcc +tgagccaaggagttccagcccagcctggacaacatagtgagatcccatctctt--aaaaa +aaaaaaaaaaaagatttgcttaattttacttttacaattttttcttttcttttttttttt +ttttttttttttttttttgagatggagtcttgctctgttaccaggctggagtgcagtggt +gtgatatcggctccctgcaacctctgcctcctgggttaaagcaattttcctgccccagcc +tcccgagtagctgggactacaggcgcgcgtcaccacacccagctaatttttgtattttta +gtagagatggggtttcaccatgttggccaggatggtctcaatctcttgatctcgtgatcc +gcccaccttggcctcccaaagtgctggaattacaggcgtgatccgccataacctggcctt +ccttcttttctttaaaaatttttttctgagacagagtctcactctgttgcccagcctgga +gtgcagtggcacaatctcggctcactgtagcctccaccttctgggttcaagtgattctcg +tgcctcagcctcccgagtagctgtgactacaggtgtgtgccctcatgcctggctaatttt +tgtatttttagtagagatggggtttcaccatgttggccaggctggtctcgaaccctgggc +tcaagtgttctgtctgcctcagccccccaaagtgctgggattacaggcatgagccaaagt +gcctggctagaaaattgtaaaagtaacttaatatctgcctcatatacttttgttttattt +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------aaaaatgcaaatcctcaaccacaaatcgaaacaagaacaaccctctgatg +acttccctccctctctctttgtacaaagaagactttctgctgtctgactctgaccacctt +ggtctattttatggagctccaaccctgccttgtttccttctcaggccatctgtcctggtt +ggcctcactgttggaaatgctcttctcaagatgttcacgtggctggttctttgtcattca +gtctcagttcaaatactccctcctccaggaagccttccctaacttcctaggtgaaagtgg +ttcccttcccctgagtcacgattatggtttcttcagtgtacttattaatggccaacactg +tctcctttattgtttgcttatgaatttaaagtctgttagcagcacctgcagcttttaaaa +gcctccttgtctctctctctttttttttttttttttttttttgaggcggagtttcgctct +tgttggccaggctggaacgcagtgatgcgatctcggctcagtgcaacctccacctcttgg +gttcaagtgattctcctgcctcagcctccttagtagctgagactacaggcatgtgccacc +atgctggctaatttttgtatttttagtagagacagggtttcgtcatattggccaagctgg +tctcgaacccctgacctcaggtgatccacccatcttggcctcccagatgctgggattaca +ggcgtgagccactgcgcctggcctaattgtcattttcgtttttttgttgagacagagttt +ctgtcacccaggctggaatgcagtggcacgatctcagctcactgcagcctctgcctcttg +ggttcaattgattctcctgcctcagcctcccaagtagctgggactacaggtgtgtgccac +cacacccagctaattttttcatttttagtagagacggggtttcaccatgttggtcaggct +tgtctcgaactcctgacctcaggtgatccgtccaacttggcctcccaaagtgctgagatt +acaggcatgagctaccgtgcccagctctcaattgtcacttttagtgcatattttctggtt +gtataaaagctctcccatgcaagagggctgatgttataacagtcgattattatactgtcc +tgcattttcatcaggtaaagaaagcttttcatgtttcactgag +>syndip_1_chr20:51952383-51954993 +ctctgtctcaaaaaaaaaaaagtcattgattgatctctttctggtttaactgctattatt +tagttttatagcattacattcaagtttttatagcattacaattcctagattctattttca +aatattgatttgcttaa--ttttttttttttttgagatggggttttgctctgtcgcccag +gctggagtgcaatggcatgatcttggctcactgcaacctctgcctcctgggttcagccat +tctcctgcctcagcctcccgagtggctgggactacaggtgcccgccaccacgcctggcta +attttttttttttatatttttagtagagacggggtttcaccatgttagccaggatggtct +cgatctcctgacctcgtgatccgcccgcctcggcctcccaaagtgctaggattacaggct +tgagccaccgcgcctggcctttaatataatttttatgaagacattatttccacttcattg +ggctctctagaattagattgcataaatactgtagttttatttcaataaaaagtcaactgt +tatttaaaccatgactaaagcttgacatgaatagagactttaaaacaataaacattgcca +gacatggtggcacatgcctgtagtctcagctactcaagaaactgagacaggaggatctcc +tgagccaaggagttccagcccagcctggacaacatagtgagatcccatctctt---aaaa +aaaaaaaaaaaagatttgcttaattttacttttacaattttttcttttcttttttttttt +ttttttttttttttttttgagatggagtcttgctctgttaccaggctggagtgcagtggt +gtgatatcggctccctgcaacctctgcctcctgggttaaagcaattttcctgccccagcc +tcccgagtagctgggactacaggcgcgcgtcaccacacccagctaatttttgtattttta +gtagagatggggtttcaccatgttggccaggatggtctcaatctcttgatctcgtgatcc +gcccaccttggcctcccaaagtgctggaattacaggcgtgatccgccataacctggcctt +ccttcttttctttaaaaatttttttctgagacagagtctcactctgttgcccagcctgga +gtgcagtggcacaatctcggctcactgtagcctccaccttctgggttcaagtgattctcg +tgcctcagcctcccgagtagctgtgactacaggtgtgtgccctcatgcctggctaatttt +tgtatttttagtagagatggggtttcaccatgttggccaggctggtctcgaaccctgggc +tcaagtgttctgtctgcctcagccccccaaagtgctgggattacaggcatgagccaaagt +gcctggctagaaaattgtaaaagtaacttaatatctgcctcatatacttttgttttattt +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------aaaaatgcaaatcctcaaccacaaatcgaaacaagaacaaccctctgatg +acttccctccctctctctttgtacaaagaagactttctgctgtctgactctgaccacctt +ggtctattttatggagctccaaccctgccttgtttccttctcaggccatctgtcctggtt +ggcctcactgttggaaatgctcttctcaagatgttcacgtggctggttctttgtcattca +gtctcagttcaaatactccctcctccaggaagccttccctaacttcctaggtgaaagtgg +ttcccttcccctgagtcacgattatggtttcttcagtgtacttattaatggccaacactg +tctcctttattgtttgcttatgaatttaaagtctgttagcagcacctgcagcttttaaaa +gcctccttgtctctctc----tatttttttttttttttttttgaggcggagtttcgctct +tgttggccaggctggaacgcagtgatgcgatctcggctcagtgcaacctccacctcttgg +gttcaagtgattctcctgcctcagcctccttagtagctgagactacaggcatgtgccacc +atgctggctaatttttgtatttttagtagagacagggtttcgtcatattggccaagctgg +tctcgaacccctgacctcaggtgatccacccatcttggcctcccagatgctgggattaca +ggcgtgagccactgcgcctggcctaattgtcattttcgtttttttgttgagacagagttt +ctgtcacccaggctggaatgcagtggcacgatctcagctcactgcagcctctgcctcttg +ggttcaattgattctcctgcctcagcctcccaagtagctgggactacaggtgtgtgccac +cacacccagctaattttttcatttttagtagagacggggtttcaccatgttggtcaggct +tgtctcgaactcctgacctcaggtgatccgtccaacttggcctcccaaagtgctgagatt +acaggcatgagctaccgtgcccagctctcaattgtcacttttagtgcatattttctggtt +gtataaaagctctcccatgcaagagggctgatgttataacagtcgattattatactgtcc +tgcattttcatcaggtaaagaaagcttttcatgtttcactgag +>syndip_2_chr20:51952383-51954993 +ctctgtctcaaaaaaaaaaaagtcattgattgatctctttctggtttaactgctattatt +tagttttatagcattacattcaagtttttatagcattacaattcctagattctattttca +aatattgatttgcttaa-tttttttttttttttgagatggggttttgctctgtcgcccag +gctggagtgcaatggcatgatcttggctcactgcaacctctgcctcctgggttcagccat +tctcctgcctcagcctcccgagtggctgggactacaggtgcccgccaccacgcctggcta +attttttttttttatatttttagtagagacggggtttcaccatgttagccaggatggtct +cgatctcctgacctcgtgatccgcccgcctcggcctcccaaagtgctaggattacaggct +tgagccaccgcgcctggcctttaatataatttttatgaagacattatttccacttcattg +ggctctctagaattagattgcataaatactgtagttttatttcaataaaaagtcaactgt +tatttaaaccatgactaaagcttgacatgaatagagactttaaaacaataaacattgcca +gacatggtggcacatgcctgtagtctcagctactcaagaaactgagacaggaggatctcc +tgagccaaggagttccagcccagcctggacaacatagtgagatcccatctcttaaaaaaa +aaaaaaaaaaaagatttgcttaattttacttttacaattttttcttttc--ttttttttt +ttttttttttttttttttgagatggagtcttgctctgttaccaggctggagtgcagtggt +gtgatatcggctccctgcaacctctgcctcctgggttaaagcaattttcctgccccagcc +tcccgagtagctgggactacaggcgcgcgtcaccacacccagctaatttttgtattttta +gtagagatggggtttcaccatgttggccaggatggtctcaatctcttgatctcgtgatcc +gcccaccttggcctcccaaagtgctggaattacaggcgtgatccgccataacctggcctt +ccttcttttctttaaaaatttttttctgagacagagtctcactctgttgcccagcctgga +gtgcagtggcacaatctcggctcactgtagcctccaccttctgggttcaagtgattctcg +tgcctcagcctcccgagtagctgtgactacaggtgtgtgccctcatgcctggctaatttt +tgtatttttagtagagatggggtttcaccatgttggccaggctggtctcgaaccctgggc +tcaagtgttctgtctgcctcagccccccaaagtgctgggattacaggcatgagccaaagt +gcctggctagaaaattgtaaaagtaacttaatatctgcctcatatacttttgttttattt +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------aaaaatgcaaatcctcaaccacaaatcgaaacaagaacaaccctctgatg +acttccctccctctctctttgtacaaagaagactttctgctgtctgactctgaccacctt +ggtctattttatggagctccaaccctgccttgtttccttctcaggccatctgtcctggtt +ggcctcactgttggaaatgctcttctcaagatgttcacgtggctggttctttgtcattca +gtctcagttcaaatactccctcctccaggaagccttccctaacttcctaggtgaaagtgg +ttcccttcccctgagtcacgattatggtttcttcagtgtacttattaatggccaacactg +tctcctttattgtttgcttatgaatttaaagtctgttagcagcacctgcagcttttaaaa +gcctccttgtctctctc--tatttttttttttttttttttttgaggcggagtttcgctct +tgttggccaggctggaacgcagtgatgcgatctcggctcagtgcaacctccacctcttgg +gttcaagtgattctcctgcctcagcctccttagtagctgagactacaggcatgtgccacc +atgctggctaatttttgtatttttagtagagacagggtttcgtcatattggccaagctgg +tctcgaacccctgacctcaggtgatccacccatcttggcctcccagatgctgggattaca +ggcgtgagccactgcgcctggcctaattgtcattttcgtttttttgttgagacagagttt +ctgtcacccaggctggaatgcagtggcacgatctcagctcactgcagcctctgcctcttg +ggttcaattgattctcctgcctcagcctcccaagtagctgggactacaggtgtgtgccac +cacacccagctaattttttcatttttagtagagacggggtttcaccatgttggtcaggct +tgtctcgaactcctgacctcaggtgatccgtccaacttggcctcccaaagtgctgagatt +acaggcatgagctaccgtgcccagctctcaattgtcacttttagtgcatattttctggtt +gtataaaagctctcccatgcaagagggctgatgttataacagtcgattattatactgtcc +tgcattttcatcaggtaaagaaagcttttcatgtttcactgag +>p:HG002_1_chr20:51952383-51954993 +ctctgtctcaaaaaaaaaaaagtcattgattgatctctttctggtttaactgctattatt +tagttttatagcattacattcaagtttttatagcattacaattcctagattctattttca +aatattgatttgcttaa-tttttttttttttttgagatggggttttgctctgtcgcccag +gctggagtgcaatggcatgatcttggctcactgcaacctccgcctcctgggttcagccat +tctcctgcctcagcctcccgagtggctgggactacaggtgcccgccaccacgcctggcta +attttttttttttatatttttagtagagacggggtttcaccatgttagccaggatggtct +cgatctcctgacctcgtgatccgcccgcctcggcctcccaaagtgctaggattacaggct +tgagccaccgcgcctggcctttaatataatttttatgaagacattatttccacttcattg +ggctctctagaattagattgcataaatactgtagttttatttcaataaaaagtcaactgt +tatttaaaccatgactaaagcttgacatgaatagagactttaaaacaataaacattgcca +gacatggtggcacatgcctgtagtctcagctactcaagaaactgagacaggaggatctcc +tgagccaaggagttccagcccagcctggacaacatagtgagatcccatctcttaaaaaaa +aaaaaaaaaaaagatttgcttaattttacttttacaattttttcttttc--ttttttttt +ttttttttttttttttttgagatggagtcttgctctgttaccaggctggagtgcagtggt +gtgatatcagctccctgcaacctctgcctcctgggttaaagcaattttcctgccccagcc +tcccgagtagctgggactacaggcgcgcgtcaccacacccagctaatttttgtattttta +gtagagatggggtttcaccatgttggccaggatggtctcaatctcttgatctcgtgatcc +gcccaccttggcctcccaaagtgctggaattacaggcgtgatccgccataacctggcctt +ccttctttcctttaaaaatttttttctgagacagagtctcactctgttgcccagcctgga +gtgcagtggcacaatctcggctcactgtagcctccaccttctgggttcaagtgattctcg +tgcctcagcctcccgagtagctgtgactacaggtgtgtgccctcatgcctggctaatttt +tgtatttttagtagagatggggtttcaccatgttggccaggctggtctcgaaccctgggc +tcaagtgttctgtctgcctcagccccccaaagtgctgggattacaggcatgagccaaagt +gcctggctagaaaattgtaaaagtaacttaatatctgcctcatatacttttgttttattt +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------aaaaatgcaaatcctcaaccacaaatcgaaacaagaacaaccctctgatg +acttccctccctctctctttgtacaaagaagactttctgctgtctgactctgaccacctt +ggtctattttatggagctccaaccctgccttgtttccttctcaggccatctgtcctggtt +ggcctcactgttggaaatgctcttctcaagatgttcacgtggctggttctttgtcattca +gtctcagttcaaatactccctcctccaggaagccttccctaacttcctaggtgaaagtgg +ttcccttcccctgagtcacgattatggtttcttcagtgtacttattaatggccaacactg +tctcctttattgtttgcttatgaatttaaagtctgttagcagcacctgcagcttttaaaa +gcctccttgtctctctc--tatttttttttttttttttttttgaggcggagtttcgctct +tgttggccaggctggaacgcagtgatgcgatctcggctcagtgcaacctccacctcttgg +gttcaagtgattctcctgcctcagcctccttagtagctgagactacaggcatgtgccacc +atgctggctaatttttgtatttttagtagagacagggtttcgtcatattggccaagctgg +tctcgaacccctgacctcaggtgatccacccatcttggcctcccagatgctgggattaca +ggcgtgagccactgcgcctggcctaattgtcattttcgtttttttgttgagacagagttt +ctgtcacccaggctggaatgcagtggcacgatctcagctcactgcagcctctgcctcttg +ggttcaattgattctcctgcctcagcctcccaagtagctgggactacaggtgtgtgccac +cacacccagctaattttttcatttttagtagagacggggtttcaccatgttggtcaggct +tgtctcgaactcctgacctcaggtgatccgtccaacttggcctcccaaagtgctgagatt +acaggcatgagctaccgtgcccagctctcaattgtcacttttagtgcatattttctggtt +gtataaaagctctcccatgcaagagggctgatgttataacagtcgattattatactgtcc +tgcattttcatcaggtaaagaaagcttttcatgtttcactgag +>p:HG002_2_chr20:51952383-51954993 +ctctgtctcaaaaaaaaaaaagtcattgattgatctctttctggtttaactgctattatt +tagttttatagcattacattcaagtttttatagcattacaattcctagattctattttca +aatattgatttgcttaa--ttttttttttttttgagatggggttttgctctgtcgcccag +gctggagtgcaatggcatgatcttggctcactgcaacctccgcctcctgggttcagccat +tctcctgcctcagcctcccgagtggctgggactacaggtgcccgccaccacgcctggcta +attttttttttttatatttttagtagagacggggtttcaccatgttagccaggatggtct +cgatctcctgacctcgtgatccgcccgcctcggcctcccaaagtgctaggattacaggct +tgagccaccgcgcctggcctttaatataatttttatgaagacattatttccacttcattg +ggctctctagaattagattgcataaatactgtagttttatttcaataaaaagtcaactgt +tatttaaaccatgactaaagcttgacatgaatagagactttaaaacaataaacattgcca +gacatggtggcacatgcctgtagtctcagctactcaagaaactgagacaggaggatctcc +tgagccaaggagttccagcccagcctggacaacatagtgagatcccatctctt---aaaa +aaaaaaaaaaaagatttgcttaattttacttttacaattttttcttttcttttttttttt +ttttttttttttttttttgagatggagtcttgctctgttaccaggctggagtgcagtggt +gtgatatcggctccctgcaacctctgcctcctgggttaaagcaattttcctgccccagcc +tcccgagtagctgggactacaggcgcgcgtcaccacacccagctaatttttgtattttca +gtagagatggggtttcaccatgttggccaggatggtctcaatctcttgatctcgtgatcc +gcccaccttggcctcccaaagtgctggaattacaggcgtgatccgccataacctggcctt +ccttcttttctttaaaaatttttttctgagacagagtctcactctgttgcccagcctgga +gtgcagtggcacaatctcggctcactgtagcctccaccttctgggttcaagtgattctcg +tgcctcagcctcccgagtagctgtgactacaggtgtgtgccctcatgcctggctaatttt +tgtatttttagtagagatggggtttcaccatgttggccaggctggtctcgaaccctgggc +tcaagtgttctgtctgcctcagccccccaaagtgctgggattacaggcatgagccaaagt +gcctggctagaaaattgtaaaagtaacttaatatctgcctcatatacttttgttttattt +aaaaatgcaaatccggccgggcgcggtggctcacgcctgtaatcccagcactttgggagg +ccgaggcgggcggatcacgaggtcaggagatcgagaccatcccggctaaaacggtgaaac +cccgtctctactaaaaatacaaaaaattagccgggcgtggtggcgggcgcctgtagtccc +agctacttgggaggctgaggcaggagaatggcgtgaacccgggaggcggagcttgcagtg +agccgagatcccgccactgcactccagcctgggcgacagagcgagactccgtctcaaaaa +aaaaaaaaaaaaaaatgcaaatcctcaaccacaaatcgaaacaagaacaaccctctgatg +acttccctccctctctctttgtacaaagaagactttctgctgtctgactctgaccacctt +ggtctattttatggagctccaaccctgccttgtttccttctcaggccatctgtcctggtt +ggcctcactgttggaaatgctcttctcaagatgttcacgtggctggttctttgtcattca +gtctcagttcaaatactccctcctccaggaagccttccctaacttcctaggtgaaagtgg +ttcccttcccctgagtcacgattatggtttcttcagtgtacttattaatggccaacactg +tctcctttattgtttgcttatgaatttaaagtctgttagcagcacctgcagcttttaaaa +gcctccttgtctctctc----tatttttttttttttttttttgaggcggagtttcgctct +tgttggccaggctggaatgcagtgatgcgatctcggctcagtgcaacctccacctcttgg +gttcaagtgattctcctgcctcagcctccttagtagctgagactacaggcatgtgccacc +atgctggctaatttttgtatttttagtagagacagggtttcgtcatattggccaagctgg +tctcgaacccctgacctcaggtgatccacccatcttggcctcccagatgctgggattaca +ggcgtgagccactgcgcctggcctaattgtcattttcgtttttttgttgagacagagttt +ctgtcacccaggctggaatgcagtggcacgatctcagctcactgcagcctctgcctcttg +ggttcaattgattctcctgcctcagcctcccaagtagctgggactacaggtgtgtgccac +cacacccagctaattttttcatttttagtagagacggggtttcaccatgttggtcaggct +tgtctcgaactcctgacctcaggtgatccgtccaacttggcctcccaaagtgctgagatt +acaggcatgagctaccgtgcccagctctcaattgtcacttttagtgcatattttctggtt +gtataaaagctctcccatgcaagagggctgatgttataacagtcgattattatactgtcc +tgcattttcatcaggtaaagaaagcttttcatgtttcactgag diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/msa.fa.fai new file mode 100644 index 00000000..64df8620 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_51952383_51954993 2923 29 60 61 +syndip_1_chr20:51952383-51954993 2923 3035 60 61 +syndip_2_chr20:51952383-51954993 2923 6041 60 61 +p:HG002_1_chr20:51952383-51954993 2923 9048 60 61 +p:HG002_2_chr20:51952383-51954993 2923 12055 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/output.vcf.gz new file mode 100644 index 00000000..d37d9617 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/output.vcf.gz.tbi new file mode 100644 index 00000000..f069aa5d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:51952483-51954893/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/base.vcf.gz new file mode 100644 index 00000000..9343b7b1 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/base.vcf.gz.tbi new file mode 100644 index 00000000..bfbfaed9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/comp.vcf.gz new file mode 100644 index 00000000..25602731 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/comp.vcf.gz.tbi new file mode 100644 index 00000000..b3d43f55 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/haps.fa new file mode 100644 index 00000000..e561c307 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/haps.fa @@ -0,0 +1,102 @@ +>ref_chr20_53203887_53204574 +CATACCACATGGGGCTACTAAGCCCTTCAAATGTGACTGGTCCAAATTAAAATATACTGTAAGTATAAAACACACTGAACTTGAAAGGCTTAGTCCAAAAACCGTAGTGCACAATATCTCCTTCATTTTTATAATATGATACTATTATATCATAATTTTATAATATACTATTATATCATATTATATGATACTATTTATATCATCATATGATGATATGATATACTATATCATCATATGATGATATGATATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATTATATCATAATATGATATAATATTTTGGACATACTAGGTTAAATAAGATATAGTTATATAAATCAATTTCACTTATTTCTTTCTCATTCTTTAATGTGACTACTGAAGCATATGAAATTCCATGCATAGCTGACATTCTACTTCTATTG +>syndip_1_chr20:53203887-53204574 +CATACCACATGGGGCTACTAAGCCCTTCAAATGTGACTGGTCCAAATTAAAATATACTGT +AAGTATAAAACACACTGAACTTGAAAGGCTTAGTCCAAAAACCGTAGTGCACAATATCTC +CTTCATTTTTATAATATGATACTATTATATCATAATTTTATAATATACTATTATATCATA +TTATATGATACTATTTATATCATCATATGATGATATACTATTATATCATCATATGATGAT +ATACTATTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACT +ATATCATCATATGATGATATACTATATCATCATATGATGATATGATACTATATCATCATA +TGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATA +TGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTA +TATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCA +TATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGA +TATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATAC +TATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCAT +CACATGATGATATGATACTATATCATCACATGATGATATGATACTATATCATCACATGAT +GATATGATACTATATCATCACATGATGATATGATACTATATCATCACATGATGATATGAT +ACTATATCATCACATGATGATATGATACTATATCATCACATGATGATATGATACTATATC +ATCACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATC +ATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCA +TCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATAT +CATCATATAACATGATGATATGATACTATTATATCATAATATGATATAATATTTTGGACA +TACTAGGTTAAATAAGATATAGTTATATAAATCAATTTCACTTATTTCTTTCTCATTCTT +TAATGTGACTACTGAAGCATATGAAATTCCATGCATAGCTGACATTCTACTTCTATTG +>syndip_2_chr20:53203887-53204574 +CATACCACATGGGGCTACTAAGCCCTTCAAATGTGACTGGTCCAAATTAAAATATACTGT +AAGTATAAAACACACTGAACTTGAAAGGCTTAGTCCAAAAACCGTAGTGCACAATATCTC +CTTCATTTTTATAATATGATACTATTATATCATAATTTTATAATATACTATTATATCATA +TTATATGATACTATTTATATCATCATATGATGATATACTATTATATCATCATATGATGAT +ATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACT +ATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATC +ATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATG +ATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATA +CTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCA +TCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGA +TGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGA +TACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATAT +CATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATAT +GATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATAT +GATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTAT +ATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCAT +ATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGAT +ATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACT +ATATCATAACATGATGATATGATACTATATCATAACATGATGATATGATACTATATCATC +ATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCA +TCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATAT +CATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTAT +ATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACT +ATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATA +CTATTATATCATAATATGATATAATATTTTGGACATACTAGGTTAAATAAGATATAGTTA +TATAAATCAATTTCACTTATTTCTTTCTCATTCTTTAATGTGACTACTGAAGCATATGAA +ATTCCATGCATAGCTGACATTCTACTTCTATTG +>p:HG002_1_chr20:53203887-53204574 +CATACCACATGGGGCTACTAAGCCCTTCAAATGTGACTGGTCCAAATTAAAATATACTGT +AAGTATAAAACACACTGAACTTGAAAGGCTTAGTCCAAAAACCGTAGTGCACAATATCTC +CTTCATTTTTATAATATGATACTATTATATCATAATTTTATAATATACTATTATATCATA +TTATATGATACTATTTATATCATCATATGATGATATACTATTATATCATCATATGATGAT +ATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACT +ATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATC +ATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATG +ATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATA +CTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCA +TCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGA +TGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGA +TACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATAT +CATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATAT +GATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATAT +GATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTAT +ATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCAT +ATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGAT +ATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACT +ATATCATAACATGATGATATGATACTATATCATAACATGATGATATGATACTATATCATC +ATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCA +TCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATAT +CATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTAT +ATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACT +ATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATA +CTATTATATCATAATATGATATAATATTTTGGACATACTAGGTTAAATAAGATATAGTTA +TATAAATCAATTTCACTTATTTCTTTCTCATTCTTTAATGTGACTACTGAAGCATATGAA +ATTCCATGCATAGCTGACATTCTACTTCTATTG +>p:HG002_2_chr20:53203887-53204574 +CATACCACATGGGGCTACTAAGCCCTTCAAATGTGACTGGTCCAAATTAAAATATACTGT +AAGTATAAAACACACTGAACTTGAAAGGCTTAGTCCAAAAACCGTAGTGCACAATATCTC +CTTCATTTTTATAATATGATACTATTATATCATAATTTTATAATATACTATTATATCATA +TTATATGATACTATTTATATCATCATATGATGATATACTATTATATCATCATATGATGAT +ATACTATTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACT +ATATCATCATATGATGATATACTATATCATCATATGATGATATGATACTATATCATCATA +TGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATA +TGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTA +TATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCA +TATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGA +TATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATAC +TATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCAT +CACATGATGATATGATACTATATCATCACATGATGATATGATACTATATCATCACATGAT +GATATGATACTATATCATCACATGATGATATGATACTATATCATCACATGATGATATGAT +ACTATATCATCACATGATGATATGATACTATATCATCACATGATGATATGATACTATATC +ATCACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATC +ATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCA +TCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATAT +CATCATATAACATGATGATATGATACTATTATATCATAATATGATATAATATTTTGGACA +TACTAGGTTAAATAAGATATAGTTATATAAATCAATTTCACTTATTTCTTTCTCATTCTT +TAATGTGACTACTGAAGCATATGAAATTCCATGCATAGCTGACATTCTACTTCTATTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/haps.fa.ref.fa new file mode 100644 index 00000000..72153792 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:53203887-53204574 +CATACCACATGGGGCTACTAAGCCCTTCAAATGTGACTGGTCCAAATTAAAATATACTGTAAGTATAAAACACACTGAACTTGAAAGGCTTAGTCCAAAAACCGTAGTGCACAATATCTCCTTCATTTTTATAATATGATACTATTATATCATAATTTTATAATATACTATTATATCATATTATATGATACTATTTATATCATCATATGATGATATGATATACTATATCATCATATGATGATATGATATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATTATATCATAATATGATATAATATTTTGGACATACTAGGTTAAATAAGATATAGTTATATAAATCAATTTCACTTATTTCTTTCTCATTCTTTAATGTGACTACTGAAGCATATGAAATTCCATGCATAGCTGACATTCTACTTCTATTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/msa.fa new file mode 100644 index 00000000..3eb02a0b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/msa.fa @@ -0,0 +1,140 @@ +>ref_chr20_53203887_53204574 +cataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgt +aagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctc +cttcatttttataatatgatactattatatcataattttataatatactattatatcata +ttatatgatactatttatatcatcatatgatgatatgat--------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------atactatatcatcatatgatgatatgatatactatatcatcatatgatgat +atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact +atatcatc---------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------atatgatgatatgatactat +atcatcat-----atgatgatatgatactatatcatcatataacatgatgatatgatact +atatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgata +ctatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatga +tactattatatcataatatgatataatattttggacatactaggttaaataagatatagt +tatataaatcaatttcacttatttctttctcattctttaatgtgactactgaagcatatg +aaattccatgcatagctgacattctacttctattg +>syndip_1_chr20:53203887-53204574 +cataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgt +aagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctc +cttcatttttataatatgatactattatatcataattttataatatactattatatcata +ttatatgatactatttatatcatcatatgatgatatactattatatcatcatatgatgat +atactattatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact +atatcatcatatgatgat---atactatatcatcatatgatgatatgatactatatcatc +atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg +atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata +ctatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatca +tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga +tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga +tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat +catcacatgatgatatgatactatatcatcacatgatgatatgatactatatcatcacat +gatgatatgatactatatcatcacatgatgatatg--atactatatcatcacatgatgat +atgatactatatcatcacatgatgatatgatactatatcatcacatgatgatatgatact +atatcatc---------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------acatgatgatatgatactat +atcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgatact +atatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgata +ctatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatga +tactattatatcataatatgatataatattttggacatactaggttaaataagatatagt +tatataaatcaatttcacttatttctttctcattctttaatgtgactactgaagcatatg +aaattccatgcatagctgacattctacttctattg +>syndip_2_chr20:53203887-53204574 +cataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgt +aagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctc +cttcatttttataatatgatactattatatcataattttataatatactattatatcata +ttatatgatactatttatatcatcatatgatgatatactattatatcatcatatgatgat +atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact +atatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatc +atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg +atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata +ctatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatca +tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga +tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga +tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat +catcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatat +gatgatatgatactatatcatcatatgatgatatg--atactatatcatcatatgatgat +atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact +atatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatc +atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg +atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata +ctatatcataacatgatgatatgatactatatcataacatgatgatatgatactatatca +tcatataacatgatgatatgatactatatcatcatataacatgatgatatgatactatat +catcatataacatgatgatatgatactatatcatcatataacatgatgatatgatactat +atcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgatact +atatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgata +ctatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatga +tactattatatcataatatgatataatattttggacatactaggttaaataagatatagt +tatataaatcaatttcacttatttctttctcattctttaatgtgactactgaagcatatg +aaattccatgcatagctgacattctacttctattg +>p:HG002_1_chr20:53203887-53204574 +cataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgt +aagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctc +cttcatttttataatatgatactattatatcataattttataatatactattatatcata +ttatatgatactatttatatcatcatatgatgatatactattatatcatcatatgatgat +atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact +atatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatc +atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg +atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata +ctatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatca +tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga +tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga +tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat +catcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatat +gatgatatgatactatatcatcatatgatgatatg--atactatatcatcatatgatgat +atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact +atatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatc +atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg +atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata +ctatatcataacatgatgatatgatactatatcataacatgatgatatgatactatatca +tcatataacatgatgatatgatactatatcatcatataacatgatgatatgatactatat +catcatataacatgatgatatgatactatatcatcatataacatgatgatatgatactat +atcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgatact +atatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgata +ctatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatga +tactattatatcataatatgatataatattttggacatactaggttaaataagatatagt +tatataaatcaatttcacttatttctttctcattctttaatgtgactactgaagcatatg +aaattccatgcatagctgacattctacttctattg +>p:HG002_2_chr20:53203887-53204574 +cataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgt +aagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctc +cttcatttttataatatgatactattatatcataattttataatatactattatatcata +ttatatgatactatttatatcatcatatgatgatatactattatatcatcatatgatgat +atactattatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact +atatcatcatatgatgat---atactatatcatcatatgatgatatgatactatatcatc +atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg +atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata +ctatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatca +tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga +tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga +tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat +catcacatgatgatatgatactatatcatcacatgatgatatgatactatatcatcacat +gatgatatgatactatatcatcacatgatgatatg--atactatatcatcacatgatgat +atgatactatatcatcacatgatgatatgatactatatcatcacatgatgatatgatact +atatcatc---------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------acatgatgatatgatactat +atcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgatact +atatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgata +ctatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatga +tactattatatcataatatgatataatattttggacatactaggttaaataagatatagt +tatataaatcaatttcacttatttctttctcattctttaatgtgactactgaagcatatg +aaattccatgcatagctgacattctacttctattg diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/msa.fa.fai new file mode 100644 index 00000000..77baaaf4 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_53203887_53204574 1595 29 60 61 +syndip_1_chr20:53203887-53204574 1595 1685 60 61 +syndip_2_chr20:53203887-53204574 1595 3341 60 61 +p:HG002_1_chr20:53203887-53204574 1595 4998 60 61 +p:HG002_2_chr20:53203887-53204574 1595 6655 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/output.vcf.gz new file mode 100644 index 00000000..c47b5db9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/output.vcf.gz.tbi new file mode 100644 index 00000000..03b61085 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:53203987-53204474/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/base.vcf.gz new file mode 100644 index 00000000..6c36716b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/base.vcf.gz.tbi new file mode 100644 index 00000000..317dc01d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/comp.vcf.gz new file mode 100644 index 00000000..e187e154 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/comp.vcf.gz.tbi new file mode 100644 index 00000000..a6793101 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/haps.fa new file mode 100644 index 00000000..95e1cd15 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/haps.fa @@ -0,0 +1,138 @@ +>ref_chr20_55624382_55625908 +ATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTCAATCAGTGAGGTGGAGGCTGCAGTGGGCCAAGATCATGCGATTGCACCCCAGCCTGGGTAAGAAAGTGAGGTCCTGTCTCCCTGTCTCTCATATATATACATAACTAAAATAATATATAGTAATATATGTTATATATTATACTATATTATATAATATACTATAATATATATAATATAGTATATATTGTATATAATATAGTATATATAATATAATAGTATATAATATAGTATAGATAGTATAGAATATATAGTATATACCTAGTATACTATATTATATAGTATAACTATTATAATATTTATAGTATATTATACTATATAATACAGTATACTGTATTATATACTATAATCTACTAGATTATAATATACTATATAATCAGTATACTATATTGTATAGTATAATATAGTATTATATTATAGTAATATATTATAAAGTATTATAGTAATATAGTATAATATACTATACATTATATAGTATAGTATATTATATAGTATACTATATATAAGTATATTTAATAGTATATTGTATATAGTAATTATATATAGTATATATAATATACAATGTATAGTATATTATAGTATACTATACGATACTGTAGTATAGTATGCTATATAGTATACTATATACGACAGTATCATATAGTATACTACAAAATATATAGTATAGCATAGTATACTATATAATATACTATATTATATATACTATATTATATATACTATACTATATTATATATACTATATTATATATACTATACTATACATAAAATACTATATATAGTATATTATATATAGTATACTATATATAGTATATAATATATAGTATACTATATATACTATATATAGTATACTATATATACTATATATAGTATACTATATATCATATATAGTATTATATACAGTATACTATATATAATATAGTATACTATACTATAATATACTATTTGTTATAATTATCTAGTATAGTATACTATATATACTATATTATATAGTATATAGTATATATAGTATATAGTATATATACTATATACTATATATACTATATACTATACTATATAATATATATACTAATATATTGTATACTATACTATGCTATAGTATGCTATATACTACACTATAGTATACTGTGTACTATACTATAGTATACAGTATACTATATACTATACTATAGTATAGTATACTATAGTATAGTATACTATATACTATAGTATAGTATATAGTATACTGTATACTATAGTATAGTATACTATATACTATACTATACTATAGTATACTCTATAGTATATAAAGACATATATATAGTCTTCAAAATGAAGATCCTGTATCCTATATATATATATAACTTCAAAAGTGAGATACATATATATGATGTAGAAACTTTAGAATATACAAAATTGTCTTCTTCAGGATAAGAAAATCCTGATATTCAGCCTAACCTCCACTGACTGTAAAGGAAGAATGGGTTTCACTTTCAGGGAAGGTCACCTTCATCC +>syndip_1_chr20:55624382-55625908 +ATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTCAATCAGTGAGGTGGAGGCTG +CAGTGGGCCAAGATCATGCGATTGCACCCCAGCCTGGGTAAGAAAGTGAGGTCCTGTCTC +CCTGTCTCTCATATATATACATAACTAAAATAATATATAGTAATATATGTTATATATTAT +ACTATATTATATAATATACTATAATATATATAATATAGTATATATTGTATATAATATAGT +ATATATAATATAATAGTATATAATATAGTATAGATAGTATAGAATATATAGTATATACCT +AGTATACTATATTATATAGTATAACTATTATAATATTTATAGTATATTATACTATATAAT +ACAGTATACTGTATTATATACTATAATCTACTAGATTATAATATACTATATAATCAGTAT +ACTATATTATATAGTATAGTATAATATAGTATTATATTATAGTAATATATTATAAAGTAT +TATAGTAATATAGTATAATATACTATACATTATATAGTATAGTATATTATATAGTATACT +ATATATAAGTATATATAATAGTATATTGTATATAGTAATTATATATAGTATATATAATAT +ACAATGTATAGTATATTATAGTATACTATACGATACTGTAGTATAGTATGCTATATAGTA +TACTATATACGACAGTATCATATAGTATACTACAAAATATATAGTATAGCATAGTATACT +ATATAATATACTATATTATATATACTATATTATATATACTACACTATATTATATATACTA +TATTATATATACTATACTATACATAAAATACTATATATAGTATATTATATATAGTATACT +ATATATAGTATATATAGTATACTATATATACTATATATAGTATACTATATAGTATACTAT +ATATAGTATATATAGTATACTATATATAGTATACTATATATAGTATATATATAGTATACT +ATATATAGTATACTATATATAGTATATATAGTATACTATATATAGTATACTATATATAGT +ATATATAGTATACTATATATAGTATACTATATATAGTATATATAGTATACTATATATAGT +ATACTATATATAGTATATATAGTATACTATATATAGTATATATAGTATACTATATATAGT +ATATATAGTATACTATATATACTATATATACTATATATAGTATACTATATATAGTATATA +TAGTATACTATATATCATATATAGTATTATATACAGTATACTATATATAATATAGTATAC +TATACTATAATATACTATTTGTTATAATTATCTAGTATAGTATACTATATATACTATATT +ATATAGTATATAGTATATATAGTATATTTATAGTATATATACTATATACTATATATACTA +TATACTATAATATATACTATATATACTAAATAAATATAATATACTTATTTAAATATATTT +AAATAAATATAAAATATTTAAATATAATTACTTAAATATATATTTAAAATATTTAATAAA +CATATATTTAAATATTTATTTAATATTTAAATATTAAATATATATAATTAATATAATTAT +ATATATATTATATACTATATATTATATATACTATATACTATATATAGTATACTAATATAA +TATACTATATATACTATATATAATATACTATATATAGTATATATAGTATAGTATACTATA +ATATACTATATTATATAATATAGTATACTATATATTGTATACTATACTATGCTATAGTAT +GCTATATACTACACTATAGTATACTGTATACTATACTATACAGTATACTGTATACTATAC +TATAGTATACAGTATACTATATACTATTGTATAGTATATAGTATACTGTATACTATAGTA +TAGTATACTATATACTATACTATACTATAGTATACTCTATAGTATATAAAGACATATATA +TAGTCTTCAAAATGAAGATCCTGTATCCTATATATATATATAACTTCAAAAGTGAGATAC +ATATATATGATGTAGAAACTTTAGAATATACAAAATTGTCTTCTTCAGGATAAGAAAATC +CTGATATTCAGCCTAACCTCCACTGACTGTAAAGGAAGAATGGGTTTCACTTTCAGGGAA +GGTCACCTTCATCC +>syndip_2_chr20:55624382-55625908 +ATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTCAATCAGTGAGGTGGAGGCTG +CAGTGGGCCAAGATCATGCGATTGCACCCCAGCCTGGGTAAGAAAGTGAGGTCCTGTCTC +CCTGTCTCTCATATATATACATAACTAAAATAATATATAGTAATATATGTTATATATTAT +ACTATATTATATAATATACTATAATATATATAATATAGTATATATTGTATATAATATAGT +ATATATAATATAATAGTATATAATATAGTATAGATAGTATAGAATATATAGTATATACCT +AGTATACTATATTATATAGTATAACTATTATAATATTTATAGTATATTATACTATATAAT +ACAGTATACTGTATTATATACTATAATCTACTAGATTATAATATACTATATAATCAGTAT +ACTATATTATATAGTATAGTATAATATAGTATTATATTATAGTAATATATTATAAAGTAT +TATAGTAATATAGTATAATATACTATACATTATATAGTATACTATATATAAGTATATATA +ATAGTATATTGTATATAGTAATTATATATAGTATATATAATATACAATGTATAGTATATT +ATAGTATACTATACGATACTGTAGTATAGTATGCTATATAGTATACTATATACGACAGTA +TCATATAGTATACTACAAAATATATAGTATAGCATAGTATACTATATAATATACTATATT +ATATATACTATATTATATATACTATACTATACATAAAATACTATATATAGTATATTATAT +ATAGTATACTATATATAGTATATATAGTATACTATATATCATATATAGTATTATATACAG +TATACTATATATAATATAGTATACTATACTATAATATACTATTTGTTATAATTATCTAGT +ATAGTATACTATATATACTATATTATATAGTATATATAGTATATTTATAGTATATATACT +ATATACTATATATACTATATAATATAATATATAATATATATACTAAATAAATATACTTAT +TTAAATATATTTAAATAAATATATTAAATATTTAAATATAATTACTTAAATATATATTTA +AAATATTTAATAAACATATATTTAAATATTTATTTAATATTTAAATATTAAATATATATA +ATTAATATAATTATATATATATTATATACTATATATTATATATACTATATAATATACTAT +ATATAGTATACTAATATAATATACTATATATACTATATATAATATACTATATATAGTATA +TATAGTATAGTATACTATAATATACTATATATAGTATATATAGTATAGTATACTATAATA +TACTATATATAGTATATAGTATACTATATATTGTATACTATACTATGCTATAGTATGCTA +TATACTACACTATAGTATACTGTATACTATACTATAGTATACAGTATACTATATACTATA +CTATAGTATAGTATACTATAGTATAGTATACTATATACTATACTATAGTATATAGTATAC +TGTATACTATAGTATACTATATACTATACTATACTATAGTATACTCTATAGTATATAAAG +ACATATATATAGTCTTCAAAATGAAGATCCTGTATCCTATATATATATATAACTTCAAAA +GTGAGATACATATATATGATGTAGAAACTTTAGAATATACAAAATTGTCTTCTTCAGGAT +AAGAAAATCCTGATATTCAGCCTAACCTCCACTGACTGTAAAGGAAGAATGGGTTTCACT +TTCAGGGAAGGTCACCTTCATCC +>p:HG002_1_chr20:55624382-55625908 +ATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTCAATCAGTGAGGTGGAGGCTG +CAGTGGGCCAAGATCATGCGATTGCACCCCAGCCTGGGTAAGAAAGTGAGGTCCTGTCTC +CCTGTCTCTCATATATATACATAACTAAAATAATATATAGTAATATATGTTATATATTAT +ACTATATTATATAATATACTATAATATATATAATATAGTATATATTGTATATAATATAGT +ATATATAATATAATAGTATATAATATAGTATAGATAGTATAGAATATATAGTATATACCT +AGTATACTATATTATATAGTATAACTATTATAATATTTATAGTATATTATACTATATAAT +ACAGTATACTGTATTATATACTATAATCTACTAGATTATAATATACTATATAATCAGTAT +ACTATATTATATAGTATAGTATAATATAGTATTATATTATAGTAATATATTATAAAGTAT +TATAGTAATATAGTATAATATACTATACATTATATAGTATACTATATATAAGTATATATA +ATAGTATATTGTATATAGTAATTATATATAGTATATATAATATACAATGTATAGTATATT +ATAGTATACTATACGATACTGTAGTATAGTATGCTATATAGTATACTATATACGACAGTA +TCATATAGTATACTACAAAATATATAGTATAGCATAGTATACTATATAATATACTATATT +ATATATACTATATTATATATACTATACTATACATAAAATACTATATATAGTATATTATAT +ATAGTATACTATATATAGTATATATAGTATACTATATATCATATATAGTATTATATACAG +TATACTATATATAATATAGTATACTATACTATAATATACTATTTGTTATAATTATCTAGT +ATAGTATACTATATATACTATATTATATAGTATATATAGTATATTTATAGTATATATACT +ATATACTATATATACTATATAATATAATATATAATATATATACTAAATAAATATACTTAT +TTAAATATATTTAAATAAATATATTAAATATTTAAATATAATTACTTAAATATATATTTA +AAATATTTAATAAACATATATTTAAATATTTATTTAATATTTAAATATTAAATATATATA +ATTAATATAATTATATATATATTATATACTATATATTATATATACTATATAATATACTAT +ATATAGTATACTAATATAATATACTATATATACTATATATAATATACTATATATAGTATA +TATAGTATAGTATACTATAATATACTATATATAGTATATATAGTATAGTATACTATAATA +TACTATATATAGTATATAGTATACTATATATTGTATACTATACTATGCTATAGTATGCTA +TATACTACACTATAGTATACTGTATACTATACTATAGTATACAGTATACTATATACTATA +CTATAGTATAGTATACTATAGTATAGTATACTATATACTATACTATAGTATATAGTATAC +TGTATACTATAGTATACTATATACTATACTATACTATAGTATACTCTATAGTATATAAAG +ACATATATATAGTCTTCAAAATGAAGATCCTGTATCCTATATATATATATAACTTCAAAA +GTGAGATACATATATATGATGTAGAAACTTTAGAATATACAAAATTGTCTTCTTCAGGAT +AAGAAAATCCTGATATTCAGCCTAACCTCCACTGACTGTAAAGGAAGAATGGGTTTCACT +TTCAGGGAAGGTCACCTTCATCC +>p:HG002_2_chr20:55624382-55625908 +ATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTCAATCAGTGAGGTGGAGGCTG +CAGTGGGCCAAGATCATGCGATTGCACCCCAGCCTGGGTAAGAAAGTGAGGTCCTGTCTC +CCTGTCTCTCATATATATACATAACTAAAATAATATATAGTAATATATGTTATATATTAT +ACTATATTATATAATATACTATAATATATATAATATAGTATATATTGTATATAATATAGT +ATATATAATATAATAGTATATAATATAGTATAGATAGTATAGAATATATAGTATATACCT +AGTATACTATATTATATAGTATAACTATTATAATATTTATAGTATATTATACTATATAAT +ACAGTATACTGTATTATATACTATAATCTACTAGATTATAATATACTATATAATCAGTAT +ACTATATTATATAGTATAGTATAATATAGTATTATATTATAGTAATATATTATAAAGTAT +TATAGTAATATAGTATAATATACTATACATTATATAGTATAGTATATTATATAGTATACT +ATATATAAGTATATATAATAGTATATTGTATATAGTAATTATATATAGTATATATAATAT +ACAATGTATAGTATATTATAGTATACTATACGATACTGTAGTATAGTATGCTATATAGTA +TACTATATACGACAGTATCATATAGTATACTACAAAATATATAGTATAGCATAGTATACT +ATATAATATACTATATTATATATACTATATTATATATACTACACTATATTATATATACTA +TATTATATATACTATACTATACATAAAATACTATATATAGTATATTATATATAGTATACT +ATATATAGTATATATAGTATACTATATATACTATATATAGTATACTATATAGTATACTAT +ATATAGTATATATAGTATACTATATATAGTATACTATATATAGTATATATATAGTATACT +ATATATAGTATACTATATATAGTATATATAGTATACTATATATAGTATACTATATATAGT +ATATATAGTATACTATATATAGTATACTATATATAGTATATATAGTATACTATATATAGT +ATACTATATATAGTATATATAGTATACTATATATAGTATATATAGTATACTATATATAGT +ATATATAGTATACTATATATACTATATATACTATATATAGTATACTATATATAGTATATA +TAGTATACTATATATCATATATAGTATTATATACAGTATACTATATATAATATAGTATAC +TATACTATAATATACTATTTGTTATAATTATCTAGTATAGTATACTATATATACTATATT +ATATAGTATATAGTATATATAGTATATTTATAGTATATATACTATATACTATATATACTA +TATACTATAATATATACTATATATACTAAATAAATATAATATACTTATTTAAATATATTT +AAATAAATATAAAATATTTAAATATAATTACTTAAATATATATTTAAAATATTTAATAAA +CATATATTTAAATATTTATTTAATATTTAAATATTAAATATATATAATTAATATAATTAT +ATATATATTATATACTATATATTATATATACTATATACTATATATAGTATACTAATATAA +TATACTATATATACTATATATAATATACTATATATAGTATATATAGTATAGTATACTATA +ATATACTATATTATATAATATAGTATACTATATATTGTATACTATACTATGCTATAGTAT +GCTATATACTACACTATAGTATACTGTATACTATACTATACAGTATACTGTATACTATAC +TATAGTATACAGTATACTATATACTATTGTATAGTATATAGTATACTGTATACTATAGTA +TAGTATACTATATACTATACTATACTATAGTATACTCTATAGTATATAAAGACATATATA +TAGTCTTCAAAATGAAGATCCTGTATCCTATATATATATATAACTTCAAAAGTGAGATAC +ATATATATGATGTAGAAACTTTAGAATATACAAAATTGTCTTCTTCAGGATAAGAAAATC +CTGATATTCAGCCTAACCTCCACTGACTGTAAAGGAAGAATGGGTTTCACTTTCAGGGAA +GGTCACCTTCATCC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/haps.fa.ref.fa new file mode 100644 index 00000000..ea49ed1d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:55624382-55625908 +ATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTCAATCAGTGAGGTGGAGGCTGCAGTGGGCCAAGATCATGCGATTGCACCCCAGCCTGGGTAAGAAAGTGAGGTCCTGTCTCCCTGTCTCTCATATATATACATAACTAAAATAATATATAGTAATATATGTTATATATTATACTATATTATATAATATACTATAATATATATAATATAGTATATATTGTATATAATATAGTATATATAATATAATAGTATATAATATAGTATAGATAGTATAGAATATATAGTATATACCTAGTATACTATATTATATAGTATAACTATTATAATATTTATAGTATATTATACTATATAATACAGTATACTGTATTATATACTATAATCTACTAGATTATAATATACTATATAATCAGTATACTATATTGTATAGTATAATATAGTATTATATTATAGTAATATATTATAAAGTATTATAGTAATATAGTATAATATACTATACATTATATAGTATAGTATATTATATAGTATACTATATATAAGTATATTTAATAGTATATTGTATATAGTAATTATATATAGTATATATAATATACAATGTATAGTATATTATAGTATACTATACGATACTGTAGTATAGTATGCTATATAGTATACTATATACGACAGTATCATATAGTATACTACAAAATATATAGTATAGCATAGTATACTATATAATATACTATATTATATATACTATATTATATATACTATACTATATTATATATACTATATTATATATACTATACTATACATAAAATACTATATATAGTATATTATATATAGTATACTATATATAGTATATAATATATAGTATACTATATATACTATATATAGTATACTATATATACTATATATAGTATACTATATATCATATATAGTATTATATACAGTATACTATATATAATATAGTATACTATACTATAATATACTATTTGTTATAATTATCTAGTATAGTATACTATATATACTATATTATATAGTATATAGTATATATAGTATATAGTATATATACTATATACTATATATACTATATACTATACTATATAATATATATACTAATATATTGTATACTATACTATGCTATAGTATGCTATATACTACACTATAGTATACTGTGTACTATACTATAGTATACAGTATACTATATACTATACTATAGTATAGTATACTATAGTATAGTATACTATATACTATAGTATAGTATATAGTATACTGTATACTATAGTATAGTATACTATATACTATACTATACTATAGTATACTCTATAGTATATAAAGACATATATATAGTCTTCAAAATGAAGATCCTGTATCCTATATATATATATAACTTCAAAAGTGAGATACATATATATGATGTAGAAACTTTAGAATATACAAAATTGTCTTCTTCAGGATAAGAAAATCCTGATATTCAGCCTAACCTCCACTGACTGTAAAGGAAGAATGGGTTTCACTTTCAGGGAAGGTCACCTTCATCC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/msa.fa new file mode 100644 index 00000000..cec18f35 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/msa.fa @@ -0,0 +1,190 @@ +>ref_chr20_55624382_55625908 +atcccagctacttgggaggctgaggcaggagaatcacttcaatcagtgaggtggaggctg +cagtgggccaagatcatgcgattgcaccccagcctgggtaagaaagtgaggtcctgtctc +cctgtctctcatatatatacataactaaaataatatatagtaatatatgttatatattat +actatattatataatatactataatatatataatatagtatatattgtatataatatagt +atatataatataatagtatataatatagtatagatagtatagaatatatagtatatacct +agtatactatattatatagtataactattataatatttatagtatattatactatataat +acagtatactgtattatatactataatctactagattataatatactatataatcagtat +actatatt-----gtatagtataatatagtattatattatagtaatatattataaagtat +tatagtaatatagtataatatactatacattatatagtatagtatattatatagtatact +atatataagtatatttaatagtatattgtatatagtaattatatatagtatatataatat +acaatgtatagtatattatagtatactatacgatactgtagtatagtatgctatatagta +tactatatacgacagtatcatatagtatactacaaaatatatagtatagcatagtatact +atataatatactatattatatatactatattatatatactatactatattatatatacta +tattatatatactatactatacataaaatactatatatagtatattatatatagtatact +atatatagtatataatatata--------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------gtatactatatatactatatatagtatactatatatactatata +tagtatactatatatcatatatagtattatatacagtatactatatataatatagtatac +tatactataatatactatttgttataattatctagtatagtatactatatatactatatt +atatagtatatagtatatatagta----tatagtatatatactatatactatatatacta +tatactatactatataatatatatacta-------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------atatattgtatactatactatgctatagtatgctatatactacacta +tagtatactgtgtactatactatagtatacagtatactatatactatactatagtatagt +atactatagtatagtatactatatactatagtatagtatatagtatactgtatactatag +tatagtatactatatactatactatactatagtatactctatagtatataaagacatata +tatagtcttcaaaatgaagatcctgtatcctatatatatatataacttcaaaagtgagat +acatatatatgatgtagaaactttagaatatacaaaattgtcttcttcaggataagaaaa +tcctgatattcagcctaacctccactgactgtaaaggaagaatgggtttcactttcaggg +aaggtcaccttcatcc +>syndip_1_chr20:55624382-55625908 +atcccagctacttgggaggctgaggcaggagaatcacttcaatcagtgaggtggaggctg +cagtgggccaagatcatgcgattgcaccccagcctgggtaagaaagtgaggtcctgtctc +cctgtctctcatatatatacataactaaaataatatatagtaatatatgttatatattat +actatattatataatatactataatatatataatatagtatatattgtatataatatagt +atatataatataatagtatataatatagtatagatagtatagaatatatagtatatacct +agtatactatattatatagtataactattataatatttatagtatattatactatataat +acagtatactgtattatatactataatctactagattataatatactatataatcagtat +actatattatatagtatagtataatatagtattatattatagtaatatattataaagtat +tatagtaatatagtataatatactatacattatatagtatagtatattatatagtatact +atatataagtatatataatagtatattgtatatagtaattatatatagtatatataatat +acaatgtatagtatattatagtatactatacgatactgtagtatagtatgctatatagta +tactatatacgacagtatcatatagtatactacaaaatatatagtatagcatagtatact +atataatatactatattatatatactatattatatatactacactatattatatatacta +tattatatatactatactatacataaaatactatatatagtatattatatatagtatact +atatatagtatatatagtatactatatatactatatatagtatactatatagtatactat +atatagtatatatagtatactatatatagtatactatatatagtatatatatagtatact +atatatagtatactatatatagtatatatagtatactatatatagtatactatatatagt +atatatagtatactatatatagtatactatatatagtatatatagtatactatatatagt +atactatatatagtatatatagtatactatatatagtatatatagtatactatatatagt +atatatagtatactatatatactatatatactatatatagtatactatatatagtatata +tagtatactatatatcatatatagtattatatacagtatactatatataatatagtatac +tatactataatatactatttgttataattatctagtatagtatactatatatactatatt +atatagtatatagtatatatagtatatttatagtatatatactatatactatatatacta +tatactataatatatactatatatactaaataaatataatatacttatttaaatatattt +aaataaatata--aaatatttaaatataattacttaaatatatatttaaaatatttaata +aacatatatttaaatatttatttaatatttaaatattaaatatatataattaatataatt +atatatatattatatactatatattatatatact-----atatactatatatagtatact +aatataatatactatatatactatatataatatactatatatagtatatatagtatagta +tactataatatactatat-------------------------------------tatat +aatatagtatactatatattgtatactatactatgctatagtatgctatatactacacta +tagtatactgtatactatac-----tatacagtatactgtatactatactatagta---- +---------tacagtatactatatactattgtatagtatatagtatactgtatactatag +tatagtatactatatactatactatactatagtatactctatagtatataaagacatata +tatagtcttcaaaatgaagatcctgtatcctatatatatatataacttcaaaagtgagat +acatatatatgatgtagaaactttagaatatacaaaattgtcttcttcaggataagaaaa +tcctgatattcagcctaacctccactgactgtaaaggaagaatgggtttcactttcaggg +aaggtcaccttcatcc +>syndip_2_chr20:55624382-55625908 +atcccagctacttgggaggctgaggcaggagaatcacttcaatcagtgaggtggaggctg +cagtgggccaagatcatgcgattgcaccccagcctgggtaagaaagtgaggtcctgtctc +cctgtctctcatatatatacataactaaaataatatatagtaatatatgttatatattat +actatattatataatatactataatatatataatatagtatatattgtatataatatagt +atatataatataatagtatataatatagtatagatagtatagaatatatagtatatacct +agtatactatattatatagtataactattataatatttatagtatattatactatataat +acagtatactgtattatatactataatctactagattataatatactatataatcagtat +actatattatatagtatagtataatatagtattatattatagtaatatattataaagtat +tatagtaatatagtataatatactatac-----------------attatatagtatact +atatataagtatatataatagtatattgtatatagtaattatatatagtatatataatat +acaatgtatagtatattatagtatactatacgatactgtagtatagtatgctatatagta +tactatatacgacagtatcatatagtatactacaaaatatatagtatagcatagtatact +atataatat---------------------------------actatattatatatacta +tattatatatactatactatacataaaatactatatatagtatat--------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------tatatatagtatactatatatagtatata +tagtatactatatatcatatatagtattatatacagtatactatatataatatagtatac +tatactataatatactatttgttataattatctagtatagtatactatatatactatat- +------tatatagtatatatagtatatttatagtatatatactatatactatatatacta +tataatataatatataatatatatactaaata-----aatatacttatttaaatatattt +aaataaatatattaaatatttaaatataattacttaaatatatatttaaaatatttaata +aacatatatttaaatatttatttaatatttaaatattaaatatatataattaatataatt +atatatatattatatactatatattatatatactatataatatactatatatagtatact +aatataatatactatatatactatatataatatactatatatagtatatatagtatagta +tactataatatactatatatagtatatatagtatagtatactataatatactatatatag +tatatagtatactatatattgtatactatactatgctatagtatgctatatactacacta +tagtatactgtatactatactatagtatacagtatactatatactatactatagtatagt +atactatagtatagtatactatatactatactatagtatatagtatactgtatac----- +tatagtatactatatactatactatactatagtatactctatagtatataaagacatata +tatagtcttcaaaatgaagatcctgtatcctatatatatatataacttcaaaagtgagat +acatatatatgatgtagaaactttagaatatacaaaattgtcttcttcaggataagaaaa +tcctgatattcagcctaacctccactgactgtaaaggaagaatgggtttcactttcaggg +aaggtcaccttcatcc +>p:HG002_1_chr20:55624382-55625908 +atcccagctacttgggaggctgaggcaggagaatcacttcaatcagtgaggtggaggctg +cagtgggccaagatcatgcgattgcaccccagcctgggtaagaaagtgaggtcctgtctc +cctgtctctcatatatatacataactaaaataatatatagtaatatatgttatatattat +actatattatataatatactataatatatataatatagtatatattgtatataatatagt +atatataatataatagtatataatatagtatagatagtatagaatatatagtatatacct +agtatactatattatatagtataactattataatatttatagtatattatactatataat +acagtatactgtattatatactataatctactagattataatatactatataatcagtat +actatattatatagtatagtataatatagtattatattatagtaatatattataaagtat +tatagtaatatagtataatatactatac-----------------attatatagtatact +atatataagtatatataatagtatattgtatatagtaattatatatagtatatataatat +acaatgtatagtatattatagtatactatacgatactgtagtatagtatgctatatagta +tactatatacgacagtatcatatagtatactacaaaatatatagtatagcatagtatact +atataatat---------------------------------actatattatatatacta +tattatatatactatactatacataaaatactatatatagtatat--------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------tatatatagtatactatatatagtatata +tagtatactatatatcatatatagtattatatacagtatactatatataatatagtatac +tatactataatatactatttgttataattatctagtatagtatactatatatactatat- +------tatatagtatatatagtatatttatagtatatatactatatactatatatacta +tataatataatatataatatatatactaaata-----aatatacttatttaaatatattt +aaataaatatattaaatatttaaatataattacttaaatatatatttaaaatatttaata +aacatatatttaaatatttatttaatatttaaatattaaatatatataattaatataatt +atatatatattatatactatatattatatatactatataatatactatatatagtatact +aatataatatactatatatactatatataatatactatatatagtatatatagtatagta +tactataatatactatatatagtatatatagtatagtatactataatatactatatatag +tatatagtatactatatattgtatactatactatgctatagtatgctatatactacacta +tagtatactgtatactatactatagtatacagtatactatatactatactatagtatagt +atactatagtatagtatactatatactatactatagtatatagtatactgtatac----- +tatagtatactatatactatactatactatagtatactctatagtatataaagacatata +tatagtcttcaaaatgaagatcctgtatcctatatatatatataacttcaaaagtgagat +acatatatatgatgtagaaactttagaatatacaaaattgtcttcttcaggataagaaaa +tcctgatattcagcctaacctccactgactgtaaaggaagaatgggtttcactttcaggg +aaggtcaccttcatcc +>p:HG002_2_chr20:55624382-55625908 +atcccagctacttgggaggctgaggcaggagaatcacttcaatcagtgaggtggaggctg +cagtgggccaagatcatgcgattgcaccccagcctgggtaagaaagtgaggtcctgtctc +cctgtctctcatatatatacataactaaaataatatatagtaatatatgttatatattat +actatattatataatatactataatatatataatatagtatatattgtatataatatagt +atatataatataatagtatataatatagtatagatagtatagaatatatagtatatacct +agtatactatattatatagtataactattataatatttatagtatattatactatataat +acagtatactgtattatatactataatctactagattataatatactatataatcagtat +actatattatatagtatagtataatatagtattatattatagtaatatattataaagtat +tatagtaatatagtataatatactatacattatatagtatagtatattatatagtatact +atatataagtatatataatagtatattgtatatagtaattatatatagtatatataatat +acaatgtatagtatattatagtatactatacgatactgtagtatagtatgctatatagta +tactatatacgacagtatcatatagtatactacaaaatatatagtatagcatagtatact +atataatatactatattatatatactatattatatatactacactatattatatatacta +tattatatatactatactatacataaaatactatatatagtatattatatatagtatact +atatatagtatatatagtatactatatatactatatatagtatactatatagtatactat +atatagtatatatagtatactatatatagtatactatatatagtatatatatagtatact +atatatagtatactatatatagtatatatagtatactatatatagtatactatatatagt +atatatagtatactatatatagtatactatatatagtatatatagtatactatatatagt +atactatatatagtatatatagtatactatatatagtatatatagtatactatatatagt +atatatagtatactatatatactatatatactatatatagtatactatatatagtatata +tagtatactatatatcatatatagtattatatacagtatactatatataatatagtatac +tatactataatatactatttgttataattatctagtatagtatactatatatactatatt +atatagtatatagtatatatagtatatttatagtatatatactatatactatatatacta +tatactataatatatactatatatactaaataaatataatatacttatttaaatatattt +aaataaatata--aaatatttaaatataattacttaaatatatatttaaaatatttaata +aacatatatttaaatatttatttaatatttaaatattaaatatatataattaatataatt +atatatatattatatactatatattatatatact-----atatactatatatagtatact +aatataatatactatatatactatatataatatactatatatagtatatatagtatagta +tactataatatactatat-------------------------------------tatat +aatatagtatactatatattgtatactatactatgctatagtatgctatatactacacta +tagtatactgtatactatac-----tatacagtatactgtatactatactatagta---- +---------tacagtatactatatactattgtatagtatatagtatactgtatactatag +tatagtatactatatactatactatactatagtatactctatagtatataaagacatata +tatagtcttcaaaatgaagatcctgtatcctatatatatatataacttcaaaagtgagat +acatatatatgatgtagaaactttagaatatacaaaattgtcttcttcaggataagaaaa +tcctgatattcagcctaacctccactgactgtaaaggaagaatgggtttcactttcaggg +aaggtcaccttcatcc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/msa.fa.fai new file mode 100644 index 00000000..05630ddf --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_55624382_55625908 2176 29 60 61 +syndip_1_chr20:55624382-55625908 2176 2276 60 61 +syndip_2_chr20:55624382-55625908 2176 4523 60 61 +p:HG002_1_chr20:55624382-55625908 2176 6771 60 61 +p:HG002_2_chr20:55624382-55625908 2176 9019 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/output.vcf.gz new file mode 100644 index 00000000..12e2884e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/output.vcf.gz.tbi new file mode 100644 index 00000000..8ad6606f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55624482-55625808/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/base.vcf.gz new file mode 100644 index 00000000..dbbc1685 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/base.vcf.gz.tbi new file mode 100644 index 00000000..995d0cd3 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/comp.vcf.gz new file mode 100644 index 00000000..cc1ba47f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/comp.vcf.gz.tbi new file mode 100644 index 00000000..258b59b4 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/haps.fa new file mode 100644 index 00000000..1c5efc0a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/haps.fa @@ -0,0 +1,90 @@ +>ref_chr20_55627244_55628551 +GTATCAGCTATCCACTACATACTTAGAAATTTGGCTAATTATCATAACATAAATTAACATTTTATGGCTGTGAAAAGAGAATAGAAATGGATTTTAGAATGTCAAGTATTTATCACTAGTATGTGTTAATATAAATAGCTTAATAAAAATAGGGCATTTATATGTATATATGTGGGTGTTCATGTATATATTTTTATATGTATATATGTGGGTGTGCATGTATACATTAAATGATGAATTTATATGTATATATTAAATGTATATATTATATGTATATATTACATATATACATATTGTATATTACATATACATAATACATAAAATGTTTAATACATACATAATATATACATAATATAATATTGTATATTATTAAATTATACATGTATATATGTATACATGTATACAAAATATGTATATAATATATACAAAAAATGTGTATTTTTGTACATATATTGTACAAAAATATGTATATTATATATACAAAATATGTATATAATATATACATATATTATGTAATATAATATATACATAATGTGTATTACATACATTATATGTAATATATACATATATATTATATACATATATATTATATACATATATGTATATATTATATACATATATGTATATATTATATATTATGTATACACATATGTATATATGTATATATTATATATTATGTATACACATATGTATATATGTATATATTATATATTATGTATACACATATGTATATATGTATATATTATATATTATGTATACACATATGTATATATGTATATATTATATATTATGTATACATATATGTATATATGTATATATTATATATTATGTATACATATATGTATATATGTATATATTATATATTATGTATACATATATGTATATATTATATATTATGTATACATATATGTATATATTATATATTATGTATACATATATGTATATATTATATATTATGTATACATATATGTATATATTATATATTATGTATACATATATGTATATATGTATGTATACATGTATATACATATATACGTATACACATATATACGTGTATATACATATATACGTATATACACGTATATATTAAATGATAAATTTATATGTATATATGCGTGTGTGCACACACACACGAGATATGTTGGTTTTGTGTAATGCAACCAAATAAATTAAGTATACATAGGAGAGAGTCACTGCCCTGACTCTTAAATGTAACCCTTATTAAAGAAAATATTTTAGTTCATTTTTTATCTATCAACCTTTTTTATCTATCAACTCTGAAATCTGCAATCAATCATATTTGGTTAT +>syndip_1_chr20:55627244-55628551 +GTATCAGCTATCCACTACATACTTAGAAATTTGGCTAATTATCATAACATAAATTAACAT +TTTATGGCTGTGAAAAGAGAATAGAAATGGATTTTAGAATGTCAAGTATTTATCACTAGT +ATGTGTTAATATAAATAGCTTAATAAAAATAGGGCATTTATATGTATATATGTGGGTGTT +CATGTATATATTTTTATATGTATATATGTGGGTGTGCATGTATACATTAAATGATGAATT +TATATGTATATATTAAATGTATATATTATATGTATATATTACATATATACATATTGTATA +TTACATATACATAATACATAAAATGTTTAATACATACATAATATATACATAATATAATAT +TGTATATTATTAAATTATACATGTATATATGTATACTATATGTATATATGTATACAAAAT +ATGTATATAATATATACAAAAATATGTGTATTTTTGTACATATATTGTACAAAAATATGT +ATATTATATATACAAAATATGTATATAATATATACATATATTATGTAATATAATATATAC +ATAATGTGTATTACATACATTATATGTAATATATACATATATTATATAATATATATGTAT +ATATTATATACATATATATTATATACATATATGTATATATTATATACATATATGTATACA +TTATATATTATGTATACATATATGTATATATGTATACATTATATATTATGTATACATATA +TGTATATATGTATACATTATATATTATGTATACATATATGTATATATGTATACATTATAT +ATTATGTATACATATATGTATATATGTATACATTATATATTATGTATACATATATGTATA +TATGTATACATTATATATTATGTATACATATATGTATATATGTATACATTATATATTATG +TATACATATATGTATATATGTATACATGTATATACATATATACGTATACACATATATACG +TGTATATACGTATATACACGTATATATTAAATGATAAATTTATATGTATATATGCGTGTG +TGCACACACACACGAGATATGTTGGTTTTGTGTAATGCAACCAAATAAATTAAGTATACA +TAGGAGAGAGTCACTGCCCTGACTCTTAAATGTAACCCTTATTAAAGAAAATATTTTAGT +TCATTTTTTATCTATCAACCTTTTTTATCTATCAACTCTGAAATCTGCAATCAATCATAT +TTGGTTAT +>syndip_2_chr20:55627244-55628551 +GTATCAGCTATCCACTACATACTTAGAAATTTGGCTAATTATCATAACATAAATTAACAT +TTTATGGCTGTGAAAAGAGAATAGAAATGGATTTTAGAATGTCAAGTATTTATCACTAGT +ATGTGTTAATATAAATAGCTTAATAAAAATAGGGCATTTATATGTATATATGTGGGTGTT +CATGTATATATTTTTATATGTATATATGTGGGTGTGCATGTATACATTAAATGATGAATT +TATATGTATATATTAAATGTATATATTATATGTATATATTACATATATACATATTGTATA +TTACATATACATAATACATAAAATGTTTAATACATACATAATATATACATAATATAATAT +TGTATATTATTAAATTATACATGTATATATGTATACATGTATACAAAATATGTATATAAT +ATATACAAAAAATGTGTATTTTTGTACATATATTGTACAAAAATATGTATATTATATATA +CAAAATATGTATATAATATATACATATATTATGTAATATAATATATACGTAATGTGTATT +ACATACATTATATGTAATATATACATATATATTATATACATATATATGTATATATTATAT +ACATATATATTATATACATATATGTATATATTATATATTATGTATACACATATGTATATA +TGTATATATTATATATTATGTATACACATATGTATATATGTATATATTATATATTATGTA +TACACATATGTATATATTATATATTATGTATACACATATGTATATATGTATATATTATAT +ATTATGTATACACATATGTATATATTATATATTATGTATACACATATGTATATATGTATA +TATTATATATTATGTATACACATATGTATATATTATATATTATGTATACACATATGTATA +TATTATATATTATGTATACACGTATATACATATATACGTATACACGTATATACGTATATA +CGTATATACGTATATACACGTATATATTAAATGATAAATTTATATGTATATATGCGTGTG +TGCACACACACACGAGATATGTTGGTTTTGTGTAATGCAACCAAATAAATTAAGTATACA +TAGGAGAGAGTCACTGCCCTGACTCTTAAATGTAACCCTTATTAAAGAAAATATTTTAGT +TCATTTTTTATCTATCAACCTTTTTTATCTATCAACTCTGAAATCTGCAATCAATCATAT +TTGGTTAT +>p:HG002_1_chr20:55627244-55628551 +GTATCAGCTATCCACTACATACTTAGAAATTTGGCTAATTATCATAACATAAATTAACAT +TTTATGGCTGTGAAAAGAGAATAGAAATGGATTTTAGAATGTCAAGTATTTATCACTAGT +ATGTGTTAATATAAATAGCTTAATAAAAATAGGGCATTTATATGTATATATGTGGGTGTT +CATGTATATATTTTTATATGTATATATGTGGGTGTGCATGTATACATTAAATGATGAATT +TATATGTATATATTAAATGTATATATTATATGTATATATTACATATATACATATTGTATA +TTACATATACATAATACATAAAATGTTTAATACATACATAATATATACATAATATAATAT +TGTATATTATTAAATTATACATGTATATATGTATACATGTATACAAAATATGTATATAAT +ATATACAAAAAATGTGTATTTTTGTACATATATTGTACAAAAATATGTATATTATATATA +CAAAATATGTATATAATATATACATATATTATGTAATATAATATATACGTAATGTGTATT +ACATACATTATATGTAATATATACATATATATTATATACATATATATGTATATATTATAT +ACATATATATTATATACATATATGTATATATTATATATTATGTATACACATATGTATATA +TGTATATATTATATATTATGTATACACATATGTATATATGTATATATTATATATTATGTA +TACACATATGTATATATTATATATTATGTATACACATATGTATATATGTATATATTATAT +ATTATGTATACACATATGTATATATTATATATTATGTATACACATATGTATATATGTATA +TATTATATATTATGTATACACATATGTATATATTATATATTATGTATACACATATGTATA +TATTATATATTATGTATACACGTATATACATATATACGTATACACGTATATACGTATATA +CGTATATACGTATATACACGTATATATTAAATGATAAATTTATATGTATATATGCGTGTG +TGCACACACACACGAGATATGTTGGTTTTGTGTAATGCAACCAAATAAATTAAGTATACA +TAGGAGAGAGTCACTGCCCTGACTCTTAAATGTAACCCTTATTAAAGAAAATATTTTAGT +TCATTTTTTATCTATCAACCTTTTTTATCTATCAACTCTGAAATCTGCAATCAATCATAT +TTGGTTAT +>p:HG002_2_chr20:55627244-55628551 +GTATCAGCTATCCACTACATACTTAGAAATTTGGCTAATTATCATAACATAAATTAACAT +TTTATGGCTGTGAAAAGAGAATAGAAATGGATTTTAGAATGTCAAGTATTTATCACTAGT +ATGTGTTAATATAAATAGCTTAATAAAAATAGGGCATTTATATGTATATATGTGGGTGTT +CATGTATATATTTTTATATGTATATATGTGGGTGTGCATGTATACATTAAATGATGAATT +TATATGTATATATTAAATGTATATATTATATGTATATATTACATATATACATATTGTATA +TTACATATACATAATACATAAAATGTTTAATACATACATAATATATACATAATATAATAT +TGTATATTATTAAATTATACATGTATATATGTATACTATATGTATATATGTATACAAAAT +ATGTATATAATATATACAAAAATATGTGTATTTTTGTACATATATTGTACAAAAATATGT +ATATTATATATACAAAATATGTATATAATATATACATATATTATGTAATATAATATATAC +ATAATGTGTATTACATACATTATATGTAATATATACATATATTATATAATATATATGTAT +ATATTATATACATATATATTATATACATATATGTATATATTATATACATATATGTATACA +TTATATATTATGTATACATATATGTATATATGTATACATTATATATTATGTATACATATA +TGTATATATGTATACATTATATATTATGTATACATATATGTATATATGTATACATTATAT +ATTATGTATACATATATGTATATATGTATACATTATATATTATGTATACATATATGTATA +TATGTATACATTATATATTATGTATACATATATGTATATATGTATACATTATATATTATG +TATACATATATGTATATATGTATACATGTATATACATATATACGTATACACATATATACG +TGTATATACGTATATACACGTATATATTAAATGATAAATTTATATGTATATATGCGTGTG +TGCACACACACACGAGATATGTTGGTTTTGTGTAATGCAACCAAATAAATTAAGTATACA +TAGGAGAGAGTCACTGCCCTGAGTCTTAAATGTAACCCTTATTAAAGAAAATATTTTAGT +TCATTTTTTATCTATCAACCTTTTTTATCTATCAACTCTGAAATCTGCAATCAATCATAT +TTGGTTAT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/haps.fa.ref.fa new file mode 100644 index 00000000..91f9904f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:55627244-55628551 +GTATCAGCTATCCACTACATACTTAGAAATTTGGCTAATTATCATAACATAAATTAACATTTTATGGCTGTGAAAAGAGAATAGAAATGGATTTTAGAATGTCAAGTATTTATCACTAGTATGTGTTAATATAAATAGCTTAATAAAAATAGGGCATTTATATGTATATATGTGGGTGTTCATGTATATATTTTTATATGTATATATGTGGGTGTGCATGTATACATTAAATGATGAATTTATATGTATATATTAAATGTATATATTATATGTATATATTACATATATACATATTGTATATTACATATACATAATACATAAAATGTTTAATACATACATAATATATACATAATATAATATTGTATATTATTAAATTATACATGTATATATGTATACATGTATACAAAATATGTATATAATATATACAAAAAATGTGTATTTTTGTACATATATTGTACAAAAATATGTATATTATATATACAAAATATGTATATAATATATACATATATTATGTAATATAATATATACATAATGTGTATTACATACATTATATGTAATATATACATATATATTATATACATATATATTATATACATATATGTATATATTATATACATATATGTATATATTATATATTATGTATACACATATGTATATATGTATATATTATATATTATGTATACACATATGTATATATGTATATATTATATATTATGTATACACATATGTATATATGTATATATTATATATTATGTATACACATATGTATATATGTATATATTATATATTATGTATACATATATGTATATATGTATATATTATATATTATGTATACATATATGTATATATGTATATATTATATATTATGTATACATATATGTATATATTATATATTATGTATACATATATGTATATATTATATATTATGTATACATATATGTATATATTATATATTATGTATACATATATGTATATATTATATATTATGTATACATATATGTATATATGTATGTATACATGTATATACATATATACGTATACACATATATACGTGTATATACATATATACGTATATACACGTATATATTAAATGATAAATTTATATGTATATATGCGTGTGTGCACACACACACGAGATATGTTGGTTTTGTGTAATGCAACCAAATAAATTAAGTATACATAGGAGAGAGTCACTGCCCTGACTCTTAAATGTAACCCTTATTAAAGAAAATATTTTAGTTCATTTTTTATCTATCAACCTTTTTTATCTATCAACTCTGAAATCTGCAATCAATCATATTTGGTTAT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/msa.fa new file mode 100644 index 00000000..f0c1c0d3 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/msa.fa @@ -0,0 +1,120 @@ +>ref_chr20_55627244_55628551 +gtatcagctatccactacatacttagaaatttggctaattatcataacataaattaacat +tttatggctgtgaaaagagaatagaaatggattttagaatgtcaagtatttatcactagt +atgtgttaatataaatagcttaataaaaatagggcatttatatgtatatatgtgggtgtt +catgtatatatttttatatgtatatatgtgggtgtgcatgtatacattaaatgatgaatt +tatatgtatatattaaatgtatatattatatgtatatattacatatatacatattgtata +ttacatatacataatacataaaatgtttaatacatacataatatatacataatataatat +tgtatattattaaattatacatgtatatatgtatac-----------atgtatacaaaat +atgtatataatatatacaaaaa-atgtgtatttttgtacatatattgtacaaaaatatgt +atattatatatacaaaatatgtatataatatatacatatattatgtaatataatatatac +ataatgtgtattacatacattatatgtaatatatacatatatattatatacatatatat- +tatata-catatatgtatatattatatacatatatgtatatattatatattatgtataca +catatgtatatatgtatatattatatattatgtatacacatatgtatatatgtatatatt +atatattatgtatacacatatgtatatatgtatatattatatattatgtatacacatatg +tatatatgtatatattatatattatgtatacatatatgtatatatgtatatattatatat +tatgtatacatatatgtatatatgtatatattatatattatgtatacatatatgtatat- +-------attatatattatgtatacatatatgtatatattatatattatgtatacatata +tgtatatattatatattatgtatacatatatgtatatattatatattatgtatacatata +tgtatatatgtatgtatacatgtatatacatatatacgtatacacatatatacgtgtata +tacatatatacgtatatacacgtatatattaaatgataaatttatatgtatatatgcgtg +tgtgcacacacacacgagatatgttggttttgtgtaatgcaaccaaataaattaagtata +cataggagagagtcactgccctgactcttaaatgtaacccttattaaagaaaatatttta +gttcattttttatctatcaaccttttttatctatcaactctgaaatctgcaatcaatcat +atttggttat +>syndip_1_chr20:55627244-55628551 +gtatcagctatccactacatacttagaaatttggctaattatcataacataaattaacat +tttatggctgtgaaaagagaatagaaatggattttagaatgtcaagtatttatcactagt +atgtgttaatataaatagcttaataaaaatagggcatttatatgtatatatgtgggtgtt +catgtatatatttttatatgtatatatgtgggtgtgcatgtatacattaaatgatgaatt +tatatgtatatattaaatgtatatattatatgtatatattacatatatacatattgtata +ttacatatacataatacataaaatgtttaatacatacataatatatacataatataatat +tgtatattattaaattatacatgtatatatgtatactatatgtatatatgtatacaaaat +atgtatataatatatacaaaaatatgtgtatttttgtacatatattgtacaaaaatatgt +atattatatatacaaaatatgtatataatatatacatatattatgtaatataatatatac +ataatgtgtattacatacattatatgtaatatatacatatattatata---atatatatg +tatatattatatacatatatattatatacatatatgtatatattatata----------- +------catatatgtatacattatatattatgtatacatatatgtatatatgtatacatt +atatattatgtatacatatatgtatatatgtatacattatatattatgtatacatatatg +tatatatgtatacattatatattatgtatacatatatgtatatatgtatacattatatat +tatgtatacatatatgtatatatgtatacattatatattatgtatacatatatgtatata +tgtatacattatatattatgtatacatatatgtata------------------------ +------------------------------------------------------------ +----------tatgtatacatgtatatacatatatacgtatacacatatatacgtg---- +----tatatacgtatatacacgtatatattaaatgataaatttatatgtatatatgcgtg +tgtgcacacacacacgagatatgttggttttgtgtaatgcaaccaaataaattaagtata +cataggagagagtcactgccctgactcttaaatgtaacccttattaaagaaaatatttta +gttcattttttatctatcaaccttttttatctatcaactctgaaatctgcaatcaatcat +atttggttat +>syndip_2_chr20:55627244-55628551 +gtatcagctatccactacatacttagaaatttggctaattatcataacataaattaacat +tttatggctgtgaaaagagaatagaaatggattttagaatgtcaagtatttatcactagt +atgtgttaatataaatagcttaataaaaatagggcatttatatgtatatatgtgggtgtt +catgtatatatttttatatgtatatatgtgggtgtgcatgtatacattaaatgatgaatt +tatatgtatatattaaatgtatatattatatgtatatattacatatatacatattgtata +ttacatatacataatacataaaatgtttaatacatacataatatatacataatataatat +tgtatattattaaattatacatgtatatatgtatac-----------atgtatacaaaat +atgtatataatatatacaaaaa-atgtgtatttttgtacatatattgtacaaaaatatgt +atattatatatacaaaatatgtatataatatatacatatattatgtaatataatatatac +gtaatgtgtattacatacattatatgtaatatatacatatatattatatacatatatatg +tatatattatatacatatatattatatacatatatgtatatattatatattatgtataca +catatgtatatatgtatatattatatattatgtatacacatatgtatatatgtatatatt +atatattatgtatacac--------atatgtatatattatatattatgtatacacatatg +tatatatgtatatattatatattatgtatac--------acatatgtatatattatatat +tatgtatacacatatgtatatatgtatatattatatattatgtatacacatatgtatat- +-------attatatattatgtatacacatatgtatatattatatat-------------- +------------------------------------------------------------ +----------tatgtatacacgtatatacatatatacgtatacacgtatatacgta--ta +tacgtatatacgtatatacacgtatatattaaatgataaatttatatgtatatatgcgtg +tgtgcacacacacacgagatatgttggttttgtgtaatgcaaccaaataaattaagtata +cataggagagagtcactgccctgactcttaaatgtaacccttattaaagaaaatatttta +gttcattttttatctatcaaccttttttatctatcaactctgaaatctgcaatcaatcat +atttggttat +>p:HG002_1_chr20:55627244-55628551 +gtatcagctatccactacatacttagaaatttggctaattatcataacataaattaacat +tttatggctgtgaaaagagaatagaaatggattttagaatgtcaagtatttatcactagt +atgtgttaatataaatagcttaataaaaatagggcatttatatgtatatatgtgggtgtt +catgtatatatttttatatgtatatatgtgggtgtgcatgtatacattaaatgatgaatt +tatatgtatatattaaatgtatatattatatgtatatattacatatatacatattgtata +ttacatatacataatacataaaatgtttaatacatacataatatatacataatataatat +tgtatattattaaattatacatgtatatatgtatac-----------atgtatacaaaat +atgtatataatatatacaaaaa-atgtgtatttttgtacatatattgtacaaaaatatgt +atattatatatacaaaatatgtatataatatatacatatattatgtaatataatatatac +gtaatgtgtattacatacattatatgtaatatatacatatatattatatacatatatatg +tatatattatatacatatatattatatacatatatgtatatattatatattatgtataca +catatgtatatatgtatatattatatattatgtatacacatatgtatatatgtatatatt +atatattatgtatacac--------atatgtatatattatatattatgtatacacatatg +tatatatgtatatattatatattatgtatac--------acatatgtatatattatatat +tatgtatacacatatgtatatatgtatatattatatattatgtatacacatatgtatat- +-------attatatattatgtatacacatatgtatatattatatat-------------- +------------------------------------------------------------ +----------tatgtatacacgtatatacatatatacgtatacacgtatatacgta--ta +tacgtatatacgtatatacacgtatatattaaatgataaatttatatgtatatatgcgtg +tgtgcacacacacacgagatatgttggttttgtgtaatgcaaccaaataaattaagtata +cataggagagagtcactgccctgactcttaaatgtaacccttattaaagaaaatatttta +gttcattttttatctatcaaccttttttatctatcaactctgaaatctgcaatcaatcat +atttggttat +>p:HG002_2_chr20:55627244-55628551 +gtatcagctatccactacatacttagaaatttggctaattatcataacataaattaacat +tttatggctgtgaaaagagaatagaaatggattttagaatgtcaagtatttatcactagt +atgtgttaatataaatagcttaataaaaatagggcatttatatgtatatatgtgggtgtt +catgtatatatttttatatgtatatatgtgggtgtgcatgtatacattaaatgatgaatt +tatatgtatatattaaatgtatatattatatgtatatattacatatatacatattgtata +ttacatatacataatacataaaatgtttaatacatacataatatatacataatataatat +tgtatattattaaattatacatgtatatatgtatactatatgtatatatgtatacaaaat +atgtatataatatatacaaaaatatgtgtatttttgtacatatattgtacaaaaatatgt +atattatatatacaaaatatgtatataatatatacatatattatgtaatataatatatac +ataatgtgtattacatacattatatgtaatatatacatatattatata---atatatatg +tatatattatatacatatatattatatacatatatgtatatattatata----------- +------catatatgtatacattatatattatgtatacatatatgtatatatgtatacatt +atatattatgtatacatatatgtatatatgtatacattatatattatgtatacatatatg +tatatatgtatacattatatattatgtatacatatatgtatatatgtatacattatatat +tatgtatacatatatgtatatatgtatacattatatattatgtatacatatatgtatata +tgtatacattatatattatgtatacatatatgtata------------------------ +------------------------------------------------------------ +----------tatgtatacatgtatatacatatatacgtatacacatatatacgtg---- +----tatatacgtatatacacgtatatattaaatgataaatttatatgtatatatgcgtg +tgtgcacacacacacgagatatgttggttttgtgtaatgcaaccaaataaattaagtata +cataggagagagtcactgccctgagtcttaaatgtaacccttattaaagaaaatatttta +gttcattttttatctatcaaccttttttatctatcaactctgaaatctgcaatcaatcat +atttggttat diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/msa.fa.fai new file mode 100644 index 00000000..048ef179 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_55627244_55628551 1330 29 60 61 +syndip_1_chr20:55627244-55628551 1330 1416 60 61 +syndip_2_chr20:55627244-55628551 1330 2803 60 61 +p:HG002_1_chr20:55627244-55628551 1330 4191 60 61 +p:HG002_2_chr20:55627244-55628551 1330 5579 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/output.vcf.gz new file mode 100644 index 00000000..5cba49e5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/output.vcf.gz.tbi new file mode 100644 index 00000000..972f84b2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55627344-55628451/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/base.vcf.gz new file mode 100644 index 00000000..f56114ce Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/base.vcf.gz.tbi new file mode 100644 index 00000000..2e78dae5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/comp.vcf.gz new file mode 100644 index 00000000..32e7b972 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/comp.vcf.gz.tbi new file mode 100644 index 00000000..f45e248e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/haps.fa new file mode 100644 index 00000000..3638376e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/haps.fa @@ -0,0 +1,148 @@ +>ref_chr20_55943819_55945908 +GTGCTGGGTACTGTCCCAGTCCTCCTACCTGTTTACCTCACTTCCACCCTTGCCTCCTTCCAAGTCAATCCCATGGGAACCAGCATTTTCTGAAACTCAATAAAATTAGCTAGCATTTCAGCCAGGTGCAGTGGCTCAAGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGTGGATCACTTGAGGTTAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCTCGCCTCTACTAAAAATACAAAAATTAGCTGGGCATGCTGGCATGTGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAACTGCTTGAGCCTGGGAGGCAGAGGTTGCAGTGAGCTGAGATGGCACCACTGCATTCCAGCTGGGCAACAGAGAGAGACTCTTTCTTAAATATATATATTTTATATATATATAGATACACACACACACACACACACACACACATATATATATATATATATATATATATATATATATGCATGCATGCCAGATGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGAGAGGCCAAGGTGGGCAGATCATCTGAGGTCAGGAGTTCCAGACCAGCCTAGCCAACATGGTGAAACTCCATCTCTACTAAAAATACAAAATTAGCTGGCTGTGGTGGCTCATGCTGGTAATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTGAACCTGGGAGGTGGAGGTTGCAGTGAGCCGAGATCACACCACTGCACTCCAGCCTGGATGACAGAGCGAGACTCCATTAAAAAAATATATCTATATCTATAGATATCTATAGATATATATCTAGATATAGATCTATGAGTATATATCTATAGATATCTAGATATATATTTATAGATAGATATATCTATAGATATCTATATATTTCTATCGATAGAGATATCTATAGATATCTATCAATATATCTATAGATTTCTAGAGATATGTATCTAGATATAAATCTATAGACATAGATATAGATATATAGATATTTAACTGCCAATGTCCTAAACACTTTATACTCAACACATTTTTTATAAAAAAAAATAGATATCGGTCTAGATAGTATCTATCTAGATATCGGTCTAGATAGTATCTATCTAGATATCTGTGTAGATGTCTAGATATCTATCTAGATATTATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTAGATAGTATCTGTCGCTATCTAGATATCTAGATAGTATCTGTCTAGATAGCTATCTAGATAGTATCTGTCTAGATAGCTATCTAGATAGTATCTGTCCAGATATCTGTAGCTATCTAGATTGTATCTGTCTAGATATCTGTAGATATCTAGATATCTATATCTATCTGGATATCTATAGATATTTAACTGCCGGGCAATGTCCTAAACCCTTTACACTCAACACATTTCATTTTATAACAAAATATGAGGTAGATATTATTATTTCCCTCAACTCACAGAGAAGAAAAAAATGAAGCATATGGAGCCCATGGGC +>syndip_1_chr20:55943819-55945908 +GTGCTGGGTACTGTCCCAGTCCTCCTACCTGTTTACCTCACTTCCACCCTTGCCTCCTTC +CAAGTCAATCCCATGGGAACCAGCATTTTCTGAAACTCAATAAAATTAGCTAGCATTTCA +GCCAGGTGCAGTGGCTCAAGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGTGGAT +CACTTGAGGTTAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCTCGCCTCTACTA +AAAATACAAAAATTAGCTGGGCATGCTGGCATGTGCCTGTAATCCCAGCTACTCAGGAGG +CTGAGGCAGGAGAACTGCTTGAGCCTGGGAGGCAGAGGTTGCAGTGAGCTGAGATGGCAC +CACTGCATTCCAGCTGGGCAACAGAGAGAGACTCTTTCTTAAATATATATATTTTATATA +TATATAGATACACACACACACACACACACACACACATATATATATATATATATATATATA +TATATATATGCATGCATGCCAGATGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGAGA +GGCCAAGGTGGGCAGATCATCTGAGGTCAGGAGTTCCAGACCAGCCTAGCCAACATGGTG +AAACTCCATCTCTACTAAAAATACAAAATTAGCTGGCTGTGGTGGCTCATGCTGGTAATC +CCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTGAACCTGGGAGGTGGAGGTTGCAG +TGAGCCGAGATCACACCACTGCACTCCAGCCTGGATGACAGAGCGAGACTCCATTAAAAA +AATATATCTATATCTATAGATATCTATAGATATATATCTAGATATAGATCTATGAGTATA +TATCTATAGATATCTAGATATATATTTATAGATAGATATATCTATAGATATCTATATATT +TCTATCGATAGAGATATCTATAGATATCTATCAATATATCTATAGATTTCTAGAGATATG +TATCTAGATATAAATCTATAGACATAGATATAGATATATAGATATTTAACTGCCAATGTC +CTAAACACTTTATACTCAACACATTTTTTATAAAAAAAAATAGATATCGGTCTAGATAGT +ATCTATCTAGATATCGGTCTAGATAGTATCTATCTAGATATCTGTGTAGATGTCTAGATA +TCTATCTAGATATTATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATCT +GTCGCTATCTAGATATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATAGTA +TCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAG +ATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCT +ATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAG +ATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCT +ATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCT +GTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATA +GTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATC +TAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATA +TCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATC +TAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTC +GCTATCTAGATATCTAGATAGTATCTGTCGCTATCTAGATATCTAGATAGTATCTGTCTA +GATAGCTATCTAGATAGTATCTGTCTAGATAGCTATCTAGATAGTATCTGTCCAGATATC +TGTAGCTATCTAGATTGTATCTGTCTAGATATCTGTAGATATCTAGATATCTATATCTAT +CTGGATATCTATAGATATTTAACTGCCGGGCAATGTCCTAAACCCTTTACACTCAACACA +TTTCATTTTATAACAAAATATGAGGTAGATATTATTATTTCCCTCAACTCACAGAGAAGA +AAAAAATGAAGCATATGGAGCCCATGGGC +>syndip_2_chr20:55943819-55945908 +GTGCTGGGTACTGTCCCAGTCCTCCTACCTGTTTACCTCACTTCCACCCTTGCCTCCTTC +CAAGTCAATCCCATGGGAACCAGCATTTTCTGAAACTCAATAAAATTAGCTAGCATTTCA +GCCAGGTGCAGTGGCTCAAGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGTGGAT +CACTTGAGGTTAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCTCGCCTCTACTA +AAAATACAAAAATTAGCTGGGCATGCTGGCATGTGCCTGTAATCCCAGCTACTCAGGAGG +CTGAGGCAGGAGAACTGCTTGAGCCTGGGAGGCAGAGGTTGCAGTGAGCTGAGATGGCAC +CACTGCATTCCAGCTGGGCAACAGAGAGAGACTCTTTCTTAAATATATATATTTTATATA +TATATAGATACACACACACACACACACACACACACACACACACACACACACACACATATA +TATATATATATATATATATATATATATATATATATATATATATGCATGCATGCCAGATGC +AGTGGCTCACGCCTGTAATCCCAGCACTTTGAGAGGCCAAGGTGGGCAGATCATCTGAGG +TCAGGAGTTCCAGACCAGCCTAGCCAACATGGTGAAACTCCATCTCTACTAAAAATACAA +AATTAGCTGGCTGTGGTGGCTCATGCTGGTAATCCCAGCTACTTGGGAGGCTGAGGCAGG +AGAATCACTTGAACCTGGGAGGTGGAGGTTGCAGTGAGCCGAGATCACACCACTGCACTC +CAGCCTGGATGACAGAGCGAGACTCCATTAAAAAAATATATCTATATCTATAGATATCTA +TAGATATATATCTAGATATAGATCTATGAGTATATATCTATAGATATCTAGATATATATT +TATAGATAGATATATCTATAGATATCTATATATTTCTATCGATAGAGATATCTATAGATA +TCTATCAATATATCTATAGATTTCTAGAGATATGTATCTAGATATAAATCTATAGACATA +GATATAGATATATAGATATTTAACTGCCAATGTCCTAAACACTTTATACTCAACACATTT +TTTATAAAAAAAAATAGATATCGGTCTAGATAGTATCTATCTAGATATCGGTCTAGATAG +TATCTATCTAGATATCGGTCTAGATAGTATCTATCTAGATATCTGCGTAGATGTCTAGAT +ATCTATCTAGATATTATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATC +TGTCGCTATCTAGATATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATC +ATCTGTCGCTATCTAGATATCTATCTAGATATCATCTGTCGCTATCTAGATATCTATCTA +GATATCATCTGTCGCTATCTAGATATCTATCTAGATATCATCTGTCGCTATCTAGATATC +TATCTAGATATCATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTA +GATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGC +TATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATC +TGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGAT +AGTATCTGTCGCTATCTAGATATCTAGATAGTATCTGTCGCTATCTAGATATCTAGATAG +TATCTGTCTAGATAGCTATCTAGATAGTATCTGTCTAGATAGCTATCTAGATAGTATCTG +TCCAGATATCTGTAGCTATCTAGATTGTATCTGTCTAGATATCTGTAGATATCTAGATAT +CTATATCTATCTGGATATCTATAGATATTTAACTGCCGGGCAATGTCCTAAACCCTTTAC +ACTCAACACATTTCATTTTATAACAAAATATGAGGTAGATATTATTATTTCCCTCAACTC +ACAGAGAAGAAAAAAATGAAGCATATGGAGCCCATGGGC +>p:HG002_1_chr20:55943819-55945908 +GTGCTGGGTACTGTCCCAGTCCTCCTACCTGTTTACCTCACTTCCACCCTTGCCTCCTTC +CAAGTCAATCCCATGGGAACCAGCATTTTCTGAAACTCAATAAAATTAGCTAGCATTTCA +GCCAGGTGCAGTGGCTCAAGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGTGGAT +CACTTGAGGTTAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCTCGCCTCTACTA +AAAATACAAAAATTAGCTGGGCATGCTGGCATGTGCCTGTAATCCCAGCTACTCAGGAGG +CTGAGGCAGGAGAACTGCTTGAGCCTGGGAGGCAGAGGTTGCAGTGAGCTGAGATGGCAC +CACTGCATTCCAGCTGGGCAACAGAGAGAGACTCTTTCTTAAATATATATATTTTATATA +TATATAGATACACACACACACACACACACACACACACACACACACACACACACACATATA +TATATATATATATATATATATATATATATATATATATATATATGCATGCATGCCAGATGC +AGTGGCTCACGCCTGTAATCCCAGCACTTTGAGAGGCCAAGGTGGGCAGATCATCTGAGG +TCAGGAGTTCCAGACCAGCCTAGCCAACATGGTGAAACTCCATCTCTACTAAAAATACAA +AATTAGCTGGCTGTGGTGGCTCATGCTGGTAATTCCAGCTACTTGGGAGGCTGAGGCAGG +AGAATCACATGAACCTGGGAGGTGGAGGTTGCAGTGAGCCGAGATCACACCACTGCACTC +CAGCCTGGATGACAGAGCGAGACTCCATTAAAAAAATATATCTATATCTATAGATATCTA +TAGATATATATCTAGATATAGATCTATGAGTATATATCTATAGATATCTAGATATATATT +TATAGATAGATATATCTATAGATATCTATATATTTCTATCGATAGAGATATCTATAGATA +TCTATCAATATATCTATAGATTTCTAGAGATATGTATCTAGATATAAATCTATAGACATA +GATATAGATATATAGATATTTAACTGCCAATGTCCTAAACACTTTATACTCAACACATTT +TTTATAAAAAAAAATAGATATCGGTCTAGATAGTATCTATCTAGATATCGGTCTAGATAG +TATCTATCTAGATATCGGTCTAGATAGTATCTATCTAGATATCTGCGTAGATGTCTAGAT +ATCTATCTAGATATTATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATC +TGTCGCTATCTAGATATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATC +ATCTGTCGCTATCTAGATATCTATCTAGATATCATCTGTCGCTATCTAGATATCTATCTA +GATATCATCTGTCGCTATCTAGATATCTATCTAGATATCATCTGTCGCTATCTAGATATC +TATCTAGATATCATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTA +GATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGC +TATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATC +TGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGAT +AGTATCTGTCGCTATCTAGATATCTAGATAGTATCTGTCGCTATCTAGATATCTAGATAG +TATCTGTCTAGATAGCTATCTAGATAGTATCTGTCTAGATAGCTATCTAGATAGTATCTG +TCCAGATATCTGTAGCTATCTAGATTGTATCTGTCTAGATATCTGTAGATATCTAGATAT +CTATATCTATCTGGATATCTATAGATATTTAACTGCCGGGCAATGTCCTAAACCCTTTAC +ACTCAACACATTTCATTTTATAACAAAATATGAGGTAGATATTATTATTTCCCTCAACTC +ACAGAGAAGAAAAAAATGAAGCATATGGAGCCCATGGGC +>p:HG002_2_chr20:55943819-55945908 +GTGCTGGGTACTGTCCCAGTCCTCCTACCTGTTTACCTCACTTCCACCCTTGCCTCCTTC +CAAGTCAATCCCATGGGAACCAGCATTTTCTGAAACTCAATAAAATTAGCTAGCATTTCA +GCCAGGTGCAGTGGCTCAAGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGTGGAT +CACTTGAGGTTAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCTCGCCTCTACTA +AAAATACAAAAATTAGCTGGGCATGCTGGCATGTGCCTGTAATCCCAGCTACTCAGGAGG +CTGAGGCAGGAGAACTGCTTGAGCCTGGGAGGCAGAGGTTGCAGTGAGCTGAGATGGCAC +CACTGCATTCCAGCTGGGCAACAGAGAGAGACTCTTTCTTAAATATATATATTTTATATA +TATATAGATACACACACACACACACACACACACACATATATATATATATATATATATATA +TATATATATGCATGCATGCCAGATGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGAGA +GGCCAAGGTGGGCAGATCATCTGAGGTCAGGAGTTCCAGACCAGCCTAGCCAACATGGTG +AAACTCCATCTCTACTAAAAATACAAAATTAGCTGGCTGTGGTGGCTCATGCTGGTAATC +CCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTGAACCTGGGAGGTGGAGGTTGCAG +TGAGCCGAGATCACACCACTGCACTCCAGCCTGGATGACAGAGCGAGACTCCATTAAAAA +AATATATCTATATCTATAGATATCTATAGATATATATCTAGATATAGATCTATGAGTATA +TATCTATAGATATCTAGATATATATTTATAGATAGATATATCTATAGATATCTATATATT +TCTATCGATAGAGATATCTATAGATATCTATCAATATATCTATAGATTTCTAGAGATATG +TATCTAGATATAAATCTATAGACATAGATATAGATATATAGATATTTAACTGCCAATGTC +CTAAACACTTTATACTCAACACATTTTTTATAAAAAAAAATAGATATCGGTCTAGATAGT +ATCTATCTAGATATCGGTCTAGATAGTATCTATCTAGATATCTGTGTAGATGTCTAGATA +TCTATCTAGATATTATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATCT +GTCGCTATCTAGATATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATAGTA +TCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAG +ATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCT +ATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAG +ATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCT +ATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCT +GTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATA +GTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATC +TAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATA +TCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATC +TAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTC +GCTATCTAGATATCTAGATAGTATCTGTCGCTATCTAGATATCTAGATAGTATCTGTCTA +GATAGCTATCTAGATAGTATCTGTCTAGATAGCTATCTAGATAGTATCTGTCCAGATATC +TGTAGCTATCTAGATTGTATCTGTCTAGATATCTGTAGATATCTAGATATCTATATCTAT +CTGGATATCTATAGATATTTAACTGCCGGGCAATGTCCTAAACCCTTTACACTCAACACA +TTTCATTTTATAACAAAATATGAGGTAGATATTATTATTTCCCTCAACTCACAGAGAAGA +AAAAAATGAAGCATATGGAGCCCATGGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/haps.fa.ref.fa new file mode 100644 index 00000000..5336576f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:55943819-55945908 +GTGCTGGGTACTGTCCCAGTCCTCCTACCTGTTTACCTCACTTCCACCCTTGCCTCCTTCCAAGTCAATCCCATGGGAACCAGCATTTTCTGAAACTCAATAAAATTAGCTAGCATTTCAGCCAGGTGCAGTGGCTCAAGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGTGGATCACTTGAGGTTAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCTCGCCTCTACTAAAAATACAAAAATTAGCTGGGCATGCTGGCATGTGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAACTGCTTGAGCCTGGGAGGCAGAGGTTGCAGTGAGCTGAGATGGCACCACTGCATTCCAGCTGGGCAACAGAGAGAGACTCTTTCTTAAATATATATATTTTATATATATATAGATACACACACACACACACACACACACACATATATATATATATATATATATATATATATATATGCATGCATGCCAGATGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGAGAGGCCAAGGTGGGCAGATCATCTGAGGTCAGGAGTTCCAGACCAGCCTAGCCAACATGGTGAAACTCCATCTCTACTAAAAATACAAAATTAGCTGGCTGTGGTGGCTCATGCTGGTAATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTGAACCTGGGAGGTGGAGGTTGCAGTGAGCCGAGATCACACCACTGCACTCCAGCCTGGATGACAGAGCGAGACTCCATTAAAAAAATATATCTATATCTATAGATATCTATAGATATATATCTAGATATAGATCTATGAGTATATATCTATAGATATCTAGATATATATTTATAGATAGATATATCTATAGATATCTATATATTTCTATCGATAGAGATATCTATAGATATCTATCAATATATCTATAGATTTCTAGAGATATGTATCTAGATATAAATCTATAGACATAGATATAGATATATAGATATTTAACTGCCAATGTCCTAAACACTTTATACTCAACACATTTTTTATAAAAAAAAATAGATATCGGTCTAGATAGTATCTATCTAGATATCGGTCTAGATAGTATCTATCTAGATATCTGTGTAGATGTCTAGATATCTATCTAGATATTATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTAGATAGTATCTGTCGCTATCTAGATATCTAGATAGTATCTGTCTAGATAGCTATCTAGATAGTATCTGTCTAGATAGCTATCTAGATAGTATCTGTCCAGATATCTGTAGCTATCTAGATTGTATCTGTCTAGATATCTGTAGATATCTAGATATCTATATCTATCTGGATATCTATAGATATTTAACTGCCGGGCAATGTCCTAAACCCTTTACACTCAACACATTTCATTTTATAACAAAATATGAGGTAGATATTATTATTTCCCTCAACTCACAGAGAAGAAAAAAATGAAGCATATGGAGCCCATGGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/msa.fa new file mode 100644 index 00000000..b99015f0 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/msa.fa @@ -0,0 +1,195 @@ +>ref_chr20_55943819_55945908 +gtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctccttc +caagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttca +gccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtggat +cacttgaggttaggagtttgagaccagcctggccaacatggtgaaacctcgcctctacta +aaaatacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggagg +ctgaggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggcac +cactgcattccagctgggcaacagagagagactctttcttaaatatatatattttatata +tatatagatacacacacacacacacacacacacac------------------------- +---------atatatatatatatatatatatatatatatatatgcatgcatgccagatgc +agtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgagg +tcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaatacaa +aattagctggctgtggtggctcatgctggtaatcccagctacttgggaggctgaggcagg +agaatcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcactc +cagcctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatcta +tagatatatatctagatatagatctatgagtatatatctatagatatctagatatatatt +tatagatagatatatctatagatatctatatatttctatcgatagagatatctatagata +tctatcaatatatctatagatttctagagatatgtatctagatataaatctatagacata +gatatagatatatagatatttaactgccaatgtcctaaacactttatactcaacacattt +tttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagatag +tatctatctagatatctgtgtagatgtctagatatctatctagatattatctatctagat +atct--gtcgctatctagatatctatctagatatctgtcgctatctagatatctatctag +a----------------------------------------------------------- +----------------------------------------tatctgtcgctatctagata +tctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatc +tagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtc +gctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagta +tctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctag +atagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatct +atctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctag +atatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgct +atctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatct +gtcgctatctagatatctatctagatagtatctgtcgctatctagatatctagatagtat +ctgtcgctatctagatatctagatagtatctgtctagatagctatctagatagtatctgt +ctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatctgt +ctagatatctgtagatatctagatatctatatctatctggatatctatagatatttaact +gccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatatgag +gtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagccca +tgggc +>syndip_1_chr20:55943819-55945908 +gtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctccttc +caagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttca +gccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtggat +cacttgaggttaggagtttgagaccagcctggccaacatggtgaaacctcgcctctacta +aaaatacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggagg +ctgaggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggcac +cactgcattccagctgggcaacagagagagactctttcttaaatatatatattttatata +tatatagatacacacacacacacacacacacacac------------------------- +---------atatatatatatatatatatatatatatatatatgcatgcatgccagatgc +agtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgagg +tcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaatacaa +aattagctggctgtggtggctcatgctggtaatcccagctacttgggaggctgaggcagg +agaatcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcactc +cagcctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatcta +tagatatatatctagatatagatctatgagtatatatctatagatatctagatatatatt +tatagatagatatatctatagatatctatatatttctatcgatagagatatctatagata +tctatcaatatatctatagatttctagagatatgtatctagatataaatctatagacata +gatatagatatatagatatttaactgccaatgtcctaaacactttatactcaacacattt +tttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagatag +tatctatctagatatctgtgtagatgtctagatatctatctagatattatctatctagat +atct--gtcgctatctagatatctatctagatatctgtcgctatctagatatctatctag +atatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatc +tagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagata +tctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatc +tagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtc +gctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagta +tctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctag +atagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatct +atctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctag +atatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgct +atctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatct +gtcgctatctagatatctatctagatagtatctgtcgctatctagatatctagatagtat +ctgtcgctatctagatatctagatagtatctgtctagatagctatctagatagtatctgt +ctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatctgt +ctagatatctgtagatatctagatatctatatctatctggatatctatagatatttaact +gccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatatgag +gtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagccca +tgggc +>syndip_2_chr20:55943819-55945908 +gtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctccttc +caagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttca +gccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtggat +cacttgaggttaggagtttgagaccagcctggccaacatggtgaaacctcgcctctacta +aaaatacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggagg +ctgaggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggcac +cactgcattccagctgggcaacagagagagactctttcttaaatatatatattttatata +tatatagatacacacacacacacacacacacacacacacacacacacacacacacatata +tatatatatatatatatatatatatatatatatatatatatatgcatgcatgccagatgc +agtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgagg +tcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaatacaa +aattagctggctgtggtggctcatgctggtaatcccagctacttgggaggctgaggcagg +agaatcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcactc +cagcctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatcta +tagatatatatctagatatagatctatgagtatatatctatagatatctagatatatatt +tatagatagatatatctatagatatctatatatttctatcgatagagatatctatagata +tctatcaatatatctatagatttctagagatatgtatctagatataaatctatagacata +gatatagatatatagatatttaactgccaatgtcctaaacactttatactcaacacattt +tttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagatag +tatctatctagatatcgg--------------------tctagatagtatctatctagat +atctgcgtagatgtctagatatctatctagatat---------------tatctatctag +a----------------------------------------------------------- +----------------------------------------tatctgtcgctatctagata +tctatctaga---tatctgtcgctatctagatatctatctaga----------------- +----------------------------------------------------tatctgtc +gctatctagatatctatctagatatcatctgtcgctatctagatatctatctagatatca +tctgtcgctatctagatatctatctagatatcatctgtcgctatctagatatctatctag +atatcatctgtcgctatctagatatctatctagatatcatctgtcgctatctagatatct +atctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctag +atatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgct +atctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatct +gtcgctatctagatatctatctagatagtatctgtcgctatctagatatctagatagtat +ctgtcgctatctagatatctagatagtatctgtctagatagctatctagatagtatctgt +ctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatctgt +ctagatatctgtagatatctagatatctatatctatctggatatctatagatatttaact +gccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatatgag +gtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagccca +tgggc +>p:HG002_1_chr20:55943819-55945908 +gtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctccttc +caagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttca +gccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtggat +cacttgaggttaggagtttgagaccagcctggccaacatggtgaaacctcgcctctacta +aaaatacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggagg +ctgaggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggcac +cactgcattccagctgggcaacagagagagactctttcttaaatatatatattttatata +tatatagatacacacacacacacacacacacacacacacacacacacacacacacatata +tatatatatatatatatatatatatatatatatatatatatatgcatgcatgccagatgc +agtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgagg +tcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaatacaa +aattagctggctgtggtggctcatgctggtaattccagctacttgggaggctgaggcagg +agaatcacatgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcactc +cagcctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatcta +tagatatatatctagatatagatctatgagtatatatctatagatatctagatatatatt +tatagatagatatatctatagatatctatatatttctatcgatagagatatctatagata +tctatcaatatatctatagatttctagagatatgtatctagatataaatctatagacata +gatatagatatatagatatttaactgccaatgtcctaaacactttatactcaacacattt +tttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagatag +tatctatctagatatcgg--------------------tctagatagtatctatctagat +atctgcgtagatgtctagatatctatctagatat---------------tatctatctag +a----------------------------------------------------------- +----------------------------------------tatctgtcgctatctagata +tctatctaga---tatctgtcgctatctagatatctatctaga----------------- +----------------------------------------------------tatctgtc +gctatctagatatctatctagatatcatctgtcgctatctagatatctatctagatatca +tctgtcgctatctagatatctatctagatatcatctgtcgctatctagatatctatctag +atatcatctgtcgctatctagatatctatctagatatcatctgtcgctatctagatatct +atctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctag +atatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgct +atctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatct +gtcgctatctagatatctatctagatagtatctgtcgctatctagatatctagatagtat +ctgtcgctatctagatatctagatagtatctgtctagatagctatctagatagtatctgt +ctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatctgt +ctagatatctgtagatatctagatatctatatctatctggatatctatagatatttaact +gccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatatgag +gtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagccca +tgggc +>p:HG002_2_chr20:55943819-55945908 +gtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctccttc +caagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttca +gccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtggat +cacttgaggttaggagtttgagaccagcctggccaacatggtgaaacctcgcctctacta +aaaatacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggagg +ctgaggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggcac +cactgcattccagctgggcaacagagagagactctttcttaaatatatatattttatata +tatatagatacacacacacacacacacacacacac------------------------- +---------atatatatatatatatatatatatatatatatatgcatgcatgccagatgc +agtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgagg +tcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaatacaa +aattagctggctgtggtggctcatgctggtaatcccagctacttgggaggctgaggcagg +agaatcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcactc +cagcctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatcta +tagatatatatctagatatagatctatgagtatatatctatagatatctagatatatatt +tatagatagatatatctatagatatctatatatttctatcgatagagatatctatagata +tctatcaatatatctatagatttctagagatatgtatctagatataaatctatagacata +gatatagatatatagatatttaactgccaatgtcctaaacactttatactcaacacattt +tttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagatag +tatctatctagatatctgtgtagatgtctagatatctatctagatattatctatctagat +atct--gtcgctatctagatatctatctagatatctgtcgctatctagatatctatctag +atatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatc +tagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagata +tctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatc +tagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtc +gctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagta +tctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctag +atagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatct +atctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctag +atatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgct +atctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatct +gtcgctatctagatatctatctagatagtatctgtcgctatctagatatctagatagtat +ctgtcgctatctagatatctagatagtatctgtctagatagctatctagatagtatctgt +ctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatctgt +ctagatatctgtagatatctagatatctatatctatctggatatctatagatatttaact +gccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatatgag +gtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagccca +tgggc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/msa.fa.fai new file mode 100644 index 00000000..3d15c300 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_55943819_55945908 2225 29 60 61 +syndip_1_chr20:55943819-55945908 2225 2326 60 61 +syndip_2_chr20:55943819-55945908 2225 4623 60 61 +p:HG002_1_chr20:55943819-55945908 2225 6921 60 61 +p:HG002_2_chr20:55943819-55945908 2225 9219 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/output.vcf.gz new file mode 100644 index 00000000..2afc778c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/output.vcf.gz.tbi new file mode 100644 index 00000000..3ad8b0cc Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:55943919-55945808/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/base.vcf.gz new file mode 100644 index 00000000..38fae46d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/base.vcf.gz.tbi new file mode 100644 index 00000000..f5ac72e6 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/comp.vcf.gz new file mode 100644 index 00000000..479ce20b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/comp.vcf.gz.tbi new file mode 100644 index 00000000..99266f05 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/haps.fa new file mode 100644 index 00000000..d8908ce9 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/haps.fa @@ -0,0 +1,154 @@ +>ref_chr20_56280322_56282215 +GGTGGACATAGTGTATCTACAGATGGGACAATCTAAGATGGTTACAACATTACTACATAGTATCGCAAATAGAAATGGAAAGCCTGAATCTAACCATGAGAAAATTTAAAATAACTATCAAAAAGGTAACATCCATATACAGATATAATATCTATAACATATATAGATATATGGATATAACATCCATATATAGATATATCTATATATCTATCTATAGCTACATCTACAGATATCTATAGCTACATCTACAGATATCTACAGATATCTATAGCTACATCTACAGATATCTATAGCTACATCTACAGATATCTACAGATATCTACAGCTACATCTACAGATATCTATAGATATCTATAGCTATATCTACAGATATCTATCGATAGATATATCTATCGATAGATATATCCACATAGATATCTAGATATATATGGATATATCTATAGATATCTATCTGGATATATCTATCGATAGATATATAGATATATATAGATAAAGCTATATAGATATATATAGATAAACCTATATAGATACATAGATATATAGAGAGAAACCTATATACATATATAGATATATAGAGAGAAACCTATATAGATATATAGATATATAGAGAGAAACCTATATAGATGTATAGATAAACCTATATAGATATATAGATAAACCTATGTAGATATATAGATATATATAGATAAATCTATATAGATATATAAAATAGATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATATATACATAAATCTATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATACATCTATACAGATATATAGATACATATAGATACATCTATACAGATATATAGATACATATAGATACATCTATACAGATATATTGATACATATAGATACATCTATATAGATATATAGATATATAGATACATCTATATAGATATATAGATATATAGATACATCTATATAGATATATATAGATACATCTATATATAGACATATAGATATATATAGATACATCTATATATAGATATATAGATATATATAGATACATCTACACAGAGAGATATATAGAAACATCTACACAGGGAGATATATAGATACATCTACACAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATAGAGATATATATAGATACATCTACATAGAGATATATATAGATACATCTATATAGAGATATATCTACCTATACTTCCTGTGAGTTGTGTTTCTCTGGAGAACTAATAGGTAGGGTGACTGTATAATTTACTCTCCATACTGGGACACTTTTAATCATTGCTATAATACATTAATTTTAATCTAATCTTCTTATCCCT +>syndip_1_chr20:56280322-56282215 +GGTGGACATAGTGTATCTACAGATGGGACAATCTAAGATGGTTACAACATTACTACATAG +TATCGCAAATAGAAATGGAAAGCCTGAATCTAACCATGAGAAAATTTAAAATAACTATCA +AAAAGGTAACATCCATATACAGATATAATATCTATAACATATATAGATATATGGATATAA +CATCCATATATAGATATATCTATATATCTATCTATAGCTACATCTACAGATATCTATAGC +CACATCTACAGATATCTATAGCTACATCTACAGATATCTACAGATATCTACAGCTACATC +TACAGATATCTATAGATATCTATAGCTATATCTACAGATATCTATCGATAGATATATCTA +TCGATAGATATATCCACATAGATATCTAGATATATATGGATATATCTATAGATATCTATC +TGGATATATCTATCGATAGATATATAGATATATATAGATAAAGCTATATAGATATATATA +GATAAACCTATATAGATACATAGATATATAGAGAGAAACCTATATACATATATAGATATA +TAGAGAGAAACCTATATAGATATATAGATATATAGAGATAAACCTATATAGATGTATAGA +TAAACCTATATAGATATATAGATAAACCTATGTAGATATATAGATATATATAGATAAATC +TATATAGATATATAAAATAGATAAATCTATATAGATATATATACATAAATCTATATAGAT +ATATATACATAAATCTATATATATACATAAATCTATATATACATAAATCTATATAGATAT +ATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAAT +CTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATAT +ATACATAAATCTATACAGATACATATACATAAATCTATACAGATACATATACATAAATCT +ATACAGATACATATACATAAATCTATACAGATATATAGATACATATAGATAAATCTATAC +AGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATACATCT +ATACAGATATATAGATACATATAGATACATCTATACAGATATATAGATACATATAGATAC +ATCTATACAGATATATAGATACATATAGATACATCTATACAGATATATAGATACATATAG +ATACATCTATACAGATATATAGATACATATAGATACATCTATACAGATATATAGATACAT +ATAGATACATCTATACAGATATATTGATACATATAGATACATCTATATAGATATATTGAT +ACATATAGATACATCTATATAGATATATTGATACATATAGATACATCTATATAGATATAT +TGATACATATAGATACATCTATATAGATTAGATATATATAGATACATCTATATAGATTAG +ATATATATAGATACATCTATATAGATTAGATATATATAGATACATCTATATATAGATATA +TAGATATATATAGATACATCTATATATAGATATATAGATATATATAGATACATCTATATA +TAGATATATAGATGTATATAGATACATCTATATATAGATATATAGATGTATATAGATACA +TCTATATATAGATATATAGATGTATATAGATACATCTATATATAGATATATAGATGTATA +TAGATACATCTATATATAGATATATAGATGTATATAGATACATCTATATATAGATATATA +GATGTATATAGATACATCTATATATAGATATATAGATGTATATAGATACATCTATATATA +GATATATAGATGTATATAGATACATCTATATATAGATATATAGATGTATATAGATACATC +TATATATAGATATATAGATGTATATAGATACATAGATATATATAGATACATTTATGTATA +TATATATGTATATATAGATATATAGATATATATAGATACATCTACACAGAGAGATATATA +GAAACATCTACACAGGGAGATATATAGATACATCTACATAGAGAGATATATAGATACATC +TACATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATAGA +GAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATAGAGAGATATA +TAGATACATCTACATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACA +TCTACATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATA +GAGAGATATATAGATACATCTACATAGAGATATATATAGATACATCTACATAGAGATATA +TATAGATACATCTATATAGAGATATATCTACCTATACTTCCTGTGAGTTGTGTTTCTCTG +GAGAACTAATAGGTAGGGTGACTGTATAATTTACTCTCCATACTGGGACACTTTTAATCA +TTGCTATAATACATTAATTTTAATCTAATCTTCTTATCCCT +>syndip_2_chr20:56280322-56282215 +GGTGGACATAGTGTATCTACAGATGGGACAATCTAAGATGGTTACAACATTACTACATAG +TATCGCAAATAGAAATGGAAAGCCTGAATCTAACCATGAGAAAATTTAAAATAACTATCA +AAAAGGTAACATCCATATACAGATATAATATCTATAACATATATAGATATATGGATATAA +CATCCATATATAGATATATCTATATATCTATCTATAGCTACATCTACAGATATCTATAGC +TACATCTACAGATATCTACAGATATCTATAGCTACATCTACAGATATCTACAGATATCTA +TAGCTACATCTACAGATATCTATAGCTACATCTACAGATATCTACAGATATCTACAGCTA +CATCTACAGATATCTATAGATATCTATAGCTATATCTACAGATATCTATCGATAGATATA +TCTATCGATAGATATATCCACATAGATATCTAGATATATATGGATATATCTATAGATATC +TATCTGGATATATCTATCGATAGATATATAGATATATATAGATAAAGCTATATAGATATA +TATAGATAAACCTATATAGATACATAGATATATAGAGAGAAACCTATATACATATATAGA +TATATAGAGAGAAACCTATATAGATATATAGATATATAGAGATAAACCTATATAGATGTA +TAGATAAACCTATATAGATATATAGATAAACCTATGTAGATATATAGATATATATAGATA +AATCTATATAGATATATAAAATAGATAAATCTATATAGATATATATACATAAATCTATAT +AGATATATATACATAAATCTATATATATACATAAATCTATATATACATAAATCTATATAG +ATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACAT +AAATCTATATAGATATATACATAAATCTATATATATATACATAAATCTATATAGATATAT +ATACATAAATCTATATAGATACATATAGATAAATCTATACAGATATATAAATATATATAG +ATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACAT +ATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGAT +ACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATAT +AGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGAT +ATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATACATCTATAT +AGATATATTGATACATATAGATACATCTATATAGATATATAGATATATAGATACATCTAT +ATAGATATATATAGATACATCTATATATAGACATATAGATATATATAGATACATCTATAT +ATAGATATATAGATATATATAGATACATCTATATATAGATATATAGATATATATAGATAC +ATCTACACAGAGAGATATATAGAAACATCTACACAGGGAGATATATAGATACATCTACAT +AGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTATATAGAGAGAT +ATATAGATACATCTATATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGAT +ACATCTACATAGAGAGATATATAGATACATCTACATAGAGATATATATAGATACATCTAC +ATAGAGATATATATAGATACATCTATATAGAGATATATCTACCTATACTTCCTGTGAGTT +GTGTTTCTCTGGAGAACTAATAGGTAGGGTGACTGTATAATTTACTCTCCATACTGGGAC +ACTTTTAATCATTGCTATAATACATTAATTTTAATCTAATCTTCTTATCCCT +>p:HG002_1_chr20:56280322-56282215 +GGTGGACATAGTGTATCTACAGATGGGACAATCTAAGATGGTTACAACATTACTACATAG +TATCGCAAATAGAAATGGAAAGCCTGAATCTAACCATGAGAAAATTTAAAATAACTATCA +AAAAGGTAACATCCATATACAGATATAATATCTATAACATATATAGATATATGGATATAA +CATCCATATATAGATATATCTATATATCTATCTATAGCTACATCTACAGATATCTATAGC +TACATCTACAGATATCTACAGATATCTATAGCTACATCTACAGATATCTACAGATATCTA +TAGCTACATCTACAGATATCTATAGCTACATCTACAGATATCTACAGATATCTACAGCTA +CATCTACAGATATCTATAGATATCTATAGCTATATCTACAGATATCTATCGATAGATATA +TCTATCGATAGATATATCCACATAGATATCTAGATATATATGGATATATCTATAGATATC +TATCTGGATATATCTATCGATAGATATATAGATATATATAGATAAAGCTATATAGATATA +TATAGATAAACCTATATAGATACATAGATATATAGAGAGAAACCTATATACATATATAGA +TATATAGAGAGAAACCTATATAGATATATAGATATATAGAGATAAACCTATATAGATGTA +TAGATAAACCTATATAGATATATAGATAAACCTATGTAGATATATAGATATATATAGATA +AATCTATATAGATATATAAAATAGATAAATCTATATAGATATATATACATAAATCTATAT +AGATATATATACATAAATCTATATATATACATAAATCTATATATACATAAATCTATATAG +ATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACAT +AAATCTATATAGATATATACATAAATCTATATATATATACATAAATCTATATAGATATAT +ATACATAAATCTATATAGATACATATAGATAAATCTATACAGATATATAAATATATATAG +ATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACAT +ATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGAT +ACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATAT +AGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGAT +ATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATACATCTATAT +AGATATATTGATACATATAGATACATCTATATAGATATATAGATATATAGATACATCTAT +ATAGATATATATAGATACATCTATATATAGACATATAGATATATATAGATACATCTATAT +ATAGATATATAGATATATATAGATACATCTATATATAGATATATAGATATATATAGATAC +ATCTACACAGAGAGATATATAGAAACATCTACACAGGGAGATATATAGATACATCTACAT +AGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTATATAGAGAGAT +ATATAGATACATCTATATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGAT +ACATCTACATAGAGAGATATATAGATACATCTACATAGAGATATATATAGATACATCTAC +ATAGAGATATATATAGATACATCTATATAGAGATATATCTACCTATACTTCCTGTGAGTT +GTGTTTCTCTGGAGAACTAATAGGTAGGGTGACTGTATAATTTACTCTCCATACTGGGAC +ACTTTTAATCATTGCTATAATACATTAATTTTAATCTAATCTTCTTATCCCT +>p:HG002_2_chr20:56280322-56282215 +GGTGGACATAGTGTATCTACAGATGGGACAATCTAAGATGGTTACAACATTACTACATAG +TATCGCAAATAGAAATGGAAAGCCTGAATCTAACCATGAGAAAATTTAAAATAACTATCA +AAAAGGTAACATCCATATACAGATATAATATCTATAACATATATAGATATATGGATATAA +CATCCATATATAGATATATCTATATATCTATCTATAGCTACATCTACAGATATCTATAGC +CACATCTACAGATATCTATAGCTACATCTACAGATATCTACAGATATCTACAGCTACATC +TACAGATATCTATAGATATCTATAGCTATATCTACAGATATCTATCGATAGATATATCTA +TCGATAGATATATCCACATAGATATCTAGATATATATGGATATATCTATAGATATCTATC +TGGATATATCTATCGATAGATATATAGATATATATAGATAAAGCTATATAGATATATATA +GATAAACCTATATAGATACATAGATATATAGAGAGAAACCTATATACATATATAGATATA +TAGAGAGAAACCTATATAGATATATAGATATATAGAGATAAACCTATATAGATGTATAGA +TAAACCTATATAGATATATAGATAAACCTATGTAGATATATAGATATATATAGATAAATC +TATATAGATATATAAAATAGATAAATCTATATAGATATATATACATAAATCTATATAGAT +ATATATACATAAATCTATATATATACATAAATCTATATATACATAAATCTATATAGATAT +ATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAAT +CTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATAT +ATACATAAATCTATACAGATACATATACATAAATCTATACAGATACATATACATAAATCT +ATACAGATACATATACATAAATCTATACAGATATATAGATACATATAGATAAATCTATAC +AGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATACATCT +ATACAGATATATAGATACATATAGATACATCTATACAGATATATAGATACATATAGATAC +ATCTATACAGATATATAGATACATATAGATACATCTATACAGATATATAGATACATATAG +ATACATCTATACAGATATATAGATACATATAGATACATCTATACAGATATATAGATACAT +ATAGATACATCTATACAGATATATTGATACATATAGATACATCTATATAGATATATTGAT +ACATATAGATACATCTATATAGATATATTGATACATATAGATACATCTATATAGATATAT +TGATACATATAGATACATCTATATAGATTAGATATATATAGATACATCTATATAGATTAG +ATATATATAGATACATCTATATAGATTAGATATATATAGATACATCTATATATAGATATA +TAGATATATATAGATACATCTATATATAGATATATAGATATATATAGATACATCTATATA +TAGATATATAGATGTATATAGATACATCTATATATAGATATATAGATGTATATAGATACA +TCTATATATAGATATATAGATGTATATAGATACATCTATATATAGATATATAGATGTATA +TAGATACATCTATATATAGATATATAGATGTATATAGATACATCTATATATAGATATATA +GATGTATATAGATACATCTATATATAGATATATAGATGTATATAGATACATCTATATATA +GATATATAGATGTATATAGATACATCTATATATAGATATATAGATGTATATAGATACATC +TATATATAGATATATAGATGTATATAGATACATAGATATATATAGATACATTTATGTATA +TATATATGTATATATAGATATATAGATATATATAGATACATCTACACAGAGAGATATATA +GAAACATCTACACAGGGAGATATATAGATACATCTACATAGAGAGATATATAGATACATC +TACATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATAGA +GAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATAGAGAGATATA +TAGATACATCTACATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACA +TCTACATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATA +GAGAGATATATAGATACATCTACATAGAGATATATATAGATACATCTACATAGAGATATA +TATAGATACATCTATATAGAGATATATCTACCTATACTTCCTGTGAGTTGTGTTTCTCTG +GAGAACTAATAGGTAGGGTGACTGTATAATTTACTCTCCATACTGGGACACTTTTAATCA +TTGCTATAATACATTAATTTTAATCTAATCTTCTTATCCCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/haps.fa.ref.fa new file mode 100644 index 00000000..cf44bd90 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:56280322-56282215 +GGTGGACATAGTGTATCTACAGATGGGACAATCTAAGATGGTTACAACATTACTACATAGTATCGCAAATAGAAATGGAAAGCCTGAATCTAACCATGAGAAAATTTAAAATAACTATCAAAAAGGTAACATCCATATACAGATATAATATCTATAACATATATAGATATATGGATATAACATCCATATATAGATATATCTATATATCTATCTATAGCTACATCTACAGATATCTATAGCTACATCTACAGATATCTACAGATATCTATAGCTACATCTACAGATATCTATAGCTACATCTACAGATATCTACAGATATCTACAGCTACATCTACAGATATCTATAGATATCTATAGCTATATCTACAGATATCTATCGATAGATATATCTATCGATAGATATATCCACATAGATATCTAGATATATATGGATATATCTATAGATATCTATCTGGATATATCTATCGATAGATATATAGATATATATAGATAAAGCTATATAGATATATATAGATAAACCTATATAGATACATAGATATATAGAGAGAAACCTATATACATATATAGATATATAGAGAGAAACCTATATAGATATATAGATATATAGAGAGAAACCTATATAGATGTATAGATAAACCTATATAGATATATAGATAAACCTATGTAGATATATAGATATATATAGATAAATCTATATAGATATATAAAATAGATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATATATACATAAATCTATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATACATCTATACAGATATATAGATACATATAGATACATCTATACAGATATATAGATACATATAGATACATCTATACAGATATATTGATACATATAGATACATCTATATAGATATATAGATATATAGATACATCTATATAGATATATAGATATATAGATACATCTATATAGATATATATAGATACATCTATATATAGACATATAGATATATATAGATACATCTATATATAGATATATAGATATATATAGATACATCTACACAGAGAGATATATAGAAACATCTACACAGGGAGATATATAGATACATCTACACAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATAGAGATATATATAGATACATCTACATAGAGATATATATAGATACATCTATATAGAGATATATCTACCTATACTTCCTGTGAGTTGTGTTTCTCTGGAGAACTAATAGGTAGGGTGACTGTATAATTTACTCTCCATACTGGGACACTTTTAATCATTGCTATAATACATTAATTTTAATCTAATCTTCTTATCCCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/msa.fa new file mode 100644 index 00000000..5dc5acec --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/msa.fa @@ -0,0 +1,225 @@ +>ref_chr20_56280322_56282215 +ggtggacatagtgtatctacagatgggacaatctaagatggttacaacattactacatag +tatcgcaaatagaaatggaaagcctgaatctaaccatgagaaaatttaaaataactatca +aaaaggtaacatccatatacagatataatatctataacatatatagatatatggatataa +catccatatatagatatatctatatatctatctatagctac------------------- +-------------atctacagatatctatagctacatctacagatatctacagatatcta +tagctacatctacagatatctatagctacatctacagatatctacagatatctacagcta +catctacagatatctatagatatctatagctatatctacagatatctatcgatagatata +tctatcgatagatatatccacatagatatctagatatatatggatatatctatagatatc +tatctggatatatctatcgatagatatatagatatatatagataaagctatatagatata +tatagataaacctatatagatacatagatatatagagagaaacctatatacatatataga +tatatagagagaaacctatatagatatatagatatatagagagaaacctatatagatgta +tagataaacctatatagatatatagataaacctatgtagatatatagatatatatagata +aatctatatagatatataaaatagataaatctatatagatatatatacataaatctatat +agatatatatacataaatctatatagatatatatacataaatctatatatatacataaat +ctatatatacataaatctatatagatatatatacataaatctatatagatatatatacat +aaatctatatagatatatatacataaatctatatag------------------------ +atatatatacataaatctatatagatatatacataaatctatatagatatatatacataa +atctatatagatatatatacataaatctatatagatatatatacataaatc--------t +atatagatacatatagataaatctatacagatatatagatacatatagataaatctatac +agatatatagatacatatagataaatctatacagatatatagatacatatagataaatct +atacagatatatagatacatatagataaatctatacagatatatagatacatatagataa +atctatacagatatatagatacatatagataaatctatacagatatatagatacatatag +atacatctatacagatatatagatacatatagatacatctatacagatatatagatacat +atagatacatctatacagatatattgatacatatagatacatctatatagatatatagat +--atatagatacatctata----------------------------------------- +------------------------------------------------------tagata +tatagatata----tagatacatctatatagatatatatagatacatctatatatagaca +tatagatatatatagatacatctatatatagatatatagat------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----atatatagatacatctacacagagagatatatagaaacatctacacagggagata +tatagatacatctacacagagagatatatagatacatctac------------------- +-------atagagagatatatagatacatctacatagagagatatatagatacatctaca +tagagagatatatagatacatctacatagagagatatatagatacatctacatagagata +tatatagatacatctacatagagatatatatagatacatctatatagagatatatctacc +tatacttcctgtgagttgtgtttctctggagaactaataggtagggtgactgtataattt +actctccatactgggacacttttaatcattgctataatacattaattttaatctaatctt +cttatccct +>syndip_1_chr20:56280322-56282215 +ggtggacatagtgtatctacagatgggacaatctaagatggttacaacattactacatag +tatcgcaaatagaaatggaaagcctgaatctaaccatgagaaaatttaaaataactatca +aaaaggtaacatccatatacagatataatatctataacatatatagatatatggatataa +catccatatatagatatatctatatatctatctatagctac------------------- +---------------------------------------------atctacagatatcta +tagccacatctacagatatctatagctacatctacagatatctacagatatctacagcta +catctacagatatctatagatatctatagctatatctacagatatctatcgatagatata +tctatcgatagatatatccacatagatatctagatatatatggatatatctatagatatc +tatctggatatatctatcgatagatatatagatatatatagataaagctatatagatata +tatagataaacctatatagatacatagatatatagagagaaacctatatacatatataga +tatatagagagaaacctatatagatatatagatatatagagataaacctatatagatgta +tagataaacctatatagatatatagataaacctatgtagatatatagatatatatagata +aatctatatagatatataaaatag------------------------ataaatctatat +agatatatatacataaatctatatagatatatatacataaatctatatatatacataaat +ctatatatacataaatctatatagatatatatacataaatctatatagatatatatacat +aaatctatatagatatatatacataaatctatatagatatatatacataaatctatatag +atatatatacataaatctatatagatatatacataaatctatacagatacatatacataa +atctatacagatacatatacataaatctatacagatacatatacataaatctatacagat +atatagatacatatagataaatctatacagatatatagatacatatagataaatctatac +agatatatagatacatatagatacatctatacagatatatagatacatatagatacatct +atacagatatatagatacatatagatacatctatacagatatatagatacatatagatac +atctatacagatatatagatacatatagatacatctatacagatatatagatacatatag +atacatctatacagatatatagatacatatagatacatctatacagatatattgatacat +atagatacatctatatagatatattgatacatatagatacatctatatagatatattgat +acatatagatacatctatatagatatattgatacatatagatacatctatatagattaga +tatatatagatacatctatatagattagatatatatagatacatctatatagattagata +tatatagatacatctatatatagatatatagatatatatagatacatctatatatagata +tatagatatatatagatacatctatatatagatatatagatgtatatagatacatctata +tatagatatatagatgtatatagatacatctatatatagatatatagatgtatatagata +catctatatatagatatatagatgtatatagatacatctatatatagatatatagatgta +tatagatacatctatatatagatatatagatgtatatagatacatctatatatagatata +tagatgtatatagatacatctatatatagatatatagatgtatatagatacatctatata +tagatatatagatgtatatagatacatctatatatagatatatagatgtatatagataca +tagatatatatagatacatttatgtatatatatatgtatatatagatatatagatatata +tagatacatctacacagagagatatatagaaacatctacacagggagatatatagataca +tctacatagagagatatatagatacatctacatagagagatatatagatacatctacata +gagagatatatagatacatctacatagagagatatatagatacatctacatagagagata +tatagatacatctacatagagagatatatagatacatctacatagagagatatatagata +catctacatagagagatatatagatacatctacatagagagatatatagatacatctaca +tagagagatatatagatacatctacatagagagatatatagatacatctacatagagata +tatatagatacatctacatagagatatatatagatacatctatatagagatatatctacc +tatacttcctgtgagttgtgtttctctggagaactaataggtagggtgactgtataattt +actctccatactgggacacttttaatcattgctataatacattaattttaatctaatctt +cttatccct +>syndip_2_chr20:56280322-56282215 +ggtggacatagtgtatctacagatgggacaatctaagatggttacaacattactacatag +tatcgcaaatagaaatggaaagcctgaatctaaccatgagaaaatttaaaataactatca +aaaaggtaacatccatatacagatataatatctataacatatatagatatatggatataa +catccatatatagatatatctatatatctatctatagctacatctacagatatctatagc +tacatctacagatatctacagatatctatagctacatctacagatatctacagatatcta +tagctacatctacagatatctatagctacatctacagatatctacagatatctacagcta +catctacagatatctatagatatctatagctatatctacagatatctatcgatagatata +tctatcgatagatatatccacatagatatctagatatatatggatatatctatagatatc +tatctggatatatctatcgatagatatatagatatatatagataaagctatatagatata +tatagataaacctatatagatacatagatatatagagagaaacctatatacatatataga +tatatagagagaaacctatatagatatatagatatatagagataaacctatatagatgta +tagataaacctatatagatatatagataaacctatgtagatatatagatatatatagata +aatctatatagatatataaaatag------------------------ataaatctatat +agatatatatacataaatctatatagatatatatacataaatctatatatatacataaat +ctatatatacataaatctatatagatatatatacataaatctatatagatatatatacat +aaatctatatagatatatatacataaatctatatag------------------------ +--atatatacataaatctatat--atatatacataaatctatatagatatatatacataa +atctatatagatacatatagataaatctatacaga------------------------t +atataaatatatatagataaatctatacagatatatagatacatatagataaatctatac +agatatatagatacatatagataaatctatacagatatatagatacatatagataaatct +atacagatatatagatacatatagataaatctatacagatatatagatacatatagataa +atctatacagatatatagatacatatagataaatctatacagatatatagatacatatag +ataaatctatacagatatatagatacatatagataaatctatacagatatatagatacat +atagatacatctatatagatatattgatacatatagatacatctatatagatatatagat +--atatagatacatctata----------------------------------------- +------------------------------------------------------tagata +tatatagatacatctatatatagacatatagatatatatagatacatctatatatagata +tatagatatatatagatacatctatatatagatatatagat------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----atatatagatacatctacacagagagatatatagaaacatctacacagggagata +tatagatacatctacatagagagatatatagatacatctacatagagagatatatagata +catctatatagagagatatatagatacatctatatagagagatatatagatacatctaca +tagagagatatatagatacatctacatagagagatatatagatacatctacatagagata +tatatagatacatctacatagagatatatatagatacatctatatagagatatatctacc +tatacttcctgtgagttgtgtttctctggagaactaataggtagggtgactgtataattt +actctccatactgggacacttttaatcattgctataatacattaattttaatctaatctt +cttatccct +>p:HG002_1_chr20:56280322-56282215 +ggtggacatagtgtatctacagatgggacaatctaagatggttacaacattactacatag +tatcgcaaatagaaatggaaagcctgaatctaaccatgagaaaatttaaaataactatca +aaaaggtaacatccatatacagatataatatctataacatatatagatatatggatataa +catccatatatagatatatctatatatctatctatagctacatctacagatatctatagc +tacatctacagatatctacagatatctatagctacatctacagatatctacagatatcta +tagctacatctacagatatctatagctacatctacagatatctacagatatctacagcta +catctacagatatctatagatatctatagctatatctacagatatctatcgatagatata +tctatcgatagatatatccacatagatatctagatatatatggatatatctatagatatc +tatctggatatatctatcgatagatatatagatatatatagataaagctatatagatata +tatagataaacctatatagatacatagatatatagagagaaacctatatacatatataga +tatatagagagaaacctatatagatatatagatatatagagataaacctatatagatgta +tagataaacctatatagatatatagataaacctatgtagatatatagatatatatagata +aatctatatagatatataaaatag------------------------ataaatctatat +agatatatatacataaatctatatagatatatatacataaatctatatatatacataaat +ctatatatacataaatctatatagatatatatacataaatctatatagatatatatacat +aaatctatatagatatatatacataaatctatatag------------------------ +--atatatacataaatctatat--atatatacataaatctatatagatatatatacataa +atctatatagatacatatagataaatctatacaga------------------------t +atataaatatatatagataaatctatacagatatatagatacatatagataaatctatac +agatatatagatacatatagataaatctatacagatatatagatacatatagataaatct +atacagatatatagatacatatagataaatctatacagatatatagatacatatagataa +atctatacagatatatagatacatatagataaatctatacagatatatagatacatatag +ataaatctatacagatatatagatacatatagataaatctatacagatatatagatacat +atagatacatctatatagatatattgatacatatagatacatctatatagatatatagat +--atatagatacatctata----------------------------------------- +------------------------------------------------------tagata +tatatagatacatctatatatagacatatagatatatatagatacatctatatatagata +tatagatatatatagatacatctatatatagatatatagat------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----atatatagatacatctacacagagagatatatagaaacatctacacagggagata +tatagatacatctacatagagagatatatagatacatctacatagagagatatatagata +catctatatagagagatatatagatacatctatatagagagatatatagatacatctaca +tagagagatatatagatacatctacatagagagatatatagatacatctacatagagata +tatatagatacatctacatagagatatatatagatacatctatatagagatatatctacc +tatacttcctgtgagttgtgtttctctggagaactaataggtagggtgactgtataattt +actctccatactgggacacttttaatcattgctataatacattaattttaatctaatctt +cttatccct +>p:HG002_2_chr20:56280322-56282215 +ggtggacatagtgtatctacagatgggacaatctaagatggttacaacattactacatag +tatcgcaaatagaaatggaaagcctgaatctaaccatgagaaaatttaaaataactatca +aaaaggtaacatccatatacagatataatatctataacatatatagatatatggatataa +catccatatatagatatatctatatatctatctatagctac------------------- +---------------------------------------------atctacagatatcta +tagccacatctacagatatctatagctacatctacagatatctacagatatctacagcta +catctacagatatctatagatatctatagctatatctacagatatctatcgatagatata +tctatcgatagatatatccacatagatatctagatatatatggatatatctatagatatc +tatctggatatatctatcgatagatatatagatatatatagataaagctatatagatata +tatagataaacctatatagatacatagatatatagagagaaacctatatacatatataga +tatatagagagaaacctatatagatatatagatatatagagataaacctatatagatgta +tagataaacctatatagatatatagataaacctatgtagatatatagatatatatagata +aatctatatagatatataaaatag------------------------ataaatctatat +agatatatatacataaatctatatagatatatatacataaatctatatatatacataaat +ctatatatacataaatctatatagatatatatacataaatctatatagatatatatacat +aaatctatatagatatatatacataaatctatatagatatatatacataaatctatatag +atatatatacataaatctatatagatatatacataaatctatacagatacatatacataa +atctatacagatacatatacataaatctatacagatacatatacataaatctatacagat +atatagatacatatagataaatctatacagatatatagatacatatagataaatctatac +agatatatagatacatatagatacatctatacagatatatagatacatatagatacatct +atacagatatatagatacatatagatacatctatacagatatatagatacatatagatac +atctatacagatatatagatacatatagatacatctatacagatatatagatacatatag +atacatctatacagatatatagatacatatagatacatctatacagatatattgatacat +atagatacatctatatagatatattgatacatatagatacatctatatagatatattgat +acatatagatacatctatatagatatattgatacatatagatacatctatatagattaga +tatatatagatacatctatatagattagatatatatagatacatctatatagattagata +tatatagatacatctatatatagatatatagatatatatagatacatctatatatagata +tatagatatatatagatacatctatatatagatatatagatgtatatagatacatctata +tatagatatatagatgtatatagatacatctatatatagatatatagatgtatatagata +catctatatatagatatatagatgtatatagatacatctatatatagatatatagatgta +tatagatacatctatatatagatatatagatgtatatagatacatctatatatagatata +tagatgtatatagatacatctatatatagatatatagatgtatatagatacatctatata +tagatatatagatgtatatagatacatctatatatagatatatagatgtatatagataca +tagatatatatagatacatttatgtatatatatatgtatatatagatatatagatatata +tagatacatctacacagagagatatatagaaacatctacacagggagatatatagataca +tctacatagagagatatatagatacatctacatagagagatatatagatacatctacata +gagagatatatagatacatctacatagagagatatatagatacatctacatagagagata +tatagatacatctacatagagagatatatagatacatctacatagagagatatatagata +catctacatagagagatatatagatacatctacatagagagatatatagatacatctaca +tagagagatatatagatacatctacatagagagatatatagatacatctacatagagata +tatatagatacatctacatagagatatatatagatacatctatatagagatatatctacc +tatacttcctgtgagttgtgtttctctggagaactaataggtagggtgactgtataattt +actctccatactgggacacttttaatcattgctataatacattaattttaatctaatctt +cttatccct diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/msa.fa.fai new file mode 100644 index 00000000..da3fb24c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_56280322_56282215 2589 29 60 61 +syndip_1_chr20:56280322-56282215 2589 2696 60 61 +syndip_2_chr20:56280322-56282215 2589 5363 60 61 +p:HG002_1_chr20:56280322-56282215 2589 8031 60 61 +p:HG002_2_chr20:56280322-56282215 2589 10699 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/output.vcf.gz new file mode 100644 index 00000000..24e8f24a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/output.vcf.gz.tbi new file mode 100644 index 00000000..35fce2c2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:56280422-56282115/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/base.vcf.gz new file mode 100644 index 00000000..01c14f16 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/base.vcf.gz.tbi new file mode 100644 index 00000000..aefa596f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/comp.vcf.gz new file mode 100644 index 00000000..fd710583 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/comp.vcf.gz.tbi new file mode 100644 index 00000000..1377c9c8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/haps.fa new file mode 100644 index 00000000..3fde0fc0 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/haps.fa @@ -0,0 +1,76 @@ +>ref_chr20_57090572_57091512 +AGCACAGTGAGGCCCACTTCAGACTTCCGAGCTCCAGACTATGAGATCAAGTGTTGTTTTAAGCCACCAAGTTTGGGAAAATTTGCCACAGCAGCAAGAGGAAACGAACGCACTCAGGTGCTCCTGCCACACACACTCACAGTTGCACAAGCTGGTGCAGCTCCAGACCCACACACCTCCACCACCACACACTCCGCCATGCACACACACCTCCACGCACACACACCTCCACCCGCACACACACACACCTTCACCACCACACACTCCACCCACACACACCTCCACCCACACACCTCCACCCACACACACCTCCGCCCACACACACCTCCGCCCACACACACCTCCGCCCACACACACCTCCACCCACACACACCTCCGCCCACACACCTCCGCCCACACACACCTCCGCCCTCACACACCTCCACCCACACACACCTCCACCCACACACGCCTCCACCCGCACACACCTCCACCACCACACACACCTCCACCCACACACACCACCCATGCACACACCTCCACCCACACACACACACCTCCACCCACACACACACACACCTCCACCCACACACACCACCCACACACACCACCCATGCACACACCTCCACCCACACACACACACCTCCACCCGCACACACCTCCACCACCACACACATCTCCACCCACACACACCACCCATGTGCACACCTCCACTGGCACACACCACCCATGCACACACCTCCACTGGCACGCACTACTCCACCTGCGTGCGCCTCCCACCTGCGTTCACCCTCCACCTGTGTTCGCTCCCACCCACTCATGCCTCTCCACCCGCAAAAGTGTGAGTGCTGAGGCTGGGACTCAACCTGAGCCGCTGGCTCTGGATTACTGGGTCCTGCCGGGCTGGCCAGGCCTGGTCACAGGCCGGGTCCCAGTCAGCAGCTCTTTACCTCAACAAGGAG +>syndip_1_chr20:57090572-57091512 +AGCACAGTGAGGCCCACTTCAGACTTCCGAGCTCCAGACTATGAGATCAAGTGTTGTTTT +AAGCCACCAAGTTTGGGAAAATTTGCCACAGCAGCAAGAGGAAACGAACGCACTCAGGTG +CTCCTGCCACACACACTCACAGTTGCACAAGCTGGTGCAGCTCCAGACCCACACACCTCC +ACCACCACACACTCCACCATGCACACACACCTCCACGCACACACACCTCCACCCGCACAC +ACACACACCTTCACCACCACACACTCCACCCACACACACCTCCACCCACACACCTCCACC +CACACACACCTCCGCCCACACACACCTCCGCCCACACACACCTCCACCCACACACACCTC +CACCCACACACCTCCGCCCACACACACCTCCGCCCTCACACACCTCCACCCACACACACC +TCCACCCACACACGCCTCCACCCGCACACACCTCCACCACCACACACACCTCCACCCACA +CACACCACCCATGCACACACCTCCACCCACACACACACACCTCCACCCACACACACCTCC +ACCCACACGCCACCCATGCACACACCTCCACCCACACACACACACACCACCCACCCACAC +ACACCTCCACCCGCACACACCTCCACCACCACACACACCTCCACCCACACACACCACCCA +TGCACACACCTCCACCCACACACACACACACCTCCACCCACACACACCTCCACCCACACA +CACCTCCACCCACACACACACACCTCCACCCACCCACACACACCTCCACCCGCACACACC +TCCACCACCACACACATCTCCACCCACACACACCACCCATGTGCACACCTCCACTGGCAC +ACACCACCCATGCACACACCTCCACTGGCACGCACTACTCCACCTGCGTGCGCCTCCCAC +CTGCGTTCACCCTCCACCTGTGTTCGCTCCCACCCACTCATGCCTCTCCACCCGCAAAAG +TGTGAGTGCTGAGGCTGGGACTCAACCTGAGCCGCTGGCTCTGGATTACTGGGTCCTGCC +GGGCTGGCCAGGCCTGGTCACAGGCCGGGTCCCAGTCAGCAGCTCTTTACCTCAACAAGG +AG +>syndip_2_chr20:57090572-57091512 +AGCACAGTGAGGCCCACTTCAGACTTCCGAGCTCCAGACTATGAGATCAAGTGTTGTTTT +AAGCCACCAAGTTTGGGAAAATTTGCCACAGCAGCAAGAGGAAACGAACGCACTCAGGTG +CTCCTGCCACACACACTCACAGTTGCACAAGCTGGTGCAGCTCCAGACCCACACACCTCC +ACCACCACACACTCCGCCATGCACACACACCTCCACGCACACACACCTCCACCCGCACAC +ACACACACCTTCACCACCACACACTCCACCCACACACACCTCCACCCACACACCTCCACC +CACACACACCTCCGCCCACACACACCTCCGCCCACACACACCTCCGCCCACACACACCTC +CACCCACACACACCTCCGCCCACACACCTCCGCCCACACACACCTCCGCCCTCACACACC +TCCACCCACACACACCTCCACCCACACACGCCTCCACCCGCACACACCTCCACCACCACA +CACACCTCCACCCACACACACCACCCATGCACACACCTCCACCCACACACACACACCTCC +ACCCACACACACACACACCTCCACCCACACACACCACCCACACACACCACCCATGCACAC +ACCTCCACCCACACACACACACCTCCACCCGCACACACCTCCACCACCACACACATCTCC +ACCCACACACACCACCCATGTGCACACCTCCACTGGCACACACCACCCATGCACACACCT +CCACTGGCACGCACTACTCCACCTGCGTGCGCCTCCCACCTGCGTTCACCCTCCACCTGT +GTTCGCTCCCACCCACTCATGCCTCTCCACCCGCAAAAGTGTGAGTGCTGAGGCTGGGAC +TCAACCTGAGCCGCTGGCTCTGGATTACTGGGTCCTGCCGGGCTGGCCAGGCCTGGTCAC +AGGCCGGGTCCCAGTCAGCAGCTCTTTACCTCAACAAGGAG +>p:HG002_1_chr20:57090572-57091512 +AGCACAGTGAGGCCCACTTCAGACTTCCGAGCTCCAGACTATGAGATCAAGTGTTGTTTT +AAGCCACCAAGTTTGGGAAAATTTGCCACAGCAGCAAGAGGAAACGAACGCACTCAGGTG +CTCCTGCCACACACACTCACAGTTGCACAAGCTGGTGCAGCTCCAGACCCACACACCTCC +ACCACCACACACTCCGCCATGCACACACACCTCCACGCACACACACCTCCACCCGCACAC +ACACACACCTTCACCACCACACACTCCACCCACACACACCTCCACCCACACACCTCCACC +CACACACACCTCCGCCCACACACACCTCCGCCCACACACACCTCCGCCCACACACACCTC +CACCCACACACACCTCCGCCCACACACCTCCGCCCACACACACCTCCGCCCTCACACACC +TCCACCCACACACACCTCCACCCACACACGCCTCCACCCGCACACACCTCCACCACCACA +CACACCTCCACCCACACACACCACCCATGCACACACCTCCACCCACACACACACACCTCC +ACCCACACACACACACACCTCCACCCACACACACCACCCACACACACCACCCATGCACAC +ACCTCCACCCACACACACACACCTCCACCCGCACACACCTCCACCACCACACACATCTCC +ACCCACACACACCACCCATGTGCACACCTCCACTGGCACACACCACCCATGCACACACCT +CCACTGGCACGCACTACTCCACCTGCGTGCGCCTCCCACCTGCGTTCACCCTCCACCTGT +GTTCGCTCCCACCCACTCATGCCTCTCCACCCGCAAAAGTGTGAGTGCTGAGGCTGGGAC +TCAACCTGAGCCGCTGGCTCTGGATTACTGGGTCCTGCCGGGCTGGCCAGGCCTGGTCAC +AGGCCGGGTCCCAGTCAGCAGCTCTTTACCTCAACAAGGAG +>p:HG002_2_chr20:57090572-57091512 +AGCACAGTGAGGCCCACTTCAGACTTCCGAGCTCCAGACTATGAGATCAAGTGTTGTTTT +AAGCCACCAAGTTTGGGAAAATTTGCCACAGCAGCAAGAGGAAACGAACGCACTCAGGTG +CTCCTGCCACACACACTCACAGTTGCACAAGCTGGTGCAGCTCCAGACCCACACACCTCC +ACCACCACACACTCCACCATGCACACACACCTCCACGCACACACACCTCCACCCGCACAC +ACACACACCTTCACCACCACACACTCCACCCACACACACCTCCACCCACACACCTCCACC +CACACACACCTCCGCCCACACACACCTCCGCCCACACACACCTCCACCCACACACACCTC +CACCCACACACCTCCGCCCACACACACCTCCGCCCTCACACACCTCCACCCACACACACC +TCCACCCACACACGCCTCCACCCGCACACACCTCCACCACCACACACACCTCCACCCACA +CACACCACCCATGCACACACCTCCACCCACACACACACACCTCCACCCACACACACCTCC +ACCCACACGCCACCCATGCACACACCTCCACCCACACACACACACACCACCCACCCACAC +ACACCTCCACCCGCACACACCTCCACCACCACACACACCTCCACCCACACACACCACCCA +TGCACACACCTCCACCCACACACACACACACCTCCACCCACACACACCTCCACCCACACA +CACCTCCACCCACACACACACACCTCCACCCACCCACACACACCTCCACCCGCACACACC +TCCACCACCACACACATCTCCACCCACACACACCACCCATGTGCACACCTCCACTGGCAC +ACACCACCCATGCACACACCTCCACTGGCACGCACTACTCCACCTGCGTGCGCCTCCCAC +CTGCGTTCACCCTCCACCTGTGTTCGCTCCCACCCACTCATGCCTCTCCACCCGCAAAAG +TGTGAGTGCTGAGGCTGGGACTCAACCTGAGCCGCTGGCTCTGGATTACTGGGTCCTGCC +GGGCTGGCCAGGCCTGGTCACAGGCCGGGTCCCAGTCAGCAGCTCTTTACCTCAACAAGG +AG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/haps.fa.ref.fa new file mode 100644 index 00000000..f9b612ec --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:57090572-57091512 +AGCACAGTGAGGCCCACTTCAGACTTCCGAGCTCCAGACTATGAGATCAAGTGTTGTTTTAAGCCACCAAGTTTGGGAAAATTTGCCACAGCAGCAAGAGGAAACGAACGCACTCAGGTGCTCCTGCCACACACACTCACAGTTGCACAAGCTGGTGCAGCTCCAGACCCACACACCTCCACCACCACACACTCCGCCATGCACACACACCTCCACGCACACACACCTCCACCCGCACACACACACACCTTCACCACCACACACTCCACCCACACACACCTCCACCCACACACCTCCACCCACACACACCTCCGCCCACACACACCTCCGCCCACACACACCTCCGCCCACACACACCTCCACCCACACACACCTCCGCCCACACACCTCCGCCCACACACACCTCCGCCCTCACACACCTCCACCCACACACACCTCCACCCACACACGCCTCCACCCGCACACACCTCCACCACCACACACACCTCCACCCACACACACCACCCATGCACACACCTCCACCCACACACACACACCTCCACCCACACACACACACACCTCCACCCACACACACCACCCACACACACCACCCATGCACACACCTCCACCCACACACACACACCTCCACCCGCACACACCTCCACCACCACACACATCTCCACCCACACACACCACCCATGTGCACACCTCCACTGGCACACACCACCCATGCACACACCTCCACTGGCACGCACTACTCCACCTGCGTGCGCCTCCCACCTGCGTTCACCCTCCACCTGTGTTCGCTCCCACCCACTCATGCCTCTCCACCCGCAAAAGTGTGAGTGCTGAGGCTGGGACTCAACCTGAGCCGCTGGCTCTGGATTACTGGGTCCTGCCGGGCTGGCCAGGCCTGGTCACAGGCCGGGTCCCAGTCAGCAGCTCTTTACCTCAACAAGGAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/msa.fa new file mode 100644 index 00000000..63e623bd --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/msa.fa @@ -0,0 +1,100 @@ +>ref_chr20_57090572_57091512 +agcacagtgaggcccacttcagacttccgagctccagactatgagatcaagtgttgtttt +aagccaccaagtttgggaaaatttgccacagcagcaagaggaaacgaacgcactcaggtg +ctcctgccacacacactcacagttgcacaagctggtgcagctccagacccacacacctcc +accaccacacactccgccatgcacacacacctccacgcacacacacctccacccgcacac +acacacaccttcaccaccacacactccacccacacacacctccacccacacacctccacc +cacacacacctccgcccacacacacctccgcccacacacacctccgcccacacacacctc +cacccacacacacctccgcccacacacctccgcccacacacacctccgccctcacacacc +tccacccacacacacctccacccacacacgcctccacccgcacacacctccaccaccaca +cacacctccacccacacacaccacccatgcacacacctccacccacacacacacacctcc +acccacacaca-----------------------cacacacctccacccacacaca---- +--------------------------------------------------------ccac +ccacacacaccacccatgcacacacctccacccaca------------------------ +--------------------------------------------------cacacacacc +tccacccgcacacacctccaccaccacacacatctccacccacacacaccacccatgtgc +acacctccactggcacacaccacccatgcacacacctccactggcacgcactactccacc +tgcgtgcgcctcccacctgcgttcaccctccacctgtgttcgctcccacccactcatgcc +tctccacccgcaaaagtgtgagtgctgaggctgggactcaacctgagccgctggctctgg +attactgggtcctgccgggctggccaggcctggtcacaggccgggtcccagtcagcagct +ctttacctcaacaaggag +>syndip_1_chr20:57090572-57091512 +agcacagtgaggcccacttcagacttccgagctccagactatgagatcaagtgttgtttt +aagccaccaagtttgggaaaatttgccacagcagcaagaggaaacgaacgcactcaggtg +ctcctgccacacacactcacagttgcacaagctggtgcagctccagacccacacacctcc +accaccacacactccaccatgcacacacacctccacgcacacacacctccacccgcacac +acacacaccttcaccaccacacactccacccacacacacctccacccacacacctcca-- +--------------cccacacacacctccgcccacacacacctccgcccacacacacctc +cacccacacacacctccacccacacacctccgcccacacacacctccgccctcacacacc +tccacccacacacacctccacccacacacgcctccacccgcacacacctccaccaccaca +cacacctccacccacacacaccacccatgcacacacctccacccacacacacacacctcc +acccacacacacctccacccacacgccacccatgcacacacctccacccacacacacaca +caccacccacccacacacacctccacccgcacacacctccaccaccacacacacctccac +ccacacacaccacccatgcacacacctccacccacacacacacacacctccacccacaca +cacctccacccacacacacctccacccacacacacacacctccacccacccacacacacc +tccacccgcacacacctccaccaccacacacatctccacccacacacaccacccatgtgc +acacctccactggcacacaccacccatgcacacacctccactggcacgcactactccacc +tgcgtgcgcctcccacctgcgttcaccctccacctgtgttcgctcccacccactcatgcc +tctccacccgcaaaagtgtgagtgctgaggctgggactcaacctgagccgctggctctgg +attactgggtcctgccgggctggccaggcctggtcacaggccgggtcccagtcagcagct +ctttacctcaacaaggag +>syndip_2_chr20:57090572-57091512 +agcacagtgaggcccacttcagacttccgagctccagactatgagatcaagtgttgtttt +aagccaccaagtttgggaaaatttgccacagcagcaagaggaaacgaacgcactcaggtg +ctcctgccacacacactcacagttgcacaagctggtgcagctccagacccacacacctcc +accaccacacactccgccatgcacacacacctccacgcacacacacctccacccgcacac +acacacaccttcaccaccacacactccacccacacacacctccacccacacacctccacc +cacacacacctccgcccacacacacctccgcccacacacacctccgcccacacacacctc +cacccacacacacctccgcccacacacctccgcccacacacacctccgccctcacacacc +tccacccacacacacctccacccacacacgcctccacccgcacacacctccaccaccaca +cacacctccacccacacacaccacccatgcacacacctccacccacacacacacacctcc +acccacacaca-----------------------cacacacctccacccacacaca---- +--------------------------------------------------------ccac +ccacacacaccacccatgcacacacctccacccaca------------------------ +--------------------------------------------------cacacacacc +tccacccgcacacacctccaccaccacacacatctccacccacacacaccacccatgtgc +acacctccactggcacacaccacccatgcacacacctccactggcacgcactactccacc +tgcgtgcgcctcccacctgcgttcaccctccacctgtgttcgctcccacccactcatgcc +tctccacccgcaaaagtgtgagtgctgaggctgggactcaacctgagccgctggctctgg +attactgggtcctgccgggctggccaggcctggtcacaggccgggtcccagtcagcagct +ctttacctcaacaaggag +>p:HG002_1_chr20:57090572-57091512 +agcacagtgaggcccacttcagacttccgagctccagactatgagatcaagtgttgtttt +aagccaccaagtttgggaaaatttgccacagcagcaagaggaaacgaacgcactcaggtg +ctcctgccacacacactcacagttgcacaagctggtgcagctccagacccacacacctcc +accaccacacactccgccatgcacacacacctccacgcacacacacctccacccgcacac +acacacaccttcaccaccacacactccacccacacacacctccacccacacacctccacc +cacacacacctccgcccacacacacctccgcccacacacacctccgcccacacacacctc +cacccacacacacctccgcccacacacctccgcccacacacacctccgccctcacacacc +tccacccacacacacctccacccacacacgcctccacccgcacacacctccaccaccaca +cacacctccacccacacacaccacccatgcacacacctccacccacacacacacacctcc +acccacacaca-----------------------cacacacctccacccacacaca---- +--------------------------------------------------------ccac +ccacacacaccacccatgcacacacctccacccaca------------------------ +--------------------------------------------------cacacacacc +tccacccgcacacacctccaccaccacacacatctccacccacacacaccacccatgtgc +acacctccactggcacacaccacccatgcacacacctccactggcacgcactactccacc +tgcgtgcgcctcccacctgcgttcaccctccacctgtgttcgctcccacccactcatgcc +tctccacccgcaaaagtgtgagtgctgaggctgggactcaacctgagccgctggctctgg +attactgggtcctgccgggctggccaggcctggtcacaggccgggtcccagtcagcagct +ctttacctcaacaaggag +>p:HG002_2_chr20:57090572-57091512 +agcacagtgaggcccacttcagacttccgagctccagactatgagatcaagtgttgtttt +aagccaccaagtttgggaaaatttgccacagcagcaagaggaaacgaacgcactcaggtg +ctcctgccacacacactcacagttgcacaagctggtgcagctccagacccacacacctcc +accaccacacactccaccatgcacacacacctccacgcacacacacctccacccgcacac +acacacaccttcaccaccacacactccacccacacacacctccacccacacacctcca-- +--------------cccacacacacctccgcccacacacacctccgcccacacacacctc +cacccacacacacctccacccacacacctccgcccacacacacctccgccctcacacacc +tccacccacacacacctccacccacacacgcctccacccgcacacacctccaccaccaca +cacacctccacccacacacaccacccatgcacacacctccacccacacacacacacctcc +acccacacacacctccacccacacgccacccatgcacacacctccacccacacacacaca +caccacccacccacacacacctccacccgcacacacctccaccaccacacacacctccac +ccacacacaccacccatgcacacacctccacccacacacacacacacctccacccacaca +cacctccacccacacacacctccacccacacacacacacctccacccacccacacacacc +tccacccgcacacacctccaccaccacacacatctccacccacacacaccacccatgtgc +acacctccactggcacacaccacccatgcacacacctccactggcacgcactactccacc +tgcgtgcgcctcccacctgcgttcaccctccacctgtgttcgctcccacccactcatgcc +tctccacccgcaaaagtgtgagtgctgaggctgggactcaacctgagccgctggctctgg +attactgggtcctgccgggctggccaggcctggtcacaggccgggtcccagtcagcagct +ctttacctcaacaaggag diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/msa.fa.fai new file mode 100644 index 00000000..9ec3571a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_57090572_57091512 1098 29 60 61 +syndip_1_chr20:57090572-57091512 1098 1180 60 61 +syndip_2_chr20:57090572-57091512 1098 2331 60 61 +p:HG002_1_chr20:57090572-57091512 1098 3483 60 61 +p:HG002_2_chr20:57090572-57091512 1098 4635 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/output.vcf.gz new file mode 100644 index 00000000..3ff08d4c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/output.vcf.gz.tbi new file mode 100644 index 00000000..a6604a42 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57090672-57091412/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57110212-57110786/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57110212-57110786/base.vcf.gz new file mode 100644 index 00000000..0d0fb046 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57110212-57110786/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57110212-57110786/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57110212-57110786/base.vcf.gz.tbi new file mode 100644 index 00000000..afcf256b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57110212-57110786/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57110212-57110786/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57110212-57110786/comp.vcf.gz new file mode 100644 index 00000000..5c909fa9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57110212-57110786/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57110212-57110786/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57110212-57110786/comp.vcf.gz.tbi new file mode 100644 index 00000000..ee98dd39 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57110212-57110786/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57110212-57110786/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57110212-57110786/haps.fa new file mode 100644 index 00000000..c43b5faf --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57110212-57110786/haps.fa @@ -0,0 +1,52 @@ +>ref_chr20_57110112_57110886 +AGAAAAATCCTCCAGAAGATGACAGTTCCAGTTGATGGGACTGACAAGCCCCCCACAGGAAGGCAGTCTCCAGCTGACCACTGTTCCGTGAGGCTGTCTGAGCAGGCTTCGCTATGCACGCATAATAGCGACAGCGCAAACAGCAGCAGCAGCAGCAGCCTCAGCTGGCTCGGCGGGGCTTGGCTCAGCGTGTGCGGGGTGCTGAGCTAAGTCTTCCCAAACGGCGTGTGCGGGGTGCTGCGCTGTCTTCCAGATCCGCTTGTGCAGGGCGCTGTGCTGTCTTCTGGTTCGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTGTCTTCCGGTTCGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGTGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTGTCTTCCGGTTCGGCGTGTGCGGGGCGTTATGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTGTCTTCCGGTTCGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGCATTCGCACTCTTTCCCTCCGACTCAACCATGGCAGTGAGGCACTGTTTTGTTTTGCTTTGCTTCTCAATTTTCCTGTGGTAAAATACACCTAATATTCACCATCTTAACCGTTTTTAAGTGTACAGTTCA +>syndip_1_chr20:57110112-57110886 +AGAAAAATCCTCCAGAAGATGACAGTTCCAGTTGATGGGACTGACAAGCCCCCCACAGGA +AGGCAGTCTCCAGCTGACCACTGTTCCGTGAGGCTGTCTGAGCAGGCTTCGCTATGCACG +CATAATAGCGACAGCGCAAACAGCAGCAGCAGCAGCAGCCTCAGCTGGCTCGGCGGGGCT +TGGCTCAGCGTGTGCGGGGTGCTGAGCTAAGTCTTCCCAAACGGCGTGTGCGGGGTGCTG +CGCTGTCTTCCAGATCCGCTTGTGCAGGGCGCTGTGCTGTCTTCTGGTTCGGCGTGTGCG +GGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGC +TGGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCT +GTCTTCCGGTTCGGCGTGTGCGGGGCGTTATGCTAAGTCTTCCGGCTGGGCGTGTGCGGG +GCGCTGTGCTGTCTTCCGGTTCGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGCA +TTCGCACTCTTTCCCTCCGACTCAACCATGGCAGTGAGGCACTGTTTTGTTTTGCTTTGC +TTCTCAATTTTCCTGTGGTAAAATACACCTAATATTCACCATCTTAACCGTTTTTAAGTG +TACAGTTCA +>syndip_2_chr20:57110112-57110886 +AGAAAAATCCTCCAGAAGATGACAGTTCCAGTTGATGGGACTGACAAGCCCCCCACAGGA +AGGCAGTCTCCAGCTGACCACTGTTCCGTGAGGCTGTCTGAGCAGGCTTCGCTATGCACG +CATAATAGCGACAGCGCAAACAGCAGCAGCAGCAGCAGCCTCAGCTGGCTCGGCGGGGCT +TGGCTCAGCGTGTGCGGGGTGCTGAGCTAAGTCTTCCCAAACGGCGTGTGCGGGGTGCTG +CGCTGTCTTCCAGATCCGCTTGTGCAGGGCGCTGTGCTGTCTTCTGGTTCGGCGTGTGCG +GGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGC +TGGGCGTGTGCGGGGCGCTGTGCTGTCTTCCGGTTCGGCGTGTGCGGGGCGTTATGCTAA +GTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTGTCTTCCGGTTCGGCGTGTGCGGGGC +GCTGTGCTAAGTCTTCCGGCTGCATTCGCACTCTTTCCCTCCGACTCAACCATGGCAGTG +AGGCACTGTTTTGTTTTGCTTTGCTTCTCAATTTTCCTGTGGTAAAATACACCTAATATT +CACCATCTTAACCGTTTTTAAGTGTACAGTTCA +>p:HG002_1_chr20:57110112-57110886 +AGAAAAATCCTCCAGAAGATGACAGTTCCAGTTGATGGGACTGACAAGCCCCCCACAGGA +AGGCAGTCTCCAGCTGACCACTGTTCCGTGAGGCTGTCTGAGCAGGCTTCGCTATGCACG +CATAATAGCGACAGCGCAAACAGCAGCAGCAGCAGCAGCCTCAGCTGGCTCGGCGGGGCT +TGGCTCAGCGTGTGCGGGGTGCTGAGCTAAGTCTTCCCAAACGGCGTGTGCGGGGTGCTG +CGCTGTCTTCCAGATCCGCTTGTGCAGGGCGCTGTGCTGTCTTCTGGTTCGGCGTGTGCG +GGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGC +TGGGCGTGTGCGGGGCGCTGTGCTGTCTTCCGGTTCGGCGTGTGCGGGGCGTTATGCTAA +GTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTGTCTTCCGGTTCGGCGTGTGCGGGGC +GCTGTGCTAAGTCTTCCGGCTGCATTCGCACTCTTTCCCTCCGACTCAACCATGGCAGTG +AGGCACTGTTTTGTTTTGCTTTGCTTCTCAATTTTCCTGTGGTAAAATACACCTAATATT +CACCATCTTAACCGTTTTTAAGTGTACAGTTCA +>p:HG002_2_chr20:57110112-57110886 +AGAAAAATCCTCCAGAAGATGACAGTTCCAGTTGATGGGACTGACAAGCCCCCCACAGGA +AGGCAGTCTCCAGCTGACCACTGTTCCGTGAGGCTGTCTGAGCAGGCTTCGCTATGCACG +CATAATAGCGACAGCGCAAACAGCAGCAGCAGCAGCAGCCTCAGCTGGCTCGGCGGGGCT +TGGCTCAGCGTGTGCGGGGTGCTGAGCTAAGTCTTCCCAAACGGCGTGTGCGGGGTGCTG +CGCTGTCTTCCAGATCCGCTTGTGCAGGGCGCTGTGCTGTCTTCTGGTTCGGCGTGTGCG +GGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGC +TGGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCT +GTCTTCCGGTTCGGCGTGTGCGGGGCGTTATGCTAAGTCTTCCGGCTGGGCGTGTGCGGG +GCGCTGTGCTGTCTTCCGGTTCGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGCA +TTCGCACTCTTTCCCTCCGACTCAACCATGGCAGTGAGGCACTGTTTTGTTTTGCTTTGC +TTCTCAATTTTCCTGTGGTAAAATACACCTAATATTCACCATCTTAACCGTTTTTAAGTG +TACAGTTCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57110212-57110786/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57110212-57110786/haps.fa.ref.fa new file mode 100644 index 00000000..c247b16d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57110212-57110786/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:57110112-57110886 +AGAAAAATCCTCCAGAAGATGACAGTTCCAGTTGATGGGACTGACAAGCCCCCCACAGGAAGGCAGTCTCCAGCTGACCACTGTTCCGTGAGGCTGTCTGAGCAGGCTTCGCTATGCACGCATAATAGCGACAGCGCAAACAGCAGCAGCAGCAGCAGCCTCAGCTGGCTCGGCGGGGCTTGGCTCAGCGTGTGCGGGGTGCTGAGCTAAGTCTTCCCAAACGGCGTGTGCGGGGTGCTGCGCTGTCTTCCAGATCCGCTTGTGCAGGGCGCTGTGCTGTCTTCTGGTTCGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTGTCTTCCGGTTCGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGTGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTGTCTTCCGGTTCGGCGTGTGCGGGGCGTTATGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTGTCTTCCGGTTCGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGCATTCGCACTCTTTCCCTCCGACTCAACCATGGCAGTGAGGCACTGTTTTGTTTTGCTTTGCTTCTCAATTTTCCTGTGGTAAAATACACCTAATATTCACCATCTTAACCGTTTTTAAGTGTACAGTTCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57110212-57110786/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57110212-57110786/msa.fa new file mode 100644 index 00000000..e9c97192 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57110212-57110786/msa.fa @@ -0,0 +1,70 @@ +>ref_chr20_57110112_57110886 +agaaaaatcctccagaagatgacagttccagttgatgggactgacaagccccccacagga +aggcagtctccagctgaccactgttccgtgaggctgtctgagcaggcttcgctatgcacg +cataatagcgacagcgcaaacagcagcagcagcagcagcctcagctggctcggcggggct +tggctcagcgtgtgcggggtgctgagctaagtcttcccaaacggcgtgtgcggggtgctg +cgctgtcttccagatccgcttgtgcagggcgctgtgctgtcttctggttcggcgtgtgcg +gggcgctgtgctaagtcttccggctgggcgtgtgcggggcgctgtgctaagtcttccggc +tgggcgtgtgcggggcgctgtgctaagtcttccggctgggcgtgtgcggggcgctgtgct +gtcttccggttcggcgtgtgcggggcgctgtgctaagtcttccggctgggcgtgtgcggg +gtgctgtgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtcttccggttcgg +cgtgtgcggggcgttatgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtct +tccggttcggcgtgtgcggggcgctgtgctaagtcttccggctgcattcgcactctttcc +ctccgactcaaccatggcagtgaggcactgttttgttttgctttgcttctcaattttcct +gtggtaaaatacacctaatattcaccatcttaaccgtttttaagtgtacagttca +>syndip_1_chr20:57110112-57110886 +agaaaaatcctccagaagatgacagttccagttgatgggactgacaagccccccacagga +aggcagtctccagctgaccactgttccgtgaggctgtctgagcaggcttcgctatgcacg +cataatagcgacagcgcaaacagcagcagcagcagcagcctcagctggctcggcggggct +tggctcagcgtgtgcggggtgctgagctaagtcttcccaaacggcgtgtgcggggtgctg +cgctgtcttccagatccgcttgtgcagggcgctgtgctgtcttctggttcggcgtgtgcg +gggcgctgtgctaagtcttccggctgggcgtgtgcggggcgctgtgctaagtcttccggc +tgggcgtgtgcggggc-------------------------------------------- +------------------------------------------------------------ +--gctgtgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtcttccggttcgg +cgtgtgcggggcgttatgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtct +tccggttcggcgtgtgcggggcgctgtgctaagtcttccggctgcattcgcactctttcc +ctccgactcaaccatggcagtgaggcactgttttgttttgctttgcttctcaattttcct +gtggtaaaatacacctaatattcaccatcttaaccgtttttaagtgtacagttca +>syndip_2_chr20:57110112-57110886 +agaaaaatcctccagaagatgacagttccagttgatgggactgacaagccccccacagga +aggcagtctccagctgaccactgttccgtgaggctgtctgagcaggcttcgctatgcacg +cataatagcgacagcgcaaacagcagcagcagcagcagcctcagctggctcggcggggct +tggctcagcgtgtgcggggtgctgagctaagtcttcccaaacggcgtgtgcggggtgctg +cgctgtcttccagatccgcttgtgcagggcgctgtgctgtcttctggttc---------- +--------------------------ggcgtgtgcggggcgctgtgctaagtcttccggc +tgggcgtgtgcggggc-------------------------------------------- +------------------------------------------------------------ +--gctgtgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtcttccggttcgg +cgtgtgcggggcgttatgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtct +tccggttcggcgtgtgcggggcgctgtgctaagtcttccggctgcattcgcactctttcc +ctccgactcaaccatggcagtgaggcactgttttgttttgctttgcttctcaattttcct +gtggtaaaatacacctaatattcaccatcttaaccgtttttaagtgtacagttca +>p:HG002_1_chr20:57110112-57110886 +agaaaaatcctccagaagatgacagttccagttgatgggactgacaagccccccacagga +aggcagtctccagctgaccactgttccgtgaggctgtctgagcaggcttcgctatgcacg +cataatagcgacagcgcaaacagcagcagcagcagcagcctcagctggctcggcggggct +tggctcagcgtgtgcggggtgctgagctaagtcttcccaaacggcgtgtgcggggtgctg +cgctgtcttccagatccgcttgtgcagggcgctgtgctgtcttctggttc---------- +--------------------------ggcgtgtgcggggcgctgtgctaagtcttccggc +tgggcgtgtgcggggc-------------------------------------------- +------------------------------------------------------------ +--gctgtgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtcttccggttcgg +cgtgtgcggggcgttatgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtct +tccggttcggcgtgtgcggggcgctgtgctaagtcttccggctgcattcgcactctttcc +ctccgactcaaccatggcagtgaggcactgttttgttttgctttgcttctcaattttcct +gtggtaaaatacacctaatattcaccatcttaaccgtttttaagtgtacagttca +>p:HG002_2_chr20:57110112-57110886 +agaaaaatcctccagaagatgacagttccagttgatgggactgacaagccccccacagga +aggcagtctccagctgaccactgttccgtgaggctgtctgagcaggcttcgctatgcacg +cataatagcgacagcgcaaacagcagcagcagcagcagcctcagctggctcggcggggct +tggctcagcgtgtgcggggtgctgagctaagtcttcccaaacggcgtgtgcggggtgctg +cgctgtcttccagatccgcttgtgcagggcgctgtgctgtcttctggttcggcgtgtgcg +gggcgctgtgctaagtcttccggctgggcgtgtgcggggcgctgtgctaagtcttccggc +tgggcgtgtgcggggc-------------------------------------------- +------------------------------------------------------------ +--gctgtgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtcttccggttcgg +cgtgtgcggggcgttatgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtct +tccggttcggcgtgtgcggggcgctgtgctaagtcttccggctgcattcgcactctttcc +ctccgactcaaccatggcagtgaggcactgttttgttttgctttgcttctcaattttcct +gtggtaaaatacacctaatattcaccatcttaaccgtttttaagtgtacagttca diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/base.vcf.gz new file mode 100644 index 00000000..3ab38092 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/base.vcf.gz.tbi new file mode 100644 index 00000000..2ce4272c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/comp.vcf.gz new file mode 100644 index 00000000..c6324122 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/comp.vcf.gz.tbi new file mode 100644 index 00000000..0488254c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/haps.fa new file mode 100644 index 00000000..ace3fa52 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/haps.fa @@ -0,0 +1,60 @@ +>ref_chr20_57189846_57190641 +CTGGGAGCTGACTGGCGAGGGAGATCAGCTCAGGGGTGCACAGTGCTGTGTCTGATGGTGGCAAGGACTAGGAAGAACCTAGGACAGGGTGGCAGGGACATGACAGTGGGGCACAGTGTACAGGGCAGAGTGAGCCATGGGAGGTTTTGGGGAGGAAATGTTCCTGGCAGAGGGAATGGCACATGCCAGGTTCATGAGAAATACACGGTGTGTGTCAGCACAGTGAAGAGGCCAGTGAGGCTGGAGAAGTGAGCCAGGAACCAGAGAGGTTGAGACTGGAGATAGTGAGCGAGGAACCGGAGGGGGTGAAGCTGGAGAGAGTGAGCCAGGAATCAGAGGAGGTGAGGCCAGAGAGAGTGAGCGAGGAACCAGAGGGGGTGAGGCTGGAGAGAGTGACCGAGGAACCAGAGGAGGTGAGGCTGGAGAGAGTGAGCCAGGAACCAGAGGAGGTGAGGCCAGAGTGAGTGAGGAGCTTGAAGGGGTGAGGCTGGAGACAGTGAGCGAGGAACCAGAGGGGGTGAGGCTGGAGAGCGTGAGTGAGGAGCCCGAGGGGGTGAGGCTGGAGAGCGTGAGTGAGGAGCCCGAGGGGGTGAGGCTGGAGAGCGTGAGTGAGGAGCCCGAGGGGGTGAGGCTGGAGAGAGTGAGTGAGGAGCCCAAGGGGGTGAAGCCGAGGTGGGTATGGGGCTGGGTCACCTGGGGTCTCCCAGCCCAGTGGGGGATTTGGGCAGGGGGCGACGTGGCCAGGGTTCTGTGGTGGGAGACCCATTCTGAATGCCGTGTGGGGAACCAACAAGGC +>syndip_1_chr20:57189846-57190641 +CTGGGAGCTGACTGGCGAGGGAGATCAGCTCAGGGGTGCACAGTGCTGTGTCTGATGGTG +GCAAGGACTAGGAAGAACCTAGGACAGGGTGGCAGGGACATGACAGTGGGGCACAGTGTA +CAGGGCAGAGTGAGCCATGGGAGGTTTTGGGGAGGAAATGTTCCTGGCAGAGGGAATGGC +ACATGCCAGGTTCATGAGAAATACACGGTGTGTGTCAGCACAGTGAAGAGGCCAGTGAGG +CTGGAGAAGTGAGCCAGGAACCAGAGAGGTTGAGACTGGAGATAGTGAGCGAGGAACCGG +AGGGGGTGAAGCTGGAGAGAGTGAGCCAGGAATCAGAGGAGGTGAGGCCAGAGAGAGTGA +GCGAGGAACCAGAGGGGGTGAGGCTGGAGAGAGTGACCGAGGAACCAGAGGAGGTGAGGC +CAGAGTGAGTGAGGAGCTTGAAGGGGTGAGGCTGGAGACAGTGAGCGAGGAACCAGAGGG +GGTGAGGCTGGAGAGAGTGAGCCAGGAACCAGAGGAGGTGAGGCCAGAGTGAGTGAGGAG +CTTGAAGGGGTGAGGCTGGAGACAGTGAGCGAGGAACCAGAGGGGGTGAGGCTGGAGAGC +GTGAGTGAGGAGCCCGAGGGGGTGAGGCTGGAGAGAGTGAGTGAGGAGCCCAAGGGGGTG +AAGCCGAGGTGGGTATGGGGCTGGGTCACCTGGGGTCTCCCAGCCCAGTGGGGGATTTGG +GCAGGGGGCGACGTGGCCAGGGTTCTGTGGTGGGAGACCCATTCTGAATGCCGTGTGGGG +AACCAACAAGGC +>syndip_2_chr20:57189846-57190641 +CTGGGAGCTGACTGGCGAGGGAGATCAGCTCAGGGGTGCACAGTGCTGTGTCTGATGGTG +GCAAGGACTAGGAAGAACCTAGGACAGGGTGGCAGGGACATGACAGTGGGGCACAGTGTA +CAGGGCAGAGTGAGCCATGGGAGGTTTTGGGGAGGAAATGTTCCTGGCAGAGGGAATGGC +ACATGCCAGGTTCATGAGAAATACACGGTGTGTGTCAGCACAGTGAAGAGGCCAGTGAGG +CTGGAGAAGTGAGCCAGGAACCAGAGGGGTTGAGGCTGGAGATAGTGAGCGAGGAACCGG +AGGGGGTGAAGCTGGAGAGAGTGAGCCAGGAATCAGAGGAGGTGAGGCCAGAGAGAGTGA +GCGAGGAACCAGAGGGGGTGAGGCTGGAGAGAGTGACCGAGGAACCAGAGGAGGTGAGGC +TGGAGAGAGTGAGCCAGGAACCAGAGGAGGTGAGGCCAGAGTGAGTGAGGAGCTTGAAGG +GGTGAGGCTGGAGACAGTGAGCGAGGAACCAGAGGGGGTGAGGCTGGAGAGCGTGAGTGA +GGAGCCCGAGGGGGTGAGGCTGGAGAGCGTGAGTGAGGAGCCCGAGGGGGTGAGGCTGGA +GAGAGTGAGTGAGGAGCCCAAGGGGGTGAAGCCGAGGTGGGTATGGGGCTGGGTCACCTG +GGGTCTCCCAGCCCAGTGGGGGATTTGGGCAGGGGGCGACGTGGCCAGGGTTCTGTGGTG +GGAGACCCATTCTGAATGCCGTGTGGGGAACCAACAAGGC +>p:HG002_1_chr20:57189846-57190641 +CTGGGAGCTGACTGGCGAGGGAGATCAGCTCAGGGGTGCACAGTGCTGTGTCTGATGGTG +GCAAGGACTAGGAAGAACCTAGGACAGGGTGGCAGGGACATGACAGTGGGGCACAGTGTA +CAGGGCAGAGTGAGCCATGGGAGGCTTTGGGGAGGAAATGTTCCTGGCAGAGGGAATGGC +ACATGCCAGGTTCATGAGAAATACACGGTGTGTGTCAGCACAGTGAAGAGGCCAGTGAGG +CTGGAGAAGTGAGCCAGGAACCAGAGGGGTTGAGGCTGGAGATAGTGAGCGAGGAACCGG +AGGGGGTGAAGCTGGAGAGAGTGAGCCAGGAATCAGAGGAGGTGAGGCCAGAGAGAGTGA +GCGAGGAACCAGAGGGGGTGAGGCTGGAGAGAGTGACCGAGGAACCAGAGGAGGTGAGGC +TGGAGAGAGTGAGCCAGGAACCAGAGGAGGTGAGGCCAGAGTGAGTGAGGAGCTTGAAGG +GGTGAGGCTGGAGACAGTGAGCGAGGAACCAGAGGGGGTGAGGCTGGAGAGCGTGAGTGA +GGAGCCCGAGGGGGTGAGGCTGGAGAGCGTGAGTGAGGAGCCCGAGGGGGTGAGGCTGGA +GAGAGTGAGTGAGGAGCCCAAGGGGGTGAAGCCGAGGTGGGTATGGGGCTGGGTCACCTG +GGGTCTCCCAGCCCAGTGGGGGATTTGGGCAGGGGGCGACGTGGCCAGGGTTCTGTGGTG +GGAGACCCATTCTGAATGCCGTGTGGGGAACCAACAAGGC +>p:HG002_2_chr20:57189846-57190641 +CTGGGAGCTGACTGGCGAGGGAGATCAGCTCAGGGGTGCACAGTGCTGTGTCTGATGGTG +GCAAGGACTAGGAAGAACCTAGGACAGGGTGGCAGGGACATGACAGTGGGGCACAGTGTA +CAGGGCAGAGTGAGCCATGGGAGGCTTTGGGGAGGAAATGTTCCTGGCAGAGGGAATGGC +ACATGCCAGGTTCATGAGAAATACACGGTGTGTGTCAGCACAGTGAAGAGGCCAGTGAGG +CTGGAGAAGTGAGCCAGGAACCAGAGAGGTTGAGACTGGAGATAGTGAGCGAGGAACCGG +AGGGGGTGAAGCTGGAGAGAGTGAGCCAGGAATCAGAGGAGGTGAGGCCAGAGAGAGTGA +GCGAGGAACCAGAGGGGGTGAGGCTGGAGAGAGTGACCGAGGAACCAGAGGAGGTGAGGC +CAGAGTGAGTGAGGAGCTTGAAGGGGTGAGGCTGGAGACAGTGAGCGAGGAACCAGAGGG +GGTGAGGCTGGAGAGAGTGAGCCAGGAACCAGAGGAGGTGAGGCCAGAGTGAGTGAGGAG +CTTGAAGGGGTGAGGCTGGAGACAGTGAGCGAGGAACCAGAGGGGGTGAGGCTGGAGAGC +GTGAGTGAGGAGCCCGAGGGGGTGAGGCTGGAGAGAGTGAGTGAGGAGCCCAAGGGGGTG +AAGCCGAGGTGGGTATGGGGCTGGGTCACCTGGGGTCTCCCAGCCCAGTGGGGGATTTGG +GCAGGGGGCGACGTGGCCAGGGTTCTGTGGTGGGAGACCCATTCTGAATGCCGTGTGGGG +AACCAACAAGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/haps.fa.ref.fa new file mode 100644 index 00000000..70908a63 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:57189846-57190641 +CTGGGAGCTGACTGGCGAGGGAGATCAGCTCAGGGGTGCACAGTGCTGTGTCTGATGGTGGCAAGGACTAGGAAGAACCTAGGACAGGGTGGCAGGGACATGACAGTGGGGCACAGTGTACAGGGCAGAGTGAGCCATGGGAGGTTTTGGGGAGGAAATGTTCCTGGCAGAGGGAATGGCACATGCCAGGTTCATGAGAAATACACGGTGTGTGTCAGCACAGTGAAGAGGCCAGTGAGGCTGGAGAAGTGAGCCAGGAACCAGAGAGGTTGAGACTGGAGATAGTGAGCGAGGAACCGGAGGGGGTGAAGCTGGAGAGAGTGAGCCAGGAATCAGAGGAGGTGAGGCCAGAGAGAGTGAGCGAGGAACCAGAGGGGGTGAGGCTGGAGAGAGTGACCGAGGAACCAGAGGAGGTGAGGCTGGAGAGAGTGAGCCAGGAACCAGAGGAGGTGAGGCCAGAGTGAGTGAGGAGCTTGAAGGGGTGAGGCTGGAGACAGTGAGCGAGGAACCAGAGGGGGTGAGGCTGGAGAGCGTGAGTGAGGAGCCCGAGGGGGTGAGGCTGGAGAGCGTGAGTGAGGAGCCCGAGGGGGTGAGGCTGGAGAGCGTGAGTGAGGAGCCCGAGGGGGTGAGGCTGGAGAGAGTGAGTGAGGAGCCCAAGGGGGTGAAGCCGAGGTGGGTATGGGGCTGGGTCACCTGGGGTCTCCCAGCCCAGTGGGGGATTTGGGCAGGGGGCGACGTGGCCAGGGTTCTGTGGTGGGAGACCCATTCTGAATGCCGTGTGGGGAACCAACAAGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/msa.fa new file mode 100644 index 00000000..ed77c0c4 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/msa.fa @@ -0,0 +1,75 @@ +>ref_chr20_57189846_57190641 +ctgggagctgactggcgagggagatcagctcaggggtgcacagtgctgtgtctgatggtg +gcaaggactaggaagaacctaggacagggtggcagggacatgacagtggggcacagtgta +cagggcagagtgagccatgggaggttttggggaggaaatgttcctggcagagggaatggc +acatgccaggttcatgagaaatacacggtgtgtgtcagcacagtgaagaggccagtgagg +ctggagaagtgagccaggaaccagagaggttgagactggagatagtgagcgaggaaccgg +agggggtgaagctggagagagtgagccaggaatcagaggaggtgaggccagagagagtga +gcgaggaaccagagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggc +tggagagagtgagccaggaaccagaggaggtgaggccag----agtgagtgaggagcttg +aaggggtgaggctggagacagtgagcgaggaaccagagggggtgaggctggagagcgtga +gtgaggagcccgagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggc +tggagagcgtgagtgaggagcccgagggggtgaggctggagagagtgagtgaggagccca +agggggtgaagccgaggtgggtatggggctgggtcacctggggtctcccagcccagtggg +ggatttgggcagggggcgacgtggccagggttctgtggtgggagacccattctgaatgcc +gtgtggggaaccaacaaggc +>syndip_1_chr20:57189846-57190641 +ctgggagctgactggcgagggagatcagctcaggggtgcacagtgctgtgtctgatggtg +gcaaggactaggaagaacctaggacagggtggcagggacatgacagtggggcacagtgta +cagggcagagtgagccatgggaggttttggggaggaaatgttcctggcagagggaatggc +acatgccaggttcatgagaaatacacggtgtgtgtcagcacagtgaagaggccagtgagg +ctggagaagtgagccaggaaccagagaggttgagactggagatagtgagcgaggaaccgg +agggggtgaagctggagagagtgagccaggaatcagaggaggtgaggccagagagagtga +gcgaggaaccagagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggc +c----agagtgagtgaggagcttgaaggggtgaggctggagacagtgagcgaggaaccag +agggggtgaggctggagagagtgagccaggaaccagaggaggtgaggccaga----gtga +gtgaggagcttgaaggggtgaggctggagacagtgagcgaggaaccagagggggtgaggc +tggagagcgtgagtgaggagcccgagggggtgaggctggagagagtgagtgaggagccca +agggggtgaagccgaggtgggtatggggctgggtcacctggggtctcccagcccagtggg +ggatttgggcagggggcgacgtggccagggttctgtggtgggagacccattctgaatgcc +gtgtggggaaccaacaaggc +>syndip_2_chr20:57189846-57190641 +ctgggagctgactggcgagggagatcagctcaggggtgcacagtgctgtgtctgatggtg +gcaaggactaggaagaacctaggacagggtggcagggacatgacagtggggcacagtgta +cagggcagagtgagccatgggaggttttggggaggaaatgttcctggcagagggaatggc +acatgccaggttcatgagaaatacacggtgtgtgtcagcacagtgaagaggccagtgagg +ctggagaagtgagccaggaaccagaggggttgaggctggagatagtgagcgaggaaccgg +agggggtgaagctggagagagtgagccaggaatcagaggaggtgaggccagagagagtga +gcgaggaaccagagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggc +tggagagagtgagccaggaaccagaggaggtgaggccag----agtgagtgaggagcttg +aaggggtgaggctggagacagtgagcgaggaacca------------------------- +-----------gagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggc +tggagagcgtgagtgaggagcccgagggggtgaggctggagagagtgagtgaggagccca +agggggtgaagccgaggtgggtatggggctgggtcacctggggtctcccagcccagtggg +ggatttgggcagggggcgacgtggccagggttctgtggtgggagacccattctgaatgcc +gtgtggggaaccaacaaggc +>p:HG002_1_chr20:57189846-57190641 +ctgggagctgactggcgagggagatcagctcaggggtgcacagtgctgtgtctgatggtg +gcaaggactaggaagaacctaggacagggtggcagggacatgacagtggggcacagtgta +cagggcagagtgagccatgggaggctttggggaggaaatgttcctggcagagggaatggc +acatgccaggttcatgagaaatacacggtgtgtgtcagcacagtgaagaggccagtgagg +ctggagaagtgagccaggaaccagaggggttgaggctggagatagtgagcgaggaaccgg +agggggtgaagctggagagagtgagccaggaatcagaggaggtgaggccagagagagtga +gcgaggaaccagagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggc +tggagagagtgagccaggaaccagaggaggtgaggccag----agtgagtgaggagcttg +aaggggtgaggctggagacagtgagcgaggaacca------------------------- +-----------gagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggc +tggagagcgtgagtgaggagcccgagggggtgaggctggagagagtgagtgaggagccca +agggggtgaagccgaggtgggtatggggctgggtcacctggggtctcccagcccagtggg +ggatttgggcagggggcgacgtggccagggttctgtggtgggagacccattctgaatgcc +gtgtggggaaccaacaaggc +>p:HG002_2_chr20:57189846-57190641 +ctgggagctgactggcgagggagatcagctcaggggtgcacagtgctgtgtctgatggtg +gcaaggactaggaagaacctaggacagggtggcagggacatgacagtggggcacagtgta +cagggcagagtgagccatgggaggctttggggaggaaatgttcctggcagagggaatggc +acatgccaggttcatgagaaatacacggtgtgtgtcagcacagtgaagaggccagtgagg +ctggagaagtgagccaggaaccagagaggttgagactggagatagtgagcgaggaaccgg +agggggtgaagctggagagagtgagccaggaatcagaggaggtgaggccagagagagtga +gcgaggaaccagagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggc +c----agagtgagtgaggagcttgaaggggtgaggctggagacagtgagcgaggaaccag +agggggtgaggctggagagagtgagccaggaaccagaggaggtgaggccaga----gtga +gtgaggagcttgaaggggtgaggctggagacagtgagcgaggaaccagagggggtgaggc +tggagagcgtgagtgaggagcccgagggggtgaggctggagagagtgagtgaggagccca +agggggtgaagccgaggtgggtatggggctgggtcacctggggtctcccagcccagtggg +ggatttgggcagggggcgacgtggccagggttctgtggtgggagacccattctgaatgcc +gtgtggggaaccaacaaggc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/msa.fa.fai new file mode 100644 index 00000000..a6dd8f20 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_57189846_57190641 800 29 60 61 +syndip_1_chr20:57189846-57190641 800 877 60 61 +syndip_2_chr20:57189846-57190641 800 1725 60 61 +p:HG002_1_chr20:57189846-57190641 800 2574 60 61 +p:HG002_2_chr20:57189846-57190641 800 3423 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/output.vcf.gz new file mode 100644 index 00000000..91547f68 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/output.vcf.gz.tbi new file mode 100644 index 00000000..041c46ff Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57189946-57190541/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/base.vcf.gz new file mode 100644 index 00000000..e1512d67 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/base.vcf.gz.tbi new file mode 100644 index 00000000..424f5155 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/comp.vcf.gz new file mode 100644 index 00000000..755629ee Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/comp.vcf.gz.tbi new file mode 100644 index 00000000..f3b14e74 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/haps.fa new file mode 100644 index 00000000..ca93c54c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/haps.fa @@ -0,0 +1,38 @@ +>ref_chr20_57350708_57351088 +AATGGCATGGTCTCGGCTCACTGCAACCTCCACCTCCTGGGTTCAAGCGATTCTCCTGCCTTAGCCTCCCAAGCAGCTGGGATTACAGGCACCCGCCACCATGCCCGGCTAATTTTTGTATTTTTAGTACTGACGGGGGGACGGGGGGGCGGGGGGGCGGGGGGACGGGGGGCGGGGGGGGCGGGGGGGGCGGGGGGACGGGGGCGGGGGGCGGGGGGGGGCGGCGCGGGGGGGCGGGGGGGGCGGGGGGCGGGGCGGTTCACGATGTTGGCCAGACTTGTCTTGAACTCCTGACCCCAGGTGATCAGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCTGGCCAGTTGCGGATTTATAAA +>syndip_1_chr20:57350708-57351088 +AATGGCATGGTCTCGGCTCACTGCAACCTCCACCTCCTGGGTTCAAGCGATTCTCCTGCC +TTAGCCTCCCAAGCAGCTGGGATTACAGGCACCCGCCACCATGCCCGGCTAATTTTTGTA +TTTTTAGTACTGACGGGGGGACGGGGGGACGGGGGACGGGGGACGGGGGGCGGGGGGGAC +GGGGGACGGGGGGCGGGGGGGGCGGGGGGGACGGGGGGCGGGGGGGGCGGGGGCCGGGGG +GGGCGGGGGGACGGGGGCGGGGGGCCGGGGGGGGCGGGGGGACGGGGGCGGGGGGGCGGG +GGGGGCGGGGGGACGGGGGCGGGGGGCGCGGGGGGGCGGGGGGGGCGGCGCGGGGGGGCG +GGGGGGGGCGGGGGGCGGGGCGGTTCACGATGTTGGCCAGACTTGTCTTGAACTCCTGAC +CCCAGGTGATCAGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCG +CGCCTGGCCAGTTGCGGATTTATAAA +>syndip_2_chr20:57350708-57351088 +AATGGCATGGTCTCGGCTCACTGCAACCTCCACCTCCTGGGTTCAAGCGATTCTCCTGCC +TTAGCCTCCCAAGCAGCTGGGATTACAGGCACCCGCCACCATGCCCGGCTAATTTTTGTA +TTTTTAGTACTGACGGGGGGACGGGGGGGCGGGGGGGCGGGGGGGCGGGGGGACGGGGGG +CGGGGGGGGCGGGGGGACGGGGGCGGGGGGCGGGGGGGGGCGGCGCGGGGGGGCGGGGGG +GGCGGGGGGCGGGGCGGTTCACGATGTTGGCCAGACTTGTCTTGAACTCCTGACCCCAGG +TGATCAGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCTG +GCCAGTTGCGGATTTATAAA +>p:HG002_1_chr20:57350708-57351088 +AATGGCATGGTCTCGGCTCACTGCAACCTCCACCTCCTGGGTTCAAGCGATTCTCCTGCC +TTAGCCTCCCAAGCAGCTGGGATTACAGGCACCCGCCACCATGCCCGGCTAATTTTTGTA +TTTTTAGTACTGACGGGGGGACGGGGGGGCGGGGGGGCGGGGGGGCGGGGGGACGGGGGG +CGGGGGGGGCGGGGGGACGGGGGCGGGGGGCGGGGGGGGGCGGCGCGGGGGGGCGGGGGG +GGCGGGGGGCGGGGCGGTTCACGATGTTGGCCAGACTTGTCTTGAACTCCTGACCCCAGG +TGATCAGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCTG +GCCAGTTGCGGATTTATAAA +>p:HG002_2_chr20:57350708-57351088 +AATGGCATGGTCTCGGCTCACTGCAACCTCCACCTCCTGGGTTCAAGCGATTCTCCTGCC +TTAGCCTCCCAAGCAGCTGGGATTACAGGCACCCGCCACCATGCCCGGCTAATTTTTGTA +TTTTTAGTACTGACGGGGGGACGGGGGGACGGGGGACGGGGGACGGGGGGCGGGGGGGAC +GGGGGACGGGGGGCGGGGGGGGCGGGGGGGACGGGGGGCGGGGGGGGCGGGGGCCGGGGG +GGGCGGGGGGACGGGGGCGGGGGGCCGGGGGGGGCGGGGGGACGGGGGCGGGGGGGCGGG +GGGGGCGGGGGGACGGGGGCGGGGGGCGCGGGGGGGCGGGGGGGGCGGCGCGGGGGGGCG +GGGGGGGGCGGGGGGCGGGGCGGTTCACGATGTTGGCCAGACTTGTCTTGAACTCCTGAC +CCCAGGTGATCAGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCG +CGCCTGGCCAGTTGCGGATTTATAAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/haps.fa.ref.fa new file mode 100644 index 00000000..b731ce98 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:57350708-57351088 +AATGGCATGGTCTCGGCTCACTGCAACCTCCACCTCCTGGGTTCAAGCGATTCTCCTGCCTTAGCCTCCCAAGCAGCTGGGATTACAGGCACCCGCCACCATGCCCGGCTAATTTTTGTATTTTTAGTACTGACGGGGGGACGGGGGGGCGGGGGGGCGGGGGGACGGGGGGCGGGGGGGGCGGGGGGGGCGGGGGGACGGGGGCGGGGGGCGGGGGGGGGCGGCGCGGGGGGGCGGGGGGGGCGGGGGGCGGGGCGGTTCACGATGTTGGCCAGACTTGTCTTGAACTCCTGACCCCAGGTGATCAGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCTGGCCAGTTGCGGATTTATAAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/msa.fa new file mode 100644 index 00000000..212f38c2 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/msa.fa @@ -0,0 +1,50 @@ +>ref_chr20_57350708_57351088 +aatggcatggtctcggctcactgcaacctccacctcctgggttcaagcgattctcctgcc +ttagcctcccaagcagctgggattacaggcacccgccaccatgcccggctaatttttgta +tttttagtactgacggggggacgggggggc------------------------------ +------------------------gggggggcggggggacggggggcggggggggcgggg +ggggcggggggacgggggcggggggcgggggggggc------------------------ +-------------------------ggcgcgggggggc---------------------- +-ggggggggcggggggcggggcggttcacgatgttggccagacttgtcttgaactcctga +ccccaggtgatcagcccgcctcggcctcccaaagtgctgggattacaggcgtgagccacc +gcgcctggccagttgcggatttataaa +>syndip_1_chr20:57350708-57351088 +aatggcatggtctcggctcactgcaacctccacctcctgggttcaagcgattctcctgcc +ttagcctcccaagcagctgggattacaggcacccgccaccatgcccggctaatttttgta +tttttagtactgacggggggacggggggacgggggacgggggacggggggcgggggggac +gggggacggggggcggggggggcgggggggacggggggcggggggg-gcgggggccgggg +ggggcggggggacgggggcggggggccggggggggcggggggacgggggcgggggggcgg +ggggggcggggggacgggggcggggggcgcgggggggcggggggggcggcgcgggggggc +gggggggggcggggggcggggcggttcacgatgttggccagacttgtcttgaactcctga +ccccaggtgatcagcccgcctcggcctcccaaagtgctgggattacaggcgtgagccacc +gcgcctggccagttgcggatttataaa +>syndip_2_chr20:57350708-57351088 +aatggcatggtctcggctcactgcaacctccacctcctgggttcaagcgattctcctgcc +ttagcctcccaagcagctgggattacaggcacccgccaccatgcccggctaatttttgta +tttttagtactgacggggggacgggggggc------------------------------ +------------------------gggggggcgggggggcgggggg-acggggggcgggg +ggggcggggggacgggggcggggggcgggggggggc------------------------ +-------------------------ggcgcgggggggc---------------------- +-ggggggggcggggggcggggcggttcacgatgttggccagacttgtcttgaactcctga +ccccaggtgatcagcccgcctcggcctcccaaagtgctgggattacaggcgtgagccacc +gcgcctggccagttgcggatttataaa +>p:HG002_1_chr20:57350708-57351088 +aatggcatggtctcggctcactgcaacctccacctcctgggttcaagcgattctcctgcc +ttagcctcccaagcagctgggattacaggcacccgccaccatgcccggctaatttttgta +tttttagtactgacggggggacgggggggc------------------------------ +------------------------gggggggcgggggggcgggggg-acggggggcgggg +ggggcggggggacgggggcggggggcgggggggggc------------------------ +-------------------------ggcgcgggggggc---------------------- +-ggggggggcggggggcggggcggttcacgatgttggccagacttgtcttgaactcctga +ccccaggtgatcagcccgcctcggcctcccaaagtgctgggattacaggcgtgagccacc +gcgcctggccagttgcggatttataaa +>p:HG002_2_chr20:57350708-57351088 +aatggcatggtctcggctcactgcaacctccacctcctgggttcaagcgattctcctgcc +ttagcctcccaagcagctgggattacaggcacccgccaccatgcccggctaatttttgta +tttttagtactgacggggggacggggggacgggggacgggggacggggggcgggggggac +gggggacggggggcggggggggcgggggggacggggggcggggggg-gcgggggccgggg +ggggcggggggacgggggcggggggccggggggggcggggggacgggggcgggggggcgg +ggggggcggggggacgggggcggggggcgcgggggggcggggggggcggcgcgggggggc +gggggggggcggggggcggggcggttcacgatgttggccagacttgtcttgaactcctga +ccccaggtgatcagcccgcctcggcctcccaaagtgctgggattacaggcgtgagccacc +gcgcctggccagttgcggatttataaa diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/msa.fa.fai new file mode 100644 index 00000000..33b2e406 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_57350708_57351088 507 29 60 61 +syndip_1_chr20:57350708-57351088 507 579 60 61 +syndip_2_chr20:57350708-57351088 507 1129 60 61 +p:HG002_1_chr20:57350708-57351088 507 1680 60 61 +p:HG002_2_chr20:57350708-57351088 507 2231 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/output.vcf.gz new file mode 100644 index 00000000..6c1d22ef Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/output.vcf.gz.tbi new file mode 100644 index 00000000..7671d31d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57350808-57350988/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/base.vcf.gz new file mode 100644 index 00000000..5482e347 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/base.vcf.gz.tbi new file mode 100644 index 00000000..5321997a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/comp.vcf.gz new file mode 100644 index 00000000..f764cf74 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/comp.vcf.gz.tbi new file mode 100644 index 00000000..745064f9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/haps.fa new file mode 100644 index 00000000..dd9dda7a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/haps.fa @@ -0,0 +1,64 @@ +>ref_chr20_57948698_57949591 +CGGAGCGGGTGTGCCCCGTGGTCTCTCTTCACTGTTCTTAAGACATTCACAACCTCATTTTGATGGTGGGACGCTGCAGCTCACGTCTGAGTCCCATCCAAGACTTGGCCCACTGCTGTGCCCTGCACAGATGGACAGATGGTTGGAAGGATGGATGGATGGATGGATGGATGGATGGATGGATGGGGTTGGATGGATGGATGGATGGATGGATGGATAGTGGATAGATGGATGAATAGTGGATGGATAAATGGATTAATGGATGGATGAATGGATGATGGATGGATGAATGAGATGGATGGATTGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGAAGAATGGATGATGGATGGATGAGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGAAGAATGGATGATGGATGGATGAGATGGATGGATGGATGGATGGATGGGGGGTTGGATGGATGGATGGATGGATGGATGGATAGTGGATAGATGGATGAATAGTGAATGGATAAATGGATTAATGGATGGATGGATAGTGGATAGATGGATGAATAGTGGATGGATAAATGGATTAATGGATGGATGAATGGATGATGGATGGATGAATGAGATGGATGGATTGATGGATGGATGGATGGATGGATGGATGGATGGAAGAATGGATGATGGATGGATGAATGAGATGGGTGGATTGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGCAGATGGATGGATCCATCTATGTCAGGCCTGCATGACACCTGGTGTGGAGGAGCCACCCAGTCAACATTTGCTGACAGGATGGACAGACAGAGAGGAGGTGAGTGACAGGGGCCCTCAGGTGCTTTTTCTTTGGAGACCTGGGC +>syndip_1_chr20:57948698-57949591 +CGGAGCGGGTGTGCCCCGTGGTCTCTCTTCACTGTTCTTAAGACATTCACAACCTCATTT +TGATGGTGGGACGCTGCAGCTCACGTCTGAGTCCCATCCAAGACTTGGCCCACTGCTGTG +CCCTGCACAGATGGACAGATGGTTGGAAGGATGGATGGATGGATGGATGGATGGATGGAT +GGGGTTGGATGGATGGATGGATGGATGGATGGATAGTGGATAGATGGATGAATAGTGGAT +GGATAAATGGATTAATGGATGGATGAATGGATGATGGATGGATGAATGAGATGGATGGAT +TGATGGATGGATGGATGGATGGATGGATGGAAGAATGGATGATGGATGGATGAGATGGAT +GGATGGATGGATGGAAGAATGGATGATGGATGGATGAGATGGATGGATGGATGGGGGGTT +GGATGGATGGATGGATGGATGGATGGATAGTGGATAGATGGATGAATAGTGGATGGATAA +ATGGATTAATGGATGGATGAATGGATGATGGATGGATGAATGAGATGGATGGATTGATGG +ATGGATGGATGGATGGAAGAATGGATGATGGATGGATGAATGAGATGGGTGGATTGATGG +ATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGCAGATGGATGGATCCATCTA +TGTCAGGCCTGCATGACACCTGGTGTGGAGGAGCCACCCAGTCAACATTTGCTGACAGGA +TGGACAGACAGAGAGGAGGTGAGTGACAGGGGCCCTCAGGTGCTTTTTCTTTGGAGACCT +GGGC +>syndip_2_chr20:57948698-57949591 +CGGAGCGGGTGTGCCCCGTGGTCTCTCTTCACTGTTCTTAAGACATTCACAACCTCATTT +TGATGGTGGGACGCTGCAGCTCACGTCTGAGTCCCATCCAAGACTTGGCCCACTGCTGTG +CCCTGCACAGATGGACAGATGGTTGGAAGGATGGATGGATGGATGGATGGATGGATGGAT +GGATGGGGTTGGATGGATGGATGGATGGATGGATGGATAGTGGATAGATGGATGAATAGT +GGATGGATAAATGGATTAATGGATGGATGAATGGATGATGGATGGATGAATGAGATGGAT +GGATTGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGAAGAATGGAT +GATGGATGGATGAGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGAAGAAT +GGATGATGGATGGATGAGATGGATGGATGGATGGATGGATGGGGGGTTGGATGGATGGAT +GGATGGATGGATGGATAGTGGATAGATGGATGAATAGTGAATGGATAAATGGATTAATGG +ATGGATGGATAGTGGATAGATGGATGAATAGTGGATGGATAAATGGATTAATGGATGGAT +GAATGGATGATGGATGGATGAATGAGATGGATGGATTGATGGATGGATGGATGGATGGAT +GGATGGATGGAAGAATGGATGATGGATGGATGAATGAGATGGGTGGATTGATGGATGGAT +GGATGGATGGATGGATGGATGGATGGATGGCAGATGGATGGATCCATCTATGTCAGGCCT +GCATGACACCTGGTGTGGAGGAGCCACCCAGTCAACATTTGCTGACAGGATGGACAGACA +GAGAGGAGGTGAGTGACAGGGGCCCTCAGGTGCTTTTTCTTTGGAGACCTGGGC +>p:HG002_1_chr20:57948698-57949591 +CGGAGCGGGTGTGCCCCGTGGTCTCTCTTCACTGTTCTTAAGACATTCACAACCTCATTT +TGATGGTGGGACGCTGCAGCTCACGTCTGAGTCCCATCCAAGACTTGGCCCACTGCTGTG +CCCTGCACAGATGGACAGATGGTTGGAAGGATGGATGGATGGATGGATGGATGGATGGAT +GGATGGGGTTGGATGGATGGATGGATGGATGGATGGATAGTGGATAGATGGATGAATAGT +GGATGGATAAATGGATTAATGGATGGATGAATGGATGATGGATGGATGAATGAGATGGAT +GGATTGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGAAGAATGGAT +GATGGATGGATGAGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGAAGAAT +GGATGATGGATGGATGAGATGGATGGATGGATGGATGGATGGGGGGTTGGATGGATGGAT +GGATGGATGGATGGATAGTGGATAGATGGATGAATAGTGAATGGATAAATGGATTAATGG +ATGGATGGATAGTGGATAGATGGATGAATAGTGGATGGATAAATGGATTAATGGATGGAT +GAATGGATGATGGATGGATGAATGAGATGGATGGATTGATGGATGGATGGATGGATGGAT +GGATGGATGGAAGAATGGATGATGGATGGATGAATGAGATGGGTGGATTGATGGATGGAT +GGATGGATGGATGGATGGATGGATGGATGGCAGATGGATGGATCCATCTATGTCAGGCCT +GCATGACACCTGGTGTGGAGGAGCCACCCAGTCAACATTTGCTGACAGGATGGACAGACA +GAGAGGAGGTGAGTGACAGGGGCCCTCAGGTGCTTTTTCTTTGGAGACCTGGGC +>p:HG002_2_chr20:57948698-57949591 +CGGAGCGGGTGTGCCCCGTGGTCTCTCTTCACTGTTCTTAAGACATTCACAACCTCATTT +TGATGGTGGGACGCTGCAGCTCACGTCTGAGTCCCATCCAAGACTTGGCCCACTGCTGTG +CCCTGCACAGATGGACAGATGGTTGGAAGGATGGATGGATGGATGGATGGATGGATGGAT +GGGGTTGGATGGATGGATGGATGGATGGATGGATAGTGGATAGATGGATGAATAGTGGAT +GGATAAATGGATTAATGGATGGATGAATGGATGATGGATGGATGAATGAGATGGATGGAT +TGATGGATGGATGGATGGATGGATGGATGGAAGAATGGATGATGGATGGATGAGATGGAT +GGATGGATGGATGGAAGAATGGATGATGGATGGATGAGATGGATGGATGGATGGGGGGTT +GGATGGATGGATGGATGGATGGATGGATAGTGGATAGATGGATGAATAGTGGATGGATAA +ATGGATTAATGGATGGATGAATGGATGATGGATGGATGAATGAGATGGATGGATTGATGG +ATGGATGGATGGATGGAAGAATGGATGATGGATGGATGAATGAGATGGGTGGATTGATGG +ATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGCAGATGGATGGATCCATCTA +TGTCAGGCCTGCATGACACCTGGTGTGGAGGAGCCACCCAGTCAACATTTGCTGACAGGA +TGGACAGACAGAGAGGAGGTGAGTGACAGGGGCCCTCAGGTGCTTTTTCTTTGGAGACCT +GGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/haps.fa.ref.fa new file mode 100644 index 00000000..cbc755d3 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:57948698-57949591 +CGGAGCGGGTGTGCCCCGTGGTCTCTCTTCACTGTTCTTAAGACATTCACAACCTCATTTTGATGGTGGGACGCTGCAGCTCACGTCTGAGTCCCATCCAAGACTTGGCCCACTGCTGTGCCCTGCACAGATGGACAGATGGTTGGAAGGATGGATGGATGGATGGATGGATGGATGGATGGATGGGGTTGGATGGATGGATGGATGGATGGATGGATAGTGGATAGATGGATGAATAGTGGATGGATAAATGGATTAATGGATGGATGAATGGATGATGGATGGATGAATGAGATGGATGGATTGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGAAGAATGGATGATGGATGGATGAGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGAAGAATGGATGATGGATGGATGAGATGGATGGATGGATGGATGGATGGGGGGTTGGATGGATGGATGGATGGATGGATGGATAGTGGATAGATGGATGAATAGTGAATGGATAAATGGATTAATGGATGGATGGATAGTGGATAGATGGATGAATAGTGGATGGATAAATGGATTAATGGATGGATGAATGGATGATGGATGGATGAATGAGATGGATGGATTGATGGATGGATGGATGGATGGATGGATGGATGGAAGAATGGATGATGGATGGATGAATGAGATGGGTGGATTGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGCAGATGGATGGATCCATCTATGTCAGGCCTGCATGACACCTGGTGTGGAGGAGCCACCCAGTCAACATTTGCTGACAGGATGGACAGACAGAGAGGAGGTGAGTGACAGGGGCCCTCAGGTGCTTTTTCTTTGGAGACCTGGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/msa.fa new file mode 100644 index 00000000..1fc076be --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/msa.fa @@ -0,0 +1,80 @@ +>ref_chr20_57948698_57949591 +cggagcgggtgtgccccgtggtctctcttcactgttcttaagacattcacaacctcattt +tgatggtgggacgctgcagctcacgtctgagtcccatccaagacttggcccactgctgtg +ccctgcacagatggacagatggttggaaggatggatggatggatggatggatggatggat +ggatggggttggatggatggatggatggatggatggatagtggatagatggatgaatagt +ggatggataaatggattaatggatggatgaatggatgatggatggatgaatgagatggat +ggattgatggatggatggatggatggatggatggatggatggatggatggaagaatggat +gatggatggatgagatggatggatggatggatggatggatggatggatggatggaagaat +ggatgatggatggatgagatggatggatggatggatggatggggggttggatggatggat +ggatggatggatggatagtggatagatggatgaatagtgaatggataaatggattaatgg +atggatggatagtggatagatggatgaatagtggatggataaatggattaatggatggat +gaatggatgatggatggatgaatgagatggatggattgatggatggatggatggatggat +ggatggatggaagaatggatgatggatggatgaatgagatgggtggatt----gatggat +ggatggatggatggatggatggatggatggatggcagatggatggatccatctatgtcag +gcctgcatgacacctggtgtggaggagccacccagtcaacatttgctgacaggatggaca +gacagagaggaggtgagtgacaggggccctcaggtgctttttctttggagacctgggc +>syndip_1_chr20:57948698-57949591 +cggagcgggtgtgccccgtggtctctcttcactgttcttaagacattcacaacctcattt +tgatggtgggacgctgcagctcacgtctgagtcccatccaagacttggcccactgctgtg +ccctgcacagatggacagatggttggaa----ggatggatggatggatggatggatggat +ggatggggttggatggatggatggatggatggatggatagtggatagatggatgaatagt +ggatggataaatggattaatggatggatgaatggatgatggatggatgaatgagatggat +ggatt----------------gatggatggatggatggatggatggatggaagaatggat +gatggatggatga--------------------gatggatggatggatggatggaagaat +ggatgatggatggatga--------gatggatggatggatggggggttggatggatggat +gg------------------------------------------------------atgg +atggatggatagtggatagatggatgaatagtggatggataaatggattaatggatggat +gaatggatgatggatggatgaatgagatggatggatt------------gatggatggat +ggatggatggaagaatggatgatggatggatgaatgagatgggtggattgatggatggat +ggatggatggatggatggatggatggatggatggcagatggatggatccatctatgtcag +gcctgcatgacacctggtgtggaggagccacccagtcaacatttgctgacaggatggaca +gacagagaggaggtgagtgacaggggccctcaggtgctttttctttggagacctgggc +>syndip_2_chr20:57948698-57949591 +cggagcgggtgtgccccgtggtctctcttcactgttcttaagacattcacaacctcattt +tgatggtgggacgctgcagctcacgtctgagtcccatccaagacttggcccactgctgtg +ccctgcacagatggacagatggttggaaggatggatggatggatggatggatggatggat +ggatggggttggatggatggatggatggatggatggatagtggatagatggatgaatagt +ggatggataaatggattaatggatggatgaatggatgatggatggatgaatgagatggat +ggattgatggatggatggatggatggatggatggatggatggatggatggaagaatggat +gatggatggatgagatggatggatggatggatggatggatggatggatggatggaagaat +ggatgatggatggatgagatggatggatggatggatggatggggggttggatggatggat +ggatggatggatggatagtggatagatggatgaatagtgaatggataaatggattaatgg +atggatggatagtggatagatggatgaatagtggatggataaatggattaatggatggat +gaatggatgatggatggatgaatgagatggatggattgatggatggatggatggatggat +ggatggatggaagaatggatgatggatggatgaatgagatgggtggatt----gatggat +ggatggatggatggatggatggatggatggatggcagatggatggatccatctatgtcag +gcctgcatgacacctggtgtggaggagccacccagtcaacatttgctgacaggatggaca +gacagagaggaggtgagtgacaggggccctcaggtgctttttctttggagacctgggc +>p:HG002_1_chr20:57948698-57949591 +cggagcgggtgtgccccgtggtctctcttcactgttcttaagacattcacaacctcattt +tgatggtgggacgctgcagctcacgtctgagtcccatccaagacttggcccactgctgtg +ccctgcacagatggacagatggttggaaggatggatggatggatggatggatggatggat +ggatggggttggatggatggatggatggatggatggatagtggatagatggatgaatagt +ggatggataaatggattaatggatggatgaatggatgatggatggatgaatgagatggat +ggattgatggatggatggatggatggatggatggatggatggatggatggaagaatggat +gatggatggatgagatggatggatggatggatggatggatggatggatggatggaagaat +ggatgatggatggatgagatggatggatggatggatggatggggggttggatggatggat +ggatggatggatggatagtggatagatggatgaatagtgaatggataaatggattaatgg +atggatggatagtggatagatggatgaatagtggatggataaatggattaatggatggat +gaatggatgatggatggatgaatgagatggatggattgatggatggatggatggatggat +ggatggatggaagaatggatgatggatggatgaatgagatgggtggatt----gatggat +ggatggatggatggatggatggatggatggatggcagatggatggatccatctatgtcag +gcctgcatgacacctggtgtggaggagccacccagtcaacatttgctgacaggatggaca +gacagagaggaggtgagtgacaggggccctcaggtgctttttctttggagacctgggc +>p:HG002_2_chr20:57948698-57949591 +cggagcgggtgtgccccgtggtctctcttcactgttcttaagacattcacaacctcattt +tgatggtgggacgctgcagctcacgtctgagtcccatccaagacttggcccactgctgtg +ccctgcacagatggacagatggttggaa----ggatggatggatggatggatggatggat +ggatggggttggatggatggatggatggatggatggatagtggatagatggatgaatagt +ggatggataaatggattaatggatggatgaatggatgatggatggatgaatgagatggat +ggatt----------------gatggatggatggatggatggatggatggaagaatggat +gatggatggatga--------------------gatggatggatggatggatggaagaat +ggatgatggatggatga--------gatggatggatggatggggggttggatggatggat +gg------------------------------------------------------atgg +atggatggatagtggatagatggatgaatagtggatggataaatggattaatggatggat +gaatggatgatggatggatgaatgagatggatggatt------------gatggatggat +ggatggatggaagaatggatgatggatggatgaatgagatgggtggattgatggatggat +ggatggatggatggatggatggatggatggatggcagatggatggatccatctatgtcag +gcctgcatgacacctggtgtggaggagccacccagtcaacatttgctgacaggatggaca +gacagagaggaggtgagtgacaggggccctcaggtgctttttctttggagacctgggc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/msa.fa.fai new file mode 100644 index 00000000..785ab6f8 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_57948698_57949591 898 29 60 61 +syndip_1_chr20:57948698-57949591 898 976 60 61 +syndip_2_chr20:57948698-57949591 898 1923 60 61 +p:HG002_1_chr20:57948698-57949591 898 2871 60 61 +p:HG002_2_chr20:57948698-57949591 898 3819 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/output.vcf.gz new file mode 100644 index 00000000..0c799b82 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/output.vcf.gz.tbi new file mode 100644 index 00000000..b4a4743c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:57948798-57949491/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/base.vcf.gz new file mode 100644 index 00000000..34715eaf Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/base.vcf.gz.tbi new file mode 100644 index 00000000..b96af4a1 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/comp.vcf.gz new file mode 100644 index 00000000..8a335e16 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/comp.vcf.gz.tbi new file mode 100644 index 00000000..aaa843c8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/haps.fa new file mode 100644 index 00000000..347e4302 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/haps.fa @@ -0,0 +1,136 @@ +>ref_chr20_59383704_59385336 +GGTTTTGTGCTTCCACCAAGCCAGGGGACTGTTCTGTGGCCCTGGAACCACCGTGAAAGCAAACAACCCTCGGCTGTGTTGGGAGACAGCTCCAGCTCCTCCATCCTCAAATGTGAGAGCTGATGATTGGGGTGGAGGAGGAGGTGAGTGGGGAGGGGGTGGGGGAGAAGGAGGTGATGGGGAAGAGATGAGTGGGCAGGAGGTGAGCAGGGAGGAGGTGAGCAGGGATGAGTGGAGGAAGGAGGTGATAGGGAGGAGGTGAGTGGGCAGGAGGTGAGCAGGGAGAAGATGAGCAGGGGGGTGGTGAGCGGGGAGGAGGTGGAGGGGAAGGAAGTGATGGGGGAGGAGGTGGGGGGAAGGAGGTGATGGGGAGGAGGTGAATGGGCAGGAGGTGACTGGGGAGGAGGTGAGCAGGGAGGAGGTGAGCAGGGAGGAGGTGAGTGGAGTGGGGATGGGAGTGGAGTGGCGGGAAGGAAGTGATAGGGAGGAGATGAGTGGGCAGGAGGTGAGCAGAGAGGAGATGAGTAGAGCAGGGATGAGTAGGGGAAGGAGGTGATAGGAGGTGAGTGGGCAGGAGGTGAGCAGGGAGGAGGCGAGCAGGGAGGAGGTAGAGGGGAAGGAAGTGATGGGGAGGAGGTGAGGGGGGAAAGAGGTGGCGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGGGGAGGAAGGTGGGGGGAAGGAGGTGATAGGGAGGATGTGGGGGAGGTGGGGGGGAAGGAGGTGAGGCAGAGGAGGGGAGTGGGGAGGGAGATGAGTAAGGAAGTGATGGGGAGAGGGTGAGTGGGGAAGTGGTGAGAGGGGAGGAGGTGAGGGGGCAAGGGAGGCGATGCGGAGGAAGGAGGTGATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGAGGGGAGGAGCTGAGTGGGGAAGGAGGTAATGAGGACAAGGTGAGGGGAAAGGAGGTAAGGGAGGGGAAGGGGAGGGAAGGAGCTGAGCGGGGCAGAGCATGTCTCCTCTCTTTAAGCATCCTCTGTATTCTGCAGAGGCCAAGCAGTCTGGATGTTGGCCTTCCTCAGTGGCCCATGAAATAACTTTGCTCCCCAGATTCTGAGCATGGGT +>syndip_1_chr20:59383704-59385336 +GGTTTTGTGCTTCCACCAAGCCAGGGGACTGTTCTGTGGCCCTGGAACCACCGTGAAAGC +AAACAACCCTCGGCTGTGTTGGGAGACAGCTCCAGCTCCTCCATCCTCAAATGTGAGAGC +TGATGATTGGGGTGGAGGAGGAGGTGAGTGGGGAGGGGGTGGGGGAGAAGGAGGTGATGG +GGAAGAGATGAGTGGGCAGGAGGTGAGCAGGGAGGAGGTGAGCAGGGATGAGTGGAGGAA +GGAGGTGATAGGGAGGAGGTGAGTGGGCAGGAGGTGAGCAGGGAGAAGATGAGCAGGGGG +GTGGTGAGCGGGGAGGAGGTGGAGGGGAAGGAAGTGATGGGGGAGGAGGTGGGGGGAAGG +AGGTGATGGGGAGGAGGTGAATGGGCAGGAGGTGACTGGGGAGGAGGTGAGCAGGGAGGA +GGTGAGCAGGGAGGAGGTGAGTGGAGTGGGGATGGGAGTGGAGTGGGGGGAAGGAAGTGA +TAGGGAGGAGATGAGTGGGCAGGAGGTGAGCAGAGAGGAGATGAGTAGAGCAGGGATGAG +TAGGGGAAGGAGGTGATAGGAGGTGAGTGGGCAGGAGGTGAGCAGGGAGGAGGCGAGCAG +GGAGGAGGTAGAGGGGAAGGAAGTGATGGGGAGGAGGTGAGGGGGGAAAGAGGTGGCGGG +GGAAGGAGGTGATGGGGAGGAGGTGAGTGGGGAGGAAGGTGGGAGGAAGGAGGTGATGGG +GAGGATGTGGGGGAGGTGGGGAGCAAGGAGGTGATGGGGAGGAGGTGAGTGGGGAGGTGG +TGAGCAGGGAGGAGGTGAGGGGGCAAGGGAGGTGATGGGGAGGAAGGAGGTTATGGGGAG +GTGGTGAGTGGGGAGGGAGGTAAGGGGTAAGGTGGTGATGTGGAGGTGGTGAGTGGGGAG +GTGGTGAGAGGGGAGGAGATGAGGGGGCAAGGGAGGTGATGGGGAGGAGGTGAGTGGGGA +GGAAGGTGGGGGGAAGGAGGTGATGGGGAGGATGTGGGGGAGGTGGGGGGGAAGGAGGTG +AGGCAGAGGAGGGGAGTGGGGAGGGAGATGAGTAAGGAAGTGATGGGGAGAGGGTGAGTG +GGGAAGTGGTGAGAGGGGAGGAGGTGAGGGGGCAAGGGAGGTGATGCGGAGGAAGGAGGT +GATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGAGGAAGGAGGTG +ATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGA +TGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGAT +GGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATG +GGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGAGGAAGGAGGTGATGG +GAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGG +AAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGA +AGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGAA +GGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGAAG +GAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGG +AGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGA +GGTGAGAGGGGAGGAGCTGAGGGGGGAAGGAGGTAATGAGGACAAGGTGAGGGGAAAGGA +GGTAAGGGAGGGGAAGGGGAGGGAAGGAGCTGAGCGGGGCAGAGCATGTCTCCTCTCTTT +AAGCATCCTCTGTATTCTGCAGAGGCCAAGCAGTCTGGATGTTGGCCTTCCTCAGTGGCC +CATGAAATAACTTTGCTCCCCAGATTCTGAGCATGGGT +>syndip_2_chr20:59383704-59385336 +GGTTTTGTGCTTCCACCAAGCCAGGGGACTGTTCTGTGGCCCTGGAACCACCGTGAAAGC +AAACAACCCTCGGCTGTGTTGGGAGACAGCTCCAGCTCCTCCATCCTCAAATGTGAGAGC +TGATGATTGGGGTGGAGGAGGAGGTGAGTGGGGAGGGGGTGGGGGAGAAGGAGGTGATGG +GGAAGAGATGAGTGGGCAGGAGGTGAGCAGGGAGGAGGTGAGCAGGGATGAGTGGAGGAA +GGAGGTGATAGGGAGGAGGTGAGTGGGCAGGAGGTGAGCAGGGAGAAGATGAGCAGGGGG +GTGGTGAGCGGGGAGGAGGTGGAGGGGAAGGAAGTGATGGGGGAGGAGGTGGGGGGAAGG +AGGTGATGGGGAGGAGGTGAATGGGCAGGAGGTGACTGGGGAGGAGGTGAGCAGGGAGGA +GGTGAGCAGGGAGGAGGTGAGTGGAGTGGGGATGGGAGTGGAGTGGGGGGAAGGAAGTGA +TAGGGAGGAGATGAGTGGGCAGGAGGTGAGCAGAGAGGAGATGAGTAGAGCAGGGATGAG +TAGGGGAAGGAGGTGATAGGAGGTGAGTGGGCAGGAGGTGAGCAGGGAGGAGGCGAGCAG +GGAGGAGGTAGAGGGGAAGGAAGTGATGGGGAGGAGGTGAGGGGGGAAAGAGGTGGCGGG +GGAAGGAGGTGATGGGGAGGAGGTGAGTGGGGAGGAAGGTGGGAGGAAGGAGGTGATGGG +GAGGATGTGGGGGAGGTGGGGAGCAAGGAGGTGATGGGGAGGAGGTGAGTGGGGAGGTGG +TGAGCAGGGAGGAGGTGAGGGGGCAAGGGAGGTGATGGGGAGGAGGTGAGTGGGGAGGTG +GTGAGCGGGGAGGAGGTGAGGGGGCAAGGGAGGTGATGGGGAGGAAGGAGGTTATGGGGA +GGTGGTGAGTGGGGAGGGAGGTAAGGGGTAAGGTGGTGATGTGGAGGTGGTGAGTGGGGA +GGTGGTGAGAGGGGAGGAGATGAGGGGGCAAGGGAGGTGATGGGGAGGAGGTGAGTGGGG +AGGAAGGTGGGGGGAAGGAGGTGATGGGGAGGATGTGGGGGAGGTGGGGGGGAAGGAGGT +GAGGCAGAGGAGGGGAGTGGGGAGGGAGATGAGTAAGGAAGTGATGGGGAGAGGGTGAGT +GGGGAAGTGGTGAGAGGGGAGGAGGTGAGGGGGCAAGGGAGGCGATGCGGAGGAAGGAGG +TGATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGAGGAAGGAGGT +GATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTG +ATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGA +TGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGAGGAAGGAGGTGAT +GGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATG +GGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGG +GGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGG +GAGGAGGTGAGAGGGGAGGAGCTGAGGGGGGAAGGAGGTAATGAGGACAAGGTGAGGGGA +AAGGAGGTAAGGGAGGGGAAGGGGAGGGAAGGAGCTGAGCGGGGCAGAGCATGTCTCCTC +TCTTTAAGCATCCTCTGTATTCTGCAGAGGCCAAGCAGTCTGGATGTTGGCCTTCCTCAG +TGGCCCATGAAATAACTTTGCTCCCCAGATTCTGAGCATGGGT +>p:HG002_1_chr20:59383704-59385336 +GGTTTTGTGCTTCCACCAAGCCAGGGGACTGTTCTGTGGCCCTGGAACCACCGTGAAAGC +AAACAACCCTCGGCTGTGTTGGGAGACAGCTCCAGCTCCTCCATCCTCAAATGTGAGAGC +TGATGATTGGGGTGGAGGAGGAGGTGAGTGGGGAGGGGGTGGGGGAGAAGGAGGTGATGG +GGAAGAGATGAGTGGGCAGGAGGTGAGCAGGGAGGAGGTGAGCAGGGATGAGTGGAGGAA +GGAGGTGATAGGGAGGAGGTGAGTGGGCAGGAGGTGAGCAGGGAGAAGATGAGCAGGGGG +GTGGTGAGCGGGGAGGAGGTGGAGGGGAAGGAAGTGATGGGGGAGGAGGTGGGGGGAAGG +AGGTGATGGGGAGGAGGTGAATGGGCAGGAGGTGACTGGGGAGGAGGTGAGCAGGGAGGA +GGTGAGCAGGGAGGAGGTGAGTGGAGTGGGGATGGGAGTGGAGTGGGGGGAAGGAAGTGA +TAGGGAGGAGATGAGTGGGCAGGAGGTGAGCAGAGAGGAGATGAGTAGAGCAGGGATGAG +TAGGGGAAGGAGGTGATAGGAGGTGAGTGGGCAGGAGGTGAGCAGGGAGGAGGCGAGCAG +GGAGGAGGTAGAGGGGAAGGAAGTGATGGGGAGGAGGTGAGGGGGGAAAGAGGTGGCGGG +GGAAGGAGGTGATGGGGAGGAGGTGAGTGGGGAGGAAGGTGGGAGGAAGGAGGTGATGGG +GAGGATGTGGGGGAGGTGGGGAGCAAGGAGGTGATGGGGAGGAGGTGAGTGGGGAGGTGG +TGAGCAGGGAGGAGGTGAGGGGGCAAGGGAGGTGATGGGGAGGAGGTGAGTGGGGAGGTG +GTGAGCGGGGAGGAGGTGAGGGGGCAAGGGAGGTGATGGGGAGGAAGGAGGTTATGGGGA +GGTGGTGAGTGGGGAGGGAGGTAAGGGGTAAGGTGGTGATGTGGAGGTGGTGAGTGGGGA +GGTGGTGAGAGGGGAGGAGATGAGGGGGCAAGGGAGGTGATGGGGAGGAGGTGAGTGGGG +AGGAAGGTGGGGGGAAGGAGGTGATGGGGAGGATGTGGGGGAGGTGGGGGGGAAGGAGGT +GAGGCAGAGGAGGGGAGTGGGGAGGGAGATGAGTAAGGAAGTGATGGGGAGAGGGTGAGT +GGGGAAGTGGTGAGAGGGGAGGAGGTGAGGGGGCAAGGGAGGCGATGCGGAGGAAGGAGG +TGATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGAGGAAGGAGGT +GATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTG +ATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGA +TGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGAGGAAGGAGGTGAT +GGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATG +GGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGG +GGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGG +GAGGAGGTGAGAGGGGAGGAGCTGAGGGGGGAAGGAGGTAATGAGGACAAGGTGAGGGGA +AAGGAGGTAAGGGAGGGGAAGGGGAGGGAAGGAGCTGAGCGGGGCAGAGCATGTCTCCTC +TCTTTAAGCATCCTCTGTATTCTGCAGAGGCCAAGCAGTCTGGATGTTGGCCTTCCTCAG +TGGCCCATGAAATAACTTTGCTCCCCAGATTCTGAGCATGGGT +>p:HG002_2_chr20:59383704-59385336 +GGTTTTGTGCTTCCACCAAGCCAGGGGACTGTTCTGTGGCCCTGGAACCACCGTGAAAGC +AAACAACCCTCGGCTGTGTTGGGAGACAGCTCCAGCTCCTCCATCCTCAAATGTGAGAGC +TGATGATTGGGGTGGAGGAGGAGGTGAGTGGGGAGGGGGTGGGGGAGAAGGAGGTGATGG +GGAAGAGATGAGTGGGCAGGAGGTGAGCAGGGAGGAGGTGAGCAGGGATGAGTGGAGGAA +GGAGGTGATAGGGAGGAGGTGAGTGGGCAGGAGGTGAGCAGGGAGAAGATGAGCAGGGGG +GTGGTGAGCGGGGAGGAGGTGGAGGGGAAGGAAGTGATGGGGGAGGAGGTGGGGGGAAGG +AGGTGATGGGGAGGAGGTGAATGGGCAGGAGGTGACTGGGGAGGAGGTGAGCAGGGAGGA +GGTGAGCAGGGAGGAGGTGAGTGGAGTGGGGATGGGAGTGGAGTGGGGGGAAGGAAGTGA +TAGGGAGGAGATGAGTGGGCAGGAGGTGAGCAGAGAGGAGATGAGTAGAGCAGGGATGAG +TAGGGGAAGGAGGTGATAGGAGGTGAGTGGGCAGGAGGTGAGCAGGGAGGAGGCGAGCAG +GGAGGAGGTAGAGGGGAAGGAAGTGATGGGGAGGAGGTGAGGGGGGAAAGAGGTGGCGGG +GGAAGGAGGTGATGGGGAGGAGGTGAGTGGGGAGGAAGGTGGGAGGAAGGAGGTGATGGG +GAGGATGTGGGGGAGGTGGGGAGCAAGGAGGTGATGGGGAGGAGGTGAGTGGGGAGGTGG +TGAGCAGGGAGGAGGTGAGGGGGCAAGGGAGGTGATGGGGAGGAAGGAGGTTATGGGGAG +GTGGTGAGTGGGGAGGGAGGTAAGGGGTAAGGTGGTGATGTGGAGGTGGTGAGTGGGGAG +GTGGTGAGAGGGGAGGAGATGAGGGGGCAAGGGAGGTGATGGGGAGGAGGTGAGTGGGGA +GGAAGGTGGGGGGAAGGAGGTGATGGGGAGGATGTGGGGGAGGTGGGGGGGAAGGAGGTG +AGGCAGAGGAGGGGAGTGGGGAGGGAGATGAGTAAGGAAGTGATGGGGAGAGGGTGAGTG +GGGAAGTGGTGAGAGGGGAGGAGGTGAGGGGGCAAGGGAGGTGATGCGGAGGAAGGAGGT +GATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGAGGAAGGAGGTG +ATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGA +TGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGAT +GGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATG +GGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGAGGAAGGAGGTGATGG +GAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGG +AAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGA +AGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGAA +GGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGAAG +GAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGG +AGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGA +GGTGAGAGGGGAGGAGCTGAGGGGGGAAGGAGGTAATGAGGACAAGGTGAGGGGAAAGGA +GGTAAGGGAGGGGAAGGGGAGGGAAGGAGCTGAGCGGGGCAGAGCATGTCTCCTCTCTTT +AAGCATCCTCTGTATTCTGCAGAGGCCAAGCAGTCTGGATGTTGGCCTTCCTCAGTGGCC +CATGAAATAACTTTGCTCCCCAGATTCTGAGCATGGGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/haps.fa.ref.fa new file mode 100644 index 00000000..cfc731bd --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:59383704-59385336 +GGTTTTGTGCTTCCACCAAGCCAGGGGACTGTTCTGTGGCCCTGGAACCACCGTGAAAGCAAACAACCCTCGGCTGTGTTGGGAGACAGCTCCAGCTCCTCCATCCTCAAATGTGAGAGCTGATGATTGGGGTGGAGGAGGAGGTGAGTGGGGAGGGGGTGGGGGAGAAGGAGGTGATGGGGAAGAGATGAGTGGGCAGGAGGTGAGCAGGGAGGAGGTGAGCAGGGATGAGTGGAGGAAGGAGGTGATAGGGAGGAGGTGAGTGGGCAGGAGGTGAGCAGGGAGAAGATGAGCAGGGGGGTGGTGAGCGGGGAGGAGGTGGAGGGGAAGGAAGTGATGGGGGAGGAGGTGGGGGGAAGGAGGTGATGGGGAGGAGGTGAATGGGCAGGAGGTGACTGGGGAGGAGGTGAGCAGGGAGGAGGTGAGCAGGGAGGAGGTGAGTGGAGTGGGGATGGGAGTGGAGTGGCGGGAAGGAAGTGATAGGGAGGAGATGAGTGGGCAGGAGGTGAGCAGAGAGGAGATGAGTAGAGCAGGGATGAGTAGGGGAAGGAGGTGATAGGAGGTGAGTGGGCAGGAGGTGAGCAGGGAGGAGGCGAGCAGGGAGGAGGTAGAGGGGAAGGAAGTGATGGGGAGGAGGTGAGGGGGGAAAGAGGTGGCGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGGGGAGGAAGGTGGGGGGAAGGAGGTGATAGGGAGGATGTGGGGGAGGTGGGGGGGAAGGAGGTGAGGCAGAGGAGGGGAGTGGGGAGGGAGATGAGTAAGGAAGTGATGGGGAGAGGGTGAGTGGGGAAGTGGTGAGAGGGGAGGAGGTGAGGGGGCAAGGGAGGCGATGCGGAGGAAGGAGGTGATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGAGGGGAGGAGCTGAGTGGGGAAGGAGGTAATGAGGACAAGGTGAGGGGAAAGGAGGTAAGGGAGGGGAAGGGGAGGGAAGGAGCTGAGCGGGGCAGAGCATGTCTCCTCTCTTTAAGCATCCTCTGTATTCTGCAGAGGCCAAGCAGTCTGGATGTTGGCCTTCCTCAGTGGCCCATGAAATAACTTTGCTCCCCAGATTCTGAGCATGGGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/msa.fa new file mode 100644 index 00000000..2a7799a9 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/msa.fa @@ -0,0 +1,180 @@ +>ref_chr20_59383704_59385336 +ggttttgtgcttccaccaagccaggggactgttctgtggccctggaaccaccgtgaaagc +aaacaaccctcggctgtgttgggagacagctccagctcctccatcctcaaatgtgagagc +tgatgattggggtggaggaggaggtgagtggggagggggtgggggagaaggaggtgatgg +ggaagagatgagtgggcaggaggtgagcagggaggaggtgagcagggatgagtggaggaa +ggaggtgatagggaggaggtgagtgggcaggaggtgagcagggagaagatgagcaggggg +gtggtgagcggggaggaggtggaggggaaggaagtgatgggggaggaggtggggggaagg +aggtgatggggaggaggtgaatgggcaggaggtgactggggaggaggtgagcagggagga +ggtgagcagggaggaggtgagtggagtggggatgggagtggagtggcgggaaggaagtga +tagggaggagatgagtgggcaggaggtgagcagagaggagatgagtagagcagggatgag +taggggaaggaggtgataggaggtgagtgggcaggaggtgagcagggaggaggcgagcag +ggaggaggtagaggggaaggaagtgatggggaggaggtgaggggggaaagaggtggcggg +ggaa-------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------ggaggtgatggggaggaggtgagtgggg +aggaaggtggggggaaggaggtgatagggaggatgtgggggaggtgggggggaaggaggt +gaggcagaggaggggagtggggagggagatgagtaaggaagtgatggggagagggtgagt +ggggaagtggtgagaggggaggaggtgagggggcaagggaggcgatgcgga--------- +------------------------------------------------------------ +-------------------------------------------------ggaaggaggtg +atgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtga +tggggaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgat +ggggaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatg +gggaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgg +gaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggg +gaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgggg +aggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgggga +ggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggag +gaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggagg +aggtgagaggggaggagctgagtggggaaggaggtaatgaggacaaggtgaggggaaagg +aggtaagggaggggaaggggagggaaggagctgagcggggcagagcatgtctcctctctt +taagcatcctctgtattctgcagaggccaagcagtctggatgttggccttcctcagtggc +ccatgaaataactttgctccccagattctgagcatgggt +>syndip_1_chr20:59383704-59385336 +ggttttgtgcttccaccaagccaggggactgttctgtggccctggaaccaccgtgaaagc +aaacaaccctcggctgtgttgggagacagctccagctcctccatcctcaaatgtgagagc +tgatgattggggtggaggaggaggtgagtggggagggggtgggggagaaggaggtgatgg +ggaagagatgagtgggcaggaggtgagcagggaggaggtgagcagggatgagtggaggaa +ggaggtgatagggaggaggtgagtgggcaggaggtgagcagggagaagatgagcaggggg +gtggtgagcggggaggaggtggaggggaaggaagtgatgggggaggaggtggggggaagg +aggtgatggggaggaggtgaatgggcaggaggtgactggggaggaggtgagcagggagga +ggtgagcagggaggaggtgagtggagtggggatgggagtggagtggggggaaggaagtga +tagggaggagatgagtgggcaggaggtgagcagagaggagatgagtagagcagggatgag +taggggaaggaggtgataggaggtgagtgggcaggaggtgagcagggaggaggcgagcag +ggaggaggtagaggggaaggaagtgatggggaggaggtgaggggggaaagaggtggcggg +ggaaggaggtgatggggaggaggtgagtggggaggaaggtgggaggaaggaggtgatggg +gaggatgtgggggaggtggggagcaaggaggtgatggggaggaggtgagtggggaggtgg +tgagca------------------------------------------------------ +-------gggaggaggtgagggggcaagggaggtgatggggaggaaggaggttatgggga +ggtggtgagtggggagggaggtaaggggtaaggtggtgatgtggaggtggtgagtgggga +ggtggtgagaggggaggagatgagggggcaagggaggtgatggggaggaggtgagtgggg +aggaaggtggggggaaggaggtgatggggaggatgtgggggaggtgggggggaaggaggt +gaggcagaggaggggagtggggagggagatgagtaaggaagtgatggggagagggtgagt +ggggaagtggtgagaggggaggaggtgagggggcaagggaggtgatgcggaggaaggagg +tgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtggggaggaaggaggt +gatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtg +atgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtga +tgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgat +gggaaggaggtgagtgtgtaggaggtaagcagggaggaagtggggaggaaggaggtgatg +ggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgg +gaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggg +aaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggga +aggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgggaa +ggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggag +gaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggagg +aggtgagaggggaggagctgaggggggaaggaggtaatgaggacaaggtgaggggaaagg +aggtaagggaggggaaggggagggaaggagctgagcggggcagagcatgtctcctctctt +taagcatcctctgtattctgcagaggccaagcagtctggatgttggccttcctcagtggc +ccatgaaataactttgctccccagattctgagcatgggt +>syndip_2_chr20:59383704-59385336 +ggttttgtgcttccaccaagccaggggactgttctgtggccctggaaccaccgtgaaagc +aaacaaccctcggctgtgttgggagacagctccagctcctccatcctcaaatgtgagagc +tgatgattggggtggaggaggaggtgagtggggagggggtgggggagaaggaggtgatgg +ggaagagatgagtgggcaggaggtgagcagggaggaggtgagcagggatgagtggaggaa +ggaggtgatagggaggaggtgagtgggcaggaggtgagcagggagaagatgagcaggggg +gtggtgagcggggaggaggtggaggggaaggaagtgatgggggaggaggtggggggaagg +aggtgatggggaggaggtgaatgggcaggaggtgactggggaggaggtgagcagggagga +ggtgagcagggaggaggtgagtggagtggggatgggagtggagtggggggaaggaagtga +tagggaggagatgagtgggcaggaggtgagcagagaggagatgagtagagcagggatgag +taggggaaggaggtgataggaggtgagtgggcaggaggtgagcagggaggaggcgagcag +ggaggaggtagaggggaaggaagtgatggggaggaggtgaggggggaaagaggtggcggg +ggaaggaggtgatggggaggaggtgagtggggaggaaggtgggaggaaggaggtgatggg +gaggatgtgggggaggtggggagcaaggaggtgatggggaggaggtgagtggggaggtgg +tgagcagggaggaggtgagggggcaagggaggtgatggggaggaggtgagtggggaggtg +gtgagcggggaggaggtgagggggcaagggaggtgatggggaggaaggaggttatgggga +ggtggtgagtggggagggaggtaaggggtaaggtggtgatgtggaggtggtgagtgggga +ggtggtgagaggggaggagatgagggggcaagggaggtgatggggaggaggtgagtgggg +aggaaggtggggggaaggaggtgatggggaggatgtgggggaggtgggggggaaggaggt +gaggcagaggaggggagtggggagggagatgagtaaggaagtgatggggagagggtgagt +ggggaagtggtgagaggggaggaggtgagggggcaagggaggcgatgcgga--------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------------------ggaaggaggtgat +gggaaggaggtgagtgtgtaggaggtaagcagggaggaagtggggaggaaggaggtgatg +ggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgg +gaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggg +gaggaggtgagtgtgtaggaggtaagcagggaggaagtggggaggaaggaggtgatggga +aggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgggaa +ggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggag +gaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggagg +aggtgagaggggaggagctgaggggggaaggaggtaatgaggacaaggtgaggggaaagg +aggtaagggaggggaaggggagggaaggagctgagcggggcagagcatgtctcctctctt +taagcatcctctgtattctgcagaggccaagcagtctggatgttggccttcctcagtggc +ccatgaaataactttgctccccagattctgagcatgggt +>p:HG002_1_chr20:59383704-59385336 +ggttttgtgcttccaccaagccaggggactgttctgtggccctggaaccaccgtgaaagc +aaacaaccctcggctgtgttgggagacagctccagctcctccatcctcaaatgtgagagc +tgatgattggggtggaggaggaggtgagtggggagggggtgggggagaaggaggtgatgg +ggaagagatgagtgggcaggaggtgagcagggaggaggtgagcagggatgagtggaggaa +ggaggtgatagggaggaggtgagtgggcaggaggtgagcagggagaagatgagcaggggg +gtggtgagcggggaggaggtggaggggaaggaagtgatgggggaggaggtggggggaagg +aggtgatggggaggaggtgaatgggcaggaggtgactggggaggaggtgagcagggagga +ggtgagcagggaggaggtgagtggagtggggatgggagtggagtggggggaaggaagtga +tagggaggagatgagtgggcaggaggtgagcagagaggagatgagtagagcagggatgag +taggggaaggaggtgataggaggtgagtgggcaggaggtgagcagggaggaggcgagcag +ggaggaggtagaggggaaggaagtgatggggaggaggtgaggggggaaagaggtggcggg +ggaaggaggtgatggggaggaggtgagtggggaggaaggtgggaggaaggaggtgatggg +gaggatgtgggggaggtggggagcaaggaggtgatggggaggaggtgagtggggaggtgg +tgagcagggaggaggtgagggggcaagggaggtgatggggaggaggtgagtggggaggtg +gtgagcggggaggaggtgagggggcaagggaggtgatggggaggaaggaggttatgggga +ggtggtgagtggggagggaggtaaggggtaaggtggtgatgtggaggtggtgagtgggga +ggtggtgagaggggaggagatgagggggcaagggaggtgatggggaggaggtgagtgggg +aggaaggtggggggaaggaggtgatggggaggatgtgggggaggtgggggggaaggaggt +gaggcagaggaggggagtggggagggagatgagtaaggaagtgatggggagagggtgagt +ggggaagtggtgagaggggaggaggtgagggggcaagggaggcgatgcgga--------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------------------ggaaggaggtgat +gggaaggaggtgagtgtgtaggaggtaagcagggaggaagtggggaggaaggaggtgatg +ggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgg +gaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggg +gaggaggtgagtgtgtaggaggtaagcagggaggaagtggggaggaaggaggtgatggga +aggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgggaa +ggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggag +gaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggagg +aggtgagaggggaggagctgaggggggaaggaggtaatgaggacaaggtgaggggaaagg +aggtaagggaggggaaggggagggaaggagctgagcggggcagagcatgtctcctctctt +taagcatcctctgtattctgcagaggccaagcagtctggatgttggccttcctcagtggc +ccatgaaataactttgctccccagattctgagcatgggt +>p:HG002_2_chr20:59383704-59385336 +ggttttgtgcttccaccaagccaggggactgttctgtggccctggaaccaccgtgaaagc +aaacaaccctcggctgtgttgggagacagctccagctcctccatcctcaaatgtgagagc +tgatgattggggtggaggaggaggtgagtggggagggggtgggggagaaggaggtgatgg +ggaagagatgagtgggcaggaggtgagcagggaggaggtgagcagggatgagtggaggaa +ggaggtgatagggaggaggtgagtgggcaggaggtgagcagggagaagatgagcaggggg +gtggtgagcggggaggaggtggaggggaaggaagtgatgggggaggaggtggggggaagg +aggtgatggggaggaggtgaatgggcaggaggtgactggggaggaggtgagcagggagga +ggtgagcagggaggaggtgagtggagtggggatgggagtggagtggggggaaggaagtga +tagggaggagatgagtgggcaggaggtgagcagagaggagatgagtagagcagggatgag +taggggaaggaggtgataggaggtgagtgggcaggaggtgagcagggaggaggcgagcag +ggaggaggtagaggggaaggaagtgatggggaggaggtgaggggggaaagaggtggcggg +ggaaggaggtgatggggaggaggtgagtggggaggaaggtgggaggaaggaggtgatggg +gaggatgtgggggaggtggggagcaaggaggtgatggggaggaggtgagtggggaggtgg +tgagca------------------------------------------------------ +-------gggaggaggtgagggggcaagggaggtgatggggaggaaggaggttatgggga +ggtggtgagtggggagggaggtaaggggtaaggtggtgatgtggaggtggtgagtgggga +ggtggtgagaggggaggagatgagggggcaagggaggtgatggggaggaggtgagtgggg +aggaaggtggggggaaggaggtgatggggaggatgtgggggaggtgggggggaaggaggt +gaggcagaggaggggagtggggagggagatgagtaaggaagtgatggggagagggtgagt +ggggaagtggtgagaggggaggaggtgagggggcaagggaggtgatgcggaggaaggagg +tgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtggggaggaaggaggt +gatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtg +atgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtga +tgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgat +gggaaggaggtgagtgtgtaggaggtaagcagggaggaagtggggaggaaggaggtgatg +ggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgg +gaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggg +aaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggga +aggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgggaa +ggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggag +gaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggagg +aggtgagaggggaggagctgaggggggaaggaggtaatgaggacaaggtgaggggaaagg +aggtaagggaggggaaggggagggaaggagctgagcggggcagagcatgtctcctctctt +taagcatcctctgtattctgcagaggccaagcagtctggatgttggccttcctcagtggc +ccatgaaataactttgctccccagattctgagcatgggt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/msa.fa.fai new file mode 100644 index 00000000..ad0f1da2 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_59383704_59385336 2079 29 60 61 +syndip_1_chr20:59383704-59385336 2079 2177 60 61 +syndip_2_chr20:59383704-59385336 2079 4325 60 61 +p:HG002_1_chr20:59383704-59385336 2079 6474 60 61 +p:HG002_2_chr20:59383704-59385336 2079 8623 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/output.vcf.gz new file mode 100644 index 00000000..561129ad Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/output.vcf.gz.tbi new file mode 100644 index 00000000..e73b2069 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:59383804-59385236/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/base.vcf.gz new file mode 100644 index 00000000..cb30439e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/base.vcf.gz.tbi new file mode 100644 index 00000000..c1afb7a4 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/comp.vcf.gz new file mode 100644 index 00000000..eed237be Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/comp.vcf.gz.tbi new file mode 100644 index 00000000..a2bc5903 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/haps.fa new file mode 100644 index 00000000..dee6dd9b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/haps.fa @@ -0,0 +1,132 @@ +>ref_chr20_60314230_60315121 +ACTTGTTTCCTCATTTATTCATTAACAATATTCATTTCTTAGCCAAGGATGGTGGTGCACACCTGTACTTCCAGCTACTCAGGAGGCTGAGGTGGAAGGATTGAAAATCCATCCATCTGTCCTCCTACCCATCCTGCTATCCATCCATCCATCCATCCTCCCATAATCTATCTTCCCATCCATTTGTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCTTCCTTCCTTCCTTCCTTCCTTCCTTCCACCCATCCATCCTCCCATTCATCCTCCCATGCATCCTCCCATCCATCCACCCAACCATCCTCCCATCCATCCTCACATCGATCTTCGCATCCATCCATCGATCGATCTATCCATCCATCCATTCTCCCATTCATCCATCCTCCCATCCATCCTCCTATCCATCCATCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCCACCCTTCCATCCATCCATCCACCCACCCTTCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCTATCCATCCATCCTCCCATCCTCCCATCCTCCCATCCATCCATCCATCCATCCATCCATCCTCCCATCCTCCCATCCTCCCATCCATCGTCCCATGTGTACATCTGTCCTGCCATCTATCCATACATCCATTTCTCCGTCCTCCCATCCATCTTCCCATCCATTCATCCATCCATCTTCCCATCCATTCATCCATCCATCCTGCCATCCATCCTTCCATTGATCCATCCATCCATCCTGCAGGAGACCAGGAGTTCAAGGCTGCCGTGAGTTATAATTGTGCCACTGCACTACAGCTTAAGTGACAGAGAGAGAAACCATCTCCAAAAATGAAAAAAAGAATATATTGATTTCAGGCCAGTTACATAGA +>syndip_1_chr20:60314230-60315121 +ACTTGTTTCCTCATTTATTCATTAACAATATTCATTTCTTAGCCAAGGATGGTGGTGCAC +ACCTGTACTTCCAGCTACTCAGGAGGCTGAGGTGGAAGGATTGAAAATCCATCCATCTGT +CCTCCTACCCATCCTGCTATCCATCCATCCATCCATCCTCCCATAATCTATCTTCCCATC +CATTTGTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC +CACCCATCCATCCTCCCATTCATCCTCCCATGCATCCTCCCATCCATCCACCCAACCATC +CTCCCATCCATCCTCACATCCATCTTCGCATCCATCCATCCATCCATCTATCCATCCATC +CATCCATCCTCCCATCCATCCTCCCATCCATTATCCCATTCATCCATCCTCCCATCCATC +CTCCTATCCATCCATCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCCACT +CTTCCATCCATCCATCCACCCACCCTTCCATCCATCCATCCTCCCATCCATCCATCCTCC +CATTCATCTATCCATCCATCCCTCGATCCTCCCATCCATCCATCCTCCCATCCATCCATC +CATCCTCCCATCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCTACCCTCC +CATCCATCCATCCTCCCACCCACCCTCCCATCCATCCATCCTCCCATCCTCCCATCCATC +CATCCATCCTCCCATCCGTCCATCCATCCTTCCATCCACCCTCCCATCCATCCATCCTCC +CATCCATCTACCCTCCCATCCATCCATCCTCCCACCCACCCTCCCATCCATCCACCCTCC +CATCCATCCATCCTCCCATCCATCTATCCATCCATCCTCCCATCCTCCCATCCATCCATC +ATCCATCCATCCATCCATCCATCCTCCCATAATCTATCTTCCCATCCATTTGTCCTTCCT +TCCTTCCTTCCTTCCTTCCTTCCTTCGTTCCACCCATCCATCCTCCCATTCATCCTCCCA +TGCATCCTCCCATCCATCCACCCAACCATCCTCCCATCCATCCTCACATCCATCTTCGCA +TCCATCCATCCATCCATCCATCTATCCATCCATCCTCCCATCCATCCTCCCATCCTCCCA +TCCATTCTCCCATTCATCCATCCTCCCATCCATCCTCCTATCCATCCATCCATCCATCCA +CCCTCCCATCCATCCATCCTCCCATCCATCCACCCTTCCATCCATCCATCCACCCACCCT +TCCATCCATCCACCCTCCCATCCATCCATCCTCCCATTCATCTATCCATCCATCCCTCGA +TCCTCCCATCCATCCATCCATCCTCCCATCCGTCCATCCATCCTTCCATCCACCCTCCCA +TCCATCCATCCTCCCATCCATCTACCCTCCCATCCATCCATCCTCCCACCCACCCTCCCA +TCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCTATCCATCCATCCTCCCATCCT +CCCATCCTCCCATCCATCCATCCATCCATCCATCCATCCTCCCATCCTCCCATCCTCCCA +TCCATCGTCCCATGTGTACATCTGTCCTGCCATCTATCCATACATCCATTTCTCCGTCCT +CCCATCCATCTTCCCATCCATTCATCCATCCATCTTCCCATCCATTCATCCATCCATCCT +GCCATCCATCCTTCCATTGATCCATCCATCCATCCTGCAGGAGACCAGGAGTTCAAGGCT +GCCGTGAGTTATAATTGTGCCACTGCACTACAGCTTAAGTGACAGAGAGAGAAACCATCT +CCAAAAATGAAAAAAAGAATATATTGATTTCAGGCCAGTTACATAGA +>syndip_2_chr20:60314230-60315121 +ACTTGTTTCCTCATTTATTCATTAACAATATTCATTTCTTAGCCAAGGATGGTGGTGCAC +ACCTGTACTTCCAGCTACTCAGGAGGCTGAGGTGGAAGGATTGAAAATCCATCCATCTGT +CGTCCTACCCATCCTGCTATCCATCCATCCATCCATCCTCCCATAATCTATCTTCCCATC +CATTTGTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCACCCATCCATCCTCCCATG +CATCCTCCCATGCATCCTCCCATCCATCCACCCAACCATCCTCCCATCCATCCTCACATC +CATCTTCGCATCCATCCATCCATCCATCTATCCATCCATCCATCCATCCTCCCATCCATC +CTCCCATCCATTATCCCATTCATCCATCCTCCCATCCATCCTCCTATCCATCCATCCATC +CATCCACCCTCTCATCCATCCATCCTCCCATCCATCCACCCTTCCATCCATCCATCCACC +CACCCTTCCATCCATCCATCCTCCCATCCATCCATCCTCCCATCCATCCATCCTCCCATT +CATCTATCCATCCATCCCTCGATCCTCCCATCCATCCATCCTCCCATCCATCCATCCATC +CTCCCATCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCTACCCTCCCATC +CATCCATCCTCCCATCCACCCTCCCATCCATCCATCCATCCATCCACCCTCTCATCCATC +CATCCTCCCATCCGTCCATCCATCCTTCCATCCACCCTCCCATCCATCCATCCTCCCATC +CATCCATCCTCCCATCCATCTACCCTCCCATCCATCCATCCTCCCACCCACCCTCCCATC +CATCCACCCTCCCATCCATCCATCCTCCCATCCATCTATCCATCCATCCTCCCATCCTCC +CATCCATCCATCATCCATCCATCCATCCATCCATCCTCCCATAATCTATCTTCCCATCCA +TTTGTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCACCCATCCATCCTCCCATTCATCCT +CCCATGCATCCTCCCATCCATCCACCCAACCATCCTCCCATCCATCCTCACATCCATCTT +CGCATCCATCCATCCATCCATCCATCTATCCATCCATCCTCCCATCCATCCTCCCATCCT +CCCATCCATCCTCCCATCCTCCCATCCATTCTCCCATTCATCCATCCTCCCATCCATCCT +CCTATCCATCCATCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCCACCCT +TCCATCCATCCATCCACCCACCCTTCCATCCATCCACCCTCCCATCCATCCATCCTCCCA +TTCATCTATCCATCCATCCCTCGATCCTCCCATCCATCCATCCATCCTCCCATCCGTCCA +TCCATCCTTCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCTACCCTCCCATCCA +TCCATCCTCCCACCCACCCTCCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCA +TCTATCCATCCATCCTCCCATCCTCCCATCCTCCCATCCATCCATCCATCCATCCATCCT +CCCATCCTCCCATCCTCCCATCCATCGTCCCATGTGTACATCTGTCCTGCCATCTATCCA +TACATCCATTTCTCCGTCCTCCCATCCATCTTCCCATCCATTCATCCATCCATCTTCCCA +TCCATTCATCCATCCATCCTGCCATCCATCCTTCCATTGATCCATCCATCCATCCTGCAG +GAGACCAGGAGTTCAAGGCTGCCGTGAGTTATAATTGTGCCACTGCACTACAGCTTAAGT +GACAGAGAGAGAAACCATCTCCAAAAATGAAAAAAAGAATATATTGATTTCAGGCCAGTT +ACATAGA +>p:HG002_1_chr20:60314230-60315121 +ACTTGTTTCCTCATTTATTCATTAACAATATTCATTTCTTAGCCAAGGATGGTGGTGCAC +ACCTGTACTTCCAGCTACTCAGGAGGCTGAGGTGGAAGGATTGAAAATCCATCCATCTGT +CGTCCTACCCATCCTGCTATCCATCCATCCATCCATCCTCCCATAATCTATCTTCCCATC +CATTTGTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCACCCATCCATCCTCCCATG +CATCCTCCCATGCATCCTCCCATCCATCCACCCAACCATCCTCCCATCCATCCTCACATC +CATCTTCGCATCCATCCATCCATCCATCTATCCATCCATCCATCCATCCTCCCATCCATC +CTCCCATCCATTATCCCATTCATCCATCCTCCCATCCATCCTCCTATCCATCCATCCATC +CATCCACCCTCTCATCCATCCATCCTCCCATCCATCCACCCTTCCATCCATCCATCCACC +CACCCTTCCATCCATCCATCCTCCCATCCATCCATCCTCCCATCCATCCATCCTCCCATT +CATCTATCCATCCATCCCTCGATCCTCCCATCCATCCATCCTCCCATCCATCCATCCATC +CTCCCATCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCTACCCTCCCATC +CATCCATCCTCCCATCCACCCTCCCATCCATCCATCCATCCATCCACCCTCTCATCCATC +CATCCTCCCATCCGTCCATCCATCCTTCCATCCACCCTCCCATCCATCCATCCTCCCATC +CATCCATCCTCCCATCCATCTACCCTCCCATCCATCCATCCTCCCACCCACCCTCCCATC +CATCCACCCTCCCATCCATCCATCCTCCCATCCATCTATCCATCCATCCTCCCATCCTCC +CATCCATCCATCATCCATCCATCCATCCATCCATCCTCCCATAATCTATCTTCCCATCCA +TTTGTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCACCCATCCATCCTCCCATTCATCCT +CCCATGCATCCTCCCATCCATCCACCCAACCATCCTCCCATCCATCCTCACATCCATCTT +CGCATCCATCCATCCATCCATCCATCTATCCATCCATCCTCCCATCCATCCTCCCATCCT +CCCATCCATCCTCCCATCCTCCCATCCATTCTCCCATTCATCCATCCTCCCATCCATCCT +CCTATCCATCCATCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCCACCCT +TCCATCCATCCATCCACCCACCCTTCCATCCATCCACCCTCCCATCCATCCATCCTCCCA +TTCATCTATCCATCCATCCCTCGATCCTCCCATCCATCCATCCATCCTCCCATCCGTCCA +TCCATCCTTCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCTACCCTCCCATCCA +TCCATCCTCCCACCCACCCTCCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCA +TCTATCCATCCATCCTCCCATCCTCCCATCCTCCCATCCATCCATCCATCCATCCATCCT +CCCATCCTCCCATCCTCCCATCCATCGTCCCATGTGTACATCTGTCCTGCCATCTATCCA +TACATCCATTTCTCCGTCCTCCCATCCATCTTCCCATCCATTCATCCATCCATCTTCCCA +TCCATTCATCCATCCATCCTGCCATCCATCCTTCCATTGATCCATCCATCCATCCTGCAG +GAGACCAGGAGTTCAAGGCTGCCGTGAGTTATAATTGTGCCACTGCACTACAGCTTAAGT +GACAGAGAGAGAAACCATCTCCAAAAATGAAAAAAAGAATATATTGATTTCAGGCCAGTT +ACATAGA +>p:HG002_2_chr20:60314230-60315121 +ACTTGTTTCCTCATTTATTCATTAACAATATTCATTTCTTAGCCAAGGATGGTGGTGCAC +ACCTGTACTTCCAGCTACTCAGGAGGCTGAGGTGGAAGGATTGAAAATCCATCCATCTGT +CCTCCTACCCATCCTGCTATCCATCCATCCATCCATCCTCCCATAATCTATCTTCCCATC +CATTTGTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC +CACCCATCCATCCTCCCATTCATCCTCCCATGCATCCTCCCATCCATCCACCCAACCATC +CTCCCATCCATCCTCACATCCATCTTCGCATCCATCCATCCATCCATCTATCCATCCATC +CATCCATCCTCCCATCCATCCTCCCATCCATTATCCCATTCATCCATCCTCCCATCCATC +CTCCTATCCATCCATCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCCACT +CTTCCATCCATCCATCCACCCACCCTTCCATCCATCCATCCTCCCATCCATCCATCCTCC +CATTCATCTATCCATCCATCCCTCGATCCTCCCATCCATCCATCCTCCCATCCATCCATC +CATCCTCCCATCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCTACCCTCC +CATCCATCCATCCTCCCACCCACCCTCCCATCCATCCATCCTCCCATCCTCCCATCCATC +CATCCATCCTCCCATCCGTCCATCCATCCTTCCATCCACCCTCCCATCCATCCATCCTCC +CATCCATCTACCCTCCCATCCATCCATCCTCCCACCCACCCTCCCATCCATCCACCCTCC +CATCCATCCATCCTCCCATCCATCTATCCATCCATCCTCCCATCCTCCCATCCATCCATC +ATCCATCCATCCATCCATCCATCCTCCCATAATCTATCTTCCCATCCATTTGTCCTTCCT +TCCTTCCTTCCTTCCTTCCTTCCTTCGTTCCACCCATCCATCCTCCCATTCATCCTCCCA +TGCATCCTCCCATCCATCCACCCAACCATCCTCCCATCCATCCTCACATCCATCTTCGCA +TCCATCCATCCATCCATCCATCTATCCATCCATCCTCCCATCCATCCTCCCATCCTCCCA +TCCATTCTCCCATTCATCCATCCTCCCATCCATCCTCCTATCCATCCATCCATCCATCCA +CCCTCCCATCCATCCATCCTCCCATCCATCCACCCTTCCATCCATCCATCCACCCACCCT +TCCATCCATCCACCCTCCCATCCATCCATCCTCCCATTCATCTATCCATCCATCCCTCGA +TCCTCCCATCCATCCATCCATCCTCCCATCCGTCCATCCATCCTTCCATCCACCCTCCCA +TCCATCCATCCTCCCATCCATCTACCCTCCCATCCATCCATCCTCCCACCCACCCTCCCA +TCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCTATCCATCCATCCTCCCATCCT +CCCATCCTCCCATCCATCCATCCATCCATCCATCCATCCTCCCATCCTCCCATCCTCCCA +TCCATCGTCCCATGTGTACATCTGTCCTGCCATCTATCCATACATCCATTTCTCCGTCCT +CCCATCCATCTTCCCATCCATTCATCCATCCATCTTCCCATCCATTCATCCATCCATCCT +GCCATCCATCCTTCCATTGATCCATCCATCCATCCTGCAGGAGACCAGGAGTTCAAGGCT +GCCGTGAGTTATAATTGTGCCACTGCACTACAGCTTAAGTGACAGAGAGAGAAACCATCT +CCAAAAATGAAAAAAAGAATATATTGATTTCAGGCCAGTTACATAGA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/haps.fa.ref.fa new file mode 100644 index 00000000..0898f1f1 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:60314230-60315121 +ACTTGTTTCCTCATTTATTCATTAACAATATTCATTTCTTAGCCAAGGATGGTGGTGCACACCTGTACTTCCAGCTACTCAGGAGGCTGAGGTGGAAGGATTGAAAATCCATCCATCTGTCCTCCTACCCATCCTGCTATCCATCCATCCATCCATCCTCCCATAATCTATCTTCCCATCCATTTGTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCTTCCTTCCTTCCTTCCTTCCTTCCTTCCACCCATCCATCCTCCCATTCATCCTCCCATGCATCCTCCCATCCATCCACCCAACCATCCTCCCATCCATCCTCACATCGATCTTCGCATCCATCCATCGATCGATCTATCCATCCATCCATTCTCCCATTCATCCATCCTCCCATCCATCCTCCTATCCATCCATCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCCACCCTTCCATCCATCCATCCACCCACCCTTCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCTATCCATCCATCCTCCCATCCTCCCATCCTCCCATCCATCCATCCATCCATCCATCCATCCTCCCATCCTCCCATCCTCCCATCCATCGTCCCATGTGTACATCTGTCCTGCCATCTATCCATACATCCATTTCTCCGTCCTCCCATCCATCTTCCCATCCATTCATCCATCCATCTTCCCATCCATTCATCCATCCATCCTGCCATCCATCCTTCCATTGATCCATCCATCCATCCTGCAGGAGACCAGGAGTTCAAGGCTGCCGTGAGTTATAATTGTGCCACTGCACTACAGCTTAAGTGACAGAGAGAGAAACCATCTCCAAAAATGAAAAAAAGAATATATTGATTTCAGGCCAGTTACATAGA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/msa.fa new file mode 100644 index 00000000..41bb252a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/msa.fa @@ -0,0 +1,165 @@ +>ref_chr20_60314230_60315121 +acttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgcac +acctgtacttccagctactcaggaggctgaggtggaaggattgaaa-------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-atccatccatctgtcctcctacccatc---ctgctatccatccatccatccatcctccc +ataatctatcttcccatccatttgtccttccttccttccttccttccttcc--------t +tct---------------------tccttccttccttccttccttccttccacccatcca +tcctcccattcatcctcccatgcatcctc----ccatccatccacccaaccatcctccca +tccatcctcacatcgatcttcgcatccatccatcgatcgatctatccatccatccattct +cccattcatccatcctcccatccatcctcctatccatccatccatccatccaccctccca +tccatccatcctcccatccatccacccttccatccatccatccacccacccttccatcca +tccaccctcccatccatccatcctcccat------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------ccatctatccatccatcctcccatcctcccatcct +cccatccatccatccatccatccatccatcctcccatcctcccatcctcccatccatcgt +cccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctcccatcca +tcttcccatccattcatccatccatcttcccatccattcatccatccatcctgccatcca +tccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccgtgag +ttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaaaaat +gaaaaaaagaatatattgatttcaggccagttacataga +>syndip_1_chr20:60314230-60315121 +acttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgcac +acctgtacttccagctactcaggaggctgaggtggaaggattgaaaatccatccatctgt +cctcctacccatcctgctatccatccatccatccatcctcccataatctatcttcccatc +catttgtccttccttccttccttccttccttccttccttccttccttccttccttccttc +cacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaaccatc +ctcccatccatcctcacatccatcttcgcatccatccatccatccatctatccatccatc +catccatcctcccatccatcctcccatccattatcccattcatccatcctcccatccatc +ctcctatccatccatccatccatccaccctcccatccatccatcctcccatccatccact +cttccatccatccatccacccaccctt----------------ccatccatccatcctcc +catccatccatcctcccattcatctatccatccatccctcgatcctcccatccatccatc +ctcccatccatccatccatcctcccatccatccatccaccctcccatccatccatcctcc +catccatctaccctcccatccatccatcctcccacccaccctcccatccatccatcctcc +catcctcccatccatccatccatcctcccatccgtccatccatccttccatccac----- +-----------cctcccatccatccatcctcccatccatctaccctcccatccatccatc +ctcccacccaccctcccatccatccaccctcccatccatccatcctcccatccatctatc +catccatcctcccatcctcccatccatccatcatccatccatccatccatccatcctccc +ataatctatcttcccatccatttgtccttccttccttccttccttccttccttccttcgt +tccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaacca +tcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatctatcca +t--------------------ccatcctcccatccatcctcccatcctcccatccattct +cccattcatccatcctcccatccatcctcctatccatccatccatccatccaccctccca +tccatccatcctcccatccatccacccttccatccatccatccacccacccttccatcca +tccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcctccca +tccatccatccatcctcccatccgtccatccatccttccatccaccctcccatccatcca +tcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatccatcca +ccctcccatccatccatcctcccatccatctatccatccatcctcccatcctcccatcct +cccatccatccatccatccatccatccatcctcccatcctcccatcctcccatccatcgt +cccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctcccatcca +tcttcccatccattcatccatccatcttcccatccattcatccatccatcctgccatcca +tccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccgtgag +ttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaaaaat +gaaaaaaagaatatattgatttcaggccagttacataga +>syndip_2_chr20:60314230-60315121 +acttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgcac +acctgtacttccagctactcaggaggctgaggtggaaggattgaaaatccatccatctgt +cgtcctacccatcctgctatccatccatccatccatcctcccataatctatcttcccatc +catttg--------------------tccttccttccttccttccttccttccttccttc +cacccatccatcctcccatgcatcctcccatgcatcctcccatccatccacccaaccatc +ctcccatccatcctcacatccatcttcgcatccatccatccatccatctatccatccatc +catccatcctcccatccatcctcccatccattatcccattcatccatcctcccatccatc +ctcctatccatccatccatccatccaccctctcatccatccatcctcccatccatccacc +cttccatccatccatccacccacccttccatccatccatcctcccatccatccatcctcc +catccatccatcctcccattcatctatccatccatccctcgatcctcccatccatccatc +ctcccatccatccatccatcctcccatccatccatccaccctcccatccatccatcctcc +catccatctaccctcccatccatccatcctcccatccaccctcccatccatccatccatc +catccaccctctcatccatccatcctcccatccgtccatccatccttccatccaccctcc +catccatccatcctcccatccatccatcctcccatccatctaccctcccatccatccatc +ctcccacccaccctcccatccatccaccctcccatccatccatcctcccatccatctatc +catccatcctcccatcctcccatccatccatcatccatccatccatccatccatcctccc +ataatctatcttcccatccatttgtccttccttccttccttccttccttcc--------t +tccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaacca +tcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatctatcca +tccatcctcccatccatcctcccatcctcccatccatcctcccatcctcccatccattct +cccattcatccatcctcccatccatcctcctatccatccatccatccatccaccctccca +tccatccatcctcccatccatccacccttccatccatccatccacccacccttccatcca +tccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcctccca +tccatccatccatcctcccatccgtccatccatccttccatccaccctcccatccatcca +tcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatccatcca +ccctcccatccatccatcctcccatccatctatccatccatcctcccatcctcccatcct +c----ccatccatccatccatccatccatcctcccatcctcccatcctcccatccatcgt +cccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctcccatcca +tcttcccatccattcatccatccatcttcccatccattcatccatccatcctgccatcca +tccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccgtgag +ttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaaaaat +gaaaaaaagaatatattgatttcaggccagttacataga +>p:HG002_1_chr20:60314230-60315121 +acttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgcac +acctgtacttccagctactcaggaggctgaggtggaaggattgaaaatccatccatctgt +cgtcctacccatcctgctatccatccatccatccatcctcccataatctatcttcccatc +catttg--------------------tccttccttccttccttccttccttccttccttc +cacccatccatcctcccatgcatcctcccatgcatcctcccatccatccacccaaccatc +ctcccatccatcctcacatccatcttcgcatccatccatccatccatctatccatccatc +catccatcctcccatccatcctcccatccattatcccattcatccatcctcccatccatc +ctcctatccatccatccatccatccaccctctcatccatccatcctcccatccatccacc +cttccatccatccatccacccacccttccatccatccatcctcccatccatccatcctcc +catccatccatcctcccattcatctatccatccatccctcgatcctcccatccatccatc +ctcccatccatccatccatcctcccatccatccatccaccctcccatccatccatcctcc +catccatctaccctcccatccatccatcctcccatccaccctcccatccatccatccatc +catccaccctctcatccatccatcctcccatccgtccatccatccttccatccaccctcc +catccatccatcctcccatccatccatcctcccatccatctaccctcccatccatccatc +ctcccacccaccctcccatccatccaccctcccatccatccatcctcccatccatctatc +catccatcctcccatcctcccatccatccatcatccatccatccatccatccatcctccc +ataatctatcttcccatccatttgtccttccttccttccttccttccttcc--------t +tccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaacca +tcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatctatcca +tccatcctcccatccatcctcccatcctcccatccatcctcccatcctcccatccattct +cccattcatccatcctcccatccatcctcctatccatccatccatccatccaccctccca +tccatccatcctcccatccatccacccttccatccatccatccacccacccttccatcca +tccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcctccca +tccatccatccatcctcccatccgtccatccatccttccatccaccctcccatccatcca +tcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatccatcca +ccctcccatccatccatcctcccatccatctatccatccatcctcccatcctcccatcct +c----ccatccatccatccatccatccatcctcccatcctcccatcctcccatccatcgt +cccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctcccatcca +tcttcccatccattcatccatccatcttcccatccattcatccatccatcctgccatcca +tccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccgtgag +ttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaaaaat +gaaaaaaagaatatattgatttcaggccagttacataga +>p:HG002_2_chr20:60314230-60315121 +acttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgcac +acctgtacttccagctactcaggaggctgaggtggaaggattgaaaatccatccatctgt +cctcctacccatcctgctatccatccatccatccatcctcccataatctatcttcccatc +catttgtccttccttccttccttccttccttccttccttccttccttccttccttccttc +cacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaaccatc +ctcccatccatcctcacatccatcttcgcatccatccatccatccatctatccatccatc +catccatcctcccatccatcctcccatccattatcccattcatccatcctcccatccatc +ctcctatccatccatccatccatccaccctcccatccatccatcctcccatccatccact +cttccatccatccatccacccaccctt----------------ccatccatccatcctcc +catccatccatcctcccattcatctatccatccatccctcgatcctcccatccatccatc +ctcccatccatccatccatcctcccatccatccatccaccctcccatccatccatcctcc +catccatctaccctcccatccatccatcctcccacccaccctcccatccatccatcctcc +catcctcccatccatccatccatcctcccatccgtccatccatccttccatccac----- +-----------cctcccatccatccatcctcccatccatctaccctcccatccatccatc +ctcccacccaccctcccatccatccaccctcccatccatccatcctcccatccatctatc +catccatcctcccatcctcccatccatccatcatccatccatccatccatccatcctccc +ataatctatcttcccatccatttgtccttccttccttccttccttccttccttccttcgt +tccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaacca +tcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatctatcca +t--------------------ccatcctcccatccatcctcccatcctcccatccattct +cccattcatccatcctcccatccatcctcctatccatccatccatccatccaccctccca +tccatccatcctcccatccatccacccttccatccatccatccacccacccttccatcca +tccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcctccca +tccatccatccatcctcccatccgtccatccatccttccatccaccctcccatccatcca +tcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatccatcca +ccctcccatccatccatcctcccatccatctatccatccatcctcccatcctcccatcct +cccatccatccatccatccatccatccatcctcccatcctcccatcctcccatccatcgt +cccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctcccatcca +tcttcccatccattcatccatccatcttcccatccattcatccatccatcctgccatcca +tccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccgtgag +ttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaaaaat +gaaaaaaagaatatattgatttcaggccagttacataga diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/msa.fa.fai new file mode 100644 index 00000000..877f09b4 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_60314230_60315121 1899 29 60 61 +syndip_1_chr20:60314230-60315121 1899 1994 60 61 +syndip_2_chr20:60314230-60315121 1899 3959 60 61 +p:HG002_1_chr20:60314230-60315121 1899 5925 60 61 +p:HG002_2_chr20:60314230-60315121 1899 7891 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/output.vcf.gz new file mode 100644 index 00000000..44830ff5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/output.vcf.gz.tbi new file mode 100644 index 00000000..be163e30 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60314330-60315021/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/base.vcf.gz new file mode 100644 index 00000000..d2f311fc Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/base.vcf.gz.tbi new file mode 100644 index 00000000..69b1a5bb Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/comp.vcf.gz new file mode 100644 index 00000000..85e9bfb3 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/comp.vcf.gz.tbi new file mode 100644 index 00000000..b0ece9be Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/haps.fa new file mode 100644 index 00000000..51c2a48b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/haps.fa @@ -0,0 +1,36 @@ +>ref_chr20_60702842_60703216 +TATGGTAACTGCATGTTGACTCTTTTGAGGAGCTTCCAGACTGTTTTTCAAAGTGATGGCACAATTTTCCTTTCCCCTCAATAATGTATGAGGGTTGCAATGTCGCTACATATTACCAACATTTGTCATTGTCTTTCTTTCTTTTCTTTCTCTCTCTCTCTTTCTTTTCCTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTTCTTTCCTTCTTTCTTTCTTTCTTTCTTTCTTTTTTTTTGGGATGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCATGATCTCGGCTCGCTGCAATCTCCACCTCCCAGGTTCAAGCGATTGAACTCACTGCCTCAGCCTCCCAAGTAGCTG +>syndip_1_chr20:60702842-60703216 +TATGGTAACTGCATGTTGACTCTTTTGAGGAGCTTCCAGACTGTTTTTCAAAGTGATGGC +ACAATTTTCCTTTCCCCTCAATAATGTATGAGGGTTGCAATGTCGCTACATATTACCAAC +ATTTGTCATTGTCTTTCTTTCTTTTCTTTCTCTCTCTCTCTTTCTTTTCCTTCTTTCTTT +CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTTCTTTCCTTCTT +CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT +CTTTCTTTCTTTCTTTCTTCTTTCTTTCTTTTTCTTTCTTTTTTTTTTGGGATGGAGTCT +CGCTCTGTCACCCAGGCTGGAGTGCAGTGGCATGATCTCGGCTCGCTGCAATCTCCACCT +CCCAGGTTCAAGCGATTGAACTCACTGCCTCAGCCTCCCAAGTAGCTG +>syndip_2_chr20:60702842-60703216 +TATGGTAACTGCATGTTGACTCTTTTGAGGAGCTTCCAGACTGTTTTTCAAAGTGATGGC +ACAATTTTCCTTTCCCCTCAATAATGTATGAGGGTTGCAATGTCGCTACATATTACCAAC +ATTTGTCATTGTCTTTCTTTCTTTTCTTTCTCTCTCTCTCTCTCTTTCTTTTCCTTCTTT +CTTTCTTTCTTTCTTTCTTTCTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT +CTTTCTTTTCTTTCCTTCTTTCTTTCTTTCTTTCTTTTTTTTTGGGATGGAGTCTCGCTC +TGTCACCCAGGCTGGAGTGCAGTGGCATGATCTCGGCTCGCTGCAATCTCCACCTCCCAG +GTTCAAGCGATTGAACTCACTGCCTCAGCCTCCCAAGTAGCTG +>p:HG002_1_chr20:60702842-60703216 +TATGGTAACTGCATGTTGACTCTTTTGAGGAGCTTCCAGACTGTTTTTCAAAGTGATGGC +ACAATTTTCCTTTCCCCTCAATAATGTATGAGGGTTGCAATGTCGCTACATATTACCAAC +ATTTGTCATTGTCTTTCTTTCTTTTCTTTCTCTCTCTCTCTCTCTTTCTTTTCCTTCTTT +CTTTCTTTCTTTCTTTCTTTCTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT +CTTTCTTTTCTTTCCTTCTTTCTTTCTTTCTTTCTTTTTTTTTGGGATGGAGTCTCGCTC +TGTCACCCAGGCTGGAGTGCAGTGGCATGATCTCGGCTCGCTGCAATCTCCACCTCCCAG +GTTCAAGCGATTGAACTCACTGCCTCAGCCTCCCAAGTAGCTG +>p:HG002_2_chr20:60702842-60703216 +TATGGTAACTGCATGTTGACTCTTTTGAGGAGCTTCCAGACTGTTTTTCAAAGTGATGGC +ACAATTTTCCTTTCCCCTCAATAATGTATGAGGGTTGCAATGTCGCTACATATTACCAAC +ATTTGTCATTGTCTTTCTTTCTTTTCTTTCTCTCTCTCTCTTTCTTTTCCTTCTTTCTTT +CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTTCTTTCCTTCTT +CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT +CTTTCTTTCTTTCTTTCTTCTTTCTTTCTTTTTCTTTCTTTTTTTTTTGGGATGGAGTCT +CGCTCTGTCACCCAGGCTGGAGTGCAGTGGCATGATCTCGGCTCGCTGCAATCTCCACCT +CCCAGGTTCAAGCGATTGAACTCACTGCCTCAGCCTCCCAAGTAGCTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/haps.fa.ref.fa new file mode 100644 index 00000000..9562d46b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:60702842-60703216 +TATGGTAACTGCATGTTGACTCTTTTGAGGAGCTTCCAGACTGTTTTTCAAAGTGATGGCACAATTTTCCTTTCCCCTCAATAATGTATGAGGGTTGCAATGTCGCTACATATTACCAACATTTGTCATTGTCTTTCTTTCTTTTCTTTCTCTCTCTCTCTTTCTTTTCCTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTTCTTTCCTTCTTTCTTTCTTTCTTTCTTTCTTTTTTTTTGGGATGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCATGATCTCGGCTCGCTGCAATCTCCACCTCCCAGGTTCAAGCGATTGAACTCACTGCCTCAGCCTCCCAAGTAGCTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/msa.fa new file mode 100644 index 00000000..40d84d0e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/msa.fa @@ -0,0 +1,45 @@ +>ref_chr20_60702842_60703216 +tatggtaactgcatgttgactcttttgaggagcttccagactgtttttcaaagtgatggc +acaattttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaac +atttgtcattgtctttctttcttttctttctctctctctctttct--------------- +-------------tttccttctttctttctttctttctttctttctttctttctttcttt +cttttc---tttccttctttctttctttctttctttc----------------------- +---------------------------------------tttttttttgggatggagtct +cgctctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatctccacct +cccaggttcaagcgattgaactcactgcctcagcctcccaagtagctg +>syndip_1_chr20:60702842-60703216 +tatggtaactgcatgttgactcttttgaggagcttccagactgtttttcaaagtgatggc +acaattttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaac +atttgtcattgtctttctttcttttctttctctctctctctttcttttccttctttcttt +ctttctttctttctttctttctttctttctttctttctttctttcttttctttccttctt +ctttctttctttctttctttctttctttctttctttctttctttctttctttctttcttt +ctttctttctttctttcttctttctttctttttctttcttttttttttgggatggagtct +cgctctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatctccacct +cccaggttcaagcgattgaactcactgcctcagcctcccaagtagctg +>syndip_2_chr20:60702842-60703216 +tatggtaactgcatgttgactcttttgaggagcttccagactgtttttcaaagtgatggc +acaattttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaac +atttgtcattgtctttctttcttttctttctctctctctctctctttcttttccttcttt +ctttctttctttctttctttcttcctttctttctttctttctttctttctttctttcttt +ctttct---tttctttccttctttctttctttctttc----------------------- +---------------------------------------tttttttttgggatggagtct +cgctctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatctccacct +cccaggttcaagcgattgaactcactgcctcagcctcccaagtagctg +>p:HG002_1_chr20:60702842-60703216 +tatggtaactgcatgttgactcttttgaggagcttccagactgtttttcaaagtgatggc +acaattttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaac +atttgtcattgtctttctttcttttctttctctctctctctctctttcttttccttcttt +ctttctttctttctttctttcttcctttctttctttctttctttctttctttctttcttt +ctttct---tttctttccttctttctttctttctttc----------------------- +---------------------------------------tttttttttgggatggagtct +cgctctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatctccacct +cccaggttcaagcgattgaactcactgcctcagcctcccaagtagctg +>p:HG002_2_chr20:60702842-60703216 +tatggtaactgcatgttgactcttttgaggagcttccagactgtttttcaaagtgatggc +acaattttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaac +atttgtcattgtctttctttcttttctttctctctctctctttcttttccttctttcttt +ctttctttctttctttctttctttctttctttctttctttctttcttttctttccttctt +ctttctttctttctttctttctttctttctttctttctttctttctttctttctttcttt +ctttctttctttctttcttctttctttctttttctttcttttttttttgggatggagtct +cgctctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatctccacct +cccaggttcaagcgattgaactcactgcctcagcctcccaagtagctg diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/msa.fa.fai new file mode 100644 index 00000000..dee59e9d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_60702842_60703216 468 29 60 61 +syndip_1_chr20:60702842-60703216 468 539 60 61 +syndip_2_chr20:60702842-60703216 468 1049 60 61 +p:HG002_1_chr20:60702842-60703216 468 1560 60 61 +p:HG002_2_chr20:60702842-60703216 468 2071 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/output.vcf.gz new file mode 100644 index 00000000..fadcc336 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/output.vcf.gz.tbi new file mode 100644 index 00000000..62cb7360 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:60702942-60703116/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/base.vcf.gz new file mode 100644 index 00000000..9efea914 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/base.vcf.gz.tbi new file mode 100644 index 00000000..f031f869 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/comp.vcf.gz new file mode 100644 index 00000000..99a0d740 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/comp.vcf.gz.tbi new file mode 100644 index 00000000..0c33f737 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/haps.fa new file mode 100644 index 00000000..b9e89818 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/haps.fa @@ -0,0 +1,154 @@ +>ref_chr20_61100692_61102788 +TTGGTACATGTACAGATTGTGCAAGACAATAGGACACCAGACAGATCCCCGGGCTCCACAGCAGAAGTCTGGTTACTGGGCAGGCAGGCCCCAAACACTGTATTTAAAACAAAACCCCACTGACAAGTCCTGTGACTGGAGAGACCCCGAGTGAAGGCAGACCTCCATGTCCTCTACATCCTGTGCCACATCTGGAGAGACCCCTGTGAGGGCAGAGAGCTACCTCCTCTTCTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCGGATGGCCACGTCTTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTACTTCCTGTGTCACACCTGGGGAGACCCTGAGTGAGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAGAGACCCCAAGAGAGGGCAGACAGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCGGATGGCCACGTCTTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTACTTCCTGTGTCACACCTGGGGAGACCCTGAGTGAGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAGAGACCCCAAGAGAGGGCAGACAGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACTCCAAGTGAGGAGAGACGGCCACATCTTCTACTTCCTGTGTCACACCTGGAGAGACCTCGAGTGAGGGCAGATGGCCACATCCTCTAATTCCTGTGTCACACCTGGAGAGACCCCAAGTGAGGGCAGACTGCCACCTCCTCTACTTCCTGTGTCACACCTAGAGAGACCCCGAGTGAGGACAGCCAGCCATGTCCTCTACTTCCTGTGCCACATCCGGAGAGATCCCGAGTGAGGGCAGACAGCCATGTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTGTCATGCCTGGAGAGACCCCGAGTGAGGGCATATGGCCACATCCTCTAATTCCTATGTCACACCTGGAGAGACCCCGAGTGAGGGTGGATGGCCACATCCTCTAATTCCTGTGTCATACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCAAGTGAGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAGAGACCCCGATGAGGGCAGACAGCTACCCCCTCTACTTCCTGTGTCACACCTGCAGAGACCCCAAGTGAGGGCAGATGGCCACCTCTTCTACTTCCTGTGTCACACCTGGAGAGGCCCCGAGTGAGGGCAGACGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTATTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTGTCACACATGGAGAGACCCCGAGTGAGGGCAGAAGGCCACATCCTCTACTTCCTGTGTCACACCTAGAGAGACCCCGAGTGAGGGCGGATGGCCACATCCTCTAATTCCTGTGTCACACCTGGGGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTAATTCCTGTGTCACACCTGGAGACACACAGAGTAAAGGTGGACAGCCACCTCCTCTACGTCCTGTGCCACACCTGGAGACACCCTGAGTTAAGGCAGATGGCCACCTCCTCTAATTATTTTTAAGAACTTTTTTGGGGTATAATTTACATGCCAGAAAGTTCACCCATTTCAAGCATATGATTCAATATTAAAGCTTAAAAATGTTATCAATTTAATAACATTGATGGTTACAGAGCTGTGTAA +>syndip_1_chr20:61100692-61102788 +TTGGTACATGTACAGATTGTGCAAGACAATAGGACACCAGACAGATCCCCGGGCTCCACA +GCAGAAGTCTGGTTACTGGGCAGGCAGGCCCCAAACACTGTATTTAAAACAAAACCCCAC +TGACAAGTCCTGTGACTGGAGAGACCCCGAGTGAAGGCAGACCTCCATGTCCTCTACATC +CTGTGCCACATCTGGAGAGACCCCTGTGAGGGCAGAGAGCTACCTCCTCTTCTTCCTGTG +TCACACCTGGAGAGACCCCGAGTGAGGGCGGATGGCCACGTCTTCTACTTCCTGTGTCAC +ACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTACTTCCTGTGTCACACCT +GGGGAGACCCTGAGTGAGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAG +AGACCCCAAGAGAGGGCAGACAGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGAC +CCCGAGTGAGGGCGGATGGCCACGTCTTCTACTTCCTGTGTCACACCTGGAGAGACCCCG +AGTGAGGGCAGATGGCCACATCCTCTACTTCCTGTGTCACACCTGGGGAGACCCTGAGTG +AGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAGAGACCCCAAGAGAGGG +CAGACAGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACTCCAAGTGAGGAGAGA +CGGCCACGTCTTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGTGGATGGC +CACATCCTCTAATTCCTGTGTCATACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACC +TCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACTGCCACCTCCT +CTACTTCCTGTGTCACACCTAGAGAGACCCCGAGTGAGGACAGCCAGCCATGTCCTCTAC +TTCCTGTGCCACATCCGGAGAGATCCCGAGTGAGGGCAGACAGCCATGTCCTCTACTTCC +TGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTG +TCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACCTCCTCTACTTCCTGTGTCAC +ACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTGTCATGCCT +GGAGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTAATTCCTATGTCACACCTGGAG +AGACCCCGAGTGAGGGTGGATGGCCACATCCTCTAATTCCTGTGTCATACCTGGAGAGAC +CCCGAGTGAGGGCAGATGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCG +AGTGAGGGCAGATGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCAAGTG +AGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAGAGACCCCGATGAGGGC +AGACAGCTACCCCCTCTACTTCCTGTGTCACACCTGCAGAGACCCCAAGTGAGGGCAGAT +GGCCACCTCTTCTACTTCCTGTGTCACACCTGGAGAGGCCCCGAGTGAGGGCAGACGGCC +ACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACAT +CCTCTATTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTC +TAATTCCTGTGTCACACATGGAGAGACCCCGAGTGAGGGCAGAAGGCCACATCCTCTACT +TCCTGTGTCACACCTAGAGAGACCCCGAGTGAGGGCGGATGGCCACATCCTCTAATTCCT +GTGTCACACCTGGGGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTAATTCCTGTGT +CACACCTGGAGACACACAGAGTAAAGGTGGACAGCCACCTCCTCTACGTCCTGTGCCACA +CCTGGAGACACCCTGAGTTAAGGCAGATGGCCACCTCCTCTAATTATTTTTAAGAACTTT +TTTGGGGTATAATTTACATGCCAGAAAGTTCACCCATTTCAAGCATATGATTCAATATTA +AAGCTTAAAAATGTTATCAATTTAATAACATTGATGGTTACAGAGCTGTGTAA +>syndip_2_chr20:61100692-61102788 +TTGGTACATGTACAGATTGTGCAAGACAATAGGACACCAGACAGATCCCCGGGCTCCACA +GCAGAAGTCTGGTTACTGGGCAGGCAGGCCCCAAACACTGTATTTAAAACAAAACCCCAC +TGACAAGTCCTGTGACTGGAGAGACCCCGAGTGAAGGCAGACCTCCATGTCCTCTACATC +CTGTGCCACATCTGGAGAGACCCCTGTGAGGGCAGAGAGCTACCTCCTCTTCTTCCTGTG +TCACACCTGGAGAGACCCCGAGTGAGGGCGGATGGCCACGTCTTCTACTTCCTGTGTCAC +ACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTACTTCCTGTGTCACACCT +GGGGAGACCCTGAGTGAGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAG +AGACCCCAAGAGAGGGCAGACAGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGAC +TCCAAGTGAGGAGAGACGGCCACGTCTTCTACTTCCTGTGTCACACCTGGAGAGACCTCG +AGTGAGGGCAGATGGCCACATCCTCTAATTCCTGTGTCACACCTGGAGAAACCCCAAGTG +AGGGCAGACTGCCACCTCCTCTACTTCCTGTGTCACACCTAGAGAGACCCCGAGTGAGGA +CAGCCAGCCATGTCCTCTACTTCCTGTGCCACATCCGGAGAGATCCCGAGTGAGGGCAGA +CAGCCATGTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACAGC +CACATCCTCTAATTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCTACA +TCCTCTAATTCCTGTGTCATGCCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACATCCT +CTAATTCCTATGTCACACCTGGAGAGACCCCGAGTGAGGGTGGATGGCCACATCCTCTAA +TTCCTGTGTCATACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACCTCCTCTACTTCC +TGTGTCACACCTGGAGAGACCCCAAGTGAGGGCAGACAGCCATGTCCTCTACGTCCTGTG +CCACATCCGGAGAGACCCCGATGAGGGCAGACAGCTACCCCCTCTACTTCCTGTGTCACA +CCTGCAGAGACCCCAAGTGAGGGCAGATGGCCACCTCTTCTACTTCCTGTGTCACACCTG +GAGAGGCCCCGAGTGAGGGCAGACGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGA +GACCCCGAGTGAGGGCAGACGGCCACATCCTCTATTTCCTGTGTCACACCTGGAGAGACC +CCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTGTCACACATGGAGAGACCCCGA +GTGAAGGCAGAAGGCCACATCCTCTACTTCCTGTGTCACACCTAGAGAGACCCCGAGTGA +GGGCGGATGGCCACATCCTCTAATTCCTATGTCACACCTGGAGAGACCCCGAGTGAGGGT +GGATGGCCACATCCTCTAATTCCTGTGTCATACCTGGAGAGACCCCGAGTGAGGGCAGAT +GGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCAAGTGAGGGCAGACAGCC +ATGTCCTCTACGTCCTGTGCCACATCCGGAGAGACCCCGATGAGGGCAGACAGCTACCCC +CTCTACTTCCTGTGTCACACCTGCAGAGACCCCAAGTGAGGGCAGATGGCCACCTCTTCT +ACTTCCTGTGTCACACCTGGAGAGGCCCCGAGTGAGGGCAGACGGCCACCTCCTCTACTT +CCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTG +TGTCACACATGGAGAGACCCTGAGTGAGGGCAGAAGGCCACATCCTCTACTTCCTGTGTC +ACACCTAGAGAGACCCCGAGTGAGGGCGGATGGCCACATCCTCTAATTCCTGTGTCACAC +CTGGGGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTGTCACACCTGG +AGACACACAGAGTAAAGGTGGACAGCCACCTCCTCTACGTCCTGTGCCACACCTGGAGAC +ACCCTGAGTTAAGGCAGATGGCCACCTCCTCTAATTATTTTTAAGAACTTTTTTGGGGTA +TAATTTACATGCCAGAAAGTTCACCCATTTCAAGCATATGATTCAATATTAAAGCTTAAA +AATGTTATCAATTTAATAACATTGATGGTTACAGAGCTGTGTAA +>p:HG002_1_chr20:61100692-61102788 +TTGGTACATGTACAGATTGTGCAAGACAATAGGACACCAGACAGATCCCCGGGCTCCACA +GCAGAAGTCTGGTTACTGGGCAGGCAGGCCCCAAACACTGTATTTAAAACAAAACCCCAC +TGACAAGTCCTGTGACTGGAGAGACCCCGAGTGAAGGCAGACCTCCATGTCCTCTACATC +CTGTGCCACATCTGGAGAGACCCCTGTGAGGGCAGAGAGCTACCTCCTCTTCTTCCTGTG +TCACACCTGGAGAGACCCCGAGTGAGGGCGGATGGCCACGTCTTCTACTTCCTGTGTCAC +ACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTACTTCCTGTGTCACACCT +GGGGAGACCCTGAGTGAGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAG +AGACCCCAAGAGAGGGCAGACAGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGAC +TCCAAGTGAGGAGAGACGGCCACGTCTTCTACTTCCTGTGTCACACCTGGAGAGACCTCG +AGTGAGGGCAGATGGCCACATCCTCTAATTCCTGTGTCACACCTGGAGAAACCCCAAGTG +AGGGCAGACTGCCACCTCCTCTACTTCCTGTGTCACACCTAGAGAGACCCCGAGTGAGGA +CAGCCAGCCATGTCCTCTACTTCCTGTGCCACATCCGGAGAGATCCCGAGTGAGGGCAGA +CAGCCATGTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACAGC +CACATCCTCTAATTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCTACA +TCCTCTAATTCCTGTGTCATGCCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACATCCT +CTAATTCCTATGTCACACCTGGAGAGACCCCGAGTGAGGGTGGATGGCCACATCCTCTAA +TTCCTGTGTCATACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACCTCCTCTACTTCC +TGTGTCACACCTGGAGAGACCCCAAGTGAGGGCAGACAGCCATGTCCTCTACGTCCTGTG +CCACATCCGGAGAGACCCCGATGAGGGCAGACAGCTACCCCCTCTACTTCCTGTGTCACA +CCTGCAGAGACCCCAAGTGAGGGCAGATGGCCACCTCTTCTACTTCCTGTGTCACACCTG +GAGAGGCCCCGAGTGAGGGCAGACGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGA +GACCCCGAGTGAGGGCAGACGGCCACATCCTCTATTTCCTGTGTCACACCTGGAGAGACC +CCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTGTCACACATGGAGAGACCCCGA +GTGAAGGCAGAAGGCCACATCCTCTACTTCCTGTGTCACACCTAGAGAGACCCCGAGTGA +GGGCGGATGGCCACATCCTCTAATTCCTATGTCACACCTGGAGAGACCCCGAGTGAGGGT +GGATGGCCACATCCTCTAATTCCTGTGTCATACCTGGAGAGACCCCGAGTGAGGGCAGAT +GGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCAAGTGAGGGCAGACAGCC +ATGTCCTCTACGTCCTGTGCCACATCCGGAGAGACCCCGATGAGGGCAGACAGCTACCCC +CTCTACTTCCTGTGTCACACCTGCAGAGACCCCAAGTGAGGGCAGATGGCCACCTCTTCT +ACTTCCTGTGTCACACCTGGAGAGGCCCCGAGTGAGGGCAGACGGCCACCTCCTCTACTT +CCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTG +TGTCACACATGGAGAGACCCTGAGTGAGGGCAGAAGGCCACATCCTCTACTTCCTGTGTC +ACACCTAGAGAGACCCCGAGTGAGGGCGGATGGCCACATCCTCTAATTCCTGTGTCACAC +CTGGGGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTGTCACACCTGG +AGACACACAGAGTAAAGGTGGACAGCCACCTCCTCTACGTCCTGTGCCACACCTGGAGAC +ACCCTGAGTTAAGGCAGATGGCCACCTCCTCTAATTATTTTTAAGAACTTTTTTGGGGTA +TAATTTACATGCCAGAAAGTTCACCCATTTCAAGCATATGATTCAATATTAAAGCTTAAA +AATGTTATCAATTTAATAACATTGATGGTTACAGAGCTGTGTAA +>p:HG002_2_chr20:61100692-61102788 +TTGGTACATGTACAGATTGTGCAAGACAATAGGACACCAGACAGATCCCCGGGCTCCACA +GCAGAAGTCTGGTTACTGGGCAGGCAGGCCCCAAACACTGTATTTAAAACAAAACCCCAC +TGACAAGTCCTGTGACTGGAGAGACCCCGAGTGAAGGCAGACCTCCATGTCCTCTACATC +CTGTGCCACATCTGGAGAGACCCCTGTGAGGGCAGAGAGCTACCTCCTCTTCTTCCTGTG +TCACACCTGGAGAGACCCCGAGTGAGGGCGGATGGCCACGTCTTCTACTTCCTGTGTCAC +ACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTACTTCCTGTGTCACACCT +GGGGAGACCCTGAGTGAGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAG +AGACCCCAAGAGAGGGCAGACAGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGAC +CCCGAGTGAGGGCGGATGGCCACGTCTTCTACTTCCTGTGTCACACCTGGAGAGACCCCG +AGTGAGGGCAGATGGCCACATCCTCTACTTCCTGTGTCACACCTGGGGAGACCCTGAGTG +AGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAGAGACCCCAAGAGAGGG +CAGACAGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACTCCAAGTGAGGAGAGA +CGGCCACGTCTTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGTGGATGGC +CACATCCTCTAATTCCTGTGTCATACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACC +TCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACTGCCACCTCCT +CTACTTCCTGTGTCACACCTAGAGAGACCCCGAGTGAGGACAGCCAGCCATGTCCTCTAC +TTCCTGTGCCACATCCGGAGAGATCCCGAGTGAGGGCAGACAGCCATGTCCTCTACTTCC +TGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTG +TCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACCTCCTCTACTTCCTGTGTCAC +ACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTGTCATGCCT +GGAGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTAATTCCTATGTCACACCTGGAG +AGACCCCGAGTGAGGGTGGATGGCCACATCCTCTAATTCCTGTGTCATACCTGGAGAGAC +CCCGAGTGAGGGCAGATGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCG +AGTGAGGGCAGATGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCAAGTG +AGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAGAGACCCCGATGAGGGC +AGACAGCTACCCCCTCTACTTCCTGTGTCACACCTGCAGAGACCCCAAGTGAGGGCAGAT +GGCCACCTCTTCTACTTCCTGTGTCACACCTGGAGAGGCCCCGAGTGAGGGCAGACGGCC +ACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACAT +CCTCTATTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTC +TAATTCCTGTGTCACACATGGAGAGACCCCGAGTGAGGGCAGAAGGCCACATCCTCTACT +TCCTGTGTCACACCTAGAGAGACCCCGAGTGAGGGCGGATGGCCACATCCTCTAATTCCT +GTGTCACACCTGGGGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTAATTCCTGTGT +CACACCTGGAGACACACAGAGTAAAGGTGGACAGCCACCTCCTCTACGTCCTGTGCCACA +CCTGGAGACACCCTGAGTTAAGGCAGATGGCCACCTCCTCTAATTATTTTTAAGAACTTT +TTTGGGGTATAATTTACATGCCAGAAAGTTCACCCATTTCAAGCATATGATTCAATATTA +AAGCTTAAAAATGTTATCAATTTAATAACATTGATGGTTACAGAGCTGTGTAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/haps.fa.ref.fa new file mode 100644 index 00000000..b7f9ff19 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:61100692-61102788 +TTGGTACATGTACAGATTGTGCAAGACAATAGGACACCAGACAGATCCCCGGGCTCCACAGCAGAAGTCTGGTTACTGGGCAGGCAGGCCCCAAACACTGTATTTAAAACAAAACCCCACTGACAAGTCCTGTGACTGGAGAGACCCCGAGTGAAGGCAGACCTCCATGTCCTCTACATCCTGTGCCACATCTGGAGAGACCCCTGTGAGGGCAGAGAGCTACCTCCTCTTCTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCGGATGGCCACGTCTTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTACTTCCTGTGTCACACCTGGGGAGACCCTGAGTGAGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAGAGACCCCAAGAGAGGGCAGACAGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCGGATGGCCACGTCTTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTACTTCCTGTGTCACACCTGGGGAGACCCTGAGTGAGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAGAGACCCCAAGAGAGGGCAGACAGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACTCCAAGTGAGGAGAGACGGCCACATCTTCTACTTCCTGTGTCACACCTGGAGAGACCTCGAGTGAGGGCAGATGGCCACATCCTCTAATTCCTGTGTCACACCTGGAGAGACCCCAAGTGAGGGCAGACTGCCACCTCCTCTACTTCCTGTGTCACACCTAGAGAGACCCCGAGTGAGGACAGCCAGCCATGTCCTCTACTTCCTGTGCCACATCCGGAGAGATCCCGAGTGAGGGCAGACAGCCATGTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTGTCATGCCTGGAGAGACCCCGAGTGAGGGCATATGGCCACATCCTCTAATTCCTATGTCACACCTGGAGAGACCCCGAGTGAGGGTGGATGGCCACATCCTCTAATTCCTGTGTCATACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCAAGTGAGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAGAGACCCCGATGAGGGCAGACAGCTACCCCCTCTACTTCCTGTGTCACACCTGCAGAGACCCCAAGTGAGGGCAGATGGCCACCTCTTCTACTTCCTGTGTCACACCTGGAGAGGCCCCGAGTGAGGGCAGACGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTATTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTGTCACACATGGAGAGACCCCGAGTGAGGGCAGAAGGCCACATCCTCTACTTCCTGTGTCACACCTAGAGAGACCCCGAGTGAGGGCGGATGGCCACATCCTCTAATTCCTGTGTCACACCTGGGGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTAATTCCTGTGTCACACCTGGAGACACACAGAGTAAAGGTGGACAGCCACCTCCTCTACGTCCTGTGCCACACCTGGAGACACCCTGAGTTAAGGCAGATGGCCACCTCCTCTAATTATTTTTAAGAACTTTTTTGGGGTATAATTTACATGCCAGAAAGTTCACCCATTTCAAGCATATGATTCAATATTAAAGCTTAAAAATGTTATCAATTTAATAACATTGATGGTTACAGAGCTGTGTAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/msa.fa new file mode 100644 index 00000000..8a037f35 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/msa.fa @@ -0,0 +1,195 @@ +>ref_chr20_61100692_61102788 +ttggtacatgtacagattgtgcaagacaataggacaccagacagatccccgggctccaca +gcagaagtctggttactgggcaggcaggccccaaacactgtatttaaaacaaaaccccac +tgacaagtcctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatc +ctgtgccacatctggagagacccctgtgagggcagagagctacctcctcttcttcctgtg +tcacacctggagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtcac +acctggagagaccccgagtgagggcagatggccacatcctctacttcctgtgtcacacct +ggggagaccctgagtgagggcagacagccatgtcctctacgtcctgtgccacatccggag +agaccccaagagagggcagacagccacctcctctacttcctgtgtcacacctggagagac +cccgagtgagggcggatggccacgtcttctacttcctgtgtcacacctggagagaccccg +agtgagggcagatggccacatcctctacttcctgtgtcacacct---------------- +------------------------------------------------------------ +------------------------------------ggggagaccctgagtgagggcaga +cagccatgtcctctacgtcctgtgccacatccggagagaccccaagagagggcagacagc +cacctcctctacttcctgtgtcacacctggagagactccaagtgaggagagacggccaca +tcttctacttcctgtgtcacacctggagagacctcgagtgagggcagatggccacatcct +ctaa-------------------------------------------------------- +ttcctgtgtcacacctggagagaccccaagtgagggcagactgccacctcctctacttcc +tgtgtcacacctagagagaccccgagtgaggacagccagccatgtcctctacttcctgtg +ccacatccggagagatcccgagtgagggcagacagccatgtcctctacttcctgtgtcac +acctggagagaccccgagtgagggcagacggccacatcctctaattcctgtgtcacacct +ggagagaccccgagtgagggcagacggccacctcctctacttcctgtgtcacacctggag +agaccccgagtgagggcagacggccacatcctctaattcctgtgtcatgcctggagagac +cccgagtgagggcatatggccacatcctctaattcctatgtcacacctggagagaccccg +agtgagggtggatggccacatcctctaattcctgtgtcatacctggagagaccccgagtg +agggcagatggccacctcctctacttcctgtgtcacacctggagagaccccgagtgaggg 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+tgacaagtcctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatc +ctgtgccacatctggagagacccctgtgagggcagagagctacctcctcttcttcctgtg +tcacacctggagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtcac +acctggagagaccccgagtgagggcagatggccacatcctctacttcctgtgtcacacct +ggggagaccctgagtgagggcagacagccatgtcctctacgtcctgtgccacatccggag +agaccccaagagagggcagacagccacctcctctacttcctgtgtcacacctggagagac +cccgagtgagggcggatggccacgtcttctacttcctgtgtcacacctggagagaccccg +agtgagggcagatggccacatcctctacttcctgtgtcacacct---------------- +------------------------------------------------------------ +------------------------------------ggggagaccctgagtgagggcaga +cagccatgtcctctacgtcctgtgccacatccggagagaccccaagagagggcagacagc +cacctcctctacttcctgtgtcacacctggagagactccaagtgaggagagacggccacg +tcttctacttcctgtgtcacacctggagagaccccgagtgagggtggatggccacatcct +ctaattcctgtgtcatacctggagagaccccgagtgagggcagatggccacctcctctac +ttcctgtgtcacacctggagagaccccgagtgagggcagactgccacctcctctacttcc +tgtgtcacacctagagagaccccgagtgaggacagccagccatgtcctctacttcctgtg 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2266 2367 60 61 +syndip_2_chr20:61100692-61102788 2266 4705 60 61 +p:HG002_1_chr20:61100692-61102788 2266 7044 60 61 +p:HG002_2_chr20:61100692-61102788 2266 9383 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/output.vcf.gz new file mode 100644 index 00000000..9de388f6 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/output.vcf.gz.tbi new file mode 100644 index 00000000..8bed9bac Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61100792-61102688/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/base.vcf.gz new file mode 100644 index 00000000..c8a97a6b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/base.vcf.gz.tbi new file mode 100644 index 00000000..ebbbb5b8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/comp.vcf.gz new file mode 100644 index 00000000..8186495b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/comp.vcf.gz.tbi new file mode 100644 index 00000000..c3282b62 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/haps.fa new file mode 100644 index 00000000..c01008e8 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/haps.fa @@ -0,0 +1,130 @@ +>ref_chr20_61201583_61202575 +AATACAGCATATCAAAATGTATGGGATGCAGCTAAAGCAGTGCTCAGAGGACAATCTATACTACTAGAGGCTTATATTAGAAAAAAAAATTTAAATCAATAACCTAAGCTTTCACCATTAGAGAAGGAATTTCCTCACTCAGGACCCTCTGCGGATGTCGCCTCCATCCTCATCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCATGGTGTCACCTCCATCCTTACTCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTCCATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTCCATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCGTGAGTGCCAGCTCTGTCTACCCTCGGGACCCTCCATGAGTGTCTCCTCTATCTACCCTCAGGACCCTCTGTGAATGTCCTCGCCATCCATACTCCCCCCTCTTAGACCCAGACTGTTTCAGGGTTGGACACTGAGCTGTGGCCCCTGAGCCTAGCTCTTCTCCGAGCTTCTCTTGGGCACCTCTCTCTCAGACTAGGCT +>syndip_1_chr20:61201583-61202575 +AATACAGCATATCAAAATGTATGGGATGCAGCTAAAGCAGTGCTCAGAGGACAATCTATA +CTACTAGAGGCTTATATTAGAAAAAAAAATTTAAATCAATAACCTAAGCTTTCACCGTTA +GAGAAGGAATTTCCTCACTCAGGACCCTCTGCGGATGTCACCTCCATCCTCATCAGGACC +CTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCATGGTGTCACCTCCATCCTTAC +TCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTC +CATCCTCACTCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGGT +GTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTCCATCCTCACCAGGATCC +CCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAG +GACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATC +CTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCA +CCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACCAGGACCCTCCAT +GAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGG +ACCCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCGCCATCC +TCACTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCA +CCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACCAGGATCCCCTGT +AAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGG +ACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCT +CACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACC +TCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATG +GTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGAC +CCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTC +ACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCA +TCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGT +CACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTC +CATGGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCA +GGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCGTGAGTGCCAGCTCTGT +CTACCCTCGGGACCCTCCATGAGTGTCTCCTCTATCTACCCTCAGGACCCTCTGTGAATG +TCCTCGCCATCCATACTCCCCCCTCTTAGACCCAGACTGTTTCAGGGTTGGACACTGAGC +TGTGGCCCCTGAGCCTAGCTCTTCTCCGAGCTTCTCTTGGGCACCTCTCTCTCAGACTAG +GCT +>syndip_2_chr20:61201583-61202575 +AATACAGCATATCAAAATGTATGGGATGCAGCTAAAGCAGTGCTCAGAGGACAATCTATA +CTACTAGAGGCTTATATTAGAAAAAAAAATTTAAATCAATAACCTAAGCTTTCACCATTA +GAGAAGGAATTTCCTCACTCAGGACCCTCTGCGGATGTCGCCTCCATCCTCATCAGGACC +CTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCATGGTGTCACCTCCATCCTTAC +TCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGGGTGTCACCTC +CATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGT +GTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCC +TCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGGTGTCACCTCCATCCTCAC +TCAGGACCCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGGTGTCACCT +CCATCCTCACTCAGGACCCTCCATGGGTGCCACCTCCATCCTCACCAGGATCCCCTGTAA +GTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAGGACCCTC +CATGAGTGTCACCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGG +ACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCT +CACTCAGGACCCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGAGTGTCA +CCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGG +TGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACC +CTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCATGGTGTCACCTCCATCCTTAC +TCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTC +CATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGAG +TGTCACCTCCATCCTCAGGACCCTCCATGGTGTCACCTCCATCCTCAGGACCCTCCATGA +GTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGAC +CCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGGTGTCACCTCCATCCT +CACTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCAC +CTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCAT +GGTGTCACCTCCATCCTTACTCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGA +CCCTCCATGAGTGCCACCTCCATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCT +CACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACC +TCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCGTG +AGTGCCAGCTCTGTCTACCCTCGGGACCCTCCATGAGTGTCTCCTCTATCTACCCTAAGG +ACCCTCTGTGAATGTCCTCGCCATCCATACTCCCCCCTCTTAGACCCAGACTGTTTCAGG +GTTGGACACTGAGCTGTGGCCCCTGAGCCTAGCTCTTCTCCGAGCTTCTCTTGGGCACCT +CTCTCTCAGACTAGGCT +>p:HG002_1_chr20:61201583-61202575 +AATACAGCATATCAAAATGTATGGGATGCAGCTAAAGCAGTGCTCAGAGGACAATCTATA +CTACTAGAGGCTTATATTAGAAAAAAAAATTTAAATCAATAACCTAAGCTTTCACCATTA +GAGAAGGAATTTCCTCACTCAGGACCCTCTGCGGATGTCGCCTCCATCCTCATCAGGACC +CTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCATGGTGTCACCTCCATCCTTAC +TCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGGGTGTCACCTC +CATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGT +GTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCC +TCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGGTGTCACCTCCATCCTCAC +TCAGGACCCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGGTGTCACCT +CCATCCTCACTCAGGACCCTCCATGGGTGCCACCTCCATCCTCACCAGGATCCCCTGTAA +GTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAGGACCCTC +CATGAGTGTCACCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGG +ACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCT +CACTCAGGACCCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGAGTGTCA +CCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGG +TGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACC +CTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCATGGTGTCACCTCCATCCTTAC +TCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTC +CATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGAG +TGTCACCTCCATCCTCAGGACCCTCCATGGTGTCACCTCCATCCTCAGGACCCTCCATGA +GTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGAC +CCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGGTGTCACCTCCATCCT +CACTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCAC +CTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCAT +GGTGTCACCTCCATCCTTACTCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGA +CCCTCCATGAGTGCCACCTCCATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCT +CACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACC +TCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCGTG +AGTGCCAGCTCTGTCTACCCTCGGGACCCTCCATGAGTGTCTCCTCTATCTACCCTAAGG +ACCCTCTGTGAATGTCCTCGCCATCCATACTCCCCCCTCTTAGACCCAGACTGTTTCAGG +GTTGGACACTGAGCTGTGGCCCCTGAGCCTAGCTCTTCTCCGAGCTTCTCTTGGGCACCT +CTCTCTCAGACTAGGCT +>p:HG002_2_chr20:61201583-61202575 +AATACAGCATATCAAAATGTATGGGATGCAGCTAAAGCAGTGCTCAGAGGACAATCTATA +CTACTAGAGGCTTATATTAGAAAAAAAAATTTAAATCAATAACCTAAGCTTTCACCGTTA +GAGAAGGAATTTCCTCACTCAGGACCCTCTGCGGATGTCACCTCCATCCTCATCAGGACC +CTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCATGGTGTCACCTCCATCCTTAC +TCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTC +CATCCTCACTCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGGT +GTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTCCATCCTCACCAGGATCC +CCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAG +GACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATC +CTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCA +CCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACCAGGACCCTCCAT +GAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGG +ACCCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCGCCATCC +TCACTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCA +CCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACCAGGATCCCCTGT +AAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGG +ACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCT +CACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACC +TCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATG +GTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGAC +CCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTC +ACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCA +TCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGT +CACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTC +CATGGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCA +GGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCGTGAGTGCCAGCTCTGT +CTACCCTCGGGACCCTCCATGAGTGTCTCCTCTATCTACCCTCAGGACCCTCTGTGAATG +TCCTCGCCATCCATACTCCCCCCTCTTAGACCCAGACTGTTTCAGGGTTGGACACTGAGC +TGTGGCCCCTGAGCCTAGCTCTTCTCCGAGCTTCTCTTGGGCACCTCTCTCTCAGACTAG +GCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/haps.fa.ref.fa new file mode 100644 index 00000000..1cfaf0a4 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:61201583-61202575 +AATACAGCATATCAAAATGTATGGGATGCAGCTAAAGCAGTGCTCAGAGGACAATCTATACTACTAGAGGCTTATATTAGAAAAAAAAATTTAAATCAATAACCTAAGCTTTCACCATTAGAGAAGGAATTTCCTCACTCAGGACCCTCTGCGGATGTCGCCTCCATCCTCATCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCATGGTGTCACCTCCATCCTTACTCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTCCATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTCCATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCGTGAGTGCCAGCTCTGTCTACCCTCGGGACCCTCCATGAGTGTCTCCTCTATCTACCCTCAGGACCCTCTGTGAATGTCCTCGCCATCCATACTCCCCCCTCTTAGACCCAGACTGTTTCAGGGTTGGACACTGAGCTGTGGCCCCTGAGCCTAGCTCTTCTCCGAGCTTCTCTTGGGCACCTCTCTCTCAGACTAGGCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/msa.fa new file mode 100644 index 00000000..6111e523 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/msa.fa @@ -0,0 +1,165 @@ +>ref_chr20_61201583_61202575 +aatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctata +ctactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccatta +gagaaggaatttcctcactcaggaccctctgcggatgtcgcctccatcctcatcaggacc +ctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatccttac +tcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccacctc +catcctcac-caggatcccctgtaagtgtcacctccatcctcaccaggaccctccatgag +tgtcacctccatcct--------------------------------------------- +----------------------------caggaccctccatgagtgtcacctccatcctc +actcaggaccctccat------------------------------------ggtgtcac +cgccatcctcactcaggaccctccatgagtgccacctccatcctcaccaggatcccctgt +aa---------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------gtgtcacctccatcctcaccaggaccctccatgagtgt +cacctccatc----ctcaggaccctccatgagtgtcacctccatcctcactcaggaccct +ccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactc +aggaccctccatg----------------------------------ggtgtcacctcca +tcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtgt +cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctc +cgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctatctaccct +caggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccagactgttt +cagggttggacactgagctgtggcccctgagcctagctcttctccgagcttctcttgggc +acctctctctcagactaggct +>syndip_1_chr20:61201583-61202575 +aatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctata +ctactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccgtta +gagaaggaatttcctcactcaggaccctctgcggatgtcacctccatcctcatcaggacc +ctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatccttac +tcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccacctc +catcctcactcaggatcccctgtaagtgtcacctccatcctcaccaggaccctccatg-g +tgtcaccgccatcctcactcaggaccctccatgagtgccacctccatcctcaccaggatc +ccctgtaagtgtcacctccatcctcac-caggaccctccatgagtgtcacctccatc--- +-ctcaggaccctccatgagtgtcacctccatcctcactcaggaccctccat-ggtgtcac +ctccatcctcactcaggaccctccat-ggtgtcacctccatcctcactcaggaccctcca +tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctca------ +----------------------ccaggaccctccatgagtgtcacctccatcctcactca +ggaccctccatggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccat +cctcactcaggaccctccat-ggtgtcaccgccatcctca-------------------- +-----------ctcaggaccctccatgagtgtcacctccatcctcactcaggaccctcca +tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcaccagga +tcccctgtaagtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcct +cactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatg-gtgtcac +ctccatcctcaccaggatcccctgtaagtgtcacctccatcctcac-caggaccctccat +gagtgtcacctccatcctca--------------------------ctcaggaccctcca +tg-gtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcag +gaccctccat-ggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccat +cctcactcaggaccctccatg-gtgtcacctccatcctcaccaggaccctccatgagtgt +cacctccatc----ctcaggaccctccatgagtgtcacctccatcctcactcaggaccct +ccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactc +aggaccctccatg-----------------------------------gtgtcacctcca +tcctcactcaggaccctccatggtgtcacctccatcctcaccaggaccctccatgagtgt +cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctc +cgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctatctaccct +caggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccagactgttt +cagggttggacactgagctgtggcccctgagcctagctcttctccgagcttctcttgggc +acctctctctcagactaggct +>syndip_2_chr20:61201583-61202575 +aatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctata +ctactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccatta +gagaaggaatttcctcactcaggaccctctgcggatgtcgcctccatcctcatcaggacc +ctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatccttac +tcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgggtgtcacctc +catcctcac-caggatcccctgtaagtgtcacctccatcctcaccaggaccctccatgag +tgtcacctccatcctcactcaggaccctccatg-gtgtcacctccatcctcactcaggac +cctccatggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctc +actcaggaccctccatgggtgtcacctccatcctcactcaggaccctccatgggtgtcac +ctccatcctcactcaggaccctccatgggtgccacctccatcctcaccaggatcccctgt +aagtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcctcaggaccc +tccatgagtgtcacctccatcctcaggaccctccatgagtgtcacctccatcctcactca +ggaccctccatggtgtcacctccatcctcactcaggaccctccat-ggtgtcacctccat +cctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccatgagtg +tcacctccatcctcaggaccctccatgagtgtcacctccatcctcactcaggaccctcca +tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcagg +accctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatcct +tactcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccac +ctccatcctcaccaggatcccctgtaagtgtcacctccatcctcactcaggaccctccat +gagtgtcacctccatcctcaggaccctccatggtgtcacctccatcctcaggaccctcca +tgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcag +gaccctccatgggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccat +cctcactcaggaccctccatgagtgtcacctccatcctcactcaggaccctccatggtgt +cacctccatcctcactcaggaccctccatg-gtgtcacctccatcctcactcaggacact +ccatggtgtcacctccatccttactcaggaccctccatggtgtcaccgccatcctcactc +aggaccctccatgagtgccacctccatcctcaccaggatcccctgtaagtgtcacctcca +tcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtgt +cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctc +cgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctatctaccct +aaggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccagactgttt +cagggttggacactgagctgtggcccctgagcctagctcttctccgagcttctcttgggc +acctctctctcagactaggct +>p:HG002_1_chr20:61201583-61202575 +aatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctata +ctactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccatta +gagaaggaatttcctcactcaggaccctctgcggatgtcgcctccatcctcatcaggacc +ctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatccttac +tcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgggtgtcacctc +catcctcac-caggatcccctgtaagtgtcacctccatcctcaccaggaccctccatgag +tgtcacctccatcctcactcaggaccctccatg-gtgtcacctccatcctcactcaggac +cctccatggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctc +actcaggaccctccatgggtgtcacctccatcctcactcaggaccctccatgggtgtcac +ctccatcctcactcaggaccctccatgggtgccacctccatcctcaccaggatcccctgt +aagtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcctcaggaccc +tccatgagtgtcacctccatcctcaggaccctccatgagtgtcacctccatcctcactca +ggaccctccatggtgtcacctccatcctcactcaggaccctccat-ggtgtcacctccat +cctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccatgagtg +tcacctccatcctcaggaccctccatgagtgtcacctccatcctcactcaggaccctcca +tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcagg +accctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatcct +tactcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccac +ctccatcctcaccaggatcccctgtaagtgtcacctccatcctcactcaggaccctccat +gagtgtcacctccatcctcaggaccctccatggtgtcacctccatcctcaggaccctcca +tgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcag +gaccctccatgggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccat +cctcactcaggaccctccatgagtgtcacctccatcctcactcaggaccctccatggtgt +cacctccatcctcactcaggaccctccatg-gtgtcacctccatcctcactcaggacact +ccatggtgtcacctccatccttactcaggaccctccatggtgtcaccgccatcctcactc +aggaccctccatgagtgccacctccatcctcaccaggatcccctgtaagtgtcacctcca +tcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtgt +cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctc +cgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctatctaccct +aaggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccagactgttt +cagggttggacactgagctgtggcccctgagcctagctcttctccgagcttctcttgggc +acctctctctcagactaggct +>p:HG002_2_chr20:61201583-61202575 +aatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctata +ctactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccgtta +gagaaggaatttcctcactcaggaccctctgcggatgtcacctccatcctcatcaggacc +ctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatccttac +tcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccacctc +catcctcactcaggatcccctgtaagtgtcacctccatcctcaccaggaccctccatg-g +tgtcaccgccatcctcactcaggaccctccatgagtgccacctccatcctcaccaggatc +ccctgtaagtgtcacctccatcctcac-caggaccctccatgagtgtcacctccatc--- +-ctcaggaccctccatgagtgtcacctccatcctcactcaggaccctccat-ggtgtcac +ctccatcctcactcaggaccctccat-ggtgtcacctccatcctcactcaggaccctcca +tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctca------ +----------------------ccaggaccctccatgagtgtcacctccatcctcactca +ggaccctccatggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccat +cctcactcaggaccctccat-ggtgtcaccgccatcctca-------------------- +-----------ctcaggaccctccatgagtgtcacctccatcctcactcaggaccctcca +tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcaccagga +tcccctgtaagtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcct +cactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatg-gtgtcac +ctccatcctcaccaggatcccctgtaagtgtcacctccatcctcac-caggaccctccat +gagtgtcacctccatcctca--------------------------ctcaggaccctcca +tg-gtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcag +gaccctccat-ggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccat +cctcactcaggaccctccatg-gtgtcacctccatcctcaccaggaccctccatgagtgt +cacctccatc----ctcaggaccctccatgagtgtcacctccatcctcactcaggaccct +ccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactc +aggaccctccatg-----------------------------------gtgtcacctcca +tcctcactcaggaccctccatggtgtcacctccatcctcaccaggaccctccatgagtgt +cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctc +cgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctatctaccct +caggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccagactgttt +cagggttggacactgagctgtggcccctgagcctagctcttctccgagcttctcttgggc +acctctctctcagactaggct diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/msa.fa.fai new file mode 100644 index 00000000..cbae1237 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_61201583_61202575 1881 29 60 61 +syndip_1_chr20:61201583-61202575 1881 1976 60 61 +syndip_2_chr20:61201583-61202575 1881 3923 60 61 +p:HG002_1_chr20:61201583-61202575 1881 5871 60 61 +p:HG002_2_chr20:61201583-61202575 1881 7819 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/output.vcf.gz new file mode 100644 index 00000000..892c44c1 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/output.vcf.gz.tbi new file mode 100644 index 00000000..0d12c18b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61201683-61202475/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/base.vcf.gz new file mode 100644 index 00000000..bffc51d4 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/base.vcf.gz.tbi new file mode 100644 index 00000000..1e222ff8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/comp.vcf.gz new file mode 100644 index 00000000..363b9c24 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/comp.vcf.gz.tbi new file mode 100644 index 00000000..49e7ad95 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/haps.fa new file mode 100644 index 00000000..98161bac --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/haps.fa @@ -0,0 +1,114 @@ +>ref_chr20_61282406_61283770 +ATAAAACATTCTGTATTTTCAAAATGCCAAAAAAATTATTGTTAAAGACTTTAGAAAACAGAAAAGTACAAAGAATAAAAGGGTAACTTCATTTCCCTCCTCTGAACAAACCACTTTTAATCTTTGGCATGGTGTGTGTGCATGTGTGTGTGTGTGTGTGTGTGTGTATGTCTATCTGTACTTGTACCTGCACACACAACTGGATGAGCATGGTGTGTGTGTACACATGTAATGTGTTCATATGTACATATGTGGGTGCCTTGTGCACACGTGTGTGGCTGTGGGATGTTCAGATGTGCATGTGAGTTGGTGTGTGTGCATGCCCACAAGCATGCATGTAAATGTGATGTGCTGTGTATGCACACGGATAAGCATGTGTGAAGGAGTGCATGAGAGTGGTGCATGGCTGTGGTGTGCACGTGTGTGCGTGTGATGCATGTGCATTTGCACGCATGTGCTGTGGTGTGTGTGATGTACGTGCATTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACGTGCATTTGCACGCGTGTGCTGTGGCGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGTGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGTGTGTGATGTAGGTGCATTTGCACGCGTGTGCTGTGGTGTGTGATGTAGGTGCATTTACACGCGTGTGCTGTGGTGTGTGATGTAGGTGCATTTGCACGTGTGTGCTGTGGTGTGTGTGATGTGTGTGCATTTGCACGTGTGTGCTGTGGTGTGTGTGTGGTGAGTGGATGGGAGGATATTTCCAGTGCTCTCCTCCTGGGACTGATGCCATGATGAAAATCTGTGTAAACCAGACAGCACATCTCTCATCATTTCTTTGTGATGGGTCATTAGAAGCAGGATTCTGAATT +>syndip_1_chr20:61282406-61283770 +ATAAAACATTCTGTATTTTCAAAATGCCAAAAAAATTATTGTTAAAGACTTTAGAAAACA +GAAAAGTACAAAGAATAAAAGGGTAACTTCATTTCCCTCCTCTGAACAAACCACTTTTAA +TCTTTGGCATGGTGTGTGTGTGTGCATGTGTGTGTGTGTGTGTGTATGTCTATCTGTACT +TGTACCTGCACACACAACTGGATGAGCATGGTGTGTGTGTACACATGTATTGTGTTCATA +TGTACATATGTGGGTGCCTTGTGCACACGTGTGTGGCTGTGGGATGTTCAGATGTGCATG +TGAGTTGGTGTGTGTGCATGCCCACAAGCATGCATGTAAATGTGATGTGCTGTGTATGCA +CACGGATAAGCATGTGTGAAGGAGTGCATGAGAGTGGTGCATGGCTGTGGTGTGCACGTG +TGTGCGTGTGATGCATGTGCATTTGCACGCATGTGCTGTGGTGTGTGTGATGTACGTGCA +TTTGCACGCATGTGCTGTGGCGTGTGTGATGTACGTGCATTTGCACGCGTGTGCTGTGTG +TGTGATGTACGTGCATTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCA +CGCGTGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGT +GATGTACGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGC +GTGTGCTGTGGTGTGTGATGTACGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGT +ACGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGTGTG +CTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACG +TGCGTTTGCACGCGTGTTCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGTGTGCTG +TGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTGTGTGC +GTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGG +CGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTGTGTGCGTT +TGCACGCGTGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGCGT +GTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGTGATGTGTGTGCGTTTGCACGCGTG +TGCTGTGGTGTGTGATGTAGGTGCATTTACACGCGTGTGCTGTGGTGTGTGATGTAGGTG +CATTTGCACGCGTGTGCTGTGGTGTGTGTGATGTGTGTGCGTTTGCACGTGTGTGCTGTG +GTGTGTGTGTGGTGAGTGGATGGGAGGATATTTCCAGTGCTCTCCTCCTGGGACTGATGC +CATGATGAAAATCTGTGTAAACCAGACAGCACATCTCTCATCATTTCTTTGTGATGGGTC +ATTAGAAGCAGGATTCTGAATT +>syndip_2_chr20:61282406-61283770 +ATAAAACATTCTGTATTTTCAAAATGCCAAAAAAATTATTGTTAAAGACTTTAGAAAACA +GAAAAGTACAAAGAATAAAAGGGTAACTTCATTTCCCTCCTCTGAACAAACCACTTTTAA +TCTTTGGCATGGTGTGTGTGTGTGCATGTGTGTGTGTGTGTGTGTATGTCTATCTGTACT +TGTACCTGCACACACAACTGGATGAGCATGGTGTGTGTGTACACATGTAATGTGTTCATA +TGTACATATGTGGGTGCCTTGTGCACACGTGTGTGGCTGTGGGATGTTCAGATGTGCATG +TGAGTTGGTGTGTGTGCATGCCCACAAGCATGCATGTAAATGTGATGTGCTGTGTATGCA +CACGGATAAGCATGTGTGAAGGAGTGCATGAGAGTGGTGCATGGCTGTGGTGTGCACGTG +TGTGCGTGTGATGCATGTGCATTTGCACGCATGTGCTGTGGTGTGTGTGATGTACGTGCA +TTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACGTGCATTTGCACGCGTGTGCTGTGTG +TGTGATGTACGTGCATTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCA +CGCGTGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGA +TGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGC +GTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGT +GGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCG +TTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGC +GTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTT +GCACGCGCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTG +TGTGATGTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCA +CGCGCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGT +GATGTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGC +GCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGAT +GTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTG +TGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGTGTGTGATGTAGG +TGCGTTTGCACGCGTGTGCTGTGGTGTGTGATGTAGGTGCGTTTGCACGCGTGTGCTGTG +GTGTGTGATGTAGGTGCATTTGCACGTGTGTGCTGTGGTGTGTGTGATGTGTGTGCATTT +GCACGTGTGTGCTGTGGTGTGTGTGTGGTGAGTGGATGGGAGGATATTTCCAGTGCTCTC +CTCCTGGGACTGATGCCATGATGAAAATCTGTGTAAACCAGACAGCACATCTCTCATCAT +TTCTTTGTGATGGGTCATTAGAAGCAGGATTCTGAATT +>p:HG002_1_chr20:61282406-61283770 +ATAAAACATTCTGTATTTTCAAAATGCCAAAAAAATTATTGTTAAAGACTTTAGAAAACA +GAAAAGTACAAAGAATAAAAGGGTAACTTCATTTCCCTCCTCTGAACAAACCACTTTTAA +TCTTTGGCATGGTGTGTGTGTGTGCATGTGTGTGTGTGTGTGTGTATGTCTATCTGTACT +TGTACCTGCACACACAACTGGATGAGCATGGTGTGTGTGTACACATGTAATGTGTTCATA +TGTACATATGTGGGTGCCTTGTGCACACGTGTGTGGCTGTGGGATGTTTAGATGTGCATG +TGAGTTGGTGTGTGTGCATGCCCACAAGCATGCATGTAAATGTGATGTGCTGTGTATGCA +CACGGATAAGCATGTGTGAAGGAGTGCATGAGAGTGGTGCATGGCTGTGGTGTGCACGTG +TGTGCGTGTGATGCATGTGCATTTGCACGCATGTGCTGTGGTGTGTGTGATGTACGTGCA +TTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACGTGCATTTGCACGCGTGTGCTGTGTG +TGTGATGTACGTGCATTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCA +CGCGTGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGA +TGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGC +GTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGT +GGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCG +TTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGC +GTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTT +GCACGCGCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTG +TGTGATGTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCA +CGCGCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGT +GATGTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGC +GCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGAT +GTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTG +TGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGTGTGTGATGTAGG +TGCGTTTGCACGCGTGTGCTGTGGTGTGTGATGTAGGTGCGTTTGCACGCGTGTGCTGTG +GTGTGTGATGTAGGTGCATTTGCACGTGTGTGCTGTGGTGTGTGTGATGTGTGTGCATTT +GCACGTGTGTGCTGTGGTGTGTGTGTGGTGAGTGGATGGGAGGATATTTCCAGTGCTCTC +CTCCTGGGACTGATGCCATGATGAAAATCTGTGTAAACCAGACAGCACATCTCTCATCAT +TTCTTTGTGATGGGTCATTAGAAGCAGGATTCTGAATT +>p:HG002_2_chr20:61282406-61283770 +ATAAAACATTCTGTATTTTCAAAATGCCAAAAAAATTATTGTTAAAGACTTTAGAAAACA +GAAAAGTACAAAGAATAAAAGGGTAACTTCATTTCCCTCCTCTGAACAAACCACTTTTAA +TCTTTGGCATGGTGTGTGTGTGTGCATGTGTGTGTGTGTGTGTGTATGTCTATCTGTACT +TGTACCTGCACACACAACTGGATGAGCATGGTGTGTGTGTACACATGTATTGTGTTCATA +TGTACATATGTGGGTGCCTTGTGCACACGTGTGTGGCTGTGGGATGTTCGGATGTGCATG +TGAGTTGGTGTGTGTGCATGCCCACAAGCATGCATGTAAATGTGATGTGCTGTGTATGCA +CACGGATAAGCATGTGTGAAGGAGTGCATGAGAGTGGTGCATGGCTGTGGTGTGCACGTG +TGTGCGTGTGATGCATGTGCATTTGCACGCATGTGCTGTGGTGTGTGTGATGTACGTGCA +TTTGCACGCATGTGCTGTGGCGTGTGTGATGTACGTGCATTTGCACGCGTGTGCTGTGTG +TGTGATGTACGTGCATTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCA +CGCGTGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGT +GATGTACGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGC +GTGTGCTGTGGTGTGTGATGTACGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGT +ACGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGTGTG +CTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACG +TGCGTTTGCACGCGTGTTCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGTGTGCTG +TGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTGTGTGC +GTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGG +CGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTGTGTGCGTT +TGCACGCGTGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGCGT +GTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGTGATGTGTGTGCGTTTGCACGCGTG +TGCTGTGGTGTGTGATGTAGGTGCATTTACACGCGTGTGCTGTGGTGTGTGATGTAGGTG +CATTTGCACGCGTGTGCTGTGGTGTGTGTGATGTGTGTGCGTTTGCACGTGTGTGCTGTG +GTGTGTGTGTGGTGAGTGGATGGGAGGATATTTCCAGTGCTCTCCTCCTGGGACTGATGC +CATGATGAAAATCTGTGTAAACCAGACAGCACATCTCTCATCATTTCTTTGTGATGGGTC +ATTAGAAGCAGGATTCTGAATT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/haps.fa.ref.fa new file mode 100644 index 00000000..e8a98649 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:61282406-61283770 +ATAAAACATTCTGTATTTTCAAAATGCCAAAAAAATTATTGTTAAAGACTTTAGAAAACAGAAAAGTACAAAGAATAAAAGGGTAACTTCATTTCCCTCCTCTGAACAAACCACTTTTAATCTTTGGCATGGTGTGTGTGCATGTGTGTGTGTGTGTGTGTGTGTGTATGTCTATCTGTACTTGTACCTGCACACACAACTGGATGAGCATGGTGTGTGTGTACACATGTAATGTGTTCATATGTACATATGTGGGTGCCTTGTGCACACGTGTGTGGCTGTGGGATGTTCAGATGTGCATGTGAGTTGGTGTGTGTGCATGCCCACAAGCATGCATGTAAATGTGATGTGCTGTGTATGCACACGGATAAGCATGTGTGAAGGAGTGCATGAGAGTGGTGCATGGCTGTGGTGTGCACGTGTGTGCGTGTGATGCATGTGCATTTGCACGCATGTGCTGTGGTGTGTGTGATGTACGTGCATTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACGTGCATTTGCACGCGTGTGCTGTGGCGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGTGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGTGTGTGATGTAGGTGCATTTGCACGCGTGTGCTGTGGTGTGTGATGTAGGTGCATTTACACGCGTGTGCTGTGGTGTGTGATGTAGGTGCATTTGCACGTGTGTGCTGTGGTGTGTGTGATGTGTGTGCATTTGCACGTGTGTGCTGTGGTGTGTGTGTGGTGAGTGGATGGGAGGATATTTCCAGTGCTCTCCTCCTGGGACTGATGCCATGATGAAAATCTGTGTAAACCAGACAGCACATCTCTCATCATTTCTTTGTGATGGGTCATTAGAAGCAGGATTCTGAATT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/msa.fa new file mode 100644 index 00000000..6fdc2ee9 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/msa.fa @@ -0,0 +1,145 @@ +>ref_chr20_61282406_61283770 +ataaaacattctgtattttcaaaatgccaaaaaaattattgttaaagactttagaaaaca +gaaaagtacaaagaataaaagggtaacttcatttccctcctctgaacaaaccacttttaa +tctttggcatggtgtgtgtgcatgtgtgtgtgtgtgtgtgtgtgtgtatgtctatctgta +cttgtacctgcacacacaactggatgagcatggtgtgtgtgtacacatgtaatgtgttca +tatgtacatatgtgggtgccttgtgcacacgtgtgtggctgtgggatgttcagatgtgca +tgtgagttggtgtgtgtgcatgcccacaagcatgcatgtaaatgtgatgtgctgtgtatg +cacacggataagcatgtgtgaaggagtgcatgagagtggtgcatggctgtggtgtgcacg +tgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctgtggtgtgtgtgatgtacgtg +catttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtg +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------gcgtgtgatgtacgtgcgtttgcacgcgcgtgctgtg----------- +-----gcgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtg +cgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtg +gcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgt +ttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcg +tgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttg +cacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggc---- +-----gtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcac +gcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggtgtgtgtg +atgtgtgtgcgtttgcacgcgtgtgc---------------------------------- +--------------------------------------------tgtggtgtgtgatgta +ggtgcatttgcacgcgtgtgctgtggtgtgtgatgtaggtgcatttacacgcgtgtgctg +tggtgtgtgatgtaggtgcatttgcacgtgtgtgctgtggtgtgtgtgatgtgtgtgcat +ttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatgggaggatatttccagtgctc +tcctcctgggactgatgccatgatgaaaatctgtgtaaaccagacagcacatctctcatc +atttctttgtgatgggtcattagaagcaggattctgaatt +>syndip_1_chr20:61282406-61283770 +ataaaacattctgtattttcaaaatgccaaaaaaattattgttaaagactttagaaaaca +gaaaagtacaaagaataaaagggtaacttcatttccctcctctgaacaaaccacttttaa +tctttggcatggtgtgtgtg--tgtgcatgtgtgtgtgtgtgtgtgtatgtctatctgta +cttgtacctgcacacacaactggatgagcatggtgtgtgtgtacacatgtattgtgttca +tatgtacatatgtgggtgccttgtgcacacgtgtgtggctgtgggatgttcagatgtgca +tgtgagttggtgtgtgtgcatgcccacaagcatgcatgtaaatgtgatgtgctgtgtatg +cacacggataagcatgtgtgaaggagtgcatgagagtggtgcatggctgtggtgtgcacg +tgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctgtggtgtgtgtgatgtacgtg +catttgcacgcatgtgctgtggcgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtg +tgtgtgatgtacgtgcatttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttg +cacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgt-------------- +-----------------------gtgctgtggcgtgtgtgatgtacgtgcgtttgcacgc +gtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtg----------- +-----gtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtg +cgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtg +gcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgt +ttgcacgcgtgttctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcg +tgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttg +cacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgt +gtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcac +gcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtg +atgtgtgtgcgtttgcacgcgtgtgc---------------------------------- +-------------------------------------------------tgtgtgatgtg +tgtgcgtttgcacgcgtgtgctgtggtgtgtgatgtaggtgcatttacacgcgtgtgctg +tggtgtgtgatgtaggtgcatttgcacgcgtgtgctgtggtgtgtgtgatgtgtgtgcgt +ttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatgggaggatatttccagtgctc +tcctcctgggactgatgccatgatgaaaatctgtgtaaaccagacagcacatctctcatc +atttctttgtgatgggtcattagaagcaggattctgaatt +>syndip_2_chr20:61282406-61283770 +ataaaacattctgtattttcaaaatgccaaaaaaattattgttaaagactttagaaaaca +gaaaagtacaaagaataaaagggtaacttcatttccctcctctgaacaaaccacttttaa +tctttggcatggtgtgtgtg--tgtgcatgtgtgtgtgtgtgtgtgtatgtctatctgta +cttgtacctgcacacacaactggatgagcatggtgtgtgtgtacacatgtaatgtgttca +tatgtacatatgtgggtgccttgtgcacacgtgtgtggctgtgggatgttcagatgtgca +tgtgagttggtgtgtgtgcatgcccacaagcatgcatgtaaatgtgatgtgctgtgtatg +cacacggataagcatgtgtgaaggagtgcatgagagtggtgcatggctgtggtgtgcacg +tgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctgtggtgtgtgtgatgtacgtg +catttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtg +tgtgtgatgtacgtgcatttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttg +cacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgt +gatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgc +gcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgat +gtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtg +cgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtg 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+tgtgagttggtgtgtgtgcatgcccacaagcatgcatgtaaatgtgatgtgctgtgtatg +cacacggataagcatgtgtgaaggagtgcatgagagtggtgcatggctgtggtgtgcacg +tgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctgtggtgtgtgtgatgtacgtg +catttgcacgcatgtgctgtggcgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtg +tgtgtgatgtacgtgcatttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttg +cacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgt-------------- +-----------------------gtgctgtggcgtgtgtgatgtacgtgcgtttgcacgc +gtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtg----------- +-----gtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtg +cgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtg +gcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgt +ttgcacgcgtgttctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcg +tgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttg +cacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgt +gtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcac +gcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtg +atgtgtgtgcgtttgcacgcgtgtgc---------------------------------- +-------------------------------------------------tgtgtgatgtg +tgtgcgtttgcacgcgtgtgctgtggtgtgtgatgtaggtgcatttacacgcgtgtgctg +tggtgtgtgatgtaggtgcatttgcacgcgtgtgctgtggtgtgtgtgatgtgtgtgcgt +ttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatgggaggatatttccagtgctc +tcctcctgggactgatgccatgatgaaaatctgtgtaaaccagacagcacatctctcatc +atttctttgtgatgggtcattagaagcaggattctgaatt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/msa.fa.fai new file mode 100644 index 00000000..c300d89b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_61282406_61283770 1660 29 60 61 +syndip_1_chr20:61282406-61283770 1660 1751 60 61 +syndip_2_chr20:61282406-61283770 1660 3473 60 61 +p:HG002_1_chr20:61282406-61283770 1660 5196 60 61 +p:HG002_2_chr20:61282406-61283770 1660 6919 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/output.vcf.gz new file mode 100644 index 00000000..77b80367 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/output.vcf.gz.tbi new file mode 100644 index 00000000..96e9830c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61282506-61283670/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/base.vcf.gz new file mode 100644 index 00000000..634e8e54 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/base.vcf.gz.tbi new file mode 100644 index 00000000..c69d2dcd Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/comp.vcf.gz new file mode 100644 index 00000000..a9f786f2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/comp.vcf.gz.tbi new file mode 100644 index 00000000..f54efc0d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/haps.fa new file mode 100644 index 00000000..67f51df0 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/haps.fa @@ -0,0 +1,80 @@ +>ref_chr20_61289525_61290656 +TGTGTGGGTGCCCAGGGGCATGAGTGCCTGGGGAGTGTGACCACAGGCCAGTGGCAGTCCCTGCCTTTGGATTAAAGAGCCCTTTGAGGCTTGCTTGGTGATGTCATGGAAAACAGCATATGACACCAAGATATCCCCATATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCGATATCCAATGAGACTTGCTGGATTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCGATATCCAATGAGACTTGCTGGATTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCGATATCCAATGAGACTTGCTGGATTTATCCCCGTATCCAATGAGACTTGCTGGATTTATCCCCATATCCAATGAGACTTGCTGGGTTTAGCACCACAGATGCCAGTCACAGAGGAAATTGATGGCATGGCAGACAGCGTGACATGTTGACTACCTGCCCTGGTCCTTGCAGATGGCATGGGCACAAAGGGGATGTGGGGTGAAGAGTTGAAACGAGTGCC +>syndip_1_chr20:61289525-61290656 +TGTGTGGGTGCCCAGGGGCATGAGTGCCTGGGGAGTGTGACCACAGGCCAGTGGCAGTCC +CTGCCTTTGGATTAAAGAGCCCTTTGAGGCTTGCTTGGTGATGTCATGGAAAACAGCATA +TGACACCAAGATATCCCCATATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGA +GACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAAC +GAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCA +ACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATC +CAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTA +TCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCG +TATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCC +CGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATC +CCCGTATCCAATGAGACTTGCTGGGTTTATCCCGATATCCAATGAGACTTGCTGGATTTA +TCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTT +TATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCGATATCCAATGAGACTTGCTGGA +TTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTG +GGTTTATCCCGATATCCAATGAGACTTGCTGGATTTATCCCCGTATCCAATGAGACTTGC +TGGATTTATCCCCATATCCAATGAGACTTGCTGGGTTTAGCACCACAGATGCCAGTCACA +GAGGAAATTGATGGCATGGCAGACAGCGTGACATGTTGACTACCTGCCCTGGTCCTTGCA +GATGGCATGGGCACAAAGGGGATGTGGGGTGAAGAGTTGAAACGAGTGCC +>syndip_2_chr20:61289525-61290656 +TGTGTGGGTGCCCAGGGGCATGAGTGCCTGGGGAGTGTGACCACAGGCCAGTGGCAGTCC +CTGCCTTTGGATTAAAGAGCCCTTTGAGGCTTGCTTGGTGATGTCATGGAAAACAGCATA +TGACACCAAGATATCCCCATATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGA +GACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAAC +GAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCA +ACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATC +CAACGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCCTA +TCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCG +TATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCC +CGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATC +CCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTA +TCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTT +TATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGG +TTTATCCCGATATCCAATGAGACTTGCTGGATTTATCCCCGTATCCAATGAGACTTGCTG +GGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCGATATCCAATGAGACTTGC +TGGATTTATCCCCGTATCCAATGAGACTTGCTGGATTTATCCCCATATCCAATGAGACTT +GCTGGGTTTAGCACCACAGATGCCAGTCACAGAGGAAATTGATGGCATGGCAGACAGCGT +GACATGTTGACTACCTGCCCTGGTCCTTGCAGATGGCATGGGCACAAAGGGGATGTGGGG +TGAAGAGTTGAAACGAGTGCC +>p:HG002_1_chr20:61289525-61290656 +TGTGTGGGTGCCCAGGGGCATGAGTGCCTGGGGAGTGTGACCACAGGCCAGTGGCAGTCC +CTGCCTTTGGATTAAAGAGCCCTTTGAGGCTTGCTTGGTGATGTCATGGAAAACAGCATA +TGACACCAAGATATCCCCATATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGA +GACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAAC +GAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCA +ACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATC +CAACGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCCTA +TCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCG +TATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCC +CGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATC +CCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTA +TCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTT +TATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGG +TTTATCCCGATATCCAATGAGACTTGCTGGATTTATCCCCGTATCCAATGAGACTTGCTG +GGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCGATATCCAATGAGACTTGC +TGGATTTATCCCCGTATCCAATGAGACTTGCTGGATTTATCCCCATATCCAATGAGACTT +GCTGGGTTTAGCACCACAGATGCCAGTCACAGAGGAAATTGATGGCATGGCAGACAGCGT +GACATGTTGACTACCTGCCCTGGTCCTTGCAGATGGCATGGGCACAAAGGGGATGTGGGG +TGAAGAGTTGAAACGAGTGCC +>p:HG002_2_chr20:61289525-61290656 +TGTGTGGGTGCCCAGGGGCATGAGTGCCTGGGGAGTGTGACCACAGGCCAGTGGCAGTCC +CTGCCTTTGGATTAAAGAGCCCTTTGAGGCTTGCTTGGTGATGTCATGGAAAACAGCATA +TGACACCAAGATATCCCCATATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGA +GACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAAC +GAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCA +ACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATC +CAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTA +TCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCG +TATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCC +CGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATC +CCCGTATCCAATGAGACTTGCTGGGTTTATCCCGATATCCAATGAGACTTGCTGGATTTA +TCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTT +TATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCGATATCCAATGAGACTTGCTGGA +TTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTG +GGTTTATCCCGATATCCAATGAGACTTGCTGGATTTATCCCCGTATCCAATGAGACTTGC +TGGATTTATCCCCATATCCAATGAGACTTGCTGGGTTTAGCACCACAGATGCCAGTCACA +GAGGAAATTGATGGCATGGCAGACAGCGTGACATGTTGACTACCTGCCCTGGTCCTTGCA +GATGGCATGGGCACAAAGGGGATGTGGGGTGAAGAGTTGAAACGAGTGCC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/haps.fa.ref.fa new file mode 100644 index 00000000..465e0be7 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:61289525-61290656 +TGTGTGGGTGCCCAGGGGCATGAGTGCCTGGGGAGTGTGACCACAGGCCAGTGGCAGTCCCTGCCTTTGGATTAAAGAGCCCTTTGAGGCTTGCTTGGTGATGTCATGGAAAACAGCATATGACACCAAGATATCCCCATATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCGATATCCAATGAGACTTGCTGGATTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCGATATCCAATGAGACTTGCTGGATTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCGATATCCAATGAGACTTGCTGGATTTATCCCCGTATCCAATGAGACTTGCTGGATTTATCCCCATATCCAATGAGACTTGCTGGGTTTAGCACCACAGATGCCAGTCACAGAGGAAATTGATGGCATGGCAGACAGCGTGACATGTTGACTACCTGCCCTGGTCCTTGCAGATGGCATGGGCACAAAGGGGATGTGGGGTGAAGAGTTGAAACGAGTGCC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/msa.fa new file mode 100644 index 00000000..1bb4efcc --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/msa.fa @@ -0,0 +1,100 @@ +>ref_chr20_61289525_61290656 +tgtgtgggtgcccaggggcatgagtgcctggggagtgtgaccacaggccagtggcagtcc +ctgcctttggattaaagagccctttgaggcttgcttggtgatgtcatggaaaacagcata +tgacaccaagatatccccatatccaacgagacttgctgggtttatccccgtatccaacga +gacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaac +gagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatcca +acgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatc +caacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgta +tccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccg +tatccaacgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccc +cgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatc +cccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggttta +tccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtt +tatcccgatatccaatgagacttgctggatttatccccgtatccaatgagacttgctggg +tttatccccgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgctg +gatttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgc +tgggtttatcccgatatccaatgagacttgctggatttatccccgtatccaatgagactt +gctggatttatccccatatccaatgagacttgctgggtttagcaccacagatgccagtca +cagaggaaattgatggcatggcagacagcgtgacatgttgactacctgccctggtccttg +cagatggcatgggcacaaaggggatgtggggtgaagagttgaaacgagtgcc +>syndip_1_chr20:61289525-61290656 +tgtgtgggtgcccaggggcatgagtgcctggggagtgtgaccacaggccagtggcagtcc +ctgcctttggattaaagagccctttgaggcttgcttggtgatgtcatggaaaacagcata +tgacaccaagatatccccatatccaacgagacttgctgggtttatccccgtatccaacga +gacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaac +gagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatcca +acgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatc +caacgagacttgctgggtttatccccg-------------------------------ta +tccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccg +tatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccc +cgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatc +cccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggttta +tcccgatatccaatgagacttgctggatttatccccgtatccaatgagacttgctggg-- +-----------------------------tttatccccgtatccaatgagacttgctggg +tttatccccgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgctg +gatttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgc +tgggtttatcccgatatccaatgagacttgctggatttatccccgtatccaatgagactt +gctggatttatccccatatccaatgagacttgctgggtttagcaccacagatgccagtca +cagaggaaattgatggcatggcagacagcgtgacatgttgactacctgccctggtccttg +cagatggcatgggcacaaaggggatgtggggtgaagagttgaaacgagtgcc +>syndip_2_chr20:61289525-61290656 +tgtgtgggtgcccaggggcatgagtgcctggggagtgtgaccacaggccagtggcagtcc +ctgcctttggattaaagagccctttgaggcttgcttggtgatgtcatggaaaacagcata +tgacaccaagatatccccatatccaacgagacttgctgggtttatccccgtatccaacga +gacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaac +gagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatcca +acgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatc +caacgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatcccccta +tccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccg +tatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccc +cgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatc +cccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggttta +tccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctggg-- +-----------------------------tttatccccgtatccaatgagacttgctggg +tttatccccgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgctg +gatttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgc +tgggtttatcccgatatccaatgagacttgctggatttatccccgtatccaatgagactt +gctggatttatccccatatccaatgagacttgctgggtttagcaccacagatgccagtca +cagaggaaattgatggcatggcagacagcgtgacatgttgactacctgccctggtccttg +cagatggcatgggcacaaaggggatgtggggtgaagagttgaaacgagtgcc +>p:HG002_1_chr20:61289525-61290656 +tgtgtgggtgcccaggggcatgagtgcctggggagtgtgaccacaggccagtggcagtcc +ctgcctttggattaaagagccctttgaggcttgcttggtgatgtcatggaaaacagcata +tgacaccaagatatccccatatccaacgagacttgctgggtttatccccgtatccaacga +gacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaac +gagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatcca +acgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatc +caacgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatcccccta +tccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccg +tatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccc +cgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatc +cccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggttta +tccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctggg-- +-----------------------------tttatccccgtatccaatgagacttgctggg +tttatccccgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgctg +gatttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgc +tgggtttatcccgatatccaatgagacttgctggatttatccccgtatccaatgagactt +gctggatttatccccatatccaatgagacttgctgggtttagcaccacagatgccagtca +cagaggaaattgatggcatggcagacagcgtgacatgttgactacctgccctggtccttg +cagatggcatgggcacaaaggggatgtggggtgaagagttgaaacgagtgcc +>p:HG002_2_chr20:61289525-61290656 +tgtgtgggtgcccaggggcatgagtgcctggggagtgtgaccacaggccagtggcagtcc +ctgcctttggattaaagagccctttgaggcttgcttggtgatgtcatggaaaacagcata +tgacaccaagatatccccatatccaacgagacttgctgggtttatccccgtatccaacga +gacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaac +gagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatcca +acgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatc +caacgagacttgctgggtttatccccg-------------------------------ta +tccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccg +tatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccc +cgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatc +cccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggttta +tcccgatatccaatgagacttgctggatttatccccgtatccaatgagacttgctggg-- +-----------------------------tttatccccgtatccaatgagacttgctggg +tttatccccgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgctg +gatttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgc +tgggtttatcccgatatccaatgagacttgctggatttatccccgtatccaatgagactt +gctggatttatccccatatccaatgagacttgctgggtttagcaccacagatgccagtca +cagaggaaattgatggcatggcagacagcgtgacatgttgactacctgccctggtccttg +cagatggcatgggcacaaaggggatgtggggtgaagagttgaaacgagtgcc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/msa.fa.fai new file mode 100644 index 00000000..3a0771e2 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_61289525_61290656 1132 29 60 61 +syndip_1_chr20:61289525-61290656 1132 1214 60 61 +syndip_2_chr20:61289525-61290656 1132 2399 60 61 +p:HG002_1_chr20:61289525-61290656 1132 3585 60 61 +p:HG002_2_chr20:61289525-61290656 1132 4771 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/output.vcf.gz new file mode 100644 index 00000000..1b1a0d91 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/output.vcf.gz.tbi new file mode 100644 index 00000000..00e0502e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61289625-61290556/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/base.vcf.gz new file mode 100644 index 00000000..f1b34918 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/base.vcf.gz.tbi new file mode 100644 index 00000000..bb297398 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/comp.vcf.gz new file mode 100644 index 00000000..469d7977 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/comp.vcf.gz.tbi new file mode 100644 index 00000000..ad36831e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/haps.fa new file mode 100644 index 00000000..58b3b250 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/haps.fa @@ -0,0 +1,73 @@ +>ref_chr20_61329158_61329678 +TTTTGTACCATCATAAAGTCAAAAAATTGTAGTTCAGCTGTCATTTAAGTTGGAGACTGTCTGTACTTGACAGTTGATATGAAATATTCACATACGTTCTGCACTGGAATCCACTCTGCTCCAGTGTTTAAGCCCAGTGTGCTGCGGTGGATTGCAGCATGCGTGGAGGGCACCCAGGTCCTCATGGTTCCCTCGTGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTGCAGTGGATTGCAGCGTGCGTGGAGGGCACCCAGGTCCTCATGGTCCCCCGTGGGTCTGGGATGTGGGTTGAGGTGGCTGTGAGTGGCTCTTCTGCCCTTGGCTTCTGTATTTTATAATAAGAGAGGGCTCTTGCTCTCTCTCTCTCTCTCCTGCTTTGTACTTTCAATCAATCTCTTTCCAGCATAGTTCCCCCTAAAACATCAGAAAGCTGAGTGAGCCTGTGCTCTCCTCTCAGAGCTTAGCCACTTGGATTCCGCAGACCCTGGATTGTCACTTTAAA +>syndip_1_chr20:61329158-61329678 +TTTTGTACCATCATAAAGTCAAAAAATTGTAGTTCAGCTGTCATTTAAGTTGGAGACTGT +CTGTACTTGACAGTTGATATGAAATATTCACATACGTTCTGCACTGGAATCCACTCTGCT +CCAGTGTTTAAGCCCAGTGTGCTGCGGTGGATTGCAGCATGCGTGGAGGGCACCCAGGTC +CTCATGGTTCCCTCGTGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTG +CAGTGGATTGCAGCGTGCGTGGAGGGCACCCAGGTCCTCATGGTCCCCCGTGGGTCTGGG +ATGTGGGTTGAGGTGGCTGTGAGTGGCTCTTCTGCCCTTGGCTTCTGTATTTTATAATAA +GAGAGGGCTCTTGCTCTCTCTCTCTCTCTCCTGCTTTGTACTTTCAATCAATCTCTTTCC +AGCATAGTTCCCCCTAAAACATCAGAAAGCTGAGTGAGCCTGTGCTCTCCTCTCAGAGCT +TAGCCACTTGGATTCCGCAGACCCTGGATTGTCACTTTAAA +>syndip_2_chr20:61329158-61329678 +TTTTGTACCATCATAAAGTCAAAAAATTGTAGTTCAGCTGTCATTTAAGTTGGAGACTGT +CTGTACTTGACAGTTGATATGAAATATTCACATACGTTCTGCACTGGAATCCACTCTGCT +CCAGTGTTTAAGCCCAGTGTGCTGCGGTGGATTGCAGCATGCGTGGAGGGCACCCAGGTC +CTCATGGTTCCCTCGTGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTG +CAGTGGATTGCAGCGTGCGTGGAGGGCACCCAGGTCCTCATGGTCCCCCGTGGGTCTGGG +ATGTGGGTTGAGGTGGCTGTGAGTGGCTCTTCTGCCCTTGGCTTCTGTATTTTATAATAA +GAGAGGGCTCTTGCTCTCTCTCTCTCTCTCCTGCTTTGTACTTTCAATCAATCTCTTTCC +AGCATAGTTCCCCCTAAAACATCAGAAAGCTGAGTGAGCCTGTGCTCTCCTCTCAGAGCT +TAGCCACTTGGATTCCGCAGACCCTGGATTGTCACTTTAAA +>p:HG002_1_chr20:61329158-61329678 +TTTTGTACCATCATAAAGTCAAAAAATTGTAGTTCAGCTGTCATTTAAGTTGGAGACTGT +CTGTACTTGACAGTTGATATGAAATATTCACATACGTTCTGCACTGGAATCCACTCTGCT +CCAGTGTTTAAGCCCAGTGTGCTGCGGTGGATTGCAGCATGCGTGGAGGGCACCCAGGTC +CTCATGGTTCCCTCGTGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTG +CGGTGGATTGCAGCGTGCGTGGAGGGCACCCAGGTCCTCATGGTCCCCTCATGGGTCTGG +GACGCGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTGCGGTGGATTGCAGCATGCGTGGAG +GGCACCCAGGTCCTCATGGTCCCCTCATGGGTCTGGGACGTGGGTCGAGGTGGCTTTAAG +CCCAGTGTGCTGCAGTGGATTGCAGCATGCGTGGAGGGCACCCAGGTCCTCATGGTCCCC +TCGTGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTGCGGTGGATTGCA +GCGTGCGTGGAGGGCACCCAGGTCCTCATGGTCCCCTCGTGGGTCTGGGACGCGGGTCGA +GGTGGCTTTAAGCCTAGTGTGCTGCGGTGGATTGCAGCATGCGTGGAGGGCACCCAGGTC +CTCATGGTCCCCTCATGGGTCTGGGACGTGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTG +CGGTGGATTGCAGCATGCGTGGAGGGCACCCAGGTCCTCATGGTTGCCTCGTGGGTCTGG +GACGCGGGTCGAGGTGGCTTTAAGCCCACTGTGCTGCAGTGGATTGCAGCATGCGTGGAG +GGCACCCAGGTCCTCATGGTTCCCCCGTGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAG +CCCACTGTGCTGCGGTGGATTGCAGCATGCGTGGAGGGCACCCAGGTCCTCATGGTCCCC +CCGTGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTGCGGTGGATTGCA +GCATGCGTGGAGGGCACCCAGGTCCTCATGGTCCCCCCGTGGGTCTGGGACGCGGGTCGA +GGTGGCTTTAAGCCCAGTGTGCTGCAGTGGATTGCAGCATGCGTGGAGGGCACCCAGGTC +CTCATGGTTCCCTCGTGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTG +CGGTGGATTGCAGCGTGCGTGGAGGGCACCCAGATCCTCATGGTTCCCCCGTGGGTCTGG +GACGCGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTGCAGTGGATTGCAGCATGCGTGGAG +GGCACCCAGATCCTCATGTTTCCCCCACGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAG +CCCAGTGTGCTGCGGTGGATTGCAGCGTGCGTGGAGGGCACCCAGGTCCTCATGGTTCCC +TCGTGGGTCTGGGACGTGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTGCAGTGGATTGCA +GCGTGCGTGGAGGGCACCCAGGTCCTCATGGTCCCCTCGTGGGTCTGGGACGCGGGTCGA +GGTGGCTTTAAGCCCAGTGTGCTGCAGTGGATTGCAGCGTGCGTGGAGGGCACCCAGGTC +CTCATGGTCCCCCGTGGGTCTGGGATGTGGGTTGAGGTGGCTGTGAGTGGCTCTTCTGCC +CTTGGCTTCTGTATTTTATAATAAGAGAGGGCTCTTGCTCTCTCTCTCTCTCTCCTGCTT +TGTACTTTCAATCAATCTCTTTCCAGCATAGTTCCCCCTAAAACATCAGAAAGCTGAGTG +AGCCTGTGCTCTCCTCTCAGAGCTTAGCCACTTGGATTCCGCAGACCCTGGATTGTCACT +TTAAA +>p:HG002_2_chr20:61329158-61329678 +TTTTGTACCATCATAAAGTCAAAAAATTGTAGTTCAGCTGTCATTTAAGTTGGAGACTGT +CTGTACTTGACAGTTGATATGAAATATTCACATACGTTCTGCACTGGAATCCACTCTGCT +CCAGTGTTTAAGCCCAGTGTGCTGCGGTGGATTGCAGCATGCGTGGAGGGCACCCAGGTC +CTCATGGTTCCCCCGTGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTG +CGGTGGATTGCAGCATGCGTGGAGGGCACCCAGATCCTCATGGTTCCCCCGTGGGTCTGG +GACGCGGGTCGAGGTGGCTTTAAGCCCACTGTGCTGCGGTGGATTGCAGCATGCGTGGAG +GGCACCCAGGTCCTCATGGTTCCCCCACGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAG +CCCAGTGTGCTGCGGTGGATTGCAGCGTGCGTGGAGGGCACCCAGGTCCTCATGGTCCCC +CCGTGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTGCGGTGGATTGCA +GCATGCGTGGAGGGCACCCAGATCCTCATGGTCCCCCCGTGGGTCTGGGACGCGGGTCGA +GGTGGCTTTAAGCCCAGTGTGCTGCGGTGGATTGCAGCATGCGTGGAGGGCACCCAGGTC +CTCATGGTCCCCCCGTGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTG +CAGTGGATTGCAGCATGCGTGGAGGGCACCCAGGTCCTCATGGTCCCCCCGTGGGTCTGG +GATGTGGGTTGAGGTGGCTGTGAGTGGCTCTTCTGCCCTTGGCTTCTGTATTTTATAATA +AGAGAGGGCTCTTGCTCTCTCTCTCTCTCTCCTGCTTTGTACTTTCAATCAATCTCTTTC +CAGCATAGTTCCCCCTAAAACATCAGAAAGCTGAGTGAGCCTGTGCTCTCCTCTCAGAGC +TTAGCCACTTGGATTCCGCAGACCCTGGATTGTCACTTTAAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/haps.fa.ref.fa new file mode 100644 index 00000000..b7b1f116 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:61329158-61329678 +TTTTGTACCATCATAAAGTCAAAAAATTGTAGTTCAGCTGTCATTTAAGTTGGAGACTGTCTGTACTTGACAGTTGATATGAAATATTCACATACGTTCTGCACTGGAATCCACTCTGCTCCAGTGTTTAAGCCCAGTGTGCTGCGGTGGATTGCAGCATGCGTGGAGGGCACCCAGGTCCTCATGGTTCCCTCGTGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTGCAGTGGATTGCAGCGTGCGTGGAGGGCACCCAGGTCCTCATGGTCCCCCGTGGGTCTGGGATGTGGGTTGAGGTGGCTGTGAGTGGCTCTTCTGCCCTTGGCTTCTGTATTTTATAATAAGAGAGGGCTCTTGCTCTCTCTCTCTCTCTCCTGCTTTGTACTTTCAATCAATCTCTTTCCAGCATAGTTCCCCCTAAAACATCAGAAAGCTGAGTGAGCCTGTGCTCTCCTCTCAGAGCTTAGCCACTTGGATTCCGCAGACCCTGGATTGTCACTTTAAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/msa.fa new file mode 100644 index 00000000..51a3634e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/msa.fa @@ -0,0 +1,165 @@ +>ref_chr20_61329158_61329678 +ttttgtaccatcataaagtcaaaaaattgtagttcagctgtcatttaagttggagactgt +ctgtacttgacagttgatatgaaatattcacatacgttctgcactggaatccactctgct +ccagtg------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------tttaagcccagtgtgctgcggtggattgca +gcatgcgtggagggcacccaggtcctcatggttccctcgtgggtctgggacgcgggtcga +ggtggctttaagcccagtgtgctgcagtggattgcagcgtgcgtggagggcacccaggtc +ctcatggt-cccccgtgggtctgggatgtgggttgaggtggctgtgagtggctcttctgc +ccttggcttctgtattttataataagagagggctcttgctctctctctctctctcctgct +ttgtactttcaatcaatctctttccagcatagttccccctaaaacatcagaaagctgagt +gagcctgtgctctcctctcagagcttagccacttggattccgcagaccctggattgtcac +tttaaa +>syndip_1_chr20:61329158-61329678 +ttttgtaccatcataaagtcaaaaaattgtagttcagctgtcatttaagttggagactgt +ctgtacttgacagttgatatgaaatattcacatacgttctgcactggaatccactctgct +ccagtg------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------tttaagcccagtgtgctgcggtggattgca +gcatgcgtggagggcacccaggtcctcatggttccctcgtgggtctgggacgcgggtcga +ggtggctttaagcccagtgtgctgcagtggattgcagcgtgcgtggagggcacccaggtc +ctcatggt-cccccgtgggtctgggatgtgggttgaggtggctgtgagtggctcttctgc +ccttggcttctgtattttataataagagagggctcttgctctctctctctctctcctgct +ttgtactttcaatcaatctctttccagcatagttccccctaaaacatcagaaagctgagt +gagcctgtgctctcctctcagagcttagccacttggattccgcagaccctggattgtcac +tttaaa +>syndip_2_chr20:61329158-61329678 +ttttgtaccatcataaagtcaaaaaattgtagttcagctgtcatttaagttggagactgt +ctgtacttgacagttgatatgaaatattcacatacgttctgcactggaatccactctgct +ccagtg------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------tttaagcccagtgtgctgcggtggattgca +gcatgcgtggagggcacccaggtcctcatggttccctcgtgggtctgggacgcgggtcga +ggtggctttaagcccagtgtgctgcagtggattgcagcgtgcgtggagggcacccaggtc +ctcatggt-cccccgtgggtctgggatgtgggttgaggtggctgtgagtggctcttctgc +ccttggcttctgtattttataataagagagggctcttgctctctctctctctctcctgct +ttgtactttcaatcaatctctttccagcatagttccccctaaaacatcagaaagctgagt +gagcctgtgctctcctctcagagcttagccacttggattccgcagaccctggattgtcac +tttaaa +>p:HG002_1_chr20:61329158-61329678 +ttttgtaccatcataaagtcaaaaaattgtagttcagctgtcatttaagttggagactgt +ctgtacttgacagttgatatgaaatattcacatacgttctgcactggaatccactctgct +ccagtgtttaagcccagtgtgctgcggtggattgcagcatgcgtggagggcacccaggtc +ctcatggttccctcgtgggtctgggacgcgggtcgaggtggctttaagcccagtgtgctg +cggtggattgcagcgtgcgtggagggcacccaggtcctcatggtcccctcatgggtctgg +gacgcgggtcgaggtggctttaagcccagtgtgctgcggtggattgcagcatgcgtggag +ggcacccaggtcctcatggtcccctcatgggtctgggacgtgggtcgaggtggctttaag +cccagtgtgctgcagtggattgcagcatgcgtggagggcacccaggtcctcatggtcccc +tcgtgggtctgggacgcgggtcgaggtggctttaagcccagtgtgctgcggtggattgca +gcgtgcgtggagggcacccaggtcctcatggtcccctcgtgggtctgggacgcgggtcga +ggtggctttaagcctagtgtgctgcggtggattgcagcatgcgtggagggcacccaggtc +ctcatggtcccctcatgggtctgggacgtgggtcgaggtggctttaagcccagtgtgctg +cggtggattgcagcatgcgtggagggcacccaggtcctcatggttgcctcgtgggtctgg +gacgcgggtcgaggtggctttaagcccactgtgctgcagtggattgcagcatgcgtggag +ggcacccaggtcctcatggttcccccgtgggtctgggacgcgggtcgaggtggctttaag +cccactgtgctgcggtggattgcagcatgcgtggagggcacccaggtcctcatggtcccc +ccgtgggtctgggacgcgggtcgaggtggctttaagcccagtgtgctgcggtggattgca +gcatgcgtggagggcacccaggtcctcatggtccccccgtgggtctgggacgcgggtcga +ggtggctttaagcccagtgtgctgcagtggattgcagcatgcgtggagggcacccaggtc +ctcatggttccctcgtgggtctgggacgcgggtcgaggtggctttaagcccagtgtgctg +cggtggattgcagcgtgcgtggagggcacccagatcctcatggttcccccgtgggtctgg +gacgcgggtcgaggtggctttaagcccagtgtgctgcagtggattgcagcatgcgtggag +ggcacccagatcctcatgtttcccccacgggtctgggacgcgggtcgaggtggctttaag +cccagtgtgctgcggtggattgcagcgtgcgtggagggcacccaggtcctcatggttccc +tcgtgggtctgggacgtgggtcgaggtggctttaagcccagtgtgctgcagtggattgca +gcgtgcgtggagggcacccaggtcctcatggtcccctcgtgggtctgggacgcgggtcga +ggtggctttaagcccagtgtgctgcagtggattgcagcgtgcgtggagggcacccaggtc +ctcatggt-cccccgtgggtctgggatgtgggttgaggtggctgtgagtggctcttctgc +ccttggcttctgtattttataataagagagggctcttgctctctctctctctctcctgct +ttgtactttcaatcaatctctttccagcatagttccccctaaaacatcagaaagctgagt +gagcctgtgctctcctctcagagcttagccacttggattccgcagaccctggattgtcac +tttaaa +>p:HG002_2_chr20:61329158-61329678 +ttttgtaccatcataaagtcaaaaaattgtagttcagctgtcatttaagttggagactgt +ctgtacttgacagttgatatgaaatattcacatacgttctgcactggaatccactctgct +ccagtg------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------tttaagcccagtgtgctgcggtggattgca +gcatgcgtggagggcacccaggtcctcatggttcccccgtgggtctgggacgcgggtcga +ggtggctttaagcccagtgtgctgcggtggattgcagcatgcgtggagggcacccagatc +ctcatggttcccccgtgggtctgggacgcgggtcgaggtggctttaagcccactgtgctg +cggtggattgcagcatgcgtggagggcacccaggtcctcatggttcccccacgggtctgg +gacgcgggtcgaggtggctttaagcccagtgtgctgcggtggattgcagcgtgcgtggag +ggcacccaggtcctcatggtccccccgtgggtctgggacgcgggtcgaggtggctttaag +cccagtgtgctgcggtggattgcagcatgcgtggagggcacccagatcctcatggtcccc +ccgtgggtctgggacgcgggtcgaggtggctttaagcccagtgtgctgcggtggattgca +gcatgcgtggagggcacccaggtcctcatggtccccccgtgggtctgggacgcgggtcga +ggtggctttaagcccagtgtgctgcagtggattgcagcatgcgtggagggcacccaggtc +ctcatggtccccccgtgggtctgggatgtgggttgaggtggctgtgagtggctcttctgc +ccttggcttctgtattttataataagagagggctcttgctctctctctctctctcctgct +ttgtactttcaatcaatctctttccagcatagttccccctaaaacatcagaaagctgagt +gagcctgtgctctcctctcagagcttagccacttggattccgcagaccctggattgtcac +tttaaa diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/msa.fa.fai new file mode 100644 index 00000000..bb2b617f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_61329158_61329678 1866 29 60 61 +syndip_1_chr20:61329158-61329678 1866 1961 60 61 +syndip_2_chr20:61329158-61329678 1866 3893 60 61 +p:HG002_1_chr20:61329158-61329678 1866 5826 60 61 +p:HG002_2_chr20:61329158-61329678 1866 7759 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/output.vcf.gz new file mode 100644 index 00000000..22586098 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/output.vcf.gz.tbi new file mode 100644 index 00000000..d8f459e7 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61329258-61329578/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/base.vcf.gz new file mode 100644 index 00000000..41251945 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/base.vcf.gz.tbi new file mode 100644 index 00000000..77c539dc Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/comp.vcf.gz new file mode 100644 index 00000000..6fd65b4e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/comp.vcf.gz.tbi new file mode 100644 index 00000000..41cba013 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/haps.fa new file mode 100644 index 00000000..e3028fce --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/haps.fa @@ -0,0 +1,66 @@ +>ref_chr20_61561820_61562604 +ACAACCCACAAAGGTTTATAGCTCCTTTCCTGTGCTGAAGAGCTGGCCCTTCTCTGGGCCCCAGTGGCTGCATGCGCCATGTTTCTGGGCAGTGACCATATGATGGCAGTAATGCTGTGTCTGGAAATCCTGACCCCAGGGCTCCCAGAGAGAGAGAGGGACCTTCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGGCCTTCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGGCCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGGGACCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCCTGTGGAGAGGTGGACCCCAGGGCTCCCAGAGAGAGAGAGGGACCTTCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGGGACCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCTGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGGGGGACCTTCGTGTGGAGAGGTGGACCCCAGGACTCCCGGAGAGAGAGAGGGGCCTCCGTGTGCAGAGGTGGTTTGTCGCTTCTTTCATCTTCAGGACAGTCATTGCCTGGGAAACTGGGGGGATTGGTCCGAACCCACCTTGTACACCCCAGACTTGGTGCGTCCCTGCAGGATCTGAGCACAGAACGGCCTGCTTCAGCCC +>syndip_1_chr20:61561820-61562604 +ACAACCCACAAAGGTTTATAGCTCCTTTCCTGTGCTGAAGAGCTGGCCCTTCTCTGGGCC +CCAGTGGCTGCATGCGCCATGTTTCTGGGCAGTGACCATATGATGGCAGTAATGCTGTGT +CTGGAAATCCTGACCCCAGGGCTCCCAGAGAGAGAGAGGGACCTTCGTGTGGAGAGGTGG +ACCCCAGGGCTCCCGGAGAGAGAGAGGGGCCTTCGTGTGGAGAGGTGGACCCCAGGGCTC +CCGGAGAGAGAGAGGGGCCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGGG +ACTTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCCTGAGA +GAGAGAGGGACCTCCCTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACC +TCCCTGTGGAGAGGTGGACCCCAGGGCTCCCAGAGAGAGAGAGGGACCTTCGTGTGGAGA +GGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCGTGTGGAGAGGTGGACCCCAG +GGCTCCCGGAGAGAGAGAGGGACCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGA +GAGGGACCTCCGTGTGGAGAGCTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCG +TGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCGTGTGGAGAGGTG +GACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTTCGTGTGGAGAGGTGGACCCCAGGACT +CCCGGAGAGAGAGAGGGGCCTCCGTGTGCAGAGGTGGTTTGTCGCTTCTTTCATCTTCAG +GACAGTCATTGCCTGGGAAACTGGGGGGATTGGTCCGAACCCACCTTGTACACCCCAGAC +TTGGTGCGTCCCTGCAGGATCTGAGCACAGAACGGCCTGCTTCAGCCC +>syndip_2_chr20:61561820-61562604 +ACAACCCACAAAGGTTTATAGCTCCTTTCCTGTGCTGAAGAGCTGGCCCTTCTCTGGGCC +CCAGTGGCTGCATGCGCCATGTTTCTGGGCAGTGACCATATGATGGCAGTAATGCTGTGT +CTGGAAATCCTGACCCCAGGGCTCCCAGAGAGAGAGAGGGACCTTCGTGTGGAGAGGTGG +ACCCCAGGGCTCCCGGAGAGAGAGAGGGGCCTTCGTGTGGAGAGGTGGACCCCAGGGCTC +CCGGAGAGAGAGAGGGGCCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGGG +ACCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCCTGTGG +AGAGGTGGACCCCAGGGCTCCCAGAGAGAGAGAGGGACCTTCGTGTGGAGAGGTGGACCC +CAGGGCTCCCGGAGAGAGAGGGACCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAG +AGAGAGAGGGACCTCTGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGAC +CTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGGGGGACCTTCGTGTGGAG +AGGTGGACCCCAGGACTCCCGGAGAGAGAGAGGGGCCTCCGTGTGCAGAGGTGGTTTGTC +GCTTCTTTCATCTTCAGGACAGTCATTGCCTGGGAAACTGGGGGGATTGGTCCGAACCCA +CCTTGTACACCCCAGACTTGGTGCGTCCCTGCAGGATCTGAGCACAGAACGGCCTGCTTC +AGCCC +>p:HG002_1_chr20:61561820-61562604 +ACAACCCACAAAGGTTTATAGCTCCTTTCCTGTGCTGAAGAGCTGGCCCTTCTCTGGGCC +CCAGTGGCTGCATGCGCCATGTTTCTGGGCAGTGACCATATGATGGCAGTAATGCTGTGT +CTGGAAATCCTGACCCCAGGGCTCCCAGAGAGAGAGAGGGACCTTCGTGTGGAGAGGTGG +ACCCCAGGGCTCCCGGAGAGAGAGAGGGGCCTTCGTGTGGAGAGGTGGACCCCAGGGCTC +CCGGAGAGAGAGAGGGGCCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGGG +ACCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCCTGTGG +AGAGGTGGACCCCAGGGCTCCCAGAGAGAGAGAGGGACCTTCGTGTGGAGAGGTGGACCC +CAGGGCTCCCGGAGAGAGAGGGACCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAG +AGAGAGAGGGACCTCTGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGAC +CTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGGGGGACCTTCGTGTGGAG +AGGTGGACCCCAGGACTCCCGGAGAGAGAGAGGGGCCTCCGTGTGCAGAGGTGGTTTGTC +GCTTCTTTCATCTTCAGGACAGTCATTGCCTGGGAAACTGGGGGGATTGGTCCGAACCCA +CCTTGTACACCCCAGACTTGGTGCGTCCCTGCAGGATCTGAGCACAGAACGGCCTGCTTC +AGCCC +>p:HG002_2_chr20:61561820-61562604 +ACAACCCACAAAGGTTTATAGCTCCTTTCCTGTGCTGAAGAGCTGGCCCTTCTCTGGGCC +CCAGTGGCTGCATGCGCCATGTTTCTGGGCAGTGACCATATGATGGCAGTAATGCTGTGT +CTGGAAATCCTGACCCCAGGGCTCCCAGAGAGAGAGAGGGACCTTCGTGTGGAGAGGTGG +ACCCCAGGGCTCCCGGAGAGAGAGAGGGGCCTTCGTGTGGAGAGGTGGACCCCAGGGCTC +CCGGAGAGAGAGAGGGGCCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGGG +ACTTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCCTGAGA +GAGAGAGGGACCTCCCTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACC +TCCCTGTGGAGAGGTGGACCCCAGGGCTCCCAGAGAGAGAGAGGGACCTTCGTGTGGAGA +GGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCGTGTGGAGAGGTGGACCCCAG +GGCTCCCGGAGAGAGAGAGGGACCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGA +GAGGGACCTCCGTGTGGAGAGCTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCG +TGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCGTGTGGAGAGGTG +GACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTTCGTGTGGAGAGGTGGACCCCAGGACT +CCCGGAGAGAGAGAGGGGCCTCCGTGTGCAGAGGTGGTTTGTCGCTTCTTTCATCTTCAG +GACAGTCATTGCCTGGGAAACTGGGGGGATTGGTCCGAACCCACCTTGTACACCCCAGAC +TTGGTGCGTCCCTGCAGGATCTGAGCACAGAACGGCCTGCTTCAGCCC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/haps.fa.ref.fa new file mode 100644 index 00000000..a158b66a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:61561820-61562604 +ACAACCCACAAAGGTTTATAGCTCCTTTCCTGTGCTGAAGAGCTGGCCCTTCTCTGGGCCCCAGTGGCTGCATGCGCCATGTTTCTGGGCAGTGACCATATGATGGCAGTAATGCTGTGTCTGGAAATCCTGACCCCAGGGCTCCCAGAGAGAGAGAGGGACCTTCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGGCCTTCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGGCCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGGGACCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCCTGTGGAGAGGTGGACCCCAGGGCTCCCAGAGAGAGAGAGGGACCTTCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGGGACCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCTGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGGGGGACCTTCGTGTGGAGAGGTGGACCCCAGGACTCCCGGAGAGAGAGAGGGGCCTCCGTGTGCAGAGGTGGTTTGTCGCTTCTTTCATCTTCAGGACAGTCATTGCCTGGGAAACTGGGGGGATTGGTCCGAACCCACCTTGTACACCCCAGACTTGGTGCGTCCCTGCAGGATCTGAGCACAGAACGGCCTGCTTCAGCCC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/msa.fa new file mode 100644 index 00000000..c5b871c8 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/msa.fa @@ -0,0 +1,85 @@ +>ref_chr20_61561820_61562604 +acaacccacaaaggtttatagctcctttcctgtgctgaagagctggcccttctctgggcc +ccagtggctgcatgcgccatgtttctgggcagtgaccatatgatggcagtaatgctgtgt +ctggaaatcctgaccccagggctcccagagagagagagggaccttcgtgtggagaggtgg +accccagggctcccggagagagagaggggccttcgtgtggagaggtggaccccagggctc +ccggagagagagaggggcctccgtgtggagaggtggaccccagggctcccggagagaggg +acctccg----------------------------------------------------- +----------------tgtggagaggtggaccccagggctcccggagagagagagggacc +tccctgtggagaggtggaccccagggctcccagagagagagagggaccttcgtgtggaga +ggtggaccccagggctcccgga-------------------------------------- +--------------------------------------------------------gaga +gagggacctccgtgtggagaggtggaccccagggctcccggagagagagagggacctctg +tgtggagaggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtg +gaccccagggctcccggagagagagggggaccttcgtgtggagaggtggaccccaggact +cccggagagagagaggggcctccgtgtgcagaggtggtttgtcgcttctttcatcttcag +gacagtcattgcctgggaaactggggggattggtccgaacccaccttgtacaccccagac +ttggtgcgtccctgcaggatctgagcacagaacggcctgcttcagccc +>syndip_1_chr20:61561820-61562604 +acaacccacaaaggtttatagctcctttcctgtgctgaagagctggcccttctctgggcc +ccagtggctgcatgcgccatgtttctgggcagtgaccatatgatggcagtaatgctgtgt +ctggaaatcctgaccccagggctcccagagagagagagggaccttcgtgtggagaggtgg +accccagggctcccggagagagagaggggccttcgtgtggagaggtggaccccagggctc +ccggagagagagaggggcctccgtgtggagaggtggaccccagggctcccggagagaggg +acttccgtgtggagaggtggaccccagggctcccggagagagagagggacctccctgaga +gagagagggacctccctgtggagaggtggaccccagggctcccggagagagagagggacc +tccctgtggagaggtggaccccagggctcccagagagagagagggaccttcgtgtggaga +ggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtggaccccag +ggctcccggagagagagagggacctccgtgtggagaggtggaccccagggctcccggaga +gagggacctccgtgtggagagctggaccccagggctcccggagagagagagggacctccg +tgtggagaggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtg +gaccccagggctcccggagagagagagggaccttcgtgtggagaggtggaccccaggact +cccggagagagagaggggcctccgtgtgcagaggtggtttgtcgcttctttcatcttcag +gacagtcattgcctgggaaactggggggattggtccgaacccaccttgtacaccccagac +ttggtgcgtccctgcaggatctgagcacagaacggcctgcttcagccc +>syndip_2_chr20:61561820-61562604 +acaacccacaaaggtttatagctcctttcctgtgctgaagagctggcccttctctgggcc +ccagtggctgcatgcgccatgtttctgggcagtgaccatatgatggcagtaatgctgtgt +ctggaaatcctgaccccagggctcccagagagagagagggaccttcgtgtggagaggtgg +accccagggctcccggagagagagaggggccttcgtgtggagaggtggaccccagggctc +ccggagagagagaggggcctccgtgtggagaggtggaccccagggctcccggagagaggg +acctccg----------------------------------------------------- +----------------tgtggagaggtggaccccagggctcccggagagagagagggacc +tccctgtggagaggtggaccccagggctcccagagagagagagggaccttcgtgtggaga +ggtggaccccagggctcccgga-------------------------------------- +--------------------------------------------------------gaga +gagggacctccgtgtggagaggtggaccccagggctcccggagagagagagggacctctg +tgtggagaggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtg +gaccccagggctcccggagagagagggggaccttcgtgtggagaggtggaccccaggact +cccggagagagagaggggcctccgtgtgcagaggtggtttgtcgcttctttcatcttcag +gacagtcattgcctgggaaactggggggattggtccgaacccaccttgtacaccccagac +ttggtgcgtccctgcaggatctgagcacagaacggcctgcttcagccc +>p:HG002_1_chr20:61561820-61562604 +acaacccacaaaggtttatagctcctttcctgtgctgaagagctggcccttctctgggcc +ccagtggctgcatgcgccatgtttctgggcagtgaccatatgatggcagtaatgctgtgt +ctggaaatcctgaccccagggctcccagagagagagagggaccttcgtgtggagaggtgg +accccagggctcccggagagagagaggggccttcgtgtggagaggtggaccccagggctc +ccggagagagagaggggcctccgtgtggagaggtggaccccagggctcccggagagaggg +acctccg----------------------------------------------------- +----------------tgtggagaggtggaccccagggctcccggagagagagagggacc +tccctgtggagaggtggaccccagggctcccagagagagagagggaccttcgtgtggaga +ggtggaccccagggctcccgga-------------------------------------- +--------------------------------------------------------gaga +gagggacctccgtgtggagaggtggaccccagggctcccggagagagagagggacctctg +tgtggagaggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtg +gaccccagggctcccggagagagagggggaccttcgtgtggagaggtggaccccaggact +cccggagagagagaggggcctccgtgtgcagaggtggtttgtcgcttctttcatcttcag +gacagtcattgcctgggaaactggggggattggtccgaacccaccttgtacaccccagac +ttggtgcgtccctgcaggatctgagcacagaacggcctgcttcagccc +>p:HG002_2_chr20:61561820-61562604 +acaacccacaaaggtttatagctcctttcctgtgctgaagagctggcccttctctgggcc +ccagtggctgcatgcgccatgtttctgggcagtgaccatatgatggcagtaatgctgtgt +ctggaaatcctgaccccagggctcccagagagagagagggaccttcgtgtggagaggtgg +accccagggctcccggagagagagaggggccttcgtgtggagaggtggaccccagggctc +ccggagagagagaggggcctccgtgtggagaggtggaccccagggctcccggagagaggg +acttccgtgtggagaggtggaccccagggctcccggagagagagagggacctccctgaga +gagagagggacctccctgtggagaggtggaccccagggctcccggagagagagagggacc +tccctgtggagaggtggaccccagggctcccagagagagagagggaccttcgtgtggaga +ggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtggaccccag +ggctcccggagagagagagggacctccgtgtggagaggtggaccccagggctcccggaga +gagggacctccgtgtggagagctggaccccagggctcccggagagagagagggacctccg +tgtggagaggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtg +gaccccagggctcccggagagagagagggaccttcgtgtggagaggtggaccccaggact +cccggagagagagaggggcctccgtgtgcagaggtggtttgtcgcttctttcatcttcag +gacagtcattgcctgggaaactggggggattggtccgaacccaccttgtacaccccagac +ttggtgcgtccctgcaggatctgagcacagaacggcctgcttcagccc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/msa.fa.fai new file mode 100644 index 00000000..c6059a5b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_61561820_61562604 948 29 60 61 +syndip_1_chr20:61561820-61562604 948 1027 60 61 +syndip_2_chr20:61561820-61562604 948 2025 60 61 +p:HG002_1_chr20:61561820-61562604 948 3024 60 61 +p:HG002_2_chr20:61561820-61562604 948 4023 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/output.vcf.gz new file mode 100644 index 00000000..ce1dd1a4 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/output.vcf.gz.tbi new file mode 100644 index 00000000..91ed720e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61561920-61562504/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/base.vcf.gz new file mode 100644 index 00000000..d7ab8246 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/base.vcf.gz.tbi new file mode 100644 index 00000000..e786a6e9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/comp.vcf.gz new file mode 100644 index 00000000..e0e42b8c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/comp.vcf.gz.tbi new file mode 100644 index 00000000..5cf8d26d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/haps.fa new file mode 100644 index 00000000..82ed0b4f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/haps.fa @@ -0,0 +1,44 @@ +>ref_chr20_61744088_61744755 +TCAAACTGGGCACTGCAAATTCTGGAATCTCTCCTACCTCCCGAAGTTTGTAGTCCACCAGGCCCAGGGCGTTCTGAAGCCTGGAGGGATGAGAAGCAAGCGGAGACTGTGTGGTTGGAAAGGAGCCAACCAGAGAGTGGGGAGGCGATGGAGAGAATAACAGAGAGGAAGGCAGGTGCAGGGAGACAGCAAAGGAGAGGGAGAAGAGAATGAGAGAGGGATGGGGAGAAAGAGAGAAGAGAGGTGGAGAGAGACAGGAAAGGAGAGGGAGGGAGAGGAAGAGAGGGAGAGAGAGAAGGAGGGAGAGAGATGGAAAGAGGTGGAGGGAGAGAGAGAAGGAAAGGGAGGGAGAGGAAGAGAGGGAGAGAGAGAAGGAGGGAGAGAGATGGAGAGAGGTGGAGGGAGAGAGAGAAGGAAAGGGAGGGGAGAGGAAGAGAGGGAGAGAGAGAAGGAGGGAGAGAGATGGAGAGAGGTGGAGGGAGAGAGAGAAGGAAAGGGAGGGAGAGAGAGAGACAGACAGACAGCTTCACACAGACATAAAACATCTGCTGTTCAGGATCCCAGCTGCCCTCCGACTCTGCCTCCTTCTAACCCGGCTGCCTGGCTCACCCGGGTGACAGGGAGGGGCGCCTTCACCATGCCCTGTCCTGAGGCTCCCTTTCATCCTG +>syndip_1_chr20:61744088-61744755 +TCAAACTGGGCACTGCAAATTCTGGAATCTCTCCTACCTCCCGAAGTTTGTAGTCCACCA +GGCCCAGGGCGTTCTGAAGCCTGGAGGGATGAGAAGCAAGCGGAGACTGTGTGGTTGGAA +AGGAGCCAACCAGAGAGTGGGGAGGCGATGGAGAGAATAACAGAGAGGAAGGCAGGTGCA +GGGAGACAGCAAAGGAGAGGGAGAAGAGAATGAGAGAGGGATGGGGAGAAAGAGAGAAGA +GAGGTGGAGAGAGACAGGAAAGGAGAGGGAGGGAGAGGAAGAGAGGGAGAGAGAGAAGGA +GGGAGAGAGATGGAAAGAGGTGGAGGGAGAGAGAGAAGGAAAGGGAGGGAGAGAGAGAGA +CAGACAGACAGCTTCACACAGACATAAAACATCTGCTGTTCAGGATCCCAGCTGCCCTCC +GACTCTGCCTCCTTCTAACCCGGCTGCCTGGCTCACCCGGGTGACAGGGAGGGGCGCCTT +CACCATGCCCTGTCCTGAGGCTCCCTTTCATCCTG +>syndip_2_chr20:61744088-61744755 +TCAAACTGGGCACTGCAAATTCTGGAATCTCTCCTACCTCCCGAAGTTTGTAGTCCACCA +GGCCCAGGGCGTTCTGAAGCCTGGAGGGATGAGAAGCAAGCGGAGACTGTGTGGTTGGAA +AGGAGCCAACCAGAGAGTGGGGAGGCGATGGAGAGAATAAGAGAGAGGAAGGCAGGTGCA +GGGAGACAGCAAAGGAGAGGGAGAAGAGAATGAGAGAGGGATGGGGAGAAAGAGAGAAGA +GAGGTGGAGAGAGACAGGAAAGGAGAGGGAGGGAGAGGAAGAGAGGGAGAGAGAGAAGGA +GGGAGAGAGATGGAAAGAGGTGGAGGGAGAGAGAGAAGGAAAGGGAGGGAGAGGAAGAGA +GGGAGAGAGAGAAGGAGGGAGAGAGATGGAGAGAGGTGGAGGGAGAGAGAGAAGGAAAGG +GAGGGAGAGAGAGAGACAGACAGCTTCACACAGACATAAAACATCTGCTGTTCAGGATCC +CAGCTGCCCTCCGACTCTGCCTCCTTCTAACCCGGCTGCCTGGCTCACCCGGGTGACAGG +GAGGGGCGCCTTCACCATGCCCTGTCCTGAGGCTCCCTTTCATCCTG +>p:HG002_1_chr20:61744088-61744755 +TCAAACTGGGCACTGCAAATTCTGGAATCTCTCCTACCTCCCGAAGTTTGTAGTCCACCA +GGCCCAGGGCGTTCTGAAGCCTGGAGGGATGAGAAGCAAGCGGAGACTGTGTGGTTGGAA +AGGAGCCAACCAGAGAGTGGGGAGGCGATGGAGAGAATAAGAGAGAGGAAGGCAGGTGCA +GGGAGACAGCAAAGGAGAGGGAGAAGAGAATGAGAGAGGGATGGGGAGAAAGAGAGAAGA +GAGGTGGAGAGAGACAGGAAAGGAGAGGGAGGGAGAGGAAGAGAGGGAGAGAGAGAAGGA +GGGAGAGAGATGGAAAGAGGTGGAGGGAGAGAGAGAAGGAAAGGGAGGGAGAGGAAGAGA +GGGAGAGAGAGAAGGAGGGAGAGAGATGGAGAGAGGTGGAGGGAGAGAGAGAAGGAAAGG +GAGGGAGAGAGAGAGACAGACAGCTTCACACAGACATAAAACATCTGCTGTTCAGGATCC +CAGCTGCCCTCCGACTCTGCCTCCTTCTAACCCGGCTGCCTGGCTCACCCGGGTGACAGG +GAGGGGCGCCTTCACCATGCCCTGTCCTGAGGCTCCCTTTCATCCTG +>p:HG002_2_chr20:61744088-61744755 +TCAAACTGGGCACTGCAAATTCTGGAATCTCTCCTACCTCCCGAAGTTTGTAGTCCACCA +GGCCCAGGGCGTTCTGAAGCCTGGAGGGATGAGAAGCAAGCGGAGACTGTGTGGTTGGAA +AGGAGCCAACCAGAGAGTGGGGAGGCGATGGAGAGAATAACAGAGAGGAAGGCAGGTGCA +GGGAGACAGCAAAGGAGAGGGAGAAGAGAATGAGAGAGGGATGGGGAGAAAGAGAGAAGA +GAGGTGGAGAGAGACAGGAAAGGAGAGGGAGGGAGAGGAAGAGAGGGAGAGAGAGAAGGA +GGGAGAGAGATGGAAAGAGGTGGAGGGAGAGAGAGAAGGAAAGGGAGGGAGAGAGAGAGA +CAGACAGACAGCTTCACACAGACATAAAACATCTGCTGTTCAGGATCCCAGCTGCCCTCC +GACTCTGCCTCCTTCTAACCCGGCTGCCTGGCTCACCCGGGTGACAGGGAGGGGCGCCTT +CACCATGCCCTGTCCTGAGGCTCCCTTTCATCCTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/haps.fa.ref.fa new file mode 100644 index 00000000..ba684156 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:61744088-61744755 +TCAAACTGGGCACTGCAAATTCTGGAATCTCTCCTACCTCCCGAAGTTTGTAGTCCACCAGGCCCAGGGCGTTCTGAAGCCTGGAGGGATGAGAAGCAAGCGGAGACTGTGTGGTTGGAAAGGAGCCAACCAGAGAGTGGGGAGGCGATGGAGAGAATAACAGAGAGGAAGGCAGGTGCAGGGAGACAGCAAAGGAGAGGGAGAAGAGAATGAGAGAGGGATGGGGAGAAAGAGAGAAGAGAGGTGGAGAGAGACAGGAAAGGAGAGGGAGGGAGAGGAAGAGAGGGAGAGAGAGAAGGAGGGAGAGAGATGGAAAGAGGTGGAGGGAGAGAGAGAAGGAAAGGGAGGGAGAGGAAGAGAGGGAGAGAGAGAAGGAGGGAGAGAGATGGAGAGAGGTGGAGGGAGAGAGAGAAGGAAAGGGAGGGGAGAGGAAGAGAGGGAGAGAGAGAAGGAGGGAGAGAGATGGAGAGAGGTGGAGGGAGAGAGAGAAGGAAAGGGAGGGAGAGAGAGAGACAGACAGACAGCTTCACACAGACATAAAACATCTGCTGTTCAGGATCCCAGCTGCCCTCCGACTCTGCCTCCTTCTAACCCGGCTGCCTGGCTCACCCGGGTGACAGGGAGGGGCGCCTTCACCATGCCCTGTCCTGAGGCTCCCTTTCATCCTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/msa.fa new file mode 100644 index 00000000..d574e4be --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/msa.fa @@ -0,0 +1,65 @@ +>ref_chr20_61744088_61744755 +tcaaactgggcactgcaaattctggaatctctcctacctcccgaagtttgtagtccacca +ggcccagggcgttctgaagcctggagggatgagaagcaagcggagactgtgtggttggaa +aggagccaaccagagagtggggaggcgatggagagaataacagagaggaaggcaggtgca +gggagacagcaaaggagagggagaagagaatgagagagggatggggagaaagagagaaga +gaggtggagagagacaggaaaggagagggagggagaggaagagagggagagagagaagga +gggagagagatggaaagaggtggagggagagagagaaggaaagggagggagaggaagaga +gggagagagagaaggagggagagagatggagagaggtggagggagagagagaaggaaagg +gaggggagaggaagagagggagagagagaaggagggagagagatggagagaggtggaggg +agagagagaaggaaagggagggagagagagagacagacagacagcttcacacagacataa +aacatctgctgttcaggatcccagctgccctccgactctgcctccttctaacccggctgc +ctggctcacccgggtgacagggaggggcgccttcaccatgccctgtcctgaggctccctt +tcatcctg +>syndip_1_chr20:61744088-61744755 +tcaaactgggcactgcaaattctggaatctctcctacctcccgaagtttgtagtccacca +ggcccagggcgttctgaagcctggagggatgagaagcaagcggagactgtgtggttggaa +aggagccaaccagagagtggggaggcgatggagagaataacagagaggaaggcaggtgca +gggagacagcaaaggagagggagaagagaatgagagagggatggggagaaagagagaaga +gaggtggagagagacaggaaaggagagggagggagaggaagagagggagagagagaagga +gggagagagatggaaagaggtggagggagagagagaaggaaagggagggaga-------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------gagagagacagacagacagcttcacacagacataa +aacatctgctgttcaggatcccagctgccctccgactctgcctccttctaacccggctgc +ctggctcacccgggtgacagggaggggcgccttcaccatgccctgtcctgaggctccctt +tcatcctg +>syndip_2_chr20:61744088-61744755 +tcaaactgggcactgcaaattctggaatctctcctacctcccgaagtttgtagtccacca +ggcccagggcgttctgaagcctggagggatgagaagcaagcggagactgtgtggttggaa +aggagccaaccagagagtggggaggcgatggagagaataagagagaggaaggcaggtgca +gggagacagcaaaggagagggagaagagaatgagagagggatggggagaaagagagaaga +gaggtggagagagacaggaaaggagagggagggagaggaagagagggagagagagaagga +gggagagagatggaaagaggtggagggagagagagaaggaaagggagggagaggaagaga +gggagagagagaaggagggagagagatggagagaggtggagggagagagagaaggaaagg +gagg-------------------------------------------------------- +-------------------------gagagagagagacagacagcttcacacagacataa +aacatctgctgttcaggatcccagctgccctccgactctgcctccttctaacccggctgc +ctggctcacccgggtgacagggaggggcgccttcaccatgccctgtcctgaggctccctt +tcatcctg +>p:HG002_1_chr20:61744088-61744755 +tcaaactgggcactgcaaattctggaatctctcctacctcccgaagtttgtagtccacca +ggcccagggcgttctgaagcctggagggatgagaagcaagcggagactgtgtggttggaa +aggagccaaccagagagtggggaggcgatggagagaataagagagaggaaggcaggtgca +gggagacagcaaaggagagggagaagagaatgagagagggatggggagaaagagagaaga +gaggtggagagagacaggaaaggagagggagggagaggaagagagggagagagagaagga +gggagagagatggaaagaggtggagggagagagagaaggaaagggagggagaggaagaga +gggagagagagaaggagggagagagatggagagaggtggagggagagagagaaggaaagg +gagg-------------------------------------------------------- +-------------------------gagagagagagacagacagcttcacacagacataa +aacatctgctgttcaggatcccagctgccctccgactctgcctccttctaacccggctgc +ctggctcacccgggtgacagggaggggcgccttcaccatgccctgtcctgaggctccctt +tcatcctg +>p:HG002_2_chr20:61744088-61744755 +tcaaactgggcactgcaaattctggaatctctcctacctcccgaagtttgtagtccacca +ggcccagggcgttctgaagcctggagggatgagaagcaagcggagactgtgtggttggaa +aggagccaaccagagagtggggaggcgatggagagaataacagagaggaaggcaggtgca +gggagacagcaaaggagagggagaagagaatgagagagggatggggagaaagagagaaga +gaggtggagagagacaggaaaggagagggagggagaggaagagagggagagagagaagga +gggagagagatggaaagaggtggagggagagagagaaggaaagggagggaga-------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------gagagagacagacagacagcttcacacagacataa +aacatctgctgttcaggatcccagctgccctccgactctgcctccttctaacccggctgc +ctggctcacccgggtgacagggaggggcgccttcaccatgccctgtcctgaggctccctt +tcatcctg diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/msa.fa.fai new file mode 100644 index 00000000..f20007eb --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_61744088_61744755 668 29 60 61 +syndip_1_chr20:61744088-61744755 668 743 60 61 +syndip_2_chr20:61744088-61744755 668 1457 60 61 +p:HG002_1_chr20:61744088-61744755 668 2172 60 61 +p:HG002_2_chr20:61744088-61744755 668 2887 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/output.vcf.gz new file mode 100644 index 00000000..3f5907f1 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/output.vcf.gz.tbi new file mode 100644 index 00000000..de20e3aa Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61744188-61744655/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/base.vcf.gz new file mode 100644 index 00000000..1f92c076 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/base.vcf.gz.tbi new file mode 100644 index 00000000..cb1a8490 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/comp.vcf.gz new file mode 100644 index 00000000..245d68ca Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/comp.vcf.gz.tbi new file mode 100644 index 00000000..2ab02e3a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/haps.fa new file mode 100644 index 00000000..581163e6 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/haps.fa @@ -0,0 +1,108 @@ +>ref_chr20_61783303_61784940 +CTCCAAAGGCACATTCTATATGATTTTTGCCCACAACCTTTCCTTAATATGTACATGTTTTCTAGATAAAAACATTAAATACAGCTAAAGTGACATCAAGGTCTCCCTCCCTTCCTTTCCTCCAATACGTGAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCGAGGCCCTCAGATGTCCTGTGCCCCCGAAAGAAATGTAATCCCAGTTCCTTGGGATAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCTGGGAGAAATGTAAGCCCAGTTCCTCAGGACAGTTCTCGAGGCCCTCAGATGTCCTGTGCTCCCAGGAGAATATAAGCCTAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCCGGGCCCTCAGATGTCCTGTGCCCCCGGGAGAAATGTAAGCCTAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTTGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTTGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAATCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCCAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGAACAGTTCTCCAGGCCCTCAGATGTCCTGTGCCCCCGGGGCCTCATCAGACATTAAGCATGCAGTCCCTTTGCAGCTCTGGATGGCGCGAGTTTCCCACGTCCCATCCCCTTCCTGGCTATGGGCAAGTGCAGGCTGGATCCTGGCCTCCTCCTTCCTGGCCTCCAG +>syndip_1_chr20:61783303-61784940 +CTCCAAAGGCACATTCTATATGATTTTTGCCCACAACCTTTCCTTAATATGTACATGTTT +TCTAGATAAAAACATTAAATACAGCTAAAGTGACATCAAGGTCTCCCTCCCTTCCTTTCC +TCCAATACGTGAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCGAGGCCCTCAGAT +GTCCTGTGCCCCCGAAAGAAATGTAATCCCAGTTCCTTGGGATAGTTCTCAAGGCCCTCC +GATATCCTGTGCCCCTGGGAGAAATGTAAGCCCAGTTCCTCAGGACAGTTCTCGAGGCCC +TCAGATGTCCTGTGCTCCCAGGAGAATATAAGCCTAGTTCCTCGGGACAGTTCTCGAGGC +CCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCCG +GGCCCTCAGATGTCCTGTGCCCCCGGGAGAAATGTAAGCCTAGTTCCTCGGGACAGTTCT +CGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGT +TCTCAAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGAC +AGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGG +ACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTTG +GGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCC +TCGGGACAGTTCTCAAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGT +TCCTTGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCA +GTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAGGAGAATGTAAGCC +CAGTTCCTTGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAA +TCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGT +AATCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAA +TGTAATCCCAGTTCCTCGGGACAGTTCTCCAGGCCCTCCGATATCCTGTGCCCCCAGGAG +AATGTAAGCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGATGTCCTGTGCCCCCAAG +AGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCC +AGGAGAATGTAAGCCCAGTTCCTCGGGACAGTTCTCCAGGCCCTCCGATATCCTGTGCCC +CCAGGAGAATGTAAGCCCAGTTCCTCGGAACAGTTCTCCAGGCCCTCAGATGTCCTGTGC +CCCCGGGGCCTCATCAGACATTAAGCATGCAGTCCCTTTGCAGCTCTGGATGGCGCGAGT +TTCCCACGTCCCATCCCCTTCCTGGCTATGGGCAAGTGCAGGCTGGATCCTGGCCTCCTC +CTTCCTGGCCTCCAG +>syndip_2_chr20:61783303-61784940 +CTCCAAAGGCACATTCTATATGATTTTTGCCCACAACCTTTCCTTAATATGTACATGTTT +TCTAGATAAAAACATTAAATACAGCTAAAGTGACATCAAGGTCTCCCTCCCTTCCTTTCC +TCCAATACGTGAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCGAGGCCCTCAGAT +GTCCTGTGCCCCCGAAAGAAATGTAATCCCAGTTCCTTGGGATAGTTCTCAAGGCCCTCC +GATATCCTGTGCCCCTGGGAGAAATGTAAGCCCAGTTCCTCAGGACAGTTCTCGAGGCCC +TCAGATGTCCTGTGCTCCCAGGAGAATATAAGCCTAGTTCCTCGGGACAGTTCTCGAGGC +CCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCCG +GGCCCTCAGATGTCCTGTGCCCCCGGGAGAAATGTAAGCCTAGTTCCTCGGGACAGTTCT +CGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGACAGT +TCTCGAGGCCCTCAGATGTCCTGTGCCCCCGGGAGAAATGTAAGCCTAGTTCCTCGGGAC +AGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGG +ACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTC +GGGACAGTTCTCAAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGTTC +CTTGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGT +TCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAGGAGAATGTAAGCCCA +GTTCCTTGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATC +CCAGTTCCTCGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAA +GCCCAGTTCCTCGGGACAGTTCTCGAGGCCTTCAGGTGTCTTGTGCCCCCAAGAGAAATG +TAATCCCAGTTCCTCGGAACAGTTCTCCAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAA +ATGTAATCCCAGTTCCTCGGGACAGTTCTCCAGGCCCTCCGATATCCTGTGCCCCCAGGA +GAATGTAAGCCCAGTTCCTCGGAACAGTTCTCCAGGCCCTCAGATGTCCTGTGCCCCCGG +GGCCTCATCAGACATTAAGCATGCAGTCCCTTTGCAGCTCTGGATGGCGCGAGTTTCCCA +CGTCCCATCCCCTTCCTGGCTATGGGCAAGTGCAGGCTGGATCCTGGCCTCCTCCTTCCT +GGCCTCCAG +>p:HG002_1_chr20:61783303-61784940 +CTCCAAAGGCACATTCTATATGATTTTTGCCCACAACCTTTCCTTAATATGTACATGTTT +TCTAGATAAAAACATTAAATACAGCTAAAGTGACATCAAGGTCTCCCTCCCTTCCTTTCC +TCCAATACGTGAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCGAGGCCCTCAGAT +GTCCTGTGCCCCCGAAAGAAATGTAATCCCAGTTCCTTGGGATAGTTCTCAAGGCCCTCC +GATATCCTGTGCCCCTGGGAGAAATGTAAGCCCAGTTCCTCAGGACAGTTCTCGAGGCCC +TCAGATGTCCTGTGCTCCCAGGAGAATATAAGCCTAGTTCCTCGGGACAGTTCTCGAGGC +CCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCCG +GGCCCTCAGATGTCCTGTGCCCCCGGGAGAAATGTAAGCCTAGTTCCTCGGGACAGTTCT +CGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGACAGT +TCTCGAGGCCCTCAGATGTCCTGTGCCCCCGGGAGAAATGTAAGCCTAGTTCCTCGGGAC +AGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGG +ACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTC +GGGACAGTTCTCAAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGTTC +CTTGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGT +TCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAGGAGAATGTAAGCCCA +GTTCCTTGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATC +CCAGTTCCTCGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAA +GCCCAGTTCCTCGGGACAGTTCTCGAGGCCTTCAGGTGTCTTGTGCCCCCAAGAGAAATG +TAATCCCAGTTCCTCGGAACAGTTCTCCAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAA +ATGTAATCCCAGTTCCTCGGGACAGTTCTCCAGGCCCTCCGATATCCTGTGCCCCCAGGA +GAATGTAAGCCCAGTTCCTCGGAACAGTTCTCCAGGCCCTCAGATGTCCTGTGCCCCCGG +GGCCTCATCAGACATTAAGCATGCAGTCCCTTTGCAGCTCTGGATGGCGCGAGTTTCCCA +CGTCCCATCCCCTTCCTGGCTATGGGCAAGTGCAGGCTGGATCCTGGCCTCCTCCTTCCT +GGCCTCCAG +>p:HG002_2_chr20:61783303-61784940 +CTCCAAAGGCACATTCTATATGATTTTTGCCCACAACCTTTCCTTAATATGTACATGTTT +TCTAGATAAAAACATTAAATACAGCTAAAGTGACATCAAGGTCTCCCTCCCTTCCTTTCC +TCCAATACGTGAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCGAGGCCCTCAGAT +GTCCTGTGCCCCCGAAAGAAATGTAATCCCAGTTCCTTGGGATAGTTCTCAAGGCCCTCC +GATATCCTGTGCCCCTGGGAGAAATGTAAGCCCAGTTCCTCAGGACAGTTCTCGAGGCCC +TCAGATGTCCTGTGCTCCCAGGAGAATATAAGCCTAGTTCCTCGGGACAGTTCTCGAGGC +CCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCCG +GGCCCTCAGATGTCCTGTGCCCCCGGGAGAAATGTAAGCCTAGTTCCTCGGGACAGTTCT +CGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGT +TCTCAAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGAC +AGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGG +ACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTTG +GGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCC +TCGGGACAGTTCTCAAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGT +TCCTTGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCA +GTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAGGAGAATGTAAGCC +CAGTTCCTTGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAA +TCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGT +AATCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAA +TGTAATCCCAGTTCCTCGGGACAGTTCTCCAGGCCCTCCGATATCCTGTGCCCCCAGGAG +AATGTAAGCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGATGTCCTGTGCCCCCAAG +AGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCC +AGGAGAATGTAAGCCCAGTTCCTCGGGACAGTTCTCCAGGCCCTCCGATATCCTGTGCCC +CCAGGAGAATGTAAGCCCAGTTCCTCGGAACAGTTCTCCAGGCCCTCAGATGTCCTGTGC +CCCCGGGGCCTCATCAGACATTAAGCATGCAGTCCCTTTGCAGCTCTGGATGGCGCGAGT +TTCCCACGTCCCATCCCCTTCCTGGCTATGGGCAAGTGCAGGCTGGATCCTGGCCTCCTC +CTTCCTGGCCTCCAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/haps.fa.ref.fa new file mode 100644 index 00000000..fe5fb8f5 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:61783303-61784940 +CTCCAAAGGCACATTCTATATGATTTTTGCCCACAACCTTTCCTTAATATGTACATGTTTTCTAGATAAAAACATTAAATACAGCTAAAGTGACATCAAGGTCTCCCTCCCTTCCTTTCCTCCAATACGTGAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCGAGGCCCTCAGATGTCCTGTGCCCCCGAAAGAAATGTAATCCCAGTTCCTTGGGATAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCTGGGAGAAATGTAAGCCCAGTTCCTCAGGACAGTTCTCGAGGCCCTCAGATGTCCTGTGCTCCCAGGAGAATATAAGCCTAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCCGGGCCCTCAGATGTCCTGTGCCCCCGGGAGAAATGTAAGCCTAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTTGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTTGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAATCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCCAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGAACAGTTCTCCAGGCCCTCAGATGTCCTGTGCCCCCGGGGCCTCATCAGACATTAAGCATGCAGTCCCTTTGCAGCTCTGGATGGCGCGAGTTTCCCACGTCCCATCCCCTTCCTGGCTATGGGCAAGTGCAGGCTGGATCCTGGCCTCCTCCTTCCTGGCCTCCAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/msa.fa new file mode 100644 index 00000000..4d970eab --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/msa.fa @@ -0,0 +1,145 @@ +>ref_chr20_61783303_61784940 +ctccaaaggcacattctatatgatttttgcccacaacctttccttaatatgtacatgttt +tctagataaaaacattaaatacagctaaagtgacatcaaggtctccctcccttcctttcc +tccaatacgtgagagaaatgtaatcccagttccttgggacagttctcgaggccctcagat +gtcctgtgcccccgaaagaaatgtaatcccagttccttgggatagttctcaaggccctcc +gatatcctgtgcccctgggagaaatgtaagcccagttcctcaggacagttctcgaggccc +tcagatgtcctgtgctcccaggagaatataagcctagttcctcgggacagttctcgaggc +cctcaggtgtcttgtgcccccaagagaaatgtaatcccagttccttgggacagttctccg +ggccctcagatgtcctgtgcccccgggagaaatgtaagcctagttcctcgggacagttct +cgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttcctcgggacagt +tctcaaggccctcagatgtcctgtgcccccaagagaaatgtaatcccagttccttgggac +agttctcaaggccctccgatatcctgtgcccccaggagaatgtaagcccagttcctcggg +acagttctcgaggccctcaggtgtcttgtgcccccaggagaatgtaagcccagttccttg +ggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttcc +tcgggacagttctcaaggccctcagatgtcctgtgcccccaagagaaatgtaatcccagt +tccttgggacagttctcaaggccctccgatatcctgtgcccccaggagaatgtaagccca +gttcctcgggacagttctcgaggccctcaggtgtcttgtgcccccaggagaatgtaagcc +cagttccttgggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaa +tcccagttcctcgggacagttctcaaggccctccgatatcctgtgcccccaggagaatgt +aatcccagttcctcgggacagttctcgaggccctcagatgtcctgtgcccccaagagaaa +tgtaatcccagttcctcgggacagttctcaaggccctccgatatcctgtgcccccaggag +aatgtaagcccagttcctcgggacagttctcgaggccctcaggtgtcttgtgcccccaag +agaaatgtaatcccagttcctcgggacagttctccaggccctccgatatcctgtgccccc +aggagaatgtaagcccagttcctcgggacagttctcgaggccctcagatgtcctgtgccc +ccaagagaaatgtaatcccagttcctcgggacagttctcaaggccctccgatatcctgtg +cccccaggagaatgtaagcccagttcctcggaacagttctccaggccctcagatgtcctg +tgcccccggggcctcatcagacattaagcatgcagtccctttgcagctctggatggcgcg +agtttcccacgtcccatccccttcctggctatgggcaagtgcaggctggatcctggcctc +ctccttcctggcctccag +>syndip_1_chr20:61783303-61784940 +ctccaaaggcacattctatatgatttttgcccacaacctttccttaatatgtacatgttt +tctagataaaaacattaaatacagctaaagtgacatcaaggtctccctcccttcctttcc +tccaatacgtgagagaaatgtaatcccagttccttgggacagttctcgaggccctcagat +gtcctgtgcccccgaaagaaatgtaatcccagttccttgggatagttctcaaggccctcc +gatatcctgtgcccctgggagaaatgtaagcccagttcctcaggacagttctcgaggccc +tcagatgtcctgtgctcccaggagaatataagcctagttcctcgggacagttctcgaggc +cctcaggtgtcttgtgcccccaagagaaatgtaatcccagttccttgggacagttctccg +ggccctcagatgtcctgtgcccccgggagaaatgtaagcctagttcctcgggacagttct +cgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttcctcgggacagt +tctcaaggccctcagatgtcctgtgcccccaagagaaatgtaatcccagttccttgggac +agttctcaaggccctccgatatcctgtgcccccaggagaatgtaagcccagttcctcggg +acagttctcgaggccctcaggtgtcttgtgcccccaggagaatgtaagcccagttccttg +ggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttcc +tcgggacagttctcaaggccctcagatgtcctgtgcccccaagagaaatgtaatcccagt +tccttgggacagttctcaaggccctccgatatcctgtgcccccaggagaatgtaagccca +gttcctcgggacagttctcgaggccctcaggtgtcttgtgcccccaggagaatgtaagcc +cagttccttgggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaa +tcccagttcctcgggacagttctcaaggccctccgatatcctgtgcccccaggagaatgt +aatcccagttcctcgggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaa +tgtaatcccagttcctcgggacagttctccaggccctccgatatcctgtgcccccaggag +aatgtaagcccagttcctcgggacagttctcgaggccctcagatgtcctgtgcccccaag +agaaatgtaatcccagttcctcgggacagttctcaaggccctccgatatcctgtgccccc +aggagaatgtaag----------------------------------------------- +----------------cccagttcctcgggacagttctccaggccctccgatatcctgtg +cccccaggagaatgtaagcccagttcctcggaacagttctccaggccctcagatgtcctg +tgcccccggggcctcatcagacattaagcatgcagtccctttgcagctctggatggcgcg +agtttcccacgtcccatccccttcctggctatgggcaagtgcaggctggatcctggcctc +ctccttcctggcctccag +>syndip_2_chr20:61783303-61784940 +ctccaaaggcacattctatatgatttttgcccacaacctttccttaatatgtacatgttt +tctagataaaaacattaaatacagctaaagtgacatcaaggtctccctcccttcctttcc +tccaatacgtgagagaaatgtaatcccagttccttgggacagttctcgaggccctcagat +gtcctgtgcccccgaaagaaatgtaatcccagttccttgggatagttctcaaggccctcc +gatatcctgtgcccctgggagaaatgtaagcccagttcctcaggacagttctcgaggccc +tcagatgtcctgtgctcccaggagaatataagcctagttcctcgggacagttctcgaggc +cctcaggtgtcttgtgcccccaagagaaatgtaatcccagttccttgggacagttctccg +ggccctcagatgtcctgtgcccccgggagaaatgtaagcctagttcctcgggacagttct +cgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttccttgggacagt +tctcgaggccctcagatgtcctgtgcccccgggagaaatgtaagcctagttcctcgggac +agttctcaaggccctccgatatcctgtgcccccaggagaatgtaagcccagttcctc--- +-----------------------------------------------------------g +ggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttcc +tcgggacagttctcaaggccctcagatgtcctgtgcccccaagagaaatgtaatcccagt +tccttgggacagttctcaaggccctccgatatcctgtgcccccaggagaatgtaagccca +gttcctcgggacagttctcgaggccctcaggtgtcttgtgcccccaggagaatgtaagcc +cagttccttgggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaa +tcccagttcctcgggacagttctcaaggccctccgatatcctgtgcccccaggagaatgt +aagcccagttcctcgggacagttctcgaggccttcaggtgtcttgtgcccccaagagaaa +tgtaatcccagttcctcggaacagttctccaggccctcagatgtcctgtgcccccaagag +a----------------------------------------------------------- +------------------------------------------------------------ +-----aatgtaat----------------------------------------------- +----------------cccagttcctcgggacagttctccaggccctccgatatcctgtg +cccccaggagaatgtaagcccagttcctcggaacagttctccaggccctcagatgtcctg +tgcccccggggcctcatcagacattaagcatgcagtccctttgcagctctggatggcgcg +agtttcccacgtcccatccccttcctggctatgggcaagtgcaggctggatcctggcctc +ctccttcctggcctccag +>p:HG002_1_chr20:61783303-61784940 +ctccaaaggcacattctatatgatttttgcccacaacctttccttaatatgtacatgttt +tctagataaaaacattaaatacagctaaagtgacatcaaggtctccctcccttcctttcc +tccaatacgtgagagaaatgtaatcccagttccttgggacagttctcgaggccctcagat +gtcctgtgcccccgaaagaaatgtaatcccagttccttgggatagttctcaaggccctcc +gatatcctgtgcccctgggagaaatgtaagcccagttcctcaggacagttctcgaggccc +tcagatgtcctgtgctcccaggagaatataagcctagttcctcgggacagttctcgaggc +cctcaggtgtcttgtgcccccaagagaaatgtaatcccagttccttgggacagttctccg +ggccctcagatgtcctgtgcccccgggagaaatgtaagcctagttcctcgggacagttct +cgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttccttgggacagt +tctcgaggccctcagatgtcctgtgcccccgggagaaatgtaagcctagttcctcgggac +agttctcaaggccctccgatatcctgtgcccccaggagaatgtaagcccagttcctc--- +-----------------------------------------------------------g +ggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttcc +tcgggacagttctcaaggccctcagatgtcctgtgcccccaagagaaatgtaatcccagt +tccttgggacagttctcaaggccctccgatatcctgtgcccccaggagaatgtaagccca +gttcctcgggacagttctcgaggccctcaggtgtcttgtgcccccaggagaatgtaagcc +cagttccttgggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaa +tcccagttcctcgggacagttctcaaggccctccgatatcctgtgcccccaggagaatgt +aagcccagttcctcgggacagttctcgaggccttcaggtgtcttgtgcccccaagagaaa +tgtaatcccagttcctcggaacagttctccaggccctcagatgtcctgtgcccccaagag +a----------------------------------------------------------- +------------------------------------------------------------ +-----aatgtaat----------------------------------------------- +----------------cccagttcctcgggacagttctccaggccctccgatatcctgtg +cccccaggagaatgtaagcccagttcctcggaacagttctccaggccctcagatgtcctg +tgcccccggggcctcatcagacattaagcatgcagtccctttgcagctctggatggcgcg +agtttcccacgtcccatccccttcctggctatgggcaagtgcaggctggatcctggcctc +ctccttcctggcctccag +>p:HG002_2_chr20:61783303-61784940 +ctccaaaggcacattctatatgatttttgcccacaacctttccttaatatgtacatgttt +tctagataaaaacattaaatacagctaaagtgacatcaaggtctccctcccttcctttcc +tccaatacgtgagagaaatgtaatcccagttccttgggacagttctcgaggccctcagat +gtcctgtgcccccgaaagaaatgtaatcccagttccttgggatagttctcaaggccctcc +gatatcctgtgcccctgggagaaatgtaagcccagttcctcaggacagttctcgaggccc +tcagatgtcctgtgctcccaggagaatataagcctagttcctcgggacagttctcgaggc +cctcaggtgtcttgtgcccccaagagaaatgtaatcccagttccttgggacagttctccg +ggccctcagatgtcctgtgcccccgggagaaatgtaagcctagttcctcgggacagttct +cgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttcctcgggacagt +tctcaaggccctcagatgtcctgtgcccccaagagaaatgtaatcccagttccttgggac +agttctcaaggccctccgatatcctgtgcccccaggagaatgtaagcccagttcctcggg +acagttctcgaggccctcaggtgtcttgtgcccccaggagaatgtaagcccagttccttg +ggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttcc +tcgggacagttctcaaggccctcagatgtcctgtgcccccaagagaaatgtaatcccagt +tccttgggacagttctcaaggccctccgatatcctgtgcccccaggagaatgtaagccca +gttcctcgggacagttctcgaggccctcaggtgtcttgtgcccccaggagaatgtaagcc +cagttccttgggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaa +tcccagttcctcgggacagttctcaaggccctccgatatcctgtgcccccaggagaatgt +aatcccagttcctcgggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaa +tgtaatcccagttcctcgggacagttctccaggccctccgatatcctgtgcccccaggag +aatgtaagcccagttcctcgggacagttctcgaggccctcagatgtcctgtgcccccaag +agaaatgtaatcccagttcctcgggacagttctcaaggccctccgatatcctgtgccccc +aggagaatgtaag----------------------------------------------- +----------------cccagttcctcgggacagttctccaggccctccgatatcctgtg +cccccaggagaatgtaagcccagttcctcggaacagttctccaggccctcagatgtcctg +tgcccccggggcctcatcagacattaagcatgcagtccctttgcagctctggatggcgcg +agtttcccacgtcccatccccttcctggctatgggcaagtgcaggctggatcctggcctc +ctccttcctggcctccag diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/msa.fa.fai new file mode 100644 index 00000000..4e9d196d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_61783303_61784940 1638 29 60 61 +syndip_1_chr20:61783303-61784940 1638 1729 60 61 +syndip_2_chr20:61783303-61784940 1638 3429 60 61 +p:HG002_1_chr20:61783303-61784940 1638 5130 60 61 +p:HG002_2_chr20:61783303-61784940 1638 6831 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/output.vcf.gz new file mode 100644 index 00000000..f583eecc Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/output.vcf.gz.tbi new file mode 100644 index 00000000..3f1c57e9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:61783403-61784840/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/base.vcf.gz new file mode 100644 index 00000000..49060430 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/base.vcf.gz.tbi new file mode 100644 index 00000000..672041d6 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/comp.vcf.gz new file mode 100644 index 00000000..2d7a6f3b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/comp.vcf.gz.tbi new file mode 100644 index 00000000..7925bd6e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/haps.fa new file mode 100644 index 00000000..0e0a7664 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/haps.fa @@ -0,0 +1,148 @@ +>ref_chr20_62057473_62059240 +TCCAAGATCCATGTACCCCAACACCACCCTACCTGGCTACGCTCCTCTCACAACTTTGAGATCAAGATGCCACGTGTGCCTTCCTCACATCGGCGCTTTCCAGTGATGCCCAGTGGGGGACACAAAGGGCCCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCTCCAGTCCCCAAACACAGTCCCCAACAGACAACTTCTCCTGTCCCCACATGCGGCTCCCAACAAACAATTTCTCCTGCCCTCACACGCGGTTCCCAACGACAACTTCTGCTCCACAACATGACACCCACGGTGGGAGAAGCTGGGGGCACTTCACTACATCATCCTGCACACTGCAGCATGGCCTGCTCCAGGCAGAAGGCAGGCCTGGAGAAGAGCCTGGGACCACCGCGGACTGACC +>syndip_1_chr20:62057473-62059240 +TCCAAGATCCATGTACCCCAACACCACCCTACCTGGCTACGCTCCTCTCACAACTTTGAG +ATCAAGATGCCACGTGTGCCTTCCTCACATCGGCGCTTTCCAGTGATGCCCAGTGGGGGA +CACAAAGGGCCCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAG +ACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTAC +ACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACG +GACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGA +CCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCC +AACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATG +GGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCA +GGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACA +GGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAG +GAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTC +AGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTC +GGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACA +GACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTA +CACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGAC +GGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAG +ACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGG +CCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAA +TGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACC +AGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACAC +AGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCA +GGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACC +TCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGC +TCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCA +CAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCT +ACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGA +CGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAG +ACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGG +CCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAA +TGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACAC +CAGGCCACAGACAGTGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGAC +ACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTC +AGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAAC +CTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGG +CTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGC +CACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGT +CTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAA +GGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAG +CAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGG +GGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGA +CAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACA +CACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGG +ACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACC +TCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAA +CCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGG +GCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGG +CCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAG +GTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGA +AGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAG +CAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGG +GGGGCCAACCTCTCCAGTCCCCAAACACAGTCCCCAACAGACAACTTCTCCTGTCCCCAC +ATGCGGCTCCCAACAAACAATTTCTCCTGCCCTCACACGCGGTTCCCAACGACAACTTCT +GCTCCACAACATGACACCCACGGTGGGAGAAGCTGGGGGCACTTCACTACATCATCCTGC +ACACTGCAGCATGGCCTGCTCCAGGCAGAAGGCAGGCCTGGAGAAGAGCCTGGGACCACC +GCGGACTGACC +>syndip_2_chr20:62057473-62059240 +TCCAAGATCCATGTACCCCAACACCACCCTACCTGGCTACGCTCCTCTCACAACTTTGAG +ATCAAGATGCCACGTGTGCCTTCCTCACATCGGCGCTTTCCAGTGATGCCCAGTGGGGGA +CACAAAGGGCCCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAG +ACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACA +CACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGG +ACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACC +TCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAA +CCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGG +GCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGC +CACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGT +CTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCTCCAGTCCCCAAACACA +GTCCCCAACAGACAACTTCTCCTGTCCTCACATGCGGCTCCCAACAAACAATTTCTCCTG +CCCTCACACGCGGTTCCCAACGACAACTTCTGCTCCACAACATGACACCCACGGTGGGAG +AAGCTGGGGGCACTTCACTACATCATCCTGCACACTGCAGCATGGCCTGCTCCAGGCAGA +AGGCAGGCCTGGAGAAGAGCCTGGGACCACCGCGGACTGACC +>p:HG002_1_chr20:62057473-62059240 +TCCAAGATCCATGTACCCCAACACCACCCTACCTGGCTACGCTCCTCTCACAACTTTGAG +ATCAAGATGCCACGTGTGCCTTCCTCACATCGGCGCTTTCCAGTGATGCCCAGTGGGGGA +CACAAAGGGCCCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAG +ACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACA +CACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGG +ACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACC +TCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAA +CCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGG +GCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGC +CACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGT +CTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCTCCAGTCCCCAAACACA +GTCCCCAACAGACAACTTCTCCTGTCCTCACATGCGGCTCCCAACAAACAATTTCTCCTG +CCCTCACACGCGGTTCCCAACGACAACTTCTGCTCCACAACATGACACCCACGGTGGGAG +AAGCTGGGGGCACTTCACTACATCATCCTGCACACTGCAGCATGGCCTGCTCCAGGCAGA +AGGCAGGCCTGGAGAAGAGCCTGGGACCACCGCGGACTGACC +>p:HG002_2_chr20:62057473-62059240 +TCCAAGATCCATGTACCCCAACACCACCCTACCTGGCTACGCTCCTCTCACAACTTTGAG +ATCAAGATGCCACGTGTGCCTTCCTCACATCGGCGCTTTCCAGTGATGCCCAGTGGGGGA +CACAAAGGGCCCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAG +ACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTAC +ACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACG +GACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGA +CCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCC +AACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATG +GGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCA +GGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACA +GGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAG +GAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTC +AGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTC +GGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACA +GACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTA +CACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGAC +GGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAG +ACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGG +CCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAA +TGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACC +AGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACAC +AGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCA +GGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACC +TCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGC +TCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCA +CAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCT +ACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGA +CGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAG +ACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGG +CCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAA +TGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACAC +CAGGCCACAGACAGTGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGAC +ACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTC +AGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAAC +CTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGG +CTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGC +CACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGT +CTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAA +GGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAG +CAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGG +GGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGA +CAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACA +CACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGG +ACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACC +TCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAA +CCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGG +GCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGG +CCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAG +GTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGA +AGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAG +CAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGG +GGGGCCAACCTCTCCAGTCCCCAAACACAGTCCCCAACAGACAACTTCTCCTGTCCCCAC +ATGCGGCTCCCAACAAACAATTTCTCCTGCCCTCACACGCGGTTCCCAACGACAACTTCT +GCTCCACAACATGACACCCACGGTGGGAGAAGCTGGGGGCACTTCACTACATCATCCTGC +ACACTGCAGCATGGCCTGCTCCAGGCAGAAGGCAGGCCTGGAGAAGAGCCTGGGACCACC +GCGGACTGACC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/haps.fa.ref.fa new file mode 100644 index 00000000..eee96022 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:62057473-62059240 +TCCAAGATCCATGTACCCCAACACCACCCTACCTGGCTACGCTCCTCTCACAACTTTGAGATCAAGATGCCACGTGTGCCTTCCTCACATCGGCGCTTTCCAGTGATGCCCAGTGGGGGACACAAAGGGCCCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCTCCAGTCCCCAAACACAGTCCCCAACAGACAACTTCTCCTGTCCCCACATGCGGCTCCCAACAAACAATTTCTCCTGCCCTCACACGCGGTTCCCAACGACAACTTCTGCTCCACAACATGACACCCACGGTGGGAGAAGCTGGGGGCACTTCACTACATCATCCTGCACACTGCAGCATGGCCTGCTCCAGGCAGAAGGCAGGCCTGGAGAAGAGCCTGGGACCACCGCGGACTGACC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/msa.fa new file mode 100644 index 00000000..dc504a6c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/msa.fa @@ -0,0 +1,285 @@ +>ref_chr20_62057473_62059240 +tccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttgag +atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga +cacaaagggcccagcaagacctcaggaaggacggacacaggcctacacaccaggccacag +acaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctac +acaccaggccacagacaatggggctcg--------------------------------- +------------------------------------------------------------ +-----------------------------------------------------gggggcc +aacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatg +gggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacca +ggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacaca +ggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcag +gaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacctc +agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc +gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccaca +gacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggccta +cacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggac +ggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaag +acctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggg +ccaacctcagcaagacctcaggaaggacggac---------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------acaggtctacacaccaggcca +cagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtct +acacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagga +cggacacaggtctacacaccaggccacagacaatggggctcg------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------------------------gg +gggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacaga +caatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctaca +caccaggccacagacaatggggctc----------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------gggggccaacctcagcaagacctcaggaaggacggacacag +gtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagga +aggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcag +caagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgg +ggggccaacctctccagtccccaaacacagtccccaacagacaacttctcctgtccccac +atgcggctcccaacaaacaatttctcctgccctcacacgcggttcccaacgacaacttct +gctccacaacatgacacccacggtgggagaagctgggggcacttcactacatcatcctgc +acactgcagcatggcctgctccaggcagaaggcaggcctggagaagagcctgggaccacc +gcggactgacc +>syndip_1_chr20:62057473-62059240 +tccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttgag +atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga +cacaaagggcccagcaagacctcaggaaggacggacacaggtctacacaccaggccacag +acaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctac +acaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacg +gacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaaga +cctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggcc +aacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatg +gggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacca +ggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacaca +ggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcag +gaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacctc +agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc +gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccaca +gacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggccta +cacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggac +ggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaag +acctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggg +ccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaa +tggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacc +aggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacac +aggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctca +ggaaggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacc +tcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggc +tcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggcca +cagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtct +acacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagga +cggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaag +acctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggg +ccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaa +tggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacac +caggccacagacagtggggctcggggggccaacctcagcaagacctcaggaaggacggac +acaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctc +aggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggccaac +ctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatgggg +ctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggc +cacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggt +ctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaa +ggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcag +caagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgg +gggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacaga +caatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctaca +caccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacgg +acacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacc +tcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaa +cctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggg +gctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccagg +ccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacag +gtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagga +aggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcag +caagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgg +ggggccaacctctccagtccccaaacacagtccccaacagacaacttctcctgtccccac +atgcggctcccaacaaacaatttctcctgccctcacacgcggttcccaacgacaacttct +gctccacaacatgacacccacggtgggagaagctgggggcacttcactacatcatcctgc +acactgcagcatggcctgctccaggcagaaggcaggcctggagaagagcctgggaccacc +gcggactgacc +>syndip_2_chr20:62057473-62059240 +tccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttgag +atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga +cacaaagggcccagcaagacctcaggaaggacggacacaggt------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------ctacacaccaggccacagacaatggggctcgggggccaacctc +agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc +gggggccaacctcagcaagacctcaggaaggacggac----------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------acaggtctacacaccaggcca +cagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtct +acacaccaggccacagacaatggggctc-------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------gggggccaacctcagcaagacctcaggaaggacggacacag +gtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagga +aggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcag +caagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc-g +ggggccaacctctccagtccccaaacacagtccccaacagacaacttctcctgtcctcac +atgcggctcccaacaaacaatttctcctgccctcacacgcggttcccaacgacaacttct +gctccacaacatgacacccacggtgggagaagctgggggcacttcactacatcatcctgc +acactgcagcatggcctgctccaggcagaaggcaggcctggagaagagcctgggaccacc +gcggactgacc +>p:HG002_1_chr20:62057473-62059240 +tccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttgag +atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga +cacaaagggcccagcaagacctcaggaaggacggacacaggt------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------ctacacaccaggccacagacaatggggctcgggggccaacctc +agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc +gggggccaacctcagcaagacctcaggaaggacggac----------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------acaggtctacacaccaggcca +cagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtct +acacaccaggccacagacaatggggctc-------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------gggggccaacctcagcaagacctcaggaaggacggacacag +gtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagga +aggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcag +caagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc-g +ggggccaacctctccagtccccaaacacagtccccaacagacaacttctcctgtcctcac +atgcggctcccaacaaacaatttctcctgccctcacacgcggttcccaacgacaacttct +gctccacaacatgacacccacggtgggagaagctgggggcacttcactacatcatcctgc +acactgcagcatggcctgctccaggcagaaggcaggcctggagaagagcctgggaccacc +gcggactgacc +>p:HG002_2_chr20:62057473-62059240 +tccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttgag +atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga +cacaaagggcccagcaagacctcaggaaggacggacacaggtctacacaccaggccacag +acaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctac +acaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacg +gacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaaga +cctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggcc +aacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatg +gggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacca +ggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacaca +ggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcag +gaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacctc +agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc +gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccaca +gacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggccta +cacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggac +ggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaag +acctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggg +ccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaa +tggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacc +aggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacac +aggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctca +ggaaggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacc +tcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggc +tcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggcca +cagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtct +acacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagga +cggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaag +acctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggg +ccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaa +tggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacac +caggccacagacagtggggctcggggggccaacctcagcaagacctcaggaaggacggac +acaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctc +aggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggccaac +ctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatgggg +ctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggc +cacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggt +ctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaa +ggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcag +caagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgg +gggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacaga +caatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctaca +caccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacgg +acacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacc +tcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaa +cctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggg +gctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccagg +ccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacag +gtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagga +aggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcag +caagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgg +ggggccaacctctccagtccccaaacacagtccccaacagacaacttctcctgtccccac +atgcggctcccaacaaacaatttctcctgccctcacacgcggttcccaacgacaacttct +gctccacaacatgacacccacggtgggagaagctgggggcacttcactacatcatcctgc +acactgcagcatggcctgctccaggcagaaggcaggcctggagaagagcctgggaccacc +gcggactgacc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/msa.fa.fai new file mode 100644 index 00000000..64a1a532 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_62057473_62059240 3311 29 60 61 +syndip_1_chr20:62057473-62059240 3311 3430 60 61 +syndip_2_chr20:62057473-62059240 3311 6831 60 61 +p:HG002_1_chr20:62057473-62059240 3311 10233 60 61 +p:HG002_2_chr20:62057473-62059240 3311 13635 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/output.vcf.gz new file mode 100644 index 00000000..4c1edaa7 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/output.vcf.gz.tbi new file mode 100644 index 00000000..540891fa Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62057573-62059140/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/base.vcf.gz new file mode 100644 index 00000000..ed2c755f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/base.vcf.gz.tbi new file mode 100644 index 00000000..3c08d7a5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/comp.vcf.gz new file mode 100644 index 00000000..0bf6c926 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/comp.vcf.gz.tbi new file mode 100644 index 00000000..ac054325 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/haps.fa new file mode 100644 index 00000000..cb0a09c0 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/haps.fa @@ -0,0 +1,70 @@ +>ref_chr20_62270179_62271195 +CGTCCTAGTCCCTGGTGCAGACGAGGAGCCTGAGAGGCTTAGCAGCTCATGTGTGTGTCAGCTGGGAACCCACAGCAAGTGGATTCCAAAGCCTGCCATGTCCCTGTTGCCACTAGCACCTCCTCCTCCACTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCCCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTTTCCTTGTCCCTTTCTGGTCTCTCTGGTCCTCTCCTTCTCTCCTTGTCCCTCTCCCTCTGCCTCTGCTTTGCCCACCCCAGACCCTGCTCCTTCCTGAAGAGCCTGCCCTGAGGTGACAGCTGTGTTTCCCTGGAATGCCTACTGCCCTTGGGATCCCTTTCCTGGAAGCCCGGTGGGAA +>syndip_1_chr20:62270179-62271195 +CGTCCTAGTCCCTGGTGCAGACGAGGAGCCTGAGAGGCTTAGCAGCTCATGTGTGTGTCA +GCTGGGAACCCACAGCAAGTGGATTCCAAAGCCTGCCATGTCCCTGTTGCCACTAGCACC +TCCTCCTCCACTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCCTGGCCTCTCTG +GGTCCTCTCCTTGTCCCTCCCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTC +TCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGG +GTCCTCTCCTTGTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTC +TCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCTGACCTCTCTGAGTCCTCTCCTTGTC +CCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCT +CTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGG +TCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTC +TCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTT +GTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCT +CCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTG +TCCCTCTCTGGCCTCTCTGGGTCCTTTCCTTGTCCCTTTCTGGTCTCTCTGGTCCTCTCC +TTCTCTCCTTGTCCCTCTCCCTCTGCCTCTGCTTTGCCCACCCCAGACCCTGCTCCTTCC +TGAAGAGCCTGCCCTGAGGTGACAGCTGTGTTTCCCTGGAATGCCTACTGCCCTTGGGAT +CCCTTTCCTGGAAGCCCGGTGGGAA +>syndip_2_chr20:62270179-62271195 +CGTCCTAGTCCCTGGTGCAGACGAGGAGCCTGAGAGGCTTAGCAGCTCATGTGTGTGTCA +GCTGGGAACCCACAGCAAGTGGATTCCAAAGCCTGCCATGTCCCTGTTGCCACTAGCACC +TCCTCCTCCACTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCCTGGCCTCTCTG +GGTCCTCTCCTTGTCCCTCCCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTC +TCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGG +GTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCT +CTCCTTGTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTT +GTCCCTCTCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCC +TCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCT +GGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTC +CTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTG +GGTCCTTTCCTTGTCCCTTTCTGGTCTCTCTGGTCCTCTCCTTCTCTCCTTGTCCCTCTC +CCTCTGCCTCTGCTTTGCCCACCCCAGACCCTGCTCCTTCCTGAAGAGCCTGCCCTGAGG +TGACAGCTGTGTTTCCCTGGAATGCCTACTGCCCTTGGGATCCCTTTCCTGGAAGCCCGG +TGGGAA +>p:HG002_1_chr20:62270179-62271195 +CGTCCTAGTCCCTGGTGCAGACGAGGAGCCTGAGAGGCTTAGCAGCTCATGTGTGTGTCA +GCTGGGAACCCACAGCAAGTGGATTCCAAAGCCTGCCATGTCCCTGTTGCCACTAGCACC +TCCTCCTCCACTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCCTGGCCTCTCTG +GGTCCTCTCCTTGTCCCTCCCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTC +TCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGG +GTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCT +CTCCTTGTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTT +GTCCCTCTCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCC +TCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCT +GGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTC +CTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTG +GGTCCTTTCCTTGTCCCTTTCTGGTCTCTCTGGTCCTCTCCTTCTCTCCTTGTCCCTCTC +CCTCTGCCTCTGCTTTGCCCACCCCAGACCCTGCTCCTTCCTGAAGAGCCTGCCCTGAGG +TGACAGCTGTGTTTCCCTGGAATGCCTACTGCCCTTGGGATCCCTTTCCTGGAAGCCCGG +TGGGAA +>p:HG002_2_chr20:62270179-62271195 +CGTCCTAGTCCCTGGTGCAGACGAGGAGCCTGAGAGGCTTAGCAGCTCATGTGTGTGTCA +GCTGGGAACCCACAGCAAGTGGATTCCAAAGCCTGCCATGTCCCTGTTGCCACTAGCACC +TCCTCCTCCACTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCCTGGCCTCTCTG +GGTCCTCTCCTTGTCCCTCCCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTC +TCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGG +GTCCTCTCCTTGTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTC +TCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCTGACCTCTCTGAGTCCTCTCCTTGTC +CCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCT +CTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGG +TCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTC +TCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTT +GTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCT +CCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTG +TCCCTCTCTGGCCTCTCTGGGTCCTTTCCTTGTCCCTTTCTGGTCTCTCTGGTCCTCTCC +TTCTCTCCTTGTCCCTCTCCCTCTGCCTCTGCTTTGCCCACCCCAGACCCTGCTCCTTCC +TGAAGAGCCTGCCCTGAGGTGACAGCTGTGTTTCCCTGGAATGCCTACTGCCCTTGGGAT +CCCTTTCCTGGAAGCCCGGTGGGAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/haps.fa.ref.fa new file mode 100644 index 00000000..232094ce --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:62270179-62271195 +CGTCCTAGTCCCTGGTGCAGACGAGGAGCCTGAGAGGCTTAGCAGCTCATGTGTGTGTCAGCTGGGAACCCACAGCAAGTGGATTCCAAAGCCTGCCATGTCCCTGTTGCCACTAGCACCTCCTCCTCCACTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCCCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTTTCCTTGTCCCTTTCTGGTCTCTCTGGTCCTCTCCTTCTCTCCTTGTCCCTCTCCCTCTGCCTCTGCTTTGCCCACCCCAGACCCTGCTCCTTCCTGAAGAGCCTGCCCTGAGGTGACAGCTGTGTTTCCCTGGAATGCCTACTGCCCTTGGGATCCCTTTCCTGGAAGCCCGGTGGGAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/msa.fa new file mode 100644 index 00000000..a2ca79af --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/msa.fa @@ -0,0 +1,90 @@ +>ref_chr20_62270179_62271195 +cgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtca +gctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcacc +tcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctg +ggtcctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcctc +tctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgg +gtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcct +ctccttgtccctc-ctggcctctctgggtcctctccttgtccctctctgggtcctctcct +tgtccctctctggcctctctgggtcctctctgacctctctgggtcctctccttgtccctc +tctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgg +gtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcct +ctccttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctggg +tcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctc +tccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcctt +gtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtccttt +ccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgcc +tctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagct +gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgggaa +>syndip_1_chr20:62270179-62271195 +cgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtca +gctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcacc +tcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctg +ggtcctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcctc +tctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgg +gtcctctccttgtccctc-ctggcctctctgggtcctctccttgtccctctctgggtcct +ctccttgtccctctctggcctctctgggtcctctct---gacctctctgagtcctctcct +tgtc-----------------------------cctctctgggtcctctccttgtccctc +tctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgg +gtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcct +ctccttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctggg +tcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctc +tccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcctt +gtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtccttt +ccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgcc +tctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagct +gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgggaa +>syndip_2_chr20:62270179-62271195 +cgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtca +gctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcacc +tcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctg +ggtcctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcctc +tctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgg +gtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcct +ctccttgtccctc-ctgg-----------------------cctctctgggtcctctcct +tgtc-------------------------------------------------------- +---------------------------------------------------cctctctgg +gtcctctccttgtccctctctgacctctctgggtcctctccttgtccctctctgggtcct +ctccttgtc-----------------------------------------cctctctggg +tcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctc +tccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcctt +gtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtccttt +ccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgcc +tctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagct +gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgggaa +>p:HG002_1_chr20:62270179-62271195 +cgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtca +gctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcacc +tcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctg +ggtcctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcctc +tctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgg +gtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcct +ctccttgtccctc-ctgg-----------------------cctctctgggtcctctcct +tgtc-------------------------------------------------------- +---------------------------------------------------cctctctgg +gtcctctccttgtccctctctgacctctctgggtcctctccttgtccctctctgggtcct +ctccttgtc-----------------------------------------cctctctggg +tcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctc +tccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcctt +gtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtccttt +ccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgcc +tctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagct +gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgggaa +>p:HG002_2_chr20:62270179-62271195 +cgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtca +gctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcacc +tcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctg +ggtcctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcctc +tctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgg +gtcctctccttgtccctc-ctggcctctctgggtcctctccttgtccctctctgggtcct +ctccttgtccctctctggcctctctgggtcctctct---gacctctctgagtcctctcct +tgtc-----------------------------cctctctgggtcctctccttgtccctc +tctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgg +gtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcct +ctccttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctggg +tcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctc +tccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcctt +gtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtccttt +ccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgcc +tctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagct +gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgggaa diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/msa.fa.fai new file mode 100644 index 00000000..a994a053 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_62270179_62271195 1018 29 60 61 +syndip_1_chr20:62270179-62271195 1018 1098 60 61 +syndip_2_chr20:62270179-62271195 1018 2167 60 61 +p:HG002_1_chr20:62270179-62271195 1018 3237 60 61 +p:HG002_2_chr20:62270179-62271195 1018 4307 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/output.vcf.gz new file mode 100644 index 00000000..0c410b43 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/output.vcf.gz.tbi new file mode 100644 index 00000000..0f467602 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62270279-62271095/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/base.vcf.gz new file mode 100644 index 00000000..e3139f7a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/base.vcf.gz.tbi new file mode 100644 index 00000000..77f0bdf8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/comp.vcf.gz new file mode 100644 index 00000000..e1be1968 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/comp.vcf.gz.tbi new file mode 100644 index 00000000..a7244bb1 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/haps.fa new file mode 100644 index 00000000..3fcd6b4e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/haps.fa @@ -0,0 +1,82 @@ +>ref_chr20_62320931_62321974 +AGGCCAGGGGAGAATGATCAGCTGGGGCCCTGGGGTCATTAGGGTGGGGAGGGCTCAGCCAGAGGTCATGAGGTCAGCTTAGGGACACAGGACCTGTGGGGAGGTCCCAGAGTTCTGGCAGAGTCATAGGGTCAGGTAGGAGTCAGATGGGAGTGAAGGGCATGGGGTCACCCAGGGAGAAGGTAGGGCCAGCACAAGGGGTTGGGGCCGGAGGTGGGGCCAGTGAAGGGGCGGGGCCGGTGGAGGCAGGGTCAGTGAAGGGGTGGGGCCAGTGGAGGAAGAGGGGGCCAGTGGAGGAGGCGGGGCCTGTGGAGGGGTGGGGCCAGTGGAGGCAGGGTCAGTGAAGGGGTGGGGCCGGTGGAGGAAGAGGGGGCCAGTGAAGGTGTGGGGCCAGTGGAGGAGGTGCAGCCAGTGGAAGAGGTGGGGCCAGTGGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGAGGACGGGTGGGTTCAGAGGACGGGTAGGGTCAGTGGAGGGGTAGGGCCAGCAGAGGGGTAGGGCCAGCAGAGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGAGGCAGGGTCAGTGAAAGGGTGGCGCCAGTGGAGGAAGAGGGGGCCAGTGGAGGCAGGGCCTGTGGAGGGGTGGGGCCAGTGGAGGTGGGGTCAGTGAAGGGGTGGGGCCAGCGGAGGAGGTGCAGCCAGTGGAAGAGGTGGGGCCAATGGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGGGGAGGCAGGGCCAGCAGAGGGGTGGGGTCAGTGGAGGGGTGGGGCCAGTGGAGGGGTGGGGTCAGTGGGGGAGGAAGGGCCAGCAGATGGGGTGGGGCCAGGGCACACAGGAAGGCTAGGGACAGTAGAGGGGTGCAGCCAGCAGTGGAGCTGCAGCGCTCCTCAGCGTGGTTGGAGTTGGACAGGCATGGGTCTCTCGGGAAATGGAAGGCAGCTGGGACCACTCTGGGAGGTCGACGTTAACACTGGGGTCACCAGGCTGTGTGGGACTTGGAT +>syndip_1_chr20:62320931-62321974 +AGGCCAGGGGAGAATGATCAGCTGGGGCCCTGGGGTCATTAGGGTGGGGAGGGCTCAGCC +AGAGGTCATGAGGTCAGCTTAGGGACACAGGACCTGTGGGGAGGTCCCAGAGTTCTGGCA +GAGTCATAGGGTCAGGTAGGAGTCAGATGGGAGTGAAGGGCATGGGGTCACCCAGGGAGA +AGGTAGGGCCAGCACAAGGGGTTGGGGCCGGAGGTGGGGCCAGTGAAGGGGCGGGGCCGG +TGGAGGCAGGGTCAGTGAAGGGGTGGGGCCAGTGGAGGAAGAGGGGGCCAGTGGAGGAGG +CGGGGCCTGTGGAGGGGTGGGGCCAGTGGAGGCAGGGTCAGTGAAGGGGTGGGGCCGGTG +GAGGAAGAGGGGGCCAGTGAAGGTGTGGGGCCAGTGGAGGAGGTGCAGCCAGTGGAAGAG +GTGGGGCCAGTGGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGAGGACAGGTGGGTTCAGA +GGACGGGTGGGTTCAGAGGACGGGTGGGTTCAGAGGACGGGTGGGGTCAGTGGAGGGGTG +GGGTCAGTGGAGGGGTAGGGTCAGAGGACGGGTAGGGTCAGTGGAGGGGTAGGGCCAGCA +GAGGGGTGGGGTCAGCGGAGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGAGGGGTGG +GGTCAGTGGAGGCAGGGTCAGTGAAAGGGTGGCGCCAGTGGAGGAAGAGGGCGCCAGTGG +AGGAAGAGGGCGCCAGTGGAGGAAGAGGGGGCCAGTGGAGGCAGGGCCTGTGGAGGGGTG +GGGCCAGTGGAGGTGGGGTCAGTGAAGGGGTGGGGCCAGCGGAGGAGGTGCAGCCAGTGG +AAGAGGTGGGGCCAATGGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGGGGAGGCAGG +GCCAGCAGAGGGGTGGGGCCAGTGGAGGGGTGGGGCCAGCGGAGGGGTGGGGTCAGTGGG +GGAGGAAGGGCCAGCAGATGGGGTGGGGCCAGGGCACACAGGAAGGCTAGGGACAGTAGA +GGGGTGCAGCCAGCAGTGGAGCTGCAGCGCTCCTCAGCGTGGTTGGAGTTGGACAGGCAT +GGGTCTCTCGGGAAATGGAAGGCAGCTGGGACCACTCTGGGAGGTCGACGTTAACACTGG +GGTCACCAGGCTGTGTGGGACTTGGAT +>syndip_2_chr20:62320931-62321974 +AGGCCAGGGGAGAATGATCAGCTGGGGCCCTGGGGTCATTAGGGTGGGGAGGGCTCAGCC +AGAGGTCATGAGGTCAGCTTAGGGACACAGGACCTGTGGGGAGGTCCCAGAGTTCTGGCA +GAGTCATAGGGTCAGGTAGGAGTCAGATGGGAGTGAAGGGCATGGGGTCACCCAGGGAGA +AGGTAGGGCCAGCACAAGGGGTTGGGGCCGGAGGTGGGGCCAGTGAAGGGGCGGGGCCGG +TGGAGGCAGGGTCAGTGAAGGGGTGGGGCCAGTGGAGGAAGAGGGGGCCAGTGGAGGAGG +CGGGGCCTGTGGAGGGGTGGGGCCAGTGGAGGCAGGGTCAGTGAAGGGGTGGGGCCGGTG +GAGGAAGAGGGGGCCAGTGAAGGTGTGGGGCCAGTGGAGGAGGTGCAGCCAGTGGCAGAG +GTGGGGCCAGTGGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGAGGACGGGTAGGGTCAGT +GGAGGGGTAGGGCCAGCAGAGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGAGGGGTG +GGGTCAGTGGAGGCAGGGTCAGTGAAAGGGTGGCGCCAGTGGAGGAAGAGGGCGCCAGTG +GAGGAAGAGGGGGCCAGTGGAGGCAGGGCCTGTGGAGGGGTGGGGCCAGTGGAGGTGGGG +TCAGTGAAGGGGTGGGGCCAGCGGAGGAGGTGCAGCCAGTGGAAGAGGTGGGGCCAATGG +GGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGGGGAGGCAGGGCCAGCAGAGGGGTGGGG +CCAGTGGAGGGGTGGGGCCAGCGGAGGGGTGGGGCCAGCGGAGGGGTGGGGTCAGTGGGG +GAGGAAGGGCCAGCAGATGGGGTGGGGCCAGGGCACACAGGAAGGCTAGGGACAGTAGAG +GGGTGCAGCCAGCAGTGGAGCTGCAGCGCTCCTCAGCGTGGTTGGAGTTGGACAGGCATG +GGTCTCTCGGGAAATGGAAGGCAGCTGGGACCACTCTGGGAGGTCGACGTTAACACTGGG +GTCACCAGGCTGTGTGGGACTTGGAT +>p:HG002_1_chr20:62320931-62321974 +AGGCCAGGGGAGAATGATCAGCTGGGGCCCTGGGGTCATTAGGGTGGGGAGGGCTCAGCC +AGAGGTCATGAGGTCAGCTTAGGGACACAGGACCTGTGGGGAGGTCCCAGAGTTCTGGCA +GAGTCATAGGGTCAGGTAGGAGTCAGATGGGAGTGAAGGGCATGGGGTCACCCAGGGAGA +AGGTAGGGCCAGCACAAGGGGTTGGGGCCGGAGGTGGGGCCAGTGAAGGGGCGGGGCCGG +TGGAGGCAGGGTCAGTGAAGGGGTGGGGCCAGTGGAGGAAGAGGGGGCCAGTGGAGGAGG +CGGGGCCTGTGGAGGGGTGGGGCCAGTGGAGGCAGGGTCAGTGAAGGGGTGGGGCCGGTG +GAGGAAGAGGGGGCCAGTGAAGGTGTGGGGCCAGTGGAGGAGGTGCAGCCAGTGGCAGAG +GTGGGGCCAGTGGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGAGGACGGGTAGGGTCAGT +GGAGGGGTAGGGCCAGCAGAGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGAGGGGTG +GGGTCAGTGGAGGCAGGGTCAGTGAAAGGGTGGCGCCAGTGGAGGAAGAGGGCGCCAGTG +GAGGAAGAGGGGGCCAGTGGAGGCAGGGCCTGTGGAGGGGTGGGGCCAGTGGAGGTGGGG +TCAGTGAAGGGGTGGGGCCAGCGGAGGAGGTGCAGCCAGTGGAAGAGGTGGGGCCAATGG +GGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGGGGAGGCAGGGCCAGCAGAGGGGTGGGG +CCAGTGGAGGGGTGGGGCCAGCGGAGGGGTGGGGCCAGCGGAGGGGTGGGGTCAGTGGGG +GAGGAAGGGCCAGCAGATGGGGTGGGGCCAGGGCACACAGGAAGGCTAGGGACAGTAGAG +GGGTGCAGCCAGCAGTGGAGCTGCAGCGCTCCTCAGCGTGGTTGGAGTTGGACAGGCATG +GGTCTCTCGGGAAATGGAAGGCAGCTGGGACCACTCTGGGAGGTCGACGTTAACACTGGG +GTCACCAGGCTGTGTGGGACTTGGAT +>p:HG002_2_chr20:62320931-62321974 +AGGCCAGGGGAGAATGATCAGCTGGGGCCCTGGGGTCATTAGGGTGGGGAGGGCTCAGCC +AGAGGTCATGAGGTCAGCTTAGGGACACAGGACCTGTGGGGAGGTCCCAGAGTTCTGGCA +GAGTCATAGGGTCAGGTAGGAGTCAGATGGGAGTGAAGGGCATGGGGTCACCCAGGGAGA +AGGTAGGGCCAGCACAAGGGGTTGGGGCCGGAGGTGGGGCCAGTGAAGGGGCGGGGCCGG +TGGAGGCAGGGTCAGTGAAGGGGTGGGGCCAGTGGAGGAAGAGGGGGCCAGTGGAGGAGG +CGGGGCCTGTGGAGGGGTGGGGCCAGTGGAGGCAGGGTCAGTGAAGGGGTGGGGCCGGTG +GAGGAAGAGGGGGCCAGTGAAGGTGTGGGGCCAGTGGAGGAGGTGCAGCCAGTGGAAGAG +GTGGGGCCAGTGGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGAGGACAGGTGGGTTCAGA +GGACGGGTGGGTTCAGAGGACGGGTGGGTTCAGAGGACGGGTGGGGTCAGTGGAGGGGTG +GGGTCAGTGGAGGGGTAGGGTCAGAGGACGGGTAGGGTCAGTGGAGGGGTAGGGCCAGCA +GAGGGGTGGGGTCAGCGGAGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGAGGGGTGG +GGTCAGTGGAGGCAGGGTCAGTGAAAGGGTGGCGCCAGTGGAGGAAGAGGGCGCCAGTGG +AGGAAGAGGGCGCCAGTGGAGGAAGAGGGGGCCAGTGGAGGCAGGGCCTGTGGAGGGGTG +GGGCCAGTGGAGGTGGGGTCAGTGAAGGGGTGGGGCCAGCGGAGGAGGTGCAGCCAGTGG +AAGAGGTGGGGCCAATGGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGGGGAGGCAGG +GCCAGCAGAGGGGTGGGGCCAGTGGAGGGGTGGGGCCAGCGGAGGGGTGGGGTCAGTGGG +GGAGGAAGGGCCAGCAGATGGGGTGGGGCCAGGGCACACAGGAAGGCTAGGGACAGTAGA +GGGGTGCAGCCAGCAGTGGAGCTGCAGCGCTCCTCAGCGTGGTTGGAGTTGGACAGGCAT +GGGTCTCTCGGGAAATGGAAGGCAGCTGGGACCACTCTGGGAGGTCGACGTTAACACTGG +GGTCACCAGGCTGTGTGGGACTTGGAT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/haps.fa.ref.fa new file mode 100644 index 00000000..f4e5333f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:62320931-62321974 +AGGCCAGGGGAGAATGATCAGCTGGGGCCCTGGGGTCATTAGGGTGGGGAGGGCTCAGCCAGAGGTCATGAGGTCAGCTTAGGGACACAGGACCTGTGGGGAGGTCCCAGAGTTCTGGCAGAGTCATAGGGTCAGGTAGGAGTCAGATGGGAGTGAAGGGCATGGGGTCACCCAGGGAGAAGGTAGGGCCAGCACAAGGGGTTGGGGCCGGAGGTGGGGCCAGTGAAGGGGCGGGGCCGGTGGAGGCAGGGTCAGTGAAGGGGTGGGGCCAGTGGAGGAAGAGGGGGCCAGTGGAGGAGGCGGGGCCTGTGGAGGGGTGGGGCCAGTGGAGGCAGGGTCAGTGAAGGGGTGGGGCCGGTGGAGGAAGAGGGGGCCAGTGAAGGTGTGGGGCCAGTGGAGGAGGTGCAGCCAGTGGAAGAGGTGGGGCCAGTGGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGAGGACGGGTGGGTTCAGAGGACGGGTAGGGTCAGTGGAGGGGTAGGGCCAGCAGAGGGGTAGGGCCAGCAGAGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGAGGCAGGGTCAGTGAAAGGGTGGCGCCAGTGGAGGAAGAGGGGGCCAGTGGAGGCAGGGCCTGTGGAGGGGTGGGGCCAGTGGAGGTGGGGTCAGTGAAGGGGTGGGGCCAGCGGAGGAGGTGCAGCCAGTGGAAGAGGTGGGGCCAATGGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGGGGAGGCAGGGCCAGCAGAGGGGTGGGGTCAGTGGAGGGGTGGGGCCAGTGGAGGGGTGGGGTCAGTGGGGGAGGAAGGGCCAGCAGATGGGGTGGGGCCAGGGCACACAGGAAGGCTAGGGACAGTAGAGGGGTGCAGCCAGCAGTGGAGCTGCAGCGCTCCTCAGCGTGGTTGGAGTTGGACAGGCATGGGTCTCTCGGGAAATGGAAGGCAGCTGGGACCACTCTGGGAGGTCGACGTTAACACTGGGGTCACCAGGCTGTGTGGGACTTGGAT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/msa.fa new file mode 100644 index 00000000..49a139cf --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/msa.fa @@ -0,0 +1,105 @@ +>ref_chr20_62320931_62321974 +aggccaggggagaatgatcagctggggccctggggtcattagggtggggagggctcagcc +agaggtcatgaggtcagcttagggacacaggacctgtggggaggtcccagagttctggca +gagtcatagggtcaggtaggagtcagatgggagtgaagggcatggggtcacccagggaga +aggtagggccagcacaaggggttggggccggaggtggggccagtgaaggggcggggccgg +tggaggcagggtcagtgaaggggtggggccagtggaggaagagggggccagtggaggagg +cggggcctgtggaggggtggggccagtggaggcagggtcagtgaaggggtggggccggtg +gaggaagagggggccagtgaaggtgtggggccagtggaggaggtgcagccagtggaagag +gtggggccagtgggggtggggtcagtggaggggtggggtcagaggacgggtgggt----- +------------------------------------------------------------ +--------------------tcagaggacgggtagggtcagtggaggggtagggccagca +gaggggtagggccagcagaggggtggggtcagtggaggggtggggtcagtggaggggtgg +ggtcagtggaggcagggtcagtgaaagggt------------------------------ +--------ggcgccagtggaggaagagggggccagtggaggcagggcctgtggaggggtg +gggccagtggaggtggggtcagtgaaggggtggggccagcggaggaggtgcagccagtgg +aagaggtggggccaatgggggtggggtcagtggaggggtggggtcagtgggggaggcagg +gccagcagaggggtggggtcagt-----------------ggaggggtggggccagtgga +ggggtggggtcagtgggggaggaagggccagcagatggggtggggccagggcacacagga +aggctagggacagtagaggggtgcagccagcagtggagctgcagcgctcctcagcgtggt +tggagttggacaggcatgggtctctcgggaaatggaaggcagctgggaccactctgggag +gtcgacgttaacactggggtcaccaggctgtgtgggacttggat +>syndip_1_chr20:62320931-62321974 +aggccaggggagaatgatcagctggggccctggggtcattagggtggggagggctcagcc +agaggtcatgaggtcagcttagggacacaggacctgtggggaggtcccagagttctggca +gagtcatagggtcaggtaggagtcagatgggagtgaagggcatggggtcacccagggaga +aggtagggccagcacaaggggttggggccggaggtggggccagtgaaggggcggggccgg +tggaggcagggtcagtgaaggggtggggccagtggaggaagagggggccagtggaggagg +cggggcctgtggaggggtggggccagtggaggcagggtcagtgaaggggtggggccggtg +gaggaagagggggccagtgaaggtgtggggccagtggaggaggtgcagccagtggaagag +gtggggccagtgggggtggggtcagtggaggggtggggtcagaggacaggtgggttcaga +ggacgggtgggttcagaggacgggtgggttcagaggacgggtggggtcagtggaggggtg +gggtcagtggaggggtagggtcagaggacgggtagggtcagtggaggggtagggccagca +gaggggtggggtcagcggaggggtggggtcagtggaggggtggggtcagtggaggggtgg +ggtcagtggaggcagggtcagtgaaagggtggcgccagtggaggaagagggcgccagtgg +aggaagagggcgccagtggaggaagagggggccagtggaggcagggcctgtggaggggtg +gggccagtggaggtggggtcagtgaaggggtggggccagcggaggaggtgcagccagtgg +aagaggtggggccaatgggggtggggtcagtggaggggtggggtcagtgggggaggcagg +gccagcagaggggtggggccagt-----------------ggaggggtggggccagcgga +ggggtggggtcagtgggggaggaagggccagcagatggggtggggccagggcacacagga +aggctagggacagtagaggggtgcagccagcagtggagctgcagcgctcctcagcgtggt +tggagttggacaggcatgggtctctcgggaaatggaaggcagctgggaccactctgggag +gtcgacgttaacactggggtcaccaggctgtgtgggacttggat +>syndip_2_chr20:62320931-62321974 +aggccaggggagaatgatcagctggggccctggggtcattagggtggggagggctcagcc +agaggtcatgaggtcagcttagggacacaggacctgtggggaggtcccagagttctggca +gagtcatagggtcaggtaggagtcagatgggagtgaagggcatggggtcacccagggaga +aggtagggccagcacaaggggttggggccggaggtggggccagtgaaggggcggggccgg +tggaggcagggtcagtgaaggggtggggccagtggaggaagagggggccagtggaggagg +cggggcctgtggaggggtggggccagtggaggcagggtcagtgaaggggtggggccggtg +gaggaagagggggccagtgaaggtgtggggccagtggaggaggtgcagccagtggcagag +gtggggccagtgggggtggggtcagtggaggggtggggtcagaggac------------- +------------------------------------------------------------ +----------------------------------------------gggtagggtcagtg +gaggggtagggccagcagaggggtggggtcagtggaggggtggggtcagtggaggggtgg +ggtcagtggaggcagggtcagtgaaagggt-------------------ggcgccagtgg +aggaagagggcgccagtggaggaagagggggccagtggaggcagggcctgtggaggggtg +gggccagtggaggtggggtcagtgaaggggtggggccagcggaggaggtgcagccagtgg +aagaggtggggccaatgggggtggggtcagtggaggggtggggtcagtgggggaggcagg +gccagcagaggggtggggccagtggaggggtggggccagcggaggggtggggccagcgga +ggggtggggtcagtgggggaggaagggccagcagatggggtggggccagggcacacagga +aggctagggacagtagaggggtgcagccagcagtggagctgcagcgctcctcagcgtggt +tggagttggacaggcatgggtctctcgggaaatggaaggcagctgggaccactctgggag +gtcgacgttaacactggggtcaccaggctgtgtgggacttggat +>p:HG002_1_chr20:62320931-62321974 +aggccaggggagaatgatcagctggggccctggggtcattagggtggggagggctcagcc +agaggtcatgaggtcagcttagggacacaggacctgtggggaggtcccagagttctggca +gagtcatagggtcaggtaggagtcagatgggagtgaagggcatggggtcacccagggaga +aggtagggccagcacaaggggttggggccggaggtggggccagtgaaggggcggggccgg +tggaggcagggtcagtgaaggggtggggccagtggaggaagagggggccagtggaggagg +cggggcctgtggaggggtggggccagtggaggcagggtcagtgaaggggtggggccggtg +gaggaagagggggccagtgaaggtgtggggccagtggaggaggtgcagccagtggcagag +gtggggccagtgggggtggggtcagtggaggggtggggtcagaggac------------- +------------------------------------------------------------ +----------------------------------------------gggtagggtcagtg +gaggggtagggccagcagaggggtggggtcagtggaggggtggggtcagtggaggggtgg +ggtcagtggaggcagggtcagtgaaagggt-------------------ggcgccagtgg +aggaagagggcgccagtggaggaagagggggccagtggaggcagggcctgtggaggggtg +gggccagtggaggtggggtcagtgaaggggtggggccagcggaggaggtgcagccagtgg +aagaggtggggccaatgggggtggggtcagtggaggggtggggtcagtgggggaggcagg +gccagcagaggggtggggccagtggaggggtggggccagcggaggggtggggccagcgga +ggggtggggtcagtgggggaggaagggccagcagatggggtggggccagggcacacagga +aggctagggacagtagaggggtgcagccagcagtggagctgcagcgctcctcagcgtggt +tggagttggacaggcatgggtctctcgggaaatggaaggcagctgggaccactctgggag +gtcgacgttaacactggggtcaccaggctgtgtgggacttggat +>p:HG002_2_chr20:62320931-62321974 +aggccaggggagaatgatcagctggggccctggggtcattagggtggggagggctcagcc +agaggtcatgaggtcagcttagggacacaggacctgtggggaggtcccagagttctggca +gagtcatagggtcaggtaggagtcagatgggagtgaagggcatggggtcacccagggaga +aggtagggccagcacaaggggttggggccggaggtggggccagtgaaggggcggggccgg +tggaggcagggtcagtgaaggggtggggccagtggaggaagagggggccagtggaggagg +cggggcctgtggaggggtggggccagtggaggcagggtcagtgaaggggtggggccggtg +gaggaagagggggccagtgaaggtgtggggccagtggaggaggtgcagccagtggaagag +gtggggccagtgggggtggggtcagtggaggggtggggtcagaggacaggtgggttcaga +ggacgggtgggttcagaggacgggtgggttcagaggacgggtggggtcagtggaggggtg +gggtcagtggaggggtagggtcagaggacgggtagggtcagtggaggggtagggccagca +gaggggtggggtcagcggaggggtggggtcagtggaggggtggggtcagtggaggggtgg +ggtcagtggaggcagggtcagtgaaagggtggcgccagtggaggaagagggcgccagtgg +aggaagagggcgccagtggaggaagagggggccagtggaggcagggcctgtggaggggtg +gggccagtggaggtggggtcagtgaaggggtggggccagcggaggaggtgcagccagtgg +aagaggtggggccaatgggggtggggtcagtggaggggtggggtcagtgggggaggcagg +gccagcagaggggtggggccagt-----------------ggaggggtggggccagcgga +ggggtggggtcagtgggggaggaagggccagcagatggggtggggccagggcacacagga +aggctagggacagtagaggggtgcagccagcagtggagctgcagcgctcctcagcgtggt +tggagttggacaggcatgggtctctcgggaaatggaaggcagctgggaccactctgggag +gtcgacgttaacactggggtcaccaggctgtgtgggacttggat diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/msa.fa.fai new file mode 100644 index 00000000..3a076f7f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_62320931_62321974 1184 29 60 61 +syndip_1_chr20:62320931-62321974 1184 1267 60 61 +syndip_2_chr20:62320931-62321974 1184 2505 60 61 +p:HG002_1_chr20:62320931-62321974 1184 3744 60 61 +p:HG002_2_chr20:62320931-62321974 1184 4983 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/output.vcf.gz new file mode 100644 index 00000000..233be3ad Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/output.vcf.gz.tbi new file mode 100644 index 00000000..01bf8ce5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62321031-62321874/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/base.vcf.gz new file mode 100644 index 00000000..0876bd7c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/base.vcf.gz.tbi new file mode 100644 index 00000000..427c1de8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/comp.vcf.gz new file mode 100644 index 00000000..087475d9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/comp.vcf.gz.tbi new file mode 100644 index 00000000..166ddc61 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/haps.fa new file mode 100644 index 00000000..46a6e858 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/haps.fa @@ -0,0 +1,102 @@ +>ref_chr20_62349512_62350033 +GAATCCTACAGTCAGCTCAACTATCATTCAAGAGGGAGGACAAAACAGCCGTTTTCAGACAATTCCGGATAGACTGTCATGGAATAGAAAAACTACAGGGTGCATTTCAGGAAGGAGGAAGCAGCAACCCAGGGGATGGGGATGGGGATGGGGATGGTGGGGGTGATGGGGGTGATGATGGTGATGGTGATGGTGATGGTGATGGTGATGGTGATGGTGGGGGTGGTGATGGGTGGGGGTGATGACGGTGGGAGTGGGGGTGATGACGGTGATGGTGGGGGTGATGACGGTGATGGTGGGGGTGATGACGGTGATGGTGGGGGTGATGATGGTGGGAGTGGGCTGGTAGTGGGGGTGATGGTTTGGGTGGGAGTAAGGTGATGGTGGAGGTAAAGAGGCAGAAAATTGCTGGCTGATGACATGGAGCCCCCTTCCCTGGAGGAGAGGTGGGGTGGCGGGTAAAGGGTGCAGGGAGAACATGGGCAGGCTAATGTTTTGGGACACTGGTGGGTGACCAGGTCC +>syndip_1_chr20:62349512-62350033 +GAATCCTACAGTCAGCTCAACTATCATTCAAGAGGGAGGACAAAACAGCCGTTTTCAGAC +AATTCCGGATAGACTGTCATGGAATAGAAAAACTACAGGGTGCATTTCAGGAAGGAGGAA +GCAGCAACCCAGGGGATGGGGATGGGGATGGGGATGGGGATGGTGGGGGTGATGGGGGTG +ATGATGGTGATGGTGGGGGTGATGATGGTGATGGTGATGGTGATGGTGGGGGTGGTGATG +GTGGGGGTGGGGGTGGTGATGGTGGGGGTGGGGGTGATGATGGTGATGGTGGGGGTGATG +ACGGTGGGGCTGGGGGTGATGATGGTGGGGGTGATGACGGTGATGATGGGGGTGGAGGGG +TGATGACGGTGATGATGGGGGTGGGGGGGTGATGACGGTGATGTGGGGGTGATGACGGTG +GGGGTGGGGGTGATGACGGTGATGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACG +GTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATG +ATGGTGATGGTGGGGGTGATGATGGTGGGGGTGGGGGTGATGATGGTGAGGGTGATGATG +GTGGGGGTAATGACGGTGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGA +TGGTGGGGGTGATGACGATGATGGTGGGGGTGATGACGGTGATGGCGGTGGGGGTGATGA +CGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGA +TGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGG +TGATGACGGTGGGGGTGGGGGTGATGACGGTGATGGTAGAGGTGATGATGGTGGGGGTGA +TGGTGGGGGTGGGGGTGGGGGTGGGGGTGATGATGGTGATGGTGGGGGTGATGATGGTGA +GGGTGATGATGGTGGGGGTGATGGTGGGGGTGGGGGTGGGGGTGGGGGTGATGACGGTGA +TGGTGGGGGTGATGATGGTGGGAGTGGGCTGGTAGTGGGGGTGATGGTTTGGGTGGGAGT +AAGGTGATGGTGGAGGTAAAGAGGCAGAAAATTGCTGGCTGATGACATGGAGCCCCCTTC +CCTGGAGGAGAGGTGGGGTGGCGGGTAAAGGGTGCAGGGAGAACATGGGCAGGCTAATGT +TTTGGGACACTGGTGGGTGACCAGGTCC +>syndip_2_chr20:62349512-62350033 +GAATCCTACAGTCAGCTCAACTATCATTCAAGAGGGAGGACAAAACAGCCGTTTTCAGAC +AATTCCGGATAGACTGTCATGGAATAGAAAAACTACAGGGTGCATTTCAGGAAGGAGGAA +GCAGCAACCCAGGGGATGGGGATGGGGATGGGGATGGGGATGGTGGGGGTGATGGGGGTG +ATGATGGTGATGGTGGGGGTGATGATGGTGATGGTGATGGTGATGGTGATGGTGGGGGTG +GTGATGGTGGGGGTGGGGGTGATGATGGTGATGGTGGGGGTGATGACGGTGGGGCTGGGG +GTGATGATGGTGGGGGTGATGACGGTGATGATGGGGGTGGAGGGGTGATGACGGTGATGA +TGGGGGTGGGGGGGTGATGACGGTGATGTGGGGGTGATGACGGTGGGGGTGGGGGTGATG +ACGGTGATGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTG +ATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGG +GTGATGATGGTGATGGTGGGGGTGATGATGGTGGGGGTGGGGGTGATGATGGTGAGGGTG +ATGATGGTGGGGGTAATGACGGTGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGA +CGGTGATGGTGGGGGTGATGACGATGATGGTGGGGGTGATGACGGTGATGGCGGTGGGGG +TGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGG +GGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGG +TGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGATGGTAGAGGTGATGATGGTGG +GGGTGGGGGTGGGGGTGGGGGTGAGGGTGATGATGGTGGGGGTGATGATGGTGATGGTGG +GGGTGATGATGGTGAGGGTGATGATGGTGGGGGTGATGGTGGGGGTGGGGGTGGGGGTAA +TGACGGTGGGGTGGGGGTAATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGT +GATGACGGTGATGGTGGGGGTGATGACGATGATGGTGGGGGTGATGACGGTGATGGCGGT +GGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGG +GGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGT +GATGGTAGAGGTGATGATGGTGGGGGTGATGGTGGGGGTGGGGGTGGGGGTGGGGGTGAT +GATGGTGATGGTGGGGGTGATGATGGTGAGGGTGATGATGGTGGGGGTGATGGTGGGGGT +GGGGGTGGGGGTGGGGGTGATGATGGTGGGAGTGGGCTGGTAGTGGGGGTGATGGTTTGG +GTGGGAGTAAGGTGATGGTGGAGGTAAAGAGGCAGAAAATTGCTGGCTGATGACATGGAG +CCCCCTTCCCTGGAGGAGAGGTGGGGTGGCGGGTAAAGGGTGCAGGGAGAACATGGGCAG +GCTAATGTTTTGGGACACTGGTGGGTGACCAGGTCC +>p:HG002_1_chr20:62349512-62350033 +GAATCCTACAGTCAGCTCAACTATCATTCAAGAGGGAGGACAAAACAGCCGTTTTCAGAC +AATTCCGGATAGACTGTCATGGAATAGAAAAACTACAGGGTGCATTTCAGGAAGGAGGAA +GCAGCAACCCAGGGGATGGGGATGGGGATGGGGATGGGGATGGTGGGGGTGATGGGGGTG +ATGATGGTGATGGTGGGGGTGATGATGGTGATGGTGATGGTGATGGTGATGGTGGGGGTG +GTGATGGTGGGGGTGGGGGTGATGATGGTGATGGTGGGGGTGATGACGGTGGGGCTGGGG +GTGATGATGGTGGGGGTGATGACGGTGATGATGGGGGTGGAGGGGTGATGACGGTGATGA +TGGGGGTGGGGGGGTGATGACGGTGATGTGGGGGTGATGACGGTGGGGGTGGGGGTGATG +ACGGTGATGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTG +ATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGG +GTGATGATGGTGATGGTGGGGGTGATGATGGTGGGGGTGGGGGTGATGATGGTGAGGGTG +ATGATGGTGGGGGTAATGACGGTGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGA +CGGTGATGGTGGGGGTGATGACGATGATGGTGGGGGTGATGACGGTGATGGCGGTGGGGG +TGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGG +GGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGG +TGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGATGGTAGAGGTGATGATGGTGG +GGGTGGGGGTGGGGGTGGGGGTGAGGGTGATGATGGTGGGGGTGATGATGGTGATGGTGG +GGGTGATGATGGTGAGGGTGATGATGGTGGGGGTGATGGTGGGGGTGGGGGTGGGGGTAA +TGACGGTGGGGTGGGGGTAATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGT +GATGACGGTGATGGTGGGGGTGATGACGATGATGGTGGGGGTGATGACGGTGATGGCGGT +GGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGG +GGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGT +GATGGTAGAGGTGATGATGGTGGGGGTGATGGTGGGGGTGGGGGTGGGGGTGGGGGTGAT +GATGGTGATGGTGGGGGTGATGATGGTGAGGGTGATGATGGTGGGGGTGATGGTGGGGGT +GGGGGTGGGGGTGGGGGTGATGATGGTGGGAGTGGGCTGGTAGTGGGGGTGATGGTTTGG +GTGGGAGTAAGGTGATGGTGGAGGTAAAGAGGCAGAAAATTGCTGGCTGATGACATGGAG +CCCCCTTCCCTGGAGGAGAGGTGGGGTGGCGGGTAAAGGGTGCAGGGAGAACATGGGCAG +GCTAATGTTTTGGGACACTGGTGGGTGACCAGGTCC +>p:HG002_2_chr20:62349512-62350033 +GAATCCTACAGTCAGCTCAACTATCATTCAAGAGGGAGGACAAAACAGCCGTTTTCAGAC +AATTCCGGATAGACTGTCATGGAATAGAAAAACTACAGGGTGCATTTCAGGAAGGAGGAA +GCAGCAACCCAGGGGATGGGGATGGGGATGGGGATGGGGATGGTGGGGGTGATGGGGGTG +ATGATGGTGATGGTGGGGGTGATGATGGTGATGGTGATGGTGATGGTGGGGGTGGTGATG +GTGGGGGTGGGGGTGGTGATGGTGGGGGTGGGGGTGATGATGGTGATGGTGGGGGTGATG +ACGGTGGGGCTGGGGGTGATGATGGTGGGGGTGATGACGGTGATGATGGGGGTGGAGGGG +TGATGACGGTGATGATGGGGGTGGGGGGGTGATGACGGTGATGTGGGGGTGATGACGGTG +GGGGTGGGGGTGATGACGGTGATGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACG +GTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATG +ATGGTGATGGTGGGGGTGATGATGGTGGGGGTGGGGGTGATGATGGTGAGGGTGATGATG +GTGGGGGTAATGACGGTGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGA +TGGTGGGGGTGATGACGATGATGGTGGGGGTGATGACGGTGATGGCGGTGGGGGTGATGA +CGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGA +TGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGG +TGATGACGGTGGGGGTGGGGGTGATGACGGTGATGGTAGAGGTGATGATGGTGGGGGTGA +TGGTGGGGGTGGGGGTGGGGGTGGGGGTGATGATGGTGATGGTGGGGGTGATGATGGTGA +GGGTGATGATGGTGGGGGTGATGGTGGGGGTGGGGGTGGGGGTGGGGGTGATGACGGTGA +TGGTGGGGGTGATGATGGTGGGAGTGGGCTGGTAGTGGGGGTGATGGTTTGGGTGGGAGT +AAGGTGATGGTGGAGGTAAAGAGGCAGAAAATTGCTGGCTGATGACATGGAGCCCCCTTC +CCTGGAGGAGAGGTGGGGTGGCGGGTAAAGGGTGCAGGGAGAACATGGGCAGGCTAATGT +TTTGGGACACTGGTGGGTGACCAGGTCC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/haps.fa.ref.fa new file mode 100644 index 00000000..8f32fa6f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:62349512-62350033 +GAATCCTACAGTCAGCTCAACTATCATTCAAGAGGGAGGACAAAACAGCCGTTTTCAGACAATTCCGGATAGACTGTCATGGAATAGAAAAACTACAGGGTGCATTTCAGGAAGGAGGAAGCAGCAACCCAGGGGATGGGGATGGGGATGGGGATGGTGGGGGTGATGGGGGTGATGATGGTGATGGTGATGGTGATGGTGATGGTGATGGTGATGGTGGGGGTGGTGATGGGTGGGGGTGATGACGGTGGGAGTGGGGGTGATGACGGTGATGGTGGGGGTGATGACGGTGATGGTGGGGGTGATGACGGTGATGGTGGGGGTGATGATGGTGGGAGTGGGCTGGTAGTGGGGGTGATGGTTTGGGTGGGAGTAAGGTGATGGTGGAGGTAAAGAGGCAGAAAATTGCTGGCTGATGACATGGAGCCCCCTTCCCTGGAGGAGAGGTGGGGTGGCGGGTAAAGGGTGCAGGGAGAACATGGGCAGGCTAATGTTTTGGGACACTGGTGGGTGACCAGGTCC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/msa.fa new file mode 100644 index 00000000..9458709a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/msa.fa @@ -0,0 +1,140 @@ +>ref_chr20_62349512_62350033 +gaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcagac +aattccggatagactgtcatggaatagaaaaactacagggtgcatttcag---------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------------gaaggaggaag +cagcaacccaggggatggggatggggatggggatggtgggggtgatgggggtgatgatgg +tgatggtgatggtgatggtgatggtgatggtgatggtggg---------ggtggtgatg- +----------ggtgggggtgatgacggtgggagtgggggtgatgacggtgatggtggggg +tgat-----------------------------------------------------gac +ggtgatggtgggggtgatgacggtgat--------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------ggtgggggtgatgatggtgggagtgggctggtagtg +ggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgctg +gctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagggtgcag +ggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtcc +>syndip_1_chr20:62349512-62350033 +gaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcagac +aattccggatagactgtcatggaatagaaaaactacagggtgcatttcaggaaggaggaa +gcagcaacccaggggatggggatggggatggggatggggatggtgggggtgatgggggtg +atgatggtgatggtgggggtgatgatggtgatggtgatggtgatggtgggggtggtgatg +gtgggggtgggggtggtgatggtgggggtgggggtgatgatggtgatggtgggggtgatg +acggtggggctgggggtgatgatggtgggggtgatgacggtgatgatgggggtggagggg +tgatgacggtgatgatgggggtgggggggtgatgacggtgatgtgggggtgatgacggtg +ggggtgggggtgatgacggtgat---------------------ggtgggggtgatgacg +gtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatg +acggtgggggtgggggtgatgatggtgatggtgggggtgatgatggtgggggtgggggtg +atgatggtgagggtgatgatggtgggggtaatgacggtggggtgggggtgatgacggtgg +gggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtgatgacgg +tgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtga +tgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtggggg +tgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtag +aggtgatgatggtgggggtgatggtgggggtgggggtggg---------ggtgggggtga +tgatggtgatggtgggggtgatgatggtgagggtgatgatggtgggggtgatggtggggg +tggg-------------------------------------------------------- +ggtgggggtgggggtgatgacggtgat--------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------ggtgggggtgatgatggtgggagtgggctggtagtg +ggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgctg +gctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagggtgcag +ggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtcc +>syndip_2_chr20:62349512-62350033 +gaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcagac +aattccggatagactgtcatggaatagaaaaactacagggtgcatttcaggaaggaggaa +gcagcaacccaggggatggggatggggatggggatggggatggtgggggtgatgggggtg +atgatggtgatggtgggggtgatgatggtgatggtga---------------tggtgatg +gtgatggtgggggtggtgatggtgggggtgggggtgatgatggtgatggtgggggtgatg +acggtggggctgggggtgatgatggtgggggtgatgacggtgatgatgggggtggagggg +tgatgacggtgatgatgggggtgggggggtgatgacggtgatgtgggggtgatgacggtg +ggggtgggggtgatgacggtgatggtgggggtgatgacggtgggggtgggggtgatgacg +gtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatg +acggtgggggtgggggtgatgatggtgatggtgggggtgatgatggtgggggtgggggtg +atgatggtgagggtgatgatggtgggggtaatgacggtggggtgggggtgatgacggtgg +gggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtgatgacgg +tgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtga +tgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtggggg +tgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtag +aggtgatgatggtgggggtgggggtgggggtgggggtgagggtgatgatggtgggggtga +tgatggtgatggtgggggtgatgatggtgagggtgatgatggtgggggtgatggtggggg +tgggggtgggggtaatgacggtggggtgggggtaatgacggtgggggtgggggtgatgac +ggtgggggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtgat +gacggtgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtggg +ggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggt +gggggtgatgacggtgatggtagaggtgatgatggtgggggtgatggtgggggtgggggt +gggggtgggggtgatgatggtgatggtgggggtgatgatggtgagggtgatgatggtggg +ggtgatggtgggggtgggggtgggggtgggggtgatgatggtgggagtgggctggtagtg +ggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgctg +gctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagggtgcag +ggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtcc +>p:HG002_1_chr20:62349512-62350033 +gaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcagac +aattccggatagactgtcatggaatagaaaaactacagggtgcatttcaggaaggaggaa +gcagcaacccaggggatggggatggggatggggatggggatggtgggggtgatgggggtg +atgatggtgatggtgggggtgatgatggtgatggtga---------------tggtgatg +gtgatggtgggggtggtgatggtgggggtgggggtgatgatggtgatggtgggggtgatg +acggtggggctgggggtgatgatggtgggggtgatgacggtgatgatgggggtggagggg +tgatgacggtgatgatgggggtgggggggtgatgacggtgatgtgggggtgatgacggtg +ggggtgggggtgatgacggtgatggtgggggtgatgacggtgggggtgggggtgatgacg +gtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatg +acggtgggggtgggggtgatgatggtgatggtgggggtgatgatggtgggggtgggggtg +atgatggtgagggtgatgatggtgggggtaatgacggtggggtgggggtgatgacggtgg +gggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtgatgacgg +tgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtga +tgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtggggg +tgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtag +aggtgatgatggtgggggtgggggtgggggtgggggtgagggtgatgatggtgggggtga +tgatggtgatggtgggggtgatgatggtgagggtgatgatggtgggggtgatggtggggg +tgggggtgggggtaatgacggtggggtgggggtaatgacggtgggggtgggggtgatgac +ggtgggggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtgat +gacggtgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtggg +ggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggt +gggggtgatgacggtgatggtagaggtgatgatggtgggggtgatggtgggggtgggggt +gggggtgggggtgatgatggtgatggtgggggtgatgatggtgagggtgatgatggtggg +ggtgatggtgggggtgggggtgggggtgggggtgatgatggtgggagtgggctggtagtg +ggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgctg +gctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagggtgcag +ggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtcc +>p:HG002_2_chr20:62349512-62350033 +gaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcagac +aattccggatagactgtcatggaatagaaaaactacagggtgcatttcaggaaggaggaa +gcagcaacccaggggatggggatggggatggggatggggatggtgggggtgatgggggtg +atgatggtgatggtgggggtgatgatggtgatggtgatggtgatggtgggggtggtgatg +gtgggggtgggggtggtgatggtgggggtgggggtgatgatggtgatggtgggggtgatg +acggtggggctgggggtgatgatggtgggggtgatgacggtgatgatgggggtggagggg +tgatgacggtgatgatgggggtgggggggtgatgacggtgatgtgggggtgatgacggtg +ggggtgggggtgatgacggtgat---------------------ggtgggggtgatgacg +gtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatg +acggtgggggtgggggtgatgatggtgatggtgggggtgatgatggtgggggtgggggtg +atgatggtgagggtgatgatggtgggggtaatgacggtggggtgggggtgatgacggtgg +gggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtgatgacgg +tgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtga +tgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtggggg +tgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtag +aggtgatgatggtgggggtgatggtgggggtgggggtggg---------ggtgggggtga +tgatggtgatggtgggggtgatgatggtgagggtgatgatggtgggggtgatggtggggg +tggg-------------------------------------------------------- +ggtgggggtgggggtgatgacggtgat--------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------ggtgggggtgatgatggtgggagtgggctggtagtg +ggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgctg +gctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagggtgcag +ggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtcc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/msa.fa.fai new file mode 100644 index 00000000..bb8b4f3c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_62349512_62350033 1611 29 60 61 +syndip_1_chr20:62349512-62350033 1611 1701 60 61 +syndip_2_chr20:62349512-62350033 1611 3373 60 61 +p:HG002_1_chr20:62349512-62350033 1611 5046 60 61 +p:HG002_2_chr20:62349512-62350033 1611 6719 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/output.vcf.gz new file mode 100644 index 00000000..5c19c542 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/output.vcf.gz.tbi new file mode 100644 index 00000000..4040a55c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62349612-62349933/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/base.vcf.gz new file mode 100644 index 00000000..47077f01 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/base.vcf.gz.tbi new file mode 100644 index 00000000..3f9a903c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/comp.vcf.gz new file mode 100644 index 00000000..6d4dc137 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/comp.vcf.gz.tbi new file mode 100644 index 00000000..8ce6d818 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/haps.fa new file mode 100644 index 00000000..0484f428 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/haps.fa @@ -0,0 +1,64 @@ +>ref_chr20_62360090_62360813 +AAGGACATTTCCCCACCCCACTCCAGGGAGTCCCTGCCCCCACCCTGACCAAGGCTGGCAGCCCCCTGGCCTAGGCCGAGACAGGGGCCTTGGTAGATACATCCACGTGGTCAGGAAAGTGGGTGAGAAGGAAGGAAGACGGTGCAGGTGTGGAGGGAGGAATGAGCAGACAGGTGGACAGATGGATGGAAACAAGGAATAAAGGGTGGGTGCTGCATAGGTAGGGGGGTGGGTGGGTGGATGGATGGGTAGGGGTGGGTGGGTGGATACGTTGGGGGTGGGTGGGTGGGTGGGTCAGCAGGCAGAGGGATGGGATAGGATAGGTGGGTGGGTGGAGGGATGGGTGAGTGGGTGGGTGGAGGGATAGATGGGTGGTGGGTGGGTGGAGGGATAGATGGGTGGTGGGTGGGTGGAGGGATAGATGGGTGGGTGGGTGGGTGGAGGGATAGATGGGTGGTGGGTGGGTGGAGGGATAGATGGGTGGATGGGTGGGTAGAAGGATAGGTAGGTGGGTGGGTGGGTGGATGGGTGGGTGGAGGGATAGATGGGTGGGTGGGTGGGTGGAGGGATAGATGGGTGGGTGGGTGGAGGGACCACTTCCCAGGTGGAGTGGAAAGGGTTCCTCTTCCCTCCGTATCATTTTACAGTTGGTGAAACTGAGGCTGTGAGAGGCAAGACGCTCACATGGCGGAACCTGATTTCTGGCCCAGAACAATCTAAAAGC +>syndip_1_chr20:62360090-62360813 +AAGGACATTTCCCCACCCCACTCCAGGGAGTCCCTGCCCCCACCCTGACCAAGGCTGGCA +GCCCCCTGGCCTAGGCCGAGACAGGGGCCTTGGTAGATACATCCACGTGGTCAGGAAAGT +GGGTGAGAAGGAAGGAAGACGGTGCAGGTGTGGAGGGAGGAATGAGCAGACAGGTGGACA +GATGGATGGAAACAAGGAATAAAGGGTGGGTGCTGCATAGGTAGGGGGGTGGGTGGGTGG +ATGGATGGGTAGGGGGTGGGTGGGTGGATACGTTGGGGGTGGGTGGGTGGGTGGGTCAGC +AGGCAGAGGGATGGGATAGGATAGGTGGGTGGGTGGGTGGATAGGGAGGGGGTGGGGTGG +GTGCATAGGTAGGGGGGTGGATGGGTCAGCAGGCAGCGGGATGGGATAGGATAGGTGGGT +GGGTGGAGGGATAGATGGGTGGTGGGTGGGTGGAGGGATAGATGGGTGGGTGGGTGGGTA +GAAGGATAGGTAGGTGGGTGGGTGGGTGGATGGATAGGTGGATGGGTGGGTGGAGGAATA +GATGGGTGGGTGGGTGGGTGGGTGGATGGATAGGTGGGTGGGTGGGTGGAGGGATAGATG +GGTGGGTGGATGGGTGGGTGGAGGGATAGATGGGTGGTGGGTGGGTGGAGGGATAGATGG +GTGGGTGGGTGGGTAGAAGGATAGGTAGGTGGGTGGGTGGGTGGATGGATAGGTGGGTGG +GTGGGTGGAGGAATAGATGGGTGGGTGGATGGGTGGGTGGAGGGATAGATGGGTGGGTGG +GTGGGTGGAGGGATAGATGGGTGGGTGGGTGGAGGGACCACTTCCCAGGTGGAGTGGAAA +GGGTTCCTCTTCCCTCCGTATCATTTTACAGTTGGTGAAACTGAGGCTGTGAGAGGCAAG +ACGCTCACATGGCGGAACCTGATTTCTGGCCCAGAACAATCTAAAAGC +>syndip_2_chr20:62360090-62360813 +AAGGACATTTCCCCACCCCACTCCAGGGAGTCCCTGCCCCCACCCTGACCAAGGCTGGCA +GCCCCCTGGCCTAGGCCGAGACAGGGGCCTTGGTAGATACATCCACGTGGTCAGGAAAGT +GGGTGAGAAGGAAGGAAGACGGTGCAGGTGTGGAGGGAGGAATGAGCAGACAGGTGGACA +GATGGATGGAAACAAGGAATAAAGGGTGGGTGCTGCATAGGTAGGGGGGTGGGTGGGTGG +ATGGATGGGTAGGGGGTGGGTGGGTGGATACGTTGGGGGTGGGTGGGTGGGTGGGTCAGC +AGGCAGAGGGATGGGATAGGATAGGTGGGTGGGTGGAGGGATAGATGGGTGGTGGGTGGG +TGGAGGGATAGATGGGTGGGTGGAGGGATAGATGGGTGGGTGGGTAGAAGGATAGGTAGG +TGGGTGGGTGGGTGGATGGATAGGTGGATGGGTGGGTGGAGGAATAGATGGGTGGGTGGG +TGGGTGGGTGGATGGATAGGTGGGTGGGTGGGTGGAGGAATAGATGGGTGGGTGGATGGG +TGGGTGGAGGGATAGATGGGTGGGTGGGTGGGTGGAGGGATAGATGGGTGGGTGGGTGGA +GGGACCACTTCCCAGGTGGAGTGGAAAGGGTTCCTCTTCCCTCCGTATCATTTTACAGTT +GGTGAAACTGAGGCTGTGAGAGGCAAGACGCTCACATGGCGGAACCTGATTTCTGGCCCA +GAACAATCTAAAAGC +>p:HG002_1_chr20:62360090-62360813 +AAGGACATTTCCCCACCCCACTCCAGGGAGTCCCTGCCCCCACCCTGACCAAGGCTGGCA +GCCCCCTGGCCTAGGCCGAGACAGGGGCCTTGGTAGATACATCCACGTGGTCAGGAAAGT +GGGTGAGAAGGAAGGAAGACGGTGCAGGTGTGGAGGGAGGAATGAGCAGACAGGTGGACA +GATGGATGGAAACAAGGAATAAAGGGTGGGTGCTGCATAGGTAGGGGGGTGGGTGGGTGG +ATGGATGGGTAGGGGGTGGGTGGGTGGATACGTTGGGGGTGGGTGGGTGGGTGGGTCAGC +AGGCAGAGGGATGGGATAGGATAGGTGGGTGGGTGGAGGGATAGATGGGTGGTGGGTGGG +TGGAGGGATAGATGGGTGGGTGGAGGGATAGATGGGTGGGTGGGTAGAAGGATAGGTAGG +TGGGTGGGTGGGTGGATGGATAGGTGGATGGGTGGGTGGAGGAATAGATGGGTGGGTGGG +TGGGTGGGTGGATGGATAGGTGGGTGGGTGGGTGGAGGAATAGATGGGTGGGTGGATGGG +TGGGTGGAGGGATAGATGGGTGGGTGGGTGGGTGGAGGGATAGATGGGTGGGTGGGTGGA +GGGACCACTTCCCAGGTGGAGTGGAAAGGGTTCCTCTTCCCTCCGTATCATTTTACAGTT +GGTGAAACTGAGGCTGTGAGAGGCAAGACGCTCACATGGCGGAACCTGATTTCTGGCCCA +GAACAATCTAAAAGC +>p:HG002_2_chr20:62360090-62360813 +AAGGACATTTCCCCACCCCACTCCAGGGAGTCCCTGCCCCCACCCTGACCAAGGCTGGCA +GCCCCCTGGCCTAGGCCGAGACAGGGGCCTTGGTAGATACATCCACGTGGTCAGGAAAGT +GGGTGAGAAGGAAGGAAGACGGTGCAGGTGTGGAGGGAGGAATGAGCAGACAGGTGGACA +GATGGATGGAAACAAGGAATAAAGGGTGGGTGCTGCATAGGTAGGGGGGTGGGTGGGTGG +ATGGATGGGTAGGGGGTGGGTGGGTGGATACGTTGGGGGTGGGTGGGTGGGTGGGTCAGC +AGGCAGAGGGATGGGATAGGATAGGTGGGTGGGTGGGTGGATAGGGAGGGGGTGGGGTGG +GTGCATAGGTAGGGGGGTGGATGGGTCAGCAGGCAGCGGGATGGGATAGGATAGGTGGGT +GGGTGGAGGGATAGATGGGTGGTGGGTGGGTGGAGGGATAGATGGGTGGGTGGGTGGGTA +GAAGGATAGGTAGGTGGGTGGGTGGGTGGATGGATAGGTGGATGGGTGGGTGGAGGAATA +GATGGGTGGGTGGGTGGGTGGGTGGATGGATAGGTGGGTGGGTGGGTGGAGGGATAGATG +GGTGGGTGGATGGGTGGGTGGAGGGATAGATGGGTGGTGGGTGGGTGGAGGGATAGATGG +GTGGGTGGGTGGGTAGAAGGATAGGTAGGTGGGTGGGTGGGTGGATGGATAGGTGGGTGG +GTGGGTGGAGGAATAGATGGGTGGGTGGATGGGTGGGTGGAGGGATAGATGGGTGGGTGG +GTGGGTGGAGGGATAGATGGGTGGGTGGGTGGAGGGACCACTTCCCAGGTGGAGTGGAAA +GGGTTCCTCTTCCCTCCGTATCATTTTACAGTTGGTGAAACTGAGGCTGTGAGAGGCAAG +ACGCTCACATGGCGGAACCTGATTTCTGGCCCAGAACAATCTAAAAGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/haps.fa.ref.fa new file mode 100644 index 00000000..bd8ab102 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:62360090-62360813 +AAGGACATTTCCCCACCCCACTCCAGGGAGTCCCTGCCCCCACCCTGACCAAGGCTGGCAGCCCCCTGGCCTAGGCCGAGACAGGGGCCTTGGTAGATACATCCACGTGGTCAGGAAAGTGGGTGAGAAGGAAGGAAGACGGTGCAGGTGTGGAGGGAGGAATGAGCAGACAGGTGGACAGATGGATGGAAACAAGGAATAAAGGGTGGGTGCTGCATAGGTAGGGGGGTGGGTGGGTGGATGGATGGGTAGGGGTGGGTGGGTGGATACGTTGGGGGTGGGTGGGTGGGTGGGTCAGCAGGCAGAGGGATGGGATAGGATAGGTGGGTGGGTGGAGGGATGGGTGAGTGGGTGGGTGGAGGGATAGATGGGTGGTGGGTGGGTGGAGGGATAGATGGGTGGTGGGTGGGTGGAGGGATAGATGGGTGGGTGGGTGGGTGGAGGGATAGATGGGTGGTGGGTGGGTGGAGGGATAGATGGGTGGATGGGTGGGTAGAAGGATAGGTAGGTGGGTGGGTGGGTGGATGGGTGGGTGGAGGGATAGATGGGTGGGTGGGTGGGTGGAGGGATAGATGGGTGGGTGGGTGGAGGGACCACTTCCCAGGTGGAGTGGAAAGGGTTCCTCTTCCCTCCGTATCATTTTACAGTTGGTGAAACTGAGGCTGTGAGAGGCAAGACGCTCACATGGCGGAACCTGATTTCTGGCCCAGAACAATCTAAAAGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/msa.fa new file mode 100644 index 00000000..12dd5f9f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/msa.fa @@ -0,0 +1,85 @@ +>ref_chr20_62360090_62360813 +aaggacatttccccaccccactccagggagtccctgcccccaccctgaccaaggctggca +gccccctggcctaggccgagacaggggccttggtagatacatccacgtggtcaggaaagt +gggtgagaaggaaggaagacggtgcaggtgtggagggaggaatgagcagacaggtggaca +gatggatggaaacaaggaataaagggtgggtgctgcataggtaggggggtgggtgggtgg +atggatgggta-ggggtgggtgggtggatacgttgggggtgggtgggtgggtgggtcagc +aggcaga----------------------------------------------------- +-------------------------------------gggatgggataggataggtgggt +gggtggagggatgggtg---agtgggtgggtggagggatagatgggtgg----------- +------------------------------------------tgggtgggtggagggata +gatgggt-ggtgggtgggtggagggatagatgggtgggtgggtgggtggagggatagatg +ggt--------------------------------------------------------- +---------------------------ggtgggtgggtggagggatagatgggtggatgg +gtgggtagaaggataggtaggtgggtgggtgggtggatgggtgggtggagggatagatgg +gtgggtgggtgggtggagggatagatgggtgggtgggtggagggaccacttcccaggtgg +agtggaaagggttcctcttccctccgtatcattttacagttggtgaaactgaggctgtga +gaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaaaagc +>syndip_1_chr20:62360090-62360813 +aaggacatttccccaccccactccagggagtccctgcccccaccctgaccaaggctggca +gccccctggcctaggccgagacaggggccttggtagatacatccacgtggtcaggaaagt +gggtgagaaggaaggaagacggtgcaggtgtggagggaggaatgagcagacaggtggaca +gatggatggaaacaaggaataaagggtgggtgctgcataggtaggggggtgggtgggtgg +atggatgggtagggggtgggtgggtggatacgttgggggtgggtgggtgggtgggtcagc +aggcagagggatgggataggataggtgggtgggtgggtggatagggagggggtggggtgg +gtgcataggtaggggggtggatgggtcagcaggcagcgggatgggataggataggtgggt +gggtggagggatagatgggtggtgggtgggtggagggatagatgggtgggtgggtgggta +gaaggataggtaggtgggtgggtgggtggatggataggtggatgggtgggtggaggaata +gatgggtgggtgggtgggtgggtggatggataggtgggtgggtgggtggagggatagatg +ggtgggtggatgggtgggtggagggatagatgggtggtgggtgggtggagggatagatgg +gtgggtgggtgggtagaaggataggtaggtgggtgggtgggtggatggataggtgggtgg +gtgggtggaggaata--------gatgggtgggtggatgggtgggtggagggatagatgg +gtgggtgggtgggtggagggatagatgggtgggtgggtggagggaccacttcccaggtgg +agtggaaagggttcctcttccctccgtatcattttacagttggtgaaactgaggctgtga +gaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaaaagc +>syndip_2_chr20:62360090-62360813 +aaggacatttccccaccccactccagggagtccctgcccccaccctgaccaaggctggca +gccccctggcctaggccgagacaggggccttggtagatacatccacgtggtcaggaaagt +gggtgagaaggaaggaagacggtgcaggtgtggagggaggaatgagcagacaggtggaca +gatggatggaaacaaggaataaagggtgggtgctgcataggtaggggggtgggtgggtgg +atggatgggtagggggtgggtgggtggatacgttgggggtgggtgggtgggtgggtcagc +aggcaga----------------------------------------------------- +-------------------------------------gggatgggataggataggtgggt +gggtggagggatagatgggtggtgggtgggtggagggatagatgggtgggtggagggata +----------------------------------------gatgggtgggtgggtagaag +gataggtaggtgggtgggtgggtggatggataggtggatgggtgggtggaggaatagatg +ggtg-------------------------------------------------------- +---------------------------ggtgggtgggtgggtggatggataggtgggtgg +gtgggtggaggaata--------gatgggtgggtggatgggtgggtggagggatagatgg +gtgggtgggtgggtggagggatagatgggtgggtgggtggagggaccacttcccaggtgg +agtggaaagggttcctcttccctccgtatcattttacagttggtgaaactgaggctgtga +gaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaaaagc +>p:HG002_1_chr20:62360090-62360813 +aaggacatttccccaccccactccagggagtccctgcccccaccctgaccaaggctggca +gccccctggcctaggccgagacaggggccttggtagatacatccacgtggtcaggaaagt +gggtgagaaggaaggaagacggtgcaggtgtggagggaggaatgagcagacaggtggaca +gatggatggaaacaaggaataaagggtgggtgctgcataggtaggggggtgggtgggtgg +atggatgggtagggggtgggtgggtggatacgttgggggtgggtgggtgggtgggtcagc +aggcaga----------------------------------------------------- +-------------------------------------gggatgggataggataggtgggt +gggtggagggatagatgggtggtgggtgggtggagggatagatgggtgggtggagggata +----------------------------------------gatgggtgggtgggtagaag +gataggtaggtgggtgggtgggtggatggataggtggatgggtgggtggaggaatagatg +ggtg-------------------------------------------------------- +---------------------------ggtgggtgggtgggtggatggataggtgggtgg +gtgggtggaggaata--------gatgggtgggtggatgggtgggtggagggatagatgg +gtgggtgggtgggtggagggatagatgggtgggtgggtggagggaccacttcccaggtgg +agtggaaagggttcctcttccctccgtatcattttacagttggtgaaactgaggctgtga +gaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaaaagc +>p:HG002_2_chr20:62360090-62360813 +aaggacatttccccaccccactccagggagtccctgcccccaccctgaccaaggctggca +gccccctggcctaggccgagacaggggccttggtagatacatccacgtggtcaggaaagt +gggtgagaaggaaggaagacggtgcaggtgtggagggaggaatgagcagacaggtggaca +gatggatggaaacaaggaataaagggtgggtgctgcataggtaggggggtgggtgggtgg +atggatgggtagggggtgggtgggtggatacgttgggggtgggtgggtgggtgggtcagc +aggcagagggatgggataggataggtgggtgggtgggtggatagggagggggtggggtgg +gtgcataggtaggggggtggatgggtcagcaggcagcgggatgggataggataggtgggt +gggtggagggatagatgggtggtgggtgggtggagggatagatgggtgggtgggtgggta +gaaggataggtaggtgggtgggtgggtggatggataggtggatgggtgggtggaggaata +gatgggtgggtgggtgggtgggtggatggataggtgggtgggtgggtggagggatagatg +ggtgggtggatgggtgggtggagggatagatgggtggtgggtgggtggagggatagatgg +gtgggtgggtgggtagaaggataggtaggtgggtgggtgggtggatggataggtgggtgg +gtgggtggaggaata--------gatgggtgggtggatgggtgggtggagggatagatgg +gtgggtgggtgggtggagggatagatgggtgggtgggtggagggaccacttcccaggtgg +agtggaaagggttcctcttccctccgtatcattttacagttggtgaaactgaggctgtga +gaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaaaagc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/msa.fa.fai new file mode 100644 index 00000000..a491333d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_62360090_62360813 956 29 60 61 +syndip_1_chr20:62360090-62360813 956 1035 60 61 +syndip_2_chr20:62360090-62360813 956 2041 60 61 +p:HG002_1_chr20:62360090-62360813 956 3048 60 61 +p:HG002_2_chr20:62360090-62360813 956 4055 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/output.vcf.gz new file mode 100644 index 00000000..26e20697 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/output.vcf.gz.tbi new file mode 100644 index 00000000..cddf881a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62360190-62360713/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/base.vcf.gz new file mode 100644 index 00000000..81989177 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/base.vcf.gz.tbi new file mode 100644 index 00000000..4b2b402b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/comp.vcf.gz new file mode 100644 index 00000000..bdbf1f46 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/comp.vcf.gz.tbi new file mode 100644 index 00000000..9ab665ab Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/haps.fa new file mode 100644 index 00000000..d53cedfb --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/haps.fa @@ -0,0 +1,52 @@ +>ref_chr20_62830512_62830939 +CCCAGGGCCAGAAGGGCAGCATGGGAGACCCCGGCCTTCCAGGCCCCCAGGGCCTCCGAGGTGACGTGGGCGACCGGGTAAGTGGCCCTCTCAGCAGGAAGCTCCCCTGCACCCCCTCTACCCATGTACCACAGTCCCCCACCCCCATGACAGTCCCCCAACCCCCACCACAGTCCCCCAACCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCACCCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCTACCACAATCCCCCACCCCCCACCACAGTCCCCTGGGACGCAGACAGGGAGAGGCCCTTGCAGCTCCCAGTGGGAAATCTGGCCATGGGCAGTGTCTCCCTGCGTGGCGGAGGCAGTGGCATCAGGGCCCCGACTGTGGCGCCTTTGGCCCCTCTGACCTTCCA +>syndip_1_chr20:62830512-62830939 +CCCAGGGCCAGAAGGGCAGCATGGGAGACCCCGGCCTTCCAGGCCCCCAGGGCCTCCGAG +GTGACGTGGGCGACCGGGTAAGTGGCCCTCTCAGCAGGAAGCTCCCCTGCACCCCCTCTA +CCCATGTACCACAGTCCCCCACCCCCCACCGTGCTCCACCCCCCACCACAGTCCCCCACC +CCCCACCCCAGTCCCCAAACCCCTACCACAGTCCCCCAACCCCACCACAGTCCCCCACCC +CCTACCACAGTCCCCCACCCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCC +CCACCACAGTCCGCCAACCCCCATGACAGTCCCTCAACCCCCACCACAGTCCCCCAACCC +CCATGACAGTCCCCCAACCCCCACCACAGTCCCCCAACCCCCACCACAGTCCCCACCCCC +TACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCTACCACAATCCCCCACCCCC +ACCACAGTCCCCTGGGACGCAGACAGGGAGAGGCCCTTGCAGCTCCCAGTGGGAAATCTG +GCCATGGGCAGTGTCTCCCTGCGTGGCGGAGGCAGTGGCATCAGGGCCCCGACTGTGGCG +CCTTTGGCCCCTCTGACCTTCCA +>syndip_2_chr20:62830512-62830939 +CCCAGGGCCAGAAGGGCAGCATGGGAGACCCCGGCCTTCCAGGCCCCCAGGGCCTCCGAG +GTGACGTGGGCGACCGGGTAAGTGGCCCTCTCAGCAGGAAGCTCCCCTGCACCCCCTCTA +CCCATGTACCACAGTCCCCCACCCCCCACCACAGTCCCCCACCCCCCACCCCAGTCCCCA +AACCCCTACCACAGTCCCCCAACCCCACCACAGTCCCCCACCCCCTACCACAGTCCCCCA +ACCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCACCACAGTCCGCCAA +CCCCCATGACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCACCACAGTCCGCCAAC +CCCCATGACAGTCCCCCAACCCCCACCACAGTCCCCCAACCCCCATGACAGTCCCCCAAC +CCCCACCACAGTCCCCCAACCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCACCC +CCTACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCTACCACAATCCCCCACCC +CCCACCACAGTCCCCTGGGACGCAGACAGGGAGAGGCCCTTGCAGCTCCCAGTGGGAAAT +CTGGCCATGGGCAGTGTCTCCCTGCGTGGCGGAGGCAGTGGCATCAGGGCCCCGACTGTG +GCGCCTTTGGCCCCTCTGACCTTCCA +>p:HG002_1_chr20:62830512-62830939 +CCCAGGGCCAGAAGGGCAGCATGGGAGACCCCGGCCTTCCAGGCCCCCAGGGCCTCCGAG +GTGACGTGGGCGACCGGGTAAGTGGCCCTCTCAGCAGGAAGCTCCCCTGCACCCCCTCTA +CCCATGTACCACAGTCCCCCACCCCCCACCACAGTCCCCCACCCCCCACCCCAGTCCCCA +AACCCCTACCACAGTCCCCCAACCCCACCACAGTCCCCCACCCCCTACCACAGTCCCCCA +ACCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCACCACAGTCCGCCAA +CCCCCATGACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCACCACAGTCCGCCAAC +CCCCATGACAGTCCCCCAACCCCCACCACAGTCCCCCAACCCCCATGACAGTCCCCCAAC +CCCCACCACAGTCCCCCAACCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCACCC +CCTACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCTACCACAATCCCCCACCC +CCCACCACAGTCCCCTGGGACGCAGACAGGGAGAGGCCCTTGCAGCTCCCAGTGGGAAAT +CTGGCCATGGGCAGTGTCTCCCTGCGTGGCGGAGGCAGTGGCATCAGGGCCCCGACTGTG +GCGCCTTTGGCCCCTCTGACCTTCCA +>p:HG002_2_chr20:62830512-62830939 +CCCAGGGCCAGAAGGGCAGCATGGGAGACCCCGGCCTTCCAGGCCCCCAGGGCCTCCGAG +GTGACGTGGGCGACCGGGTAAGTGGCCCTCTCAGCAGGAAGCTCCCCTGCACCCCCTCTA +CCCATGTACCACAGTCCCCCACCCCCCACCGTGCTCCACCCCCCACCACAGTCCCCCACC +CCCCACCCCAGTCCCCAAACCCCTACCACAGTCCCCCAACCCCACCACAGTCCCCCACCC +CCTACCACAGTCCCCCACCCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCC +CCACCACAGTCCGCCAACCCCCATGACAGTCCCTCAACCCCCACCACAGTCCCCCAACCC +CCATGACAGTCCCCCAACCCCCACCACAGTCCCCCAACCCCCACCACAGTCCCCACCCCC +TACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCTACCACAATCCCCCACCCCC +ACCACAGTCCCCTGGGACGCAGACAGGGAGAGGCCCTTGCAGCTCCCAGTGGGAAATCTG +GCCATGGGCAGTGTCTCCCTGCGTGGCGGAGGCAGTGGCATCAGGGCCCCGACTGTGGCG +CCTTTGGCCCCTCTGACCTTCCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/haps.fa.ref.fa new file mode 100644 index 00000000..df37a9a0 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:62830512-62830939 +CCCAGGGCCAGAAGGGCAGCATGGGAGACCCCGGCCTTCCAGGCCCCCAGGGCCTCCGAGGTGACGTGGGCGACCGGGTAAGTGGCCCTCTCAGCAGGAAGCTCCCCTGCACCCCCTCTACCCATGTACCACAGTCCCCCACCCCCATGACAGTCCCCCAACCCCCACCACAGTCCCCCAACCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCACCCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCTACCACAATCCCCCACCCCCCACCACAGTCCCCTGGGACGCAGACAGGGAGAGGCCCTTGCAGCTCCCAGTGGGAAATCTGGCCATGGGCAGTGTCTCCCTGCGTGGCGGAGGCAGTGGCATCAGGGCCCCGACTGTGGCGCCTTTGGCCCCTCTGACCTTCCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/msa.fa new file mode 100644 index 00000000..dc0fc966 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/msa.fa @@ -0,0 +1,65 @@ +>ref_chr20_62830512_62830939 +cccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccgag +gtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctcta +cccatgtaccacagtccccc---------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------acccccatgacagtcccccaa +cccccaccacagtcccccaacccctaccacagtcccccaacccccaccacagtccccacc +ccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatcccccacc +ccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaaa +tctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactgt +ggcgcctttggcccctctgaccttcca +>syndip_1_chr20:62830512-62830939 +cccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccgag +gtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctcta +cccatgtaccacagtcccccaccccccaccgtgctccacc-------------------- +----------------------ccccaccacagtcccccaccccccaccccagtccccaa +acccctaccacagtcccccaa-ccccaccacagtcccccaccccctaccacagtccccca +ccccctaccacagtcccccaacccccaccacagtcccccacccccaccacagtccgccaa +cccccatgacagtccctca--------------------acccccaccacagtcccccaa +cccccatgacagtcccccaacccccaccacagtcccccaacccccaccacagtccccacc +ccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatccccca-c +ccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaaa +tctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactgt +ggcgcctttggcccctctgaccttcca +>syndip_2_chr20:62830512-62830939 +cccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccgag +gtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctcta +cccatgtaccacagtcccccaccccccaccacagtcccccaccccccaccccagtcccca +aacccctaccacagtcccccaaccccaccacagtcccccaccccctaccacagtccccca +acccctaccacagtcccccaacccccaccacagtcccccaccccc-accacagtccgcca +acccccatgacagtcccccaacccccaccacagtcccccacccccaccacagtccgccaa +cccccatgacagtcccccaacccccaccacagtcccccaacccccatgacagtcccccaa +cccccaccacagtcccccaacccctaccacagtcccccaacccccaccacagtccccacc +ccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatcccccacc +ccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaaa +tctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactgt +ggcgcctttggcccctctgaccttcca +>p:HG002_1_chr20:62830512-62830939 +cccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccgag +gtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctcta +cccatgtaccacagtcccccaccccccaccacagtcccccaccccccaccccagtcccca +aacccctaccacagtcccccaaccccaccacagtcccccaccccctaccacagtccccca +acccctaccacagtcccccaacccccaccacagtcccccaccccc-accacagtccgcca +acccccatgacagtcccccaacccccaccacagtcccccacccccaccacagtccgccaa +cccccatgacagtcccccaacccccaccacagtcccccaacccccatgacagtcccccaa +cccccaccacagtcccccaacccctaccacagtcccccaacccccaccacagtccccacc +ccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatcccccacc +ccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaaa +tctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactgt +ggcgcctttggcccctctgaccttcca +>p:HG002_2_chr20:62830512-62830939 +cccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccgag +gtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctcta +cccatgtaccacagtcccccaccccccaccgtgctccacc-------------------- +----------------------ccccaccacagtcccccaccccccaccccagtccccaa +acccctaccacagtcccccaa-ccccaccacagtcccccaccccctaccacagtccccca +ccccctaccacagtcccccaacccccaccacagtcccccacccccaccacagtccgccaa +cccccatgacagtccctca--------------------acccccaccacagtcccccaa +cccccatgacagtcccccaacccccaccacagtcccccaacccccaccacagtccccacc +ccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatccccca-c +ccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaaa +tctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactgt +ggcgcctttggcccctctgaccttcca diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/msa.fa.fai new file mode 100644 index 00000000..dcf5fc89 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_62830512_62830939 687 29 60 61 +syndip_1_chr20:62830512-62830939 687 762 60 61 +syndip_2_chr20:62830512-62830939 687 1495 60 61 +p:HG002_1_chr20:62830512-62830939 687 2229 60 61 +p:HG002_2_chr20:62830512-62830939 687 2963 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/output.vcf.gz new file mode 100644 index 00000000..49e22edf Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/output.vcf.gz.tbi new file mode 100644 index 00000000..fc6693e6 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62830612-62830839/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/base.vcf.gz new file mode 100644 index 00000000..6d92851c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/base.vcf.gz.tbi new file mode 100644 index 00000000..1f2a8782 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/comp.vcf.gz new file mode 100644 index 00000000..6574c840 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/comp.vcf.gz.tbi new file mode 100644 index 00000000..d7395ed5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/haps.fa new file mode 100644 index 00000000..bf13d279 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/haps.fa @@ -0,0 +1,84 @@ +>ref_chr20_62875072_62875657 +AACTTTCCTGGCACACTGGAGAGGACGGCAGAACGCTGGGATGGATTTATCGTGCAAGACCAGCTTGATGTCCTTAGGGCTTGGAGGTCACCCCTTCACGAGGATTGTGAGGAGTGAATTCATCGGGGAGCCCCGCACCCTCACCTGCACCCTCACCCCCACCCCCACCCCCACCCCCACCCCCACCCGCACCCCCACCCCCACCCTCCCCCCCACCCGCACCCGCACCCCCACCCTCACCCGCACCCCCACCCTCACCCCCACCCTCACCCCCACCCTCACCCCCACCCCCACCCTCACCCGCACCCCCACTCGCACCCGCACCCCCACCCTCACCCGCACCCCCACCCTCACCCCCACCCTCACCCCCACCCTCACCCCCACCCCCACCCTCACCCGCACCCTCACTCGCACCGCACCCTCACTGGCACCCTCACCCACACCGCACCCACACCCACATCGGGGAAGAGCTCCATGATCATTCTTTTCTGTAGGCGAAAAACTGCGGCGGGAACTGCTGCCATGCAGCTGGGCTCCCAATGCAGTGGGGATGGTGGCGCTCTGGGCTGGCGGGAGCTATCCTGCC +>syndip_1_chr20:62875072-62875657 +AACTTTCCTGGCACACTGGAGAGGACGGCAGAACGCTGGGATGGATTTATCGTGCAAGAC +CAGCTTGATGTCCTTAGGGCTTGGAGGTCACCCCTTCACGAGGATTGTGAGGAGTGAATT +CATCGGGGAGCCCCGCACCCTCACCTGCACCCTCACCCCCACCCCCACCCCCACCCCCAC +CCCCACCCCCACCCGCACCCCCACCCCCACCCGCACCCCCACCCCCACCCCCACCCGCAC +CCCCACCCCCACCCCCACCCGCACCCCCACCCCCACCCGCACCCCCACCCCCACCCCCAC +CCGCACCCCCACCCCCACCCCCACCCGCACCCGCACCCCCACCCCCACCCGCACCCGCAC +CCCCACCCCCACCCCCACCCGCACCCCCACCCCCACCCCCACCCCCACCCGCACCCGCAC +CCGCACCCCCACCCCCACCCTCACCCGCACCCGCACCCCCACCCCCACCCCCACCCGCAC +CCGCACCCCCACCCCCACCCCCACCCCCACCCCCACCCGCACCCGCACCCGCACCCCCAC +CCTCACCCTCACCCGCACCCGCACCCCCACCCCCACCCGCACCCCCACCCGCACCCCCAC +CCCCACCCCCACCCCCACCCGCACCCGCACCCCCACCCCCACCCCCACCCCCACCCCCAC +CCCCACCCCCACCCCCACCCTCACCCGCACCCCCACCCTCACCCCCACCCTCACCCCCAC +CCTCACCCGCACCCTCACCCGCACCCGCACCCCCACCCTCACCCACACCCTCACCCCCAC +CCTCACCCCCACCCCCACCCTCACCCGCACCCGCACCCCCACCCTCACCCCCACCCCCAC +CCCCACCCTCACCCTCACCCTCACCCGCACCCGCACCCCCACCCGCACCCCCACCCTCAC +CCCCACCCTCACCCCCACCCTCACCCCCACCCCCACCCTCACCCGCACCCTCACTCGCAC +CGCACCCTCACTGGCACCCTCACCCACACCGCACCCACACCCACATCGGGGAAGAGCTCC +ATGATCATTCTTTTCTGTAGGCGAAAAACTGCGGCGGGAACTGCTGCCATGCAGCTGGGC +TCCCAATGCAGTGGGGATGGTGGCGCTCTGGGCTGGCGGGAGCTATCCTGCC +>syndip_2_chr20:62875072-62875657 +AACTTTCCTGGCACACTGGAGAGGACGGCAGAACGCTGGGATGGATTTATCGTGCAAGAC +CAGCTTGATGTCCTTAGGGCTTGGAGGTCACCCCTTCACGAGGATTGTGAGGAGTGAATT +CATCGGGGAGCCCCGCACCCTCACCTGCACCCTCACCCCCACCCCCACCCCCACCCCCAC +CCCCACCCGCACCCGCACCCCCACCCCCACCCGCACCCCCACCCCCACCCCCACCCGCAC +CCCCACCCCCACCCCCACCCGCACCCCCACCCCCACCCCCACCCGCACCCGCACCCGCAC +CCCCACCCCCACCCGCACCCCCACCCCCACCCGCACCCGCACCCCCACCCGCACCCCCAC +CCCCACCCCCACCCTCACCCCCACCCGCACCCCCACCCCCACCCCCACCCGCACCCGCAC +CCCCACCCCCACCCCCACCCGCACCCCCACCCCCACCCCCACCCGCACCCGCACCCCCAC +CCGCACCCCCACCCCCACCCCCACCCGCACCCGCACCCCCACCCGCACCCGCACCCCCAC +CCGCACCCCCACCCCCACCTCCACCCCCACCCGCACCCGCACCCCCACCCCCACCCGCAC +CCCCACCCCCACCCGCACCCCCACCCCCACCCTCACCCGCACCCCCACCCCCACCCGCAC +CCCCACCCCCACCCTCACCCCCACCCTCACCCGCACCCGCACCCCCACCCTCACCCCCAC +CCTCACCCCCACCCTCACCCGCACCCCCACCCCCACCCCCACCCCCACCCTCCCCCCCAC +CCGCACCCGCACCCCCACCCTCACCCGCACCCCCACCCTCACCCCCACCCTCACCCCCAC +CCTCACCCCCACCCCCACCCTCACCCGCACCCCCACTCGCACCCGCACCCCCACCCTCAC +CCGCACCCCCACCCTCACCCCCACCCTCACCCCCACCCTCACCCCCACCCCCACCCTCAC +CCGCACCCTCACTCGCACCGCACCCTCACTGGCACCCTCACCCACACCGCACCCACACCC +ACATCGGGGAAGAGCTCCATGATCATTCTTTTCTGTAGGCGAAAAACTGCGGCGGGAACT +GCTGCCATGCAGCTGGGCTCCCAATGCAGTGGGGATGGTGGCGCTCTGGGCTGGCGGGAG +CTATCCTGCC +>p:HG002_1_chr20:62875072-62875657 +AACTTTCCTGGCACACTGGAGAGGACGGCAGAACGCTGGGATGGATTTATCGTGCAAGAC +CAGCTTGATGTCCTTAGGGCTTGGAGGTCACCCCTTCACGAGGATTGTGAGGAGTGAATT +CATCGGGGAGCCCCGCACCCTCACCTGCACCCTCACCCCCACCCCCACCCCCACCCCCAC +CCCCACCCGCACCCGCACCCCCACCCCCACCCGCACCCCCACCCCCACCCCCACCCGCAC +CCCCACCCCCACCCCCACCCGCACCCCCACCCCCACCCCCACCCGCACCCGCACCCGCAC +CCCCACCCCCACCCGCACCCCCACCCCCACCCGCACCCGCACCCCCACCCGCACCCCCAC +CCCCACCCCCACCCTCACCCCCACCCGCACCCCCACCCCCACCCCCACCCGCACCCGCAC +CCCCACCCCCACCCCCACCCGCACCCCCACCCCCACCCCCACCCGCACCCGCACCCCCAC +CCGCACCCCCACCCCCACCCCCACCCGCACCCGCACCCCCACCCGCACCCGCACCCCCAC +CCGCACCCCCACCCCCACCTCCACCCCCACCCGCACCCGCACCCCCACCCCCACCCGCAC +CCCCACCCCCACCCGCACCCCCACCCCCACCCTCACCCGCACCCCCACCCCCACCCGCAC +CCCCACCCCCACCCTCACCCCCACCCTCACCCGCACCCGCACCCCCACCCTCACCCCCAC +CCTCACCCCCACCCTCACCCGCACCCCCACCCCCACCCCCACCCCCACCCTCCCCCCCAC +CCGCACCCGCACCCCCACCCTCACCCGCACCCCCACCCTCACCCCCACCCTCACCCCCAC +CCTCACCCCCACCCCCACCCTCACCCGCACCCCCACTCGCACCCGCACCCCCACCCTCAC +CCGCACCCCCACCCTCACCCCCACCCTCACCCCCACCCTCACCCCCACCCCCACCCTCAC +CCGCACCCTCACTCGCACCGCACCCTCACTGGCACCCTCACCCACACCGCACCCACACCC +ACATCGGGGAAGAGCTCCATGATCATTCTTTTCTGTAGGCGAAAAACTGCGGCGGGAACT +GCTGCCATGCAGCTGGGCTCCCAATGCAGTGGGGATGGTGGCGCTCTGGGCTGGCGGGAG +CTATCCTGCC +>p:HG002_2_chr20:62875072-62875657 +AACTTTCCTGGCACACTGGAGAGGACGGCAGAACGCTGGGATGGATTTATCGTGCAAGAC +CAGCTTGATGTCCTTAGGGCTTGGAGGTCACCCCTTCACGAGGATTGTGAGGAGTGAATT +CATCGGGGAGCCCCGCACCCTCACCTGCACCCTCACCCCCACCCCCACCCCCACCCCCAC +CCCCACCCCCACCCGCACCCCCACCCCCACCCGCACCCCCACCCCCACCCCCACCCGCAC +CCCCACCCCCACCCCCACCCGCACCCCCACCCCCACCCGCACCCCCACCCCCACCCCCAC +CCGCACCCCCACCCCCACCCCCACCCGCACCCGCACCCCCACCCCCACCCGCACCCGCAC +CCCCACCCCCACCCCCACCCGCACCCCCACCCCCACCCCCACCCCCACCCGCACCCGCAC +CCGCACCCCCACCCCCACCCTCACCCGCACCCGCACCCCCACCCCCACCCCCACCCGCAC +CCGCACCCCCACCCCCACCCCCACCCCCACCCCCACCCGCACCCGCACCCGCACCCCCAC +CCTCACCCTCACCCGCACCCGCACCCCCACCCCCACCCGCACCCCCACCCGCACCCCCAC +CCCCACCCCCACCCCCACCCGCACCCGCACCCCCACCCCCACCCCCACCCCCACCCCCAC +CCCCACCCCCACCCCCACCCTCACCCGCACCCCCACCCTCACCCCCACCCTCACCCCCAC +CCTCACCCGCACCCTCACCCGCACCCGCACCCCCACCCTCACCCACACCCTCACCCCCAC +CCTCACCCCCACCCCCACCCTCACCCGCACCCGCACCCCCACCCTCACCCCCACCCCCAC +CCCCACCCTCACCCTCACCCTCACCCGCACCCGCACCCCCACCCGCACCCCCACCCTCAC +CCCCACCCTCACCCCCACCCTCACCCCCACCCCCACCCTCACCCGCACCCTCACTCGCAC +CGCACCCTCACTGGCACCCTCACCCACACCGCACCCACACCCACATCGGGGAAGAGCTCC +ATGATCATTCTTTTCTGTAGGCGAAAAACTGCGGCGGGAACTGCTGCCATGCAGCTGGGC +TCCCAATGCAGTGGGGATGGTGGCGCTCTGGGCTGGCGGGAGCTATCCTGCC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/haps.fa.ref.fa new file mode 100644 index 00000000..6df8df1f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:62875072-62875657 +AACTTTCCTGGCACACTGGAGAGGACGGCAGAACGCTGGGATGGATTTATCGTGCAAGACCAGCTTGATGTCCTTAGGGCTTGGAGGTCACCCCTTCACGAGGATTGTGAGGAGTGAATTCATCGGGGAGCCCCGCACCCTCACCTGCACCCTCACCCCCACCCCCACCCCCACCCCCACCCCCACCCGCACCCCCACCCCCACCCTCCCCCCCACCCGCACCCGCACCCCCACCCTCACCCGCACCCCCACCCTCACCCCCACCCTCACCCCCACCCTCACCCCCACCCCCACCCTCACCCGCACCCCCACTCGCACCCGCACCCCCACCCTCACCCGCACCCCCACCCTCACCCCCACCCTCACCCCCACCCTCACCCCCACCCCCACCCTCACCCGCACCCTCACTCGCACCGCACCCTCACTGGCACCCTCACCCACACCGCACCCACACCCACATCGGGGAAGAGCTCCATGATCATTCTTTTCTGTAGGCGAAAAACTGCGGCGGGAACTGCTGCCATGCAGCTGGGCTCCCAATGCAGTGGGGATGGTGGCGCTCTGGGCTGGCGGGAGCTATCCTGCC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/msa.fa new file mode 100644 index 00000000..1e89c6f4 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/msa.fa @@ -0,0 +1,105 @@ +>ref_chr20_62875072_62875657 +aactttcctggcacactggagaggacggcagaacgctgggatggatttatcgtgcaagac +cagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaatt +catcggggagc------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------cccgcaccctcacctgcaccctcac +ccccacccccacccccacccccacccccacccgcacccccacccccaccctcccccccac +ccgcacccgcacccccaccctcacccgcacccccaccctcacccccaccctcacccccac +cctcacccccacccccaccctcacccgcacccccactcgcacccgcacccccaccctcac +ccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctcac +ccgcaccctcactcgcaccgcaccctcactggcaccctcacccacaccgcacccacaccc +acatcggggaagagctccatgatcattcttttctgtaggcgaaaaactgcggcgggaact +gctgccatgcagctgggctcccaatgcagtggggatggtggcgctctgggctggcgggag +ctatcctgcc +>syndip_1_chr20:62875072-62875657 +aactttcctggcacactggagaggacggcagaacgctgggatggatttatcgtgcaagac +cagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaatt +catcggggagccccgcaccctcacctgcaccctcacccccacccccacccccacccccac +ccccacccccacccgcacccccacccccacccgcacccccacccccacccccacccgcac +ccccacccccacccccacccgcacccccacccccacccgcacccccacccccacccccac +ccgcacccccacccccacccccacccgcacccgcacccccacccccacccgcacccgcac +ccccacccccacccccacccgcacccccacccccacccccacccccacccgcacccgcac +ccgcacccccacccccaccctcacccgcacccgcacccccacccccacccccacccgcac +ccgcacccccacccccacccc------------cacccccacccccacccgcacccgcac +ccgcacccccaccctcaccctcacccgcacccgcacccccacccccacccgcacccccac +ccgcacccccacccccacccccacccccacccgcacccgcacccccacccccacccccac +ccccacccccacccccacccccacccccaccctcacccgcacccccaccctcacccccac +cctcacccccaccctcacccgcaccctcacccgcacccgcacccccaccct------cac +ccacaccctcacccccaccctcacccccacccccaccctcacccgcacccgcacccccac +cctcacccccacccccacccccaccctcaccctcaccctcacccgcacccgcacccccac +ccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctcac +ccgcaccctcactcgcaccgcaccctcactggcaccctcacccacaccgcacccacaccc +acatcggggaagagctccatgatcattcttttctgtaggcgaaaaactgcggcgggaact +gctgccatgcagctgggctcccaatgcagtggggatggtggcgctctgggctggcgggag +ctatcctgcc +>syndip_2_chr20:62875072-62875657 +aactttcctggcacactggagaggacggcagaacgctgggatggatttatcgtgcaagac +cagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaatt +catcggggagccccgcaccctcacctgcaccctcacccccacccccacccccacccccac +ccccacccgcacccgcacccccacccccacccgcacccccacccccacccccacccgcac +ccccacccccacccccacccgcacccccacccccacccccacccgcacccgcacccgcac +ccccacccccacccgcacccccacccccacccgcacccgcacccccacccgcacccccac +ccccacccccaccctcacccccacccgcacccccacccccacccccacccgcacccgcac +ccccacccccacccccacccgcacccccacccccacccccacccgcacccgcacccccac +ccgcacccccacccccacccccacccgcacccgcacccccacccgcacccgcacccccac +ccgcacccccacccccacctccacccccacccgcacccgcacccccacccccacccgcac +ccccacccccacccgcacccccacccccaccctcacccgcacccccacccccacccgcac +ccccacccccaccctcacccccaccctcacccgcacccgcacccccaccctcacccccac +cctcacccccaccctcacccgcacccccacccccacccccacccccaccctcccccccac +ccgcacccgcacccccaccctcacccgcacccccaccctcacccccaccctcacccccac +cctcacccccacccccaccctcacccgcacccccactcgcacccgcacccccaccctcac +ccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctcac +ccgcaccctcactcgcaccgcaccctcactggcaccctcacccacaccgcacccacaccc +acatcggggaagagctccatgatcattcttttctgtaggcgaaaaactgcggcgggaact +gctgccatgcagctgggctcccaatgcagtggggatggtggcgctctgggctggcgggag +ctatcctgcc +>p:HG002_1_chr20:62875072-62875657 +aactttcctggcacactggagaggacggcagaacgctgggatggatttatcgtgcaagac +cagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaatt +catcggggagccccgcaccctcacctgcaccctcacccccacccccacccccacccccac +ccccacccgcacccgcacccccacccccacccgcacccccacccccacccccacccgcac +ccccacccccacccccacccgcacccccacccccacccccacccgcacccgcacccgcac +ccccacccccacccgcacccccacccccacccgcacccgcacccccacccgcacccccac +ccccacccccaccctcacccccacccgcacccccacccccacccccacccgcacccgcac +ccccacccccacccccacccgcacccccacccccacccccacccgcacccgcacccccac +ccgcacccccacccccacccccacccgcacccgcacccccacccgcacccgcacccccac +ccgcacccccacccccacctccacccccacccgcacccgcacccccacccccacccgcac +ccccacccccacccgcacccccacccccaccctcacccgcacccccacccccacccgcac +ccccacccccaccctcacccccaccctcacccgcacccgcacccccaccctcacccccac +cctcacccccaccctcacccgcacccccacccccacccccacccccaccctcccccccac +ccgcacccgcacccccaccctcacccgcacccccaccctcacccccaccctcacccccac +cctcacccccacccccaccctcacccgcacccccactcgcacccgcacccccaccctcac +ccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctcac +ccgcaccctcactcgcaccgcaccctcactggcaccctcacccacaccgcacccacaccc +acatcggggaagagctccatgatcattcttttctgtaggcgaaaaactgcggcgggaact +gctgccatgcagctgggctcccaatgcagtggggatggtggcgctctgggctggcgggag +ctatcctgcc +>p:HG002_2_chr20:62875072-62875657 +aactttcctggcacactggagaggacggcagaacgctgggatggatttatcgtgcaagac +cagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaatt +catcggggagccccgcaccctcacctgcaccctcacccccacccccacccccacccccac +ccccacccccacccgcacccccacccccacccgcacccccacccccacccccacccgcac +ccccacccccacccccacccgcacccccacccccacccgcacccccacccccacccccac +ccgcacccccacccccacccccacccgcacccgcacccccacccccacccgcacccgcac +ccccacccccacccccacccgcacccccacccccacccccacccccacccgcacccgcac +ccgcacccccacccccaccctcacccgcacccgcacccccacccccacccccacccgcac +ccgcacccccacccccacccc------------cacccccacccccacccgcacccgcac +ccgcacccccaccctcaccctcacccgcacccgcacccccacccccacccgcacccccac +ccgcacccccacccccacccccacccccacccgcacccgcacccccacccccacccccac +ccccacccccacccccacccccacccccaccctcacccgcacccccaccctcacccccac +cctcacccccaccctcacccgcaccctcacccgcacccgcacccccaccct------cac +ccacaccctcacccccaccctcacccccacccccaccctcacccgcacccgcacccccac +cctcacccccacccccacccccaccctcaccctcaccctcacccgcacccgcacccccac +ccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctcac +ccgcaccctcactcgcaccgcaccctcactggcaccctcacccacaccgcacccacaccc +acatcggggaagagctccatgatcattcttttctgtaggcgaaaaactgcggcgggaact +gctgccatgcagctgggctcccaatgcagtggggatggtggcgctctgggctggcgggag +ctatcctgcc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/msa.fa.fai new file mode 100644 index 00000000..ccd43e09 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_62875072_62875657 1150 29 60 61 +syndip_1_chr20:62875072-62875657 1150 1233 60 61 +syndip_2_chr20:62875072-62875657 1150 2437 60 61 +p:HG002_1_chr20:62875072-62875657 1150 3642 60 61 +p:HG002_2_chr20:62875072-62875657 1150 4847 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/output.vcf.gz new file mode 100644 index 00000000..e04f02af Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/output.vcf.gz.tbi new file mode 100644 index 00000000..2928af7f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:62875172-62875557/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/base.vcf.gz new file mode 100644 index 00000000..3c0ac363 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/base.vcf.gz.tbi new file mode 100644 index 00000000..56ab5dec Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/comp.vcf.gz new file mode 100644 index 00000000..eda6605c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/comp.vcf.gz.tbi new file mode 100644 index 00000000..207cc922 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/haps.fa new file mode 100644 index 00000000..c3ed29dd --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/haps.fa @@ -0,0 +1,50 @@ +>ref_chr20_63027897_63028267 +ACGGACCAGCATCTATCATGGCTGTTTTGCGTTTCTTGATTTCACGATGTCTGTTGTGTGCTCAGGCCCCTCCTCTCCAAGGTCCCAGCTGTCCTTGCCCTGTTCCCTGTGAAGAGTGAAGAACCAACGCGGGCGGGGAGTGGACCGGTGGGGAGAGGGCCGGTGGGGAGAGGACCGGTGGGGAGGGGCCGGTGGAGAGGGGGCCGGTGGGGAGGGGGCCGGCGGGGAGTGGTTTGGTGGGGAGGAGGCTGGTGAAGTAGCGTCAGGTGCGGGCCTGGCGTCGGCGAGTCAAGTCGAGCTGATCCAGGGCCTTCTTTCTGCAGCTTCATCAGGTTCTCAATTAGCGGAGGGCGCTGGCGGTGGAGGAGGGC +>syndip_1_chr20:63027897-63028267 +ACGGACCAGCATCTATCATGGCTGTTTTGCGTTTCTTGATTTCACGATGTCTGTTGTGTG +CTCAGGCCCCTCCTCTCCAAGGTCCCAGCTGTCCTTGCCCTGTTCCCTGTGAAGAGTGAA +GAACCAACGCGGGCGGGGAGTGGACCGGTGGGGAGAGGGCCGGTGGGGAGAGGGCCGGTG +GGGAGAGGACCGGTGGGGAGGGGGCCGGTGGAGAGGGGGCCGGTGGGGAGGGGGCCGGTG +GGGAGAGGACCGGTGGGGAGGGGCCGGTGGGGAGGGGGCCGGTGGGGAGAGGACCGGTGG +GGAGGGGCCGGTGGGGAGGGGGCCGGTGGGGAGAGGACCGGTGGGGAGGGGCCGGTGGGG +AGGGGGCCGGCGGGGAGGGGGCCGGCGGGGAGGGTGCCGGTGGGGAGTGGTCTGGTGGGG +AGGGGGCCGGTGGGGAGGGGGCCCGCGGGGAGGGGCCGGTGGGGAGGGGGCCTGCGGGGA +GGGGGCCGGCGGGGAGGGGCCGGTGGGGAGGGGCCGGTGGGGTGGGGCCGGTGGGGAGGG +GGCCGGTGGGGGGGGGCCTGCAGGGAGGGGGCCGGTGGGGAGGAGGCTGGTGAAGTAGCG +TCAGGTGCGGGCCTGGCGTCGGCGAGTCAAGTCGAGCTGATCCAGGGCCTTCTTTCTGCA +GCTTCATCAGGTTCTCAATTAGCGGAGGGCGCTGGCGGTGGAGGAGGGC +>syndip_2_chr20:63027897-63028267 +ACGGACCAGCATCTATCATGGCTGTTTTGCGTTTCTTGATTTCACGATGTCTGTTGTGTG +CTCAGGCCCCTCCTCTCCAAGGTCCCAGCTGTCCTTGCCCTGTTCCCTGTGAAGAGTGAA +GAACCAACGCGGGCGGGGAGTGGACCGGTGGGGAGAGGGCCGGTGGGGAGAGGACCGGTG +GGGAGGGGCCGGTGGAGAGGGGGCCGGTGGGGAGGGGGCCGGCGGGGAGTGGTTTGGTGG +GGAGGGGGCCGGTGGGGAGGGGGCCTGCGGGGAGGGGCCGGTGGGGAGGGGGCCGGTGGG +GAGGGGGCCGGCGGGGAGGGGGCCGGCGGGGAGGGGGCCGGCGGGGAGTGGTCTGGTGGG +GAGGGGGCCGGTGGGGAGGGGGCCGGCGGGGAGGGGGCCGGCGGGGAGGGGCCGGTGGGG +AGTGGTCTGGTGGGGAGGGGGCCGGTGGGGAGGAGGCTGGTGAAGTAGCGTCAGGTGCGG +GCCTGGCGTCGGCGAGTCAAGTCGAGCTGATCCAGGGCCTTCTTTCTGCAGCTTCATCAG +GTTCTCAATTAGCGGAGGGCGCTGGCGGTGGAGGAGGGC +>p:HG002_1_chr20:63027897-63028267 +ACGGACCAGCATCTATCATGGCTGTTTTGCGTTTCTTGATTTCACGATGTCTGTTGTGTG +CTCAGGCCCCTCCTCTCCAAGGTCCCAGCTGTCCTTGCCCTGTTCCCTGTGAAGAGTGAA +GAACCAACGCGGGCGGGGAGTGGACCGGTGGGGAGAGGGCCGGTGGGGAGAGGACCGGTG +GGGAGGGGCCGGTGGAGAGGGGGCCGGTGGGGAGGGGGCCGGCGGGGAGTGGTTTGGTGG +GGAGGGGGCCGGTGGGGAGGGGGCCTGCGGGGAGGGGCCGGTGGGGAGGGGGCCGGTGGG +GAGGGGGCCGGCGGGGAGGGGGCCGGCGGGGAGGGGGCCGGCGGGGAGTGGTCTGGTGGG +GAGGGGGCCGGTGGGGAGGGGGCCGGCGGGGAGGGGGCCGGCGGGGAGGGGCCGGTGGGG +AGTGGTCTGGTGGGGAGGGGGCCGGTGGGGAGGAGGCTGGTGAAGTAGCGTCAGGTGCGG +GCCTGGCGTCGGCGAGTCAAGTCGAGCTGATCCAGGGCCTTCTTTCTGCAGCTTCATCAG +GTTCTCAATTAGCGGAGGGCGCTGGCGGTGGAGGAGGGC +>p:HG002_2_chr20:63027897-63028267 +ACGGACCAGCATCTATCATGGCTGTTTTGCGTTTCTTGATTTCACGATGTCTGTTGTGTG +CTCAGGCCCCTCCTCTCCAAGGTCCCAGCTGTCCTTGCCCTGTTCCCTGTGAAGAGTGAA +GAACCAACGCGGGCGGGGAGTGGACCGGTGGGGAGAGGGCCGGTGGGGAGAGGGCCGGTG +GGGAGAGGACCGGTGGGGAGGGGGCCGGTGGAGAGGGGGCCGGTGGGGAGGGGGCCGGTG +GGGAGAGGACCGGTGGGGAGGGGCCGGTGGGGAGGGGGCCGGTGGGGAGAGGACCGGTGG +GGAGGGGCCGGTGGGGAGGGGGCCGGTGGGGAGAGGACCGGTGGGGAGGGGCCGGTGGGG +AGGGGGCCGGCGGGGAGGGGGCCGGCGGGGAGGGTGCCGGTGGGGAGTGGTCTGGTGGGG +AGGGGGCCGGTGGGGAGGGGGCCCGCGGGGAGGGGCCGGTGGGGAGGGGGCCTGCGGGGA +GGGGGCCGGCGGGGAGGGGCCGGTGGGGAGGGGCCGGTGGGGTGGGGCCGGTGGGGAGGG +GGCCGGTGGGGGGGGGCCTGCAGGGAGGGGGCCGGTGGGGAGGAGGCTGGTGAAGTAGCG +TCAGGTGCGGGCCTGGCGTCGGCGAGTCAAGTCGAGCTGATCCAGGGCCTTCTTTCTGCA +GCTTCATCAGGTTCTCAATTAGCGGAGGGCGCTGGCGGTGGAGGAGGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/haps.fa.ref.fa new file mode 100644 index 00000000..cb471bcd --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63027897-63028267 +ACGGACCAGCATCTATCATGGCTGTTTTGCGTTTCTTGATTTCACGATGTCTGTTGTGTGCTCAGGCCCCTCCTCTCCAAGGTCCCAGCTGTCCTTGCCCTGTTCCCTGTGAAGAGTGAAGAACCAACGCGGGCGGGGAGTGGACCGGTGGGGAGAGGGCCGGTGGGGAGAGGACCGGTGGGGAGGGGCCGGTGGAGAGGGGGCCGGTGGGGAGGGGGCCGGCGGGGAGTGGTTTGGTGGGGAGGAGGCTGGTGAAGTAGCGTCAGGTGCGGGCCTGGCGTCGGCGAGTCAAGTCGAGCTGATCCAGGGCCTTCTTTCTGCAGCTTCATCAGGTTCTCAATTAGCGGAGGGCGCTGGCGGTGGAGGAGGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/msa.fa new file mode 100644 index 00000000..c05441b4 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/msa.fa @@ -0,0 +1,65 @@ +>ref_chr20_63027897_63028267 +acggaccagcatctatcatggctgttttgcgtttcttgatttcacgatgtctgttgtgtg +ctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaa +gaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagaggaccggtg +ggga----------------ggggccggtggagagggggccggtggggagggggccggcg +gggag--------------tggttt----------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------ggtggggaggaggctggtgaagtagcg +tcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgca +gcttcatcaggttctcaattagcggagggcgctggcggtggaggagggc +>syndip_1_chr20:63027897-63028267 +acggaccagcatctatcatggctgttttgcgtttcttgatttcacgatgtctgttgtgtg +ctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaa +gaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagagggccggtg +gggagaggaccggtggggagggggccggtggagagggggccggtggggagggggccggtg +gggagaggaccggtggggaggggccggtggggagggggccggtggggagaggaccggtgg +ggaggggccggtggggagggggccggtggggagaggaccggtggggaggggccggtgggg +agggggccggcggggagggggccggcggggagggtgccggtggggagtggtctggtgggg +agggggccggtggggagggggcccgcggggaggggccggtggggagggggcctgcgggga +gggggccggcggggaggggccggtggggaggggccggtggggtggggccggtggggaggg +ggccggtgggggggggcctgcagggagggggccggtggggaggaggctggtgaagtagcg +tcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgca +gcttcatcaggttctcaattagcggagggcgctggcggtggaggagggc +>syndip_2_chr20:63027897-63028267 +acggaccagcatctatcatggctgttttgcgtttcttgatttcacgatgtctgttgtgtg +ctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaa +gaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagaggaccggtg +ggga----------------ggggccggtggagagggggccggtggggagggggccggcg +gggag--------------tggtttggtggggagggggccggtggggagggggcctgcgg +ggaggggccggtggggag-----------------------------ggggccggtgggg +agggggccggcggggagggggccggcggggagggggccggcggggagtggtctggtgggg +ag-----------------------------ggggccggtggggagggggccggcgggga +gggggccggcggggaggggccggtggggagtggtctg----------------------- +-------------------gtggggagggggccggtggggaggaggctggtgaagtagcg +tcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgca +gcttcatcaggttctcaattagcggagggcgctggcggtggaggagggc +>p:HG002_1_chr20:63027897-63028267 +acggaccagcatctatcatggctgttttgcgtttcttgatttcacgatgtctgttgtgtg +ctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaa +gaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagaggaccggtg +ggga----------------ggggccggtggagagggggccggtggggagggggccggcg +gggag--------------tggtttggtggggagggggccggtggggagggggcctgcgg +ggaggggccggtggggag-----------------------------ggggccggtgggg +agggggccggcggggagggggccggcggggagggggccggcggggagtggtctggtgggg +ag-----------------------------ggggccggtggggagggggccggcgggga +gggggccggcggggaggggccggtggggagtggtctg----------------------- +-------------------gtggggagggggccggtggggaggaggctggtgaagtagcg +tcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgca +gcttcatcaggttctcaattagcggagggcgctggcggtggaggagggc +>p:HG002_2_chr20:63027897-63028267 +acggaccagcatctatcatggctgttttgcgtttcttgatttcacgatgtctgttgtgtg +ctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaa +gaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagagggccggtg +gggagaggaccggtggggagggggccggtggagagggggccggtggggagggggccggtg +gggagaggaccggtggggaggggccggtggggagggggccggtggggagaggaccggtgg +ggaggggccggtggggagggggccggtggggagaggaccggtggggaggggccggtgggg +agggggccggcggggagggggccggcggggagggtgccggtggggagtggtctggtgggg +agggggccggtggggagggggcccgcggggaggggccggtggggagggggcctgcgggga +gggggccggcggggaggggccggtggggaggggccggtggggtggggccggtggggaggg +ggccggtgggggggggcctgcagggagggggccggtggggaggaggctggtgaagtagcg +tcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgca +gcttcatcaggttctcaattagcggagggcgctggcggtggaggagggc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/msa.fa.fai new file mode 100644 index 00000000..f18c8fd3 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63027897_63028267 709 29 60 61 +syndip_1_chr20:63027897-63028267 709 784 60 61 +syndip_2_chr20:63027897-63028267 709 1539 60 61 +p:HG002_1_chr20:63027897-63028267 709 2295 60 61 +p:HG002_2_chr20:63027897-63028267 709 3051 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/output.vcf.gz new file mode 100644 index 00000000..326903f9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/output.vcf.gz.tbi new file mode 100644 index 00000000..e7ee6374 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63027997-63028167/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/base.vcf.gz new file mode 100644 index 00000000..0d0de4e0 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/base.vcf.gz.tbi new file mode 100644 index 00000000..cba08c29 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/comp.vcf.gz new file mode 100644 index 00000000..af21a99d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/comp.vcf.gz.tbi new file mode 100644 index 00000000..e937e5d3 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/haps.fa new file mode 100644 index 00000000..c6e231aa --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/haps.fa @@ -0,0 +1,78 @@ +>ref_chr20_63028776_63029503 +CAACAATGCACAAGTGGCTTGAGTAGAAGAGCTGCTCCTGCTGGGAGGCGCAGGAGGCTGAGCGAGGCCCACCCTGCAGGGGCGAGGCCACGGTTTGTGTTATTTCCCATGATGACTCCAAACGCACCCGAGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTCCGTGTGCAGGTCCCCCGGGCCTCTGCGTCTCTGTGTGCAGGCTCAAGTTTGCCAACGTCCATGCACGTCTCAGCCTCTCAGCCTGGACTGGACAACTGGGCTTCGGGAATTCATTTAAATTCTACCCGCTACACGCCTTCCCTGGATTCAGGGCGGCGTCCAGTGCATTCAT +>syndip_1_chr20:63028776-63029503 +CAACAATGCACAAGTGGCTTGAGTAGAAGAGCTGCTCCTGCTGGGAGGCGCAGGAGGCTG +AGCGAGGCCCACCCTGCAGGGGCGAGGCCACGGTTTGTGTTATTTCCCATGATGACTCCA +AACGCACCCGAGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCG +CCTCCGTGTGCAGGTCCCCCGGGCCTCCGCCTCTCCGTGTGCAGGTCCCCCGGGCCTCCG +CGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGTCCCCCGGGCCTC +CGCGTCTGTGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCC +TCCGCGTCTGTGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGTCCCCCGGG +CCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCG +GGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGTCCCC +CGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTCCGTGTGCAGGTCC +CCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGT +CCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAG +GTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGC +AGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGT +GCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGT +GTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCC +GTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCT +CCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGC +CTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGC +GCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCC +GCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCT +CCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCTGCGTCTCTGTGTGCAGGCTCAAGTTTG +CCAACGTCCATGCACGTCTCAGCCTCTCAGCCTGGACTGGACAACTGGGCTTCGGGAATT +CATTTAAATTCTACCCGCTACACGCCTTCCCTGGATTCAGGGCGGCGTCCAGTGCATTCA +T +>syndip_2_chr20:63028776-63029503 +CAACAATGCACAAGTGGCTTGAGTAGAAGAGCTGCTCCTGCTGGGAGGCGCAGGAGGCTG +AGCGAGGCCCACCCTGCAGGGGCGAGGCCACGGTTTGTGTTATTTCCCATGATGACTCCA +AACGCACCCGAGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCG +CCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCG +CGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTC +CGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTCCGTGTGCAGGTCCCCCGGGCC +TCCGCGTCTGTGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGG +CCTCCGCGTCTCCGTGTGCAGGTCCCCCGGGCCCCTGCGTCTCTGTGTGCAGGCTCAAGT +TTGCCAACGTCCATGCACGTCTCAGCCTCTCAGCCTGGACTGGACAACTGGGCTTCGGGA +ATTCATTTAAATTCTACCCGCTACACGCCTTCCCTGGATTCAGGGCGGCGTCCAGTGCAT +TCAT +>p:HG002_1_chr20:63028776-63029503 +CAACAATGCACAAGTGGCTTGAGTAGAAGAGCTGCTCCTGCTGGGAGGCGCAGGAGGCTG +AGCGAGGCCCACCCTGCAGGGGCGAGGCCACGGTTTGTGTTATTTCCCATGATGACTCCA +AACGCACCCGAGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCG +CCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCG +CGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTC +CGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTCCGTGTGCAGGTCCCCCGGGCC +TCCGCGTCTGTGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGG +CCTCCGCGTCTCCGTGTGCAGGTCCCCCGGGCCCCTGCGTCTCTGTGTGCAGGCTCAAGT +TTGCCAACGTCCATGCACGTCTCAGCCTCTCAGCCTGGACTGGACAACTGGGCTTCGGGA +ATTCATTTAAATTCTACCCGCTACACGCCTTCCCTGGATTCAGGGCGGCGTCCAGTGCAT +TCAT +>p:HG002_2_chr20:63028776-63029503 +CAACAATGCACAAGTGGCTTGAGTAGAAGAGCTGCTCCTGCTGGGAGGCGCAGGAGGCTG +AGCGAGGCCCACCCTGCAGGGGCGAGGCCACGGTTTGTGTTATTTCCCATGATGACTCCA +AACGCACCCGAGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCG +CCTCCGTGTGCAGGTCCCCCGGGCCTCCGCCTCTCCGTGTGCAGGTCCCCCGGGCCTCCG +CGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGTCCCCCGGGCCTC +CGCGTCTGTGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCC +TCCGCGTCTGTGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGTCCCCCGGG +CCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCG +GGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGTCCCC +CGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTCCGTGTGCAGGTCC +CCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGT +CCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAG +GTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGC +AGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGT +GCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGT +GTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCC +GTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCT +CCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGC +CTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGC +GCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCC +GCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCT +CCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCTGCGTCTCTGTGTGCAGGCTCAAGTTTG +CCAACGTCCATGCACGTCTCAGCCTCTCAGCCTGGACTGGACAACTGGGCTTCGGGAATT +CATTTAAATTCTACCCGCTACACGCCTTCCCTGGATTCAGGGCGGCGTCCAGTGCATTCA +T diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/haps.fa.ref.fa new file mode 100644 index 00000000..fa835ef1 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63028776-63029503 +CAACAATGCACAAGTGGCTTGAGTAGAAGAGCTGCTCCTGCTGGGAGGCGCAGGAGGCTGAGCGAGGCCCACCCTGCAGGGGCGAGGCCACGGTTTGTGTTATTTCCCATGATGACTCCAAACGCACCCGAGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTCCGTGTGCAGGTCCCCCGGGCCTCTGCGTCTCTGTGTGCAGGCTCAAGTTTGCCAACGTCCATGCACGTCTCAGCCTCTCAGCCTGGACTGGACAACTGGGCTTCGGGAATTCATTTAAATTCTACCCGCTACACGCCTTCCCTGGATTCAGGGCGGCGTCCAGTGCATTCAT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/msa.fa new file mode 100644 index 00000000..3fad97e5 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/msa.fa @@ -0,0 +1,130 @@ +>ref_chr20_63028776_63029503 +caacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctg +agcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcca +aa---------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------------------cgcac +ccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgt +gtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctcc +gtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcct +ccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc +ctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgc +gcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctcc +gcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct +ccgcgtctccgtgtgcaggtcccccgggcctctgcgtctctgtgtgcaggctcaagtttg +ccaacgtccatgcacgtctcagcctctcagcctggactggacaactgggcttcgggaatt +catttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgcattca +t +>syndip_1_chr20:63028776-63029503 +caacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctg +agcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcca +aacgcacccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcg +cctccgtgtgcaggtcccccgggcctccgcctctccgtgtgcaggtcccccgggcctccg +cgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctc +cgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcc +tccgcgtctgtgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccggg +cctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccg +ggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccc +cgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctccgtgtgcaggtcc +cccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggt +cccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcag +gtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgc +aggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgt +gcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgt +gtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctcc +gtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcct +ccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc +ctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgc +gcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctcc +gcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct +ccgcgcctccgtgtgcaggtcccccgggcctctgcgtctctgtgtgcaggctcaagtttg +ccaacgtccatgcacgtctcagcctctcagcctggactggacaactgggcttcgggaatt +catttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgcattca +t +>syndip_2_chr20:63028776-63029503 +caacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctg +agcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcca +aa---------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------------------cgcac +ccga-------------------------------------------------------- +------------------------------------------------------------ +--------gtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcct +ccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc +ctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgc +gcctccgtgtgcaggtcccccgggcctccgcgtctccgtgtgcaggtcccccgggcctcc +gcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct +ccgcgtctccgtgtgcaggtcccccgggcccctgcgtctctgtgtgcaggctcaagtttg +ccaacgtccatgcacgtctcagcctctcagcctggactggacaactgggcttcgggaatt +catttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgcattca +t +>p:HG002_1_chr20:63028776-63029503 +caacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctg +agcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcca +aa---------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------------------cgcac +ccga-------------------------------------------------------- +------------------------------------------------------------ +--------gtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcct +ccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc +ctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgc +gcctccgtgtgcaggtcccccgggcctccgcgtctccgtgtgcaggtcccccgggcctcc +gcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct +ccgcgtctccgtgtgcaggtcccccgggcccctgcgtctctgtgtgcaggctcaagtttg +ccaacgtccatgcacgtctcagcctctcagcctggactggacaactgggcttcgggaatt +catttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgcattca +t +>p:HG002_2_chr20:63028776-63029503 +caacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctg +agcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcca +aacgcacccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcg +cctccgtgtgcaggtcccccgggcctccgcctctccgtgtgcaggtcccccgggcctccg +cgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctc +cgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcc +tccgcgtctgtgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccggg +cctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccg +ggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccc +cgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctccgtgtgcaggtcc +cccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggt +cccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcag +gtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgc +aggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgt +gcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgt +gtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctcc +gtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcct +ccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc +ctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgc +gcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctcc +gcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct +ccgcgcctccgtgtgcaggtcccccgggcctctgcgtctctgtgtgcaggctcaagtttg +ccaacgtccatgcacgtctcagcctctcagcctggactggacaactgggcttcgggaatt +catttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgcattca +t diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/msa.fa.fai new file mode 100644 index 00000000..b6ddf3d5 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63028776_63029503 1441 29 60 61 +syndip_1_chr20:63028776-63029503 1441 1529 60 61 +syndip_2_chr20:63028776-63029503 1441 3029 60 61 +p:HG002_1_chr20:63028776-63029503 1441 4530 60 61 +p:HG002_2_chr20:63028776-63029503 1441 6031 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/output.vcf.gz new file mode 100644 index 00000000..7a9da251 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/output.vcf.gz.tbi new file mode 100644 index 00000000..76348f55 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63028876-63029403/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/base.vcf.gz new file mode 100644 index 00000000..3066579e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/base.vcf.gz.tbi new file mode 100644 index 00000000..ec185c5d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/comp.vcf.gz new file mode 100644 index 00000000..2cc5d417 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/comp.vcf.gz.tbi new file mode 100644 index 00000000..c9e2134e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/haps.fa new file mode 100644 index 00000000..f1cc034a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/haps.fa @@ -0,0 +1,92 @@ +>ref_chr20_63048933_63049513 +GCTTGTTTGGACCTGAAGACCAGCCTGAGCGAGGAGAGTCTTGTGCAGACGGTTTATCCAGGAGGAGCCCGGGGAGAGGGGGGTGGGAAAAGCCACAGTTTTGGAGGTCAGCAAGGTCATGTGGGGGCAGACTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCCTCCTCCTCCTCTTCCTCCTCGTCCTCTTCCTCCTTCTGCCAGGACCCTTCTTCCAGGACCCCTGAGAAGCGCATAGAATAGCGTCCAGGACTGTCTGCCCCAGGCACGCTGACCACTGGCTCCACTCCCCTGGGCAAGGGTCGCCCCTGGGCTGCTGCCTCCCAGCGACACAGGCAGGACCCAGAAGCCTGGTAGAAAGTGACCATGTGTGGCAGGT +>syndip_1_chr20:63048933-63049513 +GCTTGTTTGGACCTGAAGACCAGCCTGAGCGAGGAGAGTCTTGTGCAGACGGTTTATCCA +GGAGGAGCCCGGGGAGAGGGGGGTGGGAAAAGCCACAGTTTTGGAGGTCAGCAAGGTCAT +GTGGGGGCAGACTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCTTCCTCC +TCCTCCTCCTCTTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCC +CCCTCCTCTTCCTCCTCCTCCTCTTCCTTCTCCTCCTCCTTCTCCTCCTCCTCTTCCTCC +TCTTCCTCTTCCTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCTTTCTCCTCCTCTTCC +TCTTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCC +TCCTCCTCTTCCTCCTTCTCTTCCTCTTCCTCCTCCTCTTCCTCTTCCTCCTCCTCTTCC +TCTTTCTCCTCCTCCTCCTCTTCCTCTTCCTCCTCCTCTTCCTCTTTCTCCTCCTCCTCC +TCTTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCGTCT +TCCTCCTTCTCCTCTTCCTCCTCTTCCTCTTCCTCCTCCTCTTCCTCTTCCTCTTCCTCT +TCCTCTTCCTCCTCCTCCTCCTCTTTCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCC +TCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCT +TCTTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCC +TCTTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCC +TCTTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCCTCCTCCTCCTCTTCCTCCT +CCTCCTCTTCCTCCCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCCTCC +TCCTCCTCTTCCTCCTCGTCCTCTTCCTCCTTCTGCCAGGACCCTTCTTCCAGGACCCCT +GAGAAGCGCATAGAATAGCGTCCAGGACTGTCTGCCCCAGGCACGCTGACCACTGGCTCC +ACTCCCCTGGGCAAGGGTCGCCCCTGGGCTGCTGCCTCCCAGCGACACAGGCAGGACCCA +GAAGCCTGGTAGAAAGTGACCATGTGTGGCAGGT +>syndip_2_chr20:63048933-63049513 +GCTTGTTTGGACCTGAAGACCAGCCTGAGCGAGGAGAGTCTTGTGCAGACGGTTTATCCA +GGAGGAGCCCGGGGAGAGGGGGGTGGGAAAAGCCACAGTTTTGGAGGTCAGCAAGGTCAT +GTGGGGGCAGACTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCCTCT +TCCTCTTCCTCCTCCTCCTCCTCTTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCTCCTCC +TCTTCCTCCTCCTCCTCTTCCTCCTCCCCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCC +TCCTCCTTCTCCTCCTCCTCTTCCTCCTCTTCCTCTTCCTCCTCCTCTTCCTCCTCCTCT +TTCTCCTCCTCTTCCTCTTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCC +TCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCTTCCTCCTTCTCTTCCTCTTCCTCC +TCCTCTTCCTCTTCCTCCTCCTCTTCCTCTTTCTCCTCCTCCTCCTCTTCCTCCTCTTCC +TCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCGTCTTCCTCCTTCTCCTCT +TCCTCCTCTTCCTCTTCCTCCTCCTCTTCCTCTTCCTCTTCCTCTTCCTCCTCCTCCTCC +TCTTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCC +TCCTCTTCCTCCTCCTCCTCTTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCTTCTTCC +TCCTCTTCCTCCTCCTCCTCTTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCCTCTTCC +TCCTCCTCTTCCTCCTCTTCTTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCTTCCTCC +TCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCCTCCTCTTCCTCCTCCTCCTCTTCCTCCT +CCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCCTCCTCCTCCTCTTC +CTCCTCCTCCTCTTCCTCCCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCC +CCTCCTCCTCCTCTTCCTCCTCGTCCTCTTCCTCCTTCTGCCAGGACCCTTCTTCCAGGA +CCCCTGAGAAGCGCATAGAATAGCGTCCAGGACTGTCTGCCCCAGGCACGCTGACCACTG +GCTCCACTCCCCTGGGCAAGGGTCGCCCCTGGGCTGCTGCCTCCCAGCGACACAGGCAGG +ACCCAGAAGCCTGGTAGAAAGTGACCATGTGTGGCAGGT +>p:HG002_1_chr20:63048933-63049513 +GCTTGTTTGGACCTGAAGACCAGCCTGAGCGAGGAGAGTCTTGTGCAGACGGTTTATCCA +GGAGGAGCCCGGGGAGAGGGGGGTGGGAAAAGCCACAGTTTTGGAGGTCAGCAAGGTCAT +GTGGGGGCAGACTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCCTCT +TCCTCTTCCTCCTCCTCCTCCTCTTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCTCCTCC +TCTTCCTCCTCCTCCTCTTCCTCCTCCCCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCC +TCCTCCTTCTCCTCCTCCTCTTCCTCCTCTTCCTCTTCCTCCTCCTCTTCCTCCTCCTCT +TTCTCCTCCTCTTCCTCTTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCC +TCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCTTCCTCCTTCTCTTCCTCTTCCTCC +TCCTCTTCCTCTTCCTCCTCCTCTTCCTCTTTCTCCTCCTCCTCCTCTTCCTCCTCTTCC +TCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCGTCTTCCTCCTTCTCCTCT +TCCTCCTCTTCCTCTTCCTCCTCCTCTTCCTCTTCCTCTTCCTCTTCCTCCTCCTCCTCC +TCTTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCC +TCCTCTTCCTCCTCCTCCTCTTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCTTCTTCC +TCCTCTTCCTCCTCCTCCTCTTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCCTCTTCC +TCCTCCTCTTCCTCCTCTTCTTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCTTCCTCC +TCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCCTCCTCTTCCTCCTCCTCCTCTTCCTCCT +CCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCCTCCTCCTCCTCTTC +CTCCTCCTCCTCTTCCTCCCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCC +CCTCCTCCTCCTCTTCCTCCTCGTCCTCTTCCTCCTTCTGCCAGGACCCTTCTTCCAGGA +CCCCTGAGAAGCGCATAGAATAGCGTCCAGGACTGTCTGCCCCAGGCACGCTGACCACTG +GCTCCACTCCCCTGGGCAAGGGTCGCCCCTGGGCTGCTGCCTCCCAGCGACACAGGCAGG +ACCCAGAAGCCTGGTAGAAAGTGACCATGTGTGGCAGGT +>p:HG002_2_chr20:63048933-63049513 +GCTTGTTTGGACCTGAAGACCAGCCTGAGCGAGGAGAGTCTTGTGCAGACGGTTTATCCA +GGAGGAGCCCGGGGAGAGGGGGGTGGGAAAAGCCACAGTTTTGGAGGTCAGCAAGGTCAT +GTGGGGGCAGACTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCTTCCTCC +TCCTCCTCCTCTTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCC +CCCTCCTCTTCCTCCTCCTCCTCTTCCTTCTCCTCCTCCTTCTCCTCCTCCTCTTCCTCC +TCTTCCTCTTCCTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCTTTCTCCTCCTCTTCC +TCTTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCC +TCCTCCTCTTCCTCCTTCTCTTCCTCTTCCTCCTCCTCTTCCTCTTCCTCCTCCTCTTCC +TCTTTCTCCTCCTCCTCCTCTTCCTCTTCCTCCTCCTCTTCCTCTTTCTCCTCCTCCTCC +TCTTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCGTCT +TCCTCCTTCTCCTCTTCCTCCTCTTCCTCTTCCTCCTCCTCTTCCTCTTCCTCTTCCTCT +TCCTCTTCCTCCTCCTCCTCCTCTTTCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCC +TCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCT +TCTTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCC +TCTTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCC +TCTTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCCTCCTCCTCCTCTTCCTCCT +CCTCCTCTTCCTCCCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCCTCC +TCCTCCTCTTCCTCCTCGTCCTCTTCCTCCTTCTGCCAGGACCCTTCTTCCAGGACCCCT +GAGAAGCGCATAGAATAGCGTCCAGGACTGTCTGCCCCAGGCACGCTGACCACTGGCTCC +ACTCCCCTGGGCAAGGGTCGCCCCTGGGCTGCTGCCTCCCAGCGACACAGGCAGGACCCA +GAAGCCTGGTAGAAAGTGACCATGTGTGGCAGGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/haps.fa.ref.fa new file mode 100644 index 00000000..9a0c0b1f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63048933-63049513 +GCTTGTTTGGACCTGAAGACCAGCCTGAGCGAGGAGAGTCTTGTGCAGACGGTTTATCCAGGAGGAGCCCGGGGAGAGGGGGGTGGGAAAAGCCACAGTTTTGGAGGTCAGCAAGGTCATGTGGGGGCAGACTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCCTCCTCCTCCTCTTCCTCCTCGTCCTCTTCCTCCTTCTGCCAGGACCCTTCTTCCAGGACCCCTGAGAAGCGCATAGAATAGCGTCCAGGACTGTCTGCCCCAGGCACGCTGACCACTGGCTCCACTCCCCTGGGCAAGGGTCGCCCCTGGGCTGCTGCCTCCCAGCGACACAGGCAGGACCCAGAAGCCTGGTAGAAAGTGACCATGTGTGGCAGGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/msa.fa new file mode 100644 index 00000000..82927c08 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/msa.fa @@ -0,0 +1,115 @@ +>ref_chr20_63048933_63049513 +gcttgtttggacctgaagaccagcctgagcgaggagagtcttgtgcagacggtttatcca +ggaggagcccggggagaggggggtgggaaaagccacagttttggaggtcagcaaggtcat +gtgggggcaga------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------ctcctcctcctcctcctcttcctcctcctcctcttcctcctcctcctct +tcctcttcctcctcctcctcctcttcctcctcctcctcctcttcctccctcctcttcctc +ctcctcctcttcctcctcctcttcctcctcctcctcctcttcctcccctcctcctcctct +tcctcctcctcctcttcctctcctcctcctcctcctcttcctcctcctcctcctcttcct +cccctcctcctcctcttcctcctcgtcctcttcctccttctgccaggacccttcttccag +gacccctgagaagcgcatagaatagcgtccaggactgtctgccccaggcacgctgaccac +tggctccactcccctgggcaagggtcgcccctgggctgctgcctcccagcgacacaggca +ggacccagaagcctggtagaaagtgaccatgtgtggcaggt +>syndip_1_chr20:63048933-63049513 +gcttgtttggacctgaagaccagcctgagcgaggagagtcttgtgcagacggtttatcca +ggaggagcccggggagaggggggtgggaaaagccacagttttggaggtcagcaaggtcat +gtgggggcagactcctcctcctcctcctcttcctcctcc--------------------- +------tcctcctcttcctcttcctcctcctcctcctcttcctcttcctcctcctcctcc +tcttcctcctcctcctcttcctcctccccctcctcttcctcctcctcctcttccttctcc +tcctccttctcctcctcctcttcctcctcttcctcttcctcctcctcttcctcctcctct +tcctcctcctctttctcctcctcttcctcttcctcctcttcctcctcctcttcctcctcc +tcctcttcctcctcctcctcttcctcctcctcctcttcctccttctcttcctcttcctcc +tcctcttcctcttcctcctcctcttcctctttctcctcctcctcctcttcctcttcctcc +tcc---------------------------------------tcttcctctttctcctcc +tcctcctcttcctcctcttcctcctcctcttcctcctcctcctcctcttcctcctcctcc +tcgtcttcctccttctcctcttcctcctcttcctcttcctcctcctcttcctcttcctct +tcctcttcctcttcctcctcctcctcctctttctcctcctcctcctcttcctcctcctcc +tcttcctcctcctcctcttcctcctcctcctcttcctcctcttcctcctcctcctcttcc +tcctcttcttcctcctcttcctcctcctcctcttcctcctcttcctcctcctcttcctcc +tcctcctcttcctcctcctcctcttcctcctcctcctcttcctcct-cctcctcttcctc +ctcctcctcttcctcctcctcttcctcctcctcctcctcttcctcccctcctcctcctct +tcctcctcctcctcttcctcccctcctcctcctcctcttcctcctcctcctcctcttcct +cccctcctcctcctcttcctcctcgtcctcttcctccttctgccaggacccttcttccag +gacccctgagaagcgcatagaatagcgtccaggactgtctgccccaggcacgctgaccac +tggctccactcccctgggcaagggtcgcccctgggctgctgcctcccagcgacacaggca +ggacccagaagcctggtagaaagtgaccatgtgtggcaggt +>syndip_2_chr20:63048933-63049513 +gcttgtttggacctgaagaccagcctgagcgaggagagtcttgtgcagacggtttatcca +ggaggagcccggggagaggggggtgggaaaagccacagttttggaggtcagcaaggtcat +gtgggggcagactcctcctcctcctcctcttcctcctcctcctcttcctcctcctcctct +tcctcttcctcctcctcctcctcttcctcttcctcctcctcctcctcttcctcctcctcc +tcttcctcctcctcctcttcctcctccccctcctcttcctcctcctcctcttcctcctcc +tcctccttctcctcctcctcttcctcctcttcctcttcctcctcctcttcctcctcctct +ttctcctcctcttcctcttcctcctcttcctcctcctcttcctcctcctcctcttcctcc +tcctcctcttcctcctcctcctcttcctcctcctcttcctccttctcttcctcttcctcc +tcctcttcctcttcctcctcctcttcctctttctcctcctcctcctcttcctcctcttcc +tcctcctcttcctcctcctcctcctcttcctcctcctcctcgtcttcctccttctcctct +tcctcctcttcctcttcctcctcctcttcctcttcctcttcctcttcctcctcctcctcc +tcttcctcctcctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcc +tcctcttcctcctcctcctcttcctcctcttcctcctcctcctcttcctcctcttcttcc +tcctcttcctcctcctcctcttcctcctcttcctcctcctcttcctcctcctcctcttcc +tcctcctcttcctcctcttcttcctcctcttcctcctcctcctcttcctcctcttcctcc +tcctcttcctcctcctcctcctcttcctcc-cctcctcttcctcct-cctcctcttcctc +ctcctcctcttcctcctcctcttcctcctcctcctcctcttcctcccctcctcctcctct +tcctcctcctcctcttcctcccctcctcctcctcctcttcctcctcctcctcctcttcct +cccctcctcctcctcttcctcctcgtcctcttcctccttctgccaggacccttcttccag +gacccctgagaagcgcatagaatagcgtccaggactgtctgccccaggcacgctgaccac +tggctccactcccctgggcaagggtcgcccctgggctgctgcctcccagcgacacaggca +ggacccagaagcctggtagaaagtgaccatgtgtggcaggt +>p:HG002_1_chr20:63048933-63049513 +gcttgtttggacctgaagaccagcctgagcgaggagagtcttgtgcagacggtttatcca +ggaggagcccggggagaggggggtgggaaaagccacagttttggaggtcagcaaggtcat +gtgggggcagactcctcctcctcctcctcttcctcctcctcctcttcctcctcctcctct +tcctcttcctcctcctcctcctcttcctcttcctcctcctcctcctcttcctcctcctcc +tcttcctcctcctcctcttcctcctccccctcctcttcctcctcctcctcttcctcctcc +tcctccttctcctcctcctcttcctcctcttcctcttcctcctcctcttcctcctcctct +ttctcctcctcttcctcttcctcctcttcctcctcctcttcctcctcctcctcttcctcc +tcctcctcttcctcctcctcctcttcctcctcctcttcctccttctcttcctcttcctcc +tcctcttcctcttcctcctcctcttcctctttctcctcctcctcctcttcctcctcttcc +tcctcctcttcctcctcctcctcctcttcctcctcctcctcgtcttcctccttctcctct +tcctcctcttcctcttcctcctcctcttcctcttcctcttcctcttcctcctcctcctcc +tcttcctcctcctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcc +tcctcttcctcctcctcctcttcctcctcttcctcctcctcctcttcctcctcttcttcc +tcctcttcctcctcctcctcttcctcctcttcctcctcctcttcctcctcctcctcttcc +tcctcctcttcctcctcttcttcctcctcttcctcctcctcctcttcctcctcttcctcc +tcctcttcctcctcctcctcctcttcctcc-cctcctcttcctcct-cctcctcttcctc +ctcctcctcttcctcctcctcttcctcctcctcctcctcttcctcccctcctcctcctct +tcctcctcctcctcttcctcccctcctcctcctcctcttcctcctcctcctcctcttcct +cccctcctcctcctcttcctcctcgtcctcttcctccttctgccaggacccttcttccag +gacccctgagaagcgcatagaatagcgtccaggactgtctgccccaggcacgctgaccac +tggctccactcccctgggcaagggtcgcccctgggctgctgcctcccagcgacacaggca +ggacccagaagcctggtagaaagtgaccatgtgtggcaggt +>p:HG002_2_chr20:63048933-63049513 +gcttgtttggacctgaagaccagcctgagcgaggagagtcttgtgcagacggtttatcca +ggaggagcccggggagaggggggtgggaaaagccacagttttggaggtcagcaaggtcat +gtgggggcagactcctcctcctcctcctcttcctcctcc--------------------- +------tcctcctcttcctcttcctcctcctcctcctcttcctcttcctcctcctcctcc +tcttcctcctcctcctcttcctcctccccctcctcttcctcctcctcctcttccttctcc +tcctccttctcctcctcctcttcctcctcttcctcttcctcctcctcttcctcctcctct +tcctcctcctctttctcctcctcttcctcttcctcctcttcctcctcctcttcctcctcc +tcctcttcctcctcctcctcttcctcctcctcctcttcctccttctcttcctcttcctcc +tcctcttcctcttcctcctcctcttcctctttctcctcctcctcctcttcctcttcctcc +tcc---------------------------------------tcttcctctttctcctcc +tcctcctcttcctcctcttcctcctcctcttcctcctcctcctcctcttcctcctcctcc +tcgtcttcctccttctcctcttcctcctcttcctcttcctcctcctcttcctcttcctct +tcctcttcctcttcctcctcctcctcctctttctcctcctcctcctcttcctcctcctcc +tcttcctcctcctcctcttcctcctcctcctcttcctcctcttcctcctcctcctcttcc +tcctcttcttcctcctcttcctcctcctcctcttcctcctcttcctcctcctcttcctcc +tcctcctcttcctcctcctcctcttcctcctcctcctcttcctcct-cctcctcttcctc +ctcctcctcttcctcctcctcttcctcctcctcctcctcttcctcccctcctcctcctct +tcctcctcctcctcttcctcccctcctcctcctcctcttcctcctcctcctcctcttcct +cccctcctcctcctcttcctcctcgtcctcttcctccttctgccaggacccttcttccag +gacccctgagaagcgcatagaatagcgtccaggactgtctgccccaggcacgctgaccac +tggctccactcccctgggcaagggtcgcccctgggctgctgcctcccagcgacacaggca +ggacccagaagcctggtagaaagtgaccatgtgtggcaggt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/msa.fa.fai new file mode 100644 index 00000000..ce0645af --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63048933_63049513 1301 29 60 61 +syndip_1_chr20:63048933-63049513 1301 1386 60 61 +syndip_2_chr20:63048933-63049513 1301 2743 60 61 +p:HG002_1_chr20:63048933-63049513 1301 4101 60 61 +p:HG002_2_chr20:63048933-63049513 1301 5459 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/output.vcf.gz new file mode 100644 index 00000000..fe9ffc97 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/output.vcf.gz.tbi new file mode 100644 index 00000000..9dff7397 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63049033-63049413/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/base.vcf.gz new file mode 100644 index 00000000..1e03e85a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/base.vcf.gz.tbi new file mode 100644 index 00000000..5f4a140d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/comp.vcf.gz new file mode 100644 index 00000000..bc914a27 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/comp.vcf.gz.tbi new file mode 100644 index 00000000..6ce8a8d0 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/haps.fa new file mode 100644 index 00000000..52988324 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/haps.fa @@ -0,0 +1,46 @@ +>ref_chr20_63154485_63155096 +GAAGAGGGAGATGGACTGGCCTCAGCCACCCCGGAGTACAGGGATGTCATCACACCAGCCCTCCAGCGGCTGAAAGAGCCAGTGAGAGGCAGGTGGGGGTGTGGATCAGGCCTGATCTCCCCTAGTCTCCTCCTGCAATGCCCAGATTCTTGCCCCCGTCCTTCCTTCTCCCTCCTCCCTTCCTCCTCCCTCCTCTTCCCTCCCTCCTGCTTCCTCCCTCTGCCCTCCCTCCTCCCTCTTCCTCCCTCCTCCTCCTTCCTGCTTCCTCCCTCTGCCCTCCCTCCTCCCTCTTCCTCCCTCCTCCTCCCCTCTCCTCTTTCCTCCTCCCTCTCCCTTCCTCCTCCTCCCCCCTTTCCCACCCTCCTCCCCCTTTCCCTCCCTCCTCCCGACTCCCTCTCCCCTTCTCCCTCTTCTCATCCCTTCCTCCTCCTCCCTCCTCCCTTCCTCCTCCTCCCTCCTTCCTCCCTCCTCCCTCCTCCCCACACTGTCCATTTGCAGGCTGCCTGGTCCTAGCCCATATCCAAGGGCCTGTCTCAGCTACAAAGTTCTGCTCTCTGCTTTTAAATGAGGACACAAGGTGGTTTCCAAAACACATGTACAAGGCAGAAATTG +>syndip_1_chr20:63154485-63155096 +GAAGAGGGAGATGGACTGGCCTCAGCCACCCCGGAGTACAGGGATGTCATCACACCAGCC +CTCCAGCGGCTGAAAGAGCCAGTGAGAGGCAGGTGGGGGTGTGGATCAGGCCTGATCTCC +CCTAGTCTCCTCCTGCAATGCCCAGATTCTTGCCCCCGTCCTTCCTTCTCCCTCCTCCCT +TCCTCCTCCCTCCTCTTCCCTCCCTCCTGCTTCCTCCCTCTGCCCTCCCTCCTCCCTCTT +CCTCCCTCCTCCTCCCCTCTCCTCTTTCCTCCTCCCTCTCCCTTCCTCCTCCTCCCCCCT +TTCCCACCCTCCTCCCCCTTTCCCTCCCTCCTCCCGACTCCCTCTCCCCTTCTCCCTCTT +CTCATCCCTTCCTCCTCCTCCCTCCTTCCTCCCTCCTCCCTCCTCCCCACACTGTCCATT +TGCAGGCTGCCTGGTCCTAGCCCATATCCAAGGGCCTGTCTCAGCTACAAAGTTCTGCTC +TCTGCTTTTAAATGAGGACACAAGGTGGTTTCCAAAACACATGTACAAGGCAGAAATTG +>syndip_2_chr20:63154485-63155096 +GAAGAGGGAGATGGACTGGCCTCAGCCACCCCGGAGTACAGGGATGTCATCACACCAGCC +CTCCAGCGGCTGAAAGAGCCAGTGAGAGGCAGGTGGGGGTGTGGATCAGGCCTGATCTCC +CCTAGTCTCCTCCTGCAATGCCCAGATTCTTGCCCCCGTCCTTCCTTCTCCCTCCTCCCT +TCCTCCTCCCTCCTCTTCCCTCCCTCCTGCTTCCTCCCTCTGCCCTCCCTCCTCCCTCTT +CCTCCCTCCTCTTCCCTCCCTCCTGCTTCCTCCCTCTGCCCTCCCTCCTCCCTCTTCCTC +CCTCCTCCTCCCCTCTCCTCTTTCCTCCTCCCTCTCCCTTCCTCCTCCTCCCCCCTTTCC +CACCCTCCTCCCCCTTTCCCTCCCTCCTCCCGACTCCCTCTCCCCTTCTCCCTCTTCTCA +TCCCTTCCTCCTCCTCCCTCCTCCCTTCCTCCTCCTCCCTCCTTCCTCCCTCCTCCCTCC +TCCCCACACTGTCCATTTGCAGGCTGCCTGGTCCTAGCCCATATCCAAGGGCCTGTCTCA +GCTACAAAGTTCTGCTCTCTGCTTTTAAATGAGGACACAAGGTGGTTTCCAAAACACATG +TACAAGGCAGAAATTG +>p:HG002_1_chr20:63154485-63155096 +GAAGAGGGAGATGGACTGGCCTCAGCCACCCCGGAGTACAGGGATGTCATCACACCAGCC +CTCCAGCGGCTGAAAGAGCCAGTGAGAGGCAGGTGGGGGTGTGGATCAGGCCTGATCTCC +CCTAGTCTCCTCCTGCAATGCCCAGATTCTTGCCCCCGTCCTTCCTTCTCCCTCCTCCCT +TCCTCCTCCCTCCTCTTCCCTCCCTCCTGCTTCCTCCCTCTGCCCTCCCTCCTCCCTCTT +CCTCCCTCCTCTTCCCTCCCTCCTGCTTCCTCCCTCTGCCCTCCCTCCTCCCTCTTCCTC +CCTCCTCCTCCCCTCTCCTCTTTCCTCCTCCCTCTCCCTTCCTCCTCCTCCCCCCTTTCC +CACCCTCCTCCCCCTTTCCCTCCCTCCTCCCGACTCCCTCTCCCCTTCTCCCTCTTCTCA +TCCCTTCCTCCTCCTCCCTCCTCCCTTCCTCCTCCTCCCTCCTTCCTCCCTCCTCCCTCC +TCCCCACACTGTCCATTTGCAGGCTGCCTGGTCCTAGCCCATATCCAAGGGCCTGTCTCA +GCTACAAAGTTCTGCTCTCTGCTTTTAAATGAGGACACAAGGTGGTTTCCAAAACACATG +TACAAGGCAGAAATTG +>p:HG002_2_chr20:63154485-63155096 +GAAGAGGGAGATGGACTGGCCTCAGCCACCCCGGAGTACAGGGATGTCATCACACCAGCC +CTCCAGCGGCTGAAAGAGCCAGTGAGAGGCAGGTGGGGGTGTGGATCAGGCCTGATCTCC +CCTAGTCTCCTCCTGCAATGCCCAGATTCTTGCCCCCGTCCTTCCTTCTCCCTCCTCCCT +TCCTCCTCCCTCCTCTTCCCTCCCTCCTGCTTCCTCCCTCTGCCCTCCCTCCTCCCTCTT +CCTCCCTCCTCCTCCCCTCTCCTCTTTCCTCCTCCCTCTCCCTTCCTCCTCCTCCCCCCT +TTCCCACCCTCCTCCCCCTTTCCCTCCCTCCTCCCGACTCCCTCTCCCCTTCTCCCTCTT +CTCATCCCTTCCTCCTCCTCCCTCCTTCCTCCCTCCTCCCTCCTCCCCACACTGTCCATT +TGCAGGCTGCCTGGTCCTAGCCCATATCCAAGGGCCTGTCTCAGCTACAAAGTTCTGCTC +TCTGCTTTTAAATGAGGACACAAGGTGGTTTCCAAAACACATGTACAAGGCAGAAATTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/haps.fa.ref.fa new file mode 100644 index 00000000..12643aef --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63154485-63155096 +GAAGAGGGAGATGGACTGGCCTCAGCCACCCCGGAGTACAGGGATGTCATCACACCAGCCCTCCAGCGGCTGAAAGAGCCAGTGAGAGGCAGGTGGGGGTGTGGATCAGGCCTGATCTCCCCTAGTCTCCTCCTGCAATGCCCAGATTCTTGCCCCCGTCCTTCCTTCTCCCTCCTCCCTTCCTCCTCCCTCCTCTTCCCTCCCTCCTGCTTCCTCCCTCTGCCCTCCCTCCTCCCTCTTCCTCCCTCCTCCTCCTTCCTGCTTCCTCCCTCTGCCCTCCCTCCTCCCTCTTCCTCCCTCCTCCTCCCCTCTCCTCTTTCCTCCTCCCTCTCCCTTCCTCCTCCTCCCCCCTTTCCCACCCTCCTCCCCCTTTCCCTCCCTCCTCCCGACTCCCTCTCCCCTTCTCCCTCTTCTCATCCCTTCCTCCTCCTCCCTCCTCCCTTCCTCCTCCTCCCTCCTTCCTCCCTCCTCCCTCCTCCCCACACTGTCCATTTGCAGGCTGCCTGGTCCTAGCCCATATCCAAGGGCCTGTCTCAGCTACAAAGTTCTGCTCTCTGCTTTTAAATGAGGACACAAGGTGGTTTCCAAAACACATGTACAAGGCAGAAATTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/msa.fa new file mode 100644 index 00000000..f0308c9f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/msa.fa @@ -0,0 +1,60 @@ +>ref_chr20_63154485_63155096 +gaagagggagatggactggcctcagccaccccggagtacagggatgtcatcacaccagcc +ctccagcggctgaaagagccagtgagaggcaggtgggggtgtggatcaggcctgatctcc +cctagtctcctcctgcaatgcccagattcttgcccccgtccttccttctccctcctccct +tcctcctccctcctcttccctccctcctgcttcctccctctgccctccctcctccctctt +cctccctcct----cctccttcctgcttcctccctctgccctccctcctccctcttcctc +cctcctcctcccctctcctctttcctcctccctctcccttcctcctcctcccccctttcc +caccctcctccccctttccctccctcctcccgactccctctccccttctccctcttctca +tcccttcctcctcctccctcctcccttcctcctcctccctccttcctccctcctccctcc +tccccacactgtccatttgcaggctgcctggtcctagcccatatccaagggcctgtctca +gctacaaagttctgctctctgcttttaaatgaggacacaaggtggtttccaaaacacatg +tacaaggcagaaattg +>syndip_1_chr20:63154485-63155096 +gaagagggagatggactggcctcagccaccccggagtacagggatgtcatcacaccagcc +ctccagcggctgaaagagccagtgagaggcaggtgggggtgtggatcaggcctgatctcc +cctagtctcctcctgcaatgcccagattcttgcccccgtccttccttctccctcctccct +tcctcctccctcctcttc------------------------------------------ +--------------cctccctcctgcttcctccctctgccctccctcctccctcttcctc +cctcctcctcccctctcctctttcctcctccctctcccttcctcctcctcccccctttcc +caccctcctccccctttccctccctcctcccgactccctctccccttctccctcttctca +---------------------tcccttcctcctcctccctccttcctccctcctccctcc +tccccacactgtccatttgcaggctgcctggtcctagcccatatccaagggcctgtctca +gctacaaagttctgctctctgcttttaaatgaggacacaaggtggtttccaaaacacatg +tacaaggcagaaattg +>syndip_2_chr20:63154485-63155096 +gaagagggagatggactggcctcagccaccccggagtacagggatgtcatcacaccagcc +ctccagcggctgaaagagccagtgagaggcaggtgggggtgtggatcaggcctgatctcc +cctagtctcctcctgcaatgcccagattcttgcccccgtccttccttctccctcctccct +tcctcctccctcctcttccctccctcctgcttcctccctctgccctccctcctccctctt +cctccctcctcttccctccctcctgcttcctccctctgccctccctcctccctcttcctc +cctcctcctcccctctcctctttcctcctccctctcccttcctcctcctcccccctttcc +caccctcctccccctttccctccctcctcccgactccctctccccttctccctcttctca +tcccttcctcctcctccctcctcccttcctcctcctccctccttcctccctcctccctcc +tccccacactgtccatttgcaggctgcctggtcctagcccatatccaagggcctgtctca +gctacaaagttctgctctctgcttttaaatgaggacacaaggtggtttccaaaacacatg +tacaaggcagaaattg +>p:HG002_1_chr20:63154485-63155096 +gaagagggagatggactggcctcagccaccccggagtacagggatgtcatcacaccagcc +ctccagcggctgaaagagccagtgagaggcaggtgggggtgtggatcaggcctgatctcc +cctagtctcctcctgcaatgcccagattcttgcccccgtccttccttctccctcctccct +tcctcctccctcctcttccctccctcctgcttcctccctctgccctccctcctccctctt +cctccctcctcttccctccctcctgcttcctccctctgccctccctcctccctcttcctc +cctcctcctcccctctcctctttcctcctccctctcccttcctcctcctcccccctttcc +caccctcctccccctttccctccctcctcccgactccctctccccttctccctcttctca +tcccttcctcctcctccctcctcccttcctcctcctccctccttcctccctcctccctcc +tccccacactgtccatttgcaggctgcctggtcctagcccatatccaagggcctgtctca +gctacaaagttctgctctctgcttttaaatgaggacacaaggtggtttccaaaacacatg +tacaaggcagaaattg +>p:HG002_2_chr20:63154485-63155096 +gaagagggagatggactggcctcagccaccccggagtacagggatgtcatcacaccagcc +ctccagcggctgaaagagccagtgagaggcaggtgggggtgtggatcaggcctgatctcc +cctagtctcctcctgcaatgcccagattcttgcccccgtccttccttctccctcctccct +tcctcctccctcctcttc------------------------------------------ +--------------cctccctcctgcttcctccctctgccctccctcctccctcttcctc +cctcctcctcccctctcctctttcctcctccctctcccttcctcctcctcccccctttcc +caccctcctccccctttccctccctcctcccgactccctctccccttctccctcttctca +---------------------tcccttcctcctcctccctccttcctccctcctccctcc +tccccacactgtccatttgcaggctgcctggtcctagcccatatccaagggcctgtctca +gctacaaagttctgctctctgcttttaaatgaggacacaaggtggtttccaaaacacatg +tacaaggcagaaattg diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/msa.fa.fai new file mode 100644 index 00000000..82fc522b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63154485_63155096 616 29 60 61 +syndip_1_chr20:63154485-63155096 616 690 60 61 +syndip_2_chr20:63154485-63155096 616 1351 60 61 +p:HG002_1_chr20:63154485-63155096 616 2013 60 61 +p:HG002_2_chr20:63154485-63155096 616 2675 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/output.vcf.gz new file mode 100644 index 00000000..5a0051f9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/output.vcf.gz.tbi new file mode 100644 index 00000000..cd42d948 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63154585-63154996/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/base.vcf.gz new file mode 100644 index 00000000..c435a6ae Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/base.vcf.gz.tbi new file mode 100644 index 00000000..0bcd4545 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/comp.vcf.gz new file mode 100644 index 00000000..e9b851a4 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/comp.vcf.gz.tbi new file mode 100644 index 00000000..dd74c4fd Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/haps.fa new file mode 100644 index 00000000..1efeed23 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/haps.fa @@ -0,0 +1,254 @@ +>ref_chr20_63167287_63167728 +AATGGCCAGCCCGTCCCGCCGAGGCCAGTGGACATGCCAAATCCCTCCCGCAACAAGTTGCTATCCATCCCCTCGACTAATACTTACCAAATTAATTCCAGATTTGGAGTCACTCATGGTTCCCACCAGCACTCAGCCCCATCTCAGCCCCCATCTCAGCCCCCACCGCAGCCTCACCTCAGTGCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGACCCTCCTCAGCCCCTCCTCATCCCCTCCTCAGCAGCTGCTGGAATGGGCTACCCTCAGGAGTTGGCACCCCACAGGCTCCTTCCCTTCCCACCTCCGCCACACCCTGACGAGGGAAAAATGGGGAGCTGCTGGGAGGGAACTTGCACCCTGTTGGGCGCCTTGT +>syndip_1_chr20:63167287-63167728 +AATGGCCAGCCCGTCCCGCCGAGGCCAGTGGACATGCCAAATCCCTCCCGCAACAAGTTG +CTATCCATCCCCTCGACTAATACTTACCAAATTAATTCCAGATTTGGAGTCACTCACGGT +TCCCACCAGCACTCAGCCCCATCTCAGCCCCCATCTCAGCCCCCACCGCAGCCTCACCTC +AGTGCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCTCCTCA +GCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCT +GCCCCTCCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCCG +CCCCCACCTCTGCCCCTCCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCGC +CCCCACCTCCGCCCCCACCTCTGCCCCTCCTCAGCCCCCACCTCAGCCCCCTCCTCAGCC +CCCACCTCCGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGCCCCCACCTCAGCCC +CCTCCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCCGCCCCTCCTCCGCCCC +CACCTCAGCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGCCCCC +ACCTCAGCCCCCACCTCAGCCCCCACCTCCCCCCTCCTCAGCCCCCACCTCAGCCCCCAC +CTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACC +TCCGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACC +TCCGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCTGCCCCTCCT +CAGCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGCCCCCACCTC +AGCCCCCACCTCAGCCCCCACCTCCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAG +CCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGC +CCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCTCCTCAGCC +CCCACCTCCGCCCCCACCTCCGCCCCCACCTCTGCCCCTCCTCAGCCCCCACCTCAGCCC +CCTCCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCCGCCCCTCCTCCGCCCC +CACCTCAGCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGCCCCC +ACCTCAGCCCCCACCTCAGCCCCCACCTCCCCCCTCCTCAGCCCCCACCTCAGCCCCCAC +CTCCGCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCAGCCCCCACC +TCCGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCGCCCCCACC +TCAGCCCCCACCTCTGCCCCTCCTCAGCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCT +CTGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCCCCCTCCTCAG +CCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAG +CCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCCGCC +CCCACCTCAGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGCCCCCACCTCAGCCC +CCACCTCCGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCCCCCTCCTCCGCCCCC +ACCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCCCCCTCCTCCGCCCCCAC +CTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCCCCCTCCT +CAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCT +CAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTC +AGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTC +CGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTC +AGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTC +AGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCAG +CCCCCACCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCCTCCTCAGC +CCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGC +CCCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCCTCAGCCCCCACCTCAGCCCCCA +CCTCCGCCCCCACCTCCGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCAC +CTCAGCCCCTCCTCAGCCCCCACCTCCACCCCCACCTCCGTCCCCACCTCCGCCCCCTCC +TCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCTCCT +CAGCCCCCACCTCTGCCCCCACCTCAGACCCTCCTCAGCCCCTCCTCAGCCCCTCCTCAT +CCCCTCCTCAGCAGCTGCTGGAATGGGCTACCCTCAGGAGTTGGCACCCCACAGGCTCCT +TCCCTTCCCACCTCCGCCACACCCTGACGAGGGAAAAATGGGGAGCTGCTGGGAGGGAAC +TTGCACCCTGTTGGGCGCCTTGT +>syndip_2_chr20:63167287-63167728 +AATGGCCAGCCCGTCCCGCCGAGGCCAGTGGACATGCCAAATCCCTCCCGCAACAAGTTG +CTATCCATCCCCTCGACTAATACTTACCAAATTAATTCCAGATTTGGATTCACTCACGGT +TCCCACCAGCACTCAGCCCCATCTCAGCCCCCATCTCAGCCCCCACCGCAGCCTCACCTC +AGTGCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCTCCTC +AGCCCCTCCTCCGCCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCC +GCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCTCCTCAG +CCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCG +CCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAG +CCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCTCCTCAG +CCCCCACCTCCCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCTCCCCCCCACCTCCGCC +CCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGGCCCCACCTCAGCCCCCACCTCAGCCC +CCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCC +CACCTCAGCCCCCACCTCCGCCCCTCCTCTGCCCCCACCTCAGCCCCCTCCTCAGCCCCC +ACCTCTGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCA +CCTCAGCCCCCACCTCCCCCCCTCCTCAGCCCCCACCTCCACCCCCACCTCAGCCCCCAC +CTCAGCCCCCACCTCCCCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACC +TCCGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCT +CAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCGCCCCCTCCT +CAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCACCCCCACCTCAGCCCCCACCT +CAGCCCCCACCTCCCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCA +GGCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCA +GCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCACCCCCACCTCAG +CCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGC 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+TCCGCCCCCACCTCAGCCCCCTCCTCCGCCCCTCCTCAGCCCCCACCTCCACCCCCACCT +CAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTC +AGCCCCCACCTCAGCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTC +AGCCCCCTCCTCCACCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCC +GCCCCTCCTCAGCCCCCACCTCCACCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGC +CCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCCCCCCTCCTCAGCCCCCACCTCCGCC +CCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCCACCCCCACCTCAGCCC +CCACCTCCGCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCTCCTCAGCCCCC +ACCTCCGCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCCCCCCTC +CTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACC +TCAGCCCCCACCTCCACCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCT +CAGCCCCCACCTCCGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCCGCCCCTCCTCA +GCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCC +GCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAG +ACCCCACCTCCGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGC +CCCTCCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCCGCCCCTCCTCAGCCC +CCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCC +CACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCC +CTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGCCCC +ACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCTCC +TCAGCCCCCACCTCAGCCCCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCC +GCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCCGC +CCCCACCTCCGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCC +CCCTCCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGCCCCACCTCAGCCC +CTCCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCA +CCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGCCCCTC +CTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCGCCCCCAC +CTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCT +CCGCCCCCACCTCCGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTC +AGCCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGCCCCACCTCA +GCCCCTCCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCTCCTCAGCCCCCACCTCAGC +CCCCACCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGCCCCCTCCTCAGC +CCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCCGCC +CCCACCTCAGACCCTCCTCAGCCCCTCCTCATCCCCTCCTCAGCAGCTGCTGGAATGGGC +TACCCTCAGGAGTTGGCACCCCACAGGCTCCTTCCCTTCCCACCTCCGCCACACCCTGAC +GAGGGAAAAATGGGGAGCTGCTGGGAGGGAACTTGCACCCTGTTGGGCGCCTTGT +>p:HG002_1_chr20:63167287-63167728 +AATGGCCAGCCCGTCCCGCCGAGGCCAGTGGACATGCCAAATCCCTCCCGCAACAAGTTG +CTATCCATCCCCTCGACTAATACTTACCAAATTAATTCCAGATTTGGATTCACTCACGGT +TCCCACCAGCACTCAGCCCCATCTCAGCCCCCATCTCAGCCCCCACCGCAGCCTCACCTC +AGTGCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCTCCTC +AGCCCCTCCTCCGCCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCC +GCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCTCCTCAG +CCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCG +CCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAG +CCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCTCCTCAG +CCCCCACCTCCCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCTCCCCCCCACCTCCGCC +CCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGGCCCCACCTCAGCCCCCACCTCAGCCC +CCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCC +CACCTCAGCCCCCACCTCCGCCCCTCCTCTGCCCCCACCTCAGCCCCCTCCTCAGCCCCC +ACCTCTGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCA +CCTCAGCCCCCACCTCCCCCCCTCCTCAGCCCCCACCTCCACCCCCACCTCAGCCCCCAC +CTCAGCCCCCACCTCCCCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACC +TCCGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCT +CAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCGCCCCCTCCT +CAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCACCCCCACCTCAGCCCCCACCT +CAGCCCCCACCTCCCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCA +GGCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCA +GCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCACCCCCACCTCAG +CCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGC +CCCCACCTCCGCCCCTCCTCTGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCTGCC +CCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCAGCCC +CCACCTCCCCCCCTCCTCAGCCCCCACCTCCACCCCCACCTCAGCCCCCACCTCCGCCCC +TCCTCAGCCCCCACCTCAGCCCCCACCTCCACCCCCACCTCAGCCCCCACCTCCGCCCCC +ACCTCCGCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCTCCTCAGCCCCCAC +CTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCT +CAGCCCCCACCTCCACCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCCCCCCACCTC +CGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGGCCCCACCTCAGCCCCCACCTCA +GCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAG +CCCCCACCTCAGCCCCCACCTCCACCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAG +CCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCTGCC +CCCACCTCAGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGCCCCCACCTCAGCCC +CCACCTCCGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCCCCCCTCCTCAGCCCC +CACCTCCACCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCC +ACCTCCACCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCA +CCTCCGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACC +TCCGCCCCCACCTCAGCCCCCTCCTCCGCCCCTCCTCAGCCCCCACCTCCACCCCCACCT +CAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTC +AGCCCCCACCTCAGCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTC +AGCCCCCTCCTCCACCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCC +GCCCCTCCTCAGCCCCCACCTCCACCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGC +CCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCCCCCCTCCTCAGCCCCCACCTCCGCC +CCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCCACCCCCACCTCAGCCC +CCACCTCCGCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCTCCTCAGCCCCC +ACCTCCGCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCCCCCCTC +CTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACC +TCAGCCCCCACCTCCACCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCT +CAGCCCCCACCTCCGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCCGCCCCTCCTCA +GCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCC +GCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAG +ACCCCACCTCCGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGC +CCCTCCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCCGCCCCTCCTCAGCCC +CCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCC +CACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCC +CTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGCCCC +ACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCTCC +TCAGCCCCCACCTCAGCCCCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCC +GCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCCGC +CCCCACCTCCGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCC +CCCTCCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGCCCCACCTCAGCCC +CTCCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCA +CCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGCCCCTC +CTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCGCCCCCAC +CTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCT +CCGCCCCCACCTCCGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTC +AGCCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGCCCCACCTCA +GCCCCTCCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCTCCTCAGCCCCCACCTCAGC +CCCCACCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGCCCCCTCCTCAGC +CCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCCGCC +CCCACCTCAGACCCTCCTCAGCCCCTCCTCATCCCCTCCTCAGCAGCTGCTGGAATGGGC +TACCCTCAGGAGTTGGCACCCCACAGGCTCCTTCCCTTCCCACCTCCGCCACACCCTGAC +GAGGGAAAAATGGGGAGCTGCTGGGAGGGAACTTGCACCCTGTTGGGCGCCTTGT 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+CAGCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGCCCCCACCTC +AGCCCCCACCTCAGCCCCCACCTCCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAG +CCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGC +CCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCTCCTCAGCC +CCCACCTCCGCCCCCACCTCCGCCCCCACCTCTGCCCCTCCTCAGCCCCCACCTCAGCCC +CCTCCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCCGCCCCTCCTCCGCCCC +CACCTCAGCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGCCCCC +ACCTCAGCCCCCACCTCAGCCCCCACCTCCCCCCTCCTCAGCCCCCACCTCAGCCCCCAC +CTCCGCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCAGCCCCCACC +TCCGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCGCCCCCACC +TCAGCCCCCACCTCTGCCCCTCCTCAGCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCT +CTGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCCCCCTCCTCAG +CCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAG +CCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCCGCC +CCCACCTCAGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGCCCCCACCTCAGCCC +CCACCTCCGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCCCCCTCCTCCGCCCCC +ACCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCCCCCTCCTCCGCCCCCAC +CTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCCCCCTCCT +CAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCT +CAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTC +AGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTC +CGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTC +AGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTC +AGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCAG +CCCCCACCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCCTCCTCAGC +CCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGC +CCCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCCTCAGCCCCCACCTCAGCCCCCA +CCTCCGCCCCCACCTCCGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCAC +CTCAGCCCCTCCTCAGCCCCCACCTCCACCCCCACCTCCGTCCCCACCTCCGCCCCCTCC +TCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCTCCT +CAGCCCCCACCTCTGCCCCCACCTCAGACCCTCCTCAGCCCCTCCTCAGCCCCTCCTCAT +CCCCTCCTCAGCAGCTGCTGGAATGGGCTACCCTCAGGAGTTGGCACCCCACAGGCTCCT +TCCCTTCCCACCTCCGCCACACCCTGACGAGGGAAAAATGGGGAGCTGCTGGGAGGGAAC +TTGCACCCTGTTGGGCGCCTTGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/haps.fa.ref.fa new file mode 100644 index 00000000..aababe14 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63167287-63167728 +AATGGCCAGCCCGTCCCGCCGAGGCCAGTGGACATGCCAAATCCCTCCCGCAACAAGTTGCTATCCATCCCCTCGACTAATACTTACCAAATTAATTCCAGATTTGGAGTCACTCATGGTTCCCACCAGCACTCAGCCCCATCTCAGCCCCCATCTCAGCCCCCACCGCAGCCTCACCTCAGTGCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGACCCTCCTCAGCCCCTCCTCATCCCCTCCTCAGCAGCTGCTGGAATGGGCTACCCTCAGGAGTTGGCACCCCACAGGCTCCTTCCCTTCCCACCTCCGCCACACCCTGACGAGGGAAAAATGGGGAGCTGCTGGGAGGGAACTTGCACCCTGTTGGGCGCCTTGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/msa.fa new file mode 100644 index 00000000..5af41b47 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/msa.fa @@ -0,0 +1,385 @@ +>ref_chr20_63167287_63167728 +aatggccagcccgtcccgccgaggccagtggacatgccaaatccctcccgcaacaagttg +ctatccatcccctcgactaatacttaccaaattaattccagatttggagtcactcatggt +tcccaccagcactcagccccatctcagcccccatctcagcccccaccgcagcctcacctc +agtgcccacctcagccccctcctcagccccca---------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----cctcagcccccacctccgcccccacctcagcccctcctcagcccccacctccgcc +cccacctcaga-----------ccctcctcagcccctcctcatcccctcctcagcagctg +ctggaatgggctaccctcaggagttggcaccccacaggctccttcccttcccacctccgc +cacaccctgacgagggaaaaatggggagctgctgggagggaacttgcaccctgttgggcg +ccttgt +>syndip_1_chr20:63167287-63167728 +aatggccagcccgtcccgccgaggccagtggacatgccaaatccctcccgcaacaagttg +ctatccatcccctcgactaatacttaccaaattaattccagatttggagtcactcacggt +tcccaccagcactcagccccatctcagcccccatctcagcccccaccgcagcctcacctc +agtgcccacctcagccccctcctcagcccccacctccgcccccacctcagcccct----- +-------------------cctcagcccccacctcagccccctcctcagcccccacctcc +-----------------------gcccccacctccgcccccacctctgcccct------- +------cctcagcccccacctcagccccctcctcagcccccacctccgcccccacctccg +cccccacctctgcccct-------------------------------------cctcag +cccccacctcagccccctcctcagcccccacctccgcccccacctccgcccccacctctg +cccctcctcagcccccacctcagccccctcctcag-----------cccccacctccgcc +ccctcctcagcccccacctctgcccct------------cctcagcccccacctcagccc +cctcctcagcccccacctccgcccccacctccgcccccacctccgcccctcctccgcccc +cacctcagcccccacctcc-----------------------gccccctcctcagccccc +acctctgcccctcctcagcccccacctcagcccccacctcagcccccacctc-------- +------------------------------------------------------------ +----------------------------ccccctcctcagcccccacctcagcccccacc +tcagccccctcctcagcccccacctcagcccccacctccgcccct------------cct +cagcccccacctccgcccccacctcagcccccacctcagcccccacctccgcccccacct +cagcccccacctccgcccccacctcagcccccacctccgcccccacctcagcccccacct +ctgcccctcctcagcccccacctccgccccctcctcagcccccacctctg---------- +--------------------------cccctcctcagcccccacctcagcccccacctca +gcccccacctcc-cccctcctcagcccccacctcagcccccacctcagccccctcctcag +cccccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacctcagc +ccccacctccgcccctcctcagcccccacctcag-------------------------- +------------------------------------------------------------ +--------ccccctcctcagcccccacctccgcccccacctccgcccccacctctgcccc +tcctcagcccccacctcagccccctcctcagcccccacctccgcccccacctccgccccc +acctccgcccctcctccgcccccacctcagcccccacctccgccccct------------ +----------------------cctcagcccccacctctgcccctcctcagcccccacct +cagcccccacctcagcccccacct-------------------------cccccctcctc +agcccccacctcagcccccacctccgcccctcctcagcccccacctccgccccca----- +------------------------------------------------------cctcag +cccccacctcagcccccacctccgcccccacctcagcccccacctccgcccccacctcag +cccccacctcc-----------gcccccacctcagcccccacctctgcccctcctcagcc +cccacctccgccccctcctcagcccccacctctgcccctcctcagcccccacctcagccc +ccacctcagcccccacct-------------------------cccccctcctcagcccc +ca-----------------------------------cctcagcccccacctcagccccc +tcctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagccccca +-----------------------cctcagcccccacctccgcccctcctccgcccccacc +tcagccccctcctcagcccccacctctgcccctcctcagcccccacctcagcccccacct +ccgcccccacctcagccccctcctcagcccccacctc----------------------- +--------------ccccctcctccgcccccacctcagcccccacctcagcccccacctc +agcccccacctc------------------------------------------------ +-----------------------------------------------------------c +cccctcctccgcccccacctcagccccca-----------cctcagcccccacctccgcc +cccacctcagcccccacctcc--------------------------------------- +------------------------------------------------------------ +-------cccctcctcagcccccacctcagcccccacctccgccccca-----------c +ctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacc +tccgcccccacctcagcccccacctcagcccccacctccgccccca-------------- +-------------------------------------------------------cctca +gcccccacctccgcccccacctcagcccccacctccgcccccacctcagcccccacctcc +gcccccacctccgcccccacctcc-----------gcccccacctcagcccccacctcag +cccccacctccgccccca------------------------------------------ +----cctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagccc +ccacctcagcccctcctcagcccccacctcagcccccacctcagcccccacctcagcccc +t-------------------------cctcagcccccacctcagccccctcctcagcccc +ctcctcagcccccacctcagcccccacctccgcccccacctccgcccccacctcagcccc +acctcagcccctcctcagcccccacctcagccc--------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------cctcagccccca +cctcagcccccacctccgcccccacctccgcccccacctcc------------------- +------------------------------------------------------------ +----gcccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacct +cc---------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----------acccccacctccgtccccacctccgccccctcctcagccccctcctcagc +ccccacctcagcccccacctccgcccccacctcagcccctcctcagcccccacctctgcc +cccacctcagaccctcctcagcccctcctcagcccctcctcatcccctcctcagcagctg +ctggaatgggctaccctcaggagttggcaccccacaggctccttcccttcccacctccgc +cacaccctgacgagggaaaaatggggagctgctgggagggaacttgcaccctgttgggcg +ccttgt +>syndip_2_chr20:63167287-63167728 +aatggccagcccgtcccgccgaggccagtggacatgccaaatccctcccgcaacaagttg +ctatccatcccctcgactaatacttaccaaattaattccagatttggattcactcacggt +tcccaccagcactcagccccatctcagcccccatctcagcccccaccgcagcctcacctc +agtgcccacctcagccccctcctcagcccccacctccgcccccacctccgccccctcctc +agcccctcctccgcccccacctcagcccccacctcagccccctcctcagcccccacctcc +gcccctcctcagcccccacctcagcccccacctcagcccccacctccgccccctcctcag +cccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctccg +cccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctcag +cccccacctcagccccctcctcagcccccacctcagcccccacctccgccccctcctcag +cccccacctcccccccacctccgccccctcctcagcccccacctcccccccacctccgcc +ccctcctcagcccccacctctgcccctcctcaggccccacctcagcccccacctcagccc +cctcctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagcccc +cacctcagcccccacctccgcccctcctctgcccccacctcagccccctcctcagccccc +acctctgcccctcctcagcccccacctcagcccccacctccgcccccacctcagccccca +cctcagcccccacctccccccctcctcagcccccacctccacccccacctcagcccccac +ctcagcccccacctccccccctcctcagcccccacctccgcccccacctcagcccccacc +tccgcccccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacct +cagcccccacctccgcccccacctccgcccccacctcagcccccacctccgccccctcct +cagcccccacctcagcccccacctcagcccccacctccacccccacctcagcccccacct +cagcccccacctcccccccacctccgccccctcctcagcccccacctctgcccctcctca +ggccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctca +gcccccacctccgcccctcctcagcccccacctcagcccccacctccacccccacctcag +cccccacctccgcccccacctcagcccccacctccgcccctcctcagcccccacctcagc +ccccacctccgcccctcctctgcccccacctcagccccctcctcagcccccacctctgcc +cctcctcagcccccacctcagcccccacctccgcccccacctcagcccccacctcagccc +ccacctccccccctcctcagcccccacctccacccccacctcagcccccacctccgcccc +tcctcagcccccacctcagcccccacctccacccccacctcagcccccacctccgccccc +acctccgcccctcctcagcccccacctccgcccccacctcagcccctcctcagcccccac +ctccgcccctcctcagcccccacctcagcccccacctccgcccctcctcagcccccacct +cagcccccacctccacccccacctcagcccccacctcagcccccacctcccccccacctc +cgccccctcctcagcccccacctctgcccctcctcaggccccacctcagcccccacctca +gccccctcctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcag +cccccacctcagcccccacctccacccccacctcagcccccacctccgcccccacctcag +cccccacctccgcccctcctcagcccccacctcagcccccacctccgcccctcctctgcc +cccacctcagccccctcctcagcccccacctctgcccctcctcagcccccacctcagccc +ccacctccgcccccacctcagcccccacctcagcccccacctccccccctcctcagcccc +cacctccacccccacctcagcccccacctccgcccctcctcagcccccacctcagccccc +acctccacccccacctcagcccccacctcagcccccacctccgcccctcctcagccccca +cctccgcccccacctcagcccctcctcagcccccacctccgcccctcctcagcccccacc +tccgcccccacctcagccccctcctccgcccctcctcagcccccacctccacccccacct +cagcccccacctcagccccctcctcagcccccacctccgcccctcctcagcccccacctc +agcccccacctcagcccccacctccgccccctcctcagcccccacctcagcccccacctc +agccccctcctccacccctcctcagcccccacctccgcccccacctcagcccccacctcc +gcccctcctcagcccccacctccacccccacctcagcccccacctccgcccctcctcagc +ccccacctccgcccccacctcagcccccacctccccccctcctcagcccccacctccgcc +cccacctcagcccccacctccgcccctcctcagcccccacctccacccccacctcagccc +ccacctccgcccctcctcagcccccacctccgcccccacctcagcccctcctcagccccc +acctccgcccctcctcagcccccacctccgcccccacctcagcccccacctccccccctc +ctcagcccccacctccgcccccacctcagcccccacctccgcccctcctcagcccccacc +tcagcccccacctccacccccacctcagcccccacctcagcccccacctccgcccctcct +cagcccccacctccgcccccacctcagcccctcctcagcccccacctccgcccctcctca +gcccccacctccgcccccacctcagcccccacctccgcccccacctcagcccccacctcc +gcccccacctcagcccccacctccgcccctcctcagcccccacctcagcccccacctcag +accccacctccgcccccacctccgcccctcctcagcccccacctcagcccccacctcagc +ccctcctcagcccccacctccgcccccacctccgcccccacctccgcccctcctcagccc +ccacctcagcccctcctcagcccccacctcagcccccacctcagccccctcctcagcccc +cacctcagcccccacctccgcccccacctcagccccctcctcagcccccacctcagcccc +ctcctcagcccccacctcagcccccacctccgcccccacctccgcccccacctcagcccc +acctcagcccctcctcagcccccacctcagcccctcctcagcccccacctcagcccctcc +tcagcccccacctcagccccctcagcccccacctcagcccccacctccgcccccacctcc +gcccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacctccgc +ccccacctccgcccccacctcagcccctcctcagcccccacctcagcccccacctcagcc +ccctcctcagcccccacctccgcccccacctccgcccccacctcagccccacctcagccc +ctcctcagcccccacctcagcccctcctcagcccccacctcagcccctcctcagccccca +cctcagcccccacctccgcccccacctccgcccccacctccgcccccacctcagcccctc +ctcagcccccacctcagcccccacctcagccccctcctcagcccccacctccgcccccac +ctcagcccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacct +ccgcccccacctccgcccccacctcagcccctcctcagcccccacctcagcccccacctc +agccccctcctcagcccccacctccgcccccacctccgcccccacctcagccccacctca +gcccctcctcagcccccacctcagcccctcctcagccccctcctcagcccccacctcagc +ccccacctcagcccccacctccgcccccacctccgcccccacctcagccccctcctcagc +cccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacctccgcc +cccacctcaga-----------ccctcctcagcccctcctcatcccctcctcagcagctg +ctggaatgggctaccctcaggagttggcaccccacaggctccttcccttcccacctccgc +cacaccctgacgagggaaaaatggggagctgctgggagggaacttgcaccctgttgggcg +ccttgt +>p:HG002_1_chr20:63167287-63167728 +aatggccagcccgtcccgccgaggccagtggacatgccaaatccctcccgcaacaagttg +ctatccatcccctcgactaatacttaccaaattaattccagatttggattcactcacggt +tcccaccagcactcagccccatctcagcccccatctcagcccccaccgcagcctcacctc +agtgcccacctcagccccctcctcagcccccacctccgcccccacctccgccccctcctc +agcccctcctccgcccccacctcagcccccacctcagccccctcctcagcccccacctcc +gcccctcctcagcccccacctcagcccccacctcagcccccacctccgccccctcctcag +cccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctccg +cccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctcag +cccccacctcagccccctcctcagcccccacctcagcccccacctccgccccctcctcag +cccccacctcccccccacctccgccccctcctcagcccccacctcccccccacctccgcc +ccctcctcagcccccacctctgcccctcctcaggccccacctcagcccccacctcagccc +cctcctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagcccc +cacctcagcccccacctccgcccctcctctgcccccacctcagccccctcctcagccccc +acctctgcccctcctcagcccccacctcagcccccacctccgcccccacctcagccccca +cctcagcccccacctccccccctcctcagcccccacctccacccccacctcagcccccac +ctcagcccccacctccccccctcctcagcccccacctccgcccccacctcagcccccacc +tccgcccccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacct +cagcccccacctccgcccccacctccgcccccacctcagcccccacctccgccccctcct +cagcccccacctcagcccccacctcagcccccacctccacccccacctcagcccccacct +cagcccccacctcccccccacctccgccccctcctcagcccccacctctgcccctcctca +ggccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctca +gcccccacctccgcccctcctcagcccccacctcagcccccacctccacccccacctcag +cccccacctccgcccccacctcagcccccacctccgcccctcctcagcccccacctcagc +ccccacctccgcccctcctctgcccccacctcagccccctcctcagcccccacctctgcc +cctcctcagcccccacctcagcccccacctccgcccccacctcagcccccacctcagccc +ccacctccccccctcctcagcccccacctccacccccacctcagcccccacctccgcccc +tcctcagcccccacctcagcccccacctccacccccacctcagcccccacctccgccccc +acctccgcccctcctcagcccccacctccgcccccacctcagcccctcctcagcccccac +ctccgcccctcctcagcccccacctcagcccccacctccgcccctcctcagcccccacct +cagcccccacctccacccccacctcagcccccacctcagcccccacctcccccccacctc +cgccccctcctcagcccccacctctgcccctcctcaggccccacctcagcccccacctca +gccccctcctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcag +cccccacctcagcccccacctccacccccacctcagcccccacctccgcccccacctcag +cccccacctccgcccctcctcagcccccacctcagcccccacctccgcccctcctctgcc +cccacctcagccccctcctcagcccccacctctgcccctcctcagcccccacctcagccc +ccacctccgcccccacctcagcccccacctcagcccccacctccccccctcctcagcccc +cacctccacccccacctcagcccccacctccgcccctcctcagcccccacctcagccccc +acctccacccccacctcagcccccacctcagcccccacctccgcccctcctcagccccca +cctccgcccccacctcagcccctcctcagcccccacctccgcccctcctcagcccccacc +tccgcccccacctcagccccctcctccgcccctcctcagcccccacctccacccccacct +cagcccccacctcagccccctcctcagcccccacctccgcccctcctcagcccccacctc +agcccccacctcagcccccacctccgccccctcctcagcccccacctcagcccccacctc +agccccctcctccacccctcctcagcccccacctccgcccccacctcagcccccacctcc +gcccctcctcagcccccacctccacccccacctcagcccccacctccgcccctcctcagc +ccccacctccgcccccacctcagcccccacctccccccctcctcagcccccacctccgcc +cccacctcagcccccacctccgcccctcctcagcccccacctccacccccacctcagccc +ccacctccgcccctcctcagcccccacctccgcccccacctcagcccctcctcagccccc +acctccgcccctcctcagcccccacctccgcccccacctcagcccccacctccccccctc +ctcagcccccacctccgcccccacctcagcccccacctccgcccctcctcagcccccacc +tcagcccccacctccacccccacctcagcccccacctcagcccccacctccgcccctcct +cagcccccacctccgcccccacctcagcccctcctcagcccccacctccgcccctcctca +gcccccacctccgcccccacctcagcccccacctccgcccccacctcagcccccacctcc +gcccccacctcagcccccacctccgcccctcctcagcccccacctcagcccccacctcag +accccacctccgcccccacctccgcccctcctcagcccccacctcagcccccacctcagc +ccctcctcagcccccacctccgcccccacctccgcccccacctccgcccctcctcagccc +ccacctcagcccctcctcagcccccacctcagcccccacctcagccccctcctcagcccc +cacctcagcccccacctccgcccccacctcagccccctcctcagcccccacctcagcccc +ctcctcagcccccacctcagcccccacctccgcccccacctccgcccccacctcagcccc +acctcagcccctcctcagcccccacctcagcccctcctcagcccccacctcagcccctcc +tcagcccccacctcagccccctcagcccccacctcagcccccacctccgcccccacctcc +gcccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacctccgc +ccccacctccgcccccacctcagcccctcctcagcccccacctcagcccccacctcagcc +ccctcctcagcccccacctccgcccccacctccgcccccacctcagccccacctcagccc +ctcctcagcccccacctcagcccctcctcagcccccacctcagcccctcctcagccccca +cctcagcccccacctccgcccccacctccgcccccacctccgcccccacctcagcccctc +ctcagcccccacctcagcccccacctcagccccctcctcagcccccacctccgcccccac +ctcagcccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacct +ccgcccccacctccgcccccacctcagcccctcctcagcccccacctcagcccccacctc +agccccctcctcagcccccacctccgcccccacctccgcccccacctcagccccacctca +gcccctcctcagcccccacctcagcccctcctcagccccctcctcagcccccacctcagc +ccccacctcagcccccacctccgcccccacctccgcccccacctcagccccctcctcagc +cccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacctccgcc +cccacctcaga-----------ccctcctcagcccctcctcatcccctcctcagcagctg +ctggaatgggctaccctcaggagttggcaccccacaggctccttcccttcccacctccgc +cacaccctgacgagggaaaaatggggagctgctgggagggaacttgcaccctgttgggcg +ccttgt +>p:HG002_2_chr20:63167287-63167728 +aatggccagcccgtcccgccgaggccagtggacatgccaaatccctcccgcaacaagttg +ctatccatcccctcgactaatacttaccaaattaattccagatttggagtcactcacggt +tcccaccagcactcagccccatctcagcccccatctcagcccccaccgcagcctcacctc +agtgcccacctcagccccctcctcagcccccacctccgcccccacctcagcccct----- +-------------------cctcagcccccacctcagccccctcctcagcccccacctcc +-----------------------gcccccacctccgcccccacctctgcccct------- +------cctcagcccccacctcagccccctcctcagcccccacctccgcccccacctccg +cccccacctctgcccct-------------------------------------cctcag +cccccacctcagccccctcctcagcccccacctccgcccccacctccgcccccacctctg +cccctcctcagcccccacctcagccccctcctcag-----------cccccacctccgcc +ccctcctcagcccccacctctgcccct------------cctcagcccccacctcagccc +cctcctcagcccccacctccgcccccacctccgcccccacctccgcccctcctccgcccc +cacctcagcccccacctcc-----------------------gccccctcctcagccccc +acctctgcccctcctcagcccccacctcagcccccacctcagcccccacctc-------- +------------------------------------------------------------ +----------------------------ccccctcctcagcccccacctcagcccccacc +tcagccccctcctcagcccccacctcagcccccacctccgcccct------------cct +cagcccccacctccgcccccacctcagcccccacctcagcccccacctccgcccccacct +cagcccccacctccgcccccacctcagcccccacctccgcccccacctcagcccccacct +ctgcccctcctcagcccccacctccgccccctcctcagcccccacctctg---------- +--------------------------cccctcctcagcccccacctcagcccccacctca +gcccccacctcc-cccctcctcagcccccacctcagcccccacctcagccccctcctcag +cccccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacctcagc +ccccacctccgcccctcctcagcccccacctcag-------------------------- +------------------------------------------------------------ +--------ccccctcctcagcccccacctccgcccccacctccgcccccacctctgcccc +tcctcagcccccacctcagccccctcctcagcccccacctccgcccccacctccgccccc +acctccgcccctcctccgcccccacctcagcccccacctccgccccct------------ +----------------------cctcagcccccacctctgcccctcctcagcccccacct +cagcccccacctcagcccccacct-------------------------cccccctcctc +agcccccacctcagcccccacctccgcccctcctcagcccccacctccgccccca----- +------------------------------------------------------cctcag +cccccacctcagcccccacctccgcccccacctcagcccccacctccgcccccacctcag +cccccacctcc-----------gcccccacctcagcccccacctctgcccctcctcagcc +cccacctccgccccctcctcagcccccacctctgcccctcctcagcccccacctcagccc +ccacctcagcccccacct-------------------------cccccctcctcagcccc +ca-----------------------------------cctcagcccccacctcagccccc +tcctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagccccca +-----------------------cctcagcccccacctccgcccctcctccgcccccacc +tcagccccctcctcagcccccacctctgcccctcctcagcccccacctcagcccccacct +ccgcccccacctcagccccctcctcagcccccacctc----------------------- +--------------ccccctcctccgcccccacctcagcccccacctcagcccccacctc +agcccccacctc------------------------------------------------ +-----------------------------------------------------------c +cccctcctccgcccccacctcagccccca-----------cctcagcccccacctccgcc +cccacctcagcccccacctcc--------------------------------------- +------------------------------------------------------------ +-------cccctcctcagcccccacctcagcccccacctccgccccca-----------c +ctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacc +tccgcccccacctcagcccccacctcagcccccacctccgccccca-------------- +-------------------------------------------------------cctca +gcccccacctccgcccccacctcagcccccacctccgcccccacctcagcccccacctcc +gcccccacctccgcccccacctcc-----------gcccccacctcagcccccacctcag +cccccacctccgccccca------------------------------------------ +----cctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagccc +ccacctcagcccctcctcagcccccacctcagcccccacctcagcccccacctcagcccc +t-------------------------cctcagcccccacctcagccccctcctcagcccc +ctcctcagcccccacctcagcccccacctccgcccccacctccgcccccacctcagcccc +acctcagcccctcctcagcccccacctcagccc--------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------cctcagccccca +cctcagcccccacctccgcccccacctccgcccccacctcc------------------- +------------------------------------------------------------ +----gcccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacct +cc---------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----------acccccacctccgtccccacctccgccccctcctcagccccctcctcagc +ccccacctcagcccccacctccgcccccacctcagcccctcctcagcccccacctctgcc +cccacctcagaccctcctcagcccctcctcagcccctcctcatcccctcctcagcagctg +ctggaatgggctaccctcaggagttggcaccccacaggctccttcccttcccacctccgc +cacaccctgacgagggaaaaatggggagctgctgggagggaacttgcaccctgttgggcg +ccttgt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/msa.fa.fai new file mode 100644 index 00000000..d1f0d1aa --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63167287_63167728 4506 29 60 61 +syndip_1_chr20:63167287-63167728 4506 4645 60 61 +syndip_2_chr20:63167287-63167728 4506 9261 60 61 +p:HG002_1_chr20:63167287-63167728 4506 13878 60 61 +p:HG002_2_chr20:63167287-63167728 4506 18495 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/output.vcf.gz new file mode 100644 index 00000000..13eb2914 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/output.vcf.gz.tbi new file mode 100644 index 00000000..890e183c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63167387-63167628/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/base.vcf.gz new file mode 100644 index 00000000..d2719d79 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/base.vcf.gz.tbi new file mode 100644 index 00000000..78c50a00 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/comp.vcf.gz new file mode 100644 index 00000000..9e733562 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/comp.vcf.gz.tbi new file mode 100644 index 00000000..6692fdae Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/haps.fa new file mode 100644 index 00000000..835c08c2 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/haps.fa @@ -0,0 +1,58 @@ +>ref_chr20_63221380_63221977 +TCCCACTGCAGAGAACTGTCATCTGCCTGTAAGTACCAGTGCCAGGTGCTCTGGGGCCGATGTCTCCGTTAGCCCCAAGGTGGAGGCTCAGGGAGCAGATGTGAGCGTGCCTTGCTCATCGCAGTAGCTTCGGACTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGACTGCATTGCTCTTGCAGCACCACCCGCCTCCGTGGACACCTTCAGCAGTGAGACAATGCAGGCTCTGCTACAAGAGGTGCTTACTGGGCTCTGCTCTGGTGAGGAGAGGCCTCGCCTGGCAGCCAGACAGAGTCCCAGCAGGGCAAGATGAAAATTCGGGGCCCTCGTTCAAACAGCAAGAGAAGGCTCTTTCCTTCCTTCCAGCGCCCCTCCCTGCACCT +>syndip_1_chr20:63221380-63221977 +TCCCACTGCAGAGAACTGTCATCTGCCTGTAAGTACCAGTGCCAGGTGCTCTGGGGCCGA +TGTCTCCGTTAGCCCCAAGGTGGAGGCTCAGGGAGCAGATGTGAGCGTGCCTTGCTCATC +GCAGTAGCTTCGGACTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGAC +TGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGACTGCATT +GCTCTTGCAGCACCACCCGCCTCCGTGGACACCTTCAGCAGTGAGACAATGCAGGCTCTG +CTACAAGAGGTGCTTACTGGGCTCTGCTCTGGTGAGGAGAGGCCTCGCCTGGCAGCCAGA +CAGAGTCCCAGCAGGGCAAGATGAAAATTCGGGGCCCTCGTTCAAACAGCAAGAGAAGGC +TCTTTCCTTCCTTCCAGCGCCCCTCCCTGCACCT +>syndip_2_chr20:63221380-63221977 +TCCCACTGCAGAGAACTGTCATCTGCCTGTAAGTACCAGTGCCAGGTGCTCTGGGGCCGA +TGTCTCCGTTAGCCCCAAGGTGGAGGCTCAGGGAGCAGATGTGAGCGTGCCTTGCTCATC +GCAGTAGCTTCGGACTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGAG +TGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGG +GACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGATTGC +AGGGATTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGAC +TGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGG +GATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGC +AGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGAC +TGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGG +GACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGC +AGGGATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGAT +TGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGG +GATTGCAGGGACTGCAGGGCCTGCATTGCTCTTGCAGCACCACCCGCCTCCGTGGACACC +TTCAGCAGTGAGACAATGCAGGCTCTGCTACAAGAGGTGCTTACTGGGCTCTGCTCTGGT +GAGGAGAGGCCTCGCCTGGCAGCCAGACAGAGTCCCAGCAGGGCAAGATGAAAATTCGGG +GCCCTCGTTCAAACAGCAAGAGAAGGCTCTTTCCTTCCTTCCAGCGCCCCTCCCTGCACC +T +>p:HG002_1_chr20:63221380-63221977 +TCCCACTGCAGAGAACTGTCATCTGCCTGTAAGTACCAGTGCCAGGTGCTCTGGGGCCGA +TGTCTCCGTTAGCCCCAAGGTGGAGGCTCAGGGAGCAGATGTGAGCGTGCCTTGCTCATC +GCAGTAGCTTCGGACTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGAG +TGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGG +GACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGATTGC +AGGGATTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGAC +TGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGG +GATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGC +AGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGAC +TGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGG +GACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGC +AGGGATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGAT +TGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGG +GATTGCAGGGACTGCAGGGCCTGCATTGCTCTTGCAGCACCACCCGCCTCCGTGGCCACC +TTCAGCAGTGAGACAATGCAGGCTCTGCTACAAGAGGTGCTTACTGGGCTCTGCTCTGGT +GAGGAGAGGCCTCGCCTGGCAGCCAGACAGAGTCCCAGCAGGGCAAGATGAAAATTCGGG +GCCCTCGTTCAAACAGCAAGAGAAGGCTCTTTCCTTCCTTCCAGCGCCCCTCCCTGCACC +T +>p:HG002_2_chr20:63221380-63221977 +TCCCACTGCAGAGAACTGTCATCTGCCTGTAAGTACCAGTGCCAGGTGCTCTGGGGCCGA +TGTCTCCGTTAGCCCCAAGGTGGAGGCTCAGGGAGCAGATGTGAGCGTGCCTTGCTCATC +GCAGTAGCTTCGGACTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGAC +TGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGACTGCATT +GCTCTTGCAGCACCACCCGCCTCCGTGGCCACCTTCAGCAGTGAGACAATGCAGGCTCTG +CTACAAGAGGTGCTTACTGGGCTCTGCTCTGGTGAGGAGAGGCCTCGCCTGGCAGCCAGA +CAGAGTCCCAGCAGGGCAAGATGAAAATTCGGGGCCCTCGTTCAAACAGCAAGAGAAGGC +TCTTTCCTTCCTTCCAGCGCCCCTCCCTGCACCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/haps.fa.ref.fa new file mode 100644 index 00000000..39d1febb --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63221380-63221977 +TCCCACTGCAGAGAACTGTCATCTGCCTGTAAGTACCAGTGCCAGGTGCTCTGGGGCCGATGTCTCCGTTAGCCCCAAGGTGGAGGCTCAGGGAGCAGATGTGAGCGTGCCTTGCTCATCGCAGTAGCTTCGGACTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGACTGCATTGCTCTTGCAGCACCACCCGCCTCCGTGGACACCTTCAGCAGTGAGACAATGCAGGCTCTGCTACAAGAGGTGCTTACTGGGCTCTGCTCTGGTGAGGAGAGGCCTCGCCTGGCAGCCAGACAGAGTCCCAGCAGGGCAAGATGAAAATTCGGGGCCCTCGTTCAAACAGCAAGAGAAGGCTCTTTCCTTCCTTCCAGCGCCCCTCCCTGCACCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/msa.fa new file mode 100644 index 00000000..f36fac39 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/msa.fa @@ -0,0 +1,95 @@ +>ref_chr20_63221380_63221977 +tcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccga +tgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcatc +gcagtagcttc------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------ggactgcagggattgcagggactgcagggattgcagggattgcagg +gattgcagggactgcagggattgcagggactgcagggactgcagggactgcagggactgc +agggactgcagggattgcagggattgcagggattgcagggactgcagggattgcagggac +tgcagggactgcagggattgcagggactgcagggactgcagggactgcagggattgcagg +gattgcagggactgcagggactgcattgctcttgcagcaccacccgcctccgtggacacc +ttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctggt +gaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcggg +gccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcacc +t +>syndip_1_chr20:63221380-63221977 +tcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccga +tgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcatc +gcagtagcttc------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------ggactgcagggactgcagggat +tgcagggactgcagggattgcagggactgcagggattgcagggattgcagggattgcagg +gattgcagggactgcagggactgcattgctcttgcagcaccacccgcctccgtggacacc +ttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctggt +gaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcggg +gccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcacc +t +>syndip_2_chr20:63221380-63221977 +tcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccga +tgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcatc +gcagtagcttcggactgcagggattgcagggactgcagggattgcagggattgcagggag +tgcagggactgcagggactgcagggattgcagggactgcagggactgcagggactgcagg +gactgcagggactgcagggactgcagggattgcagggactgcagggactgcagggattgc +agggattgcagggactgcagggactgcagggattgcagggactgcagggactgcagggac +tgcagggactgcagggactgcagggactgcagggattgcagggattgcagggattgcagg +gattgcagggactgcagggactgcagggactgcagggactgcagggactgcagggactgc +agggattgcagggattgcagggattgcagggattgcagggattgcagggactgcagggac +tgcagggactgcagggactgcagggattgcagggattgcagggattgcagggattgcagg +gactgcagggactgcagggattgcagggattgcagggattgcagggattgcagggattgc +agggattgcagggactgcagggactgcagggactgcagggattgcagggattgcagggat +tgcagggattgcagggactgcagggactgcagggattgcagggattgcagggattgcagg +gattgcagggactgcagggcctgcattgctcttgcagcaccacccgcctccgtggacacc +ttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctggt +gaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcggg +gccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcacc +t +>p:HG002_1_chr20:63221380-63221977 +tcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccga +tgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcatc +gcagtagcttcggactgcagggattgcagggactgcagggattgcagggattgcagggag +tgcagggactgcagggactgcagggattgcagggactgcagggactgcagggactgcagg +gactgcagggactgcagggactgcagggattgcagggactgcagggactgcagggattgc +agggattgcagggactgcagggactgcagggattgcagggactgcagggactgcagggac +tgcagggactgcagggactgcagggactgcagggattgcagggattgcagggattgcagg +gattgcagggactgcagggactgcagggactgcagggactgcagggactgcagggactgc +agggattgcagggattgcagggattgcagggattgcagggattgcagggactgcagggac +tgcagggactgcagggactgcagggattgcagggattgcagggattgcagggattgcagg +gactgcagggactgcagggattgcagggattgcagggattgcagggattgcagggattgc +agggattgcagggactgcagggactgcagggactgcagggattgcagggattgcagggat +tgcagggattgcagggactgcagggactgcagggattgcagggattgcagggattgcagg +gattgcagggactgcagggcctgcattgctcttgcagcaccacccgcctccgtggccacc +ttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctggt +gaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcggg +gccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcacc +t +>p:HG002_2_chr20:63221380-63221977 +tcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccga +tgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcatc +gcagtagcttc------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------ggactgcagggactgcagggat +tgcagggactgcagggattgcagggactgcagggattgcagggattgcagggattgcagg +gattgcagggactgcagggactgcattgctcttgcagcaccacccgcctccgtggccacc +ttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctggt +gaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcggg +gccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcacc +t diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/msa.fa.fai new file mode 100644 index 00000000..8fe1fa2d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63221380_63221977 1021 29 60 61 +syndip_1_chr20:63221380-63221977 1021 1102 60 61 +syndip_2_chr20:63221380-63221977 1021 2175 60 61 +p:HG002_1_chr20:63221380-63221977 1021 3249 60 61 +p:HG002_2_chr20:63221380-63221977 1021 4323 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/output.vcf.gz new file mode 100644 index 00000000..3b7288da Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/output.vcf.gz.tbi new file mode 100644 index 00000000..f26a52e9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63221480-63221877/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/base.vcf.gz new file mode 100644 index 00000000..d6fa2052 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/base.vcf.gz.tbi new file mode 100644 index 00000000..9835212a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/comp.vcf.gz new file mode 100644 index 00000000..89baf744 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/comp.vcf.gz.tbi new file mode 100644 index 00000000..cd054675 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/haps.fa new file mode 100644 index 00000000..4c226b02 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/haps.fa @@ -0,0 +1,52 @@ +>ref_chr20_63371965_63372792 +GGTCAGGTGAAGACTCTATTCCTGGCTCAGGAAAACCACCAGGACAGGTGAGCCCAGCAGCATCTCGTGGAGGGAGGCTCTGAGTCCCGTGAGGACAAGGACGGAACACCGGGGCTGCCACAGGTCGCAGAGACCCTGTGTCAACACCCTTGTTTTGAGGTGCAGAGACCAAAGTTGAGACCTGGCCATGCAGCAGGTCTGCAGGGACCTCAGAGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAATGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGGCCTGTCCCCAGCCCCATTAAATGCCCAGGGCCACTGTCCTGTCCCCAGTCTCATTAAACGCAGCAAACGTCTTCTGGACGTGCCGCCAGTCCCACAGAAAACCAAAGCAAGGCAGACTCACCGCTCCTGCATCCCGGAGCTCAGGTCCAGGAGGGTCTCGGGAAAGGATGGGGGCAACTGGAGTACCATCCT +>syndip_1_chr20:63371965-63372792 +GGTCAGGTGAAGACTCTATTCCTGGCTCAGGAAAACCACCAGGACAGGTGAGCCCAGCAG +CATCTCGTGGAGGGAGGCTCTGAGTCCCGTGAGGACAAGGACGGAACACCGGGGCTGCCA +CAGGTCGCAGAGACCCTGTGTCAACACCCTTGTTTTGAGGTGCAGAGACCAAAGTTGAGA +CCTGGCCATGCAGCAGGTCTGCAGGGACCTCAGAGCCCAGGGCCACTGTCCTGTCCCCAG +CCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCAC +TGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAA +ACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGGCCTGTC +CCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGG +GCCACTGGCCTGTCCCCAGCCCCATTAAATGCCCAGGGCCACTGTCCTGTCCCCAGTCTC +ATTAAACGCAGCAAACGTCTTCTGGACGTGCCGCCAGTCCCACAGAAAACCAAAGCAAGG +CAGACTCACCGCTCCTGCATCCCGGAGCTCAGGTCCAGGAGGGTCTCGGGAAAGGATGGG +GGCAACTGGAGTACCATCCT +>syndip_2_chr20:63371965-63372792 +GGTCAGGTGAAGACTCTATTCCTGGCTCAGGAAAACCACCAGGACAGGTGAGCCCAGCAG +CATCTCGTGGAGGGAGGCTCTGAGTCCCGTGAGGACAAGGACGGAACACCGGGGCTGCCA +CAGGTCGCAGAGACCCTGTGTCAACACCCTTGTTTTGAGGTGCAGAGACCAAAGTTGAGA +CCTGGCCATGCAGCAGGTCTGCAGGGACCTCAGAGCCCAGGGCCACTGTCCTGTCCCCAG +CCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCAC +TGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAA +ACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTC +CCCAGCCCCATTAAACGCCCAGGGCCACTGGCCTGTCCCCAGCCCCATTAAATGCCCAGG +GCCACTGTCCTGTCCCCAGTCTCATTAAACGCAGCAAACGTCTTCTGGACGTGCCGCCAG +TCCCACAGAAAACCAAAGCAAGGCAGACTCACCGCTCCTGCATCCCGGAGCTCAGGTCCA +GGAGGGTCTCGGGAAAGGATGGGGGCAACTGGAGTACCATCCT +>p:HG002_1_chr20:63371965-63372792 +GGTCAGGTGAAGACTCTATTCCTGGCTCAGGAAAACCACCAGGACAGGTGAGCCCAGCAG +CATCTCGTGGAGGGAGGCTCTGAGTCCCGTGAGGACAAGGACGGAACACCGGGGCTGCCA +CAGGTCGCAGAGACCCTGTGTCAACACCCTTGTTTTGAGGTGCAGAGACCAAAGTTGAGA +CCTGGCCATGCAGCAGGTCTGCAGGGACCTCAGAGCCCAGGGCCACTGTCCTGTCCCCAG +CCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCAC +TGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAA +ACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTC +CCCAGCCCCATTAAACGCCCAGGGCCACTGGCCTGTCCCCAGCCCCATTAAATGCCCAGG +GCCACTGTCCTGTCCCCAGTCTCATTAAACGCAGCAAACGTCTTCTGGACGTGCCGCCAG +TCCCACAGAAAACCAAAGCAAGGCAGACTCACCGCTCCTGCATCCCGGAGCTCAGGTCCA +GGAGGGTCTCGGGAAAGGATGGGGGCAACTGGAGTACCATCCT +>p:HG002_2_chr20:63371965-63372792 +GGTCAGGTGAAGACTCTATTCCTGGCTCAGGAAAACCACCAGGACAGGTGAGCCCAGCAG +CATCTCGTGGAGGGAGGCTCTGAGTCCCGTGAGGACAAGGACGGAACACCGGGGCTGCCA +CAGGTCGCAGAGACCCTGTGTCAACACCCTTGTTTTGAGGTGCAGAGACCAAAGTTGAGA +CCTGGCCATGCAGCAGGTCTGCAGGGACCTCAGAGCCCAGGGCCACTGTCCTGTCCCCAG +CCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCAC +TGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAA +ACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGGCCTGTC +CCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGG +GCCACTGGCCTGTCCCCAGCCCCATTAAATGCCCAGGGCCACTGTCCTGTCCCCAGTCTC +ATTAAACGCAGCAAACGTCTTCTGGACGTGCCGCCAGTCCCACAGAAAACCAAAGCAAGG +CAGACTCACCGCTCCTGCATCCCGGAGCTCAGGTCCAGGAGGGTCTCGGGAAAGGATGGG +GGCAACTGGAGTACCATCCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/haps.fa.ref.fa new file mode 100644 index 00000000..8f3869fe --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63371965-63372792 +GGTCAGGTGAAGACTCTATTCCTGGCTCAGGAAAACCACCAGGACAGGTGAGCCCAGCAGCATCTCGTGGAGGGAGGCTCTGAGTCCCGTGAGGACAAGGACGGAACACCGGGGCTGCCACAGGTCGCAGAGACCCTGTGTCAACACCCTTGTTTTGAGGTGCAGAGACCAAAGTTGAGACCTGGCCATGCAGCAGGTCTGCAGGGACCTCAGAGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAATGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGGCCTGTCCCCAGCCCCATTAAATGCCCAGGGCCACTGTCCTGTCCCCAGTCTCATTAAACGCAGCAAACGTCTTCTGGACGTGCCGCCAGTCCCACAGAAAACCAAAGCAAGGCAGACTCACCGCTCCTGCATCCCGGAGCTCAGGTCCAGGAGGGTCTCGGGAAAGGATGGGGGCAACTGGAGTACCATCCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/msa.fa new file mode 100644 index 00000000..2e53b81d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/msa.fa @@ -0,0 +1,75 @@ +>ref_chr20_63371965_63372792 +ggtcaggtgaagactctattcctggctcaggaaaaccaccaggacaggtgagcccagcag +catctcgtggagggaggctctgagtcccgtgaggacaaggacggaacaccggggctgcca +caggtcgcagagaccctgtgtcaacacccttgttttgaggtgcagagaccaaagttgaga +cctggccatgcagcaggtctgcagggacctcagagcccagggccactgtcctgtccccag +ccccattaaacgcccagggccactgtcctgtccccagccccattaaacgcccagggccac +tgtcctgtccccagccccattaaacgcccagggccactgtcctgtccccagccccattaa +acgcccagggccactgtcctgtccccagccccattaaacgcccagggccactgtcctgtc +cccagccccattaaatgcccagggccactgtcctgtccccagccccattaaacgcccagg +gccactgtcctgtccccagccccattaaacgcccagggccactgtcctgtccccagcccc +attaaacgcccagggccactgtcctgtccccagccccattaaacgcccagggccactgtc +ctgtccccagccccattaaacgcccagggccactggcctgtccccagccccattaaatgc +ccagggccactgtcctgtccccagtctcattaaacgcagcaaacgtcttctggacgtgcc +gccagtcccacagaaaaccaaagcaaggcagactcaccgctcctgcatcccggagctcag +gtccaggagggtctcgggaaaggatgggggcaactggagtaccatcct +>syndip_1_chr20:63371965-63372792 +ggtcaggtgaagactctattcctggctcaggaaaaccaccaggacaggtgagcccagcag +catctcgtggagggaggctctgagtcccgtgaggacaaggacggaacaccggggctgcca +caggtcgcagagaccctgtgtcaacacccttgttttgaggtgcagagaccaaagttgaga +cctggccatgcagcaggtctgcagggacctcagagcccagggccactgtcctgtccccag +ccccattaaacgcccagggccactgtcctgtccccagccccattaaac------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------gcccagggccactgtcctgtccccagccccattaaacgcccagg +gccactgtcctgtccccagccccattaaacgcccagggccactgtcctgtccccagcccc +attaaacgcccagggccactggcctgtccccagccccattaaacgcccagggccactgtc +ctgtccccagccccattaaacgcccagggccactggcctgtccccagccccattaaatgc +ccagggccactgtcctgtccccagtctcattaaacgcagcaaacgtcttctggacgtgcc +gccagtcccacagaaaaccaaagcaaggcagactcaccgctcctgcatcccggagctcag +gtccaggagggtctcgggaaaggatgggggcaactggagtaccatcct +>syndip_2_chr20:63371965-63372792 +ggtcaggtgaagactctattcctggctcaggaaaaccaccaggacaggtgagcccagcag +catctcgtggagggaggctctgagtcccgtgaggacaaggacggaacaccggggctgcca +caggtcgcagagaccctgtgtcaacacccttgttttgaggtgcagagaccaaagttgaga +cctggccatgcagcaggtctgcagggacctcagagcccagggccactgtcctgtccccag +ccccattaaacgcccagggccactgtcctgtccccagccccattaaac------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------gcccagggccactgtcctgtccccagccccattaaacgcccagg +gccactgtcctgtccccagccccattaaacgcccagggccactgt--------------- +----------------------cctgtccccagccccattaaacgcccagggccactgtc +ctgtccccagccccattaaacgcccagggccactggcctgtccccagccccattaaatgc +ccagggccactgtcctgtccccagtctcattaaacgcagcaaacgtcttctggacgtgcc +gccagtcccacagaaaaccaaagcaaggcagactcaccgctcctgcatcccggagctcag +gtccaggagggtctcgggaaaggatgggggcaactggagtaccatcct +>p:HG002_1_chr20:63371965-63372792 +ggtcaggtgaagactctattcctggctcaggaaaaccaccaggacaggtgagcccagcag +catctcgtggagggaggctctgagtcccgtgaggacaaggacggaacaccggggctgcca +caggtcgcagagaccctgtgtcaacacccttgttttgaggtgcagagaccaaagttgaga +cctggccatgcagcaggtctgcagggacctcagagcccagggccactgtcctgtccccag +ccccattaaacgcccagggccactgtcctgtccccagccccattaaac------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------gcccagggccactgtcctgtccccagccccattaaacgcccagg +gccactgtcctgtccccagccccattaaacgcccagggccactgt--------------- +----------------------cctgtccccagccccattaaacgcccagggccactgtc +ctgtccccagccccattaaacgcccagggccactggcctgtccccagccccattaaatgc +ccagggccactgtcctgtccccagtctcattaaacgcagcaaacgtcttctggacgtgcc +gccagtcccacagaaaaccaaagcaaggcagactcaccgctcctgcatcccggagctcag +gtccaggagggtctcgggaaaggatgggggcaactggagtaccatcct +>p:HG002_2_chr20:63371965-63372792 +ggtcaggtgaagactctattcctggctcaggaaaaccaccaggacaggtgagcccagcag +catctcgtggagggaggctctgagtcccgtgaggacaaggacggaacaccggggctgcca +caggtcgcagagaccctgtgtcaacacccttgttttgaggtgcagagaccaaagttgaga +cctggccatgcagcaggtctgcagggacctcagagcccagggccactgtcctgtccccag +ccccattaaacgcccagggccactgtcctgtccccagccccattaaac------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------gcccagggccactgtcctgtccccagccccattaaacgcccagg +gccactgtcctgtccccagccccattaaacgcccagggccactgtcctgtccccagcccc +attaaacgcccagggccactggcctgtccccagccccattaaacgcccagggccactgtc +ctgtccccagccccattaaacgcccagggccactggcctgtccccagccccattaaatgc +ccagggccactgtcctgtccccagtctcattaaacgcagcaaacgtcttctggacgtgcc +gccagtcccacagaaaaccaaagcaaggcagactcaccgctcctgcatcccggagctcag +gtccaggagggtctcgggaaaggatgggggcaactggagtaccatcct diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/msa.fa.fai new file mode 100644 index 00000000..77c587a5 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63371965_63372792 828 29 60 61 +syndip_1_chr20:63371965-63372792 828 905 60 61 +syndip_2_chr20:63371965-63372792 828 1781 60 61 +p:HG002_1_chr20:63371965-63372792 828 2658 60 61 +p:HG002_2_chr20:63371965-63372792 828 3535 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/output.vcf.gz new file mode 100644 index 00000000..a9e2f8c5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/output.vcf.gz.tbi new file mode 100644 index 00000000..d71f90ec Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63372065-63372692/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/base.vcf.gz new file mode 100644 index 00000000..174a9837 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/base.vcf.gz.tbi new file mode 100644 index 00000000..0a187dd0 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/comp.vcf.gz new file mode 100644 index 00000000..729634d5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/comp.vcf.gz.tbi new file mode 100644 index 00000000..8da83acc Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/haps.fa new file mode 100644 index 00000000..f5fce746 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/haps.fa @@ -0,0 +1,204 @@ +>ref_chr20_63491489_63493165 +GTGAGCATGATGCCCCCACAGTGCACACAGAGATGCCTGCAACATCTTTGGCTGCAGCCCACTGGCTGGGGGTCTCCTATCAGTGCCCTTCTCTAGGGTCTCAGATTTGTTTATGGTTTCTCTTCTTGGTGGGATGGATGGATGGATGGACGGATGGATGGGGAGGTGGGTGGATGGATGGATGGATGTATGAATGGGGTGGTAGATGGATGGGGAGGTGGATGGACAGAAGGATGGGTGGGGAGATGGATGAGTAGGGAGATGGATGGATGGATTGGTGGATGGATGGATGGATGGATGGATGAGGAGGTAGATGAGTGGATGGACAGAAGGATGGATGGGTAGGAAGGTGGGTGGATGAATGGATGGATGGGGAGGTGGATGGATAGATGGATGGATGGATGGATGGATGGATGGATGGATGGGGGGATAGATGGATGGATGGATGGATGGACGGACGGATGGGGAGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGAGGAGATGAACGGATGGATGAGATGGATGGATGGATGATGGAGGGAAGGATGGCTGGGTGGGGAGATGGATGGATAGAGAGGTGGATGGGTGGATGGGGAGATGGATGGATGGATGGATGGATGGGGAAGTGGATGGATGGGGAGGTGGATGGATGGATGTATGGGTGGGTAGGTGGGTGGATAGATGGATGGATGGATGGATGGATAAATGGATGGATGGAAGGATGGATGGATAGGTAGGTGGGTGGATGGATGGATGGATGGATGTACAGAAGGATGGATGGGTGGGTAGGTGGGTGAGTGGATGAATGGATGGATGGATAGATAGAAGGATGGATGGGTGGGTCAATAGATGGATGGATAGAGAGAAGGATGGATGGGTGGGTAGATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGTTGAGACAATGGATGGATGGATGGATGGATGGAGAGATGGATGGATGGATGGATGGACAGAAGGATGGATGGGTGGGGAGGTGGATGGATGGATGGAAGGATGGATGGATGGATAGAGAGAAGGATGGATGGGTGGGACAATGGATGGATGGATGCATGGATGGATGGATGGAGGGATAGAGAGAAGGATGGATGGGTGGGACAATCAATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGGTGGGGAGATGGATGGATGGATGGAGAGGTGGATGGATGGATGGATGGATGGATTGATGGACAGAAGGATGGATGGGTGGGGAGGTGGATAGATGGAGAGATGGAGGGATGGTTCGATAGAGAGAAGGATGGATGGGACAATGGATGGATGGATGGATGGAGTGAAGGATGGATGGGTGGGGAGATGGATGGATCGATGGATGGATGGATGGATAGATAGATGGATGGAGAGGTGGATAGATGGATGGGTGGATGGATGGACAGAGGATGGATGGGTGGGGAGGTGGGTGGATGGATGGATGGATGTGGGATGGACTGTCCCACAGAAAGTGTGTGGTAAGGGGAGAGATTGGAGACAGCCCAGTCTTGAGATGCCTTGTAGGGGCCCCTGGTCTAGGGCAGGCAGAGCTGGCCAGGCAGGAGCTCCAGCACAGCGCCCTTGCTCACCGCCAATCTTGTACACGTCCTGCAGCGGC +>syndip_1_chr20:63491489-63493165 +GTGAGCATGATGCCCCCACAGTGCACACAGAGATGCCTGCAACATCTTTGGCTGCAGCCC +ACTGGCTGGGGGTCTCCTATCAGTGCCCTTCTCTAGGGTCTCAGATTTGTTTATGGTTTC +TCTTCTTGGTGGGATGGATGGATGGATGGACGGATGGATGGGGAGGTGGGTGGATGGATG +GATGGATGTATGAATGGGGTGGTAGATGGATGGGGAGGTGGATGGACAGAAGGATGGGTG +GGGAGATGGATGAGTAGGGAGATGGATGGATGGATTGGTGGATGGATGGATGGATGGATG +GATGAGGAGGTAGATGAGTGGATGGACAGAAGGATGGATGGGTAGGAAGGTGGGTGGATG +AATGGATGGATGGGGAGGTGGATGGATAGATGGATGGATGGATGGATGGATGGATGGATG +GATGGATGGGGGGATAGATGGATGGATGGATGGATGGATGGACGGACGGATGGGGAGGTG +GATGGATGGATGGATGGATGGATGGATGGATGGATGAGGAGATGAATGGATGGATGAGAT +GGATGGATGGATGATGGAGGGAAGGATGGCTGGGTGGGGAGATGGATGGATAGAGAGGTG +GATGGGTGGATGGGGAGATGGATGGATGGATGGATGGATGGGGAAGTGGATGGATGGGGA +GGTGGATGGATGGATAGGTGGATGGGTGGATGGACAGAAGGATGAATGGGTAGGGAGATG +GATGGATGGATGGATGGGGAGGGATGGATGGATGGATGGATGGATGGGTGGATGGATAGA +AGGATGGATGGGTGGGGAGGTGGGTGGGTGGGTGGATGGATGGAGAGATGGATAGATGGA +TAGATGGATGGATGGATGGATGGATGGAGAGAAGGATGGATGGGTGGGGAGGTGGGTGGG 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+CAGGAGCTCCAGCACAGCGCCCTTGCTCACCGCCAATCTTGTACACGTCCTGCAGCGGC +>syndip_2_chr20:63491489-63493165 +GTGAGCATGATGCCCCCACAGTGCACACAGAGATGCCTGCAACATCTTTGGCTGCAGCCC +ACTGGCTGGGGGTCTCCTATCAGTGCCCTTCTCTAGGGTCTCAGATTTGTTTATGGTTTC +TCTTCTTGGTGGGATGGATGGATGGATGGACGGATGGATGGGGAGGTGGGTGGATGGATG +GATGGATGTATGAATGGGGTGGTAGATGGATGGGGAGGTGGATGGACAGAAGGATGGGTG +GGGAGATGGATGAGTAGGGAGATGGATGGATGGATTGGTGGATGGATGGATGGATGGATG +GATGAGGAGGTAGATGAGTGGATGGACAGAAGGATGGATGGGTAGGAAGGTGGGTGGATG +AATGGATGGATGGGGAGGTGGATGGATAGATGGATGGATGGATGGATGGATGGATGGATG +GATGGATGGGGGGATAGATGGATGGATGGATGGATGGACGGACGGATGGGGAGGTGGATG +GATGGATGGATGGATGGATGGATGGATGGATGGATGGATGAGGAGATGAATGGATGGATG +AGATGGATGGATGGATGATGGAGGGAAGGATGGCTGGGTGGGGAGATGGATGGATAGAGA +GGTGGATGGGTGGATGGGGAGATGGATGGATGGATGGATGGATGGGGAAGTGGATGGATG +GGGAGGTGGATGGATGGATAGGTGGATGGGTGGATGGACAGAAGGATGAATGGGTAGGGA +GATGGATGGATGGATGGATGCGGAGGGATGGATGGATGGATGGATGGATGGGTGGATGGA +TAGAAGGATGGATGGGTGGGGAGGTGGGTGGGTGGGTGCGTGGATGGATGGAGAGATGGA +TAGATGGATAGATGGATGGATGGATGGATGGATGGATGGAGAGAAGGATGGATGGGTGGG +GAGGTGGGTGGGTGGGTGGATGGGTGGATGGATGGATGGGTGGGGAGGTGGGCGGGTGGA +TGGATGGATGGATGCAGAGGTGGGTGGATGGATGGATGGAGAGAAGGATGGATGGGTGGG +GAGGTGGGTGGGTGGATGGATGGATGAGTGGGGAGGTGGGTGGGTGGATGGATGGATGGA +TGGATGCATGGATGGATGGATGGAGAGGTGGGTGGATGGGTGGATGGACAGAAGGATGGA +TGGGTGGGGAGGTGGGTGAGTGGGTGGATGGATGAATGGGGAGGTGGATGGATGGATGGA +TGGATGAAGGATGGATGGGTGGGGAGGTGGGTGGACGGATGGATGGATTGGGAGGTGGGT +AGATGGGTGGATGGACAGAAGGATGGATGGGTGGGGAGGTGGGTGGGTGGGTGGATGGAT +GGATGGGGAGGTGGATGGATGGATGGTTAGATGGGGAGGTGGGTGGATGGGTGGATGGAC +AGAAGGATGGATGGGTAGGGAGGTAGGTGAGTGGATGGATGGATGGGGAGATGGATGGAT +GGATAGAGAGAAGGATGGATGGGTGGGACAATGGATGGATGGATGGATAGAAGGATGGAC +GGGTGGGGAGATGGATGGATGGATGGATGGATGGATGGATGGACAGAAGGATGTATGGGT +GGGGAGGTGGGTGGATAGATGGATGGATGGATGGATGGGGAAATGGATGGATGGAAGGAT +GGATGGATAGGGAGGTGGGTGGATGGATGGATGGATGGATGTACAGAAGGATGGATGGGT +GGGGAGGTGGGTGAGTGGATGAATGGATGGATGGATAGATAGAAGGATGGATGGGTGGGA +CAATAGATGGATGGATAGAGAGAAGGATGGATGGGTGGGGAGATGGATGGATGGATGGAT 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+GGATAGATGGATGGGTGGATGGATGGACAGAGGATGGATGGGTGGGGAGGTGGGTGGATG +GATGGATGGATGTGGGATGGACTGTCCCACAGAAAGTGTGTGGTAAGGGGAGAGATTGGA +GACAGCCCAGTCTTGAGATGCCTTGTAGGGGCCCCTGGTCTAGGGCAGGCAGAGCTGGCC +AGGCAGGAGCTCCAGCACAGCGCCCTTGCTCACCGCCAATCTTGTACACGTCCTGCAGCG +GC +>p:HG002_1_chr20:63491489-63493165 +GTGAGCATGATGCCCCCACAGTGCACACAGAGATGCCTGCAACATCTTTGGCTGCAGCCC +ACTGGCTGGGGGTCTCCTATCAGTGCCCTTCTCTAGGGTCTCAGATTTGTTTATGGTTTC +TCTTCTTGGTGGGATGGATGGATGGATGGACGGATGGATGGGGAGGTGGGTGGATGGATG +GATGGATGTATGAATGGGGTGGTAGATGGATGGGGAGGTGGATGGACAGAAGGATGGGTG +GGGAGATGGATGAGTAGGGAGATGGATGGATGGATTGGTGGATGGATGGATGGATGGATG +GATGAGGAGGTAGATGAGTGGATGGACAGAAGGATGGATGGGTAGGAAGGTGGGTGGATG +AATGGATGGATGGGGAGGTGGATGGATAGATGGATGGATGGATGGATGGATGGATGGATG +GATGGATGGGGGGATAGATGGATGGATGGATGGATGGACGGACGGATGGGGAGGTGGATG +GATGGATGGATGGATGGATGGATGGATGGATGGATGGATGAGGAGATGAATGGATGGATG +AGATGGATGGATGGATGATGGAGGGAAGGATGGCTGGGTGGGGAGATGGATGGATAGAGA +GGTGGATGGGTGGATGGGGAGATGGATGGATGGATGGATGGATGGGGAAGTGGATGGATG +GGGAGGTGGATGGATGGATAGGTGGATGGGTGGATGGACAGAAGGATGAATGGGTAGGGA +GATGGATGGATGGATGGATGCGGAGGGATGGATGGATGGATGGATGGATGGGTGGATGGA +TAGAAGGATGGATGGGTGGGGAGGTGGGTGGGTGGGTGCGTGGATGGATGGAGAGATGGA +TAGATGGATAGATGGATGGATGGATGGATGGATGGATGGAGAGAAGGATGGATGGGTGGG +GAGGTGGGTGGGTGGGTGGATGGGTGGATGGATGGATGGGTGGGGAGGTGGGCGGGTGGA +TGGATGGATGGATGCAGAGGTGGGTGGATGGATGGATGGAGAGAAGGATGGATGGGTGGG +GAGGTGGGTGGGTGGATGGATGGATGAGTGGGGAGGTGGGTGGGTGGATGGATGGATGGA +TGGATGCATGGATGGATGGATGGAGAGGTGGGTGGATGGGTGGATGGACAGAAGGATGGA +TGGGTGGGGAGGTGGGTGAGTGGGTGGATGGATGAATGGGGAGGTGGATGGATGGATGGA +TGGATGAAGGATGGATGGGTGGGGAGGTGGGTGGACGGATGGATGGATTGGGAGGTGGGT +AGATGGGTGGATGGACAGAAGGATGGATGGGTGGGGAGGTGGGTGGGTGGGTGGATGGAT +GGATGGGGAGGTGGATGGATGGATGGTTAGATGGGGAGGTGGGTGGATGGGTGGATGGAC +AGAAGGATGGATGGGTAGGGAGGTAGGTGAGTGGATGGATGGATGGGGAGATGGATGGAT +GGATAGAGAGAAGGATGGATGGGTGGGACAATGGATGGATGGATGGATAGAAGGATGGAC +GGGTGGGGAGATGGATGGATGGATGGATGGATGGATGGATGGACAGAAGGATGTATGGGT +GGGGAGGTGGGTGGATAGATGGATGGATGGATGGATGGGGAAATGGATGGATGGAAGGAT 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+GAGGTGGGTGGATAGATGGATGGATGGATGGATGGGGAAATGGATGGATGGAAGGATGGA +TGGATAGGGAGGTGGGTGGATGGATGGATGGATGGATGTACAGAAGGATGGATGGGTGGG +GAGGTGGGTGAGTGGATGAATGGATGGATGGATAGATAGAAGGATGGATGGGTGGGACAA +TAGATGGATGGATAGAGAGAAGGATGGATGGGTGGGGAGATGGATGGATGGATGGATGGA +TGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGTTGAGACAATGGATGGATGGA +TGGATGGAGAGATGGATGGATGGACGGATGGACAGAAGGATGGATGGGTGGGGAGGTGGA +TGGATGGATTGAAGGATGGATGGGTGGGGACATGGATGGATGGATGGATGGATGGATGGA +TGGATGGACAGAAGGATGTATGGGTGGGGAGGTGGGTGGATAGATGGATGGATGGGGAAA +TGGATGGATGGAAGGATGGATGGATAGGGAGGTGGGTGGATGGATGGATGGATGGATGTA +CAGAAGGATGGATGGGTGGGGAGGTGGGTGAGTGGATGAATGGATGGATGGATAGATAGA +AGGATGGATGGGTGGGACAATAGATGGATGGATAGAGAGAAGGATGGATGGGTGGGGAGA +TGGATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGTTGAGACAATGGA +TGGATGGATGGATGGATGGAGAGATGGATGGATGGATGGATGGACAGAAGGATGGATGGG +TGGGGAGGTGGATGGATGGATGGAAGGATGGATGGATGGATAGAGAGAAGGATGGATGGG +TGGGACAATGGATGGATGGATGCATGGATGGATGGATGGAGGGATAGAGAGAAGGATGGA +TGGGTGGGACAATCAATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGG +TGGGGAGATGGATGGATGGATGGAGAGGTGGATGGATGGATGGATGGATGGATTGATGGA +CAGAAGGATGGATGGGTGGGGAGGTGGATAGATGGAGAGATGGAGGGATGGTTCGATAGA +GAGAAGGATGGATGGATGGGACAATGGATGGATGGATGGATGGAGTGAAGGATGGATGGG +TGGGGAGATGGATGGATCGATGGATGGATGGATGGATAGATAGATGGATGGAGAGGTGGA +TAGATGGATGGGTGGATGGATGGACAGAGGATGGATGGGTGGGGAGGTGGGTGGATGGAT +GGATGGATGTGGGATGGACTGTCCCACAGAAAGTGTGTGGTAAGGGGAGAGATTGGAGAC +AGCCCAGTCTTGAGATGCCTTGTAGGGGCCCCTGGTCTAGGGCAGGCAGAGCTGGCCAGG +CAGGAGCTCCAGCACAGCGCCCTTGCTCACCGCCAATCTTGTACACGTCCTGCAGCGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/haps.fa.ref.fa new file mode 100644 index 00000000..ebd054e8 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63491489-63493165 +GTGAGCATGATGCCCCCACAGTGCACACAGAGATGCCTGCAACATCTTTGGCTGCAGCCCACTGGCTGGGGGTCTCCTATCAGTGCCCTTCTCTAGGGTCTCAGATTTGTTTATGGTTTCTCTTCTTGGTGGGATGGATGGATGGATGGACGGATGGATGGGGAGGTGGGTGGATGGATGGATGGATGTATGAATGGGGTGGTAGATGGATGGGGAGGTGGATGGACAGAAGGATGGGTGGGGAGATGGATGAGTAGGGAGATGGATGGATGGATTGGTGGATGGATGGATGGATGGATGGATGAGGAGGTAGATGAGTGGATGGACAGAAGGATGGATGGGTAGGAAGGTGGGTGGATGAATGGATGGATGGGGAGGTGGATGGATAGATGGATGGATGGATGGATGGATGGATGGATGGATGGGGGGATAGATGGATGGATGGATGGATGGACGGACGGATGGGGAGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGAGGAGATGAACGGATGGATGAGATGGATGGATGGATGATGGAGGGAAGGATGGCTGGGTGGGGAGATGGATGGATAGAGAGGTGGATGGGTGGATGGGGAGATGGATGGATGGATGGATGGATGGGGAAGTGGATGGATGGGGAGGTGGATGGATGGATGTATGGGTGGGTAGGTGGGTGGATAGATGGATGGATGGATGGATGGATAAATGGATGGATGGAAGGATGGATGGATAGGTAGGTGGGTGGATGGATGGATGGATGGATGTACAGAAGGATGGATGGGTGGGTAGGTGGGTGAGTGGATGAATGGATGGATGGATAGATAGAAGGATGGATGGGTGGGTCAATAGATGGATGGATAGAGAGAAGGATGGATGGGTGGGTAGATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGTTGAGACAATGGATGGATGGATGGATGGATGGAGAGATGGATGGATGGATGGATGGACAGAAGGATGGATGGGTGGGGAGGTGGATGGATGGATGGAAGGATGGATGGATGGATAGAGAGAAGGATGGATGGGTGGGACAATGGATGGATGGATGCATGGATGGATGGATGGAGGGATAGAGAGAAGGATGGATGGGTGGGACAATCAATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGGTGGGGAGATGGATGGATGGATGGAGAGGTGGATGGATGGATGGATGGATGGATTGATGGACAGAAGGATGGATGGGTGGGGAGGTGGATAGATGGAGAGATGGAGGGATGGTTCGATAGAGAGAAGGATGGATGGGACAATGGATGGATGGATGGATGGAGTGAAGGATGGATGGGTGGGGAGATGGATGGATCGATGGATGGATGGATGGATAGATAGATGGATGGAGAGGTGGATAGATGGATGGGTGGATGGATGGACAGAGGATGGATGGGTGGGGAGGTGGGTGGATGGATGGATGGATGTGGGATGGACTGTCCCACAGAAAGTGTGTGGTAAGGGGAGAGATTGGAGACAGCCCAGTCTTGAGATGCCTTGTAGGGGCCCCTGGTCTAGGGCAGGCAGAGCTGGCCAGGCAGGAGCTCCAGCACAGCGCCCTTGCTCACCGCCAATCTTGTACACGTCCTGCAGCGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/msa.fa new file mode 100644 index 00000000..f21afbd6 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/msa.fa @@ -0,0 +1,260 @@ +>ref_chr20_63491489_63493165 +gtgagcatgatgcccccacagtgcacacagagatgcctgcaacatctttggctgcagccc +actggctgggggtctcctatcagtgcccttctctagggtctcagatttgtttatggtttc +tcttcttggtgggatggatggatggatggacggatggatggggaggtgggtggatggatg +gatggatgtatgaatggggtggtagatggatggggaggtggatggacagaaggatgggtg +gggagatggatgagtagggagatggatggatggattggtggatggatggatggatggatg +gatgaggaggtagatgagtggatggacagaaggatggatgggtaggaaggtgggtggatg +aatggatggatggggaggtggatggata----gatggatggatggatggatggatggatg +gatggatggggggatagatggatggatggatggatggacggacggatggggaggtggatg +gatggatggatggatggatggatggatggatggatggatgaggagatgaacggatggatg +agatggatggatggatgatggagggaaggatggctgggtggggagatggatggatagaga +ggtggatgggtggatggggagatggatggatggatggatggatggggaagtggatggatg +gggaggtggatggat--------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------------------ggatgtat +gggtgggtaggtgggtggatagatggatg------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----gatggatggatggataaatggatggatggaaggatggatggataggtaggtgggt +ggatggatggatggatggatgtacagaaggatggatgggtgggtaggtgggtgagtggat +gaatggatggatggatagatagaaggatggatgggtgggtcaatagatggatggatagag +agaaggatggatgggtgggta----gatggatggatggatggatggatggatagagagaa +ggatggatggttgagacaatggatggatggatggatggatggagagatggatggatggat +ggatggacagaaggatggatgggtggggaggtggatggatggatggaaggatggatggat +ggatagagagaaggatggatgggtgggacaatggatggatggatgcatggatggatggat 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+aatggatggatggggaggtggatggatagatggatggatggatggatggatggatggatg +gatggatggggggatagatggatggatggatggatggatggacggacg----gatgggga +ggtggatggatggatggatggatggatggatggatggatgaggagatgaatggatggatg +agatggatggatggatgatggagggaaggatggctgggtggggagatggatggatagaga +ggtggatgggtggatggggagatggatggatggatggatggatggggaagtggatggatg +gggaggtggatggatggataggtggatgggtggatggacagaaggatgaatgggtaggga +gatggatggatggatggatggggagggatggatggatggatggatggatgggtggatgga +tagaaggatggatgggtggggaggtgggtgggtgg----gtggatggatggagagatgga +tagatggata----gatggatggatggatggatggatggagagaaggatggatgggtggg +gaggtgggtgggtgggtggatgggtggatggatggatgggtggggaggtgggcgggtgga +tggatggatggatgcagaggtgggtggatggatggatggagagaaggatggatgggtggg +gaggtgggtgggtggatggatggatgagtggggaggtgggtgggtgggtggatggatgga +tggatggatgcatggatggatgga------------------------------------ +------------------------------------------------------------ +-------------------tggagaggtgggtggacggatggatggattgggaggtgggt +agatgggtggatggacagaaggatggatgggtggggaggtgggtgggtgggtggatggat +ggatggggaggtggatggatggatggttagatggggaggtgggtggatgggtggatggac +agaaggatggatgggtagggaggtaggtgagtggatggatggatggggagatggatggat +ggatagagagaaggatggatgggtgggacaatggatggatggatggatagaaggatggac +gggtggggagatggatggatggatggatggatggatggatggatggacagaaggatgtat +gggtggggaggtgggtggatagatggatggatggatggatggggaaatggatggatggaa +ggatggatggatagggaggtgggtggatggatggatggatggatgtacagaaggatggat +gggtggggaggtgggtgagtggatgaatggatggatggatagatagaaggatggatgggt +gggacaatagatggatggatagagagaaggatggatgggtggggagatggatggatggat +ggatggatggatggatggatggatggatagagagaaggatggatggttgagaca----at +ggatggatggatggatggagagatggatggatggacggatggacagaaggatggatgggt +ggggaggtggatggatggattgaaggatggatgggtgggga----catggatggatggat +ggatggatggatggatggatggacagaaggatgtatgggtggggaggtgggtggata--- +-----gatggatggatggggaaatggatggatggaaggatggatggatagggaggtgggt +ggatggatggatggatggatgtacagaaggatggatgggtggggaggtgggtgagtggat +gaatggatggatggatagatagaaggatggatgggtgggacaatagatggatggatagag +agaaggatggatgggtggggagatggatggatggatggatggatggatggatagagagaa 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+ggggaggtggatggatggattgaaggatggacgggtggggagatggatggatggatggat +ggatggatggatggatggatggacagaaggatgtatgggtggggaggtgggtggatagat +ggatggatggatggatggggaaatggatggatggaaggatggatggatagggaggtgggt +ggatggatggatggatggatgtacagaaggatggatgggtggggaggtgggtgagtggat +gaatggatggatggatagatagaaggatggatgggtgggacaaca----gatggatagag +agaaggatggatgggtgggga----gatggatggatggatggatggatggatagagagaa +ggatggatggttgagacaatggatggatggatggatggatggagagatggatggatggat +ggatggacagaaggatggatgggtggggaggtggatggatggatggaaggatggatggat +ggatagagagaaggatggatgggtgggacaatggatggatggatgcatggatggatggat +ggagggatagagagaaggatggatgggtgggacaatcaatggatggatggatggatggat +ggatagagagaaggatggatgggtggggagatggatggatggatggagaggtggatggat +ggatggatggatggattgatggacagaaggatggatgggtggggaggtggatagatggag +agatggagggatggttcgatagagagaaggatggatggatgggacaatggatggatggat +ggatggagtgaaggatggatgggtggggagatggatggatcgatggatggatggatggat +agatagatggatggagaggtggatagatggatgggtggatggatggacagaggatggatg +ggtggggaggtgggtggatggatggatggatgtgggatggactgtcccacagaaagtgtg +tggtaaggggagagattggagacagcccagtcttgagatgccttgtaggggcccctggtc +tagggcaggcagagctggccaggcaggagctccagcacagcgcccttgctcaccgccaat +cttgtacacgtcctgcagcggc +>p:HG002_2_chr20:63491489-63493165 +gtgagcatgatgcccccacagtgcacacagagatgcctgcaacatctttggctgcagccc +actggctgggggtctcctatcagtgcccttctctagggtctcagatttgtttatggtttc +tcttcttggtgggatggatggatggatggacggatggatggggaggtgggtggatggatg +gatggatgtatgaatggggtggtagatggatggggaggtggatggacagaaggatgggtg +gggagatggatgagtagggagatggatggatggattggtggatggatggatggatggatg +gatgaggaggtagatgagtggatggacagaaggatggatgggtaggaaggtgggtggatg +aatggatggatggggaggtggatggatagatggatggatggatggatggatggatggatg +gatggatggggggatagatggatggatggatggatggatggacggacg----gatgggga +ggtggatggatggatggatggatggatggatggatggatgaggagatgaatggatggatg +agatggatggatggatgatggagggaaggatggctgggtggggagatggatggatagaga +ggtggatgggtggatggggagatggatggatggatggatggatggggaagtggatggatg +gggaggtggatggatggataggtggatgggtggatggacagaaggatgaatgggtaggga +gatggatggatggatggatggggagggatggatggatggatggatggatgggtggatgga +tagaaggatggatgggtggggaggtgggtgggtgg----gtggatggatggagagatgga +tagatggata----gatggatggatggatggatggatggagagaaggatggatgggtggg +gaggtgggtgggtgggtggatgggtggatggatggatgggtggggaggtgggcgggtgga +tggatggatggatgcagaggtgggtggatggatggatggagagaaggatggatgggtggg +gaggtgggtgggtggatggatggatgagtggggaggtgggtgggtgggtggatggatgga +tggatggatgcatggatggatgga------------------------------------ +------------------------------------------------------------ +-------------------tggagaggtgggtggacggatggatggattgggaggtgggt +agatgggtggatggacagaaggatggatgggtggggaggtgggtgggtgggtggatggat +ggatggggaggtggatggatggatggttagatggggaggtgggtggatgggtggatggac +agaaggatggatgggtagggaggtaggtgagtggatggatggatggggagatggatggat +ggatagagagaaggatggatgggtgggacaatggatggatggatggatagaaggatggac +gggtggggagatggatggatggatggatggatggatggatggatggacagaaggatgtat +gggtggggaggtgggtggatagatggatggatggatggatggggaaatggatggatggaa +ggatggatggatagggaggtgggtggatggatggatggatggatgtacagaaggatggat +gggtggggaggtgggtgagtggatgaatggatggatggatagatagaaggatggatgggt +gggacaatagatggatggatagagagaaggatggatgggtggggagatggatggatggat +ggatggatggatggatggatggatggatagagagaaggatggatggttgagaca----at +ggatggatggatggatggagagatggatggatggacggatggacagaaggatggatgggt +ggggaggtggatggatggattgaaggatggatgggtgggga----catggatggatggat +ggatggatggatggatggatggacagaaggatgtatgggtggggaggtgggtggata--- +-----gatggatggatggggaaatggatggatggaaggatggatggatagggaggtgggt +ggatggatggatggatggatgtacagaaggatggatgggtggggaggtgggtgagtggat +gaatggatggatggatagatagaaggatggatgggtgggacaatagatggatggatagag +agaaggatggatgggtggggagatggatggatggatggatggatggatggatagagagaa +ggatggatggttgagacaatggatggatggatggatggatggagagatggatggatggat +ggatggacagaaggatggatgggtggggaggtggatggatggatggaaggatggatggat +ggatagagagaaggatggatgggtgggacaatggatggatggatgcatggatggatggat +ggagggatagagagaaggatggatgggtgggacaatcaatggatggatggatggatggat +ggatagagagaaggatggatgggtggggagatggatggatggatggagaggtggatggat +ggatggatggatggattgatggacagaaggatggatgggtggggaggtggatagatggag +agatggagggatggttcgatagagagaaggatggatggatgggacaatggatggatggat +ggatggagtgaaggatggatgggtggggagatggatggatcgatggatggatggatggat +agatagatggatggagaggtggatagatggatgggtggatggatggacagaggatggatg +ggtggggaggtgggtggatggatggatggatgtgggatggactgtcccacagaaagtgtg +tggtaaggggagagattggagacagcccagtcttgagatgccttgtaggggcccctggtc +tagggcaggcagagctggccaggcaggagctccagcacagcgcccttgctcaccgccaat +cttgtacacgtcctgcagcggc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/msa.fa.fai new file mode 100644 index 00000000..3c19a1c2 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63491489_63493165 3022 29 60 61 +syndip_1_chr20:63491489-63493165 3022 3136 60 61 +syndip_2_chr20:63491489-63493165 3022 6243 60 61 +p:HG002_1_chr20:63491489-63493165 3022 9351 60 61 +p:HG002_2_chr20:63491489-63493165 3022 12459 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/output.vcf.gz new file mode 100644 index 00000000..823c9b43 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/output.vcf.gz.tbi new file mode 100644 index 00000000..e956503f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63491589-63493065/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/base.vcf.gz new file mode 100644 index 00000000..4c9ca51f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/base.vcf.gz.tbi new file mode 100644 index 00000000..dd1f6c2a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/comp.vcf.gz new file mode 100644 index 00000000..53edbf61 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/comp.vcf.gz.tbi new file mode 100644 index 00000000..9cd0b752 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/haps.fa new file mode 100644 index 00000000..cb20350d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/haps.fa @@ -0,0 +1,66 @@ +>ref_chr20_63535574_63536346 +ACTTCCAGGTGGAGCTTGCAGAAGCTCCAGGTGACCTGCGCCCTTTGTGTGTCTGACTCCCTCAGGTCACTGGAACACAAACCCCACACAGAAGACCACGGCCCAGCATGGAGCCCCTGGGGTCCACCCCCTCCACTTCCGCACACCTGGAAGCACTGCCCCACCTGCCCCTCCAACCACCTGGCCTCCCGCCCCCCCCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCCCCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCACCCCGTCCTCACCTGGCCTCCCGCACCCCCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCTCCTCTCCTGGCCTCCCGCCCCCTCCTCTCCTGGCCTCCCGTCCCCTCCTCTCCTGGTCTCCCGCCCCCCCCACCTGGCCTCCCGCCCCCCCTCACCTGGCCTCCAGCCCCCCCCACCTAGCCTCCCGCTCCCCCCCCCACCTGGCCTCCCACCCCCTCCTCACCTGGCCTCCTCCCCACTTCTCACCTGGGCGAGTTCTCAGGACTCAGGGTCTTTGCACCTGGGAGCTGACCAGCCTCCGGCCAGACCCCACCCCTGCACCCCTGCTCACTAACGAGGTCGTGGGTCTGCGCGTGACCCTGCTAACGAGGTCGTGGGTCT +>syndip_1_chr20:63535574-63536346 +ACTTCCAGGTGGAGCTTGCAGAAGCTCCAGGTGACCTGCGCCCTTTGTGTGTCTGACTCC +CTCAGGTCACTGGAACACAAACCCCACACAGAAGACCACGGCCCAGCATGGAGCCCCTGG +GGTCCACCCCCTCCACTTCCGCACACCTGGAAGCACTGCCCCACCTGCCCCTCCAACCAC +CTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCC +CCTCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCACCCCGTCCTCACCTGGC +CTCCCGCACCCCCCTCACCTGGCCTCCCGCCCCCCCCTCATCTGGCCTCCCGCCCCCTCC +TCACCTGGCCTCCCGCCCCCTCCTCTCCTGGCCTCCCGCCCCCCCCCTCACCTGGCCTCC +CGCCCCCTCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCCCCCTCA +CCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCCCCCTCACCTGGCCTCCCGC +CCCCTCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCACCCCGTCCTCACCTG +GCCTCCCGCACCCCCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCGCCCCCT +CCTCTCCTGGCCTCCCGCCCCCTCCTCTCCTGGCCTCCCGTCCCCTCCTCTCCTGGTCTC +CCGCCCCCCCCACCTGGCCTCCCGCCCCCCCTCACCTGGCCTCCAGCCCCCCCCACCTGG +CCTCCCGCTCCCCCCCCACCTGGCCTCCCACCCCCTCCTCACCTGGCCTCCTCCCCACTT +CTCACCTGGGCGAGTTCTCAGGACTCAGGGTCTTTGCACCTGGGAGCTGACCAGCCTCCG +GCCAGACCCCACCCCTGCACCCCTGCTCACTAACGAGGTCGTGGGTCTGCGCGTGACCCT +GCTAACGAGGTCGTGGGTCT +>syndip_2_chr20:63535574-63536346 +ACTTCCAGGTGGAGCTTGCAGAAGCTCCAGGTGACCTGCGCCCTTTGTGTGTCTGACTCC +CTCAGGTCACTGGAACACAAACCCCACACAGAAGACCACGGCCCAGCATGGAGCCCCTGG +GGTCCACCCCCTCCACTTCCGCACACCTGGAAGCACTGCCCCACCTGCCCCTCCAACCAC +CTGGCCTCCCGCCCCCCCCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCC +CCCTCCTCACCTGGCCTCCCGCCCCCCCCCTCACCTGGCCTCCCGCCCCCTCCTCACCTG +GCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCACCCCGT +CCTCACCTGGCCTCCCGCACCCCCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTC +CCGCCCCCTCCTCACCTGGCCTCCCGCCCCCTCCTCTCCTGGCCTCCCGCCCCCTCCTCT +CCTGGCCTCCCGTCCCCTCCTCTCCTGGTCTCCCGCCCCCCCCACCTGGCCTCCCGCCCC +CCCTCACCTGGCCTCCAGCCCCCCCCACCTAGCCTCCCGCTCCCCCCCCCACCTGGCCTC +CCACCCCCTCCTCACCTGGCCTCCTCCCCACTTCTCACCTGGGCGAGTTCTCAGGACTCA +GGGTCTTTGCACCTGGGAGCTGACCAGCCTCCGGCCAGACCCCACCCCTGCACCCCTGCT +CACTAACGAGGTCGTGGGTCTGCGCGTGACCCTGCTAACGAGGTCGTGGGTCT +>p:HG002_1_chr20:63535574-63536346 +ACTTCCAGGTGGAGCTTGCAGAAGCTCCAGGTGACCTGCGCCCTTTGTGTGTCTGACTCC +CTCAGGTCACTGGAACACAAACCCCACACAGAAGACCACGGCCCAGCATGGAGCCCCTGG +GGTCCACCCCCTCCACTTCCGCACACCTGGAAGCACTGCCCCACCTGCCCCTCCAACCAC +CTGGCCTCCCGCCCCCCCCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCC +CCCTCCTCACCTGGCCTCCCGCCCCCCCCCTCACCTGGCCTCCCGCCCCCTCCTCACCTG +GCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCACCCCGT +CCTCACCTGGCCTCCCGCACCCCCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTC +CCGCCCCCTCCTCACCTGGCCTCCCGCCCCCTCCTCTCCTGGCCTCCCGCCCCCTCCTCT +CCTGGCCTCCCGTCCCCTCCTCTCCTGGTCTCCCGCCCCCCCCACCTGGCCTCCCGCCCC +CCCTCACCTGGCCTCCAGCCCCCCCCACCTAGCCTCCCGCTCCCCCCCCCACCTGGCCTC +CCACCCCCTCCTCACCTGGCCTCCTCCCCACTTCTCACCTGGGCGAGTTCTCAGGACTCA +GGGTCTTTGCACCTGGGAGCTGACCAGCCTCCGGCCAGACCCCACCCCTGCACCCCTGCT +CACTAACGAGGTCGTGGGTCTGCGCGTGACCCTGCTAACGAGGTCGTGGGTCT +>p:HG002_2_chr20:63535574-63536346 +ACTTCCAGGTGGAGCTTGCAGAAGCTCCAGGTGACCTGCGCCCTTTGTGTGTCTGACTCC +CTCAGGTCACTGGAACACAAACCCCACACAGAAGACCACGGCCCAGCATGGAGCCCCTGG +GGTCCACCCCCTCCACTTCCGCACACCTGGAAGCACTGCCCCACCTGCCCCTCCAACCAC +CTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCC +CCTCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCACCCCGTCCTCACCTGGC +CTCCCGCACCCCCCTCACCTGGCCTCCCGCCCCCCCCTCATCTGGCCTCCCGCCCCCTCC +TCACCTGGCCTCCCGCCCCCTCCTCTCCTGGCCTCCCGCCCCCCCCCTCACCTGGCCTCC +CGCCCCCTCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCCCCCTCA +CCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCCCCCTCACCTGGCCTCCCGC +CCCCTCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCACCCCGTCCTCACCTG +GCCTCCCGCACCCCCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCGCCCCCT +CCTCTCCTGGCCTCCCGCCCCCTCCTCTCCTGGCCTCCCGTCCCCTCCTCTCCTGGTCTC +CCGCCCCCCCCACCTGGCCTCCCGCCCCCCCTCACCTGGCCTCCAGCCCCCCCCACCTGG +CCTCCCGCTCCCCCCCCACCTGGCCTCCCACCCCCTCCTCACCTGGCCTCCTCCCCACTT +CTCACCTGGGCGAGTTCTCAGGACTCAGGGTCTTTGCACCTGGGAGCTGACCAGCCTCCG +GCCAGACCCCACCCCTGCACCCCTGCTCACTAACGAGGTCGTGGGTCTGCGCGTGACCCT +GCTAACGAGGTCGTGGGTCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/haps.fa.ref.fa new file mode 100644 index 00000000..32b667e8 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63535574-63536346 +ACTTCCAGGTGGAGCTTGCAGAAGCTCCAGGTGACCTGCGCCCTTTGTGTGTCTGACTCCCTCAGGTCACTGGAACACAAACCCCACACAGAAGACCACGGCCCAGCATGGAGCCCCTGGGGTCCACCCCCTCCACTTCCGCACACCTGGAAGCACTGCCCCACCTGCCCCTCCAACCACCTGGCCTCCCGCCCCCCCCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCCCCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCACCCCGTCCTCACCTGGCCTCCCGCACCCCCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCTCCTCTCCTGGCCTCCCGCCCCCTCCTCTCCTGGCCTCCCGTCCCCTCCTCTCCTGGTCTCCCGCCCCCCCCACCTGGCCTCCCGCCCCCCCTCACCTGGCCTCCAGCCCCCCCCACCTAGCCTCCCGCTCCCCCCCCCACCTGGCCTCCCACCCCCTCCTCACCTGGCCTCCTCCCCACTTCTCACCTGGGCGAGTTCTCAGGACTCAGGGTCTTTGCACCTGGGAGCTGACCAGCCTCCGGCCAGACCCCACCCCTGCACCCCTGCTCACTAACGAGGTCGTGGGTCTGCGCGTGACCCTGCTAACGAGGTCGTGGGTCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/msa.fa new file mode 100644 index 00000000..3113ce6f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/msa.fa @@ -0,0 +1,90 @@ +>ref_chr20_63535574_63536346 +acttccaggtggagcttgcagaagctccaggtgacctgcgccctttgtgtgtctgactcc +ctcaggtcactggaacacaaaccccacacagaagaccacggcccagcatggagcccctgg +ggtccaccccctccacttccgcacacctggaagcactgccccacctgcccctccaacca- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------cctggcctcccgccccccccctcacctggcctcc +cgccccctcctcacctggcctcccgccccctcctcacctggcctcccgccccccccctca +cctggcctcccgccccctcctcacctggcctcccg-ccccctcctcacctggcctcccgc +ccccccctcacctggcctcccaccccgtcctcacctggcctcccgcacccccctcacctg +gcctcccgcccccccctcacctggcctcccgccccctcctcacctggcctcccgccccct +cctctcctggcctcccgccccctcctctcctggcctcccgtcccctcctctcctggtctc +ccgccccccccacctggcctcccgccccccctcacctggcctccagccccccccacctag +cctcccgctcccccccccacctggcctcccaccccctcctcacctggcctcctccccact +tctcacctgggcgagttctcaggactcagggtctttgcacctgggagctgaccagcctcc +ggccagaccccacccctgcacccctgctcactaacgaggtcgtgggtctgcgcgtgaccc +tgctaacgaggtcgtgggtct +>syndip_1_chr20:63535574-63536346 +acttccaggtggagcttgcagaagctccaggtgacctgcgccctttgtgtgtctgactcc +ctcaggtcactggaacacaaaccccacacagaagaccacggcccagcatggagcccctgg +ggtccaccccctccacttccgcacacctggaagcactgccccacctgcccctccaaccac +ctggcctcccgcccccccctcacctggcctcccgccccctcctcacctggcctcccgccc +cctcctcacctggcctcccgcccccccctcacctggcctcccaccccgtcctcacctggc +ctcccgcacccccctcacctggcctcccgcccccccctcatctggcctcccgccccctcc +tcacctggcctcccgccccctcctctcctggcctcccgccccccccctcacctggcctcc +cgccccctcctcacctggcctcccgccccctcctcacctggcctcccgccccccccctca +cctggcctcccgccccctcctcacctggcctcccgccccccccctcacctggcctcccgc +cccctcctcacctggcctcccgcccccccctcacctggcctcccaccccgtcctcacctg +gcctcccgcacccccctcacctggcctcccgcccccccctcacctggcctcccgccccct +cctctcctggcctcccgccccctcctctcctggcctcccgtcccctcctctcctggtctc +ccgccccccccacctggcctcccgccccccctcacctggcctccagccccccccacctgg +cctcccgct-ccccccccacctggcctcccaccccctcctcacctggcctcctccccact +tctcacctgggcgagttctcaggactcagggtctttgcacctgggagctgaccagcctcc +ggccagaccccacccctgcacccctgctcactaacgaggtcgtgggtctgcgcgtgaccc +tgctaacgaggtcgtgggtct +>syndip_2_chr20:63535574-63536346 +acttccaggtggagcttgcagaagctccaggtgacctgcgccctttgtgtgtctgactcc +ctcaggtcactggaacacaaaccccacacagaagaccacggcccagcatggagcccctgg +ggtccaccccctccacttccgcacacctggaagcactgccccacctgcccctccaacca- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------cctggcctcccgccccccccctcacctggcctcc +cgccccctcctcacctggcctcccgccccctcctcacctggcctcccgccccccccctca +cctggcctcccgccccctcctcacctggcctcccg-ccccctcctcacctggcctcccgc +ccccccctcacctggcctcccaccccgtcctcacctggcctcccgcacccccctcacctg +gcctcccgcccccccctcacctggcctcccgccccctcctcacctggcctcccgccccct +cctctcctggcctcccgccccctcctctcctggcctcccgtcccctcctctcctggtctc +ccgccccccccacctggcctcccgccccccctcacctggcctccagccccccccacctag +cctcccgctcccccccccacctggcctcccaccccctcctcacctggcctcctccccact +tctcacctgggcgagttctcaggactcagggtctttgcacctgggagctgaccagcctcc +ggccagaccccacccctgcacccctgctcactaacgaggtcgtgggtctgcgcgtgaccc +tgctaacgaggtcgtgggtct +>p:HG002_1_chr20:63535574-63536346 +acttccaggtggagcttgcagaagctccaggtgacctgcgccctttgtgtgtctgactcc +ctcaggtcactggaacacaaaccccacacagaagaccacggcccagcatggagcccctgg +ggtccaccccctccacttccgcacacctggaagcactgccccacctgcccctccaacca- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------cctggcctcccgccccccccctcacctggcctcc +cgccccctcctcacctggcctcccgccccctcctcacctggcctcccgccccccccctca +cctggcctcccgccccctcctcacctggcctcccg-ccccctcctcacctggcctcccgc +ccccccctcacctggcctcccaccccgtcctcacctggcctcccgcacccccctcacctg +gcctcccgcccccccctcacctggcctcccgccccctcctcacctggcctcccgccccct +cctctcctggcctcccgccccctcctctcctggcctcccgtcccctcctctcctggtctc +ccgccccccccacctggcctcccgccccccctcacctggcctccagccccccccacctag +cctcccgctcccccccccacctggcctcccaccccctcctcacctggcctcctccccact +tctcacctgggcgagttctcaggactcagggtctttgcacctgggagctgaccagcctcc +ggccagaccccacccctgcacccctgctcactaacgaggtcgtgggtctgcgcgtgaccc +tgctaacgaggtcgtgggtct +>p:HG002_2_chr20:63535574-63536346 +acttccaggtggagcttgcagaagctccaggtgacctgcgccctttgtgtgtctgactcc +ctcaggtcactggaacacaaaccccacacagaagaccacggcccagcatggagcccctgg +ggtccaccccctccacttccgcacacctggaagcactgccccacctgcccctccaaccac +ctggcctcccgcccccccctcacctggcctcccgccccctcctcacctggcctcccgccc +cctcctcacctggcctcccgcccccccctcacctggcctcccaccccgtcctcacctggc +ctcccgcacccccctcacctggcctcccgcccccccctcatctggcctcccgccccctcc +tcacctggcctcccgccccctcctctcctggcctcccgccccccccctcacctggcctcc +cgccccctcctcacctggcctcccgccccctcctcacctggcctcccgccccccccctca +cctggcctcccgccccctcctcacctggcctcccgccccccccctcacctggcctcccgc +cccctcctcacctggcctcccgcccccccctcacctggcctcccaccccgtcctcacctg +gcctcccgcacccccctcacctggcctcccgcccccccctcacctggcctcccgccccct +cctctcctggcctcccgccccctcctctcctggcctcccgtcccctcctctcctggtctc +ccgccccccccacctggcctcccgccccccctcacctggcctccagccccccccacctgg +cctcccgct-ccccccccacctggcctcccaccccctcctcacctggcctcctccccact +tctcacctgggcgagttctcaggactcagggtctttgcacctgggagctgaccagcctcc +ggccagaccccacccctgcacccctgctcactaacgaggtcgtgggtctgcgcgtgaccc +tgctaacgaggtcgtgggtct diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/msa.fa.fai new file mode 100644 index 00000000..3b205652 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63535574_63536346 981 29 60 61 +syndip_1_chr20:63535574-63536346 981 1061 60 61 +syndip_2_chr20:63535574-63536346 981 2093 60 61 +p:HG002_1_chr20:63535574-63536346 981 3126 60 61 +p:HG002_2_chr20:63535574-63536346 981 4159 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/output.vcf.gz new file mode 100644 index 00000000..0f3f5ee8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/output.vcf.gz.tbi new file mode 100644 index 00000000..70847c3a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63535674-63536246/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/base.vcf.gz new file mode 100644 index 00000000..95303473 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/base.vcf.gz.tbi new file mode 100644 index 00000000..56576b49 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/comp.vcf.gz new file mode 100644 index 00000000..56829579 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/comp.vcf.gz.tbi new file mode 100644 index 00000000..68645061 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/haps.fa new file mode 100644 index 00000000..fda0ff17 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/haps.fa @@ -0,0 +1,54 @@ +>ref_chr20_63559188_63560064 +TGGGGGGGCCCTGGACTTTCCCTCCCAGTCCTGGCACCTTGCAGGTGGAGAGGGCTCTTCAGGAAGGCATAGTTGGCCTCCTGCAGACGCGCACCTGGCCGGCAGGCACGAGGGTCTGCTGAGCCTCGCAGAAGTCCAGGAGGCTACGCCAGAGGGGGCAGCAGCGCAGAAGGAGGTGGTCTCCTGTGAGGGTGGGAGTCAGATGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGAGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGAGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGAGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTCAGGCAGGAGTCGGCAGCTCCCTAGCCCAGCCCTGGCCTCACCTGTGTTCCCACCCTGGAAGAGCCCAGCCCCGCCCTCACCGATCAGGCAGAGCCCCTCCTGGGCCCGCGTGACAGCCACATTCACTTGGTTGGGGTCCACAACGAAGCCCAGAAACTTCTTGAGCCAGCTCTTGGTGGGCCGCTGGTCCAGGTCGCTCTTGGCACAGGTGCGGACG +>syndip_1_chr20:63559188-63560064 +TGGGGGGGCCCTGGACTTTCCCTCCCAGTCCTGGCACCTTGCAGGTGGAGAGGGCTCTTC +AGGAAGGCATAGTTGGCCTCCTGCAGACGCGCACCTGGCCGGCAGGCACGAGGGTCTGCT +GAGCCTCGCAGAAGTCCAGGAGGCTACGCCAGAGGGGGCAGCAGCGCAGAAGGAGGTGGT +CTCCTGTGAGGGTGGGAGTCAGATGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGT +CAGGTGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGA +GTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTC +AGGTGGGAGGAGTCAGGGTCAGGTGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGT +CAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGAG +TCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTCA +GGCAGGAGTCGGCAGCTCCCTAGCCCAGCCCTGGCCTCACCTGTGTTCCCACCCTGGAAG +AGCCCAGCCCCGCCCTCACCGATCAGGCAGAGCCCCTCCTGGGCCCGCGTGACAGCCACA +TTCACTTGGTTGGGGTCCACAACGAAGCCCAGAAACTTCTTGAGCCAGCTCTTGGTGGGC +CGCTGGTCCAGGTCGCTCTTGGCACAGGTGCGGACG +>syndip_2_chr20:63559188-63560064 +TGGGGGGGCCCTGGACTTTCCCTCCCAGTCCTGGCACCTTGCAGGTGGAGAGGGCTCTTC +AGGAAGGCATAGTTGGCCTCCTGCAGACGCGCACCTGGCCGGCAGGCACGAGGGTCTGCT +GAGCCTCGCAGAAGTCCAGGAGGCTACGCCAGAGGGGGCAGCAGCGCAGAAGGAGGTGGT +CTCCTGTGAGGGTGGGAGTCAGATGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGT +CAGGTGGGAGGAGTCAGGGTCAGGTGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGG +TCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGG +GTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTCAGGCAGGAGTCGGCAGCTCC +CTAGCCCAGCCCTGGCCTCACCTGTGTTCCCACCCTGGAAGAGCCCAGCCCCGCCCTCAC +CGATCAGGCAGAGCCCCTCCTGGGCCCGCGTGACAGCCACATTCACTTGGTTGGGGTCCA +CAACGAAGCCCAGAAACTTCTTGAGCCAGCTCTTGGTGGGCCGCTGGTCCAGGTCGCTCT +TGGCACAGGTGCGGACG +>p:HG002_1_chr20:63559188-63560064 +TGGGGGGGCCCTGGACTTTCCCTCCCAGTCCTGGCACCTTGCAGGTGGAGAGGGCTCTTC +AGGAAGGCATAGTTGGCCTCCTGCAGACGCGCACCTGGCCGGCAGGCACGAGGGTCTGCT +GAGCCTCGCAGAAGTCCAGGAGGCTACGCCAGAGGGGGCAGCAGCGCAGAAGGAGGTGGT +CTCCTGTGAGGGTGGGAGTCAGATGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGT +CAGGTGGGAGGAGTCAGGGTCAGGTGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGG +TCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGG +GTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTCAGGCAGGAGTCGGCAGCTCC +CTAGCCCAGCCCTGGCCTCACCTGTGTTCCCACCCTGGAAGAGCCCAGCCCCGCCCTCAC +CGATCAGGCAGAGCCCCTCCTGGGCCCGCGTGACAGCCACATTCACTTGGTTGGGGTCCA +CAACGAAGCCCAGAAACTTCTTGAGCCAGCTCTTGGTGGGCCGCTGGTCCAGGTCGCTCT +TGGCACAGGTGCGGACG +>p:HG002_2_chr20:63559188-63560064 +TGGGGGGGCCCTGGACTTTCCCTCCCAGTCCTGGCACCTTGCAGGTGGAGAGGGCTCTTC +AGGAAGGCATAGTTGGCCTCCTGCAGACGCGCACCTGGCCGGCAGGCACGAGGGTCTGCT +GAGCCTCGCAGAAGTCCAGGAGGCTACGCCAGAGGGGGCAGCAGCGCAGAAGGAGGTGGT +CTCCTGTGAGGGTGGGAGTCAGATGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGT +CAGGTGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGA +GTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTC +AGGTGGGAGGAGTCAGGGTCAGGTGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGT +CAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGAG +TCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTCA +GGCAGGAGTCGGCAGCTCCCTAGCCCAGCCCTGGCCTCACCTGTGTTCCCACCCTGGAAG +AGCCCAGCCCCGCCCTCACCGATCAGGCAGAGCCCCTCCTGGGCCCGCGTGACAGCCACA +TTCACTTGGTTGGGGTCCACAACGAAGCCCAGAAACTTCTTGAGCCAGCTCTTGGTGGGC +CGCTGGTCCAGGTCGCTCTTGGCACAGGTGCGGACG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/haps.fa.ref.fa new file mode 100644 index 00000000..8f47a2fb --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63559188-63560064 +TGGGGGGGCCCTGGACTTTCCCTCCCAGTCCTGGCACCTTGCAGGTGGAGAGGGCTCTTCAGGAAGGCATAGTTGGCCTCCTGCAGACGCGCACCTGGCCGGCAGGCACGAGGGTCTGCTGAGCCTCGCAGAAGTCCAGGAGGCTACGCCAGAGGGGGCAGCAGCGCAGAAGGAGGTGGTCTCCTGTGAGGGTGGGAGTCAGATGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGAGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGAGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGAGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTCAGGCAGGAGTCGGCAGCTCCCTAGCCCAGCCCTGGCCTCACCTGTGTTCCCACCCTGGAAGAGCCCAGCCCCGCCCTCACCGATCAGGCAGAGCCCCTCCTGGGCCCGCGTGACAGCCACATTCACTTGGTTGGGGTCCACAACGAAGCCCAGAAACTTCTTGAGCCAGCTCTTGGTGGGCCGCTGGTCCAGGTCGCTCTTGGCACAGGTGCGGACG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/msa.fa new file mode 100644 index 00000000..ac725463 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/msa.fa @@ -0,0 +1,80 @@ +>ref_chr20_63559188_63560064 +tgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctcttc +aggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgct +gagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggt +ctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcagggt +caggtgggaggagtcagggtcaggtgggagtcagtcagggtcaggtgggaggagtcaggg +tcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtcagg +gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtgggaggagtcagg +gtcagatgggagtcagtcagagtcaggtgggaggagtcagggtcaggtgggaggagtcag +ggtcaggtcggagtcagggtcaggtgggaggagtcagggtcaggtgggagtcagtcaggg +tcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcaga +gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggtc +aggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccctggaa +gagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgacagccac +attcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttggtggg +ccgctggtccaggtcgctcttggcacaggtgcggacg +>syndip_1_chr20:63559188-63560064 +tgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctcttc +aggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgct +gagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggt +ctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcagggt +caggtgggag----------------------------------------tcagtcaggg +tcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtcagg +gtcaggtgggaggagtcagggtcaggt---cggagtcagggtcaggtgggaggagtcagg +gtcaggtgggagtcagtcagggtcaggtgggagg-------------------------- +----------------------------------------------------agtcaggg +tcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcaga +gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggtc +aggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccctggaa +gagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgacagccac +attcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttggtggg +ccgctggtccaggtcgctcttggcacaggtgcggacg +>syndip_2_chr20:63559188-63560064 +tgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctcttc +aggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgct +gagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggt +ctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtggga----------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------ggagtcagggtcaggtgggaggagtcagg +gtcaggtgggagtc---------------------------------------------- +----------------------------------------------------agtcaggg +tcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcagg +gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggtc +aggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccctggaa +gagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgacagccac +attcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttggtggg +ccgctggtccaggtcgctcttggcacaggtgcggacg +>p:HG002_1_chr20:63559188-63560064 +tgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctcttc +aggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgct +gagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggt +ctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtggga----------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------ggagtcagggtcaggtgggaggagtcagg +gtcaggtgggagtc---------------------------------------------- +----------------------------------------------------agtcaggg +tcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcagg +gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggtc +aggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccctggaa +gagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgacagccac +attcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttggtggg +ccgctggtccaggtcgctcttggcacaggtgcggacg +>p:HG002_2_chr20:63559188-63560064 +tgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctcttc +aggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgct +gagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggt +ctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcagggt +caggtgggag----------------------------------------tcagtcaggg +tcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtcagg +gtcaggtgggaggagtcagggtcaggt---cggagtcagggtcaggtgggaggagtcagg +gtcaggtgggagtcagtcagggtcaggtgggagg-------------------------- +----------------------------------------------------agtcaggg +tcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcaga +gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggtc +aggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccctggaa +gagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgacagccac +attcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttggtggg +ccgctggtccaggtcgctcttggcacaggtgcggacg diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/msa.fa.fai new file mode 100644 index 00000000..30945016 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63559188_63560064 877 29 60 61 +syndip_1_chr20:63559188-63560064 877 955 60 61 +syndip_2_chr20:63559188-63560064 877 1881 60 61 +p:HG002_1_chr20:63559188-63560064 877 2808 60 61 +p:HG002_2_chr20:63559188-63560064 877 3735 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/output.vcf.gz new file mode 100644 index 00000000..f6bda72e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/output.vcf.gz.tbi new file mode 100644 index 00000000..27013b16 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63559288-63559964/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/base.vcf.gz new file mode 100644 index 00000000..2248574f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/base.vcf.gz.tbi new file mode 100644 index 00000000..ef71c854 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/comp.vcf.gz new file mode 100644 index 00000000..c6a046b2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/comp.vcf.gz.tbi new file mode 100644 index 00000000..d0bd31c7 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/haps.fa new file mode 100644 index 00000000..1add431e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/haps.fa @@ -0,0 +1,62 @@ +>ref_chr20_63641679_63642236 +TCTATTACTGCGGCTAGTTACTGTCCCGCCAGGACCAGACTCTGGACCTGCCTCGTGCGCTGCTGGGGACGCCCAGTAAACACGGGAGGAGCCCCCGACCCCCACCCCAGCTCAGCGCCTCGGAGTCCCCGGCCCCGCTCTGCGCCCCTCCGAGCTCCGCCCTAGCCCCGCCCCCGCCCAGTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCTGGCCCCGCCCCCGCCCAGTGCCCCGCCCCCTGACTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTTCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCGGCCCCGCCCCCGCACCTTCTCGCGCAGCCGCTCGCGCAGTGCGGCCAGGTGTGCCTCGCGGATCTCCTTGCTGAGCTCCATCTTGTAGTTGAGCTTCTCCTCCGCCTGGCGGCTGAAGTTGTTATTCTCCTCCAGCGCCTTGTG +>syndip_1_chr20:63641679-63642236 +TCTATTACTGCGGCTAGTTACTGTCCCGCCAGGACCAGACTCTGGACCTGCCTCGTGCGC +TGCTGGGGACGCCCAGTAAACACGGGAGGAGCCCCCGACCCCCACCCCAGCTCAGCGCCT +CGGAGTCCCCGGCCCCGCTCTGCGCCCCTCCGAGCTCCGCCCTAGCCCCGCCCCCGCCCA +GTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAG +CTCCGCCCTGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCTGGCCCCGCCCCC +CGCCCAGTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGC +TCCGAGCTCCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCTGGCCCC +GCCCCCGCCCAGTGCCCCGCCCCCTGACTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTG +CCCGCTCCGAGCTCCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCG +GCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTTCGCCCCGGCCCCGCCCCGGCCCCTGCCC +GCTCCGAGCTCCGCCCCGGCCCCGCCCCCGCACCTTCTCGCGCAGCCGCTCGCGCAGTGC +GGCCAGGTGTGCCTCGCGGATCTCCTTGCTGAGCTCCATCTTGTAGTTGAGCTTCTCCTC +CGCCTGGCGGCTGAAGTTGTTATTCTCCTCCAGCGCCTTGTG +>syndip_2_chr20:63641679-63642236 +TCTATTACTGCGGCTAGTTACTGTCCCGCCAGGACCAGACTCTGGACCTGCCTCGTGCGC +TGCTGGGGACGCCCAGTAAACACGGGAGGAGCCCCCGACCCCCACCCCAGCTCAGCGCCT +CGGAGTCCCCGGCCCCGCTCTGCGCCCCTCCGAGCTCCGCCCTAGCCCCGCCCCCGCCCA +GTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAG +CTCCGCCCTGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCTGGCCCCGCCCCC +GCCCAGTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCT +CCGAGCTCCACCCTGGCCCCGCCCCCGCCCAGTGCCCCGCCCCCTGCCTGCTGCTTGCCC +TGCCCCCTCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCGGCCCCGCCCCGGCCCAGTG +CCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTC +CGCCCTGGCCCCGCCCCCGCCCAGTGCCCCGCCCCCTGCCTGCTGCTTGCCCTGCCCCCT +CCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCGGCCTCGCCCCGGCCCCTGCCCGCTCCG +AGCTTCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTTCGCCCCGGCCCCGCCC +CGGCCCCTGCCCGCTCCGAACTCCGCCCCGGCCCCGCCCCCGCACCTTCTCGCGCAGCCG +CTCGCGCAGTGCGGCCAGGTGTGCCTCGCGGATCTCCTTGCTGAGCTCCATCTTGTAGTT +GAGCTTCTCCTCCGCCTGGCGGCTGAAGTTGTTATTCTCCTCCAGCGCCTTGTG +>p:HG002_1_chr20:63641679-63642236 +TCTATTACTGCGGCTAGTTACTGTCCCGCCAGGACCAGACTCTGGACCTGCCTCGTGCGC +TGCTGGGGACGCCCAGTAAACACGGGAGGAGCCCCCGACCCCCACCCCAGCTCAGCGCCT +CGGAGTCCCCGGCCCCGCTCTGCGCCCCTCCGAGCTCCGCCCTAGCCCCGCCCCCGCCCA +GTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAG +CTCCGCCCTGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCTGGCCCCGCCCCC +GCCCAGTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCT +CCGAGCTCCACCCTGGCCCCGCCCCCGCCCAGTGCCCCGCCCCCTGCCTGCTGCTTGCCC +TGCCCCCTCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCGGCCCCGCCCCGGCCCAGTG +CCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTC +CGCCCTGGCCCCGCCCCCGCCCAGTGCCCCGCCCCCTGCCTGCTGCTTGCCCTGCCCCCT +CCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCGGCCTCGCCCCGGCCCCTGCCCGCTCCG +AGCTTCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTTCGCCCCGGCCCCGCCC +CGGCCCCTGCCCGCTCCGAACTCCGCCCCGGCCCCGCCCCCGCACCTTCTCGCGCAGCCG +CTCGCGCAGTGCGGCCAGGTGTGCCTCGCGGATCTCCTTGCTGAGCTCCATCTTGTAGTT +GAGCTTCTCCTCCGCCTGGCGGCTGAAGTTGTTATTCTCCTCCAGCGCCTTGTG +>p:HG002_2_chr20:63641679-63642236 +TCTATTACTGCGGCTAGTTACTGTCCCGCCAGGACCAGACTCTGGACCTGCCTCGTGCGC +TGCTGGGGACGCCCAGTAAACACGGGAGGAGCCCCCGACCCCCACCCCAGCTCAGCGCCT +CGGAGTCCCCGGCCCCGCTCTGCGCCCCTCCGAGCTCCGCCCTAGCCCCGCCCCCGCCCA +GTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAG +CTCCGCCCTGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCTGGCCCCGCCCCC +CGCCCAGTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGC +TCCGAGCTCCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCTGGCCCC +GCCCCCGCCCAGTGCCCCGCCCCCTGACTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTG +CCCGCTCCGAGCTCCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCG +GCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTTCGCCCCGGCCCCGCCCCGGCCCCTGCCC +GCTCCGAGCTCCGCCCCGGCCCCGCCCCCGCACCTTCTCGCGCAGCCGCTCGCGCAGTGC +GGCCAGGTGTGCCTCGCGGATCTCCTTGCTGAGCTCCATCTTGTAGTTGAGCTTCTCCTC +CGCCTGGCGGCTGAAGTTGTTATTCTCCTCCAGCGCCTTGTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/haps.fa.ref.fa new file mode 100644 index 00000000..423b8813 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63641679-63642236 +TCTATTACTGCGGCTAGTTACTGTCCCGCCAGGACCAGACTCTGGACCTGCCTCGTGCGCTGCTGGGGACGCCCAGTAAACACGGGAGGAGCCCCCGACCCCCACCCCAGCTCAGCGCCTCGGAGTCCCCGGCCCCGCTCTGCGCCCCTCCGAGCTCCGCCCTAGCCCCGCCCCCGCCCAGTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCTGGCCCCGCCCCCGCCCAGTGCCCCGCCCCCTGACTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTTCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCGGCCCCGCCCCCGCACCTTCTCGCGCAGCCGCTCGCGCAGTGCGGCCAGGTGTGCCTCGCGGATCTCCTTGCTGAGCTCCATCTTGTAGTTGAGCTTCTCCTCCGCCTGGCGGCTGAAGTTGTTATTCTCCTCCAGCGCCTTGTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/msa.fa new file mode 100644 index 00000000..f9dc5498 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/msa.fa @@ -0,0 +1,80 @@ +>ref_chr20_63641679_63642236 +tctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcgc +tgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcct +cggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccca +gtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgag +ctccgccccggccccgccccggcccctgcccgctccgagctccgccctggccccg-cccc +cgcccagtgccccgccccctgactgctgctagccctgc---------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------ccccgccccggcccctgcccgctccgagcttcgccccggccccgcc +ccggcccctgcccgctccgagctccgccccggccccgcccccgcaccttctcgcgcagcc +gctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtagt +tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgtg +>syndip_1_chr20:63641679-63642236 +tctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcgc +tgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcct +cggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccca +gtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgag +ctccgccctggccccgccccggcccctgcccgctccgagctccgccctggccccgccccc +cgcccagtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgc +tccgagctccgccccgg------------------------------------------- +------------------------------------------------------------ +------------------------------ccccgccccggcccctgcccgctccgagct +ccgccctggccccgcccccgcccagtgccccgccccctgactgctgctagccctgccccc +gccccggcccctgcccgctccgagctccgccccggccccgccccggcccctgcccgctcc +gagctccgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgcc +ccggcccctgcccgctccgagctccgccccggccccgcccccgcaccttctcgcgcagcc +gctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtagt +tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgtg +>syndip_2_chr20:63641679-63642236 +tctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcgc +tgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcct +cggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccca +gtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgag +ctccgccctggccccgccccggcccctgcccgctccgagctccgccctggccccg-cccc +cgcccagtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgc +tccgagctccaccctggccccgcccccgcccagtgccccgccccctgcctgctgcttgcc +ctgccccctccccggcccctgcccgctccgagctccgccccggccccgccccggcccagt +gccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgagct +ccgccctggccccgcccccgcccagtgccccgccccctgcctgctgcttgccctgccccc +tccccggcccctgcccgctccgagctccgccccggcctcgccccggcccctgcccgctcc +gagcttcgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgcc +ccggcccctgcccgctccgaactccgccccggccccgcccccgcaccttctcgcgcagcc +gctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtagt +tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgtg +>p:HG002_1_chr20:63641679-63642236 +tctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcgc +tgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcct +cggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccca +gtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgag +ctccgccctggccccgccccggcccctgcccgctccgagctccgccctggccccg-cccc +cgcccagtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgc +tccgagctccaccctggccccgcccccgcccagtgccccgccccctgcctgctgcttgcc +ctgccccctccccggcccctgcccgctccgagctccgccccggccccgccccggcccagt +gccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgagct +ccgccctggccccgcccccgcccagtgccccgccccctgcctgctgcttgccctgccccc +tccccggcccctgcccgctccgagctccgccccggcctcgccccggcccctgcccgctcc +gagcttcgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgcc +ccggcccctgcccgctccgaactccgccccggccccgcccccgcaccttctcgcgcagcc +gctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtagt +tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgtg +>p:HG002_2_chr20:63641679-63642236 +tctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcgc +tgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcct +cggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccca +gtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgag +ctccgccctggccccgccccggcccctgcccgctccgagctccgccctggccccgccccc +cgcccagtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgc +tccgagctccgccccgg------------------------------------------- +------------------------------------------------------------ +------------------------------ccccgccccggcccctgcccgctccgagct +ccgccctggccccgcccccgcccagtgccccgccccctgactgctgctagccctgccccc +gccccggcccctgcccgctccgagctccgccccggccccgccccggcccctgcccgctcc +gagctccgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgcc +ccggcccctgcccgctccgagctccgccccggccccgcccccgcaccttctcgcgcagcc +gctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtagt +tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgtg diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/msa.fa.fai new file mode 100644 index 00000000..d35f8cb1 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63641679_63642236 895 29 60 61 +syndip_1_chr20:63641679-63642236 895 973 60 61 +syndip_2_chr20:63641679-63642236 895 1917 60 61 +p:HG002_1_chr20:63641679-63642236 895 2862 60 61 +p:HG002_2_chr20:63641679-63642236 895 3807 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/output.vcf.gz new file mode 100644 index 00000000..561d69c9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/output.vcf.gz.tbi new file mode 100644 index 00000000..3082ecff Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63641779-63642136/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/base.vcf.gz new file mode 100644 index 00000000..2fe83235 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/base.vcf.gz.tbi new file mode 100644 index 00000000..8af2a914 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/comp.vcf.gz new file mode 100644 index 00000000..675d13e6 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/comp.vcf.gz.tbi new file mode 100644 index 00000000..f8fae4d3 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/haps.fa new file mode 100644 index 00000000..f7b43526 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/haps.fa @@ -0,0 +1,432 @@ +>ref_chr20_63693225_63693985 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+TCGGCCTGAGCACAGCATTCCCCGAAGGCAGCGGGCACAGCCGGTCCTGGACCCCACTGGTAAATGGGGCCCCAGGTGGGACCCTCAGACTCCTGCGTGGAAGGCAGTGTGGGCCAGAGTCCTGGGCTGCTTGGGGTGGGCATCCTCGGGCCCTGCTTGGCCCCGCCTCTCTGTTCCCCTATGGGAGTGATGGGGGCCTCCACCTCCACCACCAGCACCAGCAGCACCACCTCCACCTCCACCTCCACCTCCACCTCCACCACCACCTCCACCTCCACCACCACCTCCTCCACCACCACCACCTCCACCACCACCACCACCACCACCACCTCCACCTCCACCACCTCCACCTCCACCACCACCACCTCCACCTCCACCACCACCACCTCCACCTCCACCACCACCTCCACCACCACCACCTCCACCTCCACCACCACCTCCACCACCACCACCACCACCACCACCACCACCACCACCACCTCCACCACCACCACCTGCACCACCACCTCCACCTCCACCACCACCACCACCTCCACCTCCACCAGCAGCAGCATCACTTGTTGGGGAGACCCTGTGCAACTCCATGCACAGCCCTGTCCCTGCCATAGCCCCGACCCCTAAGCACAGCCCTGTCCAACTGCCACACGTCCCCTGCCTCCCATGCATGGTCCTGGGGGGTCAACTGCACACGCCAGGGTCCTAGGGTCCTAGACCCCTGTCCTCCCTGTTTCTGCCTCTGTTTGGGGTGGAGTCCAAGTCTC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/msa.fa new file mode 100644 index 00000000..803367fa --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/msa.fa @@ -0,0 +1,660 @@ +>ref_chr20_63693225_63693985 +tcggcctgagcacagcattccccgaaggcagcgggcacagccggtcctggaccccactgg +taaatggggccccaggtgggaccctcagactcctgcgtggaaggcagtgtgggccagagt +cctgggctgcttggggtgggcatcctcgggccctgcttggccccgcctctctgttcccct +atgggagtgatgggggcctccacctccaccaccagcaccagcagcaccacctccacct-- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------ccacctccacct-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------------------------cc +acctccaccaccacctccacctccaccaccacctcctccaccaccaccacctccaccacc +accaccaccaccaccacctccacctccaccacctccacctccaccaccaccacctccacc +t----------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------------------ccaccacc +accacctccacctccaccaccacctccaccaccaccacctccacctccacca-------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------------------ccacctcc +accaccaccaccaccaccaccaccaccaccacca-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ 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+tcaactgcacacgccagggtcctagggtcctagacccctgtcctccctgtttctgcctct +gtttggggtggagtccaagtctc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/msa.fa.fai new file mode 100644 index 00000000..2a45b075 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63693225_63693985 7823 29 60 61 +syndip_1_chr20:63693225-63693985 7823 8017 60 61 +syndip_2_chr20:63693225-63693985 7823 16005 60 61 +p:HG002_1_chr20:63693225-63693985 7823 23994 60 61 +p:HG002_2_chr20:63693225-63693985 7823 31983 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/output.vcf.gz new file mode 100644 index 00000000..6a6655e3 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/output.vcf.gz.tbi new file mode 100644 index 00000000..07ac156e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63693325-63693885/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/base.vcf.gz new file mode 100644 index 00000000..ddb4d386 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/base.vcf.gz.tbi new file mode 100644 index 00000000..bb297398 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/comp.vcf.gz new file mode 100644 index 00000000..319f65d2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/comp.vcf.gz.tbi new file mode 100644 index 00000000..dbd1c030 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/haps.fa new file mode 100644 index 00000000..6370617a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/haps.fa @@ -0,0 +1,36 @@ +>ref_chr20_63770812_63771204 +TGTCCCCATTTCCTGCACGATGCGCCAGCCCACGGGGAGGTACACTCGACAGGACACCCTAGAGACCACGCTAACAAGAGGCCCAGCCCTGGAAATGCTCATCGCCTGCAACCAGCACATGGAGATGGTCGCAAGTCAGCACCGGCCACGCCCGGCACAGCAGCCACGCCGCTCGAACCACAGCAGGGGCCACGTCAGCAGGAGGTCGCAAGTCAGCACCGGCCACGCCCGGCACAGCAGCCACGCCGCTCGAACCACAGCAGGGGCTACTCGCCCTCCCAGGCCCTCTTCAGAGCTGGCCTGAGTTGAAGCTGCGTTCCTCCTGCTCTGAGGGCTGGGTACCGGGGACCCTCGCCCAGCCGAGGCCGCTCTTGTCTTCTTCTCTCTTCCGAC +>syndip_1_chr20:63770812-63771204 +TGTCCCCATTTCCTGCACGATGCGCCAGCCCACGGGGAGGTACACTCGACAGGACACCCT +AGAGACCACGCTAACAAGAGGCCCAGCCCTGGAAATGCTCATCGCCTGCAACCAGCACAT +GGAGATGGTCGCAAGTCAGCACCGGCCACGCCCGGCACAGCAGCCACGCCGCTCGAACCA +CAGCAGGGGCCACGTCAGCAGGAGGTCGCAAGTCAGCACCGGCCACGCCCGGCACAGCAG +CCACGCCGCTCGAACCACAGCAGGGGCTACTCGCCCTCCCAGGCCCTCTTCAGAGCTGGC +CTGAGTTGAAGCTGCGTTCCTCCTGCTCTGAGGGCTGGGTACCGGGGACCCTCGCCCAGC +CGAGGCCGCTCTTGTCTTCTTCTCTCTTCCGAC +>syndip_2_chr20:63770812-63771204 +TGTCCCCATTTCCTGCACGATGCGCCAGCCCACGGGGAGGTACACTCGACAGGACACCCT +AGAGACCACGCTAACAAGAGGCCCAGCCCTGGAAATGCTCATCGCCTGCAACCAGCACAT +GGAGATGGTCGCAAGTCAGCACCGGCCACGCCCGGCACAGCAGCCACGCCGCTCGAACCA +CAGCAGGGGCCACGTCAGCAGGAGGTCGCAAGTCAGCACCGGCCACGCCCGGCACAGCAG +CCACGCCGCTCGAACCACAGCAGGGGCTACTCGCCCTCCCAGGCCCTCTTCAGAGCTGGC +CTGAGTTGAAGCTGCGTTCCTCCTGCTCTGAGGGCTGGGTACCGGGGACCCTCGCCCAGC +CGAGGCCGCTCTTGTCTTCTTCTCTCTTCCGAC +>p:HG002_1_chr20:63770812-63771204 +TGTCCCCATTTCCTGCACGATGCGCCAGCCCACGGGGAGGTACACTCGACAGGACACCCT +AGAGACCACGCTAACAAGAGGCCCAGCCCTGGAAATGCTCATCGCCTGCAACCAGCACAT +GGAGATGGTCGCAAGTCAGCACCGGCCACGCCCGGCACAGCAGCCACGCCGCTCGAACCA +CAGCAGGGGCTACTCGCCCTCCCAGGCCCTCTTCAGAGCTGGCCTGAGTTGAAGCTGCGT +TCCTCCTGCTCTGAGGGCTGGGTACCGGGGACCCTCGCCCAGCCGAGGCCGCTCTTGTCT +TCTTCTCTCTTCCGAC +>p:HG002_2_chr20:63770812-63771204 +TGTCCCCATTTCCTGCACGATGCGCCAGCCCACGGGGAGGTACACTCGACAGGACACCCT +AGAGACCACGCTAACAAGAGGCCCAGCCCTGGAAATGCTCATCGCCTGCAACCAGCACAT +GGAGATGGTCGCAAGTCAGCACCGGCCACGCCCGGCACAGCGGCCACGCCGCTCGAACCA +CAGCAGGGGCCACGTCAGCAGGAGGTCGCAAGTCAGGACCGGCCACGCCCGGCACAGCGG +CCACGCCGCTCGAACCACAGCAGGGGCCACGTCAGCAGGAGGTCGCAAGTCAGGACCGGC +CACGCCCGGCACAGCGGCCACGCCGCTCGAACCACAGCAGGGGCCACGTCAGCAGGAGGT +CGCAAGTCAGCACCGGCCACGCCCGGCACAGCAGCCACGCCGCTAGAACCACAGCAGGGG +CTACTCGCCCTCCCAGGCCCTCTTCAGAGCTGGCCTGAGTTGAAGCTGCGTTCCTCCTGC +TCTGAGGGCTGGGTACCGGGGACCCTCGCCCAGCCGAGGCCGCTCTTGTCTTCTTCTCTC +TTCCGAC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/haps.fa.ref.fa new file mode 100644 index 00000000..f897c55d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63770812-63771204 +TGTCCCCATTTCCTGCACGATGCGCCAGCCCACGGGGAGGTACACTCGACAGGACACCCTAGAGACCACGCTAACAAGAGGCCCAGCCCTGGAAATGCTCATCGCCTGCAACCAGCACATGGAGATGGTCGCAAGTCAGCACCGGCCACGCCCGGCACAGCAGCCACGCCGCTCGAACCACAGCAGGGGCCACGTCAGCAGGAGGTCGCAAGTCAGCACCGGCCACGCCCGGCACAGCAGCCACGCCGCTCGAACCACAGCAGGGGCTACTCGCCCTCCCAGGCCCTCTTCAGAGCTGGCCTGAGTTGAAGCTGCGTTCCTCCTGCTCTGAGGGCTGGGTACCGGGGACCCTCGCCCAGCCGAGGCCGCTCTTGTCTTCTTCTCTCTTCCGAC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/msa.fa new file mode 100644 index 00000000..94dd95ab --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/msa.fa @@ -0,0 +1,55 @@ +>ref_chr20_63770812_63771204 +tgtccccatttcctgcacgatgcgccagcccacggggaggtacactcgacaggacaccct +agagaccacgctaacaagaggcccagccctggaaatgctcatcgcctgcaaccagcacat +ggagatggtcgcaagtcagc---------------------------------------- +------------------------------------------------------------ +------------------------------------------------------accggc +cacgcccggcacagcagccacgccgctcgaaccacagcaggggccacgtcagcaggaggt +cgcaagtcagcaccggccacgcccggcacagcagccacgccgctcgaaccacagcagggg +ctactcgccctcccaggccctcttcagagctggcctgagttgaagctgcgttcctcctgc +tctgagggctgggtaccggggaccctcgcccagccgaggccgctcttgtcttcttctctc +ttccgac +>syndip_1_chr20:63770812-63771204 +tgtccccatttcctgcacgatgcgccagcccacggggaggtacactcgacaggacaccct +agagaccacgctaacaagaggcccagccctggaaatgctcatcgcctgcaaccagcacat +ggagatggtcgcaagtcagc---------------------------------------- +------------------------------------------------------------ +------------------------------------------------------accggc +cacgcccggcacagcagccacgccgctcgaaccacagcaggggccacgtcagcaggaggt +cgcaagtcagcaccggccacgcccggcacagcagccacgccgctcgaaccacagcagggg +ctactcgccctcccaggccctcttcagagctggcctgagttgaagctgcgttcctcctgc +tctgagggctgggtaccggggaccctcgcccagccgaggccgctcttgtcttcttctctc +ttccgac +>syndip_2_chr20:63770812-63771204 +tgtccccatttcctgcacgatgcgccagcccacggggaggtacactcgacaggacaccct +agagaccacgctaacaagaggcccagccctggaaatgctcatcgcctgcaaccagcacat +ggagatggtcgcaagtcagc---------------------------------------- +------------------------------------------------------------ +------------------------------------------------------accggc +cacgcccggcacagcagccacgccgctcgaaccacagcaggggccacgtcagcaggaggt +cgcaagtcagcaccggccacgcccggcacagcagccacgccgctcgaaccacagcagggg +ctactcgccctcccaggccctcttcagagctggcctgagttgaagctgcgttcctcctgc +tctgagggctgggtaccggggaccctcgcccagccgaggccgctcttgtcttcttctctc +ttccgac +>p:HG002_1_chr20:63770812-63771204 +tgtccccatttcctgcacgatgcgccagcccacggggaggtacactcgacaggacaccct +agagaccacgctaacaagaggcccagccctggaaatgctcatcgcctgcaaccagcacat +ggagat------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------------------------ggt +cgcaagtcagcaccggccacgcccggcacagcagccacgccgctcgaaccacagcagggg +ctactcgccctcccaggccctcttcagagctggcctgagttgaagctgcgttcctcctgc +tctgagggctgggtaccggggaccctcgcccagccgaggccgctcttgtcttcttctctc +ttccgac +>p:HG002_2_chr20:63770812-63771204 +tgtccccatttcctgcacgatgcgccagcccacggggaggtacactcgacaggacaccct +agagaccacgctaacaagaggcccagccctggaaatgctcatcgcctgcaaccagcacat +ggagatggtcgcaagtcagcaccggccacgcccggcacagcggccacgccgctcgaacca +cagcaggggccacgtcagcaggaggtcgcaagtcaggaccggccacgcccggcacagcgg +ccacgccgctcgaaccacagcaggggccacgtcagcaggaggtcgcaagtcaggaccggc +cacgcccggcacagcggccacgccgctcgaaccacagcaggggccacgtcagcaggaggt +cgcaagtcagcaccggccacgcccggcacagcagccacgccgctagaaccacagcagggg +ctactcgccctcccaggccctcttcagagctggcctgagttgaagctgcgttcctcctgc +tctgagggctgggtaccggggaccctcgcccagccgaggccgctcttgtcttcttctctc +ttccgac diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/msa.fa.fai new file mode 100644 index 00000000..9f211161 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63770812_63771204 547 29 60 61 +syndip_1_chr20:63770812-63771204 547 620 60 61 +syndip_2_chr20:63770812-63771204 547 1211 60 61 +p:HG002_1_chr20:63770812-63771204 547 1803 60 61 +p:HG002_2_chr20:63770812-63771204 547 2395 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/output.vcf.gz new file mode 100644 index 00000000..f49ccbc2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/output.vcf.gz.tbi new file mode 100644 index 00000000..95da086f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63770912-63771104/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63948514-63948759/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63948514-63948759/base.vcf.gz new file mode 100644 index 00000000..0efbf926 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63948514-63948759/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63948514-63948759/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63948514-63948759/base.vcf.gz.tbi new file mode 100644 index 00000000..ebea5a9e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63948514-63948759/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63948514-63948759/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63948514-63948759/comp.vcf.gz new file mode 100644 index 00000000..eab77c5f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63948514-63948759/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63948514-63948759/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63948514-63948759/comp.vcf.gz.tbi new file mode 100644 index 00000000..144f32ed Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63948514-63948759/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63948514-63948759/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63948514-63948759/haps.fa new file mode 100644 index 00000000..b57979ec --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63948514-63948759/haps.fa @@ -0,0 +1,162 @@ +>ref_chr20_63948414_63948859 +ACAGAACACAGGTGCGGACAGGGAACGGCATCCTCAGAGCATGGTCAGGGGAGAAAAGCAAGCTGGAAGGAGAGATGATTCCATCTGTATAAAATCCAGGAAACGAAGGACGCTCACCGCCATGCGCCTCGGTGTGAGGAGGGAGGCGTGTGTGAGAGGGAGGGGATGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGTGTGTGTGAGACCGAGGGGGCGTGTAAGGGAGGGGGTGTGTGTGAGAGGGAAGCGTGTGCACACACCAGCCCTAACCATGATCACTCTCTGGCCACCAAGATTTGGAACAGCAACTTCTGTCACATTTGAATGTTTTTAAAGCAGGTGCCACTTTGTTGCCATAAACCAAACCGTAGTCTGT +>syndip_1_chr20:63948414-63948859 +ACAGAACACAGGTGCGGACAGGGAACGGCATCCTCAGAGCATGGTCAGGGGAGAAAAGCA +AGCTGGAAGGAGAGATGATTCCATCTGTATAAAATCCAGGAAACGAAGGACGCTCACCGC +CATGCGCCTCGGTGTGAGGAGGGAGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGA +GGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGTGTGTGTGAGAGGGAGGGGC +GTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGCAGGGGGCGTGTGTGTGAGGGGCGTGTG +TGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGGGGGGGCGTGTGTGAGA +GGTAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGCGTGTGTGAGAGGGA +GGGGCGTGTGTGTGAGGGAGGGGCGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGCAGGGG +CGTGTGTGTGAGGGAGGGGCGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTG +TGAGGGGGGGCGTGTGTGAGAGGTAGGGGCGTGTGTGGGAGGGGGCGTGTGTGAGAGGGA +GGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGACGGAGGGGCGTGTGTGAGAGGGAGG +GGGCGTGTGTGAGAGGGAGAGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGC +GTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGAGGCGTGT +GTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGAGA +GGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAG +GGAGGGGCGTGTGTGAAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGAGAGGGAGGGG +CGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCG +TGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGT +GTGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGAGAGGGAGGGGGCGTGTGTGAG +AGGGAGAGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGAGGGA +GGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAG +AGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGCGTGTGTGAGAGGGAGAGGC +GTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGAGGCGTGTGTGAGAGGGAGGGGCGT +GTGTGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTG +TGAGAGGGAGAGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGA +GAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGA +GGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGG +GAGGGGCGTGTGTGAAGGGAGGGGCGTGTGTGAGAGTGGGGGCGTGTGTGAGTTAGGGGC +GTGAGAGGTAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGAGA +GGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGG +AGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAG +GGGCGTGTGTGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGAGAGGGAGGGGCGT +GTGTGAGAGGGAGGGGCGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTG +AGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGAGAGGGAGGGGGCGTGTGTGAGGGAG +GGGCGTGTGTGAGAGGGAGGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAG +GGGGTGTGTGTGAGACCGAGGGGGCGTGTAAGGGAGGGGGTGTGTGTGAGAGGGAAGCGT +GTGCACACACCAGCCCTAACCATGATCACTCTCTGGCCACCAAGATTTGGAACAGCAACT +TCTGTCACATTTGAATGTTTTTAAAGCAGGTGCCACTTTGTTGCCATAAACCAAACCGTA +GTCTGT +>syndip_2_chr20:63948414-63948859 +ACAGAACACAGGTGCGGACAGGGAACGGCATCCTCAGAGCATGGTCAGGGGAGAAAAGCA +AGCTGGAAGGAGAGATGATTCCATCTGTATAAAATCCAGGAAACGAAGGACGCTCACCGC +CATGCGCCTCGGTGTGAGGAGGGAGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGA +GGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGTGTGTGTGAGAGGGAGGGG +CGTGTGTGAGAGGGAGGGGGCGTGTGTGAAAGGGAGGGGCGTGTGTGAGGGAGGGGCGTG +TGTGAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGAGGGAGGGGGCGTGTGTG +AGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGAGAGTGGGGGCGTGTGTGAGGG +GGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGTAGGGGCGTGTGTGAGAGGGAGG +GGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGGGGGGGGCGTGT +GTGAGGGGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGAGAGGGAGGGGCGTGTGTGAGA +GGGAGGGGGCGTGTGTGTGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAAGGG +AGGGGTGTGTGTGAGAGTGGGGGCGTGTGTGAGAGGGGCGTGAGAGGTAGGGGCGTGTGT +GAGAGGGAGGGGTGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAG +GGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGCGTGTGTGAGAGGGA +GGGGCGTGTGTGAGAGTGGGGGCGTGTGTGGGGGGGCGTGTGTGAGGGGGGGCGTGTGTG +AGAGGTAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGCGTGTGTGAGAGG +CAGGGGCGTGTGTGGGGGGGGGCGTGTGTGAGGGGGGGGCGTGTGTGAGAGGGAGGGGGC +GTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTG +TGTGAGAGGCAGGGGCGTGTGTGGGGGGGGCGTGTGTGAGGGGGGCGTGTGAGAGGGAGG +GGCGTGTGTGGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGT +GTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAAGGGAGGGGTGTGTGT +GAGAGTGGGGGCGTGTGTGAGAGTTAGGGGCGTGAGAGGTAGGGGCGTGTGTGAGAGGGA +GGGGCGTGTGTGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGG +CGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGCGTG +TGCGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGGGAGGGGGCGTGTGT +GAGAGGGAGGGGCGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGTGA +GGGAGGGGCGTGAGAGGGAGGGGCGTGTGTGAGGGGGGGCGTGTGTGAGAGGTAGGGGCG +TGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGT +GTGTGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGT +GAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTG +AAGGGAGGGGCGTGTGTGAGAGTGGGGGCGTGTGTGAGAGGGGCGTGAGAGGTAGGGGCG +TGTGTGAGAGGGAGGGGGCGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTG +AGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGAGA +GGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAAGGGGCGTGTGAGAGGG +AGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGG +GGGTGTGTGTGAGACCGAGGGGGCGTGTAAGGGAGGGGGTGTGTGTGAGAGGGAAGCGTG +TGCACACACCAGCCCTAACCATGATCACTCTCTGGCCACCAAGATTTGGAACAGCAACTT +CTGTCACATTTGAATGTTTTTAAAGCAGGTGCCACTTTGTTGCCATAAACCAAACCGTAG +TCTGT +>p:HG002_1_chr20:63948414-63948859 +ACAGAACACAGGTGCGGACAGGGAACGGCATCCTCAGAGCATGGTCAGGGGAGAAAAGCA +AGCTGGAAGGAGAGATGATTCCATCTGTATAAAATCCAGGAAACGAAGGACGCTCACCGC +CATGCGCCTCGGTGTGAGGAGGGAGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGA +GGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGTGTGTGTGAGAGGGAGGGG +CGTGTGTGAGAGGGAGGGGGCGTGTGTGAAAGGGAGGGGCGTGTGTGAGGGAGGGGCGTG +TGTGAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGAGGGAGGGGGCGTGTGTG +AGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGAGAGTGGGGGCGTGTGTGAGGG +GGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGTAGGGGCGTGTGTGAGAGGGAGG +GGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGGGGGGGGCGTGT +GTGAGGGGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGAGAGGGAGGGGCGTGTGTGAGA +GGGAGGGGGCGTGTGTGTGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAAGGG +AGGGGTGTGTGTGAGAGTGGGGGCGTGTGTGAGAGGGGCGTGAGAGGTAGGGGCGTGTGT +GAGAGGGAGGGGTGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAG +GGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGCGTGTGTGAGAGGGA +GGGGCGTGTGTGAGAGTGGGGGCGTGTGTGGGGGGGCGTGTGTGAGGGGGGGCGTGTGTG +AGAGGTAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGCGTGTGTGAGAGG +CAGGGGCGTGTGTGGGGGGGGGCGTGTGTGAGGGGGGGGCGTGTGTGAGAGGGAGGGGGC +GTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTG +TGTGAGAGGCAGGGGCGTGTGTGGGGGGGGCGTGTGTGAGGGGGGCGTGTGAGAGGGAGG +GGCGTGTGTGGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGT +GTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAAGGGAGGGGTGTGTGT +GAGAGTGGGGGCGTGTGTGAGAGTTAGGGGCGTGAGAGGTAGGGGCGTGTGTGAGAGGGA +GGGGCGTGTGTGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGG +CGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGCGTG +TGCGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGGGAGGGGGCGTGTGT +GAGAGGGAGGGGCGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGTGA +GGGAGGGGCGTGAGAGGGAGGGGCGTGTGTGAGGGGGGGCGTGTGTGAGAGGTAGGGGCG +TGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGT +GTGTGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGT +GAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTG +AAGGGAGGGGCGTGTGTGAGAGTGGGGGCGTGTGTGAGAGGGGCGTGAGAGGTAGGGGCG +TGTGTGAGAGGGAGGGGGCGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTG +AGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGAGA +GGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAAGGGGCGTGTGAGAGGG +AGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGG +GGGTGTGTGTGAGACCGAGGGGGCGTGTAAGGGAGGGGGTGTGTGTGAGAGGGAAGCGTG +TGCACACACCAGCCCTAACCATGATCACTCTCTGGCCACCAAGATTTGGAACAGCAACTT +CTGTCACATTTGAATGTTTTTAAAGCAGGTGCCACTTTGTTGCCATAAACCAAACCGTAG +TCTGT +>p:HG002_2_chr20:63948414-63948859 +ACAGAACACAGGTGCGGACAGGGAACGGCATCCTCAGAGCATGGTCAGGGGAGAAAAGCA +AGCTGGAAGGAGAGATGATTCCATCTGTATAAAATCCAGGAAACGAAGGACGCTCACCGC +CATGCGCCTCGGTGTGAGGAGGGAGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGA +GGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGTGTGTGTGAGAGGGAGGGGC +GTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGCAGGGGGCGTGTGTGTGAGGGGCGTGTG +TGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGGGGGGGCGTGTGTGAGA +GGTAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGCGTGTGTGAGAGGGA +GGGGCGTGTGTGTGAGGGAGGGGCGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGCAGGGG +CGTGTGTGTGAGGGAGGGGCGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTG +TGAGGGGGGGCGTGTGTGAGAGGTAGGGGCGTGTGTGGGAGGGGGCGTGTGTGAGAGGGA +GGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGACGGAGGGGCGTGTGTGAGAGGGAGG +GGGCGTGTGTGAGAGGGAGAGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGC +GTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGAGGCGTGT +GTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGAGA +GGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAG +GGAGGGGCGTGTGTGAAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGAGAGGGAGGGG +CGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCG +TGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGT +GTGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGAGAGGGAGGGGGCGTGTGTGAG +AGGGAGAGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGAGGGA +GGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAG +AGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGCGTGTGTGAGAGGGAGAGGC +GTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGAGGCGTGTGTGAGAGGGAGGGGCGT +GTGTGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTG +TGAGAGGGAGAGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGA +GAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGA +GGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGG +GAGGGGCGTGTGTGAAGGGAGGGGCGTGTGTGAGAGTGGGGGCGTGTGTGAGTTAGGGGC +GTGAGAGGTAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGAGA +GGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGG +AGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAG +GGGCGTGTGTGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGAGAGGGAGGGGCGT +GTGTGAGAGGGAGGGGCGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTG +AGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGAGAGGGAGGGGGCGTGTGTGAGGGAG +GGGCGTGTGTGAGAGGGAGGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAG +GGGGTGTGTGTGAGACCGAGGGGGCGTGTAAGGGAGGGGGTGTGTGTGAGAGGGAAGCGT +GTGCACACACCAGCCCTAACCATGATCACTCTCTGGCCACCAAGATTTGGAACAGCAACT +TCTGTCACATTTGAATGTTTTTAAAGCAGGTGCCACTTTGTTGCCATAAACCAAACCGTA +GTCTGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63948514-63948759/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63948514-63948759/haps.fa.ref.fa new file mode 100644 index 00000000..2636ea7d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63948514-63948759/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63948414-63948859 +ACAGAACACAGGTGCGGACAGGGAACGGCATCCTCAGAGCATGGTCAGGGGAGAAAAGCAAGCTGGAAGGAGAGATGATTCCATCTGTATAAAATCCAGGAAACGAAGGACGCTCACCGCCATGCGCCTCGGTGTGAGGAGGGAGGCGTGTGTGAGAGGGAGGGGATGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGTGTGTGTGAGACCGAGGGGGCGTGTAAGGGAGGGGGTGTGTGTGAGAGGGAAGCGTGTGCACACACCAGCCCTAACCATGATCACTCTCTGGCCACCAAGATTTGGAACAGCAACTTCTGTCACATTTGAATGTTTTTAAAGCAGGTGCCACTTTGTTGCCATAAACCAAACCGTAGTCTGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63948514-63948759/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63948514-63948759/msa.fa new file mode 100644 index 00000000..c2c10901 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63948514-63948759/msa.fa @@ -0,0 +1,205 @@ +>ref_chr20_63948414_63948859 +acagaacacaggtgcggacagggaacggcatcctcagagcatggtcaggggagaaaagca +agctggaaggagagatgattccatctgtataaaatccaggaaacgaaggacgctcaccgc +catgcgcctcg------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--gtgtgaggagggaggcgtgtgtgagagggaggggatgtgt---------------gtg +agagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaaggggcgtgtgtga +ga---gggaggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgtaa +gggagggggtgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcactc +tctggccaccaagatttggaacagcaacttctgtcacatttgaatgtttttaaagcaggt +gccactttgttgccataaaccaaaccgtagtctgt +>syndip_1_chr20:63948414-63948859 +acagaacacaggtgcggacagggaacggcatcctcagagcatggtcaggggagaaaagca +agctggaaggagagatgattccatctgtataaaatccaggaaacgaaggacgctcaccgc +catgcgcctcggtgtgaggagggaggcgtgtgtgagagggaggggcgtgtgtgagaggga +-ggggcgtgtgtgagagggaggggcgtgtgtgagggaggggtgtgtgtgagagggagggg +cgtgtgtgagagggagggggcgtgtgtgagaggcagggg-gcgtgtgtgtgaggggcgtg +tgtgagagggaggggcgtgtgtgagagggagggg-gcgtgtgtgagggggggcgtgtgtg +agaggtaggggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagag +gg-----------------aggggcgtgtgtgtgagggaggggcgtgtgagag-ggaggg +ggcgtgtgtgagaggcaggggcgtgtgtgtgagggaggggcgtgagagggaggggcgtgt 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+CCTGGCCTGCTTGGGTGGAATTGGGCAGGTGTCCAGGCTGTCCGCAGCCCTGCAGGGAGCAGGTGAGGTGAGGGCCAGGAGGGCCTAACTGTGGGCCCCATTACCCCCAGGCCGTGGCCGAGGAGCACCCTGACCTGGAACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACAAGCCCCCATACCTTTTCTTACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGAACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCCAACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCTGTGGCACGAGGTGCTTTGTTCTCCGACCTGGTCAGCAGCACCATTTTGCAGGGCGGTGTGTGTCTGCTGATAGCAATGGGCCTGCTGACTGTCACCGGCTTGCTGACCACAATGGGCCTGCTGACTGTCACTGGCTTGGTGACCGGCACGGGTTTCGTAACTGTCACAAGCTTTGTTACCGTAATGGGTTTGGTGACAGGTACGGGTTTGGTGACCGGCACAGACTTGGTGACTGTGATGGGTTTGGTGACCGGCATGGCCTTGGTGACGGGCATGGGCCTGCTGACTGTGACAGGTTTGGTGACTGGCACGGGCCTAGTGACCGGGATGGCCTTGGTGACTGGCATGGGTCTGCCGACCGAGACTGGCTTGCTGATGCCAATGGGTTTGCTGACACCCACAGGTTTGCCAATAGTGACAGGTTTGCTCACTCCGATGGGCTTGCTGACCCCAACAGGCCGGCTGATGGTGACCGGCCTGCTGATGGGCCCAGGCTTGGAGGCAGGCAGGGGTCGGTCCATGTGGTTCCAGATCCGGTGTTTCTCCAGCTGGGT +>syndip_1_chr20:63964668-63966718 +CCTGGCCTGCTTGGGTGGAATTGGGCAGGTGTCCAGGCTGTCCGCAGCCCTGCAGGGAGC +AGGTGAGGTGAGGGCCAGGAGGGCCTAACTGTGGGCCCCATTACCCCCAGGCCGTGGCCG +AGGAGCACCCTGACCTGGAACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTG +GGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCAT +ACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTG +TTCCTCCCTGTGGCACGAGGTGCTTTGTTCTCCGACCTGGTCAGCAGCACCATTTTGCAG +GGCGGTGTGTGTCTGCTGATAGCAATGGGCCTGCTGACTGTCACCGGCTTGCTGACCACA +ATGGGCCTGCTGACTGTCACTGGCTTGGTGACCGGCACGGGTTTCGTAACTGTCACAAGC +TTTGTTACCGTAATGGGTTTGGTGACAGGTACGGGTTTGGTGACCGGCACAGACTTGGTG +ACTGTGATGGGTTTGGTGACCGGCATGGCCTTGGTGACGGGCATGGGCCTGCTGACTGTG +ACAGGTTTGGTGACTGGCACGGGCCTAGTGACCGGGATGGCCTTGGTGACTGGCATGGGT +CTGCCGACCGAGACTGGCTTGCTGATGCCAATGGGTTTGCTGACACCCACAGGTTTGCCA +ATAGTGACAGGTTTGCTCACTCCGATGGGCTTGCTGACCCCAACAGGCCGGCTGATGGTG +ACCGGCCTGCTGATGGGCCCAGGCTTGGAGGCAGGCAGGGGTCGGTCCATGTGGTTCCAG +ATCCGGTGTTTCTCCAGCTGGGT +>syndip_2_chr20:63964668-63966718 +CCTGGCCTGCTTGGGTGGAATTGGGCAGGTGTCCAGGCTGTCCGCAGCCCTGCAGGGAGC +AGGTGAGGTGAGGGCCAGGAGGGCCTAACTGTGGGCCCCATTACCCCCAGGCCGTGGCCG +AGGAGCACCCTGACCTGGAACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTG +GGACAAGCCCCCATACCTTTTCTTACCACTGTTCCCTGACCTGGGACGAGCCCCCATACC +TTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTC +CCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGC +CCCCATACCTTTTCTCACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTC +TCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGA +CCTGGAACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCA +TACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACT +GTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGAC +GAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTT +CTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCG +ACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCCCGACCTGGGACGAGCCCCC +ATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTAC +CACTGTTCCTCCCCAACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCC +GACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCC +CATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTA +CCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCC +CGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCCCGACCTGGGACGAGCCC +CCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTTACC +ACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCCGACC +TGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATA +CCTTTTCTTACCACTGTTCCTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTTACCAC +TGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCTGTG +GCACGAGGTGCTTTGTTCTCCGACCTGGTCAGCAGCACCATTTTGCAGGGCGGTGTGTGT +CTGCTGATAGCAATGGGCCTGCTGACTGTCACCGGCTTGCTGACCACAATGGGCCTGCTG +ACTGTCACTGGCTTGGTGACCGGCACGGGTTTCGTAACTGTCACAAGCTTTGTTACCGTA +ATGGGTTTGGTGACAGGTACGGGTTTGGTGACCGGCACAGACTTGGTGACTGTGATGGGT +TTGGTGACCGGCATGGCCTTGGTGACGGGCATGGGCCTGCTGACTGTGACAGGTTTGGTG +ACTGGCACGGGCCTAGTGACCGGGATGGCCTTGGTGACTGGCATGGGTCTGCCGACCGAG +ACTGGCTTGCTGATGCCAATGGGTTTGCTGACACCCACAGGTTTGCCAATAGTGACAGGT +TTGCTCACTCCGATGGGCTTGCTGACCCCAACAGGCCGGCTGATGGTGACCGGCCTGCTG +ATGGGCCCAGGCTTGGAGGCAGGCAGGGGTCGGTCCATGTGGTTCCAGATCCGGTGTTTC +TCCAGCTGGGT +>p:HG002_1_chr20:63964668-63966718 +CCTGGCCTGCTTGGGTGGAATTGGGCAGGTGTCCAGGCTGTCCGCAGCCCTGCAGGGAGC +AGGTGAGGTGAGGGCCAGGAGGGCCTAACTGTGGGCCCCATTACCCCCAGGCCGTGGCCG +AGGAGCACCCTGACCTGGAACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTG +GGACAAGCCCCCATACCTTTTCTTACCACTGTTCCCTGACCTGGGACGAGCCCCCATACC +TTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTC +CCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGC +CCCCATACCTTTTCTCACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTC +TCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGA +CCTGGAACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCA +TACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACT +GTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGAC +GAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTT +CTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCG +ACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCCCGACCTGGGACGAGCCCCC +ATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTAC +CACTGTTCCTCCCCAACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCC +GACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCC +CATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTA +CCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCC +CGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCCCGACCTGGGACGAGCCC +CCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTTACC +ACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCCGACC +TGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATA +CCTTTTCTTACCACTGTTCCTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTTACCAC +TGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCTGTG +GCACGAGGTGCTTTGTTCTCCGACCTGGTCAGCAGCACCATTTTGCAGGGCGGTGTGTGT +CTGCTGATAGCAATGGGCCTGCTGACTGTCACCGGCTTGCTGACCACAATGGGCCTGCTG +ACTGTCACTGGCTTGGTGACCGGCACGGGTTTCGTAACTGTCACAAGCTTTGTTACCGTA +ATGGGTTTGGTGACAGGTACGGGTTTGGTGACCGGCACAGACTTGGTGACTGTGATGGGT +TTGGTGACCGGCATGGCCTTGGTGACGGGCATGGGCCTGCTGACTGTGACAGGTTTGGTG +ACTGGCACGGGCCTAGTGACCGGGATGGCCTTGGTGACTGGCATGGGTCTGCCGACCGAG +ACTGGCTTGCTGATGCCAATGGGTTTGCTGACACCCACAGGTTTGCCAATAGTGACAGGT +TTGCTCACTCCGATGGGCTTGCTGACCCCAACAGGCCGGCTGATGGTGACCGGCCTGCTG +ATGGGCCCAGGCTTGGAGGCAGGCAGGGGTCGGTCCATGTGGTTCCAGATCCGGTGTTTC +TCCAGCTGGGT +>p:HG002_2_chr20:63964668-63966718 +CCTGGCCTGCTTGGGTGGAATTGGGCAGGTGTCCAGGCTGTCCGCAGCCCTGCAGGGAGC +AGGTGAGGTGAGGGCCAGGAGGGCCTAACTGTGGGCCCCATTACCCCCAGGCCGTGGCCG +AGGAGCACCCTGACCTGGAACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTG +GGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCAT +ACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTG +TTCCTCCCTGTGGCACGAGGTGCTTTGTTCTCCGACCTGGTCAGCAGCACCATTTTGCAG +GGCGGTGTGTGTCTGCTGATAGCAATGGGCCTGCTGACTGTCACCGGCTTGCTGACCACA +ATGGGCCTGCTGACTGTCACTGGCTTGGTGACCGGCACGGGTTTCGTAACTGTCACAAGC +TTTGTGACCGTAATGGGTTTGGTGACAGGTACGGGTTTGGTGACCGGCACAGACTTGGTG +ACTGTGATGGGTTTGGTGACCGGCATGGCCTTGGTGACGGGCATGGGCCTGCTGACTGTG +ACAGGTTTGGTGACTGGCACGGGCCTAGTGACCGGGATGGCCTTGGTGACTGGCATGGGT +CTGCCGACCGAGACTGGCTTGCTGATGCCAATGGGTTTGCTGACACCCACAGGTTTGCCA +ATAGTGACAGGTTTGCTCACTCCGATGGGCTTGCTGACCCCAACAGGCCGGCTGATGGTG +ACCGGCCTGCTGATGGGCCCAGGCTTGGAGGCAGGCAGGGGTCGGTCCATGTGGTTCCAG +ATCCGGTGTTTCTCCAGCTGGGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63964768-63966618/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63964768-63966618/haps.fa.ref.fa new file mode 100644 index 00000000..16bd4f6b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63964768-63966618/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63964668-63966718 +CCTGGCCTGCTTGGGTGGAATTGGGCAGGTGTCCAGGCTGTCCGCAGCCCTGCAGGGAGCAGGTGAGGTGAGGGCCAGGAGGGCCTAACTGTGGGCCCCATTACCCCCAGGCCGTGGCCGAGGAGCACCCTGACCTGGAACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACAAGCCCCCATACCTTTTCTTACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGAACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCCAACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCTGTGGCACGAGGTGCTTTGTTCTCCGACCTGGTCAGCAGCACCATTTTGCAGGGCGGTGTGTGTCTGCTGATAGCAATGGGCCTGCTGACTGTCACCGGCTTGCTGACCACAATGGGCCTGCTGACTGTCACTGGCTTGGTGACCGGCACGGGTTTCGTAACTGTCACAAGCTTTGTTACCGTAATGGGTTTGGTGACAGGTACGGGTTTGGTGACCGGCACAGACTTGGTGACTGTGATGGGTTTGGTGACCGGCATGGCCTTGGTGACGGGCATGGGCCTGCTGACTGTGACAGGTTTGGTGACTGGCACGGGCCTAGTGACCGGGATGGCCTTGGTGACTGGCATGGGTCTGCCGACCGAGACTGGCTTGCTGATGCCAATGGGTTTGCTGACACCCACAGGTTTGCCAATAGTGACAGGTTTGCTCACTCCGATGGGCTTGCTGACCCCAACAGGCCGGCTGATGGTGACCGGCCTGCTGATGGGCCCAGGCTTGGAGGCAGGCAGGGGTCGGTCCATGTGGTTCCAGATCCGGTGTTTCTCCAGCTGGGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63964768-63966618/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63964768-63966618/msa.fa new file mode 100644 index 00000000..b5374e1a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63964768-63966618/msa.fa @@ -0,0 +1,180 @@ +>ref_chr20_63964668_63966718 +cctggcctgcttgggtggaattgggcaggtgtccaggctgtccgcagccctgcagggagc +aggtgaggtgagggccaggagggcctaactgtgggccccattacccccaggccgtggccg +aggagcaccctgacctggaacgagcccccataccttttctcaccactgttccccgacctg +ggacaagcccccataccttttcttaccactgttccctgacctgggacgagcccccatacc +ttttctcaccactgttccctgacctgggacgagcccccataccttttctcaccactgttc +cccgacctgggacgagcccccataccttttctcaccactgttccctgacctgggacgagc +ccccataccttttctcaccactgttcctccccgacctgggacgagcccccataccttttc +tcaccactgttccccgacctgggacgagcccccataccttttctcaccactgttccctga +cctggaacgagcccccataccttttctcaccactgttccccgacctgggacgagccccca +taccttttctcaccactgttccccgacctgggacgagcccccataccttttctcaccact +gttccccgacctgggacgagcccccataccttttctcaccactgttccccgacctgggac +gagcccccataccttttctcaccactgttccccgacctgggacgagcccccatacctttt +ctcaccactgttccctgacctgggacgagcccccataccttttctcaccactgttccccg +acctgggacgagcccccataccttttcttaccactgttccccgacctgggacgagccccc +ataccttttcttaccactgttcctccccgacctgggacgagcccccataccttttctcac +cactgttcctccccaacctgggacgagcccccataccttttctcaccactgttcctcccc +gacctgggacgagcccccataccttttctcaccactgttccctgacctgggacgagcccc +cataccttttcttaccactgttcctccccgacctgggacgagcccccataccttttctta +ccactgttcctccccgacctgggacgagcccccataccttttcttaccactgttcctccc +cgacctgggacgagcccccataccttttcttaccactgttccccgacctgggacgagccc +ccataccttttctcaccactgttccctgacctgggacgagcccccataccttttcttacc +actgttccctgacctgggacgagcccccataccttttctcaccactgttcctccccgacc +tgggacgagcccccataccttttctcaccactgttccccgacctgggacgagcccccata +ccttttcttaccactgttcctccctgacctgggacgagcccccataccttttcttaccac +tgttcctccccgacctgggacgagcccccataccttttcttaccactgttcctccctgtg +gcacgaggtgctttgttctccgacctggtcagcagcaccattttgcagggcggtgtgtgt +ctgctgatagcaatgggcctgctgactgtcaccggcttgctgaccacaatgggcctgctg +actgtcactggcttggtgaccggcacgggtttcgtaactgtcacaagctttgttaccgta +atgggtttggtgacaggtacgggtttggtgaccggcacagacttggtgactgtgatgggt +ttggtgaccggcatggccttggtgacgggcatgggcctgctgactgtgacaggtttggtg +actggcacgggcctagtgaccgggatggccttggtgactggcatgggtctgccgaccgag +actggcttgctgatgccaatgggtttgctgacacccacaggtttgccaatagtgacaggt +ttgctcactccgatgggcttgctgaccccaacaggccggctgatggtgaccggcctgctg +atgggcccaggcttggaggcaggcaggggtcggtccatgtggttccagatccggtgtttc +tccagctgggt +>syndip_1_chr20:63964668-63966718 +cctggcctgcttgggtggaattgggcaggtgtccaggctgtccgcagccctgcagggagc +aggtgaggtgagggccaggagggcctaactgtgggccccattacccccaggccgtggccg +aggag------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------------------caccctgacc +tggaacgagcccccataccttttctcaccactgttccctgacctgggacgagcccccata +ccttttctcaccactgttcctccccgacctgggacgagcccccataccttttctcaccac +tgt---tccctgacctgggacgagcccccataccttttcttaccactgttcctccctgtg +gcacgaggtgctttgttctccgacctggtcagcagcaccattttgcagggcggtgtgtgt +ctgctgatagcaatgggcctgctgactgtcaccggcttgctgaccacaatgggcctgctg +actgtcactggcttggtgaccggcacgggtttcgtaactgtcacaagctttgttaccgta +atgggtttggtgacaggtacgggtttggtgaccggcacagacttggtgactgtgatgggt +ttggtgaccggcatggccttggtgacgggcatgggcctgctgactgtgacaggtttggtg +actggcacgggcctagtgaccgggatggccttggtgactggcatgggtctgccgaccgag +actggcttgctgatgccaatgggtttgctgacacccacaggtttgccaatagtgacaggt +ttgctcactccgatgggcttgctgaccccaacaggccggctgatggtgaccggcctgctg +atgggcccaggcttggaggcaggcaggggtcggtccatgtggttccagatccggtgtttc +tccagctgggt +>syndip_2_chr20:63964668-63966718 +cctggcctgcttgggtggaattgggcaggtgtccaggctgtccgcagccctgcagggagc +aggtgaggtgagggccaggagggcctaactgtgggccccattacccccaggccgtggccg +aggagcaccctgacctggaacgagcccccataccttttctcaccactgttccccgacctg +ggacaagcccccataccttttcttaccactgttccctgacctgggacgagcccccatacc +ttttctcaccactgttccctgacctgggacgagcccccataccttttctcaccactgttc +cccgacctgggacgagcccccataccttttctcaccactgttccctgacctgggacgagc +ccccataccttttctcaccactgttcctccccgacctgggacgagcccccataccttttc +tcaccactgttccccgacctgggacgagcccccataccttttctcaccactgttccctga +cctggaacgagcccccataccttttctcaccactgttccccgacctgggacgagccccca +taccttttctcaccactgttccccgacctgggacgagcccccataccttttctcaccact +gttccccgacctgggacgagcccccataccttttctcaccactgttccccgacctgggac +gagcccccataccttttctcaccactgttccccgacctgggacgagcccccatacctttt +ctcaccactgttccctgacctgggacgagcccccataccttttctcaccactgttccccg +acctgggacgagcccccataccttttcttaccactgttccccgacctgggacgagccccc +ataccttttcttaccactgttcctccccgacctgggacgagcccccataccttttcttac +cactgttcctccccaacctgggacgagcccccataccttttctcaccactgttcctcccc +gacctgggacgagcccccataccttttctcaccactgttccctgacctgggacgagcccc +cataccttttcttaccactgttcctccccgacctgggacgagcccccataccttttctta +ccactgttcctccccgacctgggacgagcccccataccttttcttaccactgttcctccc +cgacctgggacgagcccccataccttttcttaccactgttccccgacctgggacgagccc +ccataccttttctcaccactgttccctgacctgggacgagcccccataccttttcttacc +actgttccctgacctgggacgagcccccataccttttctcaccactgttcctccccgacc +tgggacgagcccccataccttttctcaccactgttccccgacctgggacgagcccccata +ccttttcttaccactgttcctccctgacctgggacgagcccccataccttttcttaccac +tgttcctccccgacctgggacgagcccccataccttttcttaccactgttcctccctgtg +gcacgaggtgctttgttctccgacctggtcagcagcaccattttgcagggcggtgtgtgt +ctgctgatagcaatgggcctgctgactgtcaccggcttgctgaccacaatgggcctgctg +actgtcactggcttggtgaccggcacgggtttcgtaactgtcacaagctttgttaccgta +atgggtttggtgacaggtacgggtttggtgaccggcacagacttggtgactgtgatgggt +ttggtgaccggcatggccttggtgacgggcatgggcctgctgactgtgacaggtttggtg +actggcacgggcctagtgaccgggatggccttggtgactggcatgggtctgccgaccgag +actggcttgctgatgccaatgggtttgctgacacccacaggtttgccaatagtgacaggt +ttgctcactccgatgggcttgctgaccccaacaggccggctgatggtgaccggcctgctg +atgggcccaggcttggaggcaggcaggggtcggtccatgtggttccagatccggtgtttc +tccagctgggt +>p:HG002_1_chr20:63964668-63966718 +cctggcctgcttgggtggaattgggcaggtgtccaggctgtccgcagccctgcagggagc +aggtgaggtgagggccaggagggcctaactgtgggccccattacccccaggccgtggccg +aggagcaccctgacctggaacgagcccccataccttttctcaccactgttccccgacctg +ggacaagcccccataccttttcttaccactgttccctgacctgggacgagcccccatacc +ttttctcaccactgttccctgacctgggacgagcccccataccttttctcaccactgttc +cccgacctgggacgagcccccataccttttctcaccactgttccctgacctgggacgagc +ccccataccttttctcaccactgttcctccccgacctgggacgagcccccataccttttc +tcaccactgttccccgacctgggacgagcccccataccttttctcaccactgttccctga +cctggaacgagcccccataccttttctcaccactgttccccgacctgggacgagccccca +taccttttctcaccactgttccccgacctgggacgagcccccataccttttctcaccact +gttccccgacctgggacgagcccccataccttttctcaccactgttccccgacctgggac +gagcccccataccttttctcaccactgttccccgacctgggacgagcccccatacctttt +ctcaccactgttccctgacctgggacgagcccccataccttttctcaccactgttccccg +acctgggacgagcccccataccttttcttaccactgttccccgacctgggacgagccccc +ataccttttcttaccactgttcctccccgacctgggacgagcccccataccttttcttac +cactgttcctccccaacctgggacgagcccccataccttttctcaccactgttcctcccc +gacctgggacgagcccccataccttttctcaccactgttccctgacctgggacgagcccc +cataccttttcttaccactgttcctccccgacctgggacgagcccccataccttttctta +ccactgttcctccccgacctgggacgagcccccataccttttcttaccactgttcctccc +cgacctgggacgagcccccataccttttcttaccactgttccccgacctgggacgagccc +ccataccttttctcaccactgttccctgacctgggacgagcccccataccttttcttacc +actgttccctgacctgggacgagcccccataccttttctcaccactgttcctccccgacc +tgggacgagcccccataccttttctcaccactgttccccgacctgggacgagcccccata +ccttttcttaccactgttcctccctgacctgggacgagcccccataccttttcttaccac +tgttcctccccgacctgggacgagcccccataccttttcttaccactgttcctccctgtg +gcacgaggtgctttgttctccgacctggtcagcagcaccattttgcagggcggtgtgtgt +ctgctgatagcaatgggcctgctgactgtcaccggcttgctgaccacaatgggcctgctg +actgtcactggcttggtgaccggcacgggtttcgtaactgtcacaagctttgttaccgta +atgggtttggtgacaggtacgggtttggtgaccggcacagacttggtgactgtgatgggt +ttggtgaccggcatggccttggtgacgggcatgggcctgctgactgtgacaggtttggtg +actggcacgggcctagtgaccgggatggccttggtgactggcatgggtctgccgaccgag +actggcttgctgatgccaatgggtttgctgacacccacaggtttgccaatagtgacaggt +ttgctcactccgatgggcttgctgaccccaacaggccggctgatggtgaccggcctgctg +atgggcccaggcttggaggcaggcaggggtcggtccatgtggttccagatccggtgtttc +tccagctgggt +>p:HG002_2_chr20:63964668-63966718 +cctggcctgcttgggtggaattgggcaggtgtccaggctgtccgcagccctgcagggagc +aggtgaggtgagggccaggagggcctaactgtgggccccattacccccaggccgtggccg +aggag------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------------------caccctgacc +tggaacgagcccccataccttttctcaccactgttccctgacctgggacgagcccccata +ccttttctcaccactgttcctccccgacctgggacgagcccccataccttttctcaccac +tgt---tccctgacctgggacgagcccccataccttttcttaccactgttcctccctgtg +gcacgaggtgctttgttctccgacctggtcagcagcaccattttgcagggcggtgtgtgt +ctgctgatagcaatgggcctgctgactgtcaccggcttgctgaccacaatgggcctgctg +actgtcactggcttggtgaccggcacgggtttcgtaactgtcacaagctttgtgaccgta +atgggtttggtgacaggtacgggtttggtgaccggcacagacttggtgactgtgatgggt +ttggtgaccggcatggccttggtgacgggcatgggcctgctgactgtgacaggtttggtg +actggcacgggcctagtgaccgggatggccttggtgactggcatgggtctgccgaccgag +actggcttgctgatgccaatgggtttgctgacacccacaggtttgccaatagtgacaggt +ttgctcactccgatgggcttgctgaccccaacaggccggctgatggtgaccggcctgctg +atgggcccaggcttggaggcaggcaggggtcggtccatgtggttccagatccggtgtttc +tccagctgggt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63964768-63966618/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63964768-63966618/msa.fa.fai new file mode 100644 index 00000000..c1cd88c9 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63964768-63966618/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63964668_63966718 2051 29 60 61 +syndip_1_chr20:63964668-63966718 2051 2149 60 61 +syndip_2_chr20:63964668-63966718 2051 4269 60 61 +p:HG002_1_chr20:63964668-63966718 2051 6390 60 61 +p:HG002_2_chr20:63964668-63966718 2051 8511 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63964768-63966618/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63964768-63966618/output.vcf.gz new file mode 100644 index 00000000..1bf2cdb5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63964768-63966618/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63964768-63966618/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63964768-63966618/output.vcf.gz.tbi new file mode 100644 index 00000000..74315506 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:63964768-63966618/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/base.vcf.gz new file mode 100644 index 00000000..b7a5d37c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/base.vcf.gz.tbi new file mode 100644 index 00000000..bb297398 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/comp.vcf.gz new file mode 100644 index 00000000..1b282c23 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/comp.vcf.gz.tbi new file mode 100644 index 00000000..a8e924ea Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/haps.fa new file mode 100644 index 00000000..097dac20 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/haps.fa @@ -0,0 +1,31 @@ +>ref_chr20_64065753_64066112 +TGGAACAGTCCAGGCGAGGGGTGCTGGCCTGCTTGGGGGCAACTCAGAGGCCTGGAGGATAGATGAGGAGGGGGGCTGTGGGCCTTGTAGGTGTTGGCTGTGGCCGTGCCTGGAGTGGAGGGACCCTTGAAAGTTTGGCCTCAGCTCGGGACACTGATGTTCCCGGGTTGGCCCTTCATGAGAGTTTGGCCTCAGCTCGGGACACTGATGTTCCTGGGTTGGCCCTTCACAGCTGGTGGGCGGGGGGTGCTTTGGGGAGAGGCTGCCCTGCGCATCAGGGCATCAAGACACAGGGGAGTGAATGAACCTGGGGCTGCAGTTTCACCTGGGTGTGGCCCTGGCTGCTGGGGAGGGGCCGTG +>syndip_1_chr20:64065753-64066112 +TGGAACAGTCCAGGCGAGGGGTGCTGGCCTGCTTGGGGGCAACTCAGAGGCCTGGAGGAT +AGATGAGGAGGGGGGCTGTGGGCCTTGTAGGTGTTGGCTGTGGCCGTGCCTGGAGTGGAG +GGACCCTTGAAAGTTTGGCCTCAGCTCGGGACACTGATGTTCCCGGGTTGGCCCTTCATG +AGAGTTTGGCCTCAGCTCGGGACACTGATGTTCCTGGGTTGGCCCTTCACAGCTGGTGGG +CGGGGGGTGCTTTGGGGAGAGGCTGCCCTGCGCATCAGGGCATCAAGACACAGGGGAGTG +AATGAACCTGGGGCTGCAGTTTCACCTGGGTGTGGCCCTGGCTGCTGGGGAGGGGCCGTG +>syndip_2_chr20:64065753-64066112 +TGGAACAGTCCAGGCGAGGGGTGCTGGCCTGCTTGGGGGCAACTCAGAGGCCTGGAGGAT +AGATGAGGAGGGGGGCTGTGGGCCTTGTAGGTGTTGGCTGTGGCCGTGCCTGGAGTGGAG +GGACCCTTGAAAGTTTGGCCTCAGCTCGGGACACTGATGTTCCCGGGTTGGCCCTTCATG +AGAGTTTGGCCTCAGCTCGGGACACTGATGTTCCTGGGTTGGCCCTTCACAGCTGGTGGG +CGGGGGGTGCTTTGGGGAGAGGCTGCCCTGCGCATCAGGGCATCAAGACACAGGGGAGTG +AATGAACCTGGGGCTGCAGTTTCACCTGGGTGTGGCCCTGGCTGCTGGGGAGGGGCCGTG +>p:HG002_1_chr20:64065753-64066112 +TGGAACAGTCCAGGCGAGGGGTGCTGGCCTGCTTGGGGGCAACTCAGAGGCCTGGAGGAT +AGATGAGGAGGGGGGCTGTGGGCCTTGTAGGTGTTGGCTGTGGCCGTGCCTGGAGTGGAG +GGACCCTTGAAAGTTTGGCCTCAGCTCGGGACACTGATGTTCCCGGGTTGGCCCTTCATG +AGAGTTTGGCCTCAGCTCGGGACACTGATGTTCCTGGGTTGGCCCTTCACAGCTGGTGGG +CGGGGGGTGCTTTGGGGAGAGGCTGCCCTGCGCATCAGGGCATCAAGACACAGGGGAGTG +AATGAACCTGGGGCTGCAGTTTCACCTGGGTGTGGCCCTGGCTGCTGGGGAGGGGCCGTG +>p:HG002_2_chr20:64065753-64066112 +TGGAACAGTCCAGGCGAGGGGTGCTGGCCTGCTTGGGGGCAACTCAGAGGCCTGGAGGAT +AGATGAGGAGGGGGGCTGTGGGCCTTGTAGGTGTTGGCTGTGGCCGTGCCTGGAGTGGAG +GGACCCTTGAAAGTTTGGCCTCAGCTCGGGACACTGATGTTCCCGGGTTGGCCCTTCATG +AGAGTTTGGCCTCAGCTCGGGACACTGATGTTCCCGGGTTGGCCCTTCATGAGAGTTTGG +CCTCAGCTCGGGACACTGATGTTCCTGGGTTGGCCCTTCACAGCTGGTGGGCGGGGGGTG +CTTTGGGGAGAGGCTGCCCTGCGCATCAGGGCATCAAGACACAGGGGAGTGAATGAACCT +GGGGCTGCAGTTTCACCTGGGTGTGGCCCTGGCTGCTGGGGAGGGGCCGTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/haps.fa.ref.fa new file mode 100644 index 00000000..db9de780 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:64065753-64066112 +TGGAACAGTCCAGGCGAGGGGTGCTGGCCTGCTTGGGGGCAACTCAGAGGCCTGGAGGATAGATGAGGAGGGGGGCTGTGGGCCTTGTAGGTGTTGGCTGTGGCCGTGCCTGGAGTGGAGGGACCCTTGAAAGTTTGGCCTCAGCTCGGGACACTGATGTTCCCGGGTTGGCCCTTCATGAGAGTTTGGCCTCAGCTCGGGACACTGATGTTCCTGGGTTGGCCCTTCACAGCTGGTGGGCGGGGGGTGCTTTGGGGAGAGGCTGCCCTGCGCATCAGGGCATCAAGACACAGGGGAGTGAATGAACCTGGGGCTGCAGTTTCACCTGGGTGTGGCCCTGGCTGCTGGGGAGGGGCCGTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/msa.fa new file mode 100644 index 00000000..5c88c05c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/msa.fa @@ -0,0 +1,40 @@ +>ref_chr20_64065753_64066112 +tggaacagtccaggcgaggggtgctggcctgcttgggggcaactcagaggcctggaggat +agatgaggaggggggctgtgggccttgtaggtgttggctgtggccgtgcctggagtggag +ggacccttgaa------------------------------------------------- +--agtttggcctcagctcgggacactgatgttcccgggttggcccttcatgagagtttgg +cctcagctcgggacactgatgttcctgggttggcccttcacagctggtgggcggggggtg +ctttggggagaggctgccctgcgcatcagggcatcaagacacaggggagtgaatgaacct +ggggctgcagtttcacctgggtgtggccctggctgctggggaggggccgtg +>syndip_1_chr20:64065753-64066112 +tggaacagtccaggcgaggggtgctggcctgcttgggggcaactcagaggcctggaggat +agatgaggaggggggctgtgggccttgtaggtgttggctgtggccgtgcctggagtggag +ggacccttgaa------------------------------------------------- +--agtttggcctcagctcgggacactgatgttcccgggttggcccttcatgagagtttgg +cctcagctcgggacactgatgttcctgggttggcccttcacagctggtgggcggggggtg +ctttggggagaggctgccctgcgcatcagggcatcaagacacaggggagtgaatgaacct +ggggctgcagtttcacctgggtgtggccctggctgctggggaggggccgtg +>syndip_2_chr20:64065753-64066112 +tggaacagtccaggcgaggggtgctggcctgcttgggggcaactcagaggcctggaggat +agatgaggaggggggctgtgggccttgtaggtgttggctgtggccgtgcctggagtggag +ggacccttgaa------------------------------------------------- +--agtttggcctcagctcgggacactgatgttcccgggttggcccttcatgagagtttgg +cctcagctcgggacactgatgttcctgggttggcccttcacagctggtgggcggggggtg +ctttggggagaggctgccctgcgcatcagggcatcaagacacaggggagtgaatgaacct +ggggctgcagtttcacctgggtgtggccctggctgctggggaggggccgtg +>p:HG002_1_chr20:64065753-64066112 +tggaacagtccaggcgaggggtgctggcctgcttgggggcaactcagaggcctggaggat +agatgaggaggggggctgtgggccttgtaggtgttggctgtggccgtgcctggagtggag +ggacccttgaa------------------------------------------------- +--agtttggcctcagctcgggacactgatgttcccgggttggcccttcatgagagtttgg +cctcagctcgggacactgatgttcctgggttggcccttcacagctggtgggcggggggtg +ctttggggagaggctgccctgcgcatcagggcatcaagacacaggggagtgaatgaacct +ggggctgcagtttcacctgggtgtggccctggctgctggggaggggccgtg +>p:HG002_2_chr20:64065753-64066112 +tggaacagtccaggcgaggggtgctggcctgcttgggggcaactcagaggcctggaggat +agatgaggaggggggctgtgggccttgtaggtgttggctgtggccgtgcctggagtggag +ggacccttgaaagtttggcctcagctcgggacactgatgttcccgggttggcccttcatg +agagtttggcctcagctcgggacactgatgttcccgggttggcccttcatgagagtttgg +cctcagctcgggacactgatgttcctgggttggcccttcacagctggtgggcggggggtg +ctttggggagaggctgccctgcgcatcagggcatcaagacacaggggagtgaatgaacct +ggggctgcagtttcacctgggtgtggccctggctgctggggaggggccgtg diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/msa.fa.fai new file mode 100644 index 00000000..a31283db --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_64065753_64066112 411 29 60 61 +syndip_1_chr20:64065753-64066112 411 481 60 61 +syndip_2_chr20:64065753-64066112 411 933 60 61 +p:HG002_1_chr20:64065753-64066112 411 1386 60 61 +p:HG002_2_chr20:64065753-64066112 411 1839 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/output.vcf.gz new file mode 100644 index 00000000..0e4af5b9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/output.vcf.gz.tbi new file mode 100644 index 00000000..0806a63f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64065853-64066012/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/base.vcf.gz new file mode 100644 index 00000000..c9f823c0 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/base.vcf.gz.tbi new file mode 100644 index 00000000..bb297398 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/comp.vcf.gz new file mode 100644 index 00000000..c9ddbe22 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/comp.vcf.gz.tbi new file mode 100644 index 00000000..04493ef3 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/haps.fa new file mode 100644 index 00000000..e898806d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/haps.fa @@ -0,0 +1,58 @@ +>ref_chr20_64090604_64091490 +ACAGCCTTGACCTGTGACCTTTCATCTCAGTGGATCAGGCATGGGACCCCCGTGCTGAGAAGGAGGCAACTCTGAAGGGGCCATTCAGCTGTGTGGGTGCCAGGGGCCTGTCTGCAGGAGTGATGCTCAGCCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGGGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGGGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGGGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCGTGTCTCCAAGTGACGAACAGACCCGGGTTTCACCCCGTCTCTGCCACTGTGACAGGTGGCCTCACACCTCTGAGGCTTCGTGCTCTCAGCAGTGGCCGGGTATGGTGGGGGTGACTGAGCTCCAGGAGCA +>syndip_1_chr20:64090604-64091490 +ACAGCCTTGACCTGTGACCTTTCATCTCAGTGGATCAGGCATGGGACCCCCGTGCTGAGA +AGGAGGCAACTCTGAAGGGGCCATTCAGCTGTGTGGGTGCCAGGGGCCTGTCTGCAGGAG +TGATGCTCAGCCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTG +GGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGT +GCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGG +CCCAGCTGTGGCAGGGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCC +CTGGGCACTGATCTGGGGCCCAGCTGTGGCAGGGGTGCCCTGGGCACTGATCTGGGGCCC +AGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTG +GGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGC +TGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGC +ACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGT +GGCAGGGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACT +GATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCGTGTCTCCAAGTGACGAACAGACC +CGGGTTTCACCCCGTCTCTGCCACTGTGACAGGTGGCCTCACACCTCTGAGGCTTCGTGC +TCTCAGCAGTGGCCGGGTATGGTGGGGGTGACTGAGCTCCAGGAGCA +>syndip_2_chr20:64090604-64091490 +ACAGCCTTGACCTGTGACCTTTCATCTCAGTGGATCAGGCATGGGACCCCCGTGCTGAGA +AGGAGGCAACTCTGAAGGGGCCATTCAGCTGTGTGGGTGCCAGGGGCCTGTCTGCAGGAG +TGATGCTCAGCCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTG +GGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGT +GCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGG +CCCAGCTGTGGCAGGGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCC +CTGGGCACTGATCTGGGGCCCAGCTGTGGCAGGGGTGCCCTGGGCACTGATCTGGGGCCC +AGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTG +GGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGC +TGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGC +ACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGT +GGCAGGGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACT +GATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCGTGTCTCCAAGTGACGAACAGACC +CGGGTTTCACCCCGTCTCTGCCACTGTGACAGGTGGCCTCACACCTCTGAGGCTTCGTGC +TCTCAGCAGTGGCCGGGTATGGTGGGGGTGACTGAGCTCCAGGAGCA +>p:HG002_1_chr20:64090604-64091490 +ACAGCCTTGACCTGTGACCTTTCATCTCAGTGGATCAGGCATGGGACCCCCGTGCTGAGA +AGGAGGCAACTCTGAAGGGGCCATTCAGCTGTGTGGGTGCCAGGGGCCTGTCTGCAGGAG +TGATGCTCAGCCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTG +GGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGT +GCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGG +CCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCC +CTGGGCACTGATCTGGGGCCCAGCTGTGGCAGGGGTGCCCTGGGCACTGATCTGGGGCCC +AGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTG +GACGTGTCTCCAAGTGACGAACAGACCCGGGTTTCACCCCGTCTCTGCCACTGTGACAGG +TGGCCTCACACCTCTGAGGCTTCGTGCTCTCAGCAGTGGCCGGGTATGGTGGGGGTGACT +GAGCTCCAGGAGCA +>p:HG002_2_chr20:64090604-64091490 +ACAGCCTTGACCTGTGACCTTTCATCTCAGTGGATCAGGCATGGGACCCCCGTGCTGAGA +AGGAGGCAACTCTGAAGGGGCCATTCAGCTGTGTGGGTGCCAGGGGCCTGTCTGCAGGAG +TGATGCTCAGCCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTG +GGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGT +GCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGG +CCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCC +CTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCC +AGCTGTGGCAGGGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTG +GGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGACGTGTCTCCAAGTGACGAA +CAGACCCGGGTTTCACCCCGTCTCTGCCACTGTGACAGGTGGCCTCACACCTCTGAGGCT +TCGTGCTCTCAGCAGTGGCCGGGTATGGTGGGGGTGACTGAGCTCCAGGAGCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/haps.fa.ref.fa new file mode 100644 index 00000000..2ef1df38 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:64090604-64091490 +ACAGCCTTGACCTGTGACCTTTCATCTCAGTGGATCAGGCATGGGACCCCCGTGCTGAGAAGGAGGCAACTCTGAAGGGGCCATTCAGCTGTGTGGGTGCCAGGGGCCTGTCTGCAGGAGTGATGCTCAGCCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGGGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGGGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGGGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCGTGTCTCCAAGTGACGAACAGACCCGGGTTTCACCCCGTCTCTGCCACTGTGACAGGTGGCCTCACACCTCTGAGGCTTCGTGCTCTCAGCAGTGGCCGGGTATGGTGGGGGTGACTGAGCTCCAGGAGCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/msa.fa new file mode 100644 index 00000000..c62ab1dd --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/msa.fa @@ -0,0 +1,80 @@ +>ref_chr20_64090604_64091490 +acagccttgacctgtgacctttcatctcagtggatcaggcatgggacccccgtgctgaga +aggaggcaactctgaaggggccattcagctgtgtgggtgccaggggcctgtctgcaggag +tgatgctcagccactgatctggggcccagctgtggcagaggtgccctgggcactgatctg +gggcccagctgtggcagaggtgccctgggcactgatctggggcccagctgtggcagaggt +gccctgggcactgatctggggcccagctgtggcagaggtgccctgggcactgatctgggg +cccagctgtggcaggggtgccctgggcactgatctggggcccagctgtggcagaggtgcc +ctgggcactgatctggggcccagctgtggcaggggtgccctgggcactgatctggggccc +agctgtggcagaggtgccctgggcactgatctggggcccagctgtggcagaggtgccctg +ggcactgatctggggcccagctgtggcagaggtgccctgggcactgatctggggcccagc +tgtggcagaggtgccctgggcactgatctggggcccagctgtggcagaggtgccctgggc +actgatctggggcccagctgtggcagaggtgccctgggcactgatctggggcccagctgt +ggcaggggtgccctgggcactgatctggggcccagctgtggcagaggtgccctgggcact +gatctggggcccagctgtggcagaggtgccctgggcgtgtctccaagtgacgaacagacc +cgggtttcaccccgtctctgccactgtgacaggtggcctcacacctctgaggcttcgtgc +tctcagcagtggccgggtatggtgggggtgactgagctccaggagca +>syndip_1_chr20:64090604-64091490 +acagccttgacctgtgacctttcatctcagtggatcaggcatgggacccccgtgctgaga +aggaggcaactctgaaggggccattcagctgtgtgggtgccaggggcctgtctgcaggag +tgatgctcagccactgatctggggcccagctgtggcagaggtgccctgggcactgatctg +gggcccagctgtggcagaggtgccctgggcactgatctggggcccagctgtggcagaggt +gccctgggcactgatctggggcccagctgtggcagaggtgccctgggcactgatctgggg +cccagctgtggcaggggtgccctgggcactgatctggggcccagctgtggcagaggtgcc +ctgggcactgatctggggcccagctgtggcaggggtgccctgggcactgatctggggccc +agctgtggcagaggtgccctgggcactgatctggggcccagctgtggcagaggtgccctg +ggcactgatctggggcccagctgtggcagaggtgccctgggcactgatctggggcccagc +tgtggcagaggtgccctgggcactgatctggggcccagctgtggcagaggtgccctgggc +actgatctggggcccagctgtggcagaggtgccctgggcactgatctggggcccagctgt +ggcaggggtgccctgggcactgatctggggcccagctgtggcagaggtgccctgggcact +gatctggggcccagctgtggcagaggtgccctgggcgtgtctccaagtgacgaacagacc +cgggtttcaccccgtctctgccactgtgacaggtggcctcacacctctgaggcttcgtgc +tctcagcagtggccgggtatggtgggggtgactgagctccaggagca +>syndip_2_chr20:64090604-64091490 +acagccttgacctgtgacctttcatctcagtggatcaggcatgggacccccgtgctgaga +aggaggcaactctgaaggggccattcagctgtgtgggtgccaggggcctgtctgcaggag +tgatgctcagccactgatctggggcccagctgtggcagaggtgccctgggcactgatctg +gggcccagctgtggcagaggtgccctgggcactgatctggggcccagctgtggcagaggt +gccctgggcactgatctggggcccagctgtggcagaggtgccctgggcactgatctgggg +cccagctgtggcaggggtgccctgggcactgatctggggcccagctgtggcagaggtgcc +ctgggcactgatctggggcccagctgtggcaggggtgccctgggcactgatctggggccc +agctgtggcagaggtgccctgggcactgatctggggcccagctgtggcagaggtgccctg +ggcactgatctggggcccagctgtggcagaggtgccctgggcactgatctggggcccagc +tgtggcagaggtgccctgggcactgatctggggcccagctgtggcagaggtgccctgggc +actgatctggggcccagctgtggcagaggtgccctgggcactgatctggggcccagctgt +ggcaggggtgccctgggcactgatctggggcccagctgtggcagaggtgccctgggcact +gatctggggcccagctgtggcagaggtgccctgggcgtgtctccaagtgacgaacagacc +cgggtttcaccccgtctctgccactgtgacaggtggcctcacacctctgaggcttcgtgc +tctcagcagtggccgggtatggtgggggtgactgagctccaggagca +>p:HG002_1_chr20:64090604-64091490 +acagccttgacctgtgacctttcatctcagtggatcaggcatgggacccccgtgctgaga +aggaggcaactctgaaggggccattcagctgtgtgggtgccaggggcctgtctgcaggag +tgatgctcagc------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------------cactgatctggggccc +agctgtggcagaggtgccctgggcactgatctggggcccagctgtggcagaggtgccctg +ggcactgatctggggcccagctgtggcagaggtgccctgggcactgatctggggcccagc +tgtggcagaggtgccctgggcactgatctggggcccagctgtggcagaggtgccctgggc +actgatctggggcccagctgtggcagaggtgccctgggcactgatctggggcccagctgt +ggcaggggtgccctgggcactgatctggggcccagctgtggcagaggtgccctgggcact +gatctggggcccagctgtggcagaggtgccctggacgtgtctccaagtgacgaacagacc +cgggtttcaccccgtctctgccactgtgacaggtggcctcacacctctgaggcttcgtgc +tctcagcagtggccgggtatggtgggggtgactgagctccaggagca +>p:HG002_2_chr20:64090604-64091490 +acagccttgacctgtgacctttcatctcagtggatcaggcatgggacccccgtgctgaga +aggaggcaactctgaaggggccattcagctgtgtgggtgccaggggcctgtctgcaggag +tgatgctcagccactgatctggggcccagctgtggcaga--------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------ggtgccctgggcactgatctggggccc +agctgtggcagaggtgccctgggcactgatctggggcccagctgtggcagaggtgccctg +ggcactgatctggggcccagctgtggcagaggtgccctgggcactgatctggggcccagc +tgtggcagaggtgccctgggcactgatctggggcccagctgtggcagaggtgccctgggc +actgatctggggcccagctgtggcagaggtgccctgggcactgatctggggcccagctgt +ggcaggggtgccctgggcactgatctggggcccagctgtggcagaggtgccctgggcact +gatctggggcccagctgtggcagaggtgccctggacgtgtctccaagtgacgaacagacc +cgggtttcaccccgtctctgccactgtgacaggtggcctcacacctctgaggcttcgtgc +tctcagcagtggccgggtatggtgggggtgactgagctccaggagca diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/msa.fa.fai new file mode 100644 index 00000000..657f3e5d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_64090604_64091490 887 29 60 61 +syndip_1_chr20:64090604-64091490 887 965 60 61 +syndip_2_chr20:64090604-64091490 887 1901 60 61 +p:HG002_1_chr20:64090604-64091490 887 2838 60 61 +p:HG002_2_chr20:64090604-64091490 887 3775 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/output.vcf.gz new file mode 100644 index 00000000..d275ec6e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/output.vcf.gz.tbi new file mode 100644 index 00000000..abec3b04 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64090704-64091390/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/base.vcf.gz new file mode 100644 index 00000000..bdb28d37 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/base.vcf.gz.tbi new file mode 100644 index 00000000..bb297398 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/comp.vcf.gz new file mode 100644 index 00000000..3a388630 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/comp.vcf.gz.tbi new file mode 100644 index 00000000..0a4d26b8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/haps.fa new file mode 100644 index 00000000..366641f0 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/haps.fa @@ -0,0 +1,88 @@ +>ref_chr20_64096558_64097265 +ATTGCGGCCTCTTTGTGCTTATTCATAATCCCTCTCTAACAGGCAGAATGGAGCCCCATATTTCCTCACGGCAGCTACACTGACACAGAATAGTGTCATCTTGGGTGCTGCTGCCACTGCCAATATCGCCGCCACCATCATCATCACAATCATCACCATCACCACCATCATCACCACTATCATCATCACCACTATCACCACCACCAGCACCTTCATTATCACATTCACCATCCTCACCATCCTCACCACCACCATCACCACCATCATCACCATCATCATCATGACCATCACCACCATCACCACTATCACCACCACCACCATCATTACCATCATCATCACGACCATCACCACCATCATCACCATCACCACTATCACCACCACCACCATCATTACCATCATCATCACGACCATCACCACCATCATCACCATCACCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCATCACCATCATCACCATCATCATCATCACCACTACCATCACGCTCACAGTCATCACCATCACCACCATGATCACTGCCATCATCACCACCACCATCACCACCATAATCCCCCCCAACTATTACAACCATTAACTTATTTAACAAAAATTTATTAATCACCAACGATTTTCCCAGCCCTTTCCAGCACCATTTCAGGTGCTTGGATACACTCATACCTTATTAGCATCCCT +>syndip_1_chr20:64096558-64097265 +ATTGCGGCCTCTTTGTGCTTATTCATAATCCCTCTCTAACAGGCAGAATGGAGCCCCATA +TTTCCTCACGGCAGCTACACTGACACAGAATAGTGTCATCTTGGGTGCTGCTGCCACTGC +CAATATCGCCGCCACCATCATCATCACAATCATCACCATCACCACCATCATCACCACTAT +CATCATCACCACTATCACCACCACCAGCACCTTCATTATCACATTCACCATCCTCACCAT +CCTCACCACCACCATCACCACCATCATCACCATCATCATCATGACCATCACCACCATCAC +CACTATCACCACCACCACCATCATTACCATCATCATCACGACCATCACCACCATCATCAC +CATCACCACTATCACCACCACCACCATCATTACCATCATCATCACGACCATCACCACCAT +CATCACCATCACCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCAT +CACCATCATCACCATCATCATCATCACCACTACCATCACGCTCACAGTCATCACCATCAC +CACCATGATCACTGCCATCATCACCACCACCATCACCACCATAATCCCCCCCAACTATTA +CAACCATTAACTTATTTAACAAAAATTTATTAATCACCAACGATTTTCCCAGCCCTTTCC +AGCACCATTTCAGGTGCTTGGATACACTCATACCTTATTAGCATCCCT +>syndip_2_chr20:64096558-64097265 +ATTGCGGCCTCTTTGTGCTTATTCATAATCCCTCTCTAACAGGCAGAATGGAGCCCCATA +TTTCCTCACGGCAGCTACACTGACACAGAATAGTGTCATCTTGGGTGCTGCTGCCACTGC +CAATATCGCCGCCACCATCATCATCACAATCATCACCATCACCACCATCATCACCACTAT +CATCATCACCACTATCACCACCACCAGCACCTTCATTATCACATTCACCATCCTCACCAT +CCTCACCACCACCATCACCACCATCATCACCATCATCATCATGACCATCACCACCATCAC +CACTATCACCACCACCACCATCATTACCATCATCATCACGACCATCACCACCATCATCAC +CATCACCACTATCACCACCACCACCATCATTACCATCATCATCACGACCATCACCACCAT +CATCACCATCACCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCAT +CACCATCATCACCATCATCATCATCACCACTACCATCACGCTCACAGTCATCACCATCAC +CACCATGATCACTGCCATCATCACCACCACCATCACCACCATAATCCCCCCCAACTATTA +CAACCATTAACTTATTTAACAAAAATTTATTAATCACCAACGATTTTCCCAGCCCTTTCC +AGCACCATTTCAGGTGCTTGGATACACTCATACCTTATTAGCATCCCT +>p:HG002_1_chr20:64096558-64097265 +ATTGCGGCCTCTTTGTGCTTATTCATAATCCCTCTCTAACAGGCAGAATGGAGCCCCATA +TTTCCTCACGGCAGCTACACTGACACAGAATAGTGTCATCTTGGGTGCTGCTGCCACTGC +CAATATCGCTGCCACCATCATCATCACAATCATCACCATCACCACCATCATCACCACTAT +CATCATCACCACTATCACCACCACCAGCACCTTATCACATTCACCATCCTCACCATCCTC +ACCACCACCATCACCACCATCATCACCATCATCATCATGACCATCACCACCATCACCACT +ATCACCACCACCACCATCATTACCATCATCATCACGACCATCACCACCATCATCACCATC +ACCACTATCACCACCACCACCATCATTACCATCATCATCACGACCATCACCACCATCATC +ACCATCACCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCATCACT +GTCACCATCATCACCATCCTCACTATCACCACCACCACCATCATCACCATCACCATCATC +ACAGTCATCACCGTCACCATCATCACCATCCTCACTATCACCACCACCACCATCATCACC +ATCACCATCATCACAGTCATCACCGTCACCATCATCACCATCCTCACTATCACCACCACC +ACCATCATCACCATCACCATCATCACAGTCATCACCGTCACCATCATCACCATCCTCACT +ATCACCACCACCACCATCATCACCATCACCATCATCACAGTCATCACCGTCACCATCATC +ACCATCCTCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCATCACC +GTCACCATCATCACCATCCTCACTATCACCACCACCACCATCACCATCACCATCATCACA +GTCATCACCGTCACCATCATCACCATCCTCACTATCACCACCACCATCATCACCATCACC +ATCATCACAGTCATCACCGTCACCATCATCACCATCCTCACTATCACCACCACCACCATC +ATCACCATCACCATCATCACAGTCATCACCGTCACCATCATCACCATCCTCACTATCACC +ACCACCATCATCACCATCACCATCATCACAGTCATCACCGTCACCATCATCACCATCCTC +ACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCATCACCGTCACCATC +ATCACCATCCTCACTATCACCACCACCACCATCATCACCATCACCATCATCACAATCATC +ACCGTCACCATCATCACCATCCTCACTATCACCACCACCACCATCATCACCATCACTATC +ATCACAGTCATCACCGTCACCATCATCACCATCCTCACTATCACCACCACTACCATCATC +ATCACATTCATCATCACTATTACCATCATCATCACCACCATCACCATCACTATCACCACC +ATCATTACATTTGTCACCATCACCACCATTATCACCATCACCGCTATCACCACCACCACC +GTCATCATCACCATCATCATCATCACCACTACCATCACGCTCACAGTCATCACCATCACC +ACCATGATCACTGCCATCATCACCACCACCATCACCACCATAATCCCCCCCAACTATTAC +AACCATTAACTTATTTAACAAAAATTTATTAATCACCAACGATTTTCCCAGCCCTTTCCA +GCACCATTTCAGGTGCTTGGATACACTCATACCTTATTAGCATCCCT +>p:HG002_2_chr20:64096558-64097265 +ATTGCGGCCTCTTTGTGCTTATTCATAATCCCTCTCTAACAGGCAGAATGGAGCCCCATA +TTTCCTCACGGCAGCTACACTGACACAGAATAGTGTCATCTTGGGTGCTGCTGCCACTGC +CAATATCGCCGCCACCATCATCATCACAATCATCACCATCACCACCATCATCACCACTAT +CATCATCACCACTATCACCACCACCAGCACCTTCATTATCACATTCACCATCCTCACCAT +CCTCACCACCACCATCACCACCATCATCACCACCATCACCACTATCACCACCACCACCAT +CATTACCATCATCATCACGACCATCACCACCATCATCACCATCACCACTATCACCACCAC +CACCATCATTACCATCATCATCACGACCATCACCACCATCATCACCATCACCACTATCAC +CACCACCACCATCATCACCATCACCATCATCACAGTCATCACTGTCACCATCATCACCAT +CCTCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCATCACCGTCAC +CATCATCACCATCCTCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGT +CATCACCGTCACCATCATCACCATCCTCACTATCACCACCACCACCATCATCACCATCAC +CATCATCACAGTCATCACCGTCACCATCATCACCATCCTCACTATCACCACCACCACCAT +CATCACCATCACCATCATCACAGTCATCACCATCACCATCATCACCATCCTCACTATCAC +CACCACCACCATCATCACCATCACCATCATCACAGTCATCACCGTCACCATCATCACCAT +CCTCACTATCACCACCACCACCATCACCATCACCATCATCACAGTCATCACCGTCACCAT +CATCACCATCCTCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCAT +CACCGTCACCATCATCACCATCCTCACTATCACCACCACCACCATCATCACCATCACCAT +CATCACAGTCATCACCGTCACCATCATCACCATCCTCACTATCACCACCACCATCATCAC +CATCACCATCATCACAGTCATCACCGTCACCATCATCACCATCCTCACTATCACCACCAC +CACCATCATTACCATCACCATCATCACAGTCATCACCGTCACCATCATCACCATCCTCAC +TATCACCACCACCACCATCATCACCATCACCATCATCACAATCATCACTGTCACCATCAT +CACCATCCTCACTATCACCACCACCACCATCATTACCATCACTATCATCACAGTCATCAC +CGTCACCATCATCACCATCCTCACTATCACCACCACTACCATCATCATCACATTCATCAT +CACTATTACCATCATCATCACCACCATCACCATCACTATCACCACCATCATTACATTTGT +CACCATCACCACCATTATCACCATCACCGCTATCACCACCACCACCGTCATCATCACCAT +CATCATCATCACCACTACCATCACGCTCACAGTCATCACCATCACCACCATGATCACTGC +CATCATCACCACCACCATCACCACCATAATCCCCCCCAACTATTACAACCATTAACTTAT +TTAACAAAAATTTATTAATCACCAACGATTTTCCCAGCCCTTTCCAGCACCATTTCAGGT +GCTTGGATACACTCATACCTTATTAGCATCCCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/haps.fa.ref.fa new file mode 100644 index 00000000..066111f8 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:64096558-64097265 +ATTGCGGCCTCTTTGTGCTTATTCATAATCCCTCTCTAACAGGCAGAATGGAGCCCCATATTTCCTCACGGCAGCTACACTGACACAGAATAGTGTCATCTTGGGTGCTGCTGCCACTGCCAATATCGCCGCCACCATCATCATCACAATCATCACCATCACCACCATCATCACCACTATCATCATCACCACTATCACCACCACCAGCACCTTCATTATCACATTCACCATCCTCACCATCCTCACCACCACCATCACCACCATCATCACCATCATCATCATGACCATCACCACCATCACCACTATCACCACCACCACCATCATTACCATCATCATCACGACCATCACCACCATCATCACCATCACCACTATCACCACCACCACCATCATTACCATCATCATCACGACCATCACCACCATCATCACCATCACCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCATCACCATCATCACCATCATCATCATCACCACTACCATCACGCTCACAGTCATCACCATCACCACCATGATCACTGCCATCATCACCACCACCATCACCACCATAATCCCCCCCAACTATTACAACCATTAACTTATTTAACAAAAATTTATTAATCACCAACGATTTTCCCAGCCCTTTCCAGCACCATTTCAGGTGCTTGGATACACTCATACCTTATTAGCATCCCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/msa.fa new file mode 100644 index 00000000..c76087a2 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/msa.fa @@ -0,0 +1,150 @@ +>ref_chr20_64096558_64097265 +attgcggcctctttgtgcttattcataatccctctctaacaggcagaatggagccccata +tttcctcacggcagctacactgacacagaatagtgtcatcttgggtgctgctgccactgc +caatatcgccgccaccatcatcatcacaatcatcaccatcaccaccatcatcaccactat +catcatcaccactatcaccaccaccagcaccttcattatcacattcaccatcctcaccat +cctcaccaccaccatcaccaccatcatcaccatcatcatcatgaccatcaccaccatcac +cactatcaccaccaccaccatcattaccatcatcatcacgaccatcaccaccatcatcac +catcaccactatcaccaccaccaccatcattaccatcatcatcacgaccatcaccaccat +catcaccatcaccactatcaccaccaccaccatcatcaccatcaccatcatcacagtcat +caccatcatcaccatcatcatcatcaccactaccatcacgctcacagtcatcaccatcac +caccatgatcactgccatcatcaccaccaccatcaccaccataatcccccccaactatta +caaccattaacttatttaacaaaaatttattaatcacca--acgattttcccagcccttt +ccagcaccatttcaggtgcttggatacactcataccttattagcatc------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------------------cct +>syndip_1_chr20:64096558-64097265 +attgcggcctctttgtgcttattcataatccctctctaacaggcagaatggagccccata +tttcctcacggcagctacactgacacagaatagtgtcatcttgggtgctgctgccactgc +caatatcgccgccaccatcatcatcacaatcatcaccatcaccaccatcatcaccactat +catcatcaccactatcaccaccaccagcaccttcattatcacattcaccatcctcaccat +cctcaccaccaccatcaccaccatcatcaccatcatcatcatgaccatcaccaccatcac +cactatcaccaccaccaccatcattaccatcatcatcacgaccatcaccaccatcatcac +catcaccactatcaccaccaccaccatcattaccatcatcatcacgaccatcaccaccat +catcaccatcaccactatcaccaccaccaccatcatcaccatcaccatcatcacagtcat +caccatcatcaccatcatcatcatcaccactaccatcacgctcacagtcatcaccatcac +caccatgatcactgccatcatcaccaccaccatcaccaccataatcccccccaactatta +caaccattaacttatttaacaaaaatttattaatcacca--acgattttcccagcccttt +ccagcaccatttcaggtgcttggatacactcataccttattagcatc------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------------------cct +>syndip_2_chr20:64096558-64097265 +attgcggcctctttgtgcttattcataatccctctctaacaggcagaatggagccccata +tttcctcacggcagctacactgacacagaatagtgtcatcttgggtgctgctgccactgc +caatatcgccgccaccatcatcatcacaatcatcaccatcaccaccatcatcaccactat +catcatcaccactatcaccaccaccagcaccttcattatcacattcaccatcctcaccat +cctcaccaccaccatcaccaccatcatcaccatcatcatcatgaccatcaccaccatcac +cactatcaccaccaccaccatcattaccatcatcatcacgaccatcaccaccatcatcac +catcaccactatcaccaccaccaccatcattaccatcatcatcacgaccatcaccaccat +catcaccatcaccactatcaccaccaccaccatcatcaccatcaccatcatcacagtcat +caccatcatcaccatcatcatcatcaccactaccatcacgctcacagtcatcaccatcac +caccatgatcactgccatcatcaccaccaccatcaccaccataatcccccccaactatta +caaccattaacttatttaacaaaaatttattaatcacca--acgattttcccagcccttt +ccagcaccatttcaggtgcttggatacactcataccttattagcatc------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------------------cct +>p:HG002_1_chr20:64096558-64097265 +attgcggcctctttgtgcttattcataatccctctctaacaggcagaatggagccccata +tttcctcacggcagctacactgacacagaatagtgtcatcttgggtgctgctgccactgc +caatatcgctgccaccatcatcatcacaatcatcaccatcaccaccatcatcaccactat +catcatcaccactatcaccaccaccagcacc----ttatcacattcaccatcctcaccat +cctcaccaccaccatcaccaccatcatcaccatcatcatcatgaccatcaccaccatcac +cactatcaccaccaccaccatcattaccatcatcatcacgaccatcaccaccatcatcac +catcaccactatcaccaccaccaccatcattaccatcatcatcacgaccatcaccaccat +catcaccatcaccactatcaccaccaccaccatcatcaccatcaccatcatcacagtcat +cactgtcaccatcatcaccatcctcactatcaccaccaccaccatcatcaccatcaccat +catcacagtcatcaccgtcaccatcatcaccatcctcactatcaccaccacc-accatca +tcaccatcaccatcatcacagtcatcaccgtcaccatcatcaccatcctcactatcacca +ccaccaccatcatcaccatcaccatcatcacagtcatcaccgtcaccatcatcaccatcc +tcactatcaccaccaccaccatcatcaccatcaccatcatcacagtcatcaccgtcacca +tcatcaccatcctcactatcaccaccaccaccatcatcaccatcaccatcatcacagtca +tcaccgtcaccatcatcaccatcctcactatcaccaccaccaccatcaccatcaccatca +tcacagtcatcaccgtcaccatcatcaccatcctcactat---caccaccaccatcatca +ccatcaccatcatcacagtcatcaccgtcaccatcatcaccatcctcactatcaccacca +ccaccatcatcaccatcaccatcatcacagtcatcaccgtcaccatcatcaccatcctca +ctatcaccaccaccatcatcaccatcaccatcatcacagtcatcaccgtcaccatcatca +ccatcctcactatcaccaccaccaccatcatcaccatcaccatcatcacagtcatcaccg +tcaccatcatcaccatcctcactatcaccaccaccaccatcatcaccatcaccatcatca +caatcatcaccgtcaccatcatcaccatcctcactatcaccaccaccaccatcatcacca +tcactatcatcacagtcatcaccgtcaccatcatcaccatcctcactatcaccaccacta +ccatcatcatcacattcatcatcactattaccatcatcatcaccaccatcaccatcacta +tcaccaccatcattacatttgtcaccatcaccaccattatcaccatcaccgctatcacca +ccaccaccgtcatcatcaccatcatcatcatcaccactaccatcacgctcacagtcatca +ccatcaccaccatgatcactgccatcatcaccaccaccatcaccaccataatccccccca +actattacaaccattaacttatttaacaaaaatttattaatcaccaacgattttcccagc +cctttccagcaccatttcaggtgcttggatacactcataccttattagcatccct +>p:HG002_2_chr20:64096558-64097265 +attgcggcctctttgtgcttattcataatccctctctaacaggcagaatggagccccata +tttcctcacggcagctacactgacacagaatagtgtcatcttgggtgctgctgccactgc +caatatcgccgccaccatcatcatcacaatcatcaccatcaccaccatcatcaccactat +catcatcaccactatcaccaccaccagcaccttcattatcacattcaccatcctcaccat +cctcaccaccaccatcaccaccat---------------------catcaccaccatcac +cactatcaccaccaccaccatcattaccatcatcatcacgaccatcaccaccatcatcac +catcaccactatcaccaccaccaccatcattaccatcatcatcacgaccatcaccaccat +catcaccatcaccactatcaccaccaccaccatcatcaccatcaccatcatcacagtcat +cactgtcaccatcatcaccatcctcactatcaccaccaccaccatcatcaccatcaccat +catcacagtcatcaccgtcaccatcatcaccatcctcactatcaccaccacc-accatca +tcaccatcaccatcatcacagtcatcaccgtcaccatcatcaccatcctcactatcacca +ccaccaccatcatcaccatcaccatcatcacagtcatcaccgtcaccatcatcaccatcc +tcactatcaccaccaccaccatcatcaccatcaccatcatcacagtcatcaccatcacca +tcatcaccatcctcactatcaccaccaccaccatcatcaccatcaccatcatcacagtca +tcaccgtcaccatcatcaccatcctcactatcaccaccaccaccatcaccatcaccatca +tcacagtcatcaccgtcaccatcatcaccatcctcactatcaccaccaccaccatcatca +ccatcaccatcatcacagtcatcaccgtcaccatcatcaccatcctcactatcaccacca +ccaccatcatcaccatcaccatcatcacagtcatcaccgtcaccatcatcaccatcctca +ctatcaccaccaccatcatcaccatcaccatcatcacagtcatcaccgtcaccatcatca +ccatcctcactatcaccaccaccaccatcattaccatcaccatcatcacagtcatcaccg +tcaccatcatcaccatcctcactatcaccaccaccaccatcatcaccatcaccatcatca +caatcatcactgtcaccatcatcaccatcctcactatcaccaccaccaccatcattacca +tcactatcatcacagtcatcaccgtcaccatcatcaccatcctcactatcaccaccacta +ccatcatcatcacattcatcatcactattaccatcatcatcaccaccatcaccatcacta +tcaccaccatcattacatttgtcaccatcaccaccattatcaccatcaccgctatcacca +ccaccaccgtcatcatcaccatcatcatcatcaccactaccatcacgctcacagtcatca +ccatcaccaccatgatcactgccatcatcaccaccaccatcaccaccataatccccccca +actattacaaccattaacttatttaacaaaaatttattaatcaccaacgattttcccagc +cctttccagcaccatttcaggtgcttggatacactcataccttattagcatccct diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/msa.fa.fai new file mode 100644 index 00000000..c47b575d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_64096558_64097265 1735 29 60 61 +syndip_1_chr20:64096558-64097265 1735 1827 60 61 +syndip_2_chr20:64096558-64097265 1735 3625 60 61 +p:HG002_1_chr20:64096558-64097265 1735 5424 60 61 +p:HG002_2_chr20:64096558-64097265 1735 7223 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/output.vcf.gz new file mode 100644 index 00000000..c2eee401 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/output.vcf.gz.tbi new file mode 100644 index 00000000..e22a32e4 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64096658-64097165/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/base.vcf.gz new file mode 100644 index 00000000..52f525e9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/base.vcf.gz.tbi new file mode 100644 index 00000000..e5c693e0 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/comp.vcf.gz new file mode 100644 index 00000000..f8a3c48a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/comp.vcf.gz.tbi new file mode 100644 index 00000000..9c3b4257 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/haps.fa new file mode 100644 index 00000000..d1205380 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/haps.fa @@ -0,0 +1,174 @@ +>ref_chr20_64125009_64128075 +ATTACAGGTGTGCACCACCACACCCAGCTAATTTTTTTGTATTTTCAGTAGAGATGAGGTTTCACTGTGTTAGCCAGGATGGTCTCGATTTCCTGACCTCATGATCCACCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGCGCCCGGACACACTTTGCTAGTTTTTTTTTTTTGTTTTGTTTTTTTAGTAGCAGTGCTGGGATTACAGGTGTCAGCCACCATGCCTGGCTCAAATACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACTACACCATCTTGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTCAAATACCACACCGTCTTGATTACCAAAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATAACACACCGTCTTGATTACCACAGCTTTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTCCTATAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATACCACCCTGTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTCAAATACTACTGTCCTGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACTATCTTGATTACTACAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATAACACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTCAAATACCACACTGTCTTGATTACCACAGCTGTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACGCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACTACACTGTCTTGATTAACACAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTAACACAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTGTACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACTACACTGTCTTGATTAACACAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCTGTTTTGAGGTCAGGTAGTGTCAGTCCCTCTAACTTCATTTTTCAAAGTTGTTAGGGGATTATAGGTTCTTTGCAAATTTCTATGCAAATTTTGGAATCAGTTTGTTAATTTCCAGAAAAAAGCCTCTTGC +>syndip_1_chr20:64125009-64128075 +ATTACAGGTGTGCACCACCACACCCAGCTAATTTTTTTGTATTTTCAGTAGAGATGAGGT +TTCACTGTGTTAGCCAGGATGGTCTCGATTTCCTGACCTCATGATCCACCCACCTTGGCC +TCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGCGCCCGGACACACTTTGCTAGTTTT +TTTTTTTTGTTTTGTTTTTTTAGTAGCAGTGCTGGGATTACAGGTGTCAGCCACCATGCC +TGGCTCAAATACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACTACACCATCT +TGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTC +AAATACCACACCGTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTA +CCAAAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATAA +CACACCGTCTTGATTACCACAGCTTTATACTCAAATACTACACCGTCTTGATTACCACAG +CTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACT +GTCTTGATTCCTATAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTAT +ACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTG +ATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAA +TACCACCCTGTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTACCA +CAGCTGTATACTCAAATACTACACCGTCTTGATTACCACAGCTGTATACTCAAATACTAC +ACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACCGCTT +TATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTC +TGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTC +AAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTAC +TACAGCTTTATACTCAAATACCACACTATCTTGATTACTACAGCTTTATACTCAAATACT +ACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCT +TTATACTCAAATACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACCGT +CTTGATTACCACAGCTGTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATAC +TCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGAT +TACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATA +CCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTGATTACTACAG +CTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACT +GTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTAT +ACTCAAATACCACACTGTCTTGATTACCACAGCTGTATACTCAAATACCACACTGTCTTG +ATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACGCAA +ATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACT +ACAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACTA +CACTGTCTTGATTAACACAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCT +TTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGT +CTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATAC +TCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGAT +TACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAAT +ACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACTAT +AGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCTGTTTTGAGG +TCAGGTAGTGTCAGTCCCTCTAACTTCATTTTTCAAAGTTGTTAGGGGATTATAGGTTCT +TTGCAAATTTCTATGCAAATTTTGGAATCAGTTTGTTAATTTCCAGAAAAAAGCCTCTTG +C +>syndip_2_chr20:64125009-64128075 +ATTACAGGTGTGCACCACCACACCCAGCTAATTTTTTTGTATTTTCAGTAGAGATGAGGT +TTCACTGTGTTAGCCAGGATGGTCTCGATTTCCTGACCTCATGATCCACCCACCTTGGCC +TCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGCGCCCGGACACACTTTGCTAGTTTT +TTTTTTTTGTTTTGTTTTTTTAGTAGCAGTGCTGGGATTACAGGTGTCAGCCACCATGCC +TGGCTCAAATACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACTACACCATCT +TGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTC +AAATACCACACCGTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTA +CCAAAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATAA +CACACCGTCTTGATTACCACAGCTTTATACTCAAATACTACACCGTCTTGATTACCACAG +CTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACT +GTCTTGATTCCTATAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTAT +ACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTG +ATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAA +TACCACCCTGTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTACCA +CAGCTGTATACTCAAATACTACACCGTCTTGATTACCACAGCTGTATACTCAAATACTAC +ACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACCGCTT +TATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTC +TGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTC +AAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTAC +TACAGCTTTATACTCAAATACCACACTATCTTGATTACTACAGCTTTATACTCAAATACT +ACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCT +TTATACTCAAATACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACCGT +CTTGATTACCACAGCTGTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATAC +TCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGAT +TACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATA +CCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTGATTACTACAG +CTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACT +GTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTAT +ACTCAAATACCACACTGTCTTGATTACCACAGCTGTATACTCAAATACCACACTGTCTTG +ATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACGCAA +ATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACT +ACAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACTA +CACTGTCTTGATTAACACAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCT +TTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGT +CTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATAC +TCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGAT +TACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAAT +ACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACTAT +AGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCTGTTTTGAGG +TCAGGTAGTGTCAGTCCCTCTAACTTCATTTTTCAAAGTTGTTAGGGGATTATAGGTTCT +TTGCAAATTTCTATGCAAATTTTGGAATCAGTTTGTTAATTTCCAGAAAAAAGCCTCTTG +C +>p:HG002_1_chr20:64125009-64128075 +ATTACAGGTGTGCACCACCACACCCAGCTAATTTTTTTGTATTTTCAGTAGAGATGAGGT +TTCACTGTGTTAGCCAGGATGGTCTCGATTTCCTGACCTCATGATCCACCCACCTTGGCC +TCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGCGCCCGGACACACTTTGCTAGTTTT +TTTTTTTTGTTTTGTTTTTTTAGTAGCAGTGCTGGGATTACAGGTGTCAGCCACCATGCC +TGGCTCAAATACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACTACACCATCT +TGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTC +AAATACCACACCGTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTA +CCAAAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATAA +CACACCGTCTTGATTACCACAGCTTTATACTCAAATACTACACCGTCTTGATTACCACAG +CTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACT +GTCTTGATTCCTATAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTAT +ACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTG +ATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAA +TACCACCCTGTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTACCA +CAGCTGTATACTCAAATACTACACCGTCTTGATTACCACAGCTGTATACTCAAATACTAC +ACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACCGCTT +TATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTC +TGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTC +AAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTAC +TACAGCTTTATACTCAAATACCACACTATCTTGATTACTACAGCTTTATACTCAAATACT +ACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCT +TTATACTCAAATACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACCGT +CTTGATTACCACAGCTGTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATAC +TCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGAT +TACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATA +CCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTGATTACTACAG +CTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACT +GTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTAT +ACTCAAATACCACACTGTCTTGATTACCACAGCTGTATACTCAAATACCACACTGTCTTG +ATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACGCAA +ATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACT +ACAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACTA +CACTGTCTTGATTAACACAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCT +TTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGT +CTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATAC +TCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGAT +TACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAAT +ACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACTAT +AGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCTGTTTTGAGG +TCAGGTAGTGTCAGTCCCTCTAACTTCATTTTTCAAAGTTGTTAGGGGATTATAGGTTCT +TTGCAAATTTCTATGCAAATTTTGGAATCAGTTTGTTAATTTCCAGAAAAAAGCCTCTTG +C +>p:HG002_2_chr20:64125009-64128075 +ATTACAGGTGTGCACCACCACACCCAGCTAATTTTTTTGTATTTTCAGTAGAGATGAGGT +TTCACTGTGTTAGCCAGGATGGTCTCGATTTCCTGACCTCATGATCCACCCACCTTGGCC +TCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGCGCCCGGACACACTTTGCTAGTTTT +TTTTTTTTGTTTTGTTTTTTTAGTAGCAGTGCTGGGATTACAGGTGTCAGCCACCATGCC +TGGCTCAAATACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACTACACCATCT +TGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTC +AAATACCACACCGTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTA +CCAAAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATAA +CACACCGTCTTGATTACCACAGCTTTATACTCAAATACTACACCGTCTTGATTACCACAG +CTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACT +GTCTTGATTCCTATAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTAT +ACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTG +ATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAA +TACCACCCTGTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTACCA +CAGCTGTATACTCAAATACTACACCGTCTTGATTACCACAGCTGTATACTCAAATACTAC +ACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACCGCTT +TATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTC +TGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTC +AAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTAC +TACAGCTTTATACTCAAATACCACACTATCTTGATTACTACAGCTTTATACTCAAATACT +ACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCT +TTATACTCAAATACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACCGT +CTTGATTACCACAGCTGTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATAC +TCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGAT +TACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATA +CCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTGATTACTACAG +CTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACT +GTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTAT +ACTCAAATACCACACTGTCTTGATTACCACAGCTGTATACTCAAATACCACACTGTCTTG +ATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACGCAA +ATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACT +ACAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACTA +CACTGTCTTGATTAACACAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCT +TTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGT +CTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATAC +TCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGAT +TACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAAT +ACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACTAT +AGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCTGTTTTGAGG +TCAGGTAGTGTCAGTCCCTCTAACTTCATTTTTCAAAGTTGTTAGGGGATTATAGGTTCT +TTGCAAATTTCTATGCAAATTTTGGAATCAGTTTGTTAATTTCCAGAAAAAAGCCTCTTG +C diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/haps.fa.ref.fa new file mode 100644 index 00000000..ef619193 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:64125009-64128075 +ATTACAGGTGTGCACCACCACACCCAGCTAATTTTTTTGTATTTTCAGTAGAGATGAGGTTTCACTGTGTTAGCCAGGATGGTCTCGATTTCCTGACCTCATGATCCACCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGCGCCCGGACACACTTTGCTAGTTTTTTTTTTTTGTTTTGTTTTTTTAGTAGCAGTGCTGGGATTACAGGTGTCAGCCACCATGCCTGGCTCAAATACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACTACACCATCTTGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTCAAATACCACACCGTCTTGATTACCAAAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATAACACACCGTCTTGATTACCACAGCTTTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTCCTATAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATACCACCCTGTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTCAAATACTACTGTCCTGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACTATCTTGATTACTACAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATAACACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTCAAATACCACACTGTCTTGATTACCACAGCTGTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACGCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACTACACTGTCTTGATTAACACAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTAACACAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTGTACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACTACACTGTCTTGATTAACACAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCTGTTTTGAGGTCAGGTAGTGTCAGTCCCTCTAACTTCATTTTTCAAAGTTGTTAGGGGATTATAGGTTCTTTGCAAATTTCTATGCAAATTTTGGAATCAGTTTGTTAATTTCCAGAAAAAAGCCTCTTGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/msa.fa new file mode 100644 index 00000000..c309b2ea --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/msa.fa @@ -0,0 +1,280 @@ +>ref_chr20_64125009_64128075 +attacaggtgtgcaccaccacacccagctaatttttttgtattttcagtagagatgaggt +ttcactgtgttagccaggatggtctcgatttcctgacctcatgatccacccaccttggcc +tcccaaagtgctgggattacaggtgtgagccactgcgcccggacacactttgctagtttt +ttttttttgttttgtttttttagtagcagtgctgggattacaggtgtcagccaccatgcc +tggctcaaatactacactgtcttgattactacagctttatactcaaatactacaccatct +tgattactacagctt--------------------------------------tatactc +aaataccacaccgtcttgattaccacagctgtatactcaaataccacaccgtcttgatta +ccaaagctttatactcaaataccacactgtcttgattaccacagct-------------- +-----------------ttatactcaaataacacaccgtcttgattaccacagctttata +ctcaaatactacaccgtcttgattaccacagctttatactcaaataccacactgtcttga +ttaccacagctttatactcaaatactacactgtcttgattcctatagc------------ +-------------------tttatactcaaataccacactgtcttgattaccacagcttt +atactcaaatactacactgtcttgattactatagctttatactcaaatactacactgtct +tgattactatagctttatactcaaatactacactgtctgattactacagctttatactca +aataccaccctgtcttgattaccacagctttatactcaaataccacaccgtcttgattac +cacagctgtatactcaaatactactgtcctgattactacagctttatactcaaataccac +accgtcttgattaccacagctgtatactcaaatactacaccgtcttgattaccacagctt +tatactcaaatactacaccgtcttgattaccacagctttatactcaaataccacactgtc +ttgattactatagctttatactcaaatactacactgtctgattactacagctttatactc +aaataccacactgtcttgattaccacagctttatactcaaatactacactgtcttgatta +ctatagctttatactcaaatactacactgtctgattactacagctttatactcaaatacc +acactatcttgattactacagctttatactcaaatactacactgtctgattactacagct +ttatactcaaataccacaccgtcttgattaccacagctttatactcaaatactacactgt +cttgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatac +tcaaatactacaccgtcttgattaccacagctttatactcaaatactacaccgtcttgat +taccacagctttatactcaaataacacactgtcttgattactatagctttatactcaaat +actacactgtctgattactacagctttatactcaaataccacactgtcttgattaccaca +gctttatactcaaatactacactgtctgattactacagctttatactcaaataccacact +gtcttgattaccacagctttatactcaaatactacactgtcttgattaccacagctttat +actcaaataccacaccgtcttgattaccacagctgtatactcaaataccacactgtcttg +attaccacagctgtatactcaaataccacactgtcttgattaccacagctttatactcaa +ataccacactgtcttgattactatagctttatactcaaataccacactgtcttgattacc +acagctttatacgcaaataccacactgtcttgattactatagctttatactcaaatacca +cactgtcttgattactacagctttatactcaaataccacactgtcttgattactacagct +ttatactcaaatactacactgtcttgattaacacagctttatactcaaatactacactgt +cttgattaccacagctttatactcaaatactacactgtcttgattactatagctttatac +tcaaataccacactgtcttgattactatagctttatactcaaatactacactgtcttgat +taccacagctttatactcaaatactacactgtcttgattact------------------ +--------------------atagctttatactcaaataccacactgtcttgattaccac +--------------------------------------agctttatactcaaataccaca +ctgtcttgattaccacagctttatactcaaataccacactgtcttgattaccacagcttt +atactcaaataccacactgtcttgattactatagctttatactcaaataccacactgtct +tgattactacagctttatactcaaataccacactgtcttgattaacacagctttatactc +aaatactacactgtcttgattaccacagctttatactcaaatactacactgtcttgatta +ctatagctttatactcaaataccacactgtcttgattactatagctttatactcaaatac +tacactgtcttgattaccacagctttatactcaaatactacactgtcttgattactatag +ctttgtactcaaataccacactgtcttgattaccacagctttatactcaaataccacact +gtcttgattaccacagctttatactcaaataccacactgtcttgattactatagctttat +actcaaataccacactgtcttgattactacagctttatactcaaataccacactgtcttg +attactacagctttatactcaaatactacactgtcttgattaacacagctttatactcaa +atactacactgtcttgattaccacagctttatactcaaatactacactgtcttgattact +atagctttatactcaaataccacactgtcttgattactatagctttatactctgttttga +ggtcaggtagtgtcagtccctctaacttcatttttcaaagttgttaggggattataggtt +ctttgcaaatttctatgcaaattttggaatcagtttgttaatttccagaaaaaagcctct +tgc +>syndip_1_chr20:64125009-64128075 +attacaggtgtgcaccaccacacccagctaatttttttgtattttcagtagagatgaggt +ttcactgtgttagccaggatggtctcgatttcctgacctcatgatccacccaccttggcc +tcccaaagtgctgggattacaggtgtgagccactgcgcccggacacactttgctagtttt +ttttttttgttttgtttttttagtagcagtgctgggattacaggtgtcagccaccatgcc +tggctcaaatactacactgtcttgattactacagctttatactcaaatactacaccatct +tgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatactc +aaataccacaccgtcttgattaccacagctttatactcaaataccacaccgtcttgatta +ccaaagctttata-------------------------------ctcaaataccacactg +tcttgattaccacagctttatactcaaataacacaccgtcttgattaccacagctttata +ctcaaatactacaccgtcttgattaccacagctttatactcaaataccacactgtcttga +ttaccacagctttata-------------------------------ctcaaataccaca +ctgtcttgattcctatagctttatactcaaataccacactgtcttgattaccacagcttt +atactcaaatactacactgtcttgattactatagctttatactcaaatactacactgtct +tgattactatagctttatactcaaatactacactgtctgattactacagctttatactca +aataccaccctgtcttgattaccacagctttatactcaaataccacaccgtcttgattac +cacagctgtatactcaaatact------------------------------------ac +accgtcttgattaccacagctgtatactcaaatactacactgtcttgattaccacagctt +tatactcaaataccacactgtcttgattaccaccgctttatactcaaataccacactgtc +ttgattactatagctttatactcaaatactacactgtctgattactacagctttatactc +aaataccacactgtcttgattaccacagctttatactcaaatactacactgtcttgatta +ctatagctttatactcaaatactacactgtctgattactacagctttatactcaaatacc +acactatcttgattactacagctttatactcaaatactacactgtctgattactacagct +ttatactcaaataccacaccgtcttgattaccacagctttatactcaaatactacactgt +cttgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatac +tcaaatactacaccgtcttgattaccacagctttatactcaaatactacaccgtcttgat +taccacagctttatactcaaataccacactgtcttgattactatagctttatactcaaat +actacactgtctgattactacagctttatactcaaataccacactgtcttgattaccaca +gctttatactcaaatactacactgtctgattactacagctttatactcaaataccacact +gtcttgattaccacagctttatactcaaatactacactgtcttgattaccacagctttat +actcaaataccacaccgtcttgattaccacagctgtatactcaaataccacactgtcttg +attaccacagctgtatactcaaataccacactgtcttgattaccacagctttatactcaa +atacc------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------acactgtcttgattaccacagctttatac +gcaaataccacactgtcttgattactatagctttatactcaaataccacactgtcttgat +tactacagctttatactcaaataccacactgtcttgattactacagctttatactcaaat +actacactgtcttgattaacacagctttatactcaaatactacactgtcttgattaccac +agctttatactcaaatactacactgtcttgattactatagctttatactcaaataccaca +ctgtcttgattactatagctttatactcaaatactacactgtcttgattaccacagcttt +atactcaaatactacactgtcttgattactatagctttatactcaaataccacactgtct +tgattaccac-------------------------------------------------- +------------------------------------------------------------ +----agctttatactcaaataccacactgtcttgattaccacagctttatactcaaatac +tacactgtcttgattactac---------------------------------------- +------------------------------------agctttatactcaaatacc----- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------acactgtcttgattact +atagctttatactcaaataccacactgtcttgattactatagctttatactctgttttga +ggtcaggtagtgtcagtccctctaacttcatttttcaaagttgttaggggattataggtt +ctttgcaaatttctatgcaaattttggaatcagtttgttaatttccagaaaaaagcctct +tgc +>syndip_2_chr20:64125009-64128075 +attacaggtgtgcaccaccacacccagctaatttttttgtattttcagtagagatgaggt +ttcactgtgttagccaggatggtctcgatttcctgacctcatgatccacccaccttggcc +tcccaaagtgctgggattacaggtgtgagccactgcgcccggacacactttgctagtttt +ttttttttgttttgtttttttagtagcagtgctgggattacaggtgtcagccaccatgcc +tggctcaaatactacactgtcttgattactacagctttatactcaaatactacaccatct +tgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatactc +aaataccacaccgtcttgattaccacagctttatactcaaataccacaccgtcttgatta +ccaaagctttata-------------------------------ctcaaataccacactg +tcttgattaccacagctttatactcaaataacacaccgtcttgattaccacagctttata +ctcaaatactacaccgtcttgattaccacagctttatactcaaataccacactgtcttga +ttaccacagctttata-------------------------------ctcaaataccaca +ctgtcttgattcctatagctttatactcaaataccacactgtcttgattaccacagcttt +atactcaaatactacactgtcttgattactatagctttatactcaaatactacactgtct +tgattactatagctttatactcaaatactacactgtctgattactacagctttatactca +aataccaccctgtcttgattaccacagctttatactcaaataccacaccgtcttgattac +cacagctgtatactcaaatact------------------------------------ac +accgtcttgattaccacagctgtatactcaaatactacactgtcttgattaccacagctt +tatactcaaataccacactgtcttgattaccaccgctttatactcaaataccacactgtc +ttgattactatagctttatactcaaatactacactgtctgattactacagctttatactc +aaataccacactgtcttgattaccacagctttatactcaaatactacactgtcttgatta +ctatagctttatactcaaatactacactgtctgattactacagctttatactcaaatacc +acactatcttgattactacagctttatactcaaatactacactgtctgattactacagct +ttatactcaaataccacaccgtcttgattaccacagctttatactcaaatactacactgt +cttgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatac +tcaaatactacaccgtcttgattaccacagctttatactcaaatactacaccgtcttgat +taccacagctttatactcaaataccacactgtcttgattactatagctttatactcaaat +actacactgtctgattactacagctttatactcaaataccacactgtcttgattaccaca +gctttatactcaaatactacactgtctgattactacagctttatactcaaataccacact +gtcttgattaccacagctttatactcaaatactacactgtcttgattaccacagctttat +actcaaataccacaccgtcttgattaccacagctgtatactcaaataccacactgtcttg +attaccacagctgtatactcaaataccacactgtcttgattaccacagctttatactcaa +atacc------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------acactgtcttgattaccacagctttatac +gcaaataccacactgtcttgattactatagctttatactcaaataccacactgtcttgat +tactacagctttatactcaaataccacactgtcttgattactacagctttatactcaaat +actacactgtcttgattaacacagctttatactcaaatactacactgtcttgattaccac +agctttatactcaaatactacactgtcttgattactatagctttatactcaaataccaca +ctgtcttgattactatagctttatactcaaatactacactgtcttgattaccacagcttt +atactcaaatactacactgtcttgattactatagctttatactcaaataccacactgtct +tgattaccac-------------------------------------------------- +------------------------------------------------------------ +----agctttatactcaaataccacactgtcttgattaccacagctttatactcaaatac +cacactgtcttgattactac---------------------------------------- +------------------------------------agctttatactcaaatacc----- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------acactgtcttgattact +atagctttatactcaaataccacactgtcttgattactatagctttatactctgttttga +ggtcaggtagtgtcagtccctctaacttcatttttcaaagttgttaggggattataggtt +ctttgcaaatttctatgcaaattttggaatcagtttgttaatttccagaaaaaagcctct +tgc +>p:HG002_1_chr20:64125009-64128075 +attacaggtgtgcaccaccacacccagctaatttttttgtattttcagtagagatgaggt +ttcactgtgttagccaggatggtctcgatttcctgacctcatgatccacccaccttggcc +tcccaaagtgctgggattacaggtgtgagccactgcgcccggacacactttgctagtttt +ttttttttgttttgtttttttagtagcagtgctgggattacaggtgtcagccaccatgcc +tggctcaaatactacactgtcttgattactacagctttatactcaaatactacaccatct +tgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatactc +aaataccacaccgtcttgattaccacagctttatactcaaataccacaccgtcttgatta +ccaaagctttata-------------------------------ctcaaataccacactg +tcttgattaccacagctttatactcaaataacacaccgtcttgattaccacagctttata +ctcaaatactacaccgtcttgattaccacagctttatactcaaataccacactgtcttga +ttaccacagctttata-------------------------------ctcaaataccaca +ctgtcttgattcctatagctttatactcaaataccacactgtcttgattaccacagcttt +atactcaaatactacactgtcttgattactatagctttatactcaaatactacactgtct +tgattactatagctttatactcaaatactacactgtctgattactacagctttatactca +aataccaccctgtcttgattaccacagctttatactcaaataccacaccgtcttgattac +cacagctgtatactcaaatact------------------------------------ac +accgtcttgattaccacagctgtatactcaaatactacactgtcttgattaccacagctt +tatactcaaataccacactgtcttgattaccaccgctttatactcaaataccacactgtc +ttgattactatagctttatactcaaatactacactgtctgattactacagctttatactc +aaataccacactgtcttgattaccacagctttatactcaaatactacactgtcttgatta +ctatagctttatactcaaatactacactgtctgattactacagctttatactcaaatacc +acactatcttgattactacagctttatactcaaatactacactgtctgattactacagct +ttatactcaaataccacaccgtcttgattaccacagctttatactcaaatactacactgt +cttgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatac +tcaaatactacaccgtcttgattaccacagctttatactcaaatactacaccgtcttgat +taccacagctttatactcaaataccacactgtcttgattactatagctttatactcaaat +actacactgtctgattactacagctttatactcaaataccacactgtcttgattaccaca +gctttatactcaaatactacactgtctgattactacagctttatactcaaataccacact +gtcttgattaccacagctttatactcaaatactacactgtcttgattaccacagctttat +actcaaataccacaccgtcttgattaccacagctgtatactcaaataccacactgtcttg +attaccacagctgtatactcaaataccacactgtcttgattaccacagctttatactcaa +atacc------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------acactgtcttgattaccacagctttatac +gcaaataccacactgtcttgattactatagctttatactcaaataccacactgtcttgat +tactacagctttatactcaaataccacactgtcttgattactacagctttatactcaaat +actacactgtcttgattaacacagctttatactcaaatactacactgtcttgattaccac +agctttatactcaaatactacactgtcttgattactatagctttatactcaaataccaca +ctgtcttgattactatagctttatactcaaatactacactgtcttgattaccacagcttt +atactcaaatactacactgtcttgattactatagctttatactcaaataccacactgtct +tgattaccac-------------------------------------------------- +------------------------------------------------------------ +----agctttatactcaaataccacactgtcttgattaccacagctttatactcaaatac +cacactgtcttgattactac---------------------------------------- +------------------------------------agctttatactcaaatacc----- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------acactgtcttgattact +atagctttatactcaaataccacactgtcttgattactatagctttatactctgttttga +ggtcaggtagtgtcagtccctctaacttcatttttcaaagttgttaggggattataggtt +ctttgcaaatttctatgcaaattttggaatcagtttgttaatttccagaaaaaagcctct +tgc +>p:HG002_2_chr20:64125009-64128075 +attacaggtgtgcaccaccacacccagctaatttttttgtattttcagtagagatgaggt +ttcactgtgttagccaggatggtctcgatttcctgacctcatgatccacccaccttggcc +tcccaaagtgctgggattacaggtgtgagccactgcgcccggacacactttgctagtttt +ttttttttgttttgtttttttagtagcagtgctgggattacaggtgtcagccaccatgcc +tggctcaaatactacactgtcttgattactacagctttatactcaaatactacaccatct +tgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatactc +aaataccacaccgtcttgattaccacagctttatactcaaataccacaccgtcttgatta +ccaaagctttata-------------------------------ctcaaataccacactg +tcttgattaccacagctttatactcaaataacacaccgtcttgattaccacagctttata +ctcaaatactacaccgtcttgattaccacagctttatactcaaataccacactgtcttga +ttaccacagctttata-------------------------------ctcaaataccaca +ctgtcttgattcctatagctttatactcaaataccacactgtcttgattaccacagcttt +atactcaaatactacactgtcttgattactatagctttatactcaaatactacactgtct +tgattactatagctttatactcaaatactacactgtctgattactacagctttatactca +aataccaccctgtcttgattaccacagctttatactcaaataccacaccgtcttgattac +cacagctgtatactcaaatact------------------------------------ac +accgtcttgattaccacagctgtatactcaaatactacactgtcttgattaccacagctt +tatactcaaataccacactgtcttgattaccaccgctttatactcaaataccacactgtc +ttgattactatagctttatactcaaatactacactgtctgattactacagctttatactc +aaataccacactgtcttgattaccacagctttatactcaaatactacactgtcttgatta +ctatagctttatactcaaatactacactgtctgattactacagctttatactcaaatacc +acactatcttgattactacagctttatactcaaatactacactgtctgattactacagct +ttatactcaaataccacaccgtcttgattaccacagctttatactcaaatactacactgt +cttgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatac +tcaaatactacaccgtcttgattaccacagctttatactcaaatactacaccgtcttgat +taccacagctttatactcaaataccacactgtcttgattactatagctttatactcaaat +actacactgtctgattactacagctttatactcaaataccacactgtcttgattaccaca +gctttatactcaaatactacactgtctgattactacagctttatactcaaataccacact +gtcttgattaccacagctttatactcaaatactacactgtcttgattaccacagctttat +actcaaataccacaccgtcttgattaccacagctgtatactcaaataccacactgtcttg +attaccacagctgtatactcaaataccacactgtcttgattaccacagctttatactcaa +atacc------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------acactgtcttgattaccacagctttatac +gcaaataccacactgtcttgattactatagctttatactcaaataccacactgtcttgat +tactacagctttatactcaaataccacactgtcttgattactacagctttatactcaaat +actacactgtcttgattaacacagctttatactcaaatactacactgtcttgattaccac +agctttatactcaaatactacactgtcttgattactatagctttatactcaaataccaca +ctgtcttgattactatagctttatactcaaatactacactgtcttgattaccacagcttt +atactcaaatactacactgtcttgattactatagctttatactcaaataccacactgtct +tgattaccac-------------------------------------------------- +------------------------------------------------------------ +----agctttatactcaaataccacactgtcttgattaccacagctttatactcaaatac +tacactgtcttgattactac---------------------------------------- +------------------------------------agctttatactcaaatacc----- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------acactgtcttgattact +atagctttatactcaaataccacactgtcttgattactatagctttatactctgttttga +ggtcaggtagtgtcagtccctctaacttcatttttcaaagttgttaggggattataggtt +ctttgcaaatttctatgcaaattttggaatcagtttgttaatttccagaaaaaagcctct +tgc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/msa.fa.fai new file mode 100644 index 00000000..8e2fb2e7 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_64125009_64128075 3243 29 60 61 +syndip_1_chr20:64125009-64128075 3243 3361 60 61 +syndip_2_chr20:64125009-64128075 3243 6693 60 61 +p:HG002_1_chr20:64125009-64128075 3243 10026 60 61 +p:HG002_2_chr20:64125009-64128075 3243 13359 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/output.vcf.gz new file mode 100644 index 00000000..7a978db9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/output.vcf.gz.tbi new file mode 100644 index 00000000..87896cdb Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64125109-64127975/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/base.vcf.gz new file mode 100644 index 00000000..44d03aea Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/base.vcf.gz.tbi new file mode 100644 index 00000000..b33e92cd Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/comp.vcf.gz new file mode 100644 index 00000000..d37f252d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/comp.vcf.gz.tbi new file mode 100644 index 00000000..c7395992 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/haps.fa new file mode 100644 index 00000000..3057221c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/haps.fa @@ -0,0 +1,246 @@ +>ref_chr20_64131704_64134056 +AGGCTGTTGTAGGTGGGCCAGGAGGGGCTGGGCAGCCCATGAGGGTGAGGCTGAGACTCCACACTGAGCCCAGGTTTAGGGGACCTGGTGGGGGTCACAGCCTCCCCTGTCCCAGACTTCTCCTGGCCTCTCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCACTCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACTCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATGAGACCCCCTCACTGTCCACTCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCGCCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCGCCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACTCTCATGTCCTATGAGACCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCAACTCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCAAAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCAAAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCAAAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCATATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCATATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCAGGACCCTCTGCATTTGCTCCTTGGGTTCCCGGAACTTGAGCTTGGGTCTTGGTCCACAGCAGCTTTGGGAAGGGCCCTCGGCTGCTTTTTGCTTCAGCAGCTGGGGAGCAGTTAACTTTCAGACCCGGCCC +>syndip_1_chr20:64131704-64134056 +AGGCTGTTGTAGGTGGGCCAGGAGGGGCTGGGCAGCCCATGAGGGTGAGGCTGAGACTCC +ACACTGAGCCCAGGTTTAGGGGACCTGGTGGGGGTCACAGCCTCCCCTGTCCCAGACTTC +TCCTGGCCTCTCTCATGTCCTATGAGACCCCCTCACTGTCCACTCTCATGGCCTGTAGAG +ACCCCCTCACTGTCAACTCTCATGTCCTATAGAGACCCCCTCACTGTCAACTCTCATGTC +CTATGAGACCCCCTCACTGTCCACTCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCC +TCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACT +GTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCC +CCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATA +GAGACCCCCTCACTGTCCACTCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCAT +GTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCA +CCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTC +ACTGTCCACTCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGA +CCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCC +TGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACTCT +CATGTCCTATGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGT +CCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCC +CTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATG +AGACCCCCTCACTGTCCACTCTCATGTCCTATGAGACCCCCTCACTGTCCACTCTCATGG +CCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCAC +CCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCA +CTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGAC +CCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCT +GTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACTCT +CATGTCCTATAGAGACCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGT +CCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCC +CTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACTCTCATGTCCTATGA +GACCCCCTCACTGTCCACTCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGT +CCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCACC +CTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCAC +TGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACC +CCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCGTGTCCTA +TAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTC +ATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTC +CACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCC +TCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGA +GACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCAACTCTCATGT +CCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATGAGACCCCCTCACTGTCCACC +CTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCAC +TGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACC +CCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCAACTCTCATGTCCTA +TAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTCTCCACCCTC +ATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGT +CCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCC +TCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGA +GACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGT +CCTATAGAGACCCCCTCACTCTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCAC +CCTCGTGTCCTATAGAGACCCCCTCACTCTCCACCCTCATGGCCTATAGAGACCCCCTCA +CTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACTCTCATGTCCTATGAGAC +CCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCT +ATGAGACCCCCTCACTGTCCACTCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCA +TGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCC +ACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTC +ACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACTCTCATGTCCTATGAGA +CCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGGCCT +ATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTC +ATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGT +CCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACTCTCATGGCCTGTAGAGACCCC +CTCACTGTCCACCCATATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCAGGACCCTCT +GCATTTGCTCCTTGGGTTCCCGGAACTTGAGCTTGGGTCTTGGTCCACAGCAGCTTTGGG +AAGGGCCCTCGGCTGCTTTTTGCTTCAGCAGCTGGGGAGCAGTTAACTTTCAGACCCGGC +CC +>syndip_2_chr20:64131704-64134056 +AGGCTGTTGTAGGTGGGCCAGGAGGGGCTGGGCAGCCCATGAGGGTGAGGCTGAGACTCC +ACACTGAGCCCAGGTTTAGGGGACCTGGTGGGGGTCACAGCCTCCCCTGTCCCAGACTTC +TCCTGGCCTCTCTCATGTCCTATGAGACCCCCTCACTGTCCACTCTCATGGCCTGTAGAG +ACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGC +CTATGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCC +TCATGTCCTATAGAGACCCCTCACTGTCCACCCTCATGGCCTATGAGACCCCCTCACTGT +CCACTCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCC +CTCACTGTCCACCCTCATGTCCTATAGAGACCCCTCACTGTCCACCCTCATGGCCTATGA +GACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGT +CCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACC +CTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACT +GTCCACTCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACC +CCCTCACTGTCCACCCTCGTGTCCTATGAGACCCCCTCACTGTCCACCCTCGTGTCCTAT +AGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCA +TGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCC +ACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCT +CACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGA +GACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGG +CCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCAC +CCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCAC +TGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACC +CCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTA +TAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCA +TGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTC +CACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCC +TCACTGTCCACCCTCGTGTCCTATGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGA +GACCCCCTCACTGTCCACCCTCATGGCCTATGAGACCCCCTCACTGTCCACCCTCGTGTC +CTATGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCC +TCATGGCCTATGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTG +TCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCC +CCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTAT +GAGACCCCCTCACTGTCCACTCTCATGTCCTATAGAGACCCCTCACTGTCCACCCTCATG +GCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCA +CCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTC +ACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAG +ACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTC +CTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACC +CTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCAC +TGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACC +CCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTA +TAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTC +GTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGT +CCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCC +CTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATG +AGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATG +TCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCA +CCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTC +ACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATGAGA +CCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCC +TATAGAGACCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCT +CGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGT +CCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCC +TCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAG +AGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATG +TCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCA +CCCATATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTC +ACTGTCCACCCTCAGGACCCTCTGCATTTGCTCCTTGGGTTCCCGGAACTTGAGCTTGGG +TCTTGGTCCACAGCAGCTTTGGGAAGGGCCCTCGGCTGCTTTTTGCTTCAGCAGCTGGGG +AGCAGTTAACTTTCAGACCCGGCCC +>p:HG002_1_chr20:64131704-64134056 +AGGCTGTTGTAGGTGGGCCAGGAGGGGCTGGGCAGCCCATGAGGGTGAGGCTGAGACTCC +ACACTGAGCCCAGGTTTAGGGGACCTGGTGGGGGTCACAGCCTCCCCTGTCCCAGACTTC +TCCTGGCCTCTCTCATGTCCTATGAGACCCCCTCACTGTCCACTCTCATGGCCTGTAGAG +ACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGC +CTATGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCC +TCATGTCCTATAGAGACCCCTCACTGTCCACCCTCATGGCCTATGAGACCCCCTCACTGT +CCACTCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCC +CTCACTGTCCACCCTCATGTCCTATAGAGACCCCTCACTGTCCACCCTCATGGCCTATGA +GACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGT +CCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACC +CTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACT +GTCCACTCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACC +CCCTCACTGTCCACCCTCGTGTCCTATGAGACCCCCTCACTGTCCACCCTCGTGTCCTAT +AGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCA +TGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCC +ACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCT +CACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGA +GACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGG +CCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCAC +CCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCAC +TGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACC +CCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTA +TAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCA +TGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTC +CACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCC +TCACTGTCCACCCTCGTGTCCTATGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGA +GACCCCCTCACTGTCCACCCTCATGGCCTATGAGACCCCCTCACTGTCCACCCTCGTGTC +CTATGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCC +TCATGGCCTATGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTG +TCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCC +CCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTAT +GAGACCCCCTCACTGTCCACTCTCATGTCCTATAGAGACCCCTCACTGTCCACCCTCATG +GCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCA +CCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTC +ACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAG +ACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTC +CTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACC +CTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCAC +TGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACC +CCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTA +TAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTC +GTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGT +CCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCC +CTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATG +AGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATG +TCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCA +CCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTC +ACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATGAGA +CCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCC +TATAGAGACCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCT +CGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGT +CCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCC +TCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAG +AGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATG +TCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCA +CCCATATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTC +ACTGTCCACCCTCAGGACCCTCTGCATTTGCTCCTTGGGTTCCCGGAACTTGAGCTTGGG +TCTTGGTCCACAGCAGCTTTGGGAAGGGCCCTCGGCTGCTTTTTGCTTCAGCAGCTGGGG +AGCAGTTAACTTTCAGACCCGGCCC +>p:HG002_2_chr20:64131704-64134056 +AGGCTGTTGTAGGTGGGCCAGGAGGGGCTGGGCAGCCCATGAGGGTGAGGCTGAGACTCC +ACACTGAGCCCAGGTTTAGGGGACCTGGTGGGGGTCACAGCCTCCCCTGTCCCAGACTTC +TCCTGGCCTCTCTCATGTCCTATGAGACCCCCTCACTGTCCACTCTCATGGCCTGTAGAG +ACCCCCTCACTGTCAACTCTCATGTCCTATAGAGACCCCCTCACTGTCAACTCTCATGTC +CTATGAGACCCCCTCACTGTCCACTCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCC +TCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACT +GTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCC +CCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATA +GAGACCCCCTCACTGTCCACTCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCAT +GTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCA +CCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTC +ACTGTCCACTCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGA +CCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCC +TGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACTCT +CATGTCCTATGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGT +CCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCC +CTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATG +AGACCCCCTCACTGTCCACTCTCATGTCCTATGAGACCCCCTCACTGTCCACTCTCATGG +CCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCAC +CCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCA +CTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGAC +CCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCT +GTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACTCT +CATGTCCTATAGAGACCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGT +CCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCC +CTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACTCTCATGTCCTATGA +GACCCCCTCACTGTCCACTCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGT +CCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCACC +CTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCAC +TGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACC +CCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCGTGTCCTA +TAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTC +ATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTC +CACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCC +TCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGA +GACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCAACTCTCATGT +CCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATGAGACCCCCTCACTGTCCACC +CTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCAC +TGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACC +CCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCAACTCTCATGTCCTA +TAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTCTCCACCCTC +ATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGT +CCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCC +TCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGA +GACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGT +CCTATAGAGACCCCCTCACTCTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCAC +CCTCGTGTCCTATAGAGACCCCCTCACTCTCCACCCTCATGGCCTATAGAGACCCCCTCA +CTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACTCTCATGTCCTATGAGAC +CCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCT +ATGAGACCCCCTCACTGTCCACTCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCA +TGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCC +ACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTC +ACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACTCTCATGTCCTATGAGA +CCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGGCCT +ATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTC +ATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGT +CCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACTCTCATGGCCTGTAGAGACCCC +CTCACTGTCCACCCATATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCAGGACCCTCT +GCATTTGCTCCTTGGGTTCCCGGAACTTGAGCTTGGGTCTTGGTCCACAGCAGCTTTGGG +AAGGGCCCTCGGCTGCTTTTTGCTTCAGCAGCTGGGGAGCAGTTAACTTTCAGACCCGGC +CC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/haps.fa.ref.fa new file mode 100644 index 00000000..1dca2959 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:64131704-64134056 +AGGCTGTTGTAGGTGGGCCAGGAGGGGCTGGGCAGCCCATGAGGGTGAGGCTGAGACTCCACACTGAGCCCAGGTTTAGGGGACCTGGTGGGGGTCACAGCCTCCCCTGTCCCAGACTTCTCCTGGCCTCTCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCACTCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACTCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATGAGACCCCCTCACTGTCCACTCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCGCCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCGCCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACTCTCATGTCCTATGAGACCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCAACTCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCAAAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCAAAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCAAAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCATATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCATATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCAGGACCCTCTGCATTTGCTCCTTGGGTTCCCGGAACTTGAGCTTGGGTCTTGGTCCACAGCAGCTTTGGGAAGGGCCCTCGGCTGCTTTTTGCTTCAGCAGCTGGGGAGCAGTTAACTTTCAGACCCGGCCC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/msa.fa new file mode 100644 index 00000000..0c7d1060 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/msa.fa @@ -0,0 +1,330 @@ +>ref_chr20_64131704_64134056 +aggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactcc +acactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagacttc +tcctggcctctctcatgtcctat------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------gagaccccctcactgtccaccctcatgtcctgtagagaccccctcactgtcc +actctcatggcctatagagaccccctcactgtccaccctcatggcctgtagagaccccct +cactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctataga +gaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgt +cctatgagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccacc +ctcatgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcac +tgtccaccctca----------------------------------tgtcctgtagagac +cccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcgtgtccta +tagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctc +atgtcctat-gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgt +ccactctcatgtcctatagagaccccctcactgtccaccctcatggcctatgagaccccc +tcactgtccactctcatggcctatagagaccccctcactgtccaccctcatggcctatag +agaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatg +tcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtcca +ccctcatggcctat---------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----gagaccccctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccc +tcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccccctcact +gtccaccctcatgtcctatagagaccccctcactgtccgccctcatgtcctatgagaccc +cctcactgtccaccctcatgt--------------------------------------- +-----------------------------cctatagagaccccctcactgtccaccctca +tggcctgtagagaccccctcactgtccgccctcatgtcctat------------------ +-----------------gagaccccctcactgtccaccctcatgtcctgtagagaccccc +tcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctat-- +------------------------------------------------------------ +------------------------------------------------------------ +---------------gagaccccctcactgtccaccctcatgtcctat-gagaccccctc +actgtccaccctcatgtcctatgaga---------------------------------- +--cccctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccctcatgtc +ctat-----------------------------------gagaccccctcactgtccact +ctcatgtcctatgaga--cccctcactgtccaccctcatgtcctatagagaccccctcac +tgtccaccctcatggcctgtagagaccccctcactgtcaactctcatgtcctatgagacc +ccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcc-- +------------------------------------------------------------ +------------------------------------------------------------ +--------------aaagagaccccctcactgtccaccctcatggcctgtagagaccccc +tcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctatag +agaccccctcactgtccaccctcatgtccaaagagaccccctcactgtccaccctcatgg +cctgtagagac---------------------------------cccctcactgtccacc +ctcatggcctgta----------------------------------------------- +-------------------gagaccccctcactgtccaccctcatgtcctatagagaccc +cctcactgtccaccctcatgtccaaagagaccccctcactgtccaccctcatggcctgta +------------------------------------------------------------ +------gagaccccctcactgtccacccatatggcctgtagagaccccctcactgtccac +cctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctca +ctgtccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctgtagaga +ccccctcactgtccaccctcatggcctgtagagaccccctcactgtccacccatatggcc +tgtagagaccccctcactgtccaccctcaggaccctctgcatttgctccttgggttcccg +gaacttgagcttgggtcttggtccacagcagctttgggaagggccctcggctgctttttg +cttcagcagctggggagcagttaactttcagacccggccc +>syndip_1_chr20:64131704-64134056 +aggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactcc +acactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagacttc +tcctggcctctctcatgtcctatgagaccccctcactgtccactctcatggcctgtagag +accccctcactgtcaactctcatgtcctatagagaccccctcactgtcaactctcatgtc +ctatgagaccccctcactgtccactctcatggcctgtagagaccccctcactgtccaccc +tcatgt------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------cctatagagaccccctcactgtccaccctcatgg +cctgtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccacc +ctcatggcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcact +gtccaccctcatgtcctatagagaccccctcactgtccactctcatgtcctatagagacc +ccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctat +a----------------------------------------------------------- +--------gagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtcc +accctcatgtcctatagagaccccctcactgtccactctcatgtcctatagagaccccct +cactgtccaccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctataga +gaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgt +cctatgagaccccctcactgtccactctcatgtcctat-gagaccccctcactgtccacc +ctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcac +tgtccaccctcatggcctgtagagaccccctcactgtccaccctcgtgtcctatagagac +cccctcactgtccaccctcatgtcctatgagaccccctcactgtccactctcatgtccta +t-gagaccccctcactgtccactctcatggcctgtagagaccccctcactgtccaccctc +atgtcctgtagagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgt +ccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccc +tcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctgtag +agaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatg +gcctgtagagaccccctcactgtccactctcatgtcctatagaga-cccctcactgtcca +ccctcatggcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctc +actgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatgaga +ccccctcactgtccactctcatgtcctat-gagaccccctcactgtccactctcatggcc +tgtagagaccccctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccc +tcatgtcctgtagagaccccctcactgtccaccctcgtgtcctatagagaccccctcact +gtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccc +cctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctgt +agagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctca +tgtcctatagagaccccctcactgtccaccctcatgtcctat-gagaccccctcactgtc +caccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccc +tcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatag +agaccccctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccctcgtg +tcctatagagaccccctcactgtcaactctcatgtcctatagagaccccctcactgtcca +ccctcgtgtcctat-gagaccccctcactgtccaccctcatgtcctatagagaccccctc +actgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatagag +accccctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccctcgtgtc +ctatagagaccccctcactgtcaactctcatgtcctatagagaccccctcactgtccacc +ctcgtgtcctatagagaccccctcactctccaccctcatgtcctatagagaccccctcac +tgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctatgagacc +ccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtccta +tgagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctca +tggcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactctc +caccctcatggcctatagagaccccctcactgtccaccctcgtgtcctatagagaccccc +tcactctccaccctcatggcctatagagaccccctcactgtccaccctcatggcctatag +agaccccctcactgtccactctcatgtcctatgagaccccctcactgtccaccctcatgg +cctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccact +ctcatgtcctatgagaccccctcactgtccaccctcatggcctgtagagaccccctcact 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a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/msa.fa.fai new file mode 100644 index 00000000..0a959bfc --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_64131704_64134056 3880 29 60 61 +syndip_1_chr20:64131704-64134056 3880 4008 60 61 +syndip_2_chr20:64131704-64134056 3880 7987 60 61 +p:HG002_1_chr20:64131704-64134056 3880 11967 60 61 +p:HG002_2_chr20:64131704-64134056 3880 15947 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/output.vcf.gz new file mode 100644 index 00000000..bcf26c31 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/output.vcf.gz.tbi new file mode 100644 index 00000000..7c6908f9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64131804-64133956/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/base.vcf.gz new file mode 100644 index 00000000..23710246 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/base.vcf.gz.tbi new file mode 100644 index 00000000..dd81a1ac Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/comp.vcf.gz new file mode 100644 index 00000000..8f14ca7f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/comp.vcf.gz.tbi new file mode 100644 index 00000000..3bcf10d5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/haps.fa new file mode 100644 index 00000000..a2cd290f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/haps.fa @@ -0,0 +1,112 @@ +>ref_chr20_64134783_64136487 +AGCATTAGGTGTATCTCCTAATGCTATCCCTCCCCTCTCCCCGCACCCCACAAAAGTCCCCGGTGTGTGATGTTCCCCTTGAAAAGGAGGCGTTTCTGCTTCTCCTCTTTCCGGTCCTTGACAGTGATTCCGTGCATCACAAACACACACGCTCCCTCAGTTACACGAATCACAAACACACGCTCCCTCAGTTTTGTGCATCACAAACGCACACGCTCCCTCAGTTTTGTGCGTCACACACACGCTCCCTCAGTTTTGTGCGCCACAAACACGCGCACTCCCTCAGTTATGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACACACACGCTCCCTCAGTTTTGTGTGTCACAAACACACACGCTCCTTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTTTGTGCATCACACACACATTCCCTCAGTTTTGTGCGCCACAAACACGCGCGCTCCCTCAGTTTTGTGCATCACAAACGCACATGCTCCCTCAGTTTTGGGCATCACAAACACATTCCCTCAGTTTTGTGCATCACAAACGCACACGCTCCCTCAGTTTTGTGCGTCACAAACACACACGCTACCTCAGTTTTGTGTGTTACAAACACACACGCTCCCTCAGTTTCGTGCATCCCAAACATGCTCCCTCAGTTATGTGCGTCACAAACACGCTCCCTCAGTTTTGTGTGTCACAAACACACACGCTCCCTCAGTTTTGTGCATCACAAACACACACATTCCCTCAGTTTTGTGCGTCACAAACACGCGTGCTCTCTCAGTTATGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACACACACGCTCCCTCAGCTTTGTGCTTCACAAACACACACGCTCCCTCAGTTTTGTGTGTTACAAACACACACGCTCCCTCAGTTTCGTGCATCCCAAAGACGATTCCTCAGTTTTGTGCATCACAAACACATATGCTCCCTCAGTTTTGTGCGTCACAAACGCGCGCTCCCTCAGTTATGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACACACACGCTCCCTCAGTTTTGTGTGTCACAAACACACACGCTCCCTCAGTTTTGCGCATCACAAACACACACGCTCCCTCAGTTGTCAGGGGACTTTGCACTGTGCCTTTGCATGAAACACCATGGCTTGAAGAGGTCCCGCATCGTTAGGGCCCCCTTGCCCATGGTGTGGCGTCCCCTGACCGATTTAGCCGTTATTGAGGGACATCGAGGTT +>syndip_1_chr20:64134783-64136487 +AGCATTAGGTGTATCTCCTAATGCTATCCCTCCCCTCTCCCCGCACCCCACAAAAGTCCC +CGGTGTGTGATGTTCCCCTTGAAAAGGAGGCGTTTCTGCTTCTCCTCTTTCCGGTCCTTG +ACAGTGATTCCGTGCATCACAAACACACACGCTCCCTCAGTTACACGAATCACAAACACA +CGCTCCCTCAGTTTTGTGCATCACAAACGCACACGCTCCCTCAGTTTTGTGCGTCACACA +CACGCTCCCTCAGTTTTGTGCGTCACACACACGCTCCCTCAGTTTTGTGCGCCACAAACA +CGCGCACTCCCTCAGTTATGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCA +CAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGT +GCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAG +TTTTGTGCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTC +CCTCAGTTTTGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACACACACGC +TCCCTCAGTTTTGTGTGTCACAAACACACACGCTCCTTCAGTTTTGTGCTTCACAAACAC +ACACGCTCCCTCAGTTTTGTGCATCACACACACATTCCCTCAGTTTTGTGCGCCACAAAC +ACGCGCGCTCCCTCAGTTTTGTGCATCACAAACGCACATGCTCCCTCAGTTTTGGGCATC +ACAAACACATTCCCTCAGTTTTGTGCATCACAAACGCACACGCTCCCTCAGTTTTGTGCG +TCACAAACACACACGCTACCTCAGTTTTGTGTGTTACAAACACACACGCTCCCTCAGTTT +CGTGCATCCCAAACATGCTCCCTCAGTTATGTGCGTCACAAACACGCTCCCTCAGTTTTG +TGTGTCACAAACACACACGCTCCCTCAGTTTTGTGCATCACAAACACACACATTCCCTCA +GTTTTGTGCGTCACAAACACGCGTGCTCTCTCAGTTATGTGCGTCACAAACACAGACGCT +CCCTCAGTTTTGCGCATCACACACACGCTCCCTCAGCTTTGTGCTTCACAAACACACACG +CTCCCTCAGTTTTGTGTGTTACAAACACACACGCTCCCTCAGTTTCGTGCATCCCAAAGA +CGATTCCTCAGTTTTGTGCATCACAAACACATATGCTCCCTCAGTTTTGTGCGTCACAAA +CGCGCGCTCCCTCAGTTATGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCA +CACACACGCTCCCTCAGTTTTGTGTGTCACAAACACACACGCTCCCTCAGTTGTCAGGGG +ACTTTGCACTGTGCCTTTGCATGAAACACCATGGCTTGAAGAGGTCCCGCATCGTTAGGG +CCCCCTTGCCCATGGTGTGGCGTCCCCTGACCGATTTAGCCGTTATTGAGGGACATCGAG +GTT +>syndip_2_chr20:64134783-64136487 +AGCATTAGGTGTATCTCCTAATGCTATCCCTCCCCTCTCCCCGCACCCCACAAAAGTCCC +CGGTGTGTGATGTTCCCCTTGAAAAGGAGGCGTTTCTGCTTCTCCTCTTTCCGGTCCTTG +ACAGTGATTCCGTGCATCACAAACACACACGCTCCCTCAGTTACACGAATCACAAACACA +CGCTCCCTCAGTTTTGTGCATCACAAACGCACACGCTCCCTCAGTTTTGTGCGTCACACA +CACGCTCCCTCAGTTTTGTGCGCCACAAACACGCGCACTCCCTCAGTTATGTGCGTCACA +AACACAGACGCTCCCTCAGTTTTGCGCATCACAAACACACACGCTCCCTCAGTTATGGAC +ATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTT +ATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCC +TCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACAC +GCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCGTCACAAAC +ACAGACGCTCCCTCAGTTTTGCGCATCACACACACGCTCCCTCAGTTTTGTGTGTCACAA +ACACACACGCTCCTTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTTTGTGCA +TCACACACACATTCCCTCAGTTTTGTGCGCCACAAACACGCGCGCTCCCTCAGTTTTGTG +CATCACAAACGCACATGCTCCCTCAGTTTTGGGCATCACAAACACATTCCCTCAGTTTTG +TGCATCACAAACGCACACGCTCCCTCAGTTTTGTGCGTCACAAACACACACGCTACCTCA +GTTTTGTGTGTTACAAACACACACGCTCCCTCAGTTTCGTGCATCCCAAACATGCTCCCT +CAGTTATGTGCGTCACAAACACGCTCCCTCAGTTTTGTGTGTCACAAACACACACGCTCC +CTCAGTTTTGTGCATCACAAACACACACATTCCCTCAGTTTTGTGCGTCACAAACACGCG +TGCTCTCTCAGTTATGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACACA +CACGCTCCCTCAGCTTTGTGCTTCACAAACACACACGCTCCCTCAGTTTTGTGTGTTACA +AACACACACGCTCCCTCAGTTTCGTGCATCCCAAAGACGATTCCTCAGTTTTGTGCATCA +CAAACACATATGCTCCCTCAGTTTTGTGCGTCACAAACGCGCGCTCCCTCAGTTATGTGC +GTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACACACACGCTCCCTCAGTTTTGT +GTGTCACAAACACACACGCTCCCTCAGTTTTGCGCATCACAAACACACACGCTCCCTCAG +TTGTCAGGGGACTTTGCACTGTGCCTTTGCATGAAACACCATGGCTTGAAGAGGTCCCGC +ATCGTTAGGGCCCCCTTGCCCATGGTGTGGCGTCCCCTGACCGATTTAGCCGTTATTGAG +GGACATCGAGGTT +>p:HG002_1_chr20:64134783-64136487 +AGCATTAGGTGTATCTCCTAATGCTATCCCTCCCCTCTCCCCGCACCCCACAAAAGTCCC +CGGTGTGTGATGTTCCCCTTGAAAAGGAGGCGTTTCTGCTTCTCCTCTTTCCGGTCCTTG +ACAGTGATTCCGTGCATCACAAACACACACGCTCCCTCAGTTACACGAATCACAAACACA +CGCTCCCTCAGTTTTGTGCATCACAAACGCACACGCTCCCTCAGTTTTGTGCGTCACACA +CACGCTCCCTCAGTTTTGTGCGCCACAAACACGCGCACTCCCTCAGTTATGTGCGTCACA +AACACAGACGCTCCCTCAGTTTTGCGCATCACAAACACACACGCTCCCTCAGTTATGGAC +ATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTT +ATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCC +TCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACAC +GCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCGTCACAAAC +ACAGACGCTCCCTCAGTTTTGCGCATCACACACACGCTCCCTCAGTTTTGTGTGTCACAA +ACACACACGCTCCTTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTTTGTGCA +TCACACACACATTCCCTCAGTTTTGTGCGCCACAAACACGCGCGCTCCCTCAGTTTTGTG +CATCACAAACGCACATGCTCCCTCAGTTTTGGGCATCACAAACACATTCCCTCAGTTTTG +TGCATCACAAACGCACACGCTCCCTCAGTTTTGTGCGTCACAAACACACACGCTACCTCA +GTTTTGTGTGTTACAAACACACACGCTCCCTCAGTTTCGTGCATCCCAAACATGCTCCCT +CAGTTATGTGCGTCACAAACACGCTCCCTCAGTTTTGTGTGTCACAAACACACACGCTCC +CTCAGTTTTGTGCATCACAAACACACACATTCCCTCAGTTTTGTGCGTCACAAACACGCG +TGCTCTCTCAGTTATGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACACA +CACGCTCCCTCAGCTTTGTGCTTCACAAACACACACGCTCCCTCAGTTTTGTGTGTTACA +AACACACACGCTCCCTCAGTTTCGTGCATCCCAAAGACGATTCCTCAGTTTTGTGCATCA +CAAACACATATGCTCCCTCAGTTTTGTGCGTCACAAACGCGCGCTCCCTCAGTTATGTGC +GTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACACACACGCTCCCTCAGTTTTGT +GTGTCACAAACACACACGCTCCCTCAGTTTTGCGCATCACAAACACACACGCTCCCTCAG +TTGTCAGGGGACTTTGCACTGTGCCTTTGCATGAAACACCATGGCTTGAAGAGGTCCCGC +ATCGTTAGGGCCCCCTTGCCCATGGTGTGGCGTCCCCTGACCGATTTAGCCGTTATTGAG +GGACATCGAGGTT +>p:HG002_2_chr20:64134783-64136487 +AGCATTAGGTGTATCTCCTAATGCTATCCCTCCCCTCTCCCCGCACCCCACAAAAGTCCC +CGGTGTGTGATGTTCCCCTTGAAAAGGAGGCGTTTCTGCTTCTCCTCTTTCCGGTCCTTG +ACAGTGATTCCGTGCATCACAAACACACACGCTCCCTCAGTTACACGAATCACAAACACA +CGCTCCCTCAGTTTTGTGCATCACAAACGCACACGCTCCCTCAGTTTTGTGCGTCACACA +CACGCTCCCTCAGTTTTGTGCGTCACACACACGCTCCCTCAGTTTTGTGCGCCACAAACA +CGCGCACTCCCTCAGTTATGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCA +CAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGT +GCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAG +TTTTGTGCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTC +CCTCAGTTTTGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACACACACGC +TCCCTCAGTTTTGTGTGTCACAAACACACACGCTCCTTCAGTTTTGTGCTTCACAAACAC +ACACGCTCCCTCAGTTTTGTGCATCACACACACATTCCCTCAGTTTTGTGCGCCACAAAC +ACGCGCGCTCCCTCAGTTTTGTGCATCACAAACGCACATGCTCCCTCAGTTTTGGGCATC +ACAAACACATTCCCTCAGTTTTGTGCATCACAAACGCACACGCTCCCTCAGTTTTGTGCG +TCACAAACACACACGCTACCTCAGTTTTGTGTGTTACAAACACACACGCTCCCTCAGTTT +CGTGCATCCCAAACATGCTCCCTCAGTTATGTGCGTCACAAACACGCTCCCTCAGTTTTG +TGTGTCACAAACACACACGCTCCCTCAGTTTTGTGCATCACAAACACACACATTCCCTCA +GTTTTGTGCGTCACAAACACGCGTGCTCTCTCAGTTATGTGCGTCACAAACACAGACGCT +CCCTCAGTTTTGCGCATCACACACACGCTCCCTCAGCTTTGTGCTTCACAAACACACACG +CTCCCTCAGTTTTGTGTGTTACAAACACACACGCTCCCTCAGTTTCGTGCATCCCAAAGA +CGATTCCTCAGTTTTGTGCATCACAAACACATATGCTCCCTCAGTTTTGTGCGTCACAAA +CGCGCGCTCCCTCAGTTATGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCA +CACACACGCTCCCTCAGTTTTGTGTGTCACAAACACACACGCTCCCTCAGTTGTCAGGGG +ACTTTGCACTGTGCCTTTGCATGAAACACCATGGCTTGAAGAGGTCCCGCATCGTTAGGG +CCCCCTTGCCCATGGTGTGGCGTCCCCTGACCGATTTAGCCGTTATTGAGGGACATCGAG +GTT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/haps.fa.ref.fa new file mode 100644 index 00000000..52e034fb --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:64134783-64136487 +AGCATTAGGTGTATCTCCTAATGCTATCCCTCCCCTCTCCCCGCACCCCACAAAAGTCCCCGGTGTGTGATGTTCCCCTTGAAAAGGAGGCGTTTCTGCTTCTCCTCTTTCCGGTCCTTGACAGTGATTCCGTGCATCACAAACACACACGCTCCCTCAGTTACACGAATCACAAACACACGCTCCCTCAGTTTTGTGCATCACAAACGCACACGCTCCCTCAGTTTTGTGCGTCACACACACGCTCCCTCAGTTTTGTGCGCCACAAACACGCGCACTCCCTCAGTTATGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACACACACGCTCCCTCAGTTTTGTGTGTCACAAACACACACGCTCCTTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTTTGTGCATCACACACACATTCCCTCAGTTTTGTGCGCCACAAACACGCGCGCTCCCTCAGTTTTGTGCATCACAAACGCACATGCTCCCTCAGTTTTGGGCATCACAAACACATTCCCTCAGTTTTGTGCATCACAAACGCACACGCTCCCTCAGTTTTGTGCGTCACAAACACACACGCTACCTCAGTTTTGTGTGTTACAAACACACACGCTCCCTCAGTTTCGTGCATCCCAAACATGCTCCCTCAGTTATGTGCGTCACAAACACGCTCCCTCAGTTTTGTGTGTCACAAACACACACGCTCCCTCAGTTTTGTGCATCACAAACACACACATTCCCTCAGTTTTGTGCGTCACAAACACGCGTGCTCTCTCAGTTATGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACACACACGCTCCCTCAGCTTTGTGCTTCACAAACACACACGCTCCCTCAGTTTTGTGTGTTACAAACACACACGCTCCCTCAGTTTCGTGCATCCCAAAGACGATTCCTCAGTTTTGTGCATCACAAACACATATGCTCCCTCAGTTTTGTGCGTCACAAACGCGCGCTCCCTCAGTTATGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACACACACGCTCCCTCAGTTTTGTGTGTCACAAACACACACGCTCCCTCAGTTTTGCGCATCACAAACACACACGCTCCCTCAGTTGTCAGGGGACTTTGCACTGTGCCTTTGCATGAAACACCATGGCTTGAAGAGGTCCCGCATCGTTAGGGCCCCCTTGCCCATGGTGTGGCGTCCCCTGACCGATTTAGCCGTTATTGAGGGACATCGAGGTT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/msa.fa new file mode 100644 index 00000000..d562f23e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/msa.fa @@ -0,0 +1,150 @@ +>ref_chr20_64134783_64136487 +agcattaggtgtatctcctaatgctatccctcccctctccccgcaccccacaaaagtccc +cggtgtgtgatgttccccttgaaaaggaggcgtttctgcttctcctctttccggtccttg +acagtgattccgtgcatcacaaacacacacgctccctcagttacacgaatcacaaacaca +cgctccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaca +cacgctccctcagttttgtgcgccacaaacacgcgcactccctcagttatgtgcgtcaca +aacacagacgctccctcagttttgcgcatcacaaacacacacgctccctcagttatggac +atcacaaacacacacgctccctcagttttgtgcttcacaaacacacacgctccctcagtt +atggacatcacaaacacacacgctccctcagttttgtgcttcacaaacacacacgctccc +tcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaacacacac +gctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaac +acacacgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttc +acaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcagttttg +tgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctccctcagttt +tgtgtgtcacaaacacacacgctccttcagttttgtgcttcacaaacacacacgctccct +cagttttgtgcatcacacacacattccctcagttttgtgcgccacaaacacgcgcgctcc +ctcagttttgtgcatcacaaacgcacatgctccctcagttttgggcatcacaaacacatt +ccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaaacaca +cacgctacctcagttttgtgtgttacaaacacacacgctccctcagtttcgtgcatccca +aacatgctccctcagttatgtgcgtcacaaacacgctccctcagttttgtgtgtcacaaa +cacacacgctccctcagttttgtgcatcacaaacacacacattccctcagttttgtgcgt +cacaaacacgcgtgctctctcagttatgtgcgtcacaaacacagacgctccctcagtttt +gcgcatcacacacacgctccctcagctttgtgcttcacaaacacacacgctccctcagtt +ttgtgtgttacaaacacacacgctccctcagtttcgtgcatcccaaagacgattcctcag +ttttgtgcatcacaaacacatatgctccctcagttttgtgcgtcacaaacgcgcgctccc +tcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctc +cctcagttttgtgtgtcacaaacacacacgctccctcagttttgcgcatcacaaacacac +acgctccctcagttgtcaggggactttgcactgtgcctttgcatgaaacaccatggcttg +aagaggtcccgcatcgttagggcccccttgcccatggtgtggcgtcccctgaccgattta +gccgttattgagggacatcgaggtt +>syndip_1_chr20:64134783-64136487 +agcattaggtgtatctcctaatgctatccctcccctctccccgcaccccacaaaagtccc +cggtgtgtgatgttccccttgaaaaggaggcgtttctgcttctcctctttccggtccttg +acagtgattccgtgcatcacaaacacacacgctccctcagttacacgaatcacaaacaca +cgctccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaca +cacgctccctcagttttgtgcgtc------------------------------------ +-acacacacgctccctcagttttgtgcg-------------------------------- +------------------------------------------------------------ +----------------------------------------ccacaaacacgcgcactccc +tcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacaaacacacac +gctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaac +acacacgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttc +acaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcagttttg +tgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctccctcagttt +tgtgtgtcacaaacacacacgctccttcagttttgtgcttcacaaacacacacgctccct +cagttttgtgcatcacacacacattccctcagttttgtgcgccacaaacacgcgcgctcc +ctcagttttgtgcatcacaaacgcacatgctccctcagttttgggcatcacaaacacatt +ccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaaacaca +cacgctacctcagttttgtgtgttacaaacacacacgctccctcagtttcgtgcatccca +aacatgctccctcagttatgtgcgtcacaaacacgctccctcagttttgtgtgtcacaaa +cacacacgctccctcagttttgtgcatcacaaacacacacattccctcagttttgtgcgt +cacaaacacgcgtgctctctcagttatgtgcgtcacaaacacagacgctccctcagtttt +gcgcatcacacacacgctccctcagctttgtgcttcacaaacacacacgctccctcagtt +ttgtgtgttacaaacacacacgctccctcagtttcgtgcatcccaaagacgattcctcag +ttttgtgcatcacaaacacatatgctccctcagttttgtgcgtcacaaacgcgcgctccc +tcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctc +cctcagttttgtgtg---------------------------------tcacaaacacac +acgctccctcagttgtcaggggactttgcactgtgcctttgcatgaaacaccatggcttg +aagaggtcccgcatcgttagggcccccttgcccatggtgtggcgtcccctgaccgattta +gccgttattgagggacatcgaggtt +>syndip_2_chr20:64134783-64136487 +agcattaggtgtatctcctaatgctatccctcccctctccccgcaccccacaaaagtccc +cggtgtgtgatgttccccttgaaaaggaggcgtttctgcttctcctctttccggtccttg +acagtgattccgtgcatcacaaacacacacgctccctcagttacacgaatcacaaacaca +cgctccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaca +cacgctccctcagttttgtgcgccacaaacacgcgcactccctcagttatgtgcgtcaca +aacacagacgctccctcagttttgcgca-------------------------------- +------------------------------------------------------------ +----------------------------------------tcacaaacacacacgctccc +tcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaacacacac +gctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaac +acacacgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttc +acaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcagttttg +tgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctccctcagttt +tgtgtgtcacaaacacacacgctccttcagttttgtgcttcacaaacacacacgctccct +cagttttgtgcatcacacacacattccctcagttttgtgcgccacaaacacgcgcgctcc +ctcagttttgtgcatcacaaacgcacatgctccctcagttttgggcatcacaaacacatt +ccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaaacaca +cacgctacctcagttttgtgtgttacaaacacacacgctccctcagtttcgtgcatccca +aacatgctccctcagttatgtgcgtcacaaacacgctccctcagttttgtgtgtcacaaa +cacacacgctccctcagttttgtgcatcacaaacacacacattccctcagttttgtgcgt +cacaaacacgcgtgctctctcagttatgtgcgtcacaaacacagacgctccctcagtttt +gcgcatcacacacacgctccctcagctttgtgcttcacaaacacacacgctccctcagtt +ttgtgtgttacaaacacacacgctccctcagtttcgtgcatcccaaagacgattcctcag +ttttgtgcatcacaaacacatatgctccctcagttttgtgcgtcacaaacgcgcgctccc +tcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctc +cctcagttttgtgtgtcacaaacacacacgctccctcagttttgcgcatcacaaacacac +acgctccctcagttgtcaggggactttgcactgtgcctttgcatgaaacaccatggcttg +aagaggtcccgcatcgttagggcccccttgcccatggtgtggcgtcccctgaccgattta +gccgttattgagggacatcgaggtt +>p:HG002_1_chr20:64134783-64136487 +agcattaggtgtatctcctaatgctatccctcccctctccccgcaccccacaaaagtccc +cggtgtgtgatgttccccttgaaaaggaggcgtttctgcttctcctctttccggtccttg +acagtgattccgtgcatcacaaacacacacgctccctcagttacacgaatcacaaacaca +cgctccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaca +cacgctccctcagttttgtgcgccacaaacacgcgcactccctcagttatgtgcgtcaca +aacacagacgctccctcagttttgcgca-------------------------------- +------------------------------------------------------------ +----------------------------------------tcacaaacacacacgctccc +tcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaacacacac +gctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaac +acacacgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttc +acaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcagttttg +tgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctccctcagttt +tgtgtgtcacaaacacacacgctccttcagttttgtgcttcacaaacacacacgctccct +cagttttgtgcatcacacacacattccctcagttttgtgcgccacaaacacgcgcgctcc +ctcagttttgtgcatcacaaacgcacatgctccctcagttttgggcatcacaaacacatt +ccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaaacaca +cacgctacctcagttttgtgtgttacaaacacacacgctccctcagtttcgtgcatccca +aacatgctccctcagttatgtgcgtcacaaacacgctccctcagttttgtgtgtcacaaa +cacacacgctccctcagttttgtgcatcacaaacacacacattccctcagttttgtgcgt +cacaaacacgcgtgctctctcagttatgtgcgtcacaaacacagacgctccctcagtttt +gcgcatcacacacacgctccctcagctttgtgcttcacaaacacacacgctccctcagtt +ttgtgtgttacaaacacacacgctccctcagtttcgtgcatcccaaagacgattcctcag +ttttgtgcatcacaaacacatatgctccctcagttttgtgcgtcacaaacgcgcgctccc +tcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctc +cctcagttttgtgtgtcacaaacacacacgctccctcagttttgcgcatcacaaacacac +acgctccctcagttgtcaggggactttgcactgtgcctttgcatgaaacaccatggcttg +aagaggtcccgcatcgttagggcccccttgcccatggtgtggcgtcccctgaccgattta +gccgttattgagggacatcgaggtt +>p:HG002_2_chr20:64134783-64136487 +agcattaggtgtatctcctaatgctatccctcccctctccccgcaccccacaaaagtccc +cggtgtgtgatgttccccttgaaaaggaggcgtttctgcttctcctctttccggtccttg +acagtgattccgtgcatcacaaacacacacgctccctcagttacacgaatcacaaacaca +cgctccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaca +cacgctccctcagttttgtgcgtc------------------------------------ +-acacacacgctccctcagttttgtgcg-------------------------------- +------------------------------------------------------------ +----------------------------------------ccacaaacacgcgcactccc +tcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacaaacacacac +gctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaac +acacacgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttc +acaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcagttttg +tgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctccctcagttt +tgtgtgtcacaaacacacacgctccttcagttttgtgcttcacaaacacacacgctccct +cagttttgtgcatcacacacacattccctcagttttgtgcgccacaaacacgcgcgctcc +ctcagttttgtgcatcacaaacgcacatgctccctcagttttgggcatcacaaacacatt +ccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaaacaca +cacgctacctcagttttgtgtgttacaaacacacacgctccctcagtttcgtgcatccca +aacatgctccctcagttatgtgcgtcacaaacacgctccctcagttttgtgtgtcacaaa +cacacacgctccctcagttttgtgcatcacaaacacacacattccctcagttttgtgcgt +cacaaacacgcgtgctctctcagttatgtgcgtcacaaacacagacgctccctcagtttt +gcgcatcacacacacgctccctcagctttgtgcttcacaaacacacacgctccctcagtt +ttgtgtgttacaaacacacacgctccctcagtttcgtgcatcccaaagacgattcctcag +ttttgtgcatcacaaacacatatgctccctcagttttgtgcgtcacaaacgcgcgctccc +tcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctc +cctcagttttgtgtg---------------------------------tcacaaacacac +acgctccctcagttgtcaggggactttgcactgtgcctttgcatgaaacaccatggcttg +aagaggtcccgcatcgttagggcccccttgcccatggtgtggcgtcccctgaccgattta +gccgttattgagggacatcgaggtt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/msa.fa.fai new file mode 100644 index 00000000..ed542de2 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_64134783_64136487 1705 29 60 61 +syndip_1_chr20:64134783-64136487 1705 1797 60 61 +syndip_2_chr20:64134783-64136487 1705 3565 60 61 +p:HG002_1_chr20:64134783-64136487 1705 5334 60 61 +p:HG002_2_chr20:64134783-64136487 1705 7103 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/output.vcf.gz new file mode 100644 index 00000000..82bcb1c0 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/output.vcf.gz.tbi new file mode 100644 index 00000000..a3aa4d5f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64134883-64136387/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/base.vcf.gz new file mode 100644 index 00000000..13f40f36 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/base.vcf.gz.tbi new file mode 100644 index 00000000..c1da5b04 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/comp.vcf.gz new file mode 100644 index 00000000..9b234a36 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/comp.vcf.gz.tbi new file mode 100644 index 00000000..8e08762f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/haps.fa new file mode 100644 index 00000000..38724929 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/haps.fa @@ -0,0 +1,217 @@ +>ref_chr20_64173309_64176630 +CAGAGGTGGGCTGTTGGACAGGTGCGGCTGATAGAGTGGGTGTCTTTTGTGGGCTTCTCCCCAGCCTGTGGCCTGGCCTAGTCAGTAGAGATGGTCAGGGGAGCAGGAGGGAGCCCATACCCCAGTGCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTCCCTTTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTCCCTTTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCTTCTAGCATCTTTCCTGCTCCCTGGTAGCCTCTTGGGAGCCACCTATTTCTGGAGGTCCCCACTCTGGGTTCCTTGTCCTGGGTGTGGGGCGAATGTGCTGGACTGGGGTCACAGCATTGAACCCCACTTGGAGCTGAGGA +>syndip_1_chr20:64173309-64176630 +CAGAGGTGGGCTGTTGGACAGGTGCGGCTGATAGAGTGGGTGTCTTTTGTGGGCTTCTCC +CCAGCCTGTGGCCTGGCCTAGTCAGTAGAGATGGTCAGGGGAGCAGGAGGGAGCCCATAC +CCCAGTGCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTC +CCTTTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTAGTTG +TGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCAT +TTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCC +TGACTTCTCCTCCTGCAGCATCCTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTC +TCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCT +GCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCAT +CTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGT +AGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCC +ATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTC +CCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCT +CCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCAT +CTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGT +AGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCC +ATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTC +CCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCT +CCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTT +TCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGT +GTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCAACTTTCCTAGTTGTGTCCATTTCCCCT +CCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCC +TGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCT +TTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTG +TAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCAT +TTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTCCCCCTCCCTGG +CTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTGCAGC +ATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTA +GTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTT +CCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCT +TCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAG +CATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCC +TGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCC +ATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTC +CCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCT +CCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCCTGCAG +CATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGT +AGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTG +TCCATTCCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTT +CCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCC +CTGGCTTCTCCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGACTT +CTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCC +TGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCT +TTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAG +TTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCAT +TTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCC +TGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTC +TCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTGCAGCA +TCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAG +TTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCAT +TTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCC +TGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCC +TGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCT +TTCCCTGTAGTTGTGTTCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAG +TTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCAT +TTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCC +TGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCC +TGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCT +TTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCTTCTAGCATCTTTCCTGC +TCCCTGGTAGCCTCTTGGGAGCCACCTATTTCTGGAGGTCCCCACTCTGGGTTCCTTGTC +CTGGGTGTGGGGCGAATGTGCTGGACTGGGGTCACAGCATTGAACCCCACTTGGAGCTGA +GGA +>syndip_2_chr20:64173309-64176630 +CAGAGGTGGGCTGTTGGACAGGTGCGGCTGATAGAGTGGGTGTCTTTTGTGGGCTTCTCC +CCAGCCTGTGGCCTGGCCTAGTCAGTAGAGATGGTCAGGGGAGCAGGAGGGAGCCCATAC +CCCAGTGCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTC +CCTTTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTAGTTG +TGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCAT +TTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCC +TGACTTCTCCTCCTGCAGCATCCTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTC +TCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCT +GCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCAT +CTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGT +AGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCC +ATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCC +CTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTG +GCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTG +CAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTT +CCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTT +GTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCC +CTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCT +CCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCAT +CTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGT +TGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCC +CCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGC +TTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCA +GCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTACAGCATCTTTCC +CTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTC +CATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCT +CCCTGGCTTCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCC +TGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTC +CTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGT +CCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCC +TCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTC +CTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATC +TTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTA +GTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCTAGTTGTGTCCA +TTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCC +CTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTT +CTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGC +AGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTC +CCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTG +TGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTC +CCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGG +CTTCTCCTCTTCTAGCATCTTTCCTGCTCCCTGGTAGCCTCTTGGGAGCCACCTATTTCT +GGAGGTCCCCACTCTGGGTTCCTTGTCCTGGGTGTGGGGCGAATGTGCTGGACTGGGGTC +ACAGCATTGAACCCCACTTGGAGCTGAGGA +>p:HG002_1_chr20:64173309-64176630 +CAGAGGTGGGCTGTTGGACAGGTGCGGCTGATAGAGTGGGTGTCTTTTGTGGGCTTCTCC +CCAGCCTGTGGCCTGGCCTAGTCAGTAGAGATGGTCAGGGGAGCAGGAGGGAGCCCATAC +CCCAGTGCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTC +CCTTTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTAGTTG +TGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCAT +TTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCC +TGACTTCTCCTCCTGCAGCATCCTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTC +TCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCT +GCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCAT +CTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGT +AGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCC +ATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCC +CTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTG +GCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTG +CAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTT +CCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTT +GTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCC +CTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCT +CCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCAT +CTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGT +TGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCC +CCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGC +TTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCA +GCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTACAGCATCTTTCC +CTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTC +CATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCT +CCCTGGCTTCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCC +TGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTC +CTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGT +CCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCC +TCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTC +CTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATC +TTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTA +GTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCTAGTTGTGTCCA +TTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCC +CTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTT +CTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGC +AGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTC +CCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTG +TGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTC +CCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGG +CTTCTCCTCTTCTAGCATCTTTCCTGCTCCCTGGTAGCCTCTTGGGAGCCACCTATTTCT +GGAGGTCCCCACTCTGGGTTCCTTGTCCTGGGTGTGGGGCGAATGTGCTGGACTGGGGTC +ACAGCATTGAACCCCACTTGGAGCTGAGGA +>p:HG002_2_chr20:64173309-64176630 +CAGAGGTGGGCTGTTGGACAGGTGCGGCTGATAGAGTGGGTGTCTTTTGTGGGCTTCTCC +CCAGCCTGTGGCCTGGCCTAGTCAGTAGAGATGGTCAGGGGAGCAGGAGGGAGCCCATAC +CCCAGTGCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTC +CCTTTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTAGTTG +TGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCAT +TTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCC +TGACTTCTCCTCCTGCAGCATCCTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTC +TCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCT +GCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCAT +CTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGT +AGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCC +ATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTC +CCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCT +CCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCAT +CTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGT +AGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCC +ATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTC +CCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCT +CCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTT +TCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGT +GTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCAACTTTCCTAGTTGTGTCCATTTCCCCT +CCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCC +TGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCT +TTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAG +TTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTC +CCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTCCCCCTCCCTGGCTT +CTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTGCAGCATC +TTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTT +GTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCC +CTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCT +CCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCAT +CTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGT +AGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATT +TCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCT +GGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCT +GTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCCTGCAGCAT +CTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGT +TGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCC +ATTCCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCC +CTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTG +GCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTC +CTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGC +AGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTC +CCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTG +TGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTC +CCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGG +CTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCC +TCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTGCAGCATCT +TTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTG +TGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTC +CCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGG +CTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGC +AGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTC +CCTGTAGTTGTGTTCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTG +TGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTC +CCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGG +CTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGC +AGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTC +CCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCTTCTAGCATCTTTCCTGCTCC +CTGGTAGCCTCTTGGGAGCCACCTATTTCTGGAGGTCCCCACTCTGGGTTCCTTGTCCTG +GGTGTGGGGCGAATGTGCTGGACTGGGGTCACAGCATTGAACCCCACTTGGAGCTGAGGA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/haps.fa.ref.fa new file mode 100644 index 00000000..296e951e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:64173309-64176630 +CAGAGGTGGGCTGTTGGACAGGTGCGGCTGATAGAGTGGGTGTCTTTTGTGGGCTTCTCCCCAGCCTGTGGCCTGGCCTAGTCAGTAGAGATGGTCAGGGGAGCAGGAGGGAGCCCATACCCCAGTGCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTCCCTTTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTCCCTTTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCTTCTAGCATCTTTCCTGCTCCCTGGTAGCCTCTTGGGAGCCACCTATTTCTGGAGGTCCCCACTCTGGGTTCCTTGTCCTGGGTGTGGGGCGAATGTGCTGGACTGGGGTCACAGCATTGAACCCCACTTGGAGCTGAGGA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/msa.fa new file mode 100644 index 00000000..06fc06ba --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/msa.fa @@ -0,0 +1,365 @@ +>ref_chr20_64173309_64176630 +cagaggtgggctgttggacaggtgcggctgatagagtgggtgtcttttgtgggcttctcc +ccagcctgtggcctggcctagtcagtagagatggtcaggggagcaggagggagcccatac +cccagtgcctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatccttc +cctt--------------------------------------------------tagttg +tgtccatttcccctccctgacttctcctcctgcagcatccttccctttagttgtgtccat +ttcccctccctgacttctcctcctgcagcatctttcctagttgtgtccatttcccctccc +tgacttctcctcctgcagcatctttccttgtagttgtgtccatttcccctccctggcttc +tcctcctgcag------------------------------------------------- +----catctttccttgtagttgtgtccatttcccctccctgacttctcctcctgc----- +---------------------------------------------agcatccttccctgt +agttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcc +atttcccctccctggctt---ctcctgcagcatctttccctgtagttgtgtccatttccc +ctccctggctt---ctcctgcagcatctttccctgtagttgtgtccatttcccctccctg +gcttctcctgtagcatctttccctgtagttgtgtccattccccctccctggcttctcctg +tagcatctttcc---tagttgtgtccatttcccctccctggcttctcctgc--------- +-----------------------------------------agcatctttccctgtagtt +gtgtccatttcccctccctggcttctcctg------------------------------ +--------------------tagcatctttcc---tagttgtgtccatttcccctccctg +gcttctcctcctgcagcatctttccctgtagttgtgtccattccccctccctggcttctc +ctgtagcatctttcc---tagttgtgtccatttcccctccctggcttctcctgtagcatc +tttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagtt +gtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccattt +cccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctg +gcttctcctgtagcatctttccctgtagttgtgtccattccccctccctgacttctcctc +ctgcagcatctttccctgtagttgtgtccatttcccctccctggcgtctcctcctgcagc +atctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcc-- +-tagttgtgtccatttcccctccctggcttctc--------------------------- +------------------------------------------------------------ +----ctcctgcagcatctttccctgtagttgtgtccattccccctccctggcttctcctg +tagcatctttcc-----------------------------------------------t +agttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtccatt +tcccctccctggcttctcctgcagcatctttccc-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +-tgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgt +gtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcc +cctccctgg--------------------------------------------------- +------------------------------------------------------------ +---------------------------------------------cttctcctgcagcat +ctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgt +agttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtcc 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+------------------------------------------------------------ +---------------------------------------------cttctcctgtagcat +ctttcc---tagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgt +agttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcc +atttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctc +cctggcgtctcctcctgcagcatctttcctagttgtgtccatttcccctccctggcttct +cctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctcctgcag +catctttccctgtagttgtgtccattccccctccctggcttctcctcctgcagcatcttt +ccctgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgta +gttgtgtccattccccctccctggcttctcctcctgcagcatctttccctgtagttgtgt +ccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatttc +ccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatttcccctccc +tggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcc +tgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatct +ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag +ttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtc +cattccccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatttcc +cctccctggctt------------------------------------------------ +-----ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgta +gcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctg +tagttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtc +catttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccct +ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc +tcctgtagcatctttccctgtagttgtgttcatttcccctccctggcttctcctgcagca +tctttccctgtagttgtgtccatttcccctccctggctt--------------------- +--------------------------------ctcctgcagcatctttccctgtagttgt +gtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcc +cctccctggctt------------------------------------------------ +------------------------------------------------------------ +---------------------------------------------------ctcctgcag +catctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccc +tgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtg +tccatttcccctccctggcttctcctcttctagcatctttcctgctccctggtagcctct +tgggagccacctatttctggaggtccccactctgggttccttgtcctgggtgtggggcga +atgtgctggactggggtcacagcattgaaccccacttggagctgagga diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/msa.fa.fai new file mode 100644 index 00000000..dbcf6bde --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_64173309_64176630 4308 29 60 61 +syndip_1_chr20:64173309-64176630 4308 4443 60 61 +syndip_2_chr20:64173309-64176630 4308 8857 60 61 +p:HG002_1_chr20:64173309-64176630 4308 13272 60 61 +p:HG002_2_chr20:64173309-64176630 4308 17687 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/output.vcf.gz new file mode 100644 index 00000000..df97dce8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/output.vcf.gz.tbi new file mode 100644 index 00000000..9c4cedbd Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:64173409-64176530/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/base.vcf.gz new file mode 100644 index 00000000..7db1f8b4 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/base.vcf.gz.tbi new file mode 100644 index 00000000..31c2b2d1 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/comp.vcf.gz new file mode 100644 index 00000000..e93a2986 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/comp.vcf.gz.tbi new file mode 100644 index 00000000..4d002efd Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/haps.fa new file mode 100644 index 00000000..aeab0df0 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/haps.fa @@ -0,0 +1,98 @@ +>ref_chr20_641736_642566 +ATCATCCGGTGACAGGGATCATCATCCCTGCCTGGCATAGAAACCCGGACATCGGACCCTGCCCTCCCGCTGCTTCCGCAGGGACAGGGGGCAGCCAGCAGAGCCTCCCTCTGGGGGTGCCCCCCAATCTGGTTGCCTGGGACGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCAGCGGGGGTGAAGTTGCCTGGGGGGGGCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCAGCGGGGGTGGAGCACCCTGGACGGCCCCGCGGAGCCCCCTGCGGGAGGCGAGGGCGGCCCTCGGGCTCTGGAAGGGGCCGCGCGGCCTGGAAGACATTACACGGCTGTCGGGCGGGGGGCGGCGCTCGCAGTTCCGGAGGGGG +>syndip_1_chr20:641736-642566 +ATCATCCGGTGACAGGGATCATCATCCCTGCCTGGCATAGAAACCCGGACATCGGACCCT +GCCCTCCCGCTGCTTCCGCAGGGACAGGGGGCAGCCAGCAGAGCCTCCCTCTGGGGGTGC +CCCCCAATCTGGTTGCCTGGGAGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGG +GCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGG +GGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCT +GGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGT +TGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGG +TGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGC +GGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCC +AGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCC +AGCGGGGGTGGAGTTGCCTGGGGGGGGCCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGC +CCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGG +CCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCCAGCGGGGGTGGAGTTGCCTGGGGGGG +GGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGG +GGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCC +TGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTT +GCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGT +TGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGA +GTTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGT +GGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGCACCCTGGACGGCCCCGCGGAGCCC +CCTGCGGGAGGCGAGGGCGGCCCTCGGGCTCTGGAAGGGGCCGCGCGGCCTGGAAGACAT +TACACGGCTGTCGGGCGGGGGGCGGCGCTCGCAGTTCCGGAGGGGG +>syndip_2_chr20:641736-642566 +ATCATCCGGTGACAGGGATCATCATCCCTGCCTGGCATAGAAACCCGGACATCGGACCCT +GCCCTCCCGCTGCTTCCGCAGGGACAGGGGGCAGCCAGCAGAGCCTCCCTCTGGGGGTGC +CCCCCAATCTGGTTGCCTGGGACGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGG +CCCAGCGGGGGTGGAGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGG +GGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGC +CTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGT +TGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGG +AGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCG +GGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGC +GGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCC +AGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGG +GGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGG +GGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCAGGGGTGGAGTTGCCTG +GGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGC +CTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTG +CCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGT +TGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAG +TTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGT +GGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCG +GGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCC +AGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCC +AGCGGGGGTGGAGCACCCTGGACGGCCCCGCGGAGCCCCCTGCGGGAGGCGAGGGCGGCC +CTCGGGCTCTGGAAGGGGCCGCGCGGCCTGGAAGACATTACACGGCTGTCGGGCGGGGGG +CGGCGCTCGCAGTTCCGGAGGGGG +>p:HG002_1_chr20:641736-642566 +ATCATCCGGTGACAGGGATCATCATCCCTGCCTGGCATAGAAACCCGGACATCGGACCCT +GCCCTCCCGCTGCTTCCGCAGGGACAGGGGGCAGCCAGCAGAGCCTCCCTCTGGGGGTGC +CCCCCAATCTGGTTGCCTGGGACGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGG +CCCAGCGGGGGTGGAGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGG +GGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGC +CTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGT +TGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGG +AGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCG +GGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGC +GGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCC +AGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGG +GGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGG +GGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCAGGGGTGGAGTTGCCTG +GGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGC +CTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTG +CCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGT +TGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAG +TTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGT +GGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCG +GGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCC +AGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCC +AGCGGGGGTGGAGCACCCTGGACGGCCCCGCGGAGCCCCCTGCGGGAGGCGAGGGCGGCC +CTCGGGCTCTGGAAGGGGCCGCGCGGCCTGGAAGACATTACACGGCTGTCGGGCGGGGGG +CGGCGCTCGCAGTTCCGGAGGGGG +>p:HG002_2_chr20:641736-642566 +ATCATCCGGTGACAGGGATCATCATCCCTGCCTGGCATAGAAACCCGGACATCGGACCCT +GCCCTCCCGCTGCTTCCGCAGGGACAGGGGGCAGCCAGCAGAGCCTCCCTCTGGGGGTGC +CCCCCAATCTGGTTGCCTGGGAGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGG +GCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGG +GGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCT +GGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGT +TGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGG +TGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGC +GGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCC +AGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCC +AGCGGGGGTGGAGTTGCCTGGGGGGGGCCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGC +CCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGG +CCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCCAGCGGGGGTGGAGTTGCCTGGGGGGG +GGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGG +GGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCC +TGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTT +GCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGT +TGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGA +GTTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGT +GGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGCACCCTGGACGGCCCCGCGGAGCCC +CCTGCGGGAGGCGAGGGCGGCCCTCGGGCTCTGGAAGGGGCCGCGCGGCCTGGAAGACAT +TACACGGCTGTCGGGCGGGGGGCGGCGCTCGCAGTTCCGGAGGGGG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/haps.fa.ref.fa new file mode 100644 index 00000000..09538986 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:641736-642566 +ATCATCCGGTGACAGGGATCATCATCCCTGCCTGGCATAGAAACCCGGACATCGGACCCTGCCCTCCCGCTGCTTCCGCAGGGACAGGGGGCAGCCAGCAGAGCCTCCCTCTGGGGGTGCCCCCCAATCTGGTTGCCTGGGACGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCAGCGGGGGTGAAGTTGCCTGGGGGGGGCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCAGCGGGGGTGGAGCACCCTGGACGGCCCCGCGGAGCCCCCTGCGGGAGGCGAGGGCGGCCCTCGGGCTCTGGAAGGGGCCGCGCGGCCTGGAAGACATTACACGGCTGTCGGGCGGGGGGCGGCGCTCGCAGTTCCGGAGGGGG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/msa.fa new file mode 100644 index 00000000..12cccca8 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/msa.fa @@ -0,0 +1,125 @@ +>ref_chr20_641736_642566 +atcatccggtgacagggatcatcatccctgcctggcatagaaacccggacatcggaccct +gccctcccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtgc +cccccaatctggttgcctgggacgggggcccagcgggggtggagttgcct-ggggggggg +gcccagcgggggtggagttgcctggggggggaggcccagcgggggtggagttgcctgggg +gggggaggcccagcgggggtggagttgcctgggggggggtgcccagcgggggtggagttg +cctggggggggcccagcgggggtggagttgcctgtggggggaggcccagcgggggtggag +ttgcct-ggggggggcccagcgggggtggggttgcctggggggggaggcccagcgggggt +ggagttgcctgggggggggaggcccagcgggggtggagttgcctgggggggggtgcccag +cgggggtggagttgcct------------------------------------------- +--------------------gggggg-------------------------------ggc +ccagcgggggtggagttgcctgtggtggg---gggccagcgggggtgaagttgcctgggg +gggg----ccagcgggggtggagttgcctgggggggggccagcgggggtggagttgcctg +tgggggggggccagcgggggtggagttgcctgggggggg----ccagcgggggtggagtt +gcctgggggggg----ccagcgggggtggagcaccctggacggcccc--------gcgga +gccccctgcgggaggcgagggcggccctcgggctctggaaggggccgcgcggcctggaag +acattacacggctgtcgggcggggggcggcgctcgcagttccggaggggg---------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------ +>syndip_1_chr20:641736-642566 +atcatccggtgacagggatcatcatccctgcctggcatagaaacccggacatcggaccct +gccctcccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtgc +cccccaatctggttgcctgggaggggggcccagcgggggtggagttgcctgggggggggg +gcccagcgggggtggagttgcctgggggggg-ggcccagcgggggtggagttgcctgggg +gggggaggcccagcgggggtggagttgcctgggggggg--gcccagcgggggtggagttg +cctggg-----------------------------ggggggaggcccagcgggggtggag +ttgcctgggggggggcccagcgggggtggagttgcctgggggggg-ggcccagcgggggt +ggagttgcctgggggggggaggcccagcgggggtggagttgcctgggggggg--gcccag +cgggggtggagttgcctgggg---------------------------gggggaggccca +gcgggggtggagttgcctgggggggg-------------------------------ggc +ccagcgggggtggagttgcctg-gggggg---ggcccagcgggggtggagttgcctgggg +gggg---cccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcctg +-gggggggccccagcgggggtggagttgcctgggggggg--gcccagcgggggtggagtt +gcctgggggggg--gcccagcgggggtggagttgcctggggggggcccagcgggggtgga +gttgcctggggggggccccagcgggggtggagttgcctgggggggggcccagcgggggtg +gagttgcctggggggggggcccagcgggggtggagttgcctggggggggggcccagcggg +ggtggagttgcctgggggggggggcccagcgggggtggagttgcctgggggggggcccag +cgggggtggagttgcctg-gggggggggcccagcgggggtggagttgcct-ggggggggc +ccagcgggggtggagttgcct-gggggggggcccagcgggggtggagttgcctg-ggggg +ggggcccagcgggggtggagttgcctg-gggggggcccagcgggggtggagttgcctgtg +ggggggggcccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcct +gggggggggcccagcgggggtggagcaccctggacggccccgcggagccccctgcgggag +gcgagggcggccctcgggctctggaaggggccgcgcggcctggaagacattacacggctg +tcgggcggggggcggcgctcgcagttccggaggggg +>syndip_2_chr20:641736-642566 +atcatccggtgacagggatcatcatccctgcctggcatagaaacccggacatcggaccct +gccctcccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtgc +cccccaatctggttgcctgggacgggggcccagcgggggtggagttgcct-ggggggggg +gcccagcgggggtggagttgcctggggggggaggcccagcgggggtggagttgcctgggg +gggggaggcccagcgggggtggagttgcctgggggggggtgcccagcgggggtggagttg +cctggggggggcccagcgggggtggagttgcctgtggggggaggcccagcgggggtggag +ttgcct-ggggggggcccagcgggggtggggttgcctggggggggaggcccagcgggggt +ggagttgcctgggggggggaggcccagcgggggtggagttgcctgggggggggtgcccag +cgggggtggagttgcctgggggggggcccagcgggggtggagttgcctggggggggccca +gcgggggtggggttgcctggggggggcccagcgggggtggggttgcctggggggggaggc +ccagcgggggtggagttgcctg-ggggggggaggcccagcgggggtggagttgcctgggg +gggggtgcccagcgggggtggagttgcctggggggggcccagcgggggtggggttgcctg +-ggggggg-cccagcgggggtggggttgcctggggggggaggcccagcaggggtggagtt +gcctgggggggggtgcccagcgggggtggagttgcctggggggggcccagcgggggtgga +gttgcctgggggggg-cccagcgggggtggagttgcctgggggggggcccagcggggatg +gggttgcct-gggggggggcccagcgggggtggggttgcct-gggggggggcccagcggg +ggtggagttgcct--gggggggggcccagcgggggtggagttgcct-ggggggggcccag +cgggggtggagttgcctgtgggggggggcccagcgggggtggagttgcctgggggggggc +ccagcgggggtggagttgcctggggggggggcccagcgggggtggagttgcctgtggtgg +ggggcccagcgggggtggagttgcctgtgggggggcccagcgggggtggagttgcctgtg +ggggggggcccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcct +-ggggggggcccagcgggggtggagcaccctggacggccccgcggagccccctgcgggag +gcgagggcggccctcgggctctggaaggggccgcgcggcctggaagacattacacggctg +tcgggcggggggcggcgctcgcagttccggaggggg +>p:HG002_1_chr20:641736-642566 +atcatccggtgacagggatcatcatccctgcctggcatagaaacccggacatcggaccct +gccctcccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtgc +cccccaatctggttgcctgggacgggggcccagcgggggtggagttgcct-ggggggggg +gcccagcgggggtggagttgcctggggggggaggcccagcgggggtggagttgcctgggg +gggggaggcccagcgggggtggagttgcctgggggggggtgcccagcgggggtggagttg +cctggggggggcccagcgggggtggagttgcctgtggggggaggcccagcgggggtggag +ttgcct-ggggggggcccagcgggggtggggttgcctggggggggaggcccagcgggggt +ggagttgcctgggggggggaggcccagcgggggtggagttgcctgggggggggtgcccag +cgggggtggagttgcctgggggggggcccagcgggggtggagttgcctggggggggccca +gcgggggtggggttgcctggggggggcccagcgggggtggggttgcctggggggggaggc +ccagcgggggtggagttgcctg-ggggggggaggcccagcgggggtggagttgcctgggg +gggggtgcccagcgggggtggagttgcctggggggggcccagcgggggtggggttgcctg +-ggggggg-cccagcgggggtggggttgcctggggggggaggcccagcaggggtggagtt +gcctgggggggggtgcccagcgggggtggagttgcctggggggggcccagcgggggtgga +gttgcctgggggggg-cccagcgggggtggagttgcctgggggggggcccagcggggatg +gggttgcct-gggggggggcccagcgggggtggggttgcct-gggggggggcccagcggg +ggtggagttgcct--gggggggggcccagcgggggtggagttgcct-ggggggggcccag +cgggggtggagttgcctgtgggggggggcccagcgggggtggagttgcctgggggggggc +ccagcgggggtggagttgcctggggggggggcccagcgggggtggagttgcctgtggtgg +ggggcccagcgggggtggagttgcctgtgggggggcccagcgggggtggagttgcctgtg +ggggggggcccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcct +-ggggggggcccagcgggggtggagcaccctggacggccccgcggagccccctgcgggag +gcgagggcggccctcgggctctggaaggggccgcgcggcctggaagacattacacggctg +tcgggcggggggcggcgctcgcagttccggaggggg +>p:HG002_2_chr20:641736-642566 +atcatccggtgacagggatcatcatccctgcctggcatagaaacccggacatcggaccct +gccctcccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtgc +cccccaatctggttgcctgggaggggggcccagcgggggtggagttgcctgggggggggg +gcccagcgggggtggagttgcctgggggggg-ggcccagcgggggtggagttgcctgggg +gggggaggcccagcgggggtggagttgcctgggggggg--gcccagcgggggtggagttg +cctggg-----------------------------ggggggaggcccagcgggggtggag +ttgcctgggggggggcccagcgggggtggagttgcctgggggggg-ggcccagcgggggt +ggagttgcctgggggggggaggcccagcgggggtggagttgcctgggggggg--gcccag +cgggggtggagttgcctgggg---------------------------gggggaggccca +gcgggggtggagttgcctgggggggg-------------------------------ggc +ccagcgggggtggagttgcctg-gggggg---ggcccagcgggggtggagttgcctgggg +gggg---cccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcctg +-gggggggccccagcgggggtggagttgcctgggggggg--gcccagcgggggtggagtt +gcctgggggggg--gcccagcgggggtggagttgcctggggggggcccagcgggggtgga +gttgcctggggggggccccagcgggggtggagttgcctgggggggggcccagcgggggtg +gagttgcctggggggggggcccagcgggggtggagttgcctggggggggggcccagcggg +ggtggagttgcctgggggggggggcccagcgggggtggagttgcctgggggggggcccag +cgggggtggagttgcctg-gggggggggcccagcgggggtggagttgcct-ggggggggc +ccagcgggggtggagttgcct-gggggggggcccagcgggggtggagttgcctg-ggggg +ggggcccagcgggggtggagttgcctg-gggggggcccagcgggggtggagttgcctgtg +ggggggggcccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcct +gggggggggcccagcgggggtggagcaccctggacggccccgcggagccccctgcgggag +gcgagggcggccctcgggctctggaaggggccgcgcggcctggaagacattacacggctg +tcgggcggggggcggcgctcgcagttccggaggggg diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/msa.fa.fai new file mode 100644 index 00000000..c265ec0c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_641736_642566 1416 25 60 61 +syndip_1_chr20:641736-642566 1416 1495 60 61 +syndip_2_chr20:641736-642566 1416 2965 60 61 +p:HG002_1_chr20:641736-642566 1416 4436 60 61 +p:HG002_2_chr20:641736-642566 1416 5907 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/output.vcf.gz new file mode 100644 index 00000000..da4d05c3 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/output.vcf.gz.tbi new file mode 100644 index 00000000..35b58dc9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:641836-642466/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/base.vcf.gz new file mode 100644 index 00000000..3822c7e2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/base.vcf.gz.tbi new file mode 100644 index 00000000..bed0ef70 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/comp.vcf.gz new file mode 100644 index 00000000..72cf7841 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/comp.vcf.gz.tbi new file mode 100644 index 00000000..172389fb Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/haps.fa new file mode 100644 index 00000000..7dd3b59a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/haps.fa @@ -0,0 +1,26 @@ +>ref_chr20_7720811_7721104 +TCACACATTTAAGATACAATTCCTTTCCCCACCCCAACTCTCCAGGTTTCCTGAATTAATTGGAAGGAAACTGTTATATTTCCTTAATTCCTGAAGTGGGAGTTAAATCTAAATCTAACAAATGACATTTTCTTTTTCTTTTCTTTTCTTTCTTTTTTTTTTTTTTTTTGGGATGGAGTTCCACTCTTGTTGCCCAGGCTGGACAGGCTGGAATACAATGGCGTGATCTTGGCTCTCTGCAACCTCCGACTCCCAGGTTCAAGTGATTCTCCTGCCTCAGCCTCCCAACTAGCT +>syndip_1_chr20:7720811-7721104 +TCACACATTTAAGATACAATTCCTTTCCCCACCCCAACTCTCCAGGTTTCCTGAATTAAT +TGGAAGGAAACTGTTATATTTCCTTAATTCCTGAAGTGGGAGTTAAATCTAAATCTAACA +AATGAC*TTTTCTTTTTCTTTT*TTTTTTTTTTTGGGATGGAGTTCCACTCTTGTTGCCC +AGGCTGGACAGGCTGGAATACAATGGCGTGATCTTGGCTCTCTGCAACCTCCGACTCCCA +GGTTCAAGTGATTCTCCTGCCTCAGCCTCCCAACTAGCT +>syndip_2_chr20:7720811-7721104 +TCACACATTTAAGATACAATTCCTTTCCCCACCCCAACTCTCCAGGTTTCCTGAATTAAT +TGGAAGGAAACTGTTATATTTCCTTAATTCCTGAAGTGGGAGTTAAATCTAAATCTAACA +AATGACGTTTTCTTTTTCTTTTCTTTTTTTTTTTGGGATGGAGTTCCACTCTTGTTGCCC +AGGCTGGACAGGCTGGAATACAATGGCGTGATCTTGGCTCTCTGCAACCTCCGACTCCCA +GGTTCAAGTGATTCTCCTGCCTCAGCCTCCCAACTAGCT +>p:HG002_1_chr20:7720811-7721104 +TCACACATTTAAGATACAATTCCTTTCCCCACCCCAACTCTCCAGGTTTCCTGAATTAAT +TGGAAGGAAACTGTTATATTTCCTTAATTCCTGAAGTGGGAGTTAAATCTAAATCTAACA +AATGACGTTTTCTTTTTCTTTTCTTTTTTTTTTTGGGATGGAGTTCCACTCTTGTTGCCC +AGGCTGGACAGGCTGGAATACAATGGCGTGATCTTGGCTCTCTGCAACCTCCGACTCCCA +GGTTCAAGTGATTCTCCTGCCTCAGCCTCCCAACTAGCT +>p:HG002_2_chr20:7720811-7721104 +TCACACATTTAAGATACAATTCCTTTCCCCACCCCAACTCTCCAGGTTTCCTGAATTAAT +TGGAAGGAAACTGTTATATTTCCTTAATTCCTGAAGTGGGAGTTAAATCTAAATCTAACA +AATGACATTTTCTTTTTCTTTTCTTTTCTTTCTTTTTTTTTTTTTTTTTGGGATGGAGTT +CCACTCTTGTTGCCCAGGCTGGACAGGCTGGAATACAATGGCGTGATCTTGGCTCTCTGC +AACCTCCGACTCCCAGGTTCAAGTGATTCTCCTGCCTCAGCCTCCCAACTAGCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/haps.fa.ref.fa new file mode 100644 index 00000000..3e29a118 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:7720811-7721104 +TCACACATTTAAGATACAATTCCTTTCCCCACCCCAACTCTCCAGGTTTCCTGAATTAATTGGAAGGAAACTGTTATATTTCCTTAATTCCTGAAGTGGGAGTTAAATCTAAATCTAACAAATGACATTTTCTTTTTCTTTTCTTTTCTTTCTTTTTTTTTTTTTTTTTGGGATGGAGTTCCACTCTTGTTGCCCAGGCTGGACAGGCTGGAATACAATGGCGTGATCTTGGCTCTCTGCAACCTCCGACTCCCAGGTTCAAGTGATTCTCCTGCCTCAGCCTCCCAACTAGCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/msa.fa new file mode 100644 index 00000000..44437053 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/msa.fa @@ -0,0 +1,30 @@ +>ref_chr20_7720811_7721104 +tcacacatttaagatacaattcctttccccaccccaactctccaggtttcctgaattaat +tggaaggaaactgttatatttccttaattcctgaagtgggagttaaatctaaatctaaca +aatgacattttctttttcttttcttttctttctttttttttttttttttgggatggagtt +ccactcttgttgcccaggctggacaggctggaatacaatggcgtgatcttggctctctgc +aacctccgactcccaggttcaagtgattctcctgcctcagcctcccaactagct +>syndip_1_chr20:7720811-7721104 +tcacacatttaagatacaattcctttccccaccccaactctccaggtttcctgaattaat +tggaaggaaactgttatatttccttaattcctgaagtgggagttaaatctaaatctaaca +aatgac--ttttctttttctttt---------------tttttttttttgggatggagtt +ccactcttgttgcccaggctggacaggctggaatacaatggcgtgatcttggctctctgc +aacctccgactcccaggttcaagtgattctcctgcctcagcctcccaactagct +>syndip_2_chr20:7720811-7721104 +tcacacatttaagatacaattcctttccccaccccaactctccaggtttcctgaattaat +tggaaggaaactgttatatttccttaattcctgaagtgggagttaaatctaaatctaaca +aatgacgttttctttttcttttc---------------tttttttttttgggatggagtt +ccactcttgttgcccaggctggacaggctggaatacaatggcgtgatcttggctctctgc +aacctccgactcccaggttcaagtgattctcctgcctcagcctcccaactagct +>p:HG002_1_chr20:7720811-7721104 +tcacacatttaagatacaattcctttccccaccccaactctccaggtttcctgaattaat +tggaaggaaactgttatatttccttaattcctgaagtgggagttaaatctaaatctaaca +aatgacgttttctttttcttttc---------------tttttttttttgggatggagtt +ccactcttgttgcccaggctggacaggctggaatacaatggcgtgatcttggctctctgc +aacctccgactcccaggttcaagtgattctcctgcctcagcctcccaactagct +>p:HG002_2_chr20:7720811-7721104 +tcacacatttaagatacaattcctttccccaccccaactctccaggtttcctgaattaat +tggaaggaaactgttatatttccttaattcctgaagtgggagttaaatctaaatctaaca +aatgacattttctttttcttttcttttctttctttttttttttttttttgggatggagtt +ccactcttgttgcccaggctggacaggctggaatacaatggcgtgatcttggctctctgc +aacctccgactcccaggttcaagtgattctcctgcctcagcctcccaactagct diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/msa.fa.fai new file mode 100644 index 00000000..8651713c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_7720811_7721104 294 27 60 61 +syndip_1_chr20:7720811-7721104 294 358 60 61 +syndip_2_chr20:7720811-7721104 294 689 60 61 +p:HG002_1_chr20:7720811-7721104 294 1021 60 61 +p:HG002_2_chr20:7720811-7721104 294 1353 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/output.vcf.gz new file mode 100644 index 00000000..32eeffc5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/output.vcf.gz.tbi new file mode 100644 index 00000000..a18dbfc7 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:7720911-7721004/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/base.vcf.gz new file mode 100644 index 00000000..b517ab9d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/base.vcf.gz.tbi new file mode 100644 index 00000000..0a44f543 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/comp.vcf.gz new file mode 100644 index 00000000..40910890 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/comp.vcf.gz.tbi new file mode 100644 index 00000000..f9ca38b1 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/haps.fa new file mode 100644 index 00000000..c52bda1e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/haps.fa @@ -0,0 +1,128 @@ +>ref_chr20_8661811_8662758 +GCCAACCTACGTTAAGTAATTCATAACTTCAGTATTTAATAAATCTTCAGTGAAAGGCAAGAGGCTACACACAGTGACAGACCCAGAGATAAACCCTGTGCCCCTAGAGATTTGCACTCCTCTTAAAAGTGTATATATATATAATTATATAATTATTTATTATATAATTATATATAATTATATAATTATTTATTATATAATTATATATAATATACAATTATTTATTATATAATTATATATAATTATATATTTATTATATTTATTATACAGTTATATAATAAATAATTATATAATTATATATAATTATATATTATTTATTATCTAATTCTATATTAAATATAATTATTTATTATCTAATTCTATATTATATATAATTATTTATTATATAATTCTATATTATATATAATTATTATATAATTCTATATATAATTATTTATTATATAATTCTATACATAAGTATTTATTATATAATTATGTATATAATTATTTATTATATAATTATGTATAATATGTAATTATTTATTATATAATTATGTATAATATGTAATTATTTATTATATAATTATGTATAATATATAATTATTTATTATATAATTATGTATAATATATAATTATTTATTATATAATTATGTGTTATGTATAATTATTATATAATTATGTATAATATATATATAATTTTTTATTATATAATTATGTATAATATATAATTTTTTATAATTATGTGTAATATATAATTATTTATCATATAATTACAATATATATTATTAACATAATATCTAAATATATTAATAATCTAATATCTATAATTAATATAATATATAAATATTACTTCTTGAAATCCAACGTGCACCTGAATCACCTGAGCCGTTGTTAAAATGCAGATTCGAGATCCTGCATTTCTAACAAGTTACTGGGTGAGGCAGAAGATGCTTAGCAAAGGCCCACACC +>syndip_1_chr20:8661811-8662758 +GCCAACCTACGTTAAGTAATTCATAACTTCAGTATTTAATAAATCTTCAGTGAAAGGCAA +GAGGCTACACACAGTGACAGACCCAGAGATAAACCCTGTGCCCCTAGAGATTTGCACTCC +TCTTAAAAGTGTATATATATATAATTATATAATTATTTATTATATAATTATATATAATTA +TATAATTATTTATTATATAATTATATATAATTATATAATTATTTATTATATAATTATATA +TAATATACAATTATTTATTATATAATTATATATAATTATATATTTATTATATTTATTATA +CAGTTATATAATAAATAATTATATAATTATATATAATTATATATATATAATTATATATAA +TTATATATAATTATATAATTATATATAATTGTATATAATTATTTATTATATAATTATATA +TTATTTATTATATAATTATATAATTATATATTATTTATTATATATTATATAATTATATAA +TTATATATTATTTATTATATAATATATAATTATATATTATTTATTATATAATTATATATT +ATTTATTATATATATTATTTATTATATAATTATATATTATGTATTATATAATTATATAAT +TATATATTATGTATTATATAATTATATATTATGTATTATATAATTATATAATTATATATT +ATGTATTATATAATTATATATTATTTATTATATAATTATATAATTATATATTATTTATTA +TATAATTATATAATTATATATTATTTATTATATAATTATATAATTATATATTATTTATTA +TATAATTATATAATTATATATTATTTATTATATAATTATATATTATTTATTATATAATTA +TATATTATTTATTACATAAATATATATTATTTATTACATAAGTATATATCACTTATTATA +TAATTGCATATAATTATTTATTATATAATTGCATATAATTATTATATAATTGTATATAGT +TATTTATTATATAATTGTATATAGTTATTTATTATATAATTCTATATAATTATTTATTAT +CTAATTCTATATTAAATATAATTATTTATTATCTAATTCTATATTATATATAATTATTTA +TTATATAATTCTATATTATATATAATTATTATATAATTCTATATATAATTATTTATTATA +TAATTCTATACATAAGTATTTATTATATAATTATGTATATAATTATTTATTATATAATTA +TGTATAATATGTAATTATTTATTATATAATTATGTATAATATGTAATTATTTATTATATA +ATTATGTATAATATATAATTATTTATTATATAATTATGTATAATATATAATTATTTATTA +TATAATTATGTGTTATGTATAATTATTATATAATTATGTATAATATATATATAATTTTTT +ATTATATAATTATGTATAATATATAATTTTTTATAATTATGTGTAATATATAATTATTTA +TCATATAATTACAATATATATTATTAACATAATATCTAAATATATTAATAATCTAATATC +TATAATTAATATAATATATAAATATTACTTCTTGAAATCCAACGTGCACCTGAATCACCT +GAGCCGTTGTTAAAATGCAGATTCGAGATCCTGCATTTCTAACAAGTTACTGGGTGAGGC +AGAAGATGCTTAGCAAAGGCCCACACC +>syndip_2_chr20:8661811-8662758 +GCCAACCTACGTTAAGTAATTCATAACTTCAGTATTTAATAAATCTTCAGTGAAAGGCAA +GAGGCTACACACAGTGACAGACCCAGAGATAAACCCTGTGCCCCTAGAGATTTGCACTCC +TCTTAAAAGTGTATATATATATAATTATATAATTATTTATTATATAATGATATATAATTA +TATAATTATTTATTATATAATGATATATAATTATATAATTATTTATTATATAATTATATA +TAATTATATAATTATTTATTATATAATTATATATAATTATATAATTATTTATTATATAAT +TATATATAATTATATAATTATTTATTATATAATTATATATAATTATATAATTATTTATTA +TATAATTATATATAATTATATAATTATTTATTATATAATTATATATAATTATATAATTAT +TTATTATATAATTATATATAATTATATAATTATTTATTATATAATTATATATAATTATAT +AATTATTTATTATATAATTATATATAATATACAATTATTTATTATATAATTATATATAAT +ATACAATTATTTATTATATAATTATATATAATTATATATTTATTATATTTATTATACAGT +TATATAATAAATATATAATTATATATAAATATATAATTATATATAATTATATATATATAA +TTATATGTAATTATATATAATTATATAATTATTATATAATTGTATATAATATATAATTAT +ATAATTATATATTATTTATTATATAATATATAATTATATAATTATATATTATTTATTATA +TAATATATAATTATATAATTATATATTATTTATTATATAATTATATATTATTTATTATAT +ATATTATTTATTATATAATTATATAATTATATATTATTTATTATATAATTATATATTATT +TATTATATAATATATAATTATATATTATTTATTATATAATATATAATTATATATTATTTA +TTATATAATTATATATTATGTATTATATAATATATAATTATATATTATGTATTATATAAT +TATATAATTATATATTATTTATTATATAATTATATAATTATATATTATTTATTACATAAT +TATATATTATTTATTACATAAGTATATATTATTTATTACATAAGTATATATCACTTATTA +TATAATTGTATATAATTATTTATTATATAATTGCATATAATTATTTATTATATAATTGTA +TATAGTTATTTATTATATAATTCTATATAGTTATTTATTATATAATTCTATATAATTATT +TATTATCTAATTCTATATTATATATAATTATTTATTATCTAATTCTATATTATATATAAT +TATTTATTATATAATTCTATATTATATATAATTATTTATTATATAATTCTATATTATATA +TAATTATTATATAATTCTATATATAATTATTTATTATATAATTCTATACATAAGTATTTA +TTATATAATTATGTATATAATTATTTATTATATAATTATGTATAATATGTAATTATTTAT +TATATAATTATGTATAATATATAATTGTTTATTATATAATTATGTATAATATATAATTAT +TTATTATATAATTATGTATAATATATAATTATTTATTATATAATTATGTGTTATGTATAA +TTATTTATTATATAATTATGTATAATATATATATAATTTTTTATTATATAATTATGTATA +ATATATAATTTTTTATAATTATGTGTAATATATAATTATTTATCATATAATTACAATATA +TATTATTAACATAATATCTAAATATATTAATAATCTAATATCTATAATTAATATAATATA +TAAATATTACTTCTTGAAATCCAACGTGCACCTGAATCACCTGAGCCGTTGTTAAAATGC +AGATTCGAGATCCTGCATTTCTAACAAGTTACTGGGTGAGGCAGAAGATGCTTAGCAAAG +GCCCACACC +>p:HG002_1_chr20:8661811-8662758 +GCCAACCTACGTTAAGTAATTCATAACTTCAGTATTTAATAAATCTTCAGTGAAAGGCAA +GAGGCTACACACAGTGACAGACCCAGAGATAAACCCTGTGCCCCTAGAGATTTGCACTCC +TCTTAAAAGTGTATATATATATAATTATATAATTATTTATTATATAATGATATATAATTA +TATAATTATTTATTATATAATGATATATAATTATATAATTATTTATTATATAATTATATA +TAATTATATAATTATTTATTATATAATTATATATAATTATATAATTATTTATTATATAAT +TATATATAATTATATAATTATTTATTATATAATTATATATAATTATATAATTATTTATTA +TATAATTATATATAATTATATAATTATTTATTATATAATTATATATAATTATATAATTAT +TTATTATATAATTATATATAATTATATAATTATTTATTATATAATTATATATAATTATAT +AATTATTTATTATATAATTATATATAATATACAATTATTTATTATATAATTATATATAAT +ATACAATTATTTATTATATAATTATATATAATTATATATTTATTATATTTATTATACAGT +TATATAATAAATATATAATTATATATAAATATATAATTATATATAATTATATATATATAA +TTATATGTAATTATATATAATTATATAATTATTATATAATTGTATATAATATATAATTAT +ATAATTATATATTATTTATTATATAATATATAATTATATAATTATATATTATTTATTATA +TAATATATAATTATATAATTATATATTATTTATTATATAATTATATATTATTTATTATAT +ATATTATTTATTATATAATTATATAATTATATATTATTTATTATATAATTATATATTATT +TATTATATAATATATAATTATATATTATTTATTATATAATATATAATTATATATTATTTA +TTATATAATTATATATTATGTATTATATAATATATAATTATATATTATGTATTATATAAT +TATATAATTATATATTATTTATTATATAATTATATAATTATATATTATTTATTACATAAT +TATATATTATTTATTACATAAGTATATATTATTTATTACATAAGTATATATCACTTATTA +TATAATTGTATATAATTATTTATTATATAATTGCATATAATTATTTATTATATAATTGTA +TATAGTTATTTATTATATAATTCTATATAGTTATTTATTATATAATTCTATATAATTATT +TATTATCTAATTCTATATTATATATAATTATTTATTATCTAATTCTATATTATATATAAT +TATTTATTATATAATTCTATATTATATATAATTATTTATTATATAATTCTATATTATATA +TAATTATTATATAATTCTATATATAATTATTTATTATATAATTCTATACATAAGTATTTA +TTATATAATTATGTATATAATTATTTATTATATAATTATGTATAATATGTAATTATTTAT +TATATAATTATGTATAATATATAATTGTTTATTATATAATTATGTATAATATATAATTAT +TTATTATATAATTATGTATAATATATAATTATTTATTATATAATTATGTGTTATGTATAA +TTATTTATTATATAATTATGTATAATATATATATAATTTTTTATTATATAATTATGTATA +ATATATAATTTTTTATAATTATGTGTAATATATAATTATTTATCATATAATTACAATATA +TATTATTAACATAATATCTAAATATATTAATAATCTAATATCTATAATTAATATAATATA +TAAATATTACTTCTTGAAATCCAACGTGCACCTGAATCACCTGAGCCGTTGTTAAAATGC +AGATTCGAGATCCTGCATTTCTAACAAGTTACTGGGTGAGGCAGAAGATGCTTAGCAAAG +GCCCACACC +>p:HG002_2_chr20:8661811-8662758 +GCCAACCTACGTTAAGTAATTCATAACTTCAGTATTTAATAAATCTTCAGTGAAAGGCAA +GAGGCTACACACAGTGACAGACCCAGAGATAAACCCTGTGCCCCTAGAGATTTGCACTCC +TCTTAAAAGTGTATATATATATAATTATATAATTATTTATTATATAATTATATATAATTA +TATAATTATTTATTATATAATTATATATAATTATATAATTATTTATTATATAATTATATA +TAATATACAATTATTTATTATATAATTATATATAATTATATATTTATTATATTTATTATA +CAGTTATATAATAAATAATTATATAATTATATATAATTATATATATATAATTATATATAA +TTATATATAATTATATAATTATATATAATTGTATATAATTATTTATTATATAATTATATA +TTATTTATTATATAATTATATAATTATATATTATTTATTATATATTATATAATTATATAA +TTATATATTATTTATTATATAATATATAATTATATATTATTTATTATATAATTATATATT +ATTTATTATATATATTATTTATTATATAATTATATATTATGTATTATATAATTATATAAT +TATATATTATGTATTATATAATTATATATTATGTATTATATAATTATATAATTATATATT +ATGTATTATATAATTATATATTATTTATTATATAATTATATAATTATATATTATTTATTA +TATAATTATATAATTATATATTATTTATTATATAATTATATAATTATATATTATTTATTA +TATAATTATATAATTATATATTATTTATTATATAATTATATATTATTTATTATATAATTA +TATATTATTTATTACATAAATATATATTATTTATTACATAAGTATATATCACTTATTATA +TAATTGCATATAATTATTTATTATATAATTGCATATAATTATTATATAATTGTATATAGT +TATTTATTATATAATTGTATATAGTTATTTATTATATAATTCTATATAATTATTTATTAT +CTAATTCTATATTAAATATAATTATTTATTATCTAATTCTATATTATATATAATTATTTA +TTATATAATTCTATATTATATATAATTATTATATAATTCTATATATAATTATTTATTATA +TAATTCTATACATAAGTATTTATTATATAATTATGTATATAATTATTTATTATATAATTA +TGTATAATATGTAATTATTTATTATATAATTATGTATAATATGTAATTATTTATTATATA +ATTATGTATAATATATAATTATTTATTATATAATTATGTATAATATATAATTATTTATTA +TATAATTATGTGTTATGTATAATTATTATATAATTATGTATAATATATATATAATTTTTT +ATTATATAATTATGTATAATATATAATTTTTTATAATTATGTGTAATATATAATTATTTA +TCATATAATTACAATATATATTATTAACATAATATCTAAATATATTAATAATCTAATATC +TATAATTAATATAATATATAAATATTACTTCTTGAAATCCAACGTGCACCTGAATCACCT +GAGCCGTTGTTAAAATGCAGATTCGAGATCCTGCATTTCTAACAAGTTACTGGGTGAGGC +AGAAGATGCTTAGCAAAGGCCCACACC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/haps.fa.ref.fa new file mode 100644 index 00000000..b5e952ab --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:8661811-8662758 +GCCAACCTACGTTAAGTAATTCATAACTTCAGTATTTAATAAATCTTCAGTGAAAGGCAAGAGGCTACACACAGTGACAGACCCAGAGATAAACCCTGTGCCCCTAGAGATTTGCACTCCTCTTAAAAGTGTATATATATATAATTATATAATTATTTATTATATAATTATATATAATTATATAATTATTTATTATATAATTATATATAATATACAATTATTTATTATATAATTATATATAATTATATATTTATTATATTTATTATACAGTTATATAATAAATAATTATATAATTATATATAATTATATATTATTTATTATCTAATTCTATATTAAATATAATTATTTATTATCTAATTCTATATTATATATAATTATTTATTATATAATTCTATATTATATATAATTATTATATAATTCTATATATAATTATTTATTATATAATTCTATACATAAGTATTTATTATATAATTATGTATATAATTATTTATTATATAATTATGTATAATATGTAATTATTTATTATATAATTATGTATAATATGTAATTATTTATTATATAATTATGTATAATATATAATTATTTATTATATAATTATGTATAATATATAATTATTTATTATATAATTATGTGTTATGTATAATTATTATATAATTATGTATAATATATATATAATTTTTTATTATATAATTATGTATAATATATAATTTTTTATAATTATGTGTAATATATAATTATTTATCATATAATTACAATATATATTATTAACATAATATCTAAATATATTAATAATCTAATATCTATAATTAATATAATATATAAATATTACTTCTTGAAATCCAACGTGCACCTGAATCACCTGAGCCGTTGTTAAAATGCAGATTCGAGATCCTGCATTTCTAACAAGTTACTGGGTGAGGCAGAAGATGCTTAGCAAAGGCCCACACC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/msa.fa new file mode 100644 index 00000000..3286542a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/msa.fa @@ -0,0 +1,170 @@ +>ref_chr20_8661811_8662758 +gccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggcaa +gaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactcc +tcttaaaag--------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------tgtata +tatatataattatataattattt--------attatataattatatataattatata--- +--------attatttattatataattatatataatatac------------aattattta +ttatataattatatataattatat--------atttattatat----ttattatacagt- +-tatataataaataattatataattatatataattatat------------------att +atttattatctaattctatattaaatataattatttattatc------------------ +--------------taattctatattatatataattatttattatataattctatattat +atataattattatataattctatatataattatttattatataattctatacataagtat +ttattatataattatgtatataattatttattatataattatgtataatatgtaattatt +tattatataattatgtataatatgtaattatttattatataattatgtataatatataat +tatttattatataattatgtataatatataattatttattatataattatgtgttatgta +taa----ttattatataattatgtataatatatatataattttttattatataattatgt +ataatatataattttttataattatgtgtaatatataattatttatcatataattacaat +atatattattaacataatatctaaatatattaataatctaatatctataattaatataat +atataaatattacttcttgaaatccaacgtgcacctgaatcacctgagccgttgttaaaa +tgcagattcgagatcctgcatttctaacaagttactgggtgaggcagaagatgcttagca +aaggcccacacc +>syndip_1_chr20:8661811-8662758 +gccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggcaa +gaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactcc +tcttaaaagtgtatatatatataattatataattatttattatataattatatataatta +tataattatttattatataattatatataattatataattatttattatataattatata +taa-tatacaattatttattatataattatatataattatatatttattatatttat--- +--tatacagttatataataaataattatataattatatataattatata---------ta +tataattatatataattatata-----taattatataattatatataattg--------- +----------------------tatataattatttattatataattatat---------- +-attatttattatataattatata----------------attatat------------- +-----attatttattatata---------------------------------------- +--------------------ttatataattatataattatatattatttattatata--- +--atatataattatatat-------tatttattatataattatatattatttatta---- +-----tatatattatttattatata----------------------attatatattatg +tattatataattatataattatatattatgtattatataat----------------tat +atattatgtattatataattatataattatatattatgtattatataattatatattatt +tattatataattatataattatatattatttattatataattatataattatatattatt +tattatataat---------------------tatataattatatattatttattatata +attatataattatat-attattt--------attatataattatatattatttattatat +aattatatattatttattacataaatatatattatttattacataagtatatatcactta +ttatataattgcatataattatttattatataattgcatataa----ttattatataatt +gtatatagttatttattatataattgtatatagttatttattatataattctatataatt +atttattatctaattctatattaaatataattatttattatc------------------ +--------------taattctatattatatataattatttattatataattctatattat +atataattattatataattctatatataattatttattatataattctatacataagtat +ttattatataattatgtatataattatttattatataattatgtataatatgtaattatt +tattatataattatgtataatatgtaattatttattatataattatgtataatatataat +tatttattatataattatgtataatatataattatttattatataattatgtgttatgta +taa----ttattatataattatgtataatatatatataattttttattatataattatgt +ataatatataattttttataattatgtgtaatatataattatttatcatataattacaat +atatattattaacataatatctaaatatattaataatctaatatctataattaatataat +atataaatattacttcttgaaatccaacgtgcacctgaatcacctgagccgttgttaaaa +tgcagattcgagatcctgcatttctaacaagttactgggtgaggcagaagatgcttagca +aaggcccacacc +>syndip_2_chr20:8661811-8662758 +gccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggcaa +gaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactcc +tcttaaaagtgtatatatatataattatataattatttattatataatgatatataatta +tataattatttattatataatgatatataattatataattatttattatataattatata +taattatataattatttattatataattatatataattatataattatttattatataat +tatatataattatataattatttattatataattatatataattatataattatttatta +tataattatatataattatataattatttattatataattatatataattatataattat +ttattatataattatatataattatataattatttattatataattatatataattatat +aattatttattatataattatatataatatacaattatttattatataattatatataat +atacaattatttattatataattatatataattatatatttattatatttattatacagt +tatataataaatatataattatatataaatatataattatatataattatatatatataa +ttatatgtaattatatataattatataattattatataattgtatataatatataattat +ataattatatattatttattatataatatataattatataattatatattatttattata +taatatataattatataattatatattatttattatataattatatattatttattatat +atattatttattatataattatataattatatattatttattatataattatatattatt +tattatataa-tatataattatatattatttattatataa-tatataattatatattatt +tattatataattatatattatgtattatataatatataattatatattatgtattatata +attatataattatat-attatttattatataattatataattatatattatttattacat +aattatatattatttattacataagtatatattatttattacataagtatatatcactta +ttatataattgtatataattatttattatataattgcatataattatttattatataatt +gtatatagttatttattatataattctatatagttatttattatataattctatataatt +atttattatctaattctatattatatataattatttattatctaattctatattatatat +aattatttattatataattctatattatatataattatttattatataattctatattat +atataattattatataattctatatataattatttattatataattctatacataagtat +ttattatataattatgtatataattatttattatataattatgtataatatgtaattatt +tattatataattatgtataatatataattgtttattatataattatgtataatatataat +tatttattatataattatgtataatatataattatttattatataattatgtgttatgta +taattatttattatataattatgtataatatatatataattttttattatataattatgt +ataatatataattttttataattatgtgtaatatataattatttatcatataattacaat +atatattattaacataatatctaaatatattaataatctaatatctataattaatataat +atataaatattacttcttgaaatccaacgtgcacctgaatcacctgagccgttgttaaaa +tgcagattcgagatcctgcatttctaacaagttactgggtgaggcagaagatgcttagca +aaggcccacacc +>p:HG002_1_chr20:8661811-8662758 +gccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggcaa +gaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactcc +tcttaaaagtgtatatatatataattatataattatttattatataatgatatataatta +tataattatttattatataatgatatataattatataattatttattatataattatata +taattatataattatttattatataattatatataattatataattatttattatataat +tatatataattatataattatttattatataattatatataattatataattatttatta +tataattatatataattatataattatttattatataattatatataattatataattat +ttattatataattatatataattatataattatttattatataattatatataattatat +aattatttattatataattatatataatatacaattatttattatataattatatataat +atacaattatttattatataattatatataattatatatttattatatttattatacagt +tatataataaatatataattatatataaatatataattatatataattatatatatataa +ttatatgtaattatatataattatataattattatataattgtatataatatataattat +ataattatatattatttattatataatatataattatataattatatattatttattata +taatatataattatataattatatattatttattatataattatatattatttattatat +atattatttattatataattatataattatatattatttattatataattatatattatt +tattatataa-tatataattatatattatttattatataa-tatataattatatattatt +tattatataattatatattatgtattatataatatataattatatattatgtattatata +attatataattatat-attatttattatataattatataattatatattatttattacat +aattatatattatttattacataagtatatattatttattacataagtatatatcactta +ttatataattgtatataattatttattatataattgcatataattatttattatataatt +gtatatagttatttattatataattctatatagttatttattatataattctatataatt +atttattatctaattctatattatatataattatttattatctaattctatattatatat +aattatttattatataattctatattatatataattatttattatataattctatattat +atataattattatataattctatatataattatttattatataattctatacataagtat +ttattatataattatgtatataattatttattatataattatgtataatatgtaattatt +tattatataattatgtataatatataattgtttattatataattatgtataatatataat +tatttattatataattatgtataatatataattatttattatataattatgtgttatgta +taattatttattatataattatgtataatatatatataattttttattatataattatgt +ataatatataattttttataattatgtgtaatatataattatttatcatataattacaat +atatattattaacataatatctaaatatattaataatctaatatctataattaatataat +atataaatattacttcttgaaatccaacgtgcacctgaatcacctgagccgttgttaaaa +tgcagattcgagatcctgcatttctaacaagttactgggtgaggcagaagatgcttagca +aaggcccacacc +>p:HG002_2_chr20:8661811-8662758 +gccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggcaa +gaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactcc +tcttaaaagtgtatatatatataattatataattatttattatataattatatataatta +tataattatttattatataattatatataattatataattatttattatataattatata +taa-tatacaattatttattatataattatatataattatatatttattatatttat--- +--tatacagttatataataaataattatataattatatataattatata---------ta +tataattatatataattatata-----taattatataattatatataattg--------- +----------------------tatataattatttattatataattatat---------- +-attatttattatataattatata----------------attatat------------- +-----attatttattatata---------------------------------------- +--------------------ttatataattatataattatatattatttattatata--- +--atatataattatatat-------tatttattatataattatatattatttatta---- +-----tatatattatttattatata----------------------attatatattatg +tattatataattatataattatatattatgtattatataat----------------tat +atattatgtattatataattatataattatatattatgtattatataattatatattatt +tattatataattatataattatatattatttattatataattatataattatatattatt +tattatataat---------------------tatataattatatattatttattatata +attatataattatat-attattt--------attatataattatatattatttattatat +aattatatattatttattacataaatatatattatttattacataagtatatatcactta +ttatataattgcatataattatttattatataattgcatataa----ttattatataatt +gtatatagttatttattatataattgtatatagttatttattatataattctatataatt +atttattatctaattctatattaaatataattatttattatc------------------ +--------------taattctatattatatataattatttattatataattctatattat +atataattattatataattctatatataattatttattatataattctatacataagtat +ttattatataattatgtatataattatttattatataattatgtataatatgtaattatt +tattatataattatgtataatatgtaattatttattatataattatgtataatatataat +tatttattatataattatgtataatatataattatttattatataattatgtgttatgta +taa----ttattatataattatgtataatatatatataattttttattatataattatgt +ataatatataattttttataattatgtgtaatatataattatttatcatataattacaat +atatattattaacataatatctaaatatattaataatctaatatctataattaatataat +atataaatattacttcttgaaatccaacgtgcacctgaatcacctgagccgttgttaaaa +tgcagattcgagatcctgcatttctaacaagttactgggtgaggcagaagatgcttagca +aaggcccacacc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/msa.fa.fai new file mode 100644 index 00000000..1face17a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_8661811_8662758 1932 27 60 61 +syndip_1_chr20:8661811-8662758 1932 2024 60 61 +syndip_2_chr20:8661811-8662758 1932 4021 60 61 +p:HG002_1_chr20:8661811-8662758 1932 6019 60 61 +p:HG002_2_chr20:8661811-8662758 1932 8017 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/output.vcf.gz new file mode 100644 index 00000000..63b27473 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/output.vcf.gz.tbi new file mode 100644 index 00000000..e538cbb3 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/chr20/chr20:8661911-8662658/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/base.vcf.gz new file mode 100644 index 00000000..6c9485c5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/base.vcf.gz.tbi new file mode 100644 index 00000000..73bd98fb Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/comp.vcf.gz new file mode 100644 index 00000000..1871a961 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/comp.vcf.gz.tbi new file mode 100644 index 00000000..95dbeebc Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/haps.fa new file mode 100644 index 00000000..baa65001 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/haps.fa @@ -0,0 +1,38 @@ +>ref_chr20_10802576_10803059 +GCCCAACTTAATCCAGTGTGACTCCATTTTAAATCAATTATATCTGCAAAGATCTAATTTTCAAATGAGGTCACAGTCACAAGTATTGGGGGTTAGGACTTTTGGGGGACATAACCCACAATGTCCTCTGAATATATATATATATATCCTCCCATATATATATATATATATATATATCCTCCCATATATATATATATATATATATATATCCTCCCATATATATATATATATATATATCCTCCCATATATATATATATATATGTCCTCCCATATATATATATATATCCTCCCATATATATATATATCCTCCCATATATATATCTATCCTCCCATATATATATATATATATATATTTTCAATGTATCCCTTTATTCAAGTGATTTTAAGCAATGAAAGCAAGACAGCTGTTATAGGATTTACCTTTCTAGATGGAAAAGGACAAGTAAATAAGGTCTTAAGCTCCATGTCAAGAAAGGGGCACAAC +>syndip_1_chr20:10802576-10803059 +GCCCAACTTAATCCAGTGTGACTCCATTTTAAATCAATTATATCTGCAAAGATCTAATTT +TCAAATGAGGTCACAGTCACAAGTATTGGGGGTTAGGACTTTTGGGGGACATAACCCACA +ATGTCCTCTGAATATATATATATATATCCTCCCATATATATATATATCCTCCCATATATA +TATATATATATATATATATATATGTCCTCCCATATATATATATATCCTCCCATATATATA +TCTATCCTCCCATATATATATATATATATTTTCAATGTATCCCTTTATTCAAGTGATTTT +AAGCAATGAAAGCAAGACAGCTGTTATAGGATTTACCTTTCTAGATGGAAAAGGACAAGT +AAATAAGGTCTTAAGCTCCATGTCAAGAAAGGGGCACAAC +>syndip_2_chr20:10802576-10803059 +GCCCAACTTAATCCAGTGTGACTCCATTTTAAATCAATTATATCTGCAAAGATCTAATTT +TCAAATGAGGTCACAGTCACAAGTATTGGGGGTTAGGACTTTTGGGGGACATAACCCACA +ATGTCCTCTGAATATATATATATATATCCTCCCATATATATATATATATATATATATCCT +CCCATATATATATATATATATATATATCCTCCCATATATATATATATATATATATCCTCC +CATATATATATATATATATGTCCTCCCATATATATATATATATCCTCCCATATATATATA +TATCCTCCCATATATATATCTATCCTCCCATATATATATATATATATATATTTTCAATGT +ATCCCTTTATTCAAGTGATTTTAAGCAATGAAAGCAAGACAGCTGTTATAGGATTTACCT +TTCTAGATGGAAAAGGACAAGTAAATAAGGTCTTAAGCTCCATGTCAAGAAAGGGGCACA +AC +>p:HG002_1_chr20:10802576-10803059 +GCCCAACTTAATCCAGTGTGACTCCATTTTAAATCAATTATATCTGCAAAGATCTAATTT +TCAAATGAGGTCACAGTCACAAGTATTGGGGGTTAGGACTTTTGGGGGACATAACCCACA +ATGTCCTCTGAATATATATATATATATCCTCCCATATATATATATATATATATATATCCT +CCCATATATATATATATATATATATATCCTCCCATATATATATATATATATATATCCTCC +CATATATATATATATATATGTCCTCCCATATATATATATATATCCTCCCATATATATATA +TATCCTCCCATATATATATCTATCCTCCCATATATATATATATATATATATTTTCAATGT +ATCCCTTTATTCAAGTGATTTTAAGCAATGAAAGCAAGACAGCTGTTATAGGATTTACCT +TTCTAGATGGAAAAGGACAAGTAAATAAGGTCTTAAGCTCCATGTCAAGAAAGGGGCACA +AC +>p:HG002_2_chr20:10802576-10803059 +GCCCAACTTAATCCAGTGTGACTCCATTTTAAATCAATTATATCTGCAAAGATCTAATTT +TCAAATGAGGTCACAGTCACAAGTATTGGGGGTTAGGACTTTTGGGGGACATAACCCACA +ATGTCCTCTGAATATATATATATATATCCTCCCATATATATATATATCCTCCCATATATA +TATATATATATATATATATATATGTCCTCCCATATATATATATATCCTCCCATATATATA +TCTATCCTCCCATATATATATATATATATTTTCAATGTATCCCTTTATTCAAGTGATTTT +AAGCAATGAAAGCAAGACAGCTGTTATAGGATTTACCTTTCTAGATGGAAAAGGACAAGT +AAATAAGGTCTTAAGCTCCATGTCAAGAAAGGGGCACAAC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/haps.fa.ref.fa new file mode 100644 index 00000000..3c7e80df --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:10802576-10803059 +GCCCAACTTAATCCAGTGTGACTCCATTTTAAATCAATTATATCTGCAAAGATCTAATTTTCAAATGAGGTCACAGTCACAAGTATTGGGGGTTAGGACTTTTGGGGGACATAACCCACAATGTCCTCTGAATATATATATATATATCCTCCCATATATATATATATATATATATATCCTCCCATATATATATATATATATATATATATCCTCCCATATATATATATATATATATATCCTCCCATATATATATATATATATGTCCTCCCATATATATATATATATCCTCCCATATATATATATATCCTCCCATATATATATCTATCCTCCCATATATATATATATATATATATTTTCAATGTATCCCTTTATTCAAGTGATTTTAAGCAATGAAAGCAAGACAGCTGTTATAGGATTTACCTTTCTAGATGGAAAAGGACAAGTAAATAAGGTCTTAAGCTCCATGTCAAGAAAGGGGCACAAC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/msa.fa new file mode 100644 index 00000000..92110931 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/msa.fa @@ -0,0 +1,50 @@ +>ref_chr20_10802576_10803059 +gcccaacttaatccagtgtgactccattttaaatcaattatatctgcaaagatctaattt +tcaaatgaggtcacagtcacaagtattgggggttaggacttttgggggacataacccaca +atgtcctctgaatatatatatatatatcctcccatatatatatatatatatatatatcct +cccatatatatatatatatatatatatatcctcccatatatatatatatatatatatcct +cccatatatatatatatatatgtcctcccatatatatatatatatcctcccatatatata +tatatcctcccatatatatatctatcctcccatatatatatatatatatatattttcaat +gtatccctttattcaagtgattttaagcaatgaaagcaagacagctgttataggatttac +ctttctagatggaaaaggacaagtaaataaggtcttaagctccatgtcaagaaaggggca +caac +>syndip_1_chr20:10802576-10803059 +gcccaacttaatccagtgtgactccattttaaatcaattatatctgcaaagatctaattt +tcaaatgaggtcacagtcacaagtattgggggttaggacttttgggggacataacccaca +atgtcctctgaatatatatatatatatcctccc----------atatatatatatatcct +ccc--atatatatatatatat--------------------------------------- +-----------------------------atatatatatatatgtcctcccatatatata +tatatcctcccatatatatatctatcctccc----atatatatatatatatattttcaat +gtatccctttattcaagtgattttaagcaatgaaagcaagacagctgttataggatttac +ctttctagatggaaaaggacaagtaaataaggtcttaagctccatgtcaagaaaggggca +caac +>syndip_2_chr20:10802576-10803059 +gcccaacttaatccagtgtgactccattttaaatcaattatatctgcaaagatctaattt +tcaaatgaggtcacagtcacaagtattgggggttaggacttttgggggacataacccaca +atgtcctctgaatatatatatatatatcctcccatatatatatatatatatatatatcct +ccc--atatatatatatatatatatatatcctcccatatatatatatatatatatatcct +cccatatatatatatatatatgtcctcccatatatatatatatatcctcccatatatata +tatatcctcccatatatatatctatcctcccatatatatatatatatatatattttcaat +gtatccctttattcaagtgattttaagcaatgaaagcaagacagctgttataggatttac +ctttctagatggaaaaggacaagtaaataaggtcttaagctccatgtcaagaaaggggca +caac +>p:HG002_1_chr20:10802576-10803059 +gcccaacttaatccagtgtgactccattttaaatcaattatatctgcaaagatctaattt +tcaaatgaggtcacagtcacaagtattgggggttaggacttttgggggacataacccaca +atgtcctctgaatatatatatatatatcctcccatatatatatatatatatatatatcct +ccc--atatatatatatatatatatatatcctcccatatatatatatatatatatatcct +cccatatatatatatatatatgtcctcccatatatatatatatatcctcccatatatata +tatatcctcccatatatatatctatcctcccatatatatatatatatatatattttcaat +gtatccctttattcaagtgattttaagcaatgaaagcaagacagctgttataggatttac +ctttctagatggaaaaggacaagtaaataaggtcttaagctccatgtcaagaaaggggca +caac +>p:HG002_2_chr20:10802576-10803059 +gcccaacttaatccagtgtgactccattttaaatcaattatatctgcaaagatctaattt +tcaaatgaggtcacagtcacaagtattgggggttaggacttttgggggacataacccaca +atgtcctctgaatatatatatatatatcctccc----------atatatatatatatcct +ccc--atatatatatatatat--------------------------------------- +-----------------------------atatatatatatatgtcctcccatatatata +tatatcctcccatatatatatctatcctccc----atatatatatatatatattttcaat +gtatccctttattcaagtgattttaagcaatgaaagcaagacagctgttataggatttac +ctttctagatggaaaaggacaagtaaataaggtcttaagctccatgtcaagaaaggggca +caac diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/msa.fa.fai new file mode 100644 index 00000000..27d080c2 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_10802576_10803059 484 29 60 61 +syndip_1_chr20:10802576-10803059 484 556 60 61 +syndip_2_chr20:10802576-10803059 484 1083 60 61 +p:HG002_1_chr20:10802576-10803059 484 1611 60 61 +p:HG002_2_chr20:10802576-10803059 484 2139 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/output.vcf.gz new file mode 100644 index 00000000..c4e24f7b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/output.vcf.gz.tbi new file mode 100644 index 00000000..0886bda6 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:10802676-10802959/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/base.vcf.gz new file mode 100644 index 00000000..3dfd6e38 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/base.vcf.gz.tbi new file mode 100644 index 00000000..ad13966a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/comp.vcf.gz new file mode 100644 index 00000000..dd571f72 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/comp.vcf.gz.tbi new file mode 100644 index 00000000..ce38f9e8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/haps.fa new file mode 100644 index 00000000..f1b19697 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/haps.fa @@ -0,0 +1,60 @@ +>ref_chr20_13848064_13848750 +TCTGTAATCCCAGTTATTCAGGAGGCTGAGGCAGGAGAATCACCTGAACCCGGGAGGCAGAGGTTCCAGTGAGTCGAGATCTTGCCACTGCACTCCAGCCTGGGGGACAGAGGGAAATTGCGTCTCAAAAAAAAAAAAGAAGAAGAAAAGTAGAAGACGAAGATGAAGAAGAATAAGAAGAGAGAAAAGAAGAAGAGAAGGTTAGAGAAAAGAAGAGAAGAGAAGGAGAAGGAGAAGGAGGAGGAGAAGGAGAAGGAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGTCAAATATCTGGAGAAGAAGAAGAAGAGGAAGAAGAAGAAAAGGAAGAAGAAGAAGAAGAGGAAGAGGAAGAAAGAAGAAGAACAAGAAGAAGAAGAAGTCAAATATCTGGAGAAGAAGAAGAAGAAGAGGAAGAAGAAGAAGAAGAGGAGGAGGAAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAAATACAAATATCTGGAGCCGGGATTTGAGCCTGGCCCTTGACATATGTCCTAGGCCTCTTACACTCTCCTTACCAGCCCCTGTCCCTTAGGCCTGGGCCCCTGATTTGCCTGTCAGAGAAGCCAGAGAATC +>syndip_1_chr20:13848064-13848750 +TCTGTAATCCCAGTTATTCAGGAGGCTGAGGCAGGAGAATCACCTGAACCCGGGAGGCAG +AGGTTCCAGTGAGTCGAGATCTTGCCACTGCACTCCAGCCTGGGGGACAGAGGGAAATTG +CGTCTCAAAAAAAAAAAAGAAAAGAAAAGTAGAAGACGAAGATGAAGAAGAATAAGAAGA +GAGAAAAGAAGAAGAGAAGGTTAGAGAAAAGAAGAGAAGGAGAAGGAGAAGGAGGAGGAG +AAGGAGAAGGAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG +AAGAAGAAGAAGAAGAAGTCAAATATCTGGAGAAGAAGAAGAAGAAGAGGAAGAAGAAGA +AGAGGAAGAAGAAGAAGAAGAGGAAGAGGAAGAAAGAAGAAGAACAAGAAGAAGAAGAAG +TCAAATATCTGGAGAAGAAGAAGAAGAAGAGGAGGAAGAAGAAGAAGAAGAGGAGGAGGA +AGAAGAAGAAGAAGAAGAAGAAGAAGAAGCAGGAGCAGGAGAAGAAGAAGAAGAAGAAGA +AGAAGAGGAAGAGGAAGAGGAAGAGGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA +AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAGAAGAC +AAATATCTGGAGCCGGGATTTGAGCCTGGCCCTTGACATATGTCCTAGGCCTCTTACACT +CTCCTTACCAGCCCCTGTCCCTTAGGCCTGGGCCCCTGATTTGCCTGTCAGAGAAGCCAG +AGAATC +>syndip_2_chr20:13848064-13848750 +TCTGTAATCCCAGTTATTCAGGAGGCTGAGGCAGGAGAATCACCTGAACCCGGGAGGCAG +AGGTTCCAGTGAGTCGAGATCTTGCCACTGCACTCCAGCCTGGGGGACAGAGGGAAATTG +CGTCTCAAAAAAAAAAAAGAAAAGAAAAGTAGAAGACGAAGATGAAGAAGAATAAGAAGA +GAGAAAAGAAGAAGAGAAGGTTAGAGAAAAGAAGAGAAGGAGAAGGAGAAGGAGGAGGAG +AAGGAGAAGGAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG +AAGAAGAAGAAGAAGAAGTCAAATATCTGGAGAAGAAGAAGAAGAAGAGGAAGAAGAAGA +AGAGGAAGAAGAAGAAGAAGAGGAAGAGGAAGAAAGAAGAAGAACAAGAAGAAGAAGAAG +TCAAATATCTGGAGAAGAAGAAGAAGAAGAGGAGGAAGAAGAAGAAGAAGAGGAGGAGGA +AGAAGAAGAAGAAGAAGAAGAAGAAGAAGCAGGAGCAGGAGAAGAAGAAGAAGAAGAAGA +AGAAGAGGAAGAGGAAGAGGAAGAGGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA +AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAGAAGACAAATATCTGGAGCCG +GGATTTGAGCCTGGCCCTTGACATATGTCCTAGGCCTCTTACACTCTCCTTACCAGCCCC +TGTCCCTTAGGCCTGGGCCCCTGATTTGCCTGTCAGAGAAGCCAGAGAATC +>p:HG002_1_chr20:13848064-13848750 +TCTGTAATCCCAGTTATTCAGGAGGCTGAGGCAGGAGAATCACCTGAACCCGGGAGGCAG +AGGTTCCAGTGAGTCGAGATCTTGCCACTGCACTCCAGCCTGGGGGACAGAGGGAAATTG +CGTCTCAAAAAAAAAAAAGAAAAGAAAAGTAGAAGACGAAGATGAAGAAGAATAAGAAGA +GAGAAAAGAAGAAGAGAAGGTTAGAGAAAAGAAGAGAAGGAGAAGGAGAAGGAGGAGGAG +AAGGAGAAGGAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG +AAGAAGAAGAAGAAGAAGTCAAATATCTGGAGAAGAAGAAGAAGAAGAGGAAGAAGAAGA +AGAGGAAGAAGAAGAAGAAGAGGAAGAGGAAGAAAGAAGAAGAACAAGAAGAAGAAGAAG +TCAAATATCTGGAGAAGAAGAAGAAGAAGAGGAGGAAGAAGAAGAAGAAGAGGAGGAGGA +AGAAGAAGAAGAAGAAGAAGAAGAAGAAGCAGGAGCAGGAGAAGAAGAAGAAGAAGAAGA +AGAAGAGGAAGAGGAAGAGGAAGAGGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA +AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAGAAGACAAATATCTGGAGCCG +GGATTTGAGCCTGGCCCTTGACATATGTCCTAGGCCTCTTACACTCTCCTTACCAGCCCC +TGTCCCTTAGGCCTGGGCCCCTGATTTGCCTGTCAGAGAAGCCAGAGAATC +>p:HG002_2_chr20:13848064-13848750 +TCTGTAATCCCAGTTATTCAGGAGGCTGAGGCAGGAGAATCACCTGAACCCGGGAGGCAG +AGGTTCCAGTGAGTCGAGATCTTGCCACTGCACTCCAGCCTGGGGGACAGAGGGAAATTG +CGTCTCAAAAAAAAAAAAGAAAAGAAAAGTAGAAGACGAAGATGAAGAAGAATAAGAAGA +GAGAAAAGAAGAAGAGAAGGTTAGAGAAAAGAAGAGAAGGAGAAGGAGAAGGAGGAGGAG +AAGGAGAAGGAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG +AAGAAGAAGAAGAAGAAGTCAAATATCTGGAGAAGAAGAAGAAGAAGAGGAAGAAGAAGA +AGAGGAAGAAGAAGAAGAAGAGGAAGAGGAAGAAAGAAGAAGAACAAGAAGAAGAAGAAG +TCAAATATCTGGAGAAGAAGAAGAAGAAGAGGAGGAAGAAGAAGAAGAAGAGGAGGAGGA +AGAAGAAGAAGAAGAAGAAGAAGAAGAAGCAGGAGCAGGAGAAGAAGAAGAAGAAGAAGA +AGAAGAGGAAGAGGAAGAGGAAGAGGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA +AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAGAAGAC +AAATATCTGGAGCCGGGATTTGAGCCTGGCCCTTGACATATGTCCTAGGCCTCTTACACT +CTCCTTACCAGCCCCTGTCCCTTAGGCCTGGGCCCCTGATTTGCCTGTCAGAGAAGCCAG +AGAATC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/haps.fa.ref.fa new file mode 100644 index 00000000..660d9a4e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:13848064-13848750 +TCTGTAATCCCAGTTATTCAGGAGGCTGAGGCAGGAGAATCACCTGAACCCGGGAGGCAGAGGTTCCAGTGAGTCGAGATCTTGCCACTGCACTCCAGCCTGGGGGACAGAGGGAAATTGCGTCTCAAAAAAAAAAAAGAAGAAGAAAAGTAGAAGACGAAGATGAAGAAGAATAAGAAGAGAGAAAAGAAGAAGAGAAGGTTAGAGAAAAGAAGAGAAGAGAAGGAGAAGGAGAAGGAGGAGGAGAAGGAGAAGGAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGTCAAATATCTGGAGAAGAAGAAGAAGAGGAAGAAGAAGAAAAGGAAGAAGAAGAAGAAGAGGAAGAGGAAGAAAGAAGAAGAACAAGAAGAAGAAGAAGTCAAATATCTGGAGAAGAAGAAGAAGAAGAGGAAGAAGAAGAAGAAGAGGAGGAGGAAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAAATACAAATATCTGGAGCCGGGATTTGAGCCTGGCCCTTGACATATGTCCTAGGCCTCTTACACTCTCCTTACCAGCCCCTGTCCCTTAGGCCTGGGCCCCTGATTTGCCTGTCAGAGAAGCCAGAGAATC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/msa.fa new file mode 100644 index 00000000..19d9b767 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/msa.fa @@ -0,0 +1,75 @@ +>ref_chr20_13848064_13848750 +tctgtaatcccagttattcaggaggctgaggcaggagaatcacctgaacccgggaggcag +aggttccagtgagtcgagatcttgccactgcactccagcctgggggacagagggaaattg +cgtctcaaaaaaaaaaaagaagaagaaaagtagaagacgaagatgaagaagaataagaag +agagaaaagaagaagagaaggttagagaaaagaagagaa--------------------- +----gagaaggagaaggagaaggaggaggagaaggagaaggagaagaagaagaagaagaa +gaagaagaagaagaagaagtcaaatatctgg---agaagaagaagaagaggaagaagaag +aaaaggaagaagaagaagaagaggaagaggaagaaagaagaagaacaagaagaagaagaa +gtcaaatatctggagaagaagaagaagaagaggaagaagaagaagaagaggaggaggaag +aaggagaaggagaaggagaaggagaagga------------------------------- +-----------------------------------------gaaggagaaggagaagaag +aagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaaaata +caaatatctggagccgggatttgagcctggcccttgacatatgtcctaggcctcttacac +tctccttaccagcccctgtcccttaggcctgggcccctgatttgcctgtcagagaagcca +gagaatc +>syndip_1_chr20:13848064-13848750 +tctgtaatcccagttattcaggaggctgaggcaggagaatcacctgaacccgggaggcag +aggttccagtgagtcgagatcttgccactgcactccagcctgggggacagagggaaattg +cgtctcaaaaaaaaaaaagaa-aagaaaagtagaagacgaagatgaagaagaataagaag +agagaaaagaagaagagaaggttagagaaaagaagagaaggagaaggagaaggaggagga +gaaggagaaggagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaa +gaagaagaagaagaagaagtcaaatatctggagaagaagaagaagaagaggaagaagaag +aagaggaagaagaagaagaagaggaagaggaagaaagaagaagaacaagaagaagaagaa +gtcaaatatctggagaagaagaagaagaagaggaggaagaagaagaagaagaggaggagg +aagaagaagaagaagaagaagaagaagaagcaggagcaggagaagaagaagaagaagaag +aagaagaggaagaggaagaggaagaggaagaagaagaagaagaagaagaagaagaagaag +aagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagagaaga +caaatatctggagccgggatttgagcctggcccttgacatatgtcctaggcctcttacac +tctccttaccagcccctgtcccttaggcctgggcccctgatttgcctgtcagagaagcca +gagaatc +>syndip_2_chr20:13848064-13848750 +tctgtaatcccagttattcaggaggctgaggcaggagaatcacctgaacccgggaggcag +aggttccagtgagtcgagatcttgccactgcactccagcctgggggacagagggaaattg +cgtctcaaaaaaaaaaaagaa-aagaaaagtagaagacgaagatgaagaagaataagaag +agagaaaagaagaagagaaggttagagaaaagaagagaaggagaaggagaaggaggagga +gaaggagaaggagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaa +gaagaagaagaagaagaagtcaaatatctggagaagaagaagaagaagaggaagaagaag +aagaggaagaagaagaagaagaggaagaggaagaaagaagaagaacaagaagaagaagaa +gtcaaatatctggagaagaagaagaagaagaggaggaagaagaagaagaagaggaggagg +aagaagaagaagaagaagaagaagaagaagcaggagcaggagaagaagaagaagaagaag +aagaagaggaagaggaagaggaagag---------------gaagaagaagaagaagaag +aagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagagaaga +caaatatctggagccgggatttgagcctggcccttgacatatgtcctaggcctcttacac +tctccttaccagcccctgtcccttaggcctgggcccctgatttgcctgtcagagaagcca +gagaatc +>p:HG002_1_chr20:13848064-13848750 +tctgtaatcccagttattcaggaggctgaggcaggagaatcacctgaacccgggaggcag +aggttccagtgagtcgagatcttgccactgcactccagcctgggggacagagggaaattg +cgtctcaaaaaaaaaaaagaa-aagaaaagtagaagacgaagatgaagaagaataagaag +agagaaaagaagaagagaaggttagagaaaagaagagaaggagaaggagaaggaggagga +gaaggagaaggagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaa +gaagaagaagaagaagaagtcaaatatctggagaagaagaagaagaagaggaagaagaag +aagaggaagaagaagaagaagaggaagaggaagaaagaagaagaacaagaagaagaagaa +gtcaaatatctggagaagaagaagaagaagaggaggaagaagaagaagaagaggaggagg +aagaagaagaagaagaagaagaagaagaagcaggagcaggagaagaagaagaagaagaag +aagaagaggaagaggaagaggaagag---------------gaagaagaagaagaagaag +aagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagagaaga +caaatatctggagccgggatttgagcctggcccttgacatatgtcctaggcctcttacac +tctccttaccagcccctgtcccttaggcctgggcccctgatttgcctgtcagagaagcca +gagaatc +>p:HG002_2_chr20:13848064-13848750 +tctgtaatcccagttattcaggaggctgaggcaggagaatcacctgaacccgggaggcag +aggttccagtgagtcgagatcttgccactgcactccagcctgggggacagagggaaattg +cgtctcaaaaaaaaaaaagaa-aagaaaagtagaagacgaagatgaagaagaataagaag +agagaaaagaagaagagaaggttagagaaaagaagagaaggagaaggagaaggaggagga +gaaggagaaggagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaa +gaagaagaagaagaagaagtcaaatatctggagaagaagaagaagaagaggaagaagaag +aagaggaagaagaagaagaagaggaagaggaagaaagaagaagaacaagaagaagaagaa +gtcaaatatctggagaagaagaagaagaagaggaggaagaagaagaagaagaggaggagg +aagaagaagaagaagaagaagaagaagaagcaggagcaggagaagaagaagaagaagaag +aagaagaggaagaggaagaggaagaggaagaagaagaagaagaagaagaagaagaagaag +aagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagagaaga +caaatatctggagccgggatttgagcctggcccttgacatatgtcctaggcctcttacac +tctccttaccagcccctgtcccttaggcctgggcccctgatttgcctgtcagagaagcca +gagaatc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/msa.fa.fai new file mode 100644 index 00000000..9811e691 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_13848064_13848750 787 29 60 61 +syndip_1_chr20:13848064-13848750 787 864 60 61 +syndip_2_chr20:13848064-13848750 787 1699 60 61 +p:HG002_1_chr20:13848064-13848750 787 2535 60 61 +p:HG002_2_chr20:13848064-13848750 787 3371 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/output.vcf.gz new file mode 100644 index 00000000..0bcc04ec Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/output.vcf.gz.tbi new file mode 100644 index 00000000..d0497bfb Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:13848164-13848650/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/base.vcf.gz new file mode 100644 index 00000000..3189a6fb Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/base.vcf.gz.tbi new file mode 100644 index 00000000..cc768154 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/comp.vcf.gz new file mode 100644 index 00000000..30511b3f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/comp.vcf.gz.tbi new file mode 100644 index 00000000..0ebbf617 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/haps.fa new file mode 100644 index 00000000..d9ff76c5 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/haps.fa @@ -0,0 +1,110 @@ +>ref_chr20_14861837_14862842 +GCTCTCCTGCTGCTGGCCAAGCAGGACCCCAAGGTCCACTGGGATGTACATACTTATGGTATTATGCTCTGCAATACTTGTGGGGGCTGTGGAATGCACACTTCCAAAGTGAAATAGGACATTGGAGGTTTTATATATAAATATATATATATATATTTATATATATATTTATATATATATATTTATATATATTTATATATATTTATATATATATTTATATATATATAAATATATATAAATATATAAATATATATAAATATATATTTATACATAAATATATAAATATATAATATATATAAATATATATTATACATAAATATATAAATATATATAAATATATATAAATATATATTTATACATAAATATATAAATATATATATATATAAATATATATAAATATATATTTATATATTAATATATATAAATATATTACTATGTATATTTATATATATTTATATAAATATATATAAATATATGTAAATATATATATAAAAATATATATTAATATATAAAAATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATAAATATAAATATATATAAATATATAAAAATATATATATAAATATAAATATATATAAATATATATGTATAAATATATATATAAATATAAATATATATAAATATATATATATAAATATATATATAAATATATATATATAAATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATATATTTTTTTTTAATAGAGAGGATGAAGACCAAAGCAGTGAGTTCCACCTAAGCTGGCCCTTGCCTTTTGTCTAACAGGAAACCCAGTCCTTCCTAATGGGCACAGAATTTTCAGAGAAGAGAGCAGAAG +>syndip_1_chr20:14861837-14862842 +GCTCTCCTGCTGCTGGCCAAGCAGGACCCCAAGGTCCACTGGGATGTACATACTTATGGT +ATTATGCTCTGCAATACTTGTGGGGGCTGTGGAATGCACACTTCCAAAGTGAAATAGGAC +ATTGGAGGTTTTATATATAAATATATATATATATTTATATATATATTTATATATATATAT +ATTTATATATATTTATATATATATTTATATATATATTTATATATATATTTATATATATAT +TTATATATATATTTATATATATATTTATATATATATTTATATATATATTTATATATATTT +ATATATATTTATATATATTTTTATATATTTTTATATATATAAATATATAAAAATATATAT +AAATATATAAAAATATATAAAAATATATAAATATATATAAATATATAAATATATATAAAT +ATATATAAATATATATTTATATATAAATATATATAAATATATATTTATACATAAATATAT +ATAAATATATATTTATACATAAATATATAAATATATATAATATATATAAATATATATTAT +ACATAAATATATAAATATATATTATACATAAATATATAAATATATATAAATATATATAAA +TATATATTTATACATAAATATATAAATATATATATAAATATATATAAATATATATAAATA +TATATATAAATATATATATAAATATATATAAATATATATATAAATATATATATAAATATA +TATAAATATATATAAATATATATATAAATATATATAAATATATATAAATATATATTTATA +TATTAATATATAAATATATATAAATATATATTTATATATTAATATATAAATATATATATA +TTAATATATATAAATATATATAAATATATATTTATATATTAATATATATATATTAATATA +TATATATTTATATATTAATATATATATTTATATATTAATATATATAAATATATTACTATG +TATATTTATATATATTTATATAAATATATATAAATATATGTAAATATATATATAAAAATA +TATATTAATATATAAAATATATATATAAATATAAATAAATATATATATAAATATATATAA +ATAAATATATATATAAATATATATAAATAAATATATAAATATATATAAATATATATATAA +ATATATATAAATATATATAAATATATATAAAAATATATATAAATATATATATAAATATAT +ATAAATATATATATAAATATATATATAAATATATATATAAATATATATAAATATATATAT +AAATATATATAAATATATATATAATTATATATAAATATATATAAATATATATAAATATAT +ATATAAATATATATAAATATATATAAATATATATAAATATATATATAAATATATATAAAT +ATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATAAAT +ATATATAAATATATATATAAATATATATAAATATATATATAAATATAAATATATATGTAT +AAATATATATATAAATATAAATATATATGTATAAATATATATATAAATATATATATATAA +ATATATATATACATATATAAATATATATATAAATATATATAAAAATATATATATATATAT +TTTTTTAATAGAGAGGATGAAGACCAAAGCAGTGAGTTCCACCTAAGCTGGCCCTTGCCT +TTTGTCTAACAGGAAACCCAGTCCTTCCTAATGGGCACAGAATTTTCAGAGAAGAGAGCA +GAAG +>syndip_2_chr20:14861837-14862842 +GCTCTCCTGCTGCTGGCCAAGCAGGACCCCAAGGTCCACTGGGATGTACATACTTATGGT +ATTATGCTCTGCAATACTTGTGGGGGCTGTGGAATGCACACTTCCAAAGTGAAATAGGAC +ATTGGAGGTTTTATATATAAATATATATATATATATTTATATATATATTTATATATATAT +ATTTATATATATTTATATATATTTATATATATATTTTTATATATATTTATATATATTTAT +ATATTTATATATATTTATATATATTTTTATATATATAAATATATAAAAATATATAAATAT +ATATAAATATATAAATATATATAAATATATATTTATACATAAATATATAAATATATATAA +TATATATAAATATATATTATACATAAATATATAAATATATATTATACATAAATATATAAA +TATATATAAATATATATAAATATATATTTATACATAAATATATAAATATATATATATATA +AATATATATAAATATATATTTATATATTAATATATATAAATATATTACTATGTATATTTA +TATATATTTATATAAATATATAAATATATGTAAATATATATATAAAAATATATATTAATA +TATAAAAATATATATATAAATATATATATAAATATATATAAATAAATATATATAAATATA +TATATAAATATATATAAATATATATAAATATATATATAAATATATATAAATATATATAAA +TATATATATAAATATATATATAAATATATATAAATATATATAAATAAATATATAAATATA +TATATAAATATATATAAATATATATATAAATATATATAAATATATATATAAATATATATA +AATATATATATAAATATATATAAATATATATATAAATATATATATAAATATATATAAATA +TATATAAATATATATATATAAATATATATAAATATATATATAAATATAAATATATATAAA +TATATAAAAATATATATATAAATATAAATATATATAAATATATATGTATAAATATATATA +TAAATATAAATATATATAAATATATATATATAAATATATATATAAATATATATAAATATA +TATAAAAATATATATAAATATATATATAAATATATATATAAATATATATAAATATATATA +TAAATATATATAAAAATATATATATATTTTTTTTTTTAATAGAGAGGATGAAGACCAAAG +CAGTGAGTTCCACCTAAGCTGGCCCTTGCCTTTTGTCTAACAGGAAACCCAGTCCTTCCT +AATGGGCACAGAATTTTCAGAGAAGAGAGCAGAAG +>p:HG002_1_chr20:14861837-14862842 +GCTCTCCTGCTGCTGGCCAAGCAGGACCCCAAGGTCCACTGGGATGTACATACTTATGGT +ATTATGCTCTGCAATACTTGTGGGGGCTGTGGAATGCACACTTCCAAAGTGAAATAGGAC +ATTGGAGGTTTTATATATAAATATATATATATATATTTATATATATATTTATATATATAT +ATTTATATATATTTATATATATTTATATATATATTTTTATATATATTTATATATATTTAT +ATATTTATATATATTTATATATATTTTTATATATATAAATATATAAAAATATATAAATAT +ATATAAATATATAAATATATATAAATATATATTTATACATAAATATATAAATATATATAA +TATATATAAATATATATTATACATAAATATATAAATATATATTATACATAAATATATAAA +TATATATAAATATATATAAATATATATTTATACATAAATATATAAATATATATATATATA +AATATATATAAATATATATTTATATATTAATATATATAAATATATTACTATGTATATTTA +TATATATTTATATAAATATATAAATATATGTAAATATATATATAAAAATATATATTAATA +TATAAAAATATATATATAAATATATATATAAATATATATAAATAAATATATATAAATATA +TATATAAATATATATAAATATATATAAATATATATATAAATATATATAAATATATATAAA +TATATATATAAATATATATATAAATATATATAAATATATATAAATAAATATATAAATATA +TATATAAATATATATAAATATATATATAAATATATATAAATATATATATAAATATATATA +AATATATATATAAATATATATAAATATATATATAAATATATATATAAATATATATAAATA +TATATAAATATATATATATAAATATATATAAATATATATATAAATATAAATATATATAAA +TATATAAAAATATATATATAAATATAAATATATATAAATATATATGTATAAATATATATA +TAAATATAAATATATATAAATATATATATATAAATATATATATAAATATATATAAATATA +TATAAAAATATATATAAATATATATATAAATATATATATAAATATATATAAATATATATA +TAAATATATATAAAAATATATATATATTTTTTTTTTTAATAGAGAGGATGAAGACCAAAG +CAGTGAGTTCCACCTAAGCTGGCCCTTGCCTTTTGTCTAACAGGAAACCCAGTCCTTCCT +AATGGGCACAGAATTTTCAGAGAAGAGAGCAGAAG +>p:HG002_2_chr20:14861837-14862842 +GCTCTCCTGCTGCTGGCCAAGCAGGACCCCAAGGTCCACTGGGATGTACATACTTATGGT +ATTATGCTCTGCAATACTTGTGGGGGCTGTGGAATGCACACTTCCAAAGTGAAATAGGAC +ATTGGAGGTTTTATATATAAATATATATATATATTTATATATATATTTATATATATATAT +ATTTATATATATTTATATATATATTTATATATATATTTATATATATATTTATATATATAT +TTATATATATATTTATATATATATTTATATATATATTTATATATATATTTATATATATTT +ATATATATTTATATATATTTTTATATATTTTTATATATATAAATATATAAAAATATATAT +AAATATATAAAAATATATAAAAATATATAAATATATATAAATATATAAATATATATAAAT +ATATATAAATATATATTTATATATAAATATATATAAATATATATTTATACATAAATATAT +ATAAATATATATTTATACATAAATATATAAATATATATAATATATATAAATATATATTAT +ACATAAATATATAAATATATATTATACATAAATATATAAATATATATAAATATATATAAA +TATATATTTATACATAAATATATAAATATATATATAAATATATATAAATATATATAAATA +TATATATAAATATATATATAAATATATATAAATATATATATAAATATATATATAAATATA +TATAAATATATATAAATATATATATAAATATATATAAATATATATAAATATATATTTATA +TATTAATATATAAATATATATAAATATATATTTATATATTAATATATAAATATATATATA +TTAATATATATAAATATATATAAATATATATTTATATATTAATATATATATATTAATATA +TATATATTTATATATTAATATATATATTTATATATTAATATATATAAATATATTACTATG +TATATTTATATATATTTATATAAATATATATAAATATATGTAAATATATATATAAAAATA +TATATTAATATATAAAATATATATATAAATATAAATAAATATATATATAAATATATATAA +ATAAATATATATATAAATATATATAAATAAATATATAAATATATATAAATATATATATAA +ATATATATAAATATATATAAATATATATAAAAATATATATAAATATATATATAAATATAT +ATAAATATATATATAAATATATATATAAATATATATATAAATATATATAAATATATATAT +AAATATATATAAATATATATATAATTATATATAAATATATATAAATATATATAAATATAT +ATATAAATATATATAAATATATATAAATATATATAAATATATATATAAATATATATAAAT +ATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATAAAT +ATATATAAATATATATATAAATATATATAAATATATATATAAATATAAATATATATGTAT +AAATATATATATAAATATAAATATATATGTATAAATATATATATAAATATATATATATAA +ATATATATATACATATATAAATATATATATAAATATATATAAAAATATATATATATATAT +TTTTTTAATAGAGAGGATGAAGACCAAAGCAGTGAGTTCCACCTAAGCTGGCCCTTGCCT +TTTGTCTAACAGGAAACCCAGTCCTTCCTAATGGGCACAGAATTTTCAGAGAAGAGAGCA +GAAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/haps.fa.ref.fa new file mode 100644 index 00000000..235ee6a4 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:14861837-14862842 +GCTCTCCTGCTGCTGGCCAAGCAGGACCCCAAGGTCCACTGGGATGTACATACTTATGGTATTATGCTCTGCAATACTTGTGGGGGCTGTGGAATGCACACTTCCAAAGTGAAATAGGACATTGGAGGTTTTATATATAAATATATATATATATATTTATATATATATTTATATATATATATTTATATATATTTATATATATTTATATATATATTTATATATATATAAATATATATAAATATATAAATATATATAAATATATATTTATACATAAATATATAAATATATAATATATATAAATATATATTATACATAAATATATAAATATATATAAATATATATAAATATATATTTATACATAAATATATAAATATATATATATATAAATATATATAAATATATATTTATATATTAATATATATAAATATATTACTATGTATATTTATATATATTTATATAAATATATATAAATATATGTAAATATATATATAAAAATATATATTAATATATAAAAATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATAAATATAAATATATATAAATATATAAAAATATATATATAAATATAAATATATATAAATATATATGTATAAATATATATATAAATATAAATATATATAAATATATATATATAAATATATATATAAATATATATATATAAATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATATATTTTTTTTTAATAGAGAGGATGAAGACCAAAGCAGTGAGTTCCACCTAAGCTGGCCCTTGCCTTTTGTCTAACAGGAAACCCAGTCCTTCCTAATGGGCACAGAATTTTCAGAGAAGAGAGCAGAAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/msa.fa new file mode 100644 index 00000000..35fac4e0 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/msa.fa @@ -0,0 +1,155 @@ +>ref_chr20_14861837_14862842 +gctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggt +attatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggac +attggaggttttatatataaatatatatatatatatttatatatatatttatatatatat +atttatatatatt----------------------------------------------- +---------------tatatatatttatatatatatttatat------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------atatataaatatatataaatatataaatatat +ataaatatatatttatacataaatatataaatatata----------------------- +----atatatataaatatatattatacataaatatataaatatatataaatatatataaa +tatatatttatacataaatatataaatatat------atatatataaatatatataa--- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------atatatatttatatattaatatatataaatatattactatg +tatatttatatatatttatataaatatatataaatatatgtaaatatatatataaaaata +tatattaatatataaaa---------atatatat-------------------------- +ataaatatatataaatatatatataaat--atatataaat-------------------- +------------------------------------------------------------ +--------------------------------------atatatatataaatatatataa +atatatatataaatatatataaatatatatataaatatatataaat--------atatat +atataaatatatataa----------------------atatatatataaatatatataa +atatatatataaatataaatatatataaatatataaaaatatatatataaatataaatat +atataaatatatatgtataaatatatatataaatataaatatatataaatatatatatat +aaatatatatataaat------------------------------atatatatataaat +atatatataaatatatataaatatatatataaatatatataaatatatatatatatattt +ttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcccttgcct +tttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaagagagca +gaag +>syndip_1_chr20:14861837-14862842 +gctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggt +attatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggac +attggaggttttatatataaatatatatatatatttatatatatatttatatatatatat +atttatatatatttatatatatatttatatatatatttatatatatatttatatatatat +ttatatatatatttatatatatatttatatatatatttatatatatatttatatatattt +atatatatttatatatatttttatatatttttatatatataaatatataaaaatatatat +aaatatataaaaatatataaaaatatataaatatatataaatatataaatatatataaat +atatataaatatatatttatatataaatatatataaatatatatttatacataaatatat +ataaatatatatttatacataaatatataaatatatataatatatataaatatatattat +acataaatatataaatatatattatacataaatatataaatatatataaatatatataaa +tatatatttatacataaatatataaatatatatataaatatatataaatatatataaata +tatatataaatatatatataaatatatataaatatatatataaatatatatataaatata +tataaatatatataaatatatatataaatatatataaatatatataaatatatatttata +tattaatatataaatatatataaatatatatttatatattaatatataaatatatatata +ttaatatatataaatatatataaatatatatttatatattaatatatatatattaatata +tatatatttatatattaatatatatatttatatattaatatatataaatatattactatg +tatatttatatatatttatataaatatatataaatatatgtaaatatatatataaaaata +tatattaatatataaaatatatatataaatataaataaatatatatataaatatatataa +ataaatatatatataaatatatataaataaatatataaatatatataaatatatatataa +atatatataaatatatataaatatatataaaaatatatataaatatatatataaatatat +ataaatatatatataaatatatatataaatatatatataaatatatataaatatatatat +aaatatatataaatatatatataattatatataaatatatataaatatatataaatatat +atataaatatatataaatatatataaatatatataaatatatatataaatatatataaat +atatatatataaatatatataaatatatatataaatatatataaatatatatatataaat +atatataaatatatatataaatatatataaatatatatataaatataaatatatatgtat +aaatatatatataaatataaatatatatgtataaatatatatataaatatatatatataa +atatatatatacatatataaatatatatataaatatatataaaaatatatatatatatat +ttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcccttgcct +tttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaagagagca +gaag +>syndip_2_chr20:14861837-14862842 +gctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggt +attatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggac +attggaggttttatatataaatatatatatatatatttatatatatatttatatatatat +atttatatatatt----------------------------------------------- +---------------tatatatatttatatatatatttttatatatatttatatatatt- +-tatatatttatatatatttatatatatttttatatatataaatatataaaa-------- +------------------------------------------------------------ +----------------------------atatataaatatatataaatatataaatatat +ataaatatatatttatacataaatatataaatatatataatatatataaatatatattat +acataaatatataaatatatattatacataaatatataaatatatataaatatatataaa +tatatatttatacataaatatataaatatat------atatatataaatatatataa--- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------atatatatttatatattaatatatataaatatattactatg +tatatttatatatatttatataa--atatataaatatatgtaaatatatatataaaaata +tatattaatatataaaa---------atatatatataaatatatatataaatatatataa +ataaatatatataaatatatatataaat--atatataaatatatataaatatatatataa +atatatataaatatatataaatatatatataaatatatatataaatatatataaatatat +ataaataaatatataaatatatatataaatatatataaatatatatataaatatatataa +atatatatataaatatatataaatatatatataaatatatataaat--------atatat +ataaatatatatataaatatatataaatatatataaatatatatatataaatatatataa +atatatatataaatataaatatatataaatatataaaaatatatatataaatataaatat +atataaatatatatgtataaatatatatataaatataaatatatataaatatatatatat +aaatatatatataaatatatataaatatatataaaaatatatataaatatatatataaat +atatatataaatatatataaatatatatataaatatatataaaaatatatatatattttt +ttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcccttgcct +tttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaagagagca +gaag +>p:HG002_1_chr20:14861837-14862842 +gctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggt +attatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggac +attggaggttttatatataaatatatatatatatatttatatatatatttatatatatat +atttatatatatt----------------------------------------------- +---------------tatatatatttatatatatatttttatatatatttatatatatt- +-tatatatttatatatatttatatatatttttatatatataaatatataaaa-------- +------------------------------------------------------------ +----------------------------atatataaatatatataaatatataaatatat +ataaatatatatttatacataaatatataaatatatataatatatataaatatatattat +acataaatatataaatatatattatacataaatatataaatatatataaatatatataaa +tatatatttatacataaatatataaatatat------atatatataaatatatataa--- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------atatatatttatatattaatatatataaatatattactatg +tatatttatatatatttatataa--atatataaatatatgtaaatatatatataaaaata +tatattaatatataaaa---------atatatatataaatatatatataaatatatataa +ataaatatatataaatatatatataaat--atatataaatatatataaatatatatataa +atatatataaatatatataaatatatatataaatatatatataaatatatataaatatat +ataaataaatatataaatatatatataaatatatataaatatatatataaatatatataa +atatatatataaatatatataaatatatatataaatatatataaat--------atatat +ataaatatatatataaatatatataaatatatataaatatatatatataaatatatataa +atatatatataaatataaatatatataaatatataaaaatatatatataaatataaatat +atataaatatatatgtataaatatatatataaatataaatatatataaatatatatatat +aaatatatatataaatatatataaatatatataaaaatatatataaatatatatataaat +atatatataaatatatataaatatatatataaatatatataaaaatatatatatattttt +ttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcccttgcct +tttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaagagagca +gaag +>p:HG002_2_chr20:14861837-14862842 +gctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggt +attatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggac +attggaggttttatatataaatatatatatatatttatatatatatttatatatatatat +atttatatatatttatatatatatttatatatatatttatatatatatttatatatatat +ttatatatatatttatatatatatttatatatatatttatatatatatttatatatattt +atatatatttatatatatttttatatatttttatatatataaatatataaaaatatatat +aaatatataaaaatatataaaaatatataaatatatataaatatataaatatatataaat +atatataaatatatatttatatataaatatatataaatatatatttatacataaatatat +ataaatatatatttatacataaatatataaatatatataatatatataaatatatattat +acataaatatataaatatatattatacataaatatataaatatatataaatatatataaa +tatatatttatacataaatatataaatatatatataaatatatataaatatatataaata +tatatataaatatatatataaatatatataaatatatatataaatatatatataaatata +tataaatatatataaatatatatataaatatatataaatatatataaatatatatttata +tattaatatataaatatatataaatatatatttatatattaatatataaatatatatata +ttaatatatataaatatatataaatatatatttatatattaatatatatatattaatata +tatatatttatatattaatatatatatttatatattaatatatataaatatattactatg +tatatttatatatatttatataaatatatataaatatatgtaaatatatatataaaaata +tatattaatatataaaatatatatataaatataaataaatatatatataaatatatataa +ataaatatatatataaatatatataaataaatatataaatatatataaatatatatataa +atatatataaatatatataaatatatataaaaatatatataaatatatatataaatatat +ataaatatatatataaatatatatataaatatatatataaatatatataaatatatatat +aaatatatataaatatatatataattatatataaatatatataaatatatataaatatat +atataaatatatataaatatatataaatatatataaatatatatataaatatatataaat +atatatatataaatatatataaatatatatataaatatatataaatatatatatataaat +atatataaatatatatataaatatatataaatatatatataaatataaatatatatgtat +aaatatatatataaatataaatatatatgtataaatatatatataaatatatatatataa +atatatatatacatatataaatatatatataaatatatataaaaatatatatatatatat +ttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcccttgcct +tttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaagagagca +gaag diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/msa.fa.fai new file mode 100644 index 00000000..95952e07 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_14861837_14862842 1744 29 60 61 +syndip_1_chr20:14861837-14862842 1744 1837 60 61 +syndip_2_chr20:14861837-14862842 1744 3645 60 61 +p:HG002_1_chr20:14861837-14862842 1744 5454 60 61 +p:HG002_2_chr20:14861837-14862842 1744 7263 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/output.vcf.gz new file mode 100644 index 00000000..f289e9b9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:14861937-14862742/output.vcf.gz.tbi 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a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16257741-16259346/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16257741-16259346/haps.fa new file mode 100644 index 00000000..686b5645 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16257741-16259346/haps.fa @@ -0,0 +1,161 @@ +>ref_chr20_16257641_16259446 +CTGAGATTCCTGCCACCTTTGCCCCTTACTTTTCTCACCCCGTTCACTGAGGGCCCTCAAGTCTGTTTCTAAGCAGCAGCCTGAGGGATCCATTTTTATAATCTGAAATCAGATATCATACCCACACCCCAAAACACACACACTCCTTCCCCATCCCAAAGAGACACACCCCTTCCCCATCCCAAAGAGACACACCCCTTCCCCATCCCAAAGAGACACACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCATCCCAAACACACACACCCCTTTCCCATCCCAAACACACACACCCATTGCCCATCCTAAACACACACACACCTTGCCTTCGCAAACACACACACCCCTTCCCCATCACAAACACACACACCCTTTCCCTATCCCATGCACACACACCTTCCACTTCCCAAACACACACACCCCTTCCCCATGCCAAACACACACAACCCTTCCCCAATTCTAAACACACACACCTCTTCCCCATCCCAAACACAAACACCCCTTCCCCATCCCAAACACACCCACCCTTTCCTGCATGCCAAACACCCACACCCCTTCCCCATCCCAAACACACACCCCATCCCCAATTCCAAACACACACACCCCTTCCCCATCCCAAACACACACACCCCTTCCACATGAGAAACACACACACCCCTTCTCATCCCAAACACAAACACACCCATTCCCCATCACAAACACACGCACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCAATTGTAAACACACACACCCCTTCTCCAATTCCAAACACACACACCCCTTCCCATCACAAACACACACACACCTTCCACATCCCAAATACACACACCCCTTCCCATCTCAAACACACACATCCCTTCCCCAATTCCAAAAACACACACCCCTTCCCCATCCCAAACACCCCCACCCCTTCCCATCCCCAAACACACACCCCTTTCCCATCCCAAATACACAAACCCCTTCCCTAATTCCACACACACACACCCCTTCCCCATCCCAAACACACATACCCCTTCCCATCCCAAAGACACACACTCATTCTGCATCCCAAACACACACACCCCTTCCCATCCCAAACACACACACTACCTCCGCATCCCAAACACATATACCCCTTCCCCATCCCAAACACATACACCCCTTCCCCATCGCCAACACACACACCCCTTCCCCATCCCAAACACACACACCCCTTTCCATCCCAAACACACACCCATTCCCCATCCCAGACACACCCACCCGTTCCCCATCCCAGACACACACAACCCTTCCCCAATTCCAAACACACACCCCTTCCCATCCCAAACACACACACCCATTTCCCATCCCAGACACATCCACCCCTTCCACAACTCTGAACACCCACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCATCCCAAACACACACACCCATTCCCCATCCCAAACACACACACCCATTCCCCATCCCAAACACAACCACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCATCCCAAACACACACACACCTTCCCCATCCCAAACACACCCACCCTTACTCCATCTCAAACATGTACACCCCTTCCCCTATCCCAAAATACACACATCCATCCCTACACACCCTCACCCATTTCCCCATCCCAGAACCTATGCACCAACTCAGTTTATTTGAACATGCCAGGCACTGAACTAAGAGAACCAAAGTAGCAGGAGGAATACGGTGTTGTCCTCCCAGAACTTACCCCCTGCACGGGAGTCAGCCAGGGAAG +>syndip_1_chr20:16257641-16259446 +CTGAGATTCCTGCCACCTTTGCCCCTTACTTTTCTCACCCCGTTCACTGAGGGCCCTCAA +GTCTGTTTCTAAGCAGCAGCCTGAGGGATCCATTTTTATAATCTGAAATCAGATATCATA +CCCACACCCCAAAACACACACACTCCTTCCCCATCCCAAAGAGACACACCCCTTCCCCAT +CCCAAAGAGACACACCCCTTCCCCATCCCAAAGAGACACACCCCTTCCCCATCCCAAACA +CACACACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCATCCCAAACACACACACC +CCTTTCCCATCCCAAACACACACACCCATTGCCCATCCTAAACACACACACACCTTCCCT +TCGCAAACACACACACCCCTTCCCCATCACAAACACACACACCCTTTCCCTATCCCATGC +ACACACACCTTCCACTTCCCAAACACACACACCCCTTCCCCATCCCAAACACACACAACC +CTTCCCCAATTCTAAACACACACACCTCTTCCCCATCCCAAACACAAACACCCCTTCCCC +ATCCCAAACACACCCACCCTTTCCTGCATCCCAAACACCCACACCCCTTCCCCATCCCAA +ACACACACCCCATCCCCAATTCCAAACACACACACCCCTTCCCCATCCCAAACACACACA +CCCCTTCCACATCAGAAACACACACACCCCTTCTCATCCCAAACACAAACACACCCATTC +CCCATCACAAACACACGCACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCAATTC +TAAACACACACACCCCTTCCCCATCCCAAACACACACCCCCCTTCCCCATCCCAAACACA +CACCCCCCTTCCCCATCCCAAACACACCCACCCCTTCCCACATCCCAAACACACACACCC 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+ACACCCACCCTTACTCCATCTCAAACATGTACACCCCTTCCCCTATCCCAAAATACACAC +ATCCATCCCTACACACCCTCACCCATTTCCCCATCCCAGAACCTATGCACCAACTCAGTT +TATTTGAACATGCCAGGCACTGAACTAAGAGAACCAAAGTAGCAGGAGGAATACGGTGTT +GTCCTCCCAGAACTTACCCCCTGCACGGGAGTCAGCCAGGGAAG +>p:HG002_1_chr20:16257641-16259446 +CTGAGATTCCTGCCACCTTTGCCCCTTACTTTTCTCACCCCGTTCACTGAGGGCCCTCAA +GTCTGTTTCTAAGCAGCAGCCTGAGGGATCCATTTTTATAATCTGAAATCAGATATCATA +CCCACACCCCAAAACACACACACTCCTTCCCCATCCCAAAGAGACACACCCCTTCCCCAT +CCCAAAGAGACACACCCCTTCCCCATCCCAAAGAGACACACCCCTTCCCCATCCCAAACA +CACACACCCCTTCCCCATCCCAAACACACACACCCCTTTCCCATCCCAAACACACACACC +CATTGCCCATCCTAAACACACACACACCTTCCCTTCGCAAACACACACACCCCTTCCCCA +TCACAAACACACACACCCTTTCCCTATCCCATGCACACACACCTTCCACTTCCCAAACAC +ACACACCCCTTCCCCATCCCAAACACACACAACCCTTCCCCAATTCTAAACACACACACC +TCTTCCCCATCCCAAACACAAACACCCCTTCCCCATCCCAAACACACCCACCCTTTCCTG +CATCCCAAACACACACACCCCTTCCCCATCCCAAACACACACCCCATCCCCAATTCCAAA +CACACACACCCCTTCCCCATCCCAAACACACACACCCCTTCCACATCAGAAACACACACA 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+CTACCTCCGCATCCCAAACACATATACCCCTTCCCCATCCCAAACACATACACCCCTTCC +CCATCGCTGAACATGCCAGGCACTGAACTAAGAGAACCAAAGTAGCAGGAGGAATACGGT +GTTGTCCTCCCAGAACTTACCCCCTGCACGGGAGTCAGCCAGGGAAG +>p:HG002_2_chr20:16257641-16259446 +CTGAGATTCCTGCCACCTTTGCCCCTTACTTTTCTCACCCCGTTCACTGAGGGCCCTCAA +GTCTGTTTCTAAGCAGCAGCCTGAGGGATCCATTTTTATAATCTGAAATCAGATATCATA +CCCACACCCCAAAACACACACACTCCTTCCCCATCCCAAAGAGACACACCCCTTCCCCAT +CCCAAAGAGACACACCCCTTCCCCATCCCAAAGAGACACACCCCTTCCCCATCCCAAACA +CACACACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCATCCCAAACACACACACC +CCTTTCCCATCCCAAACACACACACCCATTGCCCATCCTAAACACACACACACCTTCCCT +TCGCAAACACACACACCCCTTCCCCATCACAAACACACACACCCTTTCCCTATCCCATGC +ACACACACCTTCCACTTCCCAAACACACACACCCCTTCCCCATCCCAAACACACACAACC +CTTCCCCAATTCTAAACACACACACCTCTTCCCCATCCCAAACACAAACACCCCTTCCCC +ATCCCAAACACACCCACCCTTTCCTGCATCCCAAACACCCACACCCCTTCCCCATCCCAA +ACACACACCCCATCCCCAATTCCAAACACACACACCCCTTCCCCATCCCAAACACACACA +CCCCTTCCACATCAGAAACACACACACCCCTTCTCATCCCAAACACAAACACACCCATTC 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a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16257741-16259346/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16257741-16259346/haps.fa.ref.fa new file mode 100644 index 00000000..4e854eb5 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16257741-16259346/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:16257641-16259446 +CTGAGATTCCTGCCACCTTTGCCCCTTACTTTTCTCACCCCGTTCACTGAGGGCCCTCAAGTCTGTTTCTAAGCAGCAGCCTGAGGGATCCATTTTTATAATCTGAAATCAGATATCATACCCACACCCCAAAACACACACACTCCTTCCCCATCCCAAAGAGACACACCCCTTCCCCATCCCAAAGAGACACACCCCTTCCCCATCCCAAAGAGACACACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCATCCCAAACACACACACCCCTTTCCCATCCCAAACACACACACCCATTGCCCATCCTAAACACACACACACCTTGCCTTCGCAAACACACACACCCCTTCCCCATCACAAACACACACACCCTTTCCCTATCCCATGCACACACACCTTCCACTTCCCAAACACACACACCCCTTCCCCATGCCAAACACACACAACCCTTCCCCAATTCTAAACACACACACCTCTTCCCCATCCCAAACACAAACACCCCTTCCCCATCCCAAACACACCCACCCTTTCCTGCATGCCAAACACCCACACCCCTTCCCCATCCCAAACACACACCCCATCCCCAATTCCAAACACACACACCCCTTCCCCATCCCAAACACACACACCCCTTCCACATGAGAAACACACACACCCCTTCTCATCCCAAACACAAACACACCCATTCCCCATCACAAACACACGCACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCAATTGTAAACACACACACCCCTTCTCCAATTCCAAACACACACACCCCTTCCCATCACAAACACACACACACCTTCCACATCCCAAATACACACACCCCTTCCCATCTCAAACACACACATCCCTTCCCCAATTCCAAAAACACACACCCCTTCCCCATCCCAAACACCCCCACCCCTTCCCATCCCCAAACACACACCCCTTTCCCATCCCAAATACACAAACCCCTTCCCTAATTCCACACACACACACCCCTTCCCCATCCCAAACACACATACCCCTTCCCATCCCAAAGACACACACTCATTCTGCATCCCAAACACACACACCCCTTCCCATCCCAAACACACACACTACCTCCGCATCCCAAACACATATACCCCTTCCCCATCCCAAACACATACACCCCTTCCCCATCGCCAACACACACACCCCTTCCCCATCCCAAACACACACACCCCTTTCCATCCCAAACACACACCCATTCCCCATCCCAGACACACCCACCCGTTCCCCATCCCAGACACACACAACCCTTCCCCAATTCCAAACACACACCCCTTCCCATCCCAAACACACACACCCATTTCCCATCCCAGACACATCCACCCCTTCCACAACTCTGAACACCCACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCATCCCAAACACACACACCCATTCCCCATCCCAAACACACACACCCATTCCCCATCCCAAACACAACCACCCCTTCCCCATCCCAAACACACACACCCCTTCCCCATCCCAAACACACACACACCTTCCCCATCCCAAACACACCCACCCTTACTCCATCTCAAACATGTACACCCCTTCCCCTATCCCAAAATACACACATCCATCCCTACACACCCTCACCCATTTCCCCATCCCAGAACCTATGCACCAACTCAGTTTATTTGAACATGCCAGGCACTGAACTAAGAGAACCAAAGTAGCAGGAGGAATACGGTGTTGTCCTCCCAGAACTTACCCCCTGCACGGGAGTCAGCCAGGGAAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16257741-16259346/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16257741-16259346/msa.fa new file mode 100644 index 00000000..25d9d886 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16257741-16259346/msa.fa @@ -0,0 +1,225 @@ +>ref_chr20_16257641_16259446 +ctgagattcctgccacctttgccccttacttttctcaccccgttcactgagggccctcaa +gtctgtttctaagcagcagcctgagggatccatttttataatctgaaatcagatatcata +cccacaccccaaaacacacacactccttccccatcccaaagagacacaccccttccccat +cccaaagagacacaccccttccccatcccaaagagacacaccccttccccatcccaaaca +cacacaccccttccccatcccaaacacacacaccccttccccatcccaaacacacacacc +cctttcccatcccaaacacacacacccattgcccatcctaaacacacacacaccttgcct +tcgcaaacacacacaccccttccccatcacaaacacacacaccctttccctatcccatgc +acacacaccttccacttcccaaacacacacaccccttccccatgccaaacacacacaacc +cttccccaattctaaacacacacacctcttccccatcccaaacacaaacaccccttcccc +atcccaaacacacccaccctttcctgcatgccaaacacccacaccccttccccatcccaa +acacacaccccatccccaattccaaacacacacaccccttccccatcccaaacacacaca +ccccttccacatgagaaacacacacaccccttctcatcccaaacacaaacacacccattc +cccatcacaaacacacg--------------------------caccccttccccatccc +aaacacacacaccccttccccaattgt--------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------aaacacacacaccccttctccaattccaaacacacacacccc +ttcccatcacaaacacacacacaccttccacatcccaaatacacacaccccttcccatct +caaacacacacatcccttccccaattccaaaaacacacaccccttccccatcccaaacac +ccccaccccttcccatcccc-aaacacacacccctttcccatcccaaatacacaaacccc +ttccctaattccacacacacacaccccttccccatcccaaacacacataccccttcccat +cccaaagacacacactcattctgcatcccaaacacacacaccccttcccatcccaaacac +acacactacctccgcatcccaaacacatataccccttccccatcccaaacacatacaccc +cttccccatcgccaacacacacaccccttccccatcccaaacacacacacccctttccat +cccaaacacacacccattccccatcccagacacacccacccgttccccatcccagacaca +cacaacccttccccaattccaaacacacaccccttcccatcccaaacacacacacccatt +tcccatcccagacacatccaccccttccacaactctgaacacccaccccttccccatccc +aaacacacacaccccttccccatcccaaacacacacacccattccccatcccaaacacac +acacccattccccatcccaaacacaaccaccccttccccatcccaaacacacacacccct +tccccatcccaaacacacacaca-------------------------ccttccccatcc +caaacacacccacccttactccatctcaaacatgtacaccccttcccctatcccaaaata +cacacatccatccctacacaccctcacccatttccccatcccagaacctatgcaccaact +cagtttatttgaacatgccaggcactgaactaagagaaccaaagtagcaggaggaatacg +gtgttgtcctcccagaacttaccccctgcacgggagtcagccagggaag +>syndip_1_chr20:16257641-16259446 +ctgagattcctgccacctttgccccttacttttctcaccccgttcactgagggccctcaa +gtctgtttctaagcagcagcctgagggatccatttttataatctgaaatcagatatcata +cccacaccccaaaacacacacactccttccccatcccaaagagacacaccccttccccat +cccaaagagacacaccccttccccatcccaaagagacacaccccttccccatcccaaaca +cacacaccccttccccatcccaaacacacacaccccttccccatcccaaacacacacacc +cctttcccatcccaaacacacacacccattgcccatcctaaacacacacacaccttccct +tcgcaaacacacacaccccttccccatcacaaacacacacaccctttccctatcccatgc +acacacaccttccacttcccaaacacacacaccccttccccatcccaaacacacacaacc +cttccccaattctaaacacacacacctcttccccatcccaaacacaaacaccccttcccc +atcccaaacacacccaccctttcctgcatcccaaacacccacaccccttccccatcccaa +acacacaccccatccccaattccaaacacacacaccccttccccatcccaaacacacaca +ccccttccacatcagaaacacacacaccccttctcatcccaaacacaaacacacccattc +cccatcacaaacacacg--------------------------caccccttccccatccc +aaacacacacaccccttccccaattctaaacacacacaccccttccccatcccaaacaca +caccccccttccccatcccaaacacacaccccccttccccatcccaaacacacccacccc +ttcccacatcccaaacacacacaccccttccctatcccaaacacacactccatccccaat +tccaaacacacacaccccttccccatcccaaacacacacaccccttcccccatcccaaac +gcacacaccccttccctatcccaaacacacaccccttccctttccaaaacacacccatcc +cttccccatcccaaacacacacaacccttcccatcccagacacacccaccccttcccatc +tcaaatacacgcaacccttccccatcccaaacacacacacctattccccatccgaaacac +acacaccccttcctcatcccacacacacccattccccatcccagacacacccatcccttc +cccatactaaacacaaccaccccttccccatcccacacacacacaccccttccccaattc +caaacacacacaccccttccccattcaaaacacacgcaccccttcccatctgaaacacac +ccactccttcccatctgaaacacacccactccttcccatcccaaacacacccactccttc +ccatcccaaacacacacaccccttccccatcccaaaaacacacaccctttcgcaatccca +aatacacaagccccttcccaaattccacacacacacacctcttccccatcccaaacaaac +ccaccctttccccattcgaaacacacacaccccttctccaattccaaacacacacacccc +ttcccatctcaaacacacggacaccttccacatcccaaatacacacaccccttcccatcc +caaacacacacatcccttccccaattccaaaaacacacaccccttccccatcccaaacac +ccccaccccttcccatccccaaaacacacacccctttcccatcccaaatacacaaacccc +ttccctaattccacacacacacaccccttccccatcccaaacacacataccccttcccat +cccaaagacacacactcattctgcatcccaaacacacacaccccttcccatcccaaacac +acacactacctccgcatcccaaacacatataccccttccccatcccaaacacatacaccc +cttccccatcgccaacacacacaccccttccccatcccaaacacacacacccctttccat +cccaaacacacacccattccccatcccagacacacccacccgttccccatcccagacaca +cacaacccttccccaattccaaacacacaccccttcccatcccaaacacacacacccatt +tcccatcccagacacatccaccccttccacaactctgaacacccaccccttccccatccc +aaacacacacaccccttccccatcccaaacacacacacccattccccatcccaaacacac +acacccattccccatcccaaacacaaccaccccttccccatcccaaacacacacacccct +tccccatcccaaacacacacaca-------------------------ccttccccatcc +caaacacacccacccttactccatctcaaacatgtacaccccttcccctatcccaaaata +cacacatccatccctacacaccctcacccatttccccatcccagaacctatgcaccaact +cagtttatttgaacatgccaggcactgaactaagagaaccaaagtagcaggaggaatacg +gtgttgtcctcccagaacttaccccctgcacgggagtcagccagggaag +>syndip_2_chr20:16257641-16259446 +ctgagattcctgccacctttgccccttacttttctcaccccgttcactgagggccctcaa +gtctgtttctaagcagcagcctgagggatccatttttataatctgaaatcagatatcata +cccacaccccaaaacacacacactccttccccatcccaaagagacacaccccttccccat +cccaaagagacacaccccttccccatcccaaagag------------------------- +-acacaccccttccccatcccaaacacacacaccccttccccatcccaaacacacacacc +cctttcccatcccaaacacacacacccattgcccatcctaaacacacacacaccttccct +tcgcaaacacacacaccccttccccatcacaaacacacacaccctttccctatcccatgc +acacacaccttccacttcccaaacacacacaccccttccccatcccaaacacacacaacc +cttccccaattctaaacacacacacctcttccccatcccaaacacaaacaccccttcccc +atcccaaacacacccaccctttcctgcatcccaaacacacacaccccttccccatcccaa +acacacaccccatccccaattccaaacacacacaccccttccccatcccaaacacacaca +ccccttccacatcagaaacacacacaccccttctcatcccaaacacaaacacacccattc +cccatcacaaacacacgcaccccttccccatcccaaacatacacaccccttccccatccc +aaacacacacaccccttccccaattctaaacacacacaccccttccccatcccaaacaca +caccccccttccccatcccaaacacacaccccccttccccatcccaaacacacccacccc +ttcccacatcccaaacacacacaccccttccctatcccaaacacacactccatccccaat +tccaaacacacacaccccttccccatcccaaacacacacaccccttcccccatcccaaac +gcacacaccccttccctatcccaaacacacaccccttccctttccaaaacacacccatcc +cttccccatcccaaacacacacaacccttcccatcccagacacacccaccccttcccatc +tcaaatacacgcaacccttc---------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------------------------------c +ccatcccaaacacacacaccccttccccatcccaaaaacacacaccctttcgcaatccca +aatacacaagccccttcccaaattccacacacacacacctcttccccatcccaaacaaac +ccaccctttccccattcgaaacacacacaccccttctccaattccaaacacacacacccc +ttcccatctcaaacacacggacaccttccacatcccaaatacacacaccccttcccatcc +caaacacacacatcccttccccaattccaaaaacacacaccccttccccatcccaaacac +ccccaccccttcccatccccaaaacacacacccctttcccatcccaaatacacaaacccc +ttccctaattccacacacacacaccccttccccatcccaaacacacataccccttcccat +cccaaagacacacactcattctgcatcccaaacacacacaccccttcccatcccaaacac +acacactacctccgcatcccaaacacatataccccttccccatcccaaacacatacaccc +cttccccatcgccaacacacacaccccttccccatcccaaacacacacacccctttccat +cccaaacacacacccattccccatcccagacacacccacccgttccccatcccagacaca +cacaacccttccccaattccaaacacacaccccttcccatcccaaacacacacacccatt +tcccatcccagacacatccaccccttccacaactccgaacacccaccccttccccatccc +aaacacacacaccccttccccatcccaaacacacacacccattccccatcccaaacacac +acacccattccccatcccaaacacaaccaccccttccccatcccaaacacacacacccct +tccccatcccaaacacacacacaccttcccatcccaaacacacacaccccttccccatcc +caaacacacccacccttactccatctcaaacatgtacaccccttcccctatcccaaaata +cacacatccatccctacacaccctcacccatttccccatcccagaacctatgcaccaact +cagtttatttgaacatgccaggcactgaactaagagaaccaaagtagcaggaggaatacg +gtgttgtcctcccagaacttaccccctgcacgggagtcagccagggaag +>p:HG002_1_chr20:16257641-16259446 +ctgagattcctgccacctttgccccttacttttctcaccccgttcactgagggccctcaa +gtctgtttctaagcagcagcctgagggatccatttttataatctgaaatcagatatcata +cccacaccccaaaacacacacactccttccccatcccaaagagacacaccccttccccat +cccaaagagacacaccccttccccatcccaaagag------------------------- +-acacaccccttccccatcccaaacacacacaccccttccccatcccaaacacacacacc +cctttcccatcccaaacacacacacccattgcccatcctaaacacacacacaccttccct +tcgcaaacacacacaccccttccccatcacaaacacacacaccctttccctatcccatgc +acacacaccttccacttcccaaacacacacaccccttccccatcccaaacacacacaacc +cttccccaattctaaacacacacacctcttccccatcccaaacacaaacaccccttcccc +atcccaaacacacccaccctttcctgcatcccaaacacacacaccccttccccatcccaa +acacacaccccatccccaattccaaacacacacaccccttccccatcccaaacacacaca +ccccttccacatcagaaacacacacaccccttctcatcccaaacacaaacacacccattc +cccatcacaaacacacgcaccccttccccatcccaaacatacacaccccttccccatccc +aaacacacacaccccttccccaattctaaacacacacaccccttccccatcccaaacaca +caccccccttccccatcccaaacacacaccccccttccccatcccaaacacacccacccc +ttcccacatcccaaacacacacaccccttccctatcccaaacacacactccatccccaat +tccaaacacacacaccccttccccatcccaaacacacacaccccttcccccatcccaaac +gcacacaccccttccctatcccaaacacacaccccttccctttccaaaacacacccatcc +cttccccatcccaaacacacacaacccttcccatcccagacacacccaccccttcccatc +tcaaatacacgcaacccttc---------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------------------------------c +ccatcccaaacacacacaccccttccccatcccaaaaacacacaccctttcgcaatccca +aatacacaagccccttcccaaattccacacacacacacctcttccccatcccaaacaaac +ccaccctttccccattcgaaacacacacaccccttctccaattccaaacacacacacccc +ttcccatctcaaacacacggacaccttccacatcccaaatacacacaccccttcccatcc +caaacacacacatcccttccccaattccaaaaacacacaccccttccccatcccaaacac +ccccaccccttcccatccccaaaacacacacccctttcccatcccaaatacacaaacccc +ttccctaattccacacacacacaccccttccccatcccaaacacacataccccttcccat +cccaaagacacacactcattctgcatcccaaacacacacaccccttcccatcccaaacac +acacactacctccgcatcccaaacacatataccccttccccatcccaaacacatacaccc +cttccccatcgctga--------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------acatgccaggcactgaactaagagaaccaaagtagcaggaggaatacg +gtgttgtcctcccagaacttaccccctgcacgggagtcagccagggaag +>p:HG002_2_chr20:16257641-16259446 +ctgagattcctgccacctttgccccttacttttctcaccccgttcactgagggccctcaa +gtctgtttctaagcagcagcctgagggatccatttttataatctgaaatcagatatcata +cccacaccccaaaacacacacactccttccccatcccaaagagacacaccccttccccat +cccaaagagacacaccccttccccatcccaaagagacacaccccttccccatcccaaaca +cacacaccccttccccatcccaaacacacacaccccttccccatcccaaacacacacacc +cctttcccatcccaaacacacacacccattgcccatcctaaacacacacacaccttccct +tcgcaaacacacacaccccttccccatcacaaacacacacaccctttccctatcccatgc +acacacaccttccacttcccaaacacacacaccccttccccatcccaaacacacacaacc +cttccccaattctaaacacacacacctcttccccatcccaaacacaaacaccccttcccc +atcccaaacacacccaccctttcctgcatcccaaacacccacaccccttccccatcccaa +acacacaccccatccccaattccaaacacacacaccccttccccatcccaaacacacaca +ccccttccacatcagaaacacacacaccccttctcatcccaaacacaaacacacccattc +cccatcacaaacacacg--------------------------caccccttccccatccc +aaacacacacaccccttccccaattctaaacacacacaccccttccccatcccaaacaca +caccccccttccccatcccaaacacacaccccccttccccatcccaaacacacccacccc +ttcccacatcccaaacacacacaccccttccctatcccaaacacacactccatccccaat +tccaaacacacacaccccttccccatcccaaacacacacaccccttcccccatcccaaac +gcacacaccccttccctatcccaaacacacaccccttccctttccaaaacacacccatcc +cttccccatcccaaacacacacaacccttcccatcccagacacacccaccccttcccatc +tcaaatacacgcaacccttccccatcccaaacacacacacctattccccatccgaaacac +acacaccccttcctcatcccacacacacccattccccatcccagacacacccatcccttc +cccatactaaacacaaccaccccttccccatcccacacacacacaccccttccccaattc +caaacacacacaccccttccccattcaaaacacacgcaccccttcccatctgaaacacac +ccactccttcccatctgaaacacacccactccttcccatcccaaacacacccactccttc +ccatcccaaacacacacaccccttccccatcccaaaaacacacaccctttcgcaatccca +aatacacaagccccttcccaaattccacacacacacacctcttccccatcccaaacaaac +ccaccctttccccattcgaaacacacacaccccttctccaattccaaacacacacacccc +ttcccatctcaaacacacggacaccttccacatcccaaatacacacaccccttcccatcc +caaacacacacatcccttccccaattccaaaaacacacaccccttccccatcccaaacac +ccccaccccttcccatccccaaaacacacacccctttcccatcccaaatacacaaacccc +ttccctaattccacacacacacaccccttccccatcccaaacacacataccccttcccat +cccaaagacacacactcattctgcatcccaaacacacacaccccttcccatcccaaacac +acacactacctccgcatcccaaacacatataccccttccccatcccaaacacatacaccc +cttccccatcgccaacacacacaccccttccccatcccaaacacacacacccctttccat +cccaaacacacacccattccccatcccagacacacccacccgttccccatcccagacaca +cacaacccttccccaattccaaacacacaccccttcccatcccaaacacacacacccatt +tcccatcccagacacatccaccccttccacaactctgaacacccaccccttccccatccc +aaacacacacaccccttccccatcccaaacacacacacccattccccatcccaaacacac +acacccattccccatcccaaacacaaccaccccttccccatcccaaacacacacacccct +tccccatcccaaacacacacaca-------------------------ccttccccatcc +caaacacacccacccttactccatctcaaacatgtacaccccttcccctatcccaaaata +cacacatccatccctacacaccctcacccatttccccatcccagaacctatgcaccaact +cagtttatttgaacatgccaggcactgaactaagagaaccaaagtagcaggaggaatacg +gtgttgtcctcccagaacttaccccctgcacgggagtcagccagggaag diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16257741-16259346/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16257741-16259346/msa.fa.fai new file mode 100644 index 00000000..4f0fd497 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16257741-16259346/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_16257641_16259446 2629 29 60 61 +syndip_1_chr20:16257641-16259446 2629 2736 60 61 +syndip_2_chr20:16257641-16259446 2629 5443 60 61 +p:HG002_1_chr20:16257641-16259446 2629 8151 60 61 +p:HG002_2_chr20:16257641-16259446 2629 10859 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16257741-16259346/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16257741-16259346/output.vcf.gz new file mode 100644 index 00000000..e6b951d3 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16257741-16259346/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16257741-16259346/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16257741-16259346/output.vcf.gz.tbi new file mode 100644 index 00000000..c25b8b9f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16257741-16259346/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/base.vcf.gz new file mode 100644 index 00000000..45f8a453 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/base.vcf.gz.tbi new file mode 100644 index 00000000..f56d3fab Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/comp.vcf.gz new file mode 100644 index 00000000..0440460c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/comp.vcf.gz.tbi new file mode 100644 index 00000000..a704c858 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/haps.fa new file mode 100644 index 00000000..019f88b3 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/haps.fa @@ -0,0 +1,38 @@ +>ref_chr20_16395049_16395522 +ACAGTCGTGGACAGCAAAGCTAAGGCTCAGTACAACAAAGGGCATACCCCTGTCATCGGTGTCTTCTTACTCTCTCCCTAATGTGATGTATTCATCCTCCCAGTTTAGTCAAGGCAGAAAGGAGATGAGGAAGGGGAGAGGAGGGGAGAGGAGGGAAGAGGAGGGGAGGGGAGGGGAGAGGAGGAGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGAAGATATGAAAGAAATAGGGAAGGAGTGGGACACAGGGAGGAAAACAAAACTATTTCCTTTCATATAAATGTTGTCATCTGGGGAGAAGCCCTCACTATCTCCTTGGTGCCTTTGGCTTTTGGTATTCAAA +>syndip_1_chr20:16395049-16395522 +ACAGTCGTGGACAGCAAAGCTAAGGCTCAGTACAACAAAGGGCATACCCCTGTCATCGGT +GTCTTCTTACTCTCTCCCTAATGTGATGTATTCATCCTCCCAGTTTAGTCAAGGCAGAAA +GGAGATGAGGAAGGGGAGAGGAGGGGAGAGGAGGGAAGAGGAGGGGAGGGGAGGGGAGAG +GAGGAGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGGGAGGAGAGGGGAGGC +CAAGGGAGGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGGGAGGA +GAGGGGAGGCCAAGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGG +GAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGAA +GATATGAAAGAAATAGGGAAGGAGTGGGACACAGGGAGGAAAACAAAACTATTTCCTTTC +ATATAAATGTTGTCATCTGGGGAGAAGCCCTCACTATCTCCTTGGTGCCTTTGGCTTTTG +GTATTCAAA +>syndip_2_chr20:16395049-16395522 +ACAGTCGTGGACAGCAAAGCTAAGGCTCAGTACAACAAAGGGCATACCCCTGTCATCGGT +GTCTTCTTACTCTCTCCCTAATGTGATGTATTCATCCTCCCAGTTTAGTCCAGGCAGAAA +GGAGATGAGGAAGGGGAGAGGAGGGGAGAGGAGGGGAGGGGAGGGGAGGGGAGAGGAGGG +GAGGCCAAGGGAGAAGATATGAAAGAAATAGGGAAGGAGTGGGACACAGGGAGGAAAACA +AAACTATTTCCTTTCATATAAATGTTGTCATCTGGGGAGAAGCCCTCACTATCTCCTTGG +TGCCTTTGGCTTTTGGTATTCAAA +>p:HG002_1_chr20:16395049-16395522 +ACAGTCGTGGACAGCAAAGCTAAGGCTCAGTACAACAAAGGGCATACCCCTGTCATCGGT +GTCTTCTTACTCTCTCCCTAATGTGATGTATTCATCCTCCCAGTTTAGTCCAGGCAGAAA +GGAGATGAGGAAGGGGAGAGGAGGGGAGAGGAGGGGAGGGGAGGGGAGGGGAGAGGAGGG +GAGGCCAAGGGAGAAGATATGAAAGAAATAGGGAAGGAGTGGGACACAGGGAGGAAAACA +AAACTATTTCCTTTCATATAAATGTTGTCATCTGGGGAGAAGCCCTCACTATCTCCTTGG +TGCCTTTGGCTTTTGGTATTCAAA +>p:HG002_2_chr20:16395049-16395522 +ACAGTCGTGGACAGCAAAGCTAAGGCTCAGTACAACAAAGGGCATACCCCTGTCATCGGT +GTCTTCTTACTCTCTCCCTAATGTGATGTATTCATCCTCCCAGTTTAGTCAAGGCAGAAA +GGAGATGAGGAAGGGGAGAGGAGGGGAGAGGAGGGAAGAGGAGGGGAGGGGAGGGGAGAG +GAGGAGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGGGAGGAGAGGGGAGGC +CAAGGGAGGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGGGAGGA +GAGGGGAGGCCAAGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGG +GAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGAA +GATATGAAAGAAATAGGGAAGGAGTGGGACACAGGGAGGAAAACAAAACTATTTCCTTTC +ATATAAATGTTGTCATCTGGGGAGAAGCCCTCACTATCTCCTTGGTGCCTTTGGCTTTTG +GTATTCAAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/haps.fa.ref.fa new file mode 100644 index 00000000..d48bb2c9 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:16395049-16395522 +ACAGTCGTGGACAGCAAAGCTAAGGCTCAGTACAACAAAGGGCATACCCCTGTCATCGGTGTCTTCTTACTCTCTCCCTAATGTGATGTATTCATCCTCCCAGTTTAGTCAAGGCAGAAAGGAGATGAGGAAGGGGAGAGGAGGGGAGAGGAGGGAAGAGGAGGGGAGGGGAGGGGAGAGGAGGAGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGGGGAGGGGAGGAGAGGGGAGGCCAAGGGAGAAGATATGAAAGAAATAGGGAAGGAGTGGGACACAGGGAGGAAAACAAAACTATTTCCTTTCATATAAATGTTGTCATCTGGGGAGAAGCCCTCACTATCTCCTTGGTGCCTTTGGCTTTTGGTATTCAAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/msa.fa new file mode 100644 index 00000000..8efb459b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/msa.fa @@ -0,0 +1,55 @@ +>ref_chr20_16395049_16395522 +acagtcgtggacagcaaagctaaggctcagtacaacaaagggcatacccctgtcatcggt +gtcttcttactctctccctaatgtgatgtattcatcctcccagtttagtcaaggcagaaa +ggagatgaggaaggggagaggaggggagaggagggaagaggaggggaggggaggggagag +gaggagaggggaggagaggggaggccaagggaggggaggggaggggaggagaggggaggc +caa-----gggaggggaggggaggagaggggaggccaagggaggggaggggaggggagga +gaggggaggccaa----------------------------------------------- +-----------------------gggaggggaggggaggagaggggaggccaagggagaa +gatatgaaagaaatagggaaggagtgggacacagggaggaaaacaaaactatttcctttc +atataaatgttgtcatctggggagaagccctcactatctccttggtgcctttggcttttg +gtattcaaa +>syndip_1_chr20:16395049-16395522 +acagtcgtggacagcaaagctaaggctcagtacaacaaagggcatacccctgtcatcggt +gtcttcttactctctccctaatgtgatgtattcatcctcccagtttagtcaaggcagaaa +ggagatgaggaaggggagaggaggggagaggagggaagaggaggggaggggaggggagag +gaggagaggggaggagaggggaggccaagggaggggaggggaggggaggagaggggaggc +caagggaggggaggggaggggaggagaggggaggccaagggaggggaggggaggggagga +gaggggaggccaagggaggggaggggaggagaggggaggccaagggaggggaggggaggg +gaggagaggggaggccaagggaggggaggggaggggaggagaggggaggccaagggagaa +gatatgaaagaaatagggaaggagtgggacacagggaggaaaacaaaactatttcctttc +atataaatgttgtcatctggggagaagccctcactatctccttggtgcctttggcttttg +gtattcaaa +>syndip_2_chr20:16395049-16395522 +acagtcgtggacagcaaagctaaggctcagtacaacaaagggcatacccctgtcatcggt +gtcttcttactctctccctaatgtgatgtattcatcctcccagtttagtccaggcagaaa +ggagatgaggaaggggagaggaggggagaggaggggag---------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------gggaggggaggggagaggaggggaggccaagggagaa +gatatgaaagaaatagggaaggagtgggacacagggaggaaaacaaaactatttcctttc +atataaatgttgtcatctggggagaagccctcactatctccttggtgcctttggcttttg +gtattcaaa +>p:HG002_1_chr20:16395049-16395522 +acagtcgtggacagcaaagctaaggctcagtacaacaaagggcatacccctgtcatcggt +gtcttcttactctctccctaatgtgatgtattcatcctcccagtttagtccaggcagaaa +ggagatgaggaaggggagaggaggggagaggaggggag---------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------gggaggggaggggagaggaggggaggccaagggagaa +gatatgaaagaaatagggaaggagtgggacacagggaggaaaacaaaactatttcctttc +atataaatgttgtcatctggggagaagccctcactatctccttggtgcctttggcttttg +gtattcaaa +>p:HG002_2_chr20:16395049-16395522 +acagtcgtggacagcaaagctaaggctcagtacaacaaagggcatacccctgtcatcggt +gtcttcttactctctccctaatgtgatgtattcatcctcccagtttagtcaaggcagaaa +ggagatgaggaaggggagaggaggggagaggagggaagaggaggggaggggaggggagag +gaggagaggggaggagaggggaggccaagggaggggaggggaggggaggagaggggaggc +caagggaggggaggggaggggaggagaggggaggccaagggaggggaggggaggggagga +gaggggaggccaagggaggggaggggaggagaggggaggccaagggaggggaggggaggg +gaggagaggggaggccaagggaggggaggggaggggaggagaggggaggccaagggagaa +gatatgaaagaaatagggaaggagtgggacacagggaggaaaacaaaactatttcctttc +atataaatgttgtcatctggggagaagccctcactatctccttggtgcctttggcttttg +gtattcaaa diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/msa.fa.fai new file mode 100644 index 00000000..45035466 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_16395049_16395522 549 29 60 61 +syndip_1_chr20:16395049-16395522 549 622 60 61 +syndip_2_chr20:16395049-16395522 549 1215 60 61 +p:HG002_1_chr20:16395049-16395522 549 1809 60 61 +p:HG002_2_chr20:16395049-16395522 549 2403 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/output.vcf.gz new file mode 100644 index 00000000..5cdb3d1e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/output.vcf.gz.tbi new file mode 100644 index 00000000..83ebc74d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:16395149-16395422/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/base.vcf.gz new file mode 100644 index 00000000..357487cf Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/base.vcf.gz.tbi new file mode 100644 index 00000000..9fa6ac23 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/comp.vcf.gz new file mode 100644 index 00000000..3f6fba66 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/comp.vcf.gz.tbi new file mode 100644 index 00000000..88dbec2d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/haps.fa new file mode 100644 index 00000000..01d063b5 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/haps.fa @@ -0,0 +1,30 @@ +>ref_chr20_17081116_17081511 +TGAATATTCTTTTATGTAGTAAAAGTATAAAACTATGGCTGGTAAAAATGCATGCCACATTGTGGATCATGACTACCTCTGGGTCAGAAGGAAATGTGATGGGTAAAGGAATCAACTCCATGTGGAATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTATTTTATTTTATTACGACAAGGTCTGGCTCTGTCGCCTAGGCTGGAGTGCATTGTGGTAATCTTGGCTTACTGCAACCTCTGCCTCCCAGACTCAACCAGTCCTCCCACCTCAGCCTCCCAAGTAGCTGGGACTACAAGTACGT +>syndip_1_chr20:17081116-17081511 +TGAATATTCTTTTATGTAGTAAAAGTATAAAACTATGGCTGGTAAAAATGCATGCCACAT +TGTGGATCATGACTACCTCTGGGTCAGAAGGAAATGTGATGGGTAAAGGAATCAACTCCA +TGTGGAATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTT +TATTTTATTTTATTTTATTACGACAAGGTCTGGCTCTGTCGCCTAGGCTGGAGTGCATTG +TGGTAATCTTGGCTTACTGCAACCTCTGCCTCCCAGACTCAACCAGTCCTCCCACCTCAG +CCTCCCAAGTAGCTGGGACTACAAGTACGT +>syndip_2_chr20:17081116-17081511 +TGAATATTCTTTTATGTAGTAAAAGTATAAAACTATGGCTGGTAAAAATGCATGCCACAT +TGTGGATCATGACTACCTCTGGGTCAGAAGGAAATGTGATGGGTAAAGGAATCAACTCCA +TGTGGAATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTT +TATTTTATTTTATTACGACAAGGTCTGGCTCTGTCGCCTAGGCTGGAGTGCATTGTGGTA +ATCTTGGCTTACTGCAACCTCTGCCTCCCAGACTCAACCAGTCCTCCCACCTCAGCCTCC +CAAGTAGCTGGGACTACAAGTACGT +>p:HG002_1_chr20:17081116-17081511 +TGAATATTCTTTTATGTAGTAAAAGTATAAAACTATGGCTGGTAAAAATGCATGCCACAT +TGTGGATCATGACTACCTCTGGGTCAGAAGGAAATGTGATGGGTAAAGGAATCAACTCCA +TGTGGAATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTT +TATTTTATTTTATTACGACAAGGTCTGGCTCTGTCGCCTAGGCTGGAGTGCATTGTGGTA +ATCTTGGCTTACTGCAACCTCTGCCTCCCAGACTCAACCAGTCCTCCCACCTCAGCCTCC +CAAGTAGCTGGGACTACAAGTACGT +>p:HG002_2_chr20:17081116-17081511 +TGAATATTCTTTTATGTAGTAAAAGTATAAAACTATGGCTGGTAAAAATGCATGCCACAT +TGTGGATCATGACTACCTCTGGGTCAGAAGGAAATGTGATGGGTAAAGGAATCAACTCCA +TGTGGAATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTT +TATTTTATTTTATTTTATTACGACAAGGTCTGGCTCTGTCGCCTAGGCTGGAGTGCATTG +TGGTAATCTTGGCTTACTGCAACCTCTGCCTCCCAGACTCAACCAGTCCTCCCACCTCAG +CCTCCCAAGTAGCTGGGACTACAAGTACGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/haps.fa.ref.fa new file mode 100644 index 00000000..0c5f103e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:17081116-17081511 +TGAATATTCTTTTATGTAGTAAAAGTATAAAACTATGGCTGGTAAAAATGCATGCCACATTGTGGATCATGACTACCTCTGGGTCAGAAGGAAATGTGATGGGTAAAGGAATCAACTCCATGTGGAATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTATTTTATTTTATTACGACAAGGTCTGGCTCTGTCGCCTAGGCTGGAGTGCATTGTGGTAATCTTGGCTTACTGCAACCTCTGCCTCCCAGACTCAACCAGTCCTCCCACCTCAGCCTCCCAAGTAGCTGGGACTACAAGTACGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/msa.fa new file mode 100644 index 00000000..07ae1836 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/msa.fa @@ -0,0 +1,40 @@ +>ref_chr20_17081116_17081511 +tgaatattcttttatgtagtaaaagtataaaactatggctggtaaaaatgcatgccacat +tgtggatcatgactacctctgggtcagaaggaaatgtgatgggtaaaggaatcaactcca +tgtggaattttattttattttattttattttattttattttattttattttattttattt +tattattttattttattttattttattttattttattttattttattttattttatttta +ttttattttattattttattttattacgacaaggtctggctctgtcgcctaggctggagt +gcattgtggtaatcttggcttactgcaacctctgcctcccagactcaaccagtcctccca +cctcagcctcccaagtagctgggactacaagtacgt +>syndip_1_chr20:17081116-17081511 +tgaatattcttttatgtagtaaaagtataaaactatggctggtaaaaatgcatgccacat +tgtggatcatgactacctctgggtcagaaggaaatgtgatgggtaaaggaatcaactcca +tgtggaattttattttattttattttattttattttattttattttattttattttattt +tatt-------------------------------------------------------- +----------ttattttattttattacgacaaggtctggctctgtcgcctaggctggagt +gcattgtggtaatcttggcttactgcaacctctgcctcccagactcaaccagtcctccca +cctcagcctcccaagtagctgggactacaagtacgt +>syndip_2_chr20:17081116-17081511 +tgaatattcttttatgtagtaaaagtataaaactatggctggtaaaaatgcatgccacat +tgtggatcatgactacctctgggtcagaaggaaatgtgatgggtaaaggaatcaactcca +tgtgga-----attttattttattttattttattttattttattttattttattttattt +tatt-------------------------------------------------------- +----------ttattttattttattacgacaaggtctggctctgtcgcctaggctggagt +gcattgtggtaatcttggcttactgcaacctctgcctcccagactcaaccagtcctccca +cctcagcctcccaagtagctgggactacaagtacgt +>p:HG002_1_chr20:17081116-17081511 +tgaatattcttttatgtagtaaaagtataaaactatggctggtaaaaatgcatgccacat +tgtggatcatgactacctctgggtcagaaggaaatgtgatgggtaaaggaatcaactcca +tgtgga-----attttattttattttattttattttattttattttattttattttattt +tatt-------------------------------------------------------- +----------ttattttattttattacgacaaggtctggctctgtcgcctaggctggagt +gcattgtggtaatcttggcttactgcaacctctgcctcccagactcaaccagtcctccca +cctcagcctcccaagtagctgggactacaagtacgt +>p:HG002_2_chr20:17081116-17081511 +tgaatattcttttatgtagtaaaagtataaaactatggctggtaaaaatgcatgccacat +tgtggatcatgactacctctgggtcagaaggaaatgtgatgggtaaaggaatcaactcca +tgtggaattttattttattttattttattttattttattttattttattttattttattt +tatt-------------------------------------------------------- +----------ttattttattttattacgacaaggtctggctctgtcgcctaggctggagt +gcattgtggtaatcttggcttactgcaacctctgcctcccagactcaaccagtcctccca +cctcagcctcccaagtagctgggactacaagtacgt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/msa.fa.fai new file mode 100644 index 00000000..ed1ece67 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_17081116_17081511 396 29 60 61 +syndip_1_chr20:17081116-17081511 396 466 60 61 +syndip_2_chr20:17081116-17081511 396 903 60 61 +p:HG002_1_chr20:17081116-17081511 396 1341 60 61 +p:HG002_2_chr20:17081116-17081511 396 1779 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/output.vcf.gz new file mode 100644 index 00000000..452ff61b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/output.vcf.gz.tbi new file mode 100644 index 00000000..04a61891 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:17081216-17081411/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/base.vcf.gz new file mode 100644 index 00000000..d9a0802f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/base.vcf.gz.tbi new file mode 100644 index 00000000..6d12980e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/comp.vcf.gz new file mode 100644 index 00000000..5f17b947 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/comp.vcf.gz.tbi new file mode 100644 index 00000000..dfcbd641 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/haps.fa new file mode 100644 index 00000000..063bc2fe --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/haps.fa @@ -0,0 +1,148 @@ +>ref_chr20_18208997_18210828 +GTATTCTTTGTACTGTTTTTATTTTTGCAACTTTTCTGTGTTTACAGTTATTTCCAAATAAAAAATAAGCAGAAAGGAAAAGCTAATCATCTCCCCCTATTCCAGTCCCCCAGGCATGTATCCTTCCGTAGCTTCTCCACACCTACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCATTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTCCACACCCACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCTAGACGATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCAGACCTTCTCCACACCCACACAGACCTAGACGATTCCTTCCACACCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTGTGCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTGCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAAACGATTCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGACAATTCCTTGCACACCTTCTCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGACAATTCCTTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGATGATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCCTAACACCCACACGAACCTAGAGAATTCCTTCCACACCTTCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAAATTCTTATACACTTAAAATGGGATTTTGTTGTTTTATTAAAATGCAGTCATTCTCTATGCATTAATTATTGTGCAGCTTGATTTTTCTCCTTTTTTTTTGTTAAATCTTCCTCCGTCATCCAGGCTGGAGTGCAG +>syndip_1_chr20:18208997-18210828 +GTATTCTTTGTACTGTTTTTATTTTTGCAACTTTTCTGTGTTTACAGTTATTTCCAAATA +AAAAATAAGCAGAAAGGAAAAGCTAATCATCTCCCCCTATTCCAGTCCCCCAGGCATGTA +TCCTTCCGTAGCTTCTCCACACCTACACGAACCTAGACGATTCCTTCCACACCTTCCCCA +CACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGAT +GAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTC +CCCACACCCATTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTCCACACCC +ACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCTAGACGATT +CCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCAGACCTTCTCCA +CACCCACACAGACCTAGACGATTCCTTCCACACCTCCACACCCACACGAACCTAGACGAA +TTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTC +CACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTA +GACGATTCCTTCCACACTTTCCCCACACCCACACGAACCTAGACGATTCCTTCCACACCT +CCACACCCACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCT +AGACGATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAATTCCTTCCACACA +CACATGAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACATGAACCTAGACGAT +TCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCACACCTTCCCC +ACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAG +ACGATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTCCACACCTT +CTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACGAACC +TAAACGATTCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCACA +CCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACAC +GAACCTAGACGATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTC +CACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCA +CACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACAATTC +CTTCCACACCTTCTCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCTCCACA +CCCACACAAACCTAGATGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGACG +ATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCT +CCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTA +GACAATTCCTTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCT +TCTCCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAA +CCTAGACGATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCA +CACCTTCCTAACACCCACACGAACCTAGAGAATTCCTTCCACACCTTCACACCCACACAA +ACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAAATTCTTAT +ACACTTAAAATGGGATTTTGTTGTTTTATTAAAATGCAGTCATTCTCTATGCATTAATTA +TTGTGCAGCTTGATTTTTCTCCTTTTTTTTTGTTAAATCTTCCTCCGTCATCCAGGCTGG +AGTGCAG +>syndip_2_chr20:18208997-18210828 +GTATTCTTTGTACTGTTTTTATTTTTGCAACTTTTCTGTGTTTACAGTTATTTCCAAATA +AAAAATAAGCAGAAAGGAAAAGCTAATCATCTCCCCCTATTCCAGTCCCCCAGGCATGTA +TCCTTCCGTAGCTTCTCCACACCTACACGAACCTAGACGATTCCTTCCACACCTTCCCCA +CACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGAT +GAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTC +CCCACACCCATTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTCCACACCC +ACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCTAGACGATT +CCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCAGACCTTCTCCA +CACCCACACAGACCTAGACGATTCCTTCCACACCTCCACACCCACACGAACCTAGACGAA +TTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTC +CACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTA +GACGATTCCTTCCACACTTTCCCCACACCCACAAGAACCTAGACGATTCCTTCCACACCT +CCACACCCACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCT +AGACGATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAATTCCTTCCACACA +CACATGAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACATGAACCTAGACGAT +TCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCACACCTTCCCC +ACACCCACACAGACCTAGACGAATTCCTTCCACACATTCTCCACACCCACACGAACCTAG +ACGATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTCCACACCTT +CTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACGAACC +TAAACGATTCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCACA +CCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACAC +GAACCTAGACGATTCCTTCCACACCACACGAACCTAGACAATTCCTTCCACACCTTCTCA +CACCCACACAAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGA +CGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACAATTCCTTCCACACCTT +CTCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACAAACC +TAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGACGATTCCTTCCACA +CCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACAC +GAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGACAATTCCTTC +CACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCA +CACAAACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGACGATTC +CTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCCTAAC +ACCCACACGAACCTAGAGAATTCCTTCCACACCTTCACACCCACACAAACCTAGACGAAT +TCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAAATTCTTATACACTTAAAATG +GGATTTTGTTGTTTTATTAAAATGCAGTCATTCTCTATGCATTAATTATTGTGCAGCTTG +ATTTTTCTCCTTTTTTTTTGTTAAATCTTCCTCCGTCATCCAGGCTGGAGTGCAG +>p:HG002_1_chr20:18208997-18210828 +GTATTCTTTGTACTGTTTTTATTTTTGCAACTTTTCTGTGTTTACAGTTATTTCCAAATA +AAAAATAAGCAGAAAGGAAAAGCTAATCATCTCCCCCTATTCCAGTCCCCCAGGCATGTA +TCCTTCCGTAGCTTCTCCACACCTACACGAACCTAGACGATTCCTTCCACACCTTCCCCA +CACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGAT +GAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTC +CCCACACCCATTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTCCACACCC +ACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCTAGACGATT +CCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCAGACCTTCTCCA +CACCCACACAGACCTAGACGATTCCTTCCACACCTCCACACCCACACGAACCTAGACGAA +TTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTC +CACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTA +GACGATTCCTTCCACACTTTCCCCACACCCACAAGAACCTAGACGATTCCTTCCACACCT +CCACACCCACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCT +AGACGATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAATTCCTTCCACACA +CACATGAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACATGAACCTAGACGAT +TCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCACACCTTCCCC +ACACCCACACAGACCTAGACGAATTCCTTCCACACATTCTCCACACCCACACGAACCTAG +ACGATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTCCACACCTT +CTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACGAACC +TAAACGATTCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCACA +CCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACAC +GAACCTAGACGATTCCTTCCACACCACACGAACCTAGACAATTCCTTCCACACCTTCTCA +CACCCACACAAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGA +CGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACAATTCCTTCCACACCTT +CTCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACAAACC +TAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGACGATTCCTTCCACA +CCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACAC +GAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGACAATTCCTTC +CACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCA +CACAAACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGACGATTC +CTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCCTAAC +ACCCACACGAACCTAGAGAATTCCTTCCACACCTTCACACCCACACAAACCTAGACGAAT +TCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAAATTCTTATACACTTAAAATG +GGATTTTGTTGTTTTATTAAAATGCAGTCATTCTCTATGCATTAATTATTGTGCAGCTTG +ATTTTTCTCCTTTTTTTTTGTTAAATCTTCCTCCGTCATCCAGGCTGGAGTGCAG +>p:HG002_2_chr20:18208997-18210828 +GTATTCTTTGTACTGTTTTTATTTTTGCAACTTTTCTGTGTTTACAGTTATTTCCAAATA +AAAAATAAGCAGAAAGGAAAAGCTAATCATCTCCCCCTATTCCAGTCCCCCAGGCATGTA +TCCTTCCGTAGCTTCTCCACACCTACACGAACCTAGACGATTCCTTCCACACCTTCCCCA +CACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGAT +GAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTC +CCCACACCCATTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTCCACACCC +ACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCTAGACGATT +CCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCAGACCTTCTCCA +CACCCACACAGACCTAGACGATTCCTTCCACACCTCCACACCCACACGAACCTAGACGAA +TTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTC +CACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTA +GACGATTCCTTCCACACTTTCCCCACACCCACACGAACCTAGACGATTCCTTCCACACCT +CCACACCCACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCT +AGACGATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAATTCCTTCCACACA +CACATGAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACATGAACCTAGACGAT +TCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCACACCTTCCCC +ACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAG +ACGATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTCCACACCTT +CTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACGAACC +TAAACGATTCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCACA +CCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACAC +GAACCTAGACGATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTC +CACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCA +CACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACAATTC +CTTCCACACCTTCTCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCTCCACA +CCCACACAAACCTAGATGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGACG +ATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCT +CCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTA +GACAATTCCTTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCT +TCTCCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAA +CCTAGACGATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCA +CACCTTCCTAACACCCACACGAACCTAGAGAATTCCTTCCACACCTTCACACCCACACAA +ACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAAATTCTTAT +ACACTTAAAATGGGATTTTGTTGTTTTATTAAAATGCAGTCATTCTCTATGCATTAATTA +TTGTGCAGCTTGATTTTTCTCCTTTTTTTTTGTTAAATCTTCCTCCGTCATCCAGGCTGG +AGTGCAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/haps.fa.ref.fa new file mode 100644 index 00000000..48f827cd --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:18208997-18210828 +GTATTCTTTGTACTGTTTTTATTTTTGCAACTTTTCTGTGTTTACAGTTATTTCCAAATAAAAAATAAGCAGAAAGGAAAAGCTAATCATCTCCCCCTATTCCAGTCCCCCAGGCATGTATCCTTCCGTAGCTTCTCCACACCTACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCATTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTCCACACCCACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCTAGACGATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCAGACCTTCTCCACACCCACACAGACCTAGACGATTCCTTCCACACCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTGTGCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTGCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAAACGATTCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGACAATTCCTTGCACACCTTCTCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGACAATTCCTTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGATGATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCCTAACACCCACACGAACCTAGAGAATTCCTTCCACACCTTCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAAATTCTTATACACTTAAAATGGGATTTTGTTGTTTTATTAAAATGCAGTCATTCTCTATGCATTAATTATTGTGCAGCTTGATTTTTCTCCTTTTTTTTTGTTAAATCTTCCTCCGTCATCCAGGCTGGAGTGCAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/msa.fa new file mode 100644 index 00000000..34f19f48 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/msa.fa @@ -0,0 +1,185 @@ +>ref_chr20_18208997_18210828 +gtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatttccaaata +aaaaataagcagaaaggaaaagctaatcatctccccctattccagtcccccaggcatgta +tccttccgtagcttctccacacct------------------------------------ +-----acacgaacctagacgattccttccacaccttccccacacccacacgaacctagat +gaattccttccacaccttctccacacccacacgaacctagacgattccttccacaccttc +cccacacccattctccacacccacacgaacctagacgattccttccacacctccacaccc +acacgaacctagatgaattccttccacaccttccccacacccacacaaacctagacgatt +ccttccacaccttctccacacccacacgaacctagacgaattccttccagaccttctcca +cacccacacagacctagacgattccttccacacctccacacccacacgaacctagacgaa +ttccttccacaccttgtgcacacccacacgaacctagacgaattccttccacaccttctc +cacacccacacgaacctagacgaattccttccacaccttctccacacccacacgaaccta +gacgattccttccacaccttccccacacccacacagacctagacgaattccttgcacacc +ttctccacacccacacgaacctagacgaattccttccacaccttctccatacccacacga +acctagacaattccttccacaccttct-------------------------------ca +cacccacacaaacctagatgaattccttccacaccttctccacacccacacgaacctaaa +cgattccttccacaccttctccacacccacacacacctagatgaattccttccacacctt +ccccacacccacacagacctagacgaattccttccacaccttctccacacccacacgaac +ctagacgattccttccacaccttctccatacccacacgaacctagacaattccttccaca +ccttctcacacccacacaa----------------------------------------- +------------------------------------------acctagatgaattccttc +cacaccttccccacacccacacagacctagacgaattccttccacaccttctccacaccc +acacgaacctagacg--------------------------------------------- +------------------------------------------------------------ +-------------------attccttccacaccttccccacacccacacgaacctagaca +attccttgcacaccttctcacacccacacaaacctagacgaattccttccacaccttctc +cacacccacacaaacctagacgaattccttccacaccttcctcacacccacacgaaccta +gacgattccttccacaccttccccacacccacacagacctagacgaattccttccacacc +ttctccacacccacacgaacctagacgattccttccacaccttccccacacccacacgaa +cctagacaattccttccacaccttctcacacccacacaaacctagatgaattccttccac +accttctccacacccacacaaacctagacgaattccttccacaccttcctcacacccaca +cgaacctagatgattccttccacaccttccccacacccacacagacctagacgaattcct +tccacaccttcctaacacccacacgaacctagagaattccttccacaccttcacacccac +acaaacctagacgaattccttccacaccttctccacacccacacaaacctagacaaattc +ttatacacttaaaatgggattttgttgttttattaaaatgcagtcattctctatgcatta +attattgtgcagcttgatttttctcctttttttttgttaaatcttcctccgtcatccagg +ctggagtgcag +>syndip_1_chr20:18208997-18210828 +gtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatttccaaata +aaaaataagcagaaaggaaaagctaatcatctccccctattccagtcccccaggcatgta +tccttccgtagcttctccacacctacacgaacctagacgattccttccacaccttcccca +cacccacacgaacctagacgattccttccacaccttccccacacccacacgaacctagat +gaattccttccacaccttctccacacccacacgaacctagacgattccttccacaccttc 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+cacacccacacaaacctagatgaattccttccacaccttcctcacacccacacgaaccta +gacgattccttccacaccttccccacacccacacagacctagacgaattccttccacacc +ttctccacacccacacgaacctagacgattccttccacaccttccccacacccacacgaa +cctagacaattccttccacaccttctcacacccacacaaacctagatgaattccttccac +accttctccacacccacacaaacctagacgaattccttccacaccttcctcacacccaca +cgaacctagacgattccttccacaccttccccacacccacacagacctagacgaattcct +tccacaccttcctaacacccacacgaacctagagaattccttccacaccttcacacccac +acaaacctagacgaattccttccacaccttctccacacccacacaaacctagacaaattc +ttatacacttaaaatgggattttgttgttttattaaaatgcagtcattctctatgcatta +attattgtgcagcttgatttttctcctttttttttgttaaatcttcctccgtcatccagg +ctggagtgcag diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/msa.fa.fai new file mode 100644 index 00000000..6620202b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_18208997_18210828 2111 29 60 61 +syndip_1_chr20:18208997-18210828 2111 2210 60 61 +syndip_2_chr20:18208997-18210828 2111 4391 60 61 +p:HG002_1_chr20:18208997-18210828 2111 6573 60 61 +p:HG002_2_chr20:18208997-18210828 2111 8755 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/output.vcf.gz new file mode 100644 index 00000000..b33d2e75 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/output.vcf.gz.tbi new file mode 100644 index 00000000..3fd5bea6 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:18209097-18210728/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/base.vcf.gz new file mode 100644 index 00000000..356a5aa0 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/base.vcf.gz.tbi new file mode 100644 index 00000000..57b1f071 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/comp.vcf.gz new file mode 100644 index 00000000..814f607c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/comp.vcf.gz.tbi new file mode 100644 index 00000000..a126af2a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/haps.fa new file mode 100644 index 00000000..5112703e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/haps.fa @@ -0,0 +1,84 @@ +>ref_chr20_20295855_20296666 +GATGCCTGTGGCAGGAGCTGAGGGCAAGGGATGAGCAGAGGAGACCAGGCCCCTGCAGCCAGAGGCTCAGTCCTGGCTTTTTCCAAACTCTTCTCCAGAGGAGCCCGCCCTTGCACACCAACGCCTGCATGCTTCCCTCCTTCCTTCCTTCCTTCCCTCCTTTCCTTCCTTCTTTCTTTTCTTCCTCCCTCCCTTCCTTCCCTTCCTTCCCTTCCTTCCCTCCTTTTCTTCCTTCTTTCCTTCCTTCCTTCCCTCCCTCCTTCCCTTCCTTCCTTCCTTCCTCCCTCCCTCCCTCCTTCCCTCCTTCATTCCTTCCTTCCCTCCTTTCCTTCCTTCACCTCCTTCCCTTCTCTCCTCCCTTCATCCCTTCCTTCCTTTCTTCCTTCCCTCCCTCTTCCTTCCTTTCTTCACCCCTCCCCCTTCCCTCATCCCTTCCCTCCTTCCCTTCCTTCCTTCCTTCCCTCCTTCCTTCCCTTCCTTCCTTCCTTGCTTCCTTCCTTCTTTCCTTTCTTCATCCCTCCTTCCCTCCCTCCCTCCTTCCTGCCTTCCTTCTTTCTTTCTTTTCTTTCTTCCTCCCTCCCTCCTTCCTTCCCTCCTTCCTGCCTTCCTTCCTTCCTTTCTTTTTCCTCCCTCCCTCCTTCCTTCTTTACTCCCTTCCTTCCTTCCTTCCTCCCCTCACTCAATTTGTTCATCAAAAAATCTAGTTCCTTGCCATGCCACAGCCTGAGTATTTAAAAATAACTTTTCCTCATTTTAGAAGTAATGATCATTTTTTAAAAATTAGAAGCTGCAGATAGTCAAATAACTGTAAG +>syndip_1_chr20:20295855-20296666 +GATGCCTGTGGCAGGAGCTGAGGGCAAGGGATGAGCAGAGGAGACCAGGCCCCTGCAGCC +AGAGGCTCAGTCCTGGCTTTTTCCAAACTCTTCTCCAGAGGAGCCCGCCCTTGCACACCA +ACGCCTGCATGCTTCCCTCCTTCCTTCCTTCCTTCCCTCCTTTCCTTCCTTCTTTCTTTT +CTTCCTCCCTCCCTTCCTTCCCTTCCTTCCCTTCCTTCCCTCCTTTTCTTCCTTCTTTCC +TTCCTTCCTTCCCTCCCTCCTTCCCTTCCTTCCTTCCTTCCCTTCCTTCCTTCTCTCCTT +CCTTCCTTCCCTCCCTCCTTCCCTTCCTTCCTTCTCTCCTTCCTTCCCTTCCTTCCTTCT +CTCCTTCCTTCCCTTCCTTCCTTCTCTCCTTCCTTCCCTTCCTTCCTTCTCTCCTTCCTT +CCCTTCCTTCCTTCTCTCCTTCCTTCCCTTGCTTCCTTTCTTCCTTCCTTTGCTTCCTTG +CTTCCTTCTTTCCTTTCTTCATCCCTCCCTCCCTCCTTCCTTCCTTTCCTTCCTTCCCTC +TATCCTTCCTTCCTTCCTTTCTTTCTCCCTCCCTTCCTTCCCTTCCTTCCTTCCCTCTTT +TCCTTCCATCTTTCCTTTCTTCCTCCCTCCCTCCCTCCTTCCCTCCTTCATTACTTCCTT +CCCTCCTTTCCTTCCTTCACCTCCTTCCCTTCTCTCCTCCCTTCATCCCTTCCTTCCTTT +CTTCCTTCCCTCCCTCTTCCTTCCTTTCTTCACCCCTCCCCCTTCCCTCATCCCTTCCCT +CCTTCCCTTCCTTCCTTCCTTCCCTCCTTCCTTCCCTTCCTTCCTTCCTTGCTTCCTTCC +TTCTTTCCTTTCTTCATCCCTCCTTCCCTCCCTCCCTCCTTCCTGCCTTCCTTCTTTCTT +TCTTTTCTTTCTTCCTCCCTCCCTCCTTCCTTCCCTCCTTCCTGCCTTCCTTCCTTCCTT +TCTTTTTCCTCCCTCCCTCCTTCCTTCTTTACTCCCTTCCTTCCTTCCTTCCTCCCCTCA +CTCAATTTGTTCATCAAAAAATCTAGTTCCTTGCCATGCCACAGCCTGAGTATTTAAAAA +TAACTTTTCCTCATTTTAGAAGTAATGATCATTTTTTAAAAATTAGAAGCTGCAGATAGT +CAAATAACTGTAAG +>syndip_2_chr20:20295855-20296666 +GATGCCTGTGGCAGGAGCTGAGGGCAAGGGATGAGCAGAGGAGACCAGGCCCCTGCAGCC +AGAGGCTCAGTCCTGGCTTTTTCCAAACTCTTCTCCAGAGGAGCCCGCCCTTGCACACCA +ACGCCTGCATGCTTCCCTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC +TTCCTGCCTGCCTGCCTGCCTTCCTGCCTTCCCTTCCTCCCTCCCTCCCTACCTCCCTCC +CTCCTTCCTTCCCTTCCTCCCTCCCTCCCTTCTTTACTTCCTTCCTCCTTCCCTCCTCCT +TTCCTCCATCCTTCCCTCCCTTCTTTCCTTTCTTCCTCCTGCCCTCCCTCCTTCTTTCCC +TTCCTCCCTCCCTTCCTTCCCATCCTCCTTCCCTCCCTCCTTCCTTCCTGCCTTCCTTCC +TTCCCTCCATCCTTCCTTCCTTCCTTTCTTCCTCCCTCCCTTCCTTCCTCCCTTCCTTCC +CTTCCTTCCTTCCCTCTTTTCCTTCCATCTTTCCTTTCTTCCTCCCTCCCTCCCTCCTTC +CCTCCTTCATTCCTTTCTTCCCTCCTTTCCTTCCTTCACCTCCTTCCCTTCTCTCCTCCC +TTCATCCCTTCCTTCCTTTCTTCCTTCCCTCCCTCTTCCTTCCTTTCTTCACCCCTCCCC +CTTCCCTCATCCCTTCCCTCCTTCCCTTCCTTCCTTCCTTCCCTCCTTCCTTCCCTTCCT +TCCTTCCTTCCCTCCTTCCTTCCCTTCCTTCCTTGCTTCCTTCCTTCCTTCCCTTCCTTC +CTTGCTTCCTTCCTTCCTTCCCTTCCTTCCTTGCTTCCTTCCTTCTTTCCTTTCTTCATC +CCTCCTTCCCTCCCTCCCTCCTTCCTGCCTTCCTTCTTTCTTTCTTTTCTTTCTTCCTCC +CTCCCTCCTTCCTTCCCTCCTTCCTGCCTTCCTTCCTTCCTTTCTTTTTCCTCCCTCCCT +CCTTCCTTCTTTACTCCCTTCCTTCCTTCCTTCCTCCCCTCACTCAATTTGTTCATCAAA +AAATCTAGTTCCTTGCCATGCCACAGCCTGAGTATTTAAAAATAACTTTTCCTCATTTTA +GAAGTAATGATCATTTTTTAAAAATTAGAAGCTGCAGATAGTCAAATAACTGTAAG +>p:HG002_1_chr20:20295855-20296666 +GATGCCTGTGGCAGGAGCTGAGGGCAAGGGATGAGCAGAGGAGACCAGGCCCCTGCAGCC +AGAGGCTCAGTCCTGGCTTTTTCCAAACTCTTCTCCAGAGGAGCCCGCCCTTGCACACCA +ACGCCTGCATGCTTCCCTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC +TTCCTGCCTGCCTGCCTGCCTTCCTGCCTTCCCTTCCTCCCTCCCTCCCTACCTCCCTCC +CTCCTTCCTTCCCTTCCTCCCTCCCTCCCTTCTTTACTTCCTTCCTCCTTCCCTCCTCCT +TTCCTCCATCCTTCCCTCCCTTCTTTCCTTTCTTCCTCCTGCCCTCCCTCCTTCTTTCCC +TTCCTCCCTCCCTTCCTTCCCATCCTCCTTCCCTCCCTCCTTCCTTCCTGCCTTCCTTCC +TTCCCTCCATCCTTCCTTCCTTCCTTTCTTCCTCCCTCCCTTCCTTCCTCCCTTCCTTCC +CTTCCTTCCTTCCCTCTTTTCCTTCCATCTTTCCTTTCTTCCTCCCTCCCTCCCTCCTTC +CCTCCTTCATTCCTTTCTTCCCTCCTTTCCTTCCTTCACCTCCTTCCCTTCTCTCCTCCC +TTCATCCCTTCCTTCCTTTCTTCCTTCCCTCCCTCTTCCTTCCTTTCTTCACCCCTCCCC +CTTCCCTCATCCCTTCCCTCCTTCCCTTCCTTCCTTCCTTCCCTCCTTCCTTCCCTTCCT +TCCTTCCTTCCCTCCTTCCTTCCCTTCCTTCCTTGCTTCCTTCCTTCCTTCCCTTCCTTC +CTTGCTTCCTTCCTTCCTTCCCTTCCTTCCTTGCTTCCTTCCTTCTTTCCTTTCTTCATC +CCTCCTTCCCTCCCTCCCTCCTTCCTGCCTTCCTTCTTTCTTTCTTTTCTTTCTTCCTCC +CTCCCTCCTTCCTTCCCTCCTTCCTGCCTTCCTTCCTTCCTTTCTTTTTCCTCCCTCCCT +CCTTCCTTCTTTACTCCCTTCCTTCCTTCCTTCCTCCCCTCACTCAATTTGTTCATCAAA +AAATCTAGTTCCTTGCCATGCCACAGCCTGAGTATTTAAAAATAACTTTTCCTCATTTTA +GAAGTAATGATCATTTTTTAAAAATTAGAAGCTGCAGATAGTCAAATAACTGTAAG +>p:HG002_2_chr20:20295855-20296666 +GATGCCTGTGGCAGGAGCTGAGGGCAAGGGATGAGCAGAGGAGACCAGGCCCCTGCAGCC +AGAGGCTCAGTCCTGGCTTTTTCCAAACTCTTCTCCAGAGGAGCCCGCCCTTGCACACCA +ACGCCTGCATGCTTCCCTCCTTCCTTCCTTCCTTCCCTCCTTTCCTTCCTTCTTTCTTTT +CTTCCTCCCTCCCTTCCTTCCCTTCCTTCCCTTCCTTCCCTCCTTTTCTTCCTTCTTTCC +TTCCTTCCTTCCCTCCCTCCTTCCCTTCCTTCCTTCCTTCCCTTCCTTCCTTCTCTCCTT +CCTTCCTTCCCTCCCTCCTTCCCTTCCTTCCTTCTCTCCTTCCTTCCCTTCCTTCCTTCT +CTCCTTCCTTCCCTTCCTTCCTTCTCTCCTTCCTTCCCTTCCTTCCTTCTCTCCTTCCTT +CCCTTCCTTCCTTCTCTCCTTCCTTCCCTTGCTTCCTTTCTTCCTTCCTTTGCTTCCTTG +CTTCCTTCTTTCCTTTCTTCATCCCTCCCTCCCTCCTTCCTTCCTTTCCTTCCTTCCCTC +TATCCTTCCTTCCTTCCTTTCTTTCTCCCTCCCTTCCTTCCCTTCCTTCCTTCCCTCTTT +TCCTTCCATCTTTCCTTTCTTCCTCCCTCCCTCCCTCCTTCCCTCCTTCATTACTTCCTT +CCCTCCTTTCCTTCCTTCACCTCCTTCCCTTCTCTCCTCCCTTCATCCCTTCCTTCCTTT +CTTCCTTCCCTCCCTCTTCCTTCCTTTCTTCACCCCTCCCCCTTCCCTCATCCCTTCCCT +CCTTCCCTTCCTTCCTTCCTTCCCTCCTTCCTTCCCTTCCTTCCTTCCTTGCTTCCTTCC +TTCTTTCCTTTCTTCATCCCTCCTTCCCTCCCTCCCTCCTTCCTGCCTTCCTTCTTTCTT +TCTTTTCTTTCTTCCTCCCTCCCTCCTTCCTTCCCTCCTTCCTGCCTTCCTTCCTTCCTT +TCTTTTTCCTCCCTCCCTCCTTCCTTCTTTACTCCCTTCCTTCCTTCCTTCCTCCCCTCA +CTCAATTTGTTCATCAAAAAATCTAGTTCCTTGCCATGCCACAGCCTGAGTATTTAAAAA +TAACTTTTCCTCATTTTAGAAGTAATGATCATTTTTTAAAAATTAGAAGCTGCAGATAGT +CAAATAACTGTAAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/haps.fa.ref.fa new file mode 100644 index 00000000..5c189ea8 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:20295855-20296666 +GATGCCTGTGGCAGGAGCTGAGGGCAAGGGATGAGCAGAGGAGACCAGGCCCCTGCAGCCAGAGGCTCAGTCCTGGCTTTTTCCAAACTCTTCTCCAGAGGAGCCCGCCCTTGCACACCAACGCCTGCATGCTTCCCTCCTTCCTTCCTTCCTTCCCTCCTTTCCTTCCTTCTTTCTTTTCTTCCTCCCTCCCTTCCTTCCCTTCCTTCCCTTCCTTCCCTCCTTTTCTTCCTTCTTTCCTTCCTTCCTTCCCTCCCTCCTTCCCTTCCTTCCTTCCTTCCTCCCTCCCTCCCTCCTTCCCTCCTTCATTCCTTCCTTCCCTCCTTTCCTTCCTTCACCTCCTTCCCTTCTCTCCTCCCTTCATCCCTTCCTTCCTTTCTTCCTTCCCTCCCTCTTCCTTCCTTTCTTCACCCCTCCCCCTTCCCTCATCCCTTCCCTCCTTCCCTTCCTTCCTTCCTTCCCTCCTTCCTTCCCTTCCTTCCTTCCTTGCTTCCTTCCTTCTTTCCTTTCTTCATCCCTCCTTCCCTCCCTCCCTCCTTCCTGCCTTCCTTCTTTCTTTCTTTTCTTTCTTCCTCCCTCCCTCCTTCCTTCCCTCCTTCCTGCCTTCCTTCCTTCCTTTCTTTTTCCTCCCTCCCTCCTTCCTTCTTTACTCCCTTCCTTCCTTCCTTCCTCCCCTCACTCAATTTGTTCATCAAAAAATCTAGTTCCTTGCCATGCCACAGCCTGAGTATTTAAAAATAACTTTTCCTCATTTTAGAAGTAATGATCATTTTTTAAAAATTAGAAGCTGCAGATAGTCAAATAACTGTAAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/msa.fa new file mode 100644 index 00000000..5636b463 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/msa.fa @@ -0,0 +1,105 @@ +>ref_chr20_20295855_20296666 +gatgcctgtggcaggagctgagggcaagggatgagcagaggagaccaggcccctgcagcc +agaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacca +acgcctgcatgcttccctccttccttccttccttccctcctttccttccttctttctttt +cttcctccctcccttcct---tcccttccttcccttccttccctcctttt--cttccttc +tttccttccttccttccctccctccttcccttccttccttc------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------cttcctccctccctccctccttccctccttcattcc +ttccttccctcctttccttccttcacctccttcccttctctcctcccttcatcccttcct +tcctttcttccttccctccctcttccttcctttcttcacccctcccccttccctcatccc +ttccctccttcccttccttccttccttccctccttccttcccttccttccttccttgctt +ccttccttctttcctttcttcatccctccttccctccctccctccttcctgccttccttc +tttctttcttttctttcttcctccctccctccttccttccctccttcctgccttccttcc +ttcctttctttttcctccctccctccttccttctttactcccttccttccttccttcctc +ccctcactcaatttgttcatcaaaaaatctagttccttgccatgccacagcctgagtatt +taaaaataacttttcctcattttagaagtaatgatcattttttaaaaattagaagctgca +gatagtcaaataactgtaag +>syndip_1_chr20:20295855-20296666 +gatgcctgtggcaggagctgagggcaagggatgagcagaggagaccaggcccctgcagcc +agaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacca +acgcctgcatgcttccctccttccttccttccttccctcctttccttccttctttctttt +cttcctccctcccttcct---tcccttccttcccttccttccctcctttt--cttccttc +tttccttccttccttccctccctccttcccttccttccttccttcc-cttccttccttct +ctccttccttccttccctccctccttcccttccttccttctctccttccttcccttcctt +ccttctctccttccttcccttccttccttctctccttccttcccttccttccttctctcc +ttccttcccttccttccttctctccttccttcccttgcttcctttcttccttcctttgct +tccttgcttccttctttcctttcttcatccctccctccctccttccttcctttccttcct +tccctctatccttccttccttcctttctttctccctcccttccttcccttccttccttcc +ctcttttccttccatctttcctttcttcctccctccctccctccttccctccttcattac +ttccttccctcctttccttccttcacctccttcccttctctcctcccttcatcccttcct +tcctttcttccttccctccctcttccttcctttcttcacccctcccccttccctcatccc +ttccctccttcccttccttccttccttccctccttccttcccttccttccttccttgctt +ccttccttctttcctttcttcatccctccttccctccctccctccttcctgccttccttc +tttctttcttttctttcttcctccctccctccttccttccctccttcctgccttccttcc +ttcctttctttttcctccctccctccttccttctttactcccttccttccttccttcctc +ccctcactcaatttgttcatcaaaaaatctagttccttgccatgccacagcctgagtatt +taaaaataacttttcctcattttagaagtaatgatcattttttaaaaattagaagctgca +gatagtcaaataactgtaag +>syndip_2_chr20:20295855-20296666 +gatgcctgtggcaggagctgagggcaagggatgagcagaggagaccaggcccctgcagcc +agaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacca +acgcctgcatgcttccctccttccttccttccttccttcctt-ccttccttccttccttc +cttcctgcctgcctgcctgccttcctgccttcccttcctccctccctccctacctccctc +cctccttccttcccttcctccctccctcccttctttacttccttcctccttccctcctcc +tttcctccatccttccctcccttctttcctttcttcctcctgccct------ccctcctt +ctttcccttcctccctcccttccttcccatcctccttccctccct--ccttccttcctgc +cttccttccttccctccatccttccttccttccttt-cttcctccctcccttccttcctc +ccttccttcccttccttccttccctcttttccttccatctttcctttcttcctccctccc +tccctccttccctccttcattcctttct---tccctcctttccttccttcacctccttcc +cttctctcctcccttcatcccttccttcctttcttccttccctccctcttccttcctttc +ttcacccctcccccttccctcatcccttccctccttcccttccttccttccttccctcct +tccttcccttccttccttc--cttccctccttcctt---------cccttccttccttgc +ttccttccttccttcccttccttccttgcttccttccttccttcccttccttccttgctt +ccttccttctttcctttcttcatccctccttccctccctccctccttcctgccttccttc +tttctttcttttctttcttcctccctccctccttccttccctccttcctgccttccttcc +ttcctttctttttcctccctccctccttccttctttactcccttccttccttccttcctc +ccctcactcaatttgttcatcaaaaaatctagttccttgccatgccacagcctgagtatt +taaaaataacttttcctcattttagaagtaatgatcattttttaaaaattagaagctgca +gatagtcaaataactgtaag +>p:HG002_1_chr20:20295855-20296666 +gatgcctgtggcaggagctgagggcaagggatgagcagaggagaccaggcccctgcagcc +agaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacca +acgcctgcatgcttccctccttccttccttccttccttcctt-ccttccttccttccttc +cttcctgcctgcctgcctgccttcctgccttcccttcctccctccctccctacctccctc +cctccttccttcccttcctccctccctcccttctttacttccttcctccttccctcctcc +tttcctccatccttccctcccttctttcctttcttcctcctgccct------ccctcctt +ctttcccttcctccctcccttccttcccatcctccttccctccct--ccttccttcctgc +cttccttccttccctccatccttccttccttccttt-cttcctccctcccttccttcctc +ccttccttcccttccttccttccctcttttccttccatctttcctttcttcctccctccc +tccctccttccctccttcattcctttct---tccctcctttccttccttcacctccttcc +cttctctcctcccttcatcccttccttcctttcttccttccctccctcttccttcctttc +ttcacccctcccccttccctcatcccttccctccttcccttccttccttccttccctcct +tccttcccttccttccttc--cttccctccttcctt---------cccttccttccttgc +ttccttccttccttcccttccttccttgcttccttccttccttcccttccttccttgctt +ccttccttctttcctttcttcatccctccttccctccctccctccttcctgccttccttc +tttctttcttttctttcttcctccctccctccttccttccctccttcctgccttccttcc +ttcctttctttttcctccctccctccttccttctttactcccttccttccttccttcctc +ccctcactcaatttgttcatcaaaaaatctagttccttgccatgccacagcctgagtatt +taaaaataacttttcctcattttagaagtaatgatcattttttaaaaattagaagctgca +gatagtcaaataactgtaag +>p:HG002_2_chr20:20295855-20296666 +gatgcctgtggcaggagctgagggcaagggatgagcagaggagaccaggcccctgcagcc +agaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacca +acgcctgcatgcttccctccttccttccttccttccctcctttccttccttctttctttt +cttcctccctcccttcct---tcccttccttcccttccttccctcctttt--cttccttc +tttccttccttccttccctccctccttcccttccttccttccttcc-cttccttccttct +ctccttccttccttccctccctccttcccttccttccttctctccttccttcccttcctt +ccttctctccttccttcccttccttccttctctccttccttcccttccttccttctctcc +ttccttcccttccttccttctctccttccttcccttgcttcctttcttccttcctttgct +tccttgcttccttctttcctttcttcatccctccctccctccttccttcctttccttcct +tccctctatccttccttccttcctttctttctccctcccttccttcccttccttccttcc +ctcttttccttccatctttcctttcttcctccctccctccctccttccctccttcattac +ttccttccctcctttccttccttcacctccttcccttctctcctcccttcatcccttcct +tcctttcttccttccctccctcttccttcctttcttcacccctcccccttccctcatccc +ttccctccttcccttccttccttccttccctccttccttcccttccttccttccttgctt +ccttccttctttcctttcttcatccctccttccctccctccctccttcctgccttccttc +tttctttcttttctttcttcctccctccctccttccttccctccttcctgccttccttcc +ttcctttctttttcctccctccctccttccttctttactcccttccttccttccttcctc +ccctcactcaatttgttcatcaaaaaatctagttccttgccatgccacagcctgagtatt +taaaaataacttttcctcattttagaagtaatgatcattttttaaaaattagaagctgca +gatagtcaaataactgtaag diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/msa.fa.fai new file mode 100644 index 00000000..e5ba32e9 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_20295855_20296666 1160 29 60 61 +syndip_1_chr20:20295855-20296666 1160 1243 60 61 +syndip_2_chr20:20295855-20296666 1160 2457 60 61 +p:HG002_1_chr20:20295855-20296666 1160 3672 60 61 +p:HG002_2_chr20:20295855-20296666 1160 4887 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/output.vcf.gz new file mode 100644 index 00000000..f522f096 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/output.vcf.gz.tbi new file mode 100644 index 00000000..be3e39e5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20295955-20296566/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/base.vcf.gz new file mode 100644 index 00000000..d8bee29c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/base.vcf.gz.tbi new file mode 100644 index 00000000..474f3cc4 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/comp.vcf.gz new file mode 100644 index 00000000..4952dd3b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/comp.vcf.gz.tbi new file mode 100644 index 00000000..ca934d45 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/haps.fa new file mode 100644 index 00000000..4fef927d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/haps.fa @@ -0,0 +1,84 @@ +>ref_chr20_20320185_20320680 +ATCCTGATTCAGATAAACTGTTAAACAAAAATCTGTGCCATTTATGAGGTGATTGGAAATTTGAAACCTGGAGAGTTAATGATGATAAGCAATTATGATTAATTTTTTTAGCAGTAAAGATGGTATTTCAGATATATAGATATATATATATTATATATATGTAATATATATAATATATGTAATATATATTATATATATGTAATATATATAATATATGTAATATATGTAATATATATTATATATGTAATATAATATATGTAATATATATTATATATGTAATATATAATATATGTAATATATAATATATGTAATATATATTATATATGTAATATATAATATATATTATATATGTAATATATATATATTTAAAAACAGAACCATTATCTTTTAGAGATACATACTGAAGTGTCTGGAGACATGCTTCAAGATAACCCAGGAGGGAGAATGGTAGAAGGAACTAGAGATGACCCAAGACTGCCCTTGAGCTAATAACTGT +>syndip_1_chr20:20320185-20320680 +ATCCTGATTCAGATAAACTGTTAAACAAAAATCTGTGCCATTTATGAGGTGATTGGAAAT +TTGAAACCTGGAGAGTTAATGATGATAAGCAATTATGATTAATTTTTTTAGCAGTAAAGA +TGGTATTTCAGATATATAGATATATATATTATATATATGTAATATATATAATATATGTAA +TATATTATATATATGTAATATATATAATATATGTAATATATTATATATATGTAATATATA +TAATATATGTAATATATATTATATATGTAATATATATAATATATGTAATATATATTATAT +ATGTAATATATATAATATATGTAATATATATTATATATGTAATATATAATATATGTAATA +TATATTATATATGTAATATAATATATGTAATATATATTATATATGTAATATATATTACAT +ATATTATATATGCAATATATATTATATATATTATATATGCAATATATATTATATATATTA +TATATGCAATATATATTATATATGCAATATATATTATATATATTATATATGCAATATATA +TTATATATATTACATATGTAATATATATTACATATGTAATATATAATATATTATATATTA +CATATGTAATATATAATATATTATATATTACATATGTAATATATAATATATATTACATAT +GTAATATATAATATATATTACATATGTAATATATTATATATTACATATGTAATATATTAT +ATATTACATATGTAATATATTATATATTACATATGTAATATATTATATATTACATATGTA +ATATATTATATATTACATATGTAATATATATAATATATTACATATGTAATATATAATATA +TTATATATGTAATATATATTACATATATAATATATATAATATATATGTAATATATTATAT +ATATTATATATGTAATATATATTACATATATAATATATATTATATATATTACATATATTA +TATATGTAATATATATTACATATGTAATATATGTAATATATATTACATATGTAATATATA +TTATATATGTAATATATATTACATATATTATATATGTAATATATATTATATATATTATAT +ATGTAATGTATAATATATATATTATATATGTAATATATATTATATATAATATATGTAATA +TATATTATATATGTAATGTATATTATATATATTATATATGTAATGTATATTATATATAAT +ATATGTAATGTATATTATATATGTAATATATATTATGTATATTATATATGTAATATATAT +TATATATATTATATATGTAATATATATTATATATATTATATATGTAATATATATTATATA +TATTATATATGTAATATATATTATATATATTATATATGTAATATATATTATATATATTAT +ATATGTAATATATATTATATATATTATATATGTAATATATATTATATATATTATATATGT +AATATATATTATATATATTATATATGTAATATATATTATATATATTATATATGTAATATA +TATTATATATATTATATATGTAATATATATTATATATATTATATATGTAATATATATTAT +ATATATTATATATGTAATATATATTATATATATTATATATGTAATATATATTATATATAT +TATATATGTAATATATATATATTTAAAAACAGAACCATTATCTTTTAGAGATACATACTG +AAGTGTCTGGAGACATGCTTCAAGATAACCCAGGAGGGAGAATGGTAGAAGGAACTAGAG +ATGACCCAAGACTGCCCTTGAGCTAATAACTGT +>syndip_2_chr20:20320185-20320680 +ATCCTGATTCAGATAAACTGTTAAACAAAAATCTGTGCCATTTATGAGGTGATTGGAAAT +TTGAAACCTGGAGAGTTAATGATGATAAGCAATTATGATTAATTTTTTTAGCAGTAAAGA +TGGTATTTCAGATATATAGATATATATATATTATATATATGTAATATATATAATATATGT +AATATATATTATATATATGTAATATATATAATATATGTAATATATGTAATATATATTATA +TATGTAATATAATATATGTAATATATATTATATATGTAATATATAATATATGTAATATAT +AATATATGTAATATATATTATATATGTAATATATAATATATATTATATATGTAATATATA +TATATTTAAAAACAGAACCATTATCTTTTAGAGATACATACTGAAGTGTCTGGAGACATG +CTTCAAGATAACCCAGGAGGGAGAATGGTAGAAGGAACTAGAGATGACCCAAGACTGCCC +TTGAGCTAATAACTGT +>p:HG002_1_chr20:20320185-20320680 +ATCCTGATTCAGATAAACTGTTAAACAAAAATCTGTGCCATTTATGAGGTGATTGGAAAT +TTGAAACCTGGAGAGTTAATGATGATAAGCAATTATGATTAATTTTTTTAGCAGTAAAGA +TGGTATTTCAGATATATAGATATATATATATTATATATATGTAATATATATAATATATGT +AATATATATTATATATATGTAATATATATAATATATGTAATATATGTAATATATATTATA +TATGTAATATAATATATGTAATATATATTATATATGTAATATATAATATATGTAATATAT +AATATATGTAATATATATTATATATGTAATATATAATATATATTATATATGTAATATATA +TATATTTAAAAACAGAACCATTATCTTTTAGAGATACATACTGAAGTGTCTGGAGACATG +CTTCAAGATAACCCAGGAGGGAGAATGGTAGAAGGAACTAGAGATGACCCAAGACTGCCC +TTGAGCTAATAACTGT +>p:HG002_2_chr20:20320185-20320680 +ATCCTGATTCAGATAAACTGTTAAACAAAAATCTGTGCCATTTATGAGGTGATTGGAAAT +TTGAAACCTGGAGAGTTAATGATGATAAGCAATTATGATTAATTTTTTTAGCAGTAAAGA +TGGTATTTCAGATATATAGATATATATATTATATATATGTAATATATATAATATATGTAA +TATATTATATATATGTAATATATATAATATATGTAATATATTATATATATGTAATATATA +TAATATATGTAATATATATTATATATGTAATATATATAATATATGTAATATATATTATAT +ATGTAATATATATAATATATGTAATATATATTATATATGTAATATATAATATATGTAATA +TATATTATATATGTAATATAATATATGTAATATATATTATATATGTAATATATATTACAT +ATATTATATATGCAATATATATTATATATATTATATATGCAATATATATTATATATATTA +TATATGCAATATATATTATATATGCAATATATATTATATATATTATATATGCAATATATA +TTATATATATTACATATGTAATATATATTACATATGTAATATATAATATATTATATATTA +CATATGTAATATATAATATATTATATATTACATATGTAATATATAATATATATTACATAT +GTAATATATAATATATATTACATATGTAATATATTATATATTACATATGTAATATATTAT +ATATTACATATGTAATATATTATATATTACATATGTAATATATTATATATTACATATGTA +ATATATTATATATTACATATGTAATATATATAATATATTACATATGTAATATATAATATA +TTATATATGTAATATATATTACATATATAATATATATAATATATATGTAATATATTATAT +ATATTATATATGTAATATATATTACATATATAATATATATTATATATATTACATATATTA +TATATGTAATATATATTACATATGTAATATATGTAATATATATTACATATGTAATATATA +TTATATATGTAATATATATTACATATATTATATATGTAATATATATTATATATATTATAT +ATGTAATGTATAATATATATATTATATATGTAATATATATTATATATAATATATGTAATA +TATATTATATATGTAATGTATATTATATATATTATATATGTAATGTATATTATATATAAT +ATATGTAATGTATATTATATATGTAATATATATTATGTATATTATATATGTAATATATAT +TATATATATTATATATGTAATATATATTATATATATTATATATGTAATATATATTATATA +TATTATATATGTAATATATATTATATATATTATATATGTAATATATATTATATATATTAT +ATATGTAATATATATTATATATATTATATATGTAATATATATTATATATATTATATATGT +AATATATATTATATATATTATATATGTAATATATATTATATATATTATATATGTAATATA +TATTATATATATTATATATGTAATATATATTATATATATTATATATGTAATATATATTAT +ATATATTATATATGTAATATATATTATATATATTATATATGTAATATATATTATATATAT +TATATATGTAATATATATATATTTAAAAACAGAACCATTATCTTTTAGAGATACATACTG +AAGTGTCTGGAGACATGCTTCAAGATAACCCAGGAGGGAGAATGGTAGAAGGAACTAGAG +ATGACCCAAGACTGCCCTTGAGCTAATAACTGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/haps.fa.ref.fa new file mode 100644 index 00000000..b9b227e4 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:20320185-20320680 +ATCCTGATTCAGATAAACTGTTAAACAAAAATCTGTGCCATTTATGAGGTGATTGGAAATTTGAAACCTGGAGAGTTAATGATGATAAGCAATTATGATTAATTTTTTTAGCAGTAAAGATGGTATTTCAGATATATAGATATATATATATTATATATATGTAATATATATAATATATGTAATATATATTATATATATGTAATATATATAATATATGTAATATATGTAATATATATTATATATGTAATATAATATATGTAATATATATTATATATGTAATATATAATATATGTAATATATAATATATGTAATATATATTATATATGTAATATATAATATATATTATATATGTAATATATATATATTTAAAAACAGAACCATTATCTTTTAGAGATACATACTGAAGTGTCTGGAGACATGCTTCAAGATAACCCAGGAGGGAGAATGGTAGAAGGAACTAGAGATGACCCAAGACTGCCCTTGAGCTAATAACTGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/msa.fa new file mode 100644 index 00000000..4c5e2abd --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/msa.fa @@ -0,0 +1,155 @@ +>ref_chr20_20320185_20320680 +atcctgattcagataaactgttaaacaaaaatctgtgccatttatgaggtgattggaaat +ttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcagtaaaga +tggtatttcagatatatagatatatatatattatatatatgtaatatatataatatatgt +aatatatattatatatatgtaatatatataatatatgta---------atatatgtaata +tatattatatatgtaatata----atatatgtaatatatattatatatgtaatatataat +atatgta----atatataatatatgtaatatatattatatatgtaatatataatatatat +tatatatgtaatatatatatatttaaaaacagaaccattatctttta-gagatacatact +gaagtgtctggagacatgcttcaagata-------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------acccaggagggagaatggtagaaggaact +agagatgacccaagactgcccttgagctaataactgt +>syndip_1_chr20:20320185-20320680 +atcctgattcagataaactgttaaacaaaaatctgtgccatttatgaggtgattggaaat +ttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcagtaaaga +tggtatttcagatatatag--atatatatattatatatatgtaatatatataatatatgt +a--atatattatatatatgtaatatatataatatatgtaatatattatatatatgtaata +tatataatatatgtaatatatattatatatgtaatatatataatatatgtaatatatatt +atatatgtaatatatataatatatgtaatatatattatatatgtaatatataatatatgt +aatatatattatatatgtaatataatatatgtaatatatattatatatgtaatatatatt +acatatattatatatgcaatatatattatatatattatatatgcaatatatattatatat +attatatatgcaatatatattatatatgcaatatatattatatatattatatatgcaata +tatattatatatattacatatgtaatatatattacatatgtaatatataatatattatat +attacatatgtaatatataatatattatatattacatatgtaatatataatatatattac +atatgtaatatataatatatattacatatgtaatatattatatattacatatgtaatata +ttatatattacatatgtaatatattatatattacatatgtaatatattatatattacata +tgtaatatattatatattacatatgtaatatatataatatattacatatgtaatatataa +tatattatatatgtaatatatattacatatataatatatataatatatatgtaatatatt +atatatattatatatgtaatatatattacatatataatatatattatatatattacatat +attatatatgtaatatatattacatatgtaatatatgtaatatatattacatatgtaata +tatattatatatgtaatatatattacatatattatatatgtaatatatattatatatatt +atatatgtaatgtataatatatatattatatatgtaatatatattatatataatatatgt +aatatatattatatatgtaatgtatattatatatattatatatgtaatgtatattatata +taatatatgtaatgtatattatatatgtaatatatattatgtatattatatatgtaatat +atattatatatattatatatgtaatatatattatatatattatatatgtaatatatatta +tatatattatatatgtaatatatattatatatattatatatgtaatatatattatatata +ttatatatgtaatatatattatatatattatatatgtaatatatattatatatattatat +atgtaatatatattatatatattatatatgtaatatatattatatatattatatatgtaa +tatatattatatatattatatatgtaatatatattatatatattatatatgtaatatata +ttatatatattatatatgtaatatatattatatatattatatatgtaatatatattatat +atattatatatgtaatatatatatatttaaaaacagaaccattatcttttagagatacat +actgaagtgtctggagacatgcttcaagataacccaggagggagaatggtagaaggaact +agagatgacccaagactgcccttgagctaataactgt +>syndip_2_chr20:20320185-20320680 +atcctgattcagataaactgttaaacaaaaatctgtgccatttatgaggtgattggaaat +ttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcagtaaaga +tggtatttcagatatatagatatatatatattatatatatgtaatatatataatatatgt +aatatatattatatatatgtaatatatataatatatgta---------atatatgtaata +tatattatatatgtaatata----atatatgtaatatatattatatatgtaatatataat +atatgta----atatataatatatgtaatatatattatatatgtaatatataatatatat +tatatatgtaatatatatatatttaaaaacagaaccattatctttta-gagatacatact +gaagtgtctggagacatgcttcaagata-------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------acccaggagggagaatggtagaaggaact +agagatgacccaagactgcccttgagctaataactgt +>p:HG002_1_chr20:20320185-20320680 +atcctgattcagataaactgttaaacaaaaatctgtgccatttatgaggtgattggaaat +ttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcagtaaaga +tggtatttcagatatatagatatatatatattatatatatgtaatatatataatatatgt +aatatatattatatatatgtaatatatataatatatgta---------atatatgtaata +tatattatatatgtaatata----atatatgtaatatatattatatatgtaatatataat +atatgta----atatataatatatgtaatatatattatatatgtaatatataatatatat +tatatatgtaatatatatatatttaaaaacagaaccattatctttta-gagatacatact +gaagtgtctggagacatgcttcaagata-------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------acccaggagggagaatggtagaaggaact +agagatgacccaagactgcccttgagctaataactgt +>p:HG002_2_chr20:20320185-20320680 +atcctgattcagataaactgttaaacaaaaatctgtgccatttatgaggtgattggaaat +ttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcagtaaaga +tggtatttcagatatatag--atatatatattatatatatgtaatatatataatatatgt +a--atatattatatatatgtaatatatataatatatgtaatatattatatatatgtaata +tatataatatatgtaatatatattatatatgtaatatatataatatatgtaatatatatt +atatatgtaatatatataatatatgtaatatatattatatatgtaatatataatatatgt +aatatatattatatatgtaatataatatatgtaatatatattatatatgtaatatatatt +acatatattatatatgcaatatatattatatatattatatatgcaatatatattatatat +attatatatgcaatatatattatatatgcaatatatattatatatattatatatgcaata +tatattatatatattacatatgtaatatatattacatatgtaatatataatatattatat +attacatatgtaatatataatatattatatattacatatgtaatatataatatatattac +atatgtaatatataatatatattacatatgtaatatattatatattacatatgtaatata +ttatatattacatatgtaatatattatatattacatatgtaatatattatatattacata +tgtaatatattatatattacatatgtaatatatataatatattacatatgtaatatataa +tatattatatatgtaatatatattacatatataatatatataatatatatgtaatatatt +atatatattatatatgtaatatatattacatatataatatatattatatatattacatat +attatatatgtaatatatattacatatgtaatatatgtaatatatattacatatgtaata +tatattatatatgtaatatatattacatatattatatatgtaatatatattatatatatt +atatatgtaatgtataatatatatattatatatgtaatatatattatatataatatatgt +aatatatattatatatgtaatgtatattatatatattatatatgtaatgtatattatata +taatatatgtaatgtatattatatatgtaatatatattatgtatattatatatgtaatat +atattatatatattatatatgtaatatatattatatatattatatatgtaatatatatta +tatatattatatatgtaatatatattatatatattatatatgtaatatatattatatata +ttatatatgtaatatatattatatatattatatatgtaatatatattatatatattatat +atgtaatatatattatatatattatatatgtaatatatattatatatattatatatgtaa +tatatattatatatattatatatgtaatatatattatatatattatatatgtaatatata +ttatatatattatatatgtaatatatattatatatattatatatgtaatatatattatat +atattatatatgtaatatatatatatttaaaaacagaaccattatcttttagagatacat +actgaagtgtctggagacatgcttcaagataacccaggagggagaatggtagaaggaact +agagatgacccaagactgcccttgagctaataactgt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/msa.fa.fai new file mode 100644 index 00000000..97aee165 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_20320185_20320680 1777 29 60 61 +syndip_1_chr20:20320185-20320680 1777 1870 60 61 +syndip_2_chr20:20320185-20320680 1777 3711 60 61 +p:HG002_1_chr20:20320185-20320680 1777 5553 60 61 +p:HG002_2_chr20:20320185-20320680 1777 7395 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/output.vcf.gz new file mode 100644 index 00000000..6303aae4 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/output.vcf.gz.tbi new file mode 100644 index 00000000..ba9ab787 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20320285-20320580/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/base.vcf.gz new file mode 100644 index 00000000..40fd5037 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/base.vcf.gz.tbi new file mode 100644 index 00000000..80f22c45 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/comp.vcf.gz new file mode 100644 index 00000000..3d7bcfa5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/comp.vcf.gz.tbi new file mode 100644 index 00000000..487fe341 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/haps.fa new file mode 100644 index 00000000..5bc69989 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/haps.fa @@ -0,0 +1,144 @@ +>ref_chr20_20337100_20337808 +TACGTGGAAGCATAGGGAAGGAAGGGATGTTTGTTGAGGGGTGGTGTGATGCAGCAGAGGAAGAGGACCAGAGGAAAGCAGCCACTGGAAATAAGGAAACAGGGTTTAGGAAGGCCTCACTAGACCTGTTAGGATGGATGCATGGATGGATGGATGGATGGACAGAATGGGTGGGTGGATGGATGGATGGATAGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGATGGATAAATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGGTGGATGGATGGATGGATGGATAGATGGGTGGGTGGGTGGATGGATGGATGGATGGATAGAATAAAAAAGAAAGCTAGGACATGGTTCTAGTGTTCTTAGCAGACGTCCCACCATGGAAGAGGTCATGGAGCACAGGGGCTTTGGGAAAGGTGTTTACAATCCTGCCTGCCTCTCACCCAGACCTCTTG +>syndip_1_chr20:20337100-20337808 +TACGTGGAAGCATAGGGAAGGAAGGGATGTTTGTTGAGGGGTGGTGTGATGCAGCAGAGG +AAGAGGACCAGAGGAAAGCAGCCACTGGAAATAAGGAAACAGGGTTTAGGAAGGCCTCAC +TAGACCTGTTAGGATGGATGCATGGATGGATGGATGGATGGACAGAATGGGTGGGTGGAT +GGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGAT +GGGTGGATGGATAGATGGGTGGATGGATAAATGGATGGATGGATGGATGGATAGATGGGT +GGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGATAGATGGGT +GGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGT +GGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATAGATGGGTGGATGGATAAATGGATGGATGGATGGAT +GGATAGATGTGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGAT +GGGTGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGT +GGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGAT +GGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGT +GGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATAGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +GGATGGATGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGT +GGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGGT +GGATGGATGGATGGATGGATGGATAGAATAAAAAGAAAGCTAGGACATGGTTCTAGTGTT +CTTAGCAGACGTCCCACCATGGAAGAGGTCATGGAGCACAGGGGCTTTGGGAAAGGTGTT +TACAATCCTGCCTGCCTCTCACCCAGACCTCTTG +>syndip_2_chr20:20337100-20337808 +TACGTGGAAGCATAGGGAAGGAAGGGATGTTTGTTGAGGGGTGGTGTGATGCAGCAGAGG +AAGAGGACCAGAGGAAAGCAGCCACTGGAAATAAGGAAACAGGGTTTAGGAAGGCCTCAC +TAGACCTGTTAGGATGGATGCATGGATGGATGGATGGATGGACAGAATGGGTGGGTGGAT +GGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGATGGATAAATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATGGATGGATGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGT +GGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGGTGGATGGATAAATGGATGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATAGATGGATAGATGGGTGGGT +GGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGATGGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGGTGGGTGGGTGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGGTGGATGGATGGAT +GGATGGATGGATAGAATAAAAAGAAAGCTAGGACATGGTTCTAGTGTTCTTAGCAGACGT +CCCACCATGGAAGAGGTCATGGAGCACAGGGGCTTTGGGAAAGGTGTTTACAATCCTGCC +TGCCTCTCACCCAGACCTCTTG +>p:HG002_1_chr20:20337100-20337808 +TACGTGGAAGCATAGGGAAGGAAGGGATGTTTGTTGAGGGGTGGTGTGATGCAGCAGAGG +AAGAGGACCAGAGGAAAGCAGCCACTGGAAATAAGGAAACAGGGTTTAGGAAGGCCTCAC +TAGACCTGTTAGGATGGATGCATGGATGGATGGATGGATGGACAGAATGGGTGGGTGGAT +GGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGATGGATAAATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATGGATGGATGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGT +GGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGGTGGATGGATAAATGGATGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATAGATGGATAGATGGGTGGGT +GGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGATGGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGGTGGGTGGGTGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGGTGGATGGATGGAT +GGATGGATGGATAGAATAAAAAGAAAGCTAGGACATGGTTCTAGTGTTCTTAGCAGACGT +CCCACCATGGAAGAGGTCATGGAGCACAGGGGCTTTGGGAAAGGTGTTTACAATCCTGCC +TGCCTCTCACCCAGACCTCTTG +>p:HG002_2_chr20:20337100-20337808 +TACGTGGAAGCATAGGGAAGGAAGGGATGTTTGTTGAGGGGTGGTGTGATGCAGCAGAGG +AAGAGGACCAGAGGAAAGCAGCCACTGGAAATAAGGAAACAGGGTTTAGGAAGGCCTCAC +TAGACCTGTTAGGATGGATGCATGGATGGATGGATGGATGGACAGAATGGGTGGGTGGAT +GGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGAT +GGGTGGATGGATAGATGGGTGGATGGATAAATGGATGGATGGATGGATGGATAGATGGGT +GGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGATAGATGGGT +GGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGT +GGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATAGATGGGTGGATGGATAAATGGATGGATGGATGGAT +GGATAGATGTGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGAT +GGGTGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGT +GGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGAT +GGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGT +GGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATAGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +GGATGGATGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGT +GGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGGT +GGATGGATGGATGGATGGATGGATAGAATAAAAAGAAAGCTAGGACATGGTTCTAGTGTT +CTTAGCAGACGTCCCACCATGGAAGAGGTCATGGAGCACAGGGGCTTTGGGAAAGGTGTT +TACAATCCTGCCTGCCTCTCACCCAGACCTCTTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/haps.fa.ref.fa new file mode 100644 index 00000000..5bb631b5 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:20337100-20337808 +TACGTGGAAGCATAGGGAAGGAAGGGATGTTTGTTGAGGGGTGGTGTGATGCAGCAGAGGAAGAGGACCAGAGGAAAGCAGCCACTGGAAATAAGGAAACAGGGTTTAGGAAGGCCTCACTAGACCTGTTAGGATGGATGCATGGATGGATGGATGGATGGACAGAATGGGTGGGTGGATGGATGGATGGATAGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGATGGATAAATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGGTGGATGGATGGATGGATGGATAGATGGGTGGGTGGGTGGATGGATGGATGGATGGATAGAATAAAAAAGAAAGCTAGGACATGGTTCTAGTGTTCTTAGCAGACGTCCCACCATGGAAGAGGTCATGGAGCACAGGGGCTTTGGGAAAGGTGTTTACAATCCTGCCTGCCTCTCACCCAGACCTCTTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/msa.fa new file mode 100644 index 00000000..11fabdd5 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/msa.fa @@ -0,0 +1,190 @@ +>ref_chr20_20337100_20337808 +tacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagagg +aagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctcac +tagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtggat +ggatggatggatagatggatggatggatggatggatggatggatggatggatggatggat +agatgggtgggtgg----gtggatgg----atggatggatggatggatggatggatggat +ggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtggat +ggatggatggatagatgggtgggtggatggatggatggatagatgggtggatggataaat +ggatggatggatggatggatagatgggtgggtggatggatggatggatggatggatggat +ggatggatagat------------------gtgggtggatggatggatggatagatgggt +gggtgggtggatggatggatggatggatagatgggtgggtgggtggatggatggatggat +ggatagaataaaaaagaaa----------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------gctaggacatggttctagtgtt +cttagcagacgtcccaccatggaagaggtcatggagcacaggggctttgggaaaggtgtt +tacaatcctgcctgcctctcacccagacctcttg +>syndip_1_chr20:20337100-20337808 +tacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagagg +aagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctcac +tagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtggat +ggatggatggatggatggatggatggatagatgggtgggtggatggatggatggatagat +gggtggatggatagatgggtggatggataaatggatggatggatggatggatagatgggt +gggtggatggatggatggatggatggatggatggatggatggatagatggatagatgggt +gggtggatggatggatggatggatggatggatggatggatggatagatgggtgggtggat +ggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggt 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+gggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggt +ggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt +gggtggatggatggatggatagatgggtgggtggatggatggatggatggatggatagat +ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat +ggatggatggatggatggatggatagatggatagatgggtgggtggatggatggatggat +agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat +ggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggat +ggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtggat +ggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggt +ggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtgggt +ggatggatggatggatggatggatagaataaaaagaaagctaggacatggttctagtgtt +cttagcagacgtcccaccatggaagaggtcatggagcacaggggctttgggaaaggtgtt +tacaatcctgcctgcctctcacccagacctcttg +>syndip_2_chr20:20337100-20337808 +tacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagagg +aagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctcac +tagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtggat +ggatggatggatggatggatggatggatggatagatgggtgggtggatggatggatggat +agatgggtggatggataaatggatgg----atggatggatggatagatgggtgggtggat +ggatggatggatggatggatggatggatggatggatagatggatagatgggtgggtggat +ggatggatggatggatggatggatggatggatggatggatggatagatgggtgggtggat +ggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggt +ggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggt +gggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat +gggtgggtggatggatggatggatagatgggtggatggataaatggatggatggatggat +ggatagatgggtgggtggatggatggatggatggatggatggatagatggataga----- +-----------tgggtgggtggatggatggatggatggatggatggatggatggatagat +gggtggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt +gggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat +gggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggat +agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat +ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat +agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat +ggatagatgggtgggtggatggatggatggatggatggatagatggatagatgggtgggt +ggatggatggatggatagatgggtggg----tggatggatggatggatggatggatggat +ggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggat +ggatggatggatagatggatagatgggtgggtggatggatggatggatagatggatagat +gggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggt +gggtggatggatggatggata--------------------gatggatagatgggtgggt +ggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt +gggtggatggatggatggatagatgggtgggtggatggatggatggataga--------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------tgggtgggtgggtggatggatggatagatgggtgggtggat +ggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggt +ggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtgggt +ggatggatggatggatggatggatagaataaaaagaaagctaggacatggttctagtgtt +cttagcagacgtcccaccatggaagaggtcatggagcacaggggctttgggaaaggtgtt +tacaatcctgcctgcctctcacccagacctcttg +>p:HG002_1_chr20:20337100-20337808 +tacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagagg +aagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctcac +tagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtggat +ggatggatggatggatggatggatggatggatagatgggtgggtggatggatggatggat +agatgggtggatggataaatggatgg----atggatggatggatagatgggtgggtggat +ggatggatggatggatggatggatggatggatggatagatggatagatgggtgggtggat +ggatggatggatggatggatggatggatggatggatggatggatagatgggtgggtggat +ggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggt +ggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggt +gggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat +gggtgggtggatggatggatggatagatgggtggatggataaatggatggatggatggat +ggatagatgggtgggtggatggatggatggatggatggatggatagatggataga----- +-----------tgggtgggtggatggatggatggatggatggatggatggatggatagat +gggtggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt +gggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat +gggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggat +agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat +ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat +agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat +ggatagatgggtgggtggatggatggatggatggatggatagatggatagatgggtgggt +ggatggatggatggatagatgggtggg----tggatggatggatggatggatggatggat +ggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggat +ggatggatggatagatggatagatgggtgggtggatggatggatggatagatggatagat +gggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggt +gggtggatggatggatggata--------------------gatggatagatgggtgggt +ggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt +gggtggatggatggatggatagatgggtgggtggatggatggatggataga--------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------tgggtgggtgggtggatggatggatagatgggtgggtggat +ggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggt +ggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtgggt +ggatggatggatggatggatggatagaataaaaagaaagctaggacatggttctagtgtt +cttagcagacgtcccaccatggaagaggtcatggagcacaggggctttgggaaaggtgtt +tacaatcctgcctgcctctcacccagacctcttg +>p:HG002_2_chr20:20337100-20337808 +tacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagagg +aagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctcac +tagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtggat +ggatggatggatggatggatggatggatagatgggtgggtggatggatggatggatagat +gggtggatggatagatgggtggatggataaatggatggatggatggatggatagatgggt +gggtggatggatggatggatggatggatggatggatggatggatagatggatagatgggt +gggtggatggatggatggatggatggatggatggatggatggatagatgggtgggtggat +ggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggt +ggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggt +gggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat +gggtgggtggatggatggatggatagatgggtggatggataaatggatggatggatggat +ggatagatgtgtgggtggatggatggatggatggatggatggatggatggatggatagat +ggatagatgggtgggtggatggatggatggatggatggatggatggatggatggatagat +gggtggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt +gggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat +gggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggat +agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat +ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat +agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat +ggatagatgggtgggtggatggatggatggatggatggatggatggatagatgggtgggt +ggatggatggatggatagatgggtgggtggatggatggatggatggatggatggatggat +ggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggat +ggatggatggatagatggatagatgggtgggtggatggatggatggatagatggatagat +gggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggt +gggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggt +ggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt +gggtggatggatggatggatagatgggtgggtggatggatggatggatggatggatagat +ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat +ggatggatggatggatggatggatagatggatagatgggtgggtggatggatggatggat +agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat +ggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggat +ggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtggat +ggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggt +ggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtgggt +ggatggatggatggatggatggatagaataaaaagaaagctaggacatggttctagtgtt +cttagcagacgtcccaccatggaagaggtcatggagcacaggggctttgggaaaggtgtt +tacaatcctgcctgcctctcacccagacctcttg diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/msa.fa.fai new file mode 100644 index 00000000..217590d1 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_20337100_20337808 2194 29 60 61 +syndip_1_chr20:20337100-20337808 2194 2294 60 61 +syndip_2_chr20:20337100-20337808 2194 4559 60 61 +p:HG002_1_chr20:20337100-20337808 2194 6825 60 61 +p:HG002_2_chr20:20337100-20337808 2194 9091 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/output.vcf.gz new file mode 100644 index 00000000..8c29abf2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/output.vcf.gz.tbi new file mode 100644 index 00000000..eb596a94 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20337200-20337708/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/base.vcf.gz new file mode 100644 index 00000000..13b3261f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/base.vcf.gz.tbi new file mode 100644 index 00000000..b91d893c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/comp.vcf.gz new file mode 100644 index 00000000..62bf632d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/comp.vcf.gz.tbi new file mode 100644 index 00000000..378ba51d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/haps.fa new file mode 100644 index 00000000..fd8e3a0a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/haps.fa @@ -0,0 +1,356 @@ +>ref_chr20_20354470_20358424 +TCCAGTCTGGGTGACAGAGAGAGACCTTGTCTCAAAAAAAAAAAAAAAAAATCAGGTACAGAAAGGTAAATACTGCACGATCTCACTTACATGTGGAATCTAAAGAAGTTGAATTCATAAGGGTAATGAGGGGAGGAAGGGGTGGTCATACTGTGTGAAGGGAGATAGTCACACTGAGGGAAGGTGGTCACACTGTGAGAAGGGAGGTAGTCACATTGTGAGAGAAAAAGTGATCACACTGTGTGAGGGGAGGTGGTCACACTGTGAGAGAAAAAGTAATCATACTGTGAAAGGGAGGTGGTCACGCTGAGAGGGGAGGTGGTCACACTGTGTCAGGGGAGGTGGTCACACTGTGAGAGAAAAAGTAATCACACTGTGAGGGGATGTGGTCACACTGAGAGGGGAGGTGGTCAGACTGTGTCAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAGATGGTCACACTGCAAGAGGGGAGGTGATCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACATTGTGAGAGGGAAGGGGGTCACTGTGAGAGGGGAGAAGGTCACACTAAGGGGAGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAGGAGGTGGTCACACTGTGAGGGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACTATGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGGGGTCACACTGTGAGGGGGAAGGTGGTCACACTGTGAGAGGGGAGAAGGTCACACTAAGGGGAGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAGGAGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACTATGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTAAGGGGAGGTGATCACACTGTGAGGGGACGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGACCACACAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGGGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGCTAGTCACACTGAGGGGAGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGCGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGCGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGAAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGGCACACTGTGAGGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTCACACTGTGAAAGAAGATGATCACAGTATGAGAGGTCATCCTTCAAGAGGCAAGTGCCCAAAAATCTGTTTATAATCTAGAGCAATATTTGCCTGAAATAAACTTTAAAAGTGGTTTTACGCTATTTAACCCAGTGTCAGA +>syndip_1_chr20:20354470-20358424 +TCCAGTCTGGGTGACAGAGAGAGACCTTGTCTCAAAAAAAAAAAAAAAAAATCAGGTACA +GAAAGGTAAATACTGCACGATCTCACTTACATGTGGAATCTAAAGAAGTTGAATTCATAA +GGGTAATGAGGGGAGGAAGGGGTGGTCATACTGTGTGAAGGGAGATGGTCACACTGAGGG +AAGGTGGTCACACTGTGAGAAGGGAGGTAGTCACATTGTGAGAGAAAAAGTGATCACACT +GTGTGAGGGGAGGTGGTCACACTGTGAGAGAAAAAGTAATCATACTGTGAAAGGGAGGTG +GTCACGCTGAGAGGGGAGGTGGTCACACTGTGTCAGGGGAGGTGGTCACACTGTGAGAGA +AAAAGTAATCACACTGTGAGGGGATGTGGTCACACTGAGAGGGGAGGTGGTCAGACTGTG +TCAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCAGA +CTCTGTCAGAGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAAGTGG +TCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAGATGGTCACACTGCAAGAGGGGA +GGTGATCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGAGA +GGGAAGGTGGTCACACTGTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACAT +TGTGAGAGGGAAGGGGGTCACTGTGAGAGGGGAGAAGGTCACACTAAGGGGAGGTAGTCA +CACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAGGAGGTGGTC +ACACTGTGAGGGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACT +ATGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACAC +TGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTACTCACA +CTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGAC +ACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGGGGTCACACTGTGAGGGGGAAGGTG +GTCACACTGTGAGAGGGGAGAAGGTCACACTAAGGGGAGGTAGTCACACTGTGAGGGGAG +GTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAGGAGGTGGTCACACTGTGAGGGGA +GGTCACACTGAGGGGAGGTAGTGACACTATGAGCAGAGATGGTCACACTGTGAGGGGAGG +TGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAG +GTGGTCACACTGAGGGGAGGTAGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGA +GGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGG +AGGGGGTCACACTGTGAGGGGGAAGGTGGTCACACTGTGAGAGGGGAGAAGGTCACACTA +AGGGGAGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGT +GAGAGGAGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACTATGA +GCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTG +AGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTCACACTGT +GAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTG +TGAGCAGAGATGGTCACACTGTAAGGGGAGGTGATCACACTGTGAGGGGACGTGGTCACA +CTGTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGACCACACAGGGGAGGTGGTCAC +ACTGAGGGGAGGTAGTGACACTGTGAGCAGAGGTGGTCACACTGTGAGGGGAGGTGGTCA +CACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCAC +ACTGAGGGGGGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCA +CACTGAGGGGAGGGGTCATACTGCGAGTGGAGGTGGTCACACTGTGAAGGGTGGTAGTCA +CACTGAGAGGAGGTGTTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAC +TGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACA +CTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACAC +TGAGGGGAGGTGGTCACAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGT +GTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACAC +TGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGA +GGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAG +GGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGG +GGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGG +GAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGG +AGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGG +TGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCATACTGTGAGTGAGG +AGGTAGTCACACTGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGG +GTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAG +GTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGA +GGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAG +GTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGAGGAGGTGGTCACACTGAGGGGAGG +TGGTCACAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAG +GTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGG +TGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGT +GGTCACAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGG +TGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGT +GGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGG +TAGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGGGG +TCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTG +GTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGG +TCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGT +CACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTC +ACAGTGTACGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGT +CACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTC +ACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCA +TAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCAT +AGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATA +GTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCAC +ACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACA +GTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCAC +ACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACA +CTGTGAGGGGAGGTGGTCACATTGAGGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCAC +ACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACA +CTGAGGAGAGGTGGTCATAGTGTGCGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAC +TGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACA +CTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAC +TGAGGGAAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCATAGT +GTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAG +TGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGGCACA +CTGTGAGGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACAC +TGAGGGGAGGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTCACACTG +AGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTCACACTGTG +AAAGAAGATGATCACAGTATGAGAGGTCATCCTTCAAGAGGCAAGTGCCCAAAAATCTGT +TTATAATCTAGAGCAATATTTGCCTGAAATAAACTTTAAAAGTGGTTTTACGCTATTTAA +CCCAGTGTCAGA +>syndip_2_chr20:20354470-20358424 +TCCAGTCTGGGTGACAGAGAGAGACCTTGTCTCAAAAAAAAAAAAAAAAAATCAGGTACA +GAAAGGTAAATACTGCACGATCTCACTTACATGTGGAATCTAAAGAAGTTGAATTCATAA +GGGTAATGAGGGGAGGAAGGGGTGGTCATACTGTGTGAAGGGAGATGGTCACACTGAGGG +AAGGTGGTCACACTGTGAGAAGGGAGGTAGTCACATTGTGAGAGAAAAAGTGATCACACT +GTGTGAGGGGAGGTGGTCACACTGTGAGAGAAAAAGTAATCATACTGTGAAAGGGAGGTG +GTCACGCTGAGAGGGGAGGTGGTCACACTGTGTCAGGGGAGGTGGTCACACTGTGAGAGA +AAAAGTAATCACACTGTGAGGGGATGTGGTCACACTGAGAGGGGAGGTGGTCAGACTGTG +TCAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCAGA +CTCTGTCAGAGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAAGTGG +TCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAGATGGTCACACTGCAAGAGGGGA +GGTGATCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGAGA +GGGAAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGTGAGGGGAGGTGGTCAC +ACTGTGAGGGGAGGTGGTCACATTGTGAGAGGGAAGGGGGTCACTGTGAGAGGGGAGAAG +GTCACACTAAGGGGAGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGG +TCACACTGTGAGAGGAGGTGGTCACACTGTGAGGGGTGGTCACACTGTGAGGGGAGGTCA +CACTGAGGGGAGGTAGTGACACTATGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTC +ACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGT +CACACTGAGGGGAGGTACTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGG +TCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGGG +GTCACACTGTGAGGGGGAAGGTGGTCACACTGTGAGAGGGGAGAAGGTCACACTAAGGGG +AGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAG +GAGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACTATGAGCAGA +GATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAG +AGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTCACACTGTGAGGG +GAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGC +AGAGATGGTCACACTGTAAGGGGAGGTGATCACACTGTGAGGGGACGTGGTCACACTGTG +AGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGACCACACAGGGGAGGTGGTCACACTGA +GGGGAGGTAGTGACACTGTGAGCAGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTG +TGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGA +GGGGGGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTG +AGGGGAGGGGTCATACTGCGAGTGGAGGTGGTCACACTGTGAAGGGTGGTAGTCACACTG +AGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGA +GGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAG +GGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGG +GGAGGTGGTCACAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGTGTGAG +GGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGG +GGAGGTGGTCACACTGTGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGA +GGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAG +GTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTG +GTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTC +ACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCA +CACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCAC +ACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACA +CTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTG +AGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAAGTGGTCACACT +GAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACAC +TGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACA +CTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTG +TGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACT +GAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTG +AGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGT +GAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTG +AGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGA +GGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAG +TGAGGAAGTAGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGG +GGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAGGGGGTCATACTGCG +AGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGA +GGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAG +GGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGA +GAGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTG +AGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGA +GTGAGGAGGTAGTCACACTGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTG +TGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGA +GGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTG +AGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGA +GGGGAGGTGGTCACAGTGTGCGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACAGTGTG +AGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGCGGGGAGGTGGTCACACTGA +GGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACACTGTG +AGGGGAGGTGGTCACACTGAGGAGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGA +GGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAG +GGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGTGA +GGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAG +GGGAGGTGGTGACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGG +GGAGGTGGTCACACTGTGAGGGGAGGTGGTCACATTGAGGAGAGGTGGTCATAGTGTGAG +GGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGG +GGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGG +GAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACAGTGTGAGG +GGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGG +GAGGTGGTCACACTGAGGGAAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGG +AGGTGGTCATAGTGTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGA +GAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGG +GGAGGTGGGCACACTGTGAGGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGG +GAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGA +GGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGG +TGGTCACACTGTGAAAGAAGATGATCACAGTATGAGAGGTCATCCTTCAAGAGGCAAGTG +CCCAAAAATCTGTTTATAATCTAGAGCAATATTTGCCTGAAATAAACTTTAAAAGTGGTT +TTACGCTATTTAACCCAGTGTCAGA +>p:HG002_1_chr20:20354470-20358424 +TCCAGTCTGGGTGACAGAGAGAGACCTTGTCTCAAAAAAAAAAAAAAAAAATCAGGTACA +GAAAGGTAAATACTGCACGATCTCACTTACATGTGGAATCTAAAGAAGTTGAATTCATAA +GGGTAATGAGGGGAGGAAGGGGTGGTCATACTGTGTGAAGGGAGATGGTCACACTGAGGG +AAGGTGGTCACACTGTGAGAAGGGAGGTAGTCACATTGTGAGAGAAAAAGTGATCACACT +GTGTGAGGGGAGGTGGTCACACTGTGAGAGAAAAAGTAATCATACTGTGAAAGGGAGGTG +GTCACGCTGAGAGGGGAGGTGGTCACACTGTGTCAGGGGAGGTGGTCACACTGTGAGAGA +AAAAGTAATCACACTGTGAGGGGATGTGGTCACACTGAGAGGGGAGGTGGTCAGACTGTG +TCAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCAGA +CTCTGTCAGAGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAAGTGG +TCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAGATGGTCACACTGCAAGAGGGGA +GGTGATCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGAGA +GGGAAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGTGAGGGGAGGTGGTCAC +ACTGTGAGGGGAGGTGGTCACATTGTGAGAGGGAAGGGGGTCACTGTGAGAGGGGAGAAG +GTCACACTAAGGGGAGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGG +TCACACTGTGAGAGGAGGTGGTCACACTGTGAGGGGTGGTCACACTGTGAGGGGAGGTCA +CACTGAGGGGAGGTAGTGACACTATGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTC +ACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGT +CACACTGAGGGGAGGTACTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGG +TCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGGG +GTCACACTGTGAGGGGGAAGGTGGTCACACTGTGAGAGGGGAGAAGGTCACACTAAGGGG +AGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAG +GAGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACTATGAGCAGA +GATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAG +AGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTCACACTGTGAGGG +GAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGC +AGAGATGGTCACACTGTAAGGGGAGGTGATCACACTGTGAGGGGACGTGGTCACACTGTG +AGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGACCACACAGGGGAGGTGGTCACACTGA +GGGGAGGTAGTGACACTGTGAGCAGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTG +TGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGA +GGGGGGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTG +AGGGGAGGGGTCATACTGCGAGTGGAGGTGGTCACACTGTGAAGGGTGGTAGTCACACTG +AGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGA +GGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAG +GGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGG +GGAGGTGGTCACAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGTGTGAG +GGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGG +GGAGGTGGTCACACTGTGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGA +GGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAG +GTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTG +GTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTC +ACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCA +CACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCAC +ACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACA +CTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTG +AGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAAGTGGTCACACT +GAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACAC +TGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACA +CTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTG +TGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACT +GAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTG +AGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGT +GAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTG +AGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGA +GGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAG +TGAGGAAGTAGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGG +GGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAGGGGGTCATACTGCG +AGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGA +GGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAG +GGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGA +GAGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTG +AGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGA +GTGAGGAGGTAGTCACACTGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTG +TGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGA +GGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTG +AGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGA +GGGGAGGTGGTCACAGTGTGCGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACAGTGTG +AGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGCGGGGAGGTGGTCACACTGA +GGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACACTGTG +AGGGGAGGTGGTCACACTGAGGAGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGA +GGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAG +GGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGTGA +GGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAG +GGGAGGTGGTGACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGG +GGAGGTGGTCACACTGTGAGGGGAGGTGGTCACATTGAGGAGAGGTGGTCATAGTGTGAG +GGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGG +GGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGG +GAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACAGTGTGAGG +GGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGG +GAGGTGGTCACACTGAGGGAAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGG +AGGTGGTCATAGTGTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGA +GAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGG +GGAGGTGGGCACACTGTGAGGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGG +GAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGA +GGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGG +TGGTCACACTGTGAAAGAAGATGATCACAGTATGAGAGGTCATCCTTCAAGAGGCAAGTG +CCCAAAAATCTGTTTATAATCTAGAGCAATATTTGCCTGAAATAAACTTTAAAAGTGGTT +TTACGCTATTTAACCCAGTGTCAGA +>p:HG002_2_chr20:20354470-20358424 +TCCAGTCTGGGTGACAGAGAGAGACCTTGTCTCAAAAAAAAAAAAAAAAAATCAGGTACA +GAAAGGTAAATACTGCACGATCTCACTTACATGTGGAATCTAAAGAAGTTGAATTCATAA +GGGTAATGAGGGGAGGAAGGGGTGGTCATACTGTGTGAAGGGAGATGGTCACACTGAGGG +AAGGTGGTCACACTGTGAGAAGGGAGGTAGTCACATTGTGAGAGAAAAAGTGATCACACT +GTGTGAGGGGAGGTGGTCACACTGTGAGAGAAAAAGTAATCATACTGTGAAAGGGAGGTG +GTCACGCTGAGAGGGGAGGTGGTCACACTGTGTCAGGGGAGGTGGTCACACTGTGAGAGA +AAAAGTAATCACACTGTGAGGGGATGTGGTCACACTGAGAGGGGAGGTGGTCAGACTGTG +TCAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCAGA +CTCTGTCAGAGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAAGTGG +TCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAGATGGTCACACTGCAAGAGGGGA +GGTGATCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGAGA +GGGAAGGTGGTCACACTGTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACAT +TGTGAGAGGGAAGGGGGTCACTGTGAGAGGGGAGAAGGTCACACTAAGGGGAGGTAGTCA +CACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAGGAGGTGGTC +ACACTGTGAGGGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACT +ATGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACAC +TGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTACTCACA +CTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGAC +ACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGGGGTCACACTGTGAGGGGGAAGGTG +GTCACACTGTGAGAGGGGAGAAGGTCACACTAAGGGGAGGTAGTCACACTGTGAGGGGAG +GTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAGGAGGTGGTCACACTGTGAGGGGA +GGTCACACTGAGGGGAGGTAGTGACACTATGAGCAGAGATGGTCACACTGTGAGGGGAGG +TGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAG +GTGGTCACACTGAGGGGAGGTAGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGA +GGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGG +AGGGGGTCACACTGTGAGGGGGAAGGTGGTCACACTGTGAGAGGGGAGAAGGTCACACTA +AGGGGAGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGT +GAGAGGAGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACTATGA +GCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTG +AGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTCACACTGT +GAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTG +TGAGCAGAGATGGTCACACTGTAAGGGGAGGTGATCACACTGTGAGGGGACGTGGTCACA +CTGTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGACCACACAGGGGAGGTGGTCAC +ACTGAGGGGAGGTAGTGACACTGTGAGCAGAGGTGGTCACACTGTGAGGGGAGGTGGTCA +CACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCAC +ACTGAGGGGGGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCA +CACTGAGGGGAGGGGTCATACTGCGAGTGGAGGTGGTCACACTGTGAAGGGTGGTAGTCA +CACTGAGAGGAGGTGTTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAC +TGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACA +CTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACAC +TGAGGGGAGGTGGTCACAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGT +GTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACAC +TGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGA +GGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAG +GGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGG +GGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGG +GAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGG +AGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGG +TGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCATACTGTGAGTGAGG +AGGTAGTCACACTGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGG +GTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAG +GTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGA +GGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAG +GTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGAGGAGGTGGTCACACTGAGGGGAGG +TGGTCACAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAG +GTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGG +TGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGT +GGTCACAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGG +TGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGT +GGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGG +TAGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGGGG +TCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTG +GTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGG +TCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGT +CACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTC +ACAGTGTACGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGT +CACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTC +ACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCA +TAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCAT +AGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATA +GTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCAC +ACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACA +GTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCAC +ACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACA +CTGTGAGGGGAGGTGGTCACATTGAGGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCAC +ACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACA +CTGAGGAGAGGTGGTCATAGTGTGCGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAC +TGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACA +CTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAC +TGAGGGAAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCATAGT +GTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAG +TGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGGCACA +CTGTGAGGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACAC +TGAGGGGAGGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTCACACTG +AGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTCACACTGTG +AAAGAAGATGATCACAGTATGAGAGGTCATCCTTCAAGAGGCAAGTGCCCAAAAATCTGT +TTATAATCTAGAGCAATATTTGCCTGAAATAAACTTTAAAAGTGGTTTTACGCTATTTAA +CCCAGTGTCAGA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/haps.fa.ref.fa new file mode 100644 index 00000000..53b76a9d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:20354470-20358424 +TCCAGTCTGGGTGACAGAGAGAGACCTTGTCTCAAAAAAAAAAAAAAAAAATCAGGTACAGAAAGGTAAATACTGCACGATCTCACTTACATGTGGAATCTAAAGAAGTTGAATTCATAAGGGTAATGAGGGGAGGAAGGGGTGGTCATACTGTGTGAAGGGAGATAGTCACACTGAGGGAAGGTGGTCACACTGTGAGAAGGGAGGTAGTCACATTGTGAGAGAAAAAGTGATCACACTGTGTGAGGGGAGGTGGTCACACTGTGAGAGAAAAAGTAATCATACTGTGAAAGGGAGGTGGTCACGCTGAGAGGGGAGGTGGTCACACTGTGTCAGGGGAGGTGGTCACACTGTGAGAGAAAAAGTAATCACACTGTGAGGGGATGTGGTCACACTGAGAGGGGAGGTGGTCAGACTGTGTCAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAGATGGTCACACTGCAAGAGGGGAGGTGATCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACATTGTGAGAGGGAAGGGGGTCACTGTGAGAGGGGAGAAGGTCACACTAAGGGGAGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAGGAGGTGGTCACACTGTGAGGGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACTATGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGGGGTCACACTGTGAGGGGGAAGGTGGTCACACTGTGAGAGGGGAGAAGGTCACACTAAGGGGAGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAGGAGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACTATGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTAAGGGGAGGTGATCACACTGTGAGGGGACGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGACCACACAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGGGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGCTAGTCACACTGAGGGGAGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGCGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGCGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGAAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGGCACACTGTGAGGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTCACACTGTGAAAGAAGATGATCACAGTATGAGAGGTCATCCTTCAAGAGGCAAGTGCCCAAAAATCTGTTTATAATCTAGAGCAATATTTGCCTGAAATAAACTTTAAAAGTGGTTTTACGCTATTTAACCCAGTGTCAGA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/msa.fa new file mode 100644 index 00000000..3f977e3f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/msa.fa @@ -0,0 +1,475 @@ +>ref_chr20_20354470_20358424 +tccagtctgggtgacagagagagaccttgtctcaaaaaaaaaaaaaaaaaatcaggtaca +gaaaggtaaatactgcacgatctcacttacatgtggaatctaaagaagttgaattcataa +gggtaatgaggggaggaaggggtggtcatactgtgtgaagggagatagtcacactgaggg +aaggtggtcacactgtgagaagggaggtagtcacattgtgagagaaaaagtgatcacact +gtgtgaggggaggtggtcacactgtgagagaaaaagtaatcatactgtgaaagggaggtg +gtcacgctgagaggggaggtggtcacactgtgtcaggggaggtggtcacactgtgagaga +aaaagtaatcacactgtgaggggatgtggtcacactgagaggggaggtggtcagactgtg +tcagaggaggtggtcacactgagg------------------------------------ +----------ggaggtggtcacactgtgagaggggaggtggtcacactgaggggaagtgg +tcacactgtgagaggggaggtggtcacactgaggggagatggtcacactgcaagagggga +ggtgatcacactgagggg-----------------------aggtggtcacactgtgaga +gggaaggtggtcacactgtgagagggaaggtggtcacactgtgtgaggggaggtggtcac +actgtgaggggaggtggtcacattgtgagagggaagggggtcactgtgagaggggagaag +gtcacactaaggggaggtagtcacactgtgaggggaggtgatcacactaaggggaggtgg +tcacactgtgagaggaggtggtcacactgtgaggggtggtcacactgtgaggggaggtca +cactgaggggaggtagtgacactatgagcagagatggtcacactgtgaggggaggtggtc +acactgaggggaggtagtgacactgtgagcagagatggtcacactgtgaggggaggtggt +cacactgaggggagg--------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---tggtcacactgtgaggggaggtggtcacactgaggggaggtggtcacactgtgaggg +gaggtggtcacactgtgaggggaggtggtcacactgaggggaggtagtgacactgtgagc +agagatggtcacactgtgaggggagggggtcacactgtgagggggaaggtggtcacactg +tgagaggggagaaggtcacactaaggggaggtagtcacactgtgaggggaggtgatcaca +ctaaggggaggtggtcacactgtgagaggaggtggtcacactgtgaggggaggtcacact +gaggggaggtagtgacactatgagcagagatggtcacactgtgaggggaggtggtcacac +tgaggggaggtagtgacactgtgagcagagatggtcacactgtgaggggaggtggtcaca +ctgaggggaggtagtcacactgtgaggggaggtggtcacactgtgaggggaggtggtcac +actgaggggaggtagtgacactgtgagcagagatggtcacactgtaaggggaggtgatca +cactgtgaggggac---gtcacactgtgaggggaggtggtcacactgtgagaggggaggt +gaccacacaggggaggtggtcacactgaggggaggtagtgacactgtgagcagagatggt +cacactgtgaggggaggtggtcacac--tgaggggaggtagtcacactgagaggaggtgg +tcacactgaggggaagtggtcacactgagggggggtggtcacactgaggggaggtggtca +tactgtgagtgaggagctagtcacactgaggggaggggtcatactgcgagtggaggtagt +cacactgtgaagggtggtagtcacactgagaggaggtggtcacactgaggggaagtggtc +acactgaggggaggtggtcatactgtgaggggaagtggtcacactgaggggaggtggtca +tagtgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcac +agtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggagatggtca +cactgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcat +agtgtgaggggaggtggtcacactggggaggtggtcacactgtgaggggaggtggtcaca +ctgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcatagtg +tgaggggaggtggtcacact----ggggaggtggtcacactgtgaggggaggtggtcaca +ctgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcacactg +aggggaggtggtcatagtgtgaggggaggtggtcacact--------------------- +ggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcacactgag +gggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtgtgagg +ggaggtggtcacac------tggggaggtggtcacactgtgaggggaggtggtcacactg +tgaggggaggtggtcacac--tgagaggaggtggtcacactgaggggaagtggtcacact +gagaggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaggtagtcacac +tgaggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatactgt +gagtgaggaggtagtcacactgaggggagggggtcatactgcgagtggaggtagtcacac +tgtgaagggtggtagtcacactgagaggaggtggtcaca--ctgaggggaagtggtcaca +ctgaggggaggtggtcatactgtgaggggaagtggtcacactgaggggaggtggtcatag +tgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcaca +ctgaggggaggtggtcaca----------------------------------------- +------------------------------------------------------------ +---------------------------------------------------------gtg +tgcggggaggtggtcatactgaggggaggtggtcacactgaggggaggtggtcacactga +ggggaggtggtcatactgtgagt------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------gaggaggtagtcacactgaggggagggggtcatact +gcgagtggaggtagtcacactgtgaagggtggtagtcaca--ctgagaggaggtggtcac +actgaggggaagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtcaca +ctgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacag +tgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgcggggaggtggtcat- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------actgaggggaggtggtcacagtgtg +aggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcatagtgt +gaggggaggtggtcacactgaggggaggtggtcacactgagggaaggtggtcacactgag +gggaggtggtcatagtgtgaggggaggtggtcatagtgtgaggggaggtggtcacagtgt +gaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcacactg +aggggaggtggtcacactgtgaggggaggtgggcacactgtgaggggtggtagtcacact +gagaggaggtggtcacactgaggggaggtggtcacactgaggggaagtggtcacactgag +gggaatggtcatactgtgaggggaggtggtcacactgaggggaagtggtcacactgaggg +gaatggtcatactgtgaggggaggtggtcacactgtgaaagaagatgatcacagtatgag +aggtcatccttcaagaggcaagtgcccaaaaatctgtttataatctagagcaatatttgc +ctgaaataaactttaaaagtggttttacgctatttaacccagtgtcaga +>syndip_1_chr20:20354470-20358424 +tccagtctgggtgacagagagagaccttgtctcaaaaaaaaaaaaaaaaaatcaggtaca +gaaaggtaaatactgcacgatctcacttacatgtggaatctaaagaagttgaattcataa +gggtaatgaggggaggaaggggtggtcatactgtgtgaagggagatggtcacactgaggg +aaggtggtcacactgtgagaagggaggtagtcacattgtgagagaaaaagtgatcacact +gtgtgaggggaggtggtcacactgtgagagaaaaagtaatcatactgtgaaagggaggtg +gtcacgctgagaggggaggtggtcacactgtgtcaggggaggtggtcacactgtgagaga +aaaagtaatcacactgtgaggggatgtggtcacactgagaggggaggtggtcagactgtg +tcagaggaggtggtcacactgaggggaggtggtcacactgtgagaggggaggtggtcaga +ctctgtcagaggaggtggtcacactgtgagaggggaggtggtcacactgaggggaagtgg +tcacactgtgagaggggaggtggtcacactgaggggagatggtcacactgcaagagggga 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+aggtcatccttcaagaggcaagtgcccaaaaatctgtttataatctagagcaatatttgc +ctgaaataaactttaaaagtggttttacgctatttaacccagtgtcaga +>p:HG002_2_chr20:20354470-20358424 +tccagtctgggtgacagagagagaccttgtctcaaaaaaaaaaaaaaaaaatcaggtaca +gaaaggtaaatactgcacgatctcacttacatgtggaatctaaagaagttgaattcataa +gggtaatgaggggaggaaggggtggtcatactgtgtgaagggagatggtcacactgaggg +aaggtggtcacactgtgagaagggaggtagtcacattgtgagagaaaaagtgatcacact +gtgtgaggggaggtggtcacactgtgagagaaaaagtaatcatactgtgaaagggaggtg +gtcacgctgagaggggaggtggtcacactgtgtcaggggaggtggtcacactgtgagaga +aaaagtaatcacactgtgaggggatgtggtcacactgagaggggaggtggtcagactgtg +tcagaggaggtggtcacactgaggggaggtggtcacactgtgagaggggaggtggtcaga +ctctgtcagaggaggtggtcacactgtgagaggggaggtggtcacactgaggggaagtgg +tcacactgtgagaggggaggtggtcacactgaggggagatggtcacactgcaagagggga +ggtgatcacactgagggg-----------------------aggtggtcacactgtgaga +gggaaggtggtcacactgtgagagggaaggtggtcacactgtgtgaggggaggtggtcac +actgtgaggggaggtggtcacattgtgagagggaagggggtcactgtgagaggggagaag +gtcacactaaggggaggtagtcacactgtgaggggaggtgatcacactaaggggaggtgg +tcacactgtgagaggaggtggtcacactgtgaggggtggtcacactgtgaggggaggtca +cactgaggggaggtagtgacactatgagcagagatggtcacactgtgaggggaggtggtc +acactgaggggaggtagtgacactgtgagcagagatggtcacactgtgaggggaggtggt +cacactgaggggaggtactcacactgtgaggggaggtggtcacactgtgaggggaggtgg +tcacactgaggggaggtagtgacactgtgagcagagatggtcacactgtgaggggagggg +gtcacactgtgagggggaaggtggtcacactgtgagaggggagaaggtcacactaagggg +aggtagtcacactgtgaggggaggtgatcacactaaggggaggtggtcacactgtgagag +gaggtggtcacactgtgaggggaggtcacactgaggggaggtagtgacactatgagcaga +gatggtcacactgtgaggggaggtggtcacactgaggggaggtagtgacactgtgagcag +agatggtcacactgtgaggggaggtggtcacactgaggggaggtagtcacactgtgaggg +gaggtggtcacactgtgaggggaggtggtcacactgaggggaggtagtgacactgtgagc +agagatggtcacactgtgaggggagggggtcacactgtgagggggaaggtggtcacactg +tgagaggggagaaggtcacactaaggggaggtagtcacactgtgaggggaggtgatcaca +ctaaggggaggtggtcacactgtgagaggaggtggtcacactgtgaggggaggtcacact +gaggggaggtagtgacactatgagcagagatggtcacactgtgaggggaggtggtcacac +tgaggggaggtagtgacactgtgagcagagatggtcacactgtgaggggaggtggtcaca +ctgaggggaggtagtcacactgtgaggggaggtggtcacactgtgaggggaggtggtcac +actgaggggaggtagtgacactgtgagcagagatggtcacactgtaaggggaggtgatca +cactgtgaggggacgtggtcacactgtgaggggaggtggtcacactgtgagaggggaggt +gaccacacaggggaggtggtcacactgaggggaggtagtgacactgtgagcagaggtggt +cacactgtgaggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtgg +tcacactgaggggaagtggtcacactgagggggggtggtcacactgaggggaggtggtca +tactgtgagtgaggaggtagtcacactgaggggaggggtcatactgcgagtggaggtggt +cacactgtgaagggtggtagtcacactgagaggaggtgttcacactgaggggaagtggtc +acactgaggggaggtggtcatactgtgaggggaagtggtcacactgaggggaggtggtca +tagtgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcac +agtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggagatggtca +cactgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcat +agtgtgaggggaggtggtcacactggggaggtggtcacactgtgaggggaggtggtcaca +ctgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcaca--c +tgaggggaggtggtcatagtgtgaggggaggtggtcacactgtgaggggaggtggtcaca +ctgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcacactg +aggggaggtggtcatagtgtgaggggaggtggtcacactggggaggtggtcacactgtga +ggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcacactgag +gggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagtgtgagg +ggaggtggtcatactgtgagtgaggaggtagtcacac--tgaggggagggggtcatactg +cgagtggaggtagtcacactgtgaagggtggtagtcacactgagaggaggtggtcacact +gaggggaagtggtcacactgaggggaggtggtcatactg--------------------- +-------------------tgaggggaagtggtcacactgaggggaggtggtcatagtgt +ga--ggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacac +--tgaggggaggtggtcacactgaggggaggtggtcacagtgtgagaggaggtggtcaca +ctgaggggaggtggtcacagtgtgaggggagatggtcacactgaggggaggtggtcacag +tgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcaca +ctgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacac +tgaggggaggtggtcacagtgtgaggggagatggtcacactgaggggaggtggtcacagt +gtgaggggaggtggtcacactgaggggaggtggtcaca-------------------gtg +tgaggggaggtggtcacactgaggggaggtggtcacactgagaggaggtggtcacactga +ggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggaagtggtcacactg +aggggaggtg------------------------------------------gtcacact +gaggggagggggtcatactgcgagtggaggtagtcacactgtgaagggtggtagtcacac +tgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcatactgt +gaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggag------------ +------------------------------------------------------------ +-----------------------------gtggtcacactgaggggaggtggtcacactg +aggggaggtggtcacagtgtga--ggggaggtggtcacactgaggggaggtggtcacagt +gtacggggaggtggtcatac--tgaggggaggtggtcacagtgtgaggggaggtggtcac +actgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcaca +ctgaggggaggtggtcacactgtgaggggaggtggtcacactgaggagaggtggtcatag +tgtgaggggaggtggtcacactgaggggaggtggtcaca-c-tgaggagaggtggtcat- +------------------agtgtgaggggaggtggtcacac------------------- +------------------------------------------------------------ +----------------------tgaggggaggtggtcacactgaggggaggtggtcatag +tgtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcaca +ctgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacag +tg--------------------------------------tgaggggaggtggtcacact +gaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactg +aggggaggtggtcatagtgtgaggggaggtggtcacactgtgaggggaggtggtcacatt +gaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactg +aggggaggtggtcatagtgtgaggggaggtggtcacactgaggagaggtggtcatagtgt +gcggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagtgtg +aggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcatagtgt +gaggggaggtggtcacactgaggggaggtggtcacactgagggaaggtggtcacactgag +gggaggtggtcatagtgtgaggggaggtggtcatagtgtgaggggaggtggtcacagtgt +gaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcacactg +aggggaggtggtcacactgtgaggggaggtgggcacactgtgaggggtggtagtcacact +gagaggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacactgag +gggaatggtcatactgtgaggggaggtggtcacactgaggggaagtggtcacactgaggg +gaatggtcatactgtgaggggaggtggtcacactgtgaaagaagatgatcacagtatgag +aggtcatccttcaagaggcaagtgcccaaaaatctgtttataatctagagcaatatttgc +ctgaaataaactttaaaagtggttttacgctatttaacccagtgtcaga diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/msa.fa.fai new file mode 100644 index 00000000..5edf4419 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_20354470_20358424 5629 29 60 61 +syndip_1_chr20:20354470-20358424 5629 5786 60 61 +syndip_2_chr20:20354470-20358424 5629 11543 60 61 +p:HG002_1_chr20:20354470-20358424 5629 17301 60 61 +p:HG002_2_chr20:20354470-20358424 5629 23059 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/output.vcf.gz new file mode 100644 index 00000000..6e8723cd Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/output.vcf.gz.tbi new file mode 100644 index 00000000..4e1eef77 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:20354570-20358324/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/base.vcf.gz new file mode 100644 index 00000000..a116ff6a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/base.vcf.gz.tbi new file mode 100644 index 00000000..5573d489 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/comp.vcf.gz new file mode 100644 index 00000000..0586215b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/comp.vcf.gz.tbi new file mode 100644 index 00000000..451e406c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/haps.fa new file mode 100644 index 00000000..02d0d23a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/haps.fa @@ -0,0 +1,34 @@ +>ref_chr20_21120112_21120640 +ACAGACTGAGACTTTGTCTTAAAATCAAATTAATTTAATTTAAAAAACAAATGCCTTTGAGCAAAGTGCTGTTAGTAACCTCATGTCTTCCTGTATTCATCAGGGTTCTTCAGAGAAACAGAACCAGTAGGACACACACACACGCACACACACACACGTGTGTGTATATATATGTGTGTATGTATATATATATATATATTTATATATATATATATTTATATATATATATTTATATATATATATTTATATATATATATATTTATATATATATATTTATATATATATATTTATATATATATATATTTATATATATATATATTTATATATATATATTTATATATATATATATTTATATATATATATTTATATATATATATATTTATATGGAGAGAGAGAGATTTATTTTTAGGAAGTGGTTCATGAGATTGTGAGGGACTTCATTCTTTTCTCCTAAGGCCTTCAACTGACTGGATGAGGCCCATCCACATTTTGGAGAGCAGTCTACTTTCCTCAAAGCCTACTGCTTCAA +>syndip_1_chr20:21120112-21120640 +ACAGACTGAGACTTTGTCTTAAAATCAAATTAATTTAATTTAAAAAACAAATGCCTTTGA +GCAAAGTGCTGTTAGTAACCTCATGTCTTCCTGTATTCATCAGGGTTCTTCAGAGAAACA +GAACCAGTAGGACACACACACACGCACACACACACACGTGTGTGTATATATATGTGTGTA +TGTATATATATATATATATATTTATATATATATATATATTTATATATATATATATTTATA +TATATATATATATATATGGAGAGAGAGAGATTTATTTTTAGGAAGTGGTTCATGAGATTG +TGAGGGACTTCATTCTTTTCTCCTAAGGCCTTCAACTGACTGGATGAGGCCCATCCACAT +TTTGGAGAGCAGTCTACTTTCCTCAAAGCCTACTGCTTCAA +>syndip_2_chr20:21120112-21120640 +ACAGACTGAGACTTTGTCTTAAAATCAAATTAATTTAATTTAAAAAACAAATGCCTTTGA +GCAAAGTGCTGTTAGTAACCTCATGTCTTCCTGTATTCATCAGGGTTCTTCAGAGAAACA +GAACCAGTAGGACACACACACACGCACACACACACACGTGTGTGTATATATATGTGTGTA +TGTATATATATATATATATATTTATATATATATATATATTTATATATATATATATATATT +TATATATATATATATATATATGGAGAGAGAGAGATTTATTTTTAGGAAGTGGTTCATGAG +ATTGTGAGGGACTTCATTCTTTTCTCCTAAGGCCTTCAACTGACTGGATGAGGCCCATCC +ACATTTTGGAGAGCAGTCTACTTTCCTCAAAGCCTACTGCTTCAA +>p:HG002_1_chr20:21120112-21120640 +ACAGACTGAGACTTTGTCTTAAAATCAAATTAATTTAATTTAAAAAACAAATGCCTTTGA +GCAAAGTGCTGTTAGTAACCTCATGTCTTCCTGTATTCATCAGGGTTCTTCAGAGAAACA +GAACCAGTAGGACACACACACACGCACACACACACACGTGTGTGTATATATATGTGTGTA +TGTATATATATATATATATATTTATATATATATATATATTTATATATATATATATATATT +TATATATATATATATATATATGGAGAGAGAGAGATTTATTTTTAGGAAGTGGTTCATGAG +ATTGTGAGGGACTTCATTCTTTTCTCCTAAGGCCTTCAACTGACTGGATGAGGCCCATCC +ACATTTTGGAGAGCAGTCTACTTTCCTCAAAGCCTACTGCTTCAA +>p:HG002_2_chr20:21120112-21120640 +ACAGACTGAGACTTTGTCTTAAAATCAAATTAATTTAATTTAAAAAACAAATGCCTTTGA +GCAAAGTGCTGTTAGTAACCTCATGTCTTCCTGTATTCATCAGGGTTCTTCAGAGAAACA +GAACCAGTAGGACACACACACACGCACACACACACACGTGTGTGTATATATATGTGTGTA +TGTATATATATATATATATATTTATATATATATATATATTTATATATATATATATTTATA +TATATATATATATATATGGAGAGAGAGAGATTTATTTTTAGGAAGTGGTTCATGAGATTG +TGAGGGACTTCATTCTTTTCTCCTAAGGCCTTCAACTGACTGGATGAGGCCCATCCACAT +TTTGGAGAGCAGTCTACTTTCCTCAAAGCCTACTGCTTCAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/haps.fa.ref.fa new file mode 100644 index 00000000..eb28f31d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:21120112-21120640 +ACAGACTGAGACTTTGTCTTAAAATCAAATTAATTTAATTTAAAAAACAAATGCCTTTGAGCAAAGTGCTGTTAGTAACCTCATGTCTTCCTGTATTCATCAGGGTTCTTCAGAGAAACAGAACCAGTAGGACACACACACACGCACACACACACACGTGTGTGTATATATATGTGTGTATGTATATATATATATATATTTATATATATATATATTTATATATATATATTTATATATATATATTTATATATATATATATTTATATATATATATTTATATATATATATTTATATATATATATATTTATATATATATATATTTATATATATATATTTATATATATATATATTTATATATATATATTTATATATATATATATTTATATGGAGAGAGAGAGATTTATTTTTAGGAAGTGGTTCATGAGATTGTGAGGGACTTCATTCTTTTCTCCTAAGGCCTTCAACTGACTGGATGAGGCCCATCCACATTTTGGAGAGCAGTCTACTTTCCTCAAAGCCTACTGCTTCAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/msa.fa new file mode 100644 index 00000000..52ea3338 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/msa.fa @@ -0,0 +1,50 @@ +>ref_chr20_21120112_21120640 +acagactgagactttgtcttaaaatcaaattaatttaatttaaaaaacaaatgcctttga +gcaaagtgctgttagtaacctcatgtcttcctgtattcatcagggttcttcagagaaaca +gaaccagtaggacacacacacacgcacacacacacacgtgtgtgtatatatatgtgtgta +tgtatatatatatatatatttatatatatatatatttatatatatatatttatatatata +tatttatatatatatatatttatatatatatatttatatatatatatttatatatatata +tatttatatatatatatatttatatatatatatttatatatatatatatttatatatata +tatttatatatatatatatttatatggagagagagagatttatttttaggaagtggttca +tgagattgtgagggacttcattcttttctcctaaggccttcaactgactggatgaggccc +atccacattttggagagcagtctactttcctcaaagcctactgcttcaa +>syndip_1_chr20:21120112-21120640 +acagactgagactttgtcttaaaatcaaattaatttaatttaaaaaacaaatgcctttga +gcaaagtgctgttagtaacctcatgtcttcctgtattcatcagggttcttcagagaaaca +gaaccagtaggacacacacacacgcacacacacacacgtgtgtgtatatatatgtgtgta +tgtatatatatatata-------------------------------------------- +------------------------------------------------------------ +--------------------tatatttatatatatatatatatt----tatatatatata +tatttatatatatatatatatatatggagagagagagatttatttttaggaagtggttca +tgagattgtgagggacttcattcttttctcctaaggccttcaactgactggatgaggccc +atccacattttggagagcagtctactttcctcaaagcctactgcttcaa +>syndip_2_chr20:21120112-21120640 +acagactgagactttgtcttaaaatcaaattaatttaatttaaaaaacaaatgcctttga +gcaaagtgctgttagtaacctcatgtcttcctgtattcatcagggttcttcagagaaaca +gaaccagtaggacacacacacacgcacacacacacacgtgtgtgtatatatatgtgtgta +tgtatatatatatata-------------------------------------------- +------------------------------------------------------------ +--------------------tatatttatatatatatatatatttatatatatatatata +tatttatatatatatatatatatatggagagagagagatttatttttaggaagtggttca +tgagattgtgagggacttcattcttttctcctaaggccttcaactgactggatgaggccc +atccacattttggagagcagtctactttcctcaaagcctactgcttcaa +>p:HG002_1_chr20:21120112-21120640 +acagactgagactttgtcttaaaatcaaattaatttaatttaaaaaacaaatgcctttga +gcaaagtgctgttagtaacctcatgtcttcctgtattcatcagggttcttcagagaaaca +gaaccagtaggacacacacacacgcacacacacacacgtgtgtgtatatatatgtgtgta +tgtatatatatatata-------------------------------------------- +------------------------------------------------------------ +--------------------tatatttatatatatatatatatttatatatatatatata +tatttatatatatatatatatatatggagagagagagatttatttttaggaagtggttca +tgagattgtgagggacttcattcttttctcctaaggccttcaactgactggatgaggccc +atccacattttggagagcagtctactttcctcaaagcctactgcttcaa +>p:HG002_2_chr20:21120112-21120640 +acagactgagactttgtcttaaaatcaaattaatttaatttaaaaaacaaatgcctttga +gcaaagtgctgttagtaacctcatgtcttcctgtattcatcagggttcttcagagaaaca +gaaccagtaggacacacacacacgcacacacacacacgtgtgtgtatatatatgtgtgta +tgtatatatatatata-------------------------------------------- +------------------------------------------------------------ +--------------------tatatttatatatatatatatatt----tatatatatata +tatttatatatatatatatatatatggagagagagagatttatttttaggaagtggttca +tgagattgtgagggacttcattcttttctcctaaggccttcaactgactggatgaggccc +atccacattttggagagcagtctactttcctcaaagcctactgcttcaa diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/msa.fa.fai new file mode 100644 index 00000000..1d0b7fc1 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_21120112_21120640 529 29 60 61 +syndip_1_chr20:21120112-21120640 529 601 60 61 +syndip_2_chr20:21120112-21120640 529 1173 60 61 +p:HG002_1_chr20:21120112-21120640 529 1746 60 61 +p:HG002_2_chr20:21120112-21120640 529 2319 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/output.vcf.gz new file mode 100644 index 00000000..2e46be01 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/output.vcf.gz.tbi new file mode 100644 index 00000000..4ba395ca Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21120212-21120540/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/base.vcf.gz new file mode 100644 index 00000000..f65fae20 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/base.vcf.gz.tbi new file mode 100644 index 00000000..1e3803c0 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/comp.vcf.gz new file mode 100644 index 00000000..9ea2cb6a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/comp.vcf.gz.tbi new file mode 100644 index 00000000..3c73a629 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/haps.fa new file mode 100644 index 00000000..412dd99e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/haps.fa @@ -0,0 +1,92 @@ +>ref_chr20_21721074_21721836 +AGTAGGGACTTGCTTTGGGTCACAGTCAGCTTTTATTAGTGTTATTATTGTTGCTGTTTTCTTCTTTTTCTTTGTACATCAACGTTTTATGGTGAATTAAATCGTGTTTTAACCTTGTAGACCACATTGGCTATTACATATATATATATAATATATATGTAATATATATATGTAATGTATATTATATATGTAATGTATATAATATATGTAATGTATATAATATATATGTAATACATATATATTATATATGTATATAATACATATATATGTATATATATGTATGTATATATATATGTATATATGTATATATATATGTATATAATACATATATATACATATATATTATATATGTAATACATATATAATATATATGTAATGTATATATATGTAATGTATATAATATATATGTAATACATATATAATATATATGTAATGTATATTATATATGTAATGTATATAATATGTATGTAATACATATATTATATATGTAATGTATATTATATATGTATTACATATATGTATTACATATATAACATATATGTATTACATATATGTATTACATATATAACATATATGTATTACATATATGTAATACACATATAATATATATGTTATATATATATATATATATAAAATTTTTTAAAAAATTGTTTCTTGAGATAGGGTCTCACTCTGTCACCCAGGCTGGAGTATAATGGTTTGATCATAGTTCACTGCAGCCTTGAACTTCTAGACTCAGGTGATCCTCCCACCTCAACCTCCT +>syndip_1_chr20:21721074-21721836 +AGTAGGGACTTGCTTTGGGTCACAGTCAGCTTTTATTAGTGTTATTATTGTTGCTGTTTT +CTTCTTTTTCTTTGTACATCAACGTTTTATGGTGAATTAAATCGTGTTTTAACCTTGTAG +ACCACATTGGCTATTACATATATATATATAATATATATGTAATATATATATGTAATGTAT +ATTATATATGTAATGTATATAATATATGTAATGTATATAATATATATGTAATACATATAT +ATTATATATGTATATAATACATATATATGTATATATATGTATGTATATATATATGTATAT +ATGTATATATATATGTATATAATACATATATATACATATATATTATATATGTAATACATA +TATAATATATATGTAATGTATATATATGTAATGTATATAATATATATGTAATACATATAT +AATATATATGTAATGTATATAATATATATGTAATACATATATAATATATATGTAATGTAT +ATTATATATGTAATGTATATAATATGTATGTAATACATATATTATATATGTAATGTATAT +TATATATGTATTACATATATGTATTACATATATAACATATATGTATTACATATATGTATT +ACATATATAACATATATGTATTACATATATGTATTACATATATAACATATATGTATTACA +TATATGTATTACATATATAACATATATGTAATACATATATGTATTACATATATAACATAT +ATGTATTACATATATGTATTACATATATAACATATATGTATTACATATATGTATTACATA +TATAACATATATGTATTACATATATGTATTACATATATAACATATATGTATTACATATAT +GTATTACATATATAACATATATGTATTACATATATGTAATACATATATAACATATATGTA +TTACATATATGTAATACATATATAACATATATGTATTACATATATGTAATACATATATAA +CATATATGTATTACATATATGTAATACATATATAACATGTATTACATATATGTAATACAT +ATATAACATGTATTACATATATGTAATACATATATAACATGTATTACATATATGTAATAC +ACATATAATATATATGTTATATATATATATATATATAAAATTTTTTAAAAAATTGTTTCT +TGAGATAGGGTCTCACTCTGTCACCCAGGCTGGAGTATAATGGTTTGATCATAGTTCACT +GCAGCCTTGAACTTCTAGACTCAGGTGATCCTCCCACCTCAACCTCCT +>syndip_2_chr20:21721074-21721836 +AGTAGGGACTTGCTTTGGGTCACAGTCAGCTTTTATTAGTGTTATTATTGTTGCTGTTTT +CTTCTTTTTCTTTGTACATCAACGTTTTATGGTGAATTAAATCGTGTTTTAACCTTGTAG +ACCACATTGGCTATTACATATATATATATAATATATATGTAATATATATATGTAATGTAT +ATTATATATGTAATGTATATAATATATGTAATGTATATAATACATATGTAATACATATAT +ATTATATATGTATATAATACATATATATGTATATATATGTATGTATATATATATGTATAT +ATGTATATATATATGTATATAATACATATATATACATATATATTATATATGTAATACATA +TATAATATATATGTAATGTATATATATGTAATGTATATAATATATATGTAATACATATAT +AATATATATGTAATGTATATAATATATATGTAATACATATATAATATATATGTAATGTAT +ATTATATATGTAATGTATATAATATGTATGTAATACATATATTATATATGTAATGTATAT +TATATATGTATTACATATATGTATTACATATATAACATATATGTATTACATATATGTATT +ACATATATAACATATATGTATTACATATATGTATTACATATATAACATATATGTATTACA +TATATGTATTACATATATAACATATATGTATTACATATATGTATTACATATATAACATAT +ATGTATTACATATATGTATTACATATATAACATATATGTATTACATATATGTATTACATA +TATAACATATATGTATTACATATATGTATTACATATATAACATATATGTATTACATATAT +GTATTACATATATAACATATATGTATTACATATATGTATTACATATATAACATATATGTA +TTACATATATGTATTACATATATAACATATATGTATTACATATATGTATTACATATATAA +CATATATGTATTACATATATGTAATACATATATAACATATATGTATTACATATATGTAAT +ACATATATAACATATATGTAATACATATATAACATATATGTATTACATATATGTAATACA +TATATAACATGTATTACATATATGTAATACACATATAATATATATGTTATATATATATAT +ATATATAAAATTTTTTAAAAAATTGTTTCTTGAGATAGGGTCTCACTCTGTCACCCAGGC +TGGAGTATAATGGTTTGATCATAGTTCACTGCAGCCTTGAACTTCTAGACTCAGGTGATC +CTCCCACCTCAACCTCCT +>p:HG002_1_chr20:21721074-21721836 +AGTAGGGACTTGCTTTGGGTCACAGTCAGCTTTTATTAGTGTTATTATTGTTGCTGTTTT +CTTCTTTTTCTTTGTACATCAACGTTTTATGGTGAATTAAATCGTGTTTTAACCTTGTAG +ACCACATTGGCTATTACATATATATATATAATATATATGTAATATATATATGTAATGTAT +ATTATATATGTAATGTATATAATATATGTAATGTATATAATACATATGTAATACATATAT +ATTATATATGTATATAATACATATATATGTATATATATGTATGTATATATATATGTATAT +ATGTATATATATATGTATATAATACATATATATACATATATATTATATATGTAATACATA +TATAATATATATGTAATGTATATATATGTAATGTATATAATATATATGTAATACATATAT +AATATATATGTAATGTATATAATATATATGTAATACATATATAATATATATGTAATGTAT +ATTATATATGTAATGTATATAATATGTATGTAATACATATATTATATATGTAATGTATAT +TATATATGTATTACATATATGTATTACATATATAACATATATGTATTACATATATGTATT +ACATATATAACATATATGTATTACATATATGTATTACATATATAACATATATGTATTACA +TATATGTATTACATATATAACATATATGTATTACATATATGTATTACATATATAACATAT +ATGTATTACATATATGTATTACATATATAACATATATGTATTACATATATGTATTACATA +TATAACATATATGTATTACATATATGTATTACATATATAACATATATGTATTACATATAT +GTATTACATATATAACATATATGTATTACATATATGTATTACATATATAACATATATGTA +TTACATATATGTATTACATATATAACATATATGTATTACATATATGTATTACATATATAA +CATATATGTATTACATATATGTAATACATATATAACATATATGTATTACATATATGTAAT +ACATATATAACATATATGTAATACATATATAACATATATGTATTACATATATGTAATACA +TATATAACATGTATTACATATATGTAATACACATATAATATATATGTTATATATATATAT +ATATATAAAATTTTTTAAAAAATTGTTTCTTGAGATAGGGTCTCACTCTGTCACCCAGGC +TGGAGTATAATGGTTTGATCATAGTTCACTGCAGCCTTGAACTTCTAGACTCAGGTGATC +CTCCCACCTCAACCTCCT +>p:HG002_2_chr20:21721074-21721836 +AGTAGGGACTTGCTTTGGGTCACAGTCAGCTTTTATTAGTGTTATTATTGTTGCTGTTTT +CTTCTTTTTCTTTGTACATCAACGTTTTATGGTGAATTAAATCGTGTTTTAACCTTGTAG +ACCACATTGGCTATTACATATATATATATAATATATATGTAATATATATATGTAATGTAT +ATTATATATGTAATGTATATAATATATGTAATGTATATAATATATATGTAATACATATAT +ATTATATATGTATATAATACATATATATGTATATATATGTATGTATATATATATGTATAT +ATGTATATATATATGTATATAATACATATATATACATATATATTATATATGTAATACATA +TATAATATATATGTAATGTATATATATGTAATGTATATAATATATATGTAATACATATAT +AATATATATGTAATGTATATAATATATATGTAATACATATATAATATATATGTAATGTAT +ATTATATATGTAATGTATATAATATGTATGTAATACATATATTATATATGTAATGTATAT +TATATATGTATTACATATATGTATTACATATATAACATATATGTATTACATATATGTATT +ACATATATAACATATATGTATTACATATATGTATTACATATATAACATATATGTATTACA +TATATGTATTACATATATAACATATATGTAATACATATATGTATTACATATATAACATAT +ATGTATTACATATATGTATTACATATATAACATATATGTATTACATATATGTATTACATA +TATAACATATATGTATTACATATATGTATTACATATATAACATATATGTATTACATATAT +GTATTACATATATAACATATATGTATTACATATATGTAATACATATATAACATATATGTA +TTACATATATGTAATACATATATAACATATATGTATTACATATATGTAATACATATATAA +CATATATGTATTACATATATGTAATACATATATAACATGTATTACATATATGTAATACAT +ATATAACATGTATTACATATATGTAATACATATATAACATGTATTACATATATGTAATAC +ACATATAATATATATGTTATATATATATATATATATAAAATTTTTTAAAAAATTGTTTCT +TGAGATAGGGTCTCACTCTGTCACCCAGGCTGGAGTATAATGGTTTGATCATAGTTCACT +GCAGCCTTGAACTTCTAGACTCAGGTGATCCTCCCACCTCAACCTCCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/haps.fa.ref.fa new file mode 100644 index 00000000..75bcdd02 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:21721074-21721836 +AGTAGGGACTTGCTTTGGGTCACAGTCAGCTTTTATTAGTGTTATTATTGTTGCTGTTTTCTTCTTTTTCTTTGTACATCAACGTTTTATGGTGAATTAAATCGTGTTTTAACCTTGTAGACCACATTGGCTATTACATATATATATATAATATATATGTAATATATATATGTAATGTATATTATATATGTAATGTATATAATATATGTAATGTATATAATATATATGTAATACATATATATTATATATGTATATAATACATATATATGTATATATATGTATGTATATATATATGTATATATGTATATATATATGTATATAATACATATATATACATATATATTATATATGTAATACATATATAATATATATGTAATGTATATATATGTAATGTATATAATATATATGTAATACATATATAATATATATGTAATGTATATTATATATGTAATGTATATAATATGTATGTAATACATATATTATATATGTAATGTATATTATATATGTATTACATATATGTATTACATATATAACATATATGTATTACATATATGTATTACATATATAACATATATGTATTACATATATGTAATACACATATAATATATATGTTATATATATATATATATATAAAATTTTTTAAAAAATTGTTTCTTGAGATAGGGTCTCACTCTGTCACCCAGGCTGGAGTATAATGGTTTGATCATAGTTCACTGCAGCCTTGAACTTCTAGACTCAGGTGATCCTCCCACCTCAACCTCCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/msa.fa new file mode 100644 index 00000000..7b4e4e00 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/msa.fa @@ -0,0 +1,115 @@ +>ref_chr20_21721074_21721836 +agtagggacttgctttgggtcacagtcagcttttattagtgttattattgttgctgtttt +cttctttttctttgtacatcaacgttttatggtgaattaaatcgtgttttaaccttgtag +accacattggctattacatatatatatataatatatatgtaatatatatatgtaatgtat +attatatatgtaatgtatataatatatgtaatgtatataatatatatgtaatacatatat +attatatatgtatataatacatatatatgtatatatatgtatgtatatatatatgtatat +atgtatatatatatgtatataatacatatatatacatatatattatatatgtaatacata +tataatatatatgtaatgt----------------------------------------- +-atatatatgtaatgtatataatatatatgtaatacatatataatatatatgtaatgtat +attatatatgtaatgtatataatatgtatgtaatacatatattatatatgtaatgtatat +tatatatgtattacatatatgtattacatatataacatatatgtattacatatatgtatt +acatatataacatatatgtattacatatatgtaatacacatataatatatatgttatata +tatatatat--------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--atataaaattttttaaaaaattgtttcttgagatagggtctcactctgtcacccaggc +tggagtataatggtttgatcatagttcactgcagccttgaacttctagactcaggtgatc +ctcccacctcaacctcct +>syndip_1_chr20:21721074-21721836 +agtagggacttgctttgggtcacagtcagcttttattagtgttattattgttgctgtttt +cttctttttctttgtacatcaacgttttatggtgaattaaatcgtgttttaaccttgtag +accacattggctattacatatatatatataatatatatgtaatatatatatgtaatgtat +attatatatgtaatgtatataatatatgtaatgtatataatatatatgtaatacatatat +attatatatgtatataatacatatatatgtatatatatgtatgtatatatatatgtatat +atgtatatatatatgtatataatacatatatatacatatatattatatatgtaatacata +tataatatatatgtaatgtatatatatgtaatgtatataatatatatgtaatacatatat +aatatatatgtaatgtatataatatatatgtaatacatatataatatatatgtaatgtat +attatatatgtaatgtatataatatgtatgtaatacatatattatatatgtaatgtatat +tatatatgtattacatatatgtattacatatataacatatatgtattacatatatgtatt +acatatataacatatatgtattacatatatgtattacatatataacatatatgtattaca +tatatgtattacatatataacatatatgtaatacatatatgtattacatatataacatat +atgtattacatatatgtattacatatataacatatatgtattacatatatgtattacata +tataacatatatgtattacatatatgtattacatatataacatatatgtattacatatat +gtattacatatataacatatatgtattacatatatgtaatacatatataacatatatgta +ttacatatatgtaatacatatataacatatatgtattacatatatgtaatacatatataa +catatatgtattacatatatgtaatacatatataac----atgtattacatatatgtaat +acatatataac--------------------------atgtattacatatatgtaataca +tatataacatgtattacatatatgtaatacacatataatatatatgttatatatatatat +atatataaaattttttaaaaaattgtttcttgagatagggtctcactctgtcacccaggc +tggagtataatggtttgatcatagttcactgcagccttgaacttctagactcaggtgatc +ctcccacctcaacctcct +>syndip_2_chr20:21721074-21721836 +agtagggacttgctttgggtcacagtcagcttttattagtgttattattgttgctgtttt +cttctttttctttgtacatcaacgttttatggtgaattaaatcgtgttttaaccttgtag +accacattggctattacatatatatatataatatatatgtaatatatatatgtaatgtat +attatatatgtaatgtatataatatatgtaatgtatataatacatatgtaatacatatat +attatatatgtatataatacatatatatgtatatatatgtatgtatatatatatgtatat +atgtatatatatatgtatataatacatatatatacatatatattatatatgtaatacata +tataatatatatgtaatgtatatatatgtaatgtatataatatatatgtaatacatatat +aatatatatgtaatgtatataatatatatgtaatacatatataatatatatgtaatgtat +attatatatgtaatgtatataatatgtatgtaatacatatattatatatgtaatgtatat +tatatatgtattacatatatgtattacatatataacatatatgtattacatatatgtatt +acatatataacatatatgtattacatatatgtattacatatataacatatatgtattaca +tatatgtattacatatataacatatatgtattacatatatgtattacatatataacatat +atgtattacatatatgtattacatatataacatatatgtattacatatatgtattacata +tataacatatatgtattacatatatgtattacatatataacatatatgtattacatatat +gtattacatatataacatatatgtattacatatatgtattacatatataacatatatgta +ttacatatatgtattacatatataacatatatgtattacatatatgtattacatatataa +catatatgtattacatatatgtaatacatatataacatatatgtattacatatatgtaat +acatatataacatatatgtaatacatatataacatatatgtattacatatatgtaataca +tatataacatgtattacatatatgtaatacacatataatatatatgttatatatatatat +atatataaaattttttaaaaaattgtttcttgagatagggtctcactctgtcacccaggc +tggagtataatggtttgatcatagttcactgcagccttgaacttctagactcaggtgatc +ctcccacctcaacctcct +>p:HG002_1_chr20:21721074-21721836 +agtagggacttgctttgggtcacagtcagcttttattagtgttattattgttgctgtttt +cttctttttctttgtacatcaacgttttatggtgaattaaatcgtgttttaaccttgtag +accacattggctattacatatatatatataatatatatgtaatatatatatgtaatgtat +attatatatgtaatgtatataatatatgtaatgtatataatacatatgtaatacatatat +attatatatgtatataatacatatatatgtatatatatgtatgtatatatatatgtatat +atgtatatatatatgtatataatacatatatatacatatatattatatatgtaatacata +tataatatatatgtaatgtatatatatgtaatgtatataatatatatgtaatacatatat +aatatatatgtaatgtatataatatatatgtaatacatatataatatatatgtaatgtat +attatatatgtaatgtatataatatgtatgtaatacatatattatatatgtaatgtatat +tatatatgtattacatatatgtattacatatataacatatatgtattacatatatgtatt +acatatataacatatatgtattacatatatgtattacatatataacatatatgtattaca +tatatgtattacatatataacatatatgtattacatatatgtattacatatataacatat +atgtattacatatatgtattacatatataacatatatgtattacatatatgtattacata +tataacatatatgtattacatatatgtattacatatataacatatatgtattacatatat +gtattacatatataacatatatgtattacatatatgtattacatatataacatatatgta +ttacatatatgtattacatatataacatatatgtattacatatatgtattacatatataa +catatatgtattacatatatgtaatacatatataacatatatgtattacatatatgtaat +acatatataacatatatgtaatacatatataacatatatgtattacatatatgtaataca +tatataacatgtattacatatatgtaatacacatataatatatatgttatatatatatat +atatataaaattttttaaaaaattgtttcttgagatagggtctcactctgtcacccaggc +tggagtataatggtttgatcatagttcactgcagccttgaacttctagactcaggtgatc +ctcccacctcaacctcct +>p:HG002_2_chr20:21721074-21721836 +agtagggacttgctttgggtcacagtcagcttttattagtgttattattgttgctgtttt +cttctttttctttgtacatcaacgttttatggtgaattaaatcgtgttttaaccttgtag +accacattggctattacatatatatatataatatatatgtaatatatatatgtaatgtat +attatatatgtaatgtatataatatatgtaatgtatataatatatatgtaatacatatat +attatatatgtatataatacatatatatgtatatatatgtatgtatatatatatgtatat +atgtatatatatatgtatataatacatatatatacatatatattatatatgtaatacata +tataatatatatgtaatgtatatatatgtaatgtatataatatatatgtaatacatatat +aatatatatgtaatgtatataatatatatgtaatacatatataatatatatgtaatgtat +attatatatgtaatgtatataatatgtatgtaatacatatattatatatgtaatgtatat +tatatatgtattacatatatgtattacatatataacatatatgtattacatatatgtatt +acatatataacatatatgtattacatatatgtattacatatataacatatatgtattaca +tatatgtattacatatataacatatatgtaatacatatatgtattacatatataacatat +atgtattacatatatgtattacatatataacatatatgtattacatatatgtattacata +tataacatatatgtattacatatatgtattacatatataacatatatgtattacatatat +gtattacatatataacatatatgtattacatatatgtaatacatatataacatatatgta +ttacatatatgtaatacatatataacatatatgtattacatatatgtaatacatatataa +catatatgtattacatatatgtaatacatatataac----atgtattacatatatgtaat +acatatataac--------------------------atgtattacatatatgtaataca +tatataacatgtattacatatatgtaatacacatataatatatatgttatatatatatat +atatataaaattttttaaaaaattgtttcttgagatagggtctcactctgtcacccaggc +tggagtataatggtttgatcatagttcactgcagccttgaacttctagactcaggtgatc +ctcccacctcaacctcct diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/msa.fa.fai new file mode 100644 index 00000000..1546e6f4 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_21721074_21721836 1278 29 60 61 +syndip_1_chr20:21721074-21721836 1278 1363 60 61 +syndip_2_chr20:21721074-21721836 1278 2697 60 61 +p:HG002_1_chr20:21721074-21721836 1278 4032 60 61 +p:HG002_2_chr20:21721074-21721836 1278 5367 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/output.vcf.gz new file mode 100644 index 00000000..53f0dd91 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/output.vcf.gz.tbi new file mode 100644 index 00000000..2ed369aa Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:21721174-21721736/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/base.vcf.gz new file mode 100644 index 00000000..fd46466a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/base.vcf.gz.tbi new file mode 100644 index 00000000..4b87cdb0 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/comp.vcf.gz new file mode 100644 index 00000000..9acc54d7 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/comp.vcf.gz.tbi new file mode 100644 index 00000000..0eafdbfe Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/haps.fa new file mode 100644 index 00000000..dcf26ec0 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/haps.fa @@ -0,0 +1,176 @@ +>ref_chr20_22081861_22084223 +GGATGGTTCCATATTTTTGCAGTTGTGTATTTTGCTGCTATAAACATGTGTGTGCAGGTGTCTTTTTCATATAACAACTTCTTTTCCTTTGGGTAGGTTTACAAAAACTATCTTTTTCCCGTTCTTTTACTTATATATGCTTATTTATATATATTATATATACACTTTTAATATATACTTATTACTATATATTAATATAATATAATAATAATACAATATAATATATGTATATATGTAGGTATATAATAATATACCTACATATATACATATATTATATATACTATCTGTATATTATATGTATAATATATGTATATATAATATATGTATATACTATACATGTATATATTATATTATACATGTATATATTATAAGTATATACTATACATGCATGTATTATATGTATATACTATACATGCATGTATTATATGTATATATTATACATGCATGTATTATATGTATATATTATACATGCATGTATTATATGTATATATTATACATGCATGTATTATATGTATATATTATACATGTATGTATTATATGTATAGATTATACATGTATATATTATATATGTATATATTACACATGTACATATATGTATATATTAAACACGTTTATATTATTTATTATACATGTAGGTATATATGACATATGCATATATCATATAGGTATATATGACATATGCATATATCATATAGGTATATATGATATATGCGCATATATCATATAGGTATATATGATATATGCGCATATATCATACAGGTATATGCGCATATATCATATAGGTATAGGTATAGGTAGATATATGATATATGCACACATATCATATAGGTATATATGATATATGCGCATATATCATATAGGTATATATGATATATGATAGGTATATATGATATATGATAGGTATATATGATATATATCATATCGGTATATATGATATATATCATATCGGTATATATAGGTATATATCATAGGTATATATAGGTATATATCACATAGGTATATATAGGTATATATCATATAGGTATATATAATATATGCATTTATATTATATAGGTATATATATTACATAGGTATATGTAATATGTGCATATATATTATATAGGTATATATATTATACAGGCATATATAATACGTATATATATTATATGGGCATATATATGTGTATATATTATATAGGTATATATAATATATGTGTATATATTATGTGGGTATATATAATATATGTGTATATATTATGTGGGTATATATAATATATGTGTACATATTATGTGGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATATATGTAATAGGAAGCAGGAATGAATGCACAGAAGACCTTAGAGTTTAAGGCATTATTTGTGTAATGAGAAATATTATATATACGTATATTAATATAGACGTATATATAATATATACATATATTAATATAGACGTATATATAATATATACATATATACATATATAGTATATACTATGTATACATATATACTATACATACGTATATTATATACATGTGTATTATATACATGTGTATTATATATATGTGTATACATATATACTATATATACATACATTATATACATACATTATATATGTGTATTATATATGTATATATTATGTATGTATATATTATATATACGTATATATTAATATACATATATATGTGTCTCATTATACCAATAATGCCTTAAACTCTAAGGTCTTCTGTGCATTCATTCCTGCTTCCTATTACATATATATTATATAGATACATATATAATATATACATATATACTACATAATATATGCATATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTGTATATGTATTATATGTATATATTACATATTATATATACTTATGTATGTATAATATATATATAATATATATATATCTTAGGCAACTTTTCATTGCTCATTTTTATTAAACCCTGAAAACTTTCACTTTACTCCATTTCTAAGTTTGATATTCTGGTAGAATTAAAGTAAGAGTTTTCTTTCTTTCATCTCCTTTTTATCTCTCTCA +>syndip_1_chr20:22081861-22084223 +GGATGGTTCCATATTTTTGCAGTTGTGTATTTTGCTGCTATAAACATGTGTGTGCAGGTG +TCTTTTTCATATAACAACTTCTTTTCCTTTGGGTAGGTTTACAAAAACTATCTTTTTCCC +GTTCTTTTACTTATATATGCTTATTTATATATATTATATATACACTTTTAATATATACTT +ATTAATATATATTAATATAATATAATAATAATACAATATAATATATGTATATATGTAGGT +ATATAATAATATACCTACATATATACATATATTATATATACTATCTGTATATTATATGTA +TAATATATGTATATATAATATATGTATATACTATACATGTATATATTATATTATACATGT +ATATATTATAAGTATATACTATACATGCATGTATTATATGTATATACTATACATGCATGT +ATTATATGTATATATTATACATGCATGTATTATATGTATATATTATACATGCATGTATTA +TATGTATATATTATACATGTATGTATTATATGTATAGATTATACATGTATATATTATATA +TGTATATATTACACATGTACATATATGTATATATTAAACACGTTTATATTATTTATTATA +CATGACTATATTATATAGGTATATATGATATATGCATATATGTCATATAGGTATATATGA +CATATATGCATATATCATGTAGGTATATATGACATATGCATATATCATATAGGTATATAT +GACATATGCATATATCATATAGGTATATATGATATATGCGCATATATCATATAGGTATAT +ATGATATATGCGCATATATCATATAGGTATATATGATATATGCGCATATATCATATAGGT +ATATATGATATATGCGCATATATCATATAGGTATATATGATATATGCGCATATATCATAT +AGGTATATATGATATATGCGCATATATCATATAGGTATATATGATATATGCGCATATATC +ATACAGGTATATGTGCATATATCATATAGGTATAGGTATAGGTAGATATATGATATATGC +ACACATATCATATAGGTATATATGATATATGATAGGTATATATGATATATGATAGGTATA +TATGATATATATCATATTGGTATATATGATATATATCATATCGGTATATATGATATATAT +CATATCGGTATATATAGGTATATATCATAGGTATATATAGGTATATATCACATAGGTATA +TATAGGTATATATCATATAGGTATATATAATATATGCATTTATATTATATAGGTATATAT +ATTACATAGGTATATGTAATATGTGCATATATATTATATAGGTATATATATTATACAGGC +ATATATAATACGTATATATATTATATGGGCATATATATGTATATATATTATATAGGTATA +TATAATATATGTGTATATATTATGTGGGTATATATAATATATGTGTACATATTATGTGGG +TATATATAATATATGTGTACATATTATGTGGGTATATATAATATATGTGTACATATTATG +TGGGTATATATAATATATGTGTATATATTATGTGGGTATATATAATATATGTGTATATAT +TATGTGGGTATATATAATATATGTGTATATATTATGTGGGTATATATAATATATGTGTAT +ATATTATGTGGGTATATATAATATATGTGTATATATTATGTGGGTATATATAATATATGT +GTATATATTATGTGGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATAT +ATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATA +ATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATA +TATAATATATGTGTATATATTATATATGTAATAGGAAGCAGGAATGAATGCACAGAAGAC +CTTAGAGTTTAAGGCATTATTTGTGTAATGAGAAATATTATATATACGTATATTAATATA +GACGTATATATAATATATACATATATACATATATAGTATATACTATGTATACATATATAC +TATACATACGTATATTATATACATGTGTATTATATACATGTGTATTATATATATGTGTAT +ACATATATACTATATATACATACATTATATACATACATTATATATGTGTATTATATATGT +ATATATTATGTATGTATATATTATATATACGTATATATTAATATGCATATATATGTGTCT +CTTTATACCAATAATGCCTTAAACTCTAAGGTCTTCTGTGCATTCATTCCTGCTTCCTAT +TACATATATATTATATAGATACATATATAATATATACATATATACTACATAATATATGCA +TATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTGTATATGTA +TATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTGTATATGTA +TATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTGTATATGTA +TATATAATATATACATATGTTGTATATGTATTATATGTATATATTACATATTATATATAC +TTATGTATGTATAATATATATATAATATATATATATCTTAGGCAACTTTTCATTGCTCAT +TTTTATTAAACCCTGAAAACTTTCACTTTACTCCATTTCTAAGTTTGATATTCTGGTAGA +ATTAAAGTAAGAGTTTTCTTTCTTTCATCTCCTTTTTATCTCTCTCA +>syndip_2_chr20:22081861-22084223 +GGATGGTTCCATATTTTTGCAGTTGTGTATTTTGCTGCTATAAACATGTGTGTGCAGGTG +TCTTTTTCATATAACAACTTCTTTTCCTTTGGGTAGGTTTACAAAAACTATCTTTTTCCC +GTTCTTTTACTTATATATGCTTATTTATATATATTATATATACACTTTTAATATATACTT +ATTACTATATATTAATATAATATAATAATAATACAATATAATATATGTATATATGTAGGT +ATATAATAATATACCTACATATATACATATATTATATATACTATCTGTATATTATATGTA +TAATATATGTATATATAATATATGTATATACTATACATGTATATATTATATTATACATGT +ATATATTATAAGTATATACTATACATGCATGTATTATATGTATATACTATACATGCATGT +ATTATATGTATATATTATACATGCATGTATTATATGTATATATTATACATGCATGTATTA +TATGTATATATTATACATGTATGTATTATATGTATAGATTATACATGTATATATTATATA +TGTATATATTACACATGTACATATATGTATATATTAAACACGTTTATATTATTTATTATA +CATGTAGGTATATATGACATATGCATATATCATATAGGTATATATGACATATGCATATAT +CATATAGGTATATATGATATATGCGCATATATCATATAGGTATATATGATATATGCGCAT +ATATCATACAGGTATATGCGCATATATCATATAGGTATAGGTATAGGTAGATATATGATA +TATGCACACATATCATATAGGTATATATGATATATGCGCATATATCATATAGGTATATAT +GATATATGATAGGTATATATGATATATGATAGGTATATATGATATATATCATATCGGTAT +ATATGATATATATCATATCGGTATATATAGGTATATATCATAGGTATATATAGGTATATA +TCACATAGGTATATATAGGTATATATCATATAGGTATATATAATATATGCATTTATATTA +TATAGGTATATATATTACATAGGTATATGTAATATGTGCATATATATTATATAGGTATAT +ATATTATACAGGCATATATAATACGTATATATATTATATGGGCATATATATGTGTATATA +TTATATAGGTATATATAATATATGTGTATATATTATGTGGGTATATATAATATATGTGTA +TATATTATGTGGGTATATATAATATATGTGTACATATTATGTGGGTATATATAATATATG +TGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATA +TATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATAT +AATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTAT +ATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAG +GTATATATAATATATGTGTATATATTATATATGTAATAGGAAGCAGGAATGAATGCACAG +AAGACCTTAGAGTTTAAGGCATTATTTGTGTAATGAGAAATATTATATATACGTATATTA +ATATAGACGTATATATAATATATACATATATTAATATAGACGTATATATAATATATACAT +ATATACATATATAGTATATACTATGTATACATATATACTATACATACGTATATTATATAC +ATGTGTATTATATACATGTGTATTATATATATGTGTATACATATATACTATATATACATA +CATTATATACATACATTATATATGTGTATTATATATGTATATATTATGTATGTATATATT +ATATATACGTATATATTAATATACATATATATGTGTCTCATTATACCAATAATGCCTTAA +ACTCTAAGGTCTTCTGTGCATTCATTCCTGCTTCCTATTACATATATATTATATAGATAC +ATATATAATATATACATATATACTACATAATATATGCATATATAATATATACATATGTTG +TATATGTATATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTG +TATATGTATATATAATATATACATATGTTGTATATGTATTATATGTATATATTACATATT +ATATATACTTATGTATGTATAATATATATATAATATATATATATCTTAGGCAACTTTTCA +TTGCTCATTTTTATTAAACCCTGAAAACTTTCACTTTACTCCATTTCTAAGTTTGATATT +CTGGTAGAATTAAAGTAAGAGTTTTCTTTCTTTCATCTCCTTTTTATCTCTCTCA +>p:HG002_1_chr20:22081861-22084223 +GGATGGTTCCATATTTTTGCAGTTGTGTATTTTGCTGCTATAAACATGTGTGTGCAGGTG +TCTTTTTCATATAACAACTTCTTTTCCTTTGGGTAGGTTTACAAAAACTATCTTTTTCCC +GTTCTTTTACTTATATATGCTTATTTATATATATTATATATACACTTTTAATATATACTT +ATTACTATATATTAATATAATATAATAATAATACAATATAATATATGTATATATGTAGGT +ATATAATAATATACCTACATATATACATATATTATATATACTATCTGTATATTATATGTA +TAATATATGTATATATAATATATGTATATACTATACATGTATATATTATATTATACATGT +ATATATTATAAGTATATACTATACATGCATGTATTATATGTATATACTATACATGCATGT +ATTATATGTATATATTATACATGCATGTATTATATGTATATATTATACATGCATGTATTA +TATGTATATATTATACATGTATGTATTATATGTATAGATTATACATGTATATATTATATA +TGTATATATTACACATGTACATATATGTATATATTAAACACGTTTATATTATTTATTATA +CATGTAGGTATATATGACATATGCATATATCATATAGGTATATATGACATATGCATATAT +CATATAGGTATATATGATATATGCGCATATATCATATAGGTATATATGATATATGCGCAT +ATATCATACAGGTATATGCGCATATATCATATAGGTATAGGTATAGGTAGATATATGATA +TATGCACACATATCATATAGGTATATATGATATATGCGCATATATCATATAGGTATATAT +GATATATGATAGGTATATATGATATATGATAGGTATATATGATATATATCATATCGGTAT +ATATGATATATATCATATCGGTATATATAGGTATATATCATAGGTATATATAGGTATATA +TCACATAGGTATATATAGGTATATATCATATAGGTATATATAATATATGCATTTATATTA +TATAGGTATATATATTACATAGGTATATGTAATATGTGCATATATATTATATAGGTATAT +ATATTATACAGGCATATATAATACGTATATATATTATATGGGCATATATATGTGTATATA +TTATATAGGTATATATAATATATGTGTATATATTATGTGGGTATATATAATATATGTGTA +TATATTATGTGGGTATATATAATATATGTGTACATATTATGTGGGTATATATAATATATG +TGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATA +TATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATAT +AATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTAT +ATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAG +GTATATATAATATATGTGTATATATTATATATGTAATAGGAAGCAGGAATGAATGCACAG +AAGACCTTAGAGTTTAAGGCATTATTTGTGTAATGAGAAATATTATATATACGTATATTA +ATATAGACGTATATATAATATATACATATATTAATATAGACGTATATATAATATATACAT +ATATACATATATAGTATATACTATGTATACATATATACTATACATACGTATATTATATAC +ATGTGTATTATATACATGTGTATTATATATATGTGTATACATATATACTATATATACATA +CATTATATACATACATTATATATGTGTATTATATATGTATATATTATGTATGTATATATT +ATATATACGTATATATTAATATACATATATATGTGTCTCATTATACCAATAATGCCTTAA +ACTCTAAGGTCTTCTGTGCATTCATTCCTGCTTCCTATTACATATATATTATATAGATAC +ATATATAATATATACATATATACTACATAATATATGCATATATAATATATACATATGTTG +TATATGTATATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTG +TATATGTATATATAATATATACATATGTTGTATATGTATTATATGTATATATTACATATT +ATATATACTTATGTATGTATAATATATATATAATATATATATATCTTAGGCAACTTTTCA +TTGCTCATTTTTATTAAACCCTGAAAACTTTCACTTTACTCCATTTCTAAGTTTGATATT +CTGGTAGAATTAAAGTAAGAGTTTTCTTTCTTTCATCTCCTTTTTATCTCTCTCA +>p:HG002_2_chr20:22081861-22084223 +GGATGGTTCCATATTTTTGCAGTTGTGTATTTTGCTGCTATAAACATGTGTGTGCAGGTG +TCTTTTTCATATAACAACTTCTTTTCCTTTGGGTAGGTTTACAAAAACTATCTTTTTCCC +GTTCTTTTACTTATATATGCTTATTTATATATATTATATATACACTTTTAATATATACTT +ATTAATATATATTAATATAATATAATAATAATACAATATAATATATGTATATATGTAGGT +ATATAATAATATACCTACATATATACATATATTATATATACTATCTGTATATTATATGTA +TAATATATGTATATATAATATATGTATATACTATACATGTATATATTATATTATACATGT +ATATATTATAAGTATATACTATACATGCATGTATTATATGTATATACTATACATGCATGT +ATTATATGTATATATTATACATGCATGTATTATATGTATATATTATACATGCATGTATTA +TATGTATATATTATACATGTATGTATTATATGTATAGATTATACATGTATATATTATATA +TGTATATATTACACATGTACATATATGTATATATTAAACACGTTTATATTATTTATTATA +CATGACTATATTATATAGGTATATATGATATATGCATATATGTCATATAGGTATATATGA +CATATATGCATATATCATGTAGGTATATATGACATATGCATATATCATATAGGTATATAT +GACATATGCATATATCATATAGGTATATATGATATATGCGCATATATCATATAGGTATAT +ATGATATATGCGCATATATCATATAGGTATATATGATATATGCGCATATATCATATAGGT +ATATATGATATATGCGCATATATCATATAGGTATATATGATATATGCGCATATATCATAT +AGGTATATATGATATATGCGCATATATCATATAGGTATATATGATATATGCGCATATATC +ATACAGGTATATGTGCATATATCATATAGGTATAGGTATAGGTAGATATATGATATATGC +ACACATATCATATAGGTATATATGATATATGATAGGTATATATGATATATGATAGGTATA +TATGATATATATCATATTGGTATATATGATATATATCATATCGGTATATATGATATATAT +CATATCGGTATATATAGGTATATATCATAGGTATATATAGGTATATATCACATAGGTATA +TATAGGTATATATCATATAGGTATATATAATATATGCATTTATATTATATAGGTATATAT +ATTACATAGGTATATGTAATATGTGCATATATATTATATAGGTATATATATTATACAGGC +ATATATAATACGTATATATATTATATGGGCATATATATGTATATATATTATATAGGTATA +TATAATATATGTGTATATATTATGTGGGTATATATAATATATGTGTACATATTATGTGGG +TATATATAATATATGTGTACATATTATGTGGGTATATATAATATATGTGTACATATTATG +TGGGTATATATAATATATGTGTATATATTATGTGGGTATATATAATATATGTGTATATAT +TATGTGGGTATATATAATATATGTGTATATATTATGTGGGTATATATAATATATGTGTAT +ATATTATGTGGGTATATATAATATATGTGTATATATTATGTGGGTATATATAATATATGT +GTATATATTATGTGGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATAT +ATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATA +ATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATA +TATAATATATGTGTATATATTATATATGTAATAGGAAGCAGGAATGAATGCACAGAAGAC +CTTAGAGTTTAAGGCATTATTTGTGTAATGAGAAATATTATATATACGTATATTAATATA +GACGTATATATAATATATACATATATACATATATAGTATATACTATGTATACATATATAC +TATACATACGTATATTATATACATGTGTATTATATACATGTGTATTATATATATGTGTAT +ACATATATACTATATATACATACATTATATACATACATTATATATGTGTATTATATATGT +ATATATTATGTATGTATATATTATATATACGTATATATTAATATGCATATATATGTGTCT +CTTTATACCAATAATGCCTTAAACTCTAAGGTCTTCTGTGCATTCATTCCTGCTTCCTAT +TACATATATATTATATAGATACATATATAATATATACATATATACTACATAATATATGCA +TATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTGTATATGTA +TATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTGTATATGTA +TATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTGTATATGTA +TATATAATATATACATATGTTGTATATGTATTATATGTATATATTACATATTATATATAC +TTATGTATGTATAATATATATATAATATATATATATCTTAGGCAACTTTTCATTGCTCAT +TTTTATTAAACCCTGAAAACTTTCACTTTACTCCATTTCTAAGTTTGATATTCTGGTAGA +ATTAAAGTAAGAGTTTTCTTTCTTTCATCTCCTTTTTATCTCTCTCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/haps.fa.ref.fa new file mode 100644 index 00000000..c53a131c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:22081861-22084223 +GGATGGTTCCATATTTTTGCAGTTGTGTATTTTGCTGCTATAAACATGTGTGTGCAGGTGTCTTTTTCATATAACAACTTCTTTTCCTTTGGGTAGGTTTACAAAAACTATCTTTTTCCCGTTCTTTTACTTATATATGCTTATTTATATATATTATATATACACTTTTAATATATACTTATTACTATATATTAATATAATATAATAATAATACAATATAATATATGTATATATGTAGGTATATAATAATATACCTACATATATACATATATTATATATACTATCTGTATATTATATGTATAATATATGTATATATAATATATGTATATACTATACATGTATATATTATATTATACATGTATATATTATAAGTATATACTATACATGCATGTATTATATGTATATACTATACATGCATGTATTATATGTATATATTATACATGCATGTATTATATGTATATATTATACATGCATGTATTATATGTATATATTATACATGCATGTATTATATGTATATATTATACATGTATGTATTATATGTATAGATTATACATGTATATATTATATATGTATATATTACACATGTACATATATGTATATATTAAACACGTTTATATTATTTATTATACATGTAGGTATATATGACATATGCATATATCATATAGGTATATATGACATATGCATATATCATATAGGTATATATGATATATGCGCATATATCATATAGGTATATATGATATATGCGCATATATCATACAGGTATATGCGCATATATCATATAGGTATAGGTATAGGTAGATATATGATATATGCACACATATCATATAGGTATATATGATATATGCGCATATATCATATAGGTATATATGATATATGATAGGTATATATGATATATGATAGGTATATATGATATATATCATATCGGTATATATGATATATATCATATCGGTATATATAGGTATATATCATAGGTATATATAGGTATATATCACATAGGTATATATAGGTATATATCATATAGGTATATATAATATATGCATTTATATTATATAGGTATATATATTACATAGGTATATGTAATATGTGCATATATATTATATAGGTATATATATTATACAGGCATATATAATACGTATATATATTATATGGGCATATATATGTGTATATATTATATAGGTATATATAATATATGTGTATATATTATGTGGGTATATATAATATATGTGTATATATTATGTGGGTATATATAATATATGTGTACATATTATGTGGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATGTAGGTATATATAATATATGTGTATATATTATATATGTAATAGGAAGCAGGAATGAATGCACAGAAGACCTTAGAGTTTAAGGCATTATTTGTGTAATGAGAAATATTATATATACGTATATTAATATAGACGTATATATAATATATACATATATTAATATAGACGTATATATAATATATACATATATACATATATAGTATATACTATGTATACATATATACTATACATACGTATATTATATACATGTGTATTATATACATGTGTATTATATATATGTGTATACATATATACTATATATACATACATTATATACATACATTATATATGTGTATTATATATGTATATATTATGTATGTATATATTATATATACGTATATATTAATATACATATATATGTGTCTCATTATACCAATAATGCCTTAAACTCTAAGGTCTTCTGTGCATTCATTCCTGCTTCCTATTACATATATATTATATAGATACATATATAATATATACATATATACTACATAATATATGCATATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTGTATATGTATATATAATATATACATATGTTGTATATGTATTATATGTATATATTACATATTATATATACTTATGTATGTATAATATATATATAATATATATATATCTTAGGCAACTTTTCATTGCTCATTTTTATTAAACCCTGAAAACTTTCACTTTACTCCATTTCTAAGTTTGATATTCTGGTAGAATTAAAGTAAGAGTTTTCTTTCTTTCATCTCCTTTTTATCTCTCTCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/msa.fa new file mode 100644 index 00000000..72dfc312 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/msa.fa @@ -0,0 +1,240 @@ +>ref_chr20_22081861_22084223 +ggatggttccatatttttgcagttgtgtattttgctgctataaacatgtgtgtgcaggtg +tctttttcatataacaacttcttttcctttgggtaggtttacaaaaactatctttttccc +gttcttttacttatatatgcttatttatatatattatatatacacttttaatatatactt +attactatatattaatataatataataataatacaatataatatatgtatatatgtaggt +atataataatatacctacatatatacatatattatatatactatctgtatattatatgta +taatatatgtatatataatatatgtatatactatacatgtatatattatattatacatgt +atatattataagtatatactatacatgcatgtattatatgtatatactatacatgcatgt +attatatgtatatattatacatgcatgtattatatgtatatattatacatgcatgtatta +tatgtatatattatacatgcatgtattatatgtatatattatacatgtatgtattatatg +tatagattatacatgtatatattatatatgtatatattacacatgtacatatatgtatat +attaaacacgtttatattatttattata-------------------------------- +-------------------------------------------catgtaggtatatatga +catatgcatatatcatataggtatatatgacatatgcatatatcatataggtatatatga +tatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatacagg----- +----tatatgcgcatatatcatataggtataggt------------------ataggtag +atatatgatatatgcacacatatcatataggtatatatgatatatgcgcatatatcatat +aggtatatatgatatatg------------------------------------------ +---------------------------------------ataggtatatatgatatatga +ta--------------------------------------------ggtatatatgatat +atatcatatcggtatatatgatatatatcatatcggtatatataggtatatatcataggt +atatataggtatatatcacataggtatatataggtatatatcatataggtatatataata +tatgcatttatattatataggtatatatattacataggtatatgtaatatgtgcatatat +attatataggtatatatattatacaggcatatataatacgtatatatattatatgggcat +atatatgtgtatatattatata-------------------------------------- +------------------------------------------------------------ +------------------------------ggtatatataatatatgtgtatatattatg +tgggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtacatat +tatgtgggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtat +atattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgt +gtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatat +atgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatata +atatatgtgtatatattatgtaggtatatataatatatgtgtatatattatatatgtaat +aggaagcaggaatgaatgcacagaagaccttagagtttaaggcattatttgtgtaatgag +aaatattatatatacgtatattaatatagacgtatatataatatatacatatattaatat +agacgtatatataatatatacatatatacatatatagtatatactatgtatacatatata +ctatacatacgtatattatatacatgtgtattatatacatgtgtattatatatatgtgta +tacatatatactatatatacatacattatatacatacattatatatgtgtattatatatg +tatatattatgtatgtatatattatatatacgtatatattaatatacatatatatgtgtc +tcattataccaataatgccttaaactctaaggtcttctgtgcattcattcctgcttccta +ttacatatatattatatagatacatatataatatatacatatatactacataatatatgc +------------------------------------------------------------ +------------------------------atatataatatatacatatgttgtatatgt +atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt +atatataatatatacatatgttgtatatgtattatatgtatatattacatattatatata +cttatgtatgtataatatatatataatatatatatatcttaggcaacttttcattgctca +tttttattaaaccctgaaaactttcactttactccatttctaagtttgatattctggtag +aattaaagtaagagttttctttctttcatctcctttttatctctctca +>syndip_1_chr20:22081861-22084223 +ggatggttccatatttttgcagttgtgtattttgctgctataaacatgtgtgtgcaggtg +tctttttcatataacaacttcttttcctttgggtaggtttacaaaaactatctttttccc +gttcttttacttatatatgcttatttatatatattatatatacacttttaatatatactt +attaatatatattaatataatataataataatacaatataatatatgtatatatgtaggt +atataataatatacctacatatatacatatattatatatactatctgtatattatatgta +taatatatgtatatataatatatgtatatactatacatgtatatattatattatacatgt +atatattataagtatatactatacatgcatgtattatatgtatatac------------- +---------------tatacatgcatgtattatatgtatatattatacatgcatgtatta +tatgtatatattatacatgcatgtattatatgtatatattatacatgtatgtattatatg +tatagattatacatgtatatattatatatgtatatattacacatgtacatatatgtatat +attaaacacgtttatattatttattatacatgactatattatataggtatatatgatata +tgcatatatgtcatataggtatatatgacatatatgcatatatcatgtaggtatatatga +catatgcatatatcatataggtatatatgacatatgcatatatcatataggtatatatga +tatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatataggtatat +atgatatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatataggt +atatatgatatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatat +aggtatatatgatatatgcgcatatatcatacaggtatatgtgcatatatcatataggta +taggtataggtagatatatgatatatgcacacatatcatataggtatatatgatatatga +taggtatatatgatatatgataggtatatatgatatatatcatattggtatatatgatat +atatcatatcggtatatatgatatatatcatatcggtatatataggtatatatcataggt +atatataggtatatatcacataggtatatataggtatatatcatataggtatatataata +tatgcatttatattatataggtatatatattacataggtatatgtaatatgtgcatatat +attatataggtatatatattatacaggcatatataatacgtatatatattatatgggcat +atatatgtatatatattatataggtatatataatatatgtgtatatattatgtgggtata +tataatatatgtgtacatattatgtgggtatatataatatatgtgtacatattatgtggg +tatatataatatatgtgtacatattatgtgggtatatataatatatgtgtatatattatg +tgggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtatatat +tatgtgggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtat +atattatgtgggtatatataatatatgtgtatatattatgtgggtatatataatatatgt +gtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatat +atgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatata +atatatgtgtatatattatgtaggtatatataatatatgtgtatatattatatatgtaat +aggaagcaggaatgaatgcacagaagaccttagagtttaaggcattatttgtgtaatgag +aaatattatatatacg---------------------------------tatattaatat +agacgtatatataatatatacatatatacatatatagtatatactatgtatacatatata +ctatacatacgtatattatatacatgtgtattatatacatgtgtattatatatatgtgta +tacatatatactatatatacatacattatatacatacattatatatgtgtattatatatg +tatatattatgtatgtatatattatatatacgtatatattaatatgcatatatatgtgtc +tctttataccaataatgccttaaactctaaggtcttctgtgcattcattcctgcttccta +ttacatatatattatatagatacatatataatatatacatatatactacataatatatgc +atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt +atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt +atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt +atatataatatatacatatgttgtatatgtattatatgtatatattacatattatatata +cttatgtatgtataatatatatataatatatatatatcttaggcaacttttcattgctca +tttttattaaaccctgaaaactttcactttactccatttctaagtttgatattctggtag +aattaaagtaagagttttctttctttcatctcctttttatctctctca +>syndip_2_chr20:22081861-22084223 +ggatggttccatatttttgcagttgtgtattttgctgctataaacatgtgtgtgcaggtg +tctttttcatataacaacttcttttcctttgggtaggtttacaaaaactatctttttccc +gttcttttacttatatatgcttatttatatatattatatatacacttttaatatatactt +attactatatattaatataatataataataatacaatataatatatgtatatatgtaggt +atataataatatacctacatatatacatatattatatatactatctgtatattatatgta +taatatatgtatatataatatatgtatatactatacatgtatatattatattatacatgt +atatattataagtatatactatacatgcatgtattatatgtatatac------------- +---------------tatacatgcatgtattatatgtatatattatacatgcatgtatta +tatgtatatattatacatgcatgtattatatgtatatattatacatgtatgtattatatg +tatagattatacatgtatatattatatatgtatatattacacatgtacatatatgtatat +attaaacacgtttatattatttattata-------------------------------- +-------------------------------------------catgtaggtatatatga +catatgcatatatcatataggtatatatgacatatgcatatatcatataggtatatatga +tatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatacagg----- +----tatatgcgcatatatcatataggtataggt------------------ataggtag +atatatgatatatgcacacatatcatataggtatatatgatatatgcgcatatatcatat +aggtatatatgatatatg------------------------------------------ +---------------------------------------ataggtatatatgatatatga +ta--------------------------------------------ggtatatatgatat +atatcatatcggtatatatgatatatatcatatcggtatatataggtatatatcataggt +atatataggtatatatcacataggtatatataggtatatatcatataggtatatataata +tatgcatttatattatataggtatatatattacataggtatatgtaatatgtgcatatat +attatataggtatatatattatacaggcatatataatacgtatatatattatatgggcat +atatatgtgtatatattatata-------------------------------------- +------------------------------------------------------------ +------------------------------ggtatatataatatatgtgtatatattatg +tgggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtacatat +tatgtgggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtat +atattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgt +gtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatat +atgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatata +atatatgtgtatatattatgtaggtatatataatatatgtgtatatattatatatgtaat +aggaagcaggaatgaatgcacagaagaccttagagtttaaggcattatttgtgtaatgag +aaatattatatatacgtatattaatatagacgtatatataatatatacatatattaatat +agacgtatatataatatatacatatatacatatatagtatatactatgtatacatatata +ctatacatacgtatattatatacatgtgtattatatacatgtgtattatatatatgtgta +tacatatatactatatatacatacattatatacatacattatatatgtgtattatatatg +tatatattatgtatgtatatattatatatacgtatatattaatatacatatatatgtgtc +tcattataccaataatgccttaaactctaaggtcttctgtgcattcattcctgcttccta +ttacatatatattatatagatacatatataatatatacatatatactacataatatatgc +------------------------------------------------------------ +------------------------------atatataatatatacatatgttgtatatgt +atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt +atatataatatatacatatgttgtatatgtattatatgtatatattacatattatatata +cttatgtatgtataatatatatataatatatatatatcttaggcaacttttcattgctca +tttttattaaaccctgaaaactttcactttactccatttctaagtttgatattctggtag +aattaaagtaagagttttctttctttcatctcctttttatctctctca +>p:HG002_1_chr20:22081861-22084223 +ggatggttccatatttttgcagttgtgtattttgctgctataaacatgtgtgtgcaggtg +tctttttcatataacaacttcttttcctttgggtaggtttacaaaaactatctttttccc +gttcttttacttatatatgcttatttatatatattatatatacacttttaatatatactt +attactatatattaatataatataataataatacaatataatatatgtatatatgtaggt +atataataatatacctacatatatacatatattatatatactatctgtatattatatgta +taatatatgtatatataatatatgtatatactatacatgtatatattatattatacatgt +atatattataagtatatactatacatgcatgtattatatgtatatac------------- +---------------tatacatgcatgtattatatgtatatattatacatgcatgtatta +tatgtatatattatacatgcatgtattatatgtatatattatacatgtatgtattatatg +tatagattatacatgtatatattatatatgtatatattacacatgtacatatatgtatat +attaaacacgtttatattatttattata-------------------------------- +-------------------------------------------catgtaggtatatatga +catatgcatatatcatataggtatatatgacatatgcatatatcatataggtatatatga +tatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatacagg----- +----tatatgcgcatatatcatataggtataggt------------------ataggtag +atatatgatatatgcacacatatcatataggtatatatgatatatgcgcatatatcatat +aggtatatatgatatatg------------------------------------------ +---------------------------------------ataggtatatatgatatatga +ta--------------------------------------------ggtatatatgatat +atatcatatcggtatatatgatatatatcatatcggtatatataggtatatatcataggt +atatataggtatatatcacataggtatatataggtatatatcatataggtatatataata +tatgcatttatattatataggtatatatattacataggtatatgtaatatgtgcatatat +attatataggtatatatattatacaggcatatataatacgtatatatattatatgggcat +atatatgtgtatatattatata-------------------------------------- +------------------------------------------------------------ +------------------------------ggtatatataatatatgtgtatatattatg +tgggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtacatat +tatgtgggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtat +atattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgt +gtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatat +atgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatata +atatatgtgtatatattatgtaggtatatataatatatgtgtatatattatatatgtaat +aggaagcaggaatgaatgcacagaagaccttagagtttaaggcattatttgtgtaatgag +aaatattatatatacgtatattaatatagacgtatatataatatatacatatattaatat +agacgtatatataatatatacatatatacatatatagtatatactatgtatacatatata +ctatacatacgtatattatatacatgtgtattatatacatgtgtattatatatatgtgta +tacatatatactatatatacatacattatatacatacattatatatgtgtattatatatg +tatatattatgtatgtatatattatatatacgtatatattaatatacatatatatgtgtc +tcattataccaataatgccttaaactctaaggtcttctgtgcattcattcctgcttccta +ttacatatatattatatagatacatatataatatatacatatatactacataatatatgc +------------------------------------------------------------ +------------------------------atatataatatatacatatgttgtatatgt +atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt +atatataatatatacatatgttgtatatgtattatatgtatatattacatattatatata +cttatgtatgtataatatatatataatatatatatatcttaggcaacttttcattgctca +tttttattaaaccctgaaaactttcactttactccatttctaagtttgatattctggtag +aattaaagtaagagttttctttctttcatctcctttttatctctctca +>p:HG002_2_chr20:22081861-22084223 +ggatggttccatatttttgcagttgtgtattttgctgctataaacatgtgtgtgcaggtg +tctttttcatataacaacttcttttcctttgggtaggtttacaaaaactatctttttccc +gttcttttacttatatatgcttatttatatatattatatatacacttttaatatatactt +attaatatatattaatataatataataataatacaatataatatatgtatatatgtaggt +atataataatatacctacatatatacatatattatatatactatctgtatattatatgta +taatatatgtatatataatatatgtatatactatacatgtatatattatattatacatgt +atatattataagtatatactatacatgcatgtattatatgtatatac------------- +---------------tatacatgcatgtattatatgtatatattatacatgcatgtatta +tatgtatatattatacatgcatgtattatatgtatatattatacatgtatgtattatatg +tatagattatacatgtatatattatatatgtatatattacacatgtacatatatgtatat +attaaacacgtttatattatttattatacatgactatattatataggtatatatgatata +tgcatatatgtcatataggtatatatgacatatatgcatatatcatgtaggtatatatga +catatgcatatatcatataggtatatatgacatatgcatatatcatataggtatatatga +tatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatataggtatat +atgatatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatataggt +atatatgatatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatat +aggtatatatgatatatgcgcatatatcatacaggtatatgtgcatatatcatataggta +taggtataggtagatatatgatatatgcacacatatcatataggtatatatgatatatga +taggtatatatgatatatgataggtatatatgatatatatcatattggtatatatgatat +atatcatatcggtatatatgatatatatcatatcggtatatataggtatatatcataggt +atatataggtatatatcacataggtatatataggtatatatcatataggtatatataata +tatgcatttatattatataggtatatatattacataggtatatgtaatatgtgcatatat +attatataggtatatatattatacaggcatatataatacgtatatatattatatgggcat +atatatgtatatatattatataggtatatataatatatgtgtatatattatgtgggtata +tataatatatgtgtacatattatgtgggtatatataatatatgtgtacatattatgtggg +tatatataatatatgtgtacatattatgtgggtatatataatatatgtgtatatattatg +tgggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtatatat +tatgtgggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtat +atattatgtgggtatatataatatatgtgtatatattatgtgggtatatataatatatgt +gtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatat +atgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatata +atatatgtgtatatattatgtaggtatatataatatatgtgtatatattatatatgtaat +aggaagcaggaatgaatgcacagaagaccttagagtttaaggcattatttgtgtaatgag +aaatattatatatacg---------------------------------tatattaatat +agacgtatatataatatatacatatatacatatatagtatatactatgtatacatatata +ctatacatacgtatattatatacatgtgtattatatacatgtgtattatatatatgtgta +tacatatatactatatatacatacattatatacatacattatatatgtgtattatatatg +tatatattatgtatgtatatattatatatacgtatatattaatatgcatatatatgtgtc +tctttataccaataatgccttaaactctaaggtcttctgtgcattcattcctgcttccta +ttacatatatattatatagatacatatataatatatacatatatactacataatatatgc +atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt +atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt +atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt +atatataatatatacatatgttgtatatgtattatatgtatatattacatattatatata +cttatgtatgtataatatatatataatatatatatatcttaggcaacttttcattgctca +tttttattaaaccctgaaaactttcactttactccatttctaagtttgatattctggtag +aattaaagtaagagttttctttctttcatctcctttttatctctctca diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/msa.fa.fai new file mode 100644 index 00000000..460d3d7e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_22081861_22084223 2808 29 60 61 +syndip_1_chr20:22081861-22084223 2808 2918 60 61 +syndip_2_chr20:22081861-22084223 2808 5807 60 61 +p:HG002_1_chr20:22081861-22084223 2808 8697 60 61 +p:HG002_2_chr20:22081861-22084223 2808 11587 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/output.vcf.gz new file mode 100644 index 00000000..957f844a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/output.vcf.gz.tbi new file mode 100644 index 00000000..fa965b47 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:22081961-22084123/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/base.vcf.gz new file mode 100644 index 00000000..ea5e9304 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/base.vcf.gz.tbi new file mode 100644 index 00000000..6b95d169 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/comp.vcf.gz new file mode 100644 index 00000000..8813d50b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/comp.vcf.gz.tbi new file mode 100644 index 00000000..dc5513d1 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/haps.fa new file mode 100644 index 00000000..87aa5032 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/haps.fa @@ -0,0 +1,74 @@ +>ref_chr20_2240825_2241827 +GTGACCCTTAGGTAAATCGTTCCAACTCTCTGAGCCTCAGTGTTGTTATCTACAAATGGGAGAATCAAGGCACCCTCCTACAAGCGGCGGCTCATCAGCTCACTTGGAAAATGTAGTCATCTTCTCAAAGTTTTCTTTTTCTTTCTTTCTTTTTCCTTTCTTTCTTTCTTTTTCTTTCTTTCTCTCTCTCTCCTTCCTTCCTTCTTTCCTTCCCTCCCTCCCTTCCTTTTTTCTTCTTTCTTTCATTTTCTTTCTTTCTCTCTTTCTTCTTTCTCTTCCTTTCTTTCCTTCCGTCCCTCCCTTCCTTCCTTTTTTCTTCTTCCTTTCATTTTCTTTCTTTCTCTCTTTCTTCTTTCTCTTCCTTTCTTCTTTCTTTTCCTCCTTCCTCCCTTCTTTCCTTCCCTTCCTTCTTCCCTCCCTCCCTCTTTGTTTCTTTCTTTCTCTCCCTCCTTCCCTCCCTCCCTTTCTGTCTCCCTCTTTCTTTCTCTTTTTTCTTTTCCTTCCTTCCGTCTTTTTCCTCCCTTCTTTCCTCCCTCCTCCCTCCCTCCCTCCTCCCTCTTTTTCTTTCTTTCTTTCTTTTTTCTTTCTCTCTTCTTTTTTTTTTTTTTTTTTTAAGAGATAGGGTCTGTTGCCCAGGCTGGAGTGCAGTGGCATGATCATGGTTCACTGCAGCCTTGAACTCCTGGGCTCAGGTGATCCTCCTACCTCAGCCTCCTAAGTAGCTGGGACTATAGGTGCATGCCATCACACCCAGCTAATTTTTTAAAAGAAATTTTGTAAAGACAGGGGTCTTGCTATGTTCCCCAGGCTGGTCTCAAACTCCTGGGCTCAAGTGATCCTCCAGCCTCAGTATCCCAAAGTGCTGGGATTATAGGTGTGAGTCACTGCAGCCAGCTCAAATATTTTCTTAAATGAATGTAAGGTTGAGGATGCATTATTATAATGGCTAATTTAGATCTAAAAAATGCTTTGCAGTTTACCAGATTCACTTATGTACATTCTC +>syndip_1_chr20:2240825-2241827 +GTGACCCTTAGGTAAATCGTTCCAACTCTCTGAGCCTCAGTGTTGTTATCTACAAATGGG +AGAATCAAGGCACCCTCCTACAAGCGGCGGCTCATCAGCTCACTTGGAAAATGTAGTCAT +CTTCTCAAAGTTTTCTTTTTCTTTCTTTCTTTTTCCTTTCTTTCTTTCTTTTTCTTTCTT +TCTCTCTCTCTCCTTCCTTCCTTCTTTCCTTCCCTCCCTCCCTTCCTTTTTTCTTCTTTC +TTTCATTTTCTTTCTTTCTCTCTTTCTTCTTTCTCTTCCTTTCTTCTTTCTTTTCCTCCT +TCCTCCCTTCTTTCCTTCCCTTCCTTCTTCCCTCCCTCCCTCTTTGTTTCTTTCTTTCTC +TCCCTCCTTCCCTCCCTCCCTTTCTTTCTCCTTTTCTTCCTTCCCTCCCTGCCTGTCTCC +CTCTTTCTTTCTCTTTTTTCTTTTCCTTCCTTCCGTCTTTTTCCTCCCTTCTTTCCTCCC +TCCTCCCTCCCTCCCTCCTCCCTCTTTTTCTTTCTTTCTTTCTTTTTTCTTTCTCTCTTC +TTTTTTTTTTTTTTTTTTAAGAGATAGGGTCTGTTGCCCAGGCTGGAGTGCAGTGGCATG +ATCATGGTTCACTGCAGCCTTGAACTCCTGGGCTCAGGTGATCCTCCTACCTCAGCCTCC +TAAGTAGCTGGGACTATAGGTGCATGCCATCACACCCAGCTAATTTTTTAAAAGAAATTT +TGTAAAGACAGGGGTCTTGCTATGTTCCCCAGGCTGGTCTCAAACTCCTGGGCTCAAGTG +ATCCTCCAGCCTCAGTATCCCAAAGTGCTGGGATTATAGGTGTGAGTCACTGCAGCCAGC +TCAAATATTTTCTTAAATGAATGTAAGGTTGAGGATGCATTATTATAATGGCTAATTTAG +ATCTAAAAAATGCTTTGCAGTTTACCAGATTCACTTATGTACATTCTC +>syndip_2_chr20:2240825-2241827 +GTGACCCTTAGGTAAATCGTTCCAACTCTCTGAGCCTCAGTGTTGTTATCTACAAATGGG +AGAATCAAGGCACCCTCCTACAAGCGGCGGCTCATCAGCTCACTTGGAAAATGTAGTCAT +CTTCTCAAAGTTTTCTTTTTCTTTCTTTCTTTTTCTTTCTTTCTCTCTCTCTCCTTCCTT +CCTTCTTTCCTTCCCTCCCTCCCTTCCTTTTTTCTTCTTCCTTTCATTTTCTTTCTTTCT +CTCTTTCTTCTTTCTCTTCCTTTCTTCTTTCTTTTCCTCCTTCCTCCCTTCTTTCCTTCC +CTTCCTTCTTCCCTCCCTCCCTCTTTGTTTCTTTCTTTCTCTCCCTCCTTCCCTCCCTCC +CTTTCTTCCTTCTTTCCTTATCCCTCCCTTCTTTCCTTCCTTCCCTTTGTTTCTCTTTCT +TTCTTTCTTTCTCTCTCTCTTCCTTCCTTCCCTCCCTCCCTCCCTCCTTCCTCCCTTCTT +TCCTTCCCTCCCTGCCTCTCTGTCTCCCTCTTTCTTTCTCTTTTTTCTTTTCCTTCCTTC +CGTCTTTTTCCTCCCTTCTTTCCTCCCTCCTCCCTCCCTCCCTCCTCCCTCTTTTTCTTT +CTTTCTTTCTTTTTTCTCTCTCTCTTCTTTTTTTTTTTTTTTTTTTAAGAGATAGGGTCT +GTTGCCCAGGCTGGAGTGCAGTGGCATGATCATGGTTCACTGCAGCCTTGAACTCCTGGG +CTCAGGTGATCCTCCTACCTCAGCCTCCTAAGTAGCTGGGACTATAGGTGCATGCCATCA +CACCCAGCTAATTTTTTAAAAGAAATTTTGTAAAGACAGGGGTCTTGCTATGTTCCCCAG +GCTGGTCTCAAACTCCTGGGCTCAAGTGATCCTCCAGCCTCAGTATCCCAAAGTGCTGGG +ATTATAGGTGTGAGTCACTGCAGCCAGCTCAAATATTTTCTTAAATGAATGTAAGGTTGA +GGATGCATTATTATAATGGCTAATTTAGATCTAAAAAATGCTTTGCAGTTTACCAGATTC +ACTTATGTACATTCTC +>p:HG002_1_chr20:2240825-2241827 +GTGACCCTTAGGTAAATCGTTCCAACTCTCTGAGCCTCAGTGTTGTTATCTACAAATGGG +AGAATCAAGGCACCCTCCTACAAGCGGCGGCTCATCAGCTCACTTGGAAAATGTAGTCAT +CTTCTCAAAGTTTTCTTTTTCTTTCTTTCTTTTTCTTTCTTTCTCTCTCTCTCCTTCCTT +CCTTCTTTCCTTCCCTCCCTCCCTTCCTTTTTTCTTCTTCCTTTCATTTTCTTTCTTTCT +CTCTTTCTTCTTTCTCTTCCTTTCTTCTTTCTTTTCCTCCTTCCTCCCTTCTTTCCTTCC +CTTCCTTCTTCCCTCCCTCCCTCTTTGTTTCTTTCTTTCTCTCCCTCCTTCCCTCCCTCC +CTTTCTTCCTTCTTTCCTTATCCCTCCCTTCTTTCCTTCCTTCCCTTTGTTTCTCTTTCT +TTCTTTCTTTCTCTCTCTCTTCCTTCCTTCCCTCCCTCCCTCCCTCCTTCCTCCCTTCTT +TCCTTCCCTCCCTGCCTCTCTGTCTCCCTCTTTCTTTCTCTTTTTTCTTTTCCTTCCTTC +CGTCTTTTTCCTCCCTTCTTTCCTCCCTCCTCCCTCCCTCCCTCCTCCCTCTTTTTCTTT +CTTTCTTTCTTTTTTCTCTCTCTCTTCTTTTTTTTTTTTTTTTTTTAAGAGATAGGGTCT +GTTGCCCAGGCTGGAGTGCAGTGGCATGATCATGGTTCACTGCAGCCTTGAACTCCTGGG +CTCAGGTGATCCTCCTACCTCAGCCTCCTAAGTAGCTGGGACTATAGGTGCATGCCATCA +CACCCAGCTAATTTTTTAAAAGAAATTTTGTAAAGACAGGGGTCTTGCTATGTTCCCCAG +GCTAGTCTCAAACTCCTGGGCTCAAGTGATCCTCCAGCCTCAGTATCCCAAAGTGCTGGG +ATTATAGGTGTGAGTCACTGCAGCCAGCTCAAATATTTTCTTAAATGAATGTAAGGTTGA +GGATGCATTATTATAATGGCTAATTTAGATCTAAAAAATGCTTTGCAGTTTACCAGATTC +ACTTATGTACATTCTC +>p:HG002_2_chr20:2240825-2241827 +GTGACCCTTAGGTAAATCGTTCCAACTCTCTGAGCCTCAGTGTTGTTATCTACAAATGGG +AGAATCAAGGCACCCTCCTACAAGCGGCGGCTCATCAGCTCACTTGGAAAATGTAGTCAT +CTTCTCAAAGTTTTCTTTTTCTTTCTTTCTTTTTCCTTTCTTTCTTTCTTTTTCTTTCTT +TCTCTCTCTCTCCTTCCTTCCTTCTTTCCTTCCCTCCCTCCCTTCCTTTTTTCTTCTTTC +TTTCATTTTCTTTCTTTCTCTCTTTCTTCTTTCTCTTCCTTTCTTCTTTCTTTTCCTCCT +TCCTCCCTTCTTTCCTTCCCTTCCTTCTTCCCTCCCTCCCTCTTTGTTTCTTTCTTTCTC +TCCCTCCTTCCCTCCCTCCCTTTCTTTCTCCTTTTCTTCCTTCCCTCCCTGCCTGTCTCC +CTCTTTCTTTCTCTTTTTTCTTTTCCTTCCTTCCGTCTTTTTCCTCCCTTCTTTCCTCCC +TCCTCCCTCCCTCCCTCCTCCCTCTTTTTCTTTCTTTCTTTCTTTTTTCTTTCTCTCTTC +TTTTTTTTTTTTTTTTTTAAGAGATAGGGTCTGTTGCCCAGGCTGGAGTGCAGTGGCATG +ATCATGGTTCACTGCAGCCTTGAACTCCTGGGCTCAGGTGATCCTCCTACCTCAGCCTCC +TAAGTAGCTGGGACTATAGGTGCATGCCATCACACCCAGCTAATTTTTTAAAAGAAATTT +TGTAAAGACAGGGGTCTTGCTATGTTCCCCAGGCTGGTCTCAAACTCCTGGGCTCAAGTG +ATCCTCCAGCCTCAGTATCCCAAAGTGCTGGGATTATAGGTGTGAGTCACTGCAGCCAGC +TCAAATATTTTCTTAAATGAATGTAAGGTTGAGGATGCATTATTATAATGGCTAATTTAG +ATCTAAAAAATGCTTTGCAGTTTACCAGATTCACTTATGTACATTCTC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/haps.fa.ref.fa new file mode 100644 index 00000000..10349967 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:2240825-2241827 +GTGACCCTTAGGTAAATCGTTCCAACTCTCTGAGCCTCAGTGTTGTTATCTACAAATGGGAGAATCAAGGCACCCTCCTACAAGCGGCGGCTCATCAGCTCACTTGGAAAATGTAGTCATCTTCTCAAAGTTTTCTTTTTCTTTCTTTCTTTTTCCTTTCTTTCTTTCTTTTTCTTTCTTTCTCTCTCTCTCCTTCCTTCCTTCTTTCCTTCCCTCCCTCCCTTCCTTTTTTCTTCTTTCTTTCATTTTCTTTCTTTCTCTCTTTCTTCTTTCTCTTCCTTTCTTTCCTTCCGTCCCTCCCTTCCTTCCTTTTTTCTTCTTCCTTTCATTTTCTTTCTTTCTCTCTTTCTTCTTTCTCTTCCTTTCTTCTTTCTTTTCCTCCTTCCTCCCTTCTTTCCTTCCCTTCCTTCTTCCCTCCCTCCCTCTTTGTTTCTTTCTTTCTCTCCCTCCTTCCCTCCCTCCCTTTCTGTCTCCCTCTTTCTTTCTCTTTTTTCTTTTCCTTCCTTCCGTCTTTTTCCTCCCTTCTTTCCTCCCTCCTCCCTCCCTCCCTCCTCCCTCTTTTTCTTTCTTTCTTTCTTTTTTCTTTCTCTCTTCTTTTTTTTTTTTTTTTTTTAAGAGATAGGGTCTGTTGCCCAGGCTGGAGTGCAGTGGCATGATCATGGTTCACTGCAGCCTTGAACTCCTGGGCTCAGGTGATCCTCCTACCTCAGCCTCCTAAGTAGCTGGGACTATAGGTGCATGCCATCACACCCAGCTAATTTTTTAAAAGAAATTTTGTAAAGACAGGGGTCTTGCTATGTTCCCCAGGCTGGTCTCAAACTCCTGGGCTCAAGTGATCCTCCAGCCTCAGTATCCCAAAGTGCTGGGATTATAGGTGTGAGTCACTGCAGCCAGCTCAAATATTTTCTTAAATGAATGTAAGGTTGAGGATGCATTATTATAATGGCTAATTTAGATCTAAAAAATGCTTTGCAGTTTACCAGATTCACTTATGTACATTCTC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/msa.fa new file mode 100644 index 00000000..59b6ae59 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/msa.fa @@ -0,0 +1,95 @@ +>ref_chr20_2240825_2241827 +gtgacccttaggtaaatcgttccaactctctgagcctcagtgttgttatctacaaatggg +agaatcaaggcaccctcctacaagcggcggctcatcagctcacttggaaaatgtagtcat +cttctcaaagttttctttttctttctttctttttcctttctttctttctttttctttctt +tctctctctctccttccttccttctttccttccctccctcccttccttttttcttctttc +tttcattttctttctttctctctttcttctttctcttcctttctt--------------- +tccttccgtccctcccttccttccttttttcttcttcctttcat--tttctttctttctc +tctttcttctttctcttcctttcttctttcttttcctccttcctcccttctttccttccc +ttcctt-----------------------------------cttccctccctccctcttt +gtttctttctttctctccctccttccctccctccctttctgtctccctctttctttctct +tttttcttttccttccttccgtctttttcctcccttctttcctccctcctccctccctcc +ctcctccctctttttctttctttctttcttttttctttctctcttctttttttttttttt +tttttaagagatagggtctgttgcccaggctggagtgcagtggcatgatcatggttcact +gcagccttgaactcctgggctcaggtgatcctcctacctcagcctcctaagtagctggga +ctataggtgcatgccatcacacccagctaattttttaaaagaaattttgtaaagacaggg +gtcttgctatgttccccaggctggtctcaaactcctgggctcaagtgatcctccagcctc +agtatcccaaagtgctgggattataggtgtgagtcactgcagccagctcaaatattttct +taaatgaatgtaaggttgaggatgcattattataatggctaatttagatctaaaaaatgc +tttgcagtttaccagattcacttatgtacattctc +>syndip_1_chr20:2240825-2241827 +gtgacccttaggtaaatcgttccaactctctgagcctcagtgttgttatctacaaatggg +agaatcaaggcaccctcctacaagcggcggctcatcagctcacttggaaaatgtagtcat +cttctcaaagttttctttttctttctttctttttcctttctttctttctttttctttctt +tctctctctctccttccttccttctttccttccctccctcccttccttttttcttctttc +tttcattttctttctttctctctttcttctttctcttcctttctt--------------- +-------------------------------------------c--tttcttttcctcct +tcctcccttctttccttcccttccttcttccctccctccctctttgtttctttctttctc +tccctc-----------------------------------cttccctccctccctttct +ttctcctt-----------ttcttccttccctccctgcctgtctccctctttctttctct +tttttcttttccttccttccgtctttttcctcccttctttcctccctcctccctccctcc +ctcctccctctttttctttctttctttcttttttctttctctcttc-ttttttttttttt +tttttaagagatagggtctgttgcccaggctggagtgcagtggcatgatcatggttcact +gcagccttgaactcctgggctcaggtgatcctcctacctcagcctcctaagtagctggga +ctataggtgcatgccatcacacccagctaattttttaaaagaaattttgtaaagacaggg +gtcttgctatgttccccaggctggtctcaaactcctgggctcaagtgatcctccagcctc +agtatcccaaagtgctgggattataggtgtgagtcactgcagccagctcaaatattttct +taaatgaatgtaaggttgaggatgcattattataatggctaatttagatctaaaaaatgc +tttgcagtttaccagattcacttatgtacattctc +>syndip_2_chr20:2240825-2241827 +gtgacccttaggtaaatcgttccaactctctgagcctcagtgttgttatctacaaatggg +agaatcaaggcaccctcctacaagcggcggctcatcagctcacttggaaaatgtagtcat +cttctcaaagttttctt-------------------tttctttctttctttttctttctt +tctctctctctccttccttccttctttccttccctccctcccttccttttttcttcttcc +tttcattttctttctttctctctttcttctttctcttcctttcttctttcttttcctcct +tcctcccttctttccttcccttccttcttccctccctccctctttgtttctttctttctc +tccctccttccctccctccctttcttccttctttccttatccctcccttctttccttcct +tccctttgtttctctttctttctttctttctctctctcttccttccttccctccctccct +ccctccttcctcccttctttccttccctccctgcctctctgtctccctctttctttctct +tttttcttttccttccttccgtctttttcctcccttctttcctccctcctccctccctcc +ctcctccctctttttctttctttctttcttttttctctctctcttctttttttttttttt +tttttaagagatagggtctgttgcccaggctggagtgcagtggcatgatcatggttcact +gcagccttgaactcctgggctcaggtgatcctcctacctcagcctcctaagtagctggga +ctataggtgcatgccatcacacccagctaattttttaaaagaaattttgtaaagacaggg +gtcttgctatgttccccaggctggtctcaaactcctgggctcaagtgatcctccagcctc +agtatcccaaagtgctgggattataggtgtgagtcactgcagccagctcaaatattttct +taaatgaatgtaaggttgaggatgcattattataatggctaatttagatctaaaaaatgc +tttgcagtttaccagattcacttatgtacattctc +>p:HG002_1_chr20:2240825-2241827 +gtgacccttaggtaaatcgttccaactctctgagcctcagtgttgttatctacaaatggg +agaatcaaggcaccctcctacaagcggcggctcatcagctcacttggaaaatgtagtcat +cttctcaaagttttctt-------------------tttctttctttctttttctttctt +tctctctctctccttccttccttctttccttccctccctcccttccttttttcttcttcc +tttcattttctttctttctctctttcttctttctcttcctttcttctttcttttcctcct +tcctcccttctttccttcccttccttcttccctccctccctctttgtttctttctttctc +tccctccttccctccctccctttcttccttctttccttatccctcccttctttccttcct +tccctttgtttctctttctttctttctttctctctctcttccttccttccctccctccct +ccctccttcctcccttctttccttccctccctgcctctctgtctccctctttctttctct +tttttcttttccttccttccgtctttttcctcccttctttcctccctcctccctccctcc +ctcctccctctttttctttctttctttcttttttctctctctcttctttttttttttttt +tttttaagagatagggtctgttgcccaggctggagtgcagtggcatgatcatggttcact +gcagccttgaactcctgggctcaggtgatcctcctacctcagcctcctaagtagctggga +ctataggtgcatgccatcacacccagctaattttttaaaagaaattttgtaaagacaggg +gtcttgctatgttccccaggctagtctcaaactcctgggctcaagtgatcctccagcctc +agtatcccaaagtgctgggattataggtgtgagtcactgcagccagctcaaatattttct +taaatgaatgtaaggttgaggatgcattattataatggctaatttagatctaaaaaatgc +tttgcagtttaccagattcacttatgtacattctc +>p:HG002_2_chr20:2240825-2241827 +gtgacccttaggtaaatcgttccaactctctgagcctcagtgttgttatctacaaatggg +agaatcaaggcaccctcctacaagcggcggctcatcagctcacttggaaaatgtagtcat +cttctcaaagttttctttttctttctttctttttcctttctttctttctttttctttctt +tctctctctctccttccttccttctttccttccctccctcccttccttttttcttctttc +tttcattttctttctttctctctttcttctttctcttcctttctt--------------- +-------------------------------------------c--tttcttttcctcct +tcctcccttctttccttcccttccttcttccctccctccctctttgtttctttctttctc +tccctc-----------------------------------cttccctccctccctttct +ttctcctt-----------ttcttccttccctccctgcctgtctccctctttctttctct +tttttcttttccttccttccgtctttttcctcccttctttcctccctcctccctccctcc +ctcctccctctttttctttctttctttcttttttctttctctcttc-ttttttttttttt +tttttaagagatagggtctgttgcccaggctggagtgcagtggcatgatcatggttcact +gcagccttgaactcctgggctcaggtgatcctcctacctcagcctcctaagtagctggga +ctataggtgcatgccatcacacccagctaattttttaaaagaaattttgtaaagacaggg +gtcttgctatgttccccaggctggtctcaaactcctgggctcaagtgatcctccagcctc +agtatcccaaagtgctgggattataggtgtgagtcactgcagccagctcaaatattttct +taaatgaatgtaaggttgaggatgcattattataatggctaatttagatctaaaaaatgc +tttgcagtttaccagattcacttatgtacattctc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/msa.fa.fai new file mode 100644 index 00000000..216b9d85 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_2240825_2241827 1055 27 60 61 +syndip_1_chr20:2240825-2241827 1055 1132 60 61 +syndip_2_chr20:2240825-2241827 1055 2237 60 61 +p:HG002_1_chr20:2240825-2241827 1055 3343 60 61 +p:HG002_2_chr20:2240825-2241827 1055 4449 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/output.vcf.gz new file mode 100644 index 00000000..6a726900 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/output.vcf.gz.tbi new file mode 100644 index 00000000..6c7562c4 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:2240925-2241727/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/base.vcf.gz new file mode 100644 index 00000000..0e4acc3b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/base.vcf.gz.tbi new file mode 100644 index 00000000..7c03422c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/comp.vcf.gz new file mode 100644 index 00000000..7c0e1e38 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/comp.vcf.gz.tbi new file mode 100644 index 00000000..f9399ed9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/haps.fa new file mode 100644 index 00000000..5e387a1b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/haps.fa @@ -0,0 +1,68 @@ +>ref_chr20_23155404_23156076 +GGGAAAGACACAGAGGTAGAATCTGCGTTAGGAATAAAAACCGCTACTCTCCGTTGTTCTGTGTGCTTTTGCAGTCATGATTGATGCAGGCAGCACCCTTCTGCAGAAGTAAATTTTGCCCTGCAGCACAAAAGAGGAAGGAAAGCAAGGGAAGGGAAGGGGAGGGGAGGAAGGGAAGGAAAAGAGAGAGAAAGAGAAAGAGAGAAAGAGAGGAAGGAAGGAAGGAAGGAGAGAGAGAAAGAAAGAAGGAAAGAGGAAGGAAGGAAGAAAGAAAAGAAAGAAAGAAAAAAGAAAGAAAGGAAGGAGAGAAAGAAATGAAAGAGAAAGAAAGAAAGAAAGAAAGAAAGGAGAGAAAAAGGAAAAACAAAGAAAGAGAAAAGAAGGAGAGAAGGAAAGGAAAAAGAAAGAAAGAAGGAAAGAAAGAAAAAAGAAGGAAAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAAAGAGAAAGGAAGGAAGGAAGGAAGGTCTTAACACCTTGGTAATTTTTGTGCTCTTCCCTGGACTTTGGACTTTGCAGCCTTAGGGAGACAGAGCTCTTTAATGTACACTTTCCCATCAGGCACTGCATGGCCAAGAACCTGCCTGCAAAGCCCCCA +>syndip_1_chr20:23155404-23156076 +GGGAAAGACACAGAGGTAGAATCTGCGTTAGGAATAAAAACCGCTACTCTCCGTTGTTCT +GTGTGCTTTTGCAGTCATGATTGATGCAGGCAGCACCCTTCTGCAGAAGTAAATTTTGCC +CTGCAGCACAAAAGAGGAAGGAAAGCAAGGGAAGGGAAGGGGAGGGGAGGAAGGGAAGGG +GAGGGGAGGAAGGGAAGGGGAGGGGAGGAAGGCGAGGTGAGGGGAGGAGAGGTGAGGGGA +GGGGGGGAGGGGAGGGGAGGGAGAGTGAGGAAGAGAGAGAGAAAGGGAGAGAGGAAGGAA +AGAAGAAAGGAAGGAAGGAAAGAAGGAAGGAAGGGAGGGAGGGAGGGAGGAAAGAAGGAA +GGAAAGGAGGGAGGAAGGGAGGGAAAGAGAGAGAGAGGAAAAGAGAGAGAAAGAGAAAGA +GAGAAAGAGAGGAAGGAAGGAAGGAAGGAGAGAGAGAAAGAAAGAAGGAAAGAGGAAGGA +AGGAAGAAAGAAAAGAAAGAAAGAAAAAAGAAAGAAAGGAAGGAGAGAAAGAAATGAAAG +AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGGAGAGAAAAAGGAAAAACAAAGAAAG +AGAAAAGAAGGAGAGAAGGAAAGGAAAAAGAAAGAAAGAAGGAAAGAAAGAAAAAAGAAG +GAAAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG +AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAAAGAGAAAGGAAGGAAGGAAGGAAG +GTCTTAACACCTTGGTAATTTTTGTGCTCTTCCCTGGACTTTGGACTTTGCAGCCTTAGG +GAGACAGAGCTCTTTAATGTACACTTTCCCATCAGGCACTGCATGGCCAAGAACCTGCCT +GCAAAGCCCCCA +>syndip_2_chr20:23155404-23156076 +GGGAAAGACACAGAGGTAGAATCTGCGTTAGGAATAAAAACCGCTACTCTCCGTTGTTCT +GTGTGCTTTTGCAGTCATGATTGATGCAGGCAGCACCCTTCTGCAGAAGTAAATTTTGCC +CTGCAGCACAAAAGAGGAAGGAAAGCAAGGGAAGGGAAGGGGAGGGGAGGAAGGGAAGGG +GAGGGGAGGAAGGCGAGGTGAGGGGAGGAGAGGTGAGGGGAGGGGGGGAGGGGAGGGGAG +GGAGAGTGAGGAAGAGAGAGAGAAAGGGAGAGAGGAAGGAAAGAAGAAAGGAAGGAAGGA +AAGAAGGAAGGAAGGGAGGGAGGGAGGGAGGAAAGAAGGAAGGAAAGGAGGGAGGAAGGG +AGGGAAAGAGAGAGAGAGGAAAAGAGAGAGAAAGAGAAAGAGAGAAAGAGAGGAAGGAAG +GAAGGAAGGAGAGAGAGAAAGAAAGAAGGAAAGAGGAAGGAAGGAAGAAAGAAAAGAAAG +AAAGAAAAAAGAAAGAAAGGAAGGAGAGAAAGAAATGAAAGAGAAAGAAAGAAAGAAAGA +AAGAAAGAAAGGAGAGAAAAAGGAAAAACAAAGAAAGAGAAAAGAAGGAGAGAAGGAAAG +GAAAAAGAAAGAAAGAAGGAAAGAAAGAAAAAAGAAGGAAAGAAAGAAGAAAGAAAGAAA +GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAAAGAGAAAGGAA +GGAAGGAAGGAAGGTCTTAACACCTTGGTAATTTTTGTGCTCTTCCCTGGACTTTGGACT +TTGCAGCCTTAGGGAGACAGAGCTCTTTAATGTACACTTTCCCATCAGGCACTGCATGGC +CAAGAACCTGCCTGCAAAGCCCCCA +>p:HG002_1_chr20:23155404-23156076 +GGGAAAGACACAGAGGTAGAATCTGCGTTAGGAATAAAAACCGCTACTCTCCGTTGTTCT +GTGTGCTTTTGCAGTCATGATTGATGCAGGCAGCACCCTTCTGCAGAAGTAAATTTTGCC +CTGCAGCACAAAAGAGGAAGGAAAGCAAGGGAAGGGAAGGGGAGGGGAGGAAGGGAAGGG +GAGGGGAGGAAGGCGAGGTGAGGGGAGGAGAGGTGAGGGGAGGGGGGGAGGGGAGGGGAG +GGAGAGTGAGGAAGAGAGAGAGAAAGGGAGAGAGGAAGGAAAGAAGAAAGGAAGGAAGGA +AAGAAGGAAGGAAGGGAGGGAGGGAGGGAGGAAAGAAGGAAGGAAAGGAGGGAGGAAGGG +AGGGAAAGAGAGAGAGAGGAAAAGAGAGAGAAAGAGAAAGAGAGAAAGAGAGGAAGGAAG +GAAGGAAGGAGAGAGAGAAAGAAAGAAGGAAAGAGGAAGGAAGGAAGAAAGAAAAGAAAG +AAAGAAAAAAGAAAGAAAGGAAGGAGAGAAAGAAATGAAAGAGAAAGAAAGAAAGAAAGA +AAGAAAGAAAGGAGAGAAAAAGGAAAAACAAAGAAAGAGAAAAGAAGGAGAGAAGGAAAG +GAAAAAGAAAGAAAGAAGGAAAGAAAGAAAAAAGAAGGAAAGAAAGAAGAAAGAAAGAAA +GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAAAGAGAAAGGAA +GGAAGGAAGGAAGGTCTTAACACCTTGGTAATTTTTGTGCTCTTCCCTGGACTTTGGACT +TTGCAGCCTTAGGGAGACAGAGCTCTTTAATGTACACTTTCCCATCAGGCACTGCATGGC +CAAGAACCTGCCTGCAAAGCCCCCA +>p:HG002_2_chr20:23155404-23156076 +GGGAAAGACACAGAGGTAGAATCTGCGTTAGGAATAAAAACCGCTACTCTCCGTTGTTCT +GTGTGCTTTTGCAGTCATGATTGATGCAGGCAGCACCCTTCTGCAGAAGTAAATTTTGCC +CTGCAGCACAAAAGAGGAAGGAAAGCAAGGGAAGGGAAGGGGAGGGGAGGAAGGGAAGGG +GAGGGGAGGAAGGGAAGGGGAGGGGAGGAAGGCGAGGTGAGGGGAGGAGAGGTGAGGGGA +GGGGGGGAGGGGAGGGGAGGGAGAGTGAGGAAGAGAGAGAGAAAGGGAGAGAGGAAGGAA +AGAAGAAAGGAAGGAAGGAAAGAAGGAAGGAAGGGAGGGAGGGAGGGAGGAAAGAAGGAA +GGAAAGGAGGGAGGAAGGGAGGGAAAGAGAGAGAGAGGAAAAGAGAGAGAAAGAGAAAGA +GAGAAAGAGAGGAAGGAAGGAAGGAAGGAGAGAGAGAAAGAAAGAAGGAAAGAGGAAGGA +AGGAAGAAAGAAAAGAAAGAAAGAAAAAAGAAAGAAAGGAAGGAGAGAAAGAAATGAAAG +AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGGAGAGAAAAAGGAAAAACAAAGAAAG +AGAAAAGAAGGAGAGAAGGAAAGGAAAAAGAAAGAAAGAAGGAAAGAAAGAAAAAAGAAG +GAAAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG +AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAAAGAGAAAGGAAGGAAGGAAGGAAG +GTCTTAACACCTTGGTAATTTTTGTGCTCTTCCCTGGACTTTGGACTTTGCAGCCTTAGG +GAGACAGAGCTCTTTAATGTACACTTTCCCATCAGGCACTGCATGGCCAAGAACCTGCCT +GCAAAGCCCCCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/haps.fa.ref.fa new file mode 100644 index 00000000..74c4f4f3 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:23155404-23156076 +GGGAAAGACACAGAGGTAGAATCTGCGTTAGGAATAAAAACCGCTACTCTCCGTTGTTCTGTGTGCTTTTGCAGTCATGATTGATGCAGGCAGCACCCTTCTGCAGAAGTAAATTTTGCCCTGCAGCACAAAAGAGGAAGGAAAGCAAGGGAAGGGAAGGGGAGGGGAGGAAGGGAAGGAAAAGAGAGAGAAAGAGAAAGAGAGAAAGAGAGGAAGGAAGGAAGGAAGGAGAGAGAGAAAGAAAGAAGGAAAGAGGAAGGAAGGAAGAAAGAAAAGAAAGAAAGAAAAAAGAAAGAAAGGAAGGAGAGAAAGAAATGAAAGAGAAAGAAAGAAAGAAAGAAAGAAAGGAGAGAAAAAGGAAAAACAAAGAAAGAGAAAAGAAGGAGAGAAGGAAAGGAAAAAGAAAGAAAGAAGGAAAGAAAGAAAAAAGAAGGAAAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAAAGAGAAAGGAAGGAAGGAAGGAAGGTCTTAACACCTTGGTAATTTTTGTGCTCTTCCCTGGACTTTGGACTTTGCAGCCTTAGGGAGACAGAGCTCTTTAATGTACACTTTCCCATCAGGCACTGCATGGCCAAGAACCTGCCTGCAAAGCCCCCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/msa.fa new file mode 100644 index 00000000..c61ccc31 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/msa.fa @@ -0,0 +1,85 @@ +>ref_chr20_23155404_23156076 +gggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttct +gtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgcc +ctgcagcacaaaagaggaaggaaagcaag-------------------ggaagggaaggg +gaggggaggaaggga--------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------aggaaaagagagagaaagagaaaga +gagaaagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaagga +aggaagaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag +--------agaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaag +agaaaagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaag +gaaagaaag------------aagaaagaaagaaagaaagaaagaaagaaagaaagaaag +aaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaag +gtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttagg +gagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcct +gcaaagccccca +>syndip_1_chr20:23155404-23156076 +gggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttct +gtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgcc +ctgcagcacaaaagaggaaggaaagcaagggaagggaaggggaggggaggaagggaaggg +gaggggaggaagggaaggggaggggaggaaggcgaggtgaggggaggagaggtgagggga +gggggggaggggaggggagggagagtgaggaagagagagagaaagggagagaggaaggaa +agaagaaaggaaggaaggaaagaaggaaggaagggagggagggagggaggaaagaaggaa +ggaaaggagggaggaagggagggaaagagagagagaggaaaagagagagaaagagaaaga +gagaaagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaagga +aggaagaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag +agaaagaaagaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaag +agaaaagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaag +gaaagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag +aaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaag +gtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttagg +gagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcct +gcaaagccccca +>syndip_2_chr20:23155404-23156076 +gggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttct +gtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgcc +ctgcagcacaaaagaggaaggaaagcaag-------------------ggaagggaaggg +gaggggaggaagggaaggggaggggaggaaggcgaggtgaggggaggagaggtgagggga +gggggggaggggaggggagggagagtgaggaagagagagagaaagggagagaggaaggaa +agaagaaaggaaggaaggaaagaaggaaggaagggagggagggagggaggaaagaaggaa +ggaaaggagggaggaagggagggaaagagagagagaggaaaagagagagaaagagaaaga +gagaaagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaagga +aggaagaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag +----agaaagaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaag +agaaaagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaag +gaaagaaag------------------------aagaaagaaagaaagaaagaaagaaag +aaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaag +gtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttagg +gagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcct +gcaaagccccca +>p:HG002_1_chr20:23155404-23156076 +gggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttct +gtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgcc +ctgcagcacaaaagaggaaggaaagcaag-------------------ggaagggaaggg +gaggggaggaagggaaggggaggggaggaaggcgaggtgaggggaggagaggtgagggga +gggggggaggggaggggagggagagtgaggaagagagagagaaagggagagaggaaggaa +agaagaaaggaaggaaggaaagaaggaaggaagggagggagggagggaggaaagaaggaa +ggaaaggagggaggaagggagggaaagagagagagaggaaaagagagagaaagagaaaga +gagaaagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaagga +aggaagaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag +----agaaagaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaag +agaaaagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaag +gaaagaaag------------------------aagaaagaaagaaagaaagaaagaaag +aaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaag +gtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttagg +gagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcct +gcaaagccccca +>p:HG002_2_chr20:23155404-23156076 +gggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttct +gtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgcc +ctgcagcacaaaagaggaaggaaagcaagggaagggaaggggaggggaggaagggaaggg +gaggggaggaagggaaggggaggggaggaaggcgaggtgaggggaggagaggtgagggga +gggggggaggggaggggagggagagtgaggaagagagagagaaagggagagaggaaggaa +agaagaaaggaaggaaggaaagaaggaaggaagggagggagggagggaggaaagaaggaa +ggaaaggagggaggaagggagggaaagagagagagaggaaaagagagagaaagagaaaga +gagaaagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaagga +aggaagaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag +agaaagaaagaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaag +agaaaagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaag +gaaagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag +aaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaag +gtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttagg +gagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcct +gcaaagccccca diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/msa.fa.fai new file mode 100644 index 00000000..bc806fd7 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_23155404_23156076 912 29 60 61 +syndip_1_chr20:23155404-23156076 912 991 60 61 +syndip_2_chr20:23155404-23156076 912 1953 60 61 +p:HG002_1_chr20:23155404-23156076 912 2916 60 61 +p:HG002_2_chr20:23155404-23156076 912 3879 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/output.vcf.gz new file mode 100644 index 00000000..cac67760 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/output.vcf.gz.tbi new file mode 100644 index 00000000..153058e9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23155504-23155976/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/base.vcf.gz new file mode 100644 index 00000000..0a58ca03 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/base.vcf.gz.tbi new file mode 100644 index 00000000..c23b7450 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/comp.vcf.gz new file mode 100644 index 00000000..895ee9e2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/comp.vcf.gz.tbi new file mode 100644 index 00000000..5b896b96 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/haps.fa new file mode 100644 index 00000000..7395e813 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/haps.fa @@ -0,0 +1,38 @@ +>ref_chr20_23560783_23561292 +TAAAATCTTCATACAGAAGATATAAGAGATTTGCAAATTACCGTTATAGTATTAGAGTATTCTGAATGTCAGTATGTACTTAGTTTCACTAGGGAGATTTTTATTCCCTAATGTTCTTCAGCATTCCTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCCTTCTTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTCTTTCTTTCTTTTTCTTTTACAGAGTCTTACTCTTGTTGCCCAGGCTGTAGTGCAGTGGTGTGATCTCGGCTCACTGCAACCTCCACCTCTGCCTCCTGCATTCAAGAAATTCTCCTGCCTCAGCCTCCAGAGTAGCTGGGAT +>syndip_1_chr20:23560783-23561292 +TAAAATCTTCATACAGAAGATATAAGAGATTTGCAAATTACCGTTATAGTATTAGAGTAT +TCTGAATGTCAGTATGTACTTAGTTTCACTAGGGAGATTTTTATTCCCTAATGTTCTTCA +GCATTCCTTTCTCTCTCTTTCTTTCTTTCTTTCTTTCTTTCCTTCCTTCCTTCCTTCCTT +CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT +TCTTTCTTTTTTTCTTTCTTTCTTTCTTTCTTTTTCTTTTACAGAGTCTTACTCTTGTTG +CCCAGGCTGTAGTGCAGTGGTGTGATCTCGGCTCACTGCAACCTCCACCTCTGCCTCCTG +CATTCAAGAAATTCTCCTGCCTCAGCCTCCAGAGTAGCTGGGAT +>syndip_2_chr20:23560783-23561292 +TAAAATCTTCATACAGAAGATATAAGAGATTTGCAAATTACCGTTATAGTATTAGAGTAT +TCTGAATGTCAGTATGTACTTAGTTTCACTAGGGAGATTTTTATTCCCTAATGTTCTTCA +GCATTCCTTTCTCTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT +CTTTCTTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCTTTCCTT +CTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTT +CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT +CTTTCTTTCTTTCTTTCTTCTTTCTTTCTTTTTCTTTTACAGAGTCTTACTCTTGTTGCC +CAGGCTGTAGTGCAGTGGTGTGATCTCGGCTCACTGCAACCTCCACCTCTGCCTCCTGCA +TTCAAGAAATTCTCCTGCCTCAGCCTCCAGAGTAGCTGGGAT +>p:HG002_1_chr20:23560783-23561292 +TAAAATCTTCATACAGAAGATATAAGAGATTTGCAAATTACCGTTATAGTATTAGAGTAT +TCTGAATGTCAGTATGTACTTAGTTTCACTAGGGAGATTTTTATTCCCTAATGTTCTTCA +GCATTCCTTTCTCTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT +CTTTCTTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCTTTCCTT +CTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTT +CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT +CTTTCTTTCTTTCTTTCTTCTTTCTTTCTTTTTCTTTTACAGAGTCTTACTCTTGTTGCC +CAGGCTGTAGTGCAGTGGTGTGATCTCGGCTCACTGCAACCTCCACCTCTGCCTCCTGCA +TTCAAGAAATTCTCCTGCCTCAGCCTCCAGAGTAGCTGGGAT +>p:HG002_2_chr20:23560783-23561292 +TAAAATCTTCATACAGAAGATATAAGAGATTTGCAAATTACCGTTATAGTATTAGAGTAT +TCTGAATGTCAGTATGTACTTAGTTTCACTAGGGAGATTTTTATTCCCTAATGTTCTTCA +GCATTCCTTTCTCTCTCTTTCTTTCTTTCTTTCTTTCTTTCCTTCCTTCCTTCCTTCCTT +CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT +TCTTTCTTTTTTTCTTTCTTTCTTTCTTTCTTTTTCTTTTACAGAGTCTTACTCTTGTTG +CCCAGGCTGTAGTGCAGTGGTGTGATCTCGGCTCACTGCAACCTCCACCTCTGCCTCCTG +CATTCAAGAAATTCTCCTGCCTCAGCCTCCAGAGTAGCTGGGAT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/haps.fa.ref.fa new file mode 100644 index 00000000..2375f67a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:23560783-23561292 +TAAAATCTTCATACAGAAGATATAAGAGATTTGCAAATTACCGTTATAGTATTAGAGTATTCTGAATGTCAGTATGTACTTAGTTTCACTAGGGAGATTTTTATTCCCTAATGTTCTTCAGCATTCCTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCCTTCTTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCCTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTCTTTCTTTCTTTTTCTTTTACAGAGTCTTACTCTTGTTGCCCAGGCTGTAGTGCAGTGGTGTGATCTCGGCTCACTGCAACCTCCACCTCTGCCTCCTGCATTCAAGAAATTCTCCTGCCTCAGCCTCCAGAGTAGCTGGGAT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/msa.fa new file mode 100644 index 00000000..360a2abb --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/msa.fa @@ -0,0 +1,50 @@ +>ref_chr20_23560783_23561292 +taaaatcttcatacagaagatataagagatttgcaaattaccgttatagtattagagtat +tctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttcttca +gcattcctttctctttctttctttctttctttctttctttctttctttctttctttcctt +ctttccttccttccttccttccttccttccttccttccttccttccttccttccttcctt +ctttccttctttccttctttccttctttccttctttccttctttccttctttcc------ +------ttctttccttctttccttctttctttctttctttctttctttctttctttcttt +ctttctttctttctttcttctttctttctttttcttttacagagtcttactcttgttgcc +caggctgtagtgcagtggtgtgatctcggctcactgcaacctccacctctgcctcctgca +ttcaagaaattctcctgcctcagcctccagagtagctgggat +>syndip_1_chr20:23560783-23561292 +taaaatcttcatacagaagatataagagatttgcaaattaccgttatagtattagagtat +tctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttcttca +gcattcctttctctctctttctttctttctttctttctttccttccttccttccttcctt +ccttccttccttccttccttccttccttcct----------------------------- +------------------------------------------------------------ +----------------------ttctttctttctttctttctttctttctttctttcttt +ttttctttct-------ttctttctttctttttcttttacagagtcttactcttgttgcc +caggctgtagtgcagtggtgtgatctcggctcactgcaacctccacctctgcctcctgca +ttcaagaaattctcctgcctcagcctccagagtagctgggat +>syndip_2_chr20:23560783-23561292 +taaaatcttcatacagaagatataagagatttgcaaattaccgttatagtattagagtat +tctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttcttca +gcattcctttctctctctttctttctttctttctttctttctttctttctttctttcttt +ctttctttccttccttccttccttccttccttccttccttccttccttccttctttcctt +ctttccttctttccttctttccttctttccttctttccttctttccttctttccttcttt +ctttctttctttctttctttctttctttctttctttctttctttctttctttctttcttt +ctttctttctttctttcttctttctttctttttcttttacagagtcttactcttgttgcc +caggctgtagtgcagtggtgtgatctcggctcactgcaacctccacctctgcctcctgca +ttcaagaaattctcctgcctcagcctccagagtagctgggat +>p:HG002_1_chr20:23560783-23561292 +taaaatcttcatacagaagatataagagatttgcaaattaccgttatagtattagagtat +tctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttcttca +gcattcctttctctctctttctttctttctttctttctttctttctttctttctttcttt +ctttctttccttccttccttccttccttccttccttccttccttccttccttctttcctt +ctttccttctttccttctttccttctttccttctttccttctttccttctttccttcttt +ctttctttctttctttctttctttctttctttctttctttctttctttctttctttcttt +ctttctttctttctttcttctttctttctttttcttttacagagtcttactcttgttgcc +caggctgtagtgcagtggtgtgatctcggctcactgcaacctccacctctgcctcctgca +ttcaagaaattctcctgcctcagcctccagagtagctgggat +>p:HG002_2_chr20:23560783-23561292 +taaaatcttcatacagaagatataagagatttgcaaattaccgttatagtattagagtat +tctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttcttca +gcattcctttctctctctttctttctttctttctttctttccttccttccttccttcctt +ccttccttccttccttccttccttccttcct----------------------------- +------------------------------------------------------------ +----------------------ttctttctttctttctttctttctttctttctttcttt +ttttctttct-------ttctttctttctttttcttttacagagtcttactcttgttgcc +caggctgtagtgcagtggtgtgatctcggctcactgcaacctccacctctgcctcctgca +ttcaagaaattctcctgcctcagcctccagagtagctgggat diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/msa.fa.fai new file mode 100644 index 00000000..efb04c69 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_23560783_23561292 522 29 60 61 +syndip_1_chr20:23560783-23561292 522 594 60 61 +syndip_2_chr20:23560783-23561292 522 1159 60 61 +p:HG002_1_chr20:23560783-23561292 522 1725 60 61 +p:HG002_2_chr20:23560783-23561292 522 2291 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/output.vcf.gz new file mode 100644 index 00000000..04efc8e2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/output.vcf.gz.tbi new file mode 100644 index 00000000..78661e86 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:23560883-23561192/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/base.vcf.gz new file mode 100644 index 00000000..ff903311 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/base.vcf.gz.tbi new file mode 100644 index 00000000..05b5a483 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/comp.vcf.gz new file mode 100644 index 00000000..69c477d5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/comp.vcf.gz.tbi new file mode 100644 index 00000000..f7d1f1ae Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/haps.fa new file mode 100644 index 00000000..9450c866 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/haps.fa @@ -0,0 +1,78 @@ +>ref_chr20_24407883_24409098 +CTCAGTTTATTCATCTATAAAACAGATGTGGCAGTGGTAGTGCCACAATTCACAGCCCAGTTCCACCTTCCTCACAGGCTCGTGATAAAGCTCCATTTCCTACCCTTCCTCTCAGTTATGTTGGAGCCACAGGAGGTGATATAGGGTGCTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGAGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGTTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGAGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTAGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCTTGGCCATCTCCTCTCCTTTAAGATACCTACACTTGTTCTTTCCCACCCACAACTGTATCAGTCAGCTTTTACTGAATAACAAAGCACCCCTAACCTCAGTGCATGATGAAACCCTGTCTCTACTAAAAGCACAAAAAT +>syndip_1_chr20:24407883-24409098 +CTCAGTTTATTCATCTATAAAACAGATGTGGCAGTGGTAGTGCCACAATTCACAGCCCAG +TTCCACCTTCCTCACAGGCTCGTGATAAAGCTCCATTTCCTACCCTTCCTCTCAGTTATG +TTGGAGCCACAGGAGGTGATATAGGGTGCTTCCGGCCCTGGCCATAGGGTACTTCTGGGA +GGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTA +TTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCTTGGC +CATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCT +GGGAGGAGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAG +GGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCT +TGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCCTGGCCATAGGGTAC +TTCTAGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGAT +ATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCA +GCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGG +TACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGT +GATATAGGATACTTCCAGCCTTGGCCATCTCCTCTCCTTTAAGATACCTACACTTGTTCT +TTCCCACCCACAACTGTATCAGTCAGCTTTTACTGAATAACAAAGCACCCCTAACCTCAG +TGCATGATGAAACCCTGTCTCTACTAAAAGCACAAAAAT +>syndip_2_chr20:24407883-24409098 +CTCAGTTTATTCATCTATAAAACAGATGTGGCAGTGGTAGTGCCACAATTCACAGCCCAG +TTCCACCTTCCTCACAGGCTCGTGATAAAGCTCCATTTCCTACCCTTCCTCTCAGTTATG +TTGGAGCCACAGGAGGTGATATAGGGTGCTTCCAGCCCTGGCCATAGGGTACTTCTGGGA +GGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTA +TTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCTTGGC +CATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCT +GGGAGGAGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAG +GGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCT +TGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCTTGGCCATAGGGTAC +TTCTGGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGAGAT +ATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCA +GCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGG +GTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTAGGAGG +TGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACT +TCCAGCCCTGGCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCAT +AGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGG +AGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGAT +ACTTCCAGCCTTGGCCATCTCCTCTCCTTTAAGATACCTACACTTGTTCTTTCCCACCCA +CAACTGTATCAGTCAGCTTTTACTGAATAACAAAGCACCCCTAACCTCAGTGCATGATGA +AACCCTGTCTCTACTAAAAGCACAAAAAT +>p:HG002_1_chr20:24407883-24409098 +CTCAGTTTATTCATCTATAAAACAGATGTGGCAGTGGTAGTGCCACAATTCACAGCCCAG +TTCCACCTTCCTCACAGGCTCGTGATAAAGCTCCATTTCCTACCCTTCCTCTCAGTTATG +TTGGAGCCACAGGAGGTGATATAGGGTGCTTCCAGCCCTGGCCATAGGGTACTTCTGGGA +GGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTA +TTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCTTGGC +CATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCT +GGGAGGAGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAG +GGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCT +TGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCTTGGCCATAGGGTAC +TTCTGGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGAGAT +ATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCA +GCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGG +GTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTAGGAGG +TGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACT +TCCAGCCCTGGCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCAT +AGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGG +AGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGAT +ACTTCCAGCCTTGGCCATCTCCTCTCCTTTAAGATACCTACACTTGTTCTTTCCCACCCA +CAACTGTATCAGTCAGCTTTTACTGAATAACAAAGCACCCCTAACCTCAGTGCATGATGA +AACCCTGTCTCTACTAAAAGCACAAAAAT +>p:HG002_2_chr20:24407883-24409098 +CTCAGTTTATTCATCTATAAAACAGATGTGGCAGTGGTAGTGCCACAATTCACAGCCCAG +TTCCACCTTCCTCACAGGCTCGTGATAAAGCTCCATTTCCTACCCTTCCTCTCAGTTATG +TTGGAGCCACAGGAGGTGATATAGGGTGCTTCCGGCCCTGGCCATAGGGTACTTCTGGGA +GGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTA +TTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCTTGGC +CATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCT +GGGAGGAGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAG +GGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCT +TGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCCTGGCCATAGGGTAC +TTCTAGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGAT +ATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCA +GCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGG +TACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGT +GATATAGGATACTTCCAGCCTTGGCCATCTCCTCTCCTTTAAGATACCTACACTTGTTCT +TTCCCACCCACAACTGTATCAGTCAGCTTTTACTGAATAACAAAGCACCCCTAACCTCAG +TGCATGATGAAACCCTGTCTCTACTAAAAGCACAAAAAT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/haps.fa.ref.fa new file mode 100644 index 00000000..382d8a68 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:24407883-24409098 +CTCAGTTTATTCATCTATAAAACAGATGTGGCAGTGGTAGTGCCACAATTCACAGCCCAGTTCCACCTTCCTCACAGGCTCGTGATAAAGCTCCATTTCCTACCCTTCCTCTCAGTTATGTTGGAGCCACAGGAGGTGATATAGGGTGCTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGAGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGTTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGAGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTGGGAGGTGATATAGGGTATTTCCAGCCTTGGCCATAGGGTACTTCTAGGAGGTGATATAGGGTACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCCTGGCCATAGGGTACTTCTGGGAGGTGATATAGGATACTTCCAGCCTTGGCCATCTCCTCTCCTTTAAGATACCTACACTTGTTCTTTCCCACCCACAACTGTATCAGTCAGCTTTTACTGAATAACAAAGCACCCCTAACCTCAGTGCATGATGAAACCCTGTCTCTACTAAAAGCACAAAAAT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/msa.fa new file mode 100644 index 00000000..5cf5e356 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/msa.fa @@ -0,0 +1,110 @@ +>ref_chr20_24407883_24409098 +ctcagtttattcatctataaaacagatgtggcagtggtagtgccacaattcacagcccag +ttccaccttcctcacaggctcgtgataaagctccatttcctacccttcctctcagttatg +ttggagccacaggaggtgatatagggtgcttccagccctggccatagggtacttctggga +ggtgatatagggtatttccagccttggccatagggtacttctgggaggtgatatagggta +cttccagccttggccatagggtacttctgggaggtgatatagggtacttccagccttggc +catagggtacttctgggaggtgatatagggtacttccagccctggccatagggtacttct +gggaggagatatagggtatttccagccttggccatagggtacttctgggaggtgatatag +gttatttccagccttggccatagggtacttctgggaggtgatatagggtatttccagcct +tggccatagggtacttctgggaggtgatatagggtacttccagccctggccatagggtac +ttctgggaggtgatatagggtacttccagccctggccatagggtacttctgggaggagat +atagggtatttccagccttggccatagggtacttctgggaggtgatatagggtatttcca +gccttggccatagggtacttctgggaggtgatatagggtatttccagccttggccatagg +gtacttctgggaggtgatatagggtatttccagccttggccatagggtacttctaggagg +tgatatagggtacttccagccctggccatagggtacttctgggaggtgatataggatact +tccagccctggccatagggtacttctgggaggtgatataggatacttccagccctggcca +tagggtacttctgggaggtgatataggatacttccagccctggccatagggtacttctgg +gaggtgatataggatacttccagccctggccatagggtacttctgggaggtgatatagga +tacttccagccctggccatagggtacttctgggaggtgatataggatacttccagccttg +gccatctcctctcctttaagatacctacacttgttctttcccacccacaactgtatcagt +cagcttttactgaataacaaagcacccctaacctcagtgcatgatgaaaccctgtctcta +ctaaaagcacaaaaat +>syndip_1_chr20:24407883-24409098 +ctcagtttattcatctataaaacagatgtggcagtggtagtgccacaattcacagcccag +ttccaccttcctcacaggctcgtgataaagctccatttcctacccttcctctcagttatg +ttggagccacaggaggtgatatagggtgcttccggccctggccatagggtacttctggga +ggtgatatagggtatttccagccttggccatagggtacttctgggaggtgatatagggta +tttccagccttggccatagggtacttctgggaggtgatatagggtacttccagccttggc +catagggtacttctgggaggtgatatagggtacttccagccctggccatagggtacttct +gggaggagatatagggtatttccagccttggccatagggtacttctgggaggtgatatag +ggtatttccagccttggccatagggtacttctgggaggtgatatagggtatttccagcct +tggccatagggtacttctgggaggtgatatagggtatttccagccctggccatagggtac +ttctaggaggtgatatagggtacttccagccctggccatagggtacttctgggaggtgat +ataggatacttccagccctggccatagggtacttctgggaggtgatataggatacttcca +g----------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------cctggccatagggtacttctgg +gaggtgatataggatacttccagccctggccatagggtacttctgggaggtgatatagga +tacttccagccctggccatagggtacttctgggaggtgatataggatacttccagccttg +gccatctcctctcctttaagatacctacacttgttctttcccacccacaactgtatcagt +cagcttttactgaataacaaagcacccctaacctcagtgcatgatgaaaccctgtctcta +ctaaaagcacaaaaat +>syndip_2_chr20:24407883-24409098 +ctcagtttattcatctataaaacagatgtggcagtggtagtgccacaattcacagcccag +ttccaccttcctcacaggctcgtgataaagctccatttcctacccttcctctcagttatg +ttggagccacaggaggtgatatagggtgcttccagccctggccatagggtacttctggga +ggtgatatagggtatttccagccttggccatagggtacttctgggaggtgatatagggta +tttccagccttggccatagggtacttctgggaggtgatatagggtacttccagccttggc +catagggtacttctgggaggtgatatagggtacttccagccctggccatagggtacttct +gggaggagatatagggtatttccagccttggccatagggtacttctgggaggtgatatag +ggtatttccagccttggccatagggtacttctgggaggtgatatagggtatttccagcct +tggccatagggtacttctgggaggtgatatagggtacttccagccttggccatagggtac +ttctgggaggtgatatagggtacttccagccctggccatagggtacttctgggaggagat +atagggtatttccagccttggccatagggtacttctgggaggtgatatagggtatttcca +gccttggccatagggtacttctgggaggtgatatagggtatttccagccttggccatagg +gtacttctgggaggtgatatagggtatttccagccttggccatagggtacttctaggagg +tgatatagggtacttccagccctggccatagggtacttctgggaggtgatataggatact +tccagccctgg-----------------------------------------------ca +tagggtacttctgggaggtgatataggatacttccagccctggccatagggtacttctgg +gaggtgatataggatacttccagccctggccatagggtacttctgggaggtgatatagga +tacttccagccctggccatagggtacttctgggaggtgatataggatacttccagccttg +gccatctcctctcctttaagatacctacacttgttctttcccacccacaactgtatcagt +cagcttttactgaataacaaagcacccctaacctcagtgcatgatgaaaccctgtctcta +ctaaaagcacaaaaat +>p:HG002_1_chr20:24407883-24409098 +ctcagtttattcatctataaaacagatgtggcagtggtagtgccacaattcacagcccag +ttccaccttcctcacaggctcgtgataaagctccatttcctacccttcctctcagttatg +ttggagccacaggaggtgatatagggtgcttccagccctggccatagggtacttctggga +ggtgatatagggtatttccagccttggccatagggtacttctgggaggtgatatagggta +tttccagccttggccatagggtacttctgggaggtgatatagggtacttccagccttggc +catagggtacttctgggaggtgatatagggtacttccagccctggccatagggtacttct +gggaggagatatagggtatttccagccttggccatagggtacttctgggaggtgatatag +ggtatttccagccttggccatagggtacttctgggaggtgatatagggtatttccagcct +tggccatagggtacttctgggaggtgatatagggtacttccagccttggccatagggtac +ttctgggaggtgatatagggtacttccagccctggccatagggtacttctgggaggagat +atagggtatttccagccttggccatagggtacttctgggaggtgatatagggtatttcca +gccttggccatagggtacttctgggaggtgatatagggtatttccagccttggccatagg +gtacttctgggaggtgatatagggtatttccagccttggccatagggtacttctaggagg +tgatatagggtacttccagccctggccatagggtacttctgggaggtgatataggatact +tccagccctgg-----------------------------------------------ca +tagggtacttctgggaggtgatataggatacttccagccctggccatagggtacttctgg +gaggtgatataggatacttccagccctggccatagggtacttctgggaggtgatatagga +tacttccagccctggccatagggtacttctgggaggtgatataggatacttccagccttg +gccatctcctctcctttaagatacctacacttgttctttcccacccacaactgtatcagt +cagcttttactgaataacaaagcacccctaacctcagtgcatgatgaaaccctgtctcta +ctaaaagcacaaaaat +>p:HG002_2_chr20:24407883-24409098 +ctcagtttattcatctataaaacagatgtggcagtggtagtgccacaattcacagcccag +ttccaccttcctcacaggctcgtgataaagctccatttcctacccttcctctcagttatg +ttggagccacaggaggtgatatagggtgcttccggccctggccatagggtacttctggga +ggtgatatagggtatttccagccttggccatagggtacttctgggaggtgatatagggta +tttccagccttggccatagggtacttctgggaggtgatatagggtacttccagccttggc +catagggtacttctgggaggtgatatagggtacttccagccctggccatagggtacttct +gggaggagatatagggtatttccagccttggccatagggtacttctgggaggtgatatag +ggtatttccagccttggccatagggtacttctgggaggtgatatagggtatttccagcct +tggccatagggtacttctgggaggtgatatagggtatttccagccctggccatagggtac +ttctaggaggtgatatagggtacttccagccctggccatagggtacttctgggaggtgat +ataggatacttccagccctggccatagggtacttctgggaggtgatataggatacttcca +g----------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------cctggccatagggtacttctgg +gaggtgatataggatacttccagccctggccatagggtacttctgggaggtgatatagga +tacttccagccctggccatagggtacttctgggaggtgatataggatacttccagccttg +gccatctcctctcctttaagatacctacacttgttctttcccacccacaactgtatcagt +cagcttttactgaataacaaagcacccctaacctcagtgcatgatgaaaccctgtctcta +ctaaaagcacaaaaat diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/msa.fa.fai new file mode 100644 index 00000000..9e3f4479 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_24407883_24409098 1216 29 60 61 +syndip_1_chr20:24407883-24409098 1216 1300 60 61 +syndip_2_chr20:24407883-24409098 1216 2571 60 61 +p:HG002_1_chr20:24407883-24409098 1216 3843 60 61 +p:HG002_2_chr20:24407883-24409098 1216 5115 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/output.vcf.gz new file mode 100644 index 00000000..faa13b1d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/output.vcf.gz.tbi new file mode 100644 index 00000000..03a7950b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24407983-24408998/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/base.vcf.gz new file mode 100644 index 00000000..47a8cb85 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/base.vcf.gz.tbi new file mode 100644 index 00000000..f1c200fd Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/comp.vcf.gz new file mode 100644 index 00000000..5e34fe2c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/comp.vcf.gz.tbi new file mode 100644 index 00000000..3f762ccf Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/haps.fa new file mode 100644 index 00000000..474a081b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/haps.fa @@ -0,0 +1,41 @@ +>ref_chr20_24681888_24682378 +CTCTGCTGCTGGGGTGTACTCGATGTCCTGGCTCGACTGACACAGTCCTGATCTTGCCAGTTGGTGTCTGTGGACCTGTGTTTTGGCATGGACAGGCACAAGGCTAAGGAGGTCAGCATGCAGCAGGAGGCAAACTGTGAAGTACCTCTCTGGCCTGGCCTTTGTGAATTACCACAGTGCGGGGTCCACCCAGGAAACTGTGAAGTACCTCTGTGGCCTTTGTGAATTACCACAGTCAGGGGTCCACCCAGGAAACTGTGAAGTACCTCTCTGGGCGTTGTGAATTACCACAGTTAGGGGTTTACCCAGGAAACTGTGAAGTATCTCTCTGGCCTTTGTGAATCACCACAGTTAGGGGTCTATGCAGGAGTACTGGTCATTCACAGACTCAGCTCATTCCAGGCCTTAGCAGTGTGCACCTCAGAGTGAAGCAGAGAGGCCCCAGGAGAAGCCATGGCCACGCCCTCAACCTCCTGCTCCGAGGAGGAGAC +>syndip_1_chr20:24681888-24682378 +CTCTGCTGCTGGGGTGTACTCGATGTCCTGGCTCGACTGACACAGTCCTGATCTTGCCAG +TTGGTGTCTGTGGACCTGTGTTTTGGCATGGACAGGCACAAGGCTAAGGAGGTCAGCATG +CAGCAGGAGGCAAACTGTGAAGTACCTCTCTGGCCTGGCCTTTGTGAATTACCACAGTGC +GGGGTCCACCCAGGAAACTGTGAAGTACCTCTCTGGGCGTTGTGAATTACCACAGTTAGG +GGTTTACCCAGGAAACTGTGAAGTATCTCTCTGGCCTTTGTGAATCACCACAGTTAGGGG +TCTATGCAGGAGTACTGGTCATTCACAGACTCAGCTCATTCCAGGCCTTAGCAGTGTGCA +CCTCAGAGTGAAGCAGAGAGGCCCCAGGAGAAGCCATGGCCACGCCCTCAACCTCCTGCT +CCGAGGAGGAGAC +>syndip_2_chr20:24681888-24682378 +CTCTGCTGCTGGGGTGTACTCGATGTCCTGGCTCGACTGACACAGTCCTGATCTTGCCAG +TTGGTGTCTGTGGACCTGTGTTTTGGCATGGACAGGCACAAGGCTAAGGAGGTCAGCATG +CAGCAGGAGGCAAACTGTGAAGTACCTCTCTGGCCTGGCCTTTGTGAATTACCACAGTCA +GGGGTCCACCCAGGAAACTGTGAAGTACCTCTGTGGCCTTTGTGAATTACCACAGTCAGG +GGTCCACCCAGGAAACTGTGAAGTACCTCTCTGGGCGTTGTGAATTACCACAGTTAGGGG +TTTACCCAGGAAACTGTGAAGTATCTCTCTGGCCTTTGTGAATCACCACAGTTAGGGGTC +TATGCAGGAGTACTGGTCATTCACAGACTCAGCTCATTCCAGGCCTTAGCAGTGTGCACC +TCAGAGTGAAGCAGAGAGGCCCCAGGAGAAGCCATGGCCACGCCCTCAACCTCCTGCTCC +GAGGAGGAGAC +>p:HG002_1_chr20:24681888-24682378 +CTCTGCTGCTGGGGTGTACTCGATGTCCTGGCTCGACTGACACAGTCCTGATCTTGCCAG +TTGGTGTCTGTGGACCTGTGTTTTGGCATGGACAGGCACAAGGCTAAGGAGGTCAGCATG +CAGCAGGAGGCAAACTGTGAAGTACCTCTCTGGCCTGGCCTTTGTGAATTACCACAGTCA +GGGGTCTACCCAGGAAACTGTGAAGTACCTCTCTGGCCTTTGTGAATTACCACAGTCAGG +GGTCCACCCAGGAAACTGTGAAGTACCTCTCTGGCCTTTGTGAATTACCACAGTCAGGGG +TCCACCCAGGAAACTGTGAAGTACCTCTCTGGGCGTTGTGAATTACCACAGTTAGGGGTT +TACCCAGGAAACTGTGAAGTATCTCTCTGGCCTTTGTGAATCACCACAGTTAGGGGTCTA +TGCAGGAGTACTGGTCATTCACAGACTCAGCTCATTCCAGGCCTTAGCAGTGTGCACCTC +AGAGTGAAGCAGAGAGGCCCCAGGAGAAGCCATGGCCACGCCCTCAACCTCCTGCTCCGA +GGAGGAGAC +>p:HG002_2_chr20:24681888-24682378 +CTCTGCTGCTGGGGTGTACTCGATGTCCTGGCTCGACTGACACAGTCCTGATCTTGCCAG +TTGGTGTCTGTGGACCTGTGTTTTGGCATGGACAGGCACAAGGCTAAGGAGGTCAGCATG +CAGCAGGAGGCAAACTGTGAAGTACCTCTCTGGCCTGGCCTTTGTGAATTACCACAGTGC +GGGGTCCACCCAGGAAACTGTGAAGTACCTCTCTGGGCGTTGTGAATTACCACAGTTAGG +GGTTTACCCAGGAAACTGTGAAGTATCTCTCTGGCCTTTGTGAATCACCACAGTTAGGGG +TCTATGCAGGAGTACTGGTCATTCACAGACTCAGCTCATTCCAGGCCTTAGCAGTGTGCA +CCTCAGAGTGAAGCAGAGAGGCCCCAGGAGAAGCCATGGCCACGCCCTCAACCTCCTGCT +CCGAGGAGGAGAC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/haps.fa.ref.fa new file mode 100644 index 00000000..4e044ed6 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:24681888-24682378 +CTCTGCTGCTGGGGTGTACTCGATGTCCTGGCTCGACTGACACAGTCCTGATCTTGCCAGTTGGTGTCTGTGGACCTGTGTTTTGGCATGGACAGGCACAAGGCTAAGGAGGTCAGCATGCAGCAGGAGGCAAACTGTGAAGTACCTCTCTGGCCTGGCCTTTGTGAATTACCACAGTGCGGGGTCCACCCAGGAAACTGTGAAGTACCTCTGTGGCCTTTGTGAATTACCACAGTCAGGGGTCCACCCAGGAAACTGTGAAGTACCTCTCTGGGCGTTGTGAATTACCACAGTTAGGGGTTTACCCAGGAAACTGTGAAGTATCTCTCTGGCCTTTGTGAATCACCACAGTTAGGGGTCTATGCAGGAGTACTGGTCATTCACAGACTCAGCTCATTCCAGGCCTTAGCAGTGTGCACCTCAGAGTGAAGCAGAGAGGCCCCAGGAGAAGCCATGGCCACGCCCTCAACCTCCTGCTCCGAGGAGGAGAC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/msa.fa new file mode 100644 index 00000000..ad3d1e33 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/msa.fa @@ -0,0 +1,55 @@ +>ref_chr20_24681888_24682378 +ctctgctgctggggtgtactcgatgtcctggctcgactgacacagtcctgatcttgccag +ttggtgtctgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcatg +cagcaggaggcaaactgtgaagtacctctctggc-------------------------- +--------------------------------ctggcctttgtgaattaccacagtgcgg +ggtccacccaggaaactgtgaagtacctctgtggcctttgtgaattaccacagtcagggg +tccacccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggtt +tacccaggaaactgtgaagtatctctctggcctttgtgaatcaccacagttaggggtcta +tgcaggagtactggtcattcacagactcagctcattccaggccttagcagtgtgcacctc +agagtgaagcagagaggccccaggagaagccatggccacgccctcaacctcctgctccga +ggaggagac +>syndip_1_chr20:24681888-24682378 +ctctgctgctggggtgtactcgatgtcctggctcgactgacacagtcctgatcttgccag +ttggtgtctgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcatg +cagcaggaggcaaactgtgaagtacctctctggc-------------------------- +------------------------------------------------------------ +------------------------------ctggcctttgtgaattaccacagtgcgggg +tccacccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggtt +tacccaggaaactgtgaagtatctctctggcctttgtgaatcaccacagttaggggtcta +tgcaggagtactggtcattcacagactcagctcattccaggccttagcagtgtgcacctc +agagtgaagcagagaggccccaggagaagccatggccacgccctcaacctcctgctccga +ggaggagac +>syndip_2_chr20:24681888-24682378 +ctctgctgctggggtgtactcgatgtcctggctcgactgacacagtcctgatcttgccag +ttggtgtctgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcatg +cagcaggaggcaaactgtgaagtacctctctggc-------------------------- +--------------------------------ctggcctttgtgaattaccacagtcagg +ggtccacccaggaaactgtgaagtacctctgtggcctttgtgaattaccacagtcagggg +tccacccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggtt +tacccaggaaactgtgaagtatctctctggcctttgtgaatcaccacagttaggggtcta +tgcaggagtactggtcattcacagactcagctcattccaggccttagcagtgtgcacctc +agagtgaagcagagaggccccaggagaagccatggccacgccctcaacctcctgctccga +ggaggagac +>p:HG002_1_chr20:24681888-24682378 +ctctgctgctggggtgtactcgatgtcctggctcgactgacacagtcctgatcttgccag +ttggtgtctgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcatg +cagcaggaggcaaactgtgaagtacctctctggcctggcctttgtgaattaccacagtca +ggggtctacccaggaaactgtgaagtacctctctggcctttgtgaattaccacagtcagg +ggtccacccaggaaactgtgaagtacctctctggcctttgtgaattaccacagtcagggg +tccacccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggtt +tacccaggaaactgtgaagtatctctctggcctttgtgaatcaccacagttaggggtcta +tgcaggagtactggtcattcacagactcagctcattccaggccttagcagtgtgcacctc +agagtgaagcagagaggccccaggagaagccatggccacgccctcaacctcctgctccga +ggaggagac +>p:HG002_2_chr20:24681888-24682378 +ctctgctgctggggtgtactcgatgtcctggctcgactgacacagtcctgatcttgccag +ttggtgtctgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcatg +cagcaggaggcaaactgtgaagtacctctctggc-------------------------- +------------------------------------------------------------ +------------------------------ctggcctttgtgaattaccacagtgcgggg +tccacccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggtt +tacccaggaaactgtgaagtatctctctggcctttgtgaatcaccacagttaggggtcta +tgcaggagtactggtcattcacagactcagctcattccaggccttagcagtgtgcacctc +agagtgaagcagagaggccccaggagaagccatggccacgccctcaacctcctgctccga +ggaggagac diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/msa.fa.fai new file mode 100644 index 00000000..5141810c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_24681888_24682378 549 29 60 61 +syndip_1_chr20:24681888-24682378 549 622 60 61 +syndip_2_chr20:24681888-24682378 549 1215 60 61 +p:HG002_1_chr20:24681888-24682378 549 1809 60 61 +p:HG002_2_chr20:24681888-24682378 549 2403 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/output.vcf.gz new file mode 100644 index 00000000..f96c1bff Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/output.vcf.gz.tbi new file mode 100644 index 00000000..5f1027aa Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:24681988-24682278/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/base.vcf.gz new file mode 100644 index 00000000..73c4c5f9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/base.vcf.gz.tbi new file mode 100644 index 00000000..bb297398 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/comp.vcf.gz new file mode 100644 index 00000000..95eb0ef2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/comp.vcf.gz.tbi new file mode 100644 index 00000000..b432405a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/haps.fa new file mode 100644 index 00000000..25da5c0a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/haps.fa @@ -0,0 +1,44 @@ +>ref_chr20_25781536_25782027 +ACAAGAATCAGTTACTTCACCAACTGTGAGACCCTGAGGGGCTGGGTTTCTATCCTACAAGATGTGTTAGAAGCCCTGACCCAAGAGCCCTGCTACCCAGAATGCATGGTTTCATGTAGCAAGGATCCTTGTGATGGTGGTGATGATGATGGTGAGGATGGTGATGGTGAAGGTGGAGGTGGTGATAATGAAGTGATAGTTATGTTGAGGATGATGAAGGTGATGATGATGGTGAGAATGGTAAAGGTGAACAAGGTGATGGTGAGAATGGCGAGGGTAAGAATGGTGATGGCGATGATGATAGTGTTGGTGATTGTAAGGATGGTGATGGCGATCATGGTGATGAAGATAATGGTGCTGACAGGGCTATGAGGTAATGGAGGCAGAAAAGTGGCAGTTTCCAGGAAGTATAGAGCCAGCTGGGAACTGCAAGGTAACCTTAGTGGGGGTGGAAGATGTAGGGTCCCTGCCTCATTTCTAGACATCTGGAGA +>syndip_1_chr20:25781536-25782027 +ACAAGAATCAGTTACTTCACCAACTGTGAGACCCTGAGGGGCTGGGTTTCTATCCTACAA +GATGTGTTAGAAGCCCTGACCCAAGAGCCCTGCTACCCAGAATGCATGGTTTCATGTAGC +AAGGATCCTTGTGATGGTGGTGATGATGATGGTGAGGATGGTGATGGTGAAGGTGGAGGT +GGTGATAATGAAGTGATAGTTATGTTGAGGATGATGAAGGTGATGATGATGGTGAGAATG +GTAAAGGTGAACAAGGTGATGGTGAGAATGGCGAGGGTAAGAATGGTGATGGCGATGATG +ATAGTGTTGGTGATTGTAAGGATGGTGATGGCGATCATGGTGATGAAGATAATGGTGCTG +ACAGGGCTATGAGGTAATGGAGGCAGAAAAGTGGCAGTTTCCAGGAAGTATAGAGCCAGC +TGGGAACTGCAAGGTAACCTTAGTGGGGGTGGAAGATGTAGGGTCCCTGCCTCATTTCTA +GACATCTGGAGA +>syndip_2_chr20:25781536-25782027 +ACAAGAATCAGTTACTTCACCAACTGTGAGACCCTGAGGGGCTGGGTTTCTATCCTACAA +GATGTGTTAGAAGCCCTGACCCAAGAGCCCTGCTACCCAGAATGCATGGTTTCATGTAGC +AAGGATCCTTGTGATGGTGGTGATGATGATGGTGAGGATGGTGATGGTGAAGGTGGAGGT +GGTGATAATGAAGTGATAGTTATGTTGAGGATGATGAAGGTGATGATGATGGTGAGAATG +GTAAAGGTGAACAAGGTGATGGTGAGAATGGCGAGGGTAAGAATGGTGATGGCGATGATG +ATAGTGTTGGTGATTGTAAGGATGGTGATGGCGATCATGGTGATGAAGATAATGGTGCTG +ACAGGGCTATGAGGTAATGGAGGCAGAAAAGTGGCAGTTTCCAGGAAGTATAGAGCCAGC +TGGGAACTGCAAGGTAACCTTAGTGGGGGTGGAAGATGTAGGGTCCCTGCCTCATTTCTA +GACATCTGGAGA +>p:HG002_1_chr20:25781536-25782027 +ACAAGAATCAGTTACTTCACCAACTGTGAGACCCTGAGGGGCTGGGTTTCTATCCTACAA +GATGTGTTAGAAGCCCTGACCCAAGAGCCCTGCTACCCAGAATGCATGGTTTCATGTAGC +AAGGATCCTTGTGATGGTGGTGATAATGATGGTGAGGATGGTGATGGTGAAGGTGGAGGT +GGTGATAATGAAGTGATAGTTATGTTGAGGATGATGAAGGTGATGATGATGGTGAGAATG +GTAAAGGTGAACAAGGTGATGGTGAGAATGGTGATGGTGGTGATTGTGATGGTGATGATA +AGGATGGTGATGGCGAAGGTGGTGATGATAGTAGTGATAGTTATGGTAAGGATAATGGTG +ATGATGATGAGGATGATGATGGTGAGAATGGTGATAGTGACGATGATAGTGATGGTAATG +ATAATGATGGTGAGAATGGCGAGGGTAAGAATGGTGATGGCGATGATGATAGTGTTGGTG +ATTGTAAGGATGGTGATGGCAATCATGGTGATGATGATAATGGTGCTGACTGGGCTATGA +GGTAATGGAGGCAGAAAAGTGGCAGTTTCCAGGAAGTATAGAGCCAGCTGGGAACTGCAA +GGTAACCTTAGTGGGGGTGGAAGATGTAGGGTCCCTGCCTCATTTCTAGACATCTGGAGA +>p:HG002_2_chr20:25781536-25782027 +ACAAGAATCAGTTACTTCACCAACTGTGAGACCCTGAGGGGCTGGGTTTCTATCCTACAA +GATGTGTTAGAAGCCCTGACCCAAGAGCCCTGCTACCCAGAATGCATGGTTTCATGTAGC +AAGGATCCTTGTGATGGTGGTGATGATGATGGTGAGGATGGTGATGGTGAAGGTGGAGGT +GGTGATAATGAAGTGATAGTTATGTTGAGGATGATGAAGGTGATGATGATGGTGAGAATG +GTAAAGGTGAACAAGGTGATGGTGAGAATGGCGAGGGTAAGAATGGTGATGGCGATGATG +ATAGTGTTGGTGATTGTAAGGATGGTGATGGCGATCATGGTGATGAAGATAATGGTGCTG +ACAGGGCTATGAGGTAATGGAGGCAGAAAAGTGGCAGTTTCCAGGAAGTATAGAGCCAGC +TGGGAACTGCAAGGTAACCTTAGTGGGGGTGGAAGATGTAGGGTCCCTGCCTCATTTCTA +GACATCTGGAGA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/haps.fa.ref.fa new file mode 100644 index 00000000..6fbf1469 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:25781536-25782027 +ACAAGAATCAGTTACTTCACCAACTGTGAGACCCTGAGGGGCTGGGTTTCTATCCTACAAGATGTGTTAGAAGCCCTGACCCAAGAGCCCTGCTACCCAGAATGCATGGTTTCATGTAGCAAGGATCCTTGTGATGGTGGTGATGATGATGGTGAGGATGGTGATGGTGAAGGTGGAGGTGGTGATAATGAAGTGATAGTTATGTTGAGGATGATGAAGGTGATGATGATGGTGAGAATGGTAAAGGTGAACAAGGTGATGGTGAGAATGGCGAGGGTAAGAATGGTGATGGCGATGATGATAGTGTTGGTGATTGTAAGGATGGTGATGGCGATCATGGTGATGAAGATAATGGTGCTGACAGGGCTATGAGGTAATGGAGGCAGAAAAGTGGCAGTTTCCAGGAAGTATAGAGCCAGCTGGGAACTGCAAGGTAACCTTAGTGGGGGTGGAAGATGTAGGGTCCCTGCCTCATTTCTAGACATCTGGAGA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/msa.fa new file mode 100644 index 00000000..e61c1bf1 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/msa.fa @@ -0,0 +1,60 @@ +>ref_chr20_25781536_25782027 +acaagaatcagttacttcaccaactgtgagaccctgaggggctgggtttctatcctacaa +gatgtgttagaagccctgacccaagagccctgctacccagaatgcatggtttcatgtagc +aaggatccttgtgatggtggtgatgatgatggtgaggatggtgatggtgaaggtggaggt +ggtgataatgaagtgatagttatgttgaggatgatgaaggtgatgatgatggtgagaatg +gtaaaggtgaacaagg-------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----tgatggtgagaatggcgagggtaagaatggtgatggcgatgatgatagtgttggtg +attgtaaggatggtgatggcgatcatggtgatgaagataatggtgctgacagggctatga +ggtaatggaggcagaaaagtggcagtttccaggaagtatagagccagctgggaactgcaa +ggtaaccttagtgggggtggaagatgtagggtccctgcctcatttctagacatctggaga +>syndip_1_chr20:25781536-25782027 +acaagaatcagttacttcaccaactgtgagaccctgaggggctgggtttctatcctacaa +gatgtgttagaagccctgacccaagagccctgctacccagaatgcatggtttcatgtagc +aaggatccttgtgatggtggtgatgatgatggtgaggatggtgatggtgaaggtggaggt +ggtgataatgaagtgatagttatgttgaggatgatgaaggtgatgatgatggtgagaatg +gtaaaggtgaacaagg-------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----tgatggtgagaatggcgagggtaagaatggtgatggcgatgatgatagtgttggtg +attgtaaggatggtgatggcgatcatggtgatgaagataatggtgctgacagggctatga +ggtaatggaggcagaaaagtggcagtttccaggaagtatagagccagctgggaactgcaa +ggtaaccttagtgggggtggaagatgtagggtccctgcctcatttctagacatctggaga +>syndip_2_chr20:25781536-25782027 +acaagaatcagttacttcaccaactgtgagaccctgaggggctgggtttctatcctacaa +gatgtgttagaagccctgacccaagagccctgctacccagaatgcatggtttcatgtagc +aaggatccttgtgatggtggtgatgatgatggtgaggatggtgatggtgaaggtggaggt +ggtgataatgaagtgatagttatgttgaggatgatgaaggtgatgatgatggtgagaatg +gtaaaggtgaacaagg-------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----tgatggtgagaatggcgagggtaagaatggtgatggcgatgatgatagtgttggtg +attgtaaggatggtgatggcgatcatggtgatgaagataatggtgctgacagggctatga +ggtaatggaggcagaaaagtggcagtttccaggaagtatagagccagctgggaactgcaa +ggtaaccttagtgggggtggaagatgtagggtccctgcctcatttctagacatctggaga +>p:HG002_1_chr20:25781536-25782027 +acaagaatcagttacttcaccaactgtgagaccctgaggggctgggtttctatcctacaa +gatgtgttagaagccctgacccaagagccctgctacccagaatgcatggtttcatgtagc +aaggatccttgtgatggtggtgataatgatggtgaggatggtgatggtgaaggtggaggt +ggtgataatgaagtgatagttatgttgaggatgatgaaggtgatgatgatggtgagaatg +gtaaaggtgaacaaggtgatggtgagaatggtgatggtggtgattgtgatggtgatgata +aggatggtgatggcgaaggtggtgatgatagtagtgatagttatggtaaggataatggtg +atgatgatgaggatgatgatggtgagaatggtgatagtgacgatgatagtgatggtaatg +ataatgatggtgagaatggcgagggtaagaatggtgatggcgatgatgatagtgttggtg +attgtaaggatggtgatggcaatcatggtgatgatgataatggtgctgactgggctatga +ggtaatggaggcagaaaagtggcagtttccaggaagtatagagccagctgggaactgcaa +ggtaaccttagtgggggtggaagatgtagggtccctgcctcatttctagacatctggaga +>p:HG002_2_chr20:25781536-25782027 +acaagaatcagttacttcaccaactgtgagaccctgaggggctgggtttctatcctacaa +gatgtgttagaagccctgacccaagagccctgctacccagaatgcatggtttcatgtagc +aaggatccttgtgatggtggtgatgatgatggtgaggatggtgatggtgaaggtggaggt +ggtgataatgaagtgatagttatgttgaggatgatgaaggtgatgatgatggtgagaatg +gtaaaggtgaacaagg-------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----tgatggtgagaatggcgagggtaagaatggtgatggcgatgatgatagtgttggtg +attgtaaggatggtgatggcgatcatggtgatgaagataatggtgctgacagggctatga +ggtaatggaggcagaaaagtggcagtttccaggaagtatagagccagctgggaactgcaa +ggtaaccttagtgggggtggaagatgtagggtccctgcctcatttctagacatctggaga diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/msa.fa.fai new file mode 100644 index 00000000..d3cc744c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_25781536_25782027 660 29 60 61 +syndip_1_chr20:25781536-25782027 660 734 60 61 +syndip_2_chr20:25781536-25782027 660 1439 60 61 +p:HG002_1_chr20:25781536-25782027 660 2145 60 61 +p:HG002_2_chr20:25781536-25782027 660 2851 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/output.vcf.gz new file mode 100644 index 00000000..433618d1 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/output.vcf.gz.tbi new file mode 100644 index 00000000..62df16c2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:25781636-25781927/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/base.vcf.gz new file mode 100644 index 00000000..14e5fb33 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/base.vcf.gz.tbi new file mode 100644 index 00000000..2cda617d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/comp.vcf.gz new file mode 100644 index 00000000..d25809ae Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/comp.vcf.gz.tbi new file mode 100644 index 00000000..49aee199 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/haps.fa new file mode 100644 index 00000000..bc114cfe --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/haps.fa @@ -0,0 +1,66 @@ +>ref_chr20_278800_279287 +GATGAAACCCATCTCGGTCCTCTTGCAAAGCCCAGGTGAGGGGAGTGAAGGGTGAAGAAATGCGTCTTCCAGGTGGAGGAAGCACCACGTGCAGTGGGCGGGGAAAGGCAGGAGAGGGCGCGCGAGTGCGCGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGAGGGACGGAGGTTGGGACGGAGGGACGGAGGGCGGGCGGATGCCGCGGGTCTCACCGCCAGGGTGTCCTGCTGCTGCAGCAGGGCCCGCACGTGCAGGGTCGTGCTGTTCTCCATCTCCTGGATGGTCTCGATCAGCTCCCGGTTGAGCTTGCTGAGGAAGTTCTCACGGC +>syndip_1_chr20:278800-279287 +GATGAAACCCATCTCGGTCCTCTTGCAAAGCCCAGGTGAGGGGAGTGAAGGGTGAAGAAA +TGCGTCTTCCAGGTGGAGGAAGCACCACGTGCAGTGGGCGGGGAAAGGCAGGAGAGGGCG +CGCGAGTGCGCGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGAGGGACGGAGG +GAGGAAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGACGGAGGGCGGGACGGCGGGAGG +GCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGG +GAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGG +GAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGTGGG +AGGGAGGGAGGGATGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGACGGAGGG +AGGGAGGGAGGGACGGAGGTTGGGACGGAGGGACGGAGGGCGGGCGGATGCCGCGGGTCT +CACCGCCAAGGTGTCCTGCTGCTGCAGCAGGGCCCGCACGTGCAGGGTCGTGCTGTTCTC +CATCTCCTGGATGGTCTCGATCAGCTCCCGGTTGAGCTTGCTGAGGAAGTTCTCACGGC +>syndip_2_chr20:278800-279287 +GATGAAACCCATCTCGGTCCTCTTGCAAAGCCCAGGTGAGGGGAGTGAAGGGTGAAGAAA +TGCGTCTTCCAGGTGGAGGAAGCACCACGTGCAGTGGGCGGGGAAAGGCAGGAGAGGGCG +CGCGAGTGCGCGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGG +GAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGG +GACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGG +GACGGAGGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGG +GAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGG +GACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGG +GAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACG +GAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGG +GAGGGCGGGACGGAGGGCGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGG +GCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGACGGAGGGAGGGAGGGAGGGAGG +GACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGG +AGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGA +GGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGCGGGACGGAGGGAGGGCGGGAGGGA +GGGACGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGAGGGACGGAGGTTGGGACGGA +GGGACGGAGGGCGGGCGGATGCCGCGGGTCTCACCGCCAAGGTGTCCTGCTGCTGCAGCA +GGGCCCGCACGTGCAGGGTCGTGCTGTTCTCCATCTCCTGGATGGTCTCGATCAGCTCCC +GGTTGAGCTTGCTGAGGAAGTTCTCACGGC +>p:HG002_1_chr20:278800-279287 +GATGAAACCCATCTCGGTCCTCTTGCAAAGCCCAGGTGAGGGGAGTGAAGGGTGAAGAAA +TGCGTCTTCCAGGTGGAGGAAGCACCACGTGCAGTGGGCGGGGAAAGGCAGGAGAGGGCG +CGCGAGTGCGCGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGG +GAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGG +GACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGG +GACGGAGGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGG +GAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGG +GACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGG +GAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACG +GAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGG +GAGGGCGGGACGGAGGGCGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGG +GCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGACGGAGGGAGGGAGGGAGGGAGG +GACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGG +AGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGA +GGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGCGGGACGGAGGGAGGGCGGGAGGGA +GGGACGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGAGGGACGGAGGTTGGGACGGA +GGGACGGAGGGCGGGCGGATGCCGCGGGTCTCACCGCCAAGGTGTCCTGCTGCTGCAGCA +GGGCCCGCACGTGCAGGGTCGTGCTGTTCTCCATCTCCTGGATGGTCTCGATCAGCTCCC +GGTTGAGCTTGCTGAGGAAGTTCTCACGGC +>p:HG002_2_chr20:278800-279287 +GATGAAACCCATCTCGGTCCTCTTGCAAAGCCCAGGTGAGGGGAGTGAAGGGTGAAGAAA +TGCGTCTTCCAGGTGGAGGAAGCACCACGTGCAGTGGGCGGGGAAAGGCAGGAGAGGGCG +CGCGAGTGCGCGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGAGGGACGGAGG +GAGGAAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGACGGAGGGCGGGACGGCGGGAGG +GCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGG +GAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGG +GAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGTGGG +AGGGAGGGAGGGATGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGACGGAGGG +AGGGAGGGAGGGACGGAGGTTGGGACGGAGGGACGGAGGGCGGGCGGATGCCGCGGGTCT +CACCGCCAAGGTGTCCTGCTGCTGCAGCAGGGCCCGCACGTGCAGGGTCGTGCTGTTCTC +CATCTCCTGGATGGTCTCGATCAGCTCCCGGTTGAGCTTGCTGAGGAAGTTCTCACGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/haps.fa.ref.fa new file mode 100644 index 00000000..601396f1 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:278800-279287 +GATGAAACCCATCTCGGTCCTCTTGCAAAGCCCAGGTGAGGGGAGTGAAGGGTGAAGAAATGCGTCTTCCAGGTGGAGGAAGCACCACGTGCAGTGGGCGGGGAAAGGCAGGAGAGGGCGCGCGAGTGCGCGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGAGGGACGGAGGTTGGGACGGAGGGACGGAGGGCGGGCGGATGCCGCGGGTCTCACCGCCAGGGTGTCCTGCTGCTGCAGCAGGGCCCGCACGTGCAGGGTCGTGCTGTTCTCCATCTCCTGGATGGTCTCGATCAGCTCCCGGTTGAGCTTGCTGAGGAAGTTCTCACGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/msa.fa new file mode 100644 index 00000000..68240cf0 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/msa.fa @@ -0,0 +1,100 @@ +>ref_chr20_278800_279287 +gatgaaacccatctcggtcctcttgcaaagcccaggtgaggggagtgaagggtgaagaaa +tgcgtcttccaggtggaggaagcaccacgtgcagt------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------------------gggcg +gggaaaggcaggagagggcgcgcgagtgcgcggagggagggcgggacggag----ggagg +gagggcg--------------------------------ggacggagggagggagggagg +gacggagggcgggacggcgggagggcgggacggagggacggagggagggcgggacggagg +gcgggagggcgggacggag----------------------------------------- +------------------------------------------------------------ +-----------------------------------------ggaggga----gggaggga +gggacggagggcgggacggagggacggagggagggagggagggacggaggttgggacgga +gggacggagggcgggcggatgccgcgggtctcaccgccagggtgtcctgctgctgcagca +gggcccgcacgtgcagggtcgtgctgttctccatctcctggatggtctcgatcagctccc +ggttgagcttgctgaggaagttctcacggc +>syndip_1_chr20:278800-279287 +gatgaaacccatctcggtcctcttgcaaagcccaggtgaggggagtgaagggtgaagaaa +tgcgtcttccaggtggaggaagcaccacgtgcagt------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------------------gggcg +gggaaaggcaggagagggcgcgcgagtgcgcggagggagggcgggacggag----ggagg +gagggcgggagggagggacggagggaggaagggcgggacggagggagggagggcgggagg +gacggagggcgggacggcgggagggcgggacggagggacggagggagggcgggacggagg +gcgggagggcgggacggagggagggag---ggagggagggcgggacggagggagggaggg +agggagggacggagggcgggacggagggagggagggcggagggagggagggcgggacgga +gggagggagggcgggacggagggtgggagggagggagggatggaggga----gggaggga +gggacggagggcgggacggagggacggagggagggagggagggacggaggttgggacgga +gggacggagggcgggcggatgccgcgggtctcaccgccaaggtgtcctgctgctgcagca +gggcccgcacgtgcagggtcgtgctgttctccatctcctggatggtctcgatcagctccc +ggttgagcttgctgaggaagttctcacggc +>syndip_2_chr20:278800-279287 +gatgaaacccatctcggtcctcttgcaaagcccaggtgaggggagtgaagggtgaagaaa +tgcgtcttccaggtggaggaagcaccacgtgcagtgggcggggaaaggcaggagagggcg +cgcgagtgcgcggagggagggcgggacggagggagggagggcgggacggagggagggagg +gagggcgggacggagggagggagggcgggacggagggagggagggagggacggagggcgg +gacggcgggagggcgggacggagggacggagggagggcgggacggagggcgggagggcgg +gacggagggagggagggagggagggcgggacggagggagggagggcgggacggagggagg +gagggagggacggagggcgggacggcgggagggcgggacggagggacggagggagggcgg +gacggagggcgggagggcgggacggagggagggagggcgggacggagggacggagggagg +gagggcgggacggagggagggagggcgggacggagggacggagggagggagggcgggacg +gagggagggagggagggacggagggcgggacggcgggagggcgggacggagggacggagg +gagggcgggacggagggcgggagggagggagggcgggacggagggagggagggagggagg +gcgggacggagggagggagggagggagggacggagggacggagggagggagggagggagg +gacggagggcgggacggagggagggagggcggagggagggagggcgggacggagggaggg +agggagggacggagggcgggacggagggagggagggcggagggagggagggcgggacgga +gggagggagggcgggagggatggagggagggagggcgggacggagggagggcgggaggga +gggacggagggcgggacggagggacggagggagggagggagggacggaggttgggacgga +gggacggagggcgggcggatgccgcgggtctcaccgccaaggtgtcctgctgctgcagca +gggcccgcacgtgcagggtcgtgctgttctccatctcctggatggtctcgatcagctccc +ggttgagcttgctgaggaagttctcacggc +>p:HG002_1_chr20:278800-279287 +gatgaaacccatctcggtcctcttgcaaagcccaggtgaggggagtgaagggtgaagaaa +tgcgtcttccaggtggaggaagcaccacgtgcagtgggcggggaaaggcaggagagggcg +cgcgagtgcgcggagggagggcgggacggagggagggagggcgggacggagggagggagg +gagggcgggacggagggagggagggcgggacggagggagggagggagggacggagggcgg +gacggcgggagggcgggacggagggacggagggagggcgggacggagggcgggagggcgg +gacggagggagggagggagggagggcgggacggagggagggagggcgggacggagggagg +gagggagggacggagggcgggacggcgggagggcgggacggagggacggagggagggcgg +gacggagggcgggagggcgggacggagggagggagggcgggacggagggacggagggagg +gagggcgggacggagggagggagggcgggacggagggacggagggagggagggcgggacg +gagggagggagggagggacggagggcgggacggcgggagggcgggacggagggacggagg +gagggcgggacggagggcgggagggagggagggcgggacggagggagggagggagggagg +gcgggacggagggagggagggagggagggacggagggacggagggagggagggagggagg +gacggagggcgggacggagggagggagggcggagggagggagggcgggacggagggaggg +agggagggacggagggcgggacggagggagggagggcggagggagggagggcgggacgga +gggagggagggcgggagggatggagggagggagggcgggacggagggagggcgggaggga +gggacggagggcgggacggagggacggagggagggagggagggacggaggttgggacgga +gggacggagggcgggcggatgccgcgggtctcaccgccaaggtgtcctgctgctgcagca +gggcccgcacgtgcagggtcgtgctgttctccatctcctggatggtctcgatcagctccc +ggttgagcttgctgaggaagttctcacggc +>p:HG002_2_chr20:278800-279287 +gatgaaacccatctcggtcctcttgcaaagcccaggtgaggggagtgaagggtgaagaaa +tgcgtcttccaggtggaggaagcaccacgtgcagt------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------------------gggcg +gggaaaggcaggagagggcgcgcgagtgcgcggagggagggcgggacggag----ggagg +gagggcgggagggagggacggagggaggaagggcgggacggagggagggagggcgggagg +gacggagggcgggacggcgggagggcgggacggagggacggagggagggcgggacggagg +gcgggagggcgggacggagggagggag---ggagggagggcgggacggagggagggaggg +agggagggacggagggcgggacggagggagggagggcggagggagggagggcgggacgga +gggagggagggcgggacggagggtgggagggagggagggatggaggga----gggaggga +gggacggagggcgggacggagggacggagggagggagggagggacggaggttgggacgga +gggacggagggcgggcggatgccgcgggtctcaccgccaaggtgtcctgctgctgcagca +gggcccgcacgtgcagggtcgtgctgttctccatctcctggatggtctcgatcagctccc +ggttgagcttgctgaggaagttctcacggc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/msa.fa.fai new file mode 100644 index 00000000..8f87f334 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_278800_279287 1110 25 60 61 +syndip_1_chr20:278800-279287 1110 1184 60 61 +syndip_2_chr20:278800-279287 1110 2343 60 61 +p:HG002_1_chr20:278800-279287 1110 3503 60 61 +p:HG002_2_chr20:278800-279287 1110 4663 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/output.vcf.gz new file mode 100644 index 00000000..5241b7ba Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/output.vcf.gz.tbi new file mode 100644 index 00000000..08d1fe8d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:278900-279187/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/base.vcf.gz new file mode 100644 index 00000000..1b2a5c76 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/base.vcf.gz.tbi new file mode 100644 index 00000000..5b885e41 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/comp.vcf.gz new file mode 100644 index 00000000..f0d772bb Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/comp.vcf.gz.tbi new file mode 100644 index 00000000..c230417d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/haps.fa new file mode 100644 index 00000000..90f0631d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/haps.fa @@ -0,0 +1,58 @@ +>ref_chr20_32722324_32723313 +ACAGAGGTCTCCTGAAAATTAGTGCCCATAACAGGTGTTTGGTAGACAGGTCTCAGCCCTCAGACAAACCCATTTCCAAAGATGAAGGCCAGAGAATGAGAATAATGATTTATCGTTCTGGCCGGGTGTGATGGCTCATGCCTGTAATCCCAGCGCTGTGGGAGGCGTGGCCGGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACTTGGTCTCTACTAAAAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGCAATCCCAGCTACCCAGAAGGCTGAGTCAGAAGAATCACTTGAACCCGGGAGGTGGAGGTTGCAGTGAGCCGAGATCGTGCCACTGCACTCCAGCCTGGGTGACAGAGTGAGACTCAGGAAAAAAAAAAAAAAGACTTGGCCGAGCCCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGTGGATCACGAGGTCAAGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCATCTCTACTAAAAAATACAAAAAATTAGCCGGGCGTGGTGGTGGGCACCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGAATGGCGTGAACCTGGTAGGCAGAGCTTGCAGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGTGACAGAGCAAGACTCCATCTCAAAAATAAATAAATAAATAAATAAATAAATAATAATAATAATAATAAAGACTTGTGATCCTCTCCCTCTCCCTCTCCCTCTCCGTCTCCCTCTCCCTCTCCCTCTCCCTCCCTCTCCGTCTCCGTCTCCGTCTCCGTCTCCCTCTCCCTCTCCCCACGGTCTCCCTCTCATGCGGAGCCGAAGCTGGACTGTACTGCTGCCATCTCGGCTCACTGCAACCTCCCTGCCTGATTCTCCTGCCTCAGCCTGCCGAGTGCCTGCGATTGCAGGCACGCGCCGCCACGCCTGACTGGTT +>syndip_1_chr20:32722324-32723313 +ACAGAGGTCTCCTGAAAATTAGTGCCCATAACAGGTGTTTGGTAGACAGGTCTCAGCCCT +CAGACAAACCCATTTCCAAAGATGAAGGCCAGAGAATGAGAATAATGATTTATCGTTCTG +GCCGGGTGTGATGGCTCATGCCTGTAATCCCAGCGCTGTGGGAGGCGTGGCCGGCAGATC +ACCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACTTGGTCTCTACTAA +AAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGCAATCCCAGCTACCCAGAAGGC +TGAGTCAGAAGAATCACTTGAACCCGGGAGGTGGAGGTTGCAGTGAGCCGAGATCGTGCC +ACTGCACTCCAGCCTGGGTGACAGAGTGAGACTCAGGAAAAAAAAAAAAAAGACTTGGCC +GAGCCCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGTGGATCAC +GAGGTCAAGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCATCTCTACTAAAAAA +TACAAAAAATTAGCCGGGCGTGGTGGTGGGCACCTGTAGTCCCAGCTACTCGGGAGGCTG +AGGCAGAATGGCGTGAACCTGGTAGGCAGAGCTTGCAGTGAGCTGAGATCACGCCACTGC +ACTCCAGCCTGGGTGACAGAGCAAGACTCCATCTCAAAAATAAATAAATAAATAAATAAA +TAAATAATAATAATAATAATAAAAAA +>syndip_2_chr20:32722324-32723313 +ACAGAGGTCTCCTGAAAATTAGTGCCCATAACAGGTGTTTGGTAGACAGGTCTCAGCCCT +CAGACAAACCCATTTCCAAAGATGAAGGCCAGAGAATGAGAATAATGATTTATCGTTCTG +GCCGGGTGTGATGGCTCATGCCTGTAATCCCAGCGCTGTGGGAGGCGTGGCCGGCAGATC +ACCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACTTGGTCTCTACTAA +AAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGCAATCCCAGCTACCCAGAAGGC +TGAGTCAGAAGAATCACTTGAACCCGGGAGGTGGAGGTTGCAGTGAGCCGAGATCGTGCC +ACTGCACTCCAGCCTGGGTGACAGAGTGAGACTCAGGAAAAAAAAAAAAAAGACTTGGCC +GAGCCCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGTGGATCAC +GAGGTCAAGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCATCTCTACTAAAAAA +TACAAAAAATTAGCCGGGCGTGGTGGTGGGCACCTGTAGTCCCAGCTACTCGGGAGGCTG +AGGCAGAATGGCGTGAACCTGGTAGGCAGAGCTTGCAGTGAGCTGAGATCACACCACTGC +ACTCCAGCCTGGGTGACAGAGCAAGACTCCATCTCAAAAATAAATAAATAAATAAATAAA +TAAATAAATAATAATAATAATAATAAT +>p:HG002_1_chr20:32722324-32723313 +ACAGAGGTCTCCTGAAAATTAGTGCCCATAACAGGTGTTTGGTAGACAGGTCTCAGCCCT +CAGACAAACCCATTTCCAAAGATGAAGGCCAGAGAATGAGAATAATGATTTATCGTTCTG +GCCGGGTGTGATGGCTCATGCCTGTAATCCCAGCGCTGTGGGAGGCGTGGCCGGCAGATC +ACCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACTTGGTCTCTACTAA +AAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGCAATCCCAGCTACCCAGAAGGC +TGAGTCAGAAGAATCACTTGAACCCGGGAGGTGGAGGTTGCAGTGAGCCGAGATCGTGCC +ACTGCACTCCAGCCTGGGTGACAGAGTGAGACTCAGGAAAAAAAAAAAAAAGACTTGGCC +GAGCCCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGTGGATCAC +GAGGTCAAGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCATCTCTACTAAAAAA +TACAAAAAATTAGCCGGGCGTGGTGGTGGGCACCTGTAGTCCCAGCTACTCGGGAGGCTG +AGGCAGAATGGCGTGAACCTGGTAGGCAGAGCTTGCAGTGAGCTGAGATCACACCACTGC +ACTCCAGCCTGGGTGACAGAGCAAGACTCCATCTCAAAAATAAATAAATAAATAAATAAA +TAAATAA +>p:HG002_2_chr20:32722324-32723313 +ACAGAGGTCTCCTGAAAATTAGTGCCCATAACAGGTGTTTGGTAGACAGGTCTCAGCCCT +CAGACAAACCCATTTCCAAAGATGAAGGCCAGAGAATGAGAATAATGATTTATCGTTCTG +GCCGGGTGTGATGGCTCATGCCTGTAATCCCAGCGCTGTGGGAGGCGTGGCCGGCAGATC +ACCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACTTGGTCTCTACTAA +AAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGCAATCCCAGCTACCCAGAAGGC +TGAGTCAGAAGAATCACTTGAACCCGGGAGGTGGAGGTTGCAGTGAGCCGAGATCGTGCC +ACTGCACTCCAGCCTGGGTGACAGAGTGAGACTCAGGAAAAAAAAAAAAAAGACTTGGCC +GAGCCCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGTGGATCAC +GAGGTCAAGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCATCTCTACTAAAAAA +TACAAAAAATTAGCCGGGCGTGGTGGTGGGCACCTGTAGTCCCAGCTACTCGGGAGGCTG +AGGCAGAATGGCGTGAACCTGGTAGGCAGAGCTTGCAGTGAGCTGAGATCACGCCACTGC +ACTCCAGCCTGGGTGACAGAGCAAGACTCCATCTCAAAAATAAATAAATAAATAAATAAA +TAAATAATAATAATAATAAT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/haps.fa.ref.fa new file mode 100644 index 00000000..d05be16a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:32722324-32723313 +ACAGAGGTCTCCTGAAAATTAGTGCCCATAACAGGTGTTTGGTAGACAGGTCTCAGCCCTCAGACAAACCCATTTCCAAAGATGAAGGCCAGAGAATGAGAATAATGATTTATCGTTCTGGCCGGGTGTGATGGCTCATGCCTGTAATCCCAGCGCTGTGGGAGGCGTGGCCGGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACTTGGTCTCTACTAAAAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGCAATCCCAGCTACCCAGAAGGCTGAGTCAGAAGAATCACTTGAACCCGGGAGGTGGAGGTTGCAGTGAGCCGAGATCGTGCCACTGCACTCCAGCCTGGGTGACAGAGTGAGACTCAGGAAAAAAAAAAAAAAGACTTGGCCGAGCCCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGTGGATCACGAGGTCAAGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCATCTCTACTAAAAAATACAAAAAATTAGCCGGGCGTGGTGGTGGGCACCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGAATGGCGTGAACCTGGTAGGCAGAGCTTGCAGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGTGACAGAGCAAGACTCCATCTCAAAAATAAATAAATAAATAAATAAATAAATAATAATAATAATAATAAAGACTTGTGATCCTCTCCCTCTCCCTCTCCCTCTCCGTCTCCCTCTCCCTCTCCCTCTCCCTCCCTCTCCGTCTCCGTCTCCGTCTCCGTCTCCCTCTCCCTCTCCCCACGGTCTCCCTCTCATGCGGAGCCGAAGCTGGACTGTACTGCTGCCATCTCGGCTCACTGCAACCTCCCTGCCTGATTCTCCTGCCTCAGCCTGCCGAGTGCCTGCGATTGCAGGCACGCGCCGCCACGCCTGACTGGTT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/msa.fa new file mode 100644 index 00000000..19c97710 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/msa.fa @@ -0,0 +1,90 @@ +>ref_chr20_32722324_32723313 +acagaggtctcctgaaaattagtgcccataacaggtgtttggtagacaggtctcagccct +cagacaaacccatttccaaagatgaaggccagagaatgagaataatgatttatcgttctg +gccgggtgtgatggctcatgcctgtaatcccagcgctgtgggaggcgtggccggcagatc +acctgaggtcaggagttcaagaccagcctggccaacatggtgaaacttggtctctactaa +aaatacaaaaattagccaggcatggtggtgggcgcctgcaatcccagctacccagaaggc +tgagtcagaagaatcacttgaacccgggaggtggaggttgcagtgagccgagatcgtgcc +actgcactccagcctgggtgacagagtgagactcaggaaaaaaaaaaaaaagacttggcc +gagcccagtggctcacacctgtaatcccagcactttgggaggctgaggcgggtggatcac +gaggtcaagagatcgagaccatcctggctaacacggtgaaaccccatctctactaaaaaa +tacaaaaaattagccgggcgtggtggtgggcacctgtagtcccagctactcgggaggctg +aggcagaatggcgtgaacctggtaggcagagcttgcagtgagctgagatcacgccactgc +actccagcctgggtgacagagcaagactccatctcaaaaataaataaataaataaataaa +taaataa-taataataataataaagacttgtgatcctctccctctccctctccctctccg +tctccctctccctctccctctccctccctctccgtctccgtctccgtctccgtctccctc +tccctctccccacggtctccctctcatgcggagccgaagctggactgtactgctgccatc +tcggctcactgcaacctccctgcctgattctcctgcctcagcctgccgagtgcctgcgat +tgcaggcacgcgccgccacgcctgactggtt +>syndip_1_chr20:32722324-32723313 +acagaggtctcctgaaaattagtgcccataacaggtgtttggtagacaggtctcagccct +cagacaaacccatttccaaagatgaaggccagagaatgagaataatgatttatcgttctg +gccgggtgtgatggctcatgcctgtaatcccagcgctgtgggaggcgtggccggcagatc +acctgaggtcaggagttcaagaccagcctggccaacatggtgaaacttggtctctactaa +aaatacaaaaattagccaggcatggtggtgggcgcctgcaatcccagctacccagaaggc +tgagtcagaagaatcacttgaacccgggaggtggaggttgcagtgagccgagatcgtgcc +actgcactccagcctgggtgacagagtgagactcaggaaaaaaaaaaaaaagacttggcc +gagcccagtggctcacacctgtaatcccagcactttgggaggctgaggcgggtggatcac +gaggtcaagagatcgagaccatcctggctaacacggtgaaaccccatctctactaaaaaa +tacaaaaaattagccgggcgtggtggtgggcacctgtagtcccagctactcgggaggctg +aggcagaatggcgtgaacctggtaggcagagcttgcagtgagctgagatcacgccactgc +actccagcctgggtgacagagcaagactccatctcaaaaataaataaataaataaataaa +taaataa-taataataataataaaaaa--------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------- +>syndip_2_chr20:32722324-32723313 +acagaggtctcctgaaaattagtgcccataacaggtgtttggtagacaggtctcagccct +cagacaaacccatttccaaagatgaaggccagagaatgagaataatgatttatcgttctg +gccgggtgtgatggctcatgcctgtaatcccagcgctgtgggaggcgtggccggcagatc +acctgaggtcaggagttcaagaccagcctggccaacatggtgaaacttggtctctactaa +aaatacaaaaattagccaggcatggtggtgggcgcctgcaatcccagctacccagaaggc +tgagtcagaagaatcacttgaacccgggaggtggaggttgcagtgagccgagatcgtgcc +actgcactccagcctgggtgacagagtgagactcaggaaaaaaaaaaaaaagacttggcc +gagcccagtggctcacacctgtaatcccagcactttgggaggctgaggcgggtggatcac +gaggtcaagagatcgagaccatcctggctaacacggtgaaaccccatctctactaaaaaa +tacaaaaaattagccgggcgtggtggtgggcacctgtagtcccagctactcgggaggctg +aggcagaatggcgtgaacctggtaggcagagcttgcagtgagctgagatcacaccactgc +actccagcctgggtgacagagcaagactccatctcaaaaataaataaataaataaataaa +taaataaataataataataataataat--------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------- +>p:HG002_1_chr20:32722324-32723313 +acagaggtctcctgaaaattagtgcccataacaggtgtttggtagacaggtctcagccct +cagacaaacccatttccaaagatgaaggccagagaatgagaataatgatttatcgttctg +gccgggtgtgatggctcatgcctgtaatcccagcgctgtgggaggcgtggccggcagatc +acctgaggtcaggagttcaagaccagcctggccaacatggtgaaacttggtctctactaa +aaatacaaaaattagccaggcatggtggtgggcgcctgcaatcccagctacccagaaggc +tgagtcagaagaatcacttgaacccgggaggtggaggttgcagtgagccgagatcgtgcc +actgcactccagcctgggtgacagagtgagactcaggaaaaaaaaaaaaaagacttggcc +gagcccagtggctcacacctgtaatcccagcactttgggaggctgaggcgggtggatcac +gaggtcaagagatcgagaccatcctggctaacacggtgaaaccccatctctactaaaaaa +tacaaaaaattagccgggcgtggtggtgggcacctgtagtcccagctactcgggaggctg +aggcagaatggcgtgaacctggtaggcagagcttgcagtgagctgagatcacaccactgc +actccagcctgggtgacagagcaagactccatctcaaaaataaataaataaataaataaa +taaataa----------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------- +>p:HG002_2_chr20:32722324-32723313 +acagaggtctcctgaaaattagtgcccataacaggtgtttggtagacaggtctcagccct +cagacaaacccatttccaaagatgaaggccagagaatgagaataatgatttatcgttctg +gccgggtgtgatggctcatgcctgtaatcccagcgctgtgggaggcgtggccggcagatc +acctgaggtcaggagttcaagaccagcctggccaacatggtgaaacttggtctctactaa +aaatacaaaaattagccaggcatggtggtgggcgcctgcaatcccagctacccagaaggc +tgagtcagaagaatcacttgaacccgggaggtggaggttgcagtgagccgagatcgtgcc +actgcactccagcctgggtgacagagtgagactcaggaaaaaaaaaaaaaagacttggcc +gagcccagtggctcacacctgtaatcccagcactttgggaggctgaggcgggtggatcac +gaggtcaagagatcgagaccatcctggctaacacggtgaaaccccatctctactaaaaaa +tacaaaaaattagccgggcgtggtggtgggcacctgtagtcccagctactcgggaggctg +aggcagaatggcgtgaacctggtaggcagagcttgcagtgagctgagatcacgccactgc +actccagcctgggtgacagagcaagactccatctcaaaaataaataaataaataaataaa +taaataa-taataataataat--------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------- diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/msa.fa.fai new file mode 100644 index 00000000..de0608cb --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_32722324_32723313 991 29 60 61 +syndip_1_chr20:32722324-32723313 991 1071 60 61 +syndip_2_chr20:32722324-32723313 991 2113 60 61 +p:HG002_1_chr20:32722324-32723313 991 3156 60 61 +p:HG002_2_chr20:32722324-32723313 991 4199 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/output.vcf.gz new file mode 100644 index 00000000..778fb976 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/output.vcf.gz.tbi new file mode 100644 index 00000000..58272588 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:32722424-32723213/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/base.vcf.gz new file mode 100644 index 00000000..e4ba3aa7 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/base.vcf.gz.tbi new file mode 100644 index 00000000..e6ba90f6 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/comp.vcf.gz new file mode 100644 index 00000000..17172bb3 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/comp.vcf.gz.tbi new file mode 100644 index 00000000..055bd4a2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/haps.fa new file mode 100644 index 00000000..e9e8c8d2 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/haps.fa @@ -0,0 +1,58 @@ +>ref_chr20_34235650_34236314 +AGCGCATGCCTGTGGCCCCTACTACTCAGGAGGCAGGGGTGGGAGGATTGCTAGAGCCCAGGAAGTCGTGGCTGAAGTGGGCTCATGATAATGCCACTGCACTCCAGCCTGTGTGACAGAGTGAGACTCTGAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAGGAAGGAAGGAAGGAAGGAAGGAAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGAAGGAAGGAAGGAGGGAGGGAGGGAAGAAGGAAAGAAGGAAGGAAGGAGAAAGAGAGAAAGAGAGAGAGAAGAAGAAAGAGAAAGAAACAGAAAAGGAAGGAAGGAGAGAGAGAAAGAAAGAGAAAGAGAAGGAAGGAAGGAAGGAGAAAGAAAGGAAAGGAAAGGAGTGGAAAGGAAAGGAGAGGAAAGGAGAAAGGAGGGAGGGAGGGAAAAGAAAGAAAGAAAGAAAAGGCTAAACCTGACTATGATATTGAATTTACTGCTAGCTCTAGGTGGTTTAAATGATTCAAGAATCATGGCCATGGCTGGGCGCAGTGGCTCACGCCTATAATCCCAGCACTTTGGGAGGCCGAAGCGGGC +>syndip_1_chr20:34235650-34236314 +AGCGCATGCCTGTGGCCCCTACTACTCAGGAGGCAGGGGTGGGAGGATTGCTAGAGCCCA +GGAAGTCGTGGCTGAAGTGGGCTCATGATAATGCCACTGCACTCCAGCCTGTGTGACAGA +GTGAGACTCTGAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG +AAAGAAAGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGGAAGGAAG +GAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGAAGGAGGAGGGAGGGAAGAAT +GAAGGAAGGAAGGAAGGAGGGAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGA +AGGAAGGAAGGAGGGAGGGAGGGAAGAAGGAAGGAGGAGGGAGGGAGGGAAGCAGGAAAG +AAGGAAGGAAGGAGAAAGAGAGAAAGAGAGAGAAGAAGAAAGAGAAAGAAACAGAAAAGG +AAGGAAGGAGAGAGAGAAAGAAAGAGAAAGAGAAGGAAGGAAGGAGAAAGAAAGGAAAAG +GAAAGGAAAGGAGTGGAAAGGAAAGGAGAGGAAAGGAGAAAGGAGGGAGGGAGGGAAAAG +AAAGAAAGAAAGAAAAGGCTAAACCTGACTATGATATTGAATTTACTGCTAGCTCTAGGT +GGTTTAAATGATTCAAGAATCATGGCCATGGCTGGGCGCAGTGGCTCACGCCTATAATCC +CAGCACTTTGGGAGGCCGAAGCGGGC +>syndip_2_chr20:34235650-34236314 +AGCGCATGCCTGTGGCCCCTACTACTCAGGAGGCAGGGGTGGGAGGATTGCTAGAGCCCA +GGAAGTCGTGGCTGAAGTGGGCTCATGATAATGCCACTGCACTCCAGCCTGTGTGACAGA +GTGAGACTCTGAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG +AAAGAAAGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGGAAGGAAG +GAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGAAGGAGGAGGGAGGGAAGAAT +GAAGGAAGGAAGGAAGGAGGGAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGA +AGGAAGGAAGGAGGGAGGGAGGGAAGAAGGAAGGAGGAGGGAGGGAGGGAAGCAGGAAAG +AAGGAAGGAAGGAGAAAGAGAGAAAGAGAGAGAAGAAGAAAGAGAAAGAAACAGAAAAGG +AAGGAAGGAGAGAGAGAAAGAAAGAGAAAGAGAAGGAAGGAAGGAGAAAGAAAGGAAAAG +GAAAGGAAAGGAGTGGAAAGGAAAGGAGAGGAAAGGAGAAAGGAGGGAGGGAGGGAAAAG +AAAGAAAGAAAGAAAAGGCTAAACCTGACTATGATATTGAATTTACTGCTAGCTCTAGGT +GGTTTAAATGATTCAAGAATCATGGCCATGGCTGGGCGCAGTGGCTCACGCCTATAATCC +CAGCACTTTGGGAGGCCGAAGCGGGC +>p:HG002_1_chr20:34235650-34236314 +AGCGCATGCCTGTGGCCCCTACTACTCAGGAGGCAGGGGTGGGAGGATTGCTAGAGCCCA +GGAAGTCGTGGCTGAAGTGGGCTCATGATAATGCCACTGCACTCCAGCCTGTGTGACAGA +GTGAGACTCTGAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG +AAAGAAAGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGGAAGGAAG +GAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGAAGGAGGAGGGAGGGAAGAAT +GAAGGAAGGAAGGAAGGAGGGAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGA +AGGAAGGAAGGAGGGAGGGAGGGAAGAAGGAAGGAGGAGGGAGGGAGGGAAGCAGGAAAG +AAGGAAGGAAGGAGAAAGAGAGAAAGAGAGAGAAGAAGAAAGAGAAAGAAACAGAAAAGG +AAGGAAGGAGAGAGAGAAAGAAAGAGAAAGAGAAGGAAGGAAGGAGAAAGAAAGGAAAAG +GAAAGGAAAGGAGTGGAAAGGAAAGGAGAGGAAAGGAGAAAGGAGGGAGGGAGGGAAAAG +AAAGAAAGAAAGAAAAGGCTAAACCTGACTATGATATTGAATTTACTGCTAGCTCTAGGT +GGTTTAAATGATTCAAGAATCATGGCCATGGCTGGGCGCAGTGGCTCACGCCTATAATCC +CAGCACTTTGGGAGGCCGAAGCGGGC +>p:HG002_2_chr20:34235650-34236314 +AGCGCATGCCTGTGGCCCCTACTACTCAGGAGGCAGGGGTGGGAGGATTGCTAGAGCCCA +GGAAGTCGTGGCTGAAGTGGGCTCATGATAATGCCACTGCACTCCAGCCTGTGTGACAGA +GTGAGACTCTGAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG +AAAGAAAGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGGAAGGAAG +GAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGAAGGAGGAGGGAGGGAAGAAT +GAAGGAAGGAAGGAAGGAGGGAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGA +AGGAAGGAAGGAGGGAGGGAGGGAAGAAGGAAGGAGGAGGGAGGGAGGGAAGCAGGAAAG +AAGGAAGGAAGGAGAAAGAGAGAAAGAGAGAGAAGAAGAAAGAGAAAGAAACAGAAAAGG +AAGGAAGGAGAGAGAGAAAGAAAGAGAAAGAGAAGGAAGGAAGGAGAAAGAAAGGAAAAG +GAAAGGAAAGGAGTGGAAAGGAAAGGAGAGGAAAGGAGAAAGGAGGGAGGGAGGGAAAAG +AAAGAAAGAAAGAAAAGGCTAAACCTGACTATGATATTGAATTTACTGCTAGCTCTAGGT +GGTTTAAATGATTCAAGAATCATGGCCATGGCTGGGCGCAGTGGCTCACGCCTATAATCC +CAGCACTTTGGGAGGCCGAAGCGGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/haps.fa.ref.fa new file mode 100644 index 00000000..83fe6093 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:34235650-34236314 +AGCGCATGCCTGTGGCCCCTACTACTCAGGAGGCAGGGGTGGGAGGATTGCTAGAGCCCAGGAAGTCGTGGCTGAAGTGGGCTCATGATAATGCCACTGCACTCCAGCCTGTGTGACAGAGTGAGACTCTGAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAGGAAGGAAGGAAGGAAGGAAGGAAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGAAGGAAGGAAGGAGGGAGGGAGGGAAGAAGGAAAGAAGGAAGGAAGGAGAAAGAGAGAAAGAGAGAGAGAAGAAGAAAGAGAAAGAAACAGAAAAGGAAGGAAGGAGAGAGAGAAAGAAAGAGAAAGAGAAGGAAGGAAGGAAGGAGAAAGAAAGGAAAGGAAAGGAGTGGAAAGGAAAGGAGAGGAAAGGAGAAAGGAGGGAGGGAGGGAAAAGAAAGAAAGAAAGAAAAGGCTAAACCTGACTATGATATTGAATTTACTGCTAGCTCTAGGTGGTTTAAATGATTCAAGAATCATGGCCATGGCTGGGCGCAGTGGCTCACGCCTATAATCCCAGCACTTTGGGAGGCCGAAGCGGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/msa.fa new file mode 100644 index 00000000..6d5785e2 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/msa.fa @@ -0,0 +1,70 @@ +>ref_chr20_34235650_34236314 +agcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccca +ggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacaga +gtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag +aaagaaagaaagaaggaaggaaggaaggaaggaaggaaaggaaggaaggaaggaaggaag +gaaggaagga-------------------------------------------------- +-----aaggaaggaaggaaggaaggaaggaaggaagcgggagggagggaagaaggaagga +aggaaggaaggagggagggagggaaga--------------------------aggaaag +aaggaaggaaggagaaagagagaaagagagagagaagaagaaagagaaagaaacagaaaa +ggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggaaggagaaag--aa +aggaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaaa +agaaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctctag +gtggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataat +cccagcactttgggaggccgaagcgggc +>syndip_1_chr20:34235650-34236314 +agcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccca +ggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacaga +gtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag +aaagaaagaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaagggaaggaag +gaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaggagggagggaagaat +gaaggaaggaaggaaggagggaaggaaggaaggaagcgggagggagggaagaaggaagga +aggaaggaaggagggagggagggaagaaggaaggaggagggagggagggaagcaggaaag +aaggaaggaaggagaaagagagaa--agagagagaagaagaaagagaaagaaacagaaaa +ggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggagaaagaaaggaaa +aggaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaaa +agaaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctctag +gtggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataat +cccagcactttgggaggccgaagcgggc +>syndip_2_chr20:34235650-34236314 +agcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccca +ggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacaga +gtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag +aaagaaagaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaagggaaggaag +gaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaggagggagggaagaat +gaaggaaggaaggaaggagggaaggaaggaaggaagcgggagggagggaagaaggaagga +aggaaggaaggagggagggagggaagaaggaaggaggagggagggagggaagcaggaaag +aaggaaggaaggagaaagagagaa--agagagagaagaagaaagagaaagaaacagaaaa +ggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggagaaagaaaggaaa +aggaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaaa +agaaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctctag +gtggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataat +cccagcactttgggaggccgaagcgggc +>p:HG002_1_chr20:34235650-34236314 +agcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccca +ggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacaga +gtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag +aaagaaagaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaagggaaggaag +gaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaggagggagggaagaat +gaaggaaggaaggaaggagggaaggaaggaaggaagcgggagggagggaagaaggaagga +aggaaggaaggagggagggagggaagaaggaaggaggagggagggagggaagcaggaaag +aaggaaggaaggagaaagagagaa--agagagagaagaagaaagagaaagaaacagaaaa +ggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggagaaagaaaggaaa +aggaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaaa +agaaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctctag +gtggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataat +cccagcactttgggaggccgaagcgggc +>p:HG002_2_chr20:34235650-34236314 +agcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccca +ggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacaga +gtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag +aaagaaagaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaagggaaggaag +gaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaggagggagggaagaat +gaaggaaggaaggaaggagggaaggaaggaaggaagcgggagggagggaagaaggaagga +aggaaggaaggagggagggagggaagaaggaaggaggagggagggagggaagcaggaaag +aaggaaggaaggagaaagagagaa--agagagagaagaagaaagagaaagaaacagaaaa +ggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggagaaagaaaggaaa +aggaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaaa +agaaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctctag +gtggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataat +cccagcactttgggaggccgaagcgggc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/msa.fa.fai new file mode 100644 index 00000000..f5d2be63 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_34235650_34236314 748 29 60 61 +syndip_1_chr20:34235650-34236314 748 824 60 61 +syndip_2_chr20:34235650-34236314 748 1619 60 61 +p:HG002_1_chr20:34235650-34236314 748 2415 60 61 +p:HG002_2_chr20:34235650-34236314 748 3211 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/output.vcf.gz new file mode 100644 index 00000000..6e4b2c0c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/output.vcf.gz.tbi new file mode 100644 index 00000000..bb0167fe Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:34235750-34236214/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/base.vcf.gz new file mode 100644 index 00000000..f966582a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/base.vcf.gz.tbi new file mode 100644 index 00000000..2634fdcb Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/comp.vcf.gz new file mode 100644 index 00000000..8acff116 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/comp.vcf.gz.tbi new file mode 100644 index 00000000..0a661f90 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/haps.fa new file mode 100644 index 00000000..50a2ab03 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/haps.fa @@ -0,0 +1,56 @@ +>ref_chr20_35539020_35539825 +TTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTAGCCAGGATGGTCTTGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACAGCGCCCGGCCTATGTTTTACATATATAACAATTTATATATAACTACATATATAATATATATAACAGTTTATATATATATATAACAGTTTATATATATAATATATATAACAGTTTATATATATATATATAACAGTTTATATATATAATATATATAACAGTTTATATATATAATATATATAACAGTTTATATATATAATATATAAGTTTATATATTATATATAACAGTTTATATATAACAGTTTATATATAATATATATAAGTTTATATATAACAGTTTATATATATAATATATATAAGTTTATATATAATATATATAAGTTTATATATATGTTTATATATAATATATATAACAGTTTATATATATAATATATATAACAGTTTATATATATAATATATATAACAGTTTATATATATAATATATATAACAGTTTATATATATAAAATATATAACAGTTTATATATATAATATATATAAGTTTATATATATAATATATATAACAGTTTATATATATTATATATATATATATGCACACACACAAAGAGAGAGAGAGAGACTCGCTCTGTCGCCCAGGCTGTAGTGCAGTGGTGTAATCACAGCTCACTATGAGGCAGGAGAACAGGGAATCAGGGTAACCGGGGGTTAAGACATAAGCAAATGAAGGGGTGCAGCCAGTTCTAGGCAGCA +>syndip_1_chr20:35539020-35539825 +TTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTAGCCAGGATGGTCTTGATCTCC +TGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCAC +AGCGCCCGGCCTATGTTTTACATATATAACAATTTATATATAACTACATATATAATATAT +ATAACAGTTTATATATATATATAACAGTTTATATATATATTATATATAACAGTTTATATA +TATAATATATATGTTTATATATTATATATAACAGTTTATATATAACAGTTTATATATAAT +ATATATAAGTTTATATATAACAGTTTATATATATAATATATATAAGTTTATATATAATAT +ATATAAGTTTATATATGTTTATATATAATATATATAACAGTTTATATATATAATATATAT +AACAGTTTATATATATAATATATATAACAGTTTATATATATAATATATATAAGTTTATAT +ATATAATATATATAACAGTTTATATATATTATATATATATATATGCACACACACAAAGAG +AGAGAGAGAGACTCGCTCTGTCGCCCAGGCTGTAGTGCAGTGGTGTAATCACAGCTCACT +ATGAGGCAGGAGAACAGGGAATCAGGGTAACCGGGGGTTAAGACATAAGCAAATGAAGGG +GTGCAGCCAGTTCTAGGCAGCA +>syndip_2_chr20:35539020-35539825 +TTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTAGCCAGGATGGTCTTGATCTCC +TGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCAC +AGCGCCCGGCCTATGTTTTACATATATAACAATTTATATATAACTACATATATAATATAT +ATAACAGTTTATATATATATATAACAGTTTATATATATAATATATATAACAGTTTATATA +TATATATAACAGTTTATATATATAATATATATAAGTTTATATATTATATATAACAGTTTA +TATATAACAGTTTATATATAATATATATAAGTTTATATATAACAGTTTATATATATAATA +TATATAAGTTTATATATAATATATATAAGTTTATATATATGTTTATATATAATATATATA +ACAGTTTATATATATAATATATATAACAGTTTATATATATAATATATATAACAGTTTATA +TATATAATATATATAACAGTTTATATATATAATATATATAAGTTTATATATATAATATAT +ATAACAGTTTATATATATTATATATATATATATGCACACACACAAAGAGAGAGAGAGAGA +CTCGCTCTGTCGCCCAGGCTGTAGTGCAGTGGTGTAATCACAGCTCACTATGAGGCAGGA +GAACAGGGAATCAGGGTAACCGGGGGTTAAGACATAAGCAAATGAAGGGGTGCAGCCAGT +TCTAGGCAGCA +>p:HG002_1_chr20:35539020-35539825 +TTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTAGCCAGGATGGTCTTGATCTCC +TGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCAC +AGCGCCCGGCCTATGTTTTACATATATAACAATTTATATATAACTACATATATAATATAT +ATAACAGTTTATATATATATATAACAGTTTATATATATAATATATATAACAGTTTATATA +TATATATAACAGTTTATATATATAATATATATAAGTTTATATATTATATATAACAGTTTA +TATATAACAGTTTATATATAATATATATAAGTTTATATATAACAGTTTATATATATAATA +TATATAAGTTTATATATAATATATATAAGTTTATATATATGTTTATATATAATATATATA +ACAGTTTATATATATAATATATATAACAGTTTATATATATAATATATATAACAGTTTATA +TATATAATATATATAACAGTTTATATATATAATATATATAAGTTTATATATATAATATAT +ATAACAGTTTATATATATTATATATATATATATGCACACACACAAAGAGAGAGAGAGAGA +CTCGCTCTGTCGCCCAGGCTGTAGTGCAGTGGTGTAATCACAGCTCACTATGAGGCAGGA +GAACAGGGAATCAGGGTAACCGGGGGTTAAGACATAAGCAAATGAAGGGGTGCAGCCAGT +TCTAGGCAGCA +>p:HG002_2_chr20:35539020-35539825 +TTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTAGCCAGGATGGTCTTGATCTCC +TGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCAC +AGCGCCCGGCCTATGTTTTACATATATAACAATTTATATATAACTACATATATAATATAT +ATAACAGTTTATATATATATATAACAGTTTATATATATATTATATATAACAGTTTATATA +TATAATATATATGTTTATATATTATATATAACAGTTTATATATAACAGTTTATATATAAT +ATATATAAGTTTATATATAACAGTTTATATATATAATATATATAAGTTTATATATAATAT +ATATAAGTTTATATATGTTTATATATAATATATATAACAGTTTATATATATAATATATAT +AACAGTTTATATATATAATATATATAACAGTTTATATATATAATATATATAAGTTTATAT +ATATAATATATATAACAGTTTATATATATTATATATATATATATGCACACACACAAAGAG +AGAGAGAGAGACTCGCTCTGTCGCCCAGGCTGTAGTGCAGTGGTGTAATCACAGCTCACT +ATGAGGCAGGAGAACAGGGAATCAGGGTAACCGGGGGTTAAGACATAAGCAAATGAAGGG +GTGCAGCCAGTTCTAGGCAGCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/haps.fa.ref.fa new file mode 100644 index 00000000..74f390c8 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:35539020-35539825 +TTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTAGCCAGGATGGTCTTGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACAGCGCCCGGCCTATGTTTTACATATATAACAATTTATATATAACTACATATATAATATATATAACAGTTTATATATATATATAACAGTTTATATATATAATATATATAACAGTTTATATATATATATATAACAGTTTATATATATAATATATATAACAGTTTATATATATAATATATATAACAGTTTATATATATAATATATAAGTTTATATATTATATATAACAGTTTATATATAACAGTTTATATATAATATATATAAGTTTATATATAACAGTTTATATATATAATATATATAAGTTTATATATAATATATATAAGTTTATATATATGTTTATATATAATATATATAACAGTTTATATATATAATATATATAACAGTTTATATATATAATATATATAACAGTTTATATATATAATATATATAACAGTTTATATATATAAAATATATAACAGTTTATATATATAATATATATAAGTTTATATATATAATATATATAACAGTTTATATATATTATATATATATATATGCACACACACAAAGAGAGAGAGAGAGACTCGCTCTGTCGCCCAGGCTGTAGTGCAGTGGTGTAATCACAGCTCACTATGAGGCAGGAGAACAGGGAATCAGGGTAACCGGGGGTTAAGACATAAGCAAATGAAGGGGTGCAGCCAGTTCTAGGCAGCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/msa.fa new file mode 100644 index 00000000..d5e3bc13 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/msa.fa @@ -0,0 +1,75 @@ +>ref_chr20_35539020_35539825 +tttttgtatttttagtagagacagggtttcaccatgttagccaggatggtcttgatctcc +tgacctcgtgatccgcccgcctcggcctcccaaagtgctgggattacaggcgtgagccac +agcgcccggcctatgttttacatatataacaatttatatataactacatatataatatat +ataacagtttatatatatatataacagtttatatatataatatatataacagtttatata +tatatatataacagtttatatatataatatatataacagtttatatatataatatatata +acagtttatatatataatatataagtttatatattatatataacagtttatatataacag +tttatatataatatatataagtttatatataacagtttatatatataatatatataagtt +tatatataatatatataagtttatatatatgtttatatataatatatataacagtttata +tatataatatatataacagtttatatatataatatatataacagtttatatatataatat +atataacagtttatatatataaaatatataacagtttatatatataatatatataagttt +atatatataatatatataacagtttatatatattatatatatatatatgcacacacacaa +agagagagagagagactcgctctgtcgcccaggctgtagtgcagtggtgtaatcacagct +cactatgaggcaggagaacagggaatcagggtaaccgggggttaagacataagcaaatga +aggggtgcagccagttctaggcagca +>syndip_1_chr20:35539020-35539825 +tttttgtatttttagtagagacagggtttcaccatgttagccaggatggtcttgatctcc +tgacctcgtgatccgcccgcctcggcctcccaaagtgctgggattacaggcgtgagccac +agcgcccggcctatgttttacatatataacaatttatatataactacatatataatatat +ataacagtttatatatatatataacagtttatatatatattatatataacagtt--tata +tatata------------------------------------------------------ +----------------atatatatgtttatatattatatataacagtttatatataacag +tttatatataatatatataagtttatatataacagtttatatatataatatatataagtt +tatatataatatatataagtttatatatg------------------------------- +---------------------tttatatataatatatataacagtttatatatataatat +atataacagtttatatatataatatatataacagtttatatatataatatatataagttt +atatatataatatatataacagtttatatatattatatatatatatatgcacacacacaa +agagagagagagagactcgctctgtcgcccaggctgtagtgcagtggtgtaatcacagct +cactatgaggcaggagaacagggaatcagggtaaccgggggttaagacataagcaaatga +aggggtgcagccagttctaggcagca +>syndip_2_chr20:35539020-35539825 +tttttgtatttttagtagagacagggtttcaccatgttagccaggatggtcttgatctcc +tgacctcgtgatccgcccgcctcggcctcccaaagtgctgggattacaggcgtgagccac +agcgcccggcctatgttttacatatataacaatttatatataactacatatataatatat +ataacagtttatatatatatataacagtttatatatataatatatataacagtt--tata +tatatatataacagtttatatatataat-------------------------------- +----------------atatataagtttatatattatatataacagtttatatataacag +tttatatataatatatataagtttatatataacagtttatatatataatatatataagtt +tatatataatatatataagtttatatatatgtttatatataatatatataacagtt---- +---------------------tatatatataatatatataacagtttatatatataatat +atataacagtttatatatataatatatataacagtttatatatataatatatataagttt +atatatataatatatataacagtttatatatattatatatatatatatgcacacacacaa +agagagagagagagactcgctctgtcgcccaggctgtagtgcagtggtgtaatcacagct +cactatgaggcaggagaacagggaatcagggtaaccgggggttaagacataagcaaatga +aggggtgcagccagttctaggcagca +>p:HG002_1_chr20:35539020-35539825 +tttttgtatttttagtagagacagggtttcaccatgttagccaggatggtcttgatctcc +tgacctcgtgatccgcccgcctcggcctcccaaagtgctgggattacaggcgtgagccac +agcgcccggcctatgttttacatatataacaatttatatataactacatatataatatat +ataacagtttatatatatatataacagtttatatatataatatatataacagtt--tata +tatatatataacagtttatatatataat-------------------------------- +----------------atatataagtttatatattatatataacagtttatatataacag +tttatatataatatatataagtttatatataacagtttatatatataatatatataagtt +tatatataatatatataagtttatatatatgtttatatataatatatataacagtt---- +---------------------tatatatataatatatataacagtttatatatataatat +atataacagtttatatatataatatatataacagtttatatatataatatatataagttt +atatatataatatatataacagtttatatatattatatatatatatatgcacacacacaa +agagagagagagagactcgctctgtcgcccaggctgtagtgcagtggtgtaatcacagct +cactatgaggcaggagaacagggaatcagggtaaccgggggttaagacataagcaaatga +aggggtgcagccagttctaggcagca +>p:HG002_2_chr20:35539020-35539825 +tttttgtatttttagtagagacagggtttcaccatgttagccaggatggtcttgatctcc +tgacctcgtgatccgcccgcctcggcctcccaaagtgctgggattacaggcgtgagccac +agcgcccggcctatgttttacatatataacaatttatatataactacatatataatatat +ataacagtttatatatatatataacagtttatatatatattatatataacagtt--tata +tatata------------------------------------------------------ +----------------atatatatgtttatatattatatataacagtttatatataacag +tttatatataatatatataagtttatatataacagtttatatatataatatatataagtt +tatatataatatatataagtttatatatg------------------------------- +---------------------tttatatataatatatataacagtttatatatataatat +atataacagtttatatatataatatatataacagtttatatatataatatatataagttt +atatatataatatatataacagtttatatatattatatatatatatatgcacacacacaa +agagagagagagagactcgctctgtcgcccaggctgtagtgcagtggtgtaatcacagct +cactatgaggcaggagaacagggaatcagggtaaccgggggttaagacataagcaaatga +aggggtgcagccagttctaggcagca diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/msa.fa.fai new file mode 100644 index 00000000..4954776a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_35539020_35539825 806 29 60 61 +syndip_1_chr20:35539020-35539825 806 883 60 61 +syndip_2_chr20:35539020-35539825 806 1737 60 61 +p:HG002_1_chr20:35539020-35539825 806 2592 60 61 +p:HG002_2_chr20:35539020-35539825 806 3447 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/output.vcf.gz new file mode 100644 index 00000000..ae5e3513 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/output.vcf.gz.tbi new file mode 100644 index 00000000..8ed81d9e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35539120-35539725/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/base.vcf.gz new file mode 100644 index 00000000..39383df5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/base.vcf.gz.tbi new file mode 100644 index 00000000..f54b5b24 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/comp.vcf.gz new file mode 100644 index 00000000..79941fcd Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/comp.vcf.gz.tbi new file mode 100644 index 00000000..ee56fe6f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/haps.fa new file mode 100644 index 00000000..51e65823 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/haps.fa @@ -0,0 +1,88 @@ +>ref_chr20_35579913_35580987 +AAAACTCCATCTCAAAAAAAAAAAAAAAAAAAAAGGGACACAATCCTGGATTCAAAAGACTGTTGTAAATATCAAATGACATAATAGAAACATAAGTACTTTGGAGCCTACAAAGTGCTGTCAGAAGCTGGGCATGGTGGCTCATGCCTGTAACCCCAGCACTTTGGGAGGCTGAGGCAGGCAGACTGCTCAAACTCAGGAGTTCGAGACCAGCCTGGGCAACATGGCAAGACACCATCTGTACCAAAAATACAAAAAAATAGCCGGGCATAGTGGTGCGCACCTGTGGTCCCAGCTACTCAGGAGGTTGAGGTGGGAGGATCACTTGAGCCCAGGGGGCGGAGGTTACAGTGAGCCAAGATTTGCACTCCAGCCTTGGTGACAGAGCAAGAGACCCTGTCTAAAATATATATGTGTATATACACACACACACACACAAATATATTTTTTGGCTGGGCATGGTGGCTGACACCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGCAGATCACTTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAAGATGATGAAATCCTGTCTCTACTAAAAATACAAAAAAATTAGCTGGGTGTGGTAACGGGTGGCTGTAATCCCAGCTACTTGGGAAGCTGAGGCAGAAGAATAGCTTGAACCTGGGAGGCACAGGTTGCAGTGAGCCGAGATCGCGCCACTGCAGCCTAGGCAGCAGAGTGAGACTCTGTCTTAAAATATATATTATGGTTTATTTTATTTTATGGTTAAAGGCCATATATATATATATATAAAATATATATATATAAAATATATATAAAATATATATATATAAAATATATATATAATATATATATATAAAATATATATATATAATATATATATATAAAATATATATATATAAAATATATATATATATAAAATATATATATATATAAAATATATATATGGAATTCCATATCTATCAATGGATCCTAAGGGAAACAATTTTACTACTGTATTGGTGGGTTTATTTTATGTATTTGTAGATATATACATATATACACATATATATGACAATTTTAGCACAAAAGAGAGGAA +>syndip_1_chr20:35579913-35580987 +AAAACTCCATCTCAAAAAAAAAAAAAAAAAAAAAGGGACACAATCCTGGATTCAAAAGAC +TGTTGTAAATATCAAATGACATAATAGAAACATAAGTACTTTGGAGCCTACAAAGTGCTG +TCAGAAGCTGGGCATGGTGGCTCATGCCTGTAACCCCAGCACTTTGGGAGGCTGAGGCAG +GCAGACTGCTCAAACTCAGGAGTTCGAGACCAGCCTGGGCAACATGGCAAGACACCATCT +GTACCAAAAATACAAAAAAATAGCCGGGCATAGTGGTGCGCACCTGTGGTCCCAGCTACT +CAGGAGGTTGAGGTGGGAGGATCACTTGAGCCCAGGGGGCGGAGGTTACAGTGAGCCAAG +ATTTGCACTCCAGCCTTGGTGACAGAGCAAGAGACCCTGTCTAAAATATATATGTGTATA +TACACACACACACACACAAATATATTTTTTGGCTGGGCATGGTGGCTGACACCTGTAATC +CCAGCACTTTGGGAGGCCAAGGCAGGCAGATCACTTGAGGTCAGGAGTTTGAGACCAGCC +TGGCCAAGATGATGAAATCCTGTCTCTACTAAAAATACAAAAAAATTAGCTGGGTGTGGT +AACGGGTGGCTGTAATCCCAGCTACTTGGGAAGCTGAGGCAGAAGAATAGCTTGAACCTG +GGAGGCACAGGTTGCAGTGAGCCGAGATCGCGCCACTGCAGCCTAGGCAGCAGAGTGAGA +CTCTGTCTTAAAATATATATTATGGTTTATTTTATTTTATGGTTAAAGGCCATATATATA +TATATATATATATATATAATATATATATATATAAAATATATATATATAAAATATATATAT +ATATAAAATATATATATATAAAATATATATATATATATAAAATATATATATATAAAATAT +ATATATATAAAATATATATATATATAAAATATATATATATATAAAATATATATATATAAA +ATATATATATATATAAAATATATATATATAAAATATATATATATAAAATATATATATATA +TAAAATATATATATATAAAATATATATATATAAAATATATATATATATAATATATATATA +TAAAATATATATATATAAAATATATATATAAAATATATATATATAAAATATATATATATA +AAATATATATATATAAAATATATATATATAAAATATATATATAAAATATATATATATAAA +ATATATATATATAAAATATATATATATAAAATATATATATGGAATTCCATATCTATCAAT +GGATCCTAAGGGAAACAATTTTACTACTGTATTGGTGGGTTTATTTTATGTATTTGTAGA +TATATACATATATACACATATATATGACAATTTTAGCACAAAAGAGAGGAA +>syndip_2_chr20:35579913-35580987 +AAAACTCCATCTCAAAAAAAAAAAAAAAAAAAAAGGGACACAATCCTGGATTCAAAAGAC +TGTTGTAAATATCAAATGACATAATAGAAACATAAGTACTTTGGAGCCTACAAAGTGCTG +TCAGAAGCTGGGCATGGTGGCTCATGCCTGTAACCCCAGCACTTTGGGAGGCTGAGGCAG +GCAGACTGCTCAAACTCAGGAGTTCGAGACCAGCCTGGGCAACATGGCAAGACACCATCT +GTACCAAAAATACAAAAAAATAGCCGGGCATAGTGGTGCGCACCTGTGGTCCCAGCTACT +CAGGAGGTTGAGGTGGGAGGATCACTTGAGCCCAGGGGGCGGAGGTTACAGTGAGCCAAG +ATTTGCACTCCAGCCTTGGTGACAGAGCAAGAGACCCTGTCTAAAATATATATGTGTATA +TACACACACACACACACAAATATATTTTTTGGCTGGGCATGGTGGCTGACACCTGTAATC +CCAGCACTTTGGGAGGCCAAGGCAGGCAGATCACTTGAGGTCAGGAGTTTGAGACCAGCC +TGGCCAAGATGATGAAATCCTGTCTCTACTAAAAATACAAAAAAATTAGCTGGGTGTGGT +AACGGGTGGCTGTAATCCCAGCTACTTGGGAAGCTGAGGCAGAAGAATAGCTTGAACCTG +GGAGGCACAGGTTGCAGTGAGCCGAGATCGCGCCACTGCAGCCTAGGCAGCAGAGTGAGA +CTCTGTCTTAAAATATATATTATGGTTTATTTTATTTTATGGTTAAAGGCCATATATATA +TATATATATATATAAAATATATATAATATATATATATATAATATATATATAAAATATATA +TAAAATATATATATATAAAATATATATATATAAAATATATATATATAAAATATATATATA +TATATAAAATATATATATGGAATTCCATATCTATCAATGGATCCTAAGGGAAACAATTTT +ACTACTGTATTGGTGGGTTTATTTTATGTATTTGTAGATATATACATATATACACATATA +TATGACAATTTTAGCACAAAAGAGAGGAA +>p:HG002_1_chr20:35579913-35580987 +AAAACTCCATCTCAAAAAAAAAAAAAAAAAAAAAGGGACACAATCCTGGATTCAAAAGAC +TGTTGTAAATATCAAATGACATAATAGAAACATAAGTACTTTGGAGCCTACAAAGTGCTG +TCAGAAGCTGGGCATGGTGGCTCATGCCTGTAACCCCAGCACTTTGGGAGGCTGAGGCAG +GCAGACTGCTCAAACTCAGGAGTTCGAGACCAGCCTGGGCAACATGGCAAGACACCATCT +GTACCAAAAATACAAAAAAATAGCCGGGCATAGTGGTGCGCACCTGTGGTCCCAGCTACT +CAGGAGGTTGAGGTGGGAGGATCACTTGAGCCCAGGGGGCGGAGGTTACAGTGAGCCAAG +ATTTGCACTCCAGCCTTGGTGACAGAGCAAGAGACCCTGTCTAAAATATATATGTGTATA +TACACACACACACACACAAATATATTTTTTGGCTGGGCATGGTGGCTGACACCTGTAATC +CCAGCACTTTGGGAGGCCAAGGCAGGCAGATCACTTGAGGTCAGGAGTTTGAGACCAGCC +TGGCCAAGATGATGAAATCCTGTCTCTACTAAAAATACAAAAAAATTAGCTGGGTGTGGT +AACGGGTGGCTGTAATCCCAGCTACTTGGGAAGCTGAGGCAGAAGAATAGCTTGAACCTG +GGAGGCACAGGTTGCAGTGAGCCGAGATCGCGCCACTGCAGCCTAGGCAGCAGAGTGAGA +CTCTGTCTTAAAATATATATTATGGTTTATTTTATTTTATGGTTAAAGGCCATATATATA +TATATATATATATAAAATATATATAATATATATATATATAATATATATATAAAATATATA +TAAAATATATATATATAAAATATATATATATAAAATATATATATATAAAATATATATATA +TATATAAAATATATATATGGAATTCCATATCTATCAATGGATCCTAAGGGAAACAATTTT +ACTACTGTATTGGTGGGTTTATTTTATGTATTTGTAGATATATACATATATACACATATA +TATGACAATTTTAGCACAAAAGAGAGGAA +>p:HG002_2_chr20:35579913-35580987 +AAAACTCCATCTCAAAAAAAAAAAAAAAAAAAAAGGGACACAATCCTGGATTCAAAAGAC +TGTTGTAAATATCAAATGACATAATAGAAACATAAGTACTTTGGAGCCTACAAAGTGCTG +TCAGAAGCTGGGCATGGTGGCTCATGCCTGTAACCCCAGCACTTTGGGAGGCTGAGGCAG +GCAGACTGCTCAAACTCAGGAGTTCGAGACCAGCCTGGGCAACATGGCAAGACACCATCT +GTACCAAAAATACAAAAAAATAGCCGGGCATAGTGGTGCGCACCTGTGGTCCCAGCTACT +CAGGAGGTTGAGGTGGGAGGATCACTTGAGCCCAGGGGGCGGAGGTTACAGTGAGCCAAG +ATTTGCACTCCAGCCTTGGTGACAGAGCAAGAGACCCTGTCTAAAATATATATGTGTATA +TACACACACACACACACAAATATATTTTTTGGCTGGGCATGGTGGCTGACACCTGTAATC +CCAGCACTTTGGGAGGCCAAGGCAGGCAGATCACTTGAGGTCAGGAGTTTGAGACCAGCC +TGGCCAAGATGATGAAATCCTGTCTCTACTAAAAATACAAAAAAATTAGCTGGGTGTGGT +AACGGGTGGCTGTAATCCCAGCTACTTGGGAAGCTGAGGCAGAAGAATAGCTTGAACCTG +GGAGGCACAGGTTGCAGTGAGCCGAGATCGTGCCACTGCAGCCTAGGCAGCAGAGTGAGA +CTCTGTCTTAAAATATATATTATGGTTTATTTTATTTTATGGTTAAAGGCCATATATATA +TATATATATATATATATAATATATATATATATAAAATATATATATATAAAATATATATAT +ATATAAAATATATATATATAAAATATATATATATATATAAAATATATATATATAAAATAT +ATATATATAAAATATATATATATATAAAATATATATATATATAAAATATATATATATAAA +ATATATATATATATAAAATATATATATATAAAATATATATATATAAAATATATATATATA +TAAAATATATATATATAAAATATATATATATAAAATATATATATATATAATATATATATA +TAAAATATATATATATAAAATATATATATAAAATATATATATATAAAATATATATATATA +AAATATATATATATAAAATATATATATATAAAATATATATATAAAATATATATATATAAA +ATATATATATATAAAATATATATATATAAAATATATATATGGAATTCCATATCTATCAAT +GGATCCTAAGGGAAACAATTTTACTACTGTATTGGTGGGTTTATTTTATGTATTTGTAGA +TATATACATATATACACATATATATGACAATTTTAGCACAAAAGAGAGGAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/haps.fa.ref.fa new file mode 100644 index 00000000..358aa93e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:35579913-35580987 +AAAACTCCATCTCAAAAAAAAAAAAAAAAAAAAAGGGACACAATCCTGGATTCAAAAGACTGTTGTAAATATCAAATGACATAATAGAAACATAAGTACTTTGGAGCCTACAAAGTGCTGTCAGAAGCTGGGCATGGTGGCTCATGCCTGTAACCCCAGCACTTTGGGAGGCTGAGGCAGGCAGACTGCTCAAACTCAGGAGTTCGAGACCAGCCTGGGCAACATGGCAAGACACCATCTGTACCAAAAATACAAAAAAATAGCCGGGCATAGTGGTGCGCACCTGTGGTCCCAGCTACTCAGGAGGTTGAGGTGGGAGGATCACTTGAGCCCAGGGGGCGGAGGTTACAGTGAGCCAAGATTTGCACTCCAGCCTTGGTGACAGAGCAAGAGACCCTGTCTAAAATATATATGTGTATATACACACACACACACACAAATATATTTTTTGGCTGGGCATGGTGGCTGACACCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGCAGATCACTTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAAGATGATGAAATCCTGTCTCTACTAAAAATACAAAAAAATTAGCTGGGTGTGGTAACGGGTGGCTGTAATCCCAGCTACTTGGGAAGCTGAGGCAGAAGAATAGCTTGAACCTGGGAGGCACAGGTTGCAGTGAGCCGAGATCGCGCCACTGCAGCCTAGGCAGCAGAGTGAGACTCTGTCTTAAAATATATATTATGGTTTATTTTATTTTATGGTTAAAGGCCATATATATATATATATAAAATATATATATATAAAATATATATAAAATATATATATATAAAATATATATATAATATATATATATAAAATATATATATATAATATATATATATAAAATATATATATATAAAATATATATATATATAAAATATATATATATATAAAATATATATATGGAATTCCATATCTATCAATGGATCCTAAGGGAAACAATTTTACTACTGTATTGGTGGGTTTATTTTATGTATTTGTAGATATATACATATATACACATATATATGACAATTTTAGCACAAAAGAGAGGAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/msa.fa new file mode 100644 index 00000000..a92e0ef2 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/msa.fa @@ -0,0 +1,120 @@ +>ref_chr20_35579913_35580987 +aaaactccatctcaaaaaaaaaaaaaaaaaaaaagggacacaatcctggattcaaaagac +tgttgtaaatatcaaatgacataatagaaacataagtactttggagcctacaaagtgctg +tcagaagctgggcatggtggctcatgcctgtaaccccagcactttgggaggctgaggcag +gcagactgctcaaactcaggagttcgagaccagcctgggcaacatggcaagacaccatct +gtaccaaaaatacaaaaaaatagccgggcatagtggtgcgcacctgtggtcccagctact +caggaggttgaggtgggaggatcacttgagcccagggggcggaggttacagtgagccaag +atttgcactccagccttggtgacagagcaagagaccctgtctaaaatatatatgtgtata +tacacacacacacacacaaatatattttttggctgggcatggtggctgacacctgtaatc +ccagcactttgggaggccaaggcaggcagatcacttgaggtcaggagtttgagaccagcc +tggccaagatgatgaaatcctgtctctactaaaaatacaaaaaaattagctgggtgtggt +aacgggtggctgtaatcccagctacttgggaagctgaggcagaagaatagcttgaacctg +ggaggcacaggttgcagtgagccgagatcgcgccactgcagcctaggcagcagagtgaga +ctctgtcttaaaatatatattatggtttattttattttatggttaaaggccatatatata +t-------------------------atatataaaatatatatatataaa------atat +atataaaatatatatatataaa-------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------atatatatataatatatatata +taa---------------aatatatatatataatatatatatataaaatatatatatata +aaatatatatatatataaaat--------------------------------------- +---------------atatatatatataaaatatatatatggaattccatatctatcaat +ggatcctaagggaaacaattttactactgtattggtgggtttattttatgtatttgtaga +tatatacatatatacacatatatatgacaattttagcacaaaagagaggaa +>syndip_1_chr20:35579913-35580987 +aaaactccatctcaaaaaaaaaaaaaaaaaaaaagggacacaatcctggattcaaaagac +tgttgtaaatatcaaatgacataatagaaacataagtactttggagcctacaaagtgctg +tcagaagctgggcatggtggctcatgcctgtaaccccagcactttgggaggctgaggcag +gcagactgctcaaactcaggagttcgagaccagcctgggcaacatggcaagacaccatct +gtaccaaaaatacaaaaaaatagccgggcatagtggtgcgcacctgtggtcccagctact +caggaggttgaggtgggaggatcacttgagcccagggggcggaggttacagtgagccaag +atttgcactccagccttggtgacagagcaagagaccctgtctaaaatatatatgtgtata +tacacacacacacacacaaatatattttttggctgggcatggtggctgacacctgtaatc +ccagcactttgggaggccaaggcaggcagatcacttgaggtcaggagtttgagaccagcc +tggccaagatgatgaaatcctgtctctactaaaaatacaaaaaaattagctgggtgtggt +aacgggtggctgtaatcccagctacttgggaagctgaggcagaagaatagcttgaacctg +ggaggcacaggttgcagtgagccgagatcgcgccactgcagcctaggcagcagagtgaga +ctctgtcttaaaatatatattatggtttattttattttatggttaaaggccatatatata +tatatatatatatatataatatatatatatataaaatatatatatataaaatatatatat +atataaaatatatatatataaaatatatatatatatataaaatatatatatataaaatat +atatatataaaatatatatatatataaaatatatatatatataaaatatatatatataaa +atatatatatatataaaatatatatatataaaatatatatatataaaatatatatatata +taaaatatatatatataaaatatatatatataaaatatatatatatataatatatatata +taaaatatatatatataaaatatatatataaaatatatatatataaaatatatatatata +aaatatatatatataaaatatatatatataaaatatatatataaaatatatatatataaa +atatatatatataaaatatatatatataaaatatatatatggaattccatatctatcaat +ggatcctaagggaaacaattttactactgtattggtgggtttattttatgtatttgtaga +tatatacatatatacacatatatatgacaattttagcacaaaagagaggaa +>syndip_2_chr20:35579913-35580987 +aaaactccatctcaaaaaaaaaaaaaaaaaaaaagggacacaatcctggattcaaaagac +tgttgtaaatatcaaatgacataatagaaacataagtactttggagcctacaaagtgctg +tcagaagctgggcatggtggctcatgcctgtaaccccagcactttgggaggctgaggcag +gcagactgctcaaactcaggagttcgagaccagcctgggcaacatggcaagacaccatct +gtaccaaaaatacaaaaaaatagccgggcatagtggtgcgcacctgtggtcccagctact +caggaggttgaggtgggaggatcacttgagcccagggggcggaggttacagtgagccaag +atttgcactccagccttggtgacagagcaagagaccctgtctaaaatatatatgtgtata +tacacacacacacacacaaatatattttttggctgggcatggtggctgacacctgtaatc +ccagcactttgggaggccaaggcaggcagatcacttgaggtcaggagtttgagaccagcc +tggccaagatgatgaaatcctgtctctactaaaaatacaaaaaaattagctgggtgtggt +aacgggtggctgtaatcccagctacttgggaagctgaggcagaagaatagcttgaacctg +ggaggcacaggttgcagtgagccgagatcgcgccactgcagcctaggcagcagagtgaga +ctctgtcttaaaatatatattatggtttattttattttatggttaaaggccatatatata +t----------------------------------atatatatatataaa------atat +atataatatatatatatata---------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------------------------atatata +tat---------------aaaatatatataaaatatatatatataaaatatatatatata +aaatatatatatataaaatat--------------------------------------- +---------------atatatatatataaaatatatatatggaattccatatctatcaat +ggatcctaagggaaacaattttactactgtattggtgggtttattttatgtatttgtaga +tatatacatatatacacatatatatgacaattttagcacaaaagagaggaa +>p:HG002_1_chr20:35579913-35580987 +aaaactccatctcaaaaaaaaaaaaaaaaaaaaagggacacaatcctggattcaaaagac +tgttgtaaatatcaaatgacataatagaaacataagtactttggagcctacaaagtgctg +tcagaagctgggcatggtggctcatgcctgtaaccccagcactttgggaggctgaggcag +gcagactgctcaaactcaggagttcgagaccagcctgggcaacatggcaagacaccatct +gtaccaaaaatacaaaaaaatagccgggcatagtggtgcgcacctgtggtcccagctact +caggaggttgaggtgggaggatcacttgagcccagggggcggaggttacagtgagccaag +atttgcactccagccttggtgacagagcaagagaccctgtctaaaatatatatgtgtata +tacacacacacacacacaaatatattttttggctgggcatggtggctgacacctgtaatc +ccagcactttgggaggccaaggcaggcagatcacttgaggtcaggagtttgagaccagcc +tggccaagatgatgaaatcctgtctctactaaaaatacaaaaaaattagctgggtgtggt +aacgggtggctgtaatcccagctacttgggaagctgaggcagaagaatagcttgaacctg +ggaggcacaggttgcagtgagccgagatcgcgccactgcagcctaggcagcagagtgaga +ctctgtcttaaaatatatattatggtttattttattttatggttaaaggccatatatata +t----------------------------------atatatatatataaa------atat +atataatatatatatatata---------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------------------------atatata +tat---------------aaaatatatataaaatatatatatataaaatatatatatata +aaatatatatatataaaatat--------------------------------------- +---------------atatatatatataaaatatatatatggaattccatatctatcaat +ggatcctaagggaaacaattttactactgtattggtgggtttattttatgtatttgtaga +tatatacatatatacacatatatatgacaattttagcacaaaagagaggaa +>p:HG002_2_chr20:35579913-35580987 +aaaactccatctcaaaaaaaaaaaaaaaaaaaaagggacacaatcctggattcaaaagac +tgttgtaaatatcaaatgacataatagaaacataagtactttggagcctacaaagtgctg +tcagaagctgggcatggtggctcatgcctgtaaccccagcactttgggaggctgaggcag +gcagactgctcaaactcaggagttcgagaccagcctgggcaacatggcaagacaccatct +gtaccaaaaatacaaaaaaatagccgggcatagtggtgcgcacctgtggtcccagctact +caggaggttgaggtgggaggatcacttgagcccagggggcggaggttacagtgagccaag +atttgcactccagccttggtgacagagcaagagaccctgtctaaaatatatatgtgtata +tacacacacacacacacaaatatattttttggctgggcatggtggctgacacctgtaatc +ccagcactttgggaggccaaggcaggcagatcacttgaggtcaggagtttgagaccagcc +tggccaagatgatgaaatcctgtctctactaaaaatacaaaaaaattagctgggtgtggt +aacgggtggctgtaatcccagctacttgggaagctgaggcagaagaatagcttgaacctg +ggaggcacaggttgcagtgagccgagatcgtgccactgcagcctaggcagcagagtgaga +ctctgtcttaaaatatatattatggtttattttattttatggttaaaggccatatatata +tatatatatatatatataatatatatatatataaaatatatatatataaaatatatatat +atataaaatatatatatataaaatatatatatatatataaaatatatatatataaaatat +atatatataaaatatatatatatataaaatatatatatatataaaatatatatatataaa +atatatatatatataaaatatatatatataaaatatatatatataaaatatatatatata +taaaatatatatatataaaatatatatatataaaatatatatatatataatatatatata +taaaatatatatatataaaatatatatataaaatatatatatataaaatatatatatata +aaatatatatatataaaatatatatatataaaatatatatataaaatatatatatataaa +atatatatatataaaatatatatatataaaatatatatatggaattccatatctatcaat +ggatcctaagggaaacaattttactactgtattggtgggtttattttatgtatttgtaga +tatatacatatatacacatatatatgacaattttagcacaaaagagaggaa diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/msa.fa.fai new file mode 100644 index 00000000..da71203f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_35579913_35580987 1371 29 60 61 +syndip_1_chr20:35579913-35580987 1371 1457 60 61 +syndip_2_chr20:35579913-35580987 1371 2885 60 61 +p:HG002_1_chr20:35579913-35580987 1371 4314 60 61 +p:HG002_2_chr20:35579913-35580987 1371 5743 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/output.vcf.gz new file mode 100644 index 00000000..bb5a8099 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/output.vcf.gz.tbi new file mode 100644 index 00000000..19d62830 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:35580013-35580887/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/base.vcf.gz new file mode 100644 index 00000000..aad818e5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/base.vcf.gz.tbi new file mode 100644 index 00000000..a6580a46 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/comp.vcf.gz new file mode 100644 index 00000000..276b8059 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/comp.vcf.gz.tbi new file mode 100644 index 00000000..f3dc9c83 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/haps.fa new file mode 100644 index 00000000..e0e8ba49 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/haps.fa @@ -0,0 +1,36 @@ +>ref_chr20_37361652_37362159 +CATCAGGGGTGGGGCAGCTGGGGGCTCTCGGAAAGATGACCTACGGCTGGGAGAGAGCAAAACTTGCCACCTCAGTGTTCTCTGTGATCCTCTCCTGACACTGAGCAGGGGCAGGGCAGGAGTGCTGCTGAGGGCCTCTGTGTGCAGGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGAGATGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGAGATGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGAGATGTAGAGATGCTGGGGTCTCTGTGTGCAGGTAGAGATGCTGGGGTCTCTGTGTGCAGGCAGAGATGCTGAAGCCCAGGTTAGCTCTTATTTATGTCTTTATTTATTTTTTTGAGACAAGGTCTCACTCTGTTGCCCAGGCTGGAGTGCAGTGGTGTAATCATAGCTCACTGCAGCCTCAAACTCCTGGGTGCAAGCAA +>syndip_1_chr20:37361652-37362159 +CATCAGGGGTGGGGCAGCTGGGGGCTCTCGGAAAGATGACCTACGGCTGGGAGAGAGCAA +AACTTGCCACCTCAGTGTTCTCTGTGATCCTCTCCTGACACTGAGCAGGGGCAGGGCAGG +AGTGCTGCTGAGGGCCTCTGTGTGCAGGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGA +GATGCCGGGGTCTCTGTGTGCAGGTAGAGATGTAGAGATGCTGGGGTCTCTGTGTGCAGG +TAGAGATGCTGGGGTCTCTGTGTGCAGGCAGAGATGCTGAAGCCCAGGTTAGCTCTTATT +TATGTCTTTATTTATTTTTTTGAGACAAGGTCTCACTCTGTTGCCCAGGCTGGAGTGCAG +TGGTGTAATCATAGCTCACTGCAGCCTCAAACTCCTGGGTGCAAGCAA +>syndip_2_chr20:37361652-37362159 +CATCAGGGGTGGGGCAGCTGGGGGCTCTCGGAAAGATGACCTACGGCTGGGAGAGAGCAA +AACTTGCCACCTCAGTGTTCTCTGTGATCCTCTCCTGACACTGAGCAGGGGCAGGGCAGG +AGTGCTGCTGAGGGCCTCTGTGTGCAGGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGA +GATGCCGGGGTCTCTGTGTGCAGGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGAGATG +CCGGGGTCTCTGTGTGCAGGTAGAGATGTAGAGATGCTGGGGTCTCTGTGTGCAGGTAGA +GATGCTGGGGTCTCTGTGTGCAGGCAGAGATGCTGAAGCCCAGGTTAGCTCTTATTTATG +TCTTTATTTATTTTTTTGAGACAAGGTCTCACTCTGTTGCCCAGGCTGGAGTGCAGTGGT +GTAATCATAGCTCACTGCAGCCTCAAACTCCTGGGTGCAAGCAA +>p:HG002_1_chr20:37361652-37362159 +CATCAGGGGTGGGGCAGCTGGGGGCTCTCGGAAAGATGACCTACGGCTGGGAGAGAGCAA +AACTTGCCACCTCAGTGTTCTCTGTGATCCTCTCCTGACACTGAGCAGGGGCAGGGCAGG +AGTGCTGCTGAGGGCCTCTGTGTGCAGGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGA +GATGCCGGGGTCTCTGTGTGCAGGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGAGATG +CCGGGGTCTCTGTGTGCAGGTAGAGATGTAGAGATGCTGGGGTCTCTGTGTGCAGGTAGA +GATGCTGGGGTCTCTGTGTGCAGGCAGAGATGCTGAAGCCCAGGTTAGCTCTTATTTATG +TCTTTATTTATTTTTTTGAGACAAGGTCTCACTCTGTTGCCCAGGCTGGAGTGCAGTGGT +GTAATCATAGCTCACTGCAGCCTCAAACTCCTGGGTGCAAGCAA +>p:HG002_2_chr20:37361652-37362159 +CATCAGGGGTGGGGCAGCTGGGGGCTCTCGGAAAGATGACCTACGGCTGGGAGAGAGCAA +AACTTGCCACCTCAGTGTTCTCTGTGATCCTCTCCTGACACTGAGCAGGGGCAGGGCAGG +AGTGCTGCTGAGGGCCTCTGTGTGCAGGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGA +GATGCCGGGGTCTCTGTGTGCAGGTAGAGATGTAGAGATGCTGGGGTCTCTGTGTGCAGG +TAGAGATGCTGGGGTCTCTGTGTGCAGGCAGAGATGCTGAAGCCCAGGTTAGCTCTTATT +TATGTCTTTATTTATTTTTTTGAGACAAGGTCTCACTCTGTTGCCCAGGCTGGAGTGCAG +TGGTGTAATCATAGCTCACTGCAGCCTCAAACTCCTGGGTGCAAGCAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/haps.fa.ref.fa new file mode 100644 index 00000000..0b1a5aca --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:37361652-37362159 +CATCAGGGGTGGGGCAGCTGGGGGCTCTCGGAAAGATGACCTACGGCTGGGAGAGAGCAAAACTTGCCACCTCAGTGTTCTCTGTGATCCTCTCCTGACACTGAGCAGGGGCAGGGCAGGAGTGCTGCTGAGGGCCTCTGTGTGCAGGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGAGATGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGAGATGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGAGATGCCGGGGTCTCTGTGTGCAGGTAGAGATGTAGAGATGCTGGGGTCTCTGTGTGCAGGTAGAGATGCTGGGGTCTCTGTGTGCAGGCAGAGATGCTGAAGCCCAGGTTAGCTCTTATTTATGTCTTTATTTATTTTTTTGAGACAAGGTCTCACTCTGTTGCCCAGGCTGGAGTGCAGTGGTGTAATCATAGCTCACTGCAGCCTCAAACTCCTGGGTGCAAGCAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/msa.fa new file mode 100644 index 00000000..c62559de --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/msa.fa @@ -0,0 +1,50 @@ +>ref_chr20_37361652_37362159 +catcaggggtggggcagctgggggctctcggaaagatgacctacggctgggagagagcaa +aacttgccacctcagtgttctctgtgatcctctcctgacactgagcaggggcagggcagg +agtgctgctgagggcctctgtgtgcaggtagagatgccggggtctctgtgtgcaggtaga +gatgtagagatgccggggtctctgtgtgcaggtagagatgtagagatgccggggtctctg +tgtgcaggtagagatgccggggtctctgtgtgcaggtagagatgccggggtctctgtgtg +caggtagagatgtagagatgctggggtctctgtgtgcaggtagagatgctggggtctctg +tgtgcaggcagagatgctgaagcccaggttagctcttatttatgtctttatttatttttt +tgagacaaggtctcactctgttgcccaggctggagtgcagtggtgtaatcatagctcact +gcagcctcaaactcctgggtgcaagcaa +>syndip_1_chr20:37361652-37362159 +catcaggggtggggcagctgggggctctcggaaagatgacctacggctgggagagagcaa +aacttgccacctcagtgttctctgtgatcctctcctgacactgagcaggggcagggcagg +agtgctgctgagggc--------------------------------------------- +-------------------------------------------------------ctctg +tgtgcaggtagagatgccggggtctctgtgtgcaggtagagatgccggggtctctgtgtg +caggtagagatgtagagatgctggggtctctgtgtgcaggtagagatgctggggtctctg +tgtgcaggcagagatgctgaagcccaggttagctcttatttatgtctttatttatttttt +tgagacaaggtctcactctgttgcccaggctggagtgcagtggtgtaatcatagctcact +gcagcctcaaactcctgggtgcaagcaa +>syndip_2_chr20:37361652-37362159 +catcaggggtggggcagctgggggctctcggaaagatgacctacggctgggagagagcaa +aacttgccacctcagtgttctctgtgatcctctcctgacactgagcaggggcagggcagg +agtgctgctgagggcctctgtgtgcaggtagagatgccggggtctctgtgtgcag----- +---------------------------------------gtagagatgccggggtctctg +tgtgcaggtagagatgccggggtctctgtgtgcaggtagagatgccggggtctctgtgtg +caggtagagatgtagagatgctggggtctctgtgtgcaggtagagatgctggggtctctg +tgtgcaggcagagatgctgaagcccaggttagctcttatttatgtctttatttatttttt +tgagacaaggtctcactctgttgcccaggctggagtgcagtggtgtaatcatagctcact +gcagcctcaaactcctgggtgcaagcaa +>p:HG002_1_chr20:37361652-37362159 +catcaggggtggggcagctgggggctctcggaaagatgacctacggctgggagagagcaa +aacttgccacctcagtgttctctgtgatcctctcctgacactgagcaggggcagggcagg +agtgctgctgagggcctctgtgtgcaggtagagatgccggggtctctgtgtgcag----- +---------------------------------------gtagagatgccggggtctctg +tgtgcaggtagagatgccggggtctctgtgtgcaggtagagatgccggggtctctgtgtg +caggtagagatgtagagatgctggggtctctgtgtgcaggtagagatgctggggtctctg +tgtgcaggcagagatgctgaagcccaggttagctcttatttatgtctttatttatttttt +tgagacaaggtctcactctgttgcccaggctggagtgcagtggtgtaatcatagctcact +gcagcctcaaactcctgggtgcaagcaa +>p:HG002_2_chr20:37361652-37362159 +catcaggggtggggcagctgggggctctcggaaagatgacctacggctgggagagagcaa +aacttgccacctcagtgttctctgtgatcctctcctgacactgagcaggggcagggcagg +agtgctgctgagggc--------------------------------------------- +-------------------------------------------------------ctctg +tgtgcaggtagagatgccggggtctctgtgtgcaggtagagatgccggggtctctgtgtg +caggtagagatgtagagatgctggggtctctgtgtgcaggtagagatgctggggtctctg +tgtgcaggcagagatgctgaagcccaggttagctcttatttatgtctttatttatttttt +tgagacaaggtctcactctgttgcccaggctggagtgcagtggtgtaatcatagctcact +gcagcctcaaactcctgggtgcaagcaa diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/msa.fa.fai new file mode 100644 index 00000000..91cfe1c6 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_37361652_37362159 508 29 60 61 +syndip_1_chr20:37361652-37362159 508 580 60 61 +syndip_2_chr20:37361652-37362159 508 1131 60 61 +p:HG002_1_chr20:37361652-37362159 508 1683 60 61 +p:HG002_2_chr20:37361652-37362159 508 2235 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/output.vcf.gz new file mode 100644 index 00000000..59a5092b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/output.vcf.gz.tbi new file mode 100644 index 00000000..7953f413 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:37361752-37362059/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/base.vcf.gz new file mode 100644 index 00000000..8fd9bde2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/base.vcf.gz.tbi new file mode 100644 index 00000000..71032ffa Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/comp.vcf.gz new file mode 100644 index 00000000..67301dd8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/comp.vcf.gz.tbi new file mode 100644 index 00000000..27d69242 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/haps.fa new file mode 100644 index 00000000..44efa372 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/haps.fa @@ -0,0 +1,146 @@ +>ref_chr20_38123490_38124806 +TTTTAAGTCCACAGCCTGTGACCAATGGCAACAGAGCAGAAGGTTAGAGCAATTACTGTGGATGGAGCTTGCCCAGTAGGCCTCCTAGCTCCATTTTCTAGCTTTGTGATCTCAGGCCTGTCCTGTAACCTCTCTGGGCCTCAGAAACCTCTCTCTCTCTCTATATATATATATATATAATAATATATAATAATAATATATAATATGTATAATAATAATATATAATATTTATAATAATAATATATATAATATGTATATATAATATACATATACCTATTATATATAATATACCTATTATATATAATATACATAAACCTATTATATATAATATACCTATTATATATAAGATACCTATTATATATAATATACCTATTATATATAAGATACCTATTATATATAATATACATATACCTATTATATATATAATATACCTATTATATATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTATATATAATACACATTATATATAATATATAACACACATTATATATAATATATAACACACATTATATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACACATTATATATTATATATAATACACATTATATATAATATATAATACACATTATATATAATACTTATTATATATTATACATAATATACATATTATATATAATACATAATATACGTATATTATATAATATACATATTATATATAATACATAATATACGTATATTATATAATATACATATTATATATATTATACTATATATAATACTCATATATATACATATTATATATACATATTATATATAATACTCATATTATATGTACATATTATACATACATATTATATATAATACACATATATACATATTATATATAATACACACACACATTATATATGTCTTATATATAATATACATATTATATATGTATTATATTATTATAGATATAATATACATATTATATCTATATATAAAATATATATGTAGAGAGAGAGAGACAGGGTCTCATTTTGTCTCCCAGGCTGGAGTGCAGTGGTGCAATCTTGGCTCACTACAACCTCCACCTCCCAGGCTCAAGGGATCCTCCAGCTTCAGCCCCCCGAGTACCTGGGACTACAGGAACGCGTCACCATGCCTGGCTAATTTTTTTTTATTTTTTGTAGAGATGGGGTTTCGCCATGTTGCCGAGGCTGGTGTCAA +>syndip_1_chr20:38123490-38124806 +TTTTAAGTCCACAGCCTGTGACCAATGGCAACAGAGCAGAAGGTTAGAGCAATTACTGTG +GATGGAGCTTGCCCAGTAGGCCTCCTAGCTCCATTTTCTAGCTTTGTGATCTCAGGCCTG +TCCTGTAACCTCTCTGGGCCTCAGAAACCTCTCTCTCTCTCTATATATATATATATAATA +ATATATAATAATAATATATAATATGTATAATAATAATATATAATATTTATAATAATAATA +TATATAATATGTATATATAATATACATATACCTATTATATATAATATACCTATTATATAT +AATATACATATACCTATTATATATAATATACCTATTATATATAAGATACCTATTATATAT +AATATACATATACCTATTATATATATAATATACCTATTATATATATATAATATACCTATT +ATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTAT +ATATATAATATACCTATTATATATAATATACCTATTATATATAAAATATACCTATTATAT +ATAATATACCTATTATATACATTATATATAATATACCTATTATATGCATTATATATAATA +TACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATACCTA +TTATATGCATTATATATAATATACCTATTATATGCATTATATAATATATTATATATAATA +TGCATATTATATGTATTATATATTATATATTATATATATAATATACATATTATATGTATT +ATATATTATATATTATATATATAATATACATATTATATGTATTATATATTATATATAATA +TACATATTATATATTATATATTATATACATATTATATATTATATATTATATACATATTAT +ATATTATATACATATTATATATTATATATTATATACATATTATACATTATATATATCTAA +AATATATAATACACATTATATATTATATAATACACATTATATATAATATATAATACACAT +TATATATTATATATAATACACATTATATATTATATATAATACACATTATATATTATATAA +TACACATTATATATTATATATAATACACATTATATATTATATATAATACACATTATATAT +TATATATAATACACATTATATATTATATAATACACATTATATATTATATATAATACACAT +TATATATATAATACACATTATATATTATATATAATACATAATACACATTATATATTATAT +ATAATACACATTATATATAATATATAACACACATTATATATAATATATAACACACATTAT +ATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACA +CATTATATATTATATATAATACACATATATTATATATAATACACATTATATATTATATAT +AATACACATTATATATAATATATAATACACATTATATATAATACTTATTATATATTATAC +ATAATATACATATTATATATAATACATAATATACGTATATTATATAATATACATATTATA +TATAATACATAATATACGTATATTATATAATATACATATTATATATATTATACTATATAT +AATACTCATATATATACATATTATATATACATATTATATATAATACTCATATTATATGTA +CATATTATACATACATATTATATATAATACACATATATACATATTATATATAATACACAC +ACACATTATATATGTCTTATATATAATATACATATTATATATGTATTATATTATTATAGA +TATAATATACATATTATATCTATATATAAAATATATATGTAGAGAGAGAGAGACAGGGTC +TCATTTTGTCTCCCAGGCTGGAGTGCAGTGGTGCAATCTTGGCTCACTACAACCTCCACC +TCCCAGGCTCAAGGGATCCTCCAGCTTCAGCCCCCCGAGTACCTGGGACTACAGGAACGC +GTCACCATGCCTGGCTAATTTTTTTTTATTTTTTGTAGAGATGGGGTTTCGCCATGTTGC +CGAGGCTGGTGTCAA +>syndip_2_chr20:38123490-38124806 +TTTTAAGTCCACAGCCTGTGACCAATGGCAACAGAGCAGAAGGTTAGAGCAATTACTGTG +GATGGAGCTTGCCCAGTAGGCCTCCTAGCTCCATTTTCTAGCTTTGTGATCTCAGGCCTG +TCCTGTAACCTCTCTGGGCCTCAGAAACCTCTCTCTCTCTCTATATATATATATATAATA +ATATATAATAATAATATATAATATGTATAATAATAATATATAATATTTATAATAATAATA +TATATAATATGTATATATAATATACATATACCTATTATATATAATATACCTATTATATAT +AATATACATATACCTATTATATATAATATACCTATTATATATAAGATACCTATTATATAT +AATATACATATACCTATTATATATATAATATACCTATTATATATATATAATATACCTATT +ATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTAT +ATATATAATATACCTATTATATATAATATACCTATTATATATAAAATATACCTATTATAT +ATAATATACCTATTATATACATTATATATAATATACCTATTATATGCATTATATATAATA +TACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATACCTA +TTATATGCATTATATAATATATTATATATAATATGCATATTATATGTATTATATATTATA +TATTATATATATAATATACATATTATATGTATTATATATTATATATTATATATATAATAT +ACATATTATATGTATTATATATTATATATAATATACATATTATATATTATATATTATATA +CATATTATATATTATATATTATATACATATTATATATTATATACATATTATATATTATAT +ATTATATACATATTATACATTATATATATCTAAAATATATAATACACATTATATATTATA +TAATACACATTATATATAATATATAATACACATTATATATTATATATAATACACATTATA +TATTATATATAATACACATTATATATTATATAATACACATTATATATTATATATAATACA +CATTATATATTATATATAATACACATTATATATTATATATAATACACATTATATATTATA +TATAATACACATTATATATTATATAATACACATTATATATTATATATAATACACATTATA +TATATAATACACATTATATATTATATATAATACATAATACACATTATATATTATATATAA +TACACATTATATATAATATATAACACACATTATATATAATATATAACACACATTATATAT +TATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACACATT +ATATATTATATATAATACACATATATTATATATAATACACATTATATATTATATATAATA +CACATTATATATAATATATAATACACATTATATATAATACTTATTATATATTATACATAA +TATACATATTATATATAATACATAATATACGTATATTATATAATATACATATTATATATA +ATACATAATATACGTATATTATATAATATACATATTATATATATTATACTATATATAATA +CTCATATATATACATATTATATATACATATTATATATAATACTCATATTATATGTACATA +TTATACATACATATTATATATAATACACATATATACATATTATATATAATACACACACAC +ATTATATATGTCTTATATATAATATACATATTATATATGTATTATATTATTATAGATATA +ATATACATATTATATCTATATATAAAATATATATGTAGAGAGAGAGAGACAGGGTCTCAT +TTTGTCTCCCAGGCTGGAGTGCAGTGGTGCAATCTTGGCTCACTACAACCTCCACCTCCC +AGGCTCAAGGGATCCTCCAGCTTCAGCCCCCCGAGTACCTGGGACTACAGGAACGCGTCA +CCATGCCTGGCTAATTTTTTTTTATTTTTTGTAGAGATGGGGTTTCGCCATGTTGCCGAG +GCTGGTGTCAA +>p:HG002_1_chr20:38123490-38124806 +TTTTAAGTCCACAGCCTGTGACCAATGGCAACAGAGCAGAAGGTTAGAGCAATTACTGTG +GATGGAGCTTGCCCAGTAGGCCTCCTAGCTCCATTTTCTAGCTTTGTGATCTCAGGCCTG +TCCTGTAACCTCTCTGGGCCTCAGAAACCTCTCTCTCTCTCTATATATATATATATAATA +ATATATAATAATAATATATAATATGTATAATAATAATATATAATATTTATAATAATAATA +TATATAATATGTATATATAATATACATATACCTATTATATATAATATACCTATTATATAT +AATATACATATACCTATTATATATAATATACCTATTATATATAAGATACCTATTATATAT +AATATACATATACCTATTATATATATAATATACCTATTATATATATATAATATACCTATT +ATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTAT +ATATATAATATACCTATTATATATAATATACCTATTATATATAAAATATACCTATTATAT +ATAATATACCTATTATATACATTATATATAATATACCTATTATATGCATTATATATAATA +TACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATACCTA +TTATATGCATTATATAATATATTATATATAATATGCATATTATATGTATTATATATTATA +TATTATATATATAATATACATATTATATGTATTATATATTATATATTATATATATAATAT +ACATATTATATGTATTATATATTATATATAATATACATATTATATATTATATATTATATA +CATATTATATATTATATATTATATACATATTATATATTATATACATATTATATATTATAT +ATTATATACATATTATACATTATATATATCTAAAATATATAATACACATTATATATTATA +TAATACACATTATATATAATATATAATACACATTATATATTATATATAATACACATTATA +TATTATATATAATACACATTATATATTATATAATACACATTATATATTATATATAATACA +CATTATATATTATATATAATACACATTATATATTATATATAATACACATTATATATTATA +TATAATACACATTATATATTATATAATACACATTATATATTATATATAATACACATTATA +TATATAATACACATTATATATTATATATAATACATAATACACATTATATATTATATATAA +TACACATTATATATAATATATAACACACATTATATATAATATATAACACACATTATATAT +TATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACACATT +ATATATTATATATAATACACATATATTATATATAATACACATTATATATTATATATAATA +CACATTATATATAATATATAATACACATTATATATAATACTTATTATATATTATACATAA +TATACATATTATATATAATACATAATATACGTATATTATATAATATACATATTATATATA +ATACATAATATACGTATATTATATAATATACATATTATATATATTATACTATATATAATA +CTCATATATATACATATTATATATACATATTATATATAATACTCATATTATATGTACATA +TTATACATACATATTATATATAATACACATATATACATATTATATATAATACACACACAC +ATTATATATGTCTTATATATAATATACATATTATATATGTATTATATTATTATAGATATA +ATATACATATTATATCTATATATAAAATATATATGTAGAGAGAGAGAGACAGGGTCTCAT +TTTGTCTCCCAGGCTGGAGTGCAGTGGTGCAATCTTGGCTCACTACAACCTCCACCTCCC +AGGCTCAAGGGATCCTCCAGCTTCAGCCCCCCGAGTACCTGGGACTACAGGAACGCGTCA +CCATGCCTGGCTAATTTTTTTTTATTTTTTGTAGAGATGGGGTTTCGCCATGTTGCCGAG +GCTGGTGTCAA +>p:HG002_2_chr20:38123490-38124806 +TTTTAAGTCCACAGCCTGTGACCAATGGCAACAGAGCAGAAGGTTAGAGCAATTACTGTG +GATGGAGCTTGCCCAGTAGGCCTCCTAGCTCCATTTTCTAGCTTTGTGATCTCAGGCCTG +TCCTGTAACCTCTCTGGGCCTCAGAAACCTCTCTCTCTCTCTATATATATATATATAATA +ATATATAATAATAATATATAATATGTATAATAATAATATATAATATTTATAATAATAATA +TATATAATATGTATATATAATATACATATACCTATTATATATAATATACCTATTATATAT +AATATACATATACCTATTATATATAATATACCTATTATATATAAGATACCTATTATATAT +AATATACATATACCTATTATATATATAATATACCTATTATATATATATAATATACCTATT +ATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTAT +ATATATAATATACCTATTATATATAATATACCTATTATATATAAAATATACCTATTATAT +ATAATATACCTATTATATACATTATATATAATATACCTATTATATGCATTATATATAATA +TACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATACCTA +TTATATGCATTATATATAATATACCTATTATATGCATTATATAATATATTATATATAATA +TGCATATTATATGTATTATATATTATATATTATATATATAATATACATATTATATGTATT +ATATATTATATATTATATATATAATATACATATTATATGTATTATATATTATATATAATA +TACATATTATATATTATATATTATATACATATTATATATTATATATTATATACATATTAT +ATATTATATACATATTATATATTATATATTATATACATATTATACATTATATATATCTAA +AATATATAATACACATTATATATTATATAATACACATTATATATAATATATAATACACAT +TATATATTATATATAATACACATTATATATTATATATAATACACATTATATATTATATAA +TACACATTATATATTATATATAATACACATTATATATTATATATAATACACATTATATAT +TATATATAATACACATTATATATTATATAATACACATTATATATTATATATAATACACAT +TATATATATAATACACATTATATATTATATATAATACATAATACACATTATATATTATAT +ATAATACACATTATATATAATATATAACACACATTATATATAATATATAACACACATTAT +ATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACA +CATTATATATTATATATAATACACATATATTATATATAATACACATTATATATTATATAT +AATACACATTATATATAATATATAATACACATTATATATAATACTTATTATATATTATAC +ATAATATACATATTATATATAATACATAATATACGTATATTATATAATATACATATTATA +TATAATACATAATATACGTATATTATATAATATACATATTATATATATTATACTATATAT +AATACTCATATATATACATATTATATATACATATTATATATAATACTCATATTATATGTA +CATATTATACATACATATTATATATAATACACATATATACATATTATATATAATACACAC +ACACATTATATATGTCTTATATATAATATACATATTATATATGTATTATATTATTATAGA +TATAATATACATATTATATCTATATATAAAATATATATGTAGAGAGAGAGAGACAGGGTC +TCATTTTGTCTCCCAGGCTGGAGTGCAGTGGTGCAATCTTGGCTCACTACAACCTCCACC +TCCCAGGCTCAAGGGATCCTCCAGCTTCAGCCCCCCGAGTACCTGGGACTACAGGAACGC +GTCACCATGCCTGGCTAATTTTTTTTTATTTTTTGTAGAGATGGGGTTTCGCCATGTTGC +CGAGGCTGGTGTCAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/haps.fa.ref.fa new file mode 100644 index 00000000..5cab64c6 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:38123490-38124806 +TTTTAAGTCCACAGCCTGTGACCAATGGCAACAGAGCAGAAGGTTAGAGCAATTACTGTGGATGGAGCTTGCCCAGTAGGCCTCCTAGCTCCATTTTCTAGCTTTGTGATCTCAGGCCTGTCCTGTAACCTCTCTGGGCCTCAGAAACCTCTCTCTCTCTCTATATATATATATATATAATAATATATAATAATAATATATAATATGTATAATAATAATATATAATATTTATAATAATAATATATATAATATGTATATATAATATACATATACCTATTATATATAATATACCTATTATATATAATATACATAAACCTATTATATATAATATACCTATTATATATAAGATACCTATTATATATAATATACCTATTATATATAAGATACCTATTATATATAATATACATATACCTATTATATATATAATATACCTATTATATATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTATATATAATACACATTATATATAATATATAACACACATTATATATAATATATAACACACATTATATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACACATTATATATTATATATAATACACATTATATATAATATATAATACACATTATATATAATACTTATTATATATTATACATAATATACATATTATATATAATACATAATATACGTATATTATATAATATACATATTATATATAATACATAATATACGTATATTATATAATATACATATTATATATATTATACTATATATAATACTCATATATATACATATTATATATACATATTATATATAATACTCATATTATATGTACATATTATACATACATATTATATATAATACACATATATACATATTATATATAATACACACACACATTATATATGTCTTATATATAATATACATATTATATATGTATTATATTATTATAGATATAATATACATATTATATCTATATATAAAATATATATGTAGAGAGAGAGAGACAGGGTCTCATTTTGTCTCCCAGGCTGGAGTGCAGTGGTGCAATCTTGGCTCACTACAACCTCCACCTCCCAGGCTCAAGGGATCCTCCAGCTTCAGCCCCCCGAGTACCTGGGACTACAGGAACGCGTCACCATGCCTGGCTAATTTTTTTTTATTTTTTGTAGAGATGGGGTTTCGCCATGTTGCCGAGGCTGGTGTCAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/msa.fa new file mode 100644 index 00000000..c856c61f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/msa.fa @@ -0,0 +1,180 @@ +>ref_chr20_38123490_38124806 +ttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgtg +gatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcctg +tcctgtaacctctctgggcctcagaaacctctctctctctctatatatatatatatataa +taatatataataataatatataatatgtataataataatatataatatttataataataa +tatatataatatgtatatataatatacatatacctattatatataatatacctattatat +ataatatacataaacctattatatataatatacctattatatataagatacctattatat +ataatatacctat------------------------------tatatataagataccta +ttatatataatatac--------------atatacctattatatatataatatacctatt +ata----------------tatatataatatacctattatatatataatatacctatta- +---------------------------------------------------tatatataa +tatacctattatatatataata-------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------tacctattatatataatacacattatatataatatataacacacatt +atatataatatataacacacattatatattatatataatacacattatatattatatata +atacacatatattatatataatacacattatatattatatataatacacatatattatat +ataatacacattatatattatatataatacacattatatataatatataatacacattat +atataatacttattatatattatacataatatacatattatatataatacataatatacg +tatattatataatatacatattatatataatacataatatacgtatattatataatatac +atattatatatattatactatatataatactcatatatatacatattatatatacatatt +atatataatactcatattatatgtacatattatacatacatattatatataatacacata +tatacatattatatataatacacacacacattatatatgtcttatatataatatacatat +tatatatgtattatattattatagatataatatacatattatatctatatataaaatata +tatgtagagagagagagacagggtctcattttgtctcccaggctggagtgcagtggtgca +atcttggctcactacaacctccacctcccaggctcaagggatcctccagcttcagccccc +cgagtacctgggactacaggaacgcgtcaccatgcctggctaatttttttttattttttg +tagagatggggtttcgccatgttgccgaggctggtgtcaa +>syndip_1_chr20:38123490-38124806 +ttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgtg +gatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcctg +tcctgtaacctctctgggcctcagaaacctctctctctctc--tatatatatatatataa +taatatataataataatatataatatgtataataataatatataatatttataataataa +tatatataatatgtatatataatatacatatacctattatatataatatacctattatat +ataatatacatatacctattatatataatatacctattatatataagatacctattatat +ataatatacatatacctattatatatataatatacctattatatatatataatataccta +ttatatataatatacctattatatatataatatacctattatatatataatatacctatt +atatatataatatacctattatatataatatacctattatatataaaatatacctattat +atataatatacctattatatacattatatataatatacctattatatgcattatatataa +tatacctattatatgcattatatataatatacctattatatgcattatatataatatacc +tattatatgcattatatataatatacctattatatgcattatataatatattatatataa +tatgcatattatatgtattatatattatatattatatatataatatacatattatatgta +ttatatattatatattatatatataatatacatattatatgtattatatattatatataa +tatacatattatatattatatattatatacatattatatattatatattatatacatatt +atatattatatacatattatatattatatattatatacatattatacattatatatatct +aaaatatataatacacattatatattatataatacacattatatataatatataatacac +attatatattatatataatacacattatatattatatataatacacattatatat----- +------------------tatataatacacattatatattatatataatacacattatat +attatatataatacacattatatattatatataatacacattatatattatataatacac +attatatattatatataatacacattatatatataatacacattatatattatatataat +acataatacacattatatattatatataatacacattatatataatatataacacacatt +atatataatatataacacacattatatattatatataatacacattatatattatatata +atacacatatattatatataatacacattatatattatatataatacacatatattatat +ataatacacattatatattatatataatacacattatatataatatataatacacattat +atataatacttattatatattatacataatatacatattatatataatacataatatacg +tatattatataatatacatattatatataatacataatatacgtatattatataatatac +atattatatatattatactatatataatactcatatatatacatattatatatacatatt +atatataatactcatattatatgtacatattatacatacatattatatataatacacata +tatacatattatatataatacacacacacattatatatgtcttatatataatatacatat +tatatatgtattatattattatagatataatatacatattatatctatatataaaatata +tatgtagagagagagagacagggtctcattttgtctcccaggctggagtgcagtggtgca +atcttggctcactacaacctccacctcccaggctcaagggatcctccagcttcagccccc +cgagtacctgggactacaggaacgcgtcaccatgcctggctaatttttttttattttttg +tagagatggggtttcgccatgttgccgaggctggtgtcaa +>syndip_2_chr20:38123490-38124806 +ttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgtg +gatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcctg +tcctgtaacctctctgggcctcagaaacctctctctctctc--tatatatatatatataa +taatatataataataatatataatatgtataataataatatataatatttataataataa +tatatataatatgtatatataatatacatatacctattatatataatatacctattatat +ataatatacatatacctattatatataatatacctattatatataagatacctattatat +ataatatacatatacctattatatatataatatacctattatatatatataatataccta +ttatatataatatacctattatatatataatatacctattatatatataatatacctatt +atatatataatatacctattatatataatatacctattatatataaaatatacctattat +atataatatacctattatata---------------------------cattatatataa +tatacctattatatgcattatatataatatacctattatatgcattatatataatatacc +tattatatgcattatatataatatacctattatatgcattatataatatattatatataa +tatgcatattatatgtattatatattatatattatatatataatatacatattatatgta +ttatatattatatattatatatataatatacatattatatgtattatatattatatataa +tatacatattatatattatatattatatacatattatatattatatattatatacatatt +atatattatatacatattatatattatatattatatacatattatacattatatatatct +aaaatatataatacacattatatattatataatacacattatatataatatataatacac +attatatattatatataatacacattatatattatatataatacacattatatattatat +aatacacattatatattatatataatacacattatatattatatataatacacattatat +attatatataatacacattatatattatatataatacacattatatattatataatacac +attatatattatatataatacacattatatatataatacacattatatattatatataat +acataatacacattatatattatatataatacacattatatataatatataacacacatt +atatataatatataacacacattatatattatatataatacacattatatattatatata +atacacatatattatatataatacacattatatattatatataatacacatatattatat +ataatacacattatatattatatataatacacattatatataatatataatacacattat +atataatacttattatatattatacataatatacatattatatataatacataatatacg +tatattatataatatacatattatatataatacataatatacgtatattatataatatac +atattatatatattatactatatataatactcatatatatacatattatatatacatatt +atatataatactcatattatatgtacatattatacatacatattatatataatacacata +tatacatattatatataatacacacacacattatatatgtcttatatataatatacatat +tatatatgtattatattattatagatataatatacatattatatctatatataaaatata +tatgtagagagagagagacagggtctcattttgtctcccaggctggagtgcagtggtgca +atcttggctcactacaacctccacctcccaggctcaagggatcctccagcttcagccccc +cgagtacctgggactacaggaacgcgtcaccatgcctggctaatttttttttattttttg +tagagatggggtttcgccatgttgccgaggctggtgtcaa +>p:HG002_1_chr20:38123490-38124806 +ttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgtg +gatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcctg +tcctgtaacctctctgggcctcagaaacctctctctctctc--tatatatatatatataa +taatatataataataatatataatatgtataataataatatataatatttataataataa +tatatataatatgtatatataatatacatatacctattatatataatatacctattatat +ataatatacatatacctattatatataatatacctattatatataagatacctattatat +ataatatacatatacctattatatatataatatacctattatatatatataatataccta +ttatatataatatacctattatatatataatatacctattatatatataatatacctatt +atatatataatatacctattatatataatatacctattatatataaaatatacctattat +atataatatacctattatata---------------------------cattatatataa +tatacctattatatgcattatatataatatacctattatatgcattatatataatatacc +tattatatgcattatatataatatacctattatatgcattatataatatattatatataa +tatgcatattatatgtattatatattatatattatatatataatatacatattatatgta +ttatatattatatattatatatataatatacatattatatgtattatatattatatataa +tatacatattatatattatatattatatacatattatatattatatattatatacatatt +atatattatatacatattatatattatatattatatacatattatacattatatatatct +aaaatatataatacacattatatattatataatacacattatatataatatataatacac +attatatattatatataatacacattatatattatatataatacacattatatattatat +aatacacattatatattatatataatacacattatatattatatataatacacattatat +attatatataatacacattatatattatatataatacacattatatattatataatacac +attatatattatatataatacacattatatatataatacacattatatattatatataat +acataatacacattatatattatatataatacacattatatataatatataacacacatt +atatataatatataacacacattatatattatatataatacacattatatattatatata +atacacatatattatatataatacacattatatattatatataatacacatatattatat +ataatacacattatatattatatataatacacattatatataatatataatacacattat +atataatacttattatatattatacataatatacatattatatataatacataatatacg +tatattatataatatacatattatatataatacataatatacgtatattatataatatac +atattatatatattatactatatataatactcatatatatacatattatatatacatatt +atatataatactcatattatatgtacatattatacatacatattatatataatacacata +tatacatattatatataatacacacacacattatatatgtcttatatataatatacatat +tatatatgtattatattattatagatataatatacatattatatctatatataaaatata +tatgtagagagagagagacagggtctcattttgtctcccaggctggagtgcagtggtgca +atcttggctcactacaacctccacctcccaggctcaagggatcctccagcttcagccccc +cgagtacctgggactacaggaacgcgtcaccatgcctggctaatttttttttattttttg +tagagatggggtttcgccatgttgccgaggctggtgtcaa +>p:HG002_2_chr20:38123490-38124806 +ttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgtg +gatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcctg +tcctgtaacctctctgggcctcagaaacctctctctctctc--tatatatatatatataa +taatatataataataatatataatatgtataataataatatataatatttataataataa +tatatataatatgtatatataatatacatatacctattatatataatatacctattatat +ataatatacatatacctattatatataatatacctattatatataagatacctattatat +ataatatacatatacctattatatatataatatacctattatatatatataatataccta +ttatatataatatacctattatatatataatatacctattatatatataatatacctatt +atatatataatatacctattatatataatatacctattatatataaaatatacctattat +atataatatacctattatatacattatatataatatacctattatatgcattatatataa +tatacctattatatgcattatatataatatacctattatatgcattatatataatatacc +tattatatgcattatatataatatacctattatatgcattatataatatattatatataa +tatgcatattatatgtattatatattatatattatatatataatatacatattatatgta +ttatatattatatattatatatataatatacatattatatgtattatatattatatataa +tatacatattatatattatatattatatacatattatatattatatattatatacatatt +atatattatatacatattatatattatatattatatacatattatacattatatatatct +aaaatatataatacacattatatattatataatacacattatatataatatataatacac +attatatattatatataatacacattatatattatatataatacacattatatat----- +------------------tatataatacacattatatattatatataatacacattatat +attatatataatacacattatatattatatataatacacattatatattatataatacac +attatatattatatataatacacattatatatataatacacattatatattatatataat +acataatacacattatatattatatataatacacattatatataatatataacacacatt +atatataatatataacacacattatatattatatataatacacattatatattatatata +atacacatatattatatataatacacattatatattatatataatacacatatattatat +ataatacacattatatattatatataatacacattatatataatatataatacacattat +atataatacttattatatattatacataatatacatattatatataatacataatatacg +tatattatataatatacatattatatataatacataatatacgtatattatataatatac +atattatatatattatactatatataatactcatatatatacatattatatatacatatt +atatataatactcatattatatgtacatattatacatacatattatatataatacacata +tatacatattatatataatacacacacacattatatatgtcttatatataatatacatat +tatatatgtattatattattatagatataatatacatattatatctatatataaaatata +tatgtagagagagagagacagggtctcattttgtctcccaggctggagtgcagtggtgca +atcttggctcactacaacctccacctcccaggctcaagggatcctccagcttcagccccc +cgagtacctgggactacaggaacgcgtcaccatgcctggctaatttttttttattttttg +tagagatggggtttcgccatgttgccgaggctggtgtcaa diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/msa.fa.fai new file mode 100644 index 00000000..0a510d7d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_38123490_38124806 2080 29 60 61 +syndip_1_chr20:38123490-38124806 2080 2178 60 61 +syndip_2_chr20:38123490-38124806 2080 4327 60 61 +p:HG002_1_chr20:38123490-38124806 2080 6477 60 61 +p:HG002_2_chr20:38123490-38124806 2080 8627 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/output.vcf.gz new file mode 100644 index 00000000..8e6f31e0 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/output.vcf.gz.tbi new file mode 100644 index 00000000..4c85f536 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38123590-38124706/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/base.vcf.gz new file mode 100644 index 00000000..93ac8ee8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/base.vcf.gz.tbi new file mode 100644 index 00000000..8771110c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/comp.vcf.gz new file mode 100644 index 00000000..46dcb10b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/comp.vcf.gz.tbi new file mode 100644 index 00000000..e4012767 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/haps.fa new file mode 100644 index 00000000..0f61fff2 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/haps.fa @@ -0,0 +1,280 @@ +>ref_chr20_38462831_38464884 +CACCATGTTACCTAGGCTGATCTTGAATTCCTGGGCTCAAGTGTTAGACTCACTTCGGCCTCCCAAAGTGTTGGGATTACAGGCGTGAGCCACTGCACCCAGCCTGTTTTGTTTGGGGCAAGGGTTTTAACATTTATATATATATAAATATATATATATTTTATATATACAAATATATATATAAATATATATTTATATATATTTATATATAATATATTATATATAAATATATTTATATATAATATATTATATATAAATATATTATATATAAAATATTATATATAAATATATATATTTATATATATAAATATATATAAATATATATATATATAAAAATACCAGCACATCAGTATCAGGAATAAATGGGCTGGGCAGTATATATATATATATATATGTATATATATATACTGTTTTTCATATATATATACTGTCTTATATATATATATACTGTTTTACATATATATACTGTTTCATATATATAATGTTTTATATATATACTGTTATATATATTATATGTACTGTTATATATTTTTTATATATATACTGTTATATATATTTTTTATATATACTGTTATATATTATATATATACTGTTATATATATATTTTACATATATACTGTTATATATATATTTTATATATATATACTGTTATATATATATATTTTATATATGTATACTGTTATATATTTATATTTTTTATATGTATACTGTTATATATATATTATATGTATACTGTTATATATATATTTTATATGTATACTGTTATATATATATATTTCATATATATATACTGTTATATATATTTTATATATATATACTGTCATATATATATTTTATATATATACTGTCATATATATATTTTATATATATATACTGTCATATATATATTTTATATATATATATACTGTCATATATATATTTTATATATATATACTGTCATATATATTTTATATATATACTGTCATATATATATTTTATATATATACTGTCATATATATATTTTATATATATACTGTCATATATATATTTTATATATATACTGTCATATATATATTTTATATATATATACTGTCATATATATATTTTATATATATATACTGTCATATATATATTTTATATATATACTGTCATATGTATATTTTATATATATACTGTCATATGTATATTTTATATATATACTGTTATATGTATATTTTATATATATATACTGTTATATATATATTTTTATATATATACTGTTATATATATTTTTTTATATATATACTGTTATATATATTTTTATATATATACTGTTATATATATATTTTATATATATACTGTTATATATATATTTTATATATACTGTTATATAGATACTGTTATATATATACTGATATATATACTGTTATATATATACTGATATATATATACTGTTATATATATACTGTTATATATATATACTGTTACATATACATATATATACTGTTATATATATACTGTTATATATATTGTTATATATATACACATATATATATACATATATATATACATATATATATACATATATATATACATATATATATACACGTATATATATACATATATATATACACATATATATATATACACACACATATATATATATATATATACTGGCTGTGTGTGGTGGTGCACACCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGCTGATGGCTTGAGCTCAGGAGTTCAAGACCAGCTAAGCAACATACTGAGATCCCATCTCTAAAAAAAATACAAAAAGGCCAGGCACAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGTGGGCAGATCACGAGGTCAGCAGTTCGAGACCAGCCTGGCCAGCATGGTGAAACCCCATCTCTACTAAAAATACAAAACATTAGCCGGACATGGTGGCACACACCTGTAATTCCAGCTACTCAGGAAGCTGAGGCAGGAGAATAGCTTGAACCCAGGAGGCGAAAGTTTCAGTCAGCCAAAATCACACCACTGCACTCCAGCCTGGGCAACAGAGCAAGACTCTGTCTCCAAAAAAA +>syndip_1_chr20:38462831-38464884 +CACCATGTTACCTAGGCTGATCTTGAATTCCTGGGCTCAAGTGTTAGACTCACTTCGGCC +TCCCAAAGTGTTGGGATTACAGGCGTGAGCCACTGCACCCAGCCTGTTTTGTTTGGGGCA +AGGGTTTTAACATTTATATATATATAAATATATATATATTTTATATATACAAATATATAT +ATAAATATATATTTATATATATTTATATATAATATATTATATATAAATATATTTATATAT +AATATATTATATATAAATATATTATATATAAAATATTATATATAAATATATATATTTATA +TATATAAATATATATAAATATATATATATATAAAAATACCAGCACATCAGTATCAGGAAT +AAATGGGCTGGGCAGTATATATATATATATATATGTATATATATATACTGTTTTTCATAT +ATATATACTGTCTTATATATATATATACTGTTTTACATATATATACTGTTTCATATATAT +AATGTTTTATATATATACTGTTATATATATTATATGTACTGTTATATATTTTTTATATAT +ATACTGTTATATATATTTTTTATATATACTGTTATATATTATATATATACTGTTATATAT +ATATTTTACATATATACTGTTATATATATATTTTATATATATATACTGTTATATATATAT +ATTTTATATATGTATACTGTTATATATTTATATTTTTTATATGTATACTGTTATATATAT +ATTATATGTATACTGTTATATATATATTTTATATGTATACTGTTATATATATATATTTCA +TATATATATACTGTTATATATATTTTATATATATATACTGTCATATATATATTTTATATA +TATACTGTCATATATATATTTTATATATATATACTGTCATATATATATTTTATATATATA +TATACTGTCATATATATATTTTATATATATATACTGTCATATATATTTTATATATATACT +GTCATATATATATTTTATATATATACTGTCATATATATATTTTATATATATACTGTCATA +TATATATTTTATATATATACTGTCATATATATATTTTATATATATATACTGTCATATATA +TATTTTATATATATATACTGTCATATATATATTTTATATATATACTGTCATATGTATATT +TTATATATATACTGTCATATGTATATTTTATATATATACTGTTATATGTATATTTTATAT +ATATATACTGTTATATATATATTTTTATATATATACTGTTATATATATTTTTTTATATAT +ATACTGTTATATATATTTTTATATATATACTGTTATATATATATTTTATATATATACTGT +TATATATATATTTTATATATACTGTTATATATATATATTTTATATATATACTGTTATATA +TAATTTTTTTCATATATATACTGTTATATATATATTTTATATATATATACTGTTATATAT +ATATTTTATATATATACTGTTATATATATATATTTTATATATATACTGTTATTTTTTATA +TATATACTGTTATATATATATTTTATATATATACTGTTATATATATATTATCTATATACT +GTTATGTGTATATTTTATCTATATACTGTTATGTGTATATTTTATCTATATACTGTTATG +TGTATATTTTACCTATATACTTTTATGTGTATATTTTATATATATACTGTTATGTGTATA +TTTTATATATATACTGTTATGTGTATATTTTTTATATATACTGTTATGTGTATATTTTAT +ATATATATACTGTTATGTGTATATTTTATATATATATACTGTTATGTGTATATTTTATAT +ATATACTGTTATGTGTATATTTTATATATATACTGTTATATATAGTTCATATATATACTG +TTATATGTATAGTTCATATATATACTGTTATATATATAGTTCATATGTATACTGTTATAT +ATATAGTTCATATATATACTGTTATATATATAGTTCATATATATACTGTTATATATATAT +AGTTCATATATATACTGTTATATATAGTTCATATATATACTGTTATATATATAGTTCATA +TATATACTGTTATATATATAGTTCATATATATACTGTTATATATAGTTCATATATATATA +CTGTTCTATATATAGTTCATATATATATACTGTTATATATATAGTTCATATATATATACT +GTTATATATAGTTCATATATATATAGTTCATATATATACTGTTATATATATAGTTCATAT +ATATACTGTTATATACATAGTTCATATATATACTGTTATATATATAGTTCATATATATAT +ACTGTTATATATATAGTTCATATATATACTGTTGTATATAGTTCATATATATACTGTTAT +ATATATAGTTCATATATTACTGTTATATATATAGTTCATATATATACTGTTATATATATA +TAGTTCATATATATACTGTTATATATAGTTTATATATATATACTGTTATATATATAGTTT +ATATATATATACTGTTATATATATAGTTTATATATATATACTGTTATATATATATAGTTT +ATATATATATACTGTTATATATATAGTTTATATATATATACTGTTATATATATATAGTTT +ATATATACTGTTATATATATAGTTTATATATATACTGTTATATATATAGTTTATATATAT +ACTGTTATATATATAGTTTATATATATACTGTTATATATATAGTTTATATATATACTGTT +ATATATATAGTTTATATATATACTGTTATATATATAGTTTATATATATACTGTTATATAT +ATAGTTTATATATATATACTGTTATATATAGTTTATATATACTGTTATATATATAGTTTA +TATACTGTTATATATAGTTTATATATATATACTGTTATATATAGTTTATATATATATACT +GTTATATATATATAGTTTATATATATATACTGTTATATATATATAGTTTATATATATACT +GTTATATATATATAGTTTATATATATACTGTTGTATATATAGTTTATATATATACTGTTA +TATATATATTTGTGTATATATACTGTTATATAAATATATTTGTGTATATATACTGTTATA +TATATATTTTATGTATATATACTGTTATATATATATTTTATGTATATATACTGTTATATA +TATATTTTATGTATATATACTGTTATATATATATTTTATGTATATATACTGTTATATATA +TATTTTATGTATATATACTGTTATATATATTTTATGTATATATACTGTTATATATATTTT +ATGTATATATACTGTTATATATATATTTTATGTATATATACTGTTATATCTGTATATTTT +ATGTTTATATACTGTTATATCTGTATATTTTATGTATATATACTGTTATATCTGTATATT +TTATGTATATACTGTTATATATATACTGTTATATATATACTGATATATATACTGTTATAT +ATATACTGATATATATATACTGTTATATATATACTGTTATATATATATACTGTTACATAT +ACATATATATACTGTTATATATATACTGTTATATATATTGTTATATATATACACATATAT +ATATACATATATATACATATATATATACATATATATATACATATATATATACACGTATAT +ATATACATATATATATACACATATATATATATACACACACATATATATATATATATATAC +TGGCTGTGTGTGGTGGTGCACACCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGCTG +ATGGCTTGAGCTCAGGAGTTCAAGACCAGCTAAGCAACATACTGAGATCCCATCTCTAAA +AAAAATACAAAAAGGCCAGGCACAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGC +TGAGGTGGGCAGATCACGAGGTCAGCAGTTCGAGACCAGCCTGGCCAGCATGGTGAAACC +CCATCTCTACTAAAAATACAAAACATTAGCCGGACATGGTGGCACACACCTGTAATTCCA +GCTACTCAGGAAGCTGAGGCAGGAGAATAGCTTGAACCCAGGAGGCGAAAGTTTCAGTCA +GCCAAAATCACACCACTGCACTCCAGCCTGGGCAACAGAGCAAGACTCTGTCTCCAAAAA +AA +>syndip_2_chr20:38462831-38464884 +CACCATGTTACCTAGGCTGATCTTGAATTCCTGGGCTCAAGTGTTAGACTCACTTCGGCC +TCCCAAAGTGTTGGGATTACAGGCGTGAGCCACTGCACCCAGCCTGTTTTGTTTGGGGCA +AGGGTTTTAACATTTATATATATATAAATATATATATATTTTATATATACAAATATATAT +ATAAATATATATTTATATATATTTATATATAATATATTATATATAATATATTTATATATA +ATATATTATATATAAATATATTATATATAAAATATTATATATAAATATATATATTTATAT +ATATAAATATATATAAATATATATATATATAAAAATACCAGCACATCAGTATCAGGAATA +AATGGGCTGGGCAGTATATATATATATATATGTATATATATATACTGTTTTTCATATATA +TATACTGTCTTATATATATATATACTGTTTTACATATATATACTGTTTCATATATATAAT +GTTTTATATATATACTGTTATATATATTATATGTACTGTTATATATTTTTTATATATATA +CTGTTATATATATTTTTTATATATACTGTTATATATTATATATATACTGTTATATATATA +TTTTACATATATACTGTTATATATATATTTTATATATATATACTGTTATATATATATATT +TTATATATGTATACTGTTATATATTTATATTTTTTATATGTATACTGTTATATATATATT +ATATGTATACTGTTATATATATATTTTATATGTATACTGTTATATATATATATTTCATAT +ATATATACTGTTATATATATTTTATATATATATACTGTCATATATATATTTTATATATAT +ACTGTCATATATATATTTTATATATATATACTGTCATATATATATTTTATATATATATAC +TGTCATATATATATTTTATATATATATACTGTCATATATATTTTATATATATACTGTCAT +ATATATATTTTATATATATACTGTCATATATATATTTTATATATATACTGTCATATATAT +ATTTTATATATATATACTGTCATATATATATTTTATATATATATACTGTCATATATATAT +TTTATATATATACTGTCATATGTATATTTTATATATATACTGTCATATGTATATTTTATA +TATATACTGTTATATGTATATTTTATATATATATACTGTTATATATATATTTTATATATA +TATACTGTTATATATATATTTTATATATATATACTGTTATATATATATTTTTATATATAT +ACTGTTATATATATTTTTTTATATATATACTGTTATATATATTTTTATATATATACTGTT +ATATATATATTTTATATATATACTGTTATATATATATTTTATATATACTGTTATATATAT +ATATTTTATATATATACTGTTATATATAATTTTTTTCATATATATACTGTTATATATATA +TTTTATATATATATACTGTTATATATATATTTTATATATATACTGTTATATATATATATT +TTATATATATACTGTTATTTTTTATATATATACTGTTATATATATATTTTATATATATAC +TGTTATATATATATTATCTATATACTGTTATGTGTATATTTTATCTATATACTGTTATGT +GTATATTTTATCTATATACTGTTATGTGTATATTTTACCTATATACTTTTATGTGTATAT +TTTATATATATACTGTTATGTGTATATTTTATATATATACTGTTATGTGTATATTTTTTA +TATATACTGTTATGTGTATATTTTATATATATATACTGTTATGTGTATATTTTATATATA +TATACTGTTATGTGTATATTTTATATATATACTGTTATGTGTATATTTTATATATATACT +GTTATATATAGTTCATATATATACTGTTATATGTATAGTTCATATATATACTGTTATATA +TATAGTTCATATGTATACTGTTATATATATAGTTCATATATATACTGTTATATATATAGT +TCATATATATACTGTTATATATATATAGTTCATATATATACTGTTATATATAGTTCATAT +ATATACTGTTATATATATAGTTCATATATATACTGTTATATATATAGTTCATATATATAC +TGTTATATATAGTTCATATATATATACTGTTCTATATATAGTTCATATATATATACTGTT +ATATATATAGTTCATATATATATACTGTTATATATAGTTCATATATATATAGTTCATATA +TATACTGTTATATATATAGTTCATATATATACTGTTATATACATAGTTCATATATATACT +GTTATATATATAGTTCATATATATATACTGTTATATATATAGTTCATATATATACTGTTG +TATATAGTTCATATATATACTGTTATATATATAGTTCATATATTACTGTTATATATATAG +TTCATATATATACTGTTATATATATATAGTTCATATATATACTGTTATATATAGTTTATA +TATATATACTGTTATATATATAGTTTATATATATATACTGTTATATATATAGTTTATATA +TATATACTGTTATATATATATAGTTTATATATATATACTGTTATATATATAGTTTATATA +TATATACTGTTATATATATAGTTTATATATACTGTTATATATATATAGTTTATATATATA +CTGTTATATATATAGTTTATATATATACTGTTATATATATAGTTTATATATATACTGTTA +TATATATAGTTTATATATATACTGTTATATATATAGTTTATATATATACTGTTATATATA +TAGTTTATATATATATACTGTTATATATATAGTTTATAAATACTGTTATATATATAGTTT +ATATACTGTTATATATAGTTTATATATATATACTGTTATATATAGTTTATATATATATAC +TGTTATATATATATAGTTTATATATATATACTGTTATATATATATAGTTTATATATATAC +TGTTATATATATATAGTTTATATATATACTGTTGTATATATAGTTTATATATATACTGTT +ATATATATATTTGTGTATATATACTGTTATATAAATATATTTGTGTATATATACTGTTAT +ATATATATTTTATGTATATATACTGTTATATATATATTTTATGTATATATACTGTTATAT +ATATATTTTATGTATATATACTGTTATATATATATTTTATGTATATATACTGTTATATAT +ATATTTTATGTATATATACTGTTATATATATTTTATGTATATATACTGTTATATATATAT +TTTATGTATATATACTGTTATATCTGTATATTTTATGTTTATATACTGTTATATCTGTAT +ATTTTATGTATATATACTGTTATATCTGTATATTTTATGTATATACTGTTATATATATAC +TGTTATATATATACTGATATATATACTGTTATATATATACTGATATATATATACTGTTAT +ATATATACTGTTATATATATATACTGTTACATATACATATATATACTGTTATATATATAC +TGTTATATATATTGTTATATATATACACATATATATATACATATATATATACATATATAT +ATACATATATATATACACGTATATATATACATATATATATACACATATATATATATACAC +ACACATATATATATATATATATACTGGCTGTGTGTGGTGGTGCACACCTGTAATCCCAGC +ACTTTGGGAGGCCAAGGCAGGCTGATGGCTTGAGCTCAGGAGTTCAAGACCAGCTAAGCA +ACATACTGAGATCCCATCTCTAAAAAAAATACAAAAAGGCCAGGCACAGTGGCTCACACC +TGTAATCCCAGCACTTTGGGAGGCTGAGGTGGGCAGATCACGAGGTCAGCAGTTCGAGAC +CAGCCTGGCCAGCATGGTGAAACCCCATCTCTACTAAAAATACAAAACATTAGCCGGACA +TGGTGGCACACACCTGTAATTCCAGCTACTCAGGAAGCTGAGGCAGGAGAATAGCTTGAA +CCCAGGAGGCGAAAGTTTCAGTCAGCCAAAATCACACCACTGCACTCCAGCCTGGGCAAC +AGAGCAAGACTCTGTCTCCAAAAAAA +>p:HG002_1_chr20:38462831-38464884 +CACCATGTTACCTAGGCTGATCTTGAATTCCTGGGCTCAAGTGTTAGACTCACTTCGGCC +TCCCAAAGTGTTGGGATTACAGGCGTGAGCCACTGCACCCAGCCTGTTTTGTTTGGGGCA +AGGGTTTTAACATTTATATATATATAAATATATATATATTTTATATATACAAATATATAT +ATAAATATATATTTATATATATTTATATATAATATATTATATATAATATATTTATATATA +ATATATTATATATAAATATATTATATATAAAATATTATATATAAATATATATATTTATAT +ATATAAATATATATAAATATATATATATATAAAAATACCAGCACATCAGTATCAGGAATA +AATGGGCTGGGCAGTATATATATATATATATGTATATATATATACTGTTTTTCATATATA +TATACTGTCTTATATATATATATACTGTTTTACATATATATACTGTTTCATATATATAAT +GTTTTATATATATACTGTTATATATATTATATGTACTGTTATATATTTTTTATATATATA +CTGTTATATATATTTTTTATATATACTGTTATATATTATATATATACTGTTATATATATA +TTTTACATATATACTGTTATATATATATTTTATATATATATACTGTTATATATATATATT +TTATATATGTATACTGTTATATATTTATATTTTTTATATGTATACTGTTATATATATATT +ATATGTATACTGTTATATATATATTTTATATGTATACTGTTATATATATATATTTCATAT +ATATATACTGTTATATATATTTTATATATATATACTGTCATATATATATTTTATATATAT +ACTGTCATATATATATTTTATATATATATACTGTCATATATATATTTTATATATATATAC +TGTCATATATATATTTTATATATATATACTGTCATATATATTTTATATATATACTGTCAT +ATATATATTTTATATATATACTGTCATATATATATTTTATATATATACTGTCATATATAT +ATTTTATATATATATACTGTCATATATATATTTTATATATATATACTGTCATATATATAT +TTTATATATATACTGTCATATGTATATTTTATATATATACTGTCATATGTATATTTTATA +TATATACTGTTATATGTATATTTTATATATATATACTGTTATATATATATTTTATATATA +TATACTGTTATATATATATTTTATATATATATACTGTTATATATATATTTTTATATATAT +ACTGTTATATATATTTTTTTATATATATACTGTTATATATATTTTTATATATATACTGTT +ATATATATATTTTATATATATACTGTTATATATATATTTTATATATACTGTTATATATAT +ATATTTTATATATATACTGTTATATATAATTTTTTTCATATATATACTGTTATATATATA +TTTTATATATATATACTGTTATATATATATTTTATATATATACTGTTATATATATATATT +TTATATATATACTGTTATTTTTTATATATATACTGTTATATATATATTTTATATATATAC +TGTTATATATATATTATCTATATACTGTTATGTGTATATTTTATCTATATACTGTTATGT +GTATATTTTATCTATATACTGTTATGTGTATATTTTACCTATATACTTTTATGTGTATAT +TTTATATATATACTGTTATGTGTATATTTTATATATATACTGTTATGTGTATATTTTTTA +TATATACTGTTATGTGTATATTTTATATATATATACTGTTATGTGTATATTTTATATATA +TATACTGTTATGTGTATATTTTATATATATACTGTTATGTGTATATTTTATATATATACT +GTTATATATAGTTCATATATATACTGTTATATGTATAGTTCATATATATACTGTTATATA +TATAGTTCATATGTATACTGTTATATATATAGTTCATATATATACTGTTATATATATAGT +TCATATATATACTGTTATATATATATAGTTCATATATATACTGTTATATATAGTTCATAT +ATATACTGTTATATATATAGTTCATATATATACTGTTATATATATAGTTCATATATATAC +TGTTATATATAGTTCATATATATATACTGTTCTATATATAGTTCATATATATATACTGTT +ATATATATAGTTCATATATATATACTGTTATATATAGTTCATATATATATAGTTCATATA +TATACTGTTATATATATAGTTCATATATATACTGTTATATACATAGTTCATATATATACT +GTTATATATATAGTTCATATATATATACTGTTATATATATAGTTCATATATATACTGTTG +TATATAGTTCATATATATACTGTTATATATATAGTTCATATATTACTGTTATATATATAG +TTCATATATATACTGTTATATATATATAGTTCATATATATACTGTTATATATAGTTTATA +TATATATACTGTTATATATATAGTTTATATATATATACTGTTATATATATAGTTTATATA +TATATACTGTTATATATATATAGTTTATATATATATACTGTTATATATATAGTTTATATA +TATATACTGTTATATATATAGTTTATATATACTGTTATATATATATAGTTTATATATATA +CTGTTATATATATAGTTTATATATATACTGTTATATATATAGTTTATATATATACTGTTA +TATATATAGTTTATATATATACTGTTATATATATAGTTTATATATATACTGTTATATATA +TAGTTTATATATATATACTGTTATATATATAGTTTATAAATACTGTTATATATATAGTTT +ATATACTGTTATATATAGTTTATATATATATACTGTTATATATAGTTTATATATATATAC +TGTTATATATATATAGTTTATATATATATACTGTTATATATATATAGTTTATATATATAC +TGTTATATATATATAGTTTATATATATACTGTTGTATATATAGTTTATATATATACTGTT +ATATATATATTTGTGTATATATACTGTTATATAAATATATTTGTGTATATATACTGTTAT +ATATATATTTTATGTATATATACTGTTATATATATATTTTATGTATATATACTGTTATAT +ATATATTTTATGTATATATACTGTTATATATATATTTTATGTATATATACTGTTATATAT +ATATTTTATGTATATATACTGTTATATATATTTTATGTATATATACTGTTATATATATAT +TTTATGTATATATACTGTTATATCTGTATATTTTATGTTTATATACTGTTATATCTGTAT +ATTTTATGTATATATACTGTTATATCTGTATATTTTATGTATATACTGTTATATATATAC +TGTTATATATATACTGATATATATACTGTTATATATATACTGATATATATATACTGTTAT +ATATATACTGTTATATATATATACTGTTACATATACATATATATACTGTTATATATATAC +TGTTATATATATTGTTATATATATACACATATATATATACATATATATATACATATATAT +ATACATATATATATACACGTATATATATACATATATATATACACATATATATATATACAC +ACACATATATATATATATATATACTGGCTGTGTGTGGTGGTGCACACCTGTAATCCCAGC +ACTTTGGGAGGCCAAGGCAGGCTGATGGCTTGAGCTCAGGAGTTCAAGACCAGCTAAGCA +ACATACTGAGATCCCATCTCTAAAAAAAATACAAAAAGGCCAGGCACAGTGGCTCACACC +TGTAATCCCAGCACTTTGGGAGGCTGAGGTGGGCAGATCACGAGGTCAGCAGTTCGAGAC +CAGCCTGGCCAGCATGGTGAAACCCCATCTCTACTAAAAATACAAAACATTAGCCGGACA +TGGTGGCACACACCTGTAATTCCAGCTACTCAGGAAGCTGAGGCAGGAGAATAGCTTGAA +CCCAGGAGGCGAAAGTTTCAGTCAGCCAAAATCACACCACTGCACTCCAGCCTGGGCAAC +AGAGCAAGACTCTGTCTCCAAAAAAA +>p:HG002_2_chr20:38462831-38464884 +CACCATGTTACCTAGGCTGATCTTGAATTCCTGGGCTCAAGTGTTAGACTCACTTCGGCC +TCCCAAAGTGTTGGGATTACAGGCGTGAGCCACTGCACCCAGCCTGTTTTGTTTGGGGCA +AGGGTTTTAACATTTATATATATATAAATATATATATATTTTATATATACAAATATATAT +ATAAATATATATTTATATATATTTATATATAATATATTATATATAAATATATTTATATAT +AATATATTATATATAAATATATTATATATAAAATATTATATATAAATATATATATTTATA +TATATAAATATATATAAATATATATATATATAAAAATACCAGCACATCAGTATCAGGAAT +AAATGGGCTGGGCAGTATATATATATATATATATGTATATATATATACTGTTTTTCATAT +ATATATACTGTCTTATATATATATATACTGTTTTACATATATATACTGTTTCATATATAT +AATGTTTTATATATATACTGTTATATATATTATATGTACTGTTATATATTTTTTATATAT +ATACTGTTATATATATTTTTTATATATACTGTTATATATTATATATATACTGTTATATAT +ATATTTTACATATATACTGTTATATATATATTTTATATATATATACTGTTATATATATAT +ATTTTATATATGTATACTGTTATATATTTATATTTTTTATATGTATACTGTTATATATAT +ATTATATGTATACTGTTATATATATATTTTATATGTATACTGTTATATATATATATTTCA +TATATATATACTGTTATATATATTTTATATATATATACTGTCATATATATATTTTATATA +TATACTGTCATATATATATTTTATATATATATACTGTCATATATATATTTTATATATATA +TATACTGTCATATATATATTTTATATATATATACTGTCATATATATTTTATATATATACT +GTCATATATATATTTTATATATATACTGTCATATATATATTTTATATATATACTGTCATA +TATATATTTTATATATATACTGTCATATATATATTTTATATATATATACTGTCATATATA +TATTTTATATATATATACTGTCATATATATATTTTATATATATACTGTCATATGTATATT +TTATATATATACTGTCATATGTATATTTTATATATATACTGTTATATGTATATTTTATAT +ATATATACTGTTATATATATATTTTTATATATATACTGTTATATATATTTTTTTATATAT +ATACTGTTATATATATTTTTATATATATACTGTTATATATATATTTTATATATATACTGT +TATATATATATTTTATATATACTGTTATATATATATATTTTATATATATACTGTTATATA +TAATTTTTTTCATATATATACTGTTATATATATATTTTATATATATATACTGTTATATAT +ATATTTTATATATATACTGTTATATATATATATTTTATATATATACTGTTATTTTTTATA +TATATACTGTTATATATATATTTTATATATATACTGTTATATATATATTATCTATATACT +GTTATGTGTATATTTTATCTATATACTGTTATGTGTATATTTTATCTATATACTGTTATG +TGTATATTTTACCTATATACTTTTATGTGTATATTTTATATATATACTGTTATGTGTATA +TTTTATATATATACTGTTATGTGTATATTTTTTATATATACTGTTATGTGTATATTTTAT +ATATATATACTGTTATGTGTATATTTTATATATATATACTGTTATGTGTATATTTTATAT +ATATACTGTTATGTGTATATTTTATATATATACTGTTATATATAGTTCATATATATACTG +TTATATGTATAGTTCATATATATACTGTTATATATATAGTTCATATGTATACTGTTATAT +ATATAGTTCATATATATACTGTTATATATATAGTTCATATATATACTGTTATATATATAT +AGTTCATATATATACTGTTATATATAGTTCATATATATACTGTTATATATATAGTTCATA +TATATACTGTTATATATATAGTTCATATATATACTGTTATATATAGTTCATATATATATA +CTGTTCTATATATAGTTCATATATATATACTGTTATATATATAGTTCATATATATATACT +GTTATATATAGTTCATATATATATAGTTCATATATATACTGTTATATATATAGTTCATAT +ATATACTGTTATATACATAGTTCATATATATACTGTTATATATATAGTTCATATATATAT +ACTGTTATATATATAGTTCATATATATACTGTTGTATATAGTTCATATATATACTGTTAT +ATATATAGTTCATATATTACTGTTATATATATAGTTCATATATATACTGTTATATATATA +TAGTTCATATATATACTGTTATATATAGTTTATATATATATACTGTTATATATATAGTTT +ATATATATATACTGTTATATATATAGTTTATATATATATACTGTTATATATATATAGTTT +ATATATATATACTGTTATATATATAGTTTATATATATATACTGTTATATATATATAGTTT +ATATATACTGTTATATATATAGTTTATATATATACTGTTATATATATAGTTTATATATAT +ACTGTTATATATATAGTTTATATATATACTGTTATATATATAGTTTATATATATACTGTT +ATATATATAGTTTATATATATACTGTTATATATATAGTTTATATATATACTGTTATATAT +ATAGTTTATATATATATACTGTTATATATAGTTTATATATACTGTTATATATATAGTTTA +TATACTGTTATATATAGTTTATATATATATACTGTTATATATAGTTTATATATATATACT +GTTATATATATATAGTTTATATATATATACTGTTATATATATATAGTTTATATATATACT +GTTATATATATATAGTTTATATATATACTGTTGTATATATAGTTTATATATATACTGTTA +TATATATATTTGTGTATATATACTGTTATATAAATATATTTGTGTATATATACTGTTATA +TATATATTTTATGTATATATACTGTTATATATATATTTTATGTATATATACTGTTATATA +TATATTTTATGTATATATACTGTTATATATATATTTTATGTATATATACTGTTATATATA +TATTTTATGTATATATACTGTTATATATATTTTATGTATATATACTGTTATATATATTTT +ATGTATATATACTGTTATATATATATTTTATGTATATATACTGTTATATCTGTATATTTT +ATGTTTATATACTGTTATATCTGTATATTTTATGTATATATACTGTTATATCTGTATATT +TTATGTATATACTGTTATATATATACTGTTATATATATACTGATATATATACTGTTATAT +ATATACTGATATATATATACTGTTATATATATACTGTTATATATATATACTGTTACATAT +ACATATATATACTGTTATATATATACTGTTATATATATTGTTATATATATACACATATAT +ATATACATATATATACATATATATATACATATATATATACATATATATATACACGTATAT +ATATACATATATATATACACATATATATATATACACACACATATATATATATATATATAC +TGGCTGTGTGTGGTGGTGCACACCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGCTG +ATGGCTTGAGCTCAGGAGTTCAAGACCAGCTAAGCAACATACTGAGATCCCATCTCTAAA +AAAAATACAAAAAGGCCAGGCACAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGC +TGAGGTGGGCAGATCACGAGGTCAGCAGTTCGAGACCAGCCTGGCCAGCATGGTGAAACC +CCATCTCTACTAAAAATACAAAACATTAGCCGGACATGGTGGCACACACCTGTAATTCCA +GCTACTCAGGAAGCTGAGGCAGGAGAATAGCTTGAACCCAGGAGGCGAAAGTTTCAGTCA +GCCAAAATCACACCACTGCACTCCAGCCTGGGCAACAGAGCAAGACTCTGTCTCCAAAAA +AA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/haps.fa.ref.fa new file mode 100644 index 00000000..c0fd3940 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:38462831-38464884 +CACCATGTTACCTAGGCTGATCTTGAATTCCTGGGCTCAAGTGTTAGACTCACTTCGGCCTCCCAAAGTGTTGGGATTACAGGCGTGAGCCACTGCACCCAGCCTGTTTTGTTTGGGGCAAGGGTTTTAACATTTATATATATATAAATATATATATATTTTATATATACAAATATATATATAAATATATATTTATATATATTTATATATAATATATTATATATAAATATATTTATATATAATATATTATATATAAATATATTATATATAAAATATTATATATAAATATATATATTTATATATATAAATATATATAAATATATATATATATAAAAATACCAGCACATCAGTATCAGGAATAAATGGGCTGGGCAGTATATATATATATATATATGTATATATATATACTGTTTTTCATATATATATACTGTCTTATATATATATATACTGTTTTACATATATATACTGTTTCATATATATAATGTTTTATATATATACTGTTATATATATTATATGTACTGTTATATATTTTTTATATATATACTGTTATATATATTTTTTATATATACTGTTATATATTATATATATACTGTTATATATATATTTTACATATATACTGTTATATATATATTTTATATATATATACTGTTATATATATATATTTTATATATGTATACTGTTATATATTTATATTTTTTATATGTATACTGTTATATATATATTATATGTATACTGTTATATATATATTTTATATGTATACTGTTATATATATATATTTCATATATATATACTGTTATATATATTTTATATATATATACTGTCATATATATATTTTATATATATACTGTCATATATATATTTTATATATATATACTGTCATATATATATTTTATATATATATATACTGTCATATATATATTTTATATATATATACTGTCATATATATTTTATATATATACTGTCATATATATATTTTATATATATACTGTCATATATATATTTTATATATATACTGTCATATATATATTTTATATATATACTGTCATATATATATTTTATATATATATACTGTCATATATATATTTTATATATATATACTGTCATATATATATTTTATATATATACTGTCATATGTATATTTTATATATATACTGTCATATGTATATTTTATATATATACTGTTATATGTATATTTTATATATATATACTGTTATATATATATTTTTATATATATACTGTTATATATATTTTTTTATATATATACTGTTATATATATTTTTATATATATACTGTTATATATATATTTTATATATATACTGTTATATATATATTTTATATATACTGTTATATAGATACTGTTATATATATACTGATATATATACTGTTATATATATACTGATATATATATACTGTTATATATATACTGTTATATATATATACTGTTACATATACATATATATACTGTTATATATATACTGTTATATATATTGTTATATATATACACATATATATATACATATATATATACATATATATATACATATATATATACATATATATATACACGTATATATATACATATATATATACACATATATATATATACACACACATATATATATATATATATACTGGCTGTGTGTGGTGGTGCACACCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGCTGATGGCTTGAGCTCAGGAGTTCAAGACCAGCTAAGCAACATACTGAGATCCCATCTCTAAAAAAAATACAAAAAGGCCAGGCACAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGTGGGCAGATCACGAGGTCAGCAGTTCGAGACCAGCCTGGCCAGCATGGTGAAACCCCATCTCTACTAAAAATACAAAACATTAGCCGGACATGGTGGCACACACCTGTAATTCCAGCTACTCAGGAAGCTGAGGCAGGAGAATAGCTTGAACCCAGGAGGCGAAAGTTTCAGTCAGCCAAAATCACACCACTGCACTCCAGCCTGGGCAACAGAGCAAGACTCTGTCTCCAAAAAAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/msa.fa new file mode 100644 index 00000000..f9c8425d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/msa.fa @@ -0,0 +1,350 @@ +>ref_chr20_38462831_38464884 +caccatgttacctaggctgatcttgaattcctgggctcaagtgttagactcacttcggcc +tcccaaagtgttgggattacaggcgtgagccactgcacccagcctgttttgtttggggca +agggttttaacatttatatatatataaatatatatatattttatatatacaaatatatat +ataaatatatatttatatatatttatatataatatattatatataaatatatttatatat +aatatattatatataaatatattatatataaaatattatatataaatatatatatttata +tatataaatatatataaatatatatatatataaaaataccagcacatcagtatcaggaat +aaatgggctgggcagtatatatatatatatatatgtatatatatatactgtttttcatat +atatatactgtcttatatatatatatactgttttacatatatatactgtttcatatatat +aatgttttatatatatactgttatatatattatatgtactgttatatattttttatatat +atactgttatatatattttttatatatactgttatatattatatatatactgttatatat +atattttacatatatactgttatatatatattttatatatatatactgttatatatatat +attttatatatgtatactgttatatatttatattttttatatgtatactgttatatatat +attatatgtatactgttatatatatattttatatgtatactgttatatatatatatttca +tatatatatactgttatatatattttatatatatatactgtcatatatatattttatata +tatactgtcatatatatattttatatatatatactgtcatatatatattttatatatata +tatactgtcatatatatattttatatatatatactgtcatatatattttatatatatact +gtcatatatatattttatatatatactgtcatatatatattttatatatatactgtcata +tatatattt--tatatatatactgtcatatatatattttatatatatatactgtcatata +tatattttatatatatatactgtcatatatatattttatatatatactgtcatatgtata +ttttatatatatactgtcatatgtatattt------------------------------ +-tatatatatactgttatatgtatattttatatatatatactgttatatatatattttta +tatatatactgttatatatatttttttatatatatactgttatatatatttttatatata +tactgttatatatatattttatatatatactgttatatatatatttta------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ 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+atatagttcatatatatactgttatatatatatagttcatatatatactgttatatatag +ttcatatatatactgttatatatatagttcatatatatactgttatatatatagttcata +tatatactgttatatatagttcatatatatatactgttctatatatagttcatatatata +tactgttatatatatagttcatatatatatactgttatatatagttcatatatatatagt +tcatatatatactgttatatatatagttcatatatatactgttatatacatagttcatat +atatactgttatatatatagttcatatatatatactgttatatatatagttcatatatat +actgttgtatatagttcatatatatactgttatatatatagttcatatattactgttata +tatatagttcatatatatactgttatatatatatagttcatatatatactgttatatata +gtttatatatatatactgttatatatatagtttatatatatatactgttatatatatagt +ttatatatatatactgttatatatatatagtttatatatatatactgttatatatatagt +ttatatatatatactgttatatatatatagtttatatatactgttatatatatagtttat +atatatactgttatatatatagtttatatatatactgttatatatatagtttatatatat +actgttatatatatagtttatatatatactgttatatatatagtttatatatatactgtt +atatatatagtttatatatatactgttatatatatagtttatatatatatactgt--tat +atatagtttatatatactgttatatatatagtttatatactgttatatatagtttatata +tatatactgttatatatagtttatatatatatactgttatatatatatagtttatatata +tatactgttatatatatatagtttatatatatactgttatatatatatagtttatatata +tactgttgtatatatagtttatatatatactgttatatatatatttgtgtatatatactg +ttatataaatatatttgtgtatatatactgttatatatatattttatgtatatatactgt +tatatatatattttatgtatatatactgttatatatatattttatgtatatatactgtta +tatatatattttatgtatatatactgttatatatatattttatgtatatatactgttata +tatattttatgtatatatactgttatatatattttatgtatatatactgttatatatata +ttttatgtatatatactgttatatctgtatattttatgtttatatactgttatatctgta +tattttatgtatatatactgttatatctgtatattttatgtatatactgttatatatata +ctgttatatatatactgatatatatactgttatatatatactgatatatatatactgtta +tatatatactgttatatatatatactgttacatatacatatatatactgttatatatata +ctgttatatatattgttatatatatacacatatatatatac--atatatatacatatata +tatacatatatatatacatatatatatacacgtatatatatacatatatatatacacata +tatatatatacacacacatatatatatatatatatactggctgtgtgtggtggtgcacac +ctgtaatcccagcactttgggaggccaaggcaggctgatggcttgagctcaggagttcaa +gaccagctaagcaacatactgagatcccatctctaaaaaaaatacaaaaaggccaggcac +agtggctcacacctgtaatcccagcactttgggaggctgaggtgggcagatcacgaggtc +agcagttcgagaccagcctggccagcatggtgaaaccccatctctactaaaaatacaaaa +cattagccggacatggtggcacacacctgtaattccagctactcaggaagctgaggcagg +agaatagcttgaacccaggaggcgaaagtttcagtcagccaaaatcacaccactgcactc +cagcctgggcaacagagcaagactctgtctccaaaaaaa diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/msa.fa.fai new file mode 100644 index 00000000..0fbd95dc --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_38462831_38464884 4119 29 60 61 +syndip_1_chr20:38462831-38464884 4119 4251 60 61 +syndip_2_chr20:38462831-38464884 4119 8473 60 61 +p:HG002_1_chr20:38462831-38464884 4119 12696 60 61 +p:HG002_2_chr20:38462831-38464884 4119 16919 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/output.vcf.gz new file mode 100644 index 00000000..d2d11b7f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/output.vcf.gz.tbi new file mode 100644 index 00000000..2eb56f31 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:38462931-38464784/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/base.vcf.gz new file mode 100644 index 00000000..6ffc7531 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/base.vcf.gz.tbi new file mode 100644 index 00000000..55d29663 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/comp.vcf.gz new file mode 100644 index 00000000..0b2659b4 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/comp.vcf.gz.tbi new file mode 100644 index 00000000..89e93fe8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/haps.fa new file mode 100644 index 00000000..5c0c9583 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/haps.fa @@ -0,0 +1,132 @@ +>ref_chr20_4032119_4033702 +CGGGATTGCAGATGAAGTCTCGTTCACTCAGTGCTCAGTGGTGTCCAGGCTGGAGTGCAGCGGCGTGATCTCGGCTCGCTACAACCACCTCCCAGCCGCCTGCCTTGGCCTCCCAAAGAGCCGAGATTGCAGCCTCTGCCCGGCCGCCACCCCGTCTGGGAAGTGAGGAGCGTCTCTGCTTGGCCACCCATCGTCTGGGATATGAGGAGCCCCTCTGCCTGGCTGCCCAGTCTGGAAAGTGAGGAGCGTCTCTGCCCGGCCGCCATCCCATCTAGGAAGCGAGGAGCGTCTCTGCCCGGCCGCCATCCCATCTAGGAAGCGAGGAGCGCCTCTTCCCGGCTGCCATCCCATCTAGGAACTGAGGAGCGTCTCTGCCCGGCCGCCCATCGTCTGAGATGTGGGGAGCACCTCTGCCCCACCGCCCTGTCTGGGATGTGAGGAGCGCCTCTGCTGGGCCGCAACCCTGTCTGGGAGGTGAGGAGCGTCTCTGCCCCGCCGCTCCGTCTGAGAAGTGAGGAAACCCTCTGCCTGGCAACCGCCCCGTCTGAGAAGTGAGGAGCCCCTCCGTCCGGCAACCACCCCGTCTGGGAAGTGAGGAGCGTCTCCGCCCGGCAGCCACCCCGTCCGGGAGGGAGGTGGGGGGGGGGGTCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCGGCCGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCGGCTGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCTGCCCCGCCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCTGGCCAGCCGCCCCATCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGGGGGAGGGGGGGTCAGCCCCCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGGGGTCAGCCCCCTTTCCGGCCGCCGCCTGTCCGGGAGGTGAGGGGCGCCTCTGCCTGGCCGCCCCTACTGGGAAGTGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGACAGCCCCCCGCCCGGCCAGCCGCCCTATCCAGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCTGGCCAGCCGCCCCGTCCGGGAGGGTAGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCATCCGGGAGGTGAGGGGCGCTTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCACGACCCCGTCTGGGAGGTGTGCCCAGCGGCTCATTGGGGATGGGCCATGATGACAATGGCGGTTTTGTGGAATAGAAAGGCGGGAAGGGTGGGGAAAAAATTGAGAAATCGGATGGTTGCCGGGTCTGTGTGGATGGAAGTAGACATG +>syndip_1_chr20:4032119-4033702 +CGGGATTGCAGATGAAGTCTCGTTCACTCAGTGCTCAGTGGTGTCCAGGCTGGAGTGCAG +CGGCGTGATCTCGGCTCGCTACAACCACCTCCCAGCCGCCTGCCTTGGCCTCCCAAAGAG +CCGAGATTGCAGCCTCTGCCCGGCCGCCACCCCGTCTGGGAAGTGAGGAGCGTCTCTGCT +TGGCCACCCATCGTCTGGGATATGAGGAGCCCCTCTGCCTGGCTGCCCAGTCTGGAAAGT +GAGGAGCGTCTCTGCCCGGCCGCCATCCCATCTAGGAAGCGAGGAGCGCCTCTTCCCGGC +TGCCATCCCATCTAGGAAGTGAGGAGCGTCTCTGCCCGGCCGCCCATCGTCTGAGATGTG +GGGAGCACCTCTGCCCCACCGCCCTGTCTGGGATGTGAGGAGCGCCTCTGCTGGGCCGCA +ACCCTGTCTGGGAGGTGAGGAGCGTCTCTGCCCCGCCGCTCCGTCTGAGAAGTGAGGAAA +CCCTCTGCCTGGCAACCGCCCCGTCTGAGAAGTGAGGAGCCCCTCCGTCCGGCAACCACC +CCGTCTGGGAAGTGAGGAGCGTCTCCGCCCGGCAGCCACCCCGTCCGGGAGGGAGGTGGG +GGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGTGAGGGGCTCCTCTGCCC +GGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGG +GAGGCGGGGGGGGGGGTCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCC +CCCGCCCGGCCGGCCGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTAC +TGGGAAGTGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGT +CAGTCCCCCGCCCGGCCGGCTGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGC +CCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCTGCCCCGCCCGGGAGGGAGGTG +GGGGGGTCAGCCCCCCGCCTGGCCAGCCGCCCCATCCGGGAGGGAGGTGGGGGGGTCAGC +CCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGGGGGAGGGGGGGTCAGCCCCCTGCCCGG +CCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCC +CCGTCCGGGAGGGAGGTGGGGGGATCAGCCCCCCGCCTGGCCAGCCGCCCCGTCCGGGAG +GTGAGGGGCGCCTCTGCCCGGCCACCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCC +AGCCGCCCCGTCCGGGAGGGAGGCGGGGGGGGGGGTCGGCCAGCCGCCCCGTCCGGGAGG +GAGGTGGGGGGGTCAGCCCCCCTTCCGGCCGGCCGCCCTGTCCGGGAGGTGAGGGGCGCC +TCTGCCTGGCCGCCCCTACTGGGAAGTGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCC +GGGAGGGAGGTGGGGGGGACAGCCCCCCGCCCGGCCAGCCGCCCTATCCAGGAGGTGAGG +GGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCCGC +CCCGTCCGGGAGGGTAGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCATCCGGGA +GGTGAGGGGCGCTTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGC +CACGACCCCGTCTGGGAGGTGTGCCCAGCGGCTCATTGGGGATGGGCCATGATGACAATG +GCGGTTTTGTGGAATAGAAAGGCGGGAAGGGTGGGGAAAAAATTGAGAAATCGGATGGTT +GCCGGGTCTGTGTGGATGGAAGTAGACATG +>syndip_2_chr20:4032119-4033702 +CGGGATTGCAGATGAAGTCTCGTTCACTCAGTGCTCAGTGGTGTCCAGGCTGGAGTGCAG +CGGCGTGATCTCGGCTCGCTACAACCACCTCCCAGCCGCCTGCCTTGGCCTCCCAAAGAG +CCGAGATTGCAGCCTCTGCCCGGCCGCCACCCCGTCTGGGAAGTGAGGAGCGTCTCTGCT +TGGCCACCCATCGTCTGGGATATGAGGAGCCCCTCTGCCTGGCTGCCCAGTCTGGAAAGT +GAGGAGCGTCTCTGCCCGGCCGCCATCCCATCTAGGAAGCGAGGAGCGTCTCTGCCCGGC +CGCCATCCCATCTAGGAAGCGAGGAGCGCCTCTTCCCGGCTGCCATCCCATCTAGGAACT +GAGGAGCGTCTCTGCCCGGCCGCCCATCGTCTGAGATGTGGGGAGCACCTCTGCCCCACC +GCCCTGTCTGGGATGTGAGGAGCGCCTCTGCTGGGCCGCAACCCTGTCTGGGAGGTGAGG +AGCGTCTCTGCCCCGCCGCTCCGTCTGAGAAGTGAGGAAACCCTCTGCCTGGCAACCGCC +CCGTCTGAGAAGTGAGGAGCCCCTCCGTCCGGCAACCACCCCGTCTGGGAAGTGAGGAGC +GTCTCCGCCCGGCAGCCACCCCGTCCGGGAGGGAGGTGGGGGGGGGGGTCGGCCAGCCGC +CCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCGGCCGCCCCGTCCGGGA +GGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGACCCCTCTGCCCGGCC +AGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCGGCTGCCCCGT +CCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTG +CCCGGCCAGCTGCCCCGCCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCTGGCCAGCC +GCCCCATCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGG +GAGGGGGGAGGGGGGGTCAGCCCCCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGG +GGGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGATC +AGCCCCCCGCCTGGCCAGCCGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCACC +CCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGCGG +GGGGGGGGGTCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCTTCC +GGCCGGCCGCCCTGTCCGGGAGGTGAGGGGCGCCTCTGCCTGGCCGCCCCTACTGGGAAG +TGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGACAGCCCC +CCGCCCGGCCAGCCGCCCTATCCAGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACT +GGGAAGTGAGGAGCCCCTCTGCCTGGCCAGCCGCCCCGTCCGGGAGGGTAGTGGGGGGGT +CAGCCCCCCGCCCGGCCAGCCGCCCCATCCGGGAGGTGAGGGGCGCTTCTGCCCGGCCGC +CCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCACGACCCCGTCTGGGAGGTGTGCCC +AGCGGCTCATTGGGGATGGGCCATGATGACAATGGCGGTTTTGTGGAATAGAAAGGCGGG +AAGGGTGGGGAAAAAATTGAGAAATCGGATGGTTGCCGGGTCTGTGTGGATGGAAGTAGA +CATG +>p:HG002_1_chr20:4032119-4033702 +CGGGATTGCAGATGAAGTCTCGTTCACTCAGTGCTCAGTGGTGTCCAGGCTGGAGTGCAG +CGGCGTGATCTCGGCTCGCTACAACCACCTCCCAGCCGCCTGCCTTGGCCTCCCAAAGAG +CCGAGATTGCAGCCTCTGCCCGGCCGCCACCCCGTCTGGGAAGTGAGGAGCGTCTCTGCT +TGGCCACCCATCGTCTGGGATATGAGGAGCCCCTCTGCCTGGCTGCCCAGTCTGGAAAGT +GAGGAGCGTCTCTGCCCGGCCGCCATCCCATCTAGGAAGCGAGGAGCGTCTCTGCCCGGC +CGCCATCCCATCTAGGAAGCGAGGAGCGCCTCTTCCCGGCTGCCATCCCATCTAGGAACT +GAGGAGCGTCTCTGCCCGGCCGCCCATCGTCTGAGATGTGGGGAGCACCTCTGCCCCACC +GCCCTGTCTGGGATGTGAGGAGCGCCTCTGCTGGGCCGCAACCCTGTCTGGGAGGTGAGG +AGCGTCTCTGCCCCGCCGCTCCGTCTGAGAAGTGAGGAAACCCTCTGCCTGGCAACCGCC +CCGTCTGAGAAGTGAGGAGCCCCTCCGTCCGGCAACCACCCCGTCTGGGAAGTGAGGAGC +GTCTCCGCCCGGCAGCCACCCCGTCCGGGAGGGAGGTGGGGGGGGGGGTCGGCCAGCCGC +CCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCGGCCGCCCCGTCCGGGA +GGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGACCCCTCTGCCCGGCC +AGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCGGCTGCCCCGT +CCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTG +CCCGGCCAGCTGCCCCGCCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCTGGCCAGCC +GCCCCATCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGG +GAGGGGGGAGGGGGGGTCAGCCCCCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGG +GGGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGATC +AGCCCCCCGCCTGGCCAGCCGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCACC +CCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGCGG +GGGGGGGGGTCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCTTCC +GGCCGGCCGCCCTGTCCGGGAGGTGAGGGGCGCCTCTGCCTGGCCGCCCCTACTGGGAAG +TGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGACAGCCCC +CCGCCCGGCCAGCCGCCCTATCCAGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACT +GGGAAGTGAGGAGCCCCTCTGCCTGGCCAGCCGCCCCGTCCGGGAGGGTAGTGGGGGGGT +CAGCCCCCCGCCCGGCCAGCCGCCCCATCCGGGAGGTGAGGGGCGCTTCTGCCCGGCCGC +CCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCACGACCCCGTCTGGGAGGTGTGCCC +AGCGGCTCATTGGGGATGGGCCATGATGACAATGGCGGTTTTGTGGAATAGAAAGGCGGG +AAGGGTGGGGAAAAAATTGAGAAATCGGATGGTTGCCGGGTCTGTGTGGATGGAAGTAGA +CATG +>p:HG002_2_chr20:4032119-4033702 +CGGGATTGCAGATGAAGTCTCGTTCACTCAGTGCTCAGTGGTGTCCAGGCTGGAGTGCAG +CGGCGTGATCTCGGCTCGCTACAACCACCTCCCAGCCGCCTGCCTTGGCCTCCCAAAGAG +CCGAGATTGCAGCCTCTGCCCGGCCGCCACCCCGTCTGGGAAGTGAGGAGCGTCTCTGCT +TGGCCACCCATCGTCTGGGATATGAGGAGCCCCTCTGCCTGGCTGCCCAGTCTGGAAAGT +GAGGAGCGTCTCTGCCCGGCCGCCATCCCATCTAGGAAGCGAGGAGCGCCTCTTCCCGGC +TGCCATCCCATCTAGGAAGTGAGGAGCGTCTCTGCCCGGCCGCCCATCGTCTGAGATGTG +GGGAGCACCTCTGCCCCACCGCCCTGTCTGGGATGTGAGGAGCGCCTCTGCTGGGCCGCA +ACCCTGTCTGGGAGGTGAGGAGCGTCTCTGCCCCGCCGCTCCGTCTGAGAAGTGAGGAAA +CCCTCTGCCTGGCAACCGCCCCGTCTGAGAAGTGAGGAGCCCCTCCGTCCGGCAACCACC +CCGTCTGGGAAGTGAGGAGCGTCTCCGCCCGGCAGCCACCCCGTCCGGGAGGGAGGTGGG +GGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGTGAGGGGCTCCTCTGCCC +GGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGG +GAGGCGGGGGGGGGGGTCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCC +CCCGCCCGGCCGGCCGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTAC +TGGGAAGTGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGT +CAGTCCCCCGCCCGGCCGGCTGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGC +CCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCTGCCCCGCCCGGGAGGGAGGTG +GGGGGGTCAGCCCCCCGCCTGGCCAGCCGCCCCATCCGGGAGGGAGGTGGGGGGGTCAGC +CCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGGGGGAGGGGGGGTCAGCCCCCTGCCCGG +CCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCC +CCGTCCGGGAGGGAGGTGGGGGGATCAGCCCCCCGCCTGGCCAGCCGCCCCGTCCGGGAG +GTGAGGGGCGCCTCTGCCCGGCCACCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCC +AGCCGCCCCGTCCGGGAGGGAGGCGGGGGGGGGGGTCGGCCAGCCGCCCCGTCCGGGAGG +GAGGTGGGGGGGTCAGCCCCCCTTCCGGCCGGCCGCCCTGTCCGGGAGGTGAGGGGCGCC +TCTGCCTGGCCGCCCCTACTGGGAAGTGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCC +GGGAGGGAGGTGGGGGGGACAGCCCCCCGCCCGGCCAGCCGCCCTATCCAGGAGGTGAGG +GGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCCGC +CCCGTCCGGGAGGGTAGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCATCCGGGA +GGTGAGGGGCGCTTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGC +CACGACCCCGTCTGGGAGGTGTGCCCAGCGGCTCATTGGGGATGGGCCATGATGACAATG +GCGGTTTTGTGGAATAGAAAGGCGGGAAGGGTGGGGAAAAAATTGAGAAATCGGATGGTT +GCCGGGTCTGTGTGGATGGAAGTAGACATG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/haps.fa.ref.fa new file mode 100644 index 00000000..5d92d772 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:4032119-4033702 +CGGGATTGCAGATGAAGTCTCGTTCACTCAGTGCTCAGTGGTGTCCAGGCTGGAGTGCAGCGGCGTGATCTCGGCTCGCTACAACCACCTCCCAGCCGCCTGCCTTGGCCTCCCAAAGAGCCGAGATTGCAGCCTCTGCCCGGCCGCCACCCCGTCTGGGAAGTGAGGAGCGTCTCTGCTTGGCCACCCATCGTCTGGGATATGAGGAGCCCCTCTGCCTGGCTGCCCAGTCTGGAAAGTGAGGAGCGTCTCTGCCCGGCCGCCATCCCATCTAGGAAGCGAGGAGCGTCTCTGCCCGGCCGCCATCCCATCTAGGAAGCGAGGAGCGCCTCTTCCCGGCTGCCATCCCATCTAGGAACTGAGGAGCGTCTCTGCCCGGCCGCCCATCGTCTGAGATGTGGGGAGCACCTCTGCCCCACCGCCCTGTCTGGGATGTGAGGAGCGCCTCTGCTGGGCCGCAACCCTGTCTGGGAGGTGAGGAGCGTCTCTGCCCCGCCGCTCCGTCTGAGAAGTGAGGAAACCCTCTGCCTGGCAACCGCCCCGTCTGAGAAGTGAGGAGCCCCTCCGTCCGGCAACCACCCCGTCTGGGAAGTGAGGAGCGTCTCCGCCCGGCAGCCACCCCGTCCGGGAGGGAGGTGGGGGGGGGGGTCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCGGCCGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCGGCTGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCTGCCCCGCCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCTGGCCAGCCGCCCCATCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGGGGGAGGGGGGGTCAGCCCCCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGGGGTCAGCCCCCTTTCCGGCCGCCGCCTGTCCGGGAGGTGAGGGGCGCCTCTGCCTGGCCGCCCCTACTGGGAAGTGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGACAGCCCCCCGCCCGGCCAGCCGCCCTATCCAGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCTGGCCAGCCGCCCCGTCCGGGAGGGTAGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCATCCGGGAGGTGAGGGGCGCTTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCACGACCCCGTCTGGGAGGTGTGCCCAGCGGCTCATTGGGGATGGGCCATGATGACAATGGCGGTTTTGTGGAATAGAAAGGCGGGAAGGGTGGGGAAAAAATTGAGAAATCGGATGGTTGCCGGGTCTGTGTGGATGGAAGTAGACATG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/msa.fa new file mode 100644 index 00000000..8f3d46af --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/msa.fa @@ -0,0 +1,170 @@ +>ref_chr20_4032119_4033702 +cgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgcag +cggcgtgatctcggctcgctacaaccacctcccagccgcctgccttggcctcccaaagag +ccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctctgct +tggccacccatcgtctgggatatgaggagcccctctgcctggctgcccagtctggaaagt +gaggagcgtctctgcccggccgccatcccatctaggaagcgaggagcgtctctgcccggc +cgccatcccatctaggaagcgaggagcgcctcttcccggctgccatcccatctaggaact +gaggagcgtctctgcccggccgcccatcgtctgagatgtggggagcacctctgccccacc +gccctgtctgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggtgagg +agcgtctctgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaaccgcc +ccgtctgagaagtgaggagcccctccgtccggcaaccaccccgtctgggaagtgaggagc +gtctccgcccggcagccaccccgtccgggagggaggt----------------------- +------------------------------------------------------------ +---------------------------------------------gggggggggggtcgg +ccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggccgcccc +gtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggacccctct +gcccggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggc +tgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggag +cccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagccccccgcct +ggccagccgccccatccgggagggaggtgggggggtcagccccccgcccggccagccgcc +ccgtccgggaggggggagggggggtcagccccctgcccggccagccgccccgtccgggag +ggaggtggg--------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------------------gggggggtcagcc +ccctttccggccg--ccgcctgtccgggaggtgaggggcgcctctgcctggccgccccta +ctgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtggggggg +acagccccccgcccggccagccgccctatccaggaggtgaggggcgcctctgcccggccg +cccctactgggaagtgaggagcccctctgcctggccagccgccccgtccgggagggtagt +gggggggtcagccccccgcccggccagccgccccatccgggaggtgaggggcgcttctgc +ccggccgcccctactgggaagtgaggagcccctctgcccggccacgaccccgtctgggag +gtgtgcccagcggctcattggggatgggccatgatgacaatggcggttttgtggaataga +aaggcgggaagggtggggaaaaaattgagaaatcggatggttgccgggtctgtgtggatg +gaagtagacatg +>syndip_1_chr20:4032119-4033702 +cgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgcag +cggcgtgatctcggctcgctacaaccacctcccagccgcctgccttggcctcccaaagag +ccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctctgct +tggccacccatcgtctgggatatgaggagcccctctgcctggctgcccagtctggaaagt +----------------------------------------gaggagcgtctctgcccggc +cgccatcccatctaggaagcgaggagcgcctcttcccggctgccatcccatctaggaagt +gaggagcgtctctgcccggccgcccatcgtctgagatgtggggagcacctctgccccacc +gccctgtctgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggtgagg +agcgtctctgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaaccgcc +ccgtctgagaagtgaggagcccctccgtccggcaaccaccccgtctgggaagtgaggagc +gtctccgcccggcagccaccccgtccgggagggaggtggggggggtcagccccccgcccg +gccagccgccccgtccgggaggtgaggggctcctctgcccggccgcccctactgggaagt +gaggagcccctctgcccggccagccgccccgtccgggagggaggcgggggggggggtcgg +ccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggccgcccc +gtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggacccctct +gcccggccagccgccccgtccgggagggaggtgggggggtcagtcccccgcccggccggc +tgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggag +cccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagccccccgcct +ggccagccgccccatccgggagggaggtgggggggtcagccccccgcccggccagccgcc +ccgtccgggaggggggagggggggtcagccccctgcccggccagccgccccgtccgggag +ggaggtggg--ggggggtcagccccccgcccggccagccgccccgtccgggagggaggtg +gggggatcagccccccgcctggccagccgccccgtccgggaggtgaggggcgcctctgcc +cggccacccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgggag +ggaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggggggtcagcc +ccccttccggccggccgccctgtccgggaggtgaggggcgcctctgcctggccgccccta +ctgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtggggggg +acagccccccgcccggccagccgccctatccaggaggtgaggggcgcctctgcccggccg +cccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgggagggtagt +gggggggtcagccccccgcccggccagccgccccatccgggaggtgaggggcgcttctgc +ccggccgcccctactgggaagtgaggagcccctctgcccggccacgaccccgtctgggag +gtgtgcccagcggctcattggggatgggccatgatgacaatggcggttttgtggaataga +aaggcgggaagggtggggaaaaaattgagaaatcggatggttgccgggtctgtgtggatg +gaagtagacatg +>syndip_2_chr20:4032119-4033702 +cgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgcag +cggcgtgatctcggctcgctacaaccacctcccagccgcctgccttggcctcccaaagag +ccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctctgct +tggccacccatcgtctgggatatgaggagcccctctgcctggctgcccagtctggaaagt +gaggagcgtctctgcccggccgccatcccatctaggaagcgaggagcgtctctgcccggc +cgccatcccatctaggaagcgaggagcgcctcttcccggctgccatcccatctaggaact +gaggagcgtctctgcccggccgcccatcgtctgagatgtggggagcacctctgccccacc +gccctgtctgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggtgagg +agcgtctctgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaaccgcc +ccgtctgagaagtgaggagcccctccgtccggcaaccaccccgtctgggaagtgaggagc +gtctccgcccggcagccaccccgtccgggagggaggt----------------------- +------------------------------------------------------------ +---------------------------------------------gggggggggggtcgg +ccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggccgcccc +gtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggacccctct +gcccggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggc +tgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggag +cccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagccccccgcct +ggccagccgccccatccgggagggaggtgggggggtcagccccccgcccggccagccgcc +ccgtccgggaggggggagggggggtcagccccctgcccggccagccgccccgtccgggag +ggaggtgggggggggggtcagccccccgcccggccagccgccccgtccgggagggaggtg +gggggatcagccccccgcctggccagccgccccgtccgggaggtgaggggcgcctctgcc +cggccacccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgggag +ggaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggggggtcagcc +ccccttccggccggccgccctgtccgggaggtgaggggcgcctctgcctggccgccccta +ctgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtggggggg +acagccccccgcccggccagccgccctatccaggaggtgaggggcgcctctgcccggccg +cccctactgggaagtgaggagcccctctgcctggccagccgccccgtccgggagggtagt +gggggggtcagccccccgcccggccagccgccccatccgggaggtgaggggcgcttctgc +ccggccgcccctactgggaagtgaggagcccctctgcccggccacgaccccgtctgggag +gtgtgcccagcggctcattggggatgggccatgatgacaatggcggttttgtggaataga +aaggcgggaagggtggggaaaaaattgagaaatcggatggttgccgggtctgtgtggatg +gaagtagacatg +>p:HG002_1_chr20:4032119-4033702 +cgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgcag +cggcgtgatctcggctcgctacaaccacctcccagccgcctgccttggcctcccaaagag +ccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctctgct +tggccacccatcgtctgggatatgaggagcccctctgcctggctgcccagtctggaaagt +gaggagcgtctctgcccggccgccatcccatctaggaagcgaggagcgtctctgcccggc +cgccatcccatctaggaagcgaggagcgcctcttcccggctgccatcccatctaggaact +gaggagcgtctctgcccggccgcccatcgtctgagatgtggggagcacctctgccccacc +gccctgtctgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggtgagg +agcgtctctgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaaccgcc +ccgtctgagaagtgaggagcccctccgtccggcaaccaccccgtctgggaagtgaggagc +gtctccgcccggcagccaccccgtccgggagggaggt----------------------- +------------------------------------------------------------ +---------------------------------------------gggggggggggtcgg +ccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggccgcccc +gtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggacccctct +gcccggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggc +tgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggag +cccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagccccccgcct +ggccagccgccccatccgggagggaggtgggggggtcagccccccgcccggccagccgcc +ccgtccgggaggggggagggggggtcagccccctgcccggccagccgccccgtccgggag +ggaggtgggggggggggtcagccccccgcccggccagccgccccgtccgggagggaggtg +gggggatcagccccccgcctggccagccgccccgtccgggaggtgaggggcgcctctgcc +cggccacccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgggag +ggaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggggggtcagcc +ccccttccggccggccgccctgtccgggaggtgaggggcgcctctgcctggccgccccta +ctgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtggggggg +acagccccccgcccggccagccgccctatccaggaggtgaggggcgcctctgcccggccg +cccctactgggaagtgaggagcccctctgcctggccagccgccccgtccgggagggtagt +gggggggtcagccccccgcccggccagccgccccatccgggaggtgaggggcgcttctgc +ccggccgcccctactgggaagtgaggagcccctctgcccggccacgaccccgtctgggag +gtgtgcccagcggctcattggggatgggccatgatgacaatggcggttttgtggaataga +aaggcgggaagggtggggaaaaaattgagaaatcggatggttgccgggtctgtgtggatg +gaagtagacatg +>p:HG002_2_chr20:4032119-4033702 +cgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgcag +cggcgtgatctcggctcgctacaaccacctcccagccgcctgccttggcctcccaaagag +ccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctctgct +tggccacccatcgtctgggatatgaggagcccctctgcctggctgcccagtctggaaagt +----------------------------------------gaggagcgtctctgcccggc +cgccatcccatctaggaagcgaggagcgcctcttcccggctgccatcccatctaggaagt +gaggagcgtctctgcccggccgcccatcgtctgagatgtggggagcacctctgccccacc +gccctgtctgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggtgagg +agcgtctctgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaaccgcc +ccgtctgagaagtgaggagcccctccgtccggcaaccaccccgtctgggaagtgaggagc +gtctccgcccggcagccaccccgtccgggagggaggtggggggggtcagccccccgcccg +gccagccgccccgtccgggaggtgaggggctcctctgcccggccgcccctactgggaagt +gaggagcccctctgcccggccagccgccccgtccgggagggaggcgggggggggggtcgg +ccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggccgcccc +gtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggacccctct +gcccggccagccgccccgtccgggagggaggtgggggggtcagtcccccgcccggccggc +tgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggag +cccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagccccccgcct +ggccagccgccccatccgggagggaggtgggggggtcagccccccgcccggccagccgcc +ccgtccgggaggggggagggggggtcagccccctgcccggccagccgccccgtccgggag +ggaggtggg--ggggggtcagccccccgcccggccagccgccccgtccgggagggaggtg +gggggatcagccccccgcctggccagccgccccgtccgggaggtgaggggcgcctctgcc +cggccacccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgggag +ggaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggggggtcagcc +ccccttccggccggccgccctgtccgggaggtgaggggcgcctctgcctggccgccccta +ctgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtggggggg +acagccccccgcccggccagccgccctatccaggaggtgaggggcgcctctgcccggccg +cccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgggagggtagt +gggggggtcagccccccgcccggccagccgccccatccgggaggtgaggggcgcttctgc +ccggccgcccctactgggaagtgaggagcccctctgcccggccacgaccccgtctgggag +gtgtgcccagcggctcattggggatgggccatgatgacaatggcggttttgtggaataga +aaggcgggaagggtggggaaaaaattgagaaatcggatggttgccgggtctgtgtggatg +gaagtagacatg diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/msa.fa.fai new file mode 100644 index 00000000..3af87227 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_4032119_4033702 1932 27 60 61 +syndip_1_chr20:4032119-4033702 1932 2024 60 61 +syndip_2_chr20:4032119-4033702 1932 4021 60 61 +p:HG002_1_chr20:4032119-4033702 1932 6019 60 61 +p:HG002_2_chr20:4032119-4033702 1932 8017 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/output.vcf.gz new file mode 100644 index 00000000..81b16563 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/output.vcf.gz.tbi new file mode 100644 index 00000000..72dfddf4 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:4032219-4033602/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/base.vcf.gz new file mode 100644 index 00000000..85516774 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/base.vcf.gz.tbi new file mode 100644 index 00000000..7837c961 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/comp.vcf.gz new file mode 100644 index 00000000..459923c8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/comp.vcf.gz.tbi new file mode 100644 index 00000000..f52c3ba1 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/haps.fa new file mode 100644 index 00000000..465bb058 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/haps.fa @@ -0,0 +1,58 @@ +>ref_chr20_41196110_41196749 +AGAGTGTTGTTGAAATCCTCTATTTCCTGATTGATCTTCTGTCTGGTTTCTATATCCATTATCGGACATGGAATATTAAAGTCTCCAACTATTTTTGTCTTTCTCCCTTTAATTCTGTCATTTCTGTTTCATATGTTTTGGAGCTCTGTTAGGGGTATATATATATATAATATATATAAATAAATATATAAAAATAAATATATATTTATAATAAATATATTTTTATTTCATATATAAATATATATCTTATAAATATATATATTTATATAACATAAATATATATTTATATATATTATATATTATATATAATATATATTTATATAAATATATATATTATATATAATATATTTATATATAATATATATTTATATATTATAAATATATATTATATATTATAAATATATATTATATATTATATATTATATAAATATTATATATAATATATATTATATATAATATATATAAAAATATATATATTTATATATATAAATATTTTATCAATATAATATCCTTGTCTCTTGTAACCTTTCTTGATTTAACATTTATTTTGTGTGCCTTTTTCAAAAGAGGACACTGGAGGTGAAGAAGGAAGCTCTTGACTCTCCTAAAGCTGATCCCAAAGTGAAGGCTTTGAAGGCCA +>syndip_1_chr20:41196110-41196749 +AGAGTGTTGTTGAAATCCTCTATTTCCTGATTGATCTTCTGTCTGGTTTCTATATCCATT +ATCGGACATGGAATATTAAAGTCTCCAACTATTTTTGTCTTTCTCCCTTTAATTCTGTCA +TTTCTGTTTCATATGTTTTGGAGCTCTGTTAGGGGTATATATATATATAATATATATAAA +TAAATATATAAAAATAAATATATATTTATAATAAATATATTTTTATTTCATATATAAATA +TATATCTTATAAATATATATATTTATATAACATAAATATATATTTATATATATTATAAAT +ATATATTATATATAATATATATTTATATAAATATATATATTATATATAATATATTTATAT +ATAATATATATTTATATATTATAAATATATATTATATATAATATATATTTATATAAATAT +ATATTATATATAAATATATATTATATATAATATATATTTATATAAATATATATTATATAT +TATATAAATATTATATATAATATATATTTATATAAATATATATTATATATTATAAATATA +TATTATATATTATATATTATATAAATATTATATATAATATATATTATATATAATATATAT +AAAAATATATATATTTATATATATAAATATTTTATCAATATAATATCCTTGTCTCTTGTA +ACCTTTCTTGATTTAACATTTATTTTGTGTGCCTTTTTCAAAAGAGGACACTGGAGGTGA +AGAAGGAAGCTCTTGACTCTCCTAAAGCTGATCCCAAAGTGAAGGCTTTGAAGGCCA +>syndip_2_chr20:41196110-41196749 +AGAGTGTTGTTGAAATCCTCTATTTCCTGATTGATCTTCTGTCTGGTTTCTATATCCATT +ATCGGACATGGAATATTAAAGTCTCCAACTATTTTTGTCTTTCTCCCTTTAATTCTGTCA +TTTCTGTTTCATATGTTTTGGAGCTCTGTTAGGGGTATATATATATATAATATATATAAA +TAAATATATAAAAATAAATATATATTTATAATAAATATATTTTTATTTCATATATAAATA +TATATCTTATAAATATATATATTTATATAACATAAATATATATTTATATATATTATATAA +CATAAATATATATTTATATATATTATATATTATATATAATATATATTTATATAAATATAT +ATATTATATATAATATATTTATATATAATATATATTTATATATTATAAATATATATTATA +TATAATATATATTTATATAAATATATATTATATATTATAAATATATATTATATATTATAT +AAATATTATATATAATATATATTTATATAAATATATAATATATATTATAAATATATATTA +TATATTATATATTATATAAATATTATATATAATATATATTATATATAATATATATAAAAA +TATATATATTTATATATATAAATATTTTATCAATATAATATCCTTGTCTCTTGTAACCTT +TCTTGATTTAACATTTATTTTGTGTGCCTTTTTCAAAAGAGGACACTGGAGGTGAAGAAG +GAAGCTCTTGACTCTCCTAAAGCTGATCCCAAAGTGAAGGCTTTGAAGGCCA +>p:HG002_1_chr20:41196110-41196749 +AGAGTGTTGTTGAAATCCTCTATTTCCTGATTGATCTTCTGTCTGGTTTCTATATCCATT +ATCGGACATGGAATATTAAAGTCTCCAACTATTTTTGTCTTTCTCCCTTTAATTCTGTCA +TTTCTGTTTCATATGTTTTGGAGCTCTGTTAGGGGTATATATATATATAATATATATAAA +TAAATATATAAAAATAAATATATATTTATAATAAATATATTTTTATTTCATATATAAATA +TATATCTTATAAATATATATATTTATATAACATAAATATATATTTATATATATTATATAA +CATAAATATATATTTATATATATTATATATTATATATAATATATATTTATATAAATATAT +ATATTATATATAATATATTTATATATAATATATATTTATATATTATAAATATATATTATA +TATAATATATATTTATATAAATATATATTATATATTATAAATATATATTATATATTATAT +AAATATTATATATAATATATATTTATATAAATATATAATATATATTATAAATATATATTA +TATATTATATATTATATAAATATTATATATAATATATATTATATATAATATATATAAAAA +TATATATATTTATATATATAAATATTTTATCAATATAATATCCTTGTCTCTTGTAACCTT +TCTTGATTTAACATTTATTTTGTGTGCCTTTTTCAAAAGAGGACACTGGAGGTGAAGAAG +GAAGCTCTTGACTCTCCTAAAGCTGATCCCAAAGTGAAGGCTTTGAAGGCCA +>p:HG002_2_chr20:41196110-41196749 +AGAGTGTTGTTGAAATCCTCTATTTCCTGATTGATCTTCTGTCTGGTTTCTATATCCATT +ATCGGACATGGAATATTAAAGTCTCCAACTATTTTTGTCTTTCTCCCTTTAATTCTGTCA +TTTCTGTTTCATATGTTTTGGAGCTCTGTTAGGGGTATATATATATATAATATATATAAA +TAAATATATAAAAATAAATATATATTTATAATAAATATATTTTTATTTCATATATAAATA +TATATCTTATAAATATATATATTTATATAACATAAATATATATTTATATATATTATAAAT +ATATATTATATATAATATATATTTATATAAATATATATATTATATATAATATATTTATAT +ATAATATATATTTATATATTATAAATATATATTATATATAATATATATTTATATAAATAT +ATATTATATATAAATATATATTATATATAATATATATTTATATAAATATATATTATATAT +TATATAAATATTATATATAATATATATTTATATAAATATATATTATATATTATAAATATA +TATTATATATTATATATTATATAAATATTATATATAATATATATTATATATAATATATAT +AAAAATATATATATTTATATATATAAATATTTTATCAATATAATATCCTTGTCTCTTGTA +ACCTTTCTTGATTTAACATTTATTTTGTGTGCCTTTTTCAAAAGAGGACACTGGAGGTGA +AGAAGGAAGCTCTTGACTCTCCTAAAGCTGATCCCAAAGTGAAGGCTTTGAAGGCCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/haps.fa.ref.fa new file mode 100644 index 00000000..e75d2a9f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:41196110-41196749 +AGAGTGTTGTTGAAATCCTCTATTTCCTGATTGATCTTCTGTCTGGTTTCTATATCCATTATCGGACATGGAATATTAAAGTCTCCAACTATTTTTGTCTTTCTCCCTTTAATTCTGTCATTTCTGTTTCATATGTTTTGGAGCTCTGTTAGGGGTATATATATATATAATATATATAAATAAATATATAAAAATAAATATATATTTATAATAAATATATTTTTATTTCATATATAAATATATATCTTATAAATATATATATTTATATAACATAAATATATATTTATATATATTATATATTATATATAATATATATTTATATAAATATATATATTATATATAATATATTTATATATAATATATATTTATATATTATAAATATATATTATATATTATAAATATATATTATATATTATATATTATATAAATATTATATATAATATATATTATATATAATATATATAAAAATATATATATTTATATATATAAATATTTTATCAATATAATATCCTTGTCTCTTGTAACCTTTCTTGATTTAACATTTATTTTGTGTGCCTTTTTCAAAAGAGGACACTGGAGGTGAAGAAGGAAGCTCTTGACTCTCCTAAAGCTGATCCCAAAGTGAAGGCTTTGAAGGCCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/msa.fa new file mode 100644 index 00000000..116ad3ca --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/msa.fa @@ -0,0 +1,75 @@ +>ref_chr20_41196110_41196749 +agagtgttgttgaaatcctctatttcctgattgatcttctgtctggtttctatatccatt +atcggacatggaatattaaagtctccaactatttttgtctttctccctttaattctgtca +tttctgtttcatatgttttggagctctgttaggggtatatatatatataatatatataaa +taaatatataaaaataaatatatatttataataaatatatttttatttcatatataaata +tatatcttataaatatatatatttatataacataaatatatatttatatat--------- +---------------------attatatattatatataatatatatttatataaatatat +atattatatataatatatttatatataatatatatttatatattataaatatatat---- +------------------------------------------------------------ +------------------------------------------------------------ +-------tatatattataaatatatattatatattatatattatataaatattatatata +atatatattatatataatatatataaaaatatatatatttatatatataaatattttatc +aatataatatccttgtctcttgtaacctttcttgatttaacatttattttgtgtgccttt +ttcaaaagaggacactggaggtgaagaaggaagctcttgactctcctaaagctgatccca +aagtgaaggctttgaaggcca +>syndip_1_chr20:41196110-41196749 +agagtgttgttgaaatcctctatttcctgattgatcttctgtctggtttctatatccatt +atcggacatggaatattaaagtctccaactatttttgtctttctccctttaattctgtca +tttctgtttcatatgttttggagctctgttaggggtatatatatatataatatatataaa +taaatatataaaaataaatatatatttataataaatatatttttatttcatatataaata +tatatcttataaatatatatatttatataacataaatatatatttatatatattata--- +---------------------aatatatattatatataatatatatttatataaatatat +atattatatataatatatttatatataatatatatttatatattataaatatatattata +tataatatatatttatataaatatatattatatataaatatatattatatataatatata +tttatataaatatatattatatattatataaatattatatataatatatatttatataaa +tatatattatatattataaatatatattatatattatatattatataaatattatatata +atatatattatatataatatatataaaaatatatatatttatatatataaatattttatc +aatataatatccttgtctcttgtaacctttcttgatttaacatttattttgtgtgccttt +ttcaaaagaggacactggaggtgaagaaggaagctcttgactctcctaaagctgatccca +aagtgaaggctttgaaggcca +>syndip_2_chr20:41196110-41196749 +agagtgttgttgaaatcctctatttcctgattgatcttctgtctggtttctatatccatt +atcggacatggaatattaaagtctccaactatttttgtctttctccctttaattctgtca +tttctgtttcatatgttttggagctctgttaggggtatatatatatataatatatataaa +taaatatataaaaataaatatatatttataataaatatatttttatttcatatataaata +tatatcttataaatatatatatttatataacataaatatatatttatatatattatataa +cataaatatatatttatatatattatatattatatataatatatatttatataaatatat +atattatatataatatatttatatataatatatatttatatattataaatatatattata +tataatatatatttatataaatatatattatatat------------------------- +----tataaatatatattatatattatataaatattatatataatatatatttatataaa +tatataatatatattataaatatatattatatattatatattatataaatattatatata +atatatattatatataatatatataaaaatatatatatttatatatataaatattttatc +aatataatatccttgtctcttgtaacctttcttgatttaacatttattttgtgtgccttt +ttcaaaagaggacactggaggtgaagaaggaagctcttgactctcctaaagctgatccca +aagtgaaggctttgaaggcca +>p:HG002_1_chr20:41196110-41196749 +agagtgttgttgaaatcctctatttcctgattgatcttctgtctggtttctatatccatt +atcggacatggaatattaaagtctccaactatttttgtctttctccctttaattctgtca +tttctgtttcatatgttttggagctctgttaggggtatatatatatataatatatataaa +taaatatataaaaataaatatatatttataataaatatatttttatttcatatataaata +tatatcttataaatatatatatttatataacataaatatatatttatatatattatataa +cataaatatatatttatatatattatatattatatataatatatatttatataaatatat +atattatatataatatatttatatataatatatatttatatattataaatatatattata +tataatatatatttatataaatatatattatatat------------------------- +----tataaatatatattatatattatataaatattatatataatatatatttatataaa +tatataatatatattataaatatatattatatattatatattatataaatattatatata +atatatattatatataatatatataaaaatatatatatttatatatataaatattttatc +aatataatatccttgtctcttgtaacctttcttgatttaacatttattttgtgtgccttt +ttcaaaagaggacactggaggtgaagaaggaagctcttgactctcctaaagctgatccca +aagtgaaggctttgaaggcca +>p:HG002_2_chr20:41196110-41196749 +agagtgttgttgaaatcctctatttcctgattgatcttctgtctggtttctatatccatt +atcggacatggaatattaaagtctccaactatttttgtctttctccctttaattctgtca +tttctgtttcatatgttttggagctctgttaggggtatatatatatataatatatataaa +taaatatataaaaataaatatatatttataataaatatatttttatttcatatataaata +tatatcttataaatatatatatttatataacataaatatatatttatatatattata--- +---------------------aatatatattatatataatatatatttatataaatatat +atattatatataatatatttatatataatatatatttatatattataaatatatattata +tataatatatatttatataaatatatattatatataaatatatattatatataatatata +tttatataaatatatattatatattatataaatattatatataatatatatttatataaa +tatatattatatattataaatatatattatatattatatattatataaatattatatata +atatatattatatataatatatataaaaatatatatatttatatatataaatattttatc +aatataatatccttgtctcttgtaacctttcttgatttaacatttattttgtgtgccttt +ttcaaaagaggacactggaggtgaagaaggaagctcttgactctcctaaagctgatccca +aagtgaaggctttgaaggcca diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/msa.fa.fai new file mode 100644 index 00000000..2d712f88 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_41196110_41196749 801 29 60 61 +syndip_1_chr20:41196110-41196749 801 878 60 61 +syndip_2_chr20:41196110-41196749 801 1727 60 61 +p:HG002_1_chr20:41196110-41196749 801 2577 60 61 +p:HG002_2_chr20:41196110-41196749 801 3427 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/output.vcf.gz new file mode 100644 index 00000000..bc9698db Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/output.vcf.gz.tbi new file mode 100644 index 00000000..1aa6f389 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41196210-41196649/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/base.vcf.gz new file mode 100644 index 00000000..57b5dc2b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/base.vcf.gz.tbi new file mode 100644 index 00000000..bb297398 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/comp.vcf.gz new file mode 100644 index 00000000..9c8c01c3 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/comp.vcf.gz.tbi new file mode 100644 index 00000000..58a3624b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/haps.fa new file mode 100644 index 00000000..ef4a7718 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/haps.fa @@ -0,0 +1,58 @@ +>ref_chr20_41257474_41258304 +AGGGGATTTAACCCTAAGCTTTCTTTCATATTCTTAATCCAGTTTCTACTCAGGTCCAAATTCATTCTCTAACTCCACAATGACTCTTAAAAGTGAGATAGAAAATAAGATCTTGTCAGGATTTGTTTTCTTTTCTTTCTTTTTTTTTTTTTTTTTGAGACAGAGTCTCACTCTGTTGCCCAGGCTGCAGTGCAGTGGCGTGATCTCAGCTCACTGCAACCTCCGCCTGCCAGCTTCAAGCAATTCTCCTGCCTCAGCCTCCTTAGTAGCTGGGACTACAGGCACACGCCACCATGCCTGGCTAAGTTTTCGTATTTTTAGTAGAGACGGGGTTTCACCATGCTAGCCAGGCTGGTCTCGAACTCCTGACCTTGTGATCTGCCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGTGTTAGCCACCACGCCCAACCCTTTTTTTTTTTGAGACGGAGTTTTGCTCTTGTCAGCCAGGCTGGGGTACAGTGGCACAGCTCACTGCAACCTCCACCTCCCAGGTTCAAGTGATTCTCCTGTCTCAGCCACCTGAGTAGCTGGGTTTACAGGCACCCGCCACCATGCCCAGATAATTTTTGTATTTTTAGTAGAGATGAGGTTTCACCAAGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGAGTGAGCCACTGCACCTAGCCAAGATTTCTTTTAAAAAATCATTTTGAGCTAATTTTAGAGTTACAGAAAAGTTGCAAAAATCGTACAGAGTTTCCATATATCCTGGCCCCAGCTTCCCCAGTGTT +>syndip_1_chr20:41257474-41258304 +AGGGGATTTAACCCTAAGCTTTCTTTCATATTCTTAATCCAGTTTCTACTCAGGTCCAAA +TTCATTCTCTAACTCCACAATGACTCTTAAAAGTGAGATAGAAAATAAGATCTTGTCAGG +ATTTGTTTTCTTTTCTTTCTTTTTTTTTTTTTTTTTGAGACAGAGTCTCACTCTGTTGCC +CAGGCTGCAGTGCAGTGGCGTGATCTCAGCTCACTGCAACCTCCGCCTGCCAGCTTCAAG +CAATTCTCCTGCCTCAGCCTCCTTAGTAGCTGGGACTACAGGCACACGCCACCATGCCTG +GCTAAGTTTTCGTATTTTTAGTAGAGACGGGGTTTCACCATGCTAGCCAGGCTGGTCTCG +AACTCCTGACCTTGTGATCTGCCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGTGTT +AGCCACCACGCCCAACCCTTTTTTTTTTTGAGACGGAGTTTTGCTCTTGTCAGCCAGGCT +GGGGTACAGTGGCACAGCTCACTGCAACCTCCACCTCCCAGGTTCAAGTGATTCTCCTGT +CTCAGCCACCTGAGTAGCTGGGTTTACAGGCACCCGCCACCATGCCCAGATAATTTTTGT +ATTTTTAGTAGAGATGAGGTTTCACCAAGTTGGCCAGGCTGGTCTCAAACTCCTGACCTC +AGGTGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGAGTGAGCCACTGCAC +CTAGCCAAGATTTCTTTTAAAAAATCATTTTGAGCTAATTTTAGAGTTACAGAAAAGTTG +CAAAAATCGTACAGAGTTTCCATATATCCTGGCCCCAGCTTCCCCAGTGTT +>syndip_2_chr20:41257474-41258304 +AGGGGATTTAACCCTAAGCTTTCTTTCATATTCTTAATCCAGTTTCTACTCAGGTCCAAA +TTCATTCTCTAACTCCACAATGACTCTTAAAAGTGAGATAGAAAATAAGATCTTGTCAGG +ATTTGTTTTCTTTTCTTTCTTTTTTTTTTTTTTTTTGAGACAGAGTCTCACTCTGTTGCC +CAGGCTGCAGTGCAGTGGCGTGATCTCAGCTCACTGCAACCTCCGCCTGCCAGCTTCAAG +CAATTCTCCTGCCTCAGCCTCCTTAGTAGCTGGGACTACAGGCACACGCCACCATGCCTG +GCTAAGTTTTCGTATTTTTAGTAGAGACGGGGTTTCACCATGCTAGCCAGGCTGGTCTCG +AACTCCTGACCTTGTGATCTGCCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGTGTT +AGCCACCACGCCCAACCCTTTTTTTTTTTGAGACGGAGTTTTGCTCTTGTCAGCCAGGCT +GGGGTACAGTGGCACAGCTCACTGCAACCTCCACCTCCCAGGTTCAAGTGATTCTCCTGT +CTCAGCCACCTGAGTAGCTGGGTTTACAGGCACCCGCCACCATGCCCAGATAATTTTTGT +ATTTTTAGTAGAGATGAGGTTTCACCAAGTTGGCCAGGCTGGTCTCAAACTCCTGACCTC +AGGTGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGAGTGAGCCACTGCAC +CTAGCCAAGATTTCTTTTAAAAAATCATTTTGAGCTAATTTTAGAGTTACAGAAAAGTTG +CAAAAATCGTACAGAGTTTCCATATATCCTGGCCCCAGCTTCCCCAGTGTT +>p:HG002_1_chr20:41257474-41258304 +AGGGGATTTAACCCTAAGCTTTCTTTCATATTCTTAATCCAGTTTCTACTCAGGTCCAAA +TTCATTCTCTAACTCCACAATGACTCTTAAAAGTGAGATAGAAAATAAGATCTTGTCAGG +ATTTGTTTTCTTTTCTTTCTTTTTTTTTTTTTTTTTGAGACAGAGTCTCACTCTGTTGCC +CAGGCTGCAGTGCAGTGGCGTGATCTCAGCTCACTGCAACCTCCGCCTGCCAGCTTCAAG +CAATTCTCCTGCCTCAGCCTCCTTAGTAGCTGGGACTACAGGCACACGCCACCATGCCTG +GCTAAGTTTTCGTATTTTTAGTAGAGACGGGGTTTCACCATGCTAGCCAGGCTGGTCTCG +AACTCCTGACCTTGTGATCTGCCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGTGTT +AGCCACCACGCCCAACCCTTTTTTTTTTTGAGACGGAGTTTTGCTCTTGTCAGCCAGGCT +GGGGTACAGTGGCACAGCTCACTGCAACCTCCACCTCCCAGGTTCAAGTGATTCTCCTGT +CTCAGCCACCTGAGTAGCTGGGTTTACAGGCACCCGCCACCATGCCCAGATAATTTTTGT +ATTTTTAGTAGAGATGAGGTTTCACCAAGTTGGCCAGGCTGGTCTCAAACTCCTGACCTC +AGGTGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGAGTGAGCCACTGCAC +CTAGCCAAGATTTCTTTTAAAAAATCATTTTGAGCTAATTTTAGAGTTACAGAAAAGTTG +CAAAAATCGTACAGAGTTTCCATATATCCTGGCCCCAGCTTCCCCAGTGTT +>p:HG002_2_chr20:41257474-41258304 +AGGGGATTTAACCCTAAGCTTTCTTTCATATTCTTAATCCAGTTTCTACTCAGGTCCAAA +TTCATTCTCTAACTCCACAATGACTCTTAAAAGTGAGATAGAAAATAAGATCTTGTCAGG +ATTTGTTTTCTTTTCTTTCTTTTTTTTTTTTTTTTTGAGACAGAGTCTCACTCTGTTGCC +CAGGCTGCAGTGCAGTGGCGTGATCTCAGCTCACTGCAACCTCCGCCTGCCAGCTTCAAG +CAATTCTCCTGTCTCAGCCACCTGAGTAGCTGGGTTTACAGGCACCCGCCACCATGCCCA +GATAATTTTTGTATTTTTAGTAGAGATGAGGTTTCACCAAGTTGGCCAGGCTGGTCTCAA +ACTCCTGACCTCAGGTGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGAGT +GAGCCACTGCACCTAGCCAAGATTTCTTTTAAAAAATCATTTTGAGCTAATTTTAGAGTT +ACAGAAAAGTTGCAAAAATCGTACAGAGTTTCCATATATCCTGGCCCCAGCTTCCCCAGT +GTT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/haps.fa.ref.fa new file mode 100644 index 00000000..dacfd787 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:41257474-41258304 +AGGGGATTTAACCCTAAGCTTTCTTTCATATTCTTAATCCAGTTTCTACTCAGGTCCAAATTCATTCTCTAACTCCACAATGACTCTTAAAAGTGAGATAGAAAATAAGATCTTGTCAGGATTTGTTTTCTTTTCTTTCTTTTTTTTTTTTTTTTTGAGACAGAGTCTCACTCTGTTGCCCAGGCTGCAGTGCAGTGGCGTGATCTCAGCTCACTGCAACCTCCGCCTGCCAGCTTCAAGCAATTCTCCTGCCTCAGCCTCCTTAGTAGCTGGGACTACAGGCACACGCCACCATGCCTGGCTAAGTTTTCGTATTTTTAGTAGAGACGGGGTTTCACCATGCTAGCCAGGCTGGTCTCGAACTCCTGACCTTGTGATCTGCCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGTGTTAGCCACCACGCCCAACCCTTTTTTTTTTTGAGACGGAGTTTTGCTCTTGTCAGCCAGGCTGGGGTACAGTGGCACAGCTCACTGCAACCTCCACCTCCCAGGTTCAAGTGATTCTCCTGTCTCAGCCACCTGAGTAGCTGGGTTTACAGGCACCCGCCACCATGCCCAGATAATTTTTGTATTTTTAGTAGAGATGAGGTTTCACCAAGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGAGTGAGCCACTGCACCTAGCCAAGATTTCTTTTAAAAAATCATTTTGAGCTAATTTTAGAGTTACAGAAAAGTTGCAAAAATCGTACAGAGTTTCCATATATCCTGGCCCCAGCTTCCCCAGTGTT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/msa.fa new file mode 100644 index 00000000..915fefe7 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/msa.fa @@ -0,0 +1,75 @@ +>ref_chr20_41257474_41258304 +aggggatttaaccctaagctttctttcatattcttaatccagtttctactcaggtccaaa +ttcattctctaactccacaatgactcttaaaagtgagatagaaaataagatcttgtcagg +atttgttttcttttctttctttttttttttttttttgagacagagtctcactctgttgcc +caggctgcagtgcagtggcgtgatctcagctcactgcaacctccgcctgccagcttcaag +caattctcctgcctcagcctccttagtagctgggactacaggcacacgccaccatgcctg +gctaagttttcgtatttttagtagagacggggtttcaccatgctagccaggctggtctcg +aactcctgaccttgtgatctgcccaccttggcctcccaaagtgctgggattacaggtgtt +agccaccacgcccaaccctttttttttttgagacggagttttgctcttgtcagccaggct +ggggtacagtggcacagctcactgcaacctccacctcccaggttcaagtgattctcctgt +ctcagccacctgagtagctgggtttacaggcacccgccaccatgcccagataatttttgt +atttttagtagagatgaggtttcaccaagttggccaggctggtctcaaactcctgacctc +aggtgatccacccgcctcggcctcccaaagtgctgggattacaggagtgagccactgcac +ctagccaagatttcttttaaaaaatcattttgagctaattttagagttacagaaaagttg +caaaaatcgtacagagtttccatatatcctggccccagcttccccagtgtt +>syndip_1_chr20:41257474-41258304 +aggggatttaaccctaagctttctttcatattcttaatccagtttctactcaggtccaaa +ttcattctctaactccacaatgactcttaaaagtgagatagaaaataagatcttgtcagg +atttgttttcttttctttctttttttttttttttttgagacagagtctcactctgttgcc +caggctgcagtgcagtggcgtgatctcagctcactgcaacctccgcctgccagcttcaag +caattctcctgcctcagcctccttagtagctgggactacaggcacacgccaccatgcctg +gctaagttttcgtatttttagtagagacggggtttcaccatgctagccaggctggtctcg +aactcctgaccttgtgatctgcccaccttggcctcccaaagtgctgggattacaggtgtt +agccaccacgcccaaccctttttttttttgagacggagttttgctcttgtcagccaggct +ggggtacagtggcacagctcactgcaacctccacctcccaggttcaagtgattctcctgt +ctcagccacctgagtagctgggtttacaggcacccgccaccatgcccagataatttttgt +atttttagtagagatgaggtttcaccaagttggccaggctggtctcaaactcctgacctc +aggtgatccacccgcctcggcctcccaaagtgctgggattacaggagtgagccactgcac +ctagccaagatttcttttaaaaaatcattttgagctaattttagagttacagaaaagttg +caaaaatcgtacagagtttccatatatcctggccccagcttccccagtgtt +>syndip_2_chr20:41257474-41258304 +aggggatttaaccctaagctttctttcatattcttaatccagtttctactcaggtccaaa +ttcattctctaactccacaatgactcttaaaagtgagatagaaaataagatcttgtcagg +atttgttttcttttctttctttttttttttttttttgagacagagtctcactctgttgcc +caggctgcagtgcagtggcgtgatctcagctcactgcaacctccgcctgccagcttcaag +caattctcctgcctcagcctccttagtagctgggactacaggcacacgccaccatgcctg +gctaagttttcgtatttttagtagagacggggtttcaccatgctagccaggctggtctcg +aactcctgaccttgtgatctgcccaccttggcctcccaaagtgctgggattacaggtgtt +agccaccacgcccaaccctttttttttttgagacggagttttgctcttgtcagccaggct +ggggtacagtggcacagctcactgcaacctccacctcccaggttcaagtgattctcctgt +ctcagccacctgagtagctgggtttacaggcacccgccaccatgcccagataatttttgt +atttttagtagagatgaggtttcaccaagttggccaggctggtctcaaactcctgacctc +aggtgatccacccgcctcggcctcccaaagtgctgggattacaggagtgagccactgcac +ctagccaagatttcttttaaaaaatcattttgagctaattttagagttacagaaaagttg +caaaaatcgtacagagtttccatatatcctggccccagcttccccagtgtt +>p:HG002_1_chr20:41257474-41258304 +aggggatttaaccctaagctttctttcatattcttaatccagtttctactcaggtccaaa +ttcattctctaactccacaatgactcttaaaagtgagatagaaaataagatcttgtcagg +atttgttttcttttctttctttttttttttttttttgagacagagtctcactctgttgcc +caggctgcagtgcagtggcgtgatctcagctcactgcaacctccgcctgccagcttcaag +caattctcctgcctcagcctccttagtagctgggactacaggcacacgccaccatgcctg +gctaagttttcgtatttttagtagagacggggtttcaccatgctagccaggctggtctcg +aactcctgaccttgtgatctgcccaccttggcctcccaaagtgctgggattacaggtgtt +agccaccacgcccaaccctttttttttttgagacggagttttgctcttgtcagccaggct +ggggtacagtggcacagctcactgcaacctccacctcccaggttcaagtgattctcctgt +ctcagccacctgagtagctgggtttacaggcacccgccaccatgcccagataatttttgt +atttttagtagagatgaggtttcaccaagttggccaggctggtctcaaactcctgacctc +aggtgatccacccgcctcggcctcccaaagtgctgggattacaggagtgagccactgcac +ctagccaagatttcttttaaaaaatcattttgagctaattttagagttacagaaaagttg +caaaaatcgtacagagtttccatatatcctggccccagcttccccagtgtt +>p:HG002_2_chr20:41257474-41258304 +aggggatttaaccctaagctttctttcatattcttaatccagtttctactcaggtccaaa +ttcattctctaactccacaatgactcttaaaagtgagatagaaaataagatcttgtcagg +atttgttttcttttctttctttttttttttttttttgagacagagtctcactctgttgcc +caggctgcagtgcagtggcgtgatctcagctcactgcaacctccgcctgccagcttcaag +ca---------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------------------attctcctgt +ctcagccacctgagtagctgggtttacaggcacccgccaccatgcccagataatttttgt +atttttagtagagatgaggtttcaccaagttggccaggctggtctcaaactcctgacctc +aggtgatccacccgcctcggcctcccaaagtgctgggattacaggagtgagccactgcac +ctagccaagatttcttttaaaaaatcattttgagctaattttagagttacagaaaagttg +caaaaatcgtacagagtttccatatatcctggccccagcttccccagtgtt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/msa.fa.fai new file mode 100644 index 00000000..a72a3a52 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_41257474_41258304 831 29 60 61 +syndip_1_chr20:41257474-41258304 831 908 60 61 +syndip_2_chr20:41257474-41258304 831 1787 60 61 +p:HG002_1_chr20:41257474-41258304 831 2667 60 61 +p:HG002_2_chr20:41257474-41258304 831 3547 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/output.vcf.gz new file mode 100644 index 00000000..bd57ec69 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/output.vcf.gz.tbi new file mode 100644 index 00000000..6297178a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:41257574-41258204/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/base.vcf.gz new file mode 100644 index 00000000..fd0d721e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/base.vcf.gz.tbi new file mode 100644 index 00000000..0c8c031b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/comp.vcf.gz new file mode 100644 index 00000000..2f3909ee Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/comp.vcf.gz.tbi new file mode 100644 index 00000000..b3f0fa74 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/haps.fa new file mode 100644 index 00000000..f1d4eec9 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/haps.fa @@ -0,0 +1,58 @@ +>ref_chr20_44763796_44764386 +GACTCCATTCTCTTTTCCAGATGGATCACTCGTCTCAACAGCATCAGAAATTAAAAGGTTGCACAGCCCTTGTGGTGATTATAGGTTATGTGATTCTCAAAGGTTTAGGAGTTTACGGGTTCCCTGTCCATCCATTCACTACATGCTCACCTATCCATCCATCCATCCATTTATCCATCCATCCATCCACCTATCACTTCATCCATCCATCCATTTATCCATCCATCCATTTATCCATCCATCCATCCATTTATCCATCCATCCATCCATTTATCCATCCATCCATCCATCCATCCACCCATCCATCCGTCCATCCATTTATCCATCCATCCATCCATCCATTTATGCATCCATTTATCCATCCATCCATCCATCCATCCATCCATCCATCCATTTATCCATCCATCCATCCATCCACCCATCCATCCATCCGTCCATCCATTCATCCATCCATCCATCCTCCCACAAACTCACCAAGCCTACAATGCAATCAATTCTGCTGTAACATGAAATATACATTTCTAAAAATTACTGTGCAACGCAAAATCTTGCTATAAAAATCACACAGCTTATGGGAAAATGGGGTCAGTG +>syndip_1_chr20:44763796-44764386 +GACTCCATTCTCTTTTCCAGATGGATCACTCGTCTCAACAGCATCAGAAATTAAAAGGTT +GCACAGCCCTTGTGGTGATTATAGGTTATGTGATTCTCAAAGGTTTAGGAGTTTACGGGT +TCCCTGTCCATCCATTCACTACATGCTCACCTATCCATCCATCCATCCATTTATCCATCC +ATCCATCCACCTATCACTTCATCCATCCATCCATTTATCCATCCATCCATTTATCCATCC +ATCCATCCATTTATCCATCCATCCATCCATTTATCCATCCATCCATCCATCCATCCACCC +ATCCATCCGTCCATCCATTTATCCATCCATCCATCCATCCATTTATCCATCCATTTATCC +ATCCATCCATCCATCCATCCATCCATCCATCCATTTATCCATCCATCCATCCATCCACCC +ATCCATCCATCCGTCCATCCATTTATCCATCCATCCATCCATCCATCCATCCATCCATCC +ATTTATCCATCCGTCCATTTATCCATCCATCCATCCACCCACCCATCCATCCATCCATCC +ACTTATCCATCCACCCATCCATCCATCCGTCCATCCATTCATCCATCCATCCATCCTCCC +ACAAACTCACCAAGCCTACAATACAATCAATTCTGCTGTAACATGAAATATACATTTCTA +AAAATTACTGTGCAACGCAAAATCTTGCTATAAAAATCACACAGCTTATGGGAAAATGGG +GTCAGTG +>syndip_2_chr20:44763796-44764386 +GACTCCATTCTCTTTTCCAGATGGATCACTCGTCTCAACAGCATCAGAAATTAAAAGGTT +GCACAGCCCTTGTGGTGATTATAGGTTATGTGATTCTCAAAGGTTTAGGAGTTTACGGGT +TCCCTGTCCATCCATTCACTACATGCTCACCTATCCATCCATCCATCCATTTATCCATCC +ATCCATCCACCTATCACTTCATCCATCCATCCATTTATCCATCCATCCATTTATCCATCC +ATCCATCCATTTATCCATCCATCCATCCATTTATCCATCCATCCATCCATCCATCCACCC +ATCCATCCGTCCATCCATTTATCCATCCATCCATCCATCCATTTATCCATCCATTTATCC +ATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATTTATCCATCCATCCATCC +ATCCACCCATCCATCCATCCGTCCATCCATTTATCCATCCATCCATCCATCCATCCATCC +ATCCATTTATCCATCCGTCCATTTATCCATCCATCCATCCACCCACCCATCCATCCATCC +ATCCATTTATCCATCCACCCATCCATCCATCCGTCCATCCATTCATCCATCCATCCATCC +TCCCACAAACTCACCAAGCCTACAATACAATCAATTCTGCTGTAACATGAAATATACATT +TCTAAAAATTACTGTGCAACGCAAAATCTTGCTATAAAAATCACACAGCTTATGGGAAAA +TGGGGTCAGTG +>p:HG002_1_chr20:44763796-44764386 +GACTCCATTCTCTTTTCCAGATGGATCACTCGTCTCAACAGCATCAGAAATTAAAAGGTT +GCACAGCCCTTGTGGTGATTATAGGTTATGTGATTCTCAAAGGTTTAGGAGTTTACGGGT +TCCCTGTCCATCCATTCACTACATGCTCACCTATCCATCCATCCATCCATTTATCCATCC +ATCCATCCACCTATCACTTCATCCATCCATCCATTTATCCATCCATCCATTTATCCATCC +ATCCATCCATTTATCCATCCATCCATCCATTTATCCATCCATCCATCCATCCATCCACCC +ATCCATCCGTCCATCCATTTATCCATCCATCCATCCATCCATTTATCCATCCATTTATCC +ATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATTTATCCATCCATCCATCC +ATCCACCCATCCATCCATCCGTCCATCCATTTATCCATCCATCCATCCATCCATCCATCC +ATCCATTTATCCATCCGTCCATTTATCCATCCATCCATCCACCCACCCATCCATCCATCC +ATCCATTTATCCATCCACCCATCCATCCATCCGTCCATCCATTCATCCATCCATCCATCC +TCCCACAAACTCACCAAGCCTACAATACAATCAATTCTGCTGTAACATGAAATATACATT +TCTAAAAATTACTGTGCAACGCAAAATCTTGCTATAAAAATCACACAGCTTATGGGAAAA +TGGGGTCAGTG +>p:HG002_2_chr20:44763796-44764386 +GACTCCATTCTCTTTTCCAGATGGATCACTCGTCTCAACAGCATCAGAAATTAAAAGGTT +GCACAGCCCTTGTGGTGATTATAGGTTATGTGATTCTCAAAGGTTTAGGAGTTTACGGGT +TCCCTGTCCATCCATTCACTACATGCTCACCTATCCATCCATCCATCCATTTATCCATCC +ATCCATCCACCTATCACTTCATCCATCCATCCATTTATCCATCCATCCATTTATCCATCC +ATCCATCCATTTATCCATCCATCCATCCATTTATCCATCCATCCATCCATCCATCCACCC +ATCCATCCGTCCATCCATTTATCCATCCATCCATCCATCCATTTATCCATCCATTTATCC +ATCCATCCATCCATCCATCCATCCATCCATCCATTTATCCATCCATCCATCCATCCACCC +ATCCATCCATCCGTCCATCCATTTATCCATCCATCCATCCATCCATCCATCCATCCATCC +ATTTATCCATCCGTCCATTTATCCATCCATCCATCCACCCACCCATCCATCCATCCATCC +ACTTATCCATCCACCCATCCATCCATCCGTCCATCCATTCATCCATCCATCCATCCTCCC +ACAAACTCACCAAGCCTACAATACAATCAATTCTGCTGTAACATGAAATATACATTTCTA +AAAATTACTGTGCAACGCAAAATCTTGCTATAAAAATCACACAGCTTATGGGAAAATGGG +GTCAGTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/haps.fa.ref.fa new file mode 100644 index 00000000..bb372205 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:44763796-44764386 +GACTCCATTCTCTTTTCCAGATGGATCACTCGTCTCAACAGCATCAGAAATTAAAAGGTTGCACAGCCCTTGTGGTGATTATAGGTTATGTGATTCTCAAAGGTTTAGGAGTTTACGGGTTCCCTGTCCATCCATTCACTACATGCTCACCTATCCATCCATCCATCCATTTATCCATCCATCCATCCACCTATCACTTCATCCATCCATCCATTTATCCATCCATCCATTTATCCATCCATCCATCCATTTATCCATCCATCCATCCATTTATCCATCCATCCATCCATCCATCCACCCATCCATCCGTCCATCCATTTATCCATCCATCCATCCATCCATTTATGCATCCATTTATCCATCCATCCATCCATCCATCCATCCATCCATCCATTTATCCATCCATCCATCCATCCACCCATCCATCCATCCGTCCATCCATTCATCCATCCATCCATCCTCCCACAAACTCACCAAGCCTACAATGCAATCAATTCTGCTGTAACATGAAATATACATTTCTAAAAATTACTGTGCAACGCAAAATCTTGCTATAAAAATCACACAGCTTATGGGAAAATGGGGTCAGTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/msa.fa new file mode 100644 index 00000000..aad2c957 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/msa.fa @@ -0,0 +1,70 @@ +>ref_chr20_44763796_44764386 +gactccattctcttttccagatggatcactcgtctcaacagcatcagaaattaaaaggtt +gcacagcccttgtggtgattataggttatgtgattctcaaaggtttaggagtttacgggt +tccctgtccatccattcactacatgctcacctatccatccatccatccatttatccatcc +atccatccacctatcacttcatccatccatccatttatccatccatccatttatccatcc +atccatccatttatccatccatccatccatttatccatccatccatccatccatccaccc +atccatccgtccatccatttatccatccatccatccatccatttatgcatccatttatcc +atccatccatccatccatccatccatccatccatttatcc-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +atccatccatccatccacccatccatccatccgtccatccattcatccatccatccatcc +tcccacaaactcaccaagcctacaatgcaatcaattctgctgtaacatgaaatatacatt +tctaaaaattactgtgcaacgcaaaatcttgctataaaaatcacacagcttatgggaaaa +tggggtcagtg +>syndip_1_chr20:44763796-44764386 +gactccattctcttttccagatggatcactcgtctcaacagcatcagaaattaaaaggtt +gcacagcccttgtggtgattataggttatgtgattctcaaaggtttaggagtttacgggt +tccctgtccatccattcactacatgctcacctatccatccatccatccatttatccatcc +atccatccacctatcacttcatccatccatccatttatccatccatccatttatccatcc +atccatccatttatccatccatccatccatttatccatccatccatccatccatccaccc +atccatccgtccatccatttatccatccatccatccatccatttatccatccatttatcc +atccatccatccatccatccatccatccatccatttatcc----atccatccatccatcc +acccatccatccatccgtccatccatttatccatccatccatccatccatccatccatcc +atccatttatccatccgtccatttatccatccatccatccacccacccatccatccatcc +atccacttatccatccacccatccatccatccgtccatccattcatccatccatccatcc +tcccacaaactcaccaagcctacaatacaatcaattctgctgtaacatgaaatatacatt +tctaaaaattactgtgcaacgcaaaatcttgctataaaaatcacacagcttatgggaaaa +tggggtcagtg +>syndip_2_chr20:44763796-44764386 +gactccattctcttttccagatggatcactcgtctcaacagcatcagaaattaaaaggtt +gcacagcccttgtggtgattataggttatgtgattctcaaaggtttaggagtttacgggt +tccctgtccatccattcactacatgctcacctatccatccatccatccatttatccatcc +atccatccacctatcacttcatccatccatccatttatccatccatccatttatccatcc +atccatccatttatccatccatccatccatttatccatccatccatccatccatccaccc +atccatccgtccatccatttatccatccatccatccatccatttatccatccatttatcc +atccatccatccatccatccatccatccatccatccatccatttatccatccatccatcc +atccacccatccatccatccgtccatccatttatccatccatccatccatccatccatcc +atccatttatccatccgtccatttatccatccatccatccacccacccatccatccatcc +atccatttatccatccacccatccatccatccgtccatccattcatccatccatccatcc +tcccacaaactcaccaagcctacaatacaatcaattctgctgtaacatgaaatatacatt +tctaaaaattactgtgcaacgcaaaatcttgctataaaaatcacacagcttatgggaaaa +tggggtcagtg +>p:HG002_1_chr20:44763796-44764386 +gactccattctcttttccagatggatcactcgtctcaacagcatcagaaattaaaaggtt +gcacagcccttgtggtgattataggttatgtgattctcaaaggtttaggagtttacgggt +tccctgtccatccattcactacatgctcacctatccatccatccatccatttatccatcc +atccatccacctatcacttcatccatccatccatttatccatccatccatttatccatcc +atccatccatttatccatccatccatccatttatccatccatccatccatccatccaccc +atccatccgtccatccatttatccatccatccatccatccatttatccatccatttatcc +atccatccatccatccatccatccatccatccatccatccatttatccatccatccatcc +atccacccatccatccatccgtccatccatttatccatccatccatccatccatccatcc +atccatttatccatccgtccatttatccatccatccatccacccacccatccatccatcc +atccatttatccatccacccatccatccatccgtccatccattcatccatccatccatcc +tcccacaaactcaccaagcctacaatacaatcaattctgctgtaacatgaaatatacatt +tctaaaaattactgtgcaacgcaaaatcttgctataaaaatcacacagcttatgggaaaa +tggggtcagtg +>p:HG002_2_chr20:44763796-44764386 +gactccattctcttttccagatggatcactcgtctcaacagcatcagaaattaaaaggtt +gcacagcccttgtggtgattataggttatgtgattctcaaaggtttaggagtttacgggt +tccctgtccatccattcactacatgctcacctatccatccatccatccatttatccatcc +atccatccacctatcacttcatccatccatccatttatccatccatccatttatccatcc +atccatccatttatccatccatccatccatttatccatccatccatccatccatccaccc +atccatccgtccatccatttatccatccatccatccatccatttatccatccatttatcc +atccatccatccatccatccatccatccatccatttatcc----atccatccatccatcc +acccatccatccatccgtccatccatttatccatccatccatccatccatccatccatcc +atccatttatccatccgtccatttatccatccatccatccacccacccatccatccatcc +atccacttatccatccacccatccatccatccgtccatccattcatccatccatccatcc +tcccacaaactcaccaagcctacaatacaatcaattctgctgtaacatgaaatatacatt +tctaaaaattactgtgcaacgcaaaatcttgctataaaaatcacacagcttatgggaaaa +tggggtcagtg diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/msa.fa.fai new file mode 100644 index 00000000..0cd24afe --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_44763796_44764386 731 29 60 61 +syndip_1_chr20:44763796-44764386 731 807 60 61 +syndip_2_chr20:44763796-44764386 731 1585 60 61 +p:HG002_1_chr20:44763796-44764386 731 2364 60 61 +p:HG002_2_chr20:44763796-44764386 731 3143 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/output.vcf.gz new file mode 100644 index 00000000..faeea307 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/output.vcf.gz.tbi new file mode 100644 index 00000000..a8492e6a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:44763896-44764286/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/base.vcf.gz new file mode 100644 index 00000000..27a0fe0a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/base.vcf.gz.tbi new file mode 100644 index 00000000..76479a45 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/comp.vcf.gz new file mode 100644 index 00000000..3a04968a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/comp.vcf.gz.tbi new file mode 100644 index 00000000..839d5ef0 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/haps.fa new file mode 100644 index 00000000..d9002f1f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/haps.fa @@ -0,0 +1,44 @@ +>ref_chr20_45600469_45600847 +AATATTGGGAATTTTACTGATGGTAAAATTAAAATAGGAGGAGGAGGTTACATCACTATCATATGGTAACATTCCCTTAAAAATCATCTCTTTATCTTTCCTAAATATTCCACTGTCTTTGACTGCTATACCTCTCTCTCTTTTCTTTCACCAAGCCTCTCTCTTTGCTTTCCTTCTGGTAAAAGCAGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATCCCCCCCTCTCCCTCTCTCTCTACCCCTGAATCTGGCCTTTCTAAACACCCTCAACTTGTGTACCTGTATACTATACTGAGCTACACTAAAGTTTCTATATTTAGCCAAATCCAGCCCATCATACCAGCTCTTCCCCTGGTATATTCCTAGGAGTGGA +>syndip_1_chr20:45600469-45600847 +AATATTGGGAATTTTACTGATGGTAAAATTAAAATAGGAGGAGGAGGTTACATCACTATC +ATATGGTAACATTCCCTTAAAAATCATCTCTTTATCTTTCCTAAATATTCCACTGTCTTT +GACTGCTATACCTCTCTCTCTTTTCTTTCACCAAGCCTCTCTCTTTGCTTTCCTTCTGGT +AAAAGCAGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATCCCCCCCTCCC +TCCCTCCTTCCCTCCCTCCCTCTCTCTCTCTCTCTCCCTTTCTCTGTCTCTCCCTCTCTC +TCTCTCTCTCTCCCTCTCTCTCTCTTTCTCCCTCTCTCTCCCTCTCTCTCTCTCTCTCTC +CCTCTCTCTCTCTTTCTCCCTCTCTCTCCCTCTCTCCCCCTCTCTCTCCCTCTCTCCCTC +TCTCCCTCTCTCTCCCTCTCTCTCTACCCCTGAATCTGGCCTTTCTAAACACCCTCAACT +TGTGTACCTGTATACTATACTGAGCTACACTAAAGTTTCTATATTTAGCCAAATCCAGCC +CATCATACCAGCTCTTCCCCTGGTATATTCCTAGGAGTGGA +>syndip_2_chr20:45600469-45600847 +AATATTGGGAATTTTACTGATGGTAAAATTAAAATAGGAGGAGGAGGTTACATCACTATC +ATATGGTAACATTCCCTTAAAAATCATCTCTTTATCTTTCCTAAATATTCCACTGTCTTT +GACTGCTATACCTCTCTCTCTTTTCTTTCACCAAGCCTCTCTCTTTGCTTTCCTTCTGGT +AAAAGCAGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATCCCCCCCTCCCTC +CCTCCTTCCCTCCCTCCCTCTCTCTCTCTCTCTCCCTTTCTCTGTCTCTCCCTCTCTCTC +TCTCTCTCTCCCTCTCTCTCCCTCTCTCCCCCTCTCTCTCCCTCTCTCCCTCTCTCCCTC +TCTCTCTACCCCTGAATCTGGCCTTTCTAAACACCCTCAACTTGTGTACCTGTATACTAT +ACTGAGCTACACTAAAGTTTCTATATTTAGCCAAATCCAGCCCATCATACCAGCTCTTCC +CCTGGTATATTCCTAGGAGTGGA +>p:HG002_1_chr20:45600469-45600847 +AATATTGGGAATTTTACTGATGGTAAAATTAAAATAGGAGGAGGAGGTTACATCACTATC +ATATGGTAACATTCCCTTAAAAATCATCTCTTTATCTTTCCTAAATATTCCACTGTCTTT +GACTGCTATACCTCTCTCTCTTTTCTTTCACCAAGCCTCTCTCTTTGCTTTCCTTCTGGT +AAAAGCAGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATCCCCCCCTCCCTC +CCTCCTTCCCTCCCTCCCTCTCTCTCTCTCTCTCCCTTTCTCTGTCTCTCCCTCTCTCTC +TCTCTCTCTCCCTCTCTCTCCCTCTCTCCCCCTCTCTCTCCCTCTCTCCCTCTCTCCCTC +TCTCTCTACCCCTGAATCTGGCCTTTCTAAACACCCTCAACTTGTGTACCTGTATACTAT +ACTGAGCTACACTAAAGTTTCTATATTTAGCCAAATCCAGCCCATCATACCAGCTCTTCC +CCTGGTATATTCCTAGGAGTGGA +>p:HG002_2_chr20:45600469-45600847 +AATATTGGGAATTTTACTGATGGTAAAATTAAAATAGGAGGAGGAGGTTACATCACTATC +ATATGGTAACATTCCCTTAAAAATCATCTCTTTATCTTTCCTAAATATTCCACTGTCTTT +GACTGCTATACCTCTCTCTCTTTTCTTTCACCAAGCCTCTCTCTTTGCTTTCCTTCTGGT +AAAAGCAGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATCCCCCCCTCCC +TCCCTCCTTCCCTCCCTCCCTCTCTCTCTCTCTCTCCCTTTCTCTGTCTCTCCCTCTCTC +TCTCTCTCTCTCCCTCTCTCTCTCTTTCTCCCTCTCTCTCCCTCTCTCTCTCTCTCTCTC +CCTCTCTCTCTCTTTCTCCCTCTCTCTCCCTCTCTCCCCCTCTCTCTCCCTCTCTCCCTC +TCTCCCTCTCTCTCCCTCTCTCTCTACCCCTGAATCTGGCCTTTCTAAACACCCTCAACT +TGTGTACCTGTATACTATACTGAGCTACACTAAAGTTTCTATATTTAGCCAAATCCAGCC +CATCATACCAGCTCTTCCCCTGGTATATTCCTAGGAGTGGA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/haps.fa.ref.fa new file mode 100644 index 00000000..ae82eca8 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:45600469-45600847 +AATATTGGGAATTTTACTGATGGTAAAATTAAAATAGGAGGAGGAGGTTACATCACTATCATATGGTAACATTCCCTTAAAAATCATCTCTTTATCTTTCCTAAATATTCCACTGTCTTTGACTGCTATACCTCTCTCTCTTTTCTTTCACCAAGCCTCTCTCTTTGCTTTCCTTCTGGTAAAAGCAGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATCCCCCCCTCTCCCTCTCTCTCTACCCCTGAATCTGGCCTTTCTAAACACCCTCAACTTGTGTACCTGTATACTATACTGAGCTACACTAAAGTTTCTATATTTAGCCAAATCCAGCCCATCATACCAGCTCTTCCCCTGGTATATTCCTAGGAGTGGA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/msa.fa new file mode 100644 index 00000000..f8425911 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/msa.fa @@ -0,0 +1,55 @@ +>ref_chr20_45600469_45600847 +aatattgggaattttactgatggtaaaattaaaataggaggaggaggttacatcactatc +atatggtaacattcccttaaaaatcatctctttatctttcctaaatattccactgtcttt +gactgctatacctctctctcttttctttcaccaagcctctctctttgctttccttctggt +aaaagcagtctctctctctctctctctctctctct------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------------------------ctc +tatccccccctctccctctctctctacccctgaatctggcctttctaaacaccctcaact +tgtgtacctgtatactatactgagctacactaaagtttctatatttagccaaatccagcc +catcataccagctcttcccctggtatattcctaggagtgga +>syndip_1_chr20:45600469-45600847 +aatattgggaattttactgatggtaaaattaaaataggaggaggaggttacatcactatc +atatggtaacattcccttaaaaatcatctctttatctttcctaaatattccactgtcttt +gactgctatacctctctctcttttctttcaccaagcctctctctttgctttccttctggt +aaaagcagtctctctctctctctctctctctctctctctctctctctatccccccctccc +tccctccttccctccctccctctctctctctctctccctttctctgtctctccctctctc +tctctctctctccctctctctctctttctccctctctctccctctctctctctctctctc +cctctctctctctttctccctctctctccctctctccccctctctctccctctctccctc +tctccctctctctccctctctctctacccctgaatctggcctttctaaacaccctcaact +tgtgtacctgtatactatactgagctacactaaagtttctatatttagccaaatccagcc +catcataccagctcttcccctggtatattcctaggagtgga +>syndip_2_chr20:45600469-45600847 +aatattgggaattttactgatggtaaaattaaaataggaggaggaggttacatcactatc +atatggtaacattcccttaaaaatcatctctttatctttcctaaatattccactgtcttt +gactgctatacctctctctcttttctttcaccaagcctctctctttgctttccttctggt +aaaagcagtctctctctctctctctctctctctct--ctctctctctatccccccctccc +tccctccttccctccctccctctctctctctctctccctttctctgtctctccctctctc +tctctctctctccctctctct--------------------------------------- +-------------------------------------ccctctctccccctctctctccc +tctctccctctctccctctctctctacccctgaatctggcctttctaaacaccctcaact +tgtgtacctgtatactatactgagctacactaaagtttctatatttagccaaatccagcc +catcataccagctcttcccctggtatattcctaggagtgga +>p:HG002_1_chr20:45600469-45600847 +aatattgggaattttactgatggtaaaattaaaataggaggaggaggttacatcactatc +atatggtaacattcccttaaaaatcatctctttatctttcctaaatattccactgtcttt +gactgctatacctctctctcttttctttcaccaagcctctctctttgctttccttctggt +aaaagcagtctctctctctctctctctctctctct--ctctctctctatccccccctccc +tccctccttccctccctccctctctctctctctctccctttctctgtctctccctctctc +tctctctctctccctctctct--------------------------------------- +-------------------------------------ccctctctccccctctctctccc +tctctccctctctccctctctctctacccctgaatctggcctttctaaacaccctcaact +tgtgtacctgtatactatactgagctacactaaagtttctatatttagccaaatccagcc +catcataccagctcttcccctggtatattcctaggagtgga +>p:HG002_2_chr20:45600469-45600847 +aatattgggaattttactgatggtaaaattaaaataggaggaggaggttacatcactatc +atatggtaacattcccttaaaaatcatctctttatctttcctaaatattccactgtcttt +gactgctatacctctctctcttttctttcaccaagcctctctctttgctttccttctggt +aaaagcagtctctctctctctctctctctctctctctctctctctctatccccccctccc +tccctccttccctccctccctctctctctctctctccctttctctgtctctccctctctc +tctctctctctccctctctctctctttctccctctctctccctctctctctctctctctc +cctctctctctctttctccctctctctccctctctccccctctctctccctctctccctc +tctccctctctctccctctctctctacccctgaatctggcctttctaaacaccctcaact +tgtgtacctgtatactatactgagctacactaaagtttctatatttagccaaatccagcc +catcataccagctcttcccctggtatattcctaggagtgga diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/msa.fa.fai new file mode 100644 index 00000000..f49d0b16 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_45600469_45600847 581 29 60 61 +syndip_1_chr20:45600469-45600847 581 654 60 61 +syndip_2_chr20:45600469-45600847 581 1279 60 61 +p:HG002_1_chr20:45600469-45600847 581 1905 60 61 +p:HG002_2_chr20:45600469-45600847 581 2531 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/output.vcf.gz new file mode 100644 index 00000000..ab827dd3 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/output.vcf.gz.tbi new file mode 100644 index 00000000..ecd78c68 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:45600569-45600747/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/base.vcf.gz new file mode 100644 index 00000000..b04846ae Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/base.vcf.gz.tbi new file mode 100644 index 00000000..ba53ed30 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/comp.vcf.gz new file mode 100644 index 00000000..254c641d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/comp.vcf.gz.tbi new file mode 100644 index 00000000..df065660 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/haps.fa new file mode 100644 index 00000000..42ff1e4e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/haps.fa @@ -0,0 +1,104 @@ +>ref_chr20_48449605_48450562 +CATGAGAATATGCTCAGTGATAAGGCAGTGGCGTTAAATCTGCAGGCAGTGGGCTATCTGTGGGTCCTTAAATCTATTTAGTGCATCTTGAACAGTATTTTTAAGCTGGGATAAGTGGAATAGGAAGGAGTGGAGTGGAGCATGATGGTATGGGATGGGATGGATGGGATGGGATGGATGGATGGATGGGGTGGGATGGGATGGGATGGGATGGGATGGATGGATGGGATGGATGGATGGGATGGGATAGGATGGATGGGGTGAGATGGGATGGAATGGATGGGATGGGATGGATGGATGGGATGGGATGGATGGGATGGGATGGATGGGATGGGATGGATGGGATGGATGGGATGGAATGGGATGGATGGGATGGGATGGGATTGGATGGGGTGGGATGGGATGGATGGATGGGATGGATGGATGGGATGGAATGGATGGATGGGATGGGATGGATGGGATGGGATGGATGGATGGGATGGGATGGATGCAATGGATGGATGGGATGGGATGGGATGGGATGGATGGAATGGATGGATGGGATGGGATGGGATGGATGGGGTGGGATGAGATGGATGGGATGGATGGGATGGGATGGATGGATGGATGGGATGGGATGGATGGATGGGATGGGATGGGATGGGGTGGATGGGATGGATGGATGGATGGGATGGGATGGATGGATGGGATGGGATGGATGGGATGGGATGGGGTGGGGTGGGGTGGGATGGGATGGGATGGGGTGGGGTGGGATGGGATTGGATGGGGTGGGATGCGATGGGATGAGATGAGATGGATGGCATGGGATGGGTGGGAGGGGATGGGATATTATCAGATGGCAAAAGTAAGAAGTGTTCATATTTTGTCTTCAAAATATAAATATGAGTGCATAATGGCTTGTGATGCAAAATACATTTCTTACTAAAGATCATGGACAAAGCACTTAAAACCACACAGT +>syndip_1_chr20:48449605-48450562 +CATGAGAATATGCTCAGTGATAAGGCAGTGGCGTTAAATCTGCAGGCAGTGGGCTATCTG +TGGGTCCTTAAATCTATTTAGTGCATCTTGAACAGTATTTTTAAGCTGGGATAAGTGGAA +TAGGAAGGAGTGGAGTGGAGCATGATGGTATGGGATGGGATGGATGGGATGGGATGGATG +GATGGATGGGGTGGGATGGGATGGGATGGGATGGATGGATGGGATGGATGGATGGGATGG +GATAGGATGGATGGGGTGAGATGGGATGGAATGGATGGGATGGGATGGATGGATGGGATG +GGATGGATGGGATGGGATGGATGGGATGGGATGGATGGGATGGATGGGATGGAATGGGAT +GGATGGGATGGGATGGGATTGGATGGGGTGGGATGGGATGGATGGATGGGATGGATGGAT +GGGATGGAATGGATGGATGGGATGGGATGGATGGGATGGGATGGATGGATGGGATGGGAT +GGATGCAATGGATGGATGGGATGGGATGGGATGGGATGGATGGAATGGATGGATGGGATG +GGATGGGATGGATGGGGTGGGATGAGATGGATGGGATGGATGGGATGGGATGGATGGATG +GATGGGATGGGATGGATGGATGGGATGGGATGGGATGGGGTGGATGGGATGGATGGATGG +ATGGGATGGGATGGATGGATGGGATGGAATGGATGAATGGGATGTGATGGATGGGATGGA +ATGGGATAGATGGGATGGGATTGGATGGGATGGGGTGGGATGGGGTAAGATGGGGTGGGA +TGGGATGGTATGGGATGGATGGATGAGATGGGATGGGATGAGATGGGATTGGATGGGGTG +GGATGCAATGGGATGAGATGAGATGAGATGAGATGGGATGGATGGCATGGGATGGGATGG +GATTGGATGGGGTGGGATGGGATGGGGTAGGATGGGATGGGATGGGATGGGATGGGATGG +GATGGGATGGGATGGGATGGGGTGGGATGGGTTGGGATGGGATGGGGTGGGTTGGGATGG +GGTGGGGTGGGATGGGATGGGATGGGATGGGGTGGGGTGGGGTGGGGTGGGATGGGGTGG +GATGGGGTGGGATGGGATGGGGTGGGATGGGATGGGATGGGGTGGGATGGGATGGGGTGG +GGTGGGGTGGGGTGGGATGAGGTGGGGTGGGATGGGATGGGATGGGGTGGGGTGGGGTGG +GATGGGATGGGATGGGGTGGGGTGGGATGGGATTGGATGGGGTGGGATGCGATGGGATGA +GATGAGATGGATGGCATGGGATGGGTGGGAGGGGATGGGATATTATCAGATGGCAAAAGT +AAGAAGTGTTCATATTTTGTCTTCAAAATATAAATATGAGTGCATAATGGCTTGTGATGC +AAAATACATTTCTTACTAAAGATCATGGACAAAGCACTTAAAACCACACAGT +>syndip_2_chr20:48449605-48450562 +CATGAGAATATGCTCAGTGATAAGGCAGTGGCGTTAAATCTGCAGGCAGTGGGCTATCTG +TGGGTCCTTAAATCTATTTAGTGCATCTTGAACAGTATTTTTAAGCTGGGATAAGTGGAA +TAGGAAGGAGTGGAGTGGAGCATGATGGTATGGGATGGGATGGATGGGATGGGATGGATG +GATGGATGGGGTGGGATGGGATGGGATGGGATGGGGTGGATGGATGGGATGGGATAGGAT +GGATGGGGTGAGATGGGATGGAATGGATGGAATGGGATGGATGGATGGGATGGGATGGAT +GGGATGGGATGGATGGGATGGATGGGATGGGATGGATGGGATGGAATGGGATGGATGGGA +TGGGATGGGATTGGATGGGGTGGGATGGGATGGATGGATGGGATGGATGGATGGGATGGA +ATGGATGGATGGGATGGGATGGATGGGATGGGATGGATGGATGGGATGGGATGGATGCAA +TGGATGGATGGGATGGGATGGGATGGGATGGATGGAATGGATGGATGGGATGGGATGGGA +TGGATGGGGTGGGATGAGATGGATGGGATGGATGGGATGGGATGGATGGATGGATGGGAT +GGGATGGATGGATGGGATGGGATGGGATGGATGGATGGGATGGGATGGGATGGGGTGGAT +GGGATGGATGGATGGATGGGATGGGATGGATGGATGGGATGGAATGGATGAATGGGATGT +GATGGATGGGATGGAATGGGATAGATGGGATGGGATTGGATGGGATGGGGTGGGATGGGG +TAAGATGGGGTGGGATGGGATGGTATGGGATGGATGGATGAGATGGGATGGGATGAGATG +GGATTGGATGGGGTGGGATGCAATGGGATGAGATGAGATGAGATGAGATGGGATGGATGG +CATGGGATGGAATGGGATTGGATGGGGTGGGATGGGATGGGGTAGGATGGGATGGGATGG +GATGGGATGGGATGGGATGGGGTGGGATGGGTTGGGATGGGATGGGGTGGGTTGGGATGG +GGTGGGGTGGGATGGGATGGGATGGGGTGGGATGGGGTGGGATGGGGTGGGATGGGGTGG +GATGGGATGGGGTGGGATGGGATGGGATGGGATGGGGTGGGATGGGGTGGGATGGGATGG +GGTGGGGTGGGGTGGGGTGGGATGAGGTGGGGTGGGATGGGATGGGATGGGGTGGGGTGG +GGTGGGATGGGATGGGATGGGGTGGGGTGGGATGGGATTGGATGGGGTGGGATGCGATGG +GATGAGATGAGATGAGATGAATGGCATGGGATGGGTGGGAGGGGATGGGATATTATCAGA +TGGCAAAAGTAAGAAGTGTTCATATTTTGTCTTCAAAATATAAATATGAGTGCATAATGG +CTTGTGATGCAAAATACATTTCTTACTAAAGATCATGGACAAAGCACTTAAAACCACACA +GT +>p:HG002_1_chr20:48449605-48450562 +CATGAGAATATGCTCAGTGATAAGGCAGTGGCGTTAAATCTGCAGGCAGTGGGCTATCTG +TGGGTCCTTAAATCTATTTAGTGCATCTTGAACAGTATTTTTAAGCTGGGATAAGTGGAA +TAGGAAGGAGTGGAGTGGAGCATGATGGTATGGGATGGGATGGATGGGATGGGATGGATG +GATGGATGGGGTGGGATGGGATGGGATGGGATGGGGTGGATGGATGGGATGGGATAGGAT +GGATGGGGTGAGATGGGATGGAATGGATGGAATGGGATGGATGGATGGGATGGGATGGAT +GGGATGGGATGGATGGGATGGATGGGATGGGATGGATGGGATGGAATGGGATGGATGGGA +TGGGATGGGATTGGATGGGGTGGGATGGGATGGATGGATGGGATGGATGGATGGGATGGA +ATGGATGGATGGGATGGGATGGATGGGATGGGATGGATGGATGGGATGGGATGGATGCAA +TGGATGGATGGGATGGGATGGGATGGGATGGATGGAATGGATGGATGGGATGGGATGGGA +TGGATGGGGTGGGATGAGATGGATGGGATGGATGGGATGGGATGGATGGATGGATGGGAT +GGGATGGATGGATGGGATGGGATGGGATGGATGGATGGGATGGGATGGGATGGGGTGGAT +GGGATGGATGGATGGATGGGATGGGATGGATGGATGGGATGGAATGGATGAATGGGATGT +GATGGATGGGATGGAATGGGATAGATGGGATGGGATTGGATGGGATGGGGTGGGATGGGG +TAAGATGGGGTGGGATGGGATGGTATGGGATGGATGGATGAGATGGGATGGGATGAGATG +GGATTGGATGGGGTGGGATGCAATGGGATGAGATGAGATGAGATGAGATGGGATGGATGG +CATGGGATGGAATGGGATTGGATGGGGTGGGATGGGATGGGGTAGGATGGGATGGGATGG +GATGGGATGGGATGGGATGGGGTGGGATGGGTTGGGATGGGATGGGGTGGGTTGGGATGG +GGTGGGGTGGGATGGGATGGGATGGGGTGGGATGGGGTGGGATGGGGTGGGATGGGGTGG +GATGGGATGGGGTGGGATGGGATGGGATGGGATGGGGTGGGATGGGGTGGGATGGGATGG +GGTGGGGTGGGGTGGGGTGGGATGAGGTGGGGTGGGATGGGATGGGATGGGGTGGGGTGG +GGTGGGATGGGATGGGATGGGGTGGGGTGGGATGGGATTGGATGGGGTGGGATGCGATGG +GATGAGATGAGATGAGATGAATGGCATGGGATGGGTGGGAGGGGATGGGATATTATCAGA +TGGCAAAAGTAAGAAGTGTTCATATTTTGTCTTCAAAATATAAATATGAGTGCATAATGG +CTTGTGATGCAAAATACATTTCTTACTAAAGATCATGGACAAAGCACTTAAAACCACACA +GT +>p:HG002_2_chr20:48449605-48450562 +CATGAGAATATGCTCAGTGATAAGGCAGTGGCGTTAAATCTGCAGGCAGTGGGCTATCTG +TGGGTCCTTAAATCTATTTAGTGCATCTTGAACAGTATTTTTAAGCTGGGATAAGTGGAA +TAGGAAGGAGTGGAGTGGAGCATGATGGTATGGGATGGGATGGATGGGATGGGATGGATG +GATGGATGGGGTGGGATGGGATGGGATGGGATGGATGGATGGGATGGATGGATGGGATGG +GATAGGATGGATGGGGTGAGATGGGATGGAATGGATGGGATGGGATGGATGGATGGGATG +GGATGGATGGGATGGGATGGATGGGATGGGATGGATGGGATGGATGGGATGGAATGGGAT +GGATGGGATGGGATGGGATTGGATGGGGTGGGATGGGATGGATGGATGGGATGGATGGAT +GGGATGGAATGGATGGATGGGATGGGATGGATGGGATGGGATGGATGGATGGGATGGGAT +GGATGCAATGGATGGATGGGATGGGATGGGATGGGATGGATGGAATGGATGGATGGGATG +GGATGGGATGGATGGGGTGGGATGAGATGGATGGGATGGATGGGATGGGATGGATGGATG +GATGGGATGGGATGGATGGATGGGATGGGATGGGATGGGGTGGATGGGATGGATGGATGG +ATGGGATGGGATGGATGGATGGGATGGAATGGATGAATGGGATGTGATGGATGGGATGGA +ATGGGATAGATGGGATGGGATTGGATGGGATGGGGTGGGATGGGGTAAGATGGGGTGGGA +TGGGATGGTATGGGATGGATGGATGAGATGGGATGGGATGAGATGGGATTGGATGGGGTG +GGATGCAATGGGATGAGATGAGATGAGATGAGATGGGATGGATGGCATGGGATGGGATGG +GATTGGATGGGGTGGGATGGGATGGGGTAGGATGGGATGGGATGGGATGGGATGGGATGG +GATGGGATGGGATGGGATGGGGTGGGATGGGTTGGGATGGGATGGGGTGGGTTGGGATGG +GGTGGGGTGGGATGGGATGGGATGGGATGGGGTGGGGTGGGGTGGGGTGGGATGGGGTGG +GATGGGGTGGGATGGGATGGGGTGGGATGGGATGGGATGGGGTGGGATGGGATGGGGTGG +GGTGGGGTGGGGTGGGATGAGGTGGGGTGGGATGGGATGGGATGGGGTGGGGTGGGGTGG +GATGGGATGGGATGGGGTGGGGTGGGATGGGATTGGATGGGGTGGGATGCGATGGGATGA +GATGAGATGGATGGCATGGGATGGGTGGGAGGGGATGGGATATTATCAGATGGCAAAAGT +AAGAAGTGTTCATATTTTGTCTTCAAAATATAAATATGAGTGCATAATGGCTTGTGATGC +AAAATACATTTCTTACTAAAGATCATGGACAAAGCACTTAAAACCACACAGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/haps.fa.ref.fa new file mode 100644 index 00000000..173876c8 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:48449605-48450562 +CATGAGAATATGCTCAGTGATAAGGCAGTGGCGTTAAATCTGCAGGCAGTGGGCTATCTGTGGGTCCTTAAATCTATTTAGTGCATCTTGAACAGTATTTTTAAGCTGGGATAAGTGGAATAGGAAGGAGTGGAGTGGAGCATGATGGTATGGGATGGGATGGATGGGATGGGATGGATGGATGGATGGGGTGGGATGGGATGGGATGGGATGGGATGGATGGATGGGATGGATGGATGGGATGGGATAGGATGGATGGGGTGAGATGGGATGGAATGGATGGGATGGGATGGATGGATGGGATGGGATGGATGGGATGGGATGGATGGGATGGGATGGATGGGATGGATGGGATGGAATGGGATGGATGGGATGGGATGGGATTGGATGGGGTGGGATGGGATGGATGGATGGGATGGATGGATGGGATGGAATGGATGGATGGGATGGGATGGATGGGATGGGATGGATGGATGGGATGGGATGGATGCAATGGATGGATGGGATGGGATGGGATGGGATGGATGGAATGGATGGATGGGATGGGATGGGATGGATGGGGTGGGATGAGATGGATGGGATGGATGGGATGGGATGGATGGATGGATGGGATGGGATGGATGGATGGGATGGGATGGGATGGGGTGGATGGGATGGATGGATGGATGGGATGGGATGGATGGATGGGATGGGATGGATGGGATGGGATGGGGTGGGGTGGGGTGGGATGGGATGGGATGGGGTGGGGTGGGATGGGATTGGATGGGGTGGGATGCGATGGGATGAGATGAGATGGATGGCATGGGATGGGTGGGAGGGGATGGGATATTATCAGATGGCAAAAGTAAGAAGTGTTCATATTTTGTCTTCAAAATATAAATATGAGTGCATAATGGCTTGTGATGCAAAATACATTTCTTACTAAAGATCATGGACAAAGCACTTAAAACCACACAGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/msa.fa new file mode 100644 index 00000000..2696ae99 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/msa.fa @@ -0,0 +1,130 @@ +>ref_chr20_48449605_48450562 +catgagaatatgctcagtgataaggcagtggcgttaaatctgcaggcagtgggctatctg +tgggtccttaaatctatttagtgcatcttgaacagtatttttaagctgggataagtggaa +taggaaggagtggagtggagcatgatggtatgggatgggatggatgggatgggatggatg +gatggatggggtgggatgggatgggatgggatgggatggatggatgggatggatggatgg +gatgggataggatggatggggtgagatgggatggaatggatgggatgggatggatggatg +ggatgggatggatgggatgggatggatgggatgggatggatgggatggatgggatggaat +gggatggatgggatgggatgggattggatggggtgggatgggatggatggatgggatgga +tggatgggatggaatggatggatgggatgggatggatgggatgggatggatggatgggat +gggatggatgcaatggatggatgggatgggatgggatgggatggatggaatggatggatg +ggatgggatgggatggatggggtgggatgagatggatgggatggatgggatgggatggat +ggat-----------------------ggatgggatgggatggatggatgggatgggatg +ggatggggtggatgggatggatggatggatgggatgggatggatggatgggatgggat-- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------------------------gga +tgggatgggatggggtggggtggggtgggatgggatgggatggggtggggtgggatggga +ttggatggggtgggatgcgatgg-----gatgagatgagatggatggcatgggatgggtg +ggaggggatgggatattatcagatggcaaaagtaagaagtgttcatattttgtcttcaaa +atataaatatgagtgcataatggcttgtgatgcaaaatacatttcttactaaagatcatg +gacaaagcacttaaaaccacacagt +>syndip_1_chr20:48449605-48450562 +catgagaatatgctcagtgataaggcagtggcgttaaatctgcaggcagtgggctatctg +tgggtccttaaatctatttagtgcatcttgaacagtatttttaagctgggataagtggaa +taggaaggagtggagtggagcatgatggtatgggatgggatggatgggatgggatggatg +gatggatggggtgggatgggatgggatg-----ggatggatggatgggatggatggatgg +gatgggataggatggatggggtgagatgggatggaatggatgggatgggatggatggatg +ggatgggatggatgggatgggatggatgggatgggatggatgggatggatgggatggaat +gggatggatgggatgggatgggattggatggggtgggatgggatggatggatgggatgga +tggatgggatggaatggatggatgggatgggatggatgggatgggatggatggatgggat +gggatggatgcaatggatggatgggatgggatgggatgggatggatggaatggatggatg +ggatgggatgggatggatggggtgggatgagatggatgggatggatgggatgggatggat +ggat-----------------------ggatgggatgggatggatggatgggatgggatg +ggatggggtggatgggatggatggatggatgggatgggatggatggatgggatggaatgg +atgaatgggatgtgatggatgggatggaatgggatagatgggatgggattggatgggatg +gggtgggatggggtaagatggggtgggatgggatggtatgggatggatggatgagatggg +atgggatgagatgggattggatggggtgggatgcaatgggatgagatgagatgagatgag +atgggatggatggcatgggatgggatgggattggatggggtgggatgggatggggtagga +tgggatgggatgggatgggatgggatgggatgggatgggatgggatggggtgggatgggt +tgggatgggatggggtgggttgggatggggtggggtgggatgggatgggatgggatgggg +tggggtggggtggggtgggatggggtgggatggggtgggatgggatggggtgggatggga +tgggatggggtgggatgggatggggtggggtggggtggggtgggatgaggtggggtggga +tgggatgggatggggtggggtggggtgggatgggatgggatggggtggggtgggatggga +ttggatggggtgggatgcgatgg-----gatgagatgagatggatggcatgggatgggtg +ggaggggatgggatattatcagatggcaaaagtaagaagtgttcatattttgtcttcaaa +atataaatatgagtgcataatggcttgtgatgcaaaatacatttcttactaaagatcatg +gacaaagcacttaaaaccacacagt +>syndip_2_chr20:48449605-48450562 +catgagaatatgctcagtgataaggcagtggcgttaaatctgcaggcagtgggctatctg +tgggtccttaaatctatttagtgcatcttgaacagtatttttaagctgggataagtggaa +taggaaggagtggagtggagcatgatggtatgggatgggatggatgggatgggatggatg +gatggatggggtgggatgggatgggatg-------------ggatggggtggatggatgg +gatgggataggatggatggggtgagatgggatggaatggatggaatgggatggatggatg +ggatgggatggatgggatgggatggatgggatggatgggatgggatggatgggatggaat +gggatggatgggatgggatgggattggatggggtgggatgggatggatggatgggatgga +tggatgggatggaatggatggatgggatgggatggatgggatgggatggatggatgggat +gggatggatgcaatggatggatgggatgggatgggatgggatggatggaatggatggatg +ggatgggatgggatggatggggtgggatgagatggatgggatggatgggatgggatggat +ggatggatgggatgggatggatggatgggatgggatgggatggatggatgggatgggatg +ggatggggtggatgggatggatggatggatgggatgggatggatggatgggatggaatgg +atgaatgggatgtgatggatgggatggaatgggatagatgggatgggattggatgggatg +gggtgggatggggtaagatggggtgggatgggatggtatgggatggatggatgagatggg +atgggatgagatgggattggatggggtgggatgcaatgggatgagatgagatgagatgag +atgggatggatggcatgggatggaatgggattggatggggtgggatgggatggggtagga +tgggatgggatgggatgggatgggatgggatggggtgggatgggttgggatgggatgggg +tgggttgggatgggg----------tggggtgggatgggatgggatggggtgggatgggg +tgggatggggtgggatggggtgggatgggatggggtgggatgggatgggatgggatgggg +tgggatggggtgggatgggatggggtggggtggggtggggtgggatgaggtggggtggga +tgggatgggatggggtggggtggggtgggatgggatgggatggggtggggtgggatggga +ttggatggggtgggatgcgatgggatgagatgagatgagatgaatggcatgggatgggtg +ggaggggatgggatattatcagatggcaaaagtaagaagtgttcatattttgtcttcaaa +atataaatatgagtgcataatggcttgtgatgcaaaatacatttcttactaaagatcatg +gacaaagcacttaaaaccacacagt +>p:HG002_1_chr20:48449605-48450562 +catgagaatatgctcagtgataaggcagtggcgttaaatctgcaggcagtgggctatctg +tgggtccttaaatctatttagtgcatcttgaacagtatttttaagctgggataagtggaa +taggaaggagtggagtggagcatgatggtatgggatgggatggatgggatgggatggatg +gatggatggggtgggatgggatgggatg-------------ggatggggtggatggatgg +gatgggataggatggatggggtgagatgggatggaatggatggaatgggatggatggatg +ggatgggatggatgggatgggatggatgggatggatgggatgggatggatgggatggaat +gggatggatgggatgggatgggattggatggggtgggatgggatggatggatgggatgga +tggatgggatggaatggatggatgggatgggatggatgggatgggatggatggatgggat +gggatggatgcaatggatggatgggatgggatgggatgggatggatggaatggatggatg +ggatgggatgggatggatggggtgggatgagatggatgggatggatgggatgggatggat +ggatggatgggatgggatggatggatgggatgggatgggatggatggatgggatgggatg +ggatggggtggatgggatggatggatggatgggatgggatggatggatgggatggaatgg +atgaatgggatgtgatggatgggatggaatgggatagatgggatgggattggatgggatg +gggtgggatggggtaagatggggtgggatgggatggtatgggatggatggatgagatggg +atgggatgagatgggattggatggggtgggatgcaatgggatgagatgagatgagatgag +atgggatggatggcatgggatggaatgggattggatggggtgggatgggatggggtagga +tgggatgggatgggatgggatgggatgggatggggtgggatgggttgggatgggatgggg +tgggttgggatgggg----------tggggtgggatgggatgggatggggtgggatgggg +tgggatggggtgggatggggtgggatgggatggggtgggatgggatgggatgggatgggg +tgggatggggtgggatgggatggggtggggtggggtggggtgggatgaggtggggtggga +tgggatgggatggggtggggtggggtgggatgggatgggatggggtggggtgggatggga +ttggatggggtgggatgcgatgggatgagatgagatgagatgaatggcatgggatgggtg +ggaggggatgggatattatcagatggcaaaagtaagaagtgttcatattttgtcttcaaa +atataaatatgagtgcataatggcttgtgatgcaaaatacatttcttactaaagatcatg +gacaaagcacttaaaaccacacagt +>p:HG002_2_chr20:48449605-48450562 +catgagaatatgctcagtgataaggcagtggcgttaaatctgcaggcagtgggctatctg +tgggtccttaaatctatttagtgcatcttgaacagtatttttaagctgggataagtggaa +taggaaggagtggagtggagcatgatggtatgggatgggatggatgggatgggatggatg +gatggatggggtgggatgggatgggatg-----ggatggatggatgggatggatggatgg +gatgggataggatggatggggtgagatgggatggaatggatgggatgggatggatggatg +ggatgggatggatgggatgggatggatgggatgggatggatgggatggatgggatggaat +gggatggatgggatgggatgggattggatggggtgggatgggatggatggatgggatgga +tggatgggatggaatggatggatgggatgggatggatgggatgggatggatggatgggat +gggatggatgcaatggatggatgggatgggatgggatgggatggatggaatggatggatg +ggatgggatgggatggatggggtgggatgagatggatgggatggatgggatgggatggat +ggat-----------------------ggatgggatgggatggatggatgggatgggatg +ggatggggtggatgggatggatggatggatgggatgggatggatggatgggatggaatgg +atgaatgggatgtgatggatgggatggaatgggatagatgggatgggattggatgggatg +gggtgggatggggtaagatggggtgggatgggatggtatgggatggatggatgagatggg +atgggatgagatgggattggatggggtgggatgcaatgggatgagatgagatgagatgag +atgggatggatggcatgggatgggatgggattggatggggtgggatgggatggggtagga +tgggatgggatgggatgggatgggatgggatgggatgggatgggatggggtgggatgggt +tgggatgggatggggtgggttgggatggggtggggtgggatgggatgggatgggatgggg +tggggtggggtggggtgggatggggtgggatggggtgggatgggatggggtgggatggga +tgggatggggtgggatgggatggggtggggtggggtggggtgggatgaggtggggtggga +tgggatgggatggggtggggtggggtgggatgggatgggatggggtggggtgggatggga +ttggatggggtgggatgcgatgg-----gatgagatgagatggatggcatgggatgggtg +ggaggggatgggatattatcagatggcaaaagtaagaagtgttcatattttgtcttcaaa +atataaatatgagtgcataatggcttgtgatgcaaaatacatttcttactaaagatcatg +gacaaagcacttaaaaccacacagt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/msa.fa.fai new file mode 100644 index 00000000..c39a55fc --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_48449605_48450562 1465 29 60 61 +syndip_1_chr20:48449605-48450562 1465 1553 60 61 +syndip_2_chr20:48449605-48450562 1465 3077 60 61 +p:HG002_1_chr20:48449605-48450562 1465 4602 60 61 +p:HG002_2_chr20:48449605-48450562 1465 6127 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/output.vcf.gz new file mode 100644 index 00000000..567e09c7 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/output.vcf.gz.tbi new file mode 100644 index 00000000..3913cabd Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:48449705-48450462/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/base.vcf.gz new file mode 100644 index 00000000..f83462d6 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/base.vcf.gz.tbi new file mode 100644 index 00000000..2d2eaccc Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/comp.vcf.gz new file mode 100644 index 00000000..1f57977c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/comp.vcf.gz.tbi new file mode 100644 index 00000000..b865b2db Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/haps.fa new file mode 100644 index 00000000..749b06cb --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/haps.fa @@ -0,0 +1,48 @@ +>ref_chr20_49834009_49834659 +GAGGCTGAGACAGGCGGATCACCTGAGGTTGGGAGTTCAAGACCAGCTTGGCCAACATGGTGAAACTCTGTCTCTGCTAAAAATACAAAAATTAGCCGGGCGTGGTGGTGCACGCTTGTAATATTAGCTTGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATATATATATATATATATATATATATATACACACACACACTATGTATATACACACACTGTATATACGCACTATATGCACTATATATACACACAGTATATGTATATACACACACTATATATACAGTGTGTATATATATATATACTGTGTATATATATATATACTGTATATATATATATACTGTGTATATATATATATACTGTGTATATATATATACTGTGTATATATATATACTGTATATATATACTGTATATATATATATATACTGTATATATATATACTGTGTATATATATATATACTGTATATATACACACACACACTATATATATGCCATATATAATATCTGGTGGCCAGTTGTGTGAAATACATTCATTTTCTCTGTTGGGTAGATTGATTTGACCTAACTATGAGCCTCAATCTCAAGAGGTAAAGTGGTAGTTTGCCAATTTAATGCTGCACAAAGGATTATTTAAG +>syndip_1_chr20:49834009-49834659 +GAGGCTGAGACAGGCGGATCACCTGAGGTTGGGAGTTCAAGACCAGCTTGGCCAACATGG +TGAAACTCTGTCTCTGCTAAAAATACAAAAATTAGCCGGGCGTGGTGGTGCACGCTTGTA +ATATTAGCTTGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATAT +ATATATATATATACACACACACACACACTATGTATATACACACACTGTATATACGCACTA +TATGCACTATATATACACACAGTATATGTATATACACACACTATATATACAGTGTGTATA +TATATATATACTGTGTGTATATATATATATACTGTATATATATATATATATACTGTGTAT +ATATATATACTGTGTATATATATATATATACTGTATATATACACACACACACTATATATA +TGCCATATATAATATCTGGTGGCCAGTTGTGTGAAATACATTCATTTTCTCTGTTGGGTA +GATTGATTTGACCTAACTATGAGCCTCAATCTCAAGAGGTAAAGTGGTAGTTTGCCAATT +TAATGCTGCACAAAGGATTATTTAAG +>syndip_2_chr20:49834009-49834659 +GAGGCTGAGACAGGCGGATCACCTGAGGTTGGGAGTTCAAGACCAGCTTGGCCAACATGG +TGAAACTCTGTCTCTGCTAAAAATACAAAAATTAGCCGGGCGTGGTGGTGCACGCTTGTA +ATATTAGCTTGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT +CTCTATATATATATATATATATATATATACACACACACACTATGTATATACACACACTGT +ATATACGCACTATATGCACTATATATACACACAGTATATGTATATACACACACTATATAT +ACAGTGTGTATATATATATATACTGTGTATATATATATATACTGTATATATATATATACT +GTGTATATATATATATACTGTATATATATATATACTGTGTATATATATATACTGTATATA +TATACTGTATATATATATATATACTGTATATATATATACTGTGTATATATATATATACTG +TATATATACACACACACACTATATATATGCCATATATAATATCTGGTGGCCAGTTGTGTG +AAATACATTCATTTTCTCTGTTGGGTAGATTGATTTGACCTAACTATGAGCCTCAATCTC +AAGAGGTAAAGTGGTAGTTTGCCAATTTAATGCTGCACAAAGGATTATTTAAG +>p:HG002_1_chr20:49834009-49834659 +GAGGCTGAGACAGGCGGATCACCTGAGGTTGGGAGTTCAAGACCAGCTTGGCCAACATGG +TGAAACTCTGTCTCTGCTAAAAATACAAAAATTAGCCGGGCGTGGTGGTGCACGCTTGTA +ATATTAGCTTGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT +CTCTATATATATATATATATATATATATACACACACACACTATGTATATACACACACTGT +ATATACGCACTATATGCACTATATATACACACAGTATATGTATATACACACACTATATAT +ACAGTGTGTATATATATATATACTGTGTATATATATATATACTGTATATATATATATACT +GTGTATATATATATATACTGTATATATATATATACTGTGTATATATATATACTGTATATA +TATACTGTATATATATATATATACTGTATATATATATACTGTGTATATATATATATACTG +TATATATACACACACACACTATATATATGCCATATATAATATCTGGTGGCCAGTTGTGTG +AAATACATTCATTTTCTCTGTTGGGTAGATTGATTTGACCTAACTATGAGCCTCAATCTC +AAGAGGTAAAGTGGTAGTTTGCCAATTTAATGCTGCACAAAGGATTATTTAAG +>p:HG002_2_chr20:49834009-49834659 +GAGGCTGAGACAGGCGGATCACCTGAGGTTGGGAGTTCAAGACCAGCTTGGCCAACATGG +TGAAACTCTGTCTCTGCTAAAAATACAAAAATTAGCCGGGCGTGGTGGTGCACGCTTGTA +ATATTAGCTTGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATAT +ATATATATATATACACACACACACACACTATGTATATACACACACTGTATATACGCACTA +TATGCACTATATATACACACAGTATATGTATATACACACACTATATATACAGTGTGTATA +TATATATATACTGTGTGTATATATATATATACTGTATATATATATATATATACTGTGTAT +ATATATATACTGTGTATATATATATATATACTGTATATATACACACACACACTATATATA +TGCCATATATAATATCTGGTGGCCAGTTGTGTGAAATACATTCATTTTCTCTGTTGGGTA +GATTGATTTGACCTAACTATGAGCCTCAATCTCAAGAGGTAAAGTGGTAGTTTGCCAATT +TAATGCTGCACAAAGGATTATTTAAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/haps.fa.ref.fa new file mode 100644 index 00000000..015f1db9 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:49834009-49834659 +GAGGCTGAGACAGGCGGATCACCTGAGGTTGGGAGTTCAAGACCAGCTTGGCCAACATGGTGAAACTCTGTCTCTGCTAAAAATACAAAAATTAGCCGGGCGTGGTGGTGCACGCTTGTAATATTAGCTTGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATATATATATATATATATATATATATATACACACACACACTATGTATATACACACACTGTATATACGCACTATATGCACTATATATACACACAGTATATGTATATACACACACTATATATACAGTGTGTATATATATATATACTGTGTATATATATATATACTGTATATATATATATACTGTGTATATATATATATACTGTGTATATATATATACTGTGTATATATATATACTGTATATATATACTGTATATATATATATATACTGTATATATATATACTGTGTATATATATATATACTGTATATATACACACACACACTATATATATGCCATATATAATATCTGGTGGCCAGTTGTGTGAAATACATTCATTTTCTCTGTTGGGTAGATTGATTTGACCTAACTATGAGCCTCAATCTCAAGAGGTAAAGTGGTAGTTTGCCAATTTAATGCTGCACAAAGGATTATTTAAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/msa.fa new file mode 100644 index 00000000..4d260dc3 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/msa.fa @@ -0,0 +1,60 @@ +>ref_chr20_49834009_49834659 +gaggctgagacaggcggatcacctgaggttgggagttcaagaccagcttggccaacatgg +tgaaactctgtctctgctaaaaatacaaaaattagccgggcgtggtggtgcacgcttgta +atattagcttg--tctctctctctctctctctctctctctctctctctctctctctctct +atatatatatatatatatatatatatatacacacacacactatgtatatacacacactgt +atatacgcactatatgcactatatatacacacagtatatgtatatacacacactatatat +acagtgtgtatatatatatatactgtgtatatatatatatactgtatatatatatatact +gtgtatatatatatatactgtgtatatatatatactgtgtatatatatatactgtatata +tatactgtatatatatatatatactgtatatatatatactgtgtatatatatatatactg +tatatatacacacacacactatatatatgccatatataatatctggtggccagttgtgtg +aaatacattcattttctctgttgggtagattgatttgacctaactatgagcctcaatctc +aagaggtaaagtggtagtttgccaatttaatgctgcacaaaggattatttaag +>syndip_1_chr20:49834009-49834659 +gaggctgagacaggcggatcacctgaggttgggagttcaagaccagcttggccaacatgg +tgaaactctgtctctgctaaaaatacaaaaattagccgggcgtggtggtgcacgcttgta +atattagcttgtctctctctctctctctctctctctctctctctctctctctctc----- +-------tatatatatatatatatacacacacacacacactatgtatatacacacactgt +atatacgcactatatgcactatatatacacacagtatatgtatatacacacactatatat +acagtgtgtatatatatatatactgtgtgtatatatatatatactgtata---------- +--------------------tatatatatatatactgtgtatatatatatactg------ +---------------------------------------tgtatatatatatatatactg +tatatatacacacacacactatatatatgccatatataatatctggtggccagttgtgtg +aaatacattcattttctctgttgggtagattgatttgacctaactatgagcctcaatctc +aagaggtaaagtggtagtttgccaatttaatgctgcacaaaggattatttaag +>syndip_2_chr20:49834009-49834659 +gaggctgagacaggcggatcacctgaggttgggagttcaagaccagcttggccaacatgg +tgaaactctgtctctgctaaaaatacaaaaattagccgggcgtggtggtgcacgcttgta +atattagcttgtctctctctctctctctctctctctctctctctctctctctctctctct +ctctatatatatatatatatatatatatacacacacacactatgtatatacacacactgt +atatacgcactatatgcactatatatacacacagtatatgtatatacacacactatatat +acagtgtgtatatatatatatactgtgtatatatatatatactgtatatatatatatact +gtgtatatatatatatactgtatatatatatatactgtgtatatatatatactgtatata +tatactgtatatatatatatatactgtatatatatatactgtgtatatatatatatactg +tatatatacacacacacactatatatatgccatatataatatctggtggccagttgtgtg +aaatacattcattttctctgttgggtagattgatttgacctaactatgagcctcaatctc +aagaggtaaagtggtagtttgccaatttaatgctgcacaaaggattatttaag +>p:HG002_1_chr20:49834009-49834659 +gaggctgagacaggcggatcacctgaggttgggagttcaagaccagcttggccaacatgg +tgaaactctgtctctgctaaaaatacaaaaattagccgggcgtggtggtgcacgcttgta +atattagcttgtctctctctctctctctctctctctctctctctctctctctctctctct +ctctatatatatatatatatatatatatacacacacacactatgtatatacacacactgt +atatacgcactatatgcactatatatacacacagtatatgtatatacacacactatatat +acagtgtgtatatatatatatactgtgtatatatatatatactgtatatatatatatact +gtgtatatatatatatactgtatatatatatatactgtgtatatatatatactgtatata +tatactgtatatatatatatatactgtatatatatatactgtgtatatatatatatactg +tatatatacacacacacactatatatatgccatatataatatctggtggccagttgtgtg +aaatacattcattttctctgttgggtagattgatttgacctaactatgagcctcaatctc +aagaggtaaagtggtagtttgccaatttaatgctgcacaaaggattatttaag +>p:HG002_2_chr20:49834009-49834659 +gaggctgagacaggcggatcacctgaggttgggagttcaagaccagcttggccaacatgg +tgaaactctgtctctgctaaaaatacaaaaattagccgggcgtggtggtgcacgcttgta +atattagcttgtctctctctctctctctctctctctctctctctctctctctctc----- +-------tatatatatatatatatacacacacacacacactatgtatatacacacactgt +atatacgcactatatgcactatatatacacacagtatatgtatatacacacactatatat +acagtgtgtatatatatatatactgtgtgtatatatatatatactgtata---------- +--------------------tatatatatatatactgtgtatatatatatactg------ +---------------------------------------tgtatatatatatatatactg +tatatatacacacacacactatatatatgccatatataatatctggtggccagttgtgtg +aaatacattcattttctctgttgggtagattgatttgacctaactatgagcctcaatctc +aagaggtaaagtggtagtttgccaatttaatgctgcacaaaggattatttaag diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/msa.fa.fai new file mode 100644 index 00000000..06e6a233 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_49834009_49834659 653 29 60 61 +syndip_1_chr20:49834009-49834659 653 727 60 61 +syndip_2_chr20:49834009-49834659 653 1425 60 61 +p:HG002_1_chr20:49834009-49834659 653 2124 60 61 +p:HG002_2_chr20:49834009-49834659 653 2823 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/output.vcf.gz new file mode 100644 index 00000000..88e63eb5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/output.vcf.gz.tbi new file mode 100644 index 00000000..ed59f036 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:49834109-49834559/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/base.vcf.gz new file mode 100644 index 00000000..e2a07495 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/base.vcf.gz.tbi new file mode 100644 index 00000000..52f3e551 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/comp.vcf.gz new file mode 100644 index 00000000..6815fae2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/comp.vcf.gz.tbi new file mode 100644 index 00000000..0eb59409 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/haps.fa new file mode 100644 index 00000000..15325c04 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/haps.fa @@ -0,0 +1,68 @@ +>ref_chr20_5039849_5040600 +AGACACAGTGTCCAGGATTGCATTATGTGGCCACCCCAGATGAAGGGGAGATGAGAATGTGAGTGTTCCGTTTTCTAATATGTATAATACAGGTAGGCTGGGCAGAAAGAGTTAGACAGGTATTGGGTTAGCCAGCCTACAGTGTCTAACACACCAACAAAATCAAGCATTGGAGAGCATTTGGATATGGAAGAGTGCTGAGAAGGTGTGGTGGCTCATGCCTATAATCCTAGTACTTTGGGAGGCTGAGGCAGGAGGATCACTTAAGTCCAGGAGTTTGAGAGCAGCCTGGGCAACAAAGTGAGACCTTGTCTCTACAAAAAATAAACAAAATTAGCTGGTGGTGGCACCTGCCTGTTGTCCCAGCTACTCAGGGGGCTGAGGTGGGAGGATGGCTTGAGCCTGGGAGATTGAAGCTTCAGTTAGCCATGATCATGCCACTGCGCTCCAGCCTGGGTGACAGAGAGAGATCCTGCCTCAAAAAAAAAATAAAAATAAAAAAGAGGGGCCGGGTGTGGTGGCTCAGGCCTGTAATCTTAGCACTCTTTGGGAGGCTGAGACTGGAGGATCCTTTGAGCCCAGGGGTTTGAGACCAGCCTGGGCAACATAGGGAGAACTTGTCTCTATTTAAAAAAAAAAATGCTCATACGTGGTTGGCAGGAGTGTAAATAGCCTCAACCAATTTGGAAAGCAATTTGCCAATACTAGTTAATATAACGATCTAGATAGTGGGCAACCCGGATTAGCCTTTT +>syndip_1_chr20:5039849-5040600 +AGACACAGTGTCCAGGATTGCATTATGTGGCCACCCCAGATGAAGGGGAGATGAGAATGT +GAGTGTTCCGTTTTCTAATATGTATAATACAGGTAGGCTGGGCAGAAAGAGTTAGACAGG +TATTGGGTTAGCCAGCCTACAGTGTCTAACACACCAACAAAATCAAGCATTGGAGAGCAT +TTGGATATGGAAGAGTGCTGAGAAGGTGTGGTGGCTCATGCCTATAATCCTAGTACTTTG +GGAGGCTGAGGCAGGAGGATCACTTAAGTCCAGGAGTTTGAGAGCAGCCTGGGCAACAAA +GTGAGACCTTGTCTCTACAAAAAATAAACAAAATTAGCTGGTGGTGGCACCTGCCTGTTG +TCCCAGCTACTCAGGGGGCTGAGGTGGGAGGATGGCTTGAGCCTGGGAGATTGAAGCTTC +AGTTAGCCATGATCATGCCACTGCGCTCCAGCCTGGGTGACAGAGAGAGATCCTGCCTCA +AAAAAAAAAATAAAAATAAAAAAGAGGGGCCGGGTGTGGTGGCTCAGGCCTGTAATCTTA +GCACTCTTTGGGAGGCTGAGACTGGAGGATCCTTTGAGCCCAGGGGTTTGAGACCAGCCT +GGGCAACATAGGGAGAACTTGTCTCTATTTAAAAAAAAAAATGCTCATACGTGGTTGGCA +GGAGTGTAAATAGCCTCAACCAATTTGGAAAGCAATTTGCCAATACTAGTTAATATAACG +ATCTAGATAGTGGGCAACCCGGATTAGCCTTTT +>syndip_2_chr20:5039849-5040600 +AGACACAGTGTCCAGGATTGCATTATGTGGCCACCCCAGATGAAGGGGAGATGAGAATGT +GAGTGTTCCGTTTTCTAATATGTATAATACAGGTAGGCTGGGCAGAAAGAGTTAGACAGG +TATTGGGTTAGCCAGCCTACAGTGTCTAACACACCAACAAAATCAAGCATTGGAGAGCAT +TTGGATATGGAAGAGTGCTGAGAAGGTGTGGTGGCTCATGCCTATAATCCTAGTACTTTG +GGAGGCTGAGGCAGGAGGATCACTTAAGTCCAGGAGTTTGAGAGCAGCCTGGGCAACAAA +GTGAGACCTTGTCTCTACAAAAAATAAACAAAATTAGCTGGTGGTGGCACCTGCCTGTTG +TCCCAGCTACTCAGGGGGCTGAGGTGGGAGGATGGCTTGAGCCTGGGAGATTGAAGCTTC +AGTTAGCCATGATCATGCCACTGCGCTCCAGCCTGGGTGACAGAGAGAGATCCTGCCTCA +AAAAAAAAATAAAAATAAAAAAGAGGGGCCGGGTGTGGTGGCTCAGGCCTGTAATCTTAG +CACTCTTTGGGAGGCTGAGACTGGAGGATCCTTTGAGCCCAGGGGTTTGAGACCAGCCTG +GGCAACATAGGGAGAACTTGTCTCTATTTAAAAAAAAAAATGCTCATACGTGGTTGGCAG +GAGTGTAAATAGCCTCAACCAATTTGGAAAGCAATTTGCCAATACTAGTTAATATAACGA +TCTAGATAGTGGGCAACCCGGATTAGCCTTTT +>p:HG002_1_chr20:5039849-5040600 +AGACACAGTGTCCAGGATTGCATTATGTGGCCACCCCAGATGAAGGGGAGATGAGAATGT +GAGTGTTCCGTTTTCTAATATGTATAATACAGGTAGGCTGGGCAGAAAGAGTTAGACAGG +TATTGGGTTAGCCAGCCTACAGTGTCTAACACACCAACAAAATCAAGCATTGGAGAGCAT +TTGGATATGGAAGAGTGCTGAGAAGGTGTGGTGGCTCATGCCTATAATCCTAGTACTTTG +GGAGGCTGAGGCAGGAGGATCACTTAAGTCCAGGAGTTTGAGAGCAGCCTGGGCAACAAA +GTGAGACCTTGTCTCTACAAAAAATAAACAAAATTAGCTGGTGGTGGCACCTGCCTGTTG +TCCCAGCTACTCAGGGGGCTGAGGTGGGAGGATGGCTTGAGCCTGGGAGATTGAAGCTTC +AGTTAGCCATGATCATGCCACTGCGCTCCAGCCTGGGTGACAGAGAGAGATCCTGCCTCA +AAAAAAAAATAAAAATAAAAAAGAGGGGCCGGGTGTGGTGGCTCAGGCCTGTAATCTTAG +CACTCTTTGGGAGGCTGAGACTGGAGGATCTTTTGAGCCCAGGGGTTTGAGACCAGCCTG +GGCAACATAGGGAGAACTTGTCTCTATTTAAAAAAAAAGGCCGGGCGCGGTGGCTCACGC +CTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCATGAGGTCAGGAGATCGAGA +CCATCCTGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGC +GCGGTGGCGGGCGCCTAGGCAGGAGAATGGCGTGAACCCGGGAAGCGGAGCTTGCAGTGA +GCCGAGATTGCGCCACTGCAGTCCGCAGTCCGACCTGGGCGACAGAGAGAGACTCCGTCT +CAAAAAAAAAAAAAAAAAAAAAAATGCTCATACGTGGTTGGCAGGAGTGTAAATAGCCTC +AACCAATTTGGAAAGCAATTTGCCAATACTAGTTAATATAACGATCTAGATAGTGGGCAA +CCCGGATTAGCCTTTT +>p:HG002_2_chr20:5039849-5040600 +AGACACAGTGTCCAGGATTGCATTATGTGGCCACCCCAGATGAAGGGGAGATGAGAATGT +GAGTGTTCCGTTTTCTAATATGTATAATACAGGTAGGCTGGGCAGAAAGAGTTAGACAGG +TATTGGGTTAGCCAGCCTACAGTGTCTAACACACCAACAAAATCAAGCATTGGAGAGCAT +TTGGATATGGAAGAGTGCTGAGAAGGTGTGGTGGCTCATGCCTATAATCCTAGTACTTTG +GGAGGCTGAGGCAGGAGGATCACTTAAGTCCAGGAGTTTGAGAGCAGCCTGGGCAACAAA +GTGAGACCTTGTCTCTACAAAAAATAAACAAAATTAGCTGGTGGTGGCACCTGCCTGTTG +TCCCAGCTACTCAGGGGGCTGAGGTGGGAGGATGGCTTGAGCCTGGGAGATTGAAGCTTC +AGTTAGCCATGATCATGCCACTGCGCTCCAGCCTGGGTGACAGAGAGAGATCCTGCCTCA +AAAAAAAAAATAAAAATAAAAAAGAGGGGCCGGGTGTGGTGGCTCAGGCCTGTAATCTTA +GCACTCTTTGGGAGGCTGAGACTGGAGGATCTTTTGAGCCCAGGGGTTTGAGACCAGCCT +GGGCAACATAGGGAGAACTTGTCTCTATTTTAAAAAAAAGGCCGGGCGCGGTGGCTCACG +CCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCATGAGGTCAGGAGATCGAG +ACCATCCTGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGG +CGCGGTGGCGGGCGCCTAGGCAGGAGAATGGCGTGAACCCGGGAAGCGGAGCTTGCAGTG +AGCCGAGATTGCGCCACTGCAGTCCGCAGTCCGACCTGGGCGACAGAGAGAGACTCCGTC +TCAAAAAAAAAAAAAAAAAAAATGCTCATACGTGGTTGGCAGGAGTGTAAATAGCCTCAA +CCAATTTGGAAAGCAATTTGCCAATACTAGTTAATATAACGATCTAGATAGTGGGCAACC +CGGATTAGCCTTTT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/haps.fa.ref.fa new file mode 100644 index 00000000..4310f49e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:5039849-5040600 +AGACACAGTGTCCAGGATTGCATTATGTGGCCACCCCAGATGAAGGGGAGATGAGAATGTGAGTGTTCCGTTTTCTAATATGTATAATACAGGTAGGCTGGGCAGAAAGAGTTAGACAGGTATTGGGTTAGCCAGCCTACAGTGTCTAACACACCAACAAAATCAAGCATTGGAGAGCATTTGGATATGGAAGAGTGCTGAGAAGGTGTGGTGGCTCATGCCTATAATCCTAGTACTTTGGGAGGCTGAGGCAGGAGGATCACTTAAGTCCAGGAGTTTGAGAGCAGCCTGGGCAACAAAGTGAGACCTTGTCTCTACAAAAAATAAACAAAATTAGCTGGTGGTGGCACCTGCCTGTTGTCCCAGCTACTCAGGGGGCTGAGGTGGGAGGATGGCTTGAGCCTGGGAGATTGAAGCTTCAGTTAGCCATGATCATGCCACTGCGCTCCAGCCTGGGTGACAGAGAGAGATCCTGCCTCAAAAAAAAAATAAAAATAAAAAAGAGGGGCCGGGTGTGGTGGCTCAGGCCTGTAATCTTAGCACTCTTTGGGAGGCTGAGACTGGAGGATCCTTTGAGCCCAGGGGTTTGAGACCAGCCTGGGCAACATAGGGAGAACTTGTCTCTATTTAAAAAAAAAAATGCTCATACGTGGTTGGCAGGAGTGTAAATAGCCTCAACCAATTTGGAAAGCAATTTGCCAATACTAGTTAATATAACGATCTAGATAGTGGGCAACCCGGATTAGCCTTTT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/msa.fa new file mode 100644 index 00000000..38363f4f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/msa.fa @@ -0,0 +1,95 @@ +>ref_chr20_5039849_5040600 +agacacagtgtccaggattgcattatgtggccaccccagatgaaggggagatgagaatgt +gagtgttccgttttctaatatgtataatacaggtaggctgggcagaaagagttagacagg +tattgggttagccagcctacagtgtctaacacaccaacaaaatcaagcattggagagcat +ttggatatggaagagtgctgagaaggtgtggtggctcatgcctataatcctagtactttg +ggaggctgaggcaggaggatcacttaagtccaggagtttgagagcagcctgggcaacaaa +gtgagaccttgtctctacaaaaaataaacaaaattagctggtggtggcacctgcctgttg +tcccagctactcagggggctgaggtgggaggatggcttgagcctgggagattgaagcttc +agttagccatgatcatgccactgcgctccagcctgggtgacagagagagatcctgcctc- +aaaaaaaaaataaaaataaaaaagaggggccgggtgtggtggctcaggcctgtaatctta +gcactctttgggaggctgagactggaggatcctttgagcccaggggtttgagaccagcct +gggcaacatagggagaacttgtctctattt------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------aaaaaaaaaaatgctcatacgtggttggcaggagtgtaaatagcct +caaccaatttggaaagcaatttgccaatactagttaatataacgatctagatagtgggca +acccggattagcctttt +>syndip_1_chr20:5039849-5040600 +agacacagtgtccaggattgcattatgtggccaccccagatgaaggggagatgagaatgt +gagtgttccgttttctaatatgtataatacaggtaggctgggcagaaagagttagacagg +tattgggttagccagcctacagtgtctaacacaccaacaaaatcaagcattggagagcat +ttggatatggaagagtgctgagaaggtgtggtggctcatgcctataatcctagtactttg +ggaggctgaggcaggaggatcacttaagtccaggagtttgagagcagcctgggcaacaaa +gtgagaccttgtctctacaaaaaataaacaaaattagctggtggtggcacctgcctgttg +tcccagctactcagggggctgaggtgggaggatggcttgagcctgggagattgaagcttc +agttagccatgatcatgccactgcgctccagcctgggtgacagagagagatcctgcctca +aaaaaaaaaataaaaataaaaaagaggggccgggtgtggtggctcaggcctgtaatctta +gcactctttgggaggctgagactggaggatcctttgagcccaggggtttgagaccagcct +gggcaacatagggagaacttgtctctattt------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------aaaaaaaaaaatgctcatacgtggttggcaggagtgtaaatagcct +caaccaatttggaaagcaatttgccaatactagttaatataacgatctagatagtgggca +acccggattagcctttt +>syndip_2_chr20:5039849-5040600 +agacacagtgtccaggattgcattatgtggccaccccagatgaaggggagatgagaatgt +gagtgttccgttttctaatatgtataatacaggtaggctgggcagaaagagttagacagg +tattgggttagccagcctacagtgtctaacacaccaacaaaatcaagcattggagagcat +ttggatatggaagagtgctgagaaggtgtggtggctcatgcctataatcctagtactttg +ggaggctgaggcaggaggatcacttaagtccaggagtttgagagcagcctgggcaacaaa +gtgagaccttgtctctacaaaaaataaacaaaattagctggtggtggcacctgcctgttg +tcccagctactcagggggctgaggtgggaggatggcttgagcctgggagattgaagcttc +agttagccatgatcatgccactgcgctccagcctgggtgacagagagagatcctgcctc- +aaaaaaaaaataaaaataaaaaagaggggccgggtgtggtggctcaggcctgtaatctta +gcactctttgggaggctgagactggaggatcctttgagcccaggggtttgagaccagcct +gggcaacatagggagaacttgtctctattt------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------aaaaaaaaaaatgctcatacgtggttggcaggagtgtaaatagcct +caaccaatttggaaagcaatttgccaatactagttaatataacgatctagatagtgggca +acccggattagcctttt +>p:HG002_1_chr20:5039849-5040600 +agacacagtgtccaggattgcattatgtggccaccccagatgaaggggagatgagaatgt +gagtgttccgttttctaatatgtataatacaggtaggctgggcagaaagagttagacagg +tattgggttagccagcctacagtgtctaacacaccaacaaaatcaagcattggagagcat +ttggatatggaagagtgctgagaaggtgtggtggctcatgcctataatcctagtactttg +ggaggctgaggcaggaggatcacttaagtccaggagtttgagagcagcctgggcaacaaa +gtgagaccttgtctctacaaaaaataaacaaaattagctggtggtggcacctgcctgttg +tcccagctactcagggggctgaggtgggaggatggcttgagcctgggagattgaagcttc +agttagccatgatcatgccactgcgctccagcctgggtgacagagagagatcctgcctc- +aaaaaaaaaataaaaataaaaaagaggggccgggtgtggtggctcaggcctgtaatctta +gcactctttgggaggctgagactggaggatcttttgagcccaggggtttgagaccagcct +gggcaacatagggagaacttgtctctatttaaaaaaaaaggccgggcgcggtggctcacg +cctgtaatcccagcactttgggaggccgaggcgggtggatcatgaggtcaggagatcgag +accatcctggctaaaacggtgaaaccccgtctctactaaaaatacaaaaaattagccggg +cgcggtggcgggcgcctaggcaggagaatggcgtgaacccgggaagcggagcttgcagtg +agccgagattgcgccactgcagtccgcagtccgacctgggcgacagagagagactccgtc +tcaaaaaaaaaaaaaaaaaaaaaaatgctcatacgtggttggcaggagtgtaaatagcct +caaccaatttggaaagcaatttgccaatactagttaatataacgatctagatagtgggca +acccggattagcctttt +>p:HG002_2_chr20:5039849-5040600 +agacacagtgtccaggattgcattatgtggccaccccagatgaaggggagatgagaatgt +gagtgttccgttttctaatatgtataatacaggtaggctgggcagaaagagttagacagg +tattgggttagccagcctacagtgtctaacacaccaacaaaatcaagcattggagagcat +ttggatatggaagagtgctgagaaggtgtggtggctcatgcctataatcctagtactttg +ggaggctgaggcaggaggatcacttaagtccaggagtttgagagcagcctgggcaacaaa +gtgagaccttgtctctacaaaaaataaacaaaattagctggtggtggcacctgcctgttg +tcccagctactcagggggctgaggtgggaggatggcttgagcctgggagattgaagcttc +agttagccatgatcatgccactgcgctccagcctgggtgacagagagagatcctgcctca +aaaaaaaaaataaaaataaaaaagaggggccgggtgtggtggctcaggcctgtaatctta +gcactctttgggaggctgagactggaggatcttttgagcccaggggtttgagaccagcct +gggcaacatagggagaacttgtctctattttaaaaaaaaggccgggcgcggtggctcacg +cctgtaatcccagcactttgggaggccgaggcgggtggatcatgaggtcaggagatcgag +accatcctggctaaaacggtgaaaccccgtctctactaaaaatacaaaaaattagccggg +cgcggtggcgggcgcctaggcaggagaatggcgtgaacccgggaagcggagcttgcagtg +agccgagattgcgccactgcagtccgcagtccgacctgggcgacagagagagactccgtc +tc---aaaaaaaaaaaaaaaaaaaatgctcatacgtggttggcaggagtgtaaatagcct +caaccaatttggaaagcaatttgccaatactagttaatataacgatctagatagtgggca +acccggattagcctttt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/msa.fa.fai new file mode 100644 index 00000000..1ff4220c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_5039849_5040600 1037 27 60 61 +syndip_1_chr20:5039849-5040600 1037 1114 60 61 +syndip_2_chr20:5039849-5040600 1037 2201 60 61 +p:HG002_1_chr20:5039849-5040600 1037 3289 60 61 +p:HG002_2_chr20:5039849-5040600 1037 4377 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/output.vcf.gz new file mode 100644 index 00000000..f0030816 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/output.vcf.gz.tbi new file mode 100644 index 00000000..3500121a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5039949-5040500/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/base.vcf.gz new file mode 100644 index 00000000..dbe5cdeb Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/base.vcf.gz.tbi new file mode 100644 index 00000000..e5014c6f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/comp.vcf.gz new file mode 100644 index 00000000..12f5e9b0 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/comp.vcf.gz.tbi new file mode 100644 index 00000000..fa73c3f0 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/haps.fa new file mode 100644 index 00000000..73c30929 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/haps.fa @@ -0,0 +1,82 @@ +>ref_chr20_5041757_5042810 +CAGTGTTGGAGCCTGCAGATGCTGACAGTGCCTGCAGCTTTCCTGCCTATTTTAGGACTTGCTAGAAGCTTGGCATGTCCTAAAAACCCTTTTTCAAGAGTCTCTCCCCAGCTGCTGCTAGCGGGATTTTTTTTTTAACTCTCTATCCTATTTAACCTCCTCACTGATGACCTTTTAATGCGTAACTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTCCCAGGCTGGAGTGCAGTGGTGTGATCTCGGCTCACTGCAACCTGTGCCTCCCAGGTTCAAGCGATCTCCTGCCTCAGCCTCCCCAGTACCTAGGATTACAGGTGCGCGCCTCCAGCATAGCTAATGTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTTATGCATAACTTTTTATCACAGATGTTTGATCTCAGTTTTAATCTTTTCAACATTTGTAAACCCTTGGTTCATTGTGCTTCTCCCTTTATTACTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTTTCGCTCTTGTTGCCCAGGCTGGAGTGCAGTGGCGCACTCTCGGTTCACTGCAATCTCCACCTCATAGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGCACACGCCACCATGCCTGGCTAATTTTTCTTTTTCTTTTTTGTATTTTTAGTAGAGATGGGGTTTCACTATGTTGGCCAGACTGGTCTTGAACTCCTGACCTCGTGATCTGCCCACCTCAGACTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCGTGCCTGGCCTAATTTTGTATTTTTAGTAGAGACGGGGTTTCTCCATGTTGGTCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCTGCTCGTCTTGGCCTCCCAAAGTGTTGGGATTATAGGCATAAGCCACCACAACCGACCTGACTGCTCATTTTTAAACTCTTGATCTGACACTGGGGGACTTTAAGCTATAATCTTGTTCTGTTTTTTTTCTTTTTCTCTTGCCTTCTATGCTTTCCATT +>syndip_1_chr20:5041757-5042810 +CAGTGTTGGAGCCTGCAGATGCTGACAGTGCCTGCAGCTTTCCTGCCTATTTTAGGACTT +GCTAGAAGCTTGGCATGTCCTAAAAACCCTTTTTCAAGAGTCTCTCCCCAGCTGCTGCTA +GCGGGATTTTTTTTTTAACTCTCTATCCTATTTAACCTCCTCACTGATGACCTTTTAATG +CATAACTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTCCCAGGCTGGAGTGCA +GTGGTGTGATCTCGGCTCACTGCAACCTGTGCCTCCCAGGTTCAAGCGATCTCCTGCCTC +AGCCTCCCCAGTACCTAGGATTACAGGTGCGCGCCTCCAGCATAGCTAATGTTTGTATTT +TTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTTATGCATAACTTTTTATCACA +GATGTTTGATCTCAGTTTTAATCTTTTCAACATTTGTAAACCCTTGGTTCATTGTGCTTC +TCCCTTTATTACTCTTTTTTTTTTTTTTTTGAGACGGAGTTTCGCTCTTGTTGCCCAGGC +TGGAGTGCAGTGGCGCACTCTCGGTTCACTGCAATCTCCACCTCATAGGTTCAAGCGATT +CTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGCACACGCCACCATGCCTGGCTAA +TTTTTCTTTTTCTTTTTTGTATTTTTAGTAGAGATGGGGTTTCACTATGTTGGCCAGACT +GGTCTTGAACTCCTGACCTCGTGATCTGCCCACCTCAGACTCCCAAAGTGCTGGGATTAC +AGGTGTGAGCCACCGTGCCTGGCCTAATTTTGTATTTTTAGTAGAGACGGGGTTTCTCCA +TGTTGGTCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCTGCTCGTCTTGGCCTCCCA +AAGTGTTGGGATTATAGGCATAAGCCACCACAACCGACCTGACTGCTCATTTTTAAACTC +TTGATCTGACACTGGGGGACTTTAAGCTATAATCTTGTTCTGTTTTTTTTCTTTTTCTCT +TGCCTTCTATGCTTTCCATT +>syndip_2_chr20:5041757-5042810 +CAGTGTTGGAGCCTGCAGATGCTGACAGTGCCTGCAGCTTTCCTGCCTATTTTAGGACTT +GCTAGAAGCTTGGCATGTCCTAAAAACCCTTTTTCAAGAGTCTCTCCCCAGCTGCTGCTA +GCGGGATTTTTTTTTTAACTCTCTATCCTATTTAACCTCCTCACTGATGACCTTTTAATG +CGTAACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGA +CGGAGTCTCGCTCTCCCAGGCTGGAGTGCAGTGGTGTGATCTCGGCTCACTGCAACCTGT +GCCTCCCAGGTTCAAGCGATCTCCTGCCTCAGCCTCCCCAGTACCTAGGATTACAGGTGC +GCGCCTCCAGCATAGCTAATGTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGC +CAGGCTGGTTATGCATAACTTTTTATCACAGATGTTTGATCTCAGTTTTAATCTTTTCAA +CATTTGTAAACCCTTGGTTCATTGTGCTTCTCCCTTTATTACTCTTTTTTTTTTTTTTTT +TTTTTTTTTTTTTTTTGAGACGGAGTTTCGCTCTTGTTGCCCAGGCTGGAGTGCAGTGGC +GCACTCTCGGTTCACTGCAATCTCCACCTCATAGGTTCAAGCGATTCTCCTGCCTCAGCC +TCCTGAGTAGCTGGGATTACAGGCACACGCCACCATGCCTGGCTAATTTTTCTTTTTCTT +TTTTGTATTTTTAGTAGAGATGGGGTTTCACTATGTTGGCCAGACTGGTCTTGAACTCCT +GACCTCGTGATCTGCCCACCTCAGACTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACC +GTGCCTGGCCTAATTTTGTATTTTTAGTAGAGACGGGGTTTCTCCATGTTGGTCAGGCTG +GTCTCGAACTCCTGACCTCAGGTGATCTGCTCGTCTTGGCCTCCCAAAGTGTTGGGATTA +TAGGCATAAGCCACCACAACCGACCTGACTGCTCATTTTTAAACTCTTGATCTGACACTG +GGGGACTTTAAGCTATAATCTTGTTCTGTTTTTTTTCTTTTTCTCTTGCCTTCTATGCTT +TCCATT +>p:HG002_1_chr20:5041757-5042810 +CAGTGTTGGAGCCTGCAGATGCTGACAGTGCCTGCAGCTTTCCTGCCTATTTTAGGACTT +GCTAGAAGCTTGGCATGTCCTAAAAACCCTTTTTCAAGAGTCTCTCCCCAGCTGCTGCTA +GCGGGATTTTTTTTTTTAACTCTCTATCCTATTTAACCTCCTCACTGATGACCTTTTAAT +GCGTAACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAG +ACGGAGTCTCGCTCTCCCAGGCTGGAGTGCAGTGGTGTGATCTCGGCTCACTGCAACCTG +TGCCTCCCAGGTTCAAGCGATCTCCTGCCTCAGCCTCCCCAGTACCTAGGATTACAGGTG +CGCGCCTCCAGCATAGCTAATGTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGG +CCAGGCTGGTTATGCATAACTTTTTATCACAGATGTTTGATCTCAGTTTTAATCTTTTCA +ACATTTGTAAACCCTTGGTTCATTGTGCTTCTCCCTTTATTACTCTTTTTTTTTTTTTTT +TTTTTTTTTTTTTTTTTGAGACGGAGTTTCGCTCTTGTTGCCCAGGCTGGAGTGCAGTGG +CGCACTCTCGGTTCACTGCAATCTCCACCTCATAGGTTCAAGCGATTCTCCTGCCTCAGC +CTCCTGAGTAGCTGGGATTACAGGCACACGCCACCATGCCTGGCTAATTTTTCTTTTTCT +TTTTTGTATTTTTAGTAGAGATGGGGTTTCACTATGTTGGCCAGACTGGTCTTGAACTCC +TGACCTCGTGATCTGCCCACCTCAGACTCCCAAAGTGCTGGGATTACAGGTGTGAGCCAC +CGTGCCTGGCCTAATTTTGTATTTTTAGTAGAGACGGGGTTTCTCCATGTTGGTCAGGCT +GGTCTCGAACTCCTGACCTCAGGTGATCTGCTCGTCTTGGCCTCCCAAAGTGTTGGGATT +ATAGGCATGAGCCACCACAACCGACCTGACTGCTCATTTTTAAACTCTTGATCTGACACT +GGGGGACTTTAAGCTATAATCTTGTTCTGTTTTTTTTCTTTTTCTCTTGCCTTCTATGCT +TTCCATT +>p:HG002_2_chr20:5041757-5042810 +CAGTGTTGGAGCCTGCAGATGCTGACAGTGCCTGCAGCTTTCCTGCCTATTTTAGGACTT +GCTAGAAGCTTGGCATGTCCTAAAAACCCTTTTTCAAGAGTCTCTCCCCAGCTGCTGCTA +GCGGGATTTTTTTTTTAACTCTCTATCCTATTTAACCTCCTCACTGATGACCTTTTAATG +CATAACTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTCCCAGGCTGGAGTGCA +GTGGTGTGATCTCGGCTCACCGCAACCTGTGCCTCCCAGGTTCAAGTGATCTCCTGCCTC +AGCCTCCCCAGTACCTAGGATTACAGGTGCGCGCCTCCAGCATAGCTAATGTTTGTATTT +TTAGTAGAAACGGGGTTTCACCATGTTGGCCAGGATGGTTATGCATAACTTTTTATCACA +GATGTTTGATCTCAGTTTTAATCTTTTCAACATTTGTAAACCCTTGGTTCATTGTGCTTC +TCCCTTTATTACTCTTTTTTTTTTTTTTTTGAGACGGAGTTTCGCTCTTGTTGCCCAGGC +TGGAGTGCAGTGGAGCACTCTCGGTTCACTGCAACCTCCACCTCATAGGTTCAAGCGATT +CTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGTGCCCACCACCATGCCCAGCTAA +TTTTTTTTTTTGAGAGTCTCACACTGTCGCCCAGGCTGGAGTGCAATGGCACTATCTTGA +CTCACTGCAACCTCCTCCTGTGTTCACGTGATTCTCCTGCCTCAGCCTCCTGAGTAGCTG +GGATTACAGGCACATGCCACCATGCCCGGCTAATTTTTCTTTTTTTTTTTTTTTGTATTT +TTAGTAGAGATGGGGTTTCACTATGTTGGCCAGACTGGTCTTGAACTCCTGACCTCGTGA +TCTGCCCGCCTCGGACTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCGTGCCCGGCC +TAATTTTGTATTTTTAGTAGAGACGGGGTTTCTCCATGTTGGTCAGGCTGGTCTCGAACT +CCCGATCTCAGGTGATCCGCTCGTCTTGGCCTCCCAAAGTGTTGGGATTACAGGCATGAG +CCACCACACCCAGCCTGACTGCTCATTTTTAAACTCTTGATCTGACACTGGGGGACTTTA +AGCTATAATCTTGTTCTGTTTTTTTTCTTTTTCTCTTGCCTTCTATGCTTTCCATT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/haps.fa.ref.fa new file mode 100644 index 00000000..bdb60847 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:5041757-5042810 +CAGTGTTGGAGCCTGCAGATGCTGACAGTGCCTGCAGCTTTCCTGCCTATTTTAGGACTTGCTAGAAGCTTGGCATGTCCTAAAAACCCTTTTTCAAGAGTCTCTCCCCAGCTGCTGCTAGCGGGATTTTTTTTTTAACTCTCTATCCTATTTAACCTCCTCACTGATGACCTTTTAATGCGTAACTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTCCCAGGCTGGAGTGCAGTGGTGTGATCTCGGCTCACTGCAACCTGTGCCTCCCAGGTTCAAGCGATCTCCTGCCTCAGCCTCCCCAGTACCTAGGATTACAGGTGCGCGCCTCCAGCATAGCTAATGTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTTATGCATAACTTTTTATCACAGATGTTTGATCTCAGTTTTAATCTTTTCAACATTTGTAAACCCTTGGTTCATTGTGCTTCTCCCTTTATTACTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTTTCGCTCTTGTTGCCCAGGCTGGAGTGCAGTGGCGCACTCTCGGTTCACTGCAATCTCCACCTCATAGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGCACACGCCACCATGCCTGGCTAATTTTTCTTTTTCTTTTTTGTATTTTTAGTAGAGATGGGGTTTCACTATGTTGGCCAGACTGGTCTTGAACTCCTGACCTCGTGATCTGCCCACCTCAGACTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCGTGCCTGGCCTAATTTTGTATTTTTAGTAGAGACGGGGTTTCTCCATGTTGGTCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCTGCTCGTCTTGGCCTCCCAAAGTGTTGGGATTATAGGCATAAGCCACCACAACCGACCTGACTGCTCATTTTTAAACTCTTGATCTGACACTGGGGGACTTTAAGCTATAATCTTGTTCTGTTTTTTTTCTTTTTCTCTTGCCTTCTATGCTTTCCATT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/msa.fa new file mode 100644 index 00000000..ca1646fc --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/msa.fa @@ -0,0 +1,110 @@ +>ref_chr20_5041757_5042810 +cagtgttggagcctgcagatgctgacagtgcctgcagctttcctgcctattttaggactt +gctagaagcttggcatgtcctaaaaaccctttttcaagagtctctccccagctgctgcta +gcggga-ttttttttttaactctctatcctatttaacctcctcactgatgaccttttaat +gcgtaac----------------------------ttttttttttttttttttttttgag +acggagtctcgctctcccaggctggagtgcagtggtgtgatctcggctcactgcaacctg +tgcctcccaggttcaagcgatctcctgcctcagcctccccagtacctaggattacaggtg +cgcgcctccagcatagctaatgtttgtatttttagtagagacggggtttcaccatgttgg +ccaggctggttatgcataactttttatcacagatgtttgatctcagttttaatcttttca +acatttgtaaacccttggttcattgtgcttctccctttattactc----ttttttttttt +tttttttttttttttttgagacggagtttcgctcttgttgcccaggctggagtgcagtgg +cgcactctcggttcactgcaatctccacctcataggttcaagcgattctcctgcctcagc +ctcctgagtagctgggattacaggcacacgccaccatgcctggctaattt---------- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------ttctttttcttttttgtatttttagtagagatgg +ggtttcactatgttggccagactggtcttgaactcctgacctcgtgatctgcccacctca +gactcccaaagtgctgggattacaggtgtgagccaccgtgcctggcctaattttgtattt +ttagtagagacggggtttctccatgttggtcaggctggtctcgaactcctgacctcaggt +gatctgctcgtcttggcctcccaaagtgttgggattataggcataagccaccacaaccga +cctgactgctcatttttaaactcttgatctgacactgggggactttaagctataatcttg +ttctgttttttttctttttctcttgccttctatgctttccatt +>syndip_1_chr20:5041757-5042810 +cagtgttggagcctgcagatgctgacagtgcctgcagctttcctgcctattttaggactt +gctagaagcttggcatgtcctaaaaaccctttttcaagagtctctccccagctgctgcta +gcggga-ttttttttttaactctctatcctatttaacctcctcactgatgaccttttaat +gcataac------------------------------ttttttttttttttttttttgag +acggagtctcgctctcccaggctggagtgcagtggtgtgatctcggctcactgcaacctg +tgcctcccaggttcaagcgatctcctgcctcagcctccccagtacctaggattacaggtg +cgcgcctccagcatagctaatgtttgtatttttagtagagacggggtttcaccatgttgg +ccaggctggttatgcataactttttatcacagatgtttgatctcagttttaatcttttca +acatttgtaaacccttggttcattgtgcttctccctttattactc--------------- +-ttttttttttttttttgagacggagtttcgctcttgttgcccaggctggagtgcagtgg +cgcactctcggttcactgcaatctccacctcataggttcaagcgattctcctgcctcagc +ctcctgagtagctgggattacaggcacacgccaccatgcctggctaattt---------- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------ttctttttcttttttgtatttttagtagagatgg +ggtttcactatgttggccagactggtcttgaactcctgacctcgtgatctgcccacctca +gactcccaaagtgctgggattacaggtgtgagccaccgtgcctggcctaattttgtattt +ttagtagagacggggtttctccatgttggtcaggctggtctcgaactcctgacctcaggt +gatctgctcgtcttggcctcccaaagtgttgggattataggcataagccaccacaaccga +cctgactgctcatttttaaactcttgatctgacactgggggactttaagctataatcttg +ttctgttttttttctttttctcttgccttctatgctttccatt +>syndip_2_chr20:5041757-5042810 +cagtgttggagcctgcagatgctgacagtgcctgcagctttcctgcctattttaggactt +gctagaagcttggcatgtcctaaaaaccctttttcaagagtctctccccagctgctgcta +gcggga-ttttttttttaactctctatcctatttaacctcctcactgatgaccttttaat +gcgtaacttttttttttttttttttttttttttttttttttttttttttttttttttgag +acggagtctcgctctcccaggctggagtgcagtggtgtgatctcggctcactgcaacctg +tgcctcccaggttcaagcgatctcctgcctcagcctccccagtacctaggattacaggtg +cgcgcctccagcatagctaatgtttgtatttttagtagagacggggtttcaccatgttgg +ccaggctggttatgcataactttttatcacagatgtttgatctcagttttaatcttttca +acatttgtaaacccttggttcattgtgcttctccctttattactcttttttttttttttt +tttttttttttttttttgagacggagtttcgctcttgttgcccaggctggagtgcagtgg +cgcactctcggttcactgcaatctccacctcataggttcaagcgattctcctgcctcagc +ctcctgagtagctgggattacaggcacacgccaccatgcctggctaattt---------- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------ttctttttcttttttgtatttttagtagagatgg +ggtttcactatgttggccagactggtcttgaactcctgacctcgtgatctgcccacctca +gactcccaaagtgctgggattacaggtgtgagccaccgtgcctggcctaattttgtattt +ttagtagagacggggtttctccatgttggtcaggctggtctcgaactcctgacctcaggt +gatctgctcgtcttggcctcccaaagtgttgggattataggcataagccaccacaaccga +cctgactgctcatttttaaactcttgatctgacactgggggactttaagctataatcttg +ttctgttttttttctttttctcttgccttctatgctttccatt +>p:HG002_1_chr20:5041757-5042810 +cagtgttggagcctgcagatgctgacagtgcctgcagctttcctgcctattttaggactt +gctagaagcttggcatgtcctaaaaaccctttttcaagagtctctccccagctgctgcta +gcgggatttttttttttaactctctatcctatttaacctcctcactgatgaccttttaat +gcgtaacttttttttttttttttttttttttttttttttttttttttttttttttttgag +acggagtctcgctctcccaggctggagtgcagtggtgtgatctcggctcactgcaacctg +tgcctcccaggttcaagcgatctcctgcctcagcctccccagtacctaggattacaggtg +cgcgcctccagcatagctaatgtttgtatttttagtagagacggggtttcaccatgttgg +ccaggctggttatgcataactttttatcacagatgtttgatctcagttttaatcttttca +acatttgtaaacccttggttcattgtgcttctccctttattactcttttttttttttttt +tttttttttttttttttgagacggagtttcgctcttgttgcccaggctggagtgcagtgg +cgcactctcggttcactgcaatctccacctcataggttcaagcgattctcctgcctcagc +ctcctgagtagctgggattacaggcacacgccaccatgcctggctaattt---------- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------ttctttttcttttttgtatttttagtagagatgg +ggtttcactatgttggccagactggtcttgaactcctgacctcgtgatctgcccacctca +gactcccaaagtgctgggattacaggtgtgagccaccgtgcctggcctaattttgtattt +ttagtagagacggggtttctccatgttggtcaggctggtctcgaactcctgacctcaggt +gatctgctcgtcttggcctcccaaagtgttgggattataggcatgagccaccacaaccga +cctgactgctcatttttaaactcttgatctgacactgggggactttaagctataatcttg +ttctgttttttttctttttctcttgccttctatgctttccatt +>p:HG002_2_chr20:5041757-5042810 +cagtgttggagcctgcagatgctgacagtgcctgcagctttcctgcctattttaggactt +gctagaagcttggcatgtcctaaaaaccctttttcaagagtctctccccagctgctgcta +gcggga-ttttttttttaactctctatcctatttaacctcctcactgatgaccttttaat +gcataac------------------------------ttttttttttttttttttttgag +acggagtctcgctctcccaggctggagtgcagtggtgtgatctcggctcaccgcaacctg +tgcctcccaggttcaagtgatctcctgcctcagcctccccagtacctaggattacaggtg +cgcgcctccagcatagctaatgtttgtatttttagtagaaacggggtttcaccatgttgg +ccaggatggttatgcataactttttatcacagatgtttgatctcagttttaatcttttca +acatttgtaaacccttggttcattgtgcttctccctttattactc--------------- +-ttttttttttttttttgagacggagtttcgctcttgttgcccaggctggagtgcagtgg +agcactctcggttcactgcaacctccacctcataggttcaagcgattctcctgcctcagc +ctcctgagtagctgggattacaggtgcccaccaccatgcccagctaatttttttttttga +gagtctcacactgtcgcccaggctggagtgcaatggcactatcttgactcactgcaacct +cctcctgtgttcacgtgattctcctgcctcagcctcctgagtagctgggattacaggcac +atgccaccatgcccggctaatttttctttttttttttttttgtatttttagtagagatgg +ggtttcactatgttggccagactggtcttgaactcctgacctcgtgatctgcccgcctcg +gactcccaaagtgctgggattacaggtgtgagccaccgtgcccggcctaattttgtattt +ttagtagagacggggtttctccatgttggtcaggctggtctcgaactcccgatctcaggt +gatccgctcgtcttggcctcccaaagtgttgggattacaggcatgagccaccacacccag +cctgactgctcatttttaaactcttgatctgacactgggggactttaagctataatcttg +ttctgttttttttctttttctcttgccttctatgctttccatt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/msa.fa.fai new file mode 100644 index 00000000..5bdcc190 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_5041757_5042810 1243 27 60 61 +syndip_1_chr20:5041757-5042810 1243 1323 60 61 +syndip_2_chr20:5041757-5042810 1243 2619 60 61 +p:HG002_1_chr20:5041757-5042810 1243 3916 60 61 +p:HG002_2_chr20:5041757-5042810 1243 5213 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/output.vcf.gz new file mode 100644 index 00000000..e61cf6d8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/output.vcf.gz.tbi new file mode 100644 index 00000000..ff79cc97 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:5041857-5042710/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/base.vcf.gz new file mode 100644 index 00000000..7574f493 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/base.vcf.gz.tbi new file mode 100644 index 00000000..2c3ea2f8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/comp.vcf.gz new file mode 100644 index 00000000..52ccf8eb Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/comp.vcf.gz.tbi new file mode 100644 index 00000000..ff990e4b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/haps.fa new file mode 100644 index 00000000..19770031 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/haps.fa @@ -0,0 +1,58 @@ +>ref_chr20_50775444_50776124 +TGAACAAAGTGAACTAATAGTAGTTCACGAAATCTACTGGTTTATAATGTCACATACCAAAGGCTTGTGTCTTTAAATCTATCTCTAGACTTGGTATTCTGCTTTCTCATTCTGTCTCTCCAAAGATTTCCATATATATATATATATATATATATATATATATATATATATATAAATATAAATATATTCTATATATTCATATATATATATTCTATATATTCATATATATAAATATATTCTATATATTCATATATAAATATATTCCATATATATAAATATATTCCATATATTTATATATAAATATATATCATATATTTATATATAAATATATATCATATATTTATATATAAATATATATCATATATTTATATATAATATATATCATATATTTATATATAAATATATATCATATATTTATATATAAATATATATCATATATTAATATATATCATATATTTATATATTAATATATATCATATATTTATATATTAATATATATCATATATTTATATATAAATATATATCATATATTTATATATAAATATATATCTACATTTTTTGAGACAGAGTCTGGCTCTGTCACCCCAGCTGGAGTGCAGTGGTACGATCTCAGCTCATTGCAACCTCCACCTCCCAGGTTCAAGCGATTCTCGTGCCTCAGCCTCCATAGTAGCTGGAATT +>syndip_1_chr20:50775444-50776124 +TGAACAAAGTGAACTAATAGTAGTTCACGAAATCTACTGGTTTATAATGTCACATACCAA +AGGCTTGTGTCTTTAAATCTATCTCTAGACTTGGTATTCTGCTTTCTCATTCTGTCTCTC +CAAAGATTTCCATATATATATATATATATATATAAATATAAATATATTCTATATATTCAT +ATATATATATTCTATATATTCATATATATAAATATATTCTATATATTCATATATATAAAT +ATATTCTATATATTCATATATAAATATATTCCATATATATAAATATATTCCATATATTTA +TATATAAATATATATCATATATTTATATATAAATATATATCATATATTTATATATAAATA +TATATCATATATTTATATATAAATATATATCATATATTTATATATAAATATATATCATAT +ATTTATATATAAATATATATCATATATTTATATATAATATATATCATATATTATATATAA +ATATATATCATATATTTATATATAAATATATATCATATATTAATATATATCATATATTTA +TATATTAATATATATCATATATTTATATATTAATATATATCATATATTTATATATAAATA +TATATCATATATTTATATATAAATATATATCTACATTTTTTGAGACAGAGTCTGGCTCTG +TCACCCCAGCTGGAGTGCAGTGGTACGATCTCAGCTCATTGCAACCTCCACCTCCCAGGT +TCAAGCGATTCTCGTGCCTCAGCCTCCATAGTAGCTGGAATT +>syndip_2_chr20:50775444-50776124 +TGAACAAAGTGAACTAATAGTAGTTCACGAAATCTACTGGTTTATAATGTCACATACCAA +AGGCTTGTGTCTTTAAATCTATCTCTAGACTTGGTATTCTGCTTTCTCATTCTGTCTCTC +CAAAGATTTCCATATATATATATATATATATATATATATATATATATATATATAAATATA +AATATATTCTATATATTCATATATATATATTCTATATATTCATATATATAAATATATTCT +ATATATTCATATATATAAATATATTCTATATATTCATATATAAATATATTCCATATATAT +AAATATATTCCATATATTTATATATAAATATATATCATATATTTATATATAAATATATAT +CATATATTTATATATAAATATATATCATATATTTATATATAAATATATATCATATATTTA +TATATAAATATATATCATATATTTATATATAATATATATCATATATTATATATAAATATA +TATCATATATTTATATATAAATATATATCATATATTAATATATATCATATATTTATATAT +TAATATATATCATATATTTATATATTAATATATATCATATATTTATATATAAATATATAT +CATATATTTATATATAAATATATATCTACATTTTTTGAGACAGAGTCTGGCTCTGTCACC +CCAGCTGGAGTGCAGTGGTACGATCTCAGCTCATTGCAACCTCCACCTCCCAGGTTCAAG +CGATTCTCGTGCCTCAGCCTCCATAGTAGCTGGAATT +>p:HG002_1_chr20:50775444-50776124 +TGAACAAAGTGAACTAATAGTAGTTCACGAAATCTACTGGTTTATAATGTCACATACCAA +AGGCTTGTGTCTTTAAATCTATCTCTAGACTTGGTATTCTGCTTTCTCATTCTGTCTCTC +CAAAGATTTCCATATATATATATATATATATATATATATATATATATATATATAAATATA +AATATATTCTATATATTCATATATATATATTCTATATATTCATATATATAAATATATTCT +ATATATTCATATATATAAATATATTCTATATATTCATATATAAATATATTCCATATATAT +AAATATATTCCATATATTTATATATAAATATATATCATATATTTATATATAAATATATAT +CATATATTTATATATAAATATATATCATATATTTATATATAAATATATATCATATATTTA +TATATAAATATATATCATATATTTATATATAATATATATCATATATTATATATAAATATA +TATCATATATTTATATATAAATATATATCATATATTAATATATATCATATATTTATATAT +TAATATATATCATATATTTATATATTAATATATATCATATATTTATATATAAATATATAT +CATATATTTATATATAAATATATATCTACATTTTTTGAGACAGAGTCTGGCTCTGTCACC +CCAGCTGGAGTGCAGTGGTACGATCTCAGCTCATTGCAACCTCCACCTCCCAGGTTCAAG +CGATTCTCGTGCCTCAGCCTCCATAGTAGCTGGAATT +>p:HG002_2_chr20:50775444-50776124 +TGAACAAAGTGAACTAATAGTAGTTCACGAAATCTACTGGTTTATAATGTCACATACCAA +AGGCTTGTGTCTTTAAATCTATCTCTAGACTTGGTATTCTGCTTTCTCATTCTGTCTCTC +CAAAGATTTCCATATATATATATATATATATATAAATATAAATATATTCTATATATTCAT +ATATATATATTCTATATATTCATATATATAAATATATTCTATATATTCATATATATAAAT +ATATTCTATATATTCATATATAAATATATTCCATATATATAAATATATTCCATATATTTA +TATATAAATATATATCATATATTTATATATAAATATATATCATATATTTATATATAAATA +TATATCATATATTTATATATAAATATATATCATATATTTATATATAAATATATATCATAT +ATTTATATATAAATATATATCATATATTTATATATAATATATATCATATATTATATATAA +ATATATATCATATATTTATATATAAATATATATCATATATTAATATATATCATATATTTA +TATATTAATATATATCATATATTTATATATTAATATATATCATATATTTATATATAAATA +TATATCATATATTTATATATAAATATATATCTACATTTTTTGAGACAGAGTCTGGCTCTG +TCACCCCAGCTGGAGTGCAGTGGTACGATCTCAGCTCATTGCAACCTCCACCTCCCAGGT +TCAAGCGATTCTCGTGCCTCAGCCTCCATAGTAGCTGGAATT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/haps.fa.ref.fa new file mode 100644 index 00000000..434fbfbe --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:50775444-50776124 +TGAACAAAGTGAACTAATAGTAGTTCACGAAATCTACTGGTTTATAATGTCACATACCAAAGGCTTGTGTCTTTAAATCTATCTCTAGACTTGGTATTCTGCTTTCTCATTCTGTCTCTCCAAAGATTTCCATATATATATATATATATATATATATATATATATATATATATAAATATAAATATATTCTATATATTCATATATATATATTCTATATATTCATATATATAAATATATTCTATATATTCATATATAAATATATTCCATATATATAAATATATTCCATATATTTATATATAAATATATATCATATATTTATATATAAATATATATCATATATTTATATATAAATATATATCATATATTTATATATAATATATATCATATATTTATATATAAATATATATCATATATTTATATATAAATATATATCATATATTAATATATATCATATATTTATATATTAATATATATCATATATTTATATATTAATATATATCATATATTTATATATAAATATATATCATATATTTATATATAAATATATATCTACATTTTTTGAGACAGAGTCTGGCTCTGTCACCCCAGCTGGAGTGCAGTGGTACGATCTCAGCTCATTGCAACCTCCACCTCCCAGGTTCAAGCGATTCTCGTGCCTCAGCCTCCATAGTAGCTGGAATT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/msa.fa new file mode 100644 index 00000000..bc7feb72 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/msa.fa @@ -0,0 +1,75 @@ +>ref_chr20_50775444_50776124 +tgaacaaagtgaactaatagtagttcacgaaatctactggtttataatgtcacataccaa +aggcttgtgtctttaaatctatctctagacttggtattctgctttctcattctgtctctc +caaagatttccatatatatatatatatatatatatatatatatatatatatataaatata +aatatattctatatattcatatat---------------------------atatattct +atatattcatatatataaatatattctatatattcatatataaatatattccatatatat +aaatatattc-------------------------catatatttatatataaatatatat +catatatttatatataaatatatatcatatatttatatataaatatatatcatatattta +tatat-aatatatatcatatat-------------------------------------- +----------ttatatataaatatatatcatatatttatatataaatatatatcatatat +taatatatatcatatatttatatattaatatatatcatatatttatatattaatatatat +catatatttatatataaatatatatcatatatttatatataaatatatatctacattttt +tgagacagagtctggctctgtcaccccagctggagtgcagtggtacgatctcagctcatt +gcaacctccacctcccaggttcaagcgattctcgtgcctcagcctccatagtagctggaa +tt +>syndip_1_chr20:50775444-50776124 +tgaacaaagtgaactaatagtagttcacgaaatctactggtttataatgtcacataccaa +aggcttgtgtctttaaatctatctctagacttggtattctgctttctcattctgtctctc +caaagatttcc--------------------atatatatatatatatatatataaatata +aatatattctatatattcatatatatatattctatatattcatatatataaatatattct +atatattcatatatataaatatattctatatattcatatataaatatattccatatatat +aaatatattccatatatttatatataaatatatatcatatatttatatataaatatatat +catatatttatatataaatatatatcatatatttatatataaatatatatcatatattta +tatataaatatatatcatatatttatatataaatatatatcatatatttatatataatat +atatcatatattatatataaatatatatcatatatttatatataaatatatatcatatat +taatatatatcatatatttatatattaatatatatcatatatttatatattaatatatat +catatatttatatataaatatatatcatatatttatatataaatatatatctacattttt +tgagacagagtctggctctgtcaccccagctggagtgcagtggtacgatctcagctcatt +gcaacctccacctcccaggttcaagcgattctcgtgcctcagcctccatagtagctggaa +tt +>syndip_2_chr20:50775444-50776124 +tgaacaaagtgaactaatagtagttcacgaaatctactggtttataatgtcacataccaa +aggcttgtgtctttaaatctatctctagacttggtattctgctttctcattctgtctctc +caaagatttccatatatatatatatatatatatatatatatatatatatatataaatata +aatatattctatatattcatatatatatattctatatattcatatatataaatatattct +atatattcatatatataaatatattctatatattcatatataaatatattccatatatat +aaatatattc-------------------------catatatttatatataaatatatat +catatatttatatataaatatatatcatatatttatatataaatatatatcatatattta +tatataaatatatatcatatatttatatataaatatatatcatatatttatatataatat +atatcatatattatatataaatatatatcatatatttatatataaatatatatcatatat +taatatatatcatatatttatatattaatatatatcatatatttatatattaatatatat +catatatttatatataaatatatatcatatatttatatataaatatatatctacattttt +tgagacagagtctggctctgtcaccccagctggagtgcagtggtacgatctcagctcatt +gcaacctccacctcccaggttcaagcgattctcgtgcctcagcctccatagtagctggaa +tt +>p:HG002_1_chr20:50775444-50776124 +tgaacaaagtgaactaatagtagttcacgaaatctactggtttataatgtcacataccaa +aggcttgtgtctttaaatctatctctagacttggtattctgctttctcattctgtctctc +caaagatttccatatatatatatatatatatatatatatatatatatatatataaatata +aatatattctatatattcatatatatatattctatatattcatatatataaatatattct +atatattcatatatataaatatattctatatattcatatataaatatattccatatatat +aaatatattc-------------------------catatatttatatataaatatatat +catatatttatatataaatatatatcatatatttatatataaatatatatcatatattta +tatataaatatatatcatatatttatatataaatatatatcatatatttatatataatat +atatcatatattatatataaatatatatcatatatttatatataaatatatatcatatat +taatatatatcatatatttatatattaatatatatcatatatttatatattaatatatat +catatatttatatataaatatatatcatatatttatatataaatatatatctacattttt +tgagacagagtctggctctgtcaccccagctggagtgcagtggtacgatctcagctcatt +gcaacctccacctcccaggttcaagcgattctcgtgcctcagcctccatagtagctggaa +tt +>p:HG002_2_chr20:50775444-50776124 +tgaacaaagtgaactaatagtagttcacgaaatctactggtttataatgtcacataccaa +aggcttgtgtctttaaatctatctctagacttggtattctgctttctcattctgtctctc +caaagatttcc--------------------atatatatatatatatatatataaatata +aatatattctatatattcatatatatatattctatatattcatatatataaatatattct +atatattcatatatataaatatattctatatattcatatataaatatattccatatatat +aaatatattccatatatttatatataaatatatatcatatatttatatataaatatatat +catatatttatatataaatatatatcatatatttatatataaatatatatcatatattta +tatataaatatatatcatatatttatatataaatatatatcatatatttatatataatat +atatcatatattatatataaatatatatcatatatttatatataaatatatatcatatat +taatatatatcatatatttatatattaatatatatcatatatttatatattaatatatat +catatatttatatataaatatatatcatatatttatatataaatatatatctacattttt +tgagacagagtctggctctgtcaccccagctggagtgcagtggtacgatctcagctcatt +gcaacctccacctcccaggttcaagcgattctcgtgcctcagcctccatagtagctggaa +tt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/msa.fa.fai new file mode 100644 index 00000000..1c7328a9 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_50775444_50776124 782 29 60 61 +syndip_1_chr20:50775444-50776124 782 859 60 61 +syndip_2_chr20:50775444-50776124 782 1689 60 61 +p:HG002_1_chr20:50775444-50776124 782 2520 60 61 +p:HG002_2_chr20:50775444-50776124 782 3351 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/output.vcf.gz new file mode 100644 index 00000000..cc54bd88 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/output.vcf.gz.tbi new file mode 100644 index 00000000..d28f75ff Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:50775544-50776024/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/base.vcf.gz new file mode 100644 index 00000000..6c94cc73 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/base.vcf.gz.tbi new file mode 100644 index 00000000..11d2f251 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/comp.vcf.gz new file mode 100644 index 00000000..e32f0953 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/comp.vcf.gz.tbi new file mode 100644 index 00000000..dd4fff64 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/haps.fa new file mode 100644 index 00000000..55d46e01 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/haps.fa @@ -0,0 +1,187 @@ +>ref_chr20_51952383_51954993 +CTCTGTCTCAAAAAAAAAAAAGTCATTGATTGATCTCTTTCTGGTTTAACTGCTATTATTTAGTTTTATAGCATTACATTCAAGTTTTTATAGCATTACAATTCCTAGATTCTATTTTCAAATATTGATTTGCTTAATTTTTTTTTTTTTTTTGAGATGGGGTTTTGCTCTGTCGCCCAGGCTGGAGTGCAATGGCATGATCTTGGCTCACTGCAACCTCTGCCTCCTGGGTTCAGCCATTCTCCTGCCTCAGCCTCCCGAGTGGCTGGGACTACAGGTGCCCGCCACCACGCCTGGCTAATTTTTTTTTTTTATATTTTTAGTAGAGACGGGGTTTCACCATGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTAGGATTACAGGCTTGAGCCACCGCGCCTGGCCTTTAATATAATTTTTATGAAGACATTATTTCCACTTCATTGGGCTCTCTAGAATTAGATTGCATAAATACTGTAGTTTTATTTCAATAAAAAGTCAACTGTTATTTAAACCATGACTAAAGCTTGACATGAATAGAGACTTTAAAACAATAAACATTGCCAGACATGGTGGCACATGCCTGTAGTCTCAGCTACTCAAGAAACTGAGACAGGAGGATCTCCTGAGCCAAGGAGTTCCAGCCCAGCCTGGACAACATAGTGAGATCCCATCTCTTAAAAAAAAAAAAAAAAAGATTTGCTTAATTTTACTTTTACAATTTTTTCTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGATGGAGTCTTGCTCTGTTACCAGGCTGGAGTGCAGTGGTGTGATATCGGCTCCCTGCAACCTCTGCCTCCTGGGTTAAAGCAATTTTCCTGCCCCAGCCTCCCGAGTAGCTGGGACTACAGGCGCGCGTCACCACACCCAGCTAATTTTTGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGATGGTCTCAATCTCTTGATCTCGTGATCCGCCCACCTTGGCCTCCCAAAGTGCTGGAATTACAGGCGTGATCCGCCATAACCTGGCCTTCCTTCTTTTCTTTAAAAATTTTTTTCTGAGACAGAGTCTCACTCTGTTGCCCAGCCTGGAGTGCAGTGGCACAATCTCGGCTCACTGTAGCCTCCACCTTCTGGGTTCAAGTGATTCTCGTGCCTCAGCCTCCCGAGTAGCTGTGACTACAGGTGTGTGCCCTCATGCCTGGCTAATTTTTGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACCCTGGGCTCAAGTGTTCTGTCTGCCTCAGCCCCCCAAAGTGCTGGGATTACAGGCATGAGCCAAAGTGCCTGGCTAGAAAATTGTAAAAGTAACTTAATATCTGCCTCATATACTTTTGTTTTATTTAAAAATGCAAATCCTCAACCACAAATCGAAACAAGAACAACCCTCTGATGACTTCCCTCCCTCTCTCTTTGTACAAAGAAGACTTTCTGCTGTCTGACTCTGACCACCTTGGTCTATTTTATGGAGCTCCAACCCTGCCTTGTTTCCTTCTCAGGCCATCTGTCCTGGTTGGCCTCACTGTTGGAAATGCTCTTCTCAAGATGTTCACGTGGCTGGTTCTTTGTCATTCAGTCTCAGTTCAAATACTCCCTCCTCCAGGAAGCCTTCCCTAACTTCCTAGGTGAAAGTGGTTCCCTTCCCCTGAGTCACGATTATGGTTTCTTCAGTGTACTTATTAATGGCCAACACTGTCTCCTTTATTGTTTGCTTATGAATTTAAAGTCTGTTAGCAGCACCTGCAGCTTTTAAAAGCCTCCTTGTCTCTCTCTCTTTTTTTTTTTTTTTTTTTTTTTGAGGCGGAGTTTCGCTCTTGTTGGCCAGGCTGGAACGCAGTGATGCGATCTCGGCTCAGTGCAACCTCCACCTCTTGGGTTCAAGTGATTCTCCTGCCTCAGCCTCCTTAGTAGCTGAGACTACAGGCATGTGCCACCATGCTGGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCGTCATATTGGCCAAGCTGGTCTCGAACCCCTGACCTCAGGTGATCCACCCATCTTGGCCTCCCAGATGCTGGGATTACAGGCGTGAGCCACTGCGCCTGGCCTAATTGTCATTTTCGTTTTTTTGTTGAGACAGAGTTTCTGTCACCCAGGCTGGAATGCAGTGGCACGATCTCAGCTCACTGCAGCCTCTGCCTCTTGGGTTCAATTGATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGTGTGTGCCACCACACCCAGCTAATTTTTTCATTTTTAGTAGAGACGGGGTTTCACCATGTTGGTCAGGCTTGTCTCGAACTCCTGACCTCAGGTGATCCGTCCAACTTGGCCTCCCAAAGTGCTGAGATTACAGGCATGAGCTACCGTGCCCAGCTCTCAATTGTCACTTTTAGTGCATATTTTCTGGTTGTATAAAAGCTCTCCCATGCAAGAGGGCTGATGTTATAACAGTCGATTATTATACTGTCCTGCATTTTCATCAGGTAAAGAAAGCTTTTCATGTTTCACTGAG +>syndip_1_chr20:51952383-51954993 +CTCTGTCTCAAAAAAAAAAAAGTCATTGATTGATCTCTTTCTGGTTTAACTGCTATTATT +TAGTTTTATAGCATTACATTCAAGTTTTTATAGCATTACAATTCCTAGATTCTATTTTCA +AATATTGATTTGCTTAATTTTTTTTTTTTTTGAGATGGGGTTTTGCTCTGTCGCCCAGGC +TGGAGTGCAATGGCATGATCTTGGCTCACTGCAACCTCTGCCTCCTGGGTTCAGCCATTC +TCCTGCCTCAGCCTCCCGAGTGGCTGGGACTACAGGTGCCCGCCACCACGCCTGGCTAAT +TTTTTTTTTTTATATTTTTAGTAGAGACGGGGTTTCACCATGTTAGCCAGGATGGTCTCG +ATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTAGGATTACAGGCTTG +AGCCACCGCGCCTGGCCTTTAATATAATTTTTATGAAGACATTATTTCCACTTCATTGGG +CTCTCTAGAATTAGATTGCATAAATACTGTAGTTTTATTTCAATAAAAAGTCAACTGTTA +TTTAAACCATGACTAAAGCTTGACATGAATAGAGACTTTAAAACAATAAACATTGCCAGA +CATGGTGGCACATGCCTGTAGTCTCAGCTACTCAAGAAACTGAGACAGGAGGATCTCCTG +AGCCAAGGAGTTCCAGCCCAGCCTGGACAACATAGTGAGATCCCATCTCTTAAAAAAAAA +AAAAAAAGATTTGCTTAATTTTACTTTTACAATTTTTTCTTTTCTTTTTTTTTTTTTTTT +TTTTTTTTTTTTTGAGATGGAGTCTTGCTCTGTTACCAGGCTGGAGTGCAGTGGTGTGAT +ATCGGCTCCCTGCAACCTCTGCCTCCTGGGTTAAAGCAATTTTCCTGCCCCAGCCTCCCG +AGTAGCTGGGACTACAGGCGCGCGTCACCACACCCAGCTAATTTTTGTATTTTTAGTAGA +GATGGGGTTTCACCATGTTGGCCAGGATGGTCTCAATCTCTTGATCTCGTGATCCGCCCA +CCTTGGCCTCCCAAAGTGCTGGAATTACAGGCGTGATCCGCCATAACCTGGCCTTCCTTC +TTTTCTTTAAAAATTTTTTTCTGAGACAGAGTCTCACTCTGTTGCCCAGCCTGGAGTGCA +GTGGCACAATCTCGGCTCACTGTAGCCTCCACCTTCTGGGTTCAAGTGATTCTCGTGCCT +CAGCCTCCCGAGTAGCTGTGACTACAGGTGTGTGCCCTCATGCCTGGCTAATTTTTGTAT +TTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACCCTGGGCTCAAG +TGTTCTGTCTGCCTCAGCCCCCCAAAGTGCTGGGATTACAGGCATGAGCCAAAGTGCCTG +GCTAGAAAATTGTAAAAGTAACTTAATATCTGCCTCATATACTTTTGTTTTATTTAAAAA +TGCAAATCCTCAACCACAAATCGAAACAAGAACAACCCTCTGATGACTTCCCTCCCTCTC +TCTTTGTACAAAGAAGACTTTCTGCTGTCTGACTCTGACCACCTTGGTCTATTTTATGGA +GCTCCAACCCTGCCTTGTTTCCTTCTCAGGCCATCTGTCCTGGTTGGCCTCACTGTTGGA +AATGCTCTTCTCAAGATGTTCACGTGGCTGGTTCTTTGTCATTCAGTCTCAGTTCAAATA +CTCCCTCCTCCAGGAAGCCTTCCCTAACTTCCTAGGTGAAAGTGGTTCCCTTCCCCTGAG +TCACGATTATGGTTTCTTCAGTGTACTTATTAATGGCCAACACTGTCTCCTTTATTGTTT +GCTTATGAATTTAAAGTCTGTTAGCAGCACCTGCAGCTTTTAAAAGCCTCCTTGTCTCTC +TCTATTTTTTTTTTTTTTTTTTTGAGGCGGAGTTTCGCTCTTGTTGGCCAGGCTGGAACG +CAGTGATGCGATCTCGGCTCAGTGCAACCTCCACCTCTTGGGTTCAAGTGATTCTCCTGC +CTCAGCCTCCTTAGTAGCTGAGACTACAGGCATGTGCCACCATGCTGGCTAATTTTTGTA +TTTTTAGTAGAGACAGGGTTTCGTCATATTGGCCAAGCTGGTCTCGAACCCCTGACCTCA +GGTGATCCACCCATCTTGGCCTCCCAGATGCTGGGATTACAGGCGTGAGCCACTGCGCCT +GGCCTAATTGTCATTTTCGTTTTTTTGTTGAGACAGAGTTTCTGTCACCCAGGCTGGAAT +GCAGTGGCACGATCTCAGCTCACTGCAGCCTCTGCCTCTTGGGTTCAATTGATTCTCCTG +CCTCAGCCTCCCAAGTAGCTGGGACTACAGGTGTGTGCCACCACACCCAGCTAATTTTTT +CATTTTTAGTAGAGACGGGGTTTCACCATGTTGGTCAGGCTTGTCTCGAACTCCTGACCT +CAGGTGATCCGTCCAACTTGGCCTCCCAAAGTGCTGAGATTACAGGCATGAGCTACCGTG +CCCAGCTCTCAATTGTCACTTTTAGTGCATATTTTCTGGTTGTATAAAAGCTCTCCCATG +CAAGAGGGCTGATGTTATAACAGTCGATTATTATACTGTCCTGCATTTTCATCAGGTAAA +GAAAGCTTTTCATGTTTCACTGAG +>syndip_2_chr20:51952383-51954993 +CTCTGTCTCAAAAAAAAAAAAGTCATTGATTGATCTCTTTCTGGTTTAACTGCTATTATT +TAGTTTTATAGCATTACATTCAAGTTTTTATAGCATTACAATTCCTAGATTCTATTTTCA +AATATTGATTTGCTTAATTTTTTTTTTTTTTTGAGATGGGGTTTTGCTCTGTCGCCCAGG +CTGGAGTGCAATGGCATGATCTTGGCTCACTGCAACCTCTGCCTCCTGGGTTCAGCCATT +CTCCTGCCTCAGCCTCCCGAGTGGCTGGGACTACAGGTGCCCGCCACCACGCCTGGCTAA +TTTTTTTTTTTTATATTTTTAGTAGAGACGGGGTTTCACCATGTTAGCCAGGATGGTCTC +GATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTAGGATTACAGGCTT +GAGCCACCGCGCCTGGCCTTTAATATAATTTTTATGAAGACATTATTTCCACTTCATTGG +GCTCTCTAGAATTAGATTGCATAAATACTGTAGTTTTATTTCAATAAAAAGTCAACTGTT +ATTTAAACCATGACTAAAGCTTGACATGAATAGAGACTTTAAAACAATAAACATTGCCAG +ACATGGTGGCACATGCCTGTAGTCTCAGCTACTCAAGAAACTGAGACAGGAGGATCTCCT +GAGCCAAGGAGTTCCAGCCCAGCCTGGACAACATAGTGAGATCCCATCTCTTAAAAAAAA +AAAAAAAAAAAGATTTGCTTAATTTTACTTTTACAATTTTTTCTTTTCTTTTTTTTTTTT +TTTTTTTTTTTTTTTGAGATGGAGTCTTGCTCTGTTACCAGGCTGGAGTGCAGTGGTGTG +ATATCGGCTCCCTGCAACCTCTGCCTCCTGGGTTAAAGCAATTTTCCTGCCCCAGCCTCC +CGAGTAGCTGGGACTACAGGCGCGCGTCACCACACCCAGCTAATTTTTGTATTTTTAGTA +GAGATGGGGTTTCACCATGTTGGCCAGGATGGTCTCAATCTCTTGATCTCGTGATCCGCC +CACCTTGGCCTCCCAAAGTGCTGGAATTACAGGCGTGATCCGCCATAACCTGGCCTTCCT +TCTTTTCTTTAAAAATTTTTTTCTGAGACAGAGTCTCACTCTGTTGCCCAGCCTGGAGTG +CAGTGGCACAATCTCGGCTCACTGTAGCCTCCACCTTCTGGGTTCAAGTGATTCTCGTGC +CTCAGCCTCCCGAGTAGCTGTGACTACAGGTGTGTGCCCTCATGCCTGGCTAATTTTTGT +ATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACCCTGGGCTCA +AGTGTTCTGTCTGCCTCAGCCCCCCAAAGTGCTGGGATTACAGGCATGAGCCAAAGTGCC +TGGCTAGAAAATTGTAAAAGTAACTTAATATCTGCCTCATATACTTTTGTTTTATTTAAA +AATGCAAATCCTCAACCACAAATCGAAACAAGAACAACCCTCTGATGACTTCCCTCCCTC +TCTCTTTGTACAAAGAAGACTTTCTGCTGTCTGACTCTGACCACCTTGGTCTATTTTATG +GAGCTCCAACCCTGCCTTGTTTCCTTCTCAGGCCATCTGTCCTGGTTGGCCTCACTGTTG +GAAATGCTCTTCTCAAGATGTTCACGTGGCTGGTTCTTTGTCATTCAGTCTCAGTTCAAA +TACTCCCTCCTCCAGGAAGCCTTCCCTAACTTCCTAGGTGAAAGTGGTTCCCTTCCCCTG +AGTCACGATTATGGTTTCTTCAGTGTACTTATTAATGGCCAACACTGTCTCCTTTATTGT +TTGCTTATGAATTTAAAGTCTGTTAGCAGCACCTGCAGCTTTTAAAAGCCTCCTTGTCTC +TCTCTATTTTTTTTTTTTTTTTTTTTTGAGGCGGAGTTTCGCTCTTGTTGGCCAGGCTGG +AACGCAGTGATGCGATCTCGGCTCAGTGCAACCTCCACCTCTTGGGTTCAAGTGATTCTC +CTGCCTCAGCCTCCTTAGTAGCTGAGACTACAGGCATGTGCCACCATGCTGGCTAATTTT +TGTATTTTTAGTAGAGACAGGGTTTCGTCATATTGGCCAAGCTGGTCTCGAACCCCTGAC +CTCAGGTGATCCACCCATCTTGGCCTCCCAGATGCTGGGATTACAGGCGTGAGCCACTGC +GCCTGGCCTAATTGTCATTTTCGTTTTTTTGTTGAGACAGAGTTTCTGTCACCCAGGCTG +GAATGCAGTGGCACGATCTCAGCTCACTGCAGCCTCTGCCTCTTGGGTTCAATTGATTCT +CCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGTGTGTGCCACCACACCCAGCTAATT +TTTTCATTTTTAGTAGAGACGGGGTTTCACCATGTTGGTCAGGCTTGTCTCGAACTCCTG +ACCTCAGGTGATCCGTCCAACTTGGCCTCCCAAAGTGCTGAGATTACAGGCATGAGCTAC +CGTGCCCAGCTCTCAATTGTCACTTTTAGTGCATATTTTCTGGTTGTATAAAAGCTCTCC +CATGCAAGAGGGCTGATGTTATAACAGTCGATTATTATACTGTCCTGCATTTTCATCAGG +TAAAGAAAGCTTTTCATGTTTCACTGAG +>p:HG002_1_chr20:51952383-51954993 +CTCTGTCTCAAAAAAAAAAAAGTCATTGATTGATCTCTTTCTGGTTTAACTGCTATTATT +TAGTTTTATAGCATTACATTCAAGTTTTTATAGCATTACAATTCCTAGATTCTATTTTCA +AATATTGATTTGCTTAATTTTTTTTTTTTTTTGAGATGGGGTTTTGCTCTGTCGCCCAGG +CTGGAGTGCAATGGCATGATCTTGGCTCACTGCAACCTCCGCCTCCTGGGTTCAGCCATT +CTCCTGCCTCAGCCTCCCGAGTGGCTGGGACTACAGGTGCCCGCCACCACGCCTGGCTAA +TTTTTTTTTTTTATATTTTTAGTAGAGACGGGGTTTCACCATGTTAGCCAGGATGGTCTC +GATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTAGGATTACAGGCTT +GAGCCACCGCGCCTGGCCTTTAATATAATTTTTATGAAGACATTATTTCCACTTCATTGG +GCTCTCTAGAATTAGATTGCATAAATACTGTAGTTTTATTTCAATAAAAAGTCAACTGTT +ATTTAAACCATGACTAAAGCTTGACATGAATAGAGACTTTAAAACAATAAACATTGCCAG +ACATGGTGGCACATGCCTGTAGTCTCAGCTACTCAAGAAACTGAGACAGGAGGATCTCCT +GAGCCAAGGAGTTCCAGCCCAGCCTGGACAACATAGTGAGATCCCATCTCTTAAAAAAAA +AAAAAAAAAAAGATTTGCTTAATTTTACTTTTACAATTTTTTCTTTTCTTTTTTTTTTTT +TTTTTTTTTTTTTTTGAGATGGAGTCTTGCTCTGTTACCAGGCTGGAGTGCAGTGGTGTG +ATATCAGCTCCCTGCAACCTCTGCCTCCTGGGTTAAAGCAATTTTCCTGCCCCAGCCTCC +CGAGTAGCTGGGACTACAGGCGCGCGTCACCACACCCAGCTAATTTTTGTATTTTTAGTA +GAGATGGGGTTTCACCATGTTGGCCAGGATGGTCTCAATCTCTTGATCTCGTGATCCGCC +CACCTTGGCCTCCCAAAGTGCTGGAATTACAGGCGTGATCCGCCATAACCTGGCCTTCCT +TCTTTCCTTTAAAAATTTTTTTCTGAGACAGAGTCTCACTCTGTTGCCCAGCCTGGAGTG +CAGTGGCACAATCTCGGCTCACTGTAGCCTCCACCTTCTGGGTTCAAGTGATTCTCGTGC +CTCAGCCTCCCGAGTAGCTGTGACTACAGGTGTGTGCCCTCATGCCTGGCTAATTTTTGT +ATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACCCTGGGCTCA +AGTGTTCTGTCTGCCTCAGCCCCCCAAAGTGCTGGGATTACAGGCATGAGCCAAAGTGCC +TGGCTAGAAAATTGTAAAAGTAACTTAATATCTGCCTCATATACTTTTGTTTTATTTAAA +AATGCAAATCCTCAACCACAAATCGAAACAAGAACAACCCTCTGATGACTTCCCTCCCTC +TCTCTTTGTACAAAGAAGACTTTCTGCTGTCTGACTCTGACCACCTTGGTCTATTTTATG +GAGCTCCAACCCTGCCTTGTTTCCTTCTCAGGCCATCTGTCCTGGTTGGCCTCACTGTTG +GAAATGCTCTTCTCAAGATGTTCACGTGGCTGGTTCTTTGTCATTCAGTCTCAGTTCAAA +TACTCCCTCCTCCAGGAAGCCTTCCCTAACTTCCTAGGTGAAAGTGGTTCCCTTCCCCTG +AGTCACGATTATGGTTTCTTCAGTGTACTTATTAATGGCCAACACTGTCTCCTTTATTGT +TTGCTTATGAATTTAAAGTCTGTTAGCAGCACCTGCAGCTTTTAAAAGCCTCCTTGTCTC +TCTCTATTTTTTTTTTTTTTTTTTTTTGAGGCGGAGTTTCGCTCTTGTTGGCCAGGCTGG +AACGCAGTGATGCGATCTCGGCTCAGTGCAACCTCCACCTCTTGGGTTCAAGTGATTCTC +CTGCCTCAGCCTCCTTAGTAGCTGAGACTACAGGCATGTGCCACCATGCTGGCTAATTTT +TGTATTTTTAGTAGAGACAGGGTTTCGTCATATTGGCCAAGCTGGTCTCGAACCCCTGAC +CTCAGGTGATCCACCCATCTTGGCCTCCCAGATGCTGGGATTACAGGCGTGAGCCACTGC +GCCTGGCCTAATTGTCATTTTCGTTTTTTTGTTGAGACAGAGTTTCTGTCACCCAGGCTG +GAATGCAGTGGCACGATCTCAGCTCACTGCAGCCTCTGCCTCTTGGGTTCAATTGATTCT +CCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGTGTGTGCCACCACACCCAGCTAATT +TTTTCATTTTTAGTAGAGACGGGGTTTCACCATGTTGGTCAGGCTTGTCTCGAACTCCTG +ACCTCAGGTGATCCGTCCAACTTGGCCTCCCAAAGTGCTGAGATTACAGGCATGAGCTAC +CGTGCCCAGCTCTCAATTGTCACTTTTAGTGCATATTTTCTGGTTGTATAAAAGCTCTCC +CATGCAAGAGGGCTGATGTTATAACAGTCGATTATTATACTGTCCTGCATTTTCATCAGG +TAAAGAAAGCTTTTCATGTTTCACTGAG +>p:HG002_2_chr20:51952383-51954993 +CTCTGTCTCAAAAAAAAAAAAGTCATTGATTGATCTCTTTCTGGTTTAACTGCTATTATT +TAGTTTTATAGCATTACATTCAAGTTTTTATAGCATTACAATTCCTAGATTCTATTTTCA +AATATTGATTTGCTTAATTTTTTTTTTTTTTGAGATGGGGTTTTGCTCTGTCGCCCAGGC +TGGAGTGCAATGGCATGATCTTGGCTCACTGCAACCTCCGCCTCCTGGGTTCAGCCATTC +TCCTGCCTCAGCCTCCCGAGTGGCTGGGACTACAGGTGCCCGCCACCACGCCTGGCTAAT +TTTTTTTTTTTATATTTTTAGTAGAGACGGGGTTTCACCATGTTAGCCAGGATGGTCTCG +ATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTAGGATTACAGGCTTG +AGCCACCGCGCCTGGCCTTTAATATAATTTTTATGAAGACATTATTTCCACTTCATTGGG +CTCTCTAGAATTAGATTGCATAAATACTGTAGTTTTATTTCAATAAAAAGTCAACTGTTA +TTTAAACCATGACTAAAGCTTGACATGAATAGAGACTTTAAAACAATAAACATTGCCAGA +CATGGTGGCACATGCCTGTAGTCTCAGCTACTCAAGAAACTGAGACAGGAGGATCTCCTG +AGCCAAGGAGTTCCAGCCCAGCCTGGACAACATAGTGAGATCCCATCTCTTAAAAAAAAA +AAAAAAAGATTTGCTTAATTTTACTTTTACAATTTTTTCTTTTCTTTTTTTTTTTTTTTT +TTTTTTTTTTTTTGAGATGGAGTCTTGCTCTGTTACCAGGCTGGAGTGCAGTGGTGTGAT +ATCGGCTCCCTGCAACCTCTGCCTCCTGGGTTAAAGCAATTTTCCTGCCCCAGCCTCCCG +AGTAGCTGGGACTACAGGCGCGCGTCACCACACCCAGCTAATTTTTGTATTTTCAGTAGA +GATGGGGTTTCACCATGTTGGCCAGGATGGTCTCAATCTCTTGATCTCGTGATCCGCCCA +CCTTGGCCTCCCAAAGTGCTGGAATTACAGGCGTGATCCGCCATAACCTGGCCTTCCTTC +TTTTCTTTAAAAATTTTTTTCTGAGACAGAGTCTCACTCTGTTGCCCAGCCTGGAGTGCA +GTGGCACAATCTCGGCTCACTGTAGCCTCCACCTTCTGGGTTCAAGTGATTCTCGTGCCT +CAGCCTCCCGAGTAGCTGTGACTACAGGTGTGTGCCCTCATGCCTGGCTAATTTTTGTAT +TTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACCCTGGGCTCAAG +TGTTCTGTCTGCCTCAGCCCCCCAAAGTGCTGGGATTACAGGCATGAGCCAAAGTGCCTG +GCTAGAAAATTGTAAAAGTAACTTAATATCTGCCTCATATACTTTTGTTTTATTTAAAAA +TGCAAATCCGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAG +GCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGT +CTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTA +CTTGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCG +AGATCCCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAA +AAAAAAAAAATGCAAATCCTCAACCACAAATCGAAACAAGAACAACCCTCTGATGACTTC +CCTCCCTCTCTCTTTGTACAAAGAAGACTTTCTGCTGTCTGACTCTGACCACCTTGGTCT +ATTTTATGGAGCTCCAACCCTGCCTTGTTTCCTTCTCAGGCCATCTGTCCTGGTTGGCCT +CACTGTTGGAAATGCTCTTCTCAAGATGTTCACGTGGCTGGTTCTTTGTCATTCAGTCTC +AGTTCAAATACTCCCTCCTCCAGGAAGCCTTCCCTAACTTCCTAGGTGAAAGTGGTTCCC +TTCCCCTGAGTCACGATTATGGTTTCTTCAGTGTACTTATTAATGGCCAACACTGTCTCC +TTTATTGTTTGCTTATGAATTTAAAGTCTGTTAGCAGCACCTGCAGCTTTTAAAAGCCTC +CTTGTCTCTCTCTATTTTTTTTTTTTTTTTTTTGAGGCGGAGTTTCGCTCTTGTTGGCCA +GGCTGGAATGCAGTGATGCGATCTCGGCTCAGTGCAACCTCCACCTCTTGGGTTCAAGTG +ATTCTCCTGCCTCAGCCTCCTTAGTAGCTGAGACTACAGGCATGTGCCACCATGCTGGCT +AATTTTTGTATTTTTAGTAGAGACAGGGTTTCGTCATATTGGCCAAGCTGGTCTCGAACC +CCTGACCTCAGGTGATCCACCCATCTTGGCCTCCCAGATGCTGGGATTACAGGCGTGAGC +CACTGCGCCTGGCCTAATTGTCATTTTCGTTTTTTTGTTGAGACAGAGTTTCTGTCACCC +AGGCTGGAATGCAGTGGCACGATCTCAGCTCACTGCAGCCTCTGCCTCTTGGGTTCAATT +GATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGTGTGTGCCACCACACCCAG +CTAATTTTTTCATTTTTAGTAGAGACGGGGTTTCACCATGTTGGTCAGGCTTGTCTCGAA +CTCCTGACCTCAGGTGATCCGTCCAACTTGGCCTCCCAAAGTGCTGAGATTACAGGCATG +AGCTACCGTGCCCAGCTCTCAATTGTCACTTTTAGTGCATATTTTCTGGTTGTATAAAAG +CTCTCCCATGCAAGAGGGCTGATGTTATAACAGTCGATTATTATACTGTCCTGCATTTTC +ATCAGGTAAAGAAAGCTTTTCATGTTTCACTGAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/haps.fa.ref.fa new file mode 100644 index 00000000..0b99d97b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:51952383-51954993 +CTCTGTCTCAAAAAAAAAAAAGTCATTGATTGATCTCTTTCTGGTTTAACTGCTATTATTTAGTTTTATAGCATTACATTCAAGTTTTTATAGCATTACAATTCCTAGATTCTATTTTCAAATATTGATTTGCTTAATTTTTTTTTTTTTTTTGAGATGGGGTTTTGCTCTGTCGCCCAGGCTGGAGTGCAATGGCATGATCTTGGCTCACTGCAACCTCTGCCTCCTGGGTTCAGCCATTCTCCTGCCTCAGCCTCCCGAGTGGCTGGGACTACAGGTGCCCGCCACCACGCCTGGCTAATTTTTTTTTTTTATATTTTTAGTAGAGACGGGGTTTCACCATGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTAGGATTACAGGCTTGAGCCACCGCGCCTGGCCTTTAATATAATTTTTATGAAGACATTATTTCCACTTCATTGGGCTCTCTAGAATTAGATTGCATAAATACTGTAGTTTTATTTCAATAAAAAGTCAACTGTTATTTAAACCATGACTAAAGCTTGACATGAATAGAGACTTTAAAACAATAAACATTGCCAGACATGGTGGCACATGCCTGTAGTCTCAGCTACTCAAGAAACTGAGACAGGAGGATCTCCTGAGCCAAGGAGTTCCAGCCCAGCCTGGACAACATAGTGAGATCCCATCTCTTAAAAAAAAAAAAAAAAAGATTTGCTTAATTTTACTTTTACAATTTTTTCTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGATGGAGTCTTGCTCTGTTACCAGGCTGGAGTGCAGTGGTGTGATATCGGCTCCCTGCAACCTCTGCCTCCTGGGTTAAAGCAATTTTCCTGCCCCAGCCTCCCGAGTAGCTGGGACTACAGGCGCGCGTCACCACACCCAGCTAATTTTTGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGATGGTCTCAATCTCTTGATCTCGTGATCCGCCCACCTTGGCCTCCCAAAGTGCTGGAATTACAGGCGTGATCCGCCATAACCTGGCCTTCCTTCTTTTCTTTAAAAATTTTTTTCTGAGACAGAGTCTCACTCTGTTGCCCAGCCTGGAGTGCAGTGGCACAATCTCGGCTCACTGTAGCCTCCACCTTCTGGGTTCAAGTGATTCTCGTGCCTCAGCCTCCCGAGTAGCTGTGACTACAGGTGTGTGCCCTCATGCCTGGCTAATTTTTGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACCCTGGGCTCAAGTGTTCTGTCTGCCTCAGCCCCCCAAAGTGCTGGGATTACAGGCATGAGCCAAAGTGCCTGGCTAGAAAATTGTAAAAGTAACTTAATATCTGCCTCATATACTTTTGTTTTATTTAAAAATGCAAATCCTCAACCACAAATCGAAACAAGAACAACCCTCTGATGACTTCCCTCCCTCTCTCTTTGTACAAAGAAGACTTTCTGCTGTCTGACTCTGACCACCTTGGTCTATTTTATGGAGCTCCAACCCTGCCTTGTTTCCTTCTCAGGCCATCTGTCCTGGTTGGCCTCACTGTTGGAAATGCTCTTCTCAAGATGTTCACGTGGCTGGTTCTTTGTCATTCAGTCTCAGTTCAAATACTCCCTCCTCCAGGAAGCCTTCCCTAACTTCCTAGGTGAAAGTGGTTCCCTTCCCCTGAGTCACGATTATGGTTTCTTCAGTGTACTTATTAATGGCCAACACTGTCTCCTTTATTGTTTGCTTATGAATTTAAAGTCTGTTAGCAGCACCTGCAGCTTTTAAAAGCCTCCTTGTCTCTCTCTCTTTTTTTTTTTTTTTTTTTTTTTGAGGCGGAGTTTCGCTCTTGTTGGCCAGGCTGGAACGCAGTGATGCGATCTCGGCTCAGTGCAACCTCCACCTCTTGGGTTCAAGTGATTCTCCTGCCTCAGCCTCCTTAGTAGCTGAGACTACAGGCATGTGCCACCATGCTGGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCGTCATATTGGCCAAGCTGGTCTCGAACCCCTGACCTCAGGTGATCCACCCATCTTGGCCTCCCAGATGCTGGGATTACAGGCGTGAGCCACTGCGCCTGGCCTAATTGTCATTTTCGTTTTTTTGTTGAGACAGAGTTTCTGTCACCCAGGCTGGAATGCAGTGGCACGATCTCAGCTCACTGCAGCCTCTGCCTCTTGGGTTCAATTGATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGTGTGTGCCACCACACCCAGCTAATTTTTTCATTTTTAGTAGAGACGGGGTTTCACCATGTTGGTCAGGCTTGTCTCGAACTCCTGACCTCAGGTGATCCGTCCAACTTGGCCTCCCAAAGTGCTGAGATTACAGGCATGAGCTACCGTGCCCAGCTCTCAATTGTCACTTTTAGTGCATATTTTCTGGTTGTATAAAAGCTCTCCCATGCAAGAGGGCTGATGTTATAACAGTCGATTATTATACTGTCCTGCATTTTCATCAGGTAAAGAAAGCTTTTCATGTTTCACTGAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/msa.fa new file mode 100644 index 00000000..980a08bc --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/msa.fa @@ -0,0 +1,250 @@ +>ref_chr20_51952383_51954993 +ctctgtctcaaaaaaaaaaaagtcattgattgatctctttctggtttaactgctattatt +tagttttatagcattacattcaagtttttatagcattacaattcctagattctattttca +aatattgatttgcttaattttttttttttttttgagatggggttttgctctgtcgcccag +gctggagtgcaatggcatgatcttggctcactgcaacctctgcctcctgggttcagccat +tctcctgcctcagcctcccgagtggctgggactacaggtgcccgccaccacgcctggcta +attttttttttttatatttttagtagagacggggtttcaccatgttagccaggatggtct +cgatctcctgacctcgtgatccgcccgcctcggcctcccaaagtgctaggattacaggct +tgagccaccgcgcctggcctttaatataatttttatgaagacattatttccacttcattg +ggctctctagaattagattgcataaatactgtagttttatttcaataaaaagtcaactgt +tatttaaaccatgactaaagcttgacatgaatagagactttaaaacaataaacattgcca +gacatggtggcacatgcctgtagtctcagctactcaagaaactgagacaggaggatctcc +tgagccaaggagttccagcccagcctggacaacatagtgagatcccatctctt--aaaaa +aaaaaaaaaaaagatttgcttaattttacttttacaattttttcttttcttttttttttt +ttttttttttttttttttgagatggagtcttgctctgttaccaggctggagtgcagtggt +gtgatatcggctccctgcaacctctgcctcctgggttaaagcaattttcctgccccagcc +tcccgagtagctgggactacaggcgcgcgtcaccacacccagctaatttttgtattttta +gtagagatggggtttcaccatgttggccaggatggtctcaatctcttgatctcgtgatcc +gcccaccttggcctcccaaagtgctggaattacaggcgtgatccgccataacctggcctt +ccttcttttctttaaaaatttttttctgagacagagtctcactctgttgcccagcctgga +gtgcagtggcacaatctcggctcactgtagcctccaccttctgggttcaagtgattctcg +tgcctcagcctcccgagtagctgtgactacaggtgtgtgccctcatgcctggctaatttt +tgtatttttagtagagatggggtttcaccatgttggccaggctggtctcgaaccctgggc +tcaagtgttctgtctgcctcagccccccaaagtgctgggattacaggcatgagccaaagt +gcctggctagaaaattgtaaaagtaacttaatatctgcctcatatacttttgttttattt +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------aaaaatgcaaatcctcaaccacaaatcgaaacaagaacaaccctctgatg +acttccctccctctctctttgtacaaagaagactttctgctgtctgactctgaccacctt +ggtctattttatggagctccaaccctgccttgtttccttctcaggccatctgtcctggtt +ggcctcactgttggaaatgctcttctcaagatgttcacgtggctggttctttgtcattca +gtctcagttcaaatactccctcctccaggaagccttccctaacttcctaggtgaaagtgg +ttcccttcccctgagtcacgattatggtttcttcagtgtacttattaatggccaacactg +tctcctttattgtttgcttatgaatttaaagtctgttagcagcacctgcagcttttaaaa +gcctccttgtctctctctctttttttttttttttttttttttgaggcggagtttcgctct +tgttggccaggctggaacgcagtgatgcgatctcggctcagtgcaacctccacctcttgg +gttcaagtgattctcctgcctcagcctccttagtagctgagactacaggcatgtgccacc +atgctggctaatttttgtatttttagtagagacagggtttcgtcatattggccaagctgg +tctcgaacccctgacctcaggtgatccacccatcttggcctcccagatgctgggattaca 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+gcccaccttggcctcccaaagtgctggaattacaggcgtgatccgccataacctggcctt +ccttcttttctttaaaaatttttttctgagacagagtctcactctgttgcccagcctgga +gtgcagtggcacaatctcggctcactgtagcctccaccttctgggttcaagtgattctcg +tgcctcagcctcccgagtagctgtgactacaggtgtgtgccctcatgcctggctaatttt +tgtatttttagtagagatggggtttcaccatgttggccaggctggtctcgaaccctgggc +tcaagtgttctgtctgcctcagccccccaaagtgctgggattacaggcatgagccaaagt +gcctggctagaaaattgtaaaagtaacttaatatctgcctcatatacttttgttttattt +aaaaatgcaaatccggccgggcgcggtggctcacgcctgtaatcccagcactttgggagg +ccgaggcgggcggatcacgaggtcaggagatcgagaccatcccggctaaaacggtgaaac +cccgtctctactaaaaatacaaaaaattagccgggcgtggtggcgggcgcctgtagtccc +agctacttgggaggctgaggcaggagaatggcgtgaacccgggaggcggagcttgcagtg +agccgagatcccgccactgcactccagcctgggcgacagagcgagactccgtctcaaaaa +aaaaaaaaaaaaaaatgcaaatcctcaaccacaaatcgaaacaagaacaaccctctgatg +acttccctccctctctctttgtacaaagaagactttctgctgtctgactctgaccacctt +ggtctattttatggagctccaaccctgccttgtttccttctcaggccatctgtcctggtt +ggcctcactgttggaaatgctcttctcaagatgttcacgtggctggttctttgtcattca +gtctcagttcaaatactccctcctccaggaagccttccctaacttcctaggtgaaagtgg +ttcccttcccctgagtcacgattatggtttcttcagtgtacttattaatggccaacactg +tctcctttattgtttgcttatgaatttaaagtctgttagcagcacctgcagcttttaaaa +gcctccttgtctctctc----tatttttttttttttttttttgaggcggagtttcgctct +tgttggccaggctggaatgcagtgatgcgatctcggctcagtgcaacctccacctcttgg +gttcaagtgattctcctgcctcagcctccttagtagctgagactacaggcatgtgccacc +atgctggctaatttttgtatttttagtagagacagggtttcgtcatattggccaagctgg +tctcgaacccctgacctcaggtgatccacccatcttggcctcccagatgctgggattaca +ggcgtgagccactgcgcctggcctaattgtcattttcgtttttttgttgagacagagttt +ctgtcacccaggctggaatgcagtggcacgatctcagctcactgcagcctctgcctcttg +ggttcaattgattctcctgcctcagcctcccaagtagctgggactacaggtgtgtgccac +cacacccagctaattttttcatttttagtagagacggggtttcaccatgttggtcaggct +tgtctcgaactcctgacctcaggtgatccgtccaacttggcctcccaaagtgctgagatt +acaggcatgagctaccgtgcccagctctcaattgtcacttttagtgcatattttctggtt +gtataaaagctctcccatgcaagagggctgatgttataacagtcgattattatactgtcc +tgcattttcatcaggtaaagaaagcttttcatgtttcactgag diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/msa.fa.fai new file mode 100644 index 00000000..64df8620 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_51952383_51954993 2923 29 60 61 +syndip_1_chr20:51952383-51954993 2923 3035 60 61 +syndip_2_chr20:51952383-51954993 2923 6041 60 61 +p:HG002_1_chr20:51952383-51954993 2923 9048 60 61 +p:HG002_2_chr20:51952383-51954993 2923 12055 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/output.vcf.gz new file mode 100644 index 00000000..d37d9617 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/output.vcf.gz.tbi new file mode 100644 index 00000000..f069aa5d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:51952483-51954893/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/base.vcf.gz new file mode 100644 index 00000000..04f8a987 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/base.vcf.gz.tbi new file mode 100644 index 00000000..3e37ccfb Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/comp.vcf.gz new file mode 100644 index 00000000..b11ccd87 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/comp.vcf.gz.tbi new file mode 100644 index 00000000..8a4fe71d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/haps.fa new file mode 100644 index 00000000..e561c307 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/haps.fa @@ -0,0 +1,102 @@ +>ref_chr20_53203887_53204574 +CATACCACATGGGGCTACTAAGCCCTTCAAATGTGACTGGTCCAAATTAAAATATACTGTAAGTATAAAACACACTGAACTTGAAAGGCTTAGTCCAAAAACCGTAGTGCACAATATCTCCTTCATTTTTATAATATGATACTATTATATCATAATTTTATAATATACTATTATATCATATTATATGATACTATTTATATCATCATATGATGATATGATATACTATATCATCATATGATGATATGATATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATTATATCATAATATGATATAATATTTTGGACATACTAGGTTAAATAAGATATAGTTATATAAATCAATTTCACTTATTTCTTTCTCATTCTTTAATGTGACTACTGAAGCATATGAAATTCCATGCATAGCTGACATTCTACTTCTATTG +>syndip_1_chr20:53203887-53204574 +CATACCACATGGGGCTACTAAGCCCTTCAAATGTGACTGGTCCAAATTAAAATATACTGT +AAGTATAAAACACACTGAACTTGAAAGGCTTAGTCCAAAAACCGTAGTGCACAATATCTC +CTTCATTTTTATAATATGATACTATTATATCATAATTTTATAATATACTATTATATCATA +TTATATGATACTATTTATATCATCATATGATGATATACTATTATATCATCATATGATGAT +ATACTATTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACT +ATATCATCATATGATGATATACTATATCATCATATGATGATATGATACTATATCATCATA +TGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATA +TGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTA +TATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCA +TATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGA +TATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATAC +TATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCAT +CACATGATGATATGATACTATATCATCACATGATGATATGATACTATATCATCACATGAT +GATATGATACTATATCATCACATGATGATATGATACTATATCATCACATGATGATATGAT +ACTATATCATCACATGATGATATGATACTATATCATCACATGATGATATGATACTATATC +ATCACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATC +ATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCA +TCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATAT +CATCATATAACATGATGATATGATACTATTATATCATAATATGATATAATATTTTGGACA +TACTAGGTTAAATAAGATATAGTTATATAAATCAATTTCACTTATTTCTTTCTCATTCTT +TAATGTGACTACTGAAGCATATGAAATTCCATGCATAGCTGACATTCTACTTCTATTG +>syndip_2_chr20:53203887-53204574 +CATACCACATGGGGCTACTAAGCCCTTCAAATGTGACTGGTCCAAATTAAAATATACTGT +AAGTATAAAACACACTGAACTTGAAAGGCTTAGTCCAAAAACCGTAGTGCACAATATCTC +CTTCATTTTTATAATATGATACTATTATATCATAATTTTATAATATACTATTATATCATA +TTATATGATACTATTTATATCATCATATGATGATATACTATTATATCATCATATGATGAT +ATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACT +ATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATC +ATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATG +ATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATA +CTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCA +TCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGA +TGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGA +TACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATAT +CATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATAT +GATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATAT +GATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTAT +ATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCAT +ATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGAT +ATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACT +ATATCATAACATGATGATATGATACTATATCATAACATGATGATATGATACTATATCATC +ATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCA +TCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATAT +CATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTAT +ATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACT +ATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATA +CTATTATATCATAATATGATATAATATTTTGGACATACTAGGTTAAATAAGATATAGTTA +TATAAATCAATTTCACTTATTTCTTTCTCATTCTTTAATGTGACTACTGAAGCATATGAA +ATTCCATGCATAGCTGACATTCTACTTCTATTG +>p:HG002_1_chr20:53203887-53204574 +CATACCACATGGGGCTACTAAGCCCTTCAAATGTGACTGGTCCAAATTAAAATATACTGT +AAGTATAAAACACACTGAACTTGAAAGGCTTAGTCCAAAAACCGTAGTGCACAATATCTC +CTTCATTTTTATAATATGATACTATTATATCATAATTTTATAATATACTATTATATCATA +TTATATGATACTATTTATATCATCATATGATGATATACTATTATATCATCATATGATGAT +ATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACT +ATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATC +ATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATG +ATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATA +CTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCA +TCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGA +TGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGA +TACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATAT +CATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATAT +GATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATAT +GATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTAT +ATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCAT +ATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGAT +ATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACT +ATATCATAACATGATGATATGATACTATATCATAACATGATGATATGATACTATATCATC +ATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCA +TCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATAT +CATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTAT +ATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACT +ATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATA +CTATTATATCATAATATGATATAATATTTTGGACATACTAGGTTAAATAAGATATAGTTA +TATAAATCAATTTCACTTATTTCTTTCTCATTCTTTAATGTGACTACTGAAGCATATGAA +ATTCCATGCATAGCTGACATTCTACTTCTATTG +>p:HG002_2_chr20:53203887-53204574 +CATACCACATGGGGCTACTAAGCCCTTCAAATGTGACTGGTCCAAATTAAAATATACTGT +AAGTATAAAACACACTGAACTTGAAAGGCTTAGTCCAAAAACCGTAGTGCACAATATCTC +CTTCATTTTTATAATATGATACTATTATATCATAATTTTATAATATACTATTATATCATA +TTATATGATACTATTTATATCATCATATGATGATATACTATTATATCATCATATGATGAT +ATACTATTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACT +ATATCATCATATGATGATATACTATATCATCATATGATGATATGATACTATATCATCATA +TGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATA +TGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTA +TATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCA +TATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGA +TATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATAC +TATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCAT +CACATGATGATATGATACTATATCATCACATGATGATATGATACTATATCATCACATGAT +GATATGATACTATATCATCACATGATGATATGATACTATATCATCACATGATGATATGAT +ACTATATCATCACATGATGATATGATACTATATCATCACATGATGATATGATACTATATC +ATCACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATC +ATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCA +TCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATAT +CATCATATAACATGATGATATGATACTATTATATCATAATATGATATAATATTTTGGACA +TACTAGGTTAAATAAGATATAGTTATATAAATCAATTTCACTTATTTCTTTCTCATTCTT +TAATGTGACTACTGAAGCATATGAAATTCCATGCATAGCTGACATTCTACTTCTATTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/haps.fa.ref.fa new file mode 100644 index 00000000..72153792 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:53203887-53204574 +CATACCACATGGGGCTACTAAGCCCTTCAAATGTGACTGGTCCAAATTAAAATATACTGTAAGTATAAAACACACTGAACTTGAAAGGCTTAGTCCAAAAACCGTAGTGCACAATATCTCCTTCATTTTTATAATATGATACTATTATATCATAATTTTATAATATACTATTATATCATATTATATGATACTATTTATATCATCATATGATGATATGATATACTATATCATCATATGATGATATGATATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATTATATCATAATATGATATAATATTTTGGACATACTAGGTTAAATAAGATATAGTTATATAAATCAATTTCACTTATTTCTTTCTCATTCTTTAATGTGACTACTGAAGCATATGAAATTCCATGCATAGCTGACATTCTACTTCTATTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/msa.fa new file mode 100644 index 00000000..3eb02a0b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/msa.fa @@ -0,0 +1,140 @@ +>ref_chr20_53203887_53204574 +cataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgt +aagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctc +cttcatttttataatatgatactattatatcataattttataatatactattatatcata +ttatatgatactatttatatcatcatatgatgatatgat--------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------atactatatcatcatatgatgatatgatatactatatcatcatatgatgat +atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact +atatcatc---------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------atatgatgatatgatactat +atcatcat-----atgatgatatgatactatatcatcatataacatgatgatatgatact +atatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgata +ctatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatga +tactattatatcataatatgatataatattttggacatactaggttaaataagatatagt +tatataaatcaatttcacttatttctttctcattctttaatgtgactactgaagcatatg +aaattccatgcatagctgacattctacttctattg +>syndip_1_chr20:53203887-53204574 +cataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgt +aagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctc +cttcatttttataatatgatactattatatcataattttataatatactattatatcata +ttatatgatactatttatatcatcatatgatgatatactattatatcatcatatgatgat +atactattatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact +atatcatcatatgatgat---atactatatcatcatatgatgatatgatactatatcatc +atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg +atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata +ctatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatca +tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga +tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga +tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat +catcacatgatgatatgatactatatcatcacatgatgatatgatactatatcatcacat +gatgatatgatactatatcatcacatgatgatatg--atactatatcatcacatgatgat +atgatactatatcatcacatgatgatatgatactatatcatcacatgatgatatgatact +atatcatc---------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------acatgatgatatgatactat +atcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgatact +atatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgata +ctatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatga +tactattatatcataatatgatataatattttggacatactaggttaaataagatatagt +tatataaatcaatttcacttatttctttctcattctttaatgtgactactgaagcatatg +aaattccatgcatagctgacattctacttctattg +>syndip_2_chr20:53203887-53204574 +cataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgt +aagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctc +cttcatttttataatatgatactattatatcataattttataatatactattatatcata +ttatatgatactatttatatcatcatatgatgatatactattatatcatcatatgatgat +atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact +atatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatc +atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg +atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata +ctatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatca +tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga +tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga +tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat +catcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatat +gatgatatgatactatatcatcatatgatgatatg--atactatatcatcatatgatgat +atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact +atatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatc +atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg +atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata +ctatatcataacatgatgatatgatactatatcataacatgatgatatgatactatatca +tcatataacatgatgatatgatactatatcatcatataacatgatgatatgatactatat +catcatataacatgatgatatgatactatatcatcatataacatgatgatatgatactat +atcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgatact +atatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgata +ctatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatga +tactattatatcataatatgatataatattttggacatactaggttaaataagatatagt +tatataaatcaatttcacttatttctttctcattctttaatgtgactactgaagcatatg +aaattccatgcatagctgacattctacttctattg +>p:HG002_1_chr20:53203887-53204574 +cataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgt +aagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctc +cttcatttttataatatgatactattatatcataattttataatatactattatatcata +ttatatgatactatttatatcatcatatgatgatatactattatatcatcatatgatgat +atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact +atatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatc +atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg +atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata +ctatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatca +tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga +tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga +tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat +catcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatat +gatgatatgatactatatcatcatatgatgatatg--atactatatcatcatatgatgat +atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact +atatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatc +atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg +atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata +ctatatcataacatgatgatatgatactatatcataacatgatgatatgatactatatca +tcatataacatgatgatatgatactatatcatcatataacatgatgatatgatactatat +catcatataacatgatgatatgatactatatcatcatataacatgatgatatgatactat +atcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgatact +atatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgata +ctatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatga +tactattatatcataatatgatataatattttggacatactaggttaaataagatatagt +tatataaatcaatttcacttatttctttctcattctttaatgtgactactgaagcatatg +aaattccatgcatagctgacattctacttctattg +>p:HG002_2_chr20:53203887-53204574 +cataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgt +aagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctc +cttcatttttataatatgatactattatatcataattttataatatactattatatcata +ttatatgatactatttatatcatcatatgatgatatactattatatcatcatatgatgat +atactattatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact +atatcatcatatgatgat---atactatatcatcatatgatgatatgatactatatcatc +atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg +atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata +ctatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatca +tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga +tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga +tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat +catcacatgatgatatgatactatatcatcacatgatgatatgatactatatcatcacat +gatgatatgatactatatcatcacatgatgatatg--atactatatcatcacatgatgat +atgatactatatcatcacatgatgatatgatactatatcatcacatgatgatatgatact +atatcatc---------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------acatgatgatatgatactat +atcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgatact +atatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgata +ctatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatga +tactattatatcataatatgatataatattttggacatactaggttaaataagatatagt +tatataaatcaatttcacttatttctttctcattctttaatgtgactactgaagcatatg +aaattccatgcatagctgacattctacttctattg diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/msa.fa.fai new file mode 100644 index 00000000..77baaaf4 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_53203887_53204574 1595 29 60 61 +syndip_1_chr20:53203887-53204574 1595 1685 60 61 +syndip_2_chr20:53203887-53204574 1595 3341 60 61 +p:HG002_1_chr20:53203887-53204574 1595 4998 60 61 +p:HG002_2_chr20:53203887-53204574 1595 6655 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/output.vcf.gz new file mode 100644 index 00000000..f5ae2942 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/output.vcf.gz.tbi new file mode 100644 index 00000000..4886a77f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:53203987-53204474/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/base.vcf.gz new file mode 100644 index 00000000..a36e0c68 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/base.vcf.gz.tbi new file mode 100644 index 00000000..317dc01d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/comp.vcf.gz new file mode 100644 index 00000000..7b170f86 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/comp.vcf.gz.tbi new file mode 100644 index 00000000..179be5de Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/haps.fa new file mode 100644 index 00000000..95e1cd15 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/haps.fa @@ -0,0 +1,138 @@ +>ref_chr20_55624382_55625908 +ATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTCAATCAGTGAGGTGGAGGCTGCAGTGGGCCAAGATCATGCGATTGCACCCCAGCCTGGGTAAGAAAGTGAGGTCCTGTCTCCCTGTCTCTCATATATATACATAACTAAAATAATATATAGTAATATATGTTATATATTATACTATATTATATAATATACTATAATATATATAATATAGTATATATTGTATATAATATAGTATATATAATATAATAGTATATAATATAGTATAGATAGTATAGAATATATAGTATATACCTAGTATACTATATTATATAGTATAACTATTATAATATTTATAGTATATTATACTATATAATACAGTATACTGTATTATATACTATAATCTACTAGATTATAATATACTATATAATCAGTATACTATATTGTATAGTATAATATAGTATTATATTATAGTAATATATTATAAAGTATTATAGTAATATAGTATAATATACTATACATTATATAGTATAGTATATTATATAGTATACTATATATAAGTATATTTAATAGTATATTGTATATAGTAATTATATATAGTATATATAATATACAATGTATAGTATATTATAGTATACTATACGATACTGTAGTATAGTATGCTATATAGTATACTATATACGACAGTATCATATAGTATACTACAAAATATATAGTATAGCATAGTATACTATATAATATACTATATTATATATACTATATTATATATACTATACTATATTATATATACTATATTATATATACTATACTATACATAAAATACTATATATAGTATATTATATATAGTATACTATATATAGTATATAATATATAGTATACTATATATACTATATATAGTATACTATATATACTATATATAGTATACTATATATCATATATAGTATTATATACAGTATACTATATATAATATAGTATACTATACTATAATATACTATTTGTTATAATTATCTAGTATAGTATACTATATATACTATATTATATAGTATATAGTATATATAGTATATAGTATATATACTATATACTATATATACTATATACTATACTATATAATATATATACTAATATATTGTATACTATACTATGCTATAGTATGCTATATACTACACTATAGTATACTGTGTACTATACTATAGTATACAGTATACTATATACTATACTATAGTATAGTATACTATAGTATAGTATACTATATACTATAGTATAGTATATAGTATACTGTATACTATAGTATAGTATACTATATACTATACTATACTATAGTATACTCTATAGTATATAAAGACATATATATAGTCTTCAAAATGAAGATCCTGTATCCTATATATATATATAACTTCAAAAGTGAGATACATATATATGATGTAGAAACTTTAGAATATACAAAATTGTCTTCTTCAGGATAAGAAAATCCTGATATTCAGCCTAACCTCCACTGACTGTAAAGGAAGAATGGGTTTCACTTTCAGGGAAGGTCACCTTCATCC +>syndip_1_chr20:55624382-55625908 +ATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTCAATCAGTGAGGTGGAGGCTG +CAGTGGGCCAAGATCATGCGATTGCACCCCAGCCTGGGTAAGAAAGTGAGGTCCTGTCTC +CCTGTCTCTCATATATATACATAACTAAAATAATATATAGTAATATATGTTATATATTAT +ACTATATTATATAATATACTATAATATATATAATATAGTATATATTGTATATAATATAGT +ATATATAATATAATAGTATATAATATAGTATAGATAGTATAGAATATATAGTATATACCT +AGTATACTATATTATATAGTATAACTATTATAATATTTATAGTATATTATACTATATAAT +ACAGTATACTGTATTATATACTATAATCTACTAGATTATAATATACTATATAATCAGTAT +ACTATATTATATAGTATAGTATAATATAGTATTATATTATAGTAATATATTATAAAGTAT +TATAGTAATATAGTATAATATACTATACATTATATAGTATAGTATATTATATAGTATACT +ATATATAAGTATATATAATAGTATATTGTATATAGTAATTATATATAGTATATATAATAT +ACAATGTATAGTATATTATAGTATACTATACGATACTGTAGTATAGTATGCTATATAGTA +TACTATATACGACAGTATCATATAGTATACTACAAAATATATAGTATAGCATAGTATACT +ATATAATATACTATATTATATATACTATATTATATATACTACACTATATTATATATACTA +TATTATATATACTATACTATACATAAAATACTATATATAGTATATTATATATAGTATACT +ATATATAGTATATATAGTATACTATATATACTATATATAGTATACTATATAGTATACTAT +ATATAGTATATATAGTATACTATATATAGTATACTATATATAGTATATATATAGTATACT +ATATATAGTATACTATATATAGTATATATAGTATACTATATATAGTATACTATATATAGT +ATATATAGTATACTATATATAGTATACTATATATAGTATATATAGTATACTATATATAGT +ATACTATATATAGTATATATAGTATACTATATATAGTATATATAGTATACTATATATAGT +ATATATAGTATACTATATATACTATATATACTATATATAGTATACTATATATAGTATATA +TAGTATACTATATATCATATATAGTATTATATACAGTATACTATATATAATATAGTATAC +TATACTATAATATACTATTTGTTATAATTATCTAGTATAGTATACTATATATACTATATT +ATATAGTATATAGTATATATAGTATATTTATAGTATATATACTATATACTATATATACTA +TATACTATAATATATACTATATATACTAAATAAATATAATATACTTATTTAAATATATTT +AAATAAATATAAAATATTTAAATATAATTACTTAAATATATATTTAAAATATTTAATAAA +CATATATTTAAATATTTATTTAATATTTAAATATTAAATATATATAATTAATATAATTAT +ATATATATTATATACTATATATTATATATACTATATACTATATATAGTATACTAATATAA +TATACTATATATACTATATATAATATACTATATATAGTATATATAGTATAGTATACTATA +ATATACTATATTATATAATATAGTATACTATATATTGTATACTATACTATGCTATAGTAT +GCTATATACTACACTATAGTATACTGTATACTATACTATACAGTATACTGTATACTATAC +TATAGTATACAGTATACTATATACTATTGTATAGTATATAGTATACTGTATACTATAGTA +TAGTATACTATATACTATACTATACTATAGTATACTCTATAGTATATAAAGACATATATA +TAGTCTTCAAAATGAAGATCCTGTATCCTATATATATATATAACTTCAAAAGTGAGATAC +ATATATATGATGTAGAAACTTTAGAATATACAAAATTGTCTTCTTCAGGATAAGAAAATC +CTGATATTCAGCCTAACCTCCACTGACTGTAAAGGAAGAATGGGTTTCACTTTCAGGGAA +GGTCACCTTCATCC +>syndip_2_chr20:55624382-55625908 +ATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTCAATCAGTGAGGTGGAGGCTG +CAGTGGGCCAAGATCATGCGATTGCACCCCAGCCTGGGTAAGAAAGTGAGGTCCTGTCTC +CCTGTCTCTCATATATATACATAACTAAAATAATATATAGTAATATATGTTATATATTAT +ACTATATTATATAATATACTATAATATATATAATATAGTATATATTGTATATAATATAGT +ATATATAATATAATAGTATATAATATAGTATAGATAGTATAGAATATATAGTATATACCT +AGTATACTATATTATATAGTATAACTATTATAATATTTATAGTATATTATACTATATAAT +ACAGTATACTGTATTATATACTATAATCTACTAGATTATAATATACTATATAATCAGTAT +ACTATATTATATAGTATAGTATAATATAGTATTATATTATAGTAATATATTATAAAGTAT +TATAGTAATATAGTATAATATACTATACATTATATAGTATACTATATATAAGTATATATA +ATAGTATATTGTATATAGTAATTATATATAGTATATATAATATACAATGTATAGTATATT +ATAGTATACTATACGATACTGTAGTATAGTATGCTATATAGTATACTATATACGACAGTA +TCATATAGTATACTACAAAATATATAGTATAGCATAGTATACTATATAATATACTATATT +ATATATACTATATTATATATACTATACTATACATAAAATACTATATATAGTATATTATAT +ATAGTATACTATATATAGTATATATAGTATACTATATATCATATATAGTATTATATACAG +TATACTATATATAATATAGTATACTATACTATAATATACTATTTGTTATAATTATCTAGT +ATAGTATACTATATATACTATATTATATAGTATATATAGTATATTTATAGTATATATACT +ATATACTATATATACTATATAATATAATATATAATATATATACTAAATAAATATACTTAT +TTAAATATATTTAAATAAATATATTAAATATTTAAATATAATTACTTAAATATATATTTA +AAATATTTAATAAACATATATTTAAATATTTATTTAATATTTAAATATTAAATATATATA +ATTAATATAATTATATATATATTATATACTATATATTATATATACTATATAATATACTAT +ATATAGTATACTAATATAATATACTATATATACTATATATAATATACTATATATAGTATA +TATAGTATAGTATACTATAATATACTATATATAGTATATATAGTATAGTATACTATAATA +TACTATATATAGTATATAGTATACTATATATTGTATACTATACTATGCTATAGTATGCTA +TATACTACACTATAGTATACTGTATACTATACTATAGTATACAGTATACTATATACTATA +CTATAGTATAGTATACTATAGTATAGTATACTATATACTATACTATAGTATATAGTATAC +TGTATACTATAGTATACTATATACTATACTATACTATAGTATACTCTATAGTATATAAAG +ACATATATATAGTCTTCAAAATGAAGATCCTGTATCCTATATATATATATAACTTCAAAA +GTGAGATACATATATATGATGTAGAAACTTTAGAATATACAAAATTGTCTTCTTCAGGAT +AAGAAAATCCTGATATTCAGCCTAACCTCCACTGACTGTAAAGGAAGAATGGGTTTCACT +TTCAGGGAAGGTCACCTTCATCC +>p:HG002_1_chr20:55624382-55625908 +ATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTCAATCAGTGAGGTGGAGGCTG +CAGTGGGCCAAGATCATGCGATTGCACCCCAGCCTGGGTAAGAAAGTGAGGTCCTGTCTC +CCTGTCTCTCATATATATACATAACTAAAATAATATATAGTAATATATGTTATATATTAT +ACTATATTATATAATATACTATAATATATATAATATAGTATATATTGTATATAATATAGT +ATATATAATATAATAGTATATAATATAGTATAGATAGTATAGAATATATAGTATATACCT +AGTATACTATATTATATAGTATAACTATTATAATATTTATAGTATATTATACTATATAAT +ACAGTATACTGTATTATATACTATAATCTACTAGATTATAATATACTATATAATCAGTAT +ACTATATTATATAGTATAGTATAATATAGTATTATATTATAGTAATATATTATAAAGTAT +TATAGTAATATAGTATAATATACTATACATTATATAGTATACTATATATAAGTATATATA +ATAGTATATTGTATATAGTAATTATATATAGTATATATAATATACAATGTATAGTATATT +ATAGTATACTATACGATACTGTAGTATAGTATGCTATATAGTATACTATATACGACAGTA +TCATATAGTATACTACAAAATATATAGTATAGCATAGTATACTATATAATATACTATATT +ATATATACTATATTATATATACTATACTATACATAAAATACTATATATAGTATATTATAT +ATAGTATACTATATATAGTATATATAGTATACTATATATCATATATAGTATTATATACAG +TATACTATATATAATATAGTATACTATACTATAATATACTATTTGTTATAATTATCTAGT +ATAGTATACTATATATACTATATTATATAGTATATATAGTATATTTATAGTATATATACT +ATATACTATATATACTATATAATATAATATATAATATATATACTAAATAAATATACTTAT +TTAAATATATTTAAATAAATATATTAAATATTTAAATATAATTACTTAAATATATATTTA +AAATATTTAATAAACATATATTTAAATATTTATTTAATATTTAAATATTAAATATATATA +ATTAATATAATTATATATATATTATATACTATATATTATATATACTATATAATATACTAT +ATATAGTATACTAATATAATATACTATATATACTATATATAATATACTATATATAGTATA +TATAGTATAGTATACTATAATATACTATATATAGTATATATAGTATAGTATACTATAATA +TACTATATATAGTATATAGTATACTATATATTGTATACTATACTATGCTATAGTATGCTA +TATACTACACTATAGTATACTGTATACTATACTATAGTATACAGTATACTATATACTATA +CTATAGTATAGTATACTATAGTATAGTATACTATATACTATACTATAGTATATAGTATAC +TGTATACTATAGTATACTATATACTATACTATACTATAGTATACTCTATAGTATATAAAG +ACATATATATAGTCTTCAAAATGAAGATCCTGTATCCTATATATATATATAACTTCAAAA +GTGAGATACATATATATGATGTAGAAACTTTAGAATATACAAAATTGTCTTCTTCAGGAT +AAGAAAATCCTGATATTCAGCCTAACCTCCACTGACTGTAAAGGAAGAATGGGTTTCACT +TTCAGGGAAGGTCACCTTCATCC +>p:HG002_2_chr20:55624382-55625908 +ATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTCAATCAGTGAGGTGGAGGCTG +CAGTGGGCCAAGATCATGCGATTGCACCCCAGCCTGGGTAAGAAAGTGAGGTCCTGTCTC +CCTGTCTCTCATATATATACATAACTAAAATAATATATAGTAATATATGTTATATATTAT +ACTATATTATATAATATACTATAATATATATAATATAGTATATATTGTATATAATATAGT +ATATATAATATAATAGTATATAATATAGTATAGATAGTATAGAATATATAGTATATACCT +AGTATACTATATTATATAGTATAACTATTATAATATTTATAGTATATTATACTATATAAT +ACAGTATACTGTATTATATACTATAATCTACTAGATTATAATATACTATATAATCAGTAT +ACTATATTATATAGTATAGTATAATATAGTATTATATTATAGTAATATATTATAAAGTAT +TATAGTAATATAGTATAATATACTATACATTATATAGTATAGTATATTATATAGTATACT +ATATATAAGTATATATAATAGTATATTGTATATAGTAATTATATATAGTATATATAATAT +ACAATGTATAGTATATTATAGTATACTATACGATACTGTAGTATAGTATGCTATATAGTA +TACTATATACGACAGTATCATATAGTATACTACAAAATATATAGTATAGCATAGTATACT +ATATAATATACTATATTATATATACTATATTATATATACTACACTATATTATATATACTA +TATTATATATACTATACTATACATAAAATACTATATATAGTATATTATATATAGTATACT +ATATATAGTATATATAGTATACTATATATACTATATATAGTATACTATATAGTATACTAT +ATATAGTATATATAGTATACTATATATAGTATACTATATATAGTATATATATAGTATACT +ATATATAGTATACTATATATAGTATATATAGTATACTATATATAGTATACTATATATAGT +ATATATAGTATACTATATATAGTATACTATATATAGTATATATAGTATACTATATATAGT +ATACTATATATAGTATATATAGTATACTATATATAGTATATATAGTATACTATATATAGT +ATATATAGTATACTATATATACTATATATACTATATATAGTATACTATATATAGTATATA +TAGTATACTATATATCATATATAGTATTATATACAGTATACTATATATAATATAGTATAC +TATACTATAATATACTATTTGTTATAATTATCTAGTATAGTATACTATATATACTATATT +ATATAGTATATAGTATATATAGTATATTTATAGTATATATACTATATACTATATATACTA +TATACTATAATATATACTATATATACTAAATAAATATAATATACTTATTTAAATATATTT +AAATAAATATAAAATATTTAAATATAATTACTTAAATATATATTTAAAATATTTAATAAA +CATATATTTAAATATTTATTTAATATTTAAATATTAAATATATATAATTAATATAATTAT +ATATATATTATATACTATATATTATATATACTATATACTATATATAGTATACTAATATAA +TATACTATATATACTATATATAATATACTATATATAGTATATATAGTATAGTATACTATA +ATATACTATATTATATAATATAGTATACTATATATTGTATACTATACTATGCTATAGTAT +GCTATATACTACACTATAGTATACTGTATACTATACTATACAGTATACTGTATACTATAC +TATAGTATACAGTATACTATATACTATTGTATAGTATATAGTATACTGTATACTATAGTA +TAGTATACTATATACTATACTATACTATAGTATACTCTATAGTATATAAAGACATATATA +TAGTCTTCAAAATGAAGATCCTGTATCCTATATATATATATAACTTCAAAAGTGAGATAC +ATATATATGATGTAGAAACTTTAGAATATACAAAATTGTCTTCTTCAGGATAAGAAAATC +CTGATATTCAGCCTAACCTCCACTGACTGTAAAGGAAGAATGGGTTTCACTTTCAGGGAA +GGTCACCTTCATCC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/haps.fa.ref.fa new file mode 100644 index 00000000..ea49ed1d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:55624382-55625908 +ATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTCAATCAGTGAGGTGGAGGCTGCAGTGGGCCAAGATCATGCGATTGCACCCCAGCCTGGGTAAGAAAGTGAGGTCCTGTCTCCCTGTCTCTCATATATATACATAACTAAAATAATATATAGTAATATATGTTATATATTATACTATATTATATAATATACTATAATATATATAATATAGTATATATTGTATATAATATAGTATATATAATATAATAGTATATAATATAGTATAGATAGTATAGAATATATAGTATATACCTAGTATACTATATTATATAGTATAACTATTATAATATTTATAGTATATTATACTATATAATACAGTATACTGTATTATATACTATAATCTACTAGATTATAATATACTATATAATCAGTATACTATATTGTATAGTATAATATAGTATTATATTATAGTAATATATTATAAAGTATTATAGTAATATAGTATAATATACTATACATTATATAGTATAGTATATTATATAGTATACTATATATAAGTATATTTAATAGTATATTGTATATAGTAATTATATATAGTATATATAATATACAATGTATAGTATATTATAGTATACTATACGATACTGTAGTATAGTATGCTATATAGTATACTATATACGACAGTATCATATAGTATACTACAAAATATATAGTATAGCATAGTATACTATATAATATACTATATTATATATACTATATTATATATACTATACTATATTATATATACTATATTATATATACTATACTATACATAAAATACTATATATAGTATATTATATATAGTATACTATATATAGTATATAATATATAGTATACTATATATACTATATATAGTATACTATATATACTATATATAGTATACTATATATCATATATAGTATTATATACAGTATACTATATATAATATAGTATACTATACTATAATATACTATTTGTTATAATTATCTAGTATAGTATACTATATATACTATATTATATAGTATATAGTATATATAGTATATAGTATATATACTATATACTATATATACTATATACTATACTATATAATATATATACTAATATATTGTATACTATACTATGCTATAGTATGCTATATACTACACTATAGTATACTGTGTACTATACTATAGTATACAGTATACTATATACTATACTATAGTATAGTATACTATAGTATAGTATACTATATACTATAGTATAGTATATAGTATACTGTATACTATAGTATAGTATACTATATACTATACTATACTATAGTATACTCTATAGTATATAAAGACATATATATAGTCTTCAAAATGAAGATCCTGTATCCTATATATATATATAACTTCAAAAGTGAGATACATATATATGATGTAGAAACTTTAGAATATACAAAATTGTCTTCTTCAGGATAAGAAAATCCTGATATTCAGCCTAACCTCCACTGACTGTAAAGGAAGAATGGGTTTCACTTTCAGGGAAGGTCACCTTCATCC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/msa.fa new file mode 100644 index 00000000..cec18f35 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/msa.fa @@ -0,0 +1,190 @@ +>ref_chr20_55624382_55625908 +atcccagctacttgggaggctgaggcaggagaatcacttcaatcagtgaggtggaggctg +cagtgggccaagatcatgcgattgcaccccagcctgggtaagaaagtgaggtcctgtctc +cctgtctctcatatatatacataactaaaataatatatagtaatatatgttatatattat +actatattatataatatactataatatatataatatagtatatattgtatataatatagt +atatataatataatagtatataatatagtatagatagtatagaatatatagtatatacct +agtatactatattatatagtataactattataatatttatagtatattatactatataat +acagtatactgtattatatactataatctactagattataatatactatataatcagtat +actatatt-----gtatagtataatatagtattatattatagtaatatattataaagtat +tatagtaatatagtataatatactatacattatatagtatagtatattatatagtatact +atatataagtatatttaatagtatattgtatatagtaattatatatagtatatataatat +acaatgtatagtatattatagtatactatacgatactgtagtatagtatgctatatagta +tactatatacgacagtatcatatagtatactacaaaatatatagtatagcatagtatact +atataatatactatattatatatactatattatatatactatactatattatatatacta +tattatatatactatactatacataaaatactatatatagtatattatatatagtatact +atatatagtatataatatata--------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------gtatactatatatactatatatagtatactatatatactatata +tagtatactatatatcatatatagtattatatacagtatactatatataatatagtatac +tatactataatatactatttgttataattatctagtatagtatactatatatactatatt +atatagtatatagtatatatagta----tatagtatatatactatatactatatatacta +tatactatactatataatatatatacta-------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------atatattgtatactatactatgctatagtatgctatatactacacta +tagtatactgtgtactatactatagtatacagtatactatatactatactatagtatagt +atactatagtatagtatactatatactatagtatagtatatagtatactgtatactatag +tatagtatactatatactatactatactatagtatactctatagtatataaagacatata +tatagtcttcaaaatgaagatcctgtatcctatatatatatataacttcaaaagtgagat +acatatatatgatgtagaaactttagaatatacaaaattgtcttcttcaggataagaaaa +tcctgatattcagcctaacctccactgactgtaaaggaagaatgggtttcactttcaggg +aaggtcaccttcatcc +>syndip_1_chr20:55624382-55625908 +atcccagctacttgggaggctgaggcaggagaatcacttcaatcagtgaggtggaggctg +cagtgggccaagatcatgcgattgcaccccagcctgggtaagaaagtgaggtcctgtctc +cctgtctctcatatatatacataactaaaataatatatagtaatatatgttatatattat +actatattatataatatactataatatatataatatagtatatattgtatataatatagt +atatataatataatagtatataatatagtatagatagtatagaatatatagtatatacct +agtatactatattatatagtataactattataatatttatagtatattatactatataat +acagtatactgtattatatactataatctactagattataatatactatataatcagtat +actatattatatagtatagtataatatagtattatattatagtaatatattataaagtat +tatagtaatatagtataatatactatacattatatagtatagtatattatatagtatact +atatataagtatatataatagtatattgtatatagtaattatatatagtatatataatat +acaatgtatagtatattatagtatactatacgatactgtagtatagtatgctatatagta +tactatatacgacagtatcatatagtatactacaaaatatatagtatagcatagtatact +atataatatactatattatatatactatattatatatactacactatattatatatacta +tattatatatactatactatacataaaatactatatatagtatattatatatagtatact +atatatagtatatatagtatactatatatactatatatagtatactatatagtatactat +atatagtatatatagtatactatatatagtatactatatatagtatatatatagtatact +atatatagtatactatatatagtatatatagtatactatatatagtatactatatatagt +atatatagtatactatatatagtatactatatatagtatatatagtatactatatatagt +atactatatatagtatatatagtatactatatatagtatatatagtatactatatatagt +atatatagtatactatatatactatatatactatatatagtatactatatatagtatata +tagtatactatatatcatatatagtattatatacagtatactatatataatatagtatac +tatactataatatactatttgttataattatctagtatagtatactatatatactatatt +atatagtatatagtatatatagtatatttatagtatatatactatatactatatatacta +tatactataatatatactatatatactaaataaatataatatacttatttaaatatattt +aaataaatata--aaatatttaaatataattacttaaatatatatttaaaatatttaata +aacatatatttaaatatttatttaatatttaaatattaaatatatataattaatataatt +atatatatattatatactatatattatatatact-----atatactatatatagtatact +aatataatatactatatatactatatataatatactatatatagtatatatagtatagta +tactataatatactatat-------------------------------------tatat +aatatagtatactatatattgtatactatactatgctatagtatgctatatactacacta +tagtatactgtatactatac-----tatacagtatactgtatactatactatagta---- +---------tacagtatactatatactattgtatagtatatagtatactgtatactatag +tatagtatactatatactatactatactatagtatactctatagtatataaagacatata +tatagtcttcaaaatgaagatcctgtatcctatatatatatataacttcaaaagtgagat +acatatatatgatgtagaaactttagaatatacaaaattgtcttcttcaggataagaaaa +tcctgatattcagcctaacctccactgactgtaaaggaagaatgggtttcactttcaggg +aaggtcaccttcatcc +>syndip_2_chr20:55624382-55625908 +atcccagctacttgggaggctgaggcaggagaatcacttcaatcagtgaggtggaggctg +cagtgggccaagatcatgcgattgcaccccagcctgggtaagaaagtgaggtcctgtctc +cctgtctctcatatatatacataactaaaataatatatagtaatatatgttatatattat +actatattatataatatactataatatatataatatagtatatattgtatataatatagt +atatataatataatagtatataatatagtatagatagtatagaatatatagtatatacct +agtatactatattatatagtataactattataatatttatagtatattatactatataat +acagtatactgtattatatactataatctactagattataatatactatataatcagtat +actatattatatagtatagtataatatagtattatattatagtaatatattataaagtat +tatagtaatatagtataatatactatac-----------------attatatagtatact +atatataagtatatataatagtatattgtatatagtaattatatatagtatatataatat +acaatgtatagtatattatagtatactatacgatactgtagtatagtatgctatatagta +tactatatacgacagtatcatatagtatactacaaaatatatagtatagcatagtatact +atataatat---------------------------------actatattatatatacta +tattatatatactatactatacataaaatactatatatagtatat--------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------tatatatagtatactatatatagtatata +tagtatactatatatcatatatagtattatatacagtatactatatataatatagtatac +tatactataatatactatttgttataattatctagtatagtatactatatatactatat- +------tatatagtatatatagtatatttatagtatatatactatatactatatatacta +tataatataatatataatatatatactaaata-----aatatacttatttaaatatattt +aaataaatatattaaatatttaaatataattacttaaatatatatttaaaatatttaata +aacatatatttaaatatttatttaatatttaaatattaaatatatataattaatataatt +atatatatattatatactatatattatatatactatataatatactatatatagtatact +aatataatatactatatatactatatataatatactatatatagtatatatagtatagta +tactataatatactatatatagtatatatagtatagtatactataatatactatatatag +tatatagtatactatatattgtatactatactatgctatagtatgctatatactacacta +tagtatactgtatactatactatagtatacagtatactatatactatactatagtatagt +atactatagtatagtatactatatactatactatagtatatagtatactgtatac----- +tatagtatactatatactatactatactatagtatactctatagtatataaagacatata +tatagtcttcaaaatgaagatcctgtatcctatatatatatataacttcaaaagtgagat +acatatatatgatgtagaaactttagaatatacaaaattgtcttcttcaggataagaaaa +tcctgatattcagcctaacctccactgactgtaaaggaagaatgggtttcactttcaggg +aaggtcaccttcatcc +>p:HG002_1_chr20:55624382-55625908 +atcccagctacttgggaggctgaggcaggagaatcacttcaatcagtgaggtggaggctg +cagtgggccaagatcatgcgattgcaccccagcctgggtaagaaagtgaggtcctgtctc +cctgtctctcatatatatacataactaaaataatatatagtaatatatgttatatattat +actatattatataatatactataatatatataatatagtatatattgtatataatatagt +atatataatataatagtatataatatagtatagatagtatagaatatatagtatatacct +agtatactatattatatagtataactattataatatttatagtatattatactatataat +acagtatactgtattatatactataatctactagattataatatactatataatcagtat +actatattatatagtatagtataatatagtattatattatagtaatatattataaagtat +tatagtaatatagtataatatactatac-----------------attatatagtatact +atatataagtatatataatagtatattgtatatagtaattatatatagtatatataatat +acaatgtatagtatattatagtatactatacgatactgtagtatagtatgctatatagta +tactatatacgacagtatcatatagtatactacaaaatatatagtatagcatagtatact +atataatat---------------------------------actatattatatatacta +tattatatatactatactatacataaaatactatatatagtatat--------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------tatatatagtatactatatatagtatata +tagtatactatatatcatatatagtattatatacagtatactatatataatatagtatac +tatactataatatactatttgttataattatctagtatagtatactatatatactatat- +------tatatagtatatatagtatatttatagtatatatactatatactatatatacta +tataatataatatataatatatatactaaata-----aatatacttatttaaatatattt +aaataaatatattaaatatttaaatataattacttaaatatatatttaaaatatttaata +aacatatatttaaatatttatttaatatttaaatattaaatatatataattaatataatt +atatatatattatatactatatattatatatactatataatatactatatatagtatact +aatataatatactatatatactatatataatatactatatatagtatatatagtatagta +tactataatatactatatatagtatatatagtatagtatactataatatactatatatag +tatatagtatactatatattgtatactatactatgctatagtatgctatatactacacta +tagtatactgtatactatactatagtatacagtatactatatactatactatagtatagt +atactatagtatagtatactatatactatactatagtatatagtatactgtatac----- +tatagtatactatatactatactatactatagtatactctatagtatataaagacatata +tatagtcttcaaaatgaagatcctgtatcctatatatatatataacttcaaaagtgagat +acatatatatgatgtagaaactttagaatatacaaaattgtcttcttcaggataagaaaa +tcctgatattcagcctaacctccactgactgtaaaggaagaatgggtttcactttcaggg +aaggtcaccttcatcc +>p:HG002_2_chr20:55624382-55625908 +atcccagctacttgggaggctgaggcaggagaatcacttcaatcagtgaggtggaggctg +cagtgggccaagatcatgcgattgcaccccagcctgggtaagaaagtgaggtcctgtctc +cctgtctctcatatatatacataactaaaataatatatagtaatatatgttatatattat +actatattatataatatactataatatatataatatagtatatattgtatataatatagt +atatataatataatagtatataatatagtatagatagtatagaatatatagtatatacct +agtatactatattatatagtataactattataatatttatagtatattatactatataat +acagtatactgtattatatactataatctactagattataatatactatataatcagtat +actatattatatagtatagtataatatagtattatattatagtaatatattataaagtat +tatagtaatatagtataatatactatacattatatagtatagtatattatatagtatact +atatataagtatatataatagtatattgtatatagtaattatatatagtatatataatat +acaatgtatagtatattatagtatactatacgatactgtagtatagtatgctatatagta +tactatatacgacagtatcatatagtatactacaaaatatatagtatagcatagtatact +atataatatactatattatatatactatattatatatactacactatattatatatacta +tattatatatactatactatacataaaatactatatatagtatattatatatagtatact +atatatagtatatatagtatactatatatactatatatagtatactatatagtatactat +atatagtatatatagtatactatatatagtatactatatatagtatatatatagtatact +atatatagtatactatatatagtatatatagtatactatatatagtatactatatatagt +atatatagtatactatatatagtatactatatatagtatatatagtatactatatatagt +atactatatatagtatatatagtatactatatatagtatatatagtatactatatatagt +atatatagtatactatatatactatatatactatatatagtatactatatatagtatata +tagtatactatatatcatatatagtattatatacagtatactatatataatatagtatac +tatactataatatactatttgttataattatctagtatagtatactatatatactatatt +atatagtatatagtatatatagtatatttatagtatatatactatatactatatatacta +tatactataatatatactatatatactaaataaatataatatacttatttaaatatattt +aaataaatata--aaatatttaaatataattacttaaatatatatttaaaatatttaata +aacatatatttaaatatttatttaatatttaaatattaaatatatataattaatataatt +atatatatattatatactatatattatatatact-----atatactatatatagtatact +aatataatatactatatatactatatataatatactatatatagtatatatagtatagta +tactataatatactatat-------------------------------------tatat +aatatagtatactatatattgtatactatactatgctatagtatgctatatactacacta +tagtatactgtatactatac-----tatacagtatactgtatactatactatagta---- +---------tacagtatactatatactattgtatagtatatagtatactgtatactatag +tatagtatactatatactatactatactatagtatactctatagtatataaagacatata +tatagtcttcaaaatgaagatcctgtatcctatatatatatataacttcaaaagtgagat +acatatatatgatgtagaaactttagaatatacaaaattgtcttcttcaggataagaaaa +tcctgatattcagcctaacctccactgactgtaaaggaagaatgggtttcactttcaggg +aaggtcaccttcatcc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/msa.fa.fai new file mode 100644 index 00000000..05630ddf --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_55624382_55625908 2176 29 60 61 +syndip_1_chr20:55624382-55625908 2176 2276 60 61 +syndip_2_chr20:55624382-55625908 2176 4523 60 61 +p:HG002_1_chr20:55624382-55625908 2176 6771 60 61 +p:HG002_2_chr20:55624382-55625908 2176 9019 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/output.vcf.gz new file mode 100644 index 00000000..dff89a31 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/output.vcf.gz.tbi new file mode 100644 index 00000000..ec6e3ed5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55624482-55625808/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/base.vcf.gz new file mode 100644 index 00000000..9d1091d8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/base.vcf.gz.tbi new file mode 100644 index 00000000..c046df78 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/comp.vcf.gz new file mode 100644 index 00000000..85b48943 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/comp.vcf.gz.tbi new file mode 100644 index 00000000..77cf8716 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/haps.fa new file mode 100644 index 00000000..1c5efc0a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/haps.fa @@ -0,0 +1,90 @@ +>ref_chr20_55627244_55628551 +GTATCAGCTATCCACTACATACTTAGAAATTTGGCTAATTATCATAACATAAATTAACATTTTATGGCTGTGAAAAGAGAATAGAAATGGATTTTAGAATGTCAAGTATTTATCACTAGTATGTGTTAATATAAATAGCTTAATAAAAATAGGGCATTTATATGTATATATGTGGGTGTTCATGTATATATTTTTATATGTATATATGTGGGTGTGCATGTATACATTAAATGATGAATTTATATGTATATATTAAATGTATATATTATATGTATATATTACATATATACATATTGTATATTACATATACATAATACATAAAATGTTTAATACATACATAATATATACATAATATAATATTGTATATTATTAAATTATACATGTATATATGTATACATGTATACAAAATATGTATATAATATATACAAAAAATGTGTATTTTTGTACATATATTGTACAAAAATATGTATATTATATATACAAAATATGTATATAATATATACATATATTATGTAATATAATATATACATAATGTGTATTACATACATTATATGTAATATATACATATATATTATATACATATATATTATATACATATATGTATATATTATATACATATATGTATATATTATATATTATGTATACACATATGTATATATGTATATATTATATATTATGTATACACATATGTATATATGTATATATTATATATTATGTATACACATATGTATATATGTATATATTATATATTATGTATACACATATGTATATATGTATATATTATATATTATGTATACATATATGTATATATGTATATATTATATATTATGTATACATATATGTATATATGTATATATTATATATTATGTATACATATATGTATATATTATATATTATGTATACATATATGTATATATTATATATTATGTATACATATATGTATATATTATATATTATGTATACATATATGTATATATTATATATTATGTATACATATATGTATATATGTATGTATACATGTATATACATATATACGTATACACATATATACGTGTATATACATATATACGTATATACACGTATATATTAAATGATAAATTTATATGTATATATGCGTGTGTGCACACACACACGAGATATGTTGGTTTTGTGTAATGCAACCAAATAAATTAAGTATACATAGGAGAGAGTCACTGCCCTGACTCTTAAATGTAACCCTTATTAAAGAAAATATTTTAGTTCATTTTTTATCTATCAACCTTTTTTATCTATCAACTCTGAAATCTGCAATCAATCATATTTGGTTAT +>syndip_1_chr20:55627244-55628551 +GTATCAGCTATCCACTACATACTTAGAAATTTGGCTAATTATCATAACATAAATTAACAT +TTTATGGCTGTGAAAAGAGAATAGAAATGGATTTTAGAATGTCAAGTATTTATCACTAGT +ATGTGTTAATATAAATAGCTTAATAAAAATAGGGCATTTATATGTATATATGTGGGTGTT +CATGTATATATTTTTATATGTATATATGTGGGTGTGCATGTATACATTAAATGATGAATT +TATATGTATATATTAAATGTATATATTATATGTATATATTACATATATACATATTGTATA +TTACATATACATAATACATAAAATGTTTAATACATACATAATATATACATAATATAATAT +TGTATATTATTAAATTATACATGTATATATGTATACTATATGTATATATGTATACAAAAT +ATGTATATAATATATACAAAAATATGTGTATTTTTGTACATATATTGTACAAAAATATGT +ATATTATATATACAAAATATGTATATAATATATACATATATTATGTAATATAATATATAC +ATAATGTGTATTACATACATTATATGTAATATATACATATATTATATAATATATATGTAT +ATATTATATACATATATATTATATACATATATGTATATATTATATACATATATGTATACA +TTATATATTATGTATACATATATGTATATATGTATACATTATATATTATGTATACATATA +TGTATATATGTATACATTATATATTATGTATACATATATGTATATATGTATACATTATAT +ATTATGTATACATATATGTATATATGTATACATTATATATTATGTATACATATATGTATA +TATGTATACATTATATATTATGTATACATATATGTATATATGTATACATTATATATTATG +TATACATATATGTATATATGTATACATGTATATACATATATACGTATACACATATATACG +TGTATATACGTATATACACGTATATATTAAATGATAAATTTATATGTATATATGCGTGTG +TGCACACACACACGAGATATGTTGGTTTTGTGTAATGCAACCAAATAAATTAAGTATACA +TAGGAGAGAGTCACTGCCCTGACTCTTAAATGTAACCCTTATTAAAGAAAATATTTTAGT +TCATTTTTTATCTATCAACCTTTTTTATCTATCAACTCTGAAATCTGCAATCAATCATAT +TTGGTTAT +>syndip_2_chr20:55627244-55628551 +GTATCAGCTATCCACTACATACTTAGAAATTTGGCTAATTATCATAACATAAATTAACAT +TTTATGGCTGTGAAAAGAGAATAGAAATGGATTTTAGAATGTCAAGTATTTATCACTAGT +ATGTGTTAATATAAATAGCTTAATAAAAATAGGGCATTTATATGTATATATGTGGGTGTT +CATGTATATATTTTTATATGTATATATGTGGGTGTGCATGTATACATTAAATGATGAATT +TATATGTATATATTAAATGTATATATTATATGTATATATTACATATATACATATTGTATA +TTACATATACATAATACATAAAATGTTTAATACATACATAATATATACATAATATAATAT +TGTATATTATTAAATTATACATGTATATATGTATACATGTATACAAAATATGTATATAAT +ATATACAAAAAATGTGTATTTTTGTACATATATTGTACAAAAATATGTATATTATATATA +CAAAATATGTATATAATATATACATATATTATGTAATATAATATATACGTAATGTGTATT +ACATACATTATATGTAATATATACATATATATTATATACATATATATGTATATATTATAT +ACATATATATTATATACATATATGTATATATTATATATTATGTATACACATATGTATATA +TGTATATATTATATATTATGTATACACATATGTATATATGTATATATTATATATTATGTA +TACACATATGTATATATTATATATTATGTATACACATATGTATATATGTATATATTATAT +ATTATGTATACACATATGTATATATTATATATTATGTATACACATATGTATATATGTATA +TATTATATATTATGTATACACATATGTATATATTATATATTATGTATACACATATGTATA +TATTATATATTATGTATACACGTATATACATATATACGTATACACGTATATACGTATATA +CGTATATACGTATATACACGTATATATTAAATGATAAATTTATATGTATATATGCGTGTG +TGCACACACACACGAGATATGTTGGTTTTGTGTAATGCAACCAAATAAATTAAGTATACA +TAGGAGAGAGTCACTGCCCTGACTCTTAAATGTAACCCTTATTAAAGAAAATATTTTAGT +TCATTTTTTATCTATCAACCTTTTTTATCTATCAACTCTGAAATCTGCAATCAATCATAT +TTGGTTAT +>p:HG002_1_chr20:55627244-55628551 +GTATCAGCTATCCACTACATACTTAGAAATTTGGCTAATTATCATAACATAAATTAACAT +TTTATGGCTGTGAAAAGAGAATAGAAATGGATTTTAGAATGTCAAGTATTTATCACTAGT +ATGTGTTAATATAAATAGCTTAATAAAAATAGGGCATTTATATGTATATATGTGGGTGTT +CATGTATATATTTTTATATGTATATATGTGGGTGTGCATGTATACATTAAATGATGAATT +TATATGTATATATTAAATGTATATATTATATGTATATATTACATATATACATATTGTATA +TTACATATACATAATACATAAAATGTTTAATACATACATAATATATACATAATATAATAT +TGTATATTATTAAATTATACATGTATATATGTATACATGTATACAAAATATGTATATAAT +ATATACAAAAAATGTGTATTTTTGTACATATATTGTACAAAAATATGTATATTATATATA +CAAAATATGTATATAATATATACATATATTATGTAATATAATATATACGTAATGTGTATT +ACATACATTATATGTAATATATACATATATATTATATACATATATATGTATATATTATAT +ACATATATATTATATACATATATGTATATATTATATATTATGTATACACATATGTATATA +TGTATATATTATATATTATGTATACACATATGTATATATGTATATATTATATATTATGTA +TACACATATGTATATATTATATATTATGTATACACATATGTATATATGTATATATTATAT +ATTATGTATACACATATGTATATATTATATATTATGTATACACATATGTATATATGTATA +TATTATATATTATGTATACACATATGTATATATTATATATTATGTATACACATATGTATA +TATTATATATTATGTATACACGTATATACATATATACGTATACACGTATATACGTATATA +CGTATATACGTATATACACGTATATATTAAATGATAAATTTATATGTATATATGCGTGTG +TGCACACACACACGAGATATGTTGGTTTTGTGTAATGCAACCAAATAAATTAAGTATACA +TAGGAGAGAGTCACTGCCCTGACTCTTAAATGTAACCCTTATTAAAGAAAATATTTTAGT +TCATTTTTTATCTATCAACCTTTTTTATCTATCAACTCTGAAATCTGCAATCAATCATAT +TTGGTTAT +>p:HG002_2_chr20:55627244-55628551 +GTATCAGCTATCCACTACATACTTAGAAATTTGGCTAATTATCATAACATAAATTAACAT +TTTATGGCTGTGAAAAGAGAATAGAAATGGATTTTAGAATGTCAAGTATTTATCACTAGT +ATGTGTTAATATAAATAGCTTAATAAAAATAGGGCATTTATATGTATATATGTGGGTGTT +CATGTATATATTTTTATATGTATATATGTGGGTGTGCATGTATACATTAAATGATGAATT +TATATGTATATATTAAATGTATATATTATATGTATATATTACATATATACATATTGTATA +TTACATATACATAATACATAAAATGTTTAATACATACATAATATATACATAATATAATAT +TGTATATTATTAAATTATACATGTATATATGTATACTATATGTATATATGTATACAAAAT +ATGTATATAATATATACAAAAATATGTGTATTTTTGTACATATATTGTACAAAAATATGT +ATATTATATATACAAAATATGTATATAATATATACATATATTATGTAATATAATATATAC +ATAATGTGTATTACATACATTATATGTAATATATACATATATTATATAATATATATGTAT +ATATTATATACATATATATTATATACATATATGTATATATTATATACATATATGTATACA +TTATATATTATGTATACATATATGTATATATGTATACATTATATATTATGTATACATATA +TGTATATATGTATACATTATATATTATGTATACATATATGTATATATGTATACATTATAT +ATTATGTATACATATATGTATATATGTATACATTATATATTATGTATACATATATGTATA +TATGTATACATTATATATTATGTATACATATATGTATATATGTATACATTATATATTATG +TATACATATATGTATATATGTATACATGTATATACATATATACGTATACACATATATACG +TGTATATACGTATATACACGTATATATTAAATGATAAATTTATATGTATATATGCGTGTG +TGCACACACACACGAGATATGTTGGTTTTGTGTAATGCAACCAAATAAATTAAGTATACA +TAGGAGAGAGTCACTGCCCTGAGTCTTAAATGTAACCCTTATTAAAGAAAATATTTTAGT +TCATTTTTTATCTATCAACCTTTTTTATCTATCAACTCTGAAATCTGCAATCAATCATAT +TTGGTTAT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/haps.fa.ref.fa new file mode 100644 index 00000000..91f9904f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:55627244-55628551 +GTATCAGCTATCCACTACATACTTAGAAATTTGGCTAATTATCATAACATAAATTAACATTTTATGGCTGTGAAAAGAGAATAGAAATGGATTTTAGAATGTCAAGTATTTATCACTAGTATGTGTTAATATAAATAGCTTAATAAAAATAGGGCATTTATATGTATATATGTGGGTGTTCATGTATATATTTTTATATGTATATATGTGGGTGTGCATGTATACATTAAATGATGAATTTATATGTATATATTAAATGTATATATTATATGTATATATTACATATATACATATTGTATATTACATATACATAATACATAAAATGTTTAATACATACATAATATATACATAATATAATATTGTATATTATTAAATTATACATGTATATATGTATACATGTATACAAAATATGTATATAATATATACAAAAAATGTGTATTTTTGTACATATATTGTACAAAAATATGTATATTATATATACAAAATATGTATATAATATATACATATATTATGTAATATAATATATACATAATGTGTATTACATACATTATATGTAATATATACATATATATTATATACATATATATTATATACATATATGTATATATTATATACATATATGTATATATTATATATTATGTATACACATATGTATATATGTATATATTATATATTATGTATACACATATGTATATATGTATATATTATATATTATGTATACACATATGTATATATGTATATATTATATATTATGTATACACATATGTATATATGTATATATTATATATTATGTATACATATATGTATATATGTATATATTATATATTATGTATACATATATGTATATATGTATATATTATATATTATGTATACATATATGTATATATTATATATTATGTATACATATATGTATATATTATATATTATGTATACATATATGTATATATTATATATTATGTATACATATATGTATATATTATATATTATGTATACATATATGTATATATGTATGTATACATGTATATACATATATACGTATACACATATATACGTGTATATACATATATACGTATATACACGTATATATTAAATGATAAATTTATATGTATATATGCGTGTGTGCACACACACACGAGATATGTTGGTTTTGTGTAATGCAACCAAATAAATTAAGTATACATAGGAGAGAGTCACTGCCCTGACTCTTAAATGTAACCCTTATTAAAGAAAATATTTTAGTTCATTTTTTATCTATCAACCTTTTTTATCTATCAACTCTGAAATCTGCAATCAATCATATTTGGTTAT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/msa.fa new file mode 100644 index 00000000..f0c1c0d3 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/msa.fa @@ -0,0 +1,120 @@ +>ref_chr20_55627244_55628551 +gtatcagctatccactacatacttagaaatttggctaattatcataacataaattaacat +tttatggctgtgaaaagagaatagaaatggattttagaatgtcaagtatttatcactagt +atgtgttaatataaatagcttaataaaaatagggcatttatatgtatatatgtgggtgtt +catgtatatatttttatatgtatatatgtgggtgtgcatgtatacattaaatgatgaatt +tatatgtatatattaaatgtatatattatatgtatatattacatatatacatattgtata +ttacatatacataatacataaaatgtttaatacatacataatatatacataatataatat +tgtatattattaaattatacatgtatatatgtatac-----------atgtatacaaaat +atgtatataatatatacaaaaa-atgtgtatttttgtacatatattgtacaaaaatatgt +atattatatatacaaaatatgtatataatatatacatatattatgtaatataatatatac +ataatgtgtattacatacattatatgtaatatatacatatatattatatacatatatat- +tatata-catatatgtatatattatatacatatatgtatatattatatattatgtataca +catatgtatatatgtatatattatatattatgtatacacatatgtatatatgtatatatt +atatattatgtatacacatatgtatatatgtatatattatatattatgtatacacatatg +tatatatgtatatattatatattatgtatacatatatgtatatatgtatatattatatat +tatgtatacatatatgtatatatgtatatattatatattatgtatacatatatgtatat- +-------attatatattatgtatacatatatgtatatattatatattatgtatacatata +tgtatatattatatattatgtatacatatatgtatatattatatattatgtatacatata +tgtatatatgtatgtatacatgtatatacatatatacgtatacacatatatacgtgtata +tacatatatacgtatatacacgtatatattaaatgataaatttatatgtatatatgcgtg +tgtgcacacacacacgagatatgttggttttgtgtaatgcaaccaaataaattaagtata +cataggagagagtcactgccctgactcttaaatgtaacccttattaaagaaaatatttta +gttcattttttatctatcaaccttttttatctatcaactctgaaatctgcaatcaatcat +atttggttat +>syndip_1_chr20:55627244-55628551 +gtatcagctatccactacatacttagaaatttggctaattatcataacataaattaacat +tttatggctgtgaaaagagaatagaaatggattttagaatgtcaagtatttatcactagt +atgtgttaatataaatagcttaataaaaatagggcatttatatgtatatatgtgggtgtt +catgtatatatttttatatgtatatatgtgggtgtgcatgtatacattaaatgatgaatt +tatatgtatatattaaatgtatatattatatgtatatattacatatatacatattgtata +ttacatatacataatacataaaatgtttaatacatacataatatatacataatataatat +tgtatattattaaattatacatgtatatatgtatactatatgtatatatgtatacaaaat +atgtatataatatatacaaaaatatgtgtatttttgtacatatattgtacaaaaatatgt +atattatatatacaaaatatgtatataatatatacatatattatgtaatataatatatac +ataatgtgtattacatacattatatgtaatatatacatatattatata---atatatatg +tatatattatatacatatatattatatacatatatgtatatattatata----------- +------catatatgtatacattatatattatgtatacatatatgtatatatgtatacatt +atatattatgtatacatatatgtatatatgtatacattatatattatgtatacatatatg +tatatatgtatacattatatattatgtatacatatatgtatatatgtatacattatatat +tatgtatacatatatgtatatatgtatacattatatattatgtatacatatatgtatata +tgtatacattatatattatgtatacatatatgtata------------------------ +------------------------------------------------------------ +----------tatgtatacatgtatatacatatatacgtatacacatatatacgtg---- +----tatatacgtatatacacgtatatattaaatgataaatttatatgtatatatgcgtg +tgtgcacacacacacgagatatgttggttttgtgtaatgcaaccaaataaattaagtata +cataggagagagtcactgccctgactcttaaatgtaacccttattaaagaaaatatttta +gttcattttttatctatcaaccttttttatctatcaactctgaaatctgcaatcaatcat +atttggttat +>syndip_2_chr20:55627244-55628551 +gtatcagctatccactacatacttagaaatttggctaattatcataacataaattaacat +tttatggctgtgaaaagagaatagaaatggattttagaatgtcaagtatttatcactagt +atgtgttaatataaatagcttaataaaaatagggcatttatatgtatatatgtgggtgtt +catgtatatatttttatatgtatatatgtgggtgtgcatgtatacattaaatgatgaatt +tatatgtatatattaaatgtatatattatatgtatatattacatatatacatattgtata +ttacatatacataatacataaaatgtttaatacatacataatatatacataatataatat +tgtatattattaaattatacatgtatatatgtatac-----------atgtatacaaaat +atgtatataatatatacaaaaa-atgtgtatttttgtacatatattgtacaaaaatatgt +atattatatatacaaaatatgtatataatatatacatatattatgtaatataatatatac +gtaatgtgtattacatacattatatgtaatatatacatatatattatatacatatatatg +tatatattatatacatatatattatatacatatatgtatatattatatattatgtataca +catatgtatatatgtatatattatatattatgtatacacatatgtatatatgtatatatt +atatattatgtatacac--------atatgtatatattatatattatgtatacacatatg +tatatatgtatatattatatattatgtatac--------acatatgtatatattatatat +tatgtatacacatatgtatatatgtatatattatatattatgtatacacatatgtatat- +-------attatatattatgtatacacatatgtatatattatatat-------------- +------------------------------------------------------------ +----------tatgtatacacgtatatacatatatacgtatacacgtatatacgta--ta +tacgtatatacgtatatacacgtatatattaaatgataaatttatatgtatatatgcgtg +tgtgcacacacacacgagatatgttggttttgtgtaatgcaaccaaataaattaagtata +cataggagagagtcactgccctgactcttaaatgtaacccttattaaagaaaatatttta +gttcattttttatctatcaaccttttttatctatcaactctgaaatctgcaatcaatcat +atttggttat +>p:HG002_1_chr20:55627244-55628551 +gtatcagctatccactacatacttagaaatttggctaattatcataacataaattaacat +tttatggctgtgaaaagagaatagaaatggattttagaatgtcaagtatttatcactagt +atgtgttaatataaatagcttaataaaaatagggcatttatatgtatatatgtgggtgtt +catgtatatatttttatatgtatatatgtgggtgtgcatgtatacattaaatgatgaatt +tatatgtatatattaaatgtatatattatatgtatatattacatatatacatattgtata +ttacatatacataatacataaaatgtttaatacatacataatatatacataatataatat +tgtatattattaaattatacatgtatatatgtatac-----------atgtatacaaaat +atgtatataatatatacaaaaa-atgtgtatttttgtacatatattgtacaaaaatatgt +atattatatatacaaaatatgtatataatatatacatatattatgtaatataatatatac +gtaatgtgtattacatacattatatgtaatatatacatatatattatatacatatatatg +tatatattatatacatatatattatatacatatatgtatatattatatattatgtataca +catatgtatatatgtatatattatatattatgtatacacatatgtatatatgtatatatt +atatattatgtatacac--------atatgtatatattatatattatgtatacacatatg +tatatatgtatatattatatattatgtatac--------acatatgtatatattatatat +tatgtatacacatatgtatatatgtatatattatatattatgtatacacatatgtatat- +-------attatatattatgtatacacatatgtatatattatatat-------------- +------------------------------------------------------------ +----------tatgtatacacgtatatacatatatacgtatacacgtatatacgta--ta +tacgtatatacgtatatacacgtatatattaaatgataaatttatatgtatatatgcgtg +tgtgcacacacacacgagatatgttggttttgtgtaatgcaaccaaataaattaagtata +cataggagagagtcactgccctgactcttaaatgtaacccttattaaagaaaatatttta +gttcattttttatctatcaaccttttttatctatcaactctgaaatctgcaatcaatcat +atttggttat +>p:HG002_2_chr20:55627244-55628551 +gtatcagctatccactacatacttagaaatttggctaattatcataacataaattaacat +tttatggctgtgaaaagagaatagaaatggattttagaatgtcaagtatttatcactagt +atgtgttaatataaatagcttaataaaaatagggcatttatatgtatatatgtgggtgtt +catgtatatatttttatatgtatatatgtgggtgtgcatgtatacattaaatgatgaatt +tatatgtatatattaaatgtatatattatatgtatatattacatatatacatattgtata +ttacatatacataatacataaaatgtttaatacatacataatatatacataatataatat +tgtatattattaaattatacatgtatatatgtatactatatgtatatatgtatacaaaat +atgtatataatatatacaaaaatatgtgtatttttgtacatatattgtacaaaaatatgt +atattatatatacaaaatatgtatataatatatacatatattatgtaatataatatatac +ataatgtgtattacatacattatatgtaatatatacatatattatata---atatatatg +tatatattatatacatatatattatatacatatatgtatatattatata----------- +------catatatgtatacattatatattatgtatacatatatgtatatatgtatacatt +atatattatgtatacatatatgtatatatgtatacattatatattatgtatacatatatg +tatatatgtatacattatatattatgtatacatatatgtatatatgtatacattatatat +tatgtatacatatatgtatatatgtatacattatatattatgtatacatatatgtatata +tgtatacattatatattatgtatacatatatgtata------------------------ +------------------------------------------------------------ +----------tatgtatacatgtatatacatatatacgtatacacatatatacgtg---- +----tatatacgtatatacacgtatatattaaatgataaatttatatgtatatatgcgtg +tgtgcacacacacacgagatatgttggttttgtgtaatgcaaccaaataaattaagtata +cataggagagagtcactgccctgagtcttaaatgtaacccttattaaagaaaatatttta +gttcattttttatctatcaaccttttttatctatcaactctgaaatctgcaatcaatcat +atttggttat diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/msa.fa.fai new file mode 100644 index 00000000..048ef179 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_55627244_55628551 1330 29 60 61 +syndip_1_chr20:55627244-55628551 1330 1416 60 61 +syndip_2_chr20:55627244-55628551 1330 2803 60 61 +p:HG002_1_chr20:55627244-55628551 1330 4191 60 61 +p:HG002_2_chr20:55627244-55628551 1330 5579 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/output.vcf.gz new file mode 100644 index 00000000..c145ce50 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/output.vcf.gz.tbi new file mode 100644 index 00000000..633f4d7f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55627344-55628451/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/base.vcf.gz new file mode 100644 index 00000000..0d50773b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/base.vcf.gz.tbi new file mode 100644 index 00000000..2e78dae5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/comp.vcf.gz new file mode 100644 index 00000000..04a0b22a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/comp.vcf.gz.tbi new file mode 100644 index 00000000..e2fffe7a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/haps.fa new file mode 100644 index 00000000..3638376e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/haps.fa @@ -0,0 +1,148 @@ +>ref_chr20_55943819_55945908 +GTGCTGGGTACTGTCCCAGTCCTCCTACCTGTTTACCTCACTTCCACCCTTGCCTCCTTCCAAGTCAATCCCATGGGAACCAGCATTTTCTGAAACTCAATAAAATTAGCTAGCATTTCAGCCAGGTGCAGTGGCTCAAGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGTGGATCACTTGAGGTTAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCTCGCCTCTACTAAAAATACAAAAATTAGCTGGGCATGCTGGCATGTGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAACTGCTTGAGCCTGGGAGGCAGAGGTTGCAGTGAGCTGAGATGGCACCACTGCATTCCAGCTGGGCAACAGAGAGAGACTCTTTCTTAAATATATATATTTTATATATATATAGATACACACACACACACACACACACACACATATATATATATATATATATATATATATATATATGCATGCATGCCAGATGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGAGAGGCCAAGGTGGGCAGATCATCTGAGGTCAGGAGTTCCAGACCAGCCTAGCCAACATGGTGAAACTCCATCTCTACTAAAAATACAAAATTAGCTGGCTGTGGTGGCTCATGCTGGTAATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTGAACCTGGGAGGTGGAGGTTGCAGTGAGCCGAGATCACACCACTGCACTCCAGCCTGGATGACAGAGCGAGACTCCATTAAAAAAATATATCTATATCTATAGATATCTATAGATATATATCTAGATATAGATCTATGAGTATATATCTATAGATATCTAGATATATATTTATAGATAGATATATCTATAGATATCTATATATTTCTATCGATAGAGATATCTATAGATATCTATCAATATATCTATAGATTTCTAGAGATATGTATCTAGATATAAATCTATAGACATAGATATAGATATATAGATATTTAACTGCCAATGTCCTAAACACTTTATACTCAACACATTTTTTATAAAAAAAAATAGATATCGGTCTAGATAGTATCTATCTAGATATCGGTCTAGATAGTATCTATCTAGATATCTGTGTAGATGTCTAGATATCTATCTAGATATTATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTAGATAGTATCTGTCGCTATCTAGATATCTAGATAGTATCTGTCTAGATAGCTATCTAGATAGTATCTGTCTAGATAGCTATCTAGATAGTATCTGTCCAGATATCTGTAGCTATCTAGATTGTATCTGTCTAGATATCTGTAGATATCTAGATATCTATATCTATCTGGATATCTATAGATATTTAACTGCCGGGCAATGTCCTAAACCCTTTACACTCAACACATTTCATTTTATAACAAAATATGAGGTAGATATTATTATTTCCCTCAACTCACAGAGAAGAAAAAAATGAAGCATATGGAGCCCATGGGC +>syndip_1_chr20:55943819-55945908 +GTGCTGGGTACTGTCCCAGTCCTCCTACCTGTTTACCTCACTTCCACCCTTGCCTCCTTC +CAAGTCAATCCCATGGGAACCAGCATTTTCTGAAACTCAATAAAATTAGCTAGCATTTCA +GCCAGGTGCAGTGGCTCAAGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGTGGAT +CACTTGAGGTTAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCTCGCCTCTACTA +AAAATACAAAAATTAGCTGGGCATGCTGGCATGTGCCTGTAATCCCAGCTACTCAGGAGG +CTGAGGCAGGAGAACTGCTTGAGCCTGGGAGGCAGAGGTTGCAGTGAGCTGAGATGGCAC +CACTGCATTCCAGCTGGGCAACAGAGAGAGACTCTTTCTTAAATATATATATTTTATATA +TATATAGATACACACACACACACACACACACACACATATATATATATATATATATATATA +TATATATATGCATGCATGCCAGATGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGAGA +GGCCAAGGTGGGCAGATCATCTGAGGTCAGGAGTTCCAGACCAGCCTAGCCAACATGGTG +AAACTCCATCTCTACTAAAAATACAAAATTAGCTGGCTGTGGTGGCTCATGCTGGTAATC +CCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTGAACCTGGGAGGTGGAGGTTGCAG +TGAGCCGAGATCACACCACTGCACTCCAGCCTGGATGACAGAGCGAGACTCCATTAAAAA +AATATATCTATATCTATAGATATCTATAGATATATATCTAGATATAGATCTATGAGTATA +TATCTATAGATATCTAGATATATATTTATAGATAGATATATCTATAGATATCTATATATT +TCTATCGATAGAGATATCTATAGATATCTATCAATATATCTATAGATTTCTAGAGATATG +TATCTAGATATAAATCTATAGACATAGATATAGATATATAGATATTTAACTGCCAATGTC +CTAAACACTTTATACTCAACACATTTTTTATAAAAAAAAATAGATATCGGTCTAGATAGT +ATCTATCTAGATATCGGTCTAGATAGTATCTATCTAGATATCTGTGTAGATGTCTAGATA +TCTATCTAGATATTATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATCT +GTCGCTATCTAGATATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATAGTA +TCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAG +ATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCT +ATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAG +ATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCT +ATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCT +GTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATA +GTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATC +TAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATA +TCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATC +TAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTC +GCTATCTAGATATCTAGATAGTATCTGTCGCTATCTAGATATCTAGATAGTATCTGTCTA +GATAGCTATCTAGATAGTATCTGTCTAGATAGCTATCTAGATAGTATCTGTCCAGATATC +TGTAGCTATCTAGATTGTATCTGTCTAGATATCTGTAGATATCTAGATATCTATATCTAT +CTGGATATCTATAGATATTTAACTGCCGGGCAATGTCCTAAACCCTTTACACTCAACACA +TTTCATTTTATAACAAAATATGAGGTAGATATTATTATTTCCCTCAACTCACAGAGAAGA +AAAAAATGAAGCATATGGAGCCCATGGGC +>syndip_2_chr20:55943819-55945908 +GTGCTGGGTACTGTCCCAGTCCTCCTACCTGTTTACCTCACTTCCACCCTTGCCTCCTTC +CAAGTCAATCCCATGGGAACCAGCATTTTCTGAAACTCAATAAAATTAGCTAGCATTTCA +GCCAGGTGCAGTGGCTCAAGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGTGGAT +CACTTGAGGTTAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCTCGCCTCTACTA +AAAATACAAAAATTAGCTGGGCATGCTGGCATGTGCCTGTAATCCCAGCTACTCAGGAGG +CTGAGGCAGGAGAACTGCTTGAGCCTGGGAGGCAGAGGTTGCAGTGAGCTGAGATGGCAC +CACTGCATTCCAGCTGGGCAACAGAGAGAGACTCTTTCTTAAATATATATATTTTATATA +TATATAGATACACACACACACACACACACACACACACACACACACACACACACACATATA +TATATATATATATATATATATATATATATATATATATATATATGCATGCATGCCAGATGC +AGTGGCTCACGCCTGTAATCCCAGCACTTTGAGAGGCCAAGGTGGGCAGATCATCTGAGG +TCAGGAGTTCCAGACCAGCCTAGCCAACATGGTGAAACTCCATCTCTACTAAAAATACAA +AATTAGCTGGCTGTGGTGGCTCATGCTGGTAATCCCAGCTACTTGGGAGGCTGAGGCAGG +AGAATCACTTGAACCTGGGAGGTGGAGGTTGCAGTGAGCCGAGATCACACCACTGCACTC +CAGCCTGGATGACAGAGCGAGACTCCATTAAAAAAATATATCTATATCTATAGATATCTA +TAGATATATATCTAGATATAGATCTATGAGTATATATCTATAGATATCTAGATATATATT +TATAGATAGATATATCTATAGATATCTATATATTTCTATCGATAGAGATATCTATAGATA +TCTATCAATATATCTATAGATTTCTAGAGATATGTATCTAGATATAAATCTATAGACATA +GATATAGATATATAGATATTTAACTGCCAATGTCCTAAACACTTTATACTCAACACATTT +TTTATAAAAAAAAATAGATATCGGTCTAGATAGTATCTATCTAGATATCGGTCTAGATAG +TATCTATCTAGATATCGGTCTAGATAGTATCTATCTAGATATCTGCGTAGATGTCTAGAT +ATCTATCTAGATATTATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATC +TGTCGCTATCTAGATATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATC +ATCTGTCGCTATCTAGATATCTATCTAGATATCATCTGTCGCTATCTAGATATCTATCTA +GATATCATCTGTCGCTATCTAGATATCTATCTAGATATCATCTGTCGCTATCTAGATATC +TATCTAGATATCATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTA +GATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGC +TATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATC +TGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGAT +AGTATCTGTCGCTATCTAGATATCTAGATAGTATCTGTCGCTATCTAGATATCTAGATAG +TATCTGTCTAGATAGCTATCTAGATAGTATCTGTCTAGATAGCTATCTAGATAGTATCTG +TCCAGATATCTGTAGCTATCTAGATTGTATCTGTCTAGATATCTGTAGATATCTAGATAT +CTATATCTATCTGGATATCTATAGATATTTAACTGCCGGGCAATGTCCTAAACCCTTTAC +ACTCAACACATTTCATTTTATAACAAAATATGAGGTAGATATTATTATTTCCCTCAACTC +ACAGAGAAGAAAAAAATGAAGCATATGGAGCCCATGGGC +>p:HG002_1_chr20:55943819-55945908 +GTGCTGGGTACTGTCCCAGTCCTCCTACCTGTTTACCTCACTTCCACCCTTGCCTCCTTC +CAAGTCAATCCCATGGGAACCAGCATTTTCTGAAACTCAATAAAATTAGCTAGCATTTCA +GCCAGGTGCAGTGGCTCAAGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGTGGAT +CACTTGAGGTTAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCTCGCCTCTACTA +AAAATACAAAAATTAGCTGGGCATGCTGGCATGTGCCTGTAATCCCAGCTACTCAGGAGG +CTGAGGCAGGAGAACTGCTTGAGCCTGGGAGGCAGAGGTTGCAGTGAGCTGAGATGGCAC +CACTGCATTCCAGCTGGGCAACAGAGAGAGACTCTTTCTTAAATATATATATTTTATATA +TATATAGATACACACACACACACACACACACACACACACACACACACACACACACATATA +TATATATATATATATATATATATATATATATATATATATATATGCATGCATGCCAGATGC +AGTGGCTCACGCCTGTAATCCCAGCACTTTGAGAGGCCAAGGTGGGCAGATCATCTGAGG +TCAGGAGTTCCAGACCAGCCTAGCCAACATGGTGAAACTCCATCTCTACTAAAAATACAA +AATTAGCTGGCTGTGGTGGCTCATGCTGGTAATTCCAGCTACTTGGGAGGCTGAGGCAGG +AGAATCACATGAACCTGGGAGGTGGAGGTTGCAGTGAGCCGAGATCACACCACTGCACTC +CAGCCTGGATGACAGAGCGAGACTCCATTAAAAAAATATATCTATATCTATAGATATCTA +TAGATATATATCTAGATATAGATCTATGAGTATATATCTATAGATATCTAGATATATATT +TATAGATAGATATATCTATAGATATCTATATATTTCTATCGATAGAGATATCTATAGATA +TCTATCAATATATCTATAGATTTCTAGAGATATGTATCTAGATATAAATCTATAGACATA +GATATAGATATATAGATATTTAACTGCCAATGTCCTAAACACTTTATACTCAACACATTT +TTTATAAAAAAAAATAGATATCGGTCTAGATAGTATCTATCTAGATATCGGTCTAGATAG +TATCTATCTAGATATCGGTCTAGATAGTATCTATCTAGATATCTGCGTAGATGTCTAGAT +ATCTATCTAGATATTATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATC +TGTCGCTATCTAGATATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATC +ATCTGTCGCTATCTAGATATCTATCTAGATATCATCTGTCGCTATCTAGATATCTATCTA +GATATCATCTGTCGCTATCTAGATATCTATCTAGATATCATCTGTCGCTATCTAGATATC +TATCTAGATATCATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTA +GATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGC +TATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATC +TGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGAT +AGTATCTGTCGCTATCTAGATATCTAGATAGTATCTGTCGCTATCTAGATATCTAGATAG +TATCTGTCTAGATAGCTATCTAGATAGTATCTGTCTAGATAGCTATCTAGATAGTATCTG +TCCAGATATCTGTAGCTATCTAGATTGTATCTGTCTAGATATCTGTAGATATCTAGATAT +CTATATCTATCTGGATATCTATAGATATTTAACTGCCGGGCAATGTCCTAAACCCTTTAC +ACTCAACACATTTCATTTTATAACAAAATATGAGGTAGATATTATTATTTCCCTCAACTC +ACAGAGAAGAAAAAAATGAAGCATATGGAGCCCATGGGC +>p:HG002_2_chr20:55943819-55945908 +GTGCTGGGTACTGTCCCAGTCCTCCTACCTGTTTACCTCACTTCCACCCTTGCCTCCTTC +CAAGTCAATCCCATGGGAACCAGCATTTTCTGAAACTCAATAAAATTAGCTAGCATTTCA +GCCAGGTGCAGTGGCTCAAGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGTGGAT +CACTTGAGGTTAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCTCGCCTCTACTA +AAAATACAAAAATTAGCTGGGCATGCTGGCATGTGCCTGTAATCCCAGCTACTCAGGAGG +CTGAGGCAGGAGAACTGCTTGAGCCTGGGAGGCAGAGGTTGCAGTGAGCTGAGATGGCAC +CACTGCATTCCAGCTGGGCAACAGAGAGAGACTCTTTCTTAAATATATATATTTTATATA +TATATAGATACACACACACACACACACACACACACATATATATATATATATATATATATA +TATATATATGCATGCATGCCAGATGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGAGA +GGCCAAGGTGGGCAGATCATCTGAGGTCAGGAGTTCCAGACCAGCCTAGCCAACATGGTG +AAACTCCATCTCTACTAAAAATACAAAATTAGCTGGCTGTGGTGGCTCATGCTGGTAATC +CCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTGAACCTGGGAGGTGGAGGTTGCAG +TGAGCCGAGATCACACCACTGCACTCCAGCCTGGATGACAGAGCGAGACTCCATTAAAAA +AATATATCTATATCTATAGATATCTATAGATATATATCTAGATATAGATCTATGAGTATA +TATCTATAGATATCTAGATATATATTTATAGATAGATATATCTATAGATATCTATATATT +TCTATCGATAGAGATATCTATAGATATCTATCAATATATCTATAGATTTCTAGAGATATG +TATCTAGATATAAATCTATAGACATAGATATAGATATATAGATATTTAACTGCCAATGTC +CTAAACACTTTATACTCAACACATTTTTTATAAAAAAAAATAGATATCGGTCTAGATAGT +ATCTATCTAGATATCGGTCTAGATAGTATCTATCTAGATATCTGTGTAGATGTCTAGATA +TCTATCTAGATATTATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATCT +GTCGCTATCTAGATATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATAGTA +TCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAG +ATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCT +ATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAG +ATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCT +ATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCT +GTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATA +GTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATC +TAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATA +TCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATC +TAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTC +GCTATCTAGATATCTAGATAGTATCTGTCGCTATCTAGATATCTAGATAGTATCTGTCTA +GATAGCTATCTAGATAGTATCTGTCTAGATAGCTATCTAGATAGTATCTGTCCAGATATC +TGTAGCTATCTAGATTGTATCTGTCTAGATATCTGTAGATATCTAGATATCTATATCTAT +CTGGATATCTATAGATATTTAACTGCCGGGCAATGTCCTAAACCCTTTACACTCAACACA +TTTCATTTTATAACAAAATATGAGGTAGATATTATTATTTCCCTCAACTCACAGAGAAGA +AAAAAATGAAGCATATGGAGCCCATGGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/haps.fa.ref.fa new file mode 100644 index 00000000..5336576f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:55943819-55945908 +GTGCTGGGTACTGTCCCAGTCCTCCTACCTGTTTACCTCACTTCCACCCTTGCCTCCTTCCAAGTCAATCCCATGGGAACCAGCATTTTCTGAAACTCAATAAAATTAGCTAGCATTTCAGCCAGGTGCAGTGGCTCAAGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGTGGATCACTTGAGGTTAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCTCGCCTCTACTAAAAATACAAAAATTAGCTGGGCATGCTGGCATGTGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAACTGCTTGAGCCTGGGAGGCAGAGGTTGCAGTGAGCTGAGATGGCACCACTGCATTCCAGCTGGGCAACAGAGAGAGACTCTTTCTTAAATATATATATTTTATATATATATAGATACACACACACACACACACACACACACATATATATATATATATATATATATATATATATATGCATGCATGCCAGATGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGAGAGGCCAAGGTGGGCAGATCATCTGAGGTCAGGAGTTCCAGACCAGCCTAGCCAACATGGTGAAACTCCATCTCTACTAAAAATACAAAATTAGCTGGCTGTGGTGGCTCATGCTGGTAATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTGAACCTGGGAGGTGGAGGTTGCAGTGAGCCGAGATCACACCACTGCACTCCAGCCTGGATGACAGAGCGAGACTCCATTAAAAAAATATATCTATATCTATAGATATCTATAGATATATATCTAGATATAGATCTATGAGTATATATCTATAGATATCTAGATATATATTTATAGATAGATATATCTATAGATATCTATATATTTCTATCGATAGAGATATCTATAGATATCTATCAATATATCTATAGATTTCTAGAGATATGTATCTAGATATAAATCTATAGACATAGATATAGATATATAGATATTTAACTGCCAATGTCCTAAACACTTTATACTCAACACATTTTTTATAAAAAAAAATAGATATCGGTCTAGATAGTATCTATCTAGATATCGGTCTAGATAGTATCTATCTAGATATCTGTGTAGATGTCTAGATATCTATCTAGATATTATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTAGATAGTATCTGTCGCTATCTAGATATCTAGATAGTATCTGTCTAGATAGCTATCTAGATAGTATCTGTCTAGATAGCTATCTAGATAGTATCTGTCCAGATATCTGTAGCTATCTAGATTGTATCTGTCTAGATATCTGTAGATATCTAGATATCTATATCTATCTGGATATCTATAGATATTTAACTGCCGGGCAATGTCCTAAACCCTTTACACTCAACACATTTCATTTTATAACAAAATATGAGGTAGATATTATTATTTCCCTCAACTCACAGAGAAGAAAAAAATGAAGCATATGGAGCCCATGGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/msa.fa new file mode 100644 index 00000000..b99015f0 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/msa.fa @@ -0,0 +1,195 @@ +>ref_chr20_55943819_55945908 +gtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctccttc +caagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttca +gccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtggat +cacttgaggttaggagtttgagaccagcctggccaacatggtgaaacctcgcctctacta +aaaatacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggagg +ctgaggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggcac +cactgcattccagctgggcaacagagagagactctttcttaaatatatatattttatata +tatatagatacacacacacacacacacacacacac------------------------- +---------atatatatatatatatatatatatatatatatatgcatgcatgccagatgc +agtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgagg +tcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaatacaa +aattagctggctgtggtggctcatgctggtaatcccagctacttgggaggctgaggcagg +agaatcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcactc +cagcctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatcta +tagatatatatctagatatagatctatgagtatatatctatagatatctagatatatatt +tatagatagatatatctatagatatctatatatttctatcgatagagatatctatagata +tctatcaatatatctatagatttctagagatatgtatctagatataaatctatagacata +gatatagatatatagatatttaactgccaatgtcctaaacactttatactcaacacattt +tttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagatag +tatctatctagatatctgtgtagatgtctagatatctatctagatattatctatctagat +atct--gtcgctatctagatatctatctagatatctgtcgctatctagatatctatctag +a----------------------------------------------------------- +----------------------------------------tatctgtcgctatctagata +tctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatc +tagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtc +gctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagta +tctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctag +atagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatct +atctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctag +atatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgct +atctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatct +gtcgctatctagatatctatctagatagtatctgtcgctatctagatatctagatagtat +ctgtcgctatctagatatctagatagtatctgtctagatagctatctagatagtatctgt +ctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatctgt +ctagatatctgtagatatctagatatctatatctatctggatatctatagatatttaact +gccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatatgag +gtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagccca +tgggc +>syndip_1_chr20:55943819-55945908 +gtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctccttc +caagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttca +gccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtggat +cacttgaggttaggagtttgagaccagcctggccaacatggtgaaacctcgcctctacta +aaaatacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggagg +ctgaggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggcac +cactgcattccagctgggcaacagagagagactctttcttaaatatatatattttatata +tatatagatacacacacacacacacacacacacac------------------------- +---------atatatatatatatatatatatatatatatatatgcatgcatgccagatgc +agtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgagg +tcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaatacaa +aattagctggctgtggtggctcatgctggtaatcccagctacttgggaggctgaggcagg +agaatcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcactc +cagcctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatcta +tagatatatatctagatatagatctatgagtatatatctatagatatctagatatatatt +tatagatagatatatctatagatatctatatatttctatcgatagagatatctatagata +tctatcaatatatctatagatttctagagatatgtatctagatataaatctatagacata +gatatagatatatagatatttaactgccaatgtcctaaacactttatactcaacacattt +tttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagatag +tatctatctagatatctgtgtagatgtctagatatctatctagatattatctatctagat +atct--gtcgctatctagatatctatctagatatctgtcgctatctagatatctatctag +atatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatc +tagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagata +tctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatc +tagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtc +gctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagta +tctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctag +atagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatct +atctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctag +atatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgct +atctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatct +gtcgctatctagatatctatctagatagtatctgtcgctatctagatatctagatagtat +ctgtcgctatctagatatctagatagtatctgtctagatagctatctagatagtatctgt +ctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatctgt +ctagatatctgtagatatctagatatctatatctatctggatatctatagatatttaact +gccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatatgag +gtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagccca +tgggc +>syndip_2_chr20:55943819-55945908 +gtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctccttc +caagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttca +gccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtggat +cacttgaggttaggagtttgagaccagcctggccaacatggtgaaacctcgcctctacta +aaaatacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggagg +ctgaggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggcac +cactgcattccagctgggcaacagagagagactctttcttaaatatatatattttatata +tatatagatacacacacacacacacacacacacacacacacacacacacacacacatata +tatatatatatatatatatatatatatatatatatatatatatgcatgcatgccagatgc +agtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgagg +tcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaatacaa +aattagctggctgtggtggctcatgctggtaatcccagctacttgggaggctgaggcagg +agaatcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcactc +cagcctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatcta +tagatatatatctagatatagatctatgagtatatatctatagatatctagatatatatt +tatagatagatatatctatagatatctatatatttctatcgatagagatatctatagata +tctatcaatatatctatagatttctagagatatgtatctagatataaatctatagacata +gatatagatatatagatatttaactgccaatgtcctaaacactttatactcaacacattt +tttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagatag +tatctatctagatatcgg--------------------tctagatagtatctatctagat +atctgcgtagatgtctagatatctatctagatat---------------tatctatctag +a----------------------------------------------------------- +----------------------------------------tatctgtcgctatctagata +tctatctaga---tatctgtcgctatctagatatctatctaga----------------- +----------------------------------------------------tatctgtc +gctatctagatatctatctagatatcatctgtcgctatctagatatctatctagatatca +tctgtcgctatctagatatctatctagatatcatctgtcgctatctagatatctatctag +atatcatctgtcgctatctagatatctatctagatatcatctgtcgctatctagatatct +atctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctag +atatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgct +atctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatct +gtcgctatctagatatctatctagatagtatctgtcgctatctagatatctagatagtat +ctgtcgctatctagatatctagatagtatctgtctagatagctatctagatagtatctgt +ctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatctgt +ctagatatctgtagatatctagatatctatatctatctggatatctatagatatttaact +gccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatatgag +gtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagccca +tgggc +>p:HG002_1_chr20:55943819-55945908 +gtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctccttc +caagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttca +gccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtggat +cacttgaggttaggagtttgagaccagcctggccaacatggtgaaacctcgcctctacta +aaaatacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggagg +ctgaggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggcac +cactgcattccagctgggcaacagagagagactctttcttaaatatatatattttatata +tatatagatacacacacacacacacacacacacacacacacacacacacacacacatata +tatatatatatatatatatatatatatatatatatatatatatgcatgcatgccagatgc +agtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgagg +tcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaatacaa +aattagctggctgtggtggctcatgctggtaattccagctacttgggaggctgaggcagg +agaatcacatgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcactc +cagcctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatcta +tagatatatatctagatatagatctatgagtatatatctatagatatctagatatatatt +tatagatagatatatctatagatatctatatatttctatcgatagagatatctatagata +tctatcaatatatctatagatttctagagatatgtatctagatataaatctatagacata +gatatagatatatagatatttaactgccaatgtcctaaacactttatactcaacacattt +tttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagatag +tatctatctagatatcgg--------------------tctagatagtatctatctagat +atctgcgtagatgtctagatatctatctagatat---------------tatctatctag +a----------------------------------------------------------- +----------------------------------------tatctgtcgctatctagata +tctatctaga---tatctgtcgctatctagatatctatctaga----------------- +----------------------------------------------------tatctgtc +gctatctagatatctatctagatatcatctgtcgctatctagatatctatctagatatca +tctgtcgctatctagatatctatctagatatcatctgtcgctatctagatatctatctag +atatcatctgtcgctatctagatatctatctagatatcatctgtcgctatctagatatct +atctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctag +atatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgct +atctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatct +gtcgctatctagatatctatctagatagtatctgtcgctatctagatatctagatagtat +ctgtcgctatctagatatctagatagtatctgtctagatagctatctagatagtatctgt +ctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatctgt +ctagatatctgtagatatctagatatctatatctatctggatatctatagatatttaact +gccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatatgag +gtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagccca +tgggc +>p:HG002_2_chr20:55943819-55945908 +gtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctccttc +caagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttca +gccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtggat +cacttgaggttaggagtttgagaccagcctggccaacatggtgaaacctcgcctctacta +aaaatacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggagg +ctgaggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggcac +cactgcattccagctgggcaacagagagagactctttcttaaatatatatattttatata +tatatagatacacacacacacacacacacacacac------------------------- +---------atatatatatatatatatatatatatatatatatgcatgcatgccagatgc +agtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgagg +tcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaatacaa +aattagctggctgtggtggctcatgctggtaatcccagctacttgggaggctgaggcagg +agaatcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcactc +cagcctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatcta +tagatatatatctagatatagatctatgagtatatatctatagatatctagatatatatt +tatagatagatatatctatagatatctatatatttctatcgatagagatatctatagata +tctatcaatatatctatagatttctagagatatgtatctagatataaatctatagacata +gatatagatatatagatatttaactgccaatgtcctaaacactttatactcaacacattt +tttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagatag +tatctatctagatatctgtgtagatgtctagatatctatctagatattatctatctagat +atct--gtcgctatctagatatctatctagatatctgtcgctatctagatatctatctag +atatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatc +tagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagata +tctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatc +tagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtc +gctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagta +tctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctag +atagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatct +atctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctag +atatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgct +atctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatct +gtcgctatctagatatctatctagatagtatctgtcgctatctagatatctagatagtat +ctgtcgctatctagatatctagatagtatctgtctagatagctatctagatagtatctgt +ctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatctgt +ctagatatctgtagatatctagatatctatatctatctggatatctatagatatttaact +gccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatatgag +gtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagccca +tgggc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/msa.fa.fai new file mode 100644 index 00000000..3d15c300 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_55943819_55945908 2225 29 60 61 +syndip_1_chr20:55943819-55945908 2225 2326 60 61 +syndip_2_chr20:55943819-55945908 2225 4623 60 61 +p:HG002_1_chr20:55943819-55945908 2225 6921 60 61 +p:HG002_2_chr20:55943819-55945908 2225 9219 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/output.vcf.gz new file mode 100644 index 00000000..6e2c16ba Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/output.vcf.gz.tbi new file mode 100644 index 00000000..c5bb6800 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:55943919-55945808/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/base.vcf.gz new file mode 100644 index 00000000..11937cc7 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/base.vcf.gz.tbi new file mode 100644 index 00000000..f5ac72e6 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/comp.vcf.gz new file mode 100644 index 00000000..a2520d17 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/comp.vcf.gz.tbi new file mode 100644 index 00000000..ea794a1f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/haps.fa new file mode 100644 index 00000000..d8908ce9 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/haps.fa @@ -0,0 +1,154 @@ +>ref_chr20_56280322_56282215 +GGTGGACATAGTGTATCTACAGATGGGACAATCTAAGATGGTTACAACATTACTACATAGTATCGCAAATAGAAATGGAAAGCCTGAATCTAACCATGAGAAAATTTAAAATAACTATCAAAAAGGTAACATCCATATACAGATATAATATCTATAACATATATAGATATATGGATATAACATCCATATATAGATATATCTATATATCTATCTATAGCTACATCTACAGATATCTATAGCTACATCTACAGATATCTACAGATATCTATAGCTACATCTACAGATATCTATAGCTACATCTACAGATATCTACAGATATCTACAGCTACATCTACAGATATCTATAGATATCTATAGCTATATCTACAGATATCTATCGATAGATATATCTATCGATAGATATATCCACATAGATATCTAGATATATATGGATATATCTATAGATATCTATCTGGATATATCTATCGATAGATATATAGATATATATAGATAAAGCTATATAGATATATATAGATAAACCTATATAGATACATAGATATATAGAGAGAAACCTATATACATATATAGATATATAGAGAGAAACCTATATAGATATATAGATATATAGAGAGAAACCTATATAGATGTATAGATAAACCTATATAGATATATAGATAAACCTATGTAGATATATAGATATATATAGATAAATCTATATAGATATATAAAATAGATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATATATACATAAATCTATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATACATCTATACAGATATATAGATACATATAGATACATCTATACAGATATATAGATACATATAGATACATCTATACAGATATATTGATACATATAGATACATCTATATAGATATATAGATATATAGATACATCTATATAGATATATAGATATATAGATACATCTATATAGATATATATAGATACATCTATATATAGACATATAGATATATATAGATACATCTATATATAGATATATAGATATATATAGATACATCTACACAGAGAGATATATAGAAACATCTACACAGGGAGATATATAGATACATCTACACAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATAGAGATATATATAGATACATCTACATAGAGATATATATAGATACATCTATATAGAGATATATCTACCTATACTTCCTGTGAGTTGTGTTTCTCTGGAGAACTAATAGGTAGGGTGACTGTATAATTTACTCTCCATACTGGGACACTTTTAATCATTGCTATAATACATTAATTTTAATCTAATCTTCTTATCCCT +>syndip_1_chr20:56280322-56282215 +GGTGGACATAGTGTATCTACAGATGGGACAATCTAAGATGGTTACAACATTACTACATAG +TATCGCAAATAGAAATGGAAAGCCTGAATCTAACCATGAGAAAATTTAAAATAACTATCA +AAAAGGTAACATCCATATACAGATATAATATCTATAACATATATAGATATATGGATATAA +CATCCATATATAGATATATCTATATATCTATCTATAGCTACATCTACAGATATCTATAGC +CACATCTACAGATATCTATAGCTACATCTACAGATATCTACAGATATCTACAGCTACATC +TACAGATATCTATAGATATCTATAGCTATATCTACAGATATCTATCGATAGATATATCTA +TCGATAGATATATCCACATAGATATCTAGATATATATGGATATATCTATAGATATCTATC +TGGATATATCTATCGATAGATATATAGATATATATAGATAAAGCTATATAGATATATATA +GATAAACCTATATAGATACATAGATATATAGAGAGAAACCTATATACATATATAGATATA +TAGAGAGAAACCTATATAGATATATAGATATATAGAGATAAACCTATATAGATGTATAGA +TAAACCTATATAGATATATAGATAAACCTATGTAGATATATAGATATATATAGATAAATC +TATATAGATATATAAAATAGATAAATCTATATAGATATATATACATAAATCTATATAGAT +ATATATACATAAATCTATATATATACATAAATCTATATATACATAAATCTATATAGATAT +ATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAAT +CTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATAT +ATACATAAATCTATACAGATACATATACATAAATCTATACAGATACATATACATAAATCT +ATACAGATACATATACATAAATCTATACAGATATATAGATACATATAGATAAATCTATAC +AGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATACATCT +ATACAGATATATAGATACATATAGATACATCTATACAGATATATAGATACATATAGATAC +ATCTATACAGATATATAGATACATATAGATACATCTATACAGATATATAGATACATATAG +ATACATCTATACAGATATATAGATACATATAGATACATCTATACAGATATATAGATACAT +ATAGATACATCTATACAGATATATTGATACATATAGATACATCTATATAGATATATTGAT +ACATATAGATACATCTATATAGATATATTGATACATATAGATACATCTATATAGATATAT +TGATACATATAGATACATCTATATAGATTAGATATATATAGATACATCTATATAGATTAG +ATATATATAGATACATCTATATAGATTAGATATATATAGATACATCTATATATAGATATA +TAGATATATATAGATACATCTATATATAGATATATAGATATATATAGATACATCTATATA +TAGATATATAGATGTATATAGATACATCTATATATAGATATATAGATGTATATAGATACA +TCTATATATAGATATATAGATGTATATAGATACATCTATATATAGATATATAGATGTATA +TAGATACATCTATATATAGATATATAGATGTATATAGATACATCTATATATAGATATATA +GATGTATATAGATACATCTATATATAGATATATAGATGTATATAGATACATCTATATATA +GATATATAGATGTATATAGATACATCTATATATAGATATATAGATGTATATAGATACATC +TATATATAGATATATAGATGTATATAGATACATAGATATATATAGATACATTTATGTATA +TATATATGTATATATAGATATATAGATATATATAGATACATCTACACAGAGAGATATATA +GAAACATCTACACAGGGAGATATATAGATACATCTACATAGAGAGATATATAGATACATC +TACATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATAGA +GAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATAGAGAGATATA +TAGATACATCTACATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACA +TCTACATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATA +GAGAGATATATAGATACATCTACATAGAGATATATATAGATACATCTACATAGAGATATA +TATAGATACATCTATATAGAGATATATCTACCTATACTTCCTGTGAGTTGTGTTTCTCTG +GAGAACTAATAGGTAGGGTGACTGTATAATTTACTCTCCATACTGGGACACTTTTAATCA +TTGCTATAATACATTAATTTTAATCTAATCTTCTTATCCCT +>syndip_2_chr20:56280322-56282215 +GGTGGACATAGTGTATCTACAGATGGGACAATCTAAGATGGTTACAACATTACTACATAG +TATCGCAAATAGAAATGGAAAGCCTGAATCTAACCATGAGAAAATTTAAAATAACTATCA +AAAAGGTAACATCCATATACAGATATAATATCTATAACATATATAGATATATGGATATAA +CATCCATATATAGATATATCTATATATCTATCTATAGCTACATCTACAGATATCTATAGC +TACATCTACAGATATCTACAGATATCTATAGCTACATCTACAGATATCTACAGATATCTA +TAGCTACATCTACAGATATCTATAGCTACATCTACAGATATCTACAGATATCTACAGCTA +CATCTACAGATATCTATAGATATCTATAGCTATATCTACAGATATCTATCGATAGATATA +TCTATCGATAGATATATCCACATAGATATCTAGATATATATGGATATATCTATAGATATC +TATCTGGATATATCTATCGATAGATATATAGATATATATAGATAAAGCTATATAGATATA +TATAGATAAACCTATATAGATACATAGATATATAGAGAGAAACCTATATACATATATAGA +TATATAGAGAGAAACCTATATAGATATATAGATATATAGAGATAAACCTATATAGATGTA +TAGATAAACCTATATAGATATATAGATAAACCTATGTAGATATATAGATATATATAGATA +AATCTATATAGATATATAAAATAGATAAATCTATATAGATATATATACATAAATCTATAT +AGATATATATACATAAATCTATATATATACATAAATCTATATATACATAAATCTATATAG +ATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACAT +AAATCTATATAGATATATACATAAATCTATATATATATACATAAATCTATATAGATATAT +ATACATAAATCTATATAGATACATATAGATAAATCTATACAGATATATAAATATATATAG +ATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACAT +ATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGAT +ACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATAT +AGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGAT +ATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATACATCTATAT +AGATATATTGATACATATAGATACATCTATATAGATATATAGATATATAGATACATCTAT +ATAGATATATATAGATACATCTATATATAGACATATAGATATATATAGATACATCTATAT +ATAGATATATAGATATATATAGATACATCTATATATAGATATATAGATATATATAGATAC +ATCTACACAGAGAGATATATAGAAACATCTACACAGGGAGATATATAGATACATCTACAT +AGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTATATAGAGAGAT +ATATAGATACATCTATATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGAT +ACATCTACATAGAGAGATATATAGATACATCTACATAGAGATATATATAGATACATCTAC +ATAGAGATATATATAGATACATCTATATAGAGATATATCTACCTATACTTCCTGTGAGTT +GTGTTTCTCTGGAGAACTAATAGGTAGGGTGACTGTATAATTTACTCTCCATACTGGGAC +ACTTTTAATCATTGCTATAATACATTAATTTTAATCTAATCTTCTTATCCCT +>p:HG002_1_chr20:56280322-56282215 +GGTGGACATAGTGTATCTACAGATGGGACAATCTAAGATGGTTACAACATTACTACATAG +TATCGCAAATAGAAATGGAAAGCCTGAATCTAACCATGAGAAAATTTAAAATAACTATCA +AAAAGGTAACATCCATATACAGATATAATATCTATAACATATATAGATATATGGATATAA +CATCCATATATAGATATATCTATATATCTATCTATAGCTACATCTACAGATATCTATAGC +TACATCTACAGATATCTACAGATATCTATAGCTACATCTACAGATATCTACAGATATCTA +TAGCTACATCTACAGATATCTATAGCTACATCTACAGATATCTACAGATATCTACAGCTA +CATCTACAGATATCTATAGATATCTATAGCTATATCTACAGATATCTATCGATAGATATA +TCTATCGATAGATATATCCACATAGATATCTAGATATATATGGATATATCTATAGATATC +TATCTGGATATATCTATCGATAGATATATAGATATATATAGATAAAGCTATATAGATATA +TATAGATAAACCTATATAGATACATAGATATATAGAGAGAAACCTATATACATATATAGA +TATATAGAGAGAAACCTATATAGATATATAGATATATAGAGATAAACCTATATAGATGTA +TAGATAAACCTATATAGATATATAGATAAACCTATGTAGATATATAGATATATATAGATA +AATCTATATAGATATATAAAATAGATAAATCTATATAGATATATATACATAAATCTATAT +AGATATATATACATAAATCTATATATATACATAAATCTATATATACATAAATCTATATAG +ATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACAT +AAATCTATATAGATATATACATAAATCTATATATATATACATAAATCTATATAGATATAT +ATACATAAATCTATATAGATACATATAGATAAATCTATACAGATATATAAATATATATAG +ATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACAT +ATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGAT +ACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATAT +AGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGAT +ATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATACATCTATAT +AGATATATTGATACATATAGATACATCTATATAGATATATAGATATATAGATACATCTAT +ATAGATATATATAGATACATCTATATATAGACATATAGATATATATAGATACATCTATAT +ATAGATATATAGATATATATAGATACATCTATATATAGATATATAGATATATATAGATAC +ATCTACACAGAGAGATATATAGAAACATCTACACAGGGAGATATATAGATACATCTACAT +AGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTATATAGAGAGAT +ATATAGATACATCTATATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGAT +ACATCTACATAGAGAGATATATAGATACATCTACATAGAGATATATATAGATACATCTAC +ATAGAGATATATATAGATACATCTATATAGAGATATATCTACCTATACTTCCTGTGAGTT +GTGTTTCTCTGGAGAACTAATAGGTAGGGTGACTGTATAATTTACTCTCCATACTGGGAC +ACTTTTAATCATTGCTATAATACATTAATTTTAATCTAATCTTCTTATCCCT +>p:HG002_2_chr20:56280322-56282215 +GGTGGACATAGTGTATCTACAGATGGGACAATCTAAGATGGTTACAACATTACTACATAG +TATCGCAAATAGAAATGGAAAGCCTGAATCTAACCATGAGAAAATTTAAAATAACTATCA +AAAAGGTAACATCCATATACAGATATAATATCTATAACATATATAGATATATGGATATAA +CATCCATATATAGATATATCTATATATCTATCTATAGCTACATCTACAGATATCTATAGC +CACATCTACAGATATCTATAGCTACATCTACAGATATCTACAGATATCTACAGCTACATC +TACAGATATCTATAGATATCTATAGCTATATCTACAGATATCTATCGATAGATATATCTA +TCGATAGATATATCCACATAGATATCTAGATATATATGGATATATCTATAGATATCTATC +TGGATATATCTATCGATAGATATATAGATATATATAGATAAAGCTATATAGATATATATA +GATAAACCTATATAGATACATAGATATATAGAGAGAAACCTATATACATATATAGATATA +TAGAGAGAAACCTATATAGATATATAGATATATAGAGATAAACCTATATAGATGTATAGA +TAAACCTATATAGATATATAGATAAACCTATGTAGATATATAGATATATATAGATAAATC +TATATAGATATATAAAATAGATAAATCTATATAGATATATATACATAAATCTATATAGAT +ATATATACATAAATCTATATATATACATAAATCTATATATACATAAATCTATATAGATAT +ATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAAT +CTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATAT +ATACATAAATCTATACAGATACATATACATAAATCTATACAGATACATATACATAAATCT +ATACAGATACATATACATAAATCTATACAGATATATAGATACATATAGATAAATCTATAC +AGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATACATCT +ATACAGATATATAGATACATATAGATACATCTATACAGATATATAGATACATATAGATAC +ATCTATACAGATATATAGATACATATAGATACATCTATACAGATATATAGATACATATAG +ATACATCTATACAGATATATAGATACATATAGATACATCTATACAGATATATAGATACAT +ATAGATACATCTATACAGATATATTGATACATATAGATACATCTATATAGATATATTGAT +ACATATAGATACATCTATATAGATATATTGATACATATAGATACATCTATATAGATATAT +TGATACATATAGATACATCTATATAGATTAGATATATATAGATACATCTATATAGATTAG +ATATATATAGATACATCTATATAGATTAGATATATATAGATACATCTATATATAGATATA +TAGATATATATAGATACATCTATATATAGATATATAGATATATATAGATACATCTATATA +TAGATATATAGATGTATATAGATACATCTATATATAGATATATAGATGTATATAGATACA +TCTATATATAGATATATAGATGTATATAGATACATCTATATATAGATATATAGATGTATA +TAGATACATCTATATATAGATATATAGATGTATATAGATACATCTATATATAGATATATA +GATGTATATAGATACATCTATATATAGATATATAGATGTATATAGATACATCTATATATA +GATATATAGATGTATATAGATACATCTATATATAGATATATAGATGTATATAGATACATC +TATATATAGATATATAGATGTATATAGATACATAGATATATATAGATACATTTATGTATA +TATATATGTATATATAGATATATAGATATATATAGATACATCTACACAGAGAGATATATA +GAAACATCTACACAGGGAGATATATAGATACATCTACATAGAGAGATATATAGATACATC +TACATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATAGA +GAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATAGAGAGATATA +TAGATACATCTACATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACA +TCTACATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATA +GAGAGATATATAGATACATCTACATAGAGATATATATAGATACATCTACATAGAGATATA +TATAGATACATCTATATAGAGATATATCTACCTATACTTCCTGTGAGTTGTGTTTCTCTG +GAGAACTAATAGGTAGGGTGACTGTATAATTTACTCTCCATACTGGGACACTTTTAATCA +TTGCTATAATACATTAATTTTAATCTAATCTTCTTATCCCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/haps.fa.ref.fa new file mode 100644 index 00000000..cf44bd90 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:56280322-56282215 +GGTGGACATAGTGTATCTACAGATGGGACAATCTAAGATGGTTACAACATTACTACATAGTATCGCAAATAGAAATGGAAAGCCTGAATCTAACCATGAGAAAATTTAAAATAACTATCAAAAAGGTAACATCCATATACAGATATAATATCTATAACATATATAGATATATGGATATAACATCCATATATAGATATATCTATATATCTATCTATAGCTACATCTACAGATATCTATAGCTACATCTACAGATATCTACAGATATCTATAGCTACATCTACAGATATCTATAGCTACATCTACAGATATCTACAGATATCTACAGCTACATCTACAGATATCTATAGATATCTATAGCTATATCTACAGATATCTATCGATAGATATATCTATCGATAGATATATCCACATAGATATCTAGATATATATGGATATATCTATAGATATCTATCTGGATATATCTATCGATAGATATATAGATATATATAGATAAAGCTATATAGATATATATAGATAAACCTATATAGATACATAGATATATAGAGAGAAACCTATATACATATATAGATATATAGAGAGAAACCTATATAGATATATAGATATATAGAGAGAAACCTATATAGATGTATAGATAAACCTATATAGATATATAGATAAACCTATGTAGATATATAGATATATATAGATAAATCTATATAGATATATAAAATAGATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATATATACATAAATCTATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATATATATACATAAATCTATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATAAATCTATACAGATATATAGATACATATAGATACATCTATACAGATATATAGATACATATAGATACATCTATACAGATATATAGATACATATAGATACATCTATACAGATATATTGATACATATAGATACATCTATATAGATATATAGATATATAGATACATCTATATAGATATATAGATATATAGATACATCTATATAGATATATATAGATACATCTATATATAGACATATAGATATATATAGATACATCTATATATAGATATATAGATATATATAGATACATCTACACAGAGAGATATATAGAAACATCTACACAGGGAGATATATAGATACATCTACACAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATAGAGAGATATATAGATACATCTACATAGAGATATATATAGATACATCTACATAGAGATATATATAGATACATCTATATAGAGATATATCTACCTATACTTCCTGTGAGTTGTGTTTCTCTGGAGAACTAATAGGTAGGGTGACTGTATAATTTACTCTCCATACTGGGACACTTTTAATCATTGCTATAATACATTAATTTTAATCTAATCTTCTTATCCCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/msa.fa new file mode 100644 index 00000000..5dc5acec --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/msa.fa @@ -0,0 +1,225 @@ +>ref_chr20_56280322_56282215 +ggtggacatagtgtatctacagatgggacaatctaagatggttacaacattactacatag +tatcgcaaatagaaatggaaagcctgaatctaaccatgagaaaatttaaaataactatca +aaaaggtaacatccatatacagatataatatctataacatatatagatatatggatataa +catccatatatagatatatctatatatctatctatagctac------------------- +-------------atctacagatatctatagctacatctacagatatctacagatatcta +tagctacatctacagatatctatagctacatctacagatatctacagatatctacagcta +catctacagatatctatagatatctatagctatatctacagatatctatcgatagatata +tctatcgatagatatatccacatagatatctagatatatatggatatatctatagatatc +tatctggatatatctatcgatagatatatagatatatatagataaagctatatagatata +tatagataaacctatatagatacatagatatatagagagaaacctatatacatatataga +tatatagagagaaacctatatagatatatagatatatagagagaaacctatatagatgta +tagataaacctatatagatatatagataaacctatgtagatatatagatatatatagata +aatctatatagatatataaaatagataaatctatatagatatatatacataaatctatat +agatatatatacataaatctatatagatatatatacataaatctatatatatacataaat +ctatatatacataaatctatatagatatatatacataaatctatatagatatatatacat +aaatctatatagatatatatacataaatctatatag------------------------ +atatatatacataaatctatatagatatatacataaatctatatagatatatatacataa +atctatatagatatatatacataaatctatatagatatatatacataaatc--------t +atatagatacatatagataaatctatacagatatatagatacatatagataaatctatac +agatatatagatacatatagataaatctatacagatatatagatacatatagataaatct +atacagatatatagatacatatagataaatctatacagatatatagatacatatagataa +atctatacagatatatagatacatatagataaatctatacagatatatagatacatatag +atacatctatacagatatatagatacatatagatacatctatacagatatatagatacat +atagatacatctatacagatatattgatacatatagatacatctatatagatatatagat +--atatagatacatctata----------------------------------------- +------------------------------------------------------tagata +tatagatata----tagatacatctatatagatatatatagatacatctatatatagaca +tatagatatatatagatacatctatatatagatatatagat------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----atatatagatacatctacacagagagatatatagaaacatctacacagggagata +tatagatacatctacacagagagatatatagatacatctac------------------- +-------atagagagatatatagatacatctacatagagagatatatagatacatctaca +tagagagatatatagatacatctacatagagagatatatagatacatctacatagagata +tatatagatacatctacatagagatatatatagatacatctatatagagatatatctacc +tatacttcctgtgagttgtgtttctctggagaactaataggtagggtgactgtataattt +actctccatactgggacacttttaatcattgctataatacattaattttaatctaatctt +cttatccct +>syndip_1_chr20:56280322-56282215 +ggtggacatagtgtatctacagatgggacaatctaagatggttacaacattactacatag +tatcgcaaatagaaatggaaagcctgaatctaaccatgagaaaatttaaaataactatca +aaaaggtaacatccatatacagatataatatctataacatatatagatatatggatataa +catccatatatagatatatctatatatctatctatagctac------------------- +---------------------------------------------atctacagatatcta +tagccacatctacagatatctatagctacatctacagatatctacagatatctacagcta +catctacagatatctatagatatctatagctatatctacagatatctatcgatagatata +tctatcgatagatatatccacatagatatctagatatatatggatatatctatagatatc +tatctggatatatctatcgatagatatatagatatatatagataaagctatatagatata +tatagataaacctatatagatacatagatatatagagagaaacctatatacatatataga +tatatagagagaaacctatatagatatatagatatatagagataaacctatatagatgta +tagataaacctatatagatatatagataaacctatgtagatatatagatatatatagata +aatctatatagatatataaaatag------------------------ataaatctatat +agatatatatacataaatctatatagatatatatacataaatctatatatatacataaat +ctatatatacataaatctatatagatatatatacataaatctatatagatatatatacat +aaatctatatagatatatatacataaatctatatagatatatatacataaatctatatag +atatatatacataaatctatatagatatatacataaatctatacagatacatatacataa +atctatacagatacatatacataaatctatacagatacatatacataaatctatacagat +atatagatacatatagataaatctatacagatatatagatacatatagataaatctatac +agatatatagatacatatagatacatctatacagatatatagatacatatagatacatct +atacagatatatagatacatatagatacatctatacagatatatagatacatatagatac +atctatacagatatatagatacatatagatacatctatacagatatatagatacatatag +atacatctatacagatatatagatacatatagatacatctatacagatatattgatacat +atagatacatctatatagatatattgatacatatagatacatctatatagatatattgat +acatatagatacatctatatagatatattgatacatatagatacatctatatagattaga +tatatatagatacatctatatagattagatatatatagatacatctatatagattagata +tatatagatacatctatatatagatatatagatatatatagatacatctatatatagata +tatagatatatatagatacatctatatatagatatatagatgtatatagatacatctata +tatagatatatagatgtatatagatacatctatatatagatatatagatgtatatagata +catctatatatagatatatagatgtatatagatacatctatatatagatatatagatgta +tatagatacatctatatatagatatatagatgtatatagatacatctatatatagatata +tagatgtatatagatacatctatatatagatatatagatgtatatagatacatctatata +tagatatatagatgtatatagatacatctatatatagatatatagatgtatatagataca +tagatatatatagatacatttatgtatatatatatgtatatatagatatatagatatata +tagatacatctacacagagagatatatagaaacatctacacagggagatatatagataca +tctacatagagagatatatagatacatctacatagagagatatatagatacatctacata +gagagatatatagatacatctacatagagagatatatagatacatctacatagagagata +tatagatacatctacatagagagatatatagatacatctacatagagagatatatagata +catctacatagagagatatatagatacatctacatagagagatatatagatacatctaca +tagagagatatatagatacatctacatagagagatatatagatacatctacatagagata +tatatagatacatctacatagagatatatatagatacatctatatagagatatatctacc +tatacttcctgtgagttgtgtttctctggagaactaataggtagggtgactgtataattt +actctccatactgggacacttttaatcattgctataatacattaattttaatctaatctt +cttatccct +>syndip_2_chr20:56280322-56282215 +ggtggacatagtgtatctacagatgggacaatctaagatggttacaacattactacatag +tatcgcaaatagaaatggaaagcctgaatctaaccatgagaaaatttaaaataactatca +aaaaggtaacatccatatacagatataatatctataacatatatagatatatggatataa +catccatatatagatatatctatatatctatctatagctacatctacagatatctatagc +tacatctacagatatctacagatatctatagctacatctacagatatctacagatatcta +tagctacatctacagatatctatagctacatctacagatatctacagatatctacagcta +catctacagatatctatagatatctatagctatatctacagatatctatcgatagatata +tctatcgatagatatatccacatagatatctagatatatatggatatatctatagatatc +tatctggatatatctatcgatagatatatagatatatatagataaagctatatagatata +tatagataaacctatatagatacatagatatatagagagaaacctatatacatatataga +tatatagagagaaacctatatagatatatagatatatagagataaacctatatagatgta +tagataaacctatatagatatatagataaacctatgtagatatatagatatatatagata +aatctatatagatatataaaatag------------------------ataaatctatat +agatatatatacataaatctatatagatatatatacataaatctatatatatacataaat +ctatatatacataaatctatatagatatatatacataaatctatatagatatatatacat +aaatctatatagatatatatacataaatctatatag------------------------ +--atatatacataaatctatat--atatatacataaatctatatagatatatatacataa +atctatatagatacatatagataaatctatacaga------------------------t +atataaatatatatagataaatctatacagatatatagatacatatagataaatctatac +agatatatagatacatatagataaatctatacagatatatagatacatatagataaatct +atacagatatatagatacatatagataaatctatacagatatatagatacatatagataa +atctatacagatatatagatacatatagataaatctatacagatatatagatacatatag +ataaatctatacagatatatagatacatatagataaatctatacagatatatagatacat +atagatacatctatatagatatattgatacatatagatacatctatatagatatatagat +--atatagatacatctata----------------------------------------- +------------------------------------------------------tagata +tatatagatacatctatatatagacatatagatatatatagatacatctatatatagata +tatagatatatatagatacatctatatatagatatatagat------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----atatatagatacatctacacagagagatatatagaaacatctacacagggagata +tatagatacatctacatagagagatatatagatacatctacatagagagatatatagata +catctatatagagagatatatagatacatctatatagagagatatatagatacatctaca +tagagagatatatagatacatctacatagagagatatatagatacatctacatagagata +tatatagatacatctacatagagatatatatagatacatctatatagagatatatctacc +tatacttcctgtgagttgtgtttctctggagaactaataggtagggtgactgtataattt +actctccatactgggacacttttaatcattgctataatacattaattttaatctaatctt +cttatccct +>p:HG002_1_chr20:56280322-56282215 +ggtggacatagtgtatctacagatgggacaatctaagatggttacaacattactacatag +tatcgcaaatagaaatggaaagcctgaatctaaccatgagaaaatttaaaataactatca +aaaaggtaacatccatatacagatataatatctataacatatatagatatatggatataa +catccatatatagatatatctatatatctatctatagctacatctacagatatctatagc +tacatctacagatatctacagatatctatagctacatctacagatatctacagatatcta +tagctacatctacagatatctatagctacatctacagatatctacagatatctacagcta +catctacagatatctatagatatctatagctatatctacagatatctatcgatagatata +tctatcgatagatatatccacatagatatctagatatatatggatatatctatagatatc +tatctggatatatctatcgatagatatatagatatatatagataaagctatatagatata +tatagataaacctatatagatacatagatatatagagagaaacctatatacatatataga +tatatagagagaaacctatatagatatatagatatatagagataaacctatatagatgta +tagataaacctatatagatatatagataaacctatgtagatatatagatatatatagata +aatctatatagatatataaaatag------------------------ataaatctatat +agatatatatacataaatctatatagatatatatacataaatctatatatatacataaat +ctatatatacataaatctatatagatatatatacataaatctatatagatatatatacat +aaatctatatagatatatatacataaatctatatag------------------------ +--atatatacataaatctatat--atatatacataaatctatatagatatatatacataa +atctatatagatacatatagataaatctatacaga------------------------t +atataaatatatatagataaatctatacagatatatagatacatatagataaatctatac +agatatatagatacatatagataaatctatacagatatatagatacatatagataaatct +atacagatatatagatacatatagataaatctatacagatatatagatacatatagataa +atctatacagatatatagatacatatagataaatctatacagatatatagatacatatag +ataaatctatacagatatatagatacatatagataaatctatacagatatatagatacat +atagatacatctatatagatatattgatacatatagatacatctatatagatatatagat +--atatagatacatctata----------------------------------------- +------------------------------------------------------tagata +tatatagatacatctatatatagacatatagatatatatagatacatctatatatagata +tatagatatatatagatacatctatatatagatatatagat------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----atatatagatacatctacacagagagatatatagaaacatctacacagggagata +tatagatacatctacatagagagatatatagatacatctacatagagagatatatagata +catctatatagagagatatatagatacatctatatagagagatatatagatacatctaca +tagagagatatatagatacatctacatagagagatatatagatacatctacatagagata +tatatagatacatctacatagagatatatatagatacatctatatagagatatatctacc +tatacttcctgtgagttgtgtttctctggagaactaataggtagggtgactgtataattt +actctccatactgggacacttttaatcattgctataatacattaattttaatctaatctt +cttatccct +>p:HG002_2_chr20:56280322-56282215 +ggtggacatagtgtatctacagatgggacaatctaagatggttacaacattactacatag +tatcgcaaatagaaatggaaagcctgaatctaaccatgagaaaatttaaaataactatca +aaaaggtaacatccatatacagatataatatctataacatatatagatatatggatataa +catccatatatagatatatctatatatctatctatagctac------------------- +---------------------------------------------atctacagatatcta +tagccacatctacagatatctatagctacatctacagatatctacagatatctacagcta +catctacagatatctatagatatctatagctatatctacagatatctatcgatagatata +tctatcgatagatatatccacatagatatctagatatatatggatatatctatagatatc +tatctggatatatctatcgatagatatatagatatatatagataaagctatatagatata +tatagataaacctatatagatacatagatatatagagagaaacctatatacatatataga +tatatagagagaaacctatatagatatatagatatatagagataaacctatatagatgta +tagataaacctatatagatatatagataaacctatgtagatatatagatatatatagata +aatctatatagatatataaaatag------------------------ataaatctatat +agatatatatacataaatctatatagatatatatacataaatctatatatatacataaat +ctatatatacataaatctatatagatatatatacataaatctatatagatatatatacat +aaatctatatagatatatatacataaatctatatagatatatatacataaatctatatag +atatatatacataaatctatatagatatatacataaatctatacagatacatatacataa +atctatacagatacatatacataaatctatacagatacatatacataaatctatacagat +atatagatacatatagataaatctatacagatatatagatacatatagataaatctatac +agatatatagatacatatagatacatctatacagatatatagatacatatagatacatct +atacagatatatagatacatatagatacatctatacagatatatagatacatatagatac +atctatacagatatatagatacatatagatacatctatacagatatatagatacatatag +atacatctatacagatatatagatacatatagatacatctatacagatatattgatacat +atagatacatctatatagatatattgatacatatagatacatctatatagatatattgat +acatatagatacatctatatagatatattgatacatatagatacatctatatagattaga +tatatatagatacatctatatagattagatatatatagatacatctatatagattagata +tatatagatacatctatatatagatatatagatatatatagatacatctatatatagata +tatagatatatatagatacatctatatatagatatatagatgtatatagatacatctata +tatagatatatagatgtatatagatacatctatatatagatatatagatgtatatagata +catctatatatagatatatagatgtatatagatacatctatatatagatatatagatgta +tatagatacatctatatatagatatatagatgtatatagatacatctatatatagatata +tagatgtatatagatacatctatatatagatatatagatgtatatagatacatctatata +tagatatatagatgtatatagatacatctatatatagatatatagatgtatatagataca +tagatatatatagatacatttatgtatatatatatgtatatatagatatatagatatata +tagatacatctacacagagagatatatagaaacatctacacagggagatatatagataca +tctacatagagagatatatagatacatctacatagagagatatatagatacatctacata +gagagatatatagatacatctacatagagagatatatagatacatctacatagagagata +tatagatacatctacatagagagatatatagatacatctacatagagagatatatagata +catctacatagagagatatatagatacatctacatagagagatatatagatacatctaca +tagagagatatatagatacatctacatagagagatatatagatacatctacatagagata +tatatagatacatctacatagagatatatatagatacatctatatagagatatatctacc +tatacttcctgtgagttgtgtttctctggagaactaataggtagggtgactgtataattt +actctccatactgggacacttttaatcattgctataatacattaattttaatctaatctt +cttatccct diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/msa.fa.fai new file mode 100644 index 00000000..da3fb24c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_56280322_56282215 2589 29 60 61 +syndip_1_chr20:56280322-56282215 2589 2696 60 61 +syndip_2_chr20:56280322-56282215 2589 5363 60 61 +p:HG002_1_chr20:56280322-56282215 2589 8031 60 61 +p:HG002_2_chr20:56280322-56282215 2589 10699 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/output.vcf.gz new file mode 100644 index 00000000..00c97a4c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/output.vcf.gz.tbi new file mode 100644 index 00000000..a03ab151 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:56280422-56282115/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/base.vcf.gz new file mode 100644 index 00000000..9e66163d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/base.vcf.gz.tbi new file mode 100644 index 00000000..3990dc41 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/comp.vcf.gz new file mode 100644 index 00000000..c74558fb Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/comp.vcf.gz.tbi new file mode 100644 index 00000000..7f1dba09 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/haps.fa new file mode 100644 index 00000000..3fde0fc0 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/haps.fa @@ -0,0 +1,76 @@ +>ref_chr20_57090572_57091512 +AGCACAGTGAGGCCCACTTCAGACTTCCGAGCTCCAGACTATGAGATCAAGTGTTGTTTTAAGCCACCAAGTTTGGGAAAATTTGCCACAGCAGCAAGAGGAAACGAACGCACTCAGGTGCTCCTGCCACACACACTCACAGTTGCACAAGCTGGTGCAGCTCCAGACCCACACACCTCCACCACCACACACTCCGCCATGCACACACACCTCCACGCACACACACCTCCACCCGCACACACACACACCTTCACCACCACACACTCCACCCACACACACCTCCACCCACACACCTCCACCCACACACACCTCCGCCCACACACACCTCCGCCCACACACACCTCCGCCCACACACACCTCCACCCACACACACCTCCGCCCACACACCTCCGCCCACACACACCTCCGCCCTCACACACCTCCACCCACACACACCTCCACCCACACACGCCTCCACCCGCACACACCTCCACCACCACACACACCTCCACCCACACACACCACCCATGCACACACCTCCACCCACACACACACACCTCCACCCACACACACACACACCTCCACCCACACACACCACCCACACACACCACCCATGCACACACCTCCACCCACACACACACACCTCCACCCGCACACACCTCCACCACCACACACATCTCCACCCACACACACCACCCATGTGCACACCTCCACTGGCACACACCACCCATGCACACACCTCCACTGGCACGCACTACTCCACCTGCGTGCGCCTCCCACCTGCGTTCACCCTCCACCTGTGTTCGCTCCCACCCACTCATGCCTCTCCACCCGCAAAAGTGTGAGTGCTGAGGCTGGGACTCAACCTGAGCCGCTGGCTCTGGATTACTGGGTCCTGCCGGGCTGGCCAGGCCTGGTCACAGGCCGGGTCCCAGTCAGCAGCTCTTTACCTCAACAAGGAG +>syndip_1_chr20:57090572-57091512 +AGCACAGTGAGGCCCACTTCAGACTTCCGAGCTCCAGACTATGAGATCAAGTGTTGTTTT +AAGCCACCAAGTTTGGGAAAATTTGCCACAGCAGCAAGAGGAAACGAACGCACTCAGGTG +CTCCTGCCACACACACTCACAGTTGCACAAGCTGGTGCAGCTCCAGACCCACACACCTCC +ACCACCACACACTCCACCATGCACACACACCTCCACGCACACACACCTCCACCCGCACAC +ACACACACCTTCACCACCACACACTCCACCCACACACACCTCCACCCACACACCTCCACC +CACACACACCTCCGCCCACACACACCTCCGCCCACACACACCTCCACCCACACACACCTC +CACCCACACACCTCCGCCCACACACACCTCCGCCCTCACACACCTCCACCCACACACACC +TCCACCCACACACGCCTCCACCCGCACACACCTCCACCACCACACACACCTCCACCCACA +CACACCACCCATGCACACACCTCCACCCACACACACACACCTCCACCCACACACACCTCC +ACCCACACGCCACCCATGCACACACCTCCACCCACACACACACACACCACCCACCCACAC +ACACCTCCACCCGCACACACCTCCACCACCACACACACCTCCACCCACACACACCACCCA +TGCACACACCTCCACCCACACACACACACACCTCCACCCACACACACCTCCACCCACACA +CACCTCCACCCACACACACACACCTCCACCCACCCACACACACCTCCACCCGCACACACC +TCCACCACCACACACATCTCCACCCACACACACCACCCATGTGCACACCTCCACTGGCAC +ACACCACCCATGCACACACCTCCACTGGCACGCACTACTCCACCTGCGTGCGCCTCCCAC +CTGCGTTCACCCTCCACCTGTGTTCGCTCCCACCCACTCATGCCTCTCCACCCGCAAAAG +TGTGAGTGCTGAGGCTGGGACTCAACCTGAGCCGCTGGCTCTGGATTACTGGGTCCTGCC +GGGCTGGCCAGGCCTGGTCACAGGCCGGGTCCCAGTCAGCAGCTCTTTACCTCAACAAGG +AG +>syndip_2_chr20:57090572-57091512 +AGCACAGTGAGGCCCACTTCAGACTTCCGAGCTCCAGACTATGAGATCAAGTGTTGTTTT +AAGCCACCAAGTTTGGGAAAATTTGCCACAGCAGCAAGAGGAAACGAACGCACTCAGGTG +CTCCTGCCACACACACTCACAGTTGCACAAGCTGGTGCAGCTCCAGACCCACACACCTCC +ACCACCACACACTCCGCCATGCACACACACCTCCACGCACACACACCTCCACCCGCACAC +ACACACACCTTCACCACCACACACTCCACCCACACACACCTCCACCCACACACCTCCACC +CACACACACCTCCGCCCACACACACCTCCGCCCACACACACCTCCGCCCACACACACCTC +CACCCACACACACCTCCGCCCACACACCTCCGCCCACACACACCTCCGCCCTCACACACC +TCCACCCACACACACCTCCACCCACACACGCCTCCACCCGCACACACCTCCACCACCACA +CACACCTCCACCCACACACACCACCCATGCACACACCTCCACCCACACACACACACCTCC +ACCCACACACACACACACCTCCACCCACACACACCACCCACACACACCACCCATGCACAC +ACCTCCACCCACACACACACACCTCCACCCGCACACACCTCCACCACCACACACATCTCC +ACCCACACACACCACCCATGTGCACACCTCCACTGGCACACACCACCCATGCACACACCT +CCACTGGCACGCACTACTCCACCTGCGTGCGCCTCCCACCTGCGTTCACCCTCCACCTGT +GTTCGCTCCCACCCACTCATGCCTCTCCACCCGCAAAAGTGTGAGTGCTGAGGCTGGGAC +TCAACCTGAGCCGCTGGCTCTGGATTACTGGGTCCTGCCGGGCTGGCCAGGCCTGGTCAC +AGGCCGGGTCCCAGTCAGCAGCTCTTTACCTCAACAAGGAG +>p:HG002_1_chr20:57090572-57091512 +AGCACAGTGAGGCCCACTTCAGACTTCCGAGCTCCAGACTATGAGATCAAGTGTTGTTTT +AAGCCACCAAGTTTGGGAAAATTTGCCACAGCAGCAAGAGGAAACGAACGCACTCAGGTG +CTCCTGCCACACACACTCACAGTTGCACAAGCTGGTGCAGCTCCAGACCCACACACCTCC +ACCACCACACACTCCGCCATGCACACACACCTCCACGCACACACACCTCCACCCGCACAC +ACACACACCTTCACCACCACACACTCCACCCACACACACCTCCACCCACACACCTCCACC +CACACACACCTCCGCCCACACACACCTCCGCCCACACACACCTCCGCCCACACACACCTC +CACCCACACACACCTCCGCCCACACACCTCCGCCCACACACACCTCCGCCCTCACACACC +TCCACCCACACACACCTCCACCCACACACGCCTCCACCCGCACACACCTCCACCACCACA +CACACCTCCACCCACACACACCACCCATGCACACACCTCCACCCACACACACACACCTCC +ACCCACACACACACACACCTCCACCCACACACACCACCCACACACACCACCCATGCACAC +ACCTCCACCCACACACACACACCTCCACCCGCACACACCTCCACCACCACACACATCTCC +ACCCACACACACCACCCATGTGCACACCTCCACTGGCACACACCACCCATGCACACACCT +CCACTGGCACGCACTACTCCACCTGCGTGCGCCTCCCACCTGCGTTCACCCTCCACCTGT +GTTCGCTCCCACCCACTCATGCCTCTCCACCCGCAAAAGTGTGAGTGCTGAGGCTGGGAC +TCAACCTGAGCCGCTGGCTCTGGATTACTGGGTCCTGCCGGGCTGGCCAGGCCTGGTCAC +AGGCCGGGTCCCAGTCAGCAGCTCTTTACCTCAACAAGGAG +>p:HG002_2_chr20:57090572-57091512 +AGCACAGTGAGGCCCACTTCAGACTTCCGAGCTCCAGACTATGAGATCAAGTGTTGTTTT +AAGCCACCAAGTTTGGGAAAATTTGCCACAGCAGCAAGAGGAAACGAACGCACTCAGGTG +CTCCTGCCACACACACTCACAGTTGCACAAGCTGGTGCAGCTCCAGACCCACACACCTCC +ACCACCACACACTCCACCATGCACACACACCTCCACGCACACACACCTCCACCCGCACAC +ACACACACCTTCACCACCACACACTCCACCCACACACACCTCCACCCACACACCTCCACC +CACACACACCTCCGCCCACACACACCTCCGCCCACACACACCTCCACCCACACACACCTC +CACCCACACACCTCCGCCCACACACACCTCCGCCCTCACACACCTCCACCCACACACACC +TCCACCCACACACGCCTCCACCCGCACACACCTCCACCACCACACACACCTCCACCCACA +CACACCACCCATGCACACACCTCCACCCACACACACACACCTCCACCCACACACACCTCC +ACCCACACGCCACCCATGCACACACCTCCACCCACACACACACACACCACCCACCCACAC +ACACCTCCACCCGCACACACCTCCACCACCACACACACCTCCACCCACACACACCACCCA +TGCACACACCTCCACCCACACACACACACACCTCCACCCACACACACCTCCACCCACACA +CACCTCCACCCACACACACACACCTCCACCCACCCACACACACCTCCACCCGCACACACC +TCCACCACCACACACATCTCCACCCACACACACCACCCATGTGCACACCTCCACTGGCAC +ACACCACCCATGCACACACCTCCACTGGCACGCACTACTCCACCTGCGTGCGCCTCCCAC +CTGCGTTCACCCTCCACCTGTGTTCGCTCCCACCCACTCATGCCTCTCCACCCGCAAAAG +TGTGAGTGCTGAGGCTGGGACTCAACCTGAGCCGCTGGCTCTGGATTACTGGGTCCTGCC +GGGCTGGCCAGGCCTGGTCACAGGCCGGGTCCCAGTCAGCAGCTCTTTACCTCAACAAGG +AG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/haps.fa.ref.fa new file mode 100644 index 00000000..f9b612ec --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:57090572-57091512 +AGCACAGTGAGGCCCACTTCAGACTTCCGAGCTCCAGACTATGAGATCAAGTGTTGTTTTAAGCCACCAAGTTTGGGAAAATTTGCCACAGCAGCAAGAGGAAACGAACGCACTCAGGTGCTCCTGCCACACACACTCACAGTTGCACAAGCTGGTGCAGCTCCAGACCCACACACCTCCACCACCACACACTCCGCCATGCACACACACCTCCACGCACACACACCTCCACCCGCACACACACACACCTTCACCACCACACACTCCACCCACACACACCTCCACCCACACACCTCCACCCACACACACCTCCGCCCACACACACCTCCGCCCACACACACCTCCGCCCACACACACCTCCACCCACACACACCTCCGCCCACACACCTCCGCCCACACACACCTCCGCCCTCACACACCTCCACCCACACACACCTCCACCCACACACGCCTCCACCCGCACACACCTCCACCACCACACACACCTCCACCCACACACACCACCCATGCACACACCTCCACCCACACACACACACCTCCACCCACACACACACACACCTCCACCCACACACACCACCCACACACACCACCCATGCACACACCTCCACCCACACACACACACCTCCACCCGCACACACCTCCACCACCACACACATCTCCACCCACACACACCACCCATGTGCACACCTCCACTGGCACACACCACCCATGCACACACCTCCACTGGCACGCACTACTCCACCTGCGTGCGCCTCCCACCTGCGTTCACCCTCCACCTGTGTTCGCTCCCACCCACTCATGCCTCTCCACCCGCAAAAGTGTGAGTGCTGAGGCTGGGACTCAACCTGAGCCGCTGGCTCTGGATTACTGGGTCCTGCCGGGCTGGCCAGGCCTGGTCACAGGCCGGGTCCCAGTCAGCAGCTCTTTACCTCAACAAGGAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/msa.fa new file mode 100644 index 00000000..63e623bd --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/msa.fa @@ -0,0 +1,100 @@ +>ref_chr20_57090572_57091512 +agcacagtgaggcccacttcagacttccgagctccagactatgagatcaagtgttgtttt +aagccaccaagtttgggaaaatttgccacagcagcaagaggaaacgaacgcactcaggtg +ctcctgccacacacactcacagttgcacaagctggtgcagctccagacccacacacctcc +accaccacacactccgccatgcacacacacctccacgcacacacacctccacccgcacac +acacacaccttcaccaccacacactccacccacacacacctccacccacacacctccacc +cacacacacctccgcccacacacacctccgcccacacacacctccgcccacacacacctc +cacccacacacacctccgcccacacacctccgcccacacacacctccgccctcacacacc +tccacccacacacacctccacccacacacgcctccacccgcacacacctccaccaccaca +cacacctccacccacacacaccacccatgcacacacctccacccacacacacacacctcc +acccacacaca-----------------------cacacacctccacccacacaca---- +--------------------------------------------------------ccac +ccacacacaccacccatgcacacacctccacccaca------------------------ +--------------------------------------------------cacacacacc +tccacccgcacacacctccaccaccacacacatctccacccacacacaccacccatgtgc +acacctccactggcacacaccacccatgcacacacctccactggcacgcactactccacc +tgcgtgcgcctcccacctgcgttcaccctccacctgtgttcgctcccacccactcatgcc +tctccacccgcaaaagtgtgagtgctgaggctgggactcaacctgagccgctggctctgg +attactgggtcctgccgggctggccaggcctggtcacaggccgggtcccagtcagcagct +ctttacctcaacaaggag +>syndip_1_chr20:57090572-57091512 +agcacagtgaggcccacttcagacttccgagctccagactatgagatcaagtgttgtttt +aagccaccaagtttgggaaaatttgccacagcagcaagaggaaacgaacgcactcaggtg +ctcctgccacacacactcacagttgcacaagctggtgcagctccagacccacacacctcc +accaccacacactccaccatgcacacacacctccacgcacacacacctccacccgcacac +acacacaccttcaccaccacacactccacccacacacacctccacccacacacctcca-- +--------------cccacacacacctccgcccacacacacctccgcccacacacacctc +cacccacacacacctccacccacacacctccgcccacacacacctccgccctcacacacc +tccacccacacacacctccacccacacacgcctccacccgcacacacctccaccaccaca +cacacctccacccacacacaccacccatgcacacacctccacccacacacacacacctcc +acccacacacacctccacccacacgccacccatgcacacacctccacccacacacacaca +caccacccacccacacacacctccacccgcacacacctccaccaccacacacacctccac +ccacacacaccacccatgcacacacctccacccacacacacacacacctccacccacaca +cacctccacccacacacacctccacccacacacacacacctccacccacccacacacacc +tccacccgcacacacctccaccaccacacacatctccacccacacacaccacccatgtgc +acacctccactggcacacaccacccatgcacacacctccactggcacgcactactccacc +tgcgtgcgcctcccacctgcgttcaccctccacctgtgttcgctcccacccactcatgcc +tctccacccgcaaaagtgtgagtgctgaggctgggactcaacctgagccgctggctctgg +attactgggtcctgccgggctggccaggcctggtcacaggccgggtcccagtcagcagct +ctttacctcaacaaggag +>syndip_2_chr20:57090572-57091512 +agcacagtgaggcccacttcagacttccgagctccagactatgagatcaagtgttgtttt +aagccaccaagtttgggaaaatttgccacagcagcaagaggaaacgaacgcactcaggtg +ctcctgccacacacactcacagttgcacaagctggtgcagctccagacccacacacctcc +accaccacacactccgccatgcacacacacctccacgcacacacacctccacccgcacac +acacacaccttcaccaccacacactccacccacacacacctccacccacacacctccacc +cacacacacctccgcccacacacacctccgcccacacacacctccgcccacacacacctc +cacccacacacacctccgcccacacacctccgcccacacacacctccgccctcacacacc +tccacccacacacacctccacccacacacgcctccacccgcacacacctccaccaccaca +cacacctccacccacacacaccacccatgcacacacctccacccacacacacacacctcc +acccacacaca-----------------------cacacacctccacccacacaca---- +--------------------------------------------------------ccac +ccacacacaccacccatgcacacacctccacccaca------------------------ +--------------------------------------------------cacacacacc +tccacccgcacacacctccaccaccacacacatctccacccacacacaccacccatgtgc +acacctccactggcacacaccacccatgcacacacctccactggcacgcactactccacc +tgcgtgcgcctcccacctgcgttcaccctccacctgtgttcgctcccacccactcatgcc +tctccacccgcaaaagtgtgagtgctgaggctgggactcaacctgagccgctggctctgg +attactgggtcctgccgggctggccaggcctggtcacaggccgggtcccagtcagcagct +ctttacctcaacaaggag +>p:HG002_1_chr20:57090572-57091512 +agcacagtgaggcccacttcagacttccgagctccagactatgagatcaagtgttgtttt +aagccaccaagtttgggaaaatttgccacagcagcaagaggaaacgaacgcactcaggtg +ctcctgccacacacactcacagttgcacaagctggtgcagctccagacccacacacctcc +accaccacacactccgccatgcacacacacctccacgcacacacacctccacccgcacac +acacacaccttcaccaccacacactccacccacacacacctccacccacacacctccacc +cacacacacctccgcccacacacacctccgcccacacacacctccgcccacacacacctc +cacccacacacacctccgcccacacacctccgcccacacacacctccgccctcacacacc +tccacccacacacacctccacccacacacgcctccacccgcacacacctccaccaccaca +cacacctccacccacacacaccacccatgcacacacctccacccacacacacacacctcc +acccacacaca-----------------------cacacacctccacccacacaca---- +--------------------------------------------------------ccac +ccacacacaccacccatgcacacacctccacccaca------------------------ +--------------------------------------------------cacacacacc +tccacccgcacacacctccaccaccacacacatctccacccacacacaccacccatgtgc +acacctccactggcacacaccacccatgcacacacctccactggcacgcactactccacc +tgcgtgcgcctcccacctgcgttcaccctccacctgtgttcgctcccacccactcatgcc +tctccacccgcaaaagtgtgagtgctgaggctgggactcaacctgagccgctggctctgg +attactgggtcctgccgggctggccaggcctggtcacaggccgggtcccagtcagcagct +ctttacctcaacaaggag +>p:HG002_2_chr20:57090572-57091512 +agcacagtgaggcccacttcagacttccgagctccagactatgagatcaagtgttgtttt +aagccaccaagtttgggaaaatttgccacagcagcaagaggaaacgaacgcactcaggtg +ctcctgccacacacactcacagttgcacaagctggtgcagctccagacccacacacctcc +accaccacacactccaccatgcacacacacctccacgcacacacacctccacccgcacac +acacacaccttcaccaccacacactccacccacacacacctccacccacacacctcca-- +--------------cccacacacacctccgcccacacacacctccgcccacacacacctc +cacccacacacacctccacccacacacctccgcccacacacacctccgccctcacacacc +tccacccacacacacctccacccacacacgcctccacccgcacacacctccaccaccaca +cacacctccacccacacacaccacccatgcacacacctccacccacacacacacacctcc +acccacacacacctccacccacacgccacccatgcacacacctccacccacacacacaca +caccacccacccacacacacctccacccgcacacacctccaccaccacacacacctccac +ccacacacaccacccatgcacacacctccacccacacacacacacacctccacccacaca +cacctccacccacacacacctccacccacacacacacacctccacccacccacacacacc +tccacccgcacacacctccaccaccacacacatctccacccacacacaccacccatgtgc +acacctccactggcacacaccacccatgcacacacctccactggcacgcactactccacc +tgcgtgcgcctcccacctgcgttcaccctccacctgtgttcgctcccacccactcatgcc +tctccacccgcaaaagtgtgagtgctgaggctgggactcaacctgagccgctggctctgg +attactgggtcctgccgggctggccaggcctggtcacaggccgggtcccagtcagcagct +ctttacctcaacaaggag diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/msa.fa.fai new file mode 100644 index 00000000..9ec3571a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_57090572_57091512 1098 29 60 61 +syndip_1_chr20:57090572-57091512 1098 1180 60 61 +syndip_2_chr20:57090572-57091512 1098 2331 60 61 +p:HG002_1_chr20:57090572-57091512 1098 3483 60 61 +p:HG002_2_chr20:57090572-57091512 1098 4635 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/output.vcf.gz new file mode 100644 index 00000000..3ff08d4c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/output.vcf.gz.tbi new file mode 100644 index 00000000..a6604a42 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57090672-57091412/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/base.vcf.gz new file mode 100644 index 00000000..5672622f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/base.vcf.gz.tbi new file mode 100644 index 00000000..0f967a11 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/comp.vcf.gz new file mode 100644 index 00000000..49c2d6ce Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/comp.vcf.gz.tbi new file mode 100644 index 00000000..352ec8f0 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/haps.fa new file mode 100644 index 00000000..c43b5faf --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/haps.fa @@ -0,0 +1,52 @@ +>ref_chr20_57110112_57110886 +AGAAAAATCCTCCAGAAGATGACAGTTCCAGTTGATGGGACTGACAAGCCCCCCACAGGAAGGCAGTCTCCAGCTGACCACTGTTCCGTGAGGCTGTCTGAGCAGGCTTCGCTATGCACGCATAATAGCGACAGCGCAAACAGCAGCAGCAGCAGCAGCCTCAGCTGGCTCGGCGGGGCTTGGCTCAGCGTGTGCGGGGTGCTGAGCTAAGTCTTCCCAAACGGCGTGTGCGGGGTGCTGCGCTGTCTTCCAGATCCGCTTGTGCAGGGCGCTGTGCTGTCTTCTGGTTCGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTGTCTTCCGGTTCGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGTGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTGTCTTCCGGTTCGGCGTGTGCGGGGCGTTATGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTGTCTTCCGGTTCGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGCATTCGCACTCTTTCCCTCCGACTCAACCATGGCAGTGAGGCACTGTTTTGTTTTGCTTTGCTTCTCAATTTTCCTGTGGTAAAATACACCTAATATTCACCATCTTAACCGTTTTTAAGTGTACAGTTCA +>syndip_1_chr20:57110112-57110886 +AGAAAAATCCTCCAGAAGATGACAGTTCCAGTTGATGGGACTGACAAGCCCCCCACAGGA +AGGCAGTCTCCAGCTGACCACTGTTCCGTGAGGCTGTCTGAGCAGGCTTCGCTATGCACG +CATAATAGCGACAGCGCAAACAGCAGCAGCAGCAGCAGCCTCAGCTGGCTCGGCGGGGCT +TGGCTCAGCGTGTGCGGGGTGCTGAGCTAAGTCTTCCCAAACGGCGTGTGCGGGGTGCTG +CGCTGTCTTCCAGATCCGCTTGTGCAGGGCGCTGTGCTGTCTTCTGGTTCGGCGTGTGCG +GGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGC +TGGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCT +GTCTTCCGGTTCGGCGTGTGCGGGGCGTTATGCTAAGTCTTCCGGCTGGGCGTGTGCGGG +GCGCTGTGCTGTCTTCCGGTTCGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGCA +TTCGCACTCTTTCCCTCCGACTCAACCATGGCAGTGAGGCACTGTTTTGTTTTGCTTTGC +TTCTCAATTTTCCTGTGGTAAAATACACCTAATATTCACCATCTTAACCGTTTTTAAGTG +TACAGTTCA +>syndip_2_chr20:57110112-57110886 +AGAAAAATCCTCCAGAAGATGACAGTTCCAGTTGATGGGACTGACAAGCCCCCCACAGGA +AGGCAGTCTCCAGCTGACCACTGTTCCGTGAGGCTGTCTGAGCAGGCTTCGCTATGCACG +CATAATAGCGACAGCGCAAACAGCAGCAGCAGCAGCAGCCTCAGCTGGCTCGGCGGGGCT +TGGCTCAGCGTGTGCGGGGTGCTGAGCTAAGTCTTCCCAAACGGCGTGTGCGGGGTGCTG +CGCTGTCTTCCAGATCCGCTTGTGCAGGGCGCTGTGCTGTCTTCTGGTTCGGCGTGTGCG +GGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGC +TGGGCGTGTGCGGGGCGCTGTGCTGTCTTCCGGTTCGGCGTGTGCGGGGCGTTATGCTAA +GTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTGTCTTCCGGTTCGGCGTGTGCGGGGC +GCTGTGCTAAGTCTTCCGGCTGCATTCGCACTCTTTCCCTCCGACTCAACCATGGCAGTG +AGGCACTGTTTTGTTTTGCTTTGCTTCTCAATTTTCCTGTGGTAAAATACACCTAATATT +CACCATCTTAACCGTTTTTAAGTGTACAGTTCA +>p:HG002_1_chr20:57110112-57110886 +AGAAAAATCCTCCAGAAGATGACAGTTCCAGTTGATGGGACTGACAAGCCCCCCACAGGA +AGGCAGTCTCCAGCTGACCACTGTTCCGTGAGGCTGTCTGAGCAGGCTTCGCTATGCACG +CATAATAGCGACAGCGCAAACAGCAGCAGCAGCAGCAGCCTCAGCTGGCTCGGCGGGGCT +TGGCTCAGCGTGTGCGGGGTGCTGAGCTAAGTCTTCCCAAACGGCGTGTGCGGGGTGCTG +CGCTGTCTTCCAGATCCGCTTGTGCAGGGCGCTGTGCTGTCTTCTGGTTCGGCGTGTGCG +GGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGC +TGGGCGTGTGCGGGGCGCTGTGCTGTCTTCCGGTTCGGCGTGTGCGGGGCGTTATGCTAA +GTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTGTCTTCCGGTTCGGCGTGTGCGGGGC +GCTGTGCTAAGTCTTCCGGCTGCATTCGCACTCTTTCCCTCCGACTCAACCATGGCAGTG +AGGCACTGTTTTGTTTTGCTTTGCTTCTCAATTTTCCTGTGGTAAAATACACCTAATATT +CACCATCTTAACCGTTTTTAAGTGTACAGTTCA +>p:HG002_2_chr20:57110112-57110886 +AGAAAAATCCTCCAGAAGATGACAGTTCCAGTTGATGGGACTGACAAGCCCCCCACAGGA +AGGCAGTCTCCAGCTGACCACTGTTCCGTGAGGCTGTCTGAGCAGGCTTCGCTATGCACG +CATAATAGCGACAGCGCAAACAGCAGCAGCAGCAGCAGCCTCAGCTGGCTCGGCGGGGCT +TGGCTCAGCGTGTGCGGGGTGCTGAGCTAAGTCTTCCCAAACGGCGTGTGCGGGGTGCTG +CGCTGTCTTCCAGATCCGCTTGTGCAGGGCGCTGTGCTGTCTTCTGGTTCGGCGTGTGCG +GGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGC +TGGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCT +GTCTTCCGGTTCGGCGTGTGCGGGGCGTTATGCTAAGTCTTCCGGCTGGGCGTGTGCGGG +GCGCTGTGCTGTCTTCCGGTTCGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGCA +TTCGCACTCTTTCCCTCCGACTCAACCATGGCAGTGAGGCACTGTTTTGTTTTGCTTTGC +TTCTCAATTTTCCTGTGGTAAAATACACCTAATATTCACCATCTTAACCGTTTTTAAGTG +TACAGTTCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/haps.fa.ref.fa new file mode 100644 index 00000000..c247b16d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:57110112-57110886 +AGAAAAATCCTCCAGAAGATGACAGTTCCAGTTGATGGGACTGACAAGCCCCCCACAGGAAGGCAGTCTCCAGCTGACCACTGTTCCGTGAGGCTGTCTGAGCAGGCTTCGCTATGCACGCATAATAGCGACAGCGCAAACAGCAGCAGCAGCAGCAGCCTCAGCTGGCTCGGCGGGGCTTGGCTCAGCGTGTGCGGGGTGCTGAGCTAAGTCTTCCCAAACGGCGTGTGCGGGGTGCTGCGCTGTCTTCCAGATCCGCTTGTGCAGGGCGCTGTGCTGTCTTCTGGTTCGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTGTCTTCCGGTTCGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGTGCTGTGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTGTCTTCCGGTTCGGCGTGTGCGGGGCGTTATGCTAAGTCTTCCGGCTGGGCGTGTGCGGGGCGCTGTGCTGTCTTCCGGTTCGGCGTGTGCGGGGCGCTGTGCTAAGTCTTCCGGCTGCATTCGCACTCTTTCCCTCCGACTCAACCATGGCAGTGAGGCACTGTTTTGTTTTGCTTTGCTTCTCAATTTTCCTGTGGTAAAATACACCTAATATTCACCATCTTAACCGTTTTTAAGTGTACAGTTCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/msa.fa new file mode 100644 index 00000000..e9c97192 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/msa.fa @@ -0,0 +1,70 @@ +>ref_chr20_57110112_57110886 +agaaaaatcctccagaagatgacagttccagttgatgggactgacaagccccccacagga +aggcagtctccagctgaccactgttccgtgaggctgtctgagcaggcttcgctatgcacg +cataatagcgacagcgcaaacagcagcagcagcagcagcctcagctggctcggcggggct +tggctcagcgtgtgcggggtgctgagctaagtcttcccaaacggcgtgtgcggggtgctg +cgctgtcttccagatccgcttgtgcagggcgctgtgctgtcttctggttcggcgtgtgcg +gggcgctgtgctaagtcttccggctgggcgtgtgcggggcgctgtgctaagtcttccggc +tgggcgtgtgcggggcgctgtgctaagtcttccggctgggcgtgtgcggggcgctgtgct +gtcttccggttcggcgtgtgcggggcgctgtgctaagtcttccggctgggcgtgtgcggg +gtgctgtgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtcttccggttcgg +cgtgtgcggggcgttatgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtct +tccggttcggcgtgtgcggggcgctgtgctaagtcttccggctgcattcgcactctttcc +ctccgactcaaccatggcagtgaggcactgttttgttttgctttgcttctcaattttcct +gtggtaaaatacacctaatattcaccatcttaaccgtttttaagtgtacagttca +>syndip_1_chr20:57110112-57110886 +agaaaaatcctccagaagatgacagttccagttgatgggactgacaagccccccacagga +aggcagtctccagctgaccactgttccgtgaggctgtctgagcaggcttcgctatgcacg +cataatagcgacagcgcaaacagcagcagcagcagcagcctcagctggctcggcggggct +tggctcagcgtgtgcggggtgctgagctaagtcttcccaaacggcgtgtgcggggtgctg +cgctgtcttccagatccgcttgtgcagggcgctgtgctgtcttctggttcggcgtgtgcg +gggcgctgtgctaagtcttccggctgggcgtgtgcggggcgctgtgctaagtcttccggc +tgggcgtgtgcggggc-------------------------------------------- +------------------------------------------------------------ +--gctgtgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtcttccggttcgg +cgtgtgcggggcgttatgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtct +tccggttcggcgtgtgcggggcgctgtgctaagtcttccggctgcattcgcactctttcc +ctccgactcaaccatggcagtgaggcactgttttgttttgctttgcttctcaattttcct +gtggtaaaatacacctaatattcaccatcttaaccgtttttaagtgtacagttca +>syndip_2_chr20:57110112-57110886 +agaaaaatcctccagaagatgacagttccagttgatgggactgacaagccccccacagga +aggcagtctccagctgaccactgttccgtgaggctgtctgagcaggcttcgctatgcacg +cataatagcgacagcgcaaacagcagcagcagcagcagcctcagctggctcggcggggct +tggctcagcgtgtgcggggtgctgagctaagtcttcccaaacggcgtgtgcggggtgctg +cgctgtcttccagatccgcttgtgcagggcgctgtgctgtcttctggttc---------- +--------------------------ggcgtgtgcggggcgctgtgctaagtcttccggc +tgggcgtgtgcggggc-------------------------------------------- +------------------------------------------------------------ +--gctgtgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtcttccggttcgg +cgtgtgcggggcgttatgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtct +tccggttcggcgtgtgcggggcgctgtgctaagtcttccggctgcattcgcactctttcc +ctccgactcaaccatggcagtgaggcactgttttgttttgctttgcttctcaattttcct +gtggtaaaatacacctaatattcaccatcttaaccgtttttaagtgtacagttca +>p:HG002_1_chr20:57110112-57110886 +agaaaaatcctccagaagatgacagttccagttgatgggactgacaagccccccacagga +aggcagtctccagctgaccactgttccgtgaggctgtctgagcaggcttcgctatgcacg +cataatagcgacagcgcaaacagcagcagcagcagcagcctcagctggctcggcggggct +tggctcagcgtgtgcggggtgctgagctaagtcttcccaaacggcgtgtgcggggtgctg +cgctgtcttccagatccgcttgtgcagggcgctgtgctgtcttctggttc---------- +--------------------------ggcgtgtgcggggcgctgtgctaagtcttccggc +tgggcgtgtgcggggc-------------------------------------------- +------------------------------------------------------------ +--gctgtgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtcttccggttcgg +cgtgtgcggggcgttatgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtct +tccggttcggcgtgtgcggggcgctgtgctaagtcttccggctgcattcgcactctttcc +ctccgactcaaccatggcagtgaggcactgttttgttttgctttgcttctcaattttcct +gtggtaaaatacacctaatattcaccatcttaaccgtttttaagtgtacagttca +>p:HG002_2_chr20:57110112-57110886 +agaaaaatcctccagaagatgacagttccagttgatgggactgacaagccccccacagga +aggcagtctccagctgaccactgttccgtgaggctgtctgagcaggcttcgctatgcacg +cataatagcgacagcgcaaacagcagcagcagcagcagcctcagctggctcggcggggct +tggctcagcgtgtgcggggtgctgagctaagtcttcccaaacggcgtgtgcggggtgctg +cgctgtcttccagatccgcttgtgcagggcgctgtgctgtcttctggttcggcgtgtgcg +gggcgctgtgctaagtcttccggctgggcgtgtgcggggcgctgtgctaagtcttccggc +tgggcgtgtgcggggc-------------------------------------------- +------------------------------------------------------------ +--gctgtgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtcttccggttcgg +cgtgtgcggggcgttatgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtct +tccggttcggcgtgtgcggggcgctgtgctaagtcttccggctgcattcgcactctttcc +ctccgactcaaccatggcagtgaggcactgttttgttttgctttgcttctcaattttcct +gtggtaaaatacacctaatattcaccatcttaaccgtttttaagtgtacagttca diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/msa.fa.fai new file mode 100644 index 00000000..d6520f5e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_57110112_57110886 775 29 60 61 +syndip_1_chr20:57110112-57110886 775 851 60 61 +syndip_2_chr20:57110112-57110886 775 1673 60 61 +p:HG002_1_chr20:57110112-57110886 775 2496 60 61 +p:HG002_2_chr20:57110112-57110886 775 3319 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/output.vcf.gz new file mode 100644 index 00000000..4187d638 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/output.vcf.gz.tbi new file mode 100644 index 00000000..e4580e00 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57110212-57110786/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/base.vcf.gz new file mode 100644 index 00000000..6d2426d5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/base.vcf.gz.tbi new file mode 100644 index 00000000..2ce4272c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/comp.vcf.gz new file mode 100644 index 00000000..b8e1e953 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/comp.vcf.gz.tbi new file mode 100644 index 00000000..3fe7a61f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/haps.fa new file mode 100644 index 00000000..ace3fa52 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/haps.fa @@ -0,0 +1,60 @@ +>ref_chr20_57189846_57190641 +CTGGGAGCTGACTGGCGAGGGAGATCAGCTCAGGGGTGCACAGTGCTGTGTCTGATGGTGGCAAGGACTAGGAAGAACCTAGGACAGGGTGGCAGGGACATGACAGTGGGGCACAGTGTACAGGGCAGAGTGAGCCATGGGAGGTTTTGGGGAGGAAATGTTCCTGGCAGAGGGAATGGCACATGCCAGGTTCATGAGAAATACACGGTGTGTGTCAGCACAGTGAAGAGGCCAGTGAGGCTGGAGAAGTGAGCCAGGAACCAGAGAGGTTGAGACTGGAGATAGTGAGCGAGGAACCGGAGGGGGTGAAGCTGGAGAGAGTGAGCCAGGAATCAGAGGAGGTGAGGCCAGAGAGAGTGAGCGAGGAACCAGAGGGGGTGAGGCTGGAGAGAGTGACCGAGGAACCAGAGGAGGTGAGGCTGGAGAGAGTGAGCCAGGAACCAGAGGAGGTGAGGCCAGAGTGAGTGAGGAGCTTGAAGGGGTGAGGCTGGAGACAGTGAGCGAGGAACCAGAGGGGGTGAGGCTGGAGAGCGTGAGTGAGGAGCCCGAGGGGGTGAGGCTGGAGAGCGTGAGTGAGGAGCCCGAGGGGGTGAGGCTGGAGAGCGTGAGTGAGGAGCCCGAGGGGGTGAGGCTGGAGAGAGTGAGTGAGGAGCCCAAGGGGGTGAAGCCGAGGTGGGTATGGGGCTGGGTCACCTGGGGTCTCCCAGCCCAGTGGGGGATTTGGGCAGGGGGCGACGTGGCCAGGGTTCTGTGGTGGGAGACCCATTCTGAATGCCGTGTGGGGAACCAACAAGGC +>syndip_1_chr20:57189846-57190641 +CTGGGAGCTGACTGGCGAGGGAGATCAGCTCAGGGGTGCACAGTGCTGTGTCTGATGGTG +GCAAGGACTAGGAAGAACCTAGGACAGGGTGGCAGGGACATGACAGTGGGGCACAGTGTA +CAGGGCAGAGTGAGCCATGGGAGGTTTTGGGGAGGAAATGTTCCTGGCAGAGGGAATGGC +ACATGCCAGGTTCATGAGAAATACACGGTGTGTGTCAGCACAGTGAAGAGGCCAGTGAGG +CTGGAGAAGTGAGCCAGGAACCAGAGAGGTTGAGACTGGAGATAGTGAGCGAGGAACCGG +AGGGGGTGAAGCTGGAGAGAGTGAGCCAGGAATCAGAGGAGGTGAGGCCAGAGAGAGTGA +GCGAGGAACCAGAGGGGGTGAGGCTGGAGAGAGTGACCGAGGAACCAGAGGAGGTGAGGC +CAGAGTGAGTGAGGAGCTTGAAGGGGTGAGGCTGGAGACAGTGAGCGAGGAACCAGAGGG +GGTGAGGCTGGAGAGAGTGAGCCAGGAACCAGAGGAGGTGAGGCCAGAGTGAGTGAGGAG +CTTGAAGGGGTGAGGCTGGAGACAGTGAGCGAGGAACCAGAGGGGGTGAGGCTGGAGAGC +GTGAGTGAGGAGCCCGAGGGGGTGAGGCTGGAGAGAGTGAGTGAGGAGCCCAAGGGGGTG +AAGCCGAGGTGGGTATGGGGCTGGGTCACCTGGGGTCTCCCAGCCCAGTGGGGGATTTGG +GCAGGGGGCGACGTGGCCAGGGTTCTGTGGTGGGAGACCCATTCTGAATGCCGTGTGGGG +AACCAACAAGGC +>syndip_2_chr20:57189846-57190641 +CTGGGAGCTGACTGGCGAGGGAGATCAGCTCAGGGGTGCACAGTGCTGTGTCTGATGGTG +GCAAGGACTAGGAAGAACCTAGGACAGGGTGGCAGGGACATGACAGTGGGGCACAGTGTA +CAGGGCAGAGTGAGCCATGGGAGGTTTTGGGGAGGAAATGTTCCTGGCAGAGGGAATGGC +ACATGCCAGGTTCATGAGAAATACACGGTGTGTGTCAGCACAGTGAAGAGGCCAGTGAGG +CTGGAGAAGTGAGCCAGGAACCAGAGGGGTTGAGGCTGGAGATAGTGAGCGAGGAACCGG +AGGGGGTGAAGCTGGAGAGAGTGAGCCAGGAATCAGAGGAGGTGAGGCCAGAGAGAGTGA +GCGAGGAACCAGAGGGGGTGAGGCTGGAGAGAGTGACCGAGGAACCAGAGGAGGTGAGGC +TGGAGAGAGTGAGCCAGGAACCAGAGGAGGTGAGGCCAGAGTGAGTGAGGAGCTTGAAGG +GGTGAGGCTGGAGACAGTGAGCGAGGAACCAGAGGGGGTGAGGCTGGAGAGCGTGAGTGA +GGAGCCCGAGGGGGTGAGGCTGGAGAGCGTGAGTGAGGAGCCCGAGGGGGTGAGGCTGGA +GAGAGTGAGTGAGGAGCCCAAGGGGGTGAAGCCGAGGTGGGTATGGGGCTGGGTCACCTG +GGGTCTCCCAGCCCAGTGGGGGATTTGGGCAGGGGGCGACGTGGCCAGGGTTCTGTGGTG +GGAGACCCATTCTGAATGCCGTGTGGGGAACCAACAAGGC +>p:HG002_1_chr20:57189846-57190641 +CTGGGAGCTGACTGGCGAGGGAGATCAGCTCAGGGGTGCACAGTGCTGTGTCTGATGGTG +GCAAGGACTAGGAAGAACCTAGGACAGGGTGGCAGGGACATGACAGTGGGGCACAGTGTA +CAGGGCAGAGTGAGCCATGGGAGGCTTTGGGGAGGAAATGTTCCTGGCAGAGGGAATGGC +ACATGCCAGGTTCATGAGAAATACACGGTGTGTGTCAGCACAGTGAAGAGGCCAGTGAGG +CTGGAGAAGTGAGCCAGGAACCAGAGGGGTTGAGGCTGGAGATAGTGAGCGAGGAACCGG +AGGGGGTGAAGCTGGAGAGAGTGAGCCAGGAATCAGAGGAGGTGAGGCCAGAGAGAGTGA +GCGAGGAACCAGAGGGGGTGAGGCTGGAGAGAGTGACCGAGGAACCAGAGGAGGTGAGGC +TGGAGAGAGTGAGCCAGGAACCAGAGGAGGTGAGGCCAGAGTGAGTGAGGAGCTTGAAGG +GGTGAGGCTGGAGACAGTGAGCGAGGAACCAGAGGGGGTGAGGCTGGAGAGCGTGAGTGA +GGAGCCCGAGGGGGTGAGGCTGGAGAGCGTGAGTGAGGAGCCCGAGGGGGTGAGGCTGGA +GAGAGTGAGTGAGGAGCCCAAGGGGGTGAAGCCGAGGTGGGTATGGGGCTGGGTCACCTG +GGGTCTCCCAGCCCAGTGGGGGATTTGGGCAGGGGGCGACGTGGCCAGGGTTCTGTGGTG +GGAGACCCATTCTGAATGCCGTGTGGGGAACCAACAAGGC +>p:HG002_2_chr20:57189846-57190641 +CTGGGAGCTGACTGGCGAGGGAGATCAGCTCAGGGGTGCACAGTGCTGTGTCTGATGGTG +GCAAGGACTAGGAAGAACCTAGGACAGGGTGGCAGGGACATGACAGTGGGGCACAGTGTA +CAGGGCAGAGTGAGCCATGGGAGGCTTTGGGGAGGAAATGTTCCTGGCAGAGGGAATGGC +ACATGCCAGGTTCATGAGAAATACACGGTGTGTGTCAGCACAGTGAAGAGGCCAGTGAGG +CTGGAGAAGTGAGCCAGGAACCAGAGAGGTTGAGACTGGAGATAGTGAGCGAGGAACCGG +AGGGGGTGAAGCTGGAGAGAGTGAGCCAGGAATCAGAGGAGGTGAGGCCAGAGAGAGTGA +GCGAGGAACCAGAGGGGGTGAGGCTGGAGAGAGTGACCGAGGAACCAGAGGAGGTGAGGC +CAGAGTGAGTGAGGAGCTTGAAGGGGTGAGGCTGGAGACAGTGAGCGAGGAACCAGAGGG +GGTGAGGCTGGAGAGAGTGAGCCAGGAACCAGAGGAGGTGAGGCCAGAGTGAGTGAGGAG +CTTGAAGGGGTGAGGCTGGAGACAGTGAGCGAGGAACCAGAGGGGGTGAGGCTGGAGAGC +GTGAGTGAGGAGCCCGAGGGGGTGAGGCTGGAGAGAGTGAGTGAGGAGCCCAAGGGGGTG +AAGCCGAGGTGGGTATGGGGCTGGGTCACCTGGGGTCTCCCAGCCCAGTGGGGGATTTGG +GCAGGGGGCGACGTGGCCAGGGTTCTGTGGTGGGAGACCCATTCTGAATGCCGTGTGGGG +AACCAACAAGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/haps.fa.ref.fa new file mode 100644 index 00000000..70908a63 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:57189846-57190641 +CTGGGAGCTGACTGGCGAGGGAGATCAGCTCAGGGGTGCACAGTGCTGTGTCTGATGGTGGCAAGGACTAGGAAGAACCTAGGACAGGGTGGCAGGGACATGACAGTGGGGCACAGTGTACAGGGCAGAGTGAGCCATGGGAGGTTTTGGGGAGGAAATGTTCCTGGCAGAGGGAATGGCACATGCCAGGTTCATGAGAAATACACGGTGTGTGTCAGCACAGTGAAGAGGCCAGTGAGGCTGGAGAAGTGAGCCAGGAACCAGAGAGGTTGAGACTGGAGATAGTGAGCGAGGAACCGGAGGGGGTGAAGCTGGAGAGAGTGAGCCAGGAATCAGAGGAGGTGAGGCCAGAGAGAGTGAGCGAGGAACCAGAGGGGGTGAGGCTGGAGAGAGTGACCGAGGAACCAGAGGAGGTGAGGCTGGAGAGAGTGAGCCAGGAACCAGAGGAGGTGAGGCCAGAGTGAGTGAGGAGCTTGAAGGGGTGAGGCTGGAGACAGTGAGCGAGGAACCAGAGGGGGTGAGGCTGGAGAGCGTGAGTGAGGAGCCCGAGGGGGTGAGGCTGGAGAGCGTGAGTGAGGAGCCCGAGGGGGTGAGGCTGGAGAGCGTGAGTGAGGAGCCCGAGGGGGTGAGGCTGGAGAGAGTGAGTGAGGAGCCCAAGGGGGTGAAGCCGAGGTGGGTATGGGGCTGGGTCACCTGGGGTCTCCCAGCCCAGTGGGGGATTTGGGCAGGGGGCGACGTGGCCAGGGTTCTGTGGTGGGAGACCCATTCTGAATGCCGTGTGGGGAACCAACAAGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/msa.fa new file mode 100644 index 00000000..ed77c0c4 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/msa.fa @@ -0,0 +1,75 @@ +>ref_chr20_57189846_57190641 +ctgggagctgactggcgagggagatcagctcaggggtgcacagtgctgtgtctgatggtg +gcaaggactaggaagaacctaggacagggtggcagggacatgacagtggggcacagtgta +cagggcagagtgagccatgggaggttttggggaggaaatgttcctggcagagggaatggc +acatgccaggttcatgagaaatacacggtgtgtgtcagcacagtgaagaggccagtgagg +ctggagaagtgagccaggaaccagagaggttgagactggagatagtgagcgaggaaccgg +agggggtgaagctggagagagtgagccaggaatcagaggaggtgaggccagagagagtga +gcgaggaaccagagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggc +tggagagagtgagccaggaaccagaggaggtgaggccag----agtgagtgaggagcttg +aaggggtgaggctggagacagtgagcgaggaaccagagggggtgaggctggagagcgtga +gtgaggagcccgagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggc +tggagagcgtgagtgaggagcccgagggggtgaggctggagagagtgagtgaggagccca +agggggtgaagccgaggtgggtatggggctgggtcacctggggtctcccagcccagtggg +ggatttgggcagggggcgacgtggccagggttctgtggtgggagacccattctgaatgcc +gtgtggggaaccaacaaggc +>syndip_1_chr20:57189846-57190641 +ctgggagctgactggcgagggagatcagctcaggggtgcacagtgctgtgtctgatggtg +gcaaggactaggaagaacctaggacagggtggcagggacatgacagtggggcacagtgta +cagggcagagtgagccatgggaggttttggggaggaaatgttcctggcagagggaatggc +acatgccaggttcatgagaaatacacggtgtgtgtcagcacagtgaagaggccagtgagg +ctggagaagtgagccaggaaccagagaggttgagactggagatagtgagcgaggaaccgg +agggggtgaagctggagagagtgagccaggaatcagaggaggtgaggccagagagagtga +gcgaggaaccagagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggc +c----agagtgagtgaggagcttgaaggggtgaggctggagacagtgagcgaggaaccag +agggggtgaggctggagagagtgagccaggaaccagaggaggtgaggccaga----gtga +gtgaggagcttgaaggggtgaggctggagacagtgagcgaggaaccagagggggtgaggc +tggagagcgtgagtgaggagcccgagggggtgaggctggagagagtgagtgaggagccca +agggggtgaagccgaggtgggtatggggctgggtcacctggggtctcccagcccagtggg +ggatttgggcagggggcgacgtggccagggttctgtggtgggagacccattctgaatgcc +gtgtggggaaccaacaaggc +>syndip_2_chr20:57189846-57190641 +ctgggagctgactggcgagggagatcagctcaggggtgcacagtgctgtgtctgatggtg +gcaaggactaggaagaacctaggacagggtggcagggacatgacagtggggcacagtgta +cagggcagagtgagccatgggaggttttggggaggaaatgttcctggcagagggaatggc +acatgccaggttcatgagaaatacacggtgtgtgtcagcacagtgaagaggccagtgagg +ctggagaagtgagccaggaaccagaggggttgaggctggagatagtgagcgaggaaccgg +agggggtgaagctggagagagtgagccaggaatcagaggaggtgaggccagagagagtga +gcgaggaaccagagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggc +tggagagagtgagccaggaaccagaggaggtgaggccag----agtgagtgaggagcttg +aaggggtgaggctggagacagtgagcgaggaacca------------------------- +-----------gagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggc +tggagagcgtgagtgaggagcccgagggggtgaggctggagagagtgagtgaggagccca +agggggtgaagccgaggtgggtatggggctgggtcacctggggtctcccagcccagtggg +ggatttgggcagggggcgacgtggccagggttctgtggtgggagacccattctgaatgcc +gtgtggggaaccaacaaggc +>p:HG002_1_chr20:57189846-57190641 +ctgggagctgactggcgagggagatcagctcaggggtgcacagtgctgtgtctgatggtg +gcaaggactaggaagaacctaggacagggtggcagggacatgacagtggggcacagtgta +cagggcagagtgagccatgggaggctttggggaggaaatgttcctggcagagggaatggc +acatgccaggttcatgagaaatacacggtgtgtgtcagcacagtgaagaggccagtgagg +ctggagaagtgagccaggaaccagaggggttgaggctggagatagtgagcgaggaaccgg +agggggtgaagctggagagagtgagccaggaatcagaggaggtgaggccagagagagtga +gcgaggaaccagagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggc +tggagagagtgagccaggaaccagaggaggtgaggccag----agtgagtgaggagcttg +aaggggtgaggctggagacagtgagcgaggaacca------------------------- +-----------gagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggc +tggagagcgtgagtgaggagcccgagggggtgaggctggagagagtgagtgaggagccca +agggggtgaagccgaggtgggtatggggctgggtcacctggggtctcccagcccagtggg +ggatttgggcagggggcgacgtggccagggttctgtggtgggagacccattctgaatgcc +gtgtggggaaccaacaaggc +>p:HG002_2_chr20:57189846-57190641 +ctgggagctgactggcgagggagatcagctcaggggtgcacagtgctgtgtctgatggtg +gcaaggactaggaagaacctaggacagggtggcagggacatgacagtggggcacagtgta +cagggcagagtgagccatgggaggctttggggaggaaatgttcctggcagagggaatggc +acatgccaggttcatgagaaatacacggtgtgtgtcagcacagtgaagaggccagtgagg +ctggagaagtgagccaggaaccagagaggttgagactggagatagtgagcgaggaaccgg +agggggtgaagctggagagagtgagccaggaatcagaggaggtgaggccagagagagtga +gcgaggaaccagagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggc +c----agagtgagtgaggagcttgaaggggtgaggctggagacagtgagcgaggaaccag +agggggtgaggctggagagagtgagccaggaaccagaggaggtgaggccaga----gtga +gtgaggagcttgaaggggtgaggctggagacagtgagcgaggaaccagagggggtgaggc +tggagagcgtgagtgaggagcccgagggggtgaggctggagagagtgagtgaggagccca +agggggtgaagccgaggtgggtatggggctgggtcacctggggtctcccagcccagtggg +ggatttgggcagggggcgacgtggccagggttctgtggtgggagacccattctgaatgcc +gtgtggggaaccaacaaggc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/msa.fa.fai new file mode 100644 index 00000000..a6dd8f20 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_57189846_57190641 800 29 60 61 +syndip_1_chr20:57189846-57190641 800 877 60 61 +syndip_2_chr20:57189846-57190641 800 1725 60 61 +p:HG002_1_chr20:57189846-57190641 800 2574 60 61 +p:HG002_2_chr20:57189846-57190641 800 3423 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/output.vcf.gz new file mode 100644 index 00000000..3f8e9c3f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/output.vcf.gz.tbi new file mode 100644 index 00000000..7bf5a505 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57189946-57190541/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/base.vcf.gz new file mode 100644 index 00000000..83893e9d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/base.vcf.gz.tbi new file mode 100644 index 00000000..f273f8d5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/comp.vcf.gz new file mode 100644 index 00000000..86266b15 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/comp.vcf.gz.tbi new file mode 100644 index 00000000..b28f47e5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/haps.fa new file mode 100644 index 00000000..ca93c54c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/haps.fa @@ -0,0 +1,38 @@ +>ref_chr20_57350708_57351088 +AATGGCATGGTCTCGGCTCACTGCAACCTCCACCTCCTGGGTTCAAGCGATTCTCCTGCCTTAGCCTCCCAAGCAGCTGGGATTACAGGCACCCGCCACCATGCCCGGCTAATTTTTGTATTTTTAGTACTGACGGGGGGACGGGGGGGCGGGGGGGCGGGGGGACGGGGGGCGGGGGGGGCGGGGGGGGCGGGGGGACGGGGGCGGGGGGCGGGGGGGGGCGGCGCGGGGGGGCGGGGGGGGCGGGGGGCGGGGCGGTTCACGATGTTGGCCAGACTTGTCTTGAACTCCTGACCCCAGGTGATCAGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCTGGCCAGTTGCGGATTTATAAA +>syndip_1_chr20:57350708-57351088 +AATGGCATGGTCTCGGCTCACTGCAACCTCCACCTCCTGGGTTCAAGCGATTCTCCTGCC +TTAGCCTCCCAAGCAGCTGGGATTACAGGCACCCGCCACCATGCCCGGCTAATTTTTGTA +TTTTTAGTACTGACGGGGGGACGGGGGGACGGGGGACGGGGGACGGGGGGCGGGGGGGAC +GGGGGACGGGGGGCGGGGGGGGCGGGGGGGACGGGGGGCGGGGGGGGCGGGGGCCGGGGG +GGGCGGGGGGACGGGGGCGGGGGGCCGGGGGGGGCGGGGGGACGGGGGCGGGGGGGCGGG +GGGGGCGGGGGGACGGGGGCGGGGGGCGCGGGGGGGCGGGGGGGGCGGCGCGGGGGGGCG +GGGGGGGGCGGGGGGCGGGGCGGTTCACGATGTTGGCCAGACTTGTCTTGAACTCCTGAC +CCCAGGTGATCAGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCG +CGCCTGGCCAGTTGCGGATTTATAAA +>syndip_2_chr20:57350708-57351088 +AATGGCATGGTCTCGGCTCACTGCAACCTCCACCTCCTGGGTTCAAGCGATTCTCCTGCC +TTAGCCTCCCAAGCAGCTGGGATTACAGGCACCCGCCACCATGCCCGGCTAATTTTTGTA +TTTTTAGTACTGACGGGGGGACGGGGGGGCGGGGGGGCGGGGGGGCGGGGGGACGGGGGG +CGGGGGGGGCGGGGGGACGGGGGCGGGGGGCGGGGGGGGGCGGCGCGGGGGGGCGGGGGG +GGCGGGGGGCGGGGCGGTTCACGATGTTGGCCAGACTTGTCTTGAACTCCTGACCCCAGG +TGATCAGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCTG +GCCAGTTGCGGATTTATAAA +>p:HG002_1_chr20:57350708-57351088 +AATGGCATGGTCTCGGCTCACTGCAACCTCCACCTCCTGGGTTCAAGCGATTCTCCTGCC +TTAGCCTCCCAAGCAGCTGGGATTACAGGCACCCGCCACCATGCCCGGCTAATTTTTGTA +TTTTTAGTACTGACGGGGGGACGGGGGGGCGGGGGGGCGGGGGGGCGGGGGGACGGGGGG +CGGGGGGGGCGGGGGGACGGGGGCGGGGGGCGGGGGGGGGCGGCGCGGGGGGGCGGGGGG +GGCGGGGGGCGGGGCGGTTCACGATGTTGGCCAGACTTGTCTTGAACTCCTGACCCCAGG +TGATCAGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCTG +GCCAGTTGCGGATTTATAAA +>p:HG002_2_chr20:57350708-57351088 +AATGGCATGGTCTCGGCTCACTGCAACCTCCACCTCCTGGGTTCAAGCGATTCTCCTGCC +TTAGCCTCCCAAGCAGCTGGGATTACAGGCACCCGCCACCATGCCCGGCTAATTTTTGTA +TTTTTAGTACTGACGGGGGGACGGGGGGACGGGGGACGGGGGACGGGGGGCGGGGGGGAC +GGGGGACGGGGGGCGGGGGGGGCGGGGGGGACGGGGGGCGGGGGGGGCGGGGGCCGGGGG +GGGCGGGGGGACGGGGGCGGGGGGCCGGGGGGGGCGGGGGGACGGGGGCGGGGGGGCGGG +GGGGGCGGGGGGACGGGGGCGGGGGGCGCGGGGGGGCGGGGGGGGCGGCGCGGGGGGGCG +GGGGGGGGCGGGGGGCGGGGCGGTTCACGATGTTGGCCAGACTTGTCTTGAACTCCTGAC +CCCAGGTGATCAGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCG +CGCCTGGCCAGTTGCGGATTTATAAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/haps.fa.ref.fa new file mode 100644 index 00000000..b731ce98 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:57350708-57351088 +AATGGCATGGTCTCGGCTCACTGCAACCTCCACCTCCTGGGTTCAAGCGATTCTCCTGCCTTAGCCTCCCAAGCAGCTGGGATTACAGGCACCCGCCACCATGCCCGGCTAATTTTTGTATTTTTAGTACTGACGGGGGGACGGGGGGGCGGGGGGGCGGGGGGACGGGGGGCGGGGGGGGCGGGGGGGGCGGGGGGACGGGGGCGGGGGGCGGGGGGGGGCGGCGCGGGGGGGCGGGGGGGGCGGGGGGCGGGGCGGTTCACGATGTTGGCCAGACTTGTCTTGAACTCCTGACCCCAGGTGATCAGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCTGGCCAGTTGCGGATTTATAAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/msa.fa new file mode 100644 index 00000000..212f38c2 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/msa.fa @@ -0,0 +1,50 @@ +>ref_chr20_57350708_57351088 +aatggcatggtctcggctcactgcaacctccacctcctgggttcaagcgattctcctgcc +ttagcctcccaagcagctgggattacaggcacccgccaccatgcccggctaatttttgta +tttttagtactgacggggggacgggggggc------------------------------ +------------------------gggggggcggggggacggggggcggggggggcgggg +ggggcggggggacgggggcggggggcgggggggggc------------------------ +-------------------------ggcgcgggggggc---------------------- +-ggggggggcggggggcggggcggttcacgatgttggccagacttgtcttgaactcctga +ccccaggtgatcagcccgcctcggcctcccaaagtgctgggattacaggcgtgagccacc +gcgcctggccagttgcggatttataaa +>syndip_1_chr20:57350708-57351088 +aatggcatggtctcggctcactgcaacctccacctcctgggttcaagcgattctcctgcc +ttagcctcccaagcagctgggattacaggcacccgccaccatgcccggctaatttttgta +tttttagtactgacggggggacggggggacgggggacgggggacggggggcgggggggac +gggggacggggggcggggggggcgggggggacggggggcggggggg-gcgggggccgggg +ggggcggggggacgggggcggggggccggggggggcggggggacgggggcgggggggcgg +ggggggcggggggacgggggcggggggcgcgggggggcggggggggcggcgcgggggggc +gggggggggcggggggcggggcggttcacgatgttggccagacttgtcttgaactcctga +ccccaggtgatcagcccgcctcggcctcccaaagtgctgggattacaggcgtgagccacc +gcgcctggccagttgcggatttataaa +>syndip_2_chr20:57350708-57351088 +aatggcatggtctcggctcactgcaacctccacctcctgggttcaagcgattctcctgcc +ttagcctcccaagcagctgggattacaggcacccgccaccatgcccggctaatttttgta +tttttagtactgacggggggacgggggggc------------------------------ +------------------------gggggggcgggggggcgggggg-acggggggcgggg +ggggcggggggacgggggcggggggcgggggggggc------------------------ +-------------------------ggcgcgggggggc---------------------- +-ggggggggcggggggcggggcggttcacgatgttggccagacttgtcttgaactcctga +ccccaggtgatcagcccgcctcggcctcccaaagtgctgggattacaggcgtgagccacc +gcgcctggccagttgcggatttataaa +>p:HG002_1_chr20:57350708-57351088 +aatggcatggtctcggctcactgcaacctccacctcctgggttcaagcgattctcctgcc +ttagcctcccaagcagctgggattacaggcacccgccaccatgcccggctaatttttgta +tttttagtactgacggggggacgggggggc------------------------------ +------------------------gggggggcgggggggcgggggg-acggggggcgggg +ggggcggggggacgggggcggggggcgggggggggc------------------------ +-------------------------ggcgcgggggggc---------------------- +-ggggggggcggggggcggggcggttcacgatgttggccagacttgtcttgaactcctga +ccccaggtgatcagcccgcctcggcctcccaaagtgctgggattacaggcgtgagccacc +gcgcctggccagttgcggatttataaa +>p:HG002_2_chr20:57350708-57351088 +aatggcatggtctcggctcactgcaacctccacctcctgggttcaagcgattctcctgcc +ttagcctcccaagcagctgggattacaggcacccgccaccatgcccggctaatttttgta +tttttagtactgacggggggacggggggacgggggacgggggacggggggcgggggggac +gggggacggggggcggggggggcgggggggacggggggcggggggg-gcgggggccgggg +ggggcggggggacgggggcggggggccggggggggcggggggacgggggcgggggggcgg +ggggggcggggggacgggggcggggggcgcgggggggcggggggggcggcgcgggggggc +gggggggggcggggggcggggcggttcacgatgttggccagacttgtcttgaactcctga +ccccaggtgatcagcccgcctcggcctcccaaagtgctgggattacaggcgtgagccacc +gcgcctggccagttgcggatttataaa diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/msa.fa.fai new file mode 100644 index 00000000..33b2e406 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_57350708_57351088 507 29 60 61 +syndip_1_chr20:57350708-57351088 507 579 60 61 +syndip_2_chr20:57350708-57351088 507 1129 60 61 +p:HG002_1_chr20:57350708-57351088 507 1680 60 61 +p:HG002_2_chr20:57350708-57351088 507 2231 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/output.vcf.gz new file mode 100644 index 00000000..e83c199e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/output.vcf.gz.tbi new file mode 100644 index 00000000..d2209c7e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57350808-57350988/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/base.vcf.gz new file mode 100644 index 00000000..7c6dca3c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/base.vcf.gz.tbi new file mode 100644 index 00000000..5321997a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/comp.vcf.gz new file mode 100644 index 00000000..c68fe7dd Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/comp.vcf.gz.tbi new file mode 100644 index 00000000..cef579dc Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/haps.fa new file mode 100644 index 00000000..dd9dda7a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/haps.fa @@ -0,0 +1,64 @@ +>ref_chr20_57948698_57949591 +CGGAGCGGGTGTGCCCCGTGGTCTCTCTTCACTGTTCTTAAGACATTCACAACCTCATTTTGATGGTGGGACGCTGCAGCTCACGTCTGAGTCCCATCCAAGACTTGGCCCACTGCTGTGCCCTGCACAGATGGACAGATGGTTGGAAGGATGGATGGATGGATGGATGGATGGATGGATGGATGGGGTTGGATGGATGGATGGATGGATGGATGGATAGTGGATAGATGGATGAATAGTGGATGGATAAATGGATTAATGGATGGATGAATGGATGATGGATGGATGAATGAGATGGATGGATTGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGAAGAATGGATGATGGATGGATGAGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGAAGAATGGATGATGGATGGATGAGATGGATGGATGGATGGATGGATGGGGGGTTGGATGGATGGATGGATGGATGGATGGATAGTGGATAGATGGATGAATAGTGAATGGATAAATGGATTAATGGATGGATGGATAGTGGATAGATGGATGAATAGTGGATGGATAAATGGATTAATGGATGGATGAATGGATGATGGATGGATGAATGAGATGGATGGATTGATGGATGGATGGATGGATGGATGGATGGATGGAAGAATGGATGATGGATGGATGAATGAGATGGGTGGATTGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGCAGATGGATGGATCCATCTATGTCAGGCCTGCATGACACCTGGTGTGGAGGAGCCACCCAGTCAACATTTGCTGACAGGATGGACAGACAGAGAGGAGGTGAGTGACAGGGGCCCTCAGGTGCTTTTTCTTTGGAGACCTGGGC +>syndip_1_chr20:57948698-57949591 +CGGAGCGGGTGTGCCCCGTGGTCTCTCTTCACTGTTCTTAAGACATTCACAACCTCATTT +TGATGGTGGGACGCTGCAGCTCACGTCTGAGTCCCATCCAAGACTTGGCCCACTGCTGTG +CCCTGCACAGATGGACAGATGGTTGGAAGGATGGATGGATGGATGGATGGATGGATGGAT +GGGGTTGGATGGATGGATGGATGGATGGATGGATAGTGGATAGATGGATGAATAGTGGAT +GGATAAATGGATTAATGGATGGATGAATGGATGATGGATGGATGAATGAGATGGATGGAT +TGATGGATGGATGGATGGATGGATGGATGGAAGAATGGATGATGGATGGATGAGATGGAT +GGATGGATGGATGGAAGAATGGATGATGGATGGATGAGATGGATGGATGGATGGGGGGTT +GGATGGATGGATGGATGGATGGATGGATAGTGGATAGATGGATGAATAGTGGATGGATAA +ATGGATTAATGGATGGATGAATGGATGATGGATGGATGAATGAGATGGATGGATTGATGG +ATGGATGGATGGATGGAAGAATGGATGATGGATGGATGAATGAGATGGGTGGATTGATGG +ATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGCAGATGGATGGATCCATCTA +TGTCAGGCCTGCATGACACCTGGTGTGGAGGAGCCACCCAGTCAACATTTGCTGACAGGA +TGGACAGACAGAGAGGAGGTGAGTGACAGGGGCCCTCAGGTGCTTTTTCTTTGGAGACCT +GGGC +>syndip_2_chr20:57948698-57949591 +CGGAGCGGGTGTGCCCCGTGGTCTCTCTTCACTGTTCTTAAGACATTCACAACCTCATTT +TGATGGTGGGACGCTGCAGCTCACGTCTGAGTCCCATCCAAGACTTGGCCCACTGCTGTG +CCCTGCACAGATGGACAGATGGTTGGAAGGATGGATGGATGGATGGATGGATGGATGGAT +GGATGGGGTTGGATGGATGGATGGATGGATGGATGGATAGTGGATAGATGGATGAATAGT +GGATGGATAAATGGATTAATGGATGGATGAATGGATGATGGATGGATGAATGAGATGGAT +GGATTGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGAAGAATGGAT +GATGGATGGATGAGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGAAGAAT +GGATGATGGATGGATGAGATGGATGGATGGATGGATGGATGGGGGGTTGGATGGATGGAT +GGATGGATGGATGGATAGTGGATAGATGGATGAATAGTGAATGGATAAATGGATTAATGG +ATGGATGGATAGTGGATAGATGGATGAATAGTGGATGGATAAATGGATTAATGGATGGAT +GAATGGATGATGGATGGATGAATGAGATGGATGGATTGATGGATGGATGGATGGATGGAT +GGATGGATGGAAGAATGGATGATGGATGGATGAATGAGATGGGTGGATTGATGGATGGAT +GGATGGATGGATGGATGGATGGATGGATGGCAGATGGATGGATCCATCTATGTCAGGCCT +GCATGACACCTGGTGTGGAGGAGCCACCCAGTCAACATTTGCTGACAGGATGGACAGACA +GAGAGGAGGTGAGTGACAGGGGCCCTCAGGTGCTTTTTCTTTGGAGACCTGGGC +>p:HG002_1_chr20:57948698-57949591 +CGGAGCGGGTGTGCCCCGTGGTCTCTCTTCACTGTTCTTAAGACATTCACAACCTCATTT +TGATGGTGGGACGCTGCAGCTCACGTCTGAGTCCCATCCAAGACTTGGCCCACTGCTGTG +CCCTGCACAGATGGACAGATGGTTGGAAGGATGGATGGATGGATGGATGGATGGATGGAT +GGATGGGGTTGGATGGATGGATGGATGGATGGATGGATAGTGGATAGATGGATGAATAGT +GGATGGATAAATGGATTAATGGATGGATGAATGGATGATGGATGGATGAATGAGATGGAT +GGATTGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGAAGAATGGAT +GATGGATGGATGAGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGAAGAAT +GGATGATGGATGGATGAGATGGATGGATGGATGGATGGATGGGGGGTTGGATGGATGGAT +GGATGGATGGATGGATAGTGGATAGATGGATGAATAGTGAATGGATAAATGGATTAATGG +ATGGATGGATAGTGGATAGATGGATGAATAGTGGATGGATAAATGGATTAATGGATGGAT +GAATGGATGATGGATGGATGAATGAGATGGATGGATTGATGGATGGATGGATGGATGGAT +GGATGGATGGAAGAATGGATGATGGATGGATGAATGAGATGGGTGGATTGATGGATGGAT +GGATGGATGGATGGATGGATGGATGGATGGCAGATGGATGGATCCATCTATGTCAGGCCT +GCATGACACCTGGTGTGGAGGAGCCACCCAGTCAACATTTGCTGACAGGATGGACAGACA +GAGAGGAGGTGAGTGACAGGGGCCCTCAGGTGCTTTTTCTTTGGAGACCTGGGC +>p:HG002_2_chr20:57948698-57949591 +CGGAGCGGGTGTGCCCCGTGGTCTCTCTTCACTGTTCTTAAGACATTCACAACCTCATTT +TGATGGTGGGACGCTGCAGCTCACGTCTGAGTCCCATCCAAGACTTGGCCCACTGCTGTG +CCCTGCACAGATGGACAGATGGTTGGAAGGATGGATGGATGGATGGATGGATGGATGGAT +GGGGTTGGATGGATGGATGGATGGATGGATGGATAGTGGATAGATGGATGAATAGTGGAT +GGATAAATGGATTAATGGATGGATGAATGGATGATGGATGGATGAATGAGATGGATGGAT +TGATGGATGGATGGATGGATGGATGGATGGAAGAATGGATGATGGATGGATGAGATGGAT +GGATGGATGGATGGAAGAATGGATGATGGATGGATGAGATGGATGGATGGATGGGGGGTT +GGATGGATGGATGGATGGATGGATGGATAGTGGATAGATGGATGAATAGTGGATGGATAA +ATGGATTAATGGATGGATGAATGGATGATGGATGGATGAATGAGATGGATGGATTGATGG +ATGGATGGATGGATGGAAGAATGGATGATGGATGGATGAATGAGATGGGTGGATTGATGG +ATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGCAGATGGATGGATCCATCTA +TGTCAGGCCTGCATGACACCTGGTGTGGAGGAGCCACCCAGTCAACATTTGCTGACAGGA +TGGACAGACAGAGAGGAGGTGAGTGACAGGGGCCCTCAGGTGCTTTTTCTTTGGAGACCT +GGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/haps.fa.ref.fa new file mode 100644 index 00000000..cbc755d3 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:57948698-57949591 +CGGAGCGGGTGTGCCCCGTGGTCTCTCTTCACTGTTCTTAAGACATTCACAACCTCATTTTGATGGTGGGACGCTGCAGCTCACGTCTGAGTCCCATCCAAGACTTGGCCCACTGCTGTGCCCTGCACAGATGGACAGATGGTTGGAAGGATGGATGGATGGATGGATGGATGGATGGATGGATGGGGTTGGATGGATGGATGGATGGATGGATGGATAGTGGATAGATGGATGAATAGTGGATGGATAAATGGATTAATGGATGGATGAATGGATGATGGATGGATGAATGAGATGGATGGATTGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGAAGAATGGATGATGGATGGATGAGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGAAGAATGGATGATGGATGGATGAGATGGATGGATGGATGGATGGATGGGGGGTTGGATGGATGGATGGATGGATGGATGGATAGTGGATAGATGGATGAATAGTGAATGGATAAATGGATTAATGGATGGATGGATAGTGGATAGATGGATGAATAGTGGATGGATAAATGGATTAATGGATGGATGAATGGATGATGGATGGATGAATGAGATGGATGGATTGATGGATGGATGGATGGATGGATGGATGGATGGAAGAATGGATGATGGATGGATGAATGAGATGGGTGGATTGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGCAGATGGATGGATCCATCTATGTCAGGCCTGCATGACACCTGGTGTGGAGGAGCCACCCAGTCAACATTTGCTGACAGGATGGACAGACAGAGAGGAGGTGAGTGACAGGGGCCCTCAGGTGCTTTTTCTTTGGAGACCTGGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/msa.fa new file mode 100644 index 00000000..1fc076be --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/msa.fa @@ -0,0 +1,80 @@ +>ref_chr20_57948698_57949591 +cggagcgggtgtgccccgtggtctctcttcactgttcttaagacattcacaacctcattt +tgatggtgggacgctgcagctcacgtctgagtcccatccaagacttggcccactgctgtg +ccctgcacagatggacagatggttggaaggatggatggatggatggatggatggatggat +ggatggggttggatggatggatggatggatggatggatagtggatagatggatgaatagt +ggatggataaatggattaatggatggatgaatggatgatggatggatgaatgagatggat +ggattgatggatggatggatggatggatggatggatggatggatggatggaagaatggat +gatggatggatgagatggatggatggatggatggatggatggatggatggatggaagaat +ggatgatggatggatgagatggatggatggatggatggatggggggttggatggatggat +ggatggatggatggatagtggatagatggatgaatagtgaatggataaatggattaatgg +atggatggatagtggatagatggatgaatagtggatggataaatggattaatggatggat +gaatggatgatggatggatgaatgagatggatggattgatggatggatggatggatggat +ggatggatggaagaatggatgatggatggatgaatgagatgggtggatt----gatggat +ggatggatggatggatggatggatggatggatggcagatggatggatccatctatgtcag +gcctgcatgacacctggtgtggaggagccacccagtcaacatttgctgacaggatggaca +gacagagaggaggtgagtgacaggggccctcaggtgctttttctttggagacctgggc +>syndip_1_chr20:57948698-57949591 +cggagcgggtgtgccccgtggtctctcttcactgttcttaagacattcacaacctcattt +tgatggtgggacgctgcagctcacgtctgagtcccatccaagacttggcccactgctgtg +ccctgcacagatggacagatggttggaa----ggatggatggatggatggatggatggat +ggatggggttggatggatggatggatggatggatggatagtggatagatggatgaatagt +ggatggataaatggattaatggatggatgaatggatgatggatggatgaatgagatggat +ggatt----------------gatggatggatggatggatggatggatggaagaatggat +gatggatggatga--------------------gatggatggatggatggatggaagaat +ggatgatggatggatga--------gatggatggatggatggggggttggatggatggat +gg------------------------------------------------------atgg +atggatggatagtggatagatggatgaatagtggatggataaatggattaatggatggat +gaatggatgatggatggatgaatgagatggatggatt------------gatggatggat +ggatggatggaagaatggatgatggatggatgaatgagatgggtggattgatggatggat +ggatggatggatggatggatggatggatggatggcagatggatggatccatctatgtcag +gcctgcatgacacctggtgtggaggagccacccagtcaacatttgctgacaggatggaca +gacagagaggaggtgagtgacaggggccctcaggtgctttttctttggagacctgggc +>syndip_2_chr20:57948698-57949591 +cggagcgggtgtgccccgtggtctctcttcactgttcttaagacattcacaacctcattt +tgatggtgggacgctgcagctcacgtctgagtcccatccaagacttggcccactgctgtg +ccctgcacagatggacagatggttggaaggatggatggatggatggatggatggatggat +ggatggggttggatggatggatggatggatggatggatagtggatagatggatgaatagt +ggatggataaatggattaatggatggatgaatggatgatggatggatgaatgagatggat +ggattgatggatggatggatggatggatggatggatggatggatggatggaagaatggat +gatggatggatgagatggatggatggatggatggatggatggatggatggatggaagaat +ggatgatggatggatgagatggatggatggatggatggatggggggttggatggatggat +ggatggatggatggatagtggatagatggatgaatagtgaatggataaatggattaatgg +atggatggatagtggatagatggatgaatagtggatggataaatggattaatggatggat +gaatggatgatggatggatgaatgagatggatggattgatggatggatggatggatggat +ggatggatggaagaatggatgatggatggatgaatgagatgggtggatt----gatggat +ggatggatggatggatggatggatggatggatggcagatggatggatccatctatgtcag +gcctgcatgacacctggtgtggaggagccacccagtcaacatttgctgacaggatggaca +gacagagaggaggtgagtgacaggggccctcaggtgctttttctttggagacctgggc +>p:HG002_1_chr20:57948698-57949591 +cggagcgggtgtgccccgtggtctctcttcactgttcttaagacattcacaacctcattt +tgatggtgggacgctgcagctcacgtctgagtcccatccaagacttggcccactgctgtg +ccctgcacagatggacagatggttggaaggatggatggatggatggatggatggatggat +ggatggggttggatggatggatggatggatggatggatagtggatagatggatgaatagt +ggatggataaatggattaatggatggatgaatggatgatggatggatgaatgagatggat +ggattgatggatggatggatggatggatggatggatggatggatggatggaagaatggat +gatggatggatgagatggatggatggatggatggatggatggatggatggatggaagaat +ggatgatggatggatgagatggatggatggatggatggatggggggttggatggatggat +ggatggatggatggatagtggatagatggatgaatagtgaatggataaatggattaatgg +atggatggatagtggatagatggatgaatagtggatggataaatggattaatggatggat +gaatggatgatggatggatgaatgagatggatggattgatggatggatggatggatggat +ggatggatggaagaatggatgatggatggatgaatgagatgggtggatt----gatggat +ggatggatggatggatggatggatggatggatggcagatggatggatccatctatgtcag +gcctgcatgacacctggtgtggaggagccacccagtcaacatttgctgacaggatggaca +gacagagaggaggtgagtgacaggggccctcaggtgctttttctttggagacctgggc +>p:HG002_2_chr20:57948698-57949591 +cggagcgggtgtgccccgtggtctctcttcactgttcttaagacattcacaacctcattt +tgatggtgggacgctgcagctcacgtctgagtcccatccaagacttggcccactgctgtg +ccctgcacagatggacagatggttggaa----ggatggatggatggatggatggatggat +ggatggggttggatggatggatggatggatggatggatagtggatagatggatgaatagt +ggatggataaatggattaatggatggatgaatggatgatggatggatgaatgagatggat +ggatt----------------gatggatggatggatggatggatggatggaagaatggat +gatggatggatga--------------------gatggatggatggatggatggaagaat +ggatgatggatggatga--------gatggatggatggatggggggttggatggatggat +gg------------------------------------------------------atgg +atggatggatagtggatagatggatgaatagtggatggataaatggattaatggatggat +gaatggatgatggatggatgaatgagatggatggatt------------gatggatggat +ggatggatggaagaatggatgatggatggatgaatgagatgggtggattgatggatggat +ggatggatggatggatggatggatggatggatggcagatggatggatccatctatgtcag +gcctgcatgacacctggtgtggaggagccacccagtcaacatttgctgacaggatggaca +gacagagaggaggtgagtgacaggggccctcaggtgctttttctttggagacctgggc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/msa.fa.fai new file mode 100644 index 00000000..785ab6f8 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_57948698_57949591 898 29 60 61 +syndip_1_chr20:57948698-57949591 898 976 60 61 +syndip_2_chr20:57948698-57949591 898 1923 60 61 +p:HG002_1_chr20:57948698-57949591 898 2871 60 61 +p:HG002_2_chr20:57948698-57949591 898 3819 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/output.vcf.gz new file mode 100644 index 00000000..0c799b82 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/output.vcf.gz.tbi new file mode 100644 index 00000000..b4a4743c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:57948798-57949491/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/base.vcf.gz new file mode 100644 index 00000000..fbf0df7e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/base.vcf.gz.tbi new file mode 100644 index 00000000..b96af4a1 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/comp.vcf.gz new file mode 100644 index 00000000..98cbef6c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/comp.vcf.gz.tbi new file mode 100644 index 00000000..4eeda189 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/haps.fa new file mode 100644 index 00000000..347e4302 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/haps.fa @@ -0,0 +1,136 @@ +>ref_chr20_59383704_59385336 +GGTTTTGTGCTTCCACCAAGCCAGGGGACTGTTCTGTGGCCCTGGAACCACCGTGAAAGCAAACAACCCTCGGCTGTGTTGGGAGACAGCTCCAGCTCCTCCATCCTCAAATGTGAGAGCTGATGATTGGGGTGGAGGAGGAGGTGAGTGGGGAGGGGGTGGGGGAGAAGGAGGTGATGGGGAAGAGATGAGTGGGCAGGAGGTGAGCAGGGAGGAGGTGAGCAGGGATGAGTGGAGGAAGGAGGTGATAGGGAGGAGGTGAGTGGGCAGGAGGTGAGCAGGGAGAAGATGAGCAGGGGGGTGGTGAGCGGGGAGGAGGTGGAGGGGAAGGAAGTGATGGGGGAGGAGGTGGGGGGAAGGAGGTGATGGGGAGGAGGTGAATGGGCAGGAGGTGACTGGGGAGGAGGTGAGCAGGGAGGAGGTGAGCAGGGAGGAGGTGAGTGGAGTGGGGATGGGAGTGGAGTGGCGGGAAGGAAGTGATAGGGAGGAGATGAGTGGGCAGGAGGTGAGCAGAGAGGAGATGAGTAGAGCAGGGATGAGTAGGGGAAGGAGGTGATAGGAGGTGAGTGGGCAGGAGGTGAGCAGGGAGGAGGCGAGCAGGGAGGAGGTAGAGGGGAAGGAAGTGATGGGGAGGAGGTGAGGGGGGAAAGAGGTGGCGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGGGGAGGAAGGTGGGGGGAAGGAGGTGATAGGGAGGATGTGGGGGAGGTGGGGGGGAAGGAGGTGAGGCAGAGGAGGGGAGTGGGGAGGGAGATGAGTAAGGAAGTGATGGGGAGAGGGTGAGTGGGGAAGTGGTGAGAGGGGAGGAGGTGAGGGGGCAAGGGAGGCGATGCGGAGGAAGGAGGTGATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGAGGGGAGGAGCTGAGTGGGGAAGGAGGTAATGAGGACAAGGTGAGGGGAAAGGAGGTAAGGGAGGGGAAGGGGAGGGAAGGAGCTGAGCGGGGCAGAGCATGTCTCCTCTCTTTAAGCATCCTCTGTATTCTGCAGAGGCCAAGCAGTCTGGATGTTGGCCTTCCTCAGTGGCCCATGAAATAACTTTGCTCCCCAGATTCTGAGCATGGGT +>syndip_1_chr20:59383704-59385336 +GGTTTTGTGCTTCCACCAAGCCAGGGGACTGTTCTGTGGCCCTGGAACCACCGTGAAAGC +AAACAACCCTCGGCTGTGTTGGGAGACAGCTCCAGCTCCTCCATCCTCAAATGTGAGAGC +TGATGATTGGGGTGGAGGAGGAGGTGAGTGGGGAGGGGGTGGGGGAGAAGGAGGTGATGG +GGAAGAGATGAGTGGGCAGGAGGTGAGCAGGGAGGAGGTGAGCAGGGATGAGTGGAGGAA +GGAGGTGATAGGGAGGAGGTGAGTGGGCAGGAGGTGAGCAGGGAGAAGATGAGCAGGGGG +GTGGTGAGCGGGGAGGAGGTGGAGGGGAAGGAAGTGATGGGGGAGGAGGTGGGGGGAAGG +AGGTGATGGGGAGGAGGTGAATGGGCAGGAGGTGACTGGGGAGGAGGTGAGCAGGGAGGA +GGTGAGCAGGGAGGAGGTGAGTGGAGTGGGGATGGGAGTGGAGTGGGGGGAAGGAAGTGA +TAGGGAGGAGATGAGTGGGCAGGAGGTGAGCAGAGAGGAGATGAGTAGAGCAGGGATGAG +TAGGGGAAGGAGGTGATAGGAGGTGAGTGGGCAGGAGGTGAGCAGGGAGGAGGCGAGCAG +GGAGGAGGTAGAGGGGAAGGAAGTGATGGGGAGGAGGTGAGGGGGGAAAGAGGTGGCGGG +GGAAGGAGGTGATGGGGAGGAGGTGAGTGGGGAGGAAGGTGGGAGGAAGGAGGTGATGGG +GAGGATGTGGGGGAGGTGGGGAGCAAGGAGGTGATGGGGAGGAGGTGAGTGGGGAGGTGG +TGAGCAGGGAGGAGGTGAGGGGGCAAGGGAGGTGATGGGGAGGAAGGAGGTTATGGGGAG +GTGGTGAGTGGGGAGGGAGGTAAGGGGTAAGGTGGTGATGTGGAGGTGGTGAGTGGGGAG +GTGGTGAGAGGGGAGGAGATGAGGGGGCAAGGGAGGTGATGGGGAGGAGGTGAGTGGGGA +GGAAGGTGGGGGGAAGGAGGTGATGGGGAGGATGTGGGGGAGGTGGGGGGGAAGGAGGTG +AGGCAGAGGAGGGGAGTGGGGAGGGAGATGAGTAAGGAAGTGATGGGGAGAGGGTGAGTG +GGGAAGTGGTGAGAGGGGAGGAGGTGAGGGGGCAAGGGAGGTGATGCGGAGGAAGGAGGT +GATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGAGGAAGGAGGTG +ATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGA +TGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGAT +GGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATG +GGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGAGGAAGGAGGTGATGG +GAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGG +AAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGA +AGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGAA +GGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGAAG +GAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGG +AGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGA +GGTGAGAGGGGAGGAGCTGAGGGGGGAAGGAGGTAATGAGGACAAGGTGAGGGGAAAGGA +GGTAAGGGAGGGGAAGGGGAGGGAAGGAGCTGAGCGGGGCAGAGCATGTCTCCTCTCTTT +AAGCATCCTCTGTATTCTGCAGAGGCCAAGCAGTCTGGATGTTGGCCTTCCTCAGTGGCC +CATGAAATAACTTTGCTCCCCAGATTCTGAGCATGGGT +>syndip_2_chr20:59383704-59385336 +GGTTTTGTGCTTCCACCAAGCCAGGGGACTGTTCTGTGGCCCTGGAACCACCGTGAAAGC +AAACAACCCTCGGCTGTGTTGGGAGACAGCTCCAGCTCCTCCATCCTCAAATGTGAGAGC +TGATGATTGGGGTGGAGGAGGAGGTGAGTGGGGAGGGGGTGGGGGAGAAGGAGGTGATGG +GGAAGAGATGAGTGGGCAGGAGGTGAGCAGGGAGGAGGTGAGCAGGGATGAGTGGAGGAA +GGAGGTGATAGGGAGGAGGTGAGTGGGCAGGAGGTGAGCAGGGAGAAGATGAGCAGGGGG +GTGGTGAGCGGGGAGGAGGTGGAGGGGAAGGAAGTGATGGGGGAGGAGGTGGGGGGAAGG +AGGTGATGGGGAGGAGGTGAATGGGCAGGAGGTGACTGGGGAGGAGGTGAGCAGGGAGGA +GGTGAGCAGGGAGGAGGTGAGTGGAGTGGGGATGGGAGTGGAGTGGGGGGAAGGAAGTGA +TAGGGAGGAGATGAGTGGGCAGGAGGTGAGCAGAGAGGAGATGAGTAGAGCAGGGATGAG +TAGGGGAAGGAGGTGATAGGAGGTGAGTGGGCAGGAGGTGAGCAGGGAGGAGGCGAGCAG +GGAGGAGGTAGAGGGGAAGGAAGTGATGGGGAGGAGGTGAGGGGGGAAAGAGGTGGCGGG +GGAAGGAGGTGATGGGGAGGAGGTGAGTGGGGAGGAAGGTGGGAGGAAGGAGGTGATGGG +GAGGATGTGGGGGAGGTGGGGAGCAAGGAGGTGATGGGGAGGAGGTGAGTGGGGAGGTGG +TGAGCAGGGAGGAGGTGAGGGGGCAAGGGAGGTGATGGGGAGGAGGTGAGTGGGGAGGTG +GTGAGCGGGGAGGAGGTGAGGGGGCAAGGGAGGTGATGGGGAGGAAGGAGGTTATGGGGA +GGTGGTGAGTGGGGAGGGAGGTAAGGGGTAAGGTGGTGATGTGGAGGTGGTGAGTGGGGA +GGTGGTGAGAGGGGAGGAGATGAGGGGGCAAGGGAGGTGATGGGGAGGAGGTGAGTGGGG +AGGAAGGTGGGGGGAAGGAGGTGATGGGGAGGATGTGGGGGAGGTGGGGGGGAAGGAGGT +GAGGCAGAGGAGGGGAGTGGGGAGGGAGATGAGTAAGGAAGTGATGGGGAGAGGGTGAGT +GGGGAAGTGGTGAGAGGGGAGGAGGTGAGGGGGCAAGGGAGGCGATGCGGAGGAAGGAGG +TGATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGAGGAAGGAGGT +GATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTG +ATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGA +TGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGAGGAAGGAGGTGAT +GGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATG +GGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGG +GGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGG +GAGGAGGTGAGAGGGGAGGAGCTGAGGGGGGAAGGAGGTAATGAGGACAAGGTGAGGGGA +AAGGAGGTAAGGGAGGGGAAGGGGAGGGAAGGAGCTGAGCGGGGCAGAGCATGTCTCCTC +TCTTTAAGCATCCTCTGTATTCTGCAGAGGCCAAGCAGTCTGGATGTTGGCCTTCCTCAG +TGGCCCATGAAATAACTTTGCTCCCCAGATTCTGAGCATGGGT +>p:HG002_1_chr20:59383704-59385336 +GGTTTTGTGCTTCCACCAAGCCAGGGGACTGTTCTGTGGCCCTGGAACCACCGTGAAAGC +AAACAACCCTCGGCTGTGTTGGGAGACAGCTCCAGCTCCTCCATCCTCAAATGTGAGAGC +TGATGATTGGGGTGGAGGAGGAGGTGAGTGGGGAGGGGGTGGGGGAGAAGGAGGTGATGG +GGAAGAGATGAGTGGGCAGGAGGTGAGCAGGGAGGAGGTGAGCAGGGATGAGTGGAGGAA +GGAGGTGATAGGGAGGAGGTGAGTGGGCAGGAGGTGAGCAGGGAGAAGATGAGCAGGGGG +GTGGTGAGCGGGGAGGAGGTGGAGGGGAAGGAAGTGATGGGGGAGGAGGTGGGGGGAAGG +AGGTGATGGGGAGGAGGTGAATGGGCAGGAGGTGACTGGGGAGGAGGTGAGCAGGGAGGA +GGTGAGCAGGGAGGAGGTGAGTGGAGTGGGGATGGGAGTGGAGTGGGGGGAAGGAAGTGA +TAGGGAGGAGATGAGTGGGCAGGAGGTGAGCAGAGAGGAGATGAGTAGAGCAGGGATGAG +TAGGGGAAGGAGGTGATAGGAGGTGAGTGGGCAGGAGGTGAGCAGGGAGGAGGCGAGCAG +GGAGGAGGTAGAGGGGAAGGAAGTGATGGGGAGGAGGTGAGGGGGGAAAGAGGTGGCGGG +GGAAGGAGGTGATGGGGAGGAGGTGAGTGGGGAGGAAGGTGGGAGGAAGGAGGTGATGGG +GAGGATGTGGGGGAGGTGGGGAGCAAGGAGGTGATGGGGAGGAGGTGAGTGGGGAGGTGG +TGAGCAGGGAGGAGGTGAGGGGGCAAGGGAGGTGATGGGGAGGAGGTGAGTGGGGAGGTG +GTGAGCGGGGAGGAGGTGAGGGGGCAAGGGAGGTGATGGGGAGGAAGGAGGTTATGGGGA +GGTGGTGAGTGGGGAGGGAGGTAAGGGGTAAGGTGGTGATGTGGAGGTGGTGAGTGGGGA +GGTGGTGAGAGGGGAGGAGATGAGGGGGCAAGGGAGGTGATGGGGAGGAGGTGAGTGGGG +AGGAAGGTGGGGGGAAGGAGGTGATGGGGAGGATGTGGGGGAGGTGGGGGGGAAGGAGGT +GAGGCAGAGGAGGGGAGTGGGGAGGGAGATGAGTAAGGAAGTGATGGGGAGAGGGTGAGT +GGGGAAGTGGTGAGAGGGGAGGAGGTGAGGGGGCAAGGGAGGCGATGCGGAGGAAGGAGG +TGATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGAGGAAGGAGGT +GATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTG +ATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGA +TGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGAGGAAGGAGGTGAT +GGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATG +GGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGG +GGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGG +GAGGAGGTGAGAGGGGAGGAGCTGAGGGGGGAAGGAGGTAATGAGGACAAGGTGAGGGGA +AAGGAGGTAAGGGAGGGGAAGGGGAGGGAAGGAGCTGAGCGGGGCAGAGCATGTCTCCTC +TCTTTAAGCATCCTCTGTATTCTGCAGAGGCCAAGCAGTCTGGATGTTGGCCTTCCTCAG +TGGCCCATGAAATAACTTTGCTCCCCAGATTCTGAGCATGGGT +>p:HG002_2_chr20:59383704-59385336 +GGTTTTGTGCTTCCACCAAGCCAGGGGACTGTTCTGTGGCCCTGGAACCACCGTGAAAGC +AAACAACCCTCGGCTGTGTTGGGAGACAGCTCCAGCTCCTCCATCCTCAAATGTGAGAGC +TGATGATTGGGGTGGAGGAGGAGGTGAGTGGGGAGGGGGTGGGGGAGAAGGAGGTGATGG +GGAAGAGATGAGTGGGCAGGAGGTGAGCAGGGAGGAGGTGAGCAGGGATGAGTGGAGGAA +GGAGGTGATAGGGAGGAGGTGAGTGGGCAGGAGGTGAGCAGGGAGAAGATGAGCAGGGGG +GTGGTGAGCGGGGAGGAGGTGGAGGGGAAGGAAGTGATGGGGGAGGAGGTGGGGGGAAGG +AGGTGATGGGGAGGAGGTGAATGGGCAGGAGGTGACTGGGGAGGAGGTGAGCAGGGAGGA +GGTGAGCAGGGAGGAGGTGAGTGGAGTGGGGATGGGAGTGGAGTGGGGGGAAGGAAGTGA +TAGGGAGGAGATGAGTGGGCAGGAGGTGAGCAGAGAGGAGATGAGTAGAGCAGGGATGAG +TAGGGGAAGGAGGTGATAGGAGGTGAGTGGGCAGGAGGTGAGCAGGGAGGAGGCGAGCAG +GGAGGAGGTAGAGGGGAAGGAAGTGATGGGGAGGAGGTGAGGGGGGAAAGAGGTGGCGGG +GGAAGGAGGTGATGGGGAGGAGGTGAGTGGGGAGGAAGGTGGGAGGAAGGAGGTGATGGG +GAGGATGTGGGGGAGGTGGGGAGCAAGGAGGTGATGGGGAGGAGGTGAGTGGGGAGGTGG +TGAGCAGGGAGGAGGTGAGGGGGCAAGGGAGGTGATGGGGAGGAAGGAGGTTATGGGGAG +GTGGTGAGTGGGGAGGGAGGTAAGGGGTAAGGTGGTGATGTGGAGGTGGTGAGTGGGGAG +GTGGTGAGAGGGGAGGAGATGAGGGGGCAAGGGAGGTGATGGGGAGGAGGTGAGTGGGGA +GGAAGGTGGGGGGAAGGAGGTGATGGGGAGGATGTGGGGGAGGTGGGGGGGAAGGAGGTG +AGGCAGAGGAGGGGAGTGGGGAGGGAGATGAGTAAGGAAGTGATGGGGAGAGGGTGAGTG +GGGAAGTGGTGAGAGGGGAGGAGGTGAGGGGGCAAGGGAGGTGATGCGGAGGAAGGAGGT +GATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGAGGAAGGAGGTG +ATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGA +TGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGAT +GGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATG +GGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGAGGAAGGAGGTGATGG +GAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGG +AAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGA +AGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGAA +GGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGAAG +GAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGG +AGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGA +GGTGAGAGGGGAGGAGCTGAGGGGGGAAGGAGGTAATGAGGACAAGGTGAGGGGAAAGGA +GGTAAGGGAGGGGAAGGGGAGGGAAGGAGCTGAGCGGGGCAGAGCATGTCTCCTCTCTTT +AAGCATCCTCTGTATTCTGCAGAGGCCAAGCAGTCTGGATGTTGGCCTTCCTCAGTGGCC +CATGAAATAACTTTGCTCCCCAGATTCTGAGCATGGGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/haps.fa.ref.fa new file mode 100644 index 00000000..cfc731bd --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:59383704-59385336 +GGTTTTGTGCTTCCACCAAGCCAGGGGACTGTTCTGTGGCCCTGGAACCACCGTGAAAGCAAACAACCCTCGGCTGTGTTGGGAGACAGCTCCAGCTCCTCCATCCTCAAATGTGAGAGCTGATGATTGGGGTGGAGGAGGAGGTGAGTGGGGAGGGGGTGGGGGAGAAGGAGGTGATGGGGAAGAGATGAGTGGGCAGGAGGTGAGCAGGGAGGAGGTGAGCAGGGATGAGTGGAGGAAGGAGGTGATAGGGAGGAGGTGAGTGGGCAGGAGGTGAGCAGGGAGAAGATGAGCAGGGGGGTGGTGAGCGGGGAGGAGGTGGAGGGGAAGGAAGTGATGGGGGAGGAGGTGGGGGGAAGGAGGTGATGGGGAGGAGGTGAATGGGCAGGAGGTGACTGGGGAGGAGGTGAGCAGGGAGGAGGTGAGCAGGGAGGAGGTGAGTGGAGTGGGGATGGGAGTGGAGTGGCGGGAAGGAAGTGATAGGGAGGAGATGAGTGGGCAGGAGGTGAGCAGAGAGGAGATGAGTAGAGCAGGGATGAGTAGGGGAAGGAGGTGATAGGAGGTGAGTGGGCAGGAGGTGAGCAGGGAGGAGGCGAGCAGGGAGGAGGTAGAGGGGAAGGAAGTGATGGGGAGGAGGTGAGGGGGGAAAGAGGTGGCGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGGGGAGGAAGGTGGGGGGAAGGAGGTGATAGGGAGGATGTGGGGGAGGTGGGGGGGAAGGAGGTGAGGCAGAGGAGGGGAGTGGGGAGGGAGATGAGTAAGGAAGTGATGGGGAGAGGGTGAGTGGGGAAGTGGTGAGAGGGGAGGAGGTGAGGGGGCAAGGGAGGCGATGCGGAGGAAGGAGGTGATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGAAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGTGTGTAGGAGGTAAGCAGGGAGGAAGTGGGGGGGAAGGAGGTGATGGGGAGGAGGTGAGAGGGGAGGAGCTGAGTGGGGAAGGAGGTAATGAGGACAAGGTGAGGGGAAAGGAGGTAAGGGAGGGGAAGGGGAGGGAAGGAGCTGAGCGGGGCAGAGCATGTCTCCTCTCTTTAAGCATCCTCTGTATTCTGCAGAGGCCAAGCAGTCTGGATGTTGGCCTTCCTCAGTGGCCCATGAAATAACTTTGCTCCCCAGATTCTGAGCATGGGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/msa.fa new file mode 100644 index 00000000..2a7799a9 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/msa.fa @@ -0,0 +1,180 @@ +>ref_chr20_59383704_59385336 +ggttttgtgcttccaccaagccaggggactgttctgtggccctggaaccaccgtgaaagc +aaacaaccctcggctgtgttgggagacagctccagctcctccatcctcaaatgtgagagc +tgatgattggggtggaggaggaggtgagtggggagggggtgggggagaaggaggtgatgg +ggaagagatgagtgggcaggaggtgagcagggaggaggtgagcagggatgagtggaggaa +ggaggtgatagggaggaggtgagtgggcaggaggtgagcagggagaagatgagcaggggg +gtggtgagcggggaggaggtggaggggaaggaagtgatgggggaggaggtggggggaagg +aggtgatggggaggaggtgaatgggcaggaggtgactggggaggaggtgagcagggagga +ggtgagcagggaggaggtgagtggagtggggatgggagtggagtggcgggaaggaagtga +tagggaggagatgagtgggcaggaggtgagcagagaggagatgagtagagcagggatgag +taggggaaggaggtgataggaggtgagtgggcaggaggtgagcagggaggaggcgagcag +ggaggaggtagaggggaaggaagtgatggggaggaggtgaggggggaaagaggtggcggg +ggaa-------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------ggaggtgatggggaggaggtgagtgggg +aggaaggtggggggaaggaggtgatagggaggatgtgggggaggtgggggggaaggaggt +gaggcagaggaggggagtggggagggagatgagtaaggaagtgatggggagagggtgagt +ggggaagtggtgagaggggaggaggtgagggggcaagggaggcgatgcgga--------- +------------------------------------------------------------ +-------------------------------------------------ggaaggaggtg +atgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtga +tggggaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgat +ggggaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatg +gggaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgg +gaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggg +gaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgggg +aggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgggga +ggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggag +gaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggagg +aggtgagaggggaggagctgagtggggaaggaggtaatgaggacaaggtgaggggaaagg +aggtaagggaggggaaggggagggaaggagctgagcggggcagagcatgtctcctctctt +taagcatcctctgtattctgcagaggccaagcagtctggatgttggccttcctcagtggc +ccatgaaataactttgctccccagattctgagcatgggt +>syndip_1_chr20:59383704-59385336 +ggttttgtgcttccaccaagccaggggactgttctgtggccctggaaccaccgtgaaagc +aaacaaccctcggctgtgttgggagacagctccagctcctccatcctcaaatgtgagagc +tgatgattggggtggaggaggaggtgagtggggagggggtgggggagaaggaggtgatgg +ggaagagatgagtgggcaggaggtgagcagggaggaggtgagcagggatgagtggaggaa +ggaggtgatagggaggaggtgagtgggcaggaggtgagcagggagaagatgagcaggggg +gtggtgagcggggaggaggtggaggggaaggaagtgatgggggaggaggtggggggaagg +aggtgatggggaggaggtgaatgggcaggaggtgactggggaggaggtgagcagggagga +ggtgagcagggaggaggtgagtggagtggggatgggagtggagtggggggaaggaagtga +tagggaggagatgagtgggcaggaggtgagcagagaggagatgagtagagcagggatgag +taggggaaggaggtgataggaggtgagtgggcaggaggtgagcagggaggaggcgagcag +ggaggaggtagaggggaaggaagtgatggggaggaggtgaggggggaaagaggtggcggg +ggaaggaggtgatggggaggaggtgagtggggaggaaggtgggaggaaggaggtgatggg +gaggatgtgggggaggtggggagcaaggaggtgatggggaggaggtgagtggggaggtgg +tgagca------------------------------------------------------ +-------gggaggaggtgagggggcaagggaggtgatggggaggaaggaggttatgggga +ggtggtgagtggggagggaggtaaggggtaaggtggtgatgtggaggtggtgagtgggga +ggtggtgagaggggaggagatgagggggcaagggaggtgatggggaggaggtgagtgggg +aggaaggtggggggaaggaggtgatggggaggatgtgggggaggtgggggggaaggaggt +gaggcagaggaggggagtggggagggagatgagtaaggaagtgatggggagagggtgagt +ggggaagtggtgagaggggaggaggtgagggggcaagggaggtgatgcggaggaaggagg +tgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtggggaggaaggaggt +gatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtg +atgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtga +tgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgat +gggaaggaggtgagtgtgtaggaggtaagcagggaggaagtggggaggaaggaggtgatg +ggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgg +gaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggg +aaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggga +aggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgggaa +ggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggag +gaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggagg +aggtgagaggggaggagctgaggggggaaggaggtaatgaggacaaggtgaggggaaagg +aggtaagggaggggaaggggagggaaggagctgagcggggcagagcatgtctcctctctt +taagcatcctctgtattctgcagaggccaagcagtctggatgttggccttcctcagtggc +ccatgaaataactttgctccccagattctgagcatgggt +>syndip_2_chr20:59383704-59385336 +ggttttgtgcttccaccaagccaggggactgttctgtggccctggaaccaccgtgaaagc +aaacaaccctcggctgtgttgggagacagctccagctcctccatcctcaaatgtgagagc +tgatgattggggtggaggaggaggtgagtggggagggggtgggggagaaggaggtgatgg +ggaagagatgagtgggcaggaggtgagcagggaggaggtgagcagggatgagtggaggaa +ggaggtgatagggaggaggtgagtgggcaggaggtgagcagggagaagatgagcaggggg +gtggtgagcggggaggaggtggaggggaaggaagtgatgggggaggaggtggggggaagg +aggtgatggggaggaggtgaatgggcaggaggtgactggggaggaggtgagcagggagga +ggtgagcagggaggaggtgagtggagtggggatgggagtggagtggggggaaggaagtga +tagggaggagatgagtgggcaggaggtgagcagagaggagatgagtagagcagggatgag +taggggaaggaggtgataggaggtgagtgggcaggaggtgagcagggaggaggcgagcag +ggaggaggtagaggggaaggaagtgatggggaggaggtgaggggggaaagaggtggcggg +ggaaggaggtgatggggaggaggtgagtggggaggaaggtgggaggaaggaggtgatggg +gaggatgtgggggaggtggggagcaaggaggtgatggggaggaggtgagtggggaggtgg +tgagcagggaggaggtgagggggcaagggaggtgatggggaggaggtgagtggggaggtg +gtgagcggggaggaggtgagggggcaagggaggtgatggggaggaaggaggttatgggga +ggtggtgagtggggagggaggtaaggggtaaggtggtgatgtggaggtggtgagtgggga +ggtggtgagaggggaggagatgagggggcaagggaggtgatggggaggaggtgagtgggg +aggaaggtggggggaaggaggtgatggggaggatgtgggggaggtgggggggaaggaggt +gaggcagaggaggggagtggggagggagatgagtaaggaagtgatggggagagggtgagt +ggggaagtggtgagaggggaggaggtgagggggcaagggaggcgatgcgga--------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------------------ggaaggaggtgat +gggaaggaggtgagtgtgtaggaggtaagcagggaggaagtggggaggaaggaggtgatg +ggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgg +gaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggg +gaggaggtgagtgtgtaggaggtaagcagggaggaagtggggaggaaggaggtgatggga +aggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgggaa +ggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggag +gaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggagg +aggtgagaggggaggagctgaggggggaaggaggtaatgaggacaaggtgaggggaaagg +aggtaagggaggggaaggggagggaaggagctgagcggggcagagcatgtctcctctctt +taagcatcctctgtattctgcagaggccaagcagtctggatgttggccttcctcagtggc +ccatgaaataactttgctccccagattctgagcatgggt +>p:HG002_1_chr20:59383704-59385336 +ggttttgtgcttccaccaagccaggggactgttctgtggccctggaaccaccgtgaaagc +aaacaaccctcggctgtgttgggagacagctccagctcctccatcctcaaatgtgagagc +tgatgattggggtggaggaggaggtgagtggggagggggtgggggagaaggaggtgatgg +ggaagagatgagtgggcaggaggtgagcagggaggaggtgagcagggatgagtggaggaa +ggaggtgatagggaggaggtgagtgggcaggaggtgagcagggagaagatgagcaggggg +gtggtgagcggggaggaggtggaggggaaggaagtgatgggggaggaggtggggggaagg +aggtgatggggaggaggtgaatgggcaggaggtgactggggaggaggtgagcagggagga +ggtgagcagggaggaggtgagtggagtggggatgggagtggagtggggggaaggaagtga +tagggaggagatgagtgggcaggaggtgagcagagaggagatgagtagagcagggatgag +taggggaaggaggtgataggaggtgagtgggcaggaggtgagcagggaggaggcgagcag +ggaggaggtagaggggaaggaagtgatggggaggaggtgaggggggaaagaggtggcggg +ggaaggaggtgatggggaggaggtgagtggggaggaaggtgggaggaaggaggtgatggg +gaggatgtgggggaggtggggagcaaggaggtgatggggaggaggtgagtggggaggtgg +tgagcagggaggaggtgagggggcaagggaggtgatggggaggaggtgagtggggaggtg +gtgagcggggaggaggtgagggggcaagggaggtgatggggaggaaggaggttatgggga +ggtggtgagtggggagggaggtaaggggtaaggtggtgatgtggaggtggtgagtgggga +ggtggtgagaggggaggagatgagggggcaagggaggtgatggggaggaggtgagtgggg +aggaaggtggggggaaggaggtgatggggaggatgtgggggaggtgggggggaaggaggt +gaggcagaggaggggagtggggagggagatgagtaaggaagtgatggggagagggtgagt +ggggaagtggtgagaggggaggaggtgagggggcaagggaggcgatgcgga--------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------------------ggaaggaggtgat +gggaaggaggtgagtgtgtaggaggtaagcagggaggaagtggggaggaaggaggtgatg +ggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgg +gaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggg +gaggaggtgagtgtgtaggaggtaagcagggaggaagtggggaggaaggaggtgatggga +aggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgggaa +ggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggag +gaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggagg +aggtgagaggggaggagctgaggggggaaggaggtaatgaggacaaggtgaggggaaagg +aggtaagggaggggaaggggagggaaggagctgagcggggcagagcatgtctcctctctt +taagcatcctctgtattctgcagaggccaagcagtctggatgttggccttcctcagtggc +ccatgaaataactttgctccccagattctgagcatgggt +>p:HG002_2_chr20:59383704-59385336 +ggttttgtgcttccaccaagccaggggactgttctgtggccctggaaccaccgtgaaagc +aaacaaccctcggctgtgttgggagacagctccagctcctccatcctcaaatgtgagagc +tgatgattggggtggaggaggaggtgagtggggagggggtgggggagaaggaggtgatgg +ggaagagatgagtgggcaggaggtgagcagggaggaggtgagcagggatgagtggaggaa +ggaggtgatagggaggaggtgagtgggcaggaggtgagcagggagaagatgagcaggggg +gtggtgagcggggaggaggtggaggggaaggaagtgatgggggaggaggtggggggaagg +aggtgatggggaggaggtgaatgggcaggaggtgactggggaggaggtgagcagggagga +ggtgagcagggaggaggtgagtggagtggggatgggagtggagtggggggaaggaagtga +tagggaggagatgagtgggcaggaggtgagcagagaggagatgagtagagcagggatgag +taggggaaggaggtgataggaggtgagtgggcaggaggtgagcagggaggaggcgagcag +ggaggaggtagaggggaaggaagtgatggggaggaggtgaggggggaaagaggtggcggg +ggaaggaggtgatggggaggaggtgagtggggaggaaggtgggaggaaggaggtgatggg +gaggatgtgggggaggtggggagcaaggaggtgatggggaggaggtgagtggggaggtgg +tgagca------------------------------------------------------ +-------gggaggaggtgagggggcaagggaggtgatggggaggaaggaggttatgggga +ggtggtgagtggggagggaggtaaggggtaaggtggtgatgtggaggtggtgagtgggga +ggtggtgagaggggaggagatgagggggcaagggaggtgatggggaggaggtgagtgggg +aggaaggtggggggaaggaggtgatggggaggatgtgggggaggtgggggggaaggaggt +gaggcagaggaggggagtggggagggagatgagtaaggaagtgatggggagagggtgagt +ggggaagtggtgagaggggaggaggtgagggggcaagggaggtgatgcggaggaaggagg +tgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtggggaggaaggaggt +gatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtg +atgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtga +tgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgat +gggaaggaggtgagtgtgtaggaggtaagcagggaggaagtggggaggaaggaggtgatg +ggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgg +gaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggg +aaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggga +aggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgggaa +ggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggag +gaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggagg +aggtgagaggggaggagctgaggggggaaggaggtaatgaggacaaggtgaggggaaagg +aggtaagggaggggaaggggagggaaggagctgagcggggcagagcatgtctcctctctt +taagcatcctctgtattctgcagaggccaagcagtctggatgttggccttcctcagtggc +ccatgaaataactttgctccccagattctgagcatgggt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/msa.fa.fai new file mode 100644 index 00000000..ad0f1da2 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_59383704_59385336 2079 29 60 61 +syndip_1_chr20:59383704-59385336 2079 2177 60 61 +syndip_2_chr20:59383704-59385336 2079 4325 60 61 +p:HG002_1_chr20:59383704-59385336 2079 6474 60 61 +p:HG002_2_chr20:59383704-59385336 2079 8623 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/output.vcf.gz new file mode 100644 index 00000000..561129ad Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/output.vcf.gz.tbi new file mode 100644 index 00000000..e73b2069 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:59383804-59385236/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/base.vcf.gz new file mode 100644 index 00000000..f0839186 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/base.vcf.gz.tbi new file mode 100644 index 00000000..8c742550 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/comp.vcf.gz new file mode 100644 index 00000000..cd50a9fa Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/comp.vcf.gz.tbi new file mode 100644 index 00000000..febc2168 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/haps.fa new file mode 100644 index 00000000..dee6dd9b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/haps.fa @@ -0,0 +1,132 @@ +>ref_chr20_60314230_60315121 +ACTTGTTTCCTCATTTATTCATTAACAATATTCATTTCTTAGCCAAGGATGGTGGTGCACACCTGTACTTCCAGCTACTCAGGAGGCTGAGGTGGAAGGATTGAAAATCCATCCATCTGTCCTCCTACCCATCCTGCTATCCATCCATCCATCCATCCTCCCATAATCTATCTTCCCATCCATTTGTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCTTCCTTCCTTCCTTCCTTCCTTCCTTCCACCCATCCATCCTCCCATTCATCCTCCCATGCATCCTCCCATCCATCCACCCAACCATCCTCCCATCCATCCTCACATCGATCTTCGCATCCATCCATCGATCGATCTATCCATCCATCCATTCTCCCATTCATCCATCCTCCCATCCATCCTCCTATCCATCCATCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCCACCCTTCCATCCATCCATCCACCCACCCTTCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCTATCCATCCATCCTCCCATCCTCCCATCCTCCCATCCATCCATCCATCCATCCATCCATCCTCCCATCCTCCCATCCTCCCATCCATCGTCCCATGTGTACATCTGTCCTGCCATCTATCCATACATCCATTTCTCCGTCCTCCCATCCATCTTCCCATCCATTCATCCATCCATCTTCCCATCCATTCATCCATCCATCCTGCCATCCATCCTTCCATTGATCCATCCATCCATCCTGCAGGAGACCAGGAGTTCAAGGCTGCCGTGAGTTATAATTGTGCCACTGCACTACAGCTTAAGTGACAGAGAGAGAAACCATCTCCAAAAATGAAAAAAAGAATATATTGATTTCAGGCCAGTTACATAGA +>syndip_1_chr20:60314230-60315121 +ACTTGTTTCCTCATTTATTCATTAACAATATTCATTTCTTAGCCAAGGATGGTGGTGCAC +ACCTGTACTTCCAGCTACTCAGGAGGCTGAGGTGGAAGGATTGAAAATCCATCCATCTGT +CCTCCTACCCATCCTGCTATCCATCCATCCATCCATCCTCCCATAATCTATCTTCCCATC +CATTTGTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC +CACCCATCCATCCTCCCATTCATCCTCCCATGCATCCTCCCATCCATCCACCCAACCATC +CTCCCATCCATCCTCACATCCATCTTCGCATCCATCCATCCATCCATCTATCCATCCATC +CATCCATCCTCCCATCCATCCTCCCATCCATTATCCCATTCATCCATCCTCCCATCCATC +CTCCTATCCATCCATCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCCACT +CTTCCATCCATCCATCCACCCACCCTTCCATCCATCCATCCTCCCATCCATCCATCCTCC +CATTCATCTATCCATCCATCCCTCGATCCTCCCATCCATCCATCCTCCCATCCATCCATC +CATCCTCCCATCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCTACCCTCC +CATCCATCCATCCTCCCACCCACCCTCCCATCCATCCATCCTCCCATCCTCCCATCCATC +CATCCATCCTCCCATCCGTCCATCCATCCTTCCATCCACCCTCCCATCCATCCATCCTCC +CATCCATCTACCCTCCCATCCATCCATCCTCCCACCCACCCTCCCATCCATCCACCCTCC +CATCCATCCATCCTCCCATCCATCTATCCATCCATCCTCCCATCCTCCCATCCATCCATC +ATCCATCCATCCATCCATCCATCCTCCCATAATCTATCTTCCCATCCATTTGTCCTTCCT +TCCTTCCTTCCTTCCTTCCTTCCTTCGTTCCACCCATCCATCCTCCCATTCATCCTCCCA +TGCATCCTCCCATCCATCCACCCAACCATCCTCCCATCCATCCTCACATCCATCTTCGCA +TCCATCCATCCATCCATCCATCTATCCATCCATCCTCCCATCCATCCTCCCATCCTCCCA +TCCATTCTCCCATTCATCCATCCTCCCATCCATCCTCCTATCCATCCATCCATCCATCCA +CCCTCCCATCCATCCATCCTCCCATCCATCCACCCTTCCATCCATCCATCCACCCACCCT +TCCATCCATCCACCCTCCCATCCATCCATCCTCCCATTCATCTATCCATCCATCCCTCGA +TCCTCCCATCCATCCATCCATCCTCCCATCCGTCCATCCATCCTTCCATCCACCCTCCCA +TCCATCCATCCTCCCATCCATCTACCCTCCCATCCATCCATCCTCCCACCCACCCTCCCA +TCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCTATCCATCCATCCTCCCATCCT +CCCATCCTCCCATCCATCCATCCATCCATCCATCCATCCTCCCATCCTCCCATCCTCCCA +TCCATCGTCCCATGTGTACATCTGTCCTGCCATCTATCCATACATCCATTTCTCCGTCCT +CCCATCCATCTTCCCATCCATTCATCCATCCATCTTCCCATCCATTCATCCATCCATCCT +GCCATCCATCCTTCCATTGATCCATCCATCCATCCTGCAGGAGACCAGGAGTTCAAGGCT +GCCGTGAGTTATAATTGTGCCACTGCACTACAGCTTAAGTGACAGAGAGAGAAACCATCT +CCAAAAATGAAAAAAAGAATATATTGATTTCAGGCCAGTTACATAGA +>syndip_2_chr20:60314230-60315121 +ACTTGTTTCCTCATTTATTCATTAACAATATTCATTTCTTAGCCAAGGATGGTGGTGCAC +ACCTGTACTTCCAGCTACTCAGGAGGCTGAGGTGGAAGGATTGAAAATCCATCCATCTGT +CGTCCTACCCATCCTGCTATCCATCCATCCATCCATCCTCCCATAATCTATCTTCCCATC +CATTTGTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCACCCATCCATCCTCCCATG +CATCCTCCCATGCATCCTCCCATCCATCCACCCAACCATCCTCCCATCCATCCTCACATC +CATCTTCGCATCCATCCATCCATCCATCTATCCATCCATCCATCCATCCTCCCATCCATC +CTCCCATCCATTATCCCATTCATCCATCCTCCCATCCATCCTCCTATCCATCCATCCATC +CATCCACCCTCTCATCCATCCATCCTCCCATCCATCCACCCTTCCATCCATCCATCCACC +CACCCTTCCATCCATCCATCCTCCCATCCATCCATCCTCCCATCCATCCATCCTCCCATT +CATCTATCCATCCATCCCTCGATCCTCCCATCCATCCATCCTCCCATCCATCCATCCATC +CTCCCATCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCTACCCTCCCATC +CATCCATCCTCCCATCCACCCTCCCATCCATCCATCCATCCATCCACCCTCTCATCCATC +CATCCTCCCATCCGTCCATCCATCCTTCCATCCACCCTCCCATCCATCCATCCTCCCATC +CATCCATCCTCCCATCCATCTACCCTCCCATCCATCCATCCTCCCACCCACCCTCCCATC +CATCCACCCTCCCATCCATCCATCCTCCCATCCATCTATCCATCCATCCTCCCATCCTCC +CATCCATCCATCATCCATCCATCCATCCATCCATCCTCCCATAATCTATCTTCCCATCCA +TTTGTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCACCCATCCATCCTCCCATTCATCCT +CCCATGCATCCTCCCATCCATCCACCCAACCATCCTCCCATCCATCCTCACATCCATCTT +CGCATCCATCCATCCATCCATCCATCTATCCATCCATCCTCCCATCCATCCTCCCATCCT +CCCATCCATCCTCCCATCCTCCCATCCATTCTCCCATTCATCCATCCTCCCATCCATCCT +CCTATCCATCCATCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCCACCCT +TCCATCCATCCATCCACCCACCCTTCCATCCATCCACCCTCCCATCCATCCATCCTCCCA +TTCATCTATCCATCCATCCCTCGATCCTCCCATCCATCCATCCATCCTCCCATCCGTCCA +TCCATCCTTCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCTACCCTCCCATCCA +TCCATCCTCCCACCCACCCTCCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCA +TCTATCCATCCATCCTCCCATCCTCCCATCCTCCCATCCATCCATCCATCCATCCATCCT +CCCATCCTCCCATCCTCCCATCCATCGTCCCATGTGTACATCTGTCCTGCCATCTATCCA +TACATCCATTTCTCCGTCCTCCCATCCATCTTCCCATCCATTCATCCATCCATCTTCCCA +TCCATTCATCCATCCATCCTGCCATCCATCCTTCCATTGATCCATCCATCCATCCTGCAG +GAGACCAGGAGTTCAAGGCTGCCGTGAGTTATAATTGTGCCACTGCACTACAGCTTAAGT +GACAGAGAGAGAAACCATCTCCAAAAATGAAAAAAAGAATATATTGATTTCAGGCCAGTT +ACATAGA +>p:HG002_1_chr20:60314230-60315121 +ACTTGTTTCCTCATTTATTCATTAACAATATTCATTTCTTAGCCAAGGATGGTGGTGCAC +ACCTGTACTTCCAGCTACTCAGGAGGCTGAGGTGGAAGGATTGAAAATCCATCCATCTGT +CGTCCTACCCATCCTGCTATCCATCCATCCATCCATCCTCCCATAATCTATCTTCCCATC +CATTTGTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCACCCATCCATCCTCCCATG +CATCCTCCCATGCATCCTCCCATCCATCCACCCAACCATCCTCCCATCCATCCTCACATC +CATCTTCGCATCCATCCATCCATCCATCTATCCATCCATCCATCCATCCTCCCATCCATC +CTCCCATCCATTATCCCATTCATCCATCCTCCCATCCATCCTCCTATCCATCCATCCATC +CATCCACCCTCTCATCCATCCATCCTCCCATCCATCCACCCTTCCATCCATCCATCCACC +CACCCTTCCATCCATCCATCCTCCCATCCATCCATCCTCCCATCCATCCATCCTCCCATT +CATCTATCCATCCATCCCTCGATCCTCCCATCCATCCATCCTCCCATCCATCCATCCATC +CTCCCATCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCTACCCTCCCATC +CATCCATCCTCCCATCCACCCTCCCATCCATCCATCCATCCATCCACCCTCTCATCCATC +CATCCTCCCATCCGTCCATCCATCCTTCCATCCACCCTCCCATCCATCCATCCTCCCATC +CATCCATCCTCCCATCCATCTACCCTCCCATCCATCCATCCTCCCACCCACCCTCCCATC +CATCCACCCTCCCATCCATCCATCCTCCCATCCATCTATCCATCCATCCTCCCATCCTCC +CATCCATCCATCATCCATCCATCCATCCATCCATCCTCCCATAATCTATCTTCCCATCCA +TTTGTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCACCCATCCATCCTCCCATTCATCCT +CCCATGCATCCTCCCATCCATCCACCCAACCATCCTCCCATCCATCCTCACATCCATCTT +CGCATCCATCCATCCATCCATCCATCTATCCATCCATCCTCCCATCCATCCTCCCATCCT +CCCATCCATCCTCCCATCCTCCCATCCATTCTCCCATTCATCCATCCTCCCATCCATCCT +CCTATCCATCCATCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCCACCCT +TCCATCCATCCATCCACCCACCCTTCCATCCATCCACCCTCCCATCCATCCATCCTCCCA +TTCATCTATCCATCCATCCCTCGATCCTCCCATCCATCCATCCATCCTCCCATCCGTCCA +TCCATCCTTCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCTACCCTCCCATCCA +TCCATCCTCCCACCCACCCTCCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCA +TCTATCCATCCATCCTCCCATCCTCCCATCCTCCCATCCATCCATCCATCCATCCATCCT +CCCATCCTCCCATCCTCCCATCCATCGTCCCATGTGTACATCTGTCCTGCCATCTATCCA +TACATCCATTTCTCCGTCCTCCCATCCATCTTCCCATCCATTCATCCATCCATCTTCCCA +TCCATTCATCCATCCATCCTGCCATCCATCCTTCCATTGATCCATCCATCCATCCTGCAG +GAGACCAGGAGTTCAAGGCTGCCGTGAGTTATAATTGTGCCACTGCACTACAGCTTAAGT +GACAGAGAGAGAAACCATCTCCAAAAATGAAAAAAAGAATATATTGATTTCAGGCCAGTT +ACATAGA +>p:HG002_2_chr20:60314230-60315121 +ACTTGTTTCCTCATTTATTCATTAACAATATTCATTTCTTAGCCAAGGATGGTGGTGCAC +ACCTGTACTTCCAGCTACTCAGGAGGCTGAGGTGGAAGGATTGAAAATCCATCCATCTGT +CCTCCTACCCATCCTGCTATCCATCCATCCATCCATCCTCCCATAATCTATCTTCCCATC +CATTTGTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC +CACCCATCCATCCTCCCATTCATCCTCCCATGCATCCTCCCATCCATCCACCCAACCATC +CTCCCATCCATCCTCACATCCATCTTCGCATCCATCCATCCATCCATCTATCCATCCATC +CATCCATCCTCCCATCCATCCTCCCATCCATTATCCCATTCATCCATCCTCCCATCCATC +CTCCTATCCATCCATCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCCACT +CTTCCATCCATCCATCCACCCACCCTTCCATCCATCCATCCTCCCATCCATCCATCCTCC +CATTCATCTATCCATCCATCCCTCGATCCTCCCATCCATCCATCCTCCCATCCATCCATC +CATCCTCCCATCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCTACCCTCC +CATCCATCCATCCTCCCACCCACCCTCCCATCCATCCATCCTCCCATCCTCCCATCCATC +CATCCATCCTCCCATCCGTCCATCCATCCTTCCATCCACCCTCCCATCCATCCATCCTCC +CATCCATCTACCCTCCCATCCATCCATCCTCCCACCCACCCTCCCATCCATCCACCCTCC +CATCCATCCATCCTCCCATCCATCTATCCATCCATCCTCCCATCCTCCCATCCATCCATC +ATCCATCCATCCATCCATCCATCCTCCCATAATCTATCTTCCCATCCATTTGTCCTTCCT +TCCTTCCTTCCTTCCTTCCTTCCTTCGTTCCACCCATCCATCCTCCCATTCATCCTCCCA +TGCATCCTCCCATCCATCCACCCAACCATCCTCCCATCCATCCTCACATCCATCTTCGCA +TCCATCCATCCATCCATCCATCTATCCATCCATCCTCCCATCCATCCTCCCATCCTCCCA +TCCATTCTCCCATTCATCCATCCTCCCATCCATCCTCCTATCCATCCATCCATCCATCCA +CCCTCCCATCCATCCATCCTCCCATCCATCCACCCTTCCATCCATCCATCCACCCACCCT +TCCATCCATCCACCCTCCCATCCATCCATCCTCCCATTCATCTATCCATCCATCCCTCGA +TCCTCCCATCCATCCATCCATCCTCCCATCCGTCCATCCATCCTTCCATCCACCCTCCCA +TCCATCCATCCTCCCATCCATCTACCCTCCCATCCATCCATCCTCCCACCCACCCTCCCA +TCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCTATCCATCCATCCTCCCATCCT +CCCATCCTCCCATCCATCCATCCATCCATCCATCCATCCTCCCATCCTCCCATCCTCCCA +TCCATCGTCCCATGTGTACATCTGTCCTGCCATCTATCCATACATCCATTTCTCCGTCCT +CCCATCCATCTTCCCATCCATTCATCCATCCATCTTCCCATCCATTCATCCATCCATCCT +GCCATCCATCCTTCCATTGATCCATCCATCCATCCTGCAGGAGACCAGGAGTTCAAGGCT +GCCGTGAGTTATAATTGTGCCACTGCACTACAGCTTAAGTGACAGAGAGAGAAACCATCT +CCAAAAATGAAAAAAAGAATATATTGATTTCAGGCCAGTTACATAGA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/haps.fa.ref.fa new file mode 100644 index 00000000..0898f1f1 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:60314230-60315121 +ACTTGTTTCCTCATTTATTCATTAACAATATTCATTTCTTAGCCAAGGATGGTGGTGCACACCTGTACTTCCAGCTACTCAGGAGGCTGAGGTGGAAGGATTGAAAATCCATCCATCTGTCCTCCTACCCATCCTGCTATCCATCCATCCATCCATCCTCCCATAATCTATCTTCCCATCCATTTGTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCTTCCTTCCTTCCTTCCTTCCTTCCTTCCACCCATCCATCCTCCCATTCATCCTCCCATGCATCCTCCCATCCATCCACCCAACCATCCTCCCATCCATCCTCACATCGATCTTCGCATCCATCCATCGATCGATCTATCCATCCATCCATTCTCCCATTCATCCATCCTCCCATCCATCCTCCTATCCATCCATCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCCACCCTTCCATCCATCCATCCACCCACCCTTCCATCCATCCACCCTCCCATCCATCCATCCTCCCATCCATCTATCCATCCATCCTCCCATCCTCCCATCCTCCCATCCATCCATCCATCCATCCATCCATCCTCCCATCCTCCCATCCTCCCATCCATCGTCCCATGTGTACATCTGTCCTGCCATCTATCCATACATCCATTTCTCCGTCCTCCCATCCATCTTCCCATCCATTCATCCATCCATCTTCCCATCCATTCATCCATCCATCCTGCCATCCATCCTTCCATTGATCCATCCATCCATCCTGCAGGAGACCAGGAGTTCAAGGCTGCCGTGAGTTATAATTGTGCCACTGCACTACAGCTTAAGTGACAGAGAGAGAAACCATCTCCAAAAATGAAAAAAAGAATATATTGATTTCAGGCCAGTTACATAGA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/msa.fa new file mode 100644 index 00000000..41bb252a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/msa.fa @@ -0,0 +1,165 @@ +>ref_chr20_60314230_60315121 +acttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgcac +acctgtacttccagctactcaggaggctgaggtggaaggattgaaa-------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-atccatccatctgtcctcctacccatc---ctgctatccatccatccatccatcctccc +ataatctatcttcccatccatttgtccttccttccttccttccttccttcc--------t +tct---------------------tccttccttccttccttccttccttccacccatcca +tcctcccattcatcctcccatgcatcctc----ccatccatccacccaaccatcctccca +tccatcctcacatcgatcttcgcatccatccatcgatcgatctatccatccatccattct +cccattcatccatcctcccatccatcctcctatccatccatccatccatccaccctccca +tccatccatcctcccatccatccacccttccatccatccatccacccacccttccatcca +tccaccctcccatccatccatcctcccat------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------ccatctatccatccatcctcccatcctcccatcct +cccatccatccatccatccatccatccatcctcccatcctcccatcctcccatccatcgt +cccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctcccatcca +tcttcccatccattcatccatccatcttcccatccattcatccatccatcctgccatcca +tccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccgtgag +ttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaaaaat +gaaaaaaagaatatattgatttcaggccagttacataga +>syndip_1_chr20:60314230-60315121 +acttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgcac +acctgtacttccagctactcaggaggctgaggtggaaggattgaaaatccatccatctgt +cctcctacccatcctgctatccatccatccatccatcctcccataatctatcttcccatc +catttgtccttccttccttccttccttccttccttccttccttccttccttccttccttc +cacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaaccatc +ctcccatccatcctcacatccatcttcgcatccatccatccatccatctatccatccatc +catccatcctcccatccatcctcccatccattatcccattcatccatcctcccatccatc +ctcctatccatccatccatccatccaccctcccatccatccatcctcccatccatccact +cttccatccatccatccacccaccctt----------------ccatccatccatcctcc +catccatccatcctcccattcatctatccatccatccctcgatcctcccatccatccatc +ctcccatccatccatccatcctcccatccatccatccaccctcccatccatccatcctcc +catccatctaccctcccatccatccatcctcccacccaccctcccatccatccatcctcc +catcctcccatccatccatccatcctcccatccgtccatccatccttccatccac----- +-----------cctcccatccatccatcctcccatccatctaccctcccatccatccatc +ctcccacccaccctcccatccatccaccctcccatccatccatcctcccatccatctatc +catccatcctcccatcctcccatccatccatcatccatccatccatccatccatcctccc +ataatctatcttcccatccatttgtccttccttccttccttccttccttccttccttcgt +tccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaacca +tcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatctatcca +t--------------------ccatcctcccatccatcctcccatcctcccatccattct +cccattcatccatcctcccatccatcctcctatccatccatccatccatccaccctccca +tccatccatcctcccatccatccacccttccatccatccatccacccacccttccatcca +tccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcctccca +tccatccatccatcctcccatccgtccatccatccttccatccaccctcccatccatcca +tcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatccatcca +ccctcccatccatccatcctcccatccatctatccatccatcctcccatcctcccatcct +cccatccatccatccatccatccatccatcctcccatcctcccatcctcccatccatcgt +cccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctcccatcca +tcttcccatccattcatccatccatcttcccatccattcatccatccatcctgccatcca +tccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccgtgag +ttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaaaaat +gaaaaaaagaatatattgatttcaggccagttacataga +>syndip_2_chr20:60314230-60315121 +acttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgcac +acctgtacttccagctactcaggaggctgaggtggaaggattgaaaatccatccatctgt +cgtcctacccatcctgctatccatccatccatccatcctcccataatctatcttcccatc +catttg--------------------tccttccttccttccttccttccttccttccttc +cacccatccatcctcccatgcatcctcccatgcatcctcccatccatccacccaaccatc +ctcccatccatcctcacatccatcttcgcatccatccatccatccatctatccatccatc +catccatcctcccatccatcctcccatccattatcccattcatccatcctcccatccatc +ctcctatccatccatccatccatccaccctctcatccatccatcctcccatccatccacc +cttccatccatccatccacccacccttccatccatccatcctcccatccatccatcctcc +catccatccatcctcccattcatctatccatccatccctcgatcctcccatccatccatc +ctcccatccatccatccatcctcccatccatccatccaccctcccatccatccatcctcc +catccatctaccctcccatccatccatcctcccatccaccctcccatccatccatccatc +catccaccctctcatccatccatcctcccatccgtccatccatccttccatccaccctcc +catccatccatcctcccatccatccatcctcccatccatctaccctcccatccatccatc +ctcccacccaccctcccatccatccaccctcccatccatccatcctcccatccatctatc +catccatcctcccatcctcccatccatccatcatccatccatccatccatccatcctccc +ataatctatcttcccatccatttgtccttccttccttccttccttccttcc--------t +tccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaacca +tcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatctatcca +tccatcctcccatccatcctcccatcctcccatccatcctcccatcctcccatccattct +cccattcatccatcctcccatccatcctcctatccatccatccatccatccaccctccca +tccatccatcctcccatccatccacccttccatccatccatccacccacccttccatcca +tccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcctccca +tccatccatccatcctcccatccgtccatccatccttccatccaccctcccatccatcca +tcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatccatcca +ccctcccatccatccatcctcccatccatctatccatccatcctcccatcctcccatcct +c----ccatccatccatccatccatccatcctcccatcctcccatcctcccatccatcgt +cccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctcccatcca +tcttcccatccattcatccatccatcttcccatccattcatccatccatcctgccatcca +tccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccgtgag +ttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaaaaat +gaaaaaaagaatatattgatttcaggccagttacataga +>p:HG002_1_chr20:60314230-60315121 +acttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgcac +acctgtacttccagctactcaggaggctgaggtggaaggattgaaaatccatccatctgt +cgtcctacccatcctgctatccatccatccatccatcctcccataatctatcttcccatc +catttg--------------------tccttccttccttccttccttccttccttccttc +cacccatccatcctcccatgcatcctcccatgcatcctcccatccatccacccaaccatc +ctcccatccatcctcacatccatcttcgcatccatccatccatccatctatccatccatc +catccatcctcccatccatcctcccatccattatcccattcatccatcctcccatccatc +ctcctatccatccatccatccatccaccctctcatccatccatcctcccatccatccacc +cttccatccatccatccacccacccttccatccatccatcctcccatccatccatcctcc +catccatccatcctcccattcatctatccatccatccctcgatcctcccatccatccatc +ctcccatccatccatccatcctcccatccatccatccaccctcccatccatccatcctcc +catccatctaccctcccatccatccatcctcccatccaccctcccatccatccatccatc +catccaccctctcatccatccatcctcccatccgtccatccatccttccatccaccctcc +catccatccatcctcccatccatccatcctcccatccatctaccctcccatccatccatc +ctcccacccaccctcccatccatccaccctcccatccatccatcctcccatccatctatc +catccatcctcccatcctcccatccatccatcatccatccatccatccatccatcctccc +ataatctatcttcccatccatttgtccttccttccttccttccttccttcc--------t +tccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaacca +tcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatctatcca +tccatcctcccatccatcctcccatcctcccatccatcctcccatcctcccatccattct +cccattcatccatcctcccatccatcctcctatccatccatccatccatccaccctccca +tccatccatcctcccatccatccacccttccatccatccatccacccacccttccatcca +tccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcctccca +tccatccatccatcctcccatccgtccatccatccttccatccaccctcccatccatcca +tcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatccatcca +ccctcccatccatccatcctcccatccatctatccatccatcctcccatcctcccatcct +c----ccatccatccatccatccatccatcctcccatcctcccatcctcccatccatcgt +cccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctcccatcca +tcttcccatccattcatccatccatcttcccatccattcatccatccatcctgccatcca +tccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccgtgag +ttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaaaaat +gaaaaaaagaatatattgatttcaggccagttacataga +>p:HG002_2_chr20:60314230-60315121 +acttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgcac +acctgtacttccagctactcaggaggctgaggtggaaggattgaaaatccatccatctgt +cctcctacccatcctgctatccatccatccatccatcctcccataatctatcttcccatc +catttgtccttccttccttccttccttccttccttccttccttccttccttccttccttc +cacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaaccatc +ctcccatccatcctcacatccatcttcgcatccatccatccatccatctatccatccatc +catccatcctcccatccatcctcccatccattatcccattcatccatcctcccatccatc +ctcctatccatccatccatccatccaccctcccatccatccatcctcccatccatccact +cttccatccatccatccacccaccctt----------------ccatccatccatcctcc +catccatccatcctcccattcatctatccatccatccctcgatcctcccatccatccatc +ctcccatccatccatccatcctcccatccatccatccaccctcccatccatccatcctcc +catccatctaccctcccatccatccatcctcccacccaccctcccatccatccatcctcc +catcctcccatccatccatccatcctcccatccgtccatccatccttccatccac----- +-----------cctcccatccatccatcctcccatccatctaccctcccatccatccatc +ctcccacccaccctcccatccatccaccctcccatccatccatcctcccatccatctatc +catccatcctcccatcctcccatccatccatcatccatccatccatccatccatcctccc +ataatctatcttcccatccatttgtccttccttccttccttccttccttccttccttcgt +tccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaacca +tcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatctatcca +t--------------------ccatcctcccatccatcctcccatcctcccatccattct +cccattcatccatcctcccatccatcctcctatccatccatccatccatccaccctccca +tccatccatcctcccatccatccacccttccatccatccatccacccacccttccatcca +tccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcctccca +tccatccatccatcctcccatccgtccatccatccttccatccaccctcccatccatcca +tcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatccatcca +ccctcccatccatccatcctcccatccatctatccatccatcctcccatcctcccatcct +cccatccatccatccatccatccatccatcctcccatcctcccatcctcccatccatcgt +cccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctcccatcca +tcttcccatccattcatccatccatcttcccatccattcatccatccatcctgccatcca +tccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccgtgag +ttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaaaaat +gaaaaaaagaatatattgatttcaggccagttacataga diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/msa.fa.fai new file mode 100644 index 00000000..877f09b4 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_60314230_60315121 1899 29 60 61 +syndip_1_chr20:60314230-60315121 1899 1994 60 61 +syndip_2_chr20:60314230-60315121 1899 3959 60 61 +p:HG002_1_chr20:60314230-60315121 1899 5925 60 61 +p:HG002_2_chr20:60314230-60315121 1899 7891 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/output.vcf.gz new file mode 100644 index 00000000..07913de7 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/output.vcf.gz.tbi new file mode 100644 index 00000000..d010bf61 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60314330-60315021/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/base.vcf.gz new file mode 100644 index 00000000..029e3318 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/base.vcf.gz.tbi new file mode 100644 index 00000000..c308e66f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/comp.vcf.gz new file mode 100644 index 00000000..d1686daa Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/comp.vcf.gz.tbi new file mode 100644 index 00000000..0dbaca72 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/haps.fa new file mode 100644 index 00000000..51c2a48b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/haps.fa @@ -0,0 +1,36 @@ +>ref_chr20_60702842_60703216 +TATGGTAACTGCATGTTGACTCTTTTGAGGAGCTTCCAGACTGTTTTTCAAAGTGATGGCACAATTTTCCTTTCCCCTCAATAATGTATGAGGGTTGCAATGTCGCTACATATTACCAACATTTGTCATTGTCTTTCTTTCTTTTCTTTCTCTCTCTCTCTTTCTTTTCCTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTTCTTTCCTTCTTTCTTTCTTTCTTTCTTTCTTTTTTTTTGGGATGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCATGATCTCGGCTCGCTGCAATCTCCACCTCCCAGGTTCAAGCGATTGAACTCACTGCCTCAGCCTCCCAAGTAGCTG +>syndip_1_chr20:60702842-60703216 +TATGGTAACTGCATGTTGACTCTTTTGAGGAGCTTCCAGACTGTTTTTCAAAGTGATGGC +ACAATTTTCCTTTCCCCTCAATAATGTATGAGGGTTGCAATGTCGCTACATATTACCAAC +ATTTGTCATTGTCTTTCTTTCTTTTCTTTCTCTCTCTCTCTTTCTTTTCCTTCTTTCTTT +CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTTCTTTCCTTCTT +CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT +CTTTCTTTCTTTCTTTCTTCTTTCTTTCTTTTTCTTTCTTTTTTTTTTGGGATGGAGTCT +CGCTCTGTCACCCAGGCTGGAGTGCAGTGGCATGATCTCGGCTCGCTGCAATCTCCACCT +CCCAGGTTCAAGCGATTGAACTCACTGCCTCAGCCTCCCAAGTAGCTG +>syndip_2_chr20:60702842-60703216 +TATGGTAACTGCATGTTGACTCTTTTGAGGAGCTTCCAGACTGTTTTTCAAAGTGATGGC +ACAATTTTCCTTTCCCCTCAATAATGTATGAGGGTTGCAATGTCGCTACATATTACCAAC +ATTTGTCATTGTCTTTCTTTCTTTTCTTTCTCTCTCTCTCTCTCTTTCTTTTCCTTCTTT +CTTTCTTTCTTTCTTTCTTTCTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT +CTTTCTTTTCTTTCCTTCTTTCTTTCTTTCTTTCTTTTTTTTTGGGATGGAGTCTCGCTC +TGTCACCCAGGCTGGAGTGCAGTGGCATGATCTCGGCTCGCTGCAATCTCCACCTCCCAG +GTTCAAGCGATTGAACTCACTGCCTCAGCCTCCCAAGTAGCTG +>p:HG002_1_chr20:60702842-60703216 +TATGGTAACTGCATGTTGACTCTTTTGAGGAGCTTCCAGACTGTTTTTCAAAGTGATGGC +ACAATTTTCCTTTCCCCTCAATAATGTATGAGGGTTGCAATGTCGCTACATATTACCAAC +ATTTGTCATTGTCTTTCTTTCTTTTCTTTCTCTCTCTCTCTCTCTTTCTTTTCCTTCTTT +CTTTCTTTCTTTCTTTCTTTCTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT +CTTTCTTTTCTTTCCTTCTTTCTTTCTTTCTTTCTTTTTTTTTGGGATGGAGTCTCGCTC +TGTCACCCAGGCTGGAGTGCAGTGGCATGATCTCGGCTCGCTGCAATCTCCACCTCCCAG +GTTCAAGCGATTGAACTCACTGCCTCAGCCTCCCAAGTAGCTG +>p:HG002_2_chr20:60702842-60703216 +TATGGTAACTGCATGTTGACTCTTTTGAGGAGCTTCCAGACTGTTTTTCAAAGTGATGGC +ACAATTTTCCTTTCCCCTCAATAATGTATGAGGGTTGCAATGTCGCTACATATTACCAAC +ATTTGTCATTGTCTTTCTTTCTTTTCTTTCTCTCTCTCTCTTTCTTTTCCTTCTTTCTTT +CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTTCTTTCCTTCTT +CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT +CTTTCTTTCTTTCTTTCTTCTTTCTTTCTTTTTCTTTCTTTTTTTTTTGGGATGGAGTCT +CGCTCTGTCACCCAGGCTGGAGTGCAGTGGCATGATCTCGGCTCGCTGCAATCTCCACCT +CCCAGGTTCAAGCGATTGAACTCACTGCCTCAGCCTCCCAAGTAGCTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/haps.fa.ref.fa new file mode 100644 index 00000000..9562d46b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:60702842-60703216 +TATGGTAACTGCATGTTGACTCTTTTGAGGAGCTTCCAGACTGTTTTTCAAAGTGATGGCACAATTTTCCTTTCCCCTCAATAATGTATGAGGGTTGCAATGTCGCTACATATTACCAACATTTGTCATTGTCTTTCTTTCTTTTCTTTCTCTCTCTCTCTTTCTTTTCCTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTTCTTTCCTTCTTTCTTTCTTTCTTTCTTTCTTTTTTTTTGGGATGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCATGATCTCGGCTCGCTGCAATCTCCACCTCCCAGGTTCAAGCGATTGAACTCACTGCCTCAGCCTCCCAAGTAGCTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/msa.fa new file mode 100644 index 00000000..40d84d0e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/msa.fa @@ -0,0 +1,45 @@ +>ref_chr20_60702842_60703216 +tatggtaactgcatgttgactcttttgaggagcttccagactgtttttcaaagtgatggc +acaattttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaac +atttgtcattgtctttctttcttttctttctctctctctctttct--------------- +-------------tttccttctttctttctttctttctttctttctttctttctttcttt +cttttc---tttccttctttctttctttctttctttc----------------------- +---------------------------------------tttttttttgggatggagtct +cgctctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatctccacct +cccaggttcaagcgattgaactcactgcctcagcctcccaagtagctg +>syndip_1_chr20:60702842-60703216 +tatggtaactgcatgttgactcttttgaggagcttccagactgtttttcaaagtgatggc +acaattttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaac +atttgtcattgtctttctttcttttctttctctctctctctttcttttccttctttcttt +ctttctttctttctttctttctttctttctttctttctttctttcttttctttccttctt +ctttctttctttctttctttctttctttctttctttctttctttctttctttctttcttt +ctttctttctttctttcttctttctttctttttctttcttttttttttgggatggagtct +cgctctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatctccacct +cccaggttcaagcgattgaactcactgcctcagcctcccaagtagctg +>syndip_2_chr20:60702842-60703216 +tatggtaactgcatgttgactcttttgaggagcttccagactgtttttcaaagtgatggc +acaattttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaac +atttgtcattgtctttctttcttttctttctctctctctctctctttcttttccttcttt +ctttctttctttctttctttcttcctttctttctttctttctttctttctttctttcttt +ctttct---tttctttccttctttctttctttctttc----------------------- +---------------------------------------tttttttttgggatggagtct +cgctctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatctccacct +cccaggttcaagcgattgaactcactgcctcagcctcccaagtagctg +>p:HG002_1_chr20:60702842-60703216 +tatggtaactgcatgttgactcttttgaggagcttccagactgtttttcaaagtgatggc +acaattttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaac +atttgtcattgtctttctttcttttctttctctctctctctctctttcttttccttcttt +ctttctttctttctttctttcttcctttctttctttctttctttctttctttctttcttt +ctttct---tttctttccttctttctttctttctttc----------------------- +---------------------------------------tttttttttgggatggagtct +cgctctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatctccacct +cccaggttcaagcgattgaactcactgcctcagcctcccaagtagctg +>p:HG002_2_chr20:60702842-60703216 +tatggtaactgcatgttgactcttttgaggagcttccagactgtttttcaaagtgatggc +acaattttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaac +atttgtcattgtctttctttcttttctttctctctctctctttcttttccttctttcttt +ctttctttctttctttctttctttctttctttctttctttctttcttttctttccttctt +ctttctttctttctttctttctttctttctttctttctttctttctttctttctttcttt +ctttctttctttctttcttctttctttctttttctttcttttttttttgggatggagtct +cgctctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatctccacct +cccaggttcaagcgattgaactcactgcctcagcctcccaagtagctg diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/msa.fa.fai new file mode 100644 index 00000000..dee59e9d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_60702842_60703216 468 29 60 61 +syndip_1_chr20:60702842-60703216 468 539 60 61 +syndip_2_chr20:60702842-60703216 468 1049 60 61 +p:HG002_1_chr20:60702842-60703216 468 1560 60 61 +p:HG002_2_chr20:60702842-60703216 468 2071 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/output.vcf.gz new file mode 100644 index 00000000..8ac2ccc9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/output.vcf.gz.tbi new file mode 100644 index 00000000..9227d7c8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:60702942-60703116/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/base.vcf.gz new file mode 100644 index 00000000..d718a1dc Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/base.vcf.gz.tbi new file mode 100644 index 00000000..f031f869 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/comp.vcf.gz new file mode 100644 index 00000000..3385d7e7 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/comp.vcf.gz.tbi new file mode 100644 index 00000000..46b5445c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/haps.fa new file mode 100644 index 00000000..b9e89818 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/haps.fa @@ -0,0 +1,154 @@ +>ref_chr20_61100692_61102788 +TTGGTACATGTACAGATTGTGCAAGACAATAGGACACCAGACAGATCCCCGGGCTCCACAGCAGAAGTCTGGTTACTGGGCAGGCAGGCCCCAAACACTGTATTTAAAACAAAACCCCACTGACAAGTCCTGTGACTGGAGAGACCCCGAGTGAAGGCAGACCTCCATGTCCTCTACATCCTGTGCCACATCTGGAGAGACCCCTGTGAGGGCAGAGAGCTACCTCCTCTTCTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCGGATGGCCACGTCTTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTACTTCCTGTGTCACACCTGGGGAGACCCTGAGTGAGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAGAGACCCCAAGAGAGGGCAGACAGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCGGATGGCCACGTCTTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTACTTCCTGTGTCACACCTGGGGAGACCCTGAGTGAGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAGAGACCCCAAGAGAGGGCAGACAGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACTCCAAGTGAGGAGAGACGGCCACATCTTCTACTTCCTGTGTCACACCTGGAGAGACCTCGAGTGAGGGCAGATGGCCACATCCTCTAATTCCTGTGTCACACCTGGAGAGACCCCAAGTGAGGGCAGACTGCCACCTCCTCTACTTCCTGTGTCACACCTAGAGAGACCCCGAGTGAGGACAGCCAGCCATGTCCTCTACTTCCTGTGCCACATCCGGAGAGATCCCGAGTGAGGGCAGACAGCCATGTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTGTCATGCCTGGAGAGACCCCGAGTGAGGGCATATGGCCACATCCTCTAATTCCTATGTCACACCTGGAGAGACCCCGAGTGAGGGTGGATGGCCACATCCTCTAATTCCTGTGTCATACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCAAGTGAGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAGAGACCCCGATGAGGGCAGACAGCTACCCCCTCTACTTCCTGTGTCACACCTGCAGAGACCCCAAGTGAGGGCAGATGGCCACCTCTTCTACTTCCTGTGTCACACCTGGAGAGGCCCCGAGTGAGGGCAGACGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTATTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTGTCACACATGGAGAGACCCCGAGTGAGGGCAGAAGGCCACATCCTCTACTTCCTGTGTCACACCTAGAGAGACCCCGAGTGAGGGCGGATGGCCACATCCTCTAATTCCTGTGTCACACCTGGGGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTAATTCCTGTGTCACACCTGGAGACACACAGAGTAAAGGTGGACAGCCACCTCCTCTACGTCCTGTGCCACACCTGGAGACACCCTGAGTTAAGGCAGATGGCCACCTCCTCTAATTATTTTTAAGAACTTTTTTGGGGTATAATTTACATGCCAGAAAGTTCACCCATTTCAAGCATATGATTCAATATTAAAGCTTAAAAATGTTATCAATTTAATAACATTGATGGTTACAGAGCTGTGTAA +>syndip_1_chr20:61100692-61102788 +TTGGTACATGTACAGATTGTGCAAGACAATAGGACACCAGACAGATCCCCGGGCTCCACA +GCAGAAGTCTGGTTACTGGGCAGGCAGGCCCCAAACACTGTATTTAAAACAAAACCCCAC +TGACAAGTCCTGTGACTGGAGAGACCCCGAGTGAAGGCAGACCTCCATGTCCTCTACATC +CTGTGCCACATCTGGAGAGACCCCTGTGAGGGCAGAGAGCTACCTCCTCTTCTTCCTGTG +TCACACCTGGAGAGACCCCGAGTGAGGGCGGATGGCCACGTCTTCTACTTCCTGTGTCAC +ACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTACTTCCTGTGTCACACCT +GGGGAGACCCTGAGTGAGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAG +AGACCCCAAGAGAGGGCAGACAGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGAC +CCCGAGTGAGGGCGGATGGCCACGTCTTCTACTTCCTGTGTCACACCTGGAGAGACCCCG +AGTGAGGGCAGATGGCCACATCCTCTACTTCCTGTGTCACACCTGGGGAGACCCTGAGTG +AGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAGAGACCCCAAGAGAGGG +CAGACAGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACTCCAAGTGAGGAGAGA +CGGCCACGTCTTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGTGGATGGC +CACATCCTCTAATTCCTGTGTCATACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACC +TCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACTGCCACCTCCT +CTACTTCCTGTGTCACACCTAGAGAGACCCCGAGTGAGGACAGCCAGCCATGTCCTCTAC +TTCCTGTGCCACATCCGGAGAGATCCCGAGTGAGGGCAGACAGCCATGTCCTCTACTTCC +TGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTG +TCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACCTCCTCTACTTCCTGTGTCAC +ACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTGTCATGCCT +GGAGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTAATTCCTATGTCACACCTGGAG +AGACCCCGAGTGAGGGTGGATGGCCACATCCTCTAATTCCTGTGTCATACCTGGAGAGAC +CCCGAGTGAGGGCAGATGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCG +AGTGAGGGCAGATGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCAAGTG +AGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAGAGACCCCGATGAGGGC +AGACAGCTACCCCCTCTACTTCCTGTGTCACACCTGCAGAGACCCCAAGTGAGGGCAGAT +GGCCACCTCTTCTACTTCCTGTGTCACACCTGGAGAGGCCCCGAGTGAGGGCAGACGGCC +ACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACAT +CCTCTATTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTC +TAATTCCTGTGTCACACATGGAGAGACCCCGAGTGAGGGCAGAAGGCCACATCCTCTACT +TCCTGTGTCACACCTAGAGAGACCCCGAGTGAGGGCGGATGGCCACATCCTCTAATTCCT +GTGTCACACCTGGGGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTAATTCCTGTGT +CACACCTGGAGACACACAGAGTAAAGGTGGACAGCCACCTCCTCTACGTCCTGTGCCACA +CCTGGAGACACCCTGAGTTAAGGCAGATGGCCACCTCCTCTAATTATTTTTAAGAACTTT +TTTGGGGTATAATTTACATGCCAGAAAGTTCACCCATTTCAAGCATATGATTCAATATTA +AAGCTTAAAAATGTTATCAATTTAATAACATTGATGGTTACAGAGCTGTGTAA +>syndip_2_chr20:61100692-61102788 +TTGGTACATGTACAGATTGTGCAAGACAATAGGACACCAGACAGATCCCCGGGCTCCACA +GCAGAAGTCTGGTTACTGGGCAGGCAGGCCCCAAACACTGTATTTAAAACAAAACCCCAC +TGACAAGTCCTGTGACTGGAGAGACCCCGAGTGAAGGCAGACCTCCATGTCCTCTACATC +CTGTGCCACATCTGGAGAGACCCCTGTGAGGGCAGAGAGCTACCTCCTCTTCTTCCTGTG +TCACACCTGGAGAGACCCCGAGTGAGGGCGGATGGCCACGTCTTCTACTTCCTGTGTCAC +ACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTACTTCCTGTGTCACACCT +GGGGAGACCCTGAGTGAGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAG +AGACCCCAAGAGAGGGCAGACAGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGAC +TCCAAGTGAGGAGAGACGGCCACGTCTTCTACTTCCTGTGTCACACCTGGAGAGACCTCG +AGTGAGGGCAGATGGCCACATCCTCTAATTCCTGTGTCACACCTGGAGAAACCCCAAGTG +AGGGCAGACTGCCACCTCCTCTACTTCCTGTGTCACACCTAGAGAGACCCCGAGTGAGGA +CAGCCAGCCATGTCCTCTACTTCCTGTGCCACATCCGGAGAGATCCCGAGTGAGGGCAGA +CAGCCATGTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACAGC +CACATCCTCTAATTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCTACA +TCCTCTAATTCCTGTGTCATGCCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACATCCT +CTAATTCCTATGTCACACCTGGAGAGACCCCGAGTGAGGGTGGATGGCCACATCCTCTAA +TTCCTGTGTCATACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACCTCCTCTACTTCC +TGTGTCACACCTGGAGAGACCCCAAGTGAGGGCAGACAGCCATGTCCTCTACGTCCTGTG +CCACATCCGGAGAGACCCCGATGAGGGCAGACAGCTACCCCCTCTACTTCCTGTGTCACA +CCTGCAGAGACCCCAAGTGAGGGCAGATGGCCACCTCTTCTACTTCCTGTGTCACACCTG +GAGAGGCCCCGAGTGAGGGCAGACGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGA +GACCCCGAGTGAGGGCAGACGGCCACATCCTCTATTTCCTGTGTCACACCTGGAGAGACC +CCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTGTCACACATGGAGAGACCCCGA +GTGAAGGCAGAAGGCCACATCCTCTACTTCCTGTGTCACACCTAGAGAGACCCCGAGTGA +GGGCGGATGGCCACATCCTCTAATTCCTATGTCACACCTGGAGAGACCCCGAGTGAGGGT +GGATGGCCACATCCTCTAATTCCTGTGTCATACCTGGAGAGACCCCGAGTGAGGGCAGAT +GGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCAAGTGAGGGCAGACAGCC +ATGTCCTCTACGTCCTGTGCCACATCCGGAGAGACCCCGATGAGGGCAGACAGCTACCCC +CTCTACTTCCTGTGTCACACCTGCAGAGACCCCAAGTGAGGGCAGATGGCCACCTCTTCT +ACTTCCTGTGTCACACCTGGAGAGGCCCCGAGTGAGGGCAGACGGCCACCTCCTCTACTT +CCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTG +TGTCACACATGGAGAGACCCTGAGTGAGGGCAGAAGGCCACATCCTCTACTTCCTGTGTC +ACACCTAGAGAGACCCCGAGTGAGGGCGGATGGCCACATCCTCTAATTCCTGTGTCACAC +CTGGGGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTGTCACACCTGG +AGACACACAGAGTAAAGGTGGACAGCCACCTCCTCTACGTCCTGTGCCACACCTGGAGAC +ACCCTGAGTTAAGGCAGATGGCCACCTCCTCTAATTATTTTTAAGAACTTTTTTGGGGTA +TAATTTACATGCCAGAAAGTTCACCCATTTCAAGCATATGATTCAATATTAAAGCTTAAA +AATGTTATCAATTTAATAACATTGATGGTTACAGAGCTGTGTAA +>p:HG002_1_chr20:61100692-61102788 +TTGGTACATGTACAGATTGTGCAAGACAATAGGACACCAGACAGATCCCCGGGCTCCACA +GCAGAAGTCTGGTTACTGGGCAGGCAGGCCCCAAACACTGTATTTAAAACAAAACCCCAC +TGACAAGTCCTGTGACTGGAGAGACCCCGAGTGAAGGCAGACCTCCATGTCCTCTACATC +CTGTGCCACATCTGGAGAGACCCCTGTGAGGGCAGAGAGCTACCTCCTCTTCTTCCTGTG +TCACACCTGGAGAGACCCCGAGTGAGGGCGGATGGCCACGTCTTCTACTTCCTGTGTCAC +ACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTACTTCCTGTGTCACACCT +GGGGAGACCCTGAGTGAGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAG +AGACCCCAAGAGAGGGCAGACAGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGAC +TCCAAGTGAGGAGAGACGGCCACGTCTTCTACTTCCTGTGTCACACCTGGAGAGACCTCG +AGTGAGGGCAGATGGCCACATCCTCTAATTCCTGTGTCACACCTGGAGAAACCCCAAGTG +AGGGCAGACTGCCACCTCCTCTACTTCCTGTGTCACACCTAGAGAGACCCCGAGTGAGGA +CAGCCAGCCATGTCCTCTACTTCCTGTGCCACATCCGGAGAGATCCCGAGTGAGGGCAGA +CAGCCATGTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACAGC +CACATCCTCTAATTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCTACA +TCCTCTAATTCCTGTGTCATGCCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACATCCT +CTAATTCCTATGTCACACCTGGAGAGACCCCGAGTGAGGGTGGATGGCCACATCCTCTAA +TTCCTGTGTCATACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACCTCCTCTACTTCC +TGTGTCACACCTGGAGAGACCCCAAGTGAGGGCAGACAGCCATGTCCTCTACGTCCTGTG +CCACATCCGGAGAGACCCCGATGAGGGCAGACAGCTACCCCCTCTACTTCCTGTGTCACA +CCTGCAGAGACCCCAAGTGAGGGCAGATGGCCACCTCTTCTACTTCCTGTGTCACACCTG +GAGAGGCCCCGAGTGAGGGCAGACGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGA +GACCCCGAGTGAGGGCAGACGGCCACATCCTCTATTTCCTGTGTCACACCTGGAGAGACC +CCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTGTCACACATGGAGAGACCCCGA +GTGAAGGCAGAAGGCCACATCCTCTACTTCCTGTGTCACACCTAGAGAGACCCCGAGTGA +GGGCGGATGGCCACATCCTCTAATTCCTATGTCACACCTGGAGAGACCCCGAGTGAGGGT +GGATGGCCACATCCTCTAATTCCTGTGTCATACCTGGAGAGACCCCGAGTGAGGGCAGAT +GGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCAAGTGAGGGCAGACAGCC +ATGTCCTCTACGTCCTGTGCCACATCCGGAGAGACCCCGATGAGGGCAGACAGCTACCCC +CTCTACTTCCTGTGTCACACCTGCAGAGACCCCAAGTGAGGGCAGATGGCCACCTCTTCT +ACTTCCTGTGTCACACCTGGAGAGGCCCCGAGTGAGGGCAGACGGCCACCTCCTCTACTT +CCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTG +TGTCACACATGGAGAGACCCTGAGTGAGGGCAGAAGGCCACATCCTCTACTTCCTGTGTC +ACACCTAGAGAGACCCCGAGTGAGGGCGGATGGCCACATCCTCTAATTCCTGTGTCACAC +CTGGGGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTGTCACACCTGG +AGACACACAGAGTAAAGGTGGACAGCCACCTCCTCTACGTCCTGTGCCACACCTGGAGAC +ACCCTGAGTTAAGGCAGATGGCCACCTCCTCTAATTATTTTTAAGAACTTTTTTGGGGTA +TAATTTACATGCCAGAAAGTTCACCCATTTCAAGCATATGATTCAATATTAAAGCTTAAA +AATGTTATCAATTTAATAACATTGATGGTTACAGAGCTGTGTAA +>p:HG002_2_chr20:61100692-61102788 +TTGGTACATGTACAGATTGTGCAAGACAATAGGACACCAGACAGATCCCCGGGCTCCACA +GCAGAAGTCTGGTTACTGGGCAGGCAGGCCCCAAACACTGTATTTAAAACAAAACCCCAC +TGACAAGTCCTGTGACTGGAGAGACCCCGAGTGAAGGCAGACCTCCATGTCCTCTACATC +CTGTGCCACATCTGGAGAGACCCCTGTGAGGGCAGAGAGCTACCTCCTCTTCTTCCTGTG +TCACACCTGGAGAGACCCCGAGTGAGGGCGGATGGCCACGTCTTCTACTTCCTGTGTCAC +ACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTACTTCCTGTGTCACACCT +GGGGAGACCCTGAGTGAGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAG +AGACCCCAAGAGAGGGCAGACAGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGAC +CCCGAGTGAGGGCGGATGGCCACGTCTTCTACTTCCTGTGTCACACCTGGAGAGACCCCG +AGTGAGGGCAGATGGCCACATCCTCTACTTCCTGTGTCACACCTGGGGAGACCCTGAGTG +AGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAGAGACCCCAAGAGAGGG +CAGACAGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACTCCAAGTGAGGAGAGA +CGGCCACGTCTTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGTGGATGGC +CACATCCTCTAATTCCTGTGTCATACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACC +TCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACTGCCACCTCCT +CTACTTCCTGTGTCACACCTAGAGAGACCCCGAGTGAGGACAGCCAGCCATGTCCTCTAC +TTCCTGTGCCACATCCGGAGAGATCCCGAGTGAGGGCAGACAGCCATGTCCTCTACTTCC +TGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTG +TCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACCTCCTCTACTTCCTGTGTCAC +ACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTGTCATGCCT +GGAGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTAATTCCTATGTCACACCTGGAG +AGACCCCGAGTGAGGGTGGATGGCCACATCCTCTAATTCCTGTGTCATACCTGGAGAGAC +CCCGAGTGAGGGCAGATGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCG +AGTGAGGGCAGATGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCAAGTG +AGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAGAGACCCCGATGAGGGC +AGACAGCTACCCCCTCTACTTCCTGTGTCACACCTGCAGAGACCCCAAGTGAGGGCAGAT +GGCCACCTCTTCTACTTCCTGTGTCACACCTGGAGAGGCCCCGAGTGAGGGCAGACGGCC +ACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACAT +CCTCTATTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTC +TAATTCCTGTGTCACACATGGAGAGACCCCGAGTGAGGGCAGAAGGCCACATCCTCTACT +TCCTGTGTCACACCTAGAGAGACCCCGAGTGAGGGCGGATGGCCACATCCTCTAATTCCT +GTGTCACACCTGGGGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTAATTCCTGTGT +CACACCTGGAGACACACAGAGTAAAGGTGGACAGCCACCTCCTCTACGTCCTGTGCCACA +CCTGGAGACACCCTGAGTTAAGGCAGATGGCCACCTCCTCTAATTATTTTTAAGAACTTT +TTTGGGGTATAATTTACATGCCAGAAAGTTCACCCATTTCAAGCATATGATTCAATATTA +AAGCTTAAAAATGTTATCAATTTAATAACATTGATGGTTACAGAGCTGTGTAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/haps.fa.ref.fa new file mode 100644 index 00000000..b7f9ff19 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:61100692-61102788 +TTGGTACATGTACAGATTGTGCAAGACAATAGGACACCAGACAGATCCCCGGGCTCCACAGCAGAAGTCTGGTTACTGGGCAGGCAGGCCCCAAACACTGTATTTAAAACAAAACCCCACTGACAAGTCCTGTGACTGGAGAGACCCCGAGTGAAGGCAGACCTCCATGTCCTCTACATCCTGTGCCACATCTGGAGAGACCCCTGTGAGGGCAGAGAGCTACCTCCTCTTCTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCGGATGGCCACGTCTTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTACTTCCTGTGTCACACCTGGGGAGACCCTGAGTGAGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAGAGACCCCAAGAGAGGGCAGACAGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCGGATGGCCACGTCTTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTACTTCCTGTGTCACACCTGGGGAGACCCTGAGTGAGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAGAGACCCCAAGAGAGGGCAGACAGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACTCCAAGTGAGGAGAGACGGCCACATCTTCTACTTCCTGTGTCACACCTGGAGAGACCTCGAGTGAGGGCAGATGGCCACATCCTCTAATTCCTGTGTCACACCTGGAGAGACCCCAAGTGAGGGCAGACTGCCACCTCCTCTACTTCCTGTGTCACACCTAGAGAGACCCCGAGTGAGGACAGCCAGCCATGTCCTCTACTTCCTGTGCCACATCCGGAGAGATCCCGAGTGAGGGCAGACAGCCATGTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTGTCATGCCTGGAGAGACCCCGAGTGAGGGCATATGGCCACATCCTCTAATTCCTATGTCACACCTGGAGAGACCCCGAGTGAGGGTGGATGGCCACATCCTCTAATTCCTGTGTCATACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGATGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCAAGTGAGGGCAGACAGCCATGTCCTCTACGTCCTGTGCCACATCCGGAGAGACCCCGATGAGGGCAGACAGCTACCCCCTCTACTTCCTGTGTCACACCTGCAGAGACCCCAAGTGAGGGCAGATGGCCACCTCTTCTACTTCCTGTGTCACACCTGGAGAGGCCCCGAGTGAGGGCAGACGGCCACCTCCTCTACTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTATTTCCTGTGTCACACCTGGAGAGACCCCGAGTGAGGGCAGACGGCCACATCCTCTAATTCCTGTGTCACACATGGAGAGACCCCGAGTGAGGGCAGAAGGCCACATCCTCTACTTCCTGTGTCACACCTAGAGAGACCCCGAGTGAGGGCGGATGGCCACATCCTCTAATTCCTGTGTCACACCTGGGGAGACCCCGAGTGAGGGCAGATGGCCACATCCTCTAATTCCTGTGTCACACCTGGAGACACACAGAGTAAAGGTGGACAGCCACCTCCTCTACGTCCTGTGCCACACCTGGAGACACCCTGAGTTAAGGCAGATGGCCACCTCCTCTAATTATTTTTAAGAACTTTTTTGGGGTATAATTTACATGCCAGAAAGTTCACCCATTTCAAGCATATGATTCAATATTAAAGCTTAAAAATGTTATCAATTTAATAACATTGATGGTTACAGAGCTGTGTAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/msa.fa new file mode 100644 index 00000000..8a037f35 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/msa.fa @@ -0,0 +1,195 @@ +>ref_chr20_61100692_61102788 +ttggtacatgtacagattgtgcaagacaataggacaccagacagatccccgggctccaca +gcagaagtctggttactgggcaggcaggccccaaacactgtatttaaaacaaaaccccac +tgacaagtcctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatc +ctgtgccacatctggagagacccctgtgagggcagagagctacctcctcttcttcctgtg +tcacacctggagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtcac +acctggagagaccccgagtgagggcagatggccacatcctctacttcctgtgtcacacct +ggggagaccctgagtgagggcagacagccatgtcctctacgtcctgtgccacatccggag +agaccccaagagagggcagacagccacctcctctacttcctgtgtcacacctggagagac +cccgagtgagggcggatggccacgtcttctacttcctgtgtcacacctggagagaccccg +agtgagggcagatggccacatcctctacttcctgtgtcacacct---------------- +------------------------------------------------------------ +------------------------------------ggggagaccctgagtgagggcaga +cagccatgtcctctacgtcctgtgccacatccggagagaccccaagagagggcagacagc +cacctcctctacttcctgtgtcacacctggagagactccaagtgaggagagacggccaca +tcttctacttcctgtgtcacacctggagagacctcgagtgagggcagatggccacatcct +ctaa-------------------------------------------------------- +ttcctgtgtcacacctggagagaccccaagtgagggcagactgccacctcctctacttcc +tgtgtcacacctagagagaccccgagtgaggacagccagccatgtcctctacttcctgtg +ccacatccggagagatcccgagtgagggcagacagccatgtcctctacttcctgtgtcac +acctggagagaccccgagtgagggcagacggccacatcctctaattcctgtgtcacacct +ggagagaccccgagtgagggcagacggccacctcctctacttcctgtgtcacacctggag +agaccccgagtgagggcagacggccacatcctctaattcctgtgtcatgcctggagagac +cccgagtgagggcatatggccacatcctctaattcctatgtcacacctggagagaccccg +agtgagggtggatggccacatcctctaattcctgtgtcatacctggagagaccccgagtg +agggcagatggccacctcctctacttcctgtgtcacacctggagagaccccgagtgaggg +cagatggccacctcctctacttcctgtgtcacacctggagagaccccaagtgagggcaga +cagccatgtcctctacgtcctgtgccacatccggagagaccccga-tgagggcagacagc +taccccctctacttcctgtgtcacacctgcagagaccccaagtgagggcagatggccacc +tcttctacttcctgtgtcacacctggagaggccccgagtgagggcagacggccacctcct +ctacttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctat +ttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctaattcc +tgtgtcacacatggagagaccccgagtgagggcagaaggccacatcctctacttcctgtg +tcacacctagagagaccccgagtgagggcggatggccacatcctctaattcctgtgtcac +acctggggagaccccgagtgagggcagatggccacatcctctaattcctgtgtcacacct +ggagacacacagagtaaaggtggacagccacctcctctacgtcctgtgccacacctggag +acaccctgagttaaggcagatggccacctcctctaattatttttaagaacttttttgggg +tataatttacatgccagaaagttcacccatttcaagcatatgattcaatattaaagctta +aaaatgttatcaatttaataacattgatggttacagagctgtgtaa +>syndip_1_chr20:61100692-61102788 +ttggtacatgtacagattgtgcaagacaataggacaccagacagatccccgggctccaca +gcagaagtctggttactgggcaggcaggccccaaacactgtatttaaaacaaaaccccac +tgacaagtcctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatc +ctgtgccacatctggagagacccctgtgagggcagagagctacctcctcttcttcctgtg +tcacacctggagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtcac +acctggagagaccccgagtgagggcagatggccacatcctctacttcctgtgtcacacct +ggggagaccctgagtgagggcagacagccatgtcctctacgtcctgtgccacatccggag +agaccccaagagagggcagacagccacctcctctacttcctgtgtcacacctggagagac +cccgagtgagggcggatggccacgtcttctacttcctgtgtcacacctggagagaccccg +agtgagggcagatggccacatcctctacttcctgtgtcacacct---------------- +------------------------------------------------------------ +------------------------------------ggggagaccctgagtgagggcaga +cagccatgtcctctacgtcctgtgccacatccggagagaccccaagagagggcagacagc +cacctcctctacttcctgtgtcacacctggagagactccaagtgaggagagacggccacg +tcttctacttcctgtgtcacacctggagagaccccgagtgagggtggatggccacatcct +ctaattcctgtgtcatacctggagagaccccgagtgagggcagatggccacctcctctac +ttcctgtgtcacacctggagagaccccgagtgagggcagactgccacctcctctacttcc +tgtgtcacacctagagagaccccgagtgaggacagccagccatgtcctctacttcctgtg +ccacatccggagagatcccgagtgagggcagacagccatgtcctctacttcctgtgtcac +acctggagagaccccgagtgagggcagacggccacatcctctaattcctgtgtcacacct +ggagagaccccgagtgagggcagacggccacctcctctacttcctgtgtcacacctggag +agaccccgagtgagggcagacggccacatcctctaattcctgtgtcatgcctggagagac +cccgagtgagggcagatggccacatcctctaattcctatgtcacacctggagagaccccg +agtgagggtggatggccacatcctctaattcctgtgtcatacctggagagaccccgagtg +agggcagatggccacctcctctacttcctgtgtcacacctggagagaccccgagtgaggg +cagatggccacctcctctacttcctgtgtcacacctggagagaccccaagtgagggcaga +cagccatgtcctctacgtcctgtgccacatccggagagaccccga-tgagggcagacagc +taccccctctacttcctgtgtcacacctgcagagaccccaagtgagggcagatggccacc +tcttctacttcctgtgtcacacctggagaggccccgagtgagggcagacggccacctcct +ctacttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctat +ttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctaattcc +tgtgtcacacatggagagaccccgagtgagggcagaaggccacatcctctacttcctgtg +tcacacctagagagaccccgagtgagggcggatggccacatcctctaattcctgtgtcac +acctggggagaccccgagtgagggcagatggccacatcctctaattcctgtgtcacacct +ggagacacacagagtaaaggtggacagccacctcctctacgtcctgtgccacacctggag +acaccctgagttaaggcagatggccacctcctctaattatttttaagaacttttttgggg +tataatttacatgccagaaagttcacccatttcaagcatatgattcaatattaaagctta +aaaatgttatcaatttaataacattgatggttacagagctgtgtaa +>syndip_2_chr20:61100692-61102788 +ttggtacatgtacagattgtgcaagacaataggacaccagacagatccccgggctccaca +gcagaagtctggttactgggcaggcaggccccaaacactgtatttaaaacaaaaccccac +tgacaagtcctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatc +ctgtgccacatctggagagacccctgtgagggcagagagctacctcctcttcttcctgtg +tcacacctggagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtcac +acctggagagaccccgagtgagggcagatggccacatcctctacttcctgtgtcacacct +ggggagaccctgagtgagggcagacagccatgtcctctacgtcctgtgccacatccggag +agaccccaagagagggcagacagccacctcctctacttcctgtgtcacacctggagagac +tccaagtgaggagagacggccacgtcttctacttcctgtgtcacacctggagagacctcg +agtgagggcagatggccacatcctctaattcctgtgtcacacctggagaaaccccaagtg +agggcagactgccacctcctctacttcctgtgtcacacctagagagaccccgagtgagga +cagccagccatgtcctctacttcctgtgccacatccggagagatcccgagtgagggcaga +cagccatgtcctctacttcctgtgtcacacctggagagaccccgagtgagggcagacagc +cacatcctctaattcctgtgtcacacctggagagaccccgagtgagggcagacggctaca +tcctctaattcctgtgtcatgcctggagagaccccgagtgagggcagatggccacatcct +ctaattcctatgtcacacctggagagaccccgagtgagggtggatggccacatcctctaa +ttcctgtgtcatacctggagagaccccgagtgagggcagatggccacctcctctacttcc +tgtgtcacacctggagagaccccaagtgagggcagacagccatgtcctctacgtcctgtg +ccacatccggagagaccccga-tgagggcagacagctaccccctctacttcctgtgtcac +acctgcagagaccccaagtgagggcagatggccacctcttctacttcctgtgtcacacct +ggagaggccccgagtgagggcagacggccacctcctctacttcctgtgtcacacctggag +agaccccgagtgagggcagacggccacatcctctatttcctgtgtcacacctggagagac +cccgagtgagggcagacggccacatcctctaattcctgtgtcacacatggagagaccccg +agtgaaggcagaaggccacatcctctacttcctgtgtcacacctagagagaccccgagtg +agggcggatggccacatcctctaattcctatgtcacacctggagagaccccgagtgaggg +tggatggccacatcctctaattcctgtgtcatacctggagagaccccgagtgagggcaga +tggccacctcctctacttcctgtgtcacacctggagagaccccaagtgagggcagacagc +catgtcctctacgtcctgtgccacatccggagagaccccga-tgagggcagacagctacc +ccctctacttcctgtgtcacacctgcagagaccccaagtgagggcagatggccacctctt +ctacttcctgtgtcacacctggagaggccccgagtgagggcagacggccacctcctctac +ttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctaattcc +tgtgtcacacatggagagaccctgagtgagggcagaaggccacatcctctacttcctgtg +tcacacctagagagaccccgagtgagggcggatggccacatcctctaattcctgtgtcac +acctggggagaccccgagtgagggcagacggccacatcctctaattcctgtgtcacacct +ggagacacacagagtaaaggtggacagccacctcctctacgtcctgtgccacacctggag +acaccctgagttaaggcagatggccacctcctctaattatttttaagaacttttttgggg +tataatttacatgccagaaagttcacccatttcaagcatatgattcaatattaaagctta +aaaatgttatcaatttaataacattgatggttacagagctgtgtaa +>p:HG002_1_chr20:61100692-61102788 +ttggtacatgtacagattgtgcaagacaataggacaccagacagatccccgggctccaca +gcagaagtctggttactgggcaggcaggccccaaacactgtatttaaaacaaaaccccac +tgacaagtcctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatc +ctgtgccacatctggagagacccctgtgagggcagagagctacctcctcttcttcctgtg +tcacacctggagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtcac +acctggagagaccccgagtgagggcagatggccacatcctctacttcctgtgtcacacct +ggggagaccctgagtgagggcagacagccatgtcctctacgtcctgtgccacatccggag +agaccccaagagagggcagacagccacctcctctacttcctgtgtcacacctggagagac +tccaagtgaggagagacggccacgtcttctacttcctgtgtcacacctggagagacctcg +agtgagggcagatggccacatcctctaattcctgtgtcacacctggagaaaccccaagtg +agggcagactgccacctcctctacttcctgtgtcacacctagagagaccccgagtgagga +cagccagccatgtcctctacttcctgtgccacatccggagagatcccgagtgagggcaga +cagccatgtcctctacttcctgtgtcacacctggagagaccccgagtgagggcagacagc +cacatcctctaattcctgtgtcacacctggagagaccccgagtgagggcagacggctaca +tcctctaattcctgtgtcatgcctggagagaccccgagtgagggcagatggccacatcct +ctaattcctatgtcacacctggagagaccccgagtgagggtggatggccacatcctctaa +ttcctgtgtcatacctggagagaccccgagtgagggcagatggccacctcctctacttcc +tgtgtcacacctggagagaccccaagtgagggcagacagccatgtcctctacgtcctgtg +ccacatccggagagaccccga-tgagggcagacagctaccccctctacttcctgtgtcac +acctgcagagaccccaagtgagggcagatggccacctcttctacttcctgtgtcacacct +ggagaggccccgagtgagggcagacggccacctcctctacttcctgtgtcacacctggag +agaccccgagtgagggcagacggccacatcctctatttcctgtgtcacacctggagagac +cccgagtgagggcagacggccacatcctctaattcctgtgtcacacatggagagaccccg +agtgaaggcagaaggccacatcctctacttcctgtgtcacacctagagagaccccgagtg +agggcggatggccacatcctctaattcctatgtcacacctggagagaccccgagtgaggg +tggatggccacatcctctaattcctgtgtcatacctggagagaccccgagtgagggcaga +tggccacctcctctacttcctgtgtcacacctggagagaccccaagtgagggcagacagc +catgtcctctacgtcctgtgccacatccggagagaccccga-tgagggcagacagctacc +ccctctacttcctgtgtcacacctgcagagaccccaagtgagggcagatggccacctctt +ctacttcctgtgtcacacctggagaggccccgagtgagggcagacggccacctcctctac +ttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctaattcc +tgtgtcacacatggagagaccctgagtgagggcagaaggccacatcctctacttcctgtg +tcacacctagagagaccccgagtgagggcggatggccacatcctctaattcctgtgtcac +acctggggagaccccgagtgagggcagacggccacatcctctaattcctgtgtcacacct +ggagacacacagagtaaaggtggacagccacctcctctacgtcctgtgccacacctggag +acaccctgagttaaggcagatggccacctcctctaattatttttaagaacttttttgggg +tataatttacatgccagaaagttcacccatttcaagcatatgattcaatattaaagctta +aaaatgttatcaatttaataacattgatggttacagagctgtgtaa +>p:HG002_2_chr20:61100692-61102788 +ttggtacatgtacagattgtgcaagacaataggacaccagacagatccccgggctccaca +gcagaagtctggttactgggcaggcaggccccaaacactgtatttaaaacaaaaccccac +tgacaagtcctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatc +ctgtgccacatctggagagacccctgtgagggcagagagctacctcctcttcttcctgtg +tcacacctggagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtcac +acctggagagaccccgagtgagggcagatggccacatcctctacttcctgtgtcacacct +ggggagaccctgagtgagggcagacagccatgtcctctacgtcctgtgccacatccggag +agaccccaagagagggcagacagccacctcctctacttcctgtgtcacacctggagagac +cccgagtgagggcggatggccacgtcttctacttcctgtgtcacacctggagagaccccg +agtgagggcagatggccacatcctctacttcctgtgtcacacct---------------- +------------------------------------------------------------ +------------------------------------ggggagaccctgagtgagggcaga +cagccatgtcctctacgtcctgtgccacatccggagagaccccaagagagggcagacagc +cacctcctctacttcctgtgtcacacctggagagactccaagtgaggagagacggccacg +tcttctacttcctgtgtcacacctggagagaccccgagtgagggtggatggccacatcct +ctaattcctgtgtcatacctggagagaccccgagtgagggcagatggccacctcctctac +ttcctgtgtcacacctggagagaccccgagtgagggcagactgccacctcctctacttcc +tgtgtcacacctagagagaccccgagtgaggacagccagccatgtcctctacttcctgtg +ccacatccggagagatcccgagtgagggcagacagccatgtcctctacttcctgtgtcac +acctggagagaccccgagtgagggcagacggccacatcctctaattcctgtgtcacacct +ggagagaccccgagtgagggcagacggccacctcctctacttcctgtgtcacacctggag +agaccccgagtgagggcagacggccacatcctctaattcctgtgtcatgcctggagagac +cccgagtgagggcagatggccacatcctctaattcctatgtcacacctggagagaccccg +agtgagggtggatggccacatcctctaattcctgtgtcatacctggagagaccccgagtg +agggcagatggccacctcctctacttcctgtgtcacacctggagagaccccgagtgaggg +cagatggccacctcctctacttcctgtgtcacacctggagagaccccaagtgagggcaga +cagccatgtcctctacgtcctgtgccacatccggagagaccccga-tgagggcagacagc +taccccctctacttcctgtgtcacacctgcagagaccccaagtgagggcagatggccacc +tcttctacttcctgtgtcacacctggagaggccccgagtgagggcagacggccacctcct +ctacttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctat +ttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctaattcc +tgtgtcacacatggagagaccccgagtgagggcagaaggccacatcctctacttcctgtg +tcacacctagagagaccccgagtgagggcggatggccacatcctctaattcctgtgtcac +acctggggagaccccgagtgagggcagatggccacatcctctaattcctgtgtcacacct +ggagacacacagagtaaaggtggacagccacctcctctacgtcctgtgccacacctggag +acaccctgagttaaggcagatggccacctcctctaattatttttaagaacttttttgggg +tataatttacatgccagaaagttcacccatttcaagcatatgattcaatattaaagctta +aaaatgttatcaatttaataacattgatggttacagagctgtgtaa diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/msa.fa.fai new file mode 100644 index 00000000..edbccfaf --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_61100692_61102788 2266 29 60 61 +syndip_1_chr20:61100692-61102788 2266 2367 60 61 +syndip_2_chr20:61100692-61102788 2266 4705 60 61 +p:HG002_1_chr20:61100692-61102788 2266 7044 60 61 +p:HG002_2_chr20:61100692-61102788 2266 9383 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/output.vcf.gz new file mode 100644 index 00000000..127e7386 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/output.vcf.gz.tbi new file mode 100644 index 00000000..3d8e62ce Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61100792-61102688/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/base.vcf.gz new file mode 100644 index 00000000..8a8f4d0d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/base.vcf.gz.tbi new file mode 100644 index 00000000..6c7c53a2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/comp.vcf.gz new file mode 100644 index 00000000..8e451473 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/comp.vcf.gz.tbi new file mode 100644 index 00000000..1be1e0b6 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/haps.fa new file mode 100644 index 00000000..c01008e8 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/haps.fa @@ -0,0 +1,130 @@ +>ref_chr20_61201583_61202575 +AATACAGCATATCAAAATGTATGGGATGCAGCTAAAGCAGTGCTCAGAGGACAATCTATACTACTAGAGGCTTATATTAGAAAAAAAAATTTAAATCAATAACCTAAGCTTTCACCATTAGAGAAGGAATTTCCTCACTCAGGACCCTCTGCGGATGTCGCCTCCATCCTCATCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCATGGTGTCACCTCCATCCTTACTCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTCCATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTCCATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCGTGAGTGCCAGCTCTGTCTACCCTCGGGACCCTCCATGAGTGTCTCCTCTATCTACCCTCAGGACCCTCTGTGAATGTCCTCGCCATCCATACTCCCCCCTCTTAGACCCAGACTGTTTCAGGGTTGGACACTGAGCTGTGGCCCCTGAGCCTAGCTCTTCTCCGAGCTTCTCTTGGGCACCTCTCTCTCAGACTAGGCT +>syndip_1_chr20:61201583-61202575 +AATACAGCATATCAAAATGTATGGGATGCAGCTAAAGCAGTGCTCAGAGGACAATCTATA +CTACTAGAGGCTTATATTAGAAAAAAAAATTTAAATCAATAACCTAAGCTTTCACCGTTA +GAGAAGGAATTTCCTCACTCAGGACCCTCTGCGGATGTCACCTCCATCCTCATCAGGACC +CTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCATGGTGTCACCTCCATCCTTAC +TCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTC +CATCCTCACTCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGGT +GTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTCCATCCTCACCAGGATCC +CCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAG +GACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATC +CTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCA +CCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACCAGGACCCTCCAT +GAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGG +ACCCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCGCCATCC +TCACTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCA +CCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACCAGGATCCCCTGT +AAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGG +ACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCT +CACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACC +TCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATG +GTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGAC +CCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTC +ACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCA +TCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGT +CACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTC +CATGGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCA +GGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCGTGAGTGCCAGCTCTGT +CTACCCTCGGGACCCTCCATGAGTGTCTCCTCTATCTACCCTCAGGACCCTCTGTGAATG +TCCTCGCCATCCATACTCCCCCCTCTTAGACCCAGACTGTTTCAGGGTTGGACACTGAGC +TGTGGCCCCTGAGCCTAGCTCTTCTCCGAGCTTCTCTTGGGCACCTCTCTCTCAGACTAG +GCT +>syndip_2_chr20:61201583-61202575 +AATACAGCATATCAAAATGTATGGGATGCAGCTAAAGCAGTGCTCAGAGGACAATCTATA +CTACTAGAGGCTTATATTAGAAAAAAAAATTTAAATCAATAACCTAAGCTTTCACCATTA +GAGAAGGAATTTCCTCACTCAGGACCCTCTGCGGATGTCGCCTCCATCCTCATCAGGACC +CTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCATGGTGTCACCTCCATCCTTAC +TCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGGGTGTCACCTC +CATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGT +GTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCC +TCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGGTGTCACCTCCATCCTCAC +TCAGGACCCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGGTGTCACCT +CCATCCTCACTCAGGACCCTCCATGGGTGCCACCTCCATCCTCACCAGGATCCCCTGTAA +GTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAGGACCCTC +CATGAGTGTCACCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGG +ACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCT +CACTCAGGACCCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGAGTGTCA +CCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGG +TGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACC +CTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCATGGTGTCACCTCCATCCTTAC +TCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTC +CATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGAG +TGTCACCTCCATCCTCAGGACCCTCCATGGTGTCACCTCCATCCTCAGGACCCTCCATGA +GTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGAC +CCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGGTGTCACCTCCATCCT +CACTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCAC +CTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCAT +GGTGTCACCTCCATCCTTACTCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGA +CCCTCCATGAGTGCCACCTCCATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCT +CACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACC +TCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCGTG +AGTGCCAGCTCTGTCTACCCTCGGGACCCTCCATGAGTGTCTCCTCTATCTACCCTAAGG +ACCCTCTGTGAATGTCCTCGCCATCCATACTCCCCCCTCTTAGACCCAGACTGTTTCAGG +GTTGGACACTGAGCTGTGGCCCCTGAGCCTAGCTCTTCTCCGAGCTTCTCTTGGGCACCT +CTCTCTCAGACTAGGCT +>p:HG002_1_chr20:61201583-61202575 +AATACAGCATATCAAAATGTATGGGATGCAGCTAAAGCAGTGCTCAGAGGACAATCTATA +CTACTAGAGGCTTATATTAGAAAAAAAAATTTAAATCAATAACCTAAGCTTTCACCATTA +GAGAAGGAATTTCCTCACTCAGGACCCTCTGCGGATGTCGCCTCCATCCTCATCAGGACC +CTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCATGGTGTCACCTCCATCCTTAC +TCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGGGTGTCACCTC +CATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGT +GTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCC +TCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGGTGTCACCTCCATCCTCAC +TCAGGACCCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGGTGTCACCT +CCATCCTCACTCAGGACCCTCCATGGGTGCCACCTCCATCCTCACCAGGATCCCCTGTAA +GTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAGGACCCTC +CATGAGTGTCACCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGG +ACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCT +CACTCAGGACCCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGAGTGTCA +CCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGG +TGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACC +CTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCATGGTGTCACCTCCATCCTTAC +TCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTC +CATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGAG +TGTCACCTCCATCCTCAGGACCCTCCATGGTGTCACCTCCATCCTCAGGACCCTCCATGA +GTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGAC +CCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGGTGTCACCTCCATCCT +CACTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCAC +CTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCAT +GGTGTCACCTCCATCCTTACTCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGA +CCCTCCATGAGTGCCACCTCCATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCT +CACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACC +TCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCGTG +AGTGCCAGCTCTGTCTACCCTCGGGACCCTCCATGAGTGTCTCCTCTATCTACCCTAAGG +ACCCTCTGTGAATGTCCTCGCCATCCATACTCCCCCCTCTTAGACCCAGACTGTTTCAGG +GTTGGACACTGAGCTGTGGCCCCTGAGCCTAGCTCTTCTCCGAGCTTCTCTTGGGCACCT +CTCTCTCAGACTAGGCT +>p:HG002_2_chr20:61201583-61202575 +AATACAGCATATCAAAATGTATGGGATGCAGCTAAAGCAGTGCTCAGAGGACAATCTATA +CTACTAGAGGCTTATATTAGAAAAAAAAATTTAAATCAATAACCTAAGCTTTCACCGTTA +GAGAAGGAATTTCCTCACTCAGGACCCTCTGCGGATGTCACCTCCATCCTCATCAGGACC +CTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCATGGTGTCACCTCCATCCTTAC +TCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTC +CATCCTCACTCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGGT +GTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTCCATCCTCACCAGGATCC +CCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAG +GACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATC +CTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCA +CCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACCAGGACCCTCCAT +GAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGG +ACCCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCGCCATCC +TCACTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCA +CCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACCAGGATCCCCTGT +AAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGG +ACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCT +CACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACC +TCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATG +GTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGAC +CCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTC +ACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCA +TCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGT +CACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTC +CATGGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCA +GGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCGTGAGTGCCAGCTCTGT +CTACCCTCGGGACCCTCCATGAGTGTCTCCTCTATCTACCCTCAGGACCCTCTGTGAATG +TCCTCGCCATCCATACTCCCCCCTCTTAGACCCAGACTGTTTCAGGGTTGGACACTGAGC +TGTGGCCCCTGAGCCTAGCTCTTCTCCGAGCTTCTCTTGGGCACCTCTCTCTCAGACTAG +GCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/haps.fa.ref.fa new file mode 100644 index 00000000..1cfaf0a4 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:61201583-61202575 +AATACAGCATATCAAAATGTATGGGATGCAGCTAAAGCAGTGCTCAGAGGACAATCTATACTACTAGAGGCTTATATTAGAAAAAAAAATTTAAATCAATAACCTAAGCTTTCACCATTAGAGAAGGAATTTCCTCACTCAGGACCCTCTGCGGATGTCGCCTCCATCCTCATCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCATGGTGTCACCTCCATCCTTACTCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTCCATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTCCATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCGTGAGTGCCAGCTCTGTCTACCCTCGGGACCCTCCATGAGTGTCTCCTCTATCTACCCTCAGGACCCTCTGTGAATGTCCTCGCCATCCATACTCCCCCCTCTTAGACCCAGACTGTTTCAGGGTTGGACACTGAGCTGTGGCCCCTGAGCCTAGCTCTTCTCCGAGCTTCTCTTGGGCACCTCTCTCTCAGACTAGGCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/msa.fa new file mode 100644 index 00000000..6111e523 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/msa.fa @@ -0,0 +1,165 @@ +>ref_chr20_61201583_61202575 +aatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctata +ctactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccatta +gagaaggaatttcctcactcaggaccctctgcggatgtcgcctccatcctcatcaggacc +ctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatccttac +tcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccacctc +catcctcac-caggatcccctgtaagtgtcacctccatcctcaccaggaccctccatgag +tgtcacctccatcct--------------------------------------------- +----------------------------caggaccctccatgagtgtcacctccatcctc +actcaggaccctccat------------------------------------ggtgtcac +cgccatcctcactcaggaccctccatgagtgccacctccatcctcaccaggatcccctgt +aa---------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------gtgtcacctccatcctcaccaggaccctccatgagtgt +cacctccatc----ctcaggaccctccatgagtgtcacctccatcctcactcaggaccct +ccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactc +aggaccctccatg----------------------------------ggtgtcacctcca +tcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtgt +cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctc +cgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctatctaccct +caggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccagactgttt +cagggttggacactgagctgtggcccctgagcctagctcttctccgagcttctcttgggc +acctctctctcagactaggct +>syndip_1_chr20:61201583-61202575 +aatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctata +ctactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccgtta +gagaaggaatttcctcactcaggaccctctgcggatgtcacctccatcctcatcaggacc +ctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatccttac +tcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccacctc +catcctcactcaggatcccctgtaagtgtcacctccatcctcaccaggaccctccatg-g +tgtcaccgccatcctcactcaggaccctccatgagtgccacctccatcctcaccaggatc +ccctgtaagtgtcacctccatcctcac-caggaccctccatgagtgtcacctccatc--- +-ctcaggaccctccatgagtgtcacctccatcctcactcaggaccctccat-ggtgtcac +ctccatcctcactcaggaccctccat-ggtgtcacctccatcctcactcaggaccctcca +tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctca------ +----------------------ccaggaccctccatgagtgtcacctccatcctcactca +ggaccctccatggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccat +cctcactcaggaccctccat-ggtgtcaccgccatcctca-------------------- +-----------ctcaggaccctccatgagtgtcacctccatcctcactcaggaccctcca +tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcaccagga +tcccctgtaagtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcct +cactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatg-gtgtcac +ctccatcctcaccaggatcccctgtaagtgtcacctccatcctcac-caggaccctccat +gagtgtcacctccatcctca--------------------------ctcaggaccctcca +tg-gtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcag +gaccctccat-ggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccat +cctcactcaggaccctccatg-gtgtcacctccatcctcaccaggaccctccatgagtgt +cacctccatc----ctcaggaccctccatgagtgtcacctccatcctcactcaggaccct +ccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactc +aggaccctccatg-----------------------------------gtgtcacctcca +tcctcactcaggaccctccatggtgtcacctccatcctcaccaggaccctccatgagtgt +cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctc +cgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctatctaccct +caggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccagactgttt +cagggttggacactgagctgtggcccctgagcctagctcttctccgagcttctcttgggc +acctctctctcagactaggct +>syndip_2_chr20:61201583-61202575 +aatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctata +ctactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccatta +gagaaggaatttcctcactcaggaccctctgcggatgtcgcctccatcctcatcaggacc +ctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatccttac +tcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgggtgtcacctc +catcctcac-caggatcccctgtaagtgtcacctccatcctcaccaggaccctccatgag +tgtcacctccatcctcactcaggaccctccatg-gtgtcacctccatcctcactcaggac +cctccatggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctc +actcaggaccctccatgggtgtcacctccatcctcactcaggaccctccatgggtgtcac +ctccatcctcactcaggaccctccatgggtgccacctccatcctcaccaggatcccctgt +aagtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcctcaggaccc +tccatgagtgtcacctccatcctcaggaccctccatgagtgtcacctccatcctcactca +ggaccctccatggtgtcacctccatcctcactcaggaccctccat-ggtgtcacctccat +cctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccatgagtg +tcacctccatcctcaggaccctccatgagtgtcacctccatcctcactcaggaccctcca +tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcagg +accctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatcct +tactcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccac +ctccatcctcaccaggatcccctgtaagtgtcacctccatcctcactcaggaccctccat +gagtgtcacctccatcctcaggaccctccatggtgtcacctccatcctcaggaccctcca +tgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcag +gaccctccatgggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccat +cctcactcaggaccctccatgagtgtcacctccatcctcactcaggaccctccatggtgt +cacctccatcctcactcaggaccctccatg-gtgtcacctccatcctcactcaggacact +ccatggtgtcacctccatccttactcaggaccctccatggtgtcaccgccatcctcactc +aggaccctccatgagtgccacctccatcctcaccaggatcccctgtaagtgtcacctcca +tcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtgt +cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctc +cgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctatctaccct +aaggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccagactgttt +cagggttggacactgagctgtggcccctgagcctagctcttctccgagcttctcttgggc +acctctctctcagactaggct +>p:HG002_1_chr20:61201583-61202575 +aatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctata +ctactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccatta +gagaaggaatttcctcactcaggaccctctgcggatgtcgcctccatcctcatcaggacc +ctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatccttac +tcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgggtgtcacctc +catcctcac-caggatcccctgtaagtgtcacctccatcctcaccaggaccctccatgag +tgtcacctccatcctcactcaggaccctccatg-gtgtcacctccatcctcactcaggac +cctccatggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctc +actcaggaccctccatgggtgtcacctccatcctcactcaggaccctccatgggtgtcac +ctccatcctcactcaggaccctccatgggtgccacctccatcctcaccaggatcccctgt +aagtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcctcaggaccc +tccatgagtgtcacctccatcctcaggaccctccatgagtgtcacctccatcctcactca +ggaccctccatggtgtcacctccatcctcactcaggaccctccat-ggtgtcacctccat +cctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccatgagtg +tcacctccatcctcaggaccctccatgagtgtcacctccatcctcactcaggaccctcca +tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcagg +accctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatcct +tactcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccac +ctccatcctcaccaggatcccctgtaagtgtcacctccatcctcactcaggaccctccat +gagtgtcacctccatcctcaggaccctccatggtgtcacctccatcctcaggaccctcca +tgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcag +gaccctccatgggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccat +cctcactcaggaccctccatgagtgtcacctccatcctcactcaggaccctccatggtgt +cacctccatcctcactcaggaccctccatg-gtgtcacctccatcctcactcaggacact +ccatggtgtcacctccatccttactcaggaccctccatggtgtcaccgccatcctcactc +aggaccctccatgagtgccacctccatcctcaccaggatcccctgtaagtgtcacctcca +tcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtgt +cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctc +cgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctatctaccct +aaggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccagactgttt +cagggttggacactgagctgtggcccctgagcctagctcttctccgagcttctcttgggc +acctctctctcagactaggct +>p:HG002_2_chr20:61201583-61202575 +aatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctata +ctactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccgtta +gagaaggaatttcctcactcaggaccctctgcggatgtcacctccatcctcatcaggacc +ctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatccttac +tcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccacctc +catcctcactcaggatcccctgtaagtgtcacctccatcctcaccaggaccctccatg-g +tgtcaccgccatcctcactcaggaccctccatgagtgccacctccatcctcaccaggatc +ccctgtaagtgtcacctccatcctcac-caggaccctccatgagtgtcacctccatc--- +-ctcaggaccctccatgagtgtcacctccatcctcactcaggaccctccat-ggtgtcac +ctccatcctcactcaggaccctccat-ggtgtcacctccatcctcactcaggaccctcca +tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctca------ +----------------------ccaggaccctccatgagtgtcacctccatcctcactca +ggaccctccatggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccat +cctcactcaggaccctccat-ggtgtcaccgccatcctca-------------------- +-----------ctcaggaccctccatgagtgtcacctccatcctcactcaggaccctcca +tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcaccagga +tcccctgtaagtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcct +cactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatg-gtgtcac +ctccatcctcaccaggatcccctgtaagtgtcacctccatcctcac-caggaccctccat +gagtgtcacctccatcctca--------------------------ctcaggaccctcca +tg-gtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcag +gaccctccat-ggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccat +cctcactcaggaccctccatg-gtgtcacctccatcctcaccaggaccctccatgagtgt +cacctccatc----ctcaggaccctccatgagtgtcacctccatcctcactcaggaccct +ccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactc +aggaccctccatg-----------------------------------gtgtcacctcca +tcctcactcaggaccctccatggtgtcacctccatcctcaccaggaccctccatgagtgt +cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctc +cgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctatctaccct +caggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccagactgttt +cagggttggacactgagctgtggcccctgagcctagctcttctccgagcttctcttgggc +acctctctctcagactaggct diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/msa.fa.fai new file mode 100644 index 00000000..cbae1237 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_61201583_61202575 1881 29 60 61 +syndip_1_chr20:61201583-61202575 1881 1976 60 61 +syndip_2_chr20:61201583-61202575 1881 3923 60 61 +p:HG002_1_chr20:61201583-61202575 1881 5871 60 61 +p:HG002_2_chr20:61201583-61202575 1881 7819 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/output.vcf.gz new file mode 100644 index 00000000..375ddfe9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/output.vcf.gz.tbi new file mode 100644 index 00000000..af2c9d22 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61201683-61202475/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/base.vcf.gz new file mode 100644 index 00000000..542aeae2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/base.vcf.gz.tbi new file mode 100644 index 00000000..02c9acb4 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/comp.vcf.gz new file mode 100644 index 00000000..8641e6ae Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/comp.vcf.gz.tbi new file mode 100644 index 00000000..87dbaefb Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/haps.fa new file mode 100644 index 00000000..98161bac --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/haps.fa @@ -0,0 +1,114 @@ +>ref_chr20_61282406_61283770 +ATAAAACATTCTGTATTTTCAAAATGCCAAAAAAATTATTGTTAAAGACTTTAGAAAACAGAAAAGTACAAAGAATAAAAGGGTAACTTCATTTCCCTCCTCTGAACAAACCACTTTTAATCTTTGGCATGGTGTGTGTGCATGTGTGTGTGTGTGTGTGTGTGTGTATGTCTATCTGTACTTGTACCTGCACACACAACTGGATGAGCATGGTGTGTGTGTACACATGTAATGTGTTCATATGTACATATGTGGGTGCCTTGTGCACACGTGTGTGGCTGTGGGATGTTCAGATGTGCATGTGAGTTGGTGTGTGTGCATGCCCACAAGCATGCATGTAAATGTGATGTGCTGTGTATGCACACGGATAAGCATGTGTGAAGGAGTGCATGAGAGTGGTGCATGGCTGTGGTGTGCACGTGTGTGCGTGTGATGCATGTGCATTTGCACGCATGTGCTGTGGTGTGTGTGATGTACGTGCATTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACGTGCATTTGCACGCGTGTGCTGTGGCGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGTGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGTGTGTGATGTAGGTGCATTTGCACGCGTGTGCTGTGGTGTGTGATGTAGGTGCATTTACACGCGTGTGCTGTGGTGTGTGATGTAGGTGCATTTGCACGTGTGTGCTGTGGTGTGTGTGATGTGTGTGCATTTGCACGTGTGTGCTGTGGTGTGTGTGTGGTGAGTGGATGGGAGGATATTTCCAGTGCTCTCCTCCTGGGACTGATGCCATGATGAAAATCTGTGTAAACCAGACAGCACATCTCTCATCATTTCTTTGTGATGGGTCATTAGAAGCAGGATTCTGAATT +>syndip_1_chr20:61282406-61283770 +ATAAAACATTCTGTATTTTCAAAATGCCAAAAAAATTATTGTTAAAGACTTTAGAAAACA +GAAAAGTACAAAGAATAAAAGGGTAACTTCATTTCCCTCCTCTGAACAAACCACTTTTAA +TCTTTGGCATGGTGTGTGTGTGTGCATGTGTGTGTGTGTGTGTGTATGTCTATCTGTACT +TGTACCTGCACACACAACTGGATGAGCATGGTGTGTGTGTACACATGTATTGTGTTCATA +TGTACATATGTGGGTGCCTTGTGCACACGTGTGTGGCTGTGGGATGTTCAGATGTGCATG +TGAGTTGGTGTGTGTGCATGCCCACAAGCATGCATGTAAATGTGATGTGCTGTGTATGCA +CACGGATAAGCATGTGTGAAGGAGTGCATGAGAGTGGTGCATGGCTGTGGTGTGCACGTG +TGTGCGTGTGATGCATGTGCATTTGCACGCATGTGCTGTGGTGTGTGTGATGTACGTGCA +TTTGCACGCATGTGCTGTGGCGTGTGTGATGTACGTGCATTTGCACGCGTGTGCTGTGTG +TGTGATGTACGTGCATTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCA +CGCGTGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGT +GATGTACGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGC +GTGTGCTGTGGTGTGTGATGTACGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGT +ACGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGTGTG +CTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACG +TGCGTTTGCACGCGTGTTCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGTGTGCTG +TGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTGTGTGC +GTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGG +CGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTGTGTGCGTT +TGCACGCGTGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGCGT +GTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGTGATGTGTGTGCGTTTGCACGCGTG +TGCTGTGGTGTGTGATGTAGGTGCATTTACACGCGTGTGCTGTGGTGTGTGATGTAGGTG +CATTTGCACGCGTGTGCTGTGGTGTGTGTGATGTGTGTGCGTTTGCACGTGTGTGCTGTG +GTGTGTGTGTGGTGAGTGGATGGGAGGATATTTCCAGTGCTCTCCTCCTGGGACTGATGC +CATGATGAAAATCTGTGTAAACCAGACAGCACATCTCTCATCATTTCTTTGTGATGGGTC +ATTAGAAGCAGGATTCTGAATT +>syndip_2_chr20:61282406-61283770 +ATAAAACATTCTGTATTTTCAAAATGCCAAAAAAATTATTGTTAAAGACTTTAGAAAACA +GAAAAGTACAAAGAATAAAAGGGTAACTTCATTTCCCTCCTCTGAACAAACCACTTTTAA +TCTTTGGCATGGTGTGTGTGTGTGCATGTGTGTGTGTGTGTGTGTATGTCTATCTGTACT +TGTACCTGCACACACAACTGGATGAGCATGGTGTGTGTGTACACATGTAATGTGTTCATA +TGTACATATGTGGGTGCCTTGTGCACACGTGTGTGGCTGTGGGATGTTCAGATGTGCATG +TGAGTTGGTGTGTGTGCATGCCCACAAGCATGCATGTAAATGTGATGTGCTGTGTATGCA +CACGGATAAGCATGTGTGAAGGAGTGCATGAGAGTGGTGCATGGCTGTGGTGTGCACGTG +TGTGCGTGTGATGCATGTGCATTTGCACGCATGTGCTGTGGTGTGTGTGATGTACGTGCA +TTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACGTGCATTTGCACGCGTGTGCTGTGTG +TGTGATGTACGTGCATTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCA +CGCGTGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGA +TGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGC +GTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGT +GGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCG +TTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGC +GTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTT +GCACGCGCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTG +TGTGATGTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCA +CGCGCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGT +GATGTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGC +GCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGAT +GTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTG +TGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGTGTGTGATGTAGG +TGCGTTTGCACGCGTGTGCTGTGGTGTGTGATGTAGGTGCGTTTGCACGCGTGTGCTGTG +GTGTGTGATGTAGGTGCATTTGCACGTGTGTGCTGTGGTGTGTGTGATGTGTGTGCATTT +GCACGTGTGTGCTGTGGTGTGTGTGTGGTGAGTGGATGGGAGGATATTTCCAGTGCTCTC +CTCCTGGGACTGATGCCATGATGAAAATCTGTGTAAACCAGACAGCACATCTCTCATCAT +TTCTTTGTGATGGGTCATTAGAAGCAGGATTCTGAATT +>p:HG002_1_chr20:61282406-61283770 +ATAAAACATTCTGTATTTTCAAAATGCCAAAAAAATTATTGTTAAAGACTTTAGAAAACA +GAAAAGTACAAAGAATAAAAGGGTAACTTCATTTCCCTCCTCTGAACAAACCACTTTTAA +TCTTTGGCATGGTGTGTGTGTGTGCATGTGTGTGTGTGTGTGTGTATGTCTATCTGTACT +TGTACCTGCACACACAACTGGATGAGCATGGTGTGTGTGTACACATGTAATGTGTTCATA +TGTACATATGTGGGTGCCTTGTGCACACGTGTGTGGCTGTGGGATGTTTAGATGTGCATG +TGAGTTGGTGTGTGTGCATGCCCACAAGCATGCATGTAAATGTGATGTGCTGTGTATGCA +CACGGATAAGCATGTGTGAAGGAGTGCATGAGAGTGGTGCATGGCTGTGGTGTGCACGTG +TGTGCGTGTGATGCATGTGCATTTGCACGCATGTGCTGTGGTGTGTGTGATGTACGTGCA +TTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACGTGCATTTGCACGCGTGTGCTGTGTG +TGTGATGTACGTGCATTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCA +CGCGTGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGA +TGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGC +GTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGT +GGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCG +TTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGC +GTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTT +GCACGCGCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTG +TGTGATGTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCA +CGCGCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGT +GATGTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGC +GCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGAT +GTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTG +TGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGTGTGTGATGTAGG +TGCGTTTGCACGCGTGTGCTGTGGTGTGTGATGTAGGTGCGTTTGCACGCGTGTGCTGTG +GTGTGTGATGTAGGTGCATTTGCACGTGTGTGCTGTGGTGTGTGTGATGTGTGTGCATTT +GCACGTGTGTGCTGTGGTGTGTGTGTGGTGAGTGGATGGGAGGATATTTCCAGTGCTCTC +CTCCTGGGACTGATGCCATGATGAAAATCTGTGTAAACCAGACAGCACATCTCTCATCAT +TTCTTTGTGATGGGTCATTAGAAGCAGGATTCTGAATT +>p:HG002_2_chr20:61282406-61283770 +ATAAAACATTCTGTATTTTCAAAATGCCAAAAAAATTATTGTTAAAGACTTTAGAAAACA +GAAAAGTACAAAGAATAAAAGGGTAACTTCATTTCCCTCCTCTGAACAAACCACTTTTAA +TCTTTGGCATGGTGTGTGTGTGTGCATGTGTGTGTGTGTGTGTGTATGTCTATCTGTACT +TGTACCTGCACACACAACTGGATGAGCATGGTGTGTGTGTACACATGTATTGTGTTCATA +TGTACATATGTGGGTGCCTTGTGCACACGTGTGTGGCTGTGGGATGTTCGGATGTGCATG +TGAGTTGGTGTGTGTGCATGCCCACAAGCATGCATGTAAATGTGATGTGCTGTGTATGCA +CACGGATAAGCATGTGTGAAGGAGTGCATGAGAGTGGTGCATGGCTGTGGTGTGCACGTG +TGTGCGTGTGATGCATGTGCATTTGCACGCATGTGCTGTGGTGTGTGTGATGTACGTGCA +TTTGCACGCATGTGCTGTGGCGTGTGTGATGTACGTGCATTTGCACGCGTGTGCTGTGTG +TGTGATGTACGTGCATTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCA +CGCGTGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGT +GATGTACGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGC +GTGTGCTGTGGTGTGTGATGTACGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGT +ACGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGTGTG +CTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACG +TGCGTTTGCACGCGTGTTCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGTGTGCTG +TGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTGTGTGC +GTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGG +CGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTGTGTGCGTT +TGCACGCGTGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGCGT +GTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGTGATGTGTGTGCGTTTGCACGCGTG +TGCTGTGGTGTGTGATGTAGGTGCATTTACACGCGTGTGCTGTGGTGTGTGATGTAGGTG +CATTTGCACGCGTGTGCTGTGGTGTGTGTGATGTGTGTGCGTTTGCACGTGTGTGCTGTG +GTGTGTGTGTGGTGAGTGGATGGGAGGATATTTCCAGTGCTCTCCTCCTGGGACTGATGC +CATGATGAAAATCTGTGTAAACCAGACAGCACATCTCTCATCATTTCTTTGTGATGGGTC +ATTAGAAGCAGGATTCTGAATT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/haps.fa.ref.fa new file mode 100644 index 00000000..e8a98649 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:61282406-61283770 +ATAAAACATTCTGTATTTTCAAAATGCCAAAAAAATTATTGTTAAAGACTTTAGAAAACAGAAAAGTACAAAGAATAAAAGGGTAACTTCATTTCCCTCCTCTGAACAAACCACTTTTAATCTTTGGCATGGTGTGTGTGCATGTGTGTGTGTGTGTGTGTGTGTGTATGTCTATCTGTACTTGTACCTGCACACACAACTGGATGAGCATGGTGTGTGTGTACACATGTAATGTGTTCATATGTACATATGTGGGTGCCTTGTGCACACGTGTGTGGCTGTGGGATGTTCAGATGTGCATGTGAGTTGGTGTGTGTGCATGCCCACAAGCATGCATGTAAATGTGATGTGCTGTGTATGCACACGGATAAGCATGTGTGAAGGAGTGCATGAGAGTGGTGCATGGCTGTGGTGTGCACGTGTGTGCGTGTGATGCATGTGCATTTGCACGCATGTGCTGTGGTGTGTGTGATGTACGTGCATTTGCACGCGTGTGCTGTGGCGTGTGTGATGTACGTGCATTTGCACGCGTGTGCTGTGGCGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTACGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGCGTTTGCACGCGCGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGCGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGTGTGTGTGATGTGTGTGCGTTTGCACGCGTGTGCTGTGGTGTGTGATGTAGGTGCATTTGCACGCGTGTGCTGTGGTGTGTGATGTAGGTGCATTTACACGCGTGTGCTGTGGTGTGTGATGTAGGTGCATTTGCACGTGTGTGCTGTGGTGTGTGTGATGTGTGTGCATTTGCACGTGTGTGCTGTGGTGTGTGTGTGGTGAGTGGATGGGAGGATATTTCCAGTGCTCTCCTCCTGGGACTGATGCCATGATGAAAATCTGTGTAAACCAGACAGCACATCTCTCATCATTTCTTTGTGATGGGTCATTAGAAGCAGGATTCTGAATT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/msa.fa new file mode 100644 index 00000000..6fdc2ee9 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/msa.fa @@ -0,0 +1,145 @@ +>ref_chr20_61282406_61283770 +ataaaacattctgtattttcaaaatgccaaaaaaattattgttaaagactttagaaaaca +gaaaagtacaaagaataaaagggtaacttcatttccctcctctgaacaaaccacttttaa +tctttggcatggtgtgtgtgcatgtgtgtgtgtgtgtgtgtgtgtgtatgtctatctgta +cttgtacctgcacacacaactggatgagcatggtgtgtgtgtacacatgtaatgtgttca +tatgtacatatgtgggtgccttgtgcacacgtgtgtggctgtgggatgttcagatgtgca +tgtgagttggtgtgtgtgcatgcccacaagcatgcatgtaaatgtgatgtgctgtgtatg +cacacggataagcatgtgtgaaggagtgcatgagagtggtgcatggctgtggtgtgcacg +tgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctgtggtgtgtgtgatgtacgtg +catttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtg +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------gcgtgtgatgtacgtgcgtttgcacgcgcgtgctgtg----------- +-----gcgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtg +cgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtg +gcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgt +ttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcg +tgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttg +cacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggc---- +-----gtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcac +gcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggtgtgtgtg +atgtgtgtgcgtttgcacgcgtgtgc---------------------------------- +--------------------------------------------tgtggtgtgtgatgta +ggtgcatttgcacgcgtgtgctgtggtgtgtgatgtaggtgcatttacacgcgtgtgctg +tggtgtgtgatgtaggtgcatttgcacgtgtgtgctgtggtgtgtgtgatgtgtgtgcat +ttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatgggaggatatttccagtgctc +tcctcctgggactgatgccatgatgaaaatctgtgtaaaccagacagcacatctctcatc +atttctttgtgatgggtcattagaagcaggattctgaatt +>syndip_1_chr20:61282406-61283770 +ataaaacattctgtattttcaaaatgccaaaaaaattattgttaaagactttagaaaaca +gaaaagtacaaagaataaaagggtaacttcatttccctcctctgaacaaaccacttttaa +tctttggcatggtgtgtgtg--tgtgcatgtgtgtgtgtgtgtgtgtatgtctatctgta +cttgtacctgcacacacaactggatgagcatggtgtgtgtgtacacatgtattgtgttca +tatgtacatatgtgggtgccttgtgcacacgtgtgtggctgtgggatgttcagatgtgca +tgtgagttggtgtgtgtgcatgcccacaagcatgcatgtaaatgtgatgtgctgtgtatg +cacacggataagcatgtgtgaaggagtgcatgagagtggtgcatggctgtggtgtgcacg +tgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctgtggtgtgtgtgatgtacgtg +catttgcacgcatgtgctgtggcgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtg +tgtgtgatgtacgtgcatttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttg +cacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgt-------------- +-----------------------gtgctgtggcgtgtgtgatgtacgtgcgtttgcacgc +gtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtg----------- +-----gtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtg +cgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtg +gcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgt +ttgcacgcgtgttctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcg +tgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttg +cacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgt +gtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcac +gcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtg +atgtgtgtgcgtttgcacgcgtgtgc---------------------------------- +-------------------------------------------------tgtgtgatgtg +tgtgcgtttgcacgcgtgtgctgtggtgtgtgatgtaggtgcatttacacgcgtgtgctg +tggtgtgtgatgtaggtgcatttgcacgcgtgtgctgtggtgtgtgtgatgtgtgtgcgt +ttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatgggaggatatttccagtgctc +tcctcctgggactgatgccatgatgaaaatctgtgtaaaccagacagcacatctctcatc +atttctttgtgatgggtcattagaagcaggattctgaatt +>syndip_2_chr20:61282406-61283770 +ataaaacattctgtattttcaaaatgccaaaaaaattattgttaaagactttagaaaaca +gaaaagtacaaagaataaaagggtaacttcatttccctcctctgaacaaaccacttttaa +tctttggcatggtgtgtgtg--tgtgcatgtgtgtgtgtgtgtgtgtatgtctatctgta +cttgtacctgcacacacaactggatgagcatggtgtgtgtgtacacatgtaatgtgttca +tatgtacatatgtgggtgccttgtgcacacgtgtgtggctgtgggatgttcagatgtgca +tgtgagttggtgtgtgtgcatgcccacaagcatgcatgtaaatgtgatgtgctgtgtatg +cacacggataagcatgtgtgaaggagtgcatgagagtggtgcatggctgtggtgtgcacg +tgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctgtggtgtgtgtgatgtacgtg +catttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtg +tgtgtgatgtacgtgcatttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttg +cacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgt +gatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgc +gcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgat +gtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtg +cgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtg +gcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgt +ttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcg +tgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttg +cacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgt +gtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcac +gcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtg +atgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcg +tgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggtgtgtgatgta +ggtgcgtttgcacgcgtgtgctgtggtgtgtgatgtaggtgcgtttgcacgcgtgtgctg +tggtgtgtgatgtaggtgcatttgcacgtgtgtgctgtggtgtgtgtgatgtgtgtgcat +ttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatgggaggatatttccagtgctc +tcctcctgggactgatgccatgatgaaaatctgtgtaaaccagacagcacatctctcatc +atttctttgtgatgggtcattagaagcaggattctgaatt +>p:HG002_1_chr20:61282406-61283770 +ataaaacattctgtattttcaaaatgccaaaaaaattattgttaaagactttagaaaaca +gaaaagtacaaagaataaaagggtaacttcatttccctcctctgaacaaaccacttttaa +tctttggcatggtgtgtgtg--tgtgcatgtgtgtgtgtgtgtgtgtatgtctatctgta +cttgtacctgcacacacaactggatgagcatggtgtgtgtgtacacatgtaatgtgttca +tatgtacatatgtgggtgccttgtgcacacgtgtgtggctgtgggatgtttagatgtgca +tgtgagttggtgtgtgtgcatgcccacaagcatgcatgtaaatgtgatgtgctgtgtatg +cacacggataagcatgtgtgaaggagtgcatgagagtggtgcatggctgtggtgtgcacg +tgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctgtggtgtgtgtgatgtacgtg +catttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtg +tgtgtgatgtacgtgcatttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttg +cacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgt +gatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgc +gcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgat +gtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtg +cgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtg +gcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgt +ttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcg +tgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttg +cacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgt +gtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcac +gcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtg +atgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcg +tgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggtgtgtgatgta +ggtgcgtttgcacgcgtgtgctgtggtgtgtgatgtaggtgcgtttgcacgcgtgtgctg +tggtgtgtgatgtaggtgcatttgcacgtgtgtgctgtggtgtgtgtgatgtgtgtgcat +ttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatgggaggatatttccagtgctc +tcctcctgggactgatgccatgatgaaaatctgtgtaaaccagacagcacatctctcatc +atttctttgtgatgggtcattagaagcaggattctgaatt +>p:HG002_2_chr20:61282406-61283770 +ataaaacattctgtattttcaaaatgccaaaaaaattattgttaaagactttagaaaaca +gaaaagtacaaagaataaaagggtaacttcatttccctcctctgaacaaaccacttttaa +tctttggcatggtgtgtgtg--tgtgcatgtgtgtgtgtgtgtgtgtatgtctatctgta +cttgtacctgcacacacaactggatgagcatggtgtgtgtgtacacatgtattgtgttca +tatgtacatatgtgggtgccttgtgcacacgtgtgtggctgtgggatgttcggatgtgca +tgtgagttggtgtgtgtgcatgcccacaagcatgcatgtaaatgtgatgtgctgtgtatg +cacacggataagcatgtgtgaaggagtgcatgagagtggtgcatggctgtggtgtgcacg +tgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctgtggtgtgtgtgatgtacgtg +catttgcacgcatgtgctgtggcgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtg +tgtgtgatgtacgtgcatttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttg +cacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgt-------------- +-----------------------gtgctgtggcgtgtgtgatgtacgtgcgtttgcacgc +gtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtg----------- +-----gtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtg +cgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtg +gcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgt +ttgcacgcgtgttctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcg +tgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttg +cacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgt +gtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcac +gcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtg +atgtgtgtgcgtttgcacgcgtgtgc---------------------------------- +-------------------------------------------------tgtgtgatgtg +tgtgcgtttgcacgcgtgtgctgtggtgtgtgatgtaggtgcatttacacgcgtgtgctg +tggtgtgtgatgtaggtgcatttgcacgcgtgtgctgtggtgtgtgtgatgtgtgtgcgt +ttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatgggaggatatttccagtgctc +tcctcctgggactgatgccatgatgaaaatctgtgtaaaccagacagcacatctctcatc +atttctttgtgatgggtcattagaagcaggattctgaatt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/msa.fa.fai new file mode 100644 index 00000000..c300d89b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_61282406_61283770 1660 29 60 61 +syndip_1_chr20:61282406-61283770 1660 1751 60 61 +syndip_2_chr20:61282406-61283770 1660 3473 60 61 +p:HG002_1_chr20:61282406-61283770 1660 5196 60 61 +p:HG002_2_chr20:61282406-61283770 1660 6919 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/output.vcf.gz new file mode 100644 index 00000000..960d2828 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/output.vcf.gz.tbi new file mode 100644 index 00000000..78bbcc70 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61282506-61283670/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/base.vcf.gz new file mode 100644 index 00000000..5d4129e6 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/base.vcf.gz.tbi new file mode 100644 index 00000000..9e7fa5d8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/comp.vcf.gz new file mode 100644 index 00000000..3f6568d3 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/comp.vcf.gz.tbi new file mode 100644 index 00000000..dd7b5c0a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/haps.fa new file mode 100644 index 00000000..67f51df0 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/haps.fa @@ -0,0 +1,80 @@ +>ref_chr20_61289525_61290656 +TGTGTGGGTGCCCAGGGGCATGAGTGCCTGGGGAGTGTGACCACAGGCCAGTGGCAGTCCCTGCCTTTGGATTAAAGAGCCCTTTGAGGCTTGCTTGGTGATGTCATGGAAAACAGCATATGACACCAAGATATCCCCATATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCGATATCCAATGAGACTTGCTGGATTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCGATATCCAATGAGACTTGCTGGATTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCGATATCCAATGAGACTTGCTGGATTTATCCCCGTATCCAATGAGACTTGCTGGATTTATCCCCATATCCAATGAGACTTGCTGGGTTTAGCACCACAGATGCCAGTCACAGAGGAAATTGATGGCATGGCAGACAGCGTGACATGTTGACTACCTGCCCTGGTCCTTGCAGATGGCATGGGCACAAAGGGGATGTGGGGTGAAGAGTTGAAACGAGTGCC +>syndip_1_chr20:61289525-61290656 +TGTGTGGGTGCCCAGGGGCATGAGTGCCTGGGGAGTGTGACCACAGGCCAGTGGCAGTCC +CTGCCTTTGGATTAAAGAGCCCTTTGAGGCTTGCTTGGTGATGTCATGGAAAACAGCATA +TGACACCAAGATATCCCCATATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGA +GACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAAC +GAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCA +ACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATC +CAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTA +TCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCG +TATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCC +CGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATC +CCCGTATCCAATGAGACTTGCTGGGTTTATCCCGATATCCAATGAGACTTGCTGGATTTA +TCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTT +TATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCGATATCCAATGAGACTTGCTGGA +TTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTG +GGTTTATCCCGATATCCAATGAGACTTGCTGGATTTATCCCCGTATCCAATGAGACTTGC +TGGATTTATCCCCATATCCAATGAGACTTGCTGGGTTTAGCACCACAGATGCCAGTCACA +GAGGAAATTGATGGCATGGCAGACAGCGTGACATGTTGACTACCTGCCCTGGTCCTTGCA +GATGGCATGGGCACAAAGGGGATGTGGGGTGAAGAGTTGAAACGAGTGCC +>syndip_2_chr20:61289525-61290656 +TGTGTGGGTGCCCAGGGGCATGAGTGCCTGGGGAGTGTGACCACAGGCCAGTGGCAGTCC +CTGCCTTTGGATTAAAGAGCCCTTTGAGGCTTGCTTGGTGATGTCATGGAAAACAGCATA +TGACACCAAGATATCCCCATATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGA +GACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAAC +GAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCA +ACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATC +CAACGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCCTA +TCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCG +TATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCC +CGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATC +CCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTA +TCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTT +TATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGG +TTTATCCCGATATCCAATGAGACTTGCTGGATTTATCCCCGTATCCAATGAGACTTGCTG +GGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCGATATCCAATGAGACTTGC +TGGATTTATCCCCGTATCCAATGAGACTTGCTGGATTTATCCCCATATCCAATGAGACTT +GCTGGGTTTAGCACCACAGATGCCAGTCACAGAGGAAATTGATGGCATGGCAGACAGCGT +GACATGTTGACTACCTGCCCTGGTCCTTGCAGATGGCATGGGCACAAAGGGGATGTGGGG +TGAAGAGTTGAAACGAGTGCC +>p:HG002_1_chr20:61289525-61290656 +TGTGTGGGTGCCCAGGGGCATGAGTGCCTGGGGAGTGTGACCACAGGCCAGTGGCAGTCC +CTGCCTTTGGATTAAAGAGCCCTTTGAGGCTTGCTTGGTGATGTCATGGAAAACAGCATA +TGACACCAAGATATCCCCATATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGA +GACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAAC +GAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCA +ACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATC +CAACGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCCTA +TCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCG +TATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCC +CGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATC +CCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTA +TCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTT +TATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGG +TTTATCCCGATATCCAATGAGACTTGCTGGATTTATCCCCGTATCCAATGAGACTTGCTG +GGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCGATATCCAATGAGACTTGC +TGGATTTATCCCCGTATCCAATGAGACTTGCTGGATTTATCCCCATATCCAATGAGACTT +GCTGGGTTTAGCACCACAGATGCCAGTCACAGAGGAAATTGATGGCATGGCAGACAGCGT +GACATGTTGACTACCTGCCCTGGTCCTTGCAGATGGCATGGGCACAAAGGGGATGTGGGG +TGAAGAGTTGAAACGAGTGCC +>p:HG002_2_chr20:61289525-61290656 +TGTGTGGGTGCCCAGGGGCATGAGTGCCTGGGGAGTGTGACCACAGGCCAGTGGCAGTCC +CTGCCTTTGGATTAAAGAGCCCTTTGAGGCTTGCTTGGTGATGTCATGGAAAACAGCATA +TGACACCAAGATATCCCCATATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGA +GACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAAC +GAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCA +ACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATC +CAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTA +TCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCG +TATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCC +CGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATC +CCCGTATCCAATGAGACTTGCTGGGTTTATCCCGATATCCAATGAGACTTGCTGGATTTA +TCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTT +TATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCGATATCCAATGAGACTTGCTGGA +TTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTG +GGTTTATCCCGATATCCAATGAGACTTGCTGGATTTATCCCCGTATCCAATGAGACTTGC +TGGATTTATCCCCATATCCAATGAGACTTGCTGGGTTTAGCACCACAGATGCCAGTCACA +GAGGAAATTGATGGCATGGCAGACAGCGTGACATGTTGACTACCTGCCCTGGTCCTTGCA +GATGGCATGGGCACAAAGGGGATGTGGGGTGAAGAGTTGAAACGAGTGCC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/haps.fa.ref.fa new file mode 100644 index 00000000..465e0be7 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:61289525-61290656 +TGTGTGGGTGCCCAGGGGCATGAGTGCCTGGGGAGTGTGACCACAGGCCAGTGGCAGTCCCTGCCTTTGGATTAAAGAGCCCTTTGAGGCTTGCTTGGTGATGTCATGGAAAACAGCATATGACACCAAGATATCCCCATATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAACGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCGATATCCAATGAGACTTGCTGGATTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCGATATCCAATGAGACTTGCTGGATTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCCGTATCCAATGAGACTTGCTGGGTTTATCCCGATATCCAATGAGACTTGCTGGATTTATCCCCGTATCCAATGAGACTTGCTGGATTTATCCCCATATCCAATGAGACTTGCTGGGTTTAGCACCACAGATGCCAGTCACAGAGGAAATTGATGGCATGGCAGACAGCGTGACATGTTGACTACCTGCCCTGGTCCTTGCAGATGGCATGGGCACAAAGGGGATGTGGGGTGAAGAGTTGAAACGAGTGCC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/msa.fa new file mode 100644 index 00000000..1bb4efcc --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/msa.fa @@ -0,0 +1,100 @@ +>ref_chr20_61289525_61290656 +tgtgtgggtgcccaggggcatgagtgcctggggagtgtgaccacaggccagtggcagtcc +ctgcctttggattaaagagccctttgaggcttgcttggtgatgtcatggaaaacagcata +tgacaccaagatatccccatatccaacgagacttgctgggtttatccccgtatccaacga +gacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaac +gagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatcca +acgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatc +caacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgta +tccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccg +tatccaacgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccc +cgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatc +cccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggttta +tccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtt +tatcccgatatccaatgagacttgctggatttatccccgtatccaatgagacttgctggg +tttatccccgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgctg +gatttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgc +tgggtttatcccgatatccaatgagacttgctggatttatccccgtatccaatgagactt +gctggatttatccccatatccaatgagacttgctgggtttagcaccacagatgccagtca +cagaggaaattgatggcatggcagacagcgtgacatgttgactacctgccctggtccttg +cagatggcatgggcacaaaggggatgtggggtgaagagttgaaacgagtgcc +>syndip_1_chr20:61289525-61290656 +tgtgtgggtgcccaggggcatgagtgcctggggagtgtgaccacaggccagtggcagtcc +ctgcctttggattaaagagccctttgaggcttgcttggtgatgtcatggaaaacagcata +tgacaccaagatatccccatatccaacgagacttgctgggtttatccccgtatccaacga +gacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaac +gagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatcca +acgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatc +caacgagacttgctgggtttatccccg-------------------------------ta +tccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccg +tatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccc +cgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatc +cccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggttta +tcccgatatccaatgagacttgctggatttatccccgtatccaatgagacttgctggg-- +-----------------------------tttatccccgtatccaatgagacttgctggg +tttatccccgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgctg +gatttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgc +tgggtttatcccgatatccaatgagacttgctggatttatccccgtatccaatgagactt +gctggatttatccccatatccaatgagacttgctgggtttagcaccacagatgccagtca +cagaggaaattgatggcatggcagacagcgtgacatgttgactacctgccctggtccttg +cagatggcatgggcacaaaggggatgtggggtgaagagttgaaacgagtgcc +>syndip_2_chr20:61289525-61290656 +tgtgtgggtgcccaggggcatgagtgcctggggagtgtgaccacaggccagtggcagtcc +ctgcctttggattaaagagccctttgaggcttgcttggtgatgtcatggaaaacagcata +tgacaccaagatatccccatatccaacgagacttgctgggtttatccccgtatccaacga +gacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaac +gagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatcca +acgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatc +caacgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatcccccta +tccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccg +tatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccc +cgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatc +cccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggttta +tccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctggg-- +-----------------------------tttatccccgtatccaatgagacttgctggg +tttatccccgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgctg +gatttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgc +tgggtttatcccgatatccaatgagacttgctggatttatccccgtatccaatgagactt +gctggatttatccccatatccaatgagacttgctgggtttagcaccacagatgccagtca +cagaggaaattgatggcatggcagacagcgtgacatgttgactacctgccctggtccttg +cagatggcatgggcacaaaggggatgtggggtgaagagttgaaacgagtgcc +>p:HG002_1_chr20:61289525-61290656 +tgtgtgggtgcccaggggcatgagtgcctggggagtgtgaccacaggccagtggcagtcc +ctgcctttggattaaagagccctttgaggcttgcttggtgatgtcatggaaaacagcata +tgacaccaagatatccccatatccaacgagacttgctgggtttatccccgtatccaacga +gacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaac +gagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatcca +acgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatc +caacgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatcccccta +tccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccg +tatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccc +cgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatc +cccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggttta +tccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctggg-- +-----------------------------tttatccccgtatccaatgagacttgctggg +tttatccccgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgctg +gatttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgc +tgggtttatcccgatatccaatgagacttgctggatttatccccgtatccaatgagactt +gctggatttatccccatatccaatgagacttgctgggtttagcaccacagatgccagtca +cagaggaaattgatggcatggcagacagcgtgacatgttgactacctgccctggtccttg +cagatggcatgggcacaaaggggatgtggggtgaagagttgaaacgagtgcc +>p:HG002_2_chr20:61289525-61290656 +tgtgtgggtgcccaggggcatgagtgcctggggagtgtgaccacaggccagtggcagtcc +ctgcctttggattaaagagccctttgaggcttgcttggtgatgtcatggaaaacagcata +tgacaccaagatatccccatatccaacgagacttgctgggtttatccccgtatccaacga +gacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaac +gagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatcca +acgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatc +caacgagacttgctgggtttatccccg-------------------------------ta +tccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccg +tatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccc +cgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatc +cccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggttta +tcccgatatccaatgagacttgctggatttatccccgtatccaatgagacttgctggg-- +-----------------------------tttatccccgtatccaatgagacttgctggg +tttatccccgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgctg +gatttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgc +tgggtttatcccgatatccaatgagacttgctggatttatccccgtatccaatgagactt +gctggatttatccccatatccaatgagacttgctgggtttagcaccacagatgccagtca +cagaggaaattgatggcatggcagacagcgtgacatgttgactacctgccctggtccttg +cagatggcatgggcacaaaggggatgtggggtgaagagttgaaacgagtgcc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/msa.fa.fai new file mode 100644 index 00000000..3a0771e2 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_61289525_61290656 1132 29 60 61 +syndip_1_chr20:61289525-61290656 1132 1214 60 61 +syndip_2_chr20:61289525-61290656 1132 2399 60 61 +p:HG002_1_chr20:61289525-61290656 1132 3585 60 61 +p:HG002_2_chr20:61289525-61290656 1132 4771 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/output.vcf.gz new file mode 100644 index 00000000..1af7b383 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/output.vcf.gz.tbi new file mode 100644 index 00000000..5377b41c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61289625-61290556/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/base.vcf.gz new file mode 100644 index 00000000..37e83f54 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/base.vcf.gz.tbi new file mode 100644 index 00000000..bb297398 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/comp.vcf.gz new file mode 100644 index 00000000..21efa0cf Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/comp.vcf.gz.tbi new file mode 100644 index 00000000..b7a9cd5b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/haps.fa new file mode 100644 index 00000000..58b3b250 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/haps.fa @@ -0,0 +1,73 @@ +>ref_chr20_61329158_61329678 +TTTTGTACCATCATAAAGTCAAAAAATTGTAGTTCAGCTGTCATTTAAGTTGGAGACTGTCTGTACTTGACAGTTGATATGAAATATTCACATACGTTCTGCACTGGAATCCACTCTGCTCCAGTGTTTAAGCCCAGTGTGCTGCGGTGGATTGCAGCATGCGTGGAGGGCACCCAGGTCCTCATGGTTCCCTCGTGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTGCAGTGGATTGCAGCGTGCGTGGAGGGCACCCAGGTCCTCATGGTCCCCCGTGGGTCTGGGATGTGGGTTGAGGTGGCTGTGAGTGGCTCTTCTGCCCTTGGCTTCTGTATTTTATAATAAGAGAGGGCTCTTGCTCTCTCTCTCTCTCTCCTGCTTTGTACTTTCAATCAATCTCTTTCCAGCATAGTTCCCCCTAAAACATCAGAAAGCTGAGTGAGCCTGTGCTCTCCTCTCAGAGCTTAGCCACTTGGATTCCGCAGACCCTGGATTGTCACTTTAAA +>syndip_1_chr20:61329158-61329678 +TTTTGTACCATCATAAAGTCAAAAAATTGTAGTTCAGCTGTCATTTAAGTTGGAGACTGT +CTGTACTTGACAGTTGATATGAAATATTCACATACGTTCTGCACTGGAATCCACTCTGCT +CCAGTGTTTAAGCCCAGTGTGCTGCGGTGGATTGCAGCATGCGTGGAGGGCACCCAGGTC +CTCATGGTTCCCTCGTGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTG +CAGTGGATTGCAGCGTGCGTGGAGGGCACCCAGGTCCTCATGGTCCCCCGTGGGTCTGGG +ATGTGGGTTGAGGTGGCTGTGAGTGGCTCTTCTGCCCTTGGCTTCTGTATTTTATAATAA +GAGAGGGCTCTTGCTCTCTCTCTCTCTCTCCTGCTTTGTACTTTCAATCAATCTCTTTCC +AGCATAGTTCCCCCTAAAACATCAGAAAGCTGAGTGAGCCTGTGCTCTCCTCTCAGAGCT +TAGCCACTTGGATTCCGCAGACCCTGGATTGTCACTTTAAA +>syndip_2_chr20:61329158-61329678 +TTTTGTACCATCATAAAGTCAAAAAATTGTAGTTCAGCTGTCATTTAAGTTGGAGACTGT +CTGTACTTGACAGTTGATATGAAATATTCACATACGTTCTGCACTGGAATCCACTCTGCT +CCAGTGTTTAAGCCCAGTGTGCTGCGGTGGATTGCAGCATGCGTGGAGGGCACCCAGGTC +CTCATGGTTCCCTCGTGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTG +CAGTGGATTGCAGCGTGCGTGGAGGGCACCCAGGTCCTCATGGTCCCCCGTGGGTCTGGG +ATGTGGGTTGAGGTGGCTGTGAGTGGCTCTTCTGCCCTTGGCTTCTGTATTTTATAATAA +GAGAGGGCTCTTGCTCTCTCTCTCTCTCTCCTGCTTTGTACTTTCAATCAATCTCTTTCC +AGCATAGTTCCCCCTAAAACATCAGAAAGCTGAGTGAGCCTGTGCTCTCCTCTCAGAGCT +TAGCCACTTGGATTCCGCAGACCCTGGATTGTCACTTTAAA +>p:HG002_1_chr20:61329158-61329678 +TTTTGTACCATCATAAAGTCAAAAAATTGTAGTTCAGCTGTCATTTAAGTTGGAGACTGT +CTGTACTTGACAGTTGATATGAAATATTCACATACGTTCTGCACTGGAATCCACTCTGCT +CCAGTGTTTAAGCCCAGTGTGCTGCGGTGGATTGCAGCATGCGTGGAGGGCACCCAGGTC +CTCATGGTTCCCTCGTGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTG +CGGTGGATTGCAGCGTGCGTGGAGGGCACCCAGGTCCTCATGGTCCCCTCATGGGTCTGG +GACGCGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTGCGGTGGATTGCAGCATGCGTGGAG +GGCACCCAGGTCCTCATGGTCCCCTCATGGGTCTGGGACGTGGGTCGAGGTGGCTTTAAG +CCCAGTGTGCTGCAGTGGATTGCAGCATGCGTGGAGGGCACCCAGGTCCTCATGGTCCCC +TCGTGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTGCGGTGGATTGCA +GCGTGCGTGGAGGGCACCCAGGTCCTCATGGTCCCCTCGTGGGTCTGGGACGCGGGTCGA +GGTGGCTTTAAGCCTAGTGTGCTGCGGTGGATTGCAGCATGCGTGGAGGGCACCCAGGTC +CTCATGGTCCCCTCATGGGTCTGGGACGTGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTG +CGGTGGATTGCAGCATGCGTGGAGGGCACCCAGGTCCTCATGGTTGCCTCGTGGGTCTGG +GACGCGGGTCGAGGTGGCTTTAAGCCCACTGTGCTGCAGTGGATTGCAGCATGCGTGGAG +GGCACCCAGGTCCTCATGGTTCCCCCGTGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAG +CCCACTGTGCTGCGGTGGATTGCAGCATGCGTGGAGGGCACCCAGGTCCTCATGGTCCCC +CCGTGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTGCGGTGGATTGCA +GCATGCGTGGAGGGCACCCAGGTCCTCATGGTCCCCCCGTGGGTCTGGGACGCGGGTCGA +GGTGGCTTTAAGCCCAGTGTGCTGCAGTGGATTGCAGCATGCGTGGAGGGCACCCAGGTC +CTCATGGTTCCCTCGTGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTG +CGGTGGATTGCAGCGTGCGTGGAGGGCACCCAGATCCTCATGGTTCCCCCGTGGGTCTGG +GACGCGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTGCAGTGGATTGCAGCATGCGTGGAG +GGCACCCAGATCCTCATGTTTCCCCCACGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAG +CCCAGTGTGCTGCGGTGGATTGCAGCGTGCGTGGAGGGCACCCAGGTCCTCATGGTTCCC +TCGTGGGTCTGGGACGTGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTGCAGTGGATTGCA +GCGTGCGTGGAGGGCACCCAGGTCCTCATGGTCCCCTCGTGGGTCTGGGACGCGGGTCGA +GGTGGCTTTAAGCCCAGTGTGCTGCAGTGGATTGCAGCGTGCGTGGAGGGCACCCAGGTC +CTCATGGTCCCCCGTGGGTCTGGGATGTGGGTTGAGGTGGCTGTGAGTGGCTCTTCTGCC +CTTGGCTTCTGTATTTTATAATAAGAGAGGGCTCTTGCTCTCTCTCTCTCTCTCCTGCTT +TGTACTTTCAATCAATCTCTTTCCAGCATAGTTCCCCCTAAAACATCAGAAAGCTGAGTG +AGCCTGTGCTCTCCTCTCAGAGCTTAGCCACTTGGATTCCGCAGACCCTGGATTGTCACT +TTAAA +>p:HG002_2_chr20:61329158-61329678 +TTTTGTACCATCATAAAGTCAAAAAATTGTAGTTCAGCTGTCATTTAAGTTGGAGACTGT +CTGTACTTGACAGTTGATATGAAATATTCACATACGTTCTGCACTGGAATCCACTCTGCT +CCAGTGTTTAAGCCCAGTGTGCTGCGGTGGATTGCAGCATGCGTGGAGGGCACCCAGGTC +CTCATGGTTCCCCCGTGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTG +CGGTGGATTGCAGCATGCGTGGAGGGCACCCAGATCCTCATGGTTCCCCCGTGGGTCTGG +GACGCGGGTCGAGGTGGCTTTAAGCCCACTGTGCTGCGGTGGATTGCAGCATGCGTGGAG +GGCACCCAGGTCCTCATGGTTCCCCCACGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAG +CCCAGTGTGCTGCGGTGGATTGCAGCGTGCGTGGAGGGCACCCAGGTCCTCATGGTCCCC +CCGTGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTGCGGTGGATTGCA +GCATGCGTGGAGGGCACCCAGATCCTCATGGTCCCCCCGTGGGTCTGGGACGCGGGTCGA +GGTGGCTTTAAGCCCAGTGTGCTGCGGTGGATTGCAGCATGCGTGGAGGGCACCCAGGTC +CTCATGGTCCCCCCGTGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTG +CAGTGGATTGCAGCATGCGTGGAGGGCACCCAGGTCCTCATGGTCCCCCCGTGGGTCTGG +GATGTGGGTTGAGGTGGCTGTGAGTGGCTCTTCTGCCCTTGGCTTCTGTATTTTATAATA +AGAGAGGGCTCTTGCTCTCTCTCTCTCTCTCCTGCTTTGTACTTTCAATCAATCTCTTTC +CAGCATAGTTCCCCCTAAAACATCAGAAAGCTGAGTGAGCCTGTGCTCTCCTCTCAGAGC +TTAGCCACTTGGATTCCGCAGACCCTGGATTGTCACTTTAAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/haps.fa.ref.fa new file mode 100644 index 00000000..b7b1f116 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:61329158-61329678 +TTTTGTACCATCATAAAGTCAAAAAATTGTAGTTCAGCTGTCATTTAAGTTGGAGACTGTCTGTACTTGACAGTTGATATGAAATATTCACATACGTTCTGCACTGGAATCCACTCTGCTCCAGTGTTTAAGCCCAGTGTGCTGCGGTGGATTGCAGCATGCGTGGAGGGCACCCAGGTCCTCATGGTTCCCTCGTGGGTCTGGGACGCGGGTCGAGGTGGCTTTAAGCCCAGTGTGCTGCAGTGGATTGCAGCGTGCGTGGAGGGCACCCAGGTCCTCATGGTCCCCCGTGGGTCTGGGATGTGGGTTGAGGTGGCTGTGAGTGGCTCTTCTGCCCTTGGCTTCTGTATTTTATAATAAGAGAGGGCTCTTGCTCTCTCTCTCTCTCTCCTGCTTTGTACTTTCAATCAATCTCTTTCCAGCATAGTTCCCCCTAAAACATCAGAAAGCTGAGTGAGCCTGTGCTCTCCTCTCAGAGCTTAGCCACTTGGATTCCGCAGACCCTGGATTGTCACTTTAAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/msa.fa new file mode 100644 index 00000000..51a3634e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/msa.fa @@ -0,0 +1,165 @@ +>ref_chr20_61329158_61329678 +ttttgtaccatcataaagtcaaaaaattgtagttcagctgtcatttaagttggagactgt +ctgtacttgacagttgatatgaaatattcacatacgttctgcactggaatccactctgct +ccagtg------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------tttaagcccagtgtgctgcggtggattgca +gcatgcgtggagggcacccaggtcctcatggttccctcgtgggtctgggacgcgggtcga +ggtggctttaagcccagtgtgctgcagtggattgcagcgtgcgtggagggcacccaggtc +ctcatggt-cccccgtgggtctgggatgtgggttgaggtggctgtgagtggctcttctgc +ccttggcttctgtattttataataagagagggctcttgctctctctctctctctcctgct +ttgtactttcaatcaatctctttccagcatagttccccctaaaacatcagaaagctgagt +gagcctgtgctctcctctcagagcttagccacttggattccgcagaccctggattgtcac +tttaaa +>syndip_1_chr20:61329158-61329678 +ttttgtaccatcataaagtcaaaaaattgtagttcagctgtcatttaagttggagactgt +ctgtacttgacagttgatatgaaatattcacatacgttctgcactggaatccactctgct +ccagtg------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------tttaagcccagtgtgctgcggtggattgca +gcatgcgtggagggcacccaggtcctcatggttccctcgtgggtctgggacgcgggtcga +ggtggctttaagcccagtgtgctgcagtggattgcagcgtgcgtggagggcacccaggtc +ctcatggt-cccccgtgggtctgggatgtgggttgaggtggctgtgagtggctcttctgc +ccttggcttctgtattttataataagagagggctcttgctctctctctctctctcctgct +ttgtactttcaatcaatctctttccagcatagttccccctaaaacatcagaaagctgagt +gagcctgtgctctcctctcagagcttagccacttggattccgcagaccctggattgtcac +tttaaa +>syndip_2_chr20:61329158-61329678 +ttttgtaccatcataaagtcaaaaaattgtagttcagctgtcatttaagttggagactgt +ctgtacttgacagttgatatgaaatattcacatacgttctgcactggaatccactctgct +ccagtg------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------tttaagcccagtgtgctgcggtggattgca +gcatgcgtggagggcacccaggtcctcatggttccctcgtgggtctgggacgcgggtcga +ggtggctttaagcccagtgtgctgcagtggattgcagcgtgcgtggagggcacccaggtc +ctcatggt-cccccgtgggtctgggatgtgggttgaggtggctgtgagtggctcttctgc +ccttggcttctgtattttataataagagagggctcttgctctctctctctctctcctgct +ttgtactttcaatcaatctctttccagcatagttccccctaaaacatcagaaagctgagt +gagcctgtgctctcctctcagagcttagccacttggattccgcagaccctggattgtcac +tttaaa +>p:HG002_1_chr20:61329158-61329678 +ttttgtaccatcataaagtcaaaaaattgtagttcagctgtcatttaagttggagactgt +ctgtacttgacagttgatatgaaatattcacatacgttctgcactggaatccactctgct +ccagtgtttaagcccagtgtgctgcggtggattgcagcatgcgtggagggcacccaggtc +ctcatggttccctcgtgggtctgggacgcgggtcgaggtggctttaagcccagtgtgctg +cggtggattgcagcgtgcgtggagggcacccaggtcctcatggtcccctcatgggtctgg +gacgcgggtcgaggtggctttaagcccagtgtgctgcggtggattgcagcatgcgtggag +ggcacccaggtcctcatggtcccctcatgggtctgggacgtgggtcgaggtggctttaag +cccagtgtgctgcagtggattgcagcatgcgtggagggcacccaggtcctcatggtcccc +tcgtgggtctgggacgcgggtcgaggtggctttaagcccagtgtgctgcggtggattgca +gcgtgcgtggagggcacccaggtcctcatggtcccctcgtgggtctgggacgcgggtcga +ggtggctttaagcctagtgtgctgcggtggattgcagcatgcgtggagggcacccaggtc +ctcatggtcccctcatgggtctgggacgtgggtcgaggtggctttaagcccagtgtgctg +cggtggattgcagcatgcgtggagggcacccaggtcctcatggttgcctcgtgggtctgg +gacgcgggtcgaggtggctttaagcccactgtgctgcagtggattgcagcatgcgtggag +ggcacccaggtcctcatggttcccccgtgggtctgggacgcgggtcgaggtggctttaag +cccactgtgctgcggtggattgcagcatgcgtggagggcacccaggtcctcatggtcccc +ccgtgggtctgggacgcgggtcgaggtggctttaagcccagtgtgctgcggtggattgca +gcatgcgtggagggcacccaggtcctcatggtccccccgtgggtctgggacgcgggtcga +ggtggctttaagcccagtgtgctgcagtggattgcagcatgcgtggagggcacccaggtc +ctcatggttccctcgtgggtctgggacgcgggtcgaggtggctttaagcccagtgtgctg +cggtggattgcagcgtgcgtggagggcacccagatcctcatggttcccccgtgggtctgg +gacgcgggtcgaggtggctttaagcccagtgtgctgcagtggattgcagcatgcgtggag +ggcacccagatcctcatgtttcccccacgggtctgggacgcgggtcgaggtggctttaag +cccagtgtgctgcggtggattgcagcgtgcgtggagggcacccaggtcctcatggttccc +tcgtgggtctgggacgtgggtcgaggtggctttaagcccagtgtgctgcagtggattgca +gcgtgcgtggagggcacccaggtcctcatggtcccctcgtgggtctgggacgcgggtcga +ggtggctttaagcccagtgtgctgcagtggattgcagcgtgcgtggagggcacccaggtc +ctcatggt-cccccgtgggtctgggatgtgggttgaggtggctgtgagtggctcttctgc +ccttggcttctgtattttataataagagagggctcttgctctctctctctctctcctgct +ttgtactttcaatcaatctctttccagcatagttccccctaaaacatcagaaagctgagt +gagcctgtgctctcctctcagagcttagccacttggattccgcagaccctggattgtcac +tttaaa +>p:HG002_2_chr20:61329158-61329678 +ttttgtaccatcataaagtcaaaaaattgtagttcagctgtcatttaagttggagactgt +ctgtacttgacagttgatatgaaatattcacatacgttctgcactggaatccactctgct +ccagtg------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------tttaagcccagtgtgctgcggtggattgca +gcatgcgtggagggcacccaggtcctcatggttcccccgtgggtctgggacgcgggtcga +ggtggctttaagcccagtgtgctgcggtggattgcagcatgcgtggagggcacccagatc +ctcatggttcccccgtgggtctgggacgcgggtcgaggtggctttaagcccactgtgctg +cggtggattgcagcatgcgtggagggcacccaggtcctcatggttcccccacgggtctgg +gacgcgggtcgaggtggctttaagcccagtgtgctgcggtggattgcagcgtgcgtggag +ggcacccaggtcctcatggtccccccgtgggtctgggacgcgggtcgaggtggctttaag +cccagtgtgctgcggtggattgcagcatgcgtggagggcacccagatcctcatggtcccc +ccgtgggtctgggacgcgggtcgaggtggctttaagcccagtgtgctgcggtggattgca +gcatgcgtggagggcacccaggtcctcatggtccccccgtgggtctgggacgcgggtcga +ggtggctttaagcccagtgtgctgcagtggattgcagcatgcgtggagggcacccaggtc +ctcatggtccccccgtgggtctgggatgtgggttgaggtggctgtgagtggctcttctgc +ccttggcttctgtattttataataagagagggctcttgctctctctctctctctcctgct +ttgtactttcaatcaatctctttccagcatagttccccctaaaacatcagaaagctgagt +gagcctgtgctctcctctcagagcttagccacttggattccgcagaccctggattgtcac +tttaaa diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/msa.fa.fai new file mode 100644 index 00000000..bb2b617f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_61329158_61329678 1866 29 60 61 +syndip_1_chr20:61329158-61329678 1866 1961 60 61 +syndip_2_chr20:61329158-61329678 1866 3893 60 61 +p:HG002_1_chr20:61329158-61329678 1866 5826 60 61 +p:HG002_2_chr20:61329158-61329678 1866 7759 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/output.vcf.gz new file mode 100644 index 00000000..22586098 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/output.vcf.gz.tbi new file mode 100644 index 00000000..d8f459e7 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61329258-61329578/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/base.vcf.gz new file mode 100644 index 00000000..a3ec6046 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/base.vcf.gz.tbi new file mode 100644 index 00000000..1911f474 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/comp.vcf.gz new file mode 100644 index 00000000..3526ee01 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/comp.vcf.gz.tbi new file mode 100644 index 00000000..c77c92ad Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/haps.fa new file mode 100644 index 00000000..e3028fce --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/haps.fa @@ -0,0 +1,66 @@ +>ref_chr20_61561820_61562604 +ACAACCCACAAAGGTTTATAGCTCCTTTCCTGTGCTGAAGAGCTGGCCCTTCTCTGGGCCCCAGTGGCTGCATGCGCCATGTTTCTGGGCAGTGACCATATGATGGCAGTAATGCTGTGTCTGGAAATCCTGACCCCAGGGCTCCCAGAGAGAGAGAGGGACCTTCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGGCCTTCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGGCCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGGGACCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCCTGTGGAGAGGTGGACCCCAGGGCTCCCAGAGAGAGAGAGGGACCTTCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGGGACCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCTGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGGGGGACCTTCGTGTGGAGAGGTGGACCCCAGGACTCCCGGAGAGAGAGAGGGGCCTCCGTGTGCAGAGGTGGTTTGTCGCTTCTTTCATCTTCAGGACAGTCATTGCCTGGGAAACTGGGGGGATTGGTCCGAACCCACCTTGTACACCCCAGACTTGGTGCGTCCCTGCAGGATCTGAGCACAGAACGGCCTGCTTCAGCCC +>syndip_1_chr20:61561820-61562604 +ACAACCCACAAAGGTTTATAGCTCCTTTCCTGTGCTGAAGAGCTGGCCCTTCTCTGGGCC +CCAGTGGCTGCATGCGCCATGTTTCTGGGCAGTGACCATATGATGGCAGTAATGCTGTGT +CTGGAAATCCTGACCCCAGGGCTCCCAGAGAGAGAGAGGGACCTTCGTGTGGAGAGGTGG +ACCCCAGGGCTCCCGGAGAGAGAGAGGGGCCTTCGTGTGGAGAGGTGGACCCCAGGGCTC +CCGGAGAGAGAGAGGGGCCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGGG +ACTTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCCTGAGA +GAGAGAGGGACCTCCCTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACC +TCCCTGTGGAGAGGTGGACCCCAGGGCTCCCAGAGAGAGAGAGGGACCTTCGTGTGGAGA +GGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCGTGTGGAGAGGTGGACCCCAG +GGCTCCCGGAGAGAGAGAGGGACCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGA +GAGGGACCTCCGTGTGGAGAGCTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCG +TGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCGTGTGGAGAGGTG +GACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTTCGTGTGGAGAGGTGGACCCCAGGACT +CCCGGAGAGAGAGAGGGGCCTCCGTGTGCAGAGGTGGTTTGTCGCTTCTTTCATCTTCAG +GACAGTCATTGCCTGGGAAACTGGGGGGATTGGTCCGAACCCACCTTGTACACCCCAGAC +TTGGTGCGTCCCTGCAGGATCTGAGCACAGAACGGCCTGCTTCAGCCC +>syndip_2_chr20:61561820-61562604 +ACAACCCACAAAGGTTTATAGCTCCTTTCCTGTGCTGAAGAGCTGGCCCTTCTCTGGGCC +CCAGTGGCTGCATGCGCCATGTTTCTGGGCAGTGACCATATGATGGCAGTAATGCTGTGT +CTGGAAATCCTGACCCCAGGGCTCCCAGAGAGAGAGAGGGACCTTCGTGTGGAGAGGTGG +ACCCCAGGGCTCCCGGAGAGAGAGAGGGGCCTTCGTGTGGAGAGGTGGACCCCAGGGCTC +CCGGAGAGAGAGAGGGGCCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGGG +ACCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCCTGTGG +AGAGGTGGACCCCAGGGCTCCCAGAGAGAGAGAGGGACCTTCGTGTGGAGAGGTGGACCC +CAGGGCTCCCGGAGAGAGAGGGACCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAG +AGAGAGAGGGACCTCTGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGAC +CTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGGGGGACCTTCGTGTGGAG +AGGTGGACCCCAGGACTCCCGGAGAGAGAGAGGGGCCTCCGTGTGCAGAGGTGGTTTGTC +GCTTCTTTCATCTTCAGGACAGTCATTGCCTGGGAAACTGGGGGGATTGGTCCGAACCCA +CCTTGTACACCCCAGACTTGGTGCGTCCCTGCAGGATCTGAGCACAGAACGGCCTGCTTC +AGCCC +>p:HG002_1_chr20:61561820-61562604 +ACAACCCACAAAGGTTTATAGCTCCTTTCCTGTGCTGAAGAGCTGGCCCTTCTCTGGGCC +CCAGTGGCTGCATGCGCCATGTTTCTGGGCAGTGACCATATGATGGCAGTAATGCTGTGT +CTGGAAATCCTGACCCCAGGGCTCCCAGAGAGAGAGAGGGACCTTCGTGTGGAGAGGTGG +ACCCCAGGGCTCCCGGAGAGAGAGAGGGGCCTTCGTGTGGAGAGGTGGACCCCAGGGCTC +CCGGAGAGAGAGAGGGGCCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGGG +ACCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCCTGTGG +AGAGGTGGACCCCAGGGCTCCCAGAGAGAGAGAGGGACCTTCGTGTGGAGAGGTGGACCC +CAGGGCTCCCGGAGAGAGAGGGACCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAG +AGAGAGAGGGACCTCTGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGAC +CTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGGGGGACCTTCGTGTGGAG +AGGTGGACCCCAGGACTCCCGGAGAGAGAGAGGGGCCTCCGTGTGCAGAGGTGGTTTGTC +GCTTCTTTCATCTTCAGGACAGTCATTGCCTGGGAAACTGGGGGGATTGGTCCGAACCCA +CCTTGTACACCCCAGACTTGGTGCGTCCCTGCAGGATCTGAGCACAGAACGGCCTGCTTC +AGCCC +>p:HG002_2_chr20:61561820-61562604 +ACAACCCACAAAGGTTTATAGCTCCTTTCCTGTGCTGAAGAGCTGGCCCTTCTCTGGGCC +CCAGTGGCTGCATGCGCCATGTTTCTGGGCAGTGACCATATGATGGCAGTAATGCTGTGT +CTGGAAATCCTGACCCCAGGGCTCCCAGAGAGAGAGAGGGACCTTCGTGTGGAGAGGTGG +ACCCCAGGGCTCCCGGAGAGAGAGAGGGGCCTTCGTGTGGAGAGGTGGACCCCAGGGCTC +CCGGAGAGAGAGAGGGGCCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGGG +ACTTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCCTGAGA +GAGAGAGGGACCTCCCTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACC +TCCCTGTGGAGAGGTGGACCCCAGGGCTCCCAGAGAGAGAGAGGGACCTTCGTGTGGAGA +GGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCGTGTGGAGAGGTGGACCCCAG +GGCTCCCGGAGAGAGAGAGGGACCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGA +GAGGGACCTCCGTGTGGAGAGCTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCG +TGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCGTGTGGAGAGGTG +GACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTTCGTGTGGAGAGGTGGACCCCAGGACT +CCCGGAGAGAGAGAGGGGCCTCCGTGTGCAGAGGTGGTTTGTCGCTTCTTTCATCTTCAG +GACAGTCATTGCCTGGGAAACTGGGGGGATTGGTCCGAACCCACCTTGTACACCCCAGAC +TTGGTGCGTCCCTGCAGGATCTGAGCACAGAACGGCCTGCTTCAGCCC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/haps.fa.ref.fa new file mode 100644 index 00000000..a158b66a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:61561820-61562604 +ACAACCCACAAAGGTTTATAGCTCCTTTCCTGTGCTGAAGAGCTGGCCCTTCTCTGGGCCCCAGTGGCTGCATGCGCCATGTTTCTGGGCAGTGACCATATGATGGCAGTAATGCTGTGTCTGGAAATCCTGACCCCAGGGCTCCCAGAGAGAGAGAGGGACCTTCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGGCCTTCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGGCCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGGGACCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCCTGTGGAGAGGTGGACCCCAGGGCTCCCAGAGAGAGAGAGGGACCTTCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGGGACCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCTGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGAGGGACCTCCGTGTGGAGAGGTGGACCCCAGGGCTCCCGGAGAGAGAGGGGGACCTTCGTGTGGAGAGGTGGACCCCAGGACTCCCGGAGAGAGAGAGGGGCCTCCGTGTGCAGAGGTGGTTTGTCGCTTCTTTCATCTTCAGGACAGTCATTGCCTGGGAAACTGGGGGGATTGGTCCGAACCCACCTTGTACACCCCAGACTTGGTGCGTCCCTGCAGGATCTGAGCACAGAACGGCCTGCTTCAGCCC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/msa.fa new file mode 100644 index 00000000..c5b871c8 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/msa.fa @@ -0,0 +1,85 @@ +>ref_chr20_61561820_61562604 +acaacccacaaaggtttatagctcctttcctgtgctgaagagctggcccttctctgggcc +ccagtggctgcatgcgccatgtttctgggcagtgaccatatgatggcagtaatgctgtgt +ctggaaatcctgaccccagggctcccagagagagagagggaccttcgtgtggagaggtgg +accccagggctcccggagagagagaggggccttcgtgtggagaggtggaccccagggctc +ccggagagagagaggggcctccgtgtggagaggtggaccccagggctcccggagagaggg +acctccg----------------------------------------------------- +----------------tgtggagaggtggaccccagggctcccggagagagagagggacc +tccctgtggagaggtggaccccagggctcccagagagagagagggaccttcgtgtggaga +ggtggaccccagggctcccgga-------------------------------------- +--------------------------------------------------------gaga +gagggacctccgtgtggagaggtggaccccagggctcccggagagagagagggacctctg +tgtggagaggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtg +gaccccagggctcccggagagagagggggaccttcgtgtggagaggtggaccccaggact +cccggagagagagaggggcctccgtgtgcagaggtggtttgtcgcttctttcatcttcag +gacagtcattgcctgggaaactggggggattggtccgaacccaccttgtacaccccagac +ttggtgcgtccctgcaggatctgagcacagaacggcctgcttcagccc +>syndip_1_chr20:61561820-61562604 +acaacccacaaaggtttatagctcctttcctgtgctgaagagctggcccttctctgggcc +ccagtggctgcatgcgccatgtttctgggcagtgaccatatgatggcagtaatgctgtgt +ctggaaatcctgaccccagggctcccagagagagagagggaccttcgtgtggagaggtgg +accccagggctcccggagagagagaggggccttcgtgtggagaggtggaccccagggctc +ccggagagagagaggggcctccgtgtggagaggtggaccccagggctcccggagagaggg +acttccgtgtggagaggtggaccccagggctcccggagagagagagggacctccctgaga +gagagagggacctccctgtggagaggtggaccccagggctcccggagagagagagggacc +tccctgtggagaggtggaccccagggctcccagagagagagagggaccttcgtgtggaga +ggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtggaccccag +ggctcccggagagagagagggacctccgtgtggagaggtggaccccagggctcccggaga +gagggacctccgtgtggagagctggaccccagggctcccggagagagagagggacctccg +tgtggagaggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtg +gaccccagggctcccggagagagagagggaccttcgtgtggagaggtggaccccaggact +cccggagagagagaggggcctccgtgtgcagaggtggtttgtcgcttctttcatcttcag +gacagtcattgcctgggaaactggggggattggtccgaacccaccttgtacaccccagac +ttggtgcgtccctgcaggatctgagcacagaacggcctgcttcagccc +>syndip_2_chr20:61561820-61562604 +acaacccacaaaggtttatagctcctttcctgtgctgaagagctggcccttctctgggcc +ccagtggctgcatgcgccatgtttctgggcagtgaccatatgatggcagtaatgctgtgt +ctggaaatcctgaccccagggctcccagagagagagagggaccttcgtgtggagaggtgg +accccagggctcccggagagagagaggggccttcgtgtggagaggtggaccccagggctc +ccggagagagagaggggcctccgtgtggagaggtggaccccagggctcccggagagaggg +acctccg----------------------------------------------------- +----------------tgtggagaggtggaccccagggctcccggagagagagagggacc +tccctgtggagaggtggaccccagggctcccagagagagagagggaccttcgtgtggaga +ggtggaccccagggctcccgga-------------------------------------- +--------------------------------------------------------gaga +gagggacctccgtgtggagaggtggaccccagggctcccggagagagagagggacctctg +tgtggagaggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtg +gaccccagggctcccggagagagagggggaccttcgtgtggagaggtggaccccaggact +cccggagagagagaggggcctccgtgtgcagaggtggtttgtcgcttctttcatcttcag +gacagtcattgcctgggaaactggggggattggtccgaacccaccttgtacaccccagac +ttggtgcgtccctgcaggatctgagcacagaacggcctgcttcagccc +>p:HG002_1_chr20:61561820-61562604 +acaacccacaaaggtttatagctcctttcctgtgctgaagagctggcccttctctgggcc +ccagtggctgcatgcgccatgtttctgggcagtgaccatatgatggcagtaatgctgtgt +ctggaaatcctgaccccagggctcccagagagagagagggaccttcgtgtggagaggtgg +accccagggctcccggagagagagaggggccttcgtgtggagaggtggaccccagggctc +ccggagagagagaggggcctccgtgtggagaggtggaccccagggctcccggagagaggg +acctccg----------------------------------------------------- +----------------tgtggagaggtggaccccagggctcccggagagagagagggacc +tccctgtggagaggtggaccccagggctcccagagagagagagggaccttcgtgtggaga +ggtggaccccagggctcccgga-------------------------------------- +--------------------------------------------------------gaga +gagggacctccgtgtggagaggtggaccccagggctcccggagagagagagggacctctg +tgtggagaggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtg +gaccccagggctcccggagagagagggggaccttcgtgtggagaggtggaccccaggact +cccggagagagagaggggcctccgtgtgcagaggtggtttgtcgcttctttcatcttcag +gacagtcattgcctgggaaactggggggattggtccgaacccaccttgtacaccccagac +ttggtgcgtccctgcaggatctgagcacagaacggcctgcttcagccc +>p:HG002_2_chr20:61561820-61562604 +acaacccacaaaggtttatagctcctttcctgtgctgaagagctggcccttctctgggcc +ccagtggctgcatgcgccatgtttctgggcagtgaccatatgatggcagtaatgctgtgt +ctggaaatcctgaccccagggctcccagagagagagagggaccttcgtgtggagaggtgg +accccagggctcccggagagagagaggggccttcgtgtggagaggtggaccccagggctc +ccggagagagagaggggcctccgtgtggagaggtggaccccagggctcccggagagaggg +acttccgtgtggagaggtggaccccagggctcccggagagagagagggacctccctgaga +gagagagggacctccctgtggagaggtggaccccagggctcccggagagagagagggacc +tccctgtggagaggtggaccccagggctcccagagagagagagggaccttcgtgtggaga +ggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtggaccccag +ggctcccggagagagagagggacctccgtgtggagaggtggaccccagggctcccggaga +gagggacctccgtgtggagagctggaccccagggctcccggagagagagagggacctccg +tgtggagaggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtg +gaccccagggctcccggagagagagagggaccttcgtgtggagaggtggaccccaggact +cccggagagagagaggggcctccgtgtgcagaggtggtttgtcgcttctttcatcttcag +gacagtcattgcctgggaaactggggggattggtccgaacccaccttgtacaccccagac +ttggtgcgtccctgcaggatctgagcacagaacggcctgcttcagccc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/msa.fa.fai new file mode 100644 index 00000000..c6059a5b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_61561820_61562604 948 29 60 61 +syndip_1_chr20:61561820-61562604 948 1027 60 61 +syndip_2_chr20:61561820-61562604 948 2025 60 61 +p:HG002_1_chr20:61561820-61562604 948 3024 60 61 +p:HG002_2_chr20:61561820-61562604 948 4023 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/output.vcf.gz new file mode 100644 index 00000000..ce1dd1a4 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/output.vcf.gz.tbi new file mode 100644 index 00000000..91ed720e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61561920-61562504/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/base.vcf.gz new file mode 100644 index 00000000..527b300a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/base.vcf.gz.tbi new file mode 100644 index 00000000..7fdddecb Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/comp.vcf.gz new file mode 100644 index 00000000..b0cba2af Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/comp.vcf.gz.tbi new file mode 100644 index 00000000..58a92aea Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/haps.fa new file mode 100644 index 00000000..82ed0b4f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/haps.fa @@ -0,0 +1,44 @@ +>ref_chr20_61744088_61744755 +TCAAACTGGGCACTGCAAATTCTGGAATCTCTCCTACCTCCCGAAGTTTGTAGTCCACCAGGCCCAGGGCGTTCTGAAGCCTGGAGGGATGAGAAGCAAGCGGAGACTGTGTGGTTGGAAAGGAGCCAACCAGAGAGTGGGGAGGCGATGGAGAGAATAACAGAGAGGAAGGCAGGTGCAGGGAGACAGCAAAGGAGAGGGAGAAGAGAATGAGAGAGGGATGGGGAGAAAGAGAGAAGAGAGGTGGAGAGAGACAGGAAAGGAGAGGGAGGGAGAGGAAGAGAGGGAGAGAGAGAAGGAGGGAGAGAGATGGAAAGAGGTGGAGGGAGAGAGAGAAGGAAAGGGAGGGAGAGGAAGAGAGGGAGAGAGAGAAGGAGGGAGAGAGATGGAGAGAGGTGGAGGGAGAGAGAGAAGGAAAGGGAGGGGAGAGGAAGAGAGGGAGAGAGAGAAGGAGGGAGAGAGATGGAGAGAGGTGGAGGGAGAGAGAGAAGGAAAGGGAGGGAGAGAGAGAGACAGACAGACAGCTTCACACAGACATAAAACATCTGCTGTTCAGGATCCCAGCTGCCCTCCGACTCTGCCTCCTTCTAACCCGGCTGCCTGGCTCACCCGGGTGACAGGGAGGGGCGCCTTCACCATGCCCTGTCCTGAGGCTCCCTTTCATCCTG +>syndip_1_chr20:61744088-61744755 +TCAAACTGGGCACTGCAAATTCTGGAATCTCTCCTACCTCCCGAAGTTTGTAGTCCACCA +GGCCCAGGGCGTTCTGAAGCCTGGAGGGATGAGAAGCAAGCGGAGACTGTGTGGTTGGAA +AGGAGCCAACCAGAGAGTGGGGAGGCGATGGAGAGAATAACAGAGAGGAAGGCAGGTGCA +GGGAGACAGCAAAGGAGAGGGAGAAGAGAATGAGAGAGGGATGGGGAGAAAGAGAGAAGA +GAGGTGGAGAGAGACAGGAAAGGAGAGGGAGGGAGAGGAAGAGAGGGAGAGAGAGAAGGA +GGGAGAGAGATGGAAAGAGGTGGAGGGAGAGAGAGAAGGAAAGGGAGGGAGAGAGAGAGA +CAGACAGACAGCTTCACACAGACATAAAACATCTGCTGTTCAGGATCCCAGCTGCCCTCC +GACTCTGCCTCCTTCTAACCCGGCTGCCTGGCTCACCCGGGTGACAGGGAGGGGCGCCTT +CACCATGCCCTGTCCTGAGGCTCCCTTTCATCCTG +>syndip_2_chr20:61744088-61744755 +TCAAACTGGGCACTGCAAATTCTGGAATCTCTCCTACCTCCCGAAGTTTGTAGTCCACCA +GGCCCAGGGCGTTCTGAAGCCTGGAGGGATGAGAAGCAAGCGGAGACTGTGTGGTTGGAA +AGGAGCCAACCAGAGAGTGGGGAGGCGATGGAGAGAATAAGAGAGAGGAAGGCAGGTGCA +GGGAGACAGCAAAGGAGAGGGAGAAGAGAATGAGAGAGGGATGGGGAGAAAGAGAGAAGA +GAGGTGGAGAGAGACAGGAAAGGAGAGGGAGGGAGAGGAAGAGAGGGAGAGAGAGAAGGA +GGGAGAGAGATGGAAAGAGGTGGAGGGAGAGAGAGAAGGAAAGGGAGGGAGAGGAAGAGA +GGGAGAGAGAGAAGGAGGGAGAGAGATGGAGAGAGGTGGAGGGAGAGAGAGAAGGAAAGG +GAGGGAGAGAGAGAGACAGACAGCTTCACACAGACATAAAACATCTGCTGTTCAGGATCC +CAGCTGCCCTCCGACTCTGCCTCCTTCTAACCCGGCTGCCTGGCTCACCCGGGTGACAGG +GAGGGGCGCCTTCACCATGCCCTGTCCTGAGGCTCCCTTTCATCCTG +>p:HG002_1_chr20:61744088-61744755 +TCAAACTGGGCACTGCAAATTCTGGAATCTCTCCTACCTCCCGAAGTTTGTAGTCCACCA +GGCCCAGGGCGTTCTGAAGCCTGGAGGGATGAGAAGCAAGCGGAGACTGTGTGGTTGGAA +AGGAGCCAACCAGAGAGTGGGGAGGCGATGGAGAGAATAAGAGAGAGGAAGGCAGGTGCA +GGGAGACAGCAAAGGAGAGGGAGAAGAGAATGAGAGAGGGATGGGGAGAAAGAGAGAAGA +GAGGTGGAGAGAGACAGGAAAGGAGAGGGAGGGAGAGGAAGAGAGGGAGAGAGAGAAGGA +GGGAGAGAGATGGAAAGAGGTGGAGGGAGAGAGAGAAGGAAAGGGAGGGAGAGGAAGAGA +GGGAGAGAGAGAAGGAGGGAGAGAGATGGAGAGAGGTGGAGGGAGAGAGAGAAGGAAAGG +GAGGGAGAGAGAGAGACAGACAGCTTCACACAGACATAAAACATCTGCTGTTCAGGATCC +CAGCTGCCCTCCGACTCTGCCTCCTTCTAACCCGGCTGCCTGGCTCACCCGGGTGACAGG +GAGGGGCGCCTTCACCATGCCCTGTCCTGAGGCTCCCTTTCATCCTG +>p:HG002_2_chr20:61744088-61744755 +TCAAACTGGGCACTGCAAATTCTGGAATCTCTCCTACCTCCCGAAGTTTGTAGTCCACCA +GGCCCAGGGCGTTCTGAAGCCTGGAGGGATGAGAAGCAAGCGGAGACTGTGTGGTTGGAA +AGGAGCCAACCAGAGAGTGGGGAGGCGATGGAGAGAATAACAGAGAGGAAGGCAGGTGCA +GGGAGACAGCAAAGGAGAGGGAGAAGAGAATGAGAGAGGGATGGGGAGAAAGAGAGAAGA +GAGGTGGAGAGAGACAGGAAAGGAGAGGGAGGGAGAGGAAGAGAGGGAGAGAGAGAAGGA +GGGAGAGAGATGGAAAGAGGTGGAGGGAGAGAGAGAAGGAAAGGGAGGGAGAGAGAGAGA +CAGACAGACAGCTTCACACAGACATAAAACATCTGCTGTTCAGGATCCCAGCTGCCCTCC +GACTCTGCCTCCTTCTAACCCGGCTGCCTGGCTCACCCGGGTGACAGGGAGGGGCGCCTT +CACCATGCCCTGTCCTGAGGCTCCCTTTCATCCTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/haps.fa.ref.fa new file mode 100644 index 00000000..ba684156 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:61744088-61744755 +TCAAACTGGGCACTGCAAATTCTGGAATCTCTCCTACCTCCCGAAGTTTGTAGTCCACCAGGCCCAGGGCGTTCTGAAGCCTGGAGGGATGAGAAGCAAGCGGAGACTGTGTGGTTGGAAAGGAGCCAACCAGAGAGTGGGGAGGCGATGGAGAGAATAACAGAGAGGAAGGCAGGTGCAGGGAGACAGCAAAGGAGAGGGAGAAGAGAATGAGAGAGGGATGGGGAGAAAGAGAGAAGAGAGGTGGAGAGAGACAGGAAAGGAGAGGGAGGGAGAGGAAGAGAGGGAGAGAGAGAAGGAGGGAGAGAGATGGAAAGAGGTGGAGGGAGAGAGAGAAGGAAAGGGAGGGAGAGGAAGAGAGGGAGAGAGAGAAGGAGGGAGAGAGATGGAGAGAGGTGGAGGGAGAGAGAGAAGGAAAGGGAGGGGAGAGGAAGAGAGGGAGAGAGAGAAGGAGGGAGAGAGATGGAGAGAGGTGGAGGGAGAGAGAGAAGGAAAGGGAGGGAGAGAGAGAGACAGACAGACAGCTTCACACAGACATAAAACATCTGCTGTTCAGGATCCCAGCTGCCCTCCGACTCTGCCTCCTTCTAACCCGGCTGCCTGGCTCACCCGGGTGACAGGGAGGGGCGCCTTCACCATGCCCTGTCCTGAGGCTCCCTTTCATCCTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/msa.fa new file mode 100644 index 00000000..d574e4be --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/msa.fa @@ -0,0 +1,65 @@ +>ref_chr20_61744088_61744755 +tcaaactgggcactgcaaattctggaatctctcctacctcccgaagtttgtagtccacca +ggcccagggcgttctgaagcctggagggatgagaagcaagcggagactgtgtggttggaa +aggagccaaccagagagtggggaggcgatggagagaataacagagaggaaggcaggtgca +gggagacagcaaaggagagggagaagagaatgagagagggatggggagaaagagagaaga +gaggtggagagagacaggaaaggagagggagggagaggaagagagggagagagagaagga +gggagagagatggaaagaggtggagggagagagagaaggaaagggagggagaggaagaga +gggagagagagaaggagggagagagatggagagaggtggagggagagagagaaggaaagg +gaggggagaggaagagagggagagagagaaggagggagagagatggagagaggtggaggg +agagagagaaggaaagggagggagagagagagacagacagacagcttcacacagacataa +aacatctgctgttcaggatcccagctgccctccgactctgcctccttctaacccggctgc +ctggctcacccgggtgacagggaggggcgccttcaccatgccctgtcctgaggctccctt +tcatcctg +>syndip_1_chr20:61744088-61744755 +tcaaactgggcactgcaaattctggaatctctcctacctcccgaagtttgtagtccacca +ggcccagggcgttctgaagcctggagggatgagaagcaagcggagactgtgtggttggaa +aggagccaaccagagagtggggaggcgatggagagaataacagagaggaaggcaggtgca +gggagacagcaaaggagagggagaagagaatgagagagggatggggagaaagagagaaga +gaggtggagagagacaggaaaggagagggagggagaggaagagagggagagagagaagga +gggagagagatggaaagaggtggagggagagagagaaggaaagggagggaga-------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------gagagagacagacagacagcttcacacagacataa +aacatctgctgttcaggatcccagctgccctccgactctgcctccttctaacccggctgc +ctggctcacccgggtgacagggaggggcgccttcaccatgccctgtcctgaggctccctt +tcatcctg +>syndip_2_chr20:61744088-61744755 +tcaaactgggcactgcaaattctggaatctctcctacctcccgaagtttgtagtccacca +ggcccagggcgttctgaagcctggagggatgagaagcaagcggagactgtgtggttggaa +aggagccaaccagagagtggggaggcgatggagagaataagagagaggaaggcaggtgca +gggagacagcaaaggagagggagaagagaatgagagagggatggggagaaagagagaaga +gaggtggagagagacaggaaaggagagggagggagaggaagagagggagagagagaagga +gggagagagatggaaagaggtggagggagagagagaaggaaagggagggagaggaagaga +gggagagagagaaggagggagagagatggagagaggtggagggagagagagaaggaaagg +gagg-------------------------------------------------------- +-------------------------gagagagagagacagacagcttcacacagacataa +aacatctgctgttcaggatcccagctgccctccgactctgcctccttctaacccggctgc +ctggctcacccgggtgacagggaggggcgccttcaccatgccctgtcctgaggctccctt +tcatcctg +>p:HG002_1_chr20:61744088-61744755 +tcaaactgggcactgcaaattctggaatctctcctacctcccgaagtttgtagtccacca +ggcccagggcgttctgaagcctggagggatgagaagcaagcggagactgtgtggttggaa +aggagccaaccagagagtggggaggcgatggagagaataagagagaggaaggcaggtgca +gggagacagcaaaggagagggagaagagaatgagagagggatggggagaaagagagaaga +gaggtggagagagacaggaaaggagagggagggagaggaagagagggagagagagaagga +gggagagagatggaaagaggtggagggagagagagaaggaaagggagggagaggaagaga +gggagagagagaaggagggagagagatggagagaggtggagggagagagagaaggaaagg +gagg-------------------------------------------------------- +-------------------------gagagagagagacagacagcttcacacagacataa +aacatctgctgttcaggatcccagctgccctccgactctgcctccttctaacccggctgc +ctggctcacccgggtgacagggaggggcgccttcaccatgccctgtcctgaggctccctt +tcatcctg +>p:HG002_2_chr20:61744088-61744755 +tcaaactgggcactgcaaattctggaatctctcctacctcccgaagtttgtagtccacca +ggcccagggcgttctgaagcctggagggatgagaagcaagcggagactgtgtggttggaa +aggagccaaccagagagtggggaggcgatggagagaataacagagaggaaggcaggtgca +gggagacagcaaaggagagggagaagagaatgagagagggatggggagaaagagagaaga +gaggtggagagagacaggaaaggagagggagggagaggaagagagggagagagagaagga +gggagagagatggaaagaggtggagggagagagagaaggaaagggagggaga-------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------gagagagacagacagacagcttcacacagacataa +aacatctgctgttcaggatcccagctgccctccgactctgcctccttctaacccggctgc +ctggctcacccgggtgacagggaggggcgccttcaccatgccctgtcctgaggctccctt +tcatcctg diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/msa.fa.fai new file mode 100644 index 00000000..f20007eb --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_61744088_61744755 668 29 60 61 +syndip_1_chr20:61744088-61744755 668 743 60 61 +syndip_2_chr20:61744088-61744755 668 1457 60 61 +p:HG002_1_chr20:61744088-61744755 668 2172 60 61 +p:HG002_2_chr20:61744088-61744755 668 2887 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/output.vcf.gz new file mode 100644 index 00000000..3f5907f1 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/output.vcf.gz.tbi new file mode 100644 index 00000000..de20e3aa Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61744188-61744655/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61783403-61784840/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61783403-61784840/base.vcf.gz new file mode 100644 index 00000000..38f579f9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61783403-61784840/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61783403-61784840/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61783403-61784840/base.vcf.gz.tbi new file mode 100644 index 00000000..cb1a8490 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61783403-61784840/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61783403-61784840/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61783403-61784840/comp.vcf.gz new file mode 100644 index 00000000..e6094735 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61783403-61784840/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61783403-61784840/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61783403-61784840/comp.vcf.gz.tbi new file mode 100644 index 00000000..44dc546f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61783403-61784840/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61783403-61784840/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61783403-61784840/haps.fa new file mode 100644 index 00000000..581163e6 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61783403-61784840/haps.fa @@ -0,0 +1,108 @@ +>ref_chr20_61783303_61784940 +CTCCAAAGGCACATTCTATATGATTTTTGCCCACAACCTTTCCTTAATATGTACATGTTTTCTAGATAAAAACATTAAATACAGCTAAAGTGACATCAAGGTCTCCCTCCCTTCCTTTCCTCCAATACGTGAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCGAGGCCCTCAGATGTCCTGTGCCCCCGAAAGAAATGTAATCCCAGTTCCTTGGGATAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCTGGGAGAAATGTAAGCCCAGTTCCTCAGGACAGTTCTCGAGGCCCTCAGATGTCCTGTGCTCCCAGGAGAATATAAGCCTAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCCGGGCCCTCAGATGTCCTGTGCCCCCGGGAGAAATGTAAGCCTAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTTGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTTGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAATCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCCAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGAACAGTTCTCCAGGCCCTCAGATGTCCTGTGCCCCCGGGGCCTCATCAGACATTAAGCATGCAGTCCCTTTGCAGCTCTGGATGGCGCGAGTTTCCCACGTCCCATCCCCTTCCTGGCTATGGGCAAGTGCAGGCTGGATCCTGGCCTCCTCCTTCCTGGCCTCCAG +>syndip_1_chr20:61783303-61784940 +CTCCAAAGGCACATTCTATATGATTTTTGCCCACAACCTTTCCTTAATATGTACATGTTT +TCTAGATAAAAACATTAAATACAGCTAAAGTGACATCAAGGTCTCCCTCCCTTCCTTTCC +TCCAATACGTGAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCGAGGCCCTCAGAT +GTCCTGTGCCCCCGAAAGAAATGTAATCCCAGTTCCTTGGGATAGTTCTCAAGGCCCTCC +GATATCCTGTGCCCCTGGGAGAAATGTAAGCCCAGTTCCTCAGGACAGTTCTCGAGGCCC +TCAGATGTCCTGTGCTCCCAGGAGAATATAAGCCTAGTTCCTCGGGACAGTTCTCGAGGC +CCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCCG +GGCCCTCAGATGTCCTGTGCCCCCGGGAGAAATGTAAGCCTAGTTCCTCGGGACAGTTCT +CGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGT +TCTCAAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGAC +AGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGG +ACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTTG +GGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCC +TCGGGACAGTTCTCAAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGT +TCCTTGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCA +GTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAGGAGAATGTAAGCC +CAGTTCCTTGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAA +TCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGT +AATCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAA +TGTAATCCCAGTTCCTCGGGACAGTTCTCCAGGCCCTCCGATATCCTGTGCCCCCAGGAG +AATGTAAGCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGATGTCCTGTGCCCCCAAG +AGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCC +AGGAGAATGTAAGCCCAGTTCCTCGGGACAGTTCTCCAGGCCCTCCGATATCCTGTGCCC +CCAGGAGAATGTAAGCCCAGTTCCTCGGAACAGTTCTCCAGGCCCTCAGATGTCCTGTGC +CCCCGGGGCCTCATCAGACATTAAGCATGCAGTCCCTTTGCAGCTCTGGATGGCGCGAGT +TTCCCACGTCCCATCCCCTTCCTGGCTATGGGCAAGTGCAGGCTGGATCCTGGCCTCCTC +CTTCCTGGCCTCCAG +>syndip_2_chr20:61783303-61784940 +CTCCAAAGGCACATTCTATATGATTTTTGCCCACAACCTTTCCTTAATATGTACATGTTT +TCTAGATAAAAACATTAAATACAGCTAAAGTGACATCAAGGTCTCCCTCCCTTCCTTTCC +TCCAATACGTGAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCGAGGCCCTCAGAT +GTCCTGTGCCCCCGAAAGAAATGTAATCCCAGTTCCTTGGGATAGTTCTCAAGGCCCTCC +GATATCCTGTGCCCCTGGGAGAAATGTAAGCCCAGTTCCTCAGGACAGTTCTCGAGGCCC +TCAGATGTCCTGTGCTCCCAGGAGAATATAAGCCTAGTTCCTCGGGACAGTTCTCGAGGC +CCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCCG +GGCCCTCAGATGTCCTGTGCCCCCGGGAGAAATGTAAGCCTAGTTCCTCGGGACAGTTCT +CGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGACAGT +TCTCGAGGCCCTCAGATGTCCTGTGCCCCCGGGAGAAATGTAAGCCTAGTTCCTCGGGAC +AGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGG +ACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTC +GGGACAGTTCTCAAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGTTC +CTTGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGT +TCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAGGAGAATGTAAGCCCA +GTTCCTTGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATC +CCAGTTCCTCGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAA +GCCCAGTTCCTCGGGACAGTTCTCGAGGCCTTCAGGTGTCTTGTGCCCCCAAGAGAAATG +TAATCCCAGTTCCTCGGAACAGTTCTCCAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAA +ATGTAATCCCAGTTCCTCGGGACAGTTCTCCAGGCCCTCCGATATCCTGTGCCCCCAGGA +GAATGTAAGCCCAGTTCCTCGGAACAGTTCTCCAGGCCCTCAGATGTCCTGTGCCCCCGG +GGCCTCATCAGACATTAAGCATGCAGTCCCTTTGCAGCTCTGGATGGCGCGAGTTTCCCA +CGTCCCATCCCCTTCCTGGCTATGGGCAAGTGCAGGCTGGATCCTGGCCTCCTCCTTCCT +GGCCTCCAG +>p:HG002_1_chr20:61783303-61784940 +CTCCAAAGGCACATTCTATATGATTTTTGCCCACAACCTTTCCTTAATATGTACATGTTT +TCTAGATAAAAACATTAAATACAGCTAAAGTGACATCAAGGTCTCCCTCCCTTCCTTTCC +TCCAATACGTGAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCGAGGCCCTCAGAT +GTCCTGTGCCCCCGAAAGAAATGTAATCCCAGTTCCTTGGGATAGTTCTCAAGGCCCTCC +GATATCCTGTGCCCCTGGGAGAAATGTAAGCCCAGTTCCTCAGGACAGTTCTCGAGGCCC +TCAGATGTCCTGTGCTCCCAGGAGAATATAAGCCTAGTTCCTCGGGACAGTTCTCGAGGC +CCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCCG +GGCCCTCAGATGTCCTGTGCCCCCGGGAGAAATGTAAGCCTAGTTCCTCGGGACAGTTCT +CGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGACAGT +TCTCGAGGCCCTCAGATGTCCTGTGCCCCCGGGAGAAATGTAAGCCTAGTTCCTCGGGAC +AGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGG +ACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTC +GGGACAGTTCTCAAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGTTC +CTTGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGT +TCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAGGAGAATGTAAGCCCA +GTTCCTTGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATC +CCAGTTCCTCGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAA +GCCCAGTTCCTCGGGACAGTTCTCGAGGCCTTCAGGTGTCTTGTGCCCCCAAGAGAAATG +TAATCCCAGTTCCTCGGAACAGTTCTCCAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAA +ATGTAATCCCAGTTCCTCGGGACAGTTCTCCAGGCCCTCCGATATCCTGTGCCCCCAGGA +GAATGTAAGCCCAGTTCCTCGGAACAGTTCTCCAGGCCCTCAGATGTCCTGTGCCCCCGG +GGCCTCATCAGACATTAAGCATGCAGTCCCTTTGCAGCTCTGGATGGCGCGAGTTTCCCA +CGTCCCATCCCCTTCCTGGCTATGGGCAAGTGCAGGCTGGATCCTGGCCTCCTCCTTCCT +GGCCTCCAG +>p:HG002_2_chr20:61783303-61784940 +CTCCAAAGGCACATTCTATATGATTTTTGCCCACAACCTTTCCTTAATATGTACATGTTT +TCTAGATAAAAACATTAAATACAGCTAAAGTGACATCAAGGTCTCCCTCCCTTCCTTTCC +TCCAATACGTGAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCGAGGCCCTCAGAT +GTCCTGTGCCCCCGAAAGAAATGTAATCCCAGTTCCTTGGGATAGTTCTCAAGGCCCTCC +GATATCCTGTGCCCCTGGGAGAAATGTAAGCCCAGTTCCTCAGGACAGTTCTCGAGGCCC +TCAGATGTCCTGTGCTCCCAGGAGAATATAAGCCTAGTTCCTCGGGACAGTTCTCGAGGC +CCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCCG +GGCCCTCAGATGTCCTGTGCCCCCGGGAGAAATGTAAGCCTAGTTCCTCGGGACAGTTCT +CGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGT +TCTCAAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGAC +AGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGG +ACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTTG +GGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCC +TCGGGACAGTTCTCAAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGT +TCCTTGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCA +GTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAGGAGAATGTAAGCC +CAGTTCCTTGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAA +TCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGT +AATCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAA +TGTAATCCCAGTTCCTCGGGACAGTTCTCCAGGCCCTCCGATATCCTGTGCCCCCAGGAG +AATGTAAGCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGATGTCCTGTGCCCCCAAG +AGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCC +AGGAGAATGTAAGCCCAGTTCCTCGGGACAGTTCTCCAGGCCCTCCGATATCCTGTGCCC +CCAGGAGAATGTAAGCCCAGTTCCTCGGAACAGTTCTCCAGGCCCTCAGATGTCCTGTGC +CCCCGGGGCCTCATCAGACATTAAGCATGCAGTCCCTTTGCAGCTCTGGATGGCGCGAGT +TTCCCACGTCCCATCCCCTTCCTGGCTATGGGCAAGTGCAGGCTGGATCCTGGCCTCCTC +CTTCCTGGCCTCCAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61783403-61784840/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61783403-61784840/haps.fa.ref.fa new file mode 100644 index 00000000..fe5fb8f5 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61783403-61784840/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:61783303-61784940 +CTCCAAAGGCACATTCTATATGATTTTTGCCCACAACCTTTCCTTAATATGTACATGTTTTCTAGATAAAAACATTAAATACAGCTAAAGTGACATCAAGGTCTCCCTCCCTTCCTTTCCTCCAATACGTGAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCGAGGCCCTCAGATGTCCTGTGCCCCCGAAAGAAATGTAATCCCAGTTCCTTGGGATAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCTGGGAGAAATGTAAGCCCAGTTCCTCAGGACAGTTCTCGAGGCCCTCAGATGTCCTGTGCTCCCAGGAGAATATAAGCCTAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCCGGGCCCTCAGATGTCCTGTGCCCCCGGGAGAAATGTAAGCCTAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTTGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTTGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTTGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAATCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGGTGTCTTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCCAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGGACAGTTCTCGAGGCCCTCAGATGTCCTGTGCCCCCAAGAGAAATGTAATCCCAGTTCCTCGGGACAGTTCTCAAGGCCCTCCGATATCCTGTGCCCCCAGGAGAATGTAAGCCCAGTTCCTCGGAACAGTTCTCCAGGCCCTCAGATGTCCTGTGCCCCCGGGGCCTCATCAGACATTAAGCATGCAGTCCCTTTGCAGCTCTGGATGGCGCGAGTTTCCCACGTCCCATCCCCTTCCTGGCTATGGGCAAGTGCAGGCTGGATCCTGGCCTCCTCCTTCCTGGCCTCCAG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61783403-61784840/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61783403-61784840/msa.fa new file mode 100644 index 00000000..4d970eab --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:61783403-61784840/msa.fa @@ -0,0 +1,145 @@ +>ref_chr20_61783303_61784940 +ctccaaaggcacattctatatgatttttgcccacaacctttccttaatatgtacatgttt +tctagataaaaacattaaatacagctaaagtgacatcaaggtctccctcccttcctttcc +tccaatacgtgagagaaatgtaatcccagttccttgggacagttctcgaggccctcagat +gtcctgtgcccccgaaagaaatgtaatcccagttccttgggatagttctcaaggccctcc +gatatcctgtgcccctgggagaaatgtaagcccagttcctcaggacagttctcgaggccc +tcagatgtcctgtgctcccaggagaatataagcctagttcctcgggacagttctcgaggc +cctcaggtgtcttgtgcccccaagagaaatgtaatcccagttccttgggacagttctccg +ggccctcagatgtcctgtgcccccgggagaaatgtaagcctagttcctcgggacagttct +cgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttcctcgggacagt +tctcaaggccctcagatgtcctgtgcccccaagagaaatgtaatcccagttccttgggac +agttctcaaggccctccgatatcctgtgcccccaggagaatgtaagcccagttcctcggg +acagttctcgaggccctcaggtgtcttgtgcccccaggagaatgtaagcccagttccttg +ggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttcc +tcgggacagttctcaaggccctcagatgtcctgtgcccccaagagaaatgtaatcccagt +tccttgggacagttctcaaggccctccgatatcctgtgcccccaggagaatgtaagccca +gttcctcgggacagttctcgaggccctcaggtgtcttgtgcccccaggagaatgtaagcc +cagttccttgggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaa +tcccagttcctcgggacagttctcaaggccctccgatatcctgtgcccccaggagaatgt +aatcccagttcctcgggacagttctcgaggccctcagatgtcctgtgcccccaagagaaa +tgtaatcccagttcctcgggacagttctcaaggccctccgatatcctgtgcccccaggag +aatgtaagcccagttcctcgggacagttctcgaggccctcaggtgtcttgtgcccccaag +agaaatgtaatcccagttcctcgggacagttctccaggccctccgatatcctgtgccccc +aggagaatgtaagcccagttcctcgggacagttctcgaggccctcagatgtcctgtgccc +ccaagagaaatgtaatcccagttcctcgggacagttctcaaggccctccgatatcctgtg +cccccaggagaatgtaagcccagttcctcggaacagttctccaggccctcagatgtcctg +tgcccccggggcctcatcagacattaagcatgcagtccctttgcagctctggatggcgcg +agtttcccacgtcccatccccttcctggctatgggcaagtgcaggctggatcctggcctc +ctccttcctggcctccag +>syndip_1_chr20:61783303-61784940 +ctccaaaggcacattctatatgatttttgcccacaacctttccttaatatgtacatgttt +tctagataaaaacattaaatacagctaaagtgacatcaaggtctccctcccttcctttcc +tccaatacgtgagagaaatgtaatcccagttccttgggacagttctcgaggccctcagat +gtcctgtgcccccgaaagaaatgtaatcccagttccttgggatagttctcaaggccctcc +gatatcctgtgcccctgggagaaatgtaagcccagttcctcaggacagttctcgaggccc +tcagatgtcctgtgctcccaggagaatataagcctagttcctcgggacagttctcgaggc +cctcaggtgtcttgtgcccccaagagaaatgtaatcccagttccttgggacagttctccg +ggccctcagatgtcctgtgcccccgggagaaatgtaagcctagttcctcgggacagttct +cgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttcctcgggacagt +tctcaaggccctcagatgtcctgtgcccccaagagaaatgtaatcccagttccttgggac +agttctcaaggccctccgatatcctgtgcccccaggagaatgtaagcccagttcctcggg +acagttctcgaggccctcaggtgtcttgtgcccccaggagaatgtaagcccagttccttg +ggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttcc +tcgggacagttctcaaggccctcagatgtcctgtgcccccaagagaaatgtaatcccagt +tccttgggacagttctcaaggccctccgatatcctgtgcccccaggagaatgtaagccca +gttcctcgggacagttctcgaggccctcaggtgtcttgtgcccccaggagaatgtaagcc +cagttccttgggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaa +tcccagttcctcgggacagttctcaaggccctccgatatcctgtgcccccaggagaatgt +aatcccagttcctcgggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaa +tgtaatcccagttcctcgggacagttctccaggccctccgatatcctgtgcccccaggag +aatgtaagcccagttcctcgggacagttctcgaggccctcagatgtcctgtgcccccaag +agaaatgtaatcccagttcctcgggacagttctcaaggccctccgatatcctgtgccccc +aggagaatgtaag----------------------------------------------- +----------------cccagttcctcgggacagttctccaggccctccgatatcctgtg +cccccaggagaatgtaagcccagttcctcggaacagttctccaggccctcagatgtcctg +tgcccccggggcctcatcagacattaagcatgcagtccctttgcagctctggatggcgcg +agtttcccacgtcccatccccttcctggctatgggcaagtgcaggctggatcctggcctc +ctccttcctggcctccag +>syndip_2_chr20:61783303-61784940 +ctccaaaggcacattctatatgatttttgcccacaacctttccttaatatgtacatgttt +tctagataaaaacattaaatacagctaaagtgacatcaaggtctccctcccttcctttcc +tccaatacgtgagagaaatgtaatcccagttccttgggacagttctcgaggccctcagat +gtcctgtgcccccgaaagaaatgtaatcccagttccttgggatagttctcaaggccctcc +gatatcctgtgcccctgggagaaatgtaagcccagttcctcaggacagttctcgaggccc +tcagatgtcctgtgctcccaggagaatataagcctagttcctcgggacagttctcgaggc +cctcaggtgtcttgtgcccccaagagaaatgtaatcccagttccttgggacagttctccg +ggccctcagatgtcctgtgcccccgggagaaatgtaagcctagttcctcgggacagttct +cgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttccttgggacagt +tctcgaggccctcagatgtcctgtgcccccgggagaaatgtaagcctagttcctcgggac +agttctcaaggccctccgatatcctgtgcccccaggagaatgtaagcccagttcctc--- +-----------------------------------------------------------g +ggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttcc +tcgggacagttctcaaggccctcagatgtcctgtgcccccaagagaaatgtaatcccagt +tccttgggacagttctcaaggccctccgatatcctgtgcccccaggagaatgtaagccca +gttcctcgggacagttctcgaggccctcaggtgtcttgtgcccccaggagaatgtaagcc +cagttccttgggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaa +tcccagttcctcgggacagttctcaaggccctccgatatcctgtgcccccaggagaatgt +aagcccagttcctcgggacagttctcgaggccttcaggtgtcttgtgcccccaagagaaa +tgtaatcccagttcctcggaacagttctccaggccctcagatgtcctgtgcccccaagag +a----------------------------------------------------------- +------------------------------------------------------------ +-----aatgtaat----------------------------------------------- +----------------cccagttcctcgggacagttctccaggccctccgatatcctgtg +cccccaggagaatgtaagcccagttcctcggaacagttctccaggccctcagatgtcctg +tgcccccggggcctcatcagacattaagcatgcagtccctttgcagctctggatggcgcg +agtttcccacgtcccatccccttcctggctatgggcaagtgcaggctggatcctggcctc +ctccttcctggcctccag +>p:HG002_1_chr20:61783303-61784940 +ctccaaaggcacattctatatgatttttgcccacaacctttccttaatatgtacatgttt +tctagataaaaacattaaatacagctaaagtgacatcaaggtctccctcccttcctttcc +tccaatacgtgagagaaatgtaatcccagttccttgggacagttctcgaggccctcagat +gtcctgtgcccccgaaagaaatgtaatcccagttccttgggatagttctcaaggccctcc +gatatcctgtgcccctgggagaaatgtaagcccagttcctcaggacagttctcgaggccc +tcagatgtcctgtgctcccaggagaatataagcctagttcctcgggacagttctcgaggc +cctcaggtgtcttgtgcccccaagagaaatgtaatcccagttccttgggacagttctccg +ggccctcagatgtcctgtgcccccgggagaaatgtaagcctagttcctcgggacagttct +cgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttccttgggacagt +tctcgaggccctcagatgtcctgtgcccccgggagaaatgtaagcctagttcctcgggac +agttctcaaggccctccgatatcctgtgcccccaggagaatgtaagcccagttcctc--- +-----------------------------------------------------------g +ggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttcc +tcgggacagttctcaaggccctcagatgtcctgtgcccccaagagaaatgtaatcccagt +tccttgggacagttctcaaggccctccgatatcctgtgcccccaggagaatgtaagccca +gttcctcgggacagttctcgaggccctcaggtgtcttgtgcccccaggagaatgtaagcc +cagttccttgggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaa +tcccagttcctcgggacagttctcaaggccctccgatatcctgtgcccccaggagaatgt +aagcccagttcctcgggacagttctcgaggccttcaggtgtcttgtgcccccaagagaaa +tgtaatcccagttcctcggaacagttctccaggccctcagatgtcctgtgcccccaagag +a----------------------------------------------------------- +------------------------------------------------------------ +-----aatgtaat----------------------------------------------- +----------------cccagttcctcgggacagttctccaggccctccgatatcctgtg +cccccaggagaatgtaagcccagttcctcggaacagttctccaggccctcagatgtcctg +tgcccccggggcctcatcagacattaagcatgcagtccctttgcagctctggatggcgcg +agtttcccacgtcccatccccttcctggctatgggcaagtgcaggctggatcctggcctc +ctccttcctggcctccag +>p:HG002_2_chr20:61783303-61784940 +ctccaaaggcacattctatatgatttttgcccacaacctttccttaatatgtacatgttt +tctagataaaaacattaaatacagctaaagtgacatcaaggtctccctcccttcctttcc +tccaatacgtgagagaaatgtaatcccagttccttgggacagttctcgaggccctcagat +gtcctgtgcccccgaaagaaatgtaatcccagttccttgggatagttctcaaggccctcc +gatatcctgtgcccctgggagaaatgtaagcccagttcctcaggacagttctcgaggccc +tcagatgtcctgtgctcccaggagaatataagcctagttcctcgggacagttctcgaggc +cctcaggtgtcttgtgcccccaagagaaatgtaatcccagttccttgggacagttctccg +ggccctcagatgtcctgtgcccccgggagaaatgtaagcctagttcctcgggacagttct +cgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttcctcgggacagt 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b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62057573-62059140/comp.vcf.gz.tbi new file mode 100644 index 00000000..2c909b6c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62057573-62059140/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62057573-62059140/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62057573-62059140/haps.fa new file mode 100644 index 00000000..0e0a7664 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62057573-62059140/haps.fa @@ -0,0 +1,148 @@ +>ref_chr20_62057473_62059240 +TCCAAGATCCATGTACCCCAACACCACCCTACCTGGCTACGCTCCTCTCACAACTTTGAGATCAAGATGCCACGTGTGCCTTCCTCACATCGGCGCTTTCCAGTGATGCCCAGTGGGGGACACAAAGGGCCCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCTCCAGTCCCCAAACACAGTCCCCAACAGACAACTTCTCCTGTCCCCACATGCGGCTCCCAACAAACAATTTCTCCTGCCCTCACACGCGGTTCCCAACGACAACTTCTGCTCCACAACATGACACCCACGGTGGGAGAAGCTGGGGGCACTTCACTACATCATCCTGCACACTGCAGCATGGCCTGCTCCAGGCAGAAGGCAGGCCTGGAGAAGAGCCTGGGACCACCGCGGACTGACC +>syndip_1_chr20:62057473-62059240 +TCCAAGATCCATGTACCCCAACACCACCCTACCTGGCTACGCTCCTCTCACAACTTTGAG +ATCAAGATGCCACGTGTGCCTTCCTCACATCGGCGCTTTCCAGTGATGCCCAGTGGGGGA +CACAAAGGGCCCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAG +ACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTAC +ACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACG +GACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGA +CCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCC +AACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATG +GGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCA +GGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACA +GGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAG +GAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTC +AGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTC +GGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACA +GACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTA +CACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGAC +GGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAG +ACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGG +CCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAA +TGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACC +AGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACAC +AGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCA +GGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACC +TCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGC +TCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCA +CAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCT +ACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGA +CGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAG +ACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGG +CCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAA +TGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACAC 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+CCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAG +GTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGA +AGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAG +CAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGG +GGGGCCAACCTCTCCAGTCCCCAAACACAGTCCCCAACAGACAACTTCTCCTGTCCCCAC +ATGCGGCTCCCAACAAACAATTTCTCCTGCCCTCACACGCGGTTCCCAACGACAACTTCT +GCTCCACAACATGACACCCACGGTGGGAGAAGCTGGGGGCACTTCACTACATCATCCTGC +ACACTGCAGCATGGCCTGCTCCAGGCAGAAGGCAGGCCTGGAGAAGAGCCTGGGACCACC +GCGGACTGACC +>syndip_2_chr20:62057473-62059240 +TCCAAGATCCATGTACCCCAACACCACCCTACCTGGCTACGCTCCTCTCACAACTTTGAG +ATCAAGATGCCACGTGTGCCTTCCTCACATCGGCGCTTTCCAGTGATGCCCAGTGGGGGA +CACAAAGGGCCCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAG +ACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACA +CACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGG +ACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACC +TCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAA 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+CCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGG +GCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGC +CACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGT +CTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCTCCAGTCCCCAAACACA +GTCCCCAACAGACAACTTCTCCTGTCCTCACATGCGGCTCCCAACAAACAATTTCTCCTG +CCCTCACACGCGGTTCCCAACGACAACTTCTGCTCCACAACATGACACCCACGGTGGGAG +AAGCTGGGGGCACTTCACTACATCATCCTGCACACTGCAGCATGGCCTGCTCCAGGCAGA +AGGCAGGCCTGGAGAAGAGCCTGGGACCACCGCGGACTGACC +>p:HG002_2_chr20:62057473-62059240 +TCCAAGATCCATGTACCCCAACACCACCCTACCTGGCTACGCTCCTCTCACAACTTTGAG +ATCAAGATGCCACGTGTGCCTTCCTCACATCGGCGCTTTCCAGTGATGCCCAGTGGGGGA +CACAAAGGGCCCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAG +ACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTAC +ACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACG +GACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGA +CCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCC +AACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATG +GGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCA +GGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACA +GGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAG +GAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTC +AGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTC +GGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACA +GACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTA +CACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGAC +GGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAG +ACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGG +CCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAA +TGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACC +AGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACAC +AGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCA +GGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACC +TCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGC +TCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCA +CAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCT +ACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGA +CGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAG +ACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGG +CCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAA +TGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACAC +CAGGCCACAGACAGTGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGAC +ACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTC +AGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAAC +CTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGG +CTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGC +CACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGT +CTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAA +GGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAG +CAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGG +GGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGA +CAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACA +CACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGG +ACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACC +TCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAA +CCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGG +GCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGG +CCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAG +GTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGA +AGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAG +CAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGG +GGGGCCAACCTCTCCAGTCCCCAAACACAGTCCCCAACAGACAACTTCTCCTGTCCCCAC +ATGCGGCTCCCAACAAACAATTTCTCCTGCCCTCACACGCGGTTCCCAACGACAACTTCT +GCTCCACAACATGACACCCACGGTGGGAGAAGCTGGGGGCACTTCACTACATCATCCTGC +ACACTGCAGCATGGCCTGCTCCAGGCAGAAGGCAGGCCTGGAGAAGAGCCTGGGACCACC +GCGGACTGACC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62057573-62059140/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62057573-62059140/haps.fa.ref.fa new file mode 100644 index 00000000..eee96022 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62057573-62059140/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:62057473-62059240 +TCCAAGATCCATGTACCCCAACACCACCCTACCTGGCTACGCTCCTCTCACAACTTTGAGATCAAGATGCCACGTGTGCCTTCCTCACATCGGCGCTTTCCAGTGATGCCCAGTGGGGGACACAAAGGGCCCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCTCCAGTCCCCAAACACAGTCCCCAACAGACAACTTCTCCTGTCCCCACATGCGGCTCCCAACAAACAATTTCTCCTGCCCTCACACGCGGTTCCCAACGACAACTTCTGCTCCACAACATGACACCCACGGTGGGAGAAGCTGGGGGCACTTCACTACATCATCCTGCACACTGCAGCATGGCCTGCTCCAGGCAGAAGGCAGGCCTGGAGAAGAGCCTGGGACCACCGCGGACTGACC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62057573-62059140/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62057573-62059140/msa.fa new file mode 100644 index 00000000..dc504a6c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62057573-62059140/msa.fa @@ -0,0 +1,285 @@ +>ref_chr20_62057473_62059240 +tccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttgag +atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga +cacaaagggcccagcaagacctcaggaaggacggacacaggcctacacaccaggccacag +acaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctac +acaccaggccacagacaatggggctcg--------------------------------- +------------------------------------------------------------ +-----------------------------------------------------gggggcc +aacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatg +gggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacca +ggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacaca +ggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcag +gaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacctc +agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc +gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccaca +gacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggccta +cacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggac +ggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaag +acctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggg +ccaacctcagcaagacctcaggaaggacggac---------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------acaggtctacacaccaggcca +cagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtct +acacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagga +cggacacaggtctacacaccaggccacagacaatggggctcg------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------------------------gg +gggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacaga +caatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctaca +caccaggccacagacaatggggctc----------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------gggggccaacctcagcaagacctcaggaaggacggacacag +gtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagga +aggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcag +caagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgg +ggggccaacctctccagtccccaaacacagtccccaacagacaacttctcctgtccccac +atgcggctcccaacaaacaatttctcctgccctcacacgcggttcccaacgacaacttct +gctccacaacatgacacccacggtgggagaagctgggggcacttcactacatcatcctgc +acactgcagcatggcctgctccaggcagaaggcaggcctggagaagagcctgggaccacc +gcggactgacc +>syndip_1_chr20:62057473-62059240 +tccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttgag +atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga +cacaaagggcccagcaagacctcaggaaggacggacacaggtctacacaccaggccacag +acaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctac +acaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacg +gacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaaga +cctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggcc +aacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatg +gggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacca +ggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacaca +ggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcag +gaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacctc +agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc +gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccaca +gacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggccta +cacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggac +ggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaag 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+aggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggccaac +ctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatgggg +ctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggc +cacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggt +ctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaa +ggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcag +caagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgg +gggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacaga +caatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctaca +caccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacgg +acacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacc +tcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaa +cctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggg +gctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccagg +ccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacag +gtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagga 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+------------------------------------------------------------ +------------------------------------------------------------ +-----------------ctacacaccaggccacagacaatggggctcgggggccaacctc +agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc +gggggccaacctcagcaagacctcaggaaggacggac----------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------acaggtctacacaccaggcca +cagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtct +acacaccaggccacagacaatggggctc-------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------gggggccaacctcagcaagacctcaggaaggacggacacag +gtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagga +aggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcag +caagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc-g +ggggccaacctctccagtccccaaacacagtccccaacagacaacttctcctgtcctcac +atgcggctcccaacaaacaatttctcctgccctcacacgcggttcccaacgacaacttct +gctccacaacatgacacccacggtgggagaagctgggggcacttcactacatcatcctgc +acactgcagcatggcctgctccaggcagaaggcaggcctggagaagagcctgggaccacc +gcggactgacc +>p:HG002_1_chr20:62057473-62059240 +tccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttgag +atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga +cacaaagggcccagcaagacctcaggaaggacggacacaggt------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------ctacacaccaggccacagacaatggggctcgggggccaacctc +agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc +gggggccaacctcagcaagacctcaggaaggacggac----------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------acaggtctacacaccaggcca +cagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtct +acacaccaggccacagacaatggggctc-------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------gggggccaacctcagcaagacctcaggaaggacggacacag +gtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagga +aggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcag +caagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc-g +ggggccaacctctccagtccccaaacacagtccccaacagacaacttctcctgtcctcac +atgcggctcccaacaaacaatttctcctgccctcacacgcggttcccaacgacaacttct +gctccacaacatgacacccacggtgggagaagctgggggcacttcactacatcatcctgc +acactgcagcatggcctgctccaggcagaaggcaggcctggagaagagcctgggaccacc +gcggactgacc +>p:HG002_2_chr20:62057473-62059240 +tccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttgag +atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga +cacaaagggcccagcaagacctcaggaaggacggacacaggtctacacaccaggccacag +acaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctac +acaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacg +gacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaaga +cctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggcc +aacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatg +gggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacca 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+cagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtct +acacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagga +cggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaag +acctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggg +ccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaa +tggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacac +caggccacagacagtggggctcggggggccaacctcagcaagacctcaggaaggacggac +acaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctc +aggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggccaac +ctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatgggg +ctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggc +cacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggt +ctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaa +ggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcag +caagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgg +gggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacaga +caatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctaca +caccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacgg +acacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacc +tcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaa +cctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggg +gctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccagg +ccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacag +gtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagga +aggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcag +caagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgg +ggggccaacctctccagtccccaaacacagtccccaacagacaacttctcctgtccccac +atgcggctcccaacaaacaatttctcctgccctcacacgcggttcccaacgacaacttct +gctccacaacatgacacccacggtgggagaagctgggggcacttcactacatcatcctgc +acactgcagcatggcctgctccaggcagaaggcaggcctggagaagagcctgggaccacc +gcggactgacc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62057573-62059140/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62057573-62059140/msa.fa.fai new file mode 100644 index 00000000..64a1a532 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62057573-62059140/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_62057473_62059240 3311 29 60 61 +syndip_1_chr20:62057473-62059240 3311 3430 60 61 +syndip_2_chr20:62057473-62059240 3311 6831 60 61 +p:HG002_1_chr20:62057473-62059240 3311 10233 60 61 +p:HG002_2_chr20:62057473-62059240 3311 13635 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62057573-62059140/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62057573-62059140/output.vcf.gz new file mode 100644 index 00000000..721cb059 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62057573-62059140/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62057573-62059140/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62057573-62059140/output.vcf.gz.tbi new file mode 100644 index 00000000..5ee45376 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62057573-62059140/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/base.vcf.gz new file mode 100644 index 00000000..56f1c0eb Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/base.vcf.gz.tbi new file mode 100644 index 00000000..ab948ce3 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/comp.vcf.gz new file mode 100644 index 00000000..6edf0d8e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/comp.vcf.gz.tbi new file mode 100644 index 00000000..1c08957e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/haps.fa new file mode 100644 index 00000000..cb0a09c0 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/haps.fa @@ -0,0 +1,70 @@ +>ref_chr20_62270179_62271195 +CGTCCTAGTCCCTGGTGCAGACGAGGAGCCTGAGAGGCTTAGCAGCTCATGTGTGTGTCAGCTGGGAACCCACAGCAAGTGGATTCCAAAGCCTGCCATGTCCCTGTTGCCACTAGCACCTCCTCCTCCACTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCCCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTTTCCTTGTCCCTTTCTGGTCTCTCTGGTCCTCTCCTTCTCTCCTTGTCCCTCTCCCTCTGCCTCTGCTTTGCCCACCCCAGACCCTGCTCCTTCCTGAAGAGCCTGCCCTGAGGTGACAGCTGTGTTTCCCTGGAATGCCTACTGCCCTTGGGATCCCTTTCCTGGAAGCCCGGTGGGAA +>syndip_1_chr20:62270179-62271195 +CGTCCTAGTCCCTGGTGCAGACGAGGAGCCTGAGAGGCTTAGCAGCTCATGTGTGTGTCA +GCTGGGAACCCACAGCAAGTGGATTCCAAAGCCTGCCATGTCCCTGTTGCCACTAGCACC +TCCTCCTCCACTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCCTGGCCTCTCTG +GGTCCTCTCCTTGTCCCTCCCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTC +TCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGG +GTCCTCTCCTTGTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTC +TCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCTGACCTCTCTGAGTCCTCTCCTTGTC +CCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCT +CTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGG +TCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTC +TCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTT +GTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCT +CCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTG +TCCCTCTCTGGCCTCTCTGGGTCCTTTCCTTGTCCCTTTCTGGTCTCTCTGGTCCTCTCC +TTCTCTCCTTGTCCCTCTCCCTCTGCCTCTGCTTTGCCCACCCCAGACCCTGCTCCTTCC +TGAAGAGCCTGCCCTGAGGTGACAGCTGTGTTTCCCTGGAATGCCTACTGCCCTTGGGAT +CCCTTTCCTGGAAGCCCGGTGGGAA +>syndip_2_chr20:62270179-62271195 +CGTCCTAGTCCCTGGTGCAGACGAGGAGCCTGAGAGGCTTAGCAGCTCATGTGTGTGTCA +GCTGGGAACCCACAGCAAGTGGATTCCAAAGCCTGCCATGTCCCTGTTGCCACTAGCACC +TCCTCCTCCACTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCCTGGCCTCTCTG +GGTCCTCTCCTTGTCCCTCCCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTC +TCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGG +GTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCT +CTCCTTGTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTT +GTCCCTCTCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCC +TCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCT +GGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTC +CTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTG +GGTCCTTTCCTTGTCCCTTTCTGGTCTCTCTGGTCCTCTCCTTCTCTCCTTGTCCCTCTC +CCTCTGCCTCTGCTTTGCCCACCCCAGACCCTGCTCCTTCCTGAAGAGCCTGCCCTGAGG +TGACAGCTGTGTTTCCCTGGAATGCCTACTGCCCTTGGGATCCCTTTCCTGGAAGCCCGG +TGGGAA +>p:HG002_1_chr20:62270179-62271195 +CGTCCTAGTCCCTGGTGCAGACGAGGAGCCTGAGAGGCTTAGCAGCTCATGTGTGTGTCA +GCTGGGAACCCACAGCAAGTGGATTCCAAAGCCTGCCATGTCCCTGTTGCCACTAGCACC +TCCTCCTCCACTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCCTGGCCTCTCTG +GGTCCTCTCCTTGTCCCTCCCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTC +TCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGG +GTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCT +CTCCTTGTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTT +GTCCCTCTCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCC +TCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCT +GGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTC +CTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTG +GGTCCTTTCCTTGTCCCTTTCTGGTCTCTCTGGTCCTCTCCTTCTCTCCTTGTCCCTCTC +CCTCTGCCTCTGCTTTGCCCACCCCAGACCCTGCTCCTTCCTGAAGAGCCTGCCCTGAGG +TGACAGCTGTGTTTCCCTGGAATGCCTACTGCCCTTGGGATCCCTTTCCTGGAAGCCCGG +TGGGAA +>p:HG002_2_chr20:62270179-62271195 +CGTCCTAGTCCCTGGTGCAGACGAGGAGCCTGAGAGGCTTAGCAGCTCATGTGTGTGTCA +GCTGGGAACCCACAGCAAGTGGATTCCAAAGCCTGCCATGTCCCTGTTGCCACTAGCACC +TCCTCCTCCACTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCCTGGCCTCTCTG +GGTCCTCTCCTTGTCCCTCCCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTC +TCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGG +GTCCTCTCCTTGTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTC +TCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCTGACCTCTCTGAGTCCTCTCCTTGTC +CCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCT +CTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGG +TCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTC +TCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTT +GTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCT +CCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTG +TCCCTCTCTGGCCTCTCTGGGTCCTTTCCTTGTCCCTTTCTGGTCTCTCTGGTCCTCTCC +TTCTCTCCTTGTCCCTCTCCCTCTGCCTCTGCTTTGCCCACCCCAGACCCTGCTCCTTCC +TGAAGAGCCTGCCCTGAGGTGACAGCTGTGTTTCCCTGGAATGCCTACTGCCCTTGGGAT +CCCTTTCCTGGAAGCCCGGTGGGAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/haps.fa.ref.fa new file mode 100644 index 00000000..232094ce --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:62270179-62271195 +CGTCCTAGTCCCTGGTGCAGACGAGGAGCCTGAGAGGCTTAGCAGCTCATGTGTGTGTCAGCTGGGAACCCACAGCAAGTGGATTCCAAAGCCTGCCATGTCCCTGTTGCCACTAGCACCTCCTCCTCCACTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCCCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTTTCCTTGTCCCTTTCTGGTCTCTCTGGTCCTCTCCTTCTCTCCTTGTCCCTCTCCCTCTGCCTCTGCTTTGCCCACCCCAGACCCTGCTCCTTCCTGAAGAGCCTGCCCTGAGGTGACAGCTGTGTTTCCCTGGAATGCCTACTGCCCTTGGGATCCCTTTCCTGGAAGCCCGGTGGGAA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/msa.fa new file mode 100644 index 00000000..a2ca79af --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/msa.fa @@ -0,0 +1,90 @@ +>ref_chr20_62270179_62271195 +cgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtca +gctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcacc +tcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctg +ggtcctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcctc +tctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgg +gtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcct +ctccttgtccctc-ctggcctctctgggtcctctccttgtccctctctgggtcctctcct +tgtccctctctggcctctctgggtcctctctgacctctctgggtcctctccttgtccctc +tctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgg +gtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcct +ctccttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctggg +tcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctc +tccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcctt +gtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtccttt +ccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgcc +tctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagct +gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgggaa +>syndip_1_chr20:62270179-62271195 +cgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtca +gctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcacc +tcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctg +ggtcctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcctc +tctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgg +gtcctctccttgtccctc-ctggcctctctgggtcctctccttgtccctctctgggtcct +ctccttgtccctctctggcctctctgggtcctctct---gacctctctgagtcctctcct +tgtc-----------------------------cctctctgggtcctctccttgtccctc +tctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgg +gtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcct +ctccttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctggg +tcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctc +tccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcctt +gtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtccttt +ccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgcc +tctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagct +gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgggaa +>syndip_2_chr20:62270179-62271195 +cgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtca +gctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcacc +tcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctg +ggtcctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcctc +tctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgg +gtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcct +ctccttgtccctc-ctgg-----------------------cctctctgggtcctctcct +tgtc-------------------------------------------------------- +---------------------------------------------------cctctctgg +gtcctctccttgtccctctctgacctctctgggtcctctccttgtccctctctgggtcct +ctccttgtc-----------------------------------------cctctctggg +tcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctc +tccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcctt +gtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtccttt +ccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgcc +tctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagct +gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgggaa +>p:HG002_1_chr20:62270179-62271195 +cgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtca +gctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcacc +tcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctg +ggtcctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcctc +tctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgg +gtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcct +ctccttgtccctc-ctgg-----------------------cctctctgggtcctctcct +tgtc-------------------------------------------------------- +---------------------------------------------------cctctctgg +gtcctctccttgtccctctctgacctctctgggtcctctccttgtccctctctgggtcct +ctccttgtc-----------------------------------------cctctctggg +tcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctc +tccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcctt +gtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtccttt +ccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgcc +tctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagct +gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgggaa +>p:HG002_2_chr20:62270179-62271195 +cgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtca +gctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcacc +tcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctg +ggtcctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcctc +tctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgg +gtcctctccttgtccctc-ctggcctctctgggtcctctccttgtccctctctgggtcct +ctccttgtccctctctggcctctctgggtcctctct---gacctctctgagtcctctcct +tgtc-----------------------------cctctctgggtcctctccttgtccctc +tctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgg +gtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcct +ctccttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctggg +tcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctc +tccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcctt +gtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtccttt +ccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgcc +tctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagct +gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgggaa diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/msa.fa.fai new file mode 100644 index 00000000..a994a053 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_62270179_62271195 1018 29 60 61 +syndip_1_chr20:62270179-62271195 1018 1098 60 61 +syndip_2_chr20:62270179-62271195 1018 2167 60 61 +p:HG002_1_chr20:62270179-62271195 1018 3237 60 61 +p:HG002_2_chr20:62270179-62271195 1018 4307 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/output.vcf.gz new file mode 100644 index 00000000..71c88976 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/output.vcf.gz.tbi new file mode 100644 index 00000000..f95766c1 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62270279-62271095/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/base.vcf.gz new file mode 100644 index 00000000..371d9582 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/base.vcf.gz.tbi new file mode 100644 index 00000000..40eb67ac Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/comp.vcf.gz new file mode 100644 index 00000000..1fd4cdba Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/comp.vcf.gz.tbi new file mode 100644 index 00000000..345c7223 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/haps.fa new file mode 100644 index 00000000..3fcd6b4e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/haps.fa @@ -0,0 +1,82 @@ +>ref_chr20_62320931_62321974 +AGGCCAGGGGAGAATGATCAGCTGGGGCCCTGGGGTCATTAGGGTGGGGAGGGCTCAGCCAGAGGTCATGAGGTCAGCTTAGGGACACAGGACCTGTGGGGAGGTCCCAGAGTTCTGGCAGAGTCATAGGGTCAGGTAGGAGTCAGATGGGAGTGAAGGGCATGGGGTCACCCAGGGAGAAGGTAGGGCCAGCACAAGGGGTTGGGGCCGGAGGTGGGGCCAGTGAAGGGGCGGGGCCGGTGGAGGCAGGGTCAGTGAAGGGGTGGGGCCAGTGGAGGAAGAGGGGGCCAGTGGAGGAGGCGGGGCCTGTGGAGGGGTGGGGCCAGTGGAGGCAGGGTCAGTGAAGGGGTGGGGCCGGTGGAGGAAGAGGGGGCCAGTGAAGGTGTGGGGCCAGTGGAGGAGGTGCAGCCAGTGGAAGAGGTGGGGCCAGTGGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGAGGACGGGTGGGTTCAGAGGACGGGTAGGGTCAGTGGAGGGGTAGGGCCAGCAGAGGGGTAGGGCCAGCAGAGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGAGGCAGGGTCAGTGAAAGGGTGGCGCCAGTGGAGGAAGAGGGGGCCAGTGGAGGCAGGGCCTGTGGAGGGGTGGGGCCAGTGGAGGTGGGGTCAGTGAAGGGGTGGGGCCAGCGGAGGAGGTGCAGCCAGTGGAAGAGGTGGGGCCAATGGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGGGGAGGCAGGGCCAGCAGAGGGGTGGGGTCAGTGGAGGGGTGGGGCCAGTGGAGGGGTGGGGTCAGTGGGGGAGGAAGGGCCAGCAGATGGGGTGGGGCCAGGGCACACAGGAAGGCTAGGGACAGTAGAGGGGTGCAGCCAGCAGTGGAGCTGCAGCGCTCCTCAGCGTGGTTGGAGTTGGACAGGCATGGGTCTCTCGGGAAATGGAAGGCAGCTGGGACCACTCTGGGAGGTCGACGTTAACACTGGGGTCACCAGGCTGTGTGGGACTTGGAT +>syndip_1_chr20:62320931-62321974 +AGGCCAGGGGAGAATGATCAGCTGGGGCCCTGGGGTCATTAGGGTGGGGAGGGCTCAGCC +AGAGGTCATGAGGTCAGCTTAGGGACACAGGACCTGTGGGGAGGTCCCAGAGTTCTGGCA +GAGTCATAGGGTCAGGTAGGAGTCAGATGGGAGTGAAGGGCATGGGGTCACCCAGGGAGA +AGGTAGGGCCAGCACAAGGGGTTGGGGCCGGAGGTGGGGCCAGTGAAGGGGCGGGGCCGG +TGGAGGCAGGGTCAGTGAAGGGGTGGGGCCAGTGGAGGAAGAGGGGGCCAGTGGAGGAGG +CGGGGCCTGTGGAGGGGTGGGGCCAGTGGAGGCAGGGTCAGTGAAGGGGTGGGGCCGGTG +GAGGAAGAGGGGGCCAGTGAAGGTGTGGGGCCAGTGGAGGAGGTGCAGCCAGTGGAAGAG +GTGGGGCCAGTGGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGAGGACAGGTGGGTTCAGA +GGACGGGTGGGTTCAGAGGACGGGTGGGTTCAGAGGACGGGTGGGGTCAGTGGAGGGGTG +GGGTCAGTGGAGGGGTAGGGTCAGAGGACGGGTAGGGTCAGTGGAGGGGTAGGGCCAGCA +GAGGGGTGGGGTCAGCGGAGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGAGGGGTGG +GGTCAGTGGAGGCAGGGTCAGTGAAAGGGTGGCGCCAGTGGAGGAAGAGGGCGCCAGTGG +AGGAAGAGGGCGCCAGTGGAGGAAGAGGGGGCCAGTGGAGGCAGGGCCTGTGGAGGGGTG +GGGCCAGTGGAGGTGGGGTCAGTGAAGGGGTGGGGCCAGCGGAGGAGGTGCAGCCAGTGG +AAGAGGTGGGGCCAATGGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGGGGAGGCAGG +GCCAGCAGAGGGGTGGGGCCAGTGGAGGGGTGGGGCCAGCGGAGGGGTGGGGTCAGTGGG +GGAGGAAGGGCCAGCAGATGGGGTGGGGCCAGGGCACACAGGAAGGCTAGGGACAGTAGA +GGGGTGCAGCCAGCAGTGGAGCTGCAGCGCTCCTCAGCGTGGTTGGAGTTGGACAGGCAT +GGGTCTCTCGGGAAATGGAAGGCAGCTGGGACCACTCTGGGAGGTCGACGTTAACACTGG +GGTCACCAGGCTGTGTGGGACTTGGAT +>syndip_2_chr20:62320931-62321974 +AGGCCAGGGGAGAATGATCAGCTGGGGCCCTGGGGTCATTAGGGTGGGGAGGGCTCAGCC +AGAGGTCATGAGGTCAGCTTAGGGACACAGGACCTGTGGGGAGGTCCCAGAGTTCTGGCA +GAGTCATAGGGTCAGGTAGGAGTCAGATGGGAGTGAAGGGCATGGGGTCACCCAGGGAGA +AGGTAGGGCCAGCACAAGGGGTTGGGGCCGGAGGTGGGGCCAGTGAAGGGGCGGGGCCGG +TGGAGGCAGGGTCAGTGAAGGGGTGGGGCCAGTGGAGGAAGAGGGGGCCAGTGGAGGAGG +CGGGGCCTGTGGAGGGGTGGGGCCAGTGGAGGCAGGGTCAGTGAAGGGGTGGGGCCGGTG +GAGGAAGAGGGGGCCAGTGAAGGTGTGGGGCCAGTGGAGGAGGTGCAGCCAGTGGCAGAG +GTGGGGCCAGTGGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGAGGACGGGTAGGGTCAGT +GGAGGGGTAGGGCCAGCAGAGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGAGGGGTG +GGGTCAGTGGAGGCAGGGTCAGTGAAAGGGTGGCGCCAGTGGAGGAAGAGGGCGCCAGTG +GAGGAAGAGGGGGCCAGTGGAGGCAGGGCCTGTGGAGGGGTGGGGCCAGTGGAGGTGGGG +TCAGTGAAGGGGTGGGGCCAGCGGAGGAGGTGCAGCCAGTGGAAGAGGTGGGGCCAATGG +GGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGGGGAGGCAGGGCCAGCAGAGGGGTGGGG +CCAGTGGAGGGGTGGGGCCAGCGGAGGGGTGGGGCCAGCGGAGGGGTGGGGTCAGTGGGG +GAGGAAGGGCCAGCAGATGGGGTGGGGCCAGGGCACACAGGAAGGCTAGGGACAGTAGAG +GGGTGCAGCCAGCAGTGGAGCTGCAGCGCTCCTCAGCGTGGTTGGAGTTGGACAGGCATG +GGTCTCTCGGGAAATGGAAGGCAGCTGGGACCACTCTGGGAGGTCGACGTTAACACTGGG +GTCACCAGGCTGTGTGGGACTTGGAT +>p:HG002_1_chr20:62320931-62321974 +AGGCCAGGGGAGAATGATCAGCTGGGGCCCTGGGGTCATTAGGGTGGGGAGGGCTCAGCC +AGAGGTCATGAGGTCAGCTTAGGGACACAGGACCTGTGGGGAGGTCCCAGAGTTCTGGCA +GAGTCATAGGGTCAGGTAGGAGTCAGATGGGAGTGAAGGGCATGGGGTCACCCAGGGAGA +AGGTAGGGCCAGCACAAGGGGTTGGGGCCGGAGGTGGGGCCAGTGAAGGGGCGGGGCCGG +TGGAGGCAGGGTCAGTGAAGGGGTGGGGCCAGTGGAGGAAGAGGGGGCCAGTGGAGGAGG +CGGGGCCTGTGGAGGGGTGGGGCCAGTGGAGGCAGGGTCAGTGAAGGGGTGGGGCCGGTG +GAGGAAGAGGGGGCCAGTGAAGGTGTGGGGCCAGTGGAGGAGGTGCAGCCAGTGGCAGAG +GTGGGGCCAGTGGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGAGGACGGGTAGGGTCAGT +GGAGGGGTAGGGCCAGCAGAGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGAGGGGTG +GGGTCAGTGGAGGCAGGGTCAGTGAAAGGGTGGCGCCAGTGGAGGAAGAGGGCGCCAGTG +GAGGAAGAGGGGGCCAGTGGAGGCAGGGCCTGTGGAGGGGTGGGGCCAGTGGAGGTGGGG +TCAGTGAAGGGGTGGGGCCAGCGGAGGAGGTGCAGCCAGTGGAAGAGGTGGGGCCAATGG +GGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGGGGAGGCAGGGCCAGCAGAGGGGTGGGG +CCAGTGGAGGGGTGGGGCCAGCGGAGGGGTGGGGCCAGCGGAGGGGTGGGGTCAGTGGGG +GAGGAAGGGCCAGCAGATGGGGTGGGGCCAGGGCACACAGGAAGGCTAGGGACAGTAGAG +GGGTGCAGCCAGCAGTGGAGCTGCAGCGCTCCTCAGCGTGGTTGGAGTTGGACAGGCATG +GGTCTCTCGGGAAATGGAAGGCAGCTGGGACCACTCTGGGAGGTCGACGTTAACACTGGG +GTCACCAGGCTGTGTGGGACTTGGAT +>p:HG002_2_chr20:62320931-62321974 +AGGCCAGGGGAGAATGATCAGCTGGGGCCCTGGGGTCATTAGGGTGGGGAGGGCTCAGCC +AGAGGTCATGAGGTCAGCTTAGGGACACAGGACCTGTGGGGAGGTCCCAGAGTTCTGGCA +GAGTCATAGGGTCAGGTAGGAGTCAGATGGGAGTGAAGGGCATGGGGTCACCCAGGGAGA +AGGTAGGGCCAGCACAAGGGGTTGGGGCCGGAGGTGGGGCCAGTGAAGGGGCGGGGCCGG +TGGAGGCAGGGTCAGTGAAGGGGTGGGGCCAGTGGAGGAAGAGGGGGCCAGTGGAGGAGG +CGGGGCCTGTGGAGGGGTGGGGCCAGTGGAGGCAGGGTCAGTGAAGGGGTGGGGCCGGTG +GAGGAAGAGGGGGCCAGTGAAGGTGTGGGGCCAGTGGAGGAGGTGCAGCCAGTGGAAGAG +GTGGGGCCAGTGGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGAGGACAGGTGGGTTCAGA +GGACGGGTGGGTTCAGAGGACGGGTGGGTTCAGAGGACGGGTGGGGTCAGTGGAGGGGTG +GGGTCAGTGGAGGGGTAGGGTCAGAGGACGGGTAGGGTCAGTGGAGGGGTAGGGCCAGCA +GAGGGGTGGGGTCAGCGGAGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGAGGGGTGG +GGTCAGTGGAGGCAGGGTCAGTGAAAGGGTGGCGCCAGTGGAGGAAGAGGGCGCCAGTGG +AGGAAGAGGGCGCCAGTGGAGGAAGAGGGGGCCAGTGGAGGCAGGGCCTGTGGAGGGGTG +GGGCCAGTGGAGGTGGGGTCAGTGAAGGGGTGGGGCCAGCGGAGGAGGTGCAGCCAGTGG +AAGAGGTGGGGCCAATGGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGGGGAGGCAGG +GCCAGCAGAGGGGTGGGGCCAGTGGAGGGGTGGGGCCAGCGGAGGGGTGGGGTCAGTGGG +GGAGGAAGGGCCAGCAGATGGGGTGGGGCCAGGGCACACAGGAAGGCTAGGGACAGTAGA +GGGGTGCAGCCAGCAGTGGAGCTGCAGCGCTCCTCAGCGTGGTTGGAGTTGGACAGGCAT +GGGTCTCTCGGGAAATGGAAGGCAGCTGGGACCACTCTGGGAGGTCGACGTTAACACTGG +GGTCACCAGGCTGTGTGGGACTTGGAT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/haps.fa.ref.fa new file mode 100644 index 00000000..f4e5333f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:62320931-62321974 +AGGCCAGGGGAGAATGATCAGCTGGGGCCCTGGGGTCATTAGGGTGGGGAGGGCTCAGCCAGAGGTCATGAGGTCAGCTTAGGGACACAGGACCTGTGGGGAGGTCCCAGAGTTCTGGCAGAGTCATAGGGTCAGGTAGGAGTCAGATGGGAGTGAAGGGCATGGGGTCACCCAGGGAGAAGGTAGGGCCAGCACAAGGGGTTGGGGCCGGAGGTGGGGCCAGTGAAGGGGCGGGGCCGGTGGAGGCAGGGTCAGTGAAGGGGTGGGGCCAGTGGAGGAAGAGGGGGCCAGTGGAGGAGGCGGGGCCTGTGGAGGGGTGGGGCCAGTGGAGGCAGGGTCAGTGAAGGGGTGGGGCCGGTGGAGGAAGAGGGGGCCAGTGAAGGTGTGGGGCCAGTGGAGGAGGTGCAGCCAGTGGAAGAGGTGGGGCCAGTGGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGAGGACGGGTGGGTTCAGAGGACGGGTAGGGTCAGTGGAGGGGTAGGGCCAGCAGAGGGGTAGGGCCAGCAGAGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGAGGCAGGGTCAGTGAAAGGGTGGCGCCAGTGGAGGAAGAGGGGGCCAGTGGAGGCAGGGCCTGTGGAGGGGTGGGGCCAGTGGAGGTGGGGTCAGTGAAGGGGTGGGGCCAGCGGAGGAGGTGCAGCCAGTGGAAGAGGTGGGGCCAATGGGGGTGGGGTCAGTGGAGGGGTGGGGTCAGTGGGGGAGGCAGGGCCAGCAGAGGGGTGGGGTCAGTGGAGGGGTGGGGCCAGTGGAGGGGTGGGGTCAGTGGGGGAGGAAGGGCCAGCAGATGGGGTGGGGCCAGGGCACACAGGAAGGCTAGGGACAGTAGAGGGGTGCAGCCAGCAGTGGAGCTGCAGCGCTCCTCAGCGTGGTTGGAGTTGGACAGGCATGGGTCTCTCGGGAAATGGAAGGCAGCTGGGACCACTCTGGGAGGTCGACGTTAACACTGGGGTCACCAGGCTGTGTGGGACTTGGAT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/msa.fa new file mode 100644 index 00000000..49a139cf --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/msa.fa @@ -0,0 +1,105 @@ +>ref_chr20_62320931_62321974 +aggccaggggagaatgatcagctggggccctggggtcattagggtggggagggctcagcc +agaggtcatgaggtcagcttagggacacaggacctgtggggaggtcccagagttctggca +gagtcatagggtcaggtaggagtcagatgggagtgaagggcatggggtcacccagggaga +aggtagggccagcacaaggggttggggccggaggtggggccagtgaaggggcggggccgg +tggaggcagggtcagtgaaggggtggggccagtggaggaagagggggccagtggaggagg +cggggcctgtggaggggtggggccagtggaggcagggtcagtgaaggggtggggccggtg +gaggaagagggggccagtgaaggtgtggggccagtggaggaggtgcagccagtggaagag +gtggggccagtgggggtggggtcagtggaggggtggggtcagaggacgggtgggt----- +------------------------------------------------------------ +--------------------tcagaggacgggtagggtcagtggaggggtagggccagca +gaggggtagggccagcagaggggtggggtcagtggaggggtggggtcagtggaggggtgg +ggtcagtggaggcagggtcagtgaaagggt------------------------------ +--------ggcgccagtggaggaagagggggccagtggaggcagggcctgtggaggggtg +gggccagtggaggtggggtcagtgaaggggtggggccagcggaggaggtgcagccagtgg +aagaggtggggccaatgggggtggggtcagtggaggggtggggtcagtgggggaggcagg +gccagcagaggggtggggtcagt-----------------ggaggggtggggccagtgga +ggggtggggtcagtgggggaggaagggccagcagatggggtggggccagggcacacagga +aggctagggacagtagaggggtgcagccagcagtggagctgcagcgctcctcagcgtggt +tggagttggacaggcatgggtctctcgggaaatggaaggcagctgggaccactctgggag +gtcgacgttaacactggggtcaccaggctgtgtgggacttggat +>syndip_1_chr20:62320931-62321974 +aggccaggggagaatgatcagctggggccctggggtcattagggtggggagggctcagcc +agaggtcatgaggtcagcttagggacacaggacctgtggggaggtcccagagttctggca +gagtcatagggtcaggtaggagtcagatgggagtgaagggcatggggtcacccagggaga +aggtagggccagcacaaggggttggggccggaggtggggccagtgaaggggcggggccgg +tggaggcagggtcagtgaaggggtggggccagtggaggaagagggggccagtggaggagg +cggggcctgtggaggggtggggccagtggaggcagggtcagtgaaggggtggggccggtg +gaggaagagggggccagtgaaggtgtggggccagtggaggaggtgcagccagtggaagag +gtggggccagtgggggtggggtcagtggaggggtggggtcagaggacaggtgggttcaga +ggacgggtgggttcagaggacgggtgggttcagaggacgggtggggtcagtggaggggtg +gggtcagtggaggggtagggtcagaggacgggtagggtcagtggaggggtagggccagca +gaggggtggggtcagcggaggggtggggtcagtggaggggtggggtcagtggaggggtgg +ggtcagtggaggcagggtcagtgaaagggtggcgccagtggaggaagagggcgccagtgg +aggaagagggcgccagtggaggaagagggggccagtggaggcagggcctgtggaggggtg +gggccagtggaggtggggtcagtgaaggggtggggccagcggaggaggtgcagccagtgg +aagaggtggggccaatgggggtggggtcagtggaggggtggggtcagtgggggaggcagg +gccagcagaggggtggggccagt-----------------ggaggggtggggccagcgga +ggggtggggtcagtgggggaggaagggccagcagatggggtggggccagggcacacagga +aggctagggacagtagaggggtgcagccagcagtggagctgcagcgctcctcagcgtggt +tggagttggacaggcatgggtctctcgggaaatggaaggcagctgggaccactctgggag +gtcgacgttaacactggggtcaccaggctgtgtgggacttggat +>syndip_2_chr20:62320931-62321974 +aggccaggggagaatgatcagctggggccctggggtcattagggtggggagggctcagcc +agaggtcatgaggtcagcttagggacacaggacctgtggggaggtcccagagttctggca +gagtcatagggtcaggtaggagtcagatgggagtgaagggcatggggtcacccagggaga +aggtagggccagcacaaggggttggggccggaggtggggccagtgaaggggcggggccgg +tggaggcagggtcagtgaaggggtggggccagtggaggaagagggggccagtggaggagg +cggggcctgtggaggggtggggccagtggaggcagggtcagtgaaggggtggggccggtg +gaggaagagggggccagtgaaggtgtggggccagtggaggaggtgcagccagtggcagag +gtggggccagtgggggtggggtcagtggaggggtggggtcagaggac------------- +------------------------------------------------------------ +----------------------------------------------gggtagggtcagtg +gaggggtagggccagcagaggggtggggtcagtggaggggtggggtcagtggaggggtgg +ggtcagtggaggcagggtcagtgaaagggt-------------------ggcgccagtgg +aggaagagggcgccagtggaggaagagggggccagtggaggcagggcctgtggaggggtg +gggccagtggaggtggggtcagtgaaggggtggggccagcggaggaggtgcagccagtgg +aagaggtggggccaatgggggtggggtcagtggaggggtggggtcagtgggggaggcagg +gccagcagaggggtggggccagtggaggggtggggccagcggaggggtggggccagcgga +ggggtggggtcagtgggggaggaagggccagcagatggggtggggccagggcacacagga +aggctagggacagtagaggggtgcagccagcagtggagctgcagcgctcctcagcgtggt +tggagttggacaggcatgggtctctcgggaaatggaaggcagctgggaccactctgggag +gtcgacgttaacactggggtcaccaggctgtgtgggacttggat +>p:HG002_1_chr20:62320931-62321974 +aggccaggggagaatgatcagctggggccctggggtcattagggtggggagggctcagcc +agaggtcatgaggtcagcttagggacacaggacctgtggggaggtcccagagttctggca +gagtcatagggtcaggtaggagtcagatgggagtgaagggcatggggtcacccagggaga +aggtagggccagcacaaggggttggggccggaggtggggccagtgaaggggcggggccgg +tggaggcagggtcagtgaaggggtggggccagtggaggaagagggggccagtggaggagg +cggggcctgtggaggggtggggccagtggaggcagggtcagtgaaggggtggggccggtg +gaggaagagggggccagtgaaggtgtggggccagtggaggaggtgcagccagtggcagag +gtggggccagtgggggtggggtcagtggaggggtggggtcagaggac------------- +------------------------------------------------------------ +----------------------------------------------gggtagggtcagtg +gaggggtagggccagcagaggggtggggtcagtggaggggtggggtcagtggaggggtgg +ggtcagtggaggcagggtcagtgaaagggt-------------------ggcgccagtgg +aggaagagggcgccagtggaggaagagggggccagtggaggcagggcctgtggaggggtg +gggccagtggaggtggggtcagtgaaggggtggggccagcggaggaggtgcagccagtgg +aagaggtggggccaatgggggtggggtcagtggaggggtggggtcagtgggggaggcagg +gccagcagaggggtggggccagtggaggggtggggccagcggaggggtggggccagcgga +ggggtggggtcagtgggggaggaagggccagcagatggggtggggccagggcacacagga +aggctagggacagtagaggggtgcagccagcagtggagctgcagcgctcctcagcgtggt +tggagttggacaggcatgggtctctcgggaaatggaaggcagctgggaccactctgggag +gtcgacgttaacactggggtcaccaggctgtgtgggacttggat +>p:HG002_2_chr20:62320931-62321974 +aggccaggggagaatgatcagctggggccctggggtcattagggtggggagggctcagcc +agaggtcatgaggtcagcttagggacacaggacctgtggggaggtcccagagttctggca +gagtcatagggtcaggtaggagtcagatgggagtgaagggcatggggtcacccagggaga +aggtagggccagcacaaggggttggggccggaggtggggccagtgaaggggcggggccgg +tggaggcagggtcagtgaaggggtggggccagtggaggaagagggggccagtggaggagg +cggggcctgtggaggggtggggccagtggaggcagggtcagtgaaggggtggggccggtg +gaggaagagggggccagtgaaggtgtggggccagtggaggaggtgcagccagtggaagag +gtggggccagtgggggtggggtcagtggaggggtggggtcagaggacaggtgggttcaga +ggacgggtgggttcagaggacgggtgggttcagaggacgggtggggtcagtggaggggtg +gggtcagtggaggggtagggtcagaggacgggtagggtcagtggaggggtagggccagca +gaggggtggggtcagcggaggggtggggtcagtggaggggtggggtcagtggaggggtgg +ggtcagtggaggcagggtcagtgaaagggtggcgccagtggaggaagagggcgccagtgg +aggaagagggcgccagtggaggaagagggggccagtggaggcagggcctgtggaggggtg +gggccagtggaggtggggtcagtgaaggggtggggccagcggaggaggtgcagccagtgg +aagaggtggggccaatgggggtggggtcagtggaggggtggggtcagtgggggaggcagg +gccagcagaggggtggggccagt-----------------ggaggggtggggccagcgga +ggggtggggtcagtgggggaggaagggccagcagatggggtggggccagggcacacagga +aggctagggacagtagaggggtgcagccagcagtggagctgcagcgctcctcagcgtggt +tggagttggacaggcatgggtctctcgggaaatggaaggcagctgggaccactctgggag +gtcgacgttaacactggggtcaccaggctgtgtgggacttggat diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/msa.fa.fai new file mode 100644 index 00000000..3a076f7f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_62320931_62321974 1184 29 60 61 +syndip_1_chr20:62320931-62321974 1184 1267 60 61 +syndip_2_chr20:62320931-62321974 1184 2505 60 61 +p:HG002_1_chr20:62320931-62321974 1184 3744 60 61 +p:HG002_2_chr20:62320931-62321974 1184 4983 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/output.vcf.gz new file mode 100644 index 00000000..096fbfd1 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/output.vcf.gz.tbi new file mode 100644 index 00000000..03007f67 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62321031-62321874/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/base.vcf.gz new file mode 100644 index 00000000..adae1dc4 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/base.vcf.gz.tbi new file mode 100644 index 00000000..eb27c026 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/comp.vcf.gz new file mode 100644 index 00000000..2d78b6a9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/comp.vcf.gz.tbi new file mode 100644 index 00000000..25244d62 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/haps.fa new file mode 100644 index 00000000..46a6e858 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/haps.fa @@ -0,0 +1,102 @@ +>ref_chr20_62349512_62350033 +GAATCCTACAGTCAGCTCAACTATCATTCAAGAGGGAGGACAAAACAGCCGTTTTCAGACAATTCCGGATAGACTGTCATGGAATAGAAAAACTACAGGGTGCATTTCAGGAAGGAGGAAGCAGCAACCCAGGGGATGGGGATGGGGATGGGGATGGTGGGGGTGATGGGGGTGATGATGGTGATGGTGATGGTGATGGTGATGGTGATGGTGATGGTGGGGGTGGTGATGGGTGGGGGTGATGACGGTGGGAGTGGGGGTGATGACGGTGATGGTGGGGGTGATGACGGTGATGGTGGGGGTGATGACGGTGATGGTGGGGGTGATGATGGTGGGAGTGGGCTGGTAGTGGGGGTGATGGTTTGGGTGGGAGTAAGGTGATGGTGGAGGTAAAGAGGCAGAAAATTGCTGGCTGATGACATGGAGCCCCCTTCCCTGGAGGAGAGGTGGGGTGGCGGGTAAAGGGTGCAGGGAGAACATGGGCAGGCTAATGTTTTGGGACACTGGTGGGTGACCAGGTCC +>syndip_1_chr20:62349512-62350033 +GAATCCTACAGTCAGCTCAACTATCATTCAAGAGGGAGGACAAAACAGCCGTTTTCAGAC +AATTCCGGATAGACTGTCATGGAATAGAAAAACTACAGGGTGCATTTCAGGAAGGAGGAA +GCAGCAACCCAGGGGATGGGGATGGGGATGGGGATGGGGATGGTGGGGGTGATGGGGGTG +ATGATGGTGATGGTGGGGGTGATGATGGTGATGGTGATGGTGATGGTGGGGGTGGTGATG +GTGGGGGTGGGGGTGGTGATGGTGGGGGTGGGGGTGATGATGGTGATGGTGGGGGTGATG +ACGGTGGGGCTGGGGGTGATGATGGTGGGGGTGATGACGGTGATGATGGGGGTGGAGGGG +TGATGACGGTGATGATGGGGGTGGGGGGGTGATGACGGTGATGTGGGGGTGATGACGGTG +GGGGTGGGGGTGATGACGGTGATGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACG +GTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATG +ATGGTGATGGTGGGGGTGATGATGGTGGGGGTGGGGGTGATGATGGTGAGGGTGATGATG +GTGGGGGTAATGACGGTGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGA +TGGTGGGGGTGATGACGATGATGGTGGGGGTGATGACGGTGATGGCGGTGGGGGTGATGA +CGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGA +TGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGG +TGATGACGGTGGGGGTGGGGGTGATGACGGTGATGGTAGAGGTGATGATGGTGGGGGTGA +TGGTGGGGGTGGGGGTGGGGGTGGGGGTGATGATGGTGATGGTGGGGGTGATGATGGTGA +GGGTGATGATGGTGGGGGTGATGGTGGGGGTGGGGGTGGGGGTGGGGGTGATGACGGTGA +TGGTGGGGGTGATGATGGTGGGAGTGGGCTGGTAGTGGGGGTGATGGTTTGGGTGGGAGT +AAGGTGATGGTGGAGGTAAAGAGGCAGAAAATTGCTGGCTGATGACATGGAGCCCCCTTC +CCTGGAGGAGAGGTGGGGTGGCGGGTAAAGGGTGCAGGGAGAACATGGGCAGGCTAATGT +TTTGGGACACTGGTGGGTGACCAGGTCC +>syndip_2_chr20:62349512-62350033 +GAATCCTACAGTCAGCTCAACTATCATTCAAGAGGGAGGACAAAACAGCCGTTTTCAGAC +AATTCCGGATAGACTGTCATGGAATAGAAAAACTACAGGGTGCATTTCAGGAAGGAGGAA +GCAGCAACCCAGGGGATGGGGATGGGGATGGGGATGGGGATGGTGGGGGTGATGGGGGTG +ATGATGGTGATGGTGGGGGTGATGATGGTGATGGTGATGGTGATGGTGATGGTGGGGGTG +GTGATGGTGGGGGTGGGGGTGATGATGGTGATGGTGGGGGTGATGACGGTGGGGCTGGGG +GTGATGATGGTGGGGGTGATGACGGTGATGATGGGGGTGGAGGGGTGATGACGGTGATGA +TGGGGGTGGGGGGGTGATGACGGTGATGTGGGGGTGATGACGGTGGGGGTGGGGGTGATG +ACGGTGATGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTG +ATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGG +GTGATGATGGTGATGGTGGGGGTGATGATGGTGGGGGTGGGGGTGATGATGGTGAGGGTG +ATGATGGTGGGGGTAATGACGGTGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGA +CGGTGATGGTGGGGGTGATGACGATGATGGTGGGGGTGATGACGGTGATGGCGGTGGGGG +TGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGG +GGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGG +TGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGATGGTAGAGGTGATGATGGTGG +GGGTGGGGGTGGGGGTGGGGGTGAGGGTGATGATGGTGGGGGTGATGATGGTGATGGTGG +GGGTGATGATGGTGAGGGTGATGATGGTGGGGGTGATGGTGGGGGTGGGGGTGGGGGTAA +TGACGGTGGGGTGGGGGTAATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGT +GATGACGGTGATGGTGGGGGTGATGACGATGATGGTGGGGGTGATGACGGTGATGGCGGT +GGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGG +GGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGT +GATGGTAGAGGTGATGATGGTGGGGGTGATGGTGGGGGTGGGGGTGGGGGTGGGGGTGAT +GATGGTGATGGTGGGGGTGATGATGGTGAGGGTGATGATGGTGGGGGTGATGGTGGGGGT +GGGGGTGGGGGTGGGGGTGATGATGGTGGGAGTGGGCTGGTAGTGGGGGTGATGGTTTGG +GTGGGAGTAAGGTGATGGTGGAGGTAAAGAGGCAGAAAATTGCTGGCTGATGACATGGAG +CCCCCTTCCCTGGAGGAGAGGTGGGGTGGCGGGTAAAGGGTGCAGGGAGAACATGGGCAG +GCTAATGTTTTGGGACACTGGTGGGTGACCAGGTCC +>p:HG002_1_chr20:62349512-62350033 +GAATCCTACAGTCAGCTCAACTATCATTCAAGAGGGAGGACAAAACAGCCGTTTTCAGAC +AATTCCGGATAGACTGTCATGGAATAGAAAAACTACAGGGTGCATTTCAGGAAGGAGGAA +GCAGCAACCCAGGGGATGGGGATGGGGATGGGGATGGGGATGGTGGGGGTGATGGGGGTG +ATGATGGTGATGGTGGGGGTGATGATGGTGATGGTGATGGTGATGGTGATGGTGGGGGTG +GTGATGGTGGGGGTGGGGGTGATGATGGTGATGGTGGGGGTGATGACGGTGGGGCTGGGG +GTGATGATGGTGGGGGTGATGACGGTGATGATGGGGGTGGAGGGGTGATGACGGTGATGA +TGGGGGTGGGGGGGTGATGACGGTGATGTGGGGGTGATGACGGTGGGGGTGGGGGTGATG +ACGGTGATGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTG +ATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGG +GTGATGATGGTGATGGTGGGGGTGATGATGGTGGGGGTGGGGGTGATGATGGTGAGGGTG +ATGATGGTGGGGGTAATGACGGTGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGA +CGGTGATGGTGGGGGTGATGACGATGATGGTGGGGGTGATGACGGTGATGGCGGTGGGGG +TGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGG +GGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGG +TGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGATGGTAGAGGTGATGATGGTGG +GGGTGGGGGTGGGGGTGGGGGTGAGGGTGATGATGGTGGGGGTGATGATGGTGATGGTGG +GGGTGATGATGGTGAGGGTGATGATGGTGGGGGTGATGGTGGGGGTGGGGGTGGGGGTAA +TGACGGTGGGGTGGGGGTAATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGT +GATGACGGTGATGGTGGGGGTGATGACGATGATGGTGGGGGTGATGACGGTGATGGCGGT +GGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGG +GGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGT +GATGGTAGAGGTGATGATGGTGGGGGTGATGGTGGGGGTGGGGGTGGGGGTGGGGGTGAT +GATGGTGATGGTGGGGGTGATGATGGTGAGGGTGATGATGGTGGGGGTGATGGTGGGGGT +GGGGGTGGGGGTGGGGGTGATGATGGTGGGAGTGGGCTGGTAGTGGGGGTGATGGTTTGG +GTGGGAGTAAGGTGATGGTGGAGGTAAAGAGGCAGAAAATTGCTGGCTGATGACATGGAG +CCCCCTTCCCTGGAGGAGAGGTGGGGTGGCGGGTAAAGGGTGCAGGGAGAACATGGGCAG +GCTAATGTTTTGGGACACTGGTGGGTGACCAGGTCC +>p:HG002_2_chr20:62349512-62350033 +GAATCCTACAGTCAGCTCAACTATCATTCAAGAGGGAGGACAAAACAGCCGTTTTCAGAC +AATTCCGGATAGACTGTCATGGAATAGAAAAACTACAGGGTGCATTTCAGGAAGGAGGAA +GCAGCAACCCAGGGGATGGGGATGGGGATGGGGATGGGGATGGTGGGGGTGATGGGGGTG +ATGATGGTGATGGTGGGGGTGATGATGGTGATGGTGATGGTGATGGTGGGGGTGGTGATG +GTGGGGGTGGGGGTGGTGATGGTGGGGGTGGGGGTGATGATGGTGATGGTGGGGGTGATG +ACGGTGGGGCTGGGGGTGATGATGGTGGGGGTGATGACGGTGATGATGGGGGTGGAGGGG +TGATGACGGTGATGATGGGGGTGGGGGGGTGATGACGGTGATGTGGGGGTGATGACGGTG +GGGGTGGGGGTGATGACGGTGATGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACG +GTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATG +ATGGTGATGGTGGGGGTGATGATGGTGGGGGTGGGGGTGATGATGGTGAGGGTGATGATG +GTGGGGGTAATGACGGTGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGA +TGGTGGGGGTGATGACGATGATGGTGGGGGTGATGACGGTGATGGCGGTGGGGGTGATGA +CGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGA +TGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGG +TGATGACGGTGGGGGTGGGGGTGATGACGGTGATGGTAGAGGTGATGATGGTGGGGGTGA +TGGTGGGGGTGGGGGTGGGGGTGGGGGTGATGATGGTGATGGTGGGGGTGATGATGGTGA +GGGTGATGATGGTGGGGGTGATGGTGGGGGTGGGGGTGGGGGTGGGGGTGATGACGGTGA +TGGTGGGGGTGATGATGGTGGGAGTGGGCTGGTAGTGGGGGTGATGGTTTGGGTGGGAGT +AAGGTGATGGTGGAGGTAAAGAGGCAGAAAATTGCTGGCTGATGACATGGAGCCCCCTTC +CCTGGAGGAGAGGTGGGGTGGCGGGTAAAGGGTGCAGGGAGAACATGGGCAGGCTAATGT +TTTGGGACACTGGTGGGTGACCAGGTCC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/haps.fa.ref.fa new file mode 100644 index 00000000..8f32fa6f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:62349512-62350033 +GAATCCTACAGTCAGCTCAACTATCATTCAAGAGGGAGGACAAAACAGCCGTTTTCAGACAATTCCGGATAGACTGTCATGGAATAGAAAAACTACAGGGTGCATTTCAGGAAGGAGGAAGCAGCAACCCAGGGGATGGGGATGGGGATGGGGATGGTGGGGGTGATGGGGGTGATGATGGTGATGGTGATGGTGATGGTGATGGTGATGGTGATGGTGGGGGTGGTGATGGGTGGGGGTGATGACGGTGGGAGTGGGGGTGATGACGGTGATGGTGGGGGTGATGACGGTGATGGTGGGGGTGATGACGGTGATGGTGGGGGTGATGATGGTGGGAGTGGGCTGGTAGTGGGGGTGATGGTTTGGGTGGGAGTAAGGTGATGGTGGAGGTAAAGAGGCAGAAAATTGCTGGCTGATGACATGGAGCCCCCTTCCCTGGAGGAGAGGTGGGGTGGCGGGTAAAGGGTGCAGGGAGAACATGGGCAGGCTAATGTTTTGGGACACTGGTGGGTGACCAGGTCC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/msa.fa new file mode 100644 index 00000000..9458709a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/msa.fa @@ -0,0 +1,140 @@ +>ref_chr20_62349512_62350033 +gaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcagac +aattccggatagactgtcatggaatagaaaaactacagggtgcatttcag---------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------------gaaggaggaag +cagcaacccaggggatggggatggggatggggatggtgggggtgatgggggtgatgatgg +tgatggtgatggtgatggtgatggtgatggtgatggtggg---------ggtggtgatg- +----------ggtgggggtgatgacggtgggagtgggggtgatgacggtgatggtggggg +tgat-----------------------------------------------------gac +ggtgatggtgggggtgatgacggtgat--------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------ggtgggggtgatgatggtgggagtgggctggtagtg +ggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgctg +gctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagggtgcag +ggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtcc +>syndip_1_chr20:62349512-62350033 +gaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcagac +aattccggatagactgtcatggaatagaaaaactacagggtgcatttcaggaaggaggaa +gcagcaacccaggggatggggatggggatggggatggggatggtgggggtgatgggggtg +atgatggtgatggtgggggtgatgatggtgatggtgatggtgatggtgggggtggtgatg +gtgggggtgggggtggtgatggtgggggtgggggtgatgatggtgatggtgggggtgatg +acggtggggctgggggtgatgatggtgggggtgatgacggtgatgatgggggtggagggg +tgatgacggtgatgatgggggtgggggggtgatgacggtgatgtgggggtgatgacggtg +ggggtgggggtgatgacggtgat---------------------ggtgggggtgatgacg +gtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatg +acggtgggggtgggggtgatgatggtgatggtgggggtgatgatggtgggggtgggggtg +atgatggtgagggtgatgatggtgggggtaatgacggtggggtgggggtgatgacggtgg +gggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtgatgacgg +tgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtga +tgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtggggg +tgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtag +aggtgatgatggtgggggtgatggtgggggtgggggtggg---------ggtgggggtga +tgatggtgatggtgggggtgatgatggtgagggtgatgatggtgggggtgatggtggggg +tggg-------------------------------------------------------- +ggtgggggtgggggtgatgacggtgat--------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------ggtgggggtgatgatggtgggagtgggctggtagtg +ggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgctg +gctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagggtgcag +ggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtcc +>syndip_2_chr20:62349512-62350033 +gaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcagac +aattccggatagactgtcatggaatagaaaaactacagggtgcatttcaggaaggaggaa +gcagcaacccaggggatggggatggggatggggatggggatggtgggggtgatgggggtg +atgatggtgatggtgggggtgatgatggtgatggtga---------------tggtgatg +gtgatggtgggggtggtgatggtgggggtgggggtgatgatggtgatggtgggggtgatg +acggtggggctgggggtgatgatggtgggggtgatgacggtgatgatgggggtggagggg +tgatgacggtgatgatgggggtgggggggtgatgacggtgatgtgggggtgatgacggtg +ggggtgggggtgatgacggtgatggtgggggtgatgacggtgggggtgggggtgatgacg +gtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatg +acggtgggggtgggggtgatgatggtgatggtgggggtgatgatggtgggggtgggggtg +atgatggtgagggtgatgatggtgggggtaatgacggtggggtgggggtgatgacggtgg +gggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtgatgacgg +tgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtga +tgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtggggg +tgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtag +aggtgatgatggtgggggtgggggtgggggtgggggtgagggtgatgatggtgggggtga +tgatggtgatggtgggggtgatgatggtgagggtgatgatggtgggggtgatggtggggg +tgggggtgggggtaatgacggtggggtgggggtaatgacggtgggggtgggggtgatgac +ggtgggggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtgat +gacggtgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtggg +ggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggt +gggggtgatgacggtgatggtagaggtgatgatggtgggggtgatggtgggggtgggggt +gggggtgggggtgatgatggtgatggtgggggtgatgatggtgagggtgatgatggtggg +ggtgatggtgggggtgggggtgggggtgggggtgatgatggtgggagtgggctggtagtg +ggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgctg +gctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagggtgcag +ggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtcc +>p:HG002_1_chr20:62349512-62350033 +gaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcagac +aattccggatagactgtcatggaatagaaaaactacagggtgcatttcaggaaggaggaa +gcagcaacccaggggatggggatggggatggggatggggatggtgggggtgatgggggtg +atgatggtgatggtgggggtgatgatggtgatggtga---------------tggtgatg +gtgatggtgggggtggtgatggtgggggtgggggtgatgatggtgatggtgggggtgatg +acggtggggctgggggtgatgatggtgggggtgatgacggtgatgatgggggtggagggg +tgatgacggtgatgatgggggtgggggggtgatgacggtgatgtgggggtgatgacggtg +ggggtgggggtgatgacggtgatggtgggggtgatgacggtgggggtgggggtgatgacg +gtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatg +acggtgggggtgggggtgatgatggtgatggtgggggtgatgatggtgggggtgggggtg +atgatggtgagggtgatgatggtgggggtaatgacggtggggtgggggtgatgacggtgg +gggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtgatgacgg +tgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtga +tgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtggggg +tgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtag +aggtgatgatggtgggggtgggggtgggggtgggggtgagggtgatgatggtgggggtga +tgatggtgatggtgggggtgatgatggtgagggtgatgatggtgggggtgatggtggggg +tgggggtgggggtaatgacggtggggtgggggtaatgacggtgggggtgggggtgatgac +ggtgggggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtgat +gacggtgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtggg +ggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggt +gggggtgatgacggtgatggtagaggtgatgatggtgggggtgatggtgggggtgggggt +gggggtgggggtgatgatggtgatggtgggggtgatgatggtgagggtgatgatggtggg +ggtgatggtgggggtgggggtgggggtgggggtgatgatggtgggagtgggctggtagtg +ggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgctg +gctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagggtgcag +ggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtcc +>p:HG002_2_chr20:62349512-62350033 +gaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcagac +aattccggatagactgtcatggaatagaaaaactacagggtgcatttcaggaaggaggaa +gcagcaacccaggggatggggatggggatggggatggggatggtgggggtgatgggggtg +atgatggtgatggtgggggtgatgatggtgatggtgatggtgatggtgggggtggtgatg +gtgggggtgggggtggtgatggtgggggtgggggtgatgatggtgatggtgggggtgatg +acggtggggctgggggtgatgatggtgggggtgatgacggtgatgatgggggtggagggg +tgatgacggtgatgatgggggtgggggggtgatgacggtgatgtgggggtgatgacggtg +ggggtgggggtgatgacggtgat---------------------ggtgggggtgatgacg +gtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatg +acggtgggggtgggggtgatgatggtgatggtgggggtgatgatggtgggggtgggggtg +atgatggtgagggtgatgatggtgggggtaatgacggtggggtgggggtgatgacggtgg +gggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtgatgacgg +tgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtga +tgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtggggg +tgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtag +aggtgatgatggtgggggtgatggtgggggtgggggtggg---------ggtgggggtga +tgatggtgatggtgggggtgatgatggtgagggtgatgatggtgggggtgatggtggggg +tggg-------------------------------------------------------- +ggtgggggtgggggtgatgacggtgat--------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------ggtgggggtgatgatggtgggagtgggctggtagtg +ggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgctg +gctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagggtgcag +ggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtcc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/msa.fa.fai new file mode 100644 index 00000000..bb8b4f3c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_62349512_62350033 1611 29 60 61 +syndip_1_chr20:62349512-62350033 1611 1701 60 61 +syndip_2_chr20:62349512-62350033 1611 3373 60 61 +p:HG002_1_chr20:62349512-62350033 1611 5046 60 61 +p:HG002_2_chr20:62349512-62350033 1611 6719 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/output.vcf.gz new file mode 100644 index 00000000..9af4d745 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/output.vcf.gz.tbi new file mode 100644 index 00000000..003fb683 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62349612-62349933/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/base.vcf.gz new file mode 100644 index 00000000..0b8336e6 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/base.vcf.gz.tbi new file mode 100644 index 00000000..3f9a903c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/comp.vcf.gz new file mode 100644 index 00000000..a40e9e26 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/comp.vcf.gz.tbi new file mode 100644 index 00000000..cb3537b9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/haps.fa new file mode 100644 index 00000000..0484f428 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/haps.fa @@ -0,0 +1,64 @@ +>ref_chr20_62360090_62360813 +AAGGACATTTCCCCACCCCACTCCAGGGAGTCCCTGCCCCCACCCTGACCAAGGCTGGCAGCCCCCTGGCCTAGGCCGAGACAGGGGCCTTGGTAGATACATCCACGTGGTCAGGAAAGTGGGTGAGAAGGAAGGAAGACGGTGCAGGTGTGGAGGGAGGAATGAGCAGACAGGTGGACAGATGGATGGAAACAAGGAATAAAGGGTGGGTGCTGCATAGGTAGGGGGGTGGGTGGGTGGATGGATGGGTAGGGGTGGGTGGGTGGATACGTTGGGGGTGGGTGGGTGGGTGGGTCAGCAGGCAGAGGGATGGGATAGGATAGGTGGGTGGGTGGAGGGATGGGTGAGTGGGTGGGTGGAGGGATAGATGGGTGGTGGGTGGGTGGAGGGATAGATGGGTGGTGGGTGGGTGGAGGGATAGATGGGTGGGTGGGTGGGTGGAGGGATAGATGGGTGGTGGGTGGGTGGAGGGATAGATGGGTGGATGGGTGGGTAGAAGGATAGGTAGGTGGGTGGGTGGGTGGATGGGTGGGTGGAGGGATAGATGGGTGGGTGGGTGGGTGGAGGGATAGATGGGTGGGTGGGTGGAGGGACCACTTCCCAGGTGGAGTGGAAAGGGTTCCTCTTCCCTCCGTATCATTTTACAGTTGGTGAAACTGAGGCTGTGAGAGGCAAGACGCTCACATGGCGGAACCTGATTTCTGGCCCAGAACAATCTAAAAGC +>syndip_1_chr20:62360090-62360813 +AAGGACATTTCCCCACCCCACTCCAGGGAGTCCCTGCCCCCACCCTGACCAAGGCTGGCA +GCCCCCTGGCCTAGGCCGAGACAGGGGCCTTGGTAGATACATCCACGTGGTCAGGAAAGT +GGGTGAGAAGGAAGGAAGACGGTGCAGGTGTGGAGGGAGGAATGAGCAGACAGGTGGACA +GATGGATGGAAACAAGGAATAAAGGGTGGGTGCTGCATAGGTAGGGGGGTGGGTGGGTGG +ATGGATGGGTAGGGGGTGGGTGGGTGGATACGTTGGGGGTGGGTGGGTGGGTGGGTCAGC +AGGCAGAGGGATGGGATAGGATAGGTGGGTGGGTGGGTGGATAGGGAGGGGGTGGGGTGG +GTGCATAGGTAGGGGGGTGGATGGGTCAGCAGGCAGCGGGATGGGATAGGATAGGTGGGT +GGGTGGAGGGATAGATGGGTGGTGGGTGGGTGGAGGGATAGATGGGTGGGTGGGTGGGTA +GAAGGATAGGTAGGTGGGTGGGTGGGTGGATGGATAGGTGGATGGGTGGGTGGAGGAATA +GATGGGTGGGTGGGTGGGTGGGTGGATGGATAGGTGGGTGGGTGGGTGGAGGGATAGATG +GGTGGGTGGATGGGTGGGTGGAGGGATAGATGGGTGGTGGGTGGGTGGAGGGATAGATGG +GTGGGTGGGTGGGTAGAAGGATAGGTAGGTGGGTGGGTGGGTGGATGGATAGGTGGGTGG +GTGGGTGGAGGAATAGATGGGTGGGTGGATGGGTGGGTGGAGGGATAGATGGGTGGGTGG +GTGGGTGGAGGGATAGATGGGTGGGTGGGTGGAGGGACCACTTCCCAGGTGGAGTGGAAA +GGGTTCCTCTTCCCTCCGTATCATTTTACAGTTGGTGAAACTGAGGCTGTGAGAGGCAAG +ACGCTCACATGGCGGAACCTGATTTCTGGCCCAGAACAATCTAAAAGC +>syndip_2_chr20:62360090-62360813 +AAGGACATTTCCCCACCCCACTCCAGGGAGTCCCTGCCCCCACCCTGACCAAGGCTGGCA +GCCCCCTGGCCTAGGCCGAGACAGGGGCCTTGGTAGATACATCCACGTGGTCAGGAAAGT +GGGTGAGAAGGAAGGAAGACGGTGCAGGTGTGGAGGGAGGAATGAGCAGACAGGTGGACA +GATGGATGGAAACAAGGAATAAAGGGTGGGTGCTGCATAGGTAGGGGGGTGGGTGGGTGG +ATGGATGGGTAGGGGGTGGGTGGGTGGATACGTTGGGGGTGGGTGGGTGGGTGGGTCAGC +AGGCAGAGGGATGGGATAGGATAGGTGGGTGGGTGGAGGGATAGATGGGTGGTGGGTGGG +TGGAGGGATAGATGGGTGGGTGGAGGGATAGATGGGTGGGTGGGTAGAAGGATAGGTAGG +TGGGTGGGTGGGTGGATGGATAGGTGGATGGGTGGGTGGAGGAATAGATGGGTGGGTGGG +TGGGTGGGTGGATGGATAGGTGGGTGGGTGGGTGGAGGAATAGATGGGTGGGTGGATGGG +TGGGTGGAGGGATAGATGGGTGGGTGGGTGGGTGGAGGGATAGATGGGTGGGTGGGTGGA +GGGACCACTTCCCAGGTGGAGTGGAAAGGGTTCCTCTTCCCTCCGTATCATTTTACAGTT +GGTGAAACTGAGGCTGTGAGAGGCAAGACGCTCACATGGCGGAACCTGATTTCTGGCCCA +GAACAATCTAAAAGC +>p:HG002_1_chr20:62360090-62360813 +AAGGACATTTCCCCACCCCACTCCAGGGAGTCCCTGCCCCCACCCTGACCAAGGCTGGCA +GCCCCCTGGCCTAGGCCGAGACAGGGGCCTTGGTAGATACATCCACGTGGTCAGGAAAGT +GGGTGAGAAGGAAGGAAGACGGTGCAGGTGTGGAGGGAGGAATGAGCAGACAGGTGGACA +GATGGATGGAAACAAGGAATAAAGGGTGGGTGCTGCATAGGTAGGGGGGTGGGTGGGTGG +ATGGATGGGTAGGGGGTGGGTGGGTGGATACGTTGGGGGTGGGTGGGTGGGTGGGTCAGC +AGGCAGAGGGATGGGATAGGATAGGTGGGTGGGTGGAGGGATAGATGGGTGGTGGGTGGG +TGGAGGGATAGATGGGTGGGTGGAGGGATAGATGGGTGGGTGGGTAGAAGGATAGGTAGG +TGGGTGGGTGGGTGGATGGATAGGTGGATGGGTGGGTGGAGGAATAGATGGGTGGGTGGG +TGGGTGGGTGGATGGATAGGTGGGTGGGTGGGTGGAGGAATAGATGGGTGGGTGGATGGG +TGGGTGGAGGGATAGATGGGTGGGTGGGTGGGTGGAGGGATAGATGGGTGGGTGGGTGGA +GGGACCACTTCCCAGGTGGAGTGGAAAGGGTTCCTCTTCCCTCCGTATCATTTTACAGTT +GGTGAAACTGAGGCTGTGAGAGGCAAGACGCTCACATGGCGGAACCTGATTTCTGGCCCA +GAACAATCTAAAAGC +>p:HG002_2_chr20:62360090-62360813 +AAGGACATTTCCCCACCCCACTCCAGGGAGTCCCTGCCCCCACCCTGACCAAGGCTGGCA +GCCCCCTGGCCTAGGCCGAGACAGGGGCCTTGGTAGATACATCCACGTGGTCAGGAAAGT +GGGTGAGAAGGAAGGAAGACGGTGCAGGTGTGGAGGGAGGAATGAGCAGACAGGTGGACA +GATGGATGGAAACAAGGAATAAAGGGTGGGTGCTGCATAGGTAGGGGGGTGGGTGGGTGG +ATGGATGGGTAGGGGGTGGGTGGGTGGATACGTTGGGGGTGGGTGGGTGGGTGGGTCAGC +AGGCAGAGGGATGGGATAGGATAGGTGGGTGGGTGGGTGGATAGGGAGGGGGTGGGGTGG +GTGCATAGGTAGGGGGGTGGATGGGTCAGCAGGCAGCGGGATGGGATAGGATAGGTGGGT +GGGTGGAGGGATAGATGGGTGGTGGGTGGGTGGAGGGATAGATGGGTGGGTGGGTGGGTA +GAAGGATAGGTAGGTGGGTGGGTGGGTGGATGGATAGGTGGATGGGTGGGTGGAGGAATA +GATGGGTGGGTGGGTGGGTGGGTGGATGGATAGGTGGGTGGGTGGGTGGAGGGATAGATG +GGTGGGTGGATGGGTGGGTGGAGGGATAGATGGGTGGTGGGTGGGTGGAGGGATAGATGG +GTGGGTGGGTGGGTAGAAGGATAGGTAGGTGGGTGGGTGGGTGGATGGATAGGTGGGTGG +GTGGGTGGAGGAATAGATGGGTGGGTGGATGGGTGGGTGGAGGGATAGATGGGTGGGTGG +GTGGGTGGAGGGATAGATGGGTGGGTGGGTGGAGGGACCACTTCCCAGGTGGAGTGGAAA +GGGTTCCTCTTCCCTCCGTATCATTTTACAGTTGGTGAAACTGAGGCTGTGAGAGGCAAG +ACGCTCACATGGCGGAACCTGATTTCTGGCCCAGAACAATCTAAAAGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/haps.fa.ref.fa new file mode 100644 index 00000000..bd8ab102 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:62360090-62360813 +AAGGACATTTCCCCACCCCACTCCAGGGAGTCCCTGCCCCCACCCTGACCAAGGCTGGCAGCCCCCTGGCCTAGGCCGAGACAGGGGCCTTGGTAGATACATCCACGTGGTCAGGAAAGTGGGTGAGAAGGAAGGAAGACGGTGCAGGTGTGGAGGGAGGAATGAGCAGACAGGTGGACAGATGGATGGAAACAAGGAATAAAGGGTGGGTGCTGCATAGGTAGGGGGGTGGGTGGGTGGATGGATGGGTAGGGGTGGGTGGGTGGATACGTTGGGGGTGGGTGGGTGGGTGGGTCAGCAGGCAGAGGGATGGGATAGGATAGGTGGGTGGGTGGAGGGATGGGTGAGTGGGTGGGTGGAGGGATAGATGGGTGGTGGGTGGGTGGAGGGATAGATGGGTGGTGGGTGGGTGGAGGGATAGATGGGTGGGTGGGTGGGTGGAGGGATAGATGGGTGGTGGGTGGGTGGAGGGATAGATGGGTGGATGGGTGGGTAGAAGGATAGGTAGGTGGGTGGGTGGGTGGATGGGTGGGTGGAGGGATAGATGGGTGGGTGGGTGGGTGGAGGGATAGATGGGTGGGTGGGTGGAGGGACCACTTCCCAGGTGGAGTGGAAAGGGTTCCTCTTCCCTCCGTATCATTTTACAGTTGGTGAAACTGAGGCTGTGAGAGGCAAGACGCTCACATGGCGGAACCTGATTTCTGGCCCAGAACAATCTAAAAGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/msa.fa new file mode 100644 index 00000000..12dd5f9f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/msa.fa @@ -0,0 +1,85 @@ +>ref_chr20_62360090_62360813 +aaggacatttccccaccccactccagggagtccctgcccccaccctgaccaaggctggca +gccccctggcctaggccgagacaggggccttggtagatacatccacgtggtcaggaaagt +gggtgagaaggaaggaagacggtgcaggtgtggagggaggaatgagcagacaggtggaca +gatggatggaaacaaggaataaagggtgggtgctgcataggtaggggggtgggtgggtgg +atggatgggta-ggggtgggtgggtggatacgttgggggtgggtgggtgggtgggtcagc +aggcaga----------------------------------------------------- +-------------------------------------gggatgggataggataggtgggt +gggtggagggatgggtg---agtgggtgggtggagggatagatgggtgg----------- +------------------------------------------tgggtgggtggagggata +gatgggt-ggtgggtgggtggagggatagatgggtgggtgggtgggtggagggatagatg +ggt--------------------------------------------------------- +---------------------------ggtgggtgggtggagggatagatgggtggatgg +gtgggtagaaggataggtaggtgggtgggtgggtggatgggtgggtggagggatagatgg +gtgggtgggtgggtggagggatagatgggtgggtgggtggagggaccacttcccaggtgg +agtggaaagggttcctcttccctccgtatcattttacagttggtgaaactgaggctgtga +gaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaaaagc +>syndip_1_chr20:62360090-62360813 +aaggacatttccccaccccactccagggagtccctgcccccaccctgaccaaggctggca +gccccctggcctaggccgagacaggggccttggtagatacatccacgtggtcaggaaagt +gggtgagaaggaaggaagacggtgcaggtgtggagggaggaatgagcagacaggtggaca +gatggatggaaacaaggaataaagggtgggtgctgcataggtaggggggtgggtgggtgg +atggatgggtagggggtgggtgggtggatacgttgggggtgggtgggtgggtgggtcagc +aggcagagggatgggataggataggtgggtgggtgggtggatagggagggggtggggtgg +gtgcataggtaggggggtggatgggtcagcaggcagcgggatgggataggataggtgggt +gggtggagggatagatgggtggtgggtgggtggagggatagatgggtgggtgggtgggta +gaaggataggtaggtgggtgggtgggtggatggataggtggatgggtgggtggaggaata +gatgggtgggtgggtgggtgggtggatggataggtgggtgggtgggtggagggatagatg +ggtgggtggatgggtgggtggagggatagatgggtggtgggtgggtggagggatagatgg +gtgggtgggtgggtagaaggataggtaggtgggtgggtgggtggatggataggtgggtgg +gtgggtggaggaata--------gatgggtgggtggatgggtgggtggagggatagatgg +gtgggtgggtgggtggagggatagatgggtgggtgggtggagggaccacttcccaggtgg +agtggaaagggttcctcttccctccgtatcattttacagttggtgaaactgaggctgtga +gaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaaaagc +>syndip_2_chr20:62360090-62360813 +aaggacatttccccaccccactccagggagtccctgcccccaccctgaccaaggctggca +gccccctggcctaggccgagacaggggccttggtagatacatccacgtggtcaggaaagt +gggtgagaaggaaggaagacggtgcaggtgtggagggaggaatgagcagacaggtggaca +gatggatggaaacaaggaataaagggtgggtgctgcataggtaggggggtgggtgggtgg +atggatgggtagggggtgggtgggtggatacgttgggggtgggtgggtgggtgggtcagc +aggcaga----------------------------------------------------- +-------------------------------------gggatgggataggataggtgggt +gggtggagggatagatgggtggtgggtgggtggagggatagatgggtgggtggagggata +----------------------------------------gatgggtgggtgggtagaag +gataggtaggtgggtgggtgggtggatggataggtggatgggtgggtggaggaatagatg +ggtg-------------------------------------------------------- +---------------------------ggtgggtgggtgggtggatggataggtgggtgg +gtgggtggaggaata--------gatgggtgggtggatgggtgggtggagggatagatgg +gtgggtgggtgggtggagggatagatgggtgggtgggtggagggaccacttcccaggtgg +agtggaaagggttcctcttccctccgtatcattttacagttggtgaaactgaggctgtga +gaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaaaagc +>p:HG002_1_chr20:62360090-62360813 +aaggacatttccccaccccactccagggagtccctgcccccaccctgaccaaggctggca +gccccctggcctaggccgagacaggggccttggtagatacatccacgtggtcaggaaagt +gggtgagaaggaaggaagacggtgcaggtgtggagggaggaatgagcagacaggtggaca +gatggatggaaacaaggaataaagggtgggtgctgcataggtaggggggtgggtgggtgg +atggatgggtagggggtgggtgggtggatacgttgggggtgggtgggtgggtgggtcagc +aggcaga----------------------------------------------------- +-------------------------------------gggatgggataggataggtgggt +gggtggagggatagatgggtggtgggtgggtggagggatagatgggtgggtggagggata +----------------------------------------gatgggtgggtgggtagaag +gataggtaggtgggtgggtgggtggatggataggtggatgggtgggtggaggaatagatg +ggtg-------------------------------------------------------- +---------------------------ggtgggtgggtgggtggatggataggtgggtgg +gtgggtggaggaata--------gatgggtgggtggatgggtgggtggagggatagatgg +gtgggtgggtgggtggagggatagatgggtgggtgggtggagggaccacttcccaggtgg +agtggaaagggttcctcttccctccgtatcattttacagttggtgaaactgaggctgtga +gaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaaaagc +>p:HG002_2_chr20:62360090-62360813 +aaggacatttccccaccccactccagggagtccctgcccccaccctgaccaaggctggca +gccccctggcctaggccgagacaggggccttggtagatacatccacgtggtcaggaaagt +gggtgagaaggaaggaagacggtgcaggtgtggagggaggaatgagcagacaggtggaca +gatggatggaaacaaggaataaagggtgggtgctgcataggtaggggggtgggtgggtgg +atggatgggtagggggtgggtgggtggatacgttgggggtgggtgggtgggtgggtcagc +aggcagagggatgggataggataggtgggtgggtgggtggatagggagggggtggggtgg +gtgcataggtaggggggtggatgggtcagcaggcagcgggatgggataggataggtgggt +gggtggagggatagatgggtggtgggtgggtggagggatagatgggtgggtgggtgggta +gaaggataggtaggtgggtgggtgggtggatggataggtggatgggtgggtggaggaata +gatgggtgggtgggtgggtgggtggatggataggtgggtgggtgggtggagggatagatg +ggtgggtggatgggtgggtggagggatagatgggtggtgggtgggtggagggatagatgg +gtgggtgggtgggtagaaggataggtaggtgggtgggtgggtggatggataggtgggtgg +gtgggtggaggaata--------gatgggtgggtggatgggtgggtggagggatagatgg +gtgggtgggtgggtggagggatagatgggtgggtgggtggagggaccacttcccaggtgg +agtggaaagggttcctcttccctccgtatcattttacagttggtgaaactgaggctgtga +gaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaaaagc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/msa.fa.fai new file mode 100644 index 00000000..a491333d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_62360090_62360813 956 29 60 61 +syndip_1_chr20:62360090-62360813 956 1035 60 61 +syndip_2_chr20:62360090-62360813 956 2041 60 61 +p:HG002_1_chr20:62360090-62360813 956 3048 60 61 +p:HG002_2_chr20:62360090-62360813 956 4055 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/output.vcf.gz new file mode 100644 index 00000000..ee59b60f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/output.vcf.gz.tbi new file mode 100644 index 00000000..7200e7a9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62360190-62360713/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/base.vcf.gz new file mode 100644 index 00000000..c5993777 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/base.vcf.gz.tbi new file mode 100644 index 00000000..dae08ce3 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/comp.vcf.gz new file mode 100644 index 00000000..d8846886 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/comp.vcf.gz.tbi new file mode 100644 index 00000000..ca645b7c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/haps.fa new file mode 100644 index 00000000..d53cedfb --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/haps.fa @@ -0,0 +1,52 @@ +>ref_chr20_62830512_62830939 +CCCAGGGCCAGAAGGGCAGCATGGGAGACCCCGGCCTTCCAGGCCCCCAGGGCCTCCGAGGTGACGTGGGCGACCGGGTAAGTGGCCCTCTCAGCAGGAAGCTCCCCTGCACCCCCTCTACCCATGTACCACAGTCCCCCACCCCCATGACAGTCCCCCAACCCCCACCACAGTCCCCCAACCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCACCCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCTACCACAATCCCCCACCCCCCACCACAGTCCCCTGGGACGCAGACAGGGAGAGGCCCTTGCAGCTCCCAGTGGGAAATCTGGCCATGGGCAGTGTCTCCCTGCGTGGCGGAGGCAGTGGCATCAGGGCCCCGACTGTGGCGCCTTTGGCCCCTCTGACCTTCCA +>syndip_1_chr20:62830512-62830939 +CCCAGGGCCAGAAGGGCAGCATGGGAGACCCCGGCCTTCCAGGCCCCCAGGGCCTCCGAG +GTGACGTGGGCGACCGGGTAAGTGGCCCTCTCAGCAGGAAGCTCCCCTGCACCCCCTCTA +CCCATGTACCACAGTCCCCCACCCCCCACCGTGCTCCACCCCCCACCACAGTCCCCCACC +CCCCACCCCAGTCCCCAAACCCCTACCACAGTCCCCCAACCCCACCACAGTCCCCCACCC +CCTACCACAGTCCCCCACCCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCC +CCACCACAGTCCGCCAACCCCCATGACAGTCCCTCAACCCCCACCACAGTCCCCCAACCC +CCATGACAGTCCCCCAACCCCCACCACAGTCCCCCAACCCCCACCACAGTCCCCACCCCC +TACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCTACCACAATCCCCCACCCCC +ACCACAGTCCCCTGGGACGCAGACAGGGAGAGGCCCTTGCAGCTCCCAGTGGGAAATCTG +GCCATGGGCAGTGTCTCCCTGCGTGGCGGAGGCAGTGGCATCAGGGCCCCGACTGTGGCG +CCTTTGGCCCCTCTGACCTTCCA +>syndip_2_chr20:62830512-62830939 +CCCAGGGCCAGAAGGGCAGCATGGGAGACCCCGGCCTTCCAGGCCCCCAGGGCCTCCGAG +GTGACGTGGGCGACCGGGTAAGTGGCCCTCTCAGCAGGAAGCTCCCCTGCACCCCCTCTA +CCCATGTACCACAGTCCCCCACCCCCCACCACAGTCCCCCACCCCCCACCCCAGTCCCCA +AACCCCTACCACAGTCCCCCAACCCCACCACAGTCCCCCACCCCCTACCACAGTCCCCCA +ACCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCACCACAGTCCGCCAA +CCCCCATGACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCACCACAGTCCGCCAAC +CCCCATGACAGTCCCCCAACCCCCACCACAGTCCCCCAACCCCCATGACAGTCCCCCAAC +CCCCACCACAGTCCCCCAACCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCACCC +CCTACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCTACCACAATCCCCCACCC +CCCACCACAGTCCCCTGGGACGCAGACAGGGAGAGGCCCTTGCAGCTCCCAGTGGGAAAT +CTGGCCATGGGCAGTGTCTCCCTGCGTGGCGGAGGCAGTGGCATCAGGGCCCCGACTGTG +GCGCCTTTGGCCCCTCTGACCTTCCA +>p:HG002_1_chr20:62830512-62830939 +CCCAGGGCCAGAAGGGCAGCATGGGAGACCCCGGCCTTCCAGGCCCCCAGGGCCTCCGAG +GTGACGTGGGCGACCGGGTAAGTGGCCCTCTCAGCAGGAAGCTCCCCTGCACCCCCTCTA +CCCATGTACCACAGTCCCCCACCCCCCACCACAGTCCCCCACCCCCCACCCCAGTCCCCA +AACCCCTACCACAGTCCCCCAACCCCACCACAGTCCCCCACCCCCTACCACAGTCCCCCA +ACCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCACCACAGTCCGCCAA +CCCCCATGACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCACCACAGTCCGCCAAC +CCCCATGACAGTCCCCCAACCCCCACCACAGTCCCCCAACCCCCATGACAGTCCCCCAAC +CCCCACCACAGTCCCCCAACCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCACCC +CCTACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCTACCACAATCCCCCACCC +CCCACCACAGTCCCCTGGGACGCAGACAGGGAGAGGCCCTTGCAGCTCCCAGTGGGAAAT +CTGGCCATGGGCAGTGTCTCCCTGCGTGGCGGAGGCAGTGGCATCAGGGCCCCGACTGTG +GCGCCTTTGGCCCCTCTGACCTTCCA +>p:HG002_2_chr20:62830512-62830939 +CCCAGGGCCAGAAGGGCAGCATGGGAGACCCCGGCCTTCCAGGCCCCCAGGGCCTCCGAG +GTGACGTGGGCGACCGGGTAAGTGGCCCTCTCAGCAGGAAGCTCCCCTGCACCCCCTCTA +CCCATGTACCACAGTCCCCCACCCCCCACCGTGCTCCACCCCCCACCACAGTCCCCCACC +CCCCACCCCAGTCCCCAAACCCCTACCACAGTCCCCCAACCCCACCACAGTCCCCCACCC +CCTACCACAGTCCCCCACCCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCC +CCACCACAGTCCGCCAACCCCCATGACAGTCCCTCAACCCCCACCACAGTCCCCCAACCC +CCATGACAGTCCCCCAACCCCCACCACAGTCCCCCAACCCCCACCACAGTCCCCACCCCC +TACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCTACCACAATCCCCCACCCCC +ACCACAGTCCCCTGGGACGCAGACAGGGAGAGGCCCTTGCAGCTCCCAGTGGGAAATCTG +GCCATGGGCAGTGTCTCCCTGCGTGGCGGAGGCAGTGGCATCAGGGCCCCGACTGTGGCG +CCTTTGGCCCCTCTGACCTTCCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/haps.fa.ref.fa new file mode 100644 index 00000000..df37a9a0 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:62830512-62830939 +CCCAGGGCCAGAAGGGCAGCATGGGAGACCCCGGCCTTCCAGGCCCCCAGGGCCTCCGAGGTGACGTGGGCGACCGGGTAAGTGGCCCTCTCAGCAGGAAGCTCCCCTGCACCCCCTCTACCCATGTACCACAGTCCCCCACCCCCATGACAGTCCCCCAACCCCCACCACAGTCCCCCAACCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCACCCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCTACCACAATCCCCCACCCCCCACCACAGTCCCCTGGGACGCAGACAGGGAGAGGCCCTTGCAGCTCCCAGTGGGAAATCTGGCCATGGGCAGTGTCTCCCTGCGTGGCGGAGGCAGTGGCATCAGGGCCCCGACTGTGGCGCCTTTGGCCCCTCTGACCTTCCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/msa.fa new file mode 100644 index 00000000..dc0fc966 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/msa.fa @@ -0,0 +1,65 @@ +>ref_chr20_62830512_62830939 +cccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccgag +gtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctcta +cccatgtaccacagtccccc---------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------acccccatgacagtcccccaa +cccccaccacagtcccccaacccctaccacagtcccccaacccccaccacagtccccacc +ccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatcccccacc +ccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaaa +tctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactgt +ggcgcctttggcccctctgaccttcca +>syndip_1_chr20:62830512-62830939 +cccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccgag +gtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctcta +cccatgtaccacagtcccccaccccccaccgtgctccacc-------------------- +----------------------ccccaccacagtcccccaccccccaccccagtccccaa +acccctaccacagtcccccaa-ccccaccacagtcccccaccccctaccacagtccccca +ccccctaccacagtcccccaacccccaccacagtcccccacccccaccacagtccgccaa +cccccatgacagtccctca--------------------acccccaccacagtcccccaa +cccccatgacagtcccccaacccccaccacagtcccccaacccccaccacagtccccacc +ccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatccccca-c +ccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaaa +tctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactgt +ggcgcctttggcccctctgaccttcca +>syndip_2_chr20:62830512-62830939 +cccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccgag +gtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctcta +cccatgtaccacagtcccccaccccccaccacagtcccccaccccccaccccagtcccca +aacccctaccacagtcccccaaccccaccacagtcccccaccccctaccacagtccccca +acccctaccacagtcccccaacccccaccacagtcccccaccccc-accacagtccgcca +acccccatgacagtcccccaacccccaccacagtcccccacccccaccacagtccgccaa +cccccatgacagtcccccaacccccaccacagtcccccaacccccatgacagtcccccaa +cccccaccacagtcccccaacccctaccacagtcccccaacccccaccacagtccccacc +ccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatcccccacc +ccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaaa +tctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactgt +ggcgcctttggcccctctgaccttcca +>p:HG002_1_chr20:62830512-62830939 +cccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccgag +gtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctcta +cccatgtaccacagtcccccaccccccaccacagtcccccaccccccaccccagtcccca +aacccctaccacagtcccccaaccccaccacagtcccccaccccctaccacagtccccca +acccctaccacagtcccccaacccccaccacagtcccccaccccc-accacagtccgcca +acccccatgacagtcccccaacccccaccacagtcccccacccccaccacagtccgccaa +cccccatgacagtcccccaacccccaccacagtcccccaacccccatgacagtcccccaa +cccccaccacagtcccccaacccctaccacagtcccccaacccccaccacagtccccacc +ccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatcccccacc +ccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaaa +tctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactgt +ggcgcctttggcccctctgaccttcca +>p:HG002_2_chr20:62830512-62830939 +cccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccgag +gtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctcta +cccatgtaccacagtcccccaccccccaccgtgctccacc-------------------- +----------------------ccccaccacagtcccccaccccccaccccagtccccaa +acccctaccacagtcccccaa-ccccaccacagtcccccaccccctaccacagtccccca +ccccctaccacagtcccccaacccccaccacagtcccccacccccaccacagtccgccaa +cccccatgacagtccctca--------------------acccccaccacagtcccccaa +cccccatgacagtcccccaacccccaccacagtcccccaacccccaccacagtccccacc +ccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatccccca-c +ccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaaa +tctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactgt +ggcgcctttggcccctctgaccttcca diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/msa.fa.fai new file mode 100644 index 00000000..dcf5fc89 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_62830512_62830939 687 29 60 61 +syndip_1_chr20:62830512-62830939 687 762 60 61 +syndip_2_chr20:62830512-62830939 687 1495 60 61 +p:HG002_1_chr20:62830512-62830939 687 2229 60 61 +p:HG002_2_chr20:62830512-62830939 687 2963 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/output.vcf.gz new file mode 100644 index 00000000..d5400033 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/output.vcf.gz.tbi new file mode 100644 index 00000000..81f766db Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62830612-62830839/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/base.vcf.gz new file mode 100644 index 00000000..e6c36ec6 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/base.vcf.gz.tbi new file mode 100644 index 00000000..1f2a8782 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/comp.vcf.gz new file mode 100644 index 00000000..8198ea61 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/comp.vcf.gz.tbi new file mode 100644 index 00000000..42c9214e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/haps.fa new file mode 100644 index 00000000..bf13d279 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/haps.fa @@ -0,0 +1,84 @@ +>ref_chr20_62875072_62875657 +AACTTTCCTGGCACACTGGAGAGGACGGCAGAACGCTGGGATGGATTTATCGTGCAAGACCAGCTTGATGTCCTTAGGGCTTGGAGGTCACCCCTTCACGAGGATTGTGAGGAGTGAATTCATCGGGGAGCCCCGCACCCTCACCTGCACCCTCACCCCCACCCCCACCCCCACCCCCACCCCCACCCGCACCCCCACCCCCACCCTCCCCCCCACCCGCACCCGCACCCCCACCCTCACCCGCACCCCCACCCTCACCCCCACCCTCACCCCCACCCTCACCCCCACCCCCACCCTCACCCGCACCCCCACTCGCACCCGCACCCCCACCCTCACCCGCACCCCCACCCTCACCCCCACCCTCACCCCCACCCTCACCCCCACCCCCACCCTCACCCGCACCCTCACTCGCACCGCACCCTCACTGGCACCCTCACCCACACCGCACCCACACCCACATCGGGGAAGAGCTCCATGATCATTCTTTTCTGTAGGCGAAAAACTGCGGCGGGAACTGCTGCCATGCAGCTGGGCTCCCAATGCAGTGGGGATGGTGGCGCTCTGGGCTGGCGGGAGCTATCCTGCC +>syndip_1_chr20:62875072-62875657 +AACTTTCCTGGCACACTGGAGAGGACGGCAGAACGCTGGGATGGATTTATCGTGCAAGAC +CAGCTTGATGTCCTTAGGGCTTGGAGGTCACCCCTTCACGAGGATTGTGAGGAGTGAATT +CATCGGGGAGCCCCGCACCCTCACCTGCACCCTCACCCCCACCCCCACCCCCACCCCCAC +CCCCACCCCCACCCGCACCCCCACCCCCACCCGCACCCCCACCCCCACCCCCACCCGCAC +CCCCACCCCCACCCCCACCCGCACCCCCACCCCCACCCGCACCCCCACCCCCACCCCCAC +CCGCACCCCCACCCCCACCCCCACCCGCACCCGCACCCCCACCCCCACCCGCACCCGCAC +CCCCACCCCCACCCCCACCCGCACCCCCACCCCCACCCCCACCCCCACCCGCACCCGCAC +CCGCACCCCCACCCCCACCCTCACCCGCACCCGCACCCCCACCCCCACCCCCACCCGCAC +CCGCACCCCCACCCCCACCCCCACCCCCACCCCCACCCGCACCCGCACCCGCACCCCCAC +CCTCACCCTCACCCGCACCCGCACCCCCACCCCCACCCGCACCCCCACCCGCACCCCCAC +CCCCACCCCCACCCCCACCCGCACCCGCACCCCCACCCCCACCCCCACCCCCACCCCCAC +CCCCACCCCCACCCCCACCCTCACCCGCACCCCCACCCTCACCCCCACCCTCACCCCCAC +CCTCACCCGCACCCTCACCCGCACCCGCACCCCCACCCTCACCCACACCCTCACCCCCAC +CCTCACCCCCACCCCCACCCTCACCCGCACCCGCACCCCCACCCTCACCCCCACCCCCAC +CCCCACCCTCACCCTCACCCTCACCCGCACCCGCACCCCCACCCGCACCCCCACCCTCAC +CCCCACCCTCACCCCCACCCTCACCCCCACCCCCACCCTCACCCGCACCCTCACTCGCAC +CGCACCCTCACTGGCACCCTCACCCACACCGCACCCACACCCACATCGGGGAAGAGCTCC +ATGATCATTCTTTTCTGTAGGCGAAAAACTGCGGCGGGAACTGCTGCCATGCAGCTGGGC +TCCCAATGCAGTGGGGATGGTGGCGCTCTGGGCTGGCGGGAGCTATCCTGCC +>syndip_2_chr20:62875072-62875657 +AACTTTCCTGGCACACTGGAGAGGACGGCAGAACGCTGGGATGGATTTATCGTGCAAGAC +CAGCTTGATGTCCTTAGGGCTTGGAGGTCACCCCTTCACGAGGATTGTGAGGAGTGAATT +CATCGGGGAGCCCCGCACCCTCACCTGCACCCTCACCCCCACCCCCACCCCCACCCCCAC +CCCCACCCGCACCCGCACCCCCACCCCCACCCGCACCCCCACCCCCACCCCCACCCGCAC +CCCCACCCCCACCCCCACCCGCACCCCCACCCCCACCCCCACCCGCACCCGCACCCGCAC +CCCCACCCCCACCCGCACCCCCACCCCCACCCGCACCCGCACCCCCACCCGCACCCCCAC +CCCCACCCCCACCCTCACCCCCACCCGCACCCCCACCCCCACCCCCACCCGCACCCGCAC +CCCCACCCCCACCCCCACCCGCACCCCCACCCCCACCCCCACCCGCACCCGCACCCCCAC +CCGCACCCCCACCCCCACCCCCACCCGCACCCGCACCCCCACCCGCACCCGCACCCCCAC +CCGCACCCCCACCCCCACCTCCACCCCCACCCGCACCCGCACCCCCACCCCCACCCGCAC +CCCCACCCCCACCCGCACCCCCACCCCCACCCTCACCCGCACCCCCACCCCCACCCGCAC +CCCCACCCCCACCCTCACCCCCACCCTCACCCGCACCCGCACCCCCACCCTCACCCCCAC +CCTCACCCCCACCCTCACCCGCACCCCCACCCCCACCCCCACCCCCACCCTCCCCCCCAC +CCGCACCCGCACCCCCACCCTCACCCGCACCCCCACCCTCACCCCCACCCTCACCCCCAC +CCTCACCCCCACCCCCACCCTCACCCGCACCCCCACTCGCACCCGCACCCCCACCCTCAC +CCGCACCCCCACCCTCACCCCCACCCTCACCCCCACCCTCACCCCCACCCCCACCCTCAC +CCGCACCCTCACTCGCACCGCACCCTCACTGGCACCCTCACCCACACCGCACCCACACCC +ACATCGGGGAAGAGCTCCATGATCATTCTTTTCTGTAGGCGAAAAACTGCGGCGGGAACT +GCTGCCATGCAGCTGGGCTCCCAATGCAGTGGGGATGGTGGCGCTCTGGGCTGGCGGGAG +CTATCCTGCC +>p:HG002_1_chr20:62875072-62875657 +AACTTTCCTGGCACACTGGAGAGGACGGCAGAACGCTGGGATGGATTTATCGTGCAAGAC +CAGCTTGATGTCCTTAGGGCTTGGAGGTCACCCCTTCACGAGGATTGTGAGGAGTGAATT +CATCGGGGAGCCCCGCACCCTCACCTGCACCCTCACCCCCACCCCCACCCCCACCCCCAC +CCCCACCCGCACCCGCACCCCCACCCCCACCCGCACCCCCACCCCCACCCCCACCCGCAC +CCCCACCCCCACCCCCACCCGCACCCCCACCCCCACCCCCACCCGCACCCGCACCCGCAC +CCCCACCCCCACCCGCACCCCCACCCCCACCCGCACCCGCACCCCCACCCGCACCCCCAC +CCCCACCCCCACCCTCACCCCCACCCGCACCCCCACCCCCACCCCCACCCGCACCCGCAC +CCCCACCCCCACCCCCACCCGCACCCCCACCCCCACCCCCACCCGCACCCGCACCCCCAC +CCGCACCCCCACCCCCACCCCCACCCGCACCCGCACCCCCACCCGCACCCGCACCCCCAC +CCGCACCCCCACCCCCACCTCCACCCCCACCCGCACCCGCACCCCCACCCCCACCCGCAC +CCCCACCCCCACCCGCACCCCCACCCCCACCCTCACCCGCACCCCCACCCCCACCCGCAC +CCCCACCCCCACCCTCACCCCCACCCTCACCCGCACCCGCACCCCCACCCTCACCCCCAC +CCTCACCCCCACCCTCACCCGCACCCCCACCCCCACCCCCACCCCCACCCTCCCCCCCAC +CCGCACCCGCACCCCCACCCTCACCCGCACCCCCACCCTCACCCCCACCCTCACCCCCAC +CCTCACCCCCACCCCCACCCTCACCCGCACCCCCACTCGCACCCGCACCCCCACCCTCAC +CCGCACCCCCACCCTCACCCCCACCCTCACCCCCACCCTCACCCCCACCCCCACCCTCAC +CCGCACCCTCACTCGCACCGCACCCTCACTGGCACCCTCACCCACACCGCACCCACACCC +ACATCGGGGAAGAGCTCCATGATCATTCTTTTCTGTAGGCGAAAAACTGCGGCGGGAACT +GCTGCCATGCAGCTGGGCTCCCAATGCAGTGGGGATGGTGGCGCTCTGGGCTGGCGGGAG +CTATCCTGCC +>p:HG002_2_chr20:62875072-62875657 +AACTTTCCTGGCACACTGGAGAGGACGGCAGAACGCTGGGATGGATTTATCGTGCAAGAC +CAGCTTGATGTCCTTAGGGCTTGGAGGTCACCCCTTCACGAGGATTGTGAGGAGTGAATT +CATCGGGGAGCCCCGCACCCTCACCTGCACCCTCACCCCCACCCCCACCCCCACCCCCAC +CCCCACCCCCACCCGCACCCCCACCCCCACCCGCACCCCCACCCCCACCCCCACCCGCAC +CCCCACCCCCACCCCCACCCGCACCCCCACCCCCACCCGCACCCCCACCCCCACCCCCAC +CCGCACCCCCACCCCCACCCCCACCCGCACCCGCACCCCCACCCCCACCCGCACCCGCAC +CCCCACCCCCACCCCCACCCGCACCCCCACCCCCACCCCCACCCCCACCCGCACCCGCAC +CCGCACCCCCACCCCCACCCTCACCCGCACCCGCACCCCCACCCCCACCCCCACCCGCAC +CCGCACCCCCACCCCCACCCCCACCCCCACCCCCACCCGCACCCGCACCCGCACCCCCAC +CCTCACCCTCACCCGCACCCGCACCCCCACCCCCACCCGCACCCCCACCCGCACCCCCAC +CCCCACCCCCACCCCCACCCGCACCCGCACCCCCACCCCCACCCCCACCCCCACCCCCAC +CCCCACCCCCACCCCCACCCTCACCCGCACCCCCACCCTCACCCCCACCCTCACCCCCAC +CCTCACCCGCACCCTCACCCGCACCCGCACCCCCACCCTCACCCACACCCTCACCCCCAC +CCTCACCCCCACCCCCACCCTCACCCGCACCCGCACCCCCACCCTCACCCCCACCCCCAC +CCCCACCCTCACCCTCACCCTCACCCGCACCCGCACCCCCACCCGCACCCCCACCCTCAC +CCCCACCCTCACCCCCACCCTCACCCCCACCCCCACCCTCACCCGCACCCTCACTCGCAC +CGCACCCTCACTGGCACCCTCACCCACACCGCACCCACACCCACATCGGGGAAGAGCTCC +ATGATCATTCTTTTCTGTAGGCGAAAAACTGCGGCGGGAACTGCTGCCATGCAGCTGGGC +TCCCAATGCAGTGGGGATGGTGGCGCTCTGGGCTGGCGGGAGCTATCCTGCC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/haps.fa.ref.fa new file mode 100644 index 00000000..6df8df1f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:62875072-62875657 +AACTTTCCTGGCACACTGGAGAGGACGGCAGAACGCTGGGATGGATTTATCGTGCAAGACCAGCTTGATGTCCTTAGGGCTTGGAGGTCACCCCTTCACGAGGATTGTGAGGAGTGAATTCATCGGGGAGCCCCGCACCCTCACCTGCACCCTCACCCCCACCCCCACCCCCACCCCCACCCCCACCCGCACCCCCACCCCCACCCTCCCCCCCACCCGCACCCGCACCCCCACCCTCACCCGCACCCCCACCCTCACCCCCACCCTCACCCCCACCCTCACCCCCACCCCCACCCTCACCCGCACCCCCACTCGCACCCGCACCCCCACCCTCACCCGCACCCCCACCCTCACCCCCACCCTCACCCCCACCCTCACCCCCACCCCCACCCTCACCCGCACCCTCACTCGCACCGCACCCTCACTGGCACCCTCACCCACACCGCACCCACACCCACATCGGGGAAGAGCTCCATGATCATTCTTTTCTGTAGGCGAAAAACTGCGGCGGGAACTGCTGCCATGCAGCTGGGCTCCCAATGCAGTGGGGATGGTGGCGCTCTGGGCTGGCGGGAGCTATCCTGCC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/msa.fa new file mode 100644 index 00000000..1e89c6f4 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/msa.fa @@ -0,0 +1,105 @@ +>ref_chr20_62875072_62875657 +aactttcctggcacactggagaggacggcagaacgctgggatggatttatcgtgcaagac +cagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaatt +catcggggagc------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------cccgcaccctcacctgcaccctcac +ccccacccccacccccacccccacccccacccgcacccccacccccaccctcccccccac +ccgcacccgcacccccaccctcacccgcacccccaccctcacccccaccctcacccccac +cctcacccccacccccaccctcacccgcacccccactcgcacccgcacccccaccctcac +ccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctcac +ccgcaccctcactcgcaccgcaccctcactggcaccctcacccacaccgcacccacaccc +acatcggggaagagctccatgatcattcttttctgtaggcgaaaaactgcggcgggaact +gctgccatgcagctgggctcccaatgcagtggggatggtggcgctctgggctggcgggag +ctatcctgcc +>syndip_1_chr20:62875072-62875657 +aactttcctggcacactggagaggacggcagaacgctgggatggatttatcgtgcaagac +cagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaatt +catcggggagccccgcaccctcacctgcaccctcacccccacccccacccccacccccac +ccccacccccacccgcacccccacccccacccgcacccccacccccacccccacccgcac +ccccacccccacccccacccgcacccccacccccacccgcacccccacccccacccccac +ccgcacccccacccccacccccacccgcacccgcacccccacccccacccgcacccgcac +ccccacccccacccccacccgcacccccacccccacccccacccccacccgcacccgcac +ccgcacccccacccccaccctcacccgcacccgcacccccacccccacccccacccgcac +ccgcacccccacccccacccc------------cacccccacccccacccgcacccgcac +ccgcacccccaccctcaccctcacccgcacccgcacccccacccccacccgcacccccac +ccgcacccccacccccacccccacccccacccgcacccgcacccccacccccacccccac +ccccacccccacccccacccccacccccaccctcacccgcacccccaccctcacccccac +cctcacccccaccctcacccgcaccctcacccgcacccgcacccccaccct------cac +ccacaccctcacccccaccctcacccccacccccaccctcacccgcacccgcacccccac +cctcacccccacccccacccccaccctcaccctcaccctcacccgcacccgcacccccac +ccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctcac +ccgcaccctcactcgcaccgcaccctcactggcaccctcacccacaccgcacccacaccc +acatcggggaagagctccatgatcattcttttctgtaggcgaaaaactgcggcgggaact +gctgccatgcagctgggctcccaatgcagtggggatggtggcgctctgggctggcgggag +ctatcctgcc +>syndip_2_chr20:62875072-62875657 +aactttcctggcacactggagaggacggcagaacgctgggatggatttatcgtgcaagac +cagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaatt +catcggggagccccgcaccctcacctgcaccctcacccccacccccacccccacccccac +ccccacccgcacccgcacccccacccccacccgcacccccacccccacccccacccgcac +ccccacccccacccccacccgcacccccacccccacccccacccgcacccgcacccgcac +ccccacccccacccgcacccccacccccacccgcacccgcacccccacccgcacccccac +ccccacccccaccctcacccccacccgcacccccacccccacccccacccgcacccgcac +ccccacccccacccccacccgcacccccacccccacccccacccgcacccgcacccccac +ccgcacccccacccccacccccacccgcacccgcacccccacccgcacccgcacccccac +ccgcacccccacccccacctccacccccacccgcacccgcacccccacccccacccgcac +ccccacccccacccgcacccccacccccaccctcacccgcacccccacccccacccgcac +ccccacccccaccctcacccccaccctcacccgcacccgcacccccaccctcacccccac +cctcacccccaccctcacccgcacccccacccccacccccacccccaccctcccccccac +ccgcacccgcacccccaccctcacccgcacccccaccctcacccccaccctcacccccac +cctcacccccacccccaccctcacccgcacccccactcgcacccgcacccccaccctcac +ccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctcac +ccgcaccctcactcgcaccgcaccctcactggcaccctcacccacaccgcacccacaccc +acatcggggaagagctccatgatcattcttttctgtaggcgaaaaactgcggcgggaact +gctgccatgcagctgggctcccaatgcagtggggatggtggcgctctgggctggcgggag +ctatcctgcc +>p:HG002_1_chr20:62875072-62875657 +aactttcctggcacactggagaggacggcagaacgctgggatggatttatcgtgcaagac +cagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaatt +catcggggagccccgcaccctcacctgcaccctcacccccacccccacccccacccccac +ccccacccgcacccgcacccccacccccacccgcacccccacccccacccccacccgcac +ccccacccccacccccacccgcacccccacccccacccccacccgcacccgcacccgcac +ccccacccccacccgcacccccacccccacccgcacccgcacccccacccgcacccccac +ccccacccccaccctcacccccacccgcacccccacccccacccccacccgcacccgcac +ccccacccccacccccacccgcacccccacccccacccccacccgcacccgcacccccac +ccgcacccccacccccacccccacccgcacccgcacccccacccgcacccgcacccccac +ccgcacccccacccccacctccacccccacccgcacccgcacccccacccccacccgcac +ccccacccccacccgcacccccacccccaccctcacccgcacccccacccccacccgcac +ccccacccccaccctcacccccaccctcacccgcacccgcacccccaccctcacccccac +cctcacccccaccctcacccgcacccccacccccacccccacccccaccctcccccccac +ccgcacccgcacccccaccctcacccgcacccccaccctcacccccaccctcacccccac +cctcacccccacccccaccctcacccgcacccccactcgcacccgcacccccaccctcac +ccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctcac +ccgcaccctcactcgcaccgcaccctcactggcaccctcacccacaccgcacccacaccc +acatcggggaagagctccatgatcattcttttctgtaggcgaaaaactgcggcgggaact +gctgccatgcagctgggctcccaatgcagtggggatggtggcgctctgggctggcgggag +ctatcctgcc +>p:HG002_2_chr20:62875072-62875657 +aactttcctggcacactggagaggacggcagaacgctgggatggatttatcgtgcaagac +cagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaatt +catcggggagccccgcaccctcacctgcaccctcacccccacccccacccccacccccac +ccccacccccacccgcacccccacccccacccgcacccccacccccacccccacccgcac +ccccacccccacccccacccgcacccccacccccacccgcacccccacccccacccccac +ccgcacccccacccccacccccacccgcacccgcacccccacccccacccgcacccgcac +ccccacccccacccccacccgcacccccacccccacccccacccccacccgcacccgcac +ccgcacccccacccccaccctcacccgcacccgcacccccacccccacccccacccgcac +ccgcacccccacccccacccc------------cacccccacccccacccgcacccgcac +ccgcacccccaccctcaccctcacccgcacccgcacccccacccccacccgcacccccac +ccgcacccccacccccacccccacccccacccgcacccgcacccccacccccacccccac +ccccacccccacccccacccccacccccaccctcacccgcacccccaccctcacccccac +cctcacccccaccctcacccgcaccctcacccgcacccgcacccccaccct------cac +ccacaccctcacccccaccctcacccccacccccaccctcacccgcacccgcacccccac +cctcacccccacccccacccccaccctcaccctcaccctcacccgcacccgcacccccac +ccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctcac +ccgcaccctcactcgcaccgcaccctcactggcaccctcacccacaccgcacccacaccc +acatcggggaagagctccatgatcattcttttctgtaggcgaaaaactgcggcgggaact +gctgccatgcagctgggctcccaatgcagtggggatggtggcgctctgggctggcgggag +ctatcctgcc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/msa.fa.fai new file mode 100644 index 00000000..ccd43e09 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_62875072_62875657 1150 29 60 61 +syndip_1_chr20:62875072-62875657 1150 1233 60 61 +syndip_2_chr20:62875072-62875657 1150 2437 60 61 +p:HG002_1_chr20:62875072-62875657 1150 3642 60 61 +p:HG002_2_chr20:62875072-62875657 1150 4847 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/output.vcf.gz new file mode 100644 index 00000000..a7b954f3 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/output.vcf.gz.tbi new file mode 100644 index 00000000..9f3aa5ad Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:62875172-62875557/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/base.vcf.gz new file mode 100644 index 00000000..952fd5ab Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/base.vcf.gz.tbi new file mode 100644 index 00000000..3177721a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/comp.vcf.gz new file mode 100644 index 00000000..6ffc1379 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/comp.vcf.gz.tbi new file mode 100644 index 00000000..dab4d336 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/haps.fa new file mode 100644 index 00000000..c3ed29dd --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/haps.fa @@ -0,0 +1,50 @@ +>ref_chr20_63027897_63028267 +ACGGACCAGCATCTATCATGGCTGTTTTGCGTTTCTTGATTTCACGATGTCTGTTGTGTGCTCAGGCCCCTCCTCTCCAAGGTCCCAGCTGTCCTTGCCCTGTTCCCTGTGAAGAGTGAAGAACCAACGCGGGCGGGGAGTGGACCGGTGGGGAGAGGGCCGGTGGGGAGAGGACCGGTGGGGAGGGGCCGGTGGAGAGGGGGCCGGTGGGGAGGGGGCCGGCGGGGAGTGGTTTGGTGGGGAGGAGGCTGGTGAAGTAGCGTCAGGTGCGGGCCTGGCGTCGGCGAGTCAAGTCGAGCTGATCCAGGGCCTTCTTTCTGCAGCTTCATCAGGTTCTCAATTAGCGGAGGGCGCTGGCGGTGGAGGAGGGC +>syndip_1_chr20:63027897-63028267 +ACGGACCAGCATCTATCATGGCTGTTTTGCGTTTCTTGATTTCACGATGTCTGTTGTGTG +CTCAGGCCCCTCCTCTCCAAGGTCCCAGCTGTCCTTGCCCTGTTCCCTGTGAAGAGTGAA +GAACCAACGCGGGCGGGGAGTGGACCGGTGGGGAGAGGGCCGGTGGGGAGAGGGCCGGTG +GGGAGAGGACCGGTGGGGAGGGGGCCGGTGGAGAGGGGGCCGGTGGGGAGGGGGCCGGTG +GGGAGAGGACCGGTGGGGAGGGGCCGGTGGGGAGGGGGCCGGTGGGGAGAGGACCGGTGG +GGAGGGGCCGGTGGGGAGGGGGCCGGTGGGGAGAGGACCGGTGGGGAGGGGCCGGTGGGG +AGGGGGCCGGCGGGGAGGGGGCCGGCGGGGAGGGTGCCGGTGGGGAGTGGTCTGGTGGGG +AGGGGGCCGGTGGGGAGGGGGCCCGCGGGGAGGGGCCGGTGGGGAGGGGGCCTGCGGGGA +GGGGGCCGGCGGGGAGGGGCCGGTGGGGAGGGGCCGGTGGGGTGGGGCCGGTGGGGAGGG +GGCCGGTGGGGGGGGGCCTGCAGGGAGGGGGCCGGTGGGGAGGAGGCTGGTGAAGTAGCG +TCAGGTGCGGGCCTGGCGTCGGCGAGTCAAGTCGAGCTGATCCAGGGCCTTCTTTCTGCA +GCTTCATCAGGTTCTCAATTAGCGGAGGGCGCTGGCGGTGGAGGAGGGC +>syndip_2_chr20:63027897-63028267 +ACGGACCAGCATCTATCATGGCTGTTTTGCGTTTCTTGATTTCACGATGTCTGTTGTGTG +CTCAGGCCCCTCCTCTCCAAGGTCCCAGCTGTCCTTGCCCTGTTCCCTGTGAAGAGTGAA +GAACCAACGCGGGCGGGGAGTGGACCGGTGGGGAGAGGGCCGGTGGGGAGAGGACCGGTG +GGGAGGGGCCGGTGGAGAGGGGGCCGGTGGGGAGGGGGCCGGCGGGGAGTGGTTTGGTGG +GGAGGGGGCCGGTGGGGAGGGGGCCTGCGGGGAGGGGCCGGTGGGGAGGGGGCCGGTGGG +GAGGGGGCCGGCGGGGAGGGGGCCGGCGGGGAGGGGGCCGGCGGGGAGTGGTCTGGTGGG +GAGGGGGCCGGTGGGGAGGGGGCCGGCGGGGAGGGGGCCGGCGGGGAGGGGCCGGTGGGG +AGTGGTCTGGTGGGGAGGGGGCCGGTGGGGAGGAGGCTGGTGAAGTAGCGTCAGGTGCGG +GCCTGGCGTCGGCGAGTCAAGTCGAGCTGATCCAGGGCCTTCTTTCTGCAGCTTCATCAG +GTTCTCAATTAGCGGAGGGCGCTGGCGGTGGAGGAGGGC +>p:HG002_1_chr20:63027897-63028267 +ACGGACCAGCATCTATCATGGCTGTTTTGCGTTTCTTGATTTCACGATGTCTGTTGTGTG +CTCAGGCCCCTCCTCTCCAAGGTCCCAGCTGTCCTTGCCCTGTTCCCTGTGAAGAGTGAA +GAACCAACGCGGGCGGGGAGTGGACCGGTGGGGAGAGGGCCGGTGGGGAGAGGACCGGTG +GGGAGGGGCCGGTGGAGAGGGGGCCGGTGGGGAGGGGGCCGGCGGGGAGTGGTTTGGTGG +GGAGGGGGCCGGTGGGGAGGGGGCCTGCGGGGAGGGGCCGGTGGGGAGGGGGCCGGTGGG +GAGGGGGCCGGCGGGGAGGGGGCCGGCGGGGAGGGGGCCGGCGGGGAGTGGTCTGGTGGG +GAGGGGGCCGGTGGGGAGGGGGCCGGCGGGGAGGGGGCCGGCGGGGAGGGGCCGGTGGGG +AGTGGTCTGGTGGGGAGGGGGCCGGTGGGGAGGAGGCTGGTGAAGTAGCGTCAGGTGCGG +GCCTGGCGTCGGCGAGTCAAGTCGAGCTGATCCAGGGCCTTCTTTCTGCAGCTTCATCAG +GTTCTCAATTAGCGGAGGGCGCTGGCGGTGGAGGAGGGC +>p:HG002_2_chr20:63027897-63028267 +ACGGACCAGCATCTATCATGGCTGTTTTGCGTTTCTTGATTTCACGATGTCTGTTGTGTG +CTCAGGCCCCTCCTCTCCAAGGTCCCAGCTGTCCTTGCCCTGTTCCCTGTGAAGAGTGAA +GAACCAACGCGGGCGGGGAGTGGACCGGTGGGGAGAGGGCCGGTGGGGAGAGGGCCGGTG +GGGAGAGGACCGGTGGGGAGGGGGCCGGTGGAGAGGGGGCCGGTGGGGAGGGGGCCGGTG +GGGAGAGGACCGGTGGGGAGGGGCCGGTGGGGAGGGGGCCGGTGGGGAGAGGACCGGTGG +GGAGGGGCCGGTGGGGAGGGGGCCGGTGGGGAGAGGACCGGTGGGGAGGGGCCGGTGGGG +AGGGGGCCGGCGGGGAGGGGGCCGGCGGGGAGGGTGCCGGTGGGGAGTGGTCTGGTGGGG +AGGGGGCCGGTGGGGAGGGGGCCCGCGGGGAGGGGCCGGTGGGGAGGGGGCCTGCGGGGA +GGGGGCCGGCGGGGAGGGGCCGGTGGGGAGGGGCCGGTGGGGTGGGGCCGGTGGGGAGGG +GGCCGGTGGGGGGGGGCCTGCAGGGAGGGGGCCGGTGGGGAGGAGGCTGGTGAAGTAGCG +TCAGGTGCGGGCCTGGCGTCGGCGAGTCAAGTCGAGCTGATCCAGGGCCTTCTTTCTGCA +GCTTCATCAGGTTCTCAATTAGCGGAGGGCGCTGGCGGTGGAGGAGGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/haps.fa.ref.fa new file mode 100644 index 00000000..cb471bcd --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63027897-63028267 +ACGGACCAGCATCTATCATGGCTGTTTTGCGTTTCTTGATTTCACGATGTCTGTTGTGTGCTCAGGCCCCTCCTCTCCAAGGTCCCAGCTGTCCTTGCCCTGTTCCCTGTGAAGAGTGAAGAACCAACGCGGGCGGGGAGTGGACCGGTGGGGAGAGGGCCGGTGGGGAGAGGACCGGTGGGGAGGGGCCGGTGGAGAGGGGGCCGGTGGGGAGGGGGCCGGCGGGGAGTGGTTTGGTGGGGAGGAGGCTGGTGAAGTAGCGTCAGGTGCGGGCCTGGCGTCGGCGAGTCAAGTCGAGCTGATCCAGGGCCTTCTTTCTGCAGCTTCATCAGGTTCTCAATTAGCGGAGGGCGCTGGCGGTGGAGGAGGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/msa.fa new file mode 100644 index 00000000..c05441b4 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/msa.fa @@ -0,0 +1,65 @@ +>ref_chr20_63027897_63028267 +acggaccagcatctatcatggctgttttgcgtttcttgatttcacgatgtctgttgtgtg +ctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaa +gaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagaggaccggtg +ggga----------------ggggccggtggagagggggccggtggggagggggccggcg +gggag--------------tggttt----------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------ggtggggaggaggctggtgaagtagcg +tcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgca +gcttcatcaggttctcaattagcggagggcgctggcggtggaggagggc +>syndip_1_chr20:63027897-63028267 +acggaccagcatctatcatggctgttttgcgtttcttgatttcacgatgtctgttgtgtg +ctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaa +gaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagagggccggtg +gggagaggaccggtggggagggggccggtggagagggggccggtggggagggggccggtg +gggagaggaccggtggggaggggccggtggggagggggccggtggggagaggaccggtgg +ggaggggccggtggggagggggccggtggggagaggaccggtggggaggggccggtgggg +agggggccggcggggagggggccggcggggagggtgccggtggggagtggtctggtgggg +agggggccggtggggagggggcccgcggggaggggccggtggggagggggcctgcgggga +gggggccggcggggaggggccggtggggaggggccggtggggtggggccggtggggaggg +ggccggtgggggggggcctgcagggagggggccggtggggaggaggctggtgaagtagcg +tcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgca +gcttcatcaggttctcaattagcggagggcgctggcggtggaggagggc +>syndip_2_chr20:63027897-63028267 +acggaccagcatctatcatggctgttttgcgtttcttgatttcacgatgtctgttgtgtg +ctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaa +gaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagaggaccggtg +ggga----------------ggggccggtggagagggggccggtggggagggggccggcg +gggag--------------tggtttggtggggagggggccggtggggagggggcctgcgg +ggaggggccggtggggag-----------------------------ggggccggtgggg +agggggccggcggggagggggccggcggggagggggccggcggggagtggtctggtgggg +ag-----------------------------ggggccggtggggagggggccggcgggga +gggggccggcggggaggggccggtggggagtggtctg----------------------- +-------------------gtggggagggggccggtggggaggaggctggtgaagtagcg +tcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgca +gcttcatcaggttctcaattagcggagggcgctggcggtggaggagggc +>p:HG002_1_chr20:63027897-63028267 +acggaccagcatctatcatggctgttttgcgtttcttgatttcacgatgtctgttgtgtg +ctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaa +gaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagaggaccggtg +ggga----------------ggggccggtggagagggggccggtggggagggggccggcg +gggag--------------tggtttggtggggagggggccggtggggagggggcctgcgg +ggaggggccggtggggag-----------------------------ggggccggtgggg +agggggccggcggggagggggccggcggggagggggccggcggggagtggtctggtgggg +ag-----------------------------ggggccggtggggagggggccggcgggga +gggggccggcggggaggggccggtggggagtggtctg----------------------- +-------------------gtggggagggggccggtggggaggaggctggtgaagtagcg +tcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgca +gcttcatcaggttctcaattagcggagggcgctggcggtggaggagggc +>p:HG002_2_chr20:63027897-63028267 +acggaccagcatctatcatggctgttttgcgtttcttgatttcacgatgtctgttgtgtg +ctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaa +gaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagagggccggtg +gggagaggaccggtggggagggggccggtggagagggggccggtggggagggggccggtg +gggagaggaccggtggggaggggccggtggggagggggccggtggggagaggaccggtgg +ggaggggccggtggggagggggccggtggggagaggaccggtggggaggggccggtgggg +agggggccggcggggagggggccggcggggagggtgccggtggggagtggtctggtgggg +agggggccggtggggagggggcccgcggggaggggccggtggggagggggcctgcgggga +gggggccggcggggaggggccggtggggaggggccggtggggtggggccggtggggaggg +ggccggtgggggggggcctgcagggagggggccggtggggaggaggctggtgaagtagcg +tcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgca +gcttcatcaggttctcaattagcggagggcgctggcggtggaggagggc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/msa.fa.fai new file mode 100644 index 00000000..f18c8fd3 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63027897_63028267 709 29 60 61 +syndip_1_chr20:63027897-63028267 709 784 60 61 +syndip_2_chr20:63027897-63028267 709 1539 60 61 +p:HG002_1_chr20:63027897-63028267 709 2295 60 61 +p:HG002_2_chr20:63027897-63028267 709 3051 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/output.vcf.gz new file mode 100644 index 00000000..cca7a5ec Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/output.vcf.gz.tbi new file mode 100644 index 00000000..caae8654 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63027997-63028167/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/base.vcf.gz new file mode 100644 index 00000000..8b3b2cd8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/base.vcf.gz.tbi new file mode 100644 index 00000000..56fbbbee Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/comp.vcf.gz new file mode 100644 index 00000000..e1096451 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/comp.vcf.gz.tbi new file mode 100644 index 00000000..a64e9cdb Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/haps.fa new file mode 100644 index 00000000..c6e231aa --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/haps.fa @@ -0,0 +1,78 @@ +>ref_chr20_63028776_63029503 +CAACAATGCACAAGTGGCTTGAGTAGAAGAGCTGCTCCTGCTGGGAGGCGCAGGAGGCTGAGCGAGGCCCACCCTGCAGGGGCGAGGCCACGGTTTGTGTTATTTCCCATGATGACTCCAAACGCACCCGAGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTCCGTGTGCAGGTCCCCCGGGCCTCTGCGTCTCTGTGTGCAGGCTCAAGTTTGCCAACGTCCATGCACGTCTCAGCCTCTCAGCCTGGACTGGACAACTGGGCTTCGGGAATTCATTTAAATTCTACCCGCTACACGCCTTCCCTGGATTCAGGGCGGCGTCCAGTGCATTCAT +>syndip_1_chr20:63028776-63029503 +CAACAATGCACAAGTGGCTTGAGTAGAAGAGCTGCTCCTGCTGGGAGGCGCAGGAGGCTG +AGCGAGGCCCACCCTGCAGGGGCGAGGCCACGGTTTGTGTTATTTCCCATGATGACTCCA +AACGCACCCGAGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCG +CCTCCGTGTGCAGGTCCCCCGGGCCTCCGCCTCTCCGTGTGCAGGTCCCCCGGGCCTCCG +CGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGTCCCCCGGGCCTC +CGCGTCTGTGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCC +TCCGCGTCTGTGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGTCCCCCGGG +CCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCG +GGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGTCCCC +CGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTCCGTGTGCAGGTCC +CCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGT +CCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAG +GTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGC +AGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGT +GCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGT +GTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCC +GTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCT +CCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGC +CTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGC +GCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCC +GCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCT +CCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCTGCGTCTCTGTGTGCAGGCTCAAGTTTG +CCAACGTCCATGCACGTCTCAGCCTCTCAGCCTGGACTGGACAACTGGGCTTCGGGAATT +CATTTAAATTCTACCCGCTACACGCCTTCCCTGGATTCAGGGCGGCGTCCAGTGCATTCA +T +>syndip_2_chr20:63028776-63029503 +CAACAATGCACAAGTGGCTTGAGTAGAAGAGCTGCTCCTGCTGGGAGGCGCAGGAGGCTG +AGCGAGGCCCACCCTGCAGGGGCGAGGCCACGGTTTGTGTTATTTCCCATGATGACTCCA +AACGCACCCGAGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCG +CCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCG +CGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTC +CGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTCCGTGTGCAGGTCCCCCGGGCC +TCCGCGTCTGTGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGG +CCTCCGCGTCTCCGTGTGCAGGTCCCCCGGGCCCCTGCGTCTCTGTGTGCAGGCTCAAGT +TTGCCAACGTCCATGCACGTCTCAGCCTCTCAGCCTGGACTGGACAACTGGGCTTCGGGA +ATTCATTTAAATTCTACCCGCTACACGCCTTCCCTGGATTCAGGGCGGCGTCCAGTGCAT +TCAT +>p:HG002_1_chr20:63028776-63029503 +CAACAATGCACAAGTGGCTTGAGTAGAAGAGCTGCTCCTGCTGGGAGGCGCAGGAGGCTG +AGCGAGGCCCACCCTGCAGGGGCGAGGCCACGGTTTGTGTTATTTCCCATGATGACTCCA +AACGCACCCGAGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCG +CCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCG +CGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTC +CGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTCCGTGTGCAGGTCCCCCGGGCC +TCCGCGTCTGTGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGG +CCTCCGCGTCTCCGTGTGCAGGTCCCCCGGGCCCCTGCGTCTCTGTGTGCAGGCTCAAGT +TTGCCAACGTCCATGCACGTCTCAGCCTCTCAGCCTGGACTGGACAACTGGGCTTCGGGA +ATTCATTTAAATTCTACCCGCTACACGCCTTCCCTGGATTCAGGGCGGCGTCCAGTGCAT +TCAT +>p:HG002_2_chr20:63028776-63029503 +CAACAATGCACAAGTGGCTTGAGTAGAAGAGCTGCTCCTGCTGGGAGGCGCAGGAGGCTG +AGCGAGGCCCACCCTGCAGGGGCGAGGCCACGGTTTGTGTTATTTCCCATGATGACTCCA +AACGCACCCGAGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCG +CCTCCGTGTGCAGGTCCCCCGGGCCTCCGCCTCTCCGTGTGCAGGTCCCCCGGGCCTCCG +CGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGTCCCCCGGGCCTC +CGCGTCTGTGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCC +TCCGCGTCTGTGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGTCCCCCGGG +CCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCG +GGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGTCCCC +CGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTCCGTGTGCAGGTCC +CCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGT +CCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAG +GTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGC +AGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGT +GCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGT +GTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCC +GTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCT +CCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGC +CTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGC +GCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCC +GCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCT +CCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCTGCGTCTCTGTGTGCAGGCTCAAGTTTG +CCAACGTCCATGCACGTCTCAGCCTCTCAGCCTGGACTGGACAACTGGGCTTCGGGAATT +CATTTAAATTCTACCCGCTACACGCCTTCCCTGGATTCAGGGCGGCGTCCAGTGCATTCA +T diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/haps.fa.ref.fa new file mode 100644 index 00000000..fa835ef1 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63028776-63029503 +CAACAATGCACAAGTGGCTTGAGTAGAAGAGCTGCTCCTGCTGGGAGGCGCAGGAGGCTGAGCGAGGCCCACCCTGCAGGGGCGAGGCCACGGTTTGTGTTATTTCCCATGATGACTCCAAACGCACCCGAGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTGTGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGCCTCCGTGTGCAGGTCCCCCGGGCCTCCGCGTCTCCGTGTGCAGGTCCCCCGGGCCTCTGCGTCTCTGTGTGCAGGCTCAAGTTTGCCAACGTCCATGCACGTCTCAGCCTCTCAGCCTGGACTGGACAACTGGGCTTCGGGAATTCATTTAAATTCTACCCGCTACACGCCTTCCCTGGATTCAGGGCGGCGTCCAGTGCATTCAT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/msa.fa new file mode 100644 index 00000000..3fad97e5 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/msa.fa @@ -0,0 +1,130 @@ +>ref_chr20_63028776_63029503 +caacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctg +agcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcca +aa---------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------------------cgcac +ccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgt +gtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctcc +gtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcct +ccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc +ctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgc +gcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctcc +gcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct +ccgcgtctccgtgtgcaggtcccccgggcctctgcgtctctgtgtgcaggctcaagtttg +ccaacgtccatgcacgtctcagcctctcagcctggactggacaactgggcttcgggaatt +catttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgcattca +t +>syndip_1_chr20:63028776-63029503 +caacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctg +agcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcca +aacgcacccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcg +cctccgtgtgcaggtcccccgggcctccgcctctccgtgtgcaggtcccccgggcctccg +cgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctc +cgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcc +tccgcgtctgtgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccggg +cctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccg +ggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccc +cgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctccgtgtgcaggtcc +cccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggt +cccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcag +gtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgc +aggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgt +gcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgt +gtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctcc +gtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcct +ccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc +ctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgc +gcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctcc +gcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct +ccgcgcctccgtgtgcaggtcccccgggcctctgcgtctctgtgtgcaggctcaagtttg +ccaacgtccatgcacgtctcagcctctcagcctggactggacaactgggcttcgggaatt +catttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgcattca +t +>syndip_2_chr20:63028776-63029503 +caacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctg +agcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcca +aa---------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------------------cgcac +ccga-------------------------------------------------------- +------------------------------------------------------------ +--------gtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcct +ccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc +ctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgc +gcctccgtgtgcaggtcccccgggcctccgcgtctccgtgtgcaggtcccccgggcctcc +gcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct +ccgcgtctccgtgtgcaggtcccccgggcccctgcgtctctgtgtgcaggctcaagtttg +ccaacgtccatgcacgtctcagcctctcagcctggactggacaactgggcttcgggaatt +catttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgcattca +t +>p:HG002_1_chr20:63028776-63029503 +caacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctg +agcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcca +aa---------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------------------cgcac +ccga-------------------------------------------------------- +------------------------------------------------------------ +--------gtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcct +ccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc +ctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgc +gcctccgtgtgcaggtcccccgggcctccgcgtctccgtgtgcaggtcccccgggcctcc +gcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct +ccgcgtctccgtgtgcaggtcccccgggcccctgcgtctctgtgtgcaggctcaagtttg +ccaacgtccatgcacgtctcagcctctcagcctggactggacaactgggcttcgggaatt +catttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgcattca +t +>p:HG002_2_chr20:63028776-63029503 +caacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctg +agcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcca +aacgcacccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcg +cctccgtgtgcaggtcccccgggcctccgcctctccgtgtgcaggtcccccgggcctccg +cgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctc +cgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcc +tccgcgtctgtgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccggg +cctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccg +ggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccc +cgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctccgtgtgcaggtcc +cccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggt +cccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcag +gtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgc +aggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgt +gcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgt +gtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctcc +gtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcct +ccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc +ctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgc +gcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctcc +gcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct +ccgcgcctccgtgtgcaggtcccccgggcctctgcgtctctgtgtgcaggctcaagtttg +ccaacgtccatgcacgtctcagcctctcagcctggactggacaactgggcttcgggaatt +catttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgcattca +t diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/msa.fa.fai new file mode 100644 index 00000000..b6ddf3d5 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63028776_63029503 1441 29 60 61 +syndip_1_chr20:63028776-63029503 1441 1529 60 61 +syndip_2_chr20:63028776-63029503 1441 3029 60 61 +p:HG002_1_chr20:63028776-63029503 1441 4530 60 61 +p:HG002_2_chr20:63028776-63029503 1441 6031 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/output.vcf.gz new file mode 100644 index 00000000..afc44e83 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/output.vcf.gz.tbi new file mode 100644 index 00000000..452987e7 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63028876-63029403/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/base.vcf.gz new file mode 100644 index 00000000..2a5ae257 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/base.vcf.gz.tbi new file mode 100644 index 00000000..d7a33d88 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/comp.vcf.gz new file mode 100644 index 00000000..54de867b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/comp.vcf.gz.tbi new file mode 100644 index 00000000..dd1fbe4a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/haps.fa new file mode 100644 index 00000000..f1cc034a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/haps.fa @@ -0,0 +1,92 @@ +>ref_chr20_63048933_63049513 +GCTTGTTTGGACCTGAAGACCAGCCTGAGCGAGGAGAGTCTTGTGCAGACGGTTTATCCAGGAGGAGCCCGGGGAGAGGGGGGTGGGAAAAGCCACAGTTTTGGAGGTCAGCAAGGTCATGTGGGGGCAGACTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCCTCCTCCTCCTCTTCCTCCTCGTCCTCTTCCTCCTTCTGCCAGGACCCTTCTTCCAGGACCCCTGAGAAGCGCATAGAATAGCGTCCAGGACTGTCTGCCCCAGGCACGCTGACCACTGGCTCCACTCCCCTGGGCAAGGGTCGCCCCTGGGCTGCTGCCTCCCAGCGACACAGGCAGGACCCAGAAGCCTGGTAGAAAGTGACCATGTGTGGCAGGT +>syndip_1_chr20:63048933-63049513 +GCTTGTTTGGACCTGAAGACCAGCCTGAGCGAGGAGAGTCTTGTGCAGACGGTTTATCCA +GGAGGAGCCCGGGGAGAGGGGGGTGGGAAAAGCCACAGTTTTGGAGGTCAGCAAGGTCAT +GTGGGGGCAGACTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCTTCCTCC +TCCTCCTCCTCTTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCC +CCCTCCTCTTCCTCCTCCTCCTCTTCCTTCTCCTCCTCCTTCTCCTCCTCCTCTTCCTCC +TCTTCCTCTTCCTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCTTTCTCCTCCTCTTCC +TCTTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCC +TCCTCCTCTTCCTCCTTCTCTTCCTCTTCCTCCTCCTCTTCCTCTTCCTCCTCCTCTTCC +TCTTTCTCCTCCTCCTCCTCTTCCTCTTCCTCCTCCTCTTCCTCTTTCTCCTCCTCCTCC +TCTTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCGTCT +TCCTCCTTCTCCTCTTCCTCCTCTTCCTCTTCCTCCTCCTCTTCCTCTTCCTCTTCCTCT +TCCTCTTCCTCCTCCTCCTCCTCTTTCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCC +TCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCT +TCTTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCC +TCTTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCC +TCTTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCCTCCTCCTCCTCTTCCTCCT +CCTCCTCTTCCTCCCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCCTCC +TCCTCCTCTTCCTCCTCGTCCTCTTCCTCCTTCTGCCAGGACCCTTCTTCCAGGACCCCT +GAGAAGCGCATAGAATAGCGTCCAGGACTGTCTGCCCCAGGCACGCTGACCACTGGCTCC +ACTCCCCTGGGCAAGGGTCGCCCCTGGGCTGCTGCCTCCCAGCGACACAGGCAGGACCCA +GAAGCCTGGTAGAAAGTGACCATGTGTGGCAGGT +>syndip_2_chr20:63048933-63049513 +GCTTGTTTGGACCTGAAGACCAGCCTGAGCGAGGAGAGTCTTGTGCAGACGGTTTATCCA +GGAGGAGCCCGGGGAGAGGGGGGTGGGAAAAGCCACAGTTTTGGAGGTCAGCAAGGTCAT +GTGGGGGCAGACTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCCTCT +TCCTCTTCCTCCTCCTCCTCCTCTTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCTCCTCC +TCTTCCTCCTCCTCCTCTTCCTCCTCCCCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCC +TCCTCCTTCTCCTCCTCCTCTTCCTCCTCTTCCTCTTCCTCCTCCTCTTCCTCCTCCTCT +TTCTCCTCCTCTTCCTCTTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCC +TCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCTTCCTCCTTCTCTTCCTCTTCCTCC +TCCTCTTCCTCTTCCTCCTCCTCTTCCTCTTTCTCCTCCTCCTCCTCTTCCTCCTCTTCC +TCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCGTCTTCCTCCTTCTCCTCT +TCCTCCTCTTCCTCTTCCTCCTCCTCTTCCTCTTCCTCTTCCTCTTCCTCCTCCTCCTCC +TCTTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCC +TCCTCTTCCTCCTCCTCCTCTTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCTTCTTCC +TCCTCTTCCTCCTCCTCCTCTTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCCTCTTCC +TCCTCCTCTTCCTCCTCTTCTTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCTTCCTCC +TCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCCTCCTCTTCCTCCTCCTCCTCTTCCTCCT +CCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCCTCCTCCTCCTCTTC +CTCCTCCTCCTCTTCCTCCCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCC +CCTCCTCCTCCTCTTCCTCCTCGTCCTCTTCCTCCTTCTGCCAGGACCCTTCTTCCAGGA +CCCCTGAGAAGCGCATAGAATAGCGTCCAGGACTGTCTGCCCCAGGCACGCTGACCACTG +GCTCCACTCCCCTGGGCAAGGGTCGCCCCTGGGCTGCTGCCTCCCAGCGACACAGGCAGG +ACCCAGAAGCCTGGTAGAAAGTGACCATGTGTGGCAGGT +>p:HG002_1_chr20:63048933-63049513 +GCTTGTTTGGACCTGAAGACCAGCCTGAGCGAGGAGAGTCTTGTGCAGACGGTTTATCCA +GGAGGAGCCCGGGGAGAGGGGGGTGGGAAAAGCCACAGTTTTGGAGGTCAGCAAGGTCAT +GTGGGGGCAGACTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCCTCT +TCCTCTTCCTCCTCCTCCTCCTCTTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCTCCTCC +TCTTCCTCCTCCTCCTCTTCCTCCTCCCCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCC +TCCTCCTTCTCCTCCTCCTCTTCCTCCTCTTCCTCTTCCTCCTCCTCTTCCTCCTCCTCT +TTCTCCTCCTCTTCCTCTTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCC +TCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCTTCCTCCTTCTCTTCCTCTTCCTCC +TCCTCTTCCTCTTCCTCCTCCTCTTCCTCTTTCTCCTCCTCCTCCTCTTCCTCCTCTTCC +TCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCGTCTTCCTCCTTCTCCTCT +TCCTCCTCTTCCTCTTCCTCCTCCTCTTCCTCTTCCTCTTCCTCTTCCTCCTCCTCCTCC +TCTTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCC +TCCTCTTCCTCCTCCTCCTCTTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCTTCTTCC +TCCTCTTCCTCCTCCTCCTCTTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCCTCTTCC +TCCTCCTCTTCCTCCTCTTCTTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCTTCCTCC +TCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCCTCCTCTTCCTCCTCCTCCTCTTCCTCCT +CCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCCTCCTCCTCCTCTTC +CTCCTCCTCCTCTTCCTCCCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCC +CCTCCTCCTCCTCTTCCTCCTCGTCCTCTTCCTCCTTCTGCCAGGACCCTTCTTCCAGGA +CCCCTGAGAAGCGCATAGAATAGCGTCCAGGACTGTCTGCCCCAGGCACGCTGACCACTG +GCTCCACTCCCCTGGGCAAGGGTCGCCCCTGGGCTGCTGCCTCCCAGCGACACAGGCAGG +ACCCAGAAGCCTGGTAGAAAGTGACCATGTGTGGCAGGT +>p:HG002_2_chr20:63048933-63049513 +GCTTGTTTGGACCTGAAGACCAGCCTGAGCGAGGAGAGTCTTGTGCAGACGGTTTATCCA +GGAGGAGCCCGGGGAGAGGGGGGTGGGAAAAGCCACAGTTTTGGAGGTCAGCAAGGTCAT +GTGGGGGCAGACTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCTTCCTCC +TCCTCCTCCTCTTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCC +CCCTCCTCTTCCTCCTCCTCCTCTTCCTTCTCCTCCTCCTTCTCCTCCTCCTCTTCCTCC +TCTTCCTCTTCCTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCTTTCTCCTCCTCTTCC +TCTTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCC +TCCTCCTCTTCCTCCTTCTCTTCCTCTTCCTCCTCCTCTTCCTCTTCCTCCTCCTCTTCC +TCTTTCTCCTCCTCCTCCTCTTCCTCTTCCTCCTCCTCTTCCTCTTTCTCCTCCTCCTCC +TCTTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCGTCT +TCCTCCTTCTCCTCTTCCTCCTCTTCCTCTTCCTCCTCCTCTTCCTCTTCCTCTTCCTCT +TCCTCTTCCTCCTCCTCCTCCTCTTTCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCC +TCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCT +TCTTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCC +TCTTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCC +TCTTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCCTCCTCCTCCTCTTCCTCCT +CCTCCTCTTCCTCCCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCCTCC +TCCTCCTCTTCCTCCTCGTCCTCTTCCTCCTTCTGCCAGGACCCTTCTTCCAGGACCCCT +GAGAAGCGCATAGAATAGCGTCCAGGACTGTCTGCCCCAGGCACGCTGACCACTGGCTCC +ACTCCCCTGGGCAAGGGTCGCCCCTGGGCTGCTGCCTCCCAGCGACACAGGCAGGACCCA +GAAGCCTGGTAGAAAGTGACCATGTGTGGCAGGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/haps.fa.ref.fa new file mode 100644 index 00000000..9a0c0b1f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63048933-63049513 +GCTTGTTTGGACCTGAAGACCAGCCTGAGCGAGGAGAGTCTTGTGCAGACGGTTTATCCAGGAGGAGCCCGGGGAGAGGGGGGTGGGAAAAGCCACAGTTTTGGAGGTCAGCAAGGTCATGTGGGGGCAGACTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCTCCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCCTCTCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCCTCTTCCTCCCCTCCTCCTCCTCTTCCTCCTCGTCCTCTTCCTCCTTCTGCCAGGACCCTTCTTCCAGGACCCCTGAGAAGCGCATAGAATAGCGTCCAGGACTGTCTGCCCCAGGCACGCTGACCACTGGCTCCACTCCCCTGGGCAAGGGTCGCCCCTGGGCTGCTGCCTCCCAGCGACACAGGCAGGACCCAGAAGCCTGGTAGAAAGTGACCATGTGTGGCAGGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/msa.fa new file mode 100644 index 00000000..82927c08 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/msa.fa @@ -0,0 +1,115 @@ +>ref_chr20_63048933_63049513 +gcttgtttggacctgaagaccagcctgagcgaggagagtcttgtgcagacggtttatcca +ggaggagcccggggagaggggggtgggaaaagccacagttttggaggtcagcaaggtcat +gtgggggcaga------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------ctcctcctcctcctcctcttcctcctcctcctcttcctcctcctcctct +tcctcttcctcctcctcctcctcttcctcctcctcctcctcttcctccctcctcttcctc +ctcctcctcttcctcctcctcttcctcctcctcctcctcttcctcccctcctcctcctct +tcctcctcctcctcttcctctcctcctcctcctcctcttcctcctcctcctcctcttcct +cccctcctcctcctcttcctcctcgtcctcttcctccttctgccaggacccttcttccag +gacccctgagaagcgcatagaatagcgtccaggactgtctgccccaggcacgctgaccac +tggctccactcccctgggcaagggtcgcccctgggctgctgcctcccagcgacacaggca +ggacccagaagcctggtagaaagtgaccatgtgtggcaggt +>syndip_1_chr20:63048933-63049513 +gcttgtttggacctgaagaccagcctgagcgaggagagtcttgtgcagacggtttatcca +ggaggagcccggggagaggggggtgggaaaagccacagttttggaggtcagcaaggtcat +gtgggggcagactcctcctcctcctcctcttcctcctcc--------------------- +------tcctcctcttcctcttcctcctcctcctcctcttcctcttcctcctcctcctcc +tcttcctcctcctcctcttcctcctccccctcctcttcctcctcctcctcttccttctcc +tcctccttctcctcctcctcttcctcctcttcctcttcctcctcctcttcctcctcctct +tcctcctcctctttctcctcctcttcctcttcctcctcttcctcctcctcttcctcctcc +tcctcttcctcctcctcctcttcctcctcctcctcttcctccttctcttcctcttcctcc +tcctcttcctcttcctcctcctcttcctctttctcctcctcctcctcttcctcttcctcc +tcc---------------------------------------tcttcctctttctcctcc +tcctcctcttcctcctcttcctcctcctcttcctcctcctcctcctcttcctcctcctcc +tcgtcttcctccttctcctcttcctcctcttcctcttcctcctcctcttcctcttcctct +tcctcttcctcttcctcctcctcctcctctttctcctcctcctcctcttcctcctcctcc +tcttcctcctcctcctcttcctcctcctcctcttcctcctcttcctcctcctcctcttcc +tcctcttcttcctcctcttcctcctcctcctcttcctcctcttcctcctcctcttcctcc +tcctcctcttcctcctcctcctcttcctcctcctcctcttcctcct-cctcctcttcctc +ctcctcctcttcctcctcctcttcctcctcctcctcctcttcctcccctcctcctcctct +tcctcctcctcctcttcctcccctcctcctcctcctcttcctcctcctcctcctcttcct +cccctcctcctcctcttcctcctcgtcctcttcctccttctgccaggacccttcttccag +gacccctgagaagcgcatagaatagcgtccaggactgtctgccccaggcacgctgaccac +tggctccactcccctgggcaagggtcgcccctgggctgctgcctcccagcgacacaggca +ggacccagaagcctggtagaaagtgaccatgtgtggcaggt +>syndip_2_chr20:63048933-63049513 +gcttgtttggacctgaagaccagcctgagcgaggagagtcttgtgcagacggtttatcca +ggaggagcccggggagaggggggtgggaaaagccacagttttggaggtcagcaaggtcat +gtgggggcagactcctcctcctcctcctcttcctcctcctcctcttcctcctcctcctct +tcctcttcctcctcctcctcctcttcctcttcctcctcctcctcctcttcctcctcctcc +tcttcctcctcctcctcttcctcctccccctcctcttcctcctcctcctcttcctcctcc +tcctccttctcctcctcctcttcctcctcttcctcttcctcctcctcttcctcctcctct +ttctcctcctcttcctcttcctcctcttcctcctcctcttcctcctcctcctcttcctcc +tcctcctcttcctcctcctcctcttcctcctcctcttcctccttctcttcctcttcctcc +tcctcttcctcttcctcctcctcttcctctttctcctcctcctcctcttcctcctcttcc +tcctcctcttcctcctcctcctcctcttcctcctcctcctcgtcttcctccttctcctct +tcctcctcttcctcttcctcctcctcttcctcttcctcttcctcttcctcctcctcctcc +tcttcctcctcctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcc +tcctcttcctcctcctcctcttcctcctcttcctcctcctcctcttcctcctcttcttcc +tcctcttcctcctcctcctcttcctcctcttcctcctcctcttcctcctcctcctcttcc +tcctcctcttcctcctcttcttcctcctcttcctcctcctcctcttcctcctcttcctcc +tcctcttcctcctcctcctcctcttcctcc-cctcctcttcctcct-cctcctcttcctc +ctcctcctcttcctcctcctcttcctcctcctcctcctcttcctcccctcctcctcctct +tcctcctcctcctcttcctcccctcctcctcctcctcttcctcctcctcctcctcttcct +cccctcctcctcctcttcctcctcgtcctcttcctccttctgccaggacccttcttccag +gacccctgagaagcgcatagaatagcgtccaggactgtctgccccaggcacgctgaccac +tggctccactcccctgggcaagggtcgcccctgggctgctgcctcccagcgacacaggca +ggacccagaagcctggtagaaagtgaccatgtgtggcaggt +>p:HG002_1_chr20:63048933-63049513 +gcttgtttggacctgaagaccagcctgagcgaggagagtcttgtgcagacggtttatcca +ggaggagcccggggagaggggggtgggaaaagccacagttttggaggtcagcaaggtcat +gtgggggcagactcctcctcctcctcctcttcctcctcctcctcttcctcctcctcctct +tcctcttcctcctcctcctcctcttcctcttcctcctcctcctcctcttcctcctcctcc +tcttcctcctcctcctcttcctcctccccctcctcttcctcctcctcctcttcctcctcc +tcctccttctcctcctcctcttcctcctcttcctcttcctcctcctcttcctcctcctct +ttctcctcctcttcctcttcctcctcttcctcctcctcttcctcctcctcctcttcctcc +tcctcctcttcctcctcctcctcttcctcctcctcttcctccttctcttcctcttcctcc +tcctcttcctcttcctcctcctcttcctctttctcctcctcctcctcttcctcctcttcc +tcctcctcttcctcctcctcctcctcttcctcctcctcctcgtcttcctccttctcctct +tcctcctcttcctcttcctcctcctcttcctcttcctcttcctcttcctcctcctcctcc +tcttcctcctcctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcc +tcctcttcctcctcctcctcttcctcctcttcctcctcctcctcttcctcctcttcttcc +tcctcttcctcctcctcctcttcctcctcttcctcctcctcttcctcctcctcctcttcc +tcctcctcttcctcctcttcttcctcctcttcctcctcctcctcttcctcctcttcctcc +tcctcttcctcctcctcctcctcttcctcc-cctcctcttcctcct-cctcctcttcctc +ctcctcctcttcctcctcctcttcctcctcctcctcctcttcctcccctcctcctcctct +tcctcctcctcctcttcctcccctcctcctcctcctcttcctcctcctcctcctcttcct +cccctcctcctcctcttcctcctcgtcctcttcctccttctgccaggacccttcttccag +gacccctgagaagcgcatagaatagcgtccaggactgtctgccccaggcacgctgaccac +tggctccactcccctgggcaagggtcgcccctgggctgctgcctcccagcgacacaggca +ggacccagaagcctggtagaaagtgaccatgtgtggcaggt +>p:HG002_2_chr20:63048933-63049513 +gcttgtttggacctgaagaccagcctgagcgaggagagtcttgtgcagacggtttatcca +ggaggagcccggggagaggggggtgggaaaagccacagttttggaggtcagcaaggtcat +gtgggggcagactcctcctcctcctcctcttcctcctcc--------------------- +------tcctcctcttcctcttcctcctcctcctcctcttcctcttcctcctcctcctcc +tcttcctcctcctcctcttcctcctccccctcctcttcctcctcctcctcttccttctcc +tcctccttctcctcctcctcttcctcctcttcctcttcctcctcctcttcctcctcctct +tcctcctcctctttctcctcctcttcctcttcctcctcttcctcctcctcttcctcctcc +tcctcttcctcctcctcctcttcctcctcctcctcttcctccttctcttcctcttcctcc +tcctcttcctcttcctcctcctcttcctctttctcctcctcctcctcttcctcttcctcc +tcc---------------------------------------tcttcctctttctcctcc +tcctcctcttcctcctcttcctcctcctcttcctcctcctcctcctcttcctcctcctcc +tcgtcttcctccttctcctcttcctcctcttcctcttcctcctcctcttcctcttcctct +tcctcttcctcttcctcctcctcctcctctttctcctcctcctcctcttcctcctcctcc +tcttcctcctcctcctcttcctcctcctcctcttcctcctcttcctcctcctcctcttcc +tcctcttcttcctcctcttcctcctcctcctcttcctcctcttcctcctcctcttcctcc +tcctcctcttcctcctcctcctcttcctcctcctcctcttcctcct-cctcctcttcctc +ctcctcctcttcctcctcctcttcctcctcctcctcctcttcctcccctcctcctcctct +tcctcctcctcctcttcctcccctcctcctcctcctcttcctcctcctcctcctcttcct +cccctcctcctcctcttcctcctcgtcctcttcctccttctgccaggacccttcttccag +gacccctgagaagcgcatagaatagcgtccaggactgtctgccccaggcacgctgaccac +tggctccactcccctgggcaagggtcgcccctgggctgctgcctcccagcgacacaggca +ggacccagaagcctggtagaaagtgaccatgtgtggcaggt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/msa.fa.fai new file mode 100644 index 00000000..ce0645af --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63048933_63049513 1301 29 60 61 +syndip_1_chr20:63048933-63049513 1301 1386 60 61 +syndip_2_chr20:63048933-63049513 1301 2743 60 61 +p:HG002_1_chr20:63048933-63049513 1301 4101 60 61 +p:HG002_2_chr20:63048933-63049513 1301 5459 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/output.vcf.gz new file mode 100644 index 00000000..fe9ffc97 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/output.vcf.gz.tbi new file mode 100644 index 00000000..9dff7397 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63049033-63049413/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/base.vcf.gz new file mode 100644 index 00000000..9dbbbf41 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/base.vcf.gz.tbi new file mode 100644 index 00000000..5f4a140d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/comp.vcf.gz new file mode 100644 index 00000000..cc01578e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/comp.vcf.gz.tbi new file mode 100644 index 00000000..bdd61883 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/haps.fa new file mode 100644 index 00000000..52988324 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/haps.fa @@ -0,0 +1,46 @@ +>ref_chr20_63154485_63155096 +GAAGAGGGAGATGGACTGGCCTCAGCCACCCCGGAGTACAGGGATGTCATCACACCAGCCCTCCAGCGGCTGAAAGAGCCAGTGAGAGGCAGGTGGGGGTGTGGATCAGGCCTGATCTCCCCTAGTCTCCTCCTGCAATGCCCAGATTCTTGCCCCCGTCCTTCCTTCTCCCTCCTCCCTTCCTCCTCCCTCCTCTTCCCTCCCTCCTGCTTCCTCCCTCTGCCCTCCCTCCTCCCTCTTCCTCCCTCCTCCTCCTTCCTGCTTCCTCCCTCTGCCCTCCCTCCTCCCTCTTCCTCCCTCCTCCTCCCCTCTCCTCTTTCCTCCTCCCTCTCCCTTCCTCCTCCTCCCCCCTTTCCCACCCTCCTCCCCCTTTCCCTCCCTCCTCCCGACTCCCTCTCCCCTTCTCCCTCTTCTCATCCCTTCCTCCTCCTCCCTCCTCCCTTCCTCCTCCTCCCTCCTTCCTCCCTCCTCCCTCCTCCCCACACTGTCCATTTGCAGGCTGCCTGGTCCTAGCCCATATCCAAGGGCCTGTCTCAGCTACAAAGTTCTGCTCTCTGCTTTTAAATGAGGACACAAGGTGGTTTCCAAAACACATGTACAAGGCAGAAATTG +>syndip_1_chr20:63154485-63155096 +GAAGAGGGAGATGGACTGGCCTCAGCCACCCCGGAGTACAGGGATGTCATCACACCAGCC +CTCCAGCGGCTGAAAGAGCCAGTGAGAGGCAGGTGGGGGTGTGGATCAGGCCTGATCTCC +CCTAGTCTCCTCCTGCAATGCCCAGATTCTTGCCCCCGTCCTTCCTTCTCCCTCCTCCCT +TCCTCCTCCCTCCTCTTCCCTCCCTCCTGCTTCCTCCCTCTGCCCTCCCTCCTCCCTCTT +CCTCCCTCCTCCTCCCCTCTCCTCTTTCCTCCTCCCTCTCCCTTCCTCCTCCTCCCCCCT +TTCCCACCCTCCTCCCCCTTTCCCTCCCTCCTCCCGACTCCCTCTCCCCTTCTCCCTCTT +CTCATCCCTTCCTCCTCCTCCCTCCTTCCTCCCTCCTCCCTCCTCCCCACACTGTCCATT +TGCAGGCTGCCTGGTCCTAGCCCATATCCAAGGGCCTGTCTCAGCTACAAAGTTCTGCTC +TCTGCTTTTAAATGAGGACACAAGGTGGTTTCCAAAACACATGTACAAGGCAGAAATTG +>syndip_2_chr20:63154485-63155096 +GAAGAGGGAGATGGACTGGCCTCAGCCACCCCGGAGTACAGGGATGTCATCACACCAGCC +CTCCAGCGGCTGAAAGAGCCAGTGAGAGGCAGGTGGGGGTGTGGATCAGGCCTGATCTCC +CCTAGTCTCCTCCTGCAATGCCCAGATTCTTGCCCCCGTCCTTCCTTCTCCCTCCTCCCT +TCCTCCTCCCTCCTCTTCCCTCCCTCCTGCTTCCTCCCTCTGCCCTCCCTCCTCCCTCTT +CCTCCCTCCTCTTCCCTCCCTCCTGCTTCCTCCCTCTGCCCTCCCTCCTCCCTCTTCCTC +CCTCCTCCTCCCCTCTCCTCTTTCCTCCTCCCTCTCCCTTCCTCCTCCTCCCCCCTTTCC +CACCCTCCTCCCCCTTTCCCTCCCTCCTCCCGACTCCCTCTCCCCTTCTCCCTCTTCTCA +TCCCTTCCTCCTCCTCCCTCCTCCCTTCCTCCTCCTCCCTCCTTCCTCCCTCCTCCCTCC +TCCCCACACTGTCCATTTGCAGGCTGCCTGGTCCTAGCCCATATCCAAGGGCCTGTCTCA +GCTACAAAGTTCTGCTCTCTGCTTTTAAATGAGGACACAAGGTGGTTTCCAAAACACATG +TACAAGGCAGAAATTG +>p:HG002_1_chr20:63154485-63155096 +GAAGAGGGAGATGGACTGGCCTCAGCCACCCCGGAGTACAGGGATGTCATCACACCAGCC +CTCCAGCGGCTGAAAGAGCCAGTGAGAGGCAGGTGGGGGTGTGGATCAGGCCTGATCTCC +CCTAGTCTCCTCCTGCAATGCCCAGATTCTTGCCCCCGTCCTTCCTTCTCCCTCCTCCCT +TCCTCCTCCCTCCTCTTCCCTCCCTCCTGCTTCCTCCCTCTGCCCTCCCTCCTCCCTCTT +CCTCCCTCCTCTTCCCTCCCTCCTGCTTCCTCCCTCTGCCCTCCCTCCTCCCTCTTCCTC +CCTCCTCCTCCCCTCTCCTCTTTCCTCCTCCCTCTCCCTTCCTCCTCCTCCCCCCTTTCC +CACCCTCCTCCCCCTTTCCCTCCCTCCTCCCGACTCCCTCTCCCCTTCTCCCTCTTCTCA +TCCCTTCCTCCTCCTCCCTCCTCCCTTCCTCCTCCTCCCTCCTTCCTCCCTCCTCCCTCC +TCCCCACACTGTCCATTTGCAGGCTGCCTGGTCCTAGCCCATATCCAAGGGCCTGTCTCA +GCTACAAAGTTCTGCTCTCTGCTTTTAAATGAGGACACAAGGTGGTTTCCAAAACACATG +TACAAGGCAGAAATTG +>p:HG002_2_chr20:63154485-63155096 +GAAGAGGGAGATGGACTGGCCTCAGCCACCCCGGAGTACAGGGATGTCATCACACCAGCC +CTCCAGCGGCTGAAAGAGCCAGTGAGAGGCAGGTGGGGGTGTGGATCAGGCCTGATCTCC +CCTAGTCTCCTCCTGCAATGCCCAGATTCTTGCCCCCGTCCTTCCTTCTCCCTCCTCCCT +TCCTCCTCCCTCCTCTTCCCTCCCTCCTGCTTCCTCCCTCTGCCCTCCCTCCTCCCTCTT +CCTCCCTCCTCCTCCCCTCTCCTCTTTCCTCCTCCCTCTCCCTTCCTCCTCCTCCCCCCT +TTCCCACCCTCCTCCCCCTTTCCCTCCCTCCTCCCGACTCCCTCTCCCCTTCTCCCTCTT +CTCATCCCTTCCTCCTCCTCCCTCCTTCCTCCCTCCTCCCTCCTCCCCACACTGTCCATT +TGCAGGCTGCCTGGTCCTAGCCCATATCCAAGGGCCTGTCTCAGCTACAAAGTTCTGCTC +TCTGCTTTTAAATGAGGACACAAGGTGGTTTCCAAAACACATGTACAAGGCAGAAATTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/haps.fa.ref.fa new file mode 100644 index 00000000..12643aef --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63154485-63155096 +GAAGAGGGAGATGGACTGGCCTCAGCCACCCCGGAGTACAGGGATGTCATCACACCAGCCCTCCAGCGGCTGAAAGAGCCAGTGAGAGGCAGGTGGGGGTGTGGATCAGGCCTGATCTCCCCTAGTCTCCTCCTGCAATGCCCAGATTCTTGCCCCCGTCCTTCCTTCTCCCTCCTCCCTTCCTCCTCCCTCCTCTTCCCTCCCTCCTGCTTCCTCCCTCTGCCCTCCCTCCTCCCTCTTCCTCCCTCCTCCTCCTTCCTGCTTCCTCCCTCTGCCCTCCCTCCTCCCTCTTCCTCCCTCCTCCTCCCCTCTCCTCTTTCCTCCTCCCTCTCCCTTCCTCCTCCTCCCCCCTTTCCCACCCTCCTCCCCCTTTCCCTCCCTCCTCCCGACTCCCTCTCCCCTTCTCCCTCTTCTCATCCCTTCCTCCTCCTCCCTCCTCCCTTCCTCCTCCTCCCTCCTTCCTCCCTCCTCCCTCCTCCCCACACTGTCCATTTGCAGGCTGCCTGGTCCTAGCCCATATCCAAGGGCCTGTCTCAGCTACAAAGTTCTGCTCTCTGCTTTTAAATGAGGACACAAGGTGGTTTCCAAAACACATGTACAAGGCAGAAATTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/msa.fa new file mode 100644 index 00000000..f0308c9f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/msa.fa @@ -0,0 +1,60 @@ +>ref_chr20_63154485_63155096 +gaagagggagatggactggcctcagccaccccggagtacagggatgtcatcacaccagcc +ctccagcggctgaaagagccagtgagaggcaggtgggggtgtggatcaggcctgatctcc +cctagtctcctcctgcaatgcccagattcttgcccccgtccttccttctccctcctccct +tcctcctccctcctcttccctccctcctgcttcctccctctgccctccctcctccctctt +cctccctcct----cctccttcctgcttcctccctctgccctccctcctccctcttcctc +cctcctcctcccctctcctctttcctcctccctctcccttcctcctcctcccccctttcc +caccctcctccccctttccctccctcctcccgactccctctccccttctccctcttctca +tcccttcctcctcctccctcctcccttcctcctcctccctccttcctccctcctccctcc +tccccacactgtccatttgcaggctgcctggtcctagcccatatccaagggcctgtctca +gctacaaagttctgctctctgcttttaaatgaggacacaaggtggtttccaaaacacatg +tacaaggcagaaattg +>syndip_1_chr20:63154485-63155096 +gaagagggagatggactggcctcagccaccccggagtacagggatgtcatcacaccagcc +ctccagcggctgaaagagccagtgagaggcaggtgggggtgtggatcaggcctgatctcc +cctagtctcctcctgcaatgcccagattcttgcccccgtccttccttctccctcctccct +tcctcctccctcctcttc------------------------------------------ +--------------cctccctcctgcttcctccctctgccctccctcctccctcttcctc +cctcctcctcccctctcctctttcctcctccctctcccttcctcctcctcccccctttcc +caccctcctccccctttccctccctcctcccgactccctctccccttctccctcttctca +---------------------tcccttcctcctcctccctccttcctccctcctccctcc +tccccacactgtccatttgcaggctgcctggtcctagcccatatccaagggcctgtctca +gctacaaagttctgctctctgcttttaaatgaggacacaaggtggtttccaaaacacatg +tacaaggcagaaattg +>syndip_2_chr20:63154485-63155096 +gaagagggagatggactggcctcagccaccccggagtacagggatgtcatcacaccagcc +ctccagcggctgaaagagccagtgagaggcaggtgggggtgtggatcaggcctgatctcc +cctagtctcctcctgcaatgcccagattcttgcccccgtccttccttctccctcctccct +tcctcctccctcctcttccctccctcctgcttcctccctctgccctccctcctccctctt +cctccctcctcttccctccctcctgcttcctccctctgccctccctcctccctcttcctc +cctcctcctcccctctcctctttcctcctccctctcccttcctcctcctcccccctttcc +caccctcctccccctttccctccctcctcccgactccctctccccttctccctcttctca +tcccttcctcctcctccctcctcccttcctcctcctccctccttcctccctcctccctcc +tccccacactgtccatttgcaggctgcctggtcctagcccatatccaagggcctgtctca +gctacaaagttctgctctctgcttttaaatgaggacacaaggtggtttccaaaacacatg +tacaaggcagaaattg +>p:HG002_1_chr20:63154485-63155096 +gaagagggagatggactggcctcagccaccccggagtacagggatgtcatcacaccagcc +ctccagcggctgaaagagccagtgagaggcaggtgggggtgtggatcaggcctgatctcc +cctagtctcctcctgcaatgcccagattcttgcccccgtccttccttctccctcctccct +tcctcctccctcctcttccctccctcctgcttcctccctctgccctccctcctccctctt +cctccctcctcttccctccctcctgcttcctccctctgccctccctcctccctcttcctc +cctcctcctcccctctcctctttcctcctccctctcccttcctcctcctcccccctttcc +caccctcctccccctttccctccctcctcccgactccctctccccttctccctcttctca +tcccttcctcctcctccctcctcccttcctcctcctccctccttcctccctcctccctcc +tccccacactgtccatttgcaggctgcctggtcctagcccatatccaagggcctgtctca +gctacaaagttctgctctctgcttttaaatgaggacacaaggtggtttccaaaacacatg +tacaaggcagaaattg +>p:HG002_2_chr20:63154485-63155096 +gaagagggagatggactggcctcagccaccccggagtacagggatgtcatcacaccagcc +ctccagcggctgaaagagccagtgagaggcaggtgggggtgtggatcaggcctgatctcc +cctagtctcctcctgcaatgcccagattcttgcccccgtccttccttctccctcctccct +tcctcctccctcctcttc------------------------------------------ +--------------cctccctcctgcttcctccctctgccctccctcctccctcttcctc +cctcctcctcccctctcctctttcctcctccctctcccttcctcctcctcccccctttcc +caccctcctccccctttccctccctcctcccgactccctctccccttctccctcttctca +---------------------tcccttcctcctcctccctccttcctccctcctccctcc +tccccacactgtccatttgcaggctgcctggtcctagcccatatccaagggcctgtctca +gctacaaagttctgctctctgcttttaaatgaggacacaaggtggtttccaaaacacatg +tacaaggcagaaattg diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/msa.fa.fai new file mode 100644 index 00000000..82fc522b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63154485_63155096 616 29 60 61 +syndip_1_chr20:63154485-63155096 616 690 60 61 +syndip_2_chr20:63154485-63155096 616 1351 60 61 +p:HG002_1_chr20:63154485-63155096 616 2013 60 61 +p:HG002_2_chr20:63154485-63155096 616 2675 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/output.vcf.gz new file mode 100644 index 00000000..5a0051f9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/output.vcf.gz.tbi new file mode 100644 index 00000000..cd42d948 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63154585-63154996/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/base.vcf.gz new file mode 100644 index 00000000..ad3ed66d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/base.vcf.gz.tbi new file mode 100644 index 00000000..546f22e3 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/comp.vcf.gz new file mode 100644 index 00000000..ca7fe369 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/comp.vcf.gz.tbi new file mode 100644 index 00000000..715a02b7 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/haps.fa new file mode 100644 index 00000000..1efeed23 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/haps.fa @@ -0,0 +1,254 @@ +>ref_chr20_63167287_63167728 +AATGGCCAGCCCGTCCCGCCGAGGCCAGTGGACATGCCAAATCCCTCCCGCAACAAGTTGCTATCCATCCCCTCGACTAATACTTACCAAATTAATTCCAGATTTGGAGTCACTCATGGTTCCCACCAGCACTCAGCCCCATCTCAGCCCCCATCTCAGCCCCCACCGCAGCCTCACCTCAGTGCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGACCCTCCTCAGCCCCTCCTCATCCCCTCCTCAGCAGCTGCTGGAATGGGCTACCCTCAGGAGTTGGCACCCCACAGGCTCCTTCCCTTCCCACCTCCGCCACACCCTGACGAGGGAAAAATGGGGAGCTGCTGGGAGGGAACTTGCACCCTGTTGGGCGCCTTGT +>syndip_1_chr20:63167287-63167728 +AATGGCCAGCCCGTCCCGCCGAGGCCAGTGGACATGCCAAATCCCTCCCGCAACAAGTTG +CTATCCATCCCCTCGACTAATACTTACCAAATTAATTCCAGATTTGGAGTCACTCACGGT +TCCCACCAGCACTCAGCCCCATCTCAGCCCCCATCTCAGCCCCCACCGCAGCCTCACCTC +AGTGCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCTCCTCA +GCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCT +GCCCCTCCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCCG +CCCCCACCTCTGCCCCTCCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCGC +CCCCACCTCCGCCCCCACCTCTGCCCCTCCTCAGCCCCCACCTCAGCCCCCTCCTCAGCC +CCCACCTCCGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGCCCCCACCTCAGCCC +CCTCCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCCGCCCCTCCTCCGCCCC +CACCTCAGCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGCCCCC +ACCTCAGCCCCCACCTCAGCCCCCACCTCCCCCCTCCTCAGCCCCCACCTCAGCCCCCAC +CTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACC +TCCGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACC +TCCGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCTGCCCCTCCT +CAGCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGCCCCCACCTC +AGCCCCCACCTCAGCCCCCACCTCCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAG +CCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGC +CCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCTCCTCAGCC +CCCACCTCCGCCCCCACCTCCGCCCCCACCTCTGCCCCTCCTCAGCCCCCACCTCAGCCC +CCTCCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCCGCCCCTCCTCCGCCCC +CACCTCAGCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGCCCCC +ACCTCAGCCCCCACCTCAGCCCCCACCTCCCCCCTCCTCAGCCCCCACCTCAGCCCCCAC +CTCCGCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCAGCCCCCACC +TCCGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCGCCCCCACC +TCAGCCCCCACCTCTGCCCCTCCTCAGCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCT +CTGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCCCCCTCCTCAG +CCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAG +CCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCCGCC +CCCACCTCAGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGCCCCCACCTCAGCCC +CCACCTCCGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCCCCCTCCTCCGCCCCC +ACCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCCCCCTCCTCCGCCCCCAC +CTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCCCCCTCCT +CAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCT +CAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTC +AGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTC +CGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTC +AGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTC +AGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCAG +CCCCCACCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCCTCCTCAGC +CCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGC +CCCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCCTCAGCCCCCACCTCAGCCCCCA +CCTCCGCCCCCACCTCCGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCAC +CTCAGCCCCTCCTCAGCCCCCACCTCCACCCCCACCTCCGTCCCCACCTCCGCCCCCTCC +TCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCTCCT +CAGCCCCCACCTCTGCCCCCACCTCAGACCCTCCTCAGCCCCTCCTCAGCCCCTCCTCAT +CCCCTCCTCAGCAGCTGCTGGAATGGGCTACCCTCAGGAGTTGGCACCCCACAGGCTCCT +TCCCTTCCCACCTCCGCCACACCCTGACGAGGGAAAAATGGGGAGCTGCTGGGAGGGAAC +TTGCACCCTGTTGGGCGCCTTGT +>syndip_2_chr20:63167287-63167728 +AATGGCCAGCCCGTCCCGCCGAGGCCAGTGGACATGCCAAATCCCTCCCGCAACAAGTTG +CTATCCATCCCCTCGACTAATACTTACCAAATTAATTCCAGATTTGGATTCACTCACGGT +TCCCACCAGCACTCAGCCCCATCTCAGCCCCCATCTCAGCCCCCACCGCAGCCTCACCTC +AGTGCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCTCCTC +AGCCCCTCCTCCGCCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCC +GCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCTCCTCAG +CCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCG +CCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAG +CCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCTCCTCAG +CCCCCACCTCCCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCTCCCCCCCACCTCCGCC +CCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGGCCCCACCTCAGCCCCCACCTCAGCCC +CCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCC +CACCTCAGCCCCCACCTCCGCCCCTCCTCTGCCCCCACCTCAGCCCCCTCCTCAGCCCCC +ACCTCTGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCA +CCTCAGCCCCCACCTCCCCCCCTCCTCAGCCCCCACCTCCACCCCCACCTCAGCCCCCAC +CTCAGCCCCCACCTCCCCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACC +TCCGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCT +CAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCGCCCCCTCCT +CAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCACCCCCACCTCAGCCCCCACCT +CAGCCCCCACCTCCCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCA +GGCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCA +GCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCACCCCCACCTCAG +CCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGC +CCCCACCTCCGCCCCTCCTCTGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCTGCC +CCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCAGCCC +CCACCTCCCCCCCTCCTCAGCCCCCACCTCCACCCCCACCTCAGCCCCCACCTCCGCCCC +TCCTCAGCCCCCACCTCAGCCCCCACCTCCACCCCCACCTCAGCCCCCACCTCCGCCCCC +ACCTCCGCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCTCCTCAGCCCCCAC +CTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCT +CAGCCCCCACCTCCACCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCCCCCCACCTC +CGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGGCCCCACCTCAGCCCCCACCTCA +GCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAG +CCCCCACCTCAGCCCCCACCTCCACCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAG +CCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCTGCC +CCCACCTCAGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGCCCCCACCTCAGCCC +CCACCTCCGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCCCCCCTCCTCAGCCCC +CACCTCCACCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCC +ACCTCCACCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCA +CCTCCGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACC +TCCGCCCCCACCTCAGCCCCCTCCTCCGCCCCTCCTCAGCCCCCACCTCCACCCCCACCT +CAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTC +AGCCCCCACCTCAGCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTC +AGCCCCCTCCTCCACCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCC +GCCCCTCCTCAGCCCCCACCTCCACCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGC +CCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCCCCCCTCCTCAGCCCCCACCTCCGCC +CCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCCACCCCCACCTCAGCCC +CCACCTCCGCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCTCCTCAGCCCCC +ACCTCCGCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCCCCCCTC +CTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACC +TCAGCCCCCACCTCCACCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCT +CAGCCCCCACCTCCGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCCGCCCCTCCTCA +GCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCC +GCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAG +ACCCCACCTCCGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGC +CCCTCCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCCGCCCCTCCTCAGCCC +CCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCC +CACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCC +CTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGCCCC +ACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCTCC +TCAGCCCCCACCTCAGCCCCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCC +GCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCCGC +CCCCACCTCCGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCC +CCCTCCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGCCCCACCTCAGCCC +CTCCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCA +CCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGCCCCTC +CTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCGCCCCCAC +CTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCT +CCGCCCCCACCTCCGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTC +AGCCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGCCCCACCTCA +GCCCCTCCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCTCCTCAGCCCCCACCTCAGC +CCCCACCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGCCCCCTCCTCAGC +CCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCCGCC +CCCACCTCAGACCCTCCTCAGCCCCTCCTCATCCCCTCCTCAGCAGCTGCTGGAATGGGC +TACCCTCAGGAGTTGGCACCCCACAGGCTCCTTCCCTTCCCACCTCCGCCACACCCTGAC +GAGGGAAAAATGGGGAGCTGCTGGGAGGGAACTTGCACCCTGTTGGGCGCCTTGT +>p:HG002_1_chr20:63167287-63167728 +AATGGCCAGCCCGTCCCGCCGAGGCCAGTGGACATGCCAAATCCCTCCCGCAACAAGTTG +CTATCCATCCCCTCGACTAATACTTACCAAATTAATTCCAGATTTGGATTCACTCACGGT +TCCCACCAGCACTCAGCCCCATCTCAGCCCCCATCTCAGCCCCCACCGCAGCCTCACCTC +AGTGCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCTCCTC +AGCCCCTCCTCCGCCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCC +GCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCTCCTCAG +CCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCG +CCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAG +CCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCTCCTCAG +CCCCCACCTCCCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCTCCCCCCCACCTCCGCC +CCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGGCCCCACCTCAGCCCCCACCTCAGCCC +CCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCC +CACCTCAGCCCCCACCTCCGCCCCTCCTCTGCCCCCACCTCAGCCCCCTCCTCAGCCCCC +ACCTCTGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCA +CCTCAGCCCCCACCTCCCCCCCTCCTCAGCCCCCACCTCCACCCCCACCTCAGCCCCCAC +CTCAGCCCCCACCTCCCCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACC +TCCGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCT +CAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCGCCCCCTCCT +CAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCACCCCCACCTCAGCCCCCACCT +CAGCCCCCACCTCCCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCA +GGCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCA +GCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCACCCCCACCTCAG +CCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGC +CCCCACCTCCGCCCCTCCTCTGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCTGCC +CCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCAGCCC +CCACCTCCCCCCCTCCTCAGCCCCCACCTCCACCCCCACCTCAGCCCCCACCTCCGCCCC +TCCTCAGCCCCCACCTCAGCCCCCACCTCCACCCCCACCTCAGCCCCCACCTCCGCCCCC +ACCTCCGCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCTCCTCAGCCCCCAC +CTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCT +CAGCCCCCACCTCCACCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCCCCCCACCTC +CGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGGCCCCACCTCAGCCCCCACCTCA +GCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAG +CCCCCACCTCAGCCCCCACCTCCACCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAG +CCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCTGCC +CCCACCTCAGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGCCCCCACCTCAGCCC +CCACCTCCGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCCCCCCTCCTCAGCCCC +CACCTCCACCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCC +ACCTCCACCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCA +CCTCCGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACC +TCCGCCCCCACCTCAGCCCCCTCCTCCGCCCCTCCTCAGCCCCCACCTCCACCCCCACCT +CAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTC +AGCCCCCACCTCAGCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTC +AGCCCCCTCCTCCACCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCC +GCCCCTCCTCAGCCCCCACCTCCACCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGC +CCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCCCCCCTCCTCAGCCCCCACCTCCGCC +CCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCCACCCCCACCTCAGCCC +CCACCTCCGCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCTCCTCAGCCCCC +ACCTCCGCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCCCCCCTC +CTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACC +TCAGCCCCCACCTCCACCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCT +CAGCCCCCACCTCCGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCCGCCCCTCCTCA +GCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCC +GCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAG +ACCCCACCTCCGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGC +CCCTCCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCCGCCCCTCCTCAGCCC +CCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCC +CACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCC +CTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGCCCC +ACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCTCC +TCAGCCCCCACCTCAGCCCCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCC +GCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCCGC +CCCCACCTCCGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCC +CCCTCCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGCCCCACCTCAGCCC +CTCCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCA +CCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGCCCCTC +CTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCGCCCCCAC +CTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCT +CCGCCCCCACCTCCGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTC +AGCCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGCCCCACCTCA +GCCCCTCCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCTCCTCAGCCCCCACCTCAGC +CCCCACCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGCCCCCTCCTCAGC +CCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCCGCC +CCCACCTCAGACCCTCCTCAGCCCCTCCTCATCCCCTCCTCAGCAGCTGCTGGAATGGGC +TACCCTCAGGAGTTGGCACCCCACAGGCTCCTTCCCTTCCCACCTCCGCCACACCCTGAC +GAGGGAAAAATGGGGAGCTGCTGGGAGGGAACTTGCACCCTGTTGGGCGCCTTGT +>p:HG002_2_chr20:63167287-63167728 +AATGGCCAGCCCGTCCCGCCGAGGCCAGTGGACATGCCAAATCCCTCCCGCAACAAGTTG +CTATCCATCCCCTCGACTAATACTTACCAAATTAATTCCAGATTTGGAGTCACTCACGGT +TCCCACCAGCACTCAGCCCCATCTCAGCCCCCATCTCAGCCCCCACCGCAGCCTCACCTC +AGTGCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCTCCTCA +GCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCT +GCCCCTCCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCCG +CCCCCACCTCTGCCCCTCCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCGC +CCCCACCTCCGCCCCCACCTCTGCCCCTCCTCAGCCCCCACCTCAGCCCCCTCCTCAGCC +CCCACCTCCGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGCCCCCACCTCAGCCC +CCTCCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCCGCCCCTCCTCCGCCCC +CACCTCAGCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGCCCCC +ACCTCAGCCCCCACCTCAGCCCCCACCTCCCCCCTCCTCAGCCCCCACCTCAGCCCCCAC +CTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACC +TCCGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACC +TCCGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCTGCCCCTCCT +CAGCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGCCCCCACCTC +AGCCCCCACCTCAGCCCCCACCTCCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAG +CCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGC +CCCCACCTCAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCTCCTCAGCC +CCCACCTCCGCCCCCACCTCCGCCCCCACCTCTGCCCCTCCTCAGCCCCCACCTCAGCCC +CCTCCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCCGCCCCTCCTCCGCCCC +CACCTCAGCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGCCCCC +ACCTCAGCCCCCACCTCAGCCCCCACCTCCCCCCTCCTCAGCCCCCACCTCAGCCCCCAC +CTCCGCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCAGCCCCCACC +TCCGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCGCCCCCACC +TCAGCCCCCACCTCTGCCCCTCCTCAGCCCCCACCTCCGCCCCCTCCTCAGCCCCCACCT +CTGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCCCCCTCCTCAG +CCCCCACCTCAGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCAG +CCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCTCCTCCGCC +CCCACCTCAGCCCCCTCCTCAGCCCCCACCTCTGCCCCTCCTCAGCCCCCACCTCAGCCC +CCACCTCCGCCCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCCCCCCTCCTCCGCCCCC +ACCTCAGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTCCCCCCTCCTCCGCCCCCAC +CTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCCCCCTCCT +CAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCT +CAGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTC +AGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTC +CGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTC +AGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCCACCTCAGCCCCCACCTC +AGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCAG +CCCCCACCTCAGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCCTCCTCAGC +CCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCCGCCCCCACCTCAGC +CCCACCTCAGCCCCTCCTCAGCCCCCACCTCAGCCCCCTCAGCCCCCACCTCAGCCCCCA +CCTCCGCCCCCACCTCCGCCCCCACCTCCGCCCCTCCTCAGCCCCCACCTCAGCCCCCAC +CTCAGCCCCTCCTCAGCCCCCACCTCCACCCCCACCTCCGTCCCCACCTCCGCCCCCTCC +TCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCTCCT +CAGCCCCCACCTCTGCCCCCACCTCAGACCCTCCTCAGCCCCTCCTCAGCCCCTCCTCAT +CCCCTCCTCAGCAGCTGCTGGAATGGGCTACCCTCAGGAGTTGGCACCCCACAGGCTCCT +TCCCTTCCCACCTCCGCCACACCCTGACGAGGGAAAAATGGGGAGCTGCTGGGAGGGAAC +TTGCACCCTGTTGGGCGCCTTGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/haps.fa.ref.fa new file mode 100644 index 00000000..aababe14 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63167287-63167728 +AATGGCCAGCCCGTCCCGCCGAGGCCAGTGGACATGCCAAATCCCTCCCGCAACAAGTTGCTATCCATCCCCTCGACTAATACTTACCAAATTAATTCCAGATTTGGAGTCACTCATGGTTCCCACCAGCACTCAGCCCCATCTCAGCCCCCATCTCAGCCCCCACCGCAGCCTCACCTCAGTGCCCACCTCAGCCCCCTCCTCAGCCCCCACCTCAGCCCCCACCTCCGCCCCCACCTCAGCCCCTCCTCAGCCCCCACCTCCGCCCCCACCTCAGACCCTCCTCAGCCCCTCCTCATCCCCTCCTCAGCAGCTGCTGGAATGGGCTACCCTCAGGAGTTGGCACCCCACAGGCTCCTTCCCTTCCCACCTCCGCCACACCCTGACGAGGGAAAAATGGGGAGCTGCTGGGAGGGAACTTGCACCCTGTTGGGCGCCTTGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/msa.fa new file mode 100644 index 00000000..5af41b47 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/msa.fa @@ -0,0 +1,385 @@ +>ref_chr20_63167287_63167728 +aatggccagcccgtcccgccgaggccagtggacatgccaaatccctcccgcaacaagttg +ctatccatcccctcgactaatacttaccaaattaattccagatttggagtcactcatggt +tcccaccagcactcagccccatctcagcccccatctcagcccccaccgcagcctcacctc +agtgcccacctcagccccctcctcagccccca---------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----cctcagcccccacctccgcccccacctcagcccctcctcagcccccacctccgcc +cccacctcaga-----------ccctcctcagcccctcctcatcccctcctcagcagctg +ctggaatgggctaccctcaggagttggcaccccacaggctccttcccttcccacctccgc +cacaccctgacgagggaaaaatggggagctgctgggagggaacttgcaccctgttgggcg +ccttgt +>syndip_1_chr20:63167287-63167728 +aatggccagcccgtcccgccgaggccagtggacatgccaaatccctcccgcaacaagttg +ctatccatcccctcgactaatacttaccaaattaattccagatttggagtcactcacggt +tcccaccagcactcagccccatctcagcccccatctcagcccccaccgcagcctcacctc +agtgcccacctcagccccctcctcagcccccacctccgcccccacctcagcccct----- +-------------------cctcagcccccacctcagccccctcctcagcccccacctcc +-----------------------gcccccacctccgcccccacctctgcccct------- +------cctcagcccccacctcagccccctcctcagcccccacctccgcccccacctccg +cccccacctctgcccct-------------------------------------cctcag +cccccacctcagccccctcctcagcccccacctccgcccccacctccgcccccacctctg +cccctcctcagcccccacctcagccccctcctcag-----------cccccacctccgcc +ccctcctcagcccccacctctgcccct------------cctcagcccccacctcagccc +cctcctcagcccccacctccgcccccacctccgcccccacctccgcccctcctccgcccc +cacctcagcccccacctcc-----------------------gccccctcctcagccccc +acctctgcccctcctcagcccccacctcagcccccacctcagcccccacctc-------- +------------------------------------------------------------ +----------------------------ccccctcctcagcccccacctcagcccccacc +tcagccccctcctcagcccccacctcagcccccacctccgcccct------------cct +cagcccccacctccgcccccacctcagcccccacctcagcccccacctccgcccccacct +cagcccccacctccgcccccacctcagcccccacctccgcccccacctcagcccccacct +ctgcccctcctcagcccccacctccgccccctcctcagcccccacctctg---------- +--------------------------cccctcctcagcccccacctcagcccccacctca +gcccccacctcc-cccctcctcagcccccacctcagcccccacctcagccccctcctcag +cccccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacctcagc +ccccacctccgcccctcctcagcccccacctcag-------------------------- +------------------------------------------------------------ +--------ccccctcctcagcccccacctccgcccccacctccgcccccacctctgcccc +tcctcagcccccacctcagccccctcctcagcccccacctccgcccccacctccgccccc +acctccgcccctcctccgcccccacctcagcccccacctccgccccct------------ +----------------------cctcagcccccacctctgcccctcctcagcccccacct +cagcccccacctcagcccccacct-------------------------cccccctcctc +agcccccacctcagcccccacctccgcccctcctcagcccccacctccgccccca----- +------------------------------------------------------cctcag +cccccacctcagcccccacctccgcccccacctcagcccccacctccgcccccacctcag +cccccacctcc-----------gcccccacctcagcccccacctctgcccctcctcagcc +cccacctccgccccctcctcagcccccacctctgcccctcctcagcccccacctcagccc +ccacctcagcccccacct-------------------------cccccctcctcagcccc +ca-----------------------------------cctcagcccccacctcagccccc +tcctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagccccca +-----------------------cctcagcccccacctccgcccctcctccgcccccacc +tcagccccctcctcagcccccacctctgcccctcctcagcccccacctcagcccccacct +ccgcccccacctcagccccctcctcagcccccacctc----------------------- +--------------ccccctcctccgcccccacctcagcccccacctcagcccccacctc +agcccccacctc------------------------------------------------ +-----------------------------------------------------------c +cccctcctccgcccccacctcagccccca-----------cctcagcccccacctccgcc +cccacctcagcccccacctcc--------------------------------------- +------------------------------------------------------------ +-------cccctcctcagcccccacctcagcccccacctccgccccca-----------c +ctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacc +tccgcccccacctcagcccccacctcagcccccacctccgccccca-------------- +-------------------------------------------------------cctca +gcccccacctccgcccccacctcagcccccacctccgcccccacctcagcccccacctcc +gcccccacctccgcccccacctcc-----------gcccccacctcagcccccacctcag +cccccacctccgccccca------------------------------------------ +----cctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagccc +ccacctcagcccctcctcagcccccacctcagcccccacctcagcccccacctcagcccc +t-------------------------cctcagcccccacctcagccccctcctcagcccc +ctcctcagcccccacctcagcccccacctccgcccccacctccgcccccacctcagcccc +acctcagcccctcctcagcccccacctcagccc--------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------cctcagccccca +cctcagcccccacctccgcccccacctccgcccccacctcc------------------- +------------------------------------------------------------ +----gcccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacct +cc---------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----------acccccacctccgtccccacctccgccccctcctcagccccctcctcagc +ccccacctcagcccccacctccgcccccacctcagcccctcctcagcccccacctctgcc +cccacctcagaccctcctcagcccctcctcagcccctcctcatcccctcctcagcagctg +ctggaatgggctaccctcaggagttggcaccccacaggctccttcccttcccacctccgc +cacaccctgacgagggaaaaatggggagctgctgggagggaacttgcaccctgttgggcg +ccttgt +>syndip_2_chr20:63167287-63167728 +aatggccagcccgtcccgccgaggccagtggacatgccaaatccctcccgcaacaagttg +ctatccatcccctcgactaatacttaccaaattaattccagatttggattcactcacggt +tcccaccagcactcagccccatctcagcccccatctcagcccccaccgcagcctcacctc +agtgcccacctcagccccctcctcagcccccacctccgcccccacctccgccccctcctc +agcccctcctccgcccccacctcagcccccacctcagccccctcctcagcccccacctcc +gcccctcctcagcccccacctcagcccccacctcagcccccacctccgccccctcctcag +cccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctccg +cccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctcag +cccccacctcagccccctcctcagcccccacctcagcccccacctccgccccctcctcag +cccccacctcccccccacctccgccccctcctcagcccccacctcccccccacctccgcc +ccctcctcagcccccacctctgcccctcctcaggccccacctcagcccccacctcagccc +cctcctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagcccc +cacctcagcccccacctccgcccctcctctgcccccacctcagccccctcctcagccccc +acctctgcccctcctcagcccccacctcagcccccacctccgcccccacctcagccccca +cctcagcccccacctccccccctcctcagcccccacctccacccccacctcagcccccac +ctcagcccccacctccccccctcctcagcccccacctccgcccccacctcagcccccacc +tccgcccccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacct +cagcccccacctccgcccccacctccgcccccacctcagcccccacctccgccccctcct +cagcccccacctcagcccccacctcagcccccacctccacccccacctcagcccccacct +cagcccccacctcccccccacctccgccccctcctcagcccccacctctgcccctcctca +ggccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctca +gcccccacctccgcccctcctcagcccccacctcagcccccacctccacccccacctcag +cccccacctccgcccccacctcagcccccacctccgcccctcctcagcccccacctcagc +ccccacctccgcccctcctctgcccccacctcagccccctcctcagcccccacctctgcc +cctcctcagcccccacctcagcccccacctccgcccccacctcagcccccacctcagccc +ccacctccccccctcctcagcccccacctccacccccacctcagcccccacctccgcccc +tcctcagcccccacctcagcccccacctccacccccacctcagcccccacctccgccccc +acctccgcccctcctcagcccccacctccgcccccacctcagcccctcctcagcccccac +ctccgcccctcctcagcccccacctcagcccccacctccgcccctcctcagcccccacct +cagcccccacctccacccccacctcagcccccacctcagcccccacctcccccccacctc +cgccccctcctcagcccccacctctgcccctcctcaggccccacctcagcccccacctca +gccccctcctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcag +cccccacctcagcccccacctccacccccacctcagcccccacctccgcccccacctcag +cccccacctccgcccctcctcagcccccacctcagcccccacctccgcccctcctctgcc +cccacctcagccccctcctcagcccccacctctgcccctcctcagcccccacctcagccc +ccacctccgcccccacctcagcccccacctcagcccccacctccccccctcctcagcccc +cacctccacccccacctcagcccccacctccgcccctcctcagcccccacctcagccccc +acctccacccccacctcagcccccacctcagcccccacctccgcccctcctcagccccca +cctccgcccccacctcagcccctcctcagcccccacctccgcccctcctcagcccccacc +tccgcccccacctcagccccctcctccgcccctcctcagcccccacctccacccccacct +cagcccccacctcagccccctcctcagcccccacctccgcccctcctcagcccccacctc +agcccccacctcagcccccacctccgccccctcctcagcccccacctcagcccccacctc 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+cctcagcccccacctccccccctcctcagcccccacctccacccccacctcagcccccac +ctcagcccccacctccccccctcctcagcccccacctccgcccccacctcagcccccacc +tccgcccccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacct +cagcccccacctccgcccccacctccgcccccacctcagcccccacctccgccccctcct +cagcccccacctcagcccccacctcagcccccacctccacccccacctcagcccccacct +cagcccccacctcccccccacctccgccccctcctcagcccccacctctgcccctcctca +ggccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctca +gcccccacctccgcccctcctcagcccccacctcagcccccacctccacccccacctcag +cccccacctccgcccccacctcagcccccacctccgcccctcctcagcccccacctcagc +ccccacctccgcccctcctctgcccccacctcagccccctcctcagcccccacctctgcc +cctcctcagcccccacctcagcccccacctccgcccccacctcagcccccacctcagccc +ccacctccccccctcctcagcccccacctccacccccacctcagcccccacctccgcccc +tcctcagcccccacctcagcccccacctccacccccacctcagcccccacctccgccccc +acctccgcccctcctcagcccccacctccgcccccacctcagcccctcctcagcccccac +ctccgcccctcctcagcccccacctcagcccccacctccgcccctcctcagcccccacct +cagcccccacctccacccccacctcagcccccacctcagcccccacctcccccccacctc +cgccccctcctcagcccccacctctgcccctcctcaggccccacctcagcccccacctca +gccccctcctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcag +cccccacctcagcccccacctccacccccacctcagcccccacctccgcccccacctcag +cccccacctccgcccctcctcagcccccacctcagcccccacctccgcccctcctctgcc +cccacctcagccccctcctcagcccccacctctgcccctcctcagcccccacctcagccc +ccacctccgcccccacctcagcccccacctcagcccccacctccccccctcctcagcccc +cacctccacccccacctcagcccccacctccgcccctcctcagcccccacctcagccccc +acctccacccccacctcagcccccacctcagcccccacctccgcccctcctcagccccca +cctccgcccccacctcagcccctcctcagcccccacctccgcccctcctcagcccccacc +tccgcccccacctcagccccctcctccgcccctcctcagcccccacctccacccccacct +cagcccccacctcagccccctcctcagcccccacctccgcccctcctcagcccccacctc +agcccccacctcagcccccacctccgccccctcctcagcccccacctcagcccccacctc +agccccctcctccacccctcctcagcccccacctccgcccccacctcagcccccacctcc +gcccctcctcagcccccacctccacccccacctcagcccccacctccgcccctcctcagc +ccccacctccgcccccacctcagcccccacctccccccctcctcagcccccacctccgcc +cccacctcagcccccacctccgcccctcctcagcccccacctccacccccacctcagccc 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+ccctcctcagcccccacctccgcccccacctccgcccccacctcagccccacctcagccc +ctcctcagcccccacctcagcccctcctcagcccccacctcagcccctcctcagccccca +cctcagcccccacctccgcccccacctccgcccccacctccgcccccacctcagcccctc +ctcagcccccacctcagcccccacctcagccccctcctcagcccccacctccgcccccac +ctcagcccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacct +ccgcccccacctccgcccccacctcagcccctcctcagcccccacctcagcccccacctc +agccccctcctcagcccccacctccgcccccacctccgcccccacctcagccccacctca +gcccctcctcagcccccacctcagcccctcctcagccccctcctcagcccccacctcagc +ccccacctcagcccccacctccgcccccacctccgcccccacctcagccccctcctcagc +cccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacctccgcc +cccacctcaga-----------ccctcctcagcccctcctcatcccctcctcagcagctg +ctggaatgggctaccctcaggagttggcaccccacaggctccttcccttcccacctccgc +cacaccctgacgagggaaaaatggggagctgctgggagggaacttgcaccctgttgggcg +ccttgt +>p:HG002_2_chr20:63167287-63167728 +aatggccagcccgtcccgccgaggccagtggacatgccaaatccctcccgcaacaagttg +ctatccatcccctcgactaatacttaccaaattaattccagatttggagtcactcacggt +tcccaccagcactcagccccatctcagcccccatctcagcccccaccgcagcctcacctc +agtgcccacctcagccccctcctcagcccccacctccgcccccacctcagcccct----- +-------------------cctcagcccccacctcagccccctcctcagcccccacctcc +-----------------------gcccccacctccgcccccacctctgcccct------- +------cctcagcccccacctcagccccctcctcagcccccacctccgcccccacctccg +cccccacctctgcccct-------------------------------------cctcag +cccccacctcagccccctcctcagcccccacctccgcccccacctccgcccccacctctg +cccctcctcagcccccacctcagccccctcctcag-----------cccccacctccgcc +ccctcctcagcccccacctctgcccct------------cctcagcccccacctcagccc +cctcctcagcccccacctccgcccccacctccgcccccacctccgcccctcctccgcccc +cacctcagcccccacctcc-----------------------gccccctcctcagccccc +acctctgcccctcctcagcccccacctcagcccccacctcagcccccacctc-------- +------------------------------------------------------------ +----------------------------ccccctcctcagcccccacctcagcccccacc +tcagccccctcctcagcccccacctcagcccccacctccgcccct------------cct +cagcccccacctccgcccccacctcagcccccacctcagcccccacctccgcccccacct +cagcccccacctccgcccccacctcagcccccacctccgcccccacctcagcccccacct +ctgcccctcctcagcccccacctccgccccctcctcagcccccacctctg---------- +--------------------------cccctcctcagcccccacctcagcccccacctca +gcccccacctcc-cccctcctcagcccccacctcagcccccacctcagccccctcctcag +cccccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacctcagc +ccccacctccgcccctcctcagcccccacctcag-------------------------- +------------------------------------------------------------ +--------ccccctcctcagcccccacctccgcccccacctccgcccccacctctgcccc +tcctcagcccccacctcagccccctcctcagcccccacctccgcccccacctccgccccc +acctccgcccctcctccgcccccacctcagcccccacctccgccccct------------ +----------------------cctcagcccccacctctgcccctcctcagcccccacct +cagcccccacctcagcccccacct-------------------------cccccctcctc +agcccccacctcagcccccacctccgcccctcctcagcccccacctccgccccca----- +------------------------------------------------------cctcag +cccccacctcagcccccacctccgcccccacctcagcccccacctccgcccccacctcag +cccccacctcc-----------gcccccacctcagcccccacctctgcccctcctcagcc +cccacctccgccccctcctcagcccccacctctgcccctcctcagcccccacctcagccc +ccacctcagcccccacct-------------------------cccccctcctcagcccc +ca-----------------------------------cctcagcccccacctcagccccc +tcctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagccccca +-----------------------cctcagcccccacctccgcccctcctccgcccccacc +tcagccccctcctcagcccccacctctgcccctcctcagcccccacctcagcccccacct +ccgcccccacctcagccccctcctcagcccccacctc----------------------- +--------------ccccctcctccgcccccacctcagcccccacctcagcccccacctc +agcccccacctc------------------------------------------------ +-----------------------------------------------------------c +cccctcctccgcccccacctcagccccca-----------cctcagcccccacctccgcc +cccacctcagcccccacctcc--------------------------------------- +------------------------------------------------------------ +-------cccctcctcagcccccacctcagcccccacctccgccccca-----------c +ctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacc +tccgcccccacctcagcccccacctcagcccccacctccgccccca-------------- +-------------------------------------------------------cctca +gcccccacctccgcccccacctcagcccccacctccgcccccacctcagcccccacctcc +gcccccacctccgcccccacctcc-----------gcccccacctcagcccccacctcag +cccccacctccgccccca------------------------------------------ +----cctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagccc +ccacctcagcccctcctcagcccccacctcagcccccacctcagcccccacctcagcccc +t-------------------------cctcagcccccacctcagccccctcctcagcccc +ctcctcagcccccacctcagcccccacctccgcccccacctccgcccccacctcagcccc +acctcagcccctcctcagcccccacctcagccc--------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------cctcagccccca +cctcagcccccacctccgcccccacctccgcccccacctcc------------------- +------------------------------------------------------------ +----gcccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacct +cc---------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----------acccccacctccgtccccacctccgccccctcctcagccccctcctcagc +ccccacctcagcccccacctccgcccccacctcagcccctcctcagcccccacctctgcc +cccacctcagaccctcctcagcccctcctcagcccctcctcatcccctcctcagcagctg +ctggaatgggctaccctcaggagttggcaccccacaggctccttcccttcccacctccgc +cacaccctgacgagggaaaaatggggagctgctgggagggaacttgcaccctgttgggcg +ccttgt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/msa.fa.fai new file mode 100644 index 00000000..d1f0d1aa --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63167287_63167728 4506 29 60 61 +syndip_1_chr20:63167287-63167728 4506 4645 60 61 +syndip_2_chr20:63167287-63167728 4506 9261 60 61 +p:HG002_1_chr20:63167287-63167728 4506 13878 60 61 +p:HG002_2_chr20:63167287-63167728 4506 18495 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/output.vcf.gz new file mode 100644 index 00000000..13eb2914 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/output.vcf.gz.tbi new file mode 100644 index 00000000..890e183c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63167387-63167628/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/base.vcf.gz new file mode 100644 index 00000000..9ac2e013 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/base.vcf.gz.tbi new file mode 100644 index 00000000..78c50a00 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/comp.vcf.gz new file mode 100644 index 00000000..ffec51c5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/comp.vcf.gz.tbi new file mode 100644 index 00000000..d5517d51 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/haps.fa new file mode 100644 index 00000000..835c08c2 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/haps.fa @@ -0,0 +1,58 @@ +>ref_chr20_63221380_63221977 +TCCCACTGCAGAGAACTGTCATCTGCCTGTAAGTACCAGTGCCAGGTGCTCTGGGGCCGATGTCTCCGTTAGCCCCAAGGTGGAGGCTCAGGGAGCAGATGTGAGCGTGCCTTGCTCATCGCAGTAGCTTCGGACTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGACTGCATTGCTCTTGCAGCACCACCCGCCTCCGTGGACACCTTCAGCAGTGAGACAATGCAGGCTCTGCTACAAGAGGTGCTTACTGGGCTCTGCTCTGGTGAGGAGAGGCCTCGCCTGGCAGCCAGACAGAGTCCCAGCAGGGCAAGATGAAAATTCGGGGCCCTCGTTCAAACAGCAAGAGAAGGCTCTTTCCTTCCTTCCAGCGCCCCTCCCTGCACCT +>syndip_1_chr20:63221380-63221977 +TCCCACTGCAGAGAACTGTCATCTGCCTGTAAGTACCAGTGCCAGGTGCTCTGGGGCCGA +TGTCTCCGTTAGCCCCAAGGTGGAGGCTCAGGGAGCAGATGTGAGCGTGCCTTGCTCATC +GCAGTAGCTTCGGACTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGAC +TGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGACTGCATT +GCTCTTGCAGCACCACCCGCCTCCGTGGACACCTTCAGCAGTGAGACAATGCAGGCTCTG +CTACAAGAGGTGCTTACTGGGCTCTGCTCTGGTGAGGAGAGGCCTCGCCTGGCAGCCAGA +CAGAGTCCCAGCAGGGCAAGATGAAAATTCGGGGCCCTCGTTCAAACAGCAAGAGAAGGC +TCTTTCCTTCCTTCCAGCGCCCCTCCCTGCACCT +>syndip_2_chr20:63221380-63221977 +TCCCACTGCAGAGAACTGTCATCTGCCTGTAAGTACCAGTGCCAGGTGCTCTGGGGCCGA +TGTCTCCGTTAGCCCCAAGGTGGAGGCTCAGGGAGCAGATGTGAGCGTGCCTTGCTCATC +GCAGTAGCTTCGGACTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGAG +TGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGG +GACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGATTGC +AGGGATTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGAC +TGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGG +GATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGC +AGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGAC +TGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGG +GACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGC +AGGGATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGAT +TGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGG +GATTGCAGGGACTGCAGGGCCTGCATTGCTCTTGCAGCACCACCCGCCTCCGTGGACACC +TTCAGCAGTGAGACAATGCAGGCTCTGCTACAAGAGGTGCTTACTGGGCTCTGCTCTGGT +GAGGAGAGGCCTCGCCTGGCAGCCAGACAGAGTCCCAGCAGGGCAAGATGAAAATTCGGG +GCCCTCGTTCAAACAGCAAGAGAAGGCTCTTTCCTTCCTTCCAGCGCCCCTCCCTGCACC +T +>p:HG002_1_chr20:63221380-63221977 +TCCCACTGCAGAGAACTGTCATCTGCCTGTAAGTACCAGTGCCAGGTGCTCTGGGGCCGA +TGTCTCCGTTAGCCCCAAGGTGGAGGCTCAGGGAGCAGATGTGAGCGTGCCTTGCTCATC +GCAGTAGCTTCGGACTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGAG +TGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGG +GACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGATTGC +AGGGATTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGAC +TGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGG +GATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGC +AGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGAC +TGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGG +GACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGC +AGGGATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGAT +TGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGG +GATTGCAGGGACTGCAGGGCCTGCATTGCTCTTGCAGCACCACCCGCCTCCGTGGCCACC +TTCAGCAGTGAGACAATGCAGGCTCTGCTACAAGAGGTGCTTACTGGGCTCTGCTCTGGT +GAGGAGAGGCCTCGCCTGGCAGCCAGACAGAGTCCCAGCAGGGCAAGATGAAAATTCGGG +GCCCTCGTTCAAACAGCAAGAGAAGGCTCTTTCCTTCCTTCCAGCGCCCCTCCCTGCACC +T +>p:HG002_2_chr20:63221380-63221977 +TCCCACTGCAGAGAACTGTCATCTGCCTGTAAGTACCAGTGCCAGGTGCTCTGGGGCCGA +TGTCTCCGTTAGCCCCAAGGTGGAGGCTCAGGGAGCAGATGTGAGCGTGCCTTGCTCATC +GCAGTAGCTTCGGACTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGAC +TGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGACTGCATT +GCTCTTGCAGCACCACCCGCCTCCGTGGCCACCTTCAGCAGTGAGACAATGCAGGCTCTG +CTACAAGAGGTGCTTACTGGGCTCTGCTCTGGTGAGGAGAGGCCTCGCCTGGCAGCCAGA +CAGAGTCCCAGCAGGGCAAGATGAAAATTCGGGGCCCTCGTTCAAACAGCAAGAGAAGGC +TCTTTCCTTCCTTCCAGCGCCCCTCCCTGCACCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/haps.fa.ref.fa new file mode 100644 index 00000000..39d1febb --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63221380-63221977 +TCCCACTGCAGAGAACTGTCATCTGCCTGTAAGTACCAGTGCCAGGTGCTCTGGGGCCGATGTCTCCGTTAGCCCCAAGGTGGAGGCTCAGGGAGCAGATGTGAGCGTGCCTTGCTCATCGCAGTAGCTTCGGACTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGACTGCATTGCTCTTGCAGCACCACCCGCCTCCGTGGACACCTTCAGCAGTGAGACAATGCAGGCTCTGCTACAAGAGGTGCTTACTGGGCTCTGCTCTGGTGAGGAGAGGCCTCGCCTGGCAGCCAGACAGAGTCCCAGCAGGGCAAGATGAAAATTCGGGGCCCTCGTTCAAACAGCAAGAGAAGGCTCTTTCCTTCCTTCCAGCGCCCCTCCCTGCACCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/msa.fa new file mode 100644 index 00000000..f36fac39 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/msa.fa @@ -0,0 +1,95 @@ +>ref_chr20_63221380_63221977 +tcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccga +tgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcatc +gcagtagcttc------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------ggactgcagggattgcagggactgcagggattgcagggattgcagg +gattgcagggactgcagggattgcagggactgcagggactgcagggactgcagggactgc +agggactgcagggattgcagggattgcagggattgcagggactgcagggattgcagggac +tgcagggactgcagggattgcagggactgcagggactgcagggactgcagggattgcagg +gattgcagggactgcagggactgcattgctcttgcagcaccacccgcctccgtggacacc +ttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctggt +gaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcggg +gccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcacc +t +>syndip_1_chr20:63221380-63221977 +tcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccga +tgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcatc +gcagtagcttc------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------ggactgcagggactgcagggat +tgcagggactgcagggattgcagggactgcagggattgcagggattgcagggattgcagg +gattgcagggactgcagggactgcattgctcttgcagcaccacccgcctccgtggacacc +ttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctggt +gaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcggg +gccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcacc +t +>syndip_2_chr20:63221380-63221977 +tcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccga +tgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcatc +gcagtagcttcggactgcagggattgcagggactgcagggattgcagggattgcagggag +tgcagggactgcagggactgcagggattgcagggactgcagggactgcagggactgcagg +gactgcagggactgcagggactgcagggattgcagggactgcagggactgcagggattgc +agggattgcagggactgcagggactgcagggattgcagggactgcagggactgcagggac +tgcagggactgcagggactgcagggactgcagggattgcagggattgcagggattgcagg +gattgcagggactgcagggactgcagggactgcagggactgcagggactgcagggactgc +agggattgcagggattgcagggattgcagggattgcagggattgcagggactgcagggac +tgcagggactgcagggactgcagggattgcagggattgcagggattgcagggattgcagg +gactgcagggactgcagggattgcagggattgcagggattgcagggattgcagggattgc +agggattgcagggactgcagggactgcagggactgcagggattgcagggattgcagggat +tgcagggattgcagggactgcagggactgcagggattgcagggattgcagggattgcagg +gattgcagggactgcagggcctgcattgctcttgcagcaccacccgcctccgtggacacc +ttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctggt +gaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcggg +gccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcacc +t +>p:HG002_1_chr20:63221380-63221977 +tcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccga +tgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcatc +gcagtagcttcggactgcagggattgcagggactgcagggattgcagggattgcagggag +tgcagggactgcagggactgcagggattgcagggactgcagggactgcagggactgcagg +gactgcagggactgcagggactgcagggattgcagggactgcagggactgcagggattgc +agggattgcagggactgcagggactgcagggattgcagggactgcagggactgcagggac +tgcagggactgcagggactgcagggactgcagggattgcagggattgcagggattgcagg +gattgcagggactgcagggactgcagggactgcagggactgcagggactgcagggactgc +agggattgcagggattgcagggattgcagggattgcagggattgcagggactgcagggac +tgcagggactgcagggactgcagggattgcagggattgcagggattgcagggattgcagg +gactgcagggactgcagggattgcagggattgcagggattgcagggattgcagggattgc +agggattgcagggactgcagggactgcagggactgcagggattgcagggattgcagggat +tgcagggattgcagggactgcagggactgcagggattgcagggattgcagggattgcagg +gattgcagggactgcagggcctgcattgctcttgcagcaccacccgcctccgtggccacc +ttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctggt +gaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcggg +gccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcacc +t +>p:HG002_2_chr20:63221380-63221977 +tcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccga +tgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcatc +gcagtagcttc------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------ggactgcagggactgcagggat +tgcagggactgcagggattgcagggactgcagggattgcagggattgcagggattgcagg +gattgcagggactgcagggactgcattgctcttgcagcaccacccgcctccgtggccacc +ttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctggt +gaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcggg +gccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcacc +t diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/msa.fa.fai new file mode 100644 index 00000000..8fe1fa2d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63221380_63221977 1021 29 60 61 +syndip_1_chr20:63221380-63221977 1021 1102 60 61 +syndip_2_chr20:63221380-63221977 1021 2175 60 61 +p:HG002_1_chr20:63221380-63221977 1021 3249 60 61 +p:HG002_2_chr20:63221380-63221977 1021 4323 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/output.vcf.gz new file mode 100644 index 00000000..3b7288da Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/output.vcf.gz.tbi new file mode 100644 index 00000000..f26a52e9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63221480-63221877/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/base.vcf.gz new file mode 100644 index 00000000..bddd1ed8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/base.vcf.gz.tbi new file mode 100644 index 00000000..034660c3 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/comp.vcf.gz new file mode 100644 index 00000000..3f74e33a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/comp.vcf.gz.tbi new file mode 100644 index 00000000..6a1d7d88 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/haps.fa new file mode 100644 index 00000000..4c226b02 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/haps.fa @@ -0,0 +1,52 @@ +>ref_chr20_63371965_63372792 +GGTCAGGTGAAGACTCTATTCCTGGCTCAGGAAAACCACCAGGACAGGTGAGCCCAGCAGCATCTCGTGGAGGGAGGCTCTGAGTCCCGTGAGGACAAGGACGGAACACCGGGGCTGCCACAGGTCGCAGAGACCCTGTGTCAACACCCTTGTTTTGAGGTGCAGAGACCAAAGTTGAGACCTGGCCATGCAGCAGGTCTGCAGGGACCTCAGAGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAATGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGGCCTGTCCCCAGCCCCATTAAATGCCCAGGGCCACTGTCCTGTCCCCAGTCTCATTAAACGCAGCAAACGTCTTCTGGACGTGCCGCCAGTCCCACAGAAAACCAAAGCAAGGCAGACTCACCGCTCCTGCATCCCGGAGCTCAGGTCCAGGAGGGTCTCGGGAAAGGATGGGGGCAACTGGAGTACCATCCT +>syndip_1_chr20:63371965-63372792 +GGTCAGGTGAAGACTCTATTCCTGGCTCAGGAAAACCACCAGGACAGGTGAGCCCAGCAG +CATCTCGTGGAGGGAGGCTCTGAGTCCCGTGAGGACAAGGACGGAACACCGGGGCTGCCA +CAGGTCGCAGAGACCCTGTGTCAACACCCTTGTTTTGAGGTGCAGAGACCAAAGTTGAGA +CCTGGCCATGCAGCAGGTCTGCAGGGACCTCAGAGCCCAGGGCCACTGTCCTGTCCCCAG +CCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCAC +TGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAA +ACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGGCCTGTC +CCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGG +GCCACTGGCCTGTCCCCAGCCCCATTAAATGCCCAGGGCCACTGTCCTGTCCCCAGTCTC +ATTAAACGCAGCAAACGTCTTCTGGACGTGCCGCCAGTCCCACAGAAAACCAAAGCAAGG +CAGACTCACCGCTCCTGCATCCCGGAGCTCAGGTCCAGGAGGGTCTCGGGAAAGGATGGG +GGCAACTGGAGTACCATCCT +>syndip_2_chr20:63371965-63372792 +GGTCAGGTGAAGACTCTATTCCTGGCTCAGGAAAACCACCAGGACAGGTGAGCCCAGCAG +CATCTCGTGGAGGGAGGCTCTGAGTCCCGTGAGGACAAGGACGGAACACCGGGGCTGCCA +CAGGTCGCAGAGACCCTGTGTCAACACCCTTGTTTTGAGGTGCAGAGACCAAAGTTGAGA +CCTGGCCATGCAGCAGGTCTGCAGGGACCTCAGAGCCCAGGGCCACTGTCCTGTCCCCAG +CCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCAC +TGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAA +ACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTC +CCCAGCCCCATTAAACGCCCAGGGCCACTGGCCTGTCCCCAGCCCCATTAAATGCCCAGG +GCCACTGTCCTGTCCCCAGTCTCATTAAACGCAGCAAACGTCTTCTGGACGTGCCGCCAG +TCCCACAGAAAACCAAAGCAAGGCAGACTCACCGCTCCTGCATCCCGGAGCTCAGGTCCA +GGAGGGTCTCGGGAAAGGATGGGGGCAACTGGAGTACCATCCT +>p:HG002_1_chr20:63371965-63372792 +GGTCAGGTGAAGACTCTATTCCTGGCTCAGGAAAACCACCAGGACAGGTGAGCCCAGCAG +CATCTCGTGGAGGGAGGCTCTGAGTCCCGTGAGGACAAGGACGGAACACCGGGGCTGCCA +CAGGTCGCAGAGACCCTGTGTCAACACCCTTGTTTTGAGGTGCAGAGACCAAAGTTGAGA +CCTGGCCATGCAGCAGGTCTGCAGGGACCTCAGAGCCCAGGGCCACTGTCCTGTCCCCAG +CCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCAC +TGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAA +ACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTC +CCCAGCCCCATTAAACGCCCAGGGCCACTGGCCTGTCCCCAGCCCCATTAAATGCCCAGG +GCCACTGTCCTGTCCCCAGTCTCATTAAACGCAGCAAACGTCTTCTGGACGTGCCGCCAG +TCCCACAGAAAACCAAAGCAAGGCAGACTCACCGCTCCTGCATCCCGGAGCTCAGGTCCA +GGAGGGTCTCGGGAAAGGATGGGGGCAACTGGAGTACCATCCT +>p:HG002_2_chr20:63371965-63372792 +GGTCAGGTGAAGACTCTATTCCTGGCTCAGGAAAACCACCAGGACAGGTGAGCCCAGCAG +CATCTCGTGGAGGGAGGCTCTGAGTCCCGTGAGGACAAGGACGGAACACCGGGGCTGCCA +CAGGTCGCAGAGACCCTGTGTCAACACCCTTGTTTTGAGGTGCAGAGACCAAAGTTGAGA +CCTGGCCATGCAGCAGGTCTGCAGGGACCTCAGAGCCCAGGGCCACTGTCCTGTCCCCAG +CCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCAC +TGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAA +ACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGGCCTGTC +CCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGG +GCCACTGGCCTGTCCCCAGCCCCATTAAATGCCCAGGGCCACTGTCCTGTCCCCAGTCTC +ATTAAACGCAGCAAACGTCTTCTGGACGTGCCGCCAGTCCCACAGAAAACCAAAGCAAGG +CAGACTCACCGCTCCTGCATCCCGGAGCTCAGGTCCAGGAGGGTCTCGGGAAAGGATGGG +GGCAACTGGAGTACCATCCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/haps.fa.ref.fa new file mode 100644 index 00000000..8f3869fe --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63371965-63372792 +GGTCAGGTGAAGACTCTATTCCTGGCTCAGGAAAACCACCAGGACAGGTGAGCCCAGCAGCATCTCGTGGAGGGAGGCTCTGAGTCCCGTGAGGACAAGGACGGAACACCGGGGCTGCCACAGGTCGCAGAGACCCTGTGTCAACACCCTTGTTTTGAGGTGCAGAGACCAAAGTTGAGACCTGGCCATGCAGCAGGTCTGCAGGGACCTCAGAGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAATGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGTCCTGTCCCCAGCCCCATTAAACGCCCAGGGCCACTGGCCTGTCCCCAGCCCCATTAAATGCCCAGGGCCACTGTCCTGTCCCCAGTCTCATTAAACGCAGCAAACGTCTTCTGGACGTGCCGCCAGTCCCACAGAAAACCAAAGCAAGGCAGACTCACCGCTCCTGCATCCCGGAGCTCAGGTCCAGGAGGGTCTCGGGAAAGGATGGGGGCAACTGGAGTACCATCCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/msa.fa new file mode 100644 index 00000000..2e53b81d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/msa.fa @@ -0,0 +1,75 @@ +>ref_chr20_63371965_63372792 +ggtcaggtgaagactctattcctggctcaggaaaaccaccaggacaggtgagcccagcag +catctcgtggagggaggctctgagtcccgtgaggacaaggacggaacaccggggctgcca +caggtcgcagagaccctgtgtcaacacccttgttttgaggtgcagagaccaaagttgaga +cctggccatgcagcaggtctgcagggacctcagagcccagggccactgtcctgtccccag +ccccattaaacgcccagggccactgtcctgtccccagccccattaaacgcccagggccac +tgtcctgtccccagccccattaaacgcccagggccactgtcctgtccccagccccattaa +acgcccagggccactgtcctgtccccagccccattaaacgcccagggccactgtcctgtc +cccagccccattaaatgcccagggccactgtcctgtccccagccccattaaacgcccagg +gccactgtcctgtccccagccccattaaacgcccagggccactgtcctgtccccagcccc +attaaacgcccagggccactgtcctgtccccagccccattaaacgcccagggccactgtc +ctgtccccagccccattaaacgcccagggccactggcctgtccccagccccattaaatgc +ccagggccactgtcctgtccccagtctcattaaacgcagcaaacgtcttctggacgtgcc +gccagtcccacagaaaaccaaagcaaggcagactcaccgctcctgcatcccggagctcag +gtccaggagggtctcgggaaaggatgggggcaactggagtaccatcct +>syndip_1_chr20:63371965-63372792 +ggtcaggtgaagactctattcctggctcaggaaaaccaccaggacaggtgagcccagcag +catctcgtggagggaggctctgagtcccgtgaggacaaggacggaacaccggggctgcca +caggtcgcagagaccctgtgtcaacacccttgttttgaggtgcagagaccaaagttgaga +cctggccatgcagcaggtctgcagggacctcagagcccagggccactgtcctgtccccag +ccccattaaacgcccagggccactgtcctgtccccagccccattaaac------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------gcccagggccactgtcctgtccccagccccattaaacgcccagg +gccactgtcctgtccccagccccattaaacgcccagggccactgtcctgtccccagcccc +attaaacgcccagggccactggcctgtccccagccccattaaacgcccagggccactgtc +ctgtccccagccccattaaacgcccagggccactggcctgtccccagccccattaaatgc +ccagggccactgtcctgtccccagtctcattaaacgcagcaaacgtcttctggacgtgcc +gccagtcccacagaaaaccaaagcaaggcagactcaccgctcctgcatcccggagctcag +gtccaggagggtctcgggaaaggatgggggcaactggagtaccatcct +>syndip_2_chr20:63371965-63372792 +ggtcaggtgaagactctattcctggctcaggaaaaccaccaggacaggtgagcccagcag +catctcgtggagggaggctctgagtcccgtgaggacaaggacggaacaccggggctgcca +caggtcgcagagaccctgtgtcaacacccttgttttgaggtgcagagaccaaagttgaga +cctggccatgcagcaggtctgcagggacctcagagcccagggccactgtcctgtccccag +ccccattaaacgcccagggccactgtcctgtccccagccccattaaac------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------gcccagggccactgtcctgtccccagccccattaaacgcccagg +gccactgtcctgtccccagccccattaaacgcccagggccactgt--------------- +----------------------cctgtccccagccccattaaacgcccagggccactgtc +ctgtccccagccccattaaacgcccagggccactggcctgtccccagccccattaaatgc +ccagggccactgtcctgtccccagtctcattaaacgcagcaaacgtcttctggacgtgcc +gccagtcccacagaaaaccaaagcaaggcagactcaccgctcctgcatcccggagctcag +gtccaggagggtctcgggaaaggatgggggcaactggagtaccatcct +>p:HG002_1_chr20:63371965-63372792 +ggtcaggtgaagactctattcctggctcaggaaaaccaccaggacaggtgagcccagcag +catctcgtggagggaggctctgagtcccgtgaggacaaggacggaacaccggggctgcca +caggtcgcagagaccctgtgtcaacacccttgttttgaggtgcagagaccaaagttgaga +cctggccatgcagcaggtctgcagggacctcagagcccagggccactgtcctgtccccag +ccccattaaacgcccagggccactgtcctgtccccagccccattaaac------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------gcccagggccactgtcctgtccccagccccattaaacgcccagg +gccactgtcctgtccccagccccattaaacgcccagggccactgt--------------- +----------------------cctgtccccagccccattaaacgcccagggccactgtc +ctgtccccagccccattaaacgcccagggccactggcctgtccccagccccattaaatgc +ccagggccactgtcctgtccccagtctcattaaacgcagcaaacgtcttctggacgtgcc +gccagtcccacagaaaaccaaagcaaggcagactcaccgctcctgcatcccggagctcag +gtccaggagggtctcgggaaaggatgggggcaactggagtaccatcct +>p:HG002_2_chr20:63371965-63372792 +ggtcaggtgaagactctattcctggctcaggaaaaccaccaggacaggtgagcccagcag +catctcgtggagggaggctctgagtcccgtgaggacaaggacggaacaccggggctgcca +caggtcgcagagaccctgtgtcaacacccttgttttgaggtgcagagaccaaagttgaga +cctggccatgcagcaggtctgcagggacctcagagcccagggccactgtcctgtccccag +ccccattaaacgcccagggccactgtcctgtccccagccccattaaac------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------gcccagggccactgtcctgtccccagccccattaaacgcccagg +gccactgtcctgtccccagccccattaaacgcccagggccactgtcctgtccccagcccc +attaaacgcccagggccactggcctgtccccagccccattaaacgcccagggccactgtc +ctgtccccagccccattaaacgcccagggccactggcctgtccccagccccattaaatgc +ccagggccactgtcctgtccccagtctcattaaacgcagcaaacgtcttctggacgtgcc +gccagtcccacagaaaaccaaagcaaggcagactcaccgctcctgcatcccggagctcag +gtccaggagggtctcgggaaaggatgggggcaactggagtaccatcct diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/msa.fa.fai new file mode 100644 index 00000000..77c587a5 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63371965_63372792 828 29 60 61 +syndip_1_chr20:63371965-63372792 828 905 60 61 +syndip_2_chr20:63371965-63372792 828 1781 60 61 +p:HG002_1_chr20:63371965-63372792 828 2658 60 61 +p:HG002_2_chr20:63371965-63372792 828 3535 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/output.vcf.gz new file mode 100644 index 00000000..a9e2f8c5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/output.vcf.gz.tbi new file mode 100644 index 00000000..d71f90ec Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63372065-63372692/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/base.vcf.gz new file mode 100644 index 00000000..5867e3ed Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/base.vcf.gz.tbi new file mode 100644 index 00000000..0a187dd0 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/comp.vcf.gz new file mode 100644 index 00000000..b5430fad Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/comp.vcf.gz.tbi new file mode 100644 index 00000000..ac41102c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/haps.fa new file mode 100644 index 00000000..f5fce746 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/haps.fa @@ -0,0 +1,204 @@ +>ref_chr20_63491489_63493165 +GTGAGCATGATGCCCCCACAGTGCACACAGAGATGCCTGCAACATCTTTGGCTGCAGCCCACTGGCTGGGGGTCTCCTATCAGTGCCCTTCTCTAGGGTCTCAGATTTGTTTATGGTTTCTCTTCTTGGTGGGATGGATGGATGGATGGACGGATGGATGGGGAGGTGGGTGGATGGATGGATGGATGTATGAATGGGGTGGTAGATGGATGGGGAGGTGGATGGACAGAAGGATGGGTGGGGAGATGGATGAGTAGGGAGATGGATGGATGGATTGGTGGATGGATGGATGGATGGATGGATGAGGAGGTAGATGAGTGGATGGACAGAAGGATGGATGGGTAGGAAGGTGGGTGGATGAATGGATGGATGGGGAGGTGGATGGATAGATGGATGGATGGATGGATGGATGGATGGATGGATGGGGGGATAGATGGATGGATGGATGGATGGACGGACGGATGGGGAGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGAGGAGATGAACGGATGGATGAGATGGATGGATGGATGATGGAGGGAAGGATGGCTGGGTGGGGAGATGGATGGATAGAGAGGTGGATGGGTGGATGGGGAGATGGATGGATGGATGGATGGATGGGGAAGTGGATGGATGGGGAGGTGGATGGATGGATGTATGGGTGGGTAGGTGGGTGGATAGATGGATGGATGGATGGATGGATAAATGGATGGATGGAAGGATGGATGGATAGGTAGGTGGGTGGATGGATGGATGGATGGATGTACAGAAGGATGGATGGGTGGGTAGGTGGGTGAGTGGATGAATGGATGGATGGATAGATAGAAGGATGGATGGGTGGGTCAATAGATGGATGGATAGAGAGAAGGATGGATGGGTGGGTAGATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGTTGAGACAATGGATGGATGGATGGATGGATGGAGAGATGGATGGATGGATGGATGGACAGAAGGATGGATGGGTGGGGAGGTGGATGGATGGATGGAAGGATGGATGGATGGATAGAGAGAAGGATGGATGGGTGGGACAATGGATGGATGGATGCATGGATGGATGGATGGAGGGATAGAGAGAAGGATGGATGGGTGGGACAATCAATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGGTGGGGAGATGGATGGATGGATGGAGAGGTGGATGGATGGATGGATGGATGGATTGATGGACAGAAGGATGGATGGGTGGGGAGGTGGATAGATGGAGAGATGGAGGGATGGTTCGATAGAGAGAAGGATGGATGGGACAATGGATGGATGGATGGATGGAGTGAAGGATGGATGGGTGGGGAGATGGATGGATCGATGGATGGATGGATGGATAGATAGATGGATGGAGAGGTGGATAGATGGATGGGTGGATGGATGGACAGAGGATGGATGGGTGGGGAGGTGGGTGGATGGATGGATGGATGTGGGATGGACTGTCCCACAGAAAGTGTGTGGTAAGGGGAGAGATTGGAGACAGCCCAGTCTTGAGATGCCTTGTAGGGGCCCCTGGTCTAGGGCAGGCAGAGCTGGCCAGGCAGGAGCTCCAGCACAGCGCCCTTGCTCACCGCCAATCTTGTACACGTCCTGCAGCGGC +>syndip_1_chr20:63491489-63493165 +GTGAGCATGATGCCCCCACAGTGCACACAGAGATGCCTGCAACATCTTTGGCTGCAGCCC +ACTGGCTGGGGGTCTCCTATCAGTGCCCTTCTCTAGGGTCTCAGATTTGTTTATGGTTTC +TCTTCTTGGTGGGATGGATGGATGGATGGACGGATGGATGGGGAGGTGGGTGGATGGATG +GATGGATGTATGAATGGGGTGGTAGATGGATGGGGAGGTGGATGGACAGAAGGATGGGTG +GGGAGATGGATGAGTAGGGAGATGGATGGATGGATTGGTGGATGGATGGATGGATGGATG +GATGAGGAGGTAGATGAGTGGATGGACAGAAGGATGGATGGGTAGGAAGGTGGGTGGATG +AATGGATGGATGGGGAGGTGGATGGATAGATGGATGGATGGATGGATGGATGGATGGATG +GATGGATGGGGGGATAGATGGATGGATGGATGGATGGATGGACGGACGGATGGGGAGGTG +GATGGATGGATGGATGGATGGATGGATGGATGGATGAGGAGATGAATGGATGGATGAGAT +GGATGGATGGATGATGGAGGGAAGGATGGCTGGGTGGGGAGATGGATGGATAGAGAGGTG +GATGGGTGGATGGGGAGATGGATGGATGGATGGATGGATGGGGAAGTGGATGGATGGGGA +GGTGGATGGATGGATAGGTGGATGGGTGGATGGACAGAAGGATGAATGGGTAGGGAGATG +GATGGATGGATGGATGGGGAGGGATGGATGGATGGATGGATGGATGGGTGGATGGATAGA +AGGATGGATGGGTGGGGAGGTGGGTGGGTGGGTGGATGGATGGAGAGATGGATAGATGGA +TAGATGGATGGATGGATGGATGGATGGAGAGAAGGATGGATGGGTGGGGAGGTGGGTGGG +TGGGTGGATGGGTGGATGGATGGATGGGTGGGGAGGTGGGCGGGTGGATGGATGGATGGA +TGCAGAGGTGGGTGGATGGATGGATGGAGAGAAGGATGGATGGGTGGGGAGGTGGGTGGG +TGGATGGATGGATGAGTGGGGAGGTGGGTGGGTGGGTGGATGGATGGATGGATGGATGCA +TGGATGGATGGATGGAGAGGTGGGTGGACGGATGGATGGATTGGGAGGTGGGTAGATGGG +TGGATGGACAGAAGGATGGATGGGTGGGGAGGTGGGTGGGTGGGTGGATGGATGGATGGG +GAGGTGGATGGATGGATGGTTAGATGGGGAGGTGGGTGGATGGGTGGATGGACAGAAGGA +TGGATGGGTAGGGAGGTAGGTGAGTGGATGGATGGATGGGGAGATGGATGGATGGATAGA +GAGAAGGATGGATGGGTGGGACAATGGATGGATGGATGGATAGAAGGATGGACGGGTGGG +GAGATGGATGGATGGATGGATGGATGGATGGATGGATGGACAGAAGGATGTATGGGTGGG +GAGGTGGGTGGATAGATGGATGGATGGATGGATGGGGAAATGGATGGATGGAAGGATGGA +TGGATAGGGAGGTGGGTGGATGGATGGATGGATGGATGTACAGAAGGATGGATGGGTGGG +GAGGTGGGTGAGTGGATGAATGGATGGATGGATAGATAGAAGGATGGATGGGTGGGACAA +TAGATGGATGGATAGAGAGAAGGATGGATGGGTGGGGAGATGGATGGATGGATGGATGGA +TGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGTTGAGACAATGGATGGATGGA +TGGATGGAGAGATGGATGGATGGACGGATGGACAGAAGGATGGATGGGTGGGGAGGTGGA +TGGATGGATTGAAGGATGGATGGGTGGGGACATGGATGGATGGATGGATGGATGGATGGA +TGGATGGACAGAAGGATGTATGGGTGGGGAGGTGGGTGGATAGATGGATGGATGGGGAAA +TGGATGGATGGAAGGATGGATGGATAGGGAGGTGGGTGGATGGATGGATGGATGGATGTA +CAGAAGGATGGATGGGTGGGGAGGTGGGTGAGTGGATGAATGGATGGATGGATAGATAGA +AGGATGGATGGGTGGGACAATAGATGGATGGATAGAGAGAAGGATGGATGGGTGGGGAGA +TGGATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGTTGAGACAATGGA +TGGATGGATGGATGGATGGAGAGATGGATGGATGGATGGATGGACAGAAGGATGGATGGG +TGGGGAGGTGGATGGATGGATGGAAGGATGGATGGATGGATAGAGAGAAGGATGGATGGG +TGGGACAATGGATGGATGGATGCATGGATGGATGGATGGAGGGATAGAGAGAAGGATGGA +TGGGTGGGACAATCAATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGG +TGGGGAGATGGATGGATGGATGGAGAGGTGGATGGATGGATGGATGGATGGATTGATGGA +CAGAAGGATGGATGGGTGGGGAGGTGGATAGATGGAGAGATGGAGGGATGGTTCGATAGA +GAGAAGGATGGATGGATGGGACAATGGATGGATGGATGGATGGAGTGAAGGATGGATGGG +TGGGGAGATGGATGGATCGATGGATGGATGGATGGATAGATAGATGGATGGAGAGGTGGA +TAGATGGATGGGTGGATGGATGGACAGAGGATGGATGGGTGGGGAGGTGGGTGGATGGAT +GGATGGATGTGGGATGGACTGTCCCACAGAAAGTGTGTGGTAAGGGGAGAGATTGGAGAC +AGCCCAGTCTTGAGATGCCTTGTAGGGGCCCCTGGTCTAGGGCAGGCAGAGCTGGCCAGG +CAGGAGCTCCAGCACAGCGCCCTTGCTCACCGCCAATCTTGTACACGTCCTGCAGCGGC +>syndip_2_chr20:63491489-63493165 +GTGAGCATGATGCCCCCACAGTGCACACAGAGATGCCTGCAACATCTTTGGCTGCAGCCC +ACTGGCTGGGGGTCTCCTATCAGTGCCCTTCTCTAGGGTCTCAGATTTGTTTATGGTTTC +TCTTCTTGGTGGGATGGATGGATGGATGGACGGATGGATGGGGAGGTGGGTGGATGGATG +GATGGATGTATGAATGGGGTGGTAGATGGATGGGGAGGTGGATGGACAGAAGGATGGGTG +GGGAGATGGATGAGTAGGGAGATGGATGGATGGATTGGTGGATGGATGGATGGATGGATG +GATGAGGAGGTAGATGAGTGGATGGACAGAAGGATGGATGGGTAGGAAGGTGGGTGGATG +AATGGATGGATGGGGAGGTGGATGGATAGATGGATGGATGGATGGATGGATGGATGGATG +GATGGATGGGGGGATAGATGGATGGATGGATGGATGGACGGACGGATGGGGAGGTGGATG +GATGGATGGATGGATGGATGGATGGATGGATGGATGGATGAGGAGATGAATGGATGGATG +AGATGGATGGATGGATGATGGAGGGAAGGATGGCTGGGTGGGGAGATGGATGGATAGAGA +GGTGGATGGGTGGATGGGGAGATGGATGGATGGATGGATGGATGGGGAAGTGGATGGATG +GGGAGGTGGATGGATGGATAGGTGGATGGGTGGATGGACAGAAGGATGAATGGGTAGGGA +GATGGATGGATGGATGGATGCGGAGGGATGGATGGATGGATGGATGGATGGGTGGATGGA +TAGAAGGATGGATGGGTGGGGAGGTGGGTGGGTGGGTGCGTGGATGGATGGAGAGATGGA +TAGATGGATAGATGGATGGATGGATGGATGGATGGATGGAGAGAAGGATGGATGGGTGGG +GAGGTGGGTGGGTGGGTGGATGGGTGGATGGATGGATGGGTGGGGAGGTGGGCGGGTGGA +TGGATGGATGGATGCAGAGGTGGGTGGATGGATGGATGGAGAGAAGGATGGATGGGTGGG +GAGGTGGGTGGGTGGATGGATGGATGAGTGGGGAGGTGGGTGGGTGGATGGATGGATGGA +TGGATGCATGGATGGATGGATGGAGAGGTGGGTGGATGGGTGGATGGACAGAAGGATGGA +TGGGTGGGGAGGTGGGTGAGTGGGTGGATGGATGAATGGGGAGGTGGATGGATGGATGGA +TGGATGAAGGATGGATGGGTGGGGAGGTGGGTGGACGGATGGATGGATTGGGAGGTGGGT +AGATGGGTGGATGGACAGAAGGATGGATGGGTGGGGAGGTGGGTGGGTGGGTGGATGGAT +GGATGGGGAGGTGGATGGATGGATGGTTAGATGGGGAGGTGGGTGGATGGGTGGATGGAC +AGAAGGATGGATGGGTAGGGAGGTAGGTGAGTGGATGGATGGATGGGGAGATGGATGGAT +GGATAGAGAGAAGGATGGATGGGTGGGACAATGGATGGATGGATGGATAGAAGGATGGAC +GGGTGGGGAGATGGATGGATGGATGGATGGATGGATGGATGGACAGAAGGATGTATGGGT +GGGGAGGTGGGTGGATAGATGGATGGATGGATGGATGGGGAAATGGATGGATGGAAGGAT +GGATGGATAGGGAGGTGGGTGGATGGATGGATGGATGGATGTACAGAAGGATGGATGGGT +GGGGAGGTGGGTGAGTGGATGAATGGATGGATGGATAGATAGAAGGATGGATGGGTGGGA +CAATAGATGGATGGATAGAGAGAAGGATGGATGGGTGGGGAGATGGATGGATGGATGGAT +GGATGGATGGATGGATAGAGAGAAGGATGGATGGTTGAGACAATGGATGGATGGATGGAT +GGATGGAGAGATGGATGGATGGATGGATGGACAGAAGGATGGATGGGTGGGGAGGTGGAT +GGATGGATTGAAGGATGGACGGGTGGGGAGATGGATGGATGGATGGATGGATGGATGGAT +GGATGGATGGACAGAAGGATGTATGGGTGGGGAGGTGGGTGGATAGATGGATGGATGGAT +GGATGGGGAAATGGATGGATGGAAGGATGGATGGATAGGGAGGTGGGTGGATGGATGGAT +GGATGGATGTACAGAAGGATGGATGGGTGGGGAGGTGGGTGAGTGGATGAATGGATGGAT +GGATAGATAGAAGGATGGATGGGTGGGACAACAGATGGATAGAGAGAAGGATGGATGGGT +GGGGAGATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGTTGAGACAAT +GGATGGATGGATGGATGGATGGAGAGATGGATGGATGGATGGATGGACAGAAGGATGGAT +GGGTGGGGAGGTGGATGGATGGATGGAAGGATGGATGGATGGATAGAGAGAAGGATGGAT +GGGTGGGACAATGGATGGATGGATGCATGGATGGATGGATGGAGGGATAGAGAGAAGGAT +GGATGGGTGGGACAATCAATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGAT +GGGTGGGGAGATGGATGGATGGATGGAGAGGTGGATGGATGGATGGATGGATGGATTGAT +GGACAGAAGGATGGATGGGTGGGGAGGTGGATAGATGGAGAGATGGAGGGATGGTTCGAT +AGAGAGAAGGATGGATGGATGGGACAATGGATGGATGGATGGATGGAGTGAAGGATGGAT +GGGTGGGGAGATGGATGGATCGATGGATGGATGGATGGATAGATAGATGGATGGAGAGGT +GGATAGATGGATGGGTGGATGGATGGACAGAGGATGGATGGGTGGGGAGGTGGGTGGATG +GATGGATGGATGTGGGATGGACTGTCCCACAGAAAGTGTGTGGTAAGGGGAGAGATTGGA +GACAGCCCAGTCTTGAGATGCCTTGTAGGGGCCCCTGGTCTAGGGCAGGCAGAGCTGGCC +AGGCAGGAGCTCCAGCACAGCGCCCTTGCTCACCGCCAATCTTGTACACGTCCTGCAGCG +GC +>p:HG002_1_chr20:63491489-63493165 +GTGAGCATGATGCCCCCACAGTGCACACAGAGATGCCTGCAACATCTTTGGCTGCAGCCC +ACTGGCTGGGGGTCTCCTATCAGTGCCCTTCTCTAGGGTCTCAGATTTGTTTATGGTTTC +TCTTCTTGGTGGGATGGATGGATGGATGGACGGATGGATGGGGAGGTGGGTGGATGGATG +GATGGATGTATGAATGGGGTGGTAGATGGATGGGGAGGTGGATGGACAGAAGGATGGGTG +GGGAGATGGATGAGTAGGGAGATGGATGGATGGATTGGTGGATGGATGGATGGATGGATG +GATGAGGAGGTAGATGAGTGGATGGACAGAAGGATGGATGGGTAGGAAGGTGGGTGGATG +AATGGATGGATGGGGAGGTGGATGGATAGATGGATGGATGGATGGATGGATGGATGGATG +GATGGATGGGGGGATAGATGGATGGATGGATGGATGGACGGACGGATGGGGAGGTGGATG +GATGGATGGATGGATGGATGGATGGATGGATGGATGGATGAGGAGATGAATGGATGGATG +AGATGGATGGATGGATGATGGAGGGAAGGATGGCTGGGTGGGGAGATGGATGGATAGAGA +GGTGGATGGGTGGATGGGGAGATGGATGGATGGATGGATGGATGGGGAAGTGGATGGATG +GGGAGGTGGATGGATGGATAGGTGGATGGGTGGATGGACAGAAGGATGAATGGGTAGGGA +GATGGATGGATGGATGGATGCGGAGGGATGGATGGATGGATGGATGGATGGGTGGATGGA +TAGAAGGATGGATGGGTGGGGAGGTGGGTGGGTGGGTGCGTGGATGGATGGAGAGATGGA +TAGATGGATAGATGGATGGATGGATGGATGGATGGATGGAGAGAAGGATGGATGGGTGGG +GAGGTGGGTGGGTGGGTGGATGGGTGGATGGATGGATGGGTGGGGAGGTGGGCGGGTGGA +TGGATGGATGGATGCAGAGGTGGGTGGATGGATGGATGGAGAGAAGGATGGATGGGTGGG +GAGGTGGGTGGGTGGATGGATGGATGAGTGGGGAGGTGGGTGGGTGGATGGATGGATGGA +TGGATGCATGGATGGATGGATGGAGAGGTGGGTGGATGGGTGGATGGACAGAAGGATGGA +TGGGTGGGGAGGTGGGTGAGTGGGTGGATGGATGAATGGGGAGGTGGATGGATGGATGGA +TGGATGAAGGATGGATGGGTGGGGAGGTGGGTGGACGGATGGATGGATTGGGAGGTGGGT +AGATGGGTGGATGGACAGAAGGATGGATGGGTGGGGAGGTGGGTGGGTGGGTGGATGGAT +GGATGGGGAGGTGGATGGATGGATGGTTAGATGGGGAGGTGGGTGGATGGGTGGATGGAC +AGAAGGATGGATGGGTAGGGAGGTAGGTGAGTGGATGGATGGATGGGGAGATGGATGGAT +GGATAGAGAGAAGGATGGATGGGTGGGACAATGGATGGATGGATGGATAGAAGGATGGAC +GGGTGGGGAGATGGATGGATGGATGGATGGATGGATGGATGGACAGAAGGATGTATGGGT +GGGGAGGTGGGTGGATAGATGGATGGATGGATGGATGGGGAAATGGATGGATGGAAGGAT +GGATGGATAGGGAGGTGGGTGGATGGATGGATGGATGGATGTACAGAAGGATGGATGGGT +GGGGAGGTGGGTGAGTGGATGAATGGATGGATGGATAGATAGAAGGATGGATGGGTGGGA +CAATAGATGGATGGATAGAGAGAAGGATGGATGGGTGGGGAGATGGATGGATGGATGGAT +GGATGGATGGATGGATAGAGAGAAGGATGGATGGTTGAGACAATGGATGGATGGATGGAT +GGATGGAGAGATGGATGGATGGATGGATGGACAGAAGGATGGATGGGTGGGGAGGTGGAT +GGATGGATTGAAGGATGGACGGGTGGGGAGATGGATGGATGGATGGATGGATGGATGGAT +GGATGGATGGACAGAAGGATGTATGGGTGGGGAGGTGGGTGGATAGATGGATGGATGGAT +GGATGGGGAAATGGATGGATGGAAGGATGGATGGATAGGGAGGTGGGTGGATGGATGGAT +GGATGGATGTACAGAAGGATGGATGGGTGGGGAGGTGGGTGAGTGGATGAATGGATGGAT +GGATAGATAGAAGGATGGATGGGTGGGACAACAGATGGATAGAGAGAAGGATGGATGGGT +GGGGAGATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGTTGAGACAAT +GGATGGATGGATGGATGGATGGAGAGATGGATGGATGGATGGATGGACAGAAGGATGGAT +GGGTGGGGAGGTGGATGGATGGATGGAAGGATGGATGGATGGATAGAGAGAAGGATGGAT +GGGTGGGACAATGGATGGATGGATGCATGGATGGATGGATGGAGGGATAGAGAGAAGGAT +GGATGGGTGGGACAATCAATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGAT +GGGTGGGGAGATGGATGGATGGATGGAGAGGTGGATGGATGGATGGATGGATGGATTGAT +GGACAGAAGGATGGATGGGTGGGGAGGTGGATAGATGGAGAGATGGAGGGATGGTTCGAT +AGAGAGAAGGATGGATGGATGGGACAATGGATGGATGGATGGATGGAGTGAAGGATGGAT +GGGTGGGGAGATGGATGGATCGATGGATGGATGGATGGATAGATAGATGGATGGAGAGGT +GGATAGATGGATGGGTGGATGGATGGACAGAGGATGGATGGGTGGGGAGGTGGGTGGATG +GATGGATGGATGTGGGATGGACTGTCCCACAGAAAGTGTGTGGTAAGGGGAGAGATTGGA +GACAGCCCAGTCTTGAGATGCCTTGTAGGGGCCCCTGGTCTAGGGCAGGCAGAGCTGGCC +AGGCAGGAGCTCCAGCACAGCGCCCTTGCTCACCGCCAATCTTGTACACGTCCTGCAGCG +GC +>p:HG002_2_chr20:63491489-63493165 +GTGAGCATGATGCCCCCACAGTGCACACAGAGATGCCTGCAACATCTTTGGCTGCAGCCC +ACTGGCTGGGGGTCTCCTATCAGTGCCCTTCTCTAGGGTCTCAGATTTGTTTATGGTTTC +TCTTCTTGGTGGGATGGATGGATGGATGGACGGATGGATGGGGAGGTGGGTGGATGGATG +GATGGATGTATGAATGGGGTGGTAGATGGATGGGGAGGTGGATGGACAGAAGGATGGGTG +GGGAGATGGATGAGTAGGGAGATGGATGGATGGATTGGTGGATGGATGGATGGATGGATG +GATGAGGAGGTAGATGAGTGGATGGACAGAAGGATGGATGGGTAGGAAGGTGGGTGGATG +AATGGATGGATGGGGAGGTGGATGGATAGATGGATGGATGGATGGATGGATGGATGGATG +GATGGATGGGGGGATAGATGGATGGATGGATGGATGGATGGACGGACGGATGGGGAGGTG +GATGGATGGATGGATGGATGGATGGATGGATGGATGAGGAGATGAATGGATGGATGAGAT +GGATGGATGGATGATGGAGGGAAGGATGGCTGGGTGGGGAGATGGATGGATAGAGAGGTG +GATGGGTGGATGGGGAGATGGATGGATGGATGGATGGATGGGGAAGTGGATGGATGGGGA +GGTGGATGGATGGATAGGTGGATGGGTGGATGGACAGAAGGATGAATGGGTAGGGAGATG +GATGGATGGATGGATGGGGAGGGATGGATGGATGGATGGATGGATGGGTGGATGGATAGA +AGGATGGATGGGTGGGGAGGTGGGTGGGTGGGTGGATGGATGGAGAGATGGATAGATGGA +TAGATGGATGGATGGATGGATGGATGGAGAGAAGGATGGATGGGTGGGGAGGTGGGTGGG +TGGGTGGATGGGTGGATGGATGGATGGGTGGGGAGGTGGGCGGGTGGATGGATGGATGGA +TGCAGAGGTGGGTGGATGGATGGATGGAGAGAAGGATGGATGGGTGGGGAGGTGGGTGGG +TGGATGGATGGATGAGTGGGGAGGTGGGTGGGTGGGTGGATGGATGGATGGATGGATGCA +TGGATGGATGGATGGAGAGGTGGGTGGACGGATGGATGGATTGGGAGGTGGGTAGATGGG +TGGATGGACAGAAGGATGGATGGGTGGGGAGGTGGGTGGGTGGGTGGATGGATGGATGGG +GAGGTGGATGGATGGATGGTTAGATGGGGAGGTGGGTGGATGGGTGGATGGACAGAAGGA +TGGATGGGTAGGGAGGTAGGTGAGTGGATGGATGGATGGGGAGATGGATGGATGGATAGA +GAGAAGGATGGATGGGTGGGACAATGGATGGATGGATGGATAGAAGGATGGACGGGTGGG +GAGATGGATGGATGGATGGATGGATGGATGGATGGATGGACAGAAGGATGTATGGGTGGG +GAGGTGGGTGGATAGATGGATGGATGGATGGATGGGGAAATGGATGGATGGAAGGATGGA +TGGATAGGGAGGTGGGTGGATGGATGGATGGATGGATGTACAGAAGGATGGATGGGTGGG +GAGGTGGGTGAGTGGATGAATGGATGGATGGATAGATAGAAGGATGGATGGGTGGGACAA +TAGATGGATGGATAGAGAGAAGGATGGATGGGTGGGGAGATGGATGGATGGATGGATGGA +TGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGTTGAGACAATGGATGGATGGA +TGGATGGAGAGATGGATGGATGGACGGATGGACAGAAGGATGGATGGGTGGGGAGGTGGA +TGGATGGATTGAAGGATGGATGGGTGGGGACATGGATGGATGGATGGATGGATGGATGGA +TGGATGGACAGAAGGATGTATGGGTGGGGAGGTGGGTGGATAGATGGATGGATGGGGAAA +TGGATGGATGGAAGGATGGATGGATAGGGAGGTGGGTGGATGGATGGATGGATGGATGTA +CAGAAGGATGGATGGGTGGGGAGGTGGGTGAGTGGATGAATGGATGGATGGATAGATAGA +AGGATGGATGGGTGGGACAATAGATGGATGGATAGAGAGAAGGATGGATGGGTGGGGAGA +TGGATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGTTGAGACAATGGA +TGGATGGATGGATGGATGGAGAGATGGATGGATGGATGGATGGACAGAAGGATGGATGGG +TGGGGAGGTGGATGGATGGATGGAAGGATGGATGGATGGATAGAGAGAAGGATGGATGGG +TGGGACAATGGATGGATGGATGCATGGATGGATGGATGGAGGGATAGAGAGAAGGATGGA +TGGGTGGGACAATCAATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGG +TGGGGAGATGGATGGATGGATGGAGAGGTGGATGGATGGATGGATGGATGGATTGATGGA +CAGAAGGATGGATGGGTGGGGAGGTGGATAGATGGAGAGATGGAGGGATGGTTCGATAGA +GAGAAGGATGGATGGATGGGACAATGGATGGATGGATGGATGGAGTGAAGGATGGATGGG +TGGGGAGATGGATGGATCGATGGATGGATGGATGGATAGATAGATGGATGGAGAGGTGGA +TAGATGGATGGGTGGATGGATGGACAGAGGATGGATGGGTGGGGAGGTGGGTGGATGGAT +GGATGGATGTGGGATGGACTGTCCCACAGAAAGTGTGTGGTAAGGGGAGAGATTGGAGAC +AGCCCAGTCTTGAGATGCCTTGTAGGGGCCCCTGGTCTAGGGCAGGCAGAGCTGGCCAGG +CAGGAGCTCCAGCACAGCGCCCTTGCTCACCGCCAATCTTGTACACGTCCTGCAGCGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/haps.fa.ref.fa new file mode 100644 index 00000000..ebd054e8 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63491489-63493165 +GTGAGCATGATGCCCCCACAGTGCACACAGAGATGCCTGCAACATCTTTGGCTGCAGCCCACTGGCTGGGGGTCTCCTATCAGTGCCCTTCTCTAGGGTCTCAGATTTGTTTATGGTTTCTCTTCTTGGTGGGATGGATGGATGGATGGACGGATGGATGGGGAGGTGGGTGGATGGATGGATGGATGTATGAATGGGGTGGTAGATGGATGGGGAGGTGGATGGACAGAAGGATGGGTGGGGAGATGGATGAGTAGGGAGATGGATGGATGGATTGGTGGATGGATGGATGGATGGATGGATGAGGAGGTAGATGAGTGGATGGACAGAAGGATGGATGGGTAGGAAGGTGGGTGGATGAATGGATGGATGGGGAGGTGGATGGATAGATGGATGGATGGATGGATGGATGGATGGATGGATGGGGGGATAGATGGATGGATGGATGGATGGACGGACGGATGGGGAGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGAGGAGATGAACGGATGGATGAGATGGATGGATGGATGATGGAGGGAAGGATGGCTGGGTGGGGAGATGGATGGATAGAGAGGTGGATGGGTGGATGGGGAGATGGATGGATGGATGGATGGATGGGGAAGTGGATGGATGGGGAGGTGGATGGATGGATGTATGGGTGGGTAGGTGGGTGGATAGATGGATGGATGGATGGATGGATAAATGGATGGATGGAAGGATGGATGGATAGGTAGGTGGGTGGATGGATGGATGGATGGATGTACAGAAGGATGGATGGGTGGGTAGGTGGGTGAGTGGATGAATGGATGGATGGATAGATAGAAGGATGGATGGGTGGGTCAATAGATGGATGGATAGAGAGAAGGATGGATGGGTGGGTAGATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGTTGAGACAATGGATGGATGGATGGATGGATGGAGAGATGGATGGATGGATGGATGGACAGAAGGATGGATGGGTGGGGAGGTGGATGGATGGATGGAAGGATGGATGGATGGATAGAGAGAAGGATGGATGGGTGGGACAATGGATGGATGGATGCATGGATGGATGGATGGAGGGATAGAGAGAAGGATGGATGGGTGGGACAATCAATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGGTGGGGAGATGGATGGATGGATGGAGAGGTGGATGGATGGATGGATGGATGGATTGATGGACAGAAGGATGGATGGGTGGGGAGGTGGATAGATGGAGAGATGGAGGGATGGTTCGATAGAGAGAAGGATGGATGGGACAATGGATGGATGGATGGATGGAGTGAAGGATGGATGGGTGGGGAGATGGATGGATCGATGGATGGATGGATGGATAGATAGATGGATGGAGAGGTGGATAGATGGATGGGTGGATGGATGGACAGAGGATGGATGGGTGGGGAGGTGGGTGGATGGATGGATGGATGTGGGATGGACTGTCCCACAGAAAGTGTGTGGTAAGGGGAGAGATTGGAGACAGCCCAGTCTTGAGATGCCTTGTAGGGGCCCCTGGTCTAGGGCAGGCAGAGCTGGCCAGGCAGGAGCTCCAGCACAGCGCCCTTGCTCACCGCCAATCTTGTACACGTCCTGCAGCGGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/msa.fa new file mode 100644 index 00000000..f21afbd6 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/msa.fa @@ -0,0 +1,260 @@ +>ref_chr20_63491489_63493165 +gtgagcatgatgcccccacagtgcacacagagatgcctgcaacatctttggctgcagccc +actggctgggggtctcctatcagtgcccttctctagggtctcagatttgtttatggtttc +tcttcttggtgggatggatggatggatggacggatggatggggaggtgggtggatggatg +gatggatgtatgaatggggtggtagatggatggggaggtggatggacagaaggatgggtg +gggagatggatgagtagggagatggatggatggattggtggatggatggatggatggatg +gatgaggaggtagatgagtggatggacagaaggatggatgggtaggaaggtgggtggatg +aatggatggatggggaggtggatggata----gatggatggatggatggatggatggatg +gatggatggggggatagatggatggatggatggatggacggacggatggggaggtggatg +gatggatggatggatggatggatggatggatggatggatgaggagatgaacggatggatg +agatggatggatggatgatggagggaaggatggctgggtggggagatggatggatagaga +ggtggatgggtggatggggagatggatggatggatggatggatggggaagtggatggatg +gggaggtggatggat--------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------------------ggatgtat +gggtgggtaggtgggtggatagatggatg------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----gatggatggatggataaatggatggatggaaggatggatggataggtaggtgggt +ggatggatggatggatggatgtacagaaggatggatgggtgggtaggtgggtgagtggat +gaatggatggatggatagatagaaggatggatgggtgggtcaatagatggatggatagag +agaaggatggatgggtgggta----gatggatggatggatggatggatggatagagagaa +ggatggatggttgagacaatggatggatggatggatggatggagagatggatggatggat +ggatggacagaaggatggatgggtggggaggtggatggatggatggaaggatggatggat +ggatagagagaaggatggatgggtgggacaatggatggatggatgcatggatggatggat +ggagggatagagagaaggatggatgggtgggacaatcaatggatggatggatggatggat +ggatagagagaaggatggatgggtggggagatggatggatggatggagaggtggatggat +ggatggatggatggattgatggacagaaggatggatgggtggggaggtggatagatggag +agatggagggatggttcgatagagagaa----ggatggatgggacaatggatggatggat +ggatggagtgaaggatggatgggtggggagatggatggatcgatggatggatggatggat +agatagatggatggagaggtggatagatggatgggtggatggatggacagaggatggatg +ggtggggaggtgggtggatggatggatggatgtgggatggactgtcccacagaaagtgtg +tggtaaggggagagattggagacagcccagtcttgagatgccttgtaggggcccctggtc +tagggcaggcagagctggccaggcaggagctccagcacagcgcccttgctcaccgccaat +cttgtacacgtcctgcagcggc +>syndip_1_chr20:63491489-63493165 +gtgagcatgatgcccccacagtgcacacagagatgcctgcaacatctttggctgcagccc +actggctgggggtctcctatcagtgcccttctctagggtctcagatttgtttatggtttc +tcttcttggtgggatggatggatggatggacggatggatggggaggtgggtggatggatg +gatggatgtatgaatggggtggtagatggatggggaggtggatggacagaaggatgggtg +gggagatggatgagtagggagatggatggatggattggtggatggatggatggatggatg +gatgaggaggtagatgagtggatggacagaaggatggatgggtaggaaggtgggtggatg +aatggatggatggggaggtggatggatagatggatggatggatggatggatggatggatg +gatggatggggggatagatggatggatggatggatggatggacggacg----gatgggga +ggtggatggatggatggatggatggatggatggatggatgaggagatgaatggatggatg +agatggatggatggatgatggagggaaggatggctgggtggggagatggatggatagaga +ggtggatgggtggatggggagatggatggatggatggatggatggggaagtggatggatg +gggaggtggatggatggataggtggatgggtggatggacagaaggatgaatgggtaggga +gatggatggatggatggatggggagggatggatggatggatggatggatgggtggatgga +tagaaggatggatgggtggggaggtgggtgggtgg----gtggatggatggagagatgga +tagatggata----gatggatggatggatggatggatggagagaaggatggatgggtggg +gaggtgggtgggtgggtggatgggtggatggatggatgggtggggaggtgggcgggtgga +tggatggatggatgcagaggtgggtggatggatggatggagagaaggatggatgggtggg +gaggtgggtgggtggatggatggatgagtggggaggtgggtgggtgggtggatggatgga +tggatggatgcatggatggatgga------------------------------------ +------------------------------------------------------------ +-------------------tggagaggtgggtggacggatggatggattgggaggtgggt +agatgggtggatggacagaaggatggatgggtggggaggtgggtgggtgggtggatggat +ggatggggaggtggatggatggatggttagatggggaggtgggtggatgggtggatggac +agaaggatggatgggtagggaggtaggtgagtggatggatggatggggagatggatggat +ggatagagagaaggatggatgggtgggacaatggatggatggatggatagaaggatggac +gggtggggagatggatggatggatggatggatggatggatggatggacagaaggatgtat +gggtggggaggtgggtggatagatggatggatggatggatggggaaatggatggatggaa +ggatggatggatagggaggtgggtggatggatggatggatggatgtacagaaggatggat +gggtggggaggtgggtgagtggatgaatggatggatggatagatagaaggatggatgggt +gggacaatagatggatggatagagagaaggatggatgggtggggagatggatggatggat +ggatggatggatggatggatggatggatagagagaaggatggatggttgagaca----at +ggatggatggatggatggagagatggatggatggacggatggacagaaggatggatgggt +ggggaggtggatggatggattgaaggatggatgggtgggga----catggatggatggat +ggatggatggatggatggatggacagaaggatgtatgggtggggaggtgggtggata--- +-----gatggatggatggggaaatggatggatggaaggatggatggatagggaggtgggt +ggatggatggatggatggatgtacagaaggatggatgggtggggaggtgggtgagtggat +gaatggatggatggatagatagaaggatggatgggtgggacaatagatggatggatagag +agaaggatggatgggtggggagatggatggatggatggatggatggatggatagagagaa +ggatggatggttgagacaatggatggatggatggatggatggagagatggatggatggat +ggatggacagaaggatggatgggtggggaggtggatggatggatggaaggatggatggat +ggatagagagaaggatggatgggtgggacaatggatggatggatgcatggatggatggat +ggagggatagagagaaggatggatgggtgggacaatcaatggatggatggatggatggat +ggatagagagaaggatggatgggtggggagatggatggatggatggagaggtggatggat +ggatggatggatggattgatggacagaaggatggatgggtggggaggtggatagatggag +agatggagggatggttcgatagagagaaggatggatggatgggacaatggatggatggat +ggatggagtgaaggatggatgggtggggagatggatggatcgatggatggatggatggat +agatagatggatggagaggtggatagatggatgggtggatggatggacagaggatggatg +ggtggggaggtgggtggatggatggatggatgtgggatggactgtcccacagaaagtgtg +tggtaaggggagagattggagacagcccagtcttgagatgccttgtaggggcccctggtc +tagggcaggcagagctggccaggcaggagctccagcacagcgcccttgctcaccgccaat +cttgtacacgtcctgcagcggc +>syndip_2_chr20:63491489-63493165 +gtgagcatgatgcccccacagtgcacacagagatgcctgcaacatctttggctgcagccc +actggctgggggtctcctatcagtgcccttctctagggtctcagatttgtttatggtttc +tcttcttggtgggatggatggatggatggacggatggatggggaggtgggtggatggatg 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+ggatggagtgaaggatggatgggtggggagatggatggatcgatggatggatggatggat +agatagatggatggagaggtggatagatggatgggtggatggatggacagaggatggatg +ggtggggaggtgggtggatggatggatggatgtgggatggactgtcccacagaaagtgtg +tggtaaggggagagattggagacagcccagtcttgagatgccttgtaggggcccctggtc +tagggcaggcagagctggccaggcaggagctccagcacagcgcccttgctcaccgccaat +cttgtacacgtcctgcagcggc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/msa.fa.fai new file mode 100644 index 00000000..3c19a1c2 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63491489_63493165 3022 29 60 61 +syndip_1_chr20:63491489-63493165 3022 3136 60 61 +syndip_2_chr20:63491489-63493165 3022 6243 60 61 +p:HG002_1_chr20:63491489-63493165 3022 9351 60 61 +p:HG002_2_chr20:63491489-63493165 3022 12459 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/output.vcf.gz new file mode 100644 index 00000000..af11b81c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/output.vcf.gz.tbi new file mode 100644 index 00000000..a904a9f3 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63491589-63493065/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63535674-63536246/base.vcf.gz 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b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63535674-63536246/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63535674-63536246/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63535674-63536246/comp.vcf.gz.tbi new file mode 100644 index 00000000..63987ce6 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63535674-63536246/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63535674-63536246/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63535674-63536246/haps.fa new file mode 100644 index 00000000..cb20350d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63535674-63536246/haps.fa @@ -0,0 +1,66 @@ +>ref_chr20_63535574_63536346 +ACTTCCAGGTGGAGCTTGCAGAAGCTCCAGGTGACCTGCGCCCTTTGTGTGTCTGACTCCCTCAGGTCACTGGAACACAAACCCCACACAGAAGACCACGGCCCAGCATGGAGCCCCTGGGGTCCACCCCCTCCACTTCCGCACACCTGGAAGCACTGCCCCACCTGCCCCTCCAACCACCTGGCCTCCCGCCCCCCCCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCCCCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCACCCCGTCCTCACCTGGCCTCCCGCACCCCCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCTCCTCTCCTGGCCTCCCGCCCCCTCCTCTCCTGGCCTCCCGTCCCCTCCTCTCCTGGTCTCCCGCCCCCCCCACCTGGCCTCCCGCCCCCCCTCACCTGGCCTCCAGCCCCCCCCACCTAGCCTCCCGCTCCCCCCCCCACCTGGCCTCCCACCCCCTCCTCACCTGGCCTCCTCCCCACTTCTCACCTGGGCGAGTTCTCAGGACTCAGGGTCTTTGCACCTGGGAGCTGACCAGCCTCCGGCCAGACCCCACCCCTGCACCCCTGCTCACTAACGAGGTCGTGGGTCTGCGCGTGACCCTGCTAACGAGGTCGTGGGTCT +>syndip_1_chr20:63535574-63536346 +ACTTCCAGGTGGAGCTTGCAGAAGCTCCAGGTGACCTGCGCCCTTTGTGTGTCTGACTCC +CTCAGGTCACTGGAACACAAACCCCACACAGAAGACCACGGCCCAGCATGGAGCCCCTGG +GGTCCACCCCCTCCACTTCCGCACACCTGGAAGCACTGCCCCACCTGCCCCTCCAACCAC +CTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCC +CCTCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCACCCCGTCCTCACCTGGC +CTCCCGCACCCCCCTCACCTGGCCTCCCGCCCCCCCCTCATCTGGCCTCCCGCCCCCTCC +TCACCTGGCCTCCCGCCCCCTCCTCTCCTGGCCTCCCGCCCCCCCCCTCACCTGGCCTCC +CGCCCCCTCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCCCCCTCA +CCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCCCCCTCACCTGGCCTCCCGC +CCCCTCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCACCCCGTCCTCACCTG +GCCTCCCGCACCCCCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCGCCCCCT +CCTCTCCTGGCCTCCCGCCCCCTCCTCTCCTGGCCTCCCGTCCCCTCCTCTCCTGGTCTC +CCGCCCCCCCCACCTGGCCTCCCGCCCCCCCTCACCTGGCCTCCAGCCCCCCCCACCTGG +CCTCCCGCTCCCCCCCCACCTGGCCTCCCACCCCCTCCTCACCTGGCCTCCTCCCCACTT +CTCACCTGGGCGAGTTCTCAGGACTCAGGGTCTTTGCACCTGGGAGCTGACCAGCCTCCG +GCCAGACCCCACCCCTGCACCCCTGCTCACTAACGAGGTCGTGGGTCTGCGCGTGACCCT +GCTAACGAGGTCGTGGGTCT +>syndip_2_chr20:63535574-63536346 +ACTTCCAGGTGGAGCTTGCAGAAGCTCCAGGTGACCTGCGCCCTTTGTGTGTCTGACTCC +CTCAGGTCACTGGAACACAAACCCCACACAGAAGACCACGGCCCAGCATGGAGCCCCTGG +GGTCCACCCCCTCCACTTCCGCACACCTGGAAGCACTGCCCCACCTGCCCCTCCAACCAC +CTGGCCTCCCGCCCCCCCCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCC +CCCTCCTCACCTGGCCTCCCGCCCCCCCCCTCACCTGGCCTCCCGCCCCCTCCTCACCTG +GCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCACCCCGT +CCTCACCTGGCCTCCCGCACCCCCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTC +CCGCCCCCTCCTCACCTGGCCTCCCGCCCCCTCCTCTCCTGGCCTCCCGCCCCCTCCTCT +CCTGGCCTCCCGTCCCCTCCTCTCCTGGTCTCCCGCCCCCCCCACCTGGCCTCCCGCCCC +CCCTCACCTGGCCTCCAGCCCCCCCCACCTAGCCTCCCGCTCCCCCCCCCACCTGGCCTC +CCACCCCCTCCTCACCTGGCCTCCTCCCCACTTCTCACCTGGGCGAGTTCTCAGGACTCA +GGGTCTTTGCACCTGGGAGCTGACCAGCCTCCGGCCAGACCCCACCCCTGCACCCCTGCT +CACTAACGAGGTCGTGGGTCTGCGCGTGACCCTGCTAACGAGGTCGTGGGTCT +>p:HG002_1_chr20:63535574-63536346 +ACTTCCAGGTGGAGCTTGCAGAAGCTCCAGGTGACCTGCGCCCTTTGTGTGTCTGACTCC +CTCAGGTCACTGGAACACAAACCCCACACAGAAGACCACGGCCCAGCATGGAGCCCCTGG +GGTCCACCCCCTCCACTTCCGCACACCTGGAAGCACTGCCCCACCTGCCCCTCCAACCAC +CTGGCCTCCCGCCCCCCCCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCC +CCCTCCTCACCTGGCCTCCCGCCCCCCCCCTCACCTGGCCTCCCGCCCCCTCCTCACCTG +GCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCACCCCGT +CCTCACCTGGCCTCCCGCACCCCCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTC +CCGCCCCCTCCTCACCTGGCCTCCCGCCCCCTCCTCTCCTGGCCTCCCGCCCCCTCCTCT +CCTGGCCTCCCGTCCCCTCCTCTCCTGGTCTCCCGCCCCCCCCACCTGGCCTCCCGCCCC +CCCTCACCTGGCCTCCAGCCCCCCCCACCTAGCCTCCCGCTCCCCCCCCCACCTGGCCTC +CCACCCCCTCCTCACCTGGCCTCCTCCCCACTTCTCACCTGGGCGAGTTCTCAGGACTCA +GGGTCTTTGCACCTGGGAGCTGACCAGCCTCCGGCCAGACCCCACCCCTGCACCCCTGCT +CACTAACGAGGTCGTGGGTCTGCGCGTGACCCTGCTAACGAGGTCGTGGGTCT +>p:HG002_2_chr20:63535574-63536346 +ACTTCCAGGTGGAGCTTGCAGAAGCTCCAGGTGACCTGCGCCCTTTGTGTGTCTGACTCC +CTCAGGTCACTGGAACACAAACCCCACACAGAAGACCACGGCCCAGCATGGAGCCCCTGG +GGTCCACCCCCTCCACTTCCGCACACCTGGAAGCACTGCCCCACCTGCCCCTCCAACCAC +CTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCC +CCTCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCACCCCGTCCTCACCTGGC +CTCCCGCACCCCCCTCACCTGGCCTCCCGCCCCCCCCTCATCTGGCCTCCCGCCCCCTCC +TCACCTGGCCTCCCGCCCCCTCCTCTCCTGGCCTCCCGCCCCCCCCCTCACCTGGCCTCC +CGCCCCCTCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCCCCCTCA +CCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCCCCCTCACCTGGCCTCCCGC +CCCCTCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCACCCCGTCCTCACCTG +GCCTCCCGCACCCCCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCGCCCCCT +CCTCTCCTGGCCTCCCGCCCCCTCCTCTCCTGGCCTCCCGTCCCCTCCTCTCCTGGTCTC +CCGCCCCCCCCACCTGGCCTCCCGCCCCCCCTCACCTGGCCTCCAGCCCCCCCCACCTGG +CCTCCCGCTCCCCCCCCACCTGGCCTCCCACCCCCTCCTCACCTGGCCTCCTCCCCACTT +CTCACCTGGGCGAGTTCTCAGGACTCAGGGTCTTTGCACCTGGGAGCTGACCAGCCTCCG +GCCAGACCCCACCCCTGCACCCCTGCTCACTAACGAGGTCGTGGGTCTGCGCGTGACCCT +GCTAACGAGGTCGTGGGTCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63535674-63536246/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63535674-63536246/haps.fa.ref.fa new file mode 100644 index 00000000..32b667e8 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63535674-63536246/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63535574-63536346 +ACTTCCAGGTGGAGCTTGCAGAAGCTCCAGGTGACCTGCGCCCTTTGTGTGTCTGACTCCCTCAGGTCACTGGAACACAAACCCCACACAGAAGACCACGGCCCAGCATGGAGCCCCTGGGGTCCACCCCCTCCACTTCCGCACACCTGGAAGCACTGCCCCACCTGCCCCTCCAACCACCTGGCCTCCCGCCCCCCCCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCCCCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCACCCCGTCCTCACCTGGCCTCCCGCACCCCCCTCACCTGGCCTCCCGCCCCCCCCTCACCTGGCCTCCCGCCCCCTCCTCACCTGGCCTCCCGCCCCCTCCTCTCCTGGCCTCCCGCCCCCTCCTCTCCTGGCCTCCCGTCCCCTCCTCTCCTGGTCTCCCGCCCCCCCCACCTGGCCTCCCGCCCCCCCTCACCTGGCCTCCAGCCCCCCCCACCTAGCCTCCCGCTCCCCCCCCCACCTGGCCTCCCACCCCCTCCTCACCTGGCCTCCTCCCCACTTCTCACCTGGGCGAGTTCTCAGGACTCAGGGTCTTTGCACCTGGGAGCTGACCAGCCTCCGGCCAGACCCCACCCCTGCACCCCTGCTCACTAACGAGGTCGTGGGTCTGCGCGTGACCCTGCTAACGAGGTCGTGGGTCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63535674-63536246/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63535674-63536246/msa.fa new file mode 100644 index 00000000..3113ce6f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63535674-63536246/msa.fa @@ -0,0 +1,90 @@ +>ref_chr20_63535574_63536346 +acttccaggtggagcttgcagaagctccaggtgacctgcgccctttgtgtgtctgactcc +ctcaggtcactggaacacaaaccccacacagaagaccacggcccagcatggagcccctgg +ggtccaccccctccacttccgcacacctggaagcactgccccacctgcccctccaacca- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------cctggcctcccgccccccccctcacctggcctcc +cgccccctcctcacctggcctcccgccccctcctcacctggcctcccgccccccccctca +cctggcctcccgccccctcctcacctggcctcccg-ccccctcctcacctggcctcccgc +ccccccctcacctggcctcccaccccgtcctcacctggcctcccgcacccccctcacctg +gcctcccgcccccccctcacctggcctcccgccccctcctcacctggcctcccgccccct +cctctcctggcctcccgccccctcctctcctggcctcccgtcccctcctctcctggtctc +ccgccccccccacctggcctcccgccccccctcacctggcctccagccccccccacctag +cctcccgctcccccccccacctggcctcccaccccctcctcacctggcctcctccccact +tctcacctgggcgagttctcaggactcagggtctttgcacctgggagctgaccagcctcc +ggccagaccccacccctgcacccctgctcactaacgaggtcgtgggtctgcgcgtgaccc +tgctaacgaggtcgtgggtct +>syndip_1_chr20:63535574-63536346 +acttccaggtggagcttgcagaagctccaggtgacctgcgccctttgtgtgtctgactcc +ctcaggtcactggaacacaaaccccacacagaagaccacggcccagcatggagcccctgg +ggtccaccccctccacttccgcacacctggaagcactgccccacctgcccctccaaccac +ctggcctcccgcccccccctcacctggcctcccgccccctcctcacctggcctcccgccc +cctcctcacctggcctcccgcccccccctcacctggcctcccaccccgtcctcacctggc +ctcccgcacccccctcacctggcctcccgcccccccctcatctggcctcccgccccctcc +tcacctggcctcccgccccctcctctcctggcctcccgccccccccctcacctggcctcc +cgccccctcctcacctggcctcccgccccctcctcacctggcctcccgccccccccctca +cctggcctcccgccccctcctcacctggcctcccgccccccccctcacctggcctcccgc +cccctcctcacctggcctcccgcccccccctcacctggcctcccaccccgtcctcacctg +gcctcccgcacccccctcacctggcctcccgcccccccctcacctggcctcccgccccct +cctctcctggcctcccgccccctcctctcctggcctcccgtcccctcctctcctggtctc +ccgccccccccacctggcctcccgccccccctcacctggcctccagccccccccacctgg +cctcccgct-ccccccccacctggcctcccaccccctcctcacctggcctcctccccact +tctcacctgggcgagttctcaggactcagggtctttgcacctgggagctgaccagcctcc +ggccagaccccacccctgcacccctgctcactaacgaggtcgtgggtctgcgcgtgaccc +tgctaacgaggtcgtgggtct +>syndip_2_chr20:63535574-63536346 +acttccaggtggagcttgcagaagctccaggtgacctgcgccctttgtgtgtctgactcc +ctcaggtcactggaacacaaaccccacacagaagaccacggcccagcatggagcccctgg +ggtccaccccctccacttccgcacacctggaagcactgccccacctgcccctccaacca- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------cctggcctcccgccccccccctcacctggcctcc +cgccccctcctcacctggcctcccgccccctcctcacctggcctcccgccccccccctca +cctggcctcccgccccctcctcacctggcctcccg-ccccctcctcacctggcctcccgc +ccccccctcacctggcctcccaccccgtcctcacctggcctcccgcacccccctcacctg +gcctcccgcccccccctcacctggcctcccgccccctcctcacctggcctcccgccccct +cctctcctggcctcccgccccctcctctcctggcctcccgtcccctcctctcctggtctc +ccgccccccccacctggcctcccgccccccctcacctggcctccagccccccccacctag +cctcccgctcccccccccacctggcctcccaccccctcctcacctggcctcctccccact +tctcacctgggcgagttctcaggactcagggtctttgcacctgggagctgaccagcctcc +ggccagaccccacccctgcacccctgctcactaacgaggtcgtgggtctgcgcgtgaccc +tgctaacgaggtcgtgggtct +>p:HG002_1_chr20:63535574-63536346 +acttccaggtggagcttgcagaagctccaggtgacctgcgccctttgtgtgtctgactcc +ctcaggtcactggaacacaaaccccacacagaagaccacggcccagcatggagcccctgg +ggtccaccccctccacttccgcacacctggaagcactgccccacctgcccctccaacca- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------cctggcctcccgccccccccctcacctggcctcc +cgccccctcctcacctggcctcccgccccctcctcacctggcctcccgccccccccctca +cctggcctcccgccccctcctcacctggcctcccg-ccccctcctcacctggcctcccgc +ccccccctcacctggcctcccaccccgtcctcacctggcctcccgcacccccctcacctg +gcctcccgcccccccctcacctggcctcccgccccctcctcacctggcctcccgccccct +cctctcctggcctcccgccccctcctctcctggcctcccgtcccctcctctcctggtctc +ccgccccccccacctggcctcccgccccccctcacctggcctccagccccccccacctag +cctcccgctcccccccccacctggcctcccaccccctcctcacctggcctcctccccact +tctcacctgggcgagttctcaggactcagggtctttgcacctgggagctgaccagcctcc +ggccagaccccacccctgcacccctgctcactaacgaggtcgtgggtctgcgcgtgaccc +tgctaacgaggtcgtgggtct +>p:HG002_2_chr20:63535574-63536346 +acttccaggtggagcttgcagaagctccaggtgacctgcgccctttgtgtgtctgactcc +ctcaggtcactggaacacaaaccccacacagaagaccacggcccagcatggagcccctgg +ggtccaccccctccacttccgcacacctggaagcactgccccacctgcccctccaaccac +ctggcctcccgcccccccctcacctggcctcccgccccctcctcacctggcctcccgccc +cctcctcacctggcctcccgcccccccctcacctggcctcccaccccgtcctcacctggc +ctcccgcacccccctcacctggcctcccgcccccccctcatctggcctcccgccccctcc +tcacctggcctcccgccccctcctctcctggcctcccgccccccccctcacctggcctcc +cgccccctcctcacctggcctcccgccccctcctcacctggcctcccgccccccccctca +cctggcctcccgccccctcctcacctggcctcccgccccccccctcacctggcctcccgc +cccctcctcacctggcctcccgcccccccctcacctggcctcccaccccgtcctcacctg +gcctcccgcacccccctcacctggcctcccgcccccccctcacctggcctcccgccccct +cctctcctggcctcccgccccctcctctcctggcctcccgtcccctcctctcctggtctc +ccgccccccccacctggcctcccgccccccctcacctggcctccagccccccccacctgg +cctcccgct-ccccccccacctggcctcccaccccctcctcacctggcctcctccccact +tctcacctgggcgagttctcaggactcagggtctttgcacctgggagctgaccagcctcc +ggccagaccccacccctgcacccctgctcactaacgaggtcgtgggtctgcgcgtgaccc +tgctaacgaggtcgtgggtct diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63535674-63536246/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63535674-63536246/msa.fa.fai new file mode 100644 index 00000000..3b205652 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63535674-63536246/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63535574_63536346 981 29 60 61 +syndip_1_chr20:63535574-63536346 981 1061 60 61 +syndip_2_chr20:63535574-63536346 981 2093 60 61 +p:HG002_1_chr20:63535574-63536346 981 3126 60 61 +p:HG002_2_chr20:63535574-63536346 981 4159 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63535674-63536246/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63535674-63536246/output.vcf.gz new file mode 100644 index 00000000..32cbdf01 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63535674-63536246/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63535674-63536246/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63535674-63536246/output.vcf.gz.tbi new file mode 100644 index 00000000..9a65e867 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63535674-63536246/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/base.vcf.gz new file mode 100644 index 00000000..410b4c89 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/base.vcf.gz.tbi new file mode 100644 index 00000000..21761b61 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/comp.vcf.gz new file mode 100644 index 00000000..777b47aa Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/comp.vcf.gz.tbi new file mode 100644 index 00000000..28cfad52 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/haps.fa new file mode 100644 index 00000000..fda0ff17 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/haps.fa @@ -0,0 +1,54 @@ +>ref_chr20_63559188_63560064 +TGGGGGGGCCCTGGACTTTCCCTCCCAGTCCTGGCACCTTGCAGGTGGAGAGGGCTCTTCAGGAAGGCATAGTTGGCCTCCTGCAGACGCGCACCTGGCCGGCAGGCACGAGGGTCTGCTGAGCCTCGCAGAAGTCCAGGAGGCTACGCCAGAGGGGGCAGCAGCGCAGAAGGAGGTGGTCTCCTGTGAGGGTGGGAGTCAGATGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGAGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGAGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGAGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTCAGGCAGGAGTCGGCAGCTCCCTAGCCCAGCCCTGGCCTCACCTGTGTTCCCACCCTGGAAGAGCCCAGCCCCGCCCTCACCGATCAGGCAGAGCCCCTCCTGGGCCCGCGTGACAGCCACATTCACTTGGTTGGGGTCCACAACGAAGCCCAGAAACTTCTTGAGCCAGCTCTTGGTGGGCCGCTGGTCCAGGTCGCTCTTGGCACAGGTGCGGACG +>syndip_1_chr20:63559188-63560064 +TGGGGGGGCCCTGGACTTTCCCTCCCAGTCCTGGCACCTTGCAGGTGGAGAGGGCTCTTC +AGGAAGGCATAGTTGGCCTCCTGCAGACGCGCACCTGGCCGGCAGGCACGAGGGTCTGCT +GAGCCTCGCAGAAGTCCAGGAGGCTACGCCAGAGGGGGCAGCAGCGCAGAAGGAGGTGGT +CTCCTGTGAGGGTGGGAGTCAGATGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGT +CAGGTGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGA +GTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTC +AGGTGGGAGGAGTCAGGGTCAGGTGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGT +CAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGAG +TCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTCA +GGCAGGAGTCGGCAGCTCCCTAGCCCAGCCCTGGCCTCACCTGTGTTCCCACCCTGGAAG +AGCCCAGCCCCGCCCTCACCGATCAGGCAGAGCCCCTCCTGGGCCCGCGTGACAGCCACA +TTCACTTGGTTGGGGTCCACAACGAAGCCCAGAAACTTCTTGAGCCAGCTCTTGGTGGGC +CGCTGGTCCAGGTCGCTCTTGGCACAGGTGCGGACG +>syndip_2_chr20:63559188-63560064 +TGGGGGGGCCCTGGACTTTCCCTCCCAGTCCTGGCACCTTGCAGGTGGAGAGGGCTCTTC +AGGAAGGCATAGTTGGCCTCCTGCAGACGCGCACCTGGCCGGCAGGCACGAGGGTCTGCT +GAGCCTCGCAGAAGTCCAGGAGGCTACGCCAGAGGGGGCAGCAGCGCAGAAGGAGGTGGT +CTCCTGTGAGGGTGGGAGTCAGATGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGT +CAGGTGGGAGGAGTCAGGGTCAGGTGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGG +TCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGG +GTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTCAGGCAGGAGTCGGCAGCTCC +CTAGCCCAGCCCTGGCCTCACCTGTGTTCCCACCCTGGAAGAGCCCAGCCCCGCCCTCAC +CGATCAGGCAGAGCCCCTCCTGGGCCCGCGTGACAGCCACATTCACTTGGTTGGGGTCCA +CAACGAAGCCCAGAAACTTCTTGAGCCAGCTCTTGGTGGGCCGCTGGTCCAGGTCGCTCT +TGGCACAGGTGCGGACG +>p:HG002_1_chr20:63559188-63560064 +TGGGGGGGCCCTGGACTTTCCCTCCCAGTCCTGGCACCTTGCAGGTGGAGAGGGCTCTTC +AGGAAGGCATAGTTGGCCTCCTGCAGACGCGCACCTGGCCGGCAGGCACGAGGGTCTGCT +GAGCCTCGCAGAAGTCCAGGAGGCTACGCCAGAGGGGGCAGCAGCGCAGAAGGAGGTGGT +CTCCTGTGAGGGTGGGAGTCAGATGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGT +CAGGTGGGAGGAGTCAGGGTCAGGTGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGG +TCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGG +GTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTCAGGCAGGAGTCGGCAGCTCC +CTAGCCCAGCCCTGGCCTCACCTGTGTTCCCACCCTGGAAGAGCCCAGCCCCGCCCTCAC +CGATCAGGCAGAGCCCCTCCTGGGCCCGCGTGACAGCCACATTCACTTGGTTGGGGTCCA +CAACGAAGCCCAGAAACTTCTTGAGCCAGCTCTTGGTGGGCCGCTGGTCCAGGTCGCTCT +TGGCACAGGTGCGGACG +>p:HG002_2_chr20:63559188-63560064 +TGGGGGGGCCCTGGACTTTCCCTCCCAGTCCTGGCACCTTGCAGGTGGAGAGGGCTCTTC +AGGAAGGCATAGTTGGCCTCCTGCAGACGCGCACCTGGCCGGCAGGCACGAGGGTCTGCT +GAGCCTCGCAGAAGTCCAGGAGGCTACGCCAGAGGGGGCAGCAGCGCAGAAGGAGGTGGT +CTCCTGTGAGGGTGGGAGTCAGATGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGT +CAGGTGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGA +GTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTC +AGGTGGGAGGAGTCAGGGTCAGGTGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGT +CAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGAG +TCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTCA +GGCAGGAGTCGGCAGCTCCCTAGCCCAGCCCTGGCCTCACCTGTGTTCCCACCCTGGAAG +AGCCCAGCCCCGCCCTCACCGATCAGGCAGAGCCCCTCCTGGGCCCGCGTGACAGCCACA +TTCACTTGGTTGGGGTCCACAACGAAGCCCAGAAACTTCTTGAGCCAGCTCTTGGTGGGC +CGCTGGTCCAGGTCGCTCTTGGCACAGGTGCGGACG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/haps.fa.ref.fa new file mode 100644 index 00000000..8f47a2fb --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63559188-63560064 +TGGGGGGGCCCTGGACTTTCCCTCCCAGTCCTGGCACCTTGCAGGTGGAGAGGGCTCTTCAGGAAGGCATAGTTGGCCTCCTGCAGACGCGCACCTGGCCGGCAGGCACGAGGGTCTGCTGAGCCTCGCAGAAGTCCAGGAGGCTACGCCAGAGGGGGCAGCAGCGCAGAAGGAGGTGGTCTCCTGTGAGGGTGGGAGTCAGATGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGAGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGAGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGAGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTCAGGCAGGAGTCGGCAGCTCCCTAGCCCAGCCCTGGCCTCACCTGTGTTCCCACCCTGGAAGAGCCCAGCCCCGCCCTCACCGATCAGGCAGAGCCCCTCCTGGGCCCGCGTGACAGCCACATTCACTTGGTTGGGGTCCACAACGAAGCCCAGAAACTTCTTGAGCCAGCTCTTGGTGGGCCGCTGGTCCAGGTCGCTCTTGGCACAGGTGCGGACG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/msa.fa new file mode 100644 index 00000000..ac725463 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/msa.fa @@ -0,0 +1,80 @@ +>ref_chr20_63559188_63560064 +tgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctcttc +aggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgct +gagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggt +ctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcagggt +caggtgggaggagtcagggtcaggtgggagtcagtcagggtcaggtgggaggagtcaggg +tcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtcagg +gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtgggaggagtcagg +gtcagatgggagtcagtcagagtcaggtgggaggagtcagggtcaggtgggaggagtcag +ggtcaggtcggagtcagggtcaggtgggaggagtcagggtcaggtgggagtcagtcaggg +tcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcaga +gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggtc +aggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccctggaa +gagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgacagccac +attcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttggtggg +ccgctggtccaggtcgctcttggcacaggtgcggacg +>syndip_1_chr20:63559188-63560064 +tgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctcttc +aggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgct +gagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggt +ctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcagggt +caggtgggag----------------------------------------tcagtcaggg +tcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtcagg +gtcaggtgggaggagtcagggtcaggt---cggagtcagggtcaggtgggaggagtcagg +gtcaggtgggagtcagtcagggtcaggtgggagg-------------------------- +----------------------------------------------------agtcaggg +tcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcaga +gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggtc +aggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccctggaa +gagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgacagccac +attcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttggtggg +ccgctggtccaggtcgctcttggcacaggtgcggacg +>syndip_2_chr20:63559188-63560064 +tgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctcttc +aggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgct +gagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggt +ctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtggga----------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------ggagtcagggtcaggtgggaggagtcagg +gtcaggtgggagtc---------------------------------------------- +----------------------------------------------------agtcaggg +tcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcagg +gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggtc +aggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccctggaa +gagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgacagccac +attcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttggtggg +ccgctggtccaggtcgctcttggcacaggtgcggacg +>p:HG002_1_chr20:63559188-63560064 +tgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctcttc +aggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgct +gagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggt +ctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtggga----------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------ggagtcagggtcaggtgggaggagtcagg +gtcaggtgggagtc---------------------------------------------- +----------------------------------------------------agtcaggg +tcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcagg +gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggtc +aggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccctggaa +gagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgacagccac +attcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttggtggg +ccgctggtccaggtcgctcttggcacaggtgcggacg +>p:HG002_2_chr20:63559188-63560064 +tgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctcttc +aggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgct +gagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggt +ctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcagggt +caggtgggag----------------------------------------tcagtcaggg +tcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtcagg +gtcaggtgggaggagtcagggtcaggt---cggagtcagggtcaggtgggaggagtcagg +gtcaggtgggagtcagtcagggtcaggtgggagg-------------------------- +----------------------------------------------------agtcaggg +tcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcaga +gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggtc +aggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccctggaa +gagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgacagccac +attcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttggtggg +ccgctggtccaggtcgctcttggcacaggtgcggacg diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/msa.fa.fai new file mode 100644 index 00000000..30945016 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63559188_63560064 877 29 60 61 +syndip_1_chr20:63559188-63560064 877 955 60 61 +syndip_2_chr20:63559188-63560064 877 1881 60 61 +p:HG002_1_chr20:63559188-63560064 877 2808 60 61 +p:HG002_2_chr20:63559188-63560064 877 3735 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/output.vcf.gz new file mode 100644 index 00000000..c2145186 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/output.vcf.gz.tbi new file mode 100644 index 00000000..cda09c6e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63559288-63559964/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/base.vcf.gz new file mode 100644 index 00000000..7fb8e05f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/base.vcf.gz.tbi new file mode 100644 index 00000000..953b65cf Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/comp.vcf.gz new file mode 100644 index 00000000..a340841c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/comp.vcf.gz.tbi new file mode 100644 index 00000000..1073cdc1 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/haps.fa new file mode 100644 index 00000000..1add431e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/haps.fa @@ -0,0 +1,62 @@ +>ref_chr20_63641679_63642236 +TCTATTACTGCGGCTAGTTACTGTCCCGCCAGGACCAGACTCTGGACCTGCCTCGTGCGCTGCTGGGGACGCCCAGTAAACACGGGAGGAGCCCCCGACCCCCACCCCAGCTCAGCGCCTCGGAGTCCCCGGCCCCGCTCTGCGCCCCTCCGAGCTCCGCCCTAGCCCCGCCCCCGCCCAGTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCTGGCCCCGCCCCCGCCCAGTGCCCCGCCCCCTGACTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTTCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCGGCCCCGCCCCCGCACCTTCTCGCGCAGCCGCTCGCGCAGTGCGGCCAGGTGTGCCTCGCGGATCTCCTTGCTGAGCTCCATCTTGTAGTTGAGCTTCTCCTCCGCCTGGCGGCTGAAGTTGTTATTCTCCTCCAGCGCCTTGTG +>syndip_1_chr20:63641679-63642236 +TCTATTACTGCGGCTAGTTACTGTCCCGCCAGGACCAGACTCTGGACCTGCCTCGTGCGC +TGCTGGGGACGCCCAGTAAACACGGGAGGAGCCCCCGACCCCCACCCCAGCTCAGCGCCT +CGGAGTCCCCGGCCCCGCTCTGCGCCCCTCCGAGCTCCGCCCTAGCCCCGCCCCCGCCCA +GTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAG +CTCCGCCCTGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCTGGCCCCGCCCCC +CGCCCAGTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGC +TCCGAGCTCCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCTGGCCCC +GCCCCCGCCCAGTGCCCCGCCCCCTGACTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTG +CCCGCTCCGAGCTCCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCG +GCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTTCGCCCCGGCCCCGCCCCGGCCCCTGCCC +GCTCCGAGCTCCGCCCCGGCCCCGCCCCCGCACCTTCTCGCGCAGCCGCTCGCGCAGTGC +GGCCAGGTGTGCCTCGCGGATCTCCTTGCTGAGCTCCATCTTGTAGTTGAGCTTCTCCTC +CGCCTGGCGGCTGAAGTTGTTATTCTCCTCCAGCGCCTTGTG +>syndip_2_chr20:63641679-63642236 +TCTATTACTGCGGCTAGTTACTGTCCCGCCAGGACCAGACTCTGGACCTGCCTCGTGCGC +TGCTGGGGACGCCCAGTAAACACGGGAGGAGCCCCCGACCCCCACCCCAGCTCAGCGCCT +CGGAGTCCCCGGCCCCGCTCTGCGCCCCTCCGAGCTCCGCCCTAGCCCCGCCCCCGCCCA +GTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAG +CTCCGCCCTGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCTGGCCCCGCCCCC +GCCCAGTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCT +CCGAGCTCCACCCTGGCCCCGCCCCCGCCCAGTGCCCCGCCCCCTGCCTGCTGCTTGCCC +TGCCCCCTCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCGGCCCCGCCCCGGCCCAGTG +CCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTC +CGCCCTGGCCCCGCCCCCGCCCAGTGCCCCGCCCCCTGCCTGCTGCTTGCCCTGCCCCCT +CCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCGGCCTCGCCCCGGCCCCTGCCCGCTCCG +AGCTTCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTTCGCCCCGGCCCCGCCC +CGGCCCCTGCCCGCTCCGAACTCCGCCCCGGCCCCGCCCCCGCACCTTCTCGCGCAGCCG +CTCGCGCAGTGCGGCCAGGTGTGCCTCGCGGATCTCCTTGCTGAGCTCCATCTTGTAGTT +GAGCTTCTCCTCCGCCTGGCGGCTGAAGTTGTTATTCTCCTCCAGCGCCTTGTG +>p:HG002_1_chr20:63641679-63642236 +TCTATTACTGCGGCTAGTTACTGTCCCGCCAGGACCAGACTCTGGACCTGCCTCGTGCGC +TGCTGGGGACGCCCAGTAAACACGGGAGGAGCCCCCGACCCCCACCCCAGCTCAGCGCCT +CGGAGTCCCCGGCCCCGCTCTGCGCCCCTCCGAGCTCCGCCCTAGCCCCGCCCCCGCCCA +GTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAG +CTCCGCCCTGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCTGGCCCCGCCCCC +GCCCAGTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCT +CCGAGCTCCACCCTGGCCCCGCCCCCGCCCAGTGCCCCGCCCCCTGCCTGCTGCTTGCCC +TGCCCCCTCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCGGCCCCGCCCCGGCCCAGTG +CCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTC +CGCCCTGGCCCCGCCCCCGCCCAGTGCCCCGCCCCCTGCCTGCTGCTTGCCCTGCCCCCT +CCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCGGCCTCGCCCCGGCCCCTGCCCGCTCCG +AGCTTCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTTCGCCCCGGCCCCGCCC +CGGCCCCTGCCCGCTCCGAACTCCGCCCCGGCCCCGCCCCCGCACCTTCTCGCGCAGCCG +CTCGCGCAGTGCGGCCAGGTGTGCCTCGCGGATCTCCTTGCTGAGCTCCATCTTGTAGTT +GAGCTTCTCCTCCGCCTGGCGGCTGAAGTTGTTATTCTCCTCCAGCGCCTTGTG +>p:HG002_2_chr20:63641679-63642236 +TCTATTACTGCGGCTAGTTACTGTCCCGCCAGGACCAGACTCTGGACCTGCCTCGTGCGC +TGCTGGGGACGCCCAGTAAACACGGGAGGAGCCCCCGACCCCCACCCCAGCTCAGCGCCT +CGGAGTCCCCGGCCCCGCTCTGCGCCCCTCCGAGCTCCGCCCTAGCCCCGCCCCCGCCCA +GTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAG +CTCCGCCCTGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCTGGCCCCGCCCCC +CGCCCAGTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGC +TCCGAGCTCCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCTGGCCCC +GCCCCCGCCCAGTGCCCCGCCCCCTGACTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTG +CCCGCTCCGAGCTCCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCG +GCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTTCGCCCCGGCCCCGCCCCGGCCCCTGCCC +GCTCCGAGCTCCGCCCCGGCCCCGCCCCCGCACCTTCTCGCGCAGCCGCTCGCGCAGTGC +GGCCAGGTGTGCCTCGCGGATCTCCTTGCTGAGCTCCATCTTGTAGTTGAGCTTCTCCTC +CGCCTGGCGGCTGAAGTTGTTATTCTCCTCCAGCGCCTTGTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/haps.fa.ref.fa new file mode 100644 index 00000000..423b8813 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63641679-63642236 +TCTATTACTGCGGCTAGTTACTGTCCCGCCAGGACCAGACTCTGGACCTGCCTCGTGCGCTGCTGGGGACGCCCAGTAAACACGGGAGGAGCCCCCGACCCCCACCCCAGCTCAGCGCCTCGGAGTCCCCGGCCCCGCTCTGCGCCCCTCCGAGCTCCGCCCTAGCCCCGCCCCCGCCCAGTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCTGGCCCCGCCCCCGCCCAGTGCCCCGCCCCCTGACTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTTCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCGGCCCCGCCCCCGCACCTTCTCGCGCAGCCGCTCGCGCAGTGCGGCCAGGTGTGCCTCGCGGATCTCCTTGCTGAGCTCCATCTTGTAGTTGAGCTTCTCCTCCGCCTGGCGGCTGAAGTTGTTATTCTCCTCCAGCGCCTTGTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/msa.fa new file mode 100644 index 00000000..f9dc5498 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/msa.fa @@ -0,0 +1,80 @@ +>ref_chr20_63641679_63642236 +tctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcgc +tgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcct +cggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccca +gtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgag +ctccgccccggccccgccccggcccctgcccgctccgagctccgccctggccccg-cccc +cgcccagtgccccgccccctgactgctgctagccctgc---------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------ccccgccccggcccctgcccgctccgagcttcgccccggccccgcc +ccggcccctgcccgctccgagctccgccccggccccgcccccgcaccttctcgcgcagcc +gctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtagt +tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgtg +>syndip_1_chr20:63641679-63642236 +tctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcgc +tgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcct +cggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccca +gtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgag +ctccgccctggccccgccccggcccctgcccgctccgagctccgccctggccccgccccc +cgcccagtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgc +tccgagctccgccccgg------------------------------------------- +------------------------------------------------------------ +------------------------------ccccgccccggcccctgcccgctccgagct +ccgccctggccccgcccccgcccagtgccccgccccctgactgctgctagccctgccccc +gccccggcccctgcccgctccgagctccgccccggccccgccccggcccctgcccgctcc +gagctccgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgcc +ccggcccctgcccgctccgagctccgccccggccccgcccccgcaccttctcgcgcagcc +gctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtagt +tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgtg +>syndip_2_chr20:63641679-63642236 +tctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcgc +tgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcct +cggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccca +gtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgag +ctccgccctggccccgccccggcccctgcccgctccgagctccgccctggccccg-cccc +cgcccagtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgc +tccgagctccaccctggccccgcccccgcccagtgccccgccccctgcctgctgcttgcc +ctgccccctccccggcccctgcccgctccgagctccgccccggccccgccccggcccagt +gccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgagct +ccgccctggccccgcccccgcccagtgccccgccccctgcctgctgcttgccctgccccc +tccccggcccctgcccgctccgagctccgccccggcctcgccccggcccctgcccgctcc +gagcttcgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgcc +ccggcccctgcccgctccgaactccgccccggccccgcccccgcaccttctcgcgcagcc +gctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtagt +tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgtg +>p:HG002_1_chr20:63641679-63642236 +tctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcgc +tgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcct +cggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccca +gtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgag +ctccgccctggccccgccccggcccctgcccgctccgagctccgccctggccccg-cccc +cgcccagtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgc +tccgagctccaccctggccccgcccccgcccagtgccccgccccctgcctgctgcttgcc +ctgccccctccccggcccctgcccgctccgagctccgccccggccccgccccggcccagt +gccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgagct +ccgccctggccccgcccccgcccagtgccccgccccctgcctgctgcttgccctgccccc +tccccggcccctgcccgctccgagctccgccccggcctcgccccggcccctgcccgctcc +gagcttcgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgcc +ccggcccctgcccgctccgaactccgccccggccccgcccccgcaccttctcgcgcagcc +gctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtagt +tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgtg +>p:HG002_2_chr20:63641679-63642236 +tctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcgc +tgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcct +cggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccca +gtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgag +ctccgccctggccccgccccggcccctgcccgctccgagctccgccctggccccgccccc +cgcccagtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgc +tccgagctccgccccgg------------------------------------------- +------------------------------------------------------------ +------------------------------ccccgccccggcccctgcccgctccgagct +ccgccctggccccgcccccgcccagtgccccgccccctgactgctgctagccctgccccc +gccccggcccctgcccgctccgagctccgccccggccccgccccggcccctgcccgctcc +gagctccgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgcc +ccggcccctgcccgctccgagctccgccccggccccgcccccgcaccttctcgcgcagcc +gctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtagt +tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgtg diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/msa.fa.fai new file mode 100644 index 00000000..d35f8cb1 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63641679_63642236 895 29 60 61 +syndip_1_chr20:63641679-63642236 895 973 60 61 +syndip_2_chr20:63641679-63642236 895 1917 60 61 +p:HG002_1_chr20:63641679-63642236 895 2862 60 61 +p:HG002_2_chr20:63641679-63642236 895 3807 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/output.vcf.gz new file mode 100644 index 00000000..561d69c9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/output.vcf.gz.tbi new file mode 100644 index 00000000..3082ecff Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63641779-63642136/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63693325-63693885/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63693325-63693885/base.vcf.gz new file mode 100644 index 00000000..2d417017 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63693325-63693885/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63693325-63693885/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63693325-63693885/base.vcf.gz.tbi new file mode 100644 index 00000000..51cb1aa8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63693325-63693885/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63693325-63693885/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63693325-63693885/comp.vcf.gz new file mode 100644 index 00000000..f15b6206 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63693325-63693885/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63693325-63693885/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63693325-63693885/comp.vcf.gz.tbi new file mode 100644 index 00000000..b49c7d22 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63693325-63693885/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63693325-63693885/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63693325-63693885/haps.fa new file mode 100644 index 00000000..f7b43526 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63693325-63693885/haps.fa @@ -0,0 +1,432 @@ +>ref_chr20_63693225_63693985 +TCGGCCTGAGCACAGCATTCCCCGAAGGCAGCGGGCACAGCCGGTCCTGGACCCCACTGGTAAATGGGGCCCCAGGTGGGACCCTCAGACTCCTGCGTGGAAGGCAGTGTGGGCCAGAGTCCTGGGCTGCTTGGGGTGGGCATCCTCGGGCCCTGCTTGGCCCCGCCTCTCTGTTCCCCTATGGGAGTGATGGGGGCCTCCACCTCCACCACCAGCACCAGCAGCACCACCTCCACCTCCACCTCCACCTCCACCTCCACCACCACCTCCACCTCCACCACCACCTCCTCCACCACCACCACCTCCACCACCACCACCACCACCACCACCTCCACCTCCACCACCTCCACCTCCACCACCACCACCTCCACCTCCACCACCACCACCTCCACCTCCACCACCACCTCCACCACCACCACCTCCACCTCCACCACCACCTCCACCACCACCACCACCACCACCACCACCACCACCACCACCTCCACCACCACCACCTGCACCACCACCTCCACCTCCACCACCACCACCACCTCCACCTCCACCAGCAGCAGCATCACTTGTTGGGGAGACCCTGTGCAACTCCATGCACAGCCCTGTCCCTGCCATAGCCCCGACCCCTAAGCACAGCCCTGTCCAACTGCCACACGTCCCCTGCCTCCCATGCATGGTCCTGGGGGGTCAACTGCACACGCCAGGGTCCTAGGGTCCTAGACCCCTGTCCTCCCTGTTTCTGCCTCTGTTTGGGGTGGAGTCCAAGTCTC +>syndip_1_chr20:63693225-63693985 +TCGGCCTGAGCACAGCATTCCCCGAAGGCAGCGGGCACAGCCGGTCCTGGACCCCACTGG +TAAATGGGGCCCCAGGTGGGACCCTCAGACTCCTGCGTGGAAGGCAGTGTGGGCCAGAGT +CCTGGGCTGCTTGGGGTGGGCATCCTCGGGCCCTGCTTGGCCCCGCCTCTCTGTTCCCCT +ATGGGAGTGATGGGGGCCTCCACCTCCACCACCAGCACCAGCAGCACCACCTCCACCTTC +ACCACCACCACCTCCACCACCACCTCCACCACCTCCACCTCCACCACCTCCACCACCTCC +ACCACCACCACCTCCACCACCACCACCTCCACCACCACCACCACCACCACCTCCACCACC +ACCACCACCACCACCACCTCCACCTCCACCACCTCCACCACCACCTCCACCTCCACCACC +ACCTCCACCTCCACCTCCACCACCACCACCTCCACCACCTCCACCACCTCCACCTCCACC +ACCACCTCCACCTCCACCACCACCTCCACCTCCACCTCCACCTCCACCTCCACCACCACC +ACCTCCACCACCTCCACCACCTCCACCTCCACCACCACCACCTCCACCTCCACCTCCACC +ACCTCCACCTCCACCACCTCCACCTCCACCACCTCCACCACCACCACCACCACCACCACC +ACCTCCACCACCACCACCACCACCACCTCCACCACCTCCACCTCCACCACCTCCACCACC +ACCACCTCCACCACCACCTCCACCACCACCTCCACCTCCACCACCTCCACCTCCACCACC +TCCACCTCCACCTCCACCACCACCTCCACCACCTCCACCACCACCTCCACCACCTCCACC +TCCACCACCACCACCTCCACCACCACCACCACCACCACCTCCACCACCTCCACCTCCACC +ACCTCCACCACCACCACCTCCACCACCACCTCCACCACCACCTCCACCTCCACCACCTCC +ACCTCCACCACCTCCACCTCCACCTCCACCACCACCTCCACCACCTCCACCACCACCTCC +ACCACCTCCACCACCTCCACCACCACCTCCACCACCTCCACCTCCACCACCACCACCTCC +ACCTCCACCACCACCACCTCCACCACCACCTCCACCTCCACCACCACCACCTCCACCTCC +ACCACCACCACCTCCACCACCACCTCCACCACCACCACCACCACCACCACCTCCACCTCC +ACCACCTCCACCACCACCACCACCACCTCCACCTCCACCACCTCCACCACCTCCACCACC +ACCACCACCACCTCCACCACCTCCACCACCACCTCCACCACCTCCACCTCCACCACCACC +ACCTCCACCACCACCACCTCCACCTCCACCTCCACCTCCACCTCCACCACCACCTCCACC +TCCACCACCACCTCCACCACCACCTCCACCTCCACCACCTCCACCTCCACCTCCACCACC +TCCACCACCACCACCACCACCACCACCACCACCACCACCTCCACCACCTCCACCTCCACC +TCCACCACCACCACCACCACCTCCACCACCACCACCACCACCTCCACCACCTCCACCACC +ACCTCCACCACCACCACCACCACCACCACCACCACCTCCACCACCTCCACCTCCACCTCC +ACCTCCACCACCTCCACCACCTCCACCACCACCTCCACCACCACCACCACCACCTCCACC +ACCACCTCCACCTCCACCACCACCTCCACCACCACCTCCACCTCCACCACCTCCACCTCC +ACCACCTCCACCACCTCCACCTCCACCACCTCCACCTCCACCTCCACCACCTCCACCACC +ACCACCACCACCACCACCACCACCACCACCTCCACCACCACCACCTCCACCACCACCTCC +ACCACCTCCACCACCACCTCCACCACCACCACCACCACCACCACCACCACCACCACCTCC +ACCACCACCTCCACCTCCACCACCACCTCCACCACCACCTCCACCTCCACCACCTCCACC +TCCACCACCTCCACCACCTCCACCACCACCACCACCACCTCCACCACCACCTCCACCTCC +ACCACCACCACCACCACCACCACCTCCACCACCACCACCTCCACCACCACCTCCACCACC +TCCACCACCACCTCCACCTCCACCACCTCCACCACCACCTCCACCACCACCTCCACCACC +ACCACCTCCACCACCACCTCCACCACCTCCACCACCACCTCCACCTCCACCACCTCCACC +ACCACCTCCACCACCACCTCCACCACCACCACCTCCACCACCACCTCCACCACCTCCACC +ACCACCTCCACCTCCACCACCTCCACCTCCACCTCCACCACCTCCACCACCACCACCACC +ACCACCACCACCACCACCACCACCACCACCACCACCTCCACCTCCACCTCCACCACCTCC +ACCTCCACCACCTCCACCACCACCTCCACCTCCACCACCTCCACCTCCACCTCCACCACC +TCCACCTCCACCACCTCCACCTCCACCTCCACCACCTCCACCACCACCACCTCCACCACC +ACCTCCACCACCTCCACCACCACCTCCACCTCCACCACCTCCACCACCACCTCCACCACC +ACCTCCACCACCACCACCTCCACCACCACCTCCACCACCTCCACCACCACCTCCACCTCC +ACCACCTCCACCTCCACCTCCACCACCTCCACCACCACCACCACCACCACCACCACCACC +ACCACCTCCACCACCACCACCTCCACCACCACCTCCACCACCACCACCACCACCTCCACC +ACCACCACCACCACCTCCACCACCACCTCCACCACCTCCACCACCACCACCACCACCACC +ACCACCTCCACCACCACCTCCACCACCACCACCACCACCACCACCACCTCCACCACCTCC +ACCTCCACCACCACCACCACCTCCACCACCACCACCACCACCACCTCCACCTCCACCACC +ACCACCTCCACCACCACCACCACCTCCACCACCACCTCCACCACCACCACCACCACCACC +ACCACCACCTCCACCACCTCCACCACCTCCACCACCACCTCCACCACCTCCACCACCACC +ACCACCACCTCCACCACCACCTCCACCACCACCACCACCACCACCACCTCCACCTCCACC +TCCACCACCTCCACCTCCACCACCTCCACCTCCACCACCTCCACCTCCACCTCCACCACC +TCCACCACCACCTCCACCTCCACCACCACCTCCTCCACCACCACCACCTCCACCACCACC +TCCACCACCACCACCTCCACCTCCACCACCTCCACCTCCACCACCACCACCTCCACCTCC +ACCACCACCACCTCCACCACCTCCACCACCACCTCCACCACCTCCACCTCCACCACCACC +ACCTCCACCACCACCACCTCCACCTCCACCACCACCACCACCACCACCTCCACCTCCACC +ACCACCTCCACCACCACCTCCACCTCCACCTCCACCACCTCCACCACCACCTCCACCACC +TCCACCACCTCCACCTCCACCACCACCACCACCTCCACCACCACCACCACCACCTCTACC +ACCTCTACCACCACCACCACCACCTCCACCACCACCACCACCACCTCCACCACCACCACC +ACCACCACCTCCACCACCACCTCCACCACCTCCACCACCACCACCACCACCTCTACCACC +TCCACCTCCACCACCACCACCACCTCTACCACCACCACCACCACCTCCACCACCACCACC +ACCTCCACCACCACCACCACCTCCACCACCACCTCCACCACCACCTCCACCACCTCCACC +ACCACCACCACCTCCACCTCCACCACCTCCACCACCACCTCCACCACCACCACCACCACC +ACCTCCACCACCACCTCCACCACCTCCACCACCACCACCACCACCTCTACCACCTCCACC +TCCACCACCACCACCACCTCCACCTCCACCACCACCACCACCACCACCACCACCACCACC +TCCACCACCACCACCACCACCACCTCTACCACCACCACCACCACCTCCACCACCACCACC +ACCTCCACCACCACCACCACCTCCACCACCACCTCCACCACCACCACCACCACCACCACC +ACCTCTACCACCACCACCACCACCTCCACCACCACCACCACCTCCACCACCACCACCACC +TCCACCACCACCTCCACCACCACCACCACCTCCACCACCACCTCCACCACCACCTCCACC +ACCTCCACCACCACCACCACCACCTCCACCACCACCTCCACCTCCACCACCACCACCACC +ACCTCCACCACCACCACCACCACCACCACCTCCACCACCACCTCCACCACCACCTCCACC +ACCTCCACCACCACCACCACCACCTCCACCACCACCTCCACCTCCACCACCACCACCACC +ACCTCCACCACCACCTCCACCACCACCACCACCACCACCTCCACCACCACCTCCACCACC +TCCACCACCACCACCACCACCTCTACCACCTCTACCACCACCACCACCACCTCCACCACC +ACCACCACCTCCACCACCACCACCACCTCCACCACCACCACCTCCACCTCCACCACCACC +ACCTCCACCACCTCCACCACCACCTCCACCACCACCACCTCCACCTCCACCACCACCACC +TCCACCACCTCCACCACCACCACCACCACCACCACCACCTCCACCACCACCACCACCACC +ACCTCCACCACCACCTCCACCACCTCCACCACCACCACCACCACCTCTACCACCTCTACC +ACCACCACCACCACCTCCACCACCACCACCACCTCCACCACCACCACCACCTCCACCACC +ACCTCCACCACCACCACCTCCACCTCCACCACCACCACCTCCACCACCACCACCTCCACC +TCCACCACCACCACCTCCACCACCTCCACCACCACCTCCACCACCACCACCTCCACCTCC +ACCACCACCACCTCCACCACCTCCACCACCACCACCTCCACCACCACCACCTCCACCACC +TCCACCACCACCACCACCACCTCCACCACCTCCACCACCTCCACCACCACCACCACCACC +TCCACCTCCACCTCCACCACCTCCACCACCACCACCTCCACCACCACCACCACCACCACC +ACCACCTCCACCTCCACCTCCACCACCTCCACCTCCACCACCACCACCACCACCACCACC +ACCACCACCACCTCCACCTCCACCTCCACCACCTCCACCACCACCACCTCCACCACCACC +ACCTCCACCTCCACCACCTCCACCACCACCTCCACCACCACCACCTCCACCTCCACCACC +ACCACCTCCACCACCACCACCTCCACCTCCACCACCACCACCTCCACCACCTCCACCACC +ACCTCCACCACCACCACCTCCACCTCCACCACCACCACCTCCACCACCTCCACCACCACC +ACCTCCACCACCACCACCTCCACCACCTCCACCACCACCACCACCACCTCCACCACCTCC +ACCACCTCCACCACCACCACCACCACCTCCACCTCCACCTCCACCACCTCCACCACCACC +ACCTCCACCACCACCACCACCACCACCTCCACCACCTCCACCACCACCACCACCACCTCC +ACCTCCACCTCCACCACCTCCACCACCACCACCTCCACCACCACCACCACCACCACCACC +ACCACCTCCACCTCCACCTCCACCACCTCCACCTCCACCACCACCACCACCACCACCACC +TCCACCACCACCTCCACCTCCACCTCCACCACCTCCACCTCCACCACCACCACCACCACC +ACCACCACCACCACCACCTCCACCTCCACCTCCACCACCACCACCTCTACCACCACCTCC +ACCACCACCACCACCACCACCACCACCACCTCCACCACCTCCACCACCACCACCTCCACC +ACCACCACCTCCACCTCCACCACCACCACCACCTCCACCACCTCCACCACCACCTCCACC +TCCACCTCCACCACCTCCACCACCACCACCTCCACCACCACCACCACCACCACCACCTCC +ACCACCTCCACCACCACCACCTCCACCACCACCACCTCCACCTCCACCACCTCCACCACC +TCCACCACCACCACCACCTCCACCACCACCACCACCACCACCTCCACCTCCACCACCTCT +ACCACCACCTCCACCACCACCACCACCACCACCTCCACCTCCACCACCTCCACCTCCACC +ACCTCTACCACCACCTCCACCACCACCACCTCCACCTCCACCTCCACCACCACCACCTCC +ACCTCCACCTCCACCACCACCACCACCACCACCACCTCCACCACCACCACCACCACCACC +ACCACCACCTCCACCTCCACCACCACCACCTCCACCACCACCACCTCCACCACCTCCACC +ACCACCTCCACCTCCACCACCACCACCTCCACCTCCACCTCCACCACCACCACCACCACC +TCCACCACCACCACCTCCACCACCAACACCTCCACCTCCACCTCCACCACCACCACCACC +ACCTCCACCTCCACCACCACCTCCACCACCACCACCTCCACCTCCACCACCACCACCTCC +ACCACCACCTCCACCACCTCCACCACCACCACCTCCACCACCACCTCCACCACCACCACC +ACCACCACCTCCACCTCCACCTCCACCACCACCACCTCTACCACCACCTCCACCACCACC +ACCACCACCACCACCACCACCTCCACCTCCACCTCCACCACCTCCACCTCCACCACCACC +ACCACCACCACCACCTCCACCACCACCTCCACCTCCACCTCCACCACCTCCACCTCCACC +ACCACCACCACCACCACCACCACCACCACCACCTCCACCTCCACCTCCACCACCACCACC +TCTACCACCACCTCCACCACCACCACCACCACCACCACCACCACCTCCACCACCACCACC 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+TCGGCCTGAGCACAGCATTCCCCGAAGGCAGCGGGCACAGCCGGTCCTGGACCCCACTGGTAAATGGGGCCCCAGGTGGGACCCTCAGACTCCTGCGTGGAAGGCAGTGTGGGCCAGAGTCCTGGGCTGCTTGGGGTGGGCATCCTCGGGCCCTGCTTGGCCCCGCCTCTCTGTTCCCCTATGGGAGTGATGGGGGCCTCCACCTCCACCACCAGCACCAGCAGCACCACCTCCACCTCCACCTCCACCTCCACCTCCACCACCACCTCCACCTCCACCACCACCTCCTCCACCACCACCACCTCCACCACCACCACCACCACCACCACCTCCACCTCCACCACCTCCACCTCCACCACCACCACCTCCACCTCCACCACCACCACCTCCACCTCCACCACCACCTCCACCACCACCACCTCCACCTCCACCACCACCTCCACCACCACCACCACCACCACCACCACCACCACCACCACCTCCACCACCACCACCTGCACCACCACCTCCACCTCCACCACCACCACCACCTCCACCTCCACCAGCAGCAGCATCACTTGTTGGGGAGACCCTGTGCAACTCCATGCACAGCCCTGTCCCTGCCATAGCCCCGACCCCTAAGCACAGCCCTGTCCAACTGCCACACGTCCCCTGCCTCCCATGCATGGTCCTGGGGGGTCAACTGCACACGCCAGGGTCCTAGGGTCCTAGACCCCTGTCCTCCCTGTTTCTGCCTCTGTTTGGGGTGGAGTCCAAGTCTC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63693325-63693885/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63693325-63693885/msa.fa new file mode 100644 index 00000000..803367fa --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63693325-63693885/msa.fa @@ -0,0 +1,660 @@ +>ref_chr20_63693225_63693985 +tcggcctgagcacagcattccccgaaggcagcgggcacagccggtcctggaccccactgg +taaatggggccccaggtgggaccctcagactcctgcgtggaaggcagtgtgggccagagt +cctgggctgcttggggtgggcatcctcgggccctgcttggccccgcctctctgttcccct +atgggagtgatgggggcctccacctccaccaccagcaccagcagcaccacctccacct-- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ 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+------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------------------ccacctcc +accaccaccaccaccaccaccaccaccaccacca-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ 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files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63693325-63693885/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63693325-63693885/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63693325-63693885/output.vcf.gz.tbi new file mode 100644 index 00000000..0a9e269b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63693325-63693885/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/base.vcf.gz new file mode 100644 index 00000000..61939413 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/base.vcf.gz.tbi new file mode 100644 index 00000000..bb297398 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/comp.vcf.gz new file mode 100644 index 00000000..f7a4cd31 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/comp.vcf.gz.tbi new file mode 100644 index 00000000..b0541a1f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/haps.fa new file mode 100644 index 00000000..6370617a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/haps.fa @@ -0,0 +1,36 @@ +>ref_chr20_63770812_63771204 +TGTCCCCATTTCCTGCACGATGCGCCAGCCCACGGGGAGGTACACTCGACAGGACACCCTAGAGACCACGCTAACAAGAGGCCCAGCCCTGGAAATGCTCATCGCCTGCAACCAGCACATGGAGATGGTCGCAAGTCAGCACCGGCCACGCCCGGCACAGCAGCCACGCCGCTCGAACCACAGCAGGGGCCACGTCAGCAGGAGGTCGCAAGTCAGCACCGGCCACGCCCGGCACAGCAGCCACGCCGCTCGAACCACAGCAGGGGCTACTCGCCCTCCCAGGCCCTCTTCAGAGCTGGCCTGAGTTGAAGCTGCGTTCCTCCTGCTCTGAGGGCTGGGTACCGGGGACCCTCGCCCAGCCGAGGCCGCTCTTGTCTTCTTCTCTCTTCCGAC +>syndip_1_chr20:63770812-63771204 +TGTCCCCATTTCCTGCACGATGCGCCAGCCCACGGGGAGGTACACTCGACAGGACACCCT +AGAGACCACGCTAACAAGAGGCCCAGCCCTGGAAATGCTCATCGCCTGCAACCAGCACAT +GGAGATGGTCGCAAGTCAGCACCGGCCACGCCCGGCACAGCAGCCACGCCGCTCGAACCA +CAGCAGGGGCCACGTCAGCAGGAGGTCGCAAGTCAGCACCGGCCACGCCCGGCACAGCAG +CCACGCCGCTCGAACCACAGCAGGGGCTACTCGCCCTCCCAGGCCCTCTTCAGAGCTGGC +CTGAGTTGAAGCTGCGTTCCTCCTGCTCTGAGGGCTGGGTACCGGGGACCCTCGCCCAGC +CGAGGCCGCTCTTGTCTTCTTCTCTCTTCCGAC +>syndip_2_chr20:63770812-63771204 +TGTCCCCATTTCCTGCACGATGCGCCAGCCCACGGGGAGGTACACTCGACAGGACACCCT +AGAGACCACGCTAACAAGAGGCCCAGCCCTGGAAATGCTCATCGCCTGCAACCAGCACAT +GGAGATGGTCGCAAGTCAGCACCGGCCACGCCCGGCACAGCAGCCACGCCGCTCGAACCA +CAGCAGGGGCCACGTCAGCAGGAGGTCGCAAGTCAGCACCGGCCACGCCCGGCACAGCAG +CCACGCCGCTCGAACCACAGCAGGGGCTACTCGCCCTCCCAGGCCCTCTTCAGAGCTGGC +CTGAGTTGAAGCTGCGTTCCTCCTGCTCTGAGGGCTGGGTACCGGGGACCCTCGCCCAGC +CGAGGCCGCTCTTGTCTTCTTCTCTCTTCCGAC +>p:HG002_1_chr20:63770812-63771204 +TGTCCCCATTTCCTGCACGATGCGCCAGCCCACGGGGAGGTACACTCGACAGGACACCCT +AGAGACCACGCTAACAAGAGGCCCAGCCCTGGAAATGCTCATCGCCTGCAACCAGCACAT +GGAGATGGTCGCAAGTCAGCACCGGCCACGCCCGGCACAGCAGCCACGCCGCTCGAACCA +CAGCAGGGGCTACTCGCCCTCCCAGGCCCTCTTCAGAGCTGGCCTGAGTTGAAGCTGCGT +TCCTCCTGCTCTGAGGGCTGGGTACCGGGGACCCTCGCCCAGCCGAGGCCGCTCTTGTCT +TCTTCTCTCTTCCGAC +>p:HG002_2_chr20:63770812-63771204 +TGTCCCCATTTCCTGCACGATGCGCCAGCCCACGGGGAGGTACACTCGACAGGACACCCT +AGAGACCACGCTAACAAGAGGCCCAGCCCTGGAAATGCTCATCGCCTGCAACCAGCACAT +GGAGATGGTCGCAAGTCAGCACCGGCCACGCCCGGCACAGCGGCCACGCCGCTCGAACCA +CAGCAGGGGCCACGTCAGCAGGAGGTCGCAAGTCAGGACCGGCCACGCCCGGCACAGCGG +CCACGCCGCTCGAACCACAGCAGGGGCCACGTCAGCAGGAGGTCGCAAGTCAGGACCGGC +CACGCCCGGCACAGCGGCCACGCCGCTCGAACCACAGCAGGGGCCACGTCAGCAGGAGGT +CGCAAGTCAGCACCGGCCACGCCCGGCACAGCAGCCACGCCGCTAGAACCACAGCAGGGG +CTACTCGCCCTCCCAGGCCCTCTTCAGAGCTGGCCTGAGTTGAAGCTGCGTTCCTCCTGC +TCTGAGGGCTGGGTACCGGGGACCCTCGCCCAGCCGAGGCCGCTCTTGTCTTCTTCTCTC +TTCCGAC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/haps.fa.ref.fa new file mode 100644 index 00000000..f897c55d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63770812-63771204 +TGTCCCCATTTCCTGCACGATGCGCCAGCCCACGGGGAGGTACACTCGACAGGACACCCTAGAGACCACGCTAACAAGAGGCCCAGCCCTGGAAATGCTCATCGCCTGCAACCAGCACATGGAGATGGTCGCAAGTCAGCACCGGCCACGCCCGGCACAGCAGCCACGCCGCTCGAACCACAGCAGGGGCCACGTCAGCAGGAGGTCGCAAGTCAGCACCGGCCACGCCCGGCACAGCAGCCACGCCGCTCGAACCACAGCAGGGGCTACTCGCCCTCCCAGGCCCTCTTCAGAGCTGGCCTGAGTTGAAGCTGCGTTCCTCCTGCTCTGAGGGCTGGGTACCGGGGACCCTCGCCCAGCCGAGGCCGCTCTTGTCTTCTTCTCTCTTCCGAC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/msa.fa new file mode 100644 index 00000000..94dd95ab --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/msa.fa @@ -0,0 +1,55 @@ +>ref_chr20_63770812_63771204 +tgtccccatttcctgcacgatgcgccagcccacggggaggtacactcgacaggacaccct +agagaccacgctaacaagaggcccagccctggaaatgctcatcgcctgcaaccagcacat +ggagatggtcgcaagtcagc---------------------------------------- +------------------------------------------------------------ +------------------------------------------------------accggc +cacgcccggcacagcagccacgccgctcgaaccacagcaggggccacgtcagcaggaggt +cgcaagtcagcaccggccacgcccggcacagcagccacgccgctcgaaccacagcagggg +ctactcgccctcccaggccctcttcagagctggcctgagttgaagctgcgttcctcctgc +tctgagggctgggtaccggggaccctcgcccagccgaggccgctcttgtcttcttctctc +ttccgac +>syndip_1_chr20:63770812-63771204 +tgtccccatttcctgcacgatgcgccagcccacggggaggtacactcgacaggacaccct +agagaccacgctaacaagaggcccagccctggaaatgctcatcgcctgcaaccagcacat +ggagatggtcgcaagtcagc---------------------------------------- +------------------------------------------------------------ +------------------------------------------------------accggc +cacgcccggcacagcagccacgccgctcgaaccacagcaggggccacgtcagcaggaggt +cgcaagtcagcaccggccacgcccggcacagcagccacgccgctcgaaccacagcagggg +ctactcgccctcccaggccctcttcagagctggcctgagttgaagctgcgttcctcctgc +tctgagggctgggtaccggggaccctcgcccagccgaggccgctcttgtcttcttctctc +ttccgac +>syndip_2_chr20:63770812-63771204 +tgtccccatttcctgcacgatgcgccagcccacggggaggtacactcgacaggacaccct +agagaccacgctaacaagaggcccagccctggaaatgctcatcgcctgcaaccagcacat +ggagatggtcgcaagtcagc---------------------------------------- +------------------------------------------------------------ +------------------------------------------------------accggc +cacgcccggcacagcagccacgccgctcgaaccacagcaggggccacgtcagcaggaggt +cgcaagtcagcaccggccacgcccggcacagcagccacgccgctcgaaccacagcagggg +ctactcgccctcccaggccctcttcagagctggcctgagttgaagctgcgttcctcctgc +tctgagggctgggtaccggggaccctcgcccagccgaggccgctcttgtcttcttctctc +ttccgac +>p:HG002_1_chr20:63770812-63771204 +tgtccccatttcctgcacgatgcgccagcccacggggaggtacactcgacaggacaccct +agagaccacgctaacaagaggcccagccctggaaatgctcatcgcctgcaaccagcacat +ggagat------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------------------------ggt +cgcaagtcagcaccggccacgcccggcacagcagccacgccgctcgaaccacagcagggg +ctactcgccctcccaggccctcttcagagctggcctgagttgaagctgcgttcctcctgc +tctgagggctgggtaccggggaccctcgcccagccgaggccgctcttgtcttcttctctc +ttccgac +>p:HG002_2_chr20:63770812-63771204 +tgtccccatttcctgcacgatgcgccagcccacggggaggtacactcgacaggacaccct +agagaccacgctaacaagaggcccagccctggaaatgctcatcgcctgcaaccagcacat +ggagatggtcgcaagtcagcaccggccacgcccggcacagcggccacgccgctcgaacca +cagcaggggccacgtcagcaggaggtcgcaagtcaggaccggccacgcccggcacagcgg +ccacgccgctcgaaccacagcaggggccacgtcagcaggaggtcgcaagtcaggaccggc +cacgcccggcacagcggccacgccgctcgaaccacagcaggggccacgtcagcaggaggt +cgcaagtcagcaccggccacgcccggcacagcagccacgccgctagaaccacagcagggg +ctactcgccctcccaggccctcttcagagctggcctgagttgaagctgcgttcctcctgc +tctgagggctgggtaccggggaccctcgcccagccgaggccgctcttgtcttcttctctc +ttccgac diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/msa.fa.fai new file mode 100644 index 00000000..9f211161 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63770812_63771204 547 29 60 61 +syndip_1_chr20:63770812-63771204 547 620 60 61 +syndip_2_chr20:63770812-63771204 547 1211 60 61 +p:HG002_1_chr20:63770812-63771204 547 1803 60 61 +p:HG002_2_chr20:63770812-63771204 547 2395 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/output.vcf.gz new file mode 100644 index 00000000..f49ccbc2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/output.vcf.gz.tbi new file mode 100644 index 00000000..95da086f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63770912-63771104/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/base.vcf.gz new file mode 100644 index 00000000..bbb01d44 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/base.vcf.gz.tbi new file mode 100644 index 00000000..912fc502 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/comp.vcf.gz new file mode 100644 index 00000000..4db159e1 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/comp.vcf.gz.tbi new file mode 100644 index 00000000..e27fde67 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/haps.fa new file mode 100644 index 00000000..b57979ec --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/haps.fa @@ -0,0 +1,162 @@ +>ref_chr20_63948414_63948859 +ACAGAACACAGGTGCGGACAGGGAACGGCATCCTCAGAGCATGGTCAGGGGAGAAAAGCAAGCTGGAAGGAGAGATGATTCCATCTGTATAAAATCCAGGAAACGAAGGACGCTCACCGCCATGCGCCTCGGTGTGAGGAGGGAGGCGTGTGTGAGAGGGAGGGGATGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGTGTGTGTGAGACCGAGGGGGCGTGTAAGGGAGGGGGTGTGTGTGAGAGGGAAGCGTGTGCACACACCAGCCCTAACCATGATCACTCTCTGGCCACCAAGATTTGGAACAGCAACTTCTGTCACATTTGAATGTTTTTAAAGCAGGTGCCACTTTGTTGCCATAAACCAAACCGTAGTCTGT +>syndip_1_chr20:63948414-63948859 +ACAGAACACAGGTGCGGACAGGGAACGGCATCCTCAGAGCATGGTCAGGGGAGAAAAGCA +AGCTGGAAGGAGAGATGATTCCATCTGTATAAAATCCAGGAAACGAAGGACGCTCACCGC +CATGCGCCTCGGTGTGAGGAGGGAGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGA +GGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGTGTGTGTGAGAGGGAGGGGC +GTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGCAGGGGGCGTGTGTGTGAGGGGCGTGTG +TGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGGGGGGGCGTGTGTGAGA +GGTAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGCGTGTGTGAGAGGGA +GGGGCGTGTGTGTGAGGGAGGGGCGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGCAGGGG +CGTGTGTGTGAGGGAGGGGCGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTG +TGAGGGGGGGCGTGTGTGAGAGGTAGGGGCGTGTGTGGGAGGGGGCGTGTGTGAGAGGGA +GGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGACGGAGGGGCGTGTGTGAGAGGGAGG +GGGCGTGTGTGAGAGGGAGAGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGC +GTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGAGGCGTGT +GTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGAGA +GGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAG +GGAGGGGCGTGTGTGAAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGAGAGGGAGGGG +CGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCG +TGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGT +GTGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGAGAGGGAGGGGGCGTGTGTGAG +AGGGAGAGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGAGGGA +GGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAG +AGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGCGTGTGTGAGAGGGAGAGGC +GTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGAGGCGTGTGTGAGAGGGAGGGGCGT +GTGTGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTG +TGAGAGGGAGAGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGA +GAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGA +GGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGG +GAGGGGCGTGTGTGAAGGGAGGGGCGTGTGTGAGAGTGGGGGCGTGTGTGAGTTAGGGGC +GTGAGAGGTAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGAGA +GGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGG +AGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAG +GGGCGTGTGTGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGAGAGGGAGGGGCGT +GTGTGAGAGGGAGGGGCGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTG +AGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGAGAGGGAGGGGGCGTGTGTGAGGGAG +GGGCGTGTGTGAGAGGGAGGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAG +GGGGTGTGTGTGAGACCGAGGGGGCGTGTAAGGGAGGGGGTGTGTGTGAGAGGGAAGCGT +GTGCACACACCAGCCCTAACCATGATCACTCTCTGGCCACCAAGATTTGGAACAGCAACT +TCTGTCACATTTGAATGTTTTTAAAGCAGGTGCCACTTTGTTGCCATAAACCAAACCGTA +GTCTGT +>syndip_2_chr20:63948414-63948859 +ACAGAACACAGGTGCGGACAGGGAACGGCATCCTCAGAGCATGGTCAGGGGAGAAAAGCA +AGCTGGAAGGAGAGATGATTCCATCTGTATAAAATCCAGGAAACGAAGGACGCTCACCGC +CATGCGCCTCGGTGTGAGGAGGGAGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGA +GGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGTGTGTGTGAGAGGGAGGGG +CGTGTGTGAGAGGGAGGGGGCGTGTGTGAAAGGGAGGGGCGTGTGTGAGGGAGGGGCGTG +TGTGAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGAGGGAGGGGGCGTGTGTG +AGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGAGAGTGGGGGCGTGTGTGAGGG +GGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGTAGGGGCGTGTGTGAGAGGGAGG +GGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGGGGGGGGCGTGT +GTGAGGGGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGAGAGGGAGGGGCGTGTGTGAGA +GGGAGGGGGCGTGTGTGTGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAAGGG +AGGGGTGTGTGTGAGAGTGGGGGCGTGTGTGAGAGGGGCGTGAGAGGTAGGGGCGTGTGT +GAGAGGGAGGGGTGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAG +GGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGCGTGTGTGAGAGGGA +GGGGCGTGTGTGAGAGTGGGGGCGTGTGTGGGGGGGCGTGTGTGAGGGGGGGCGTGTGTG +AGAGGTAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGCGTGTGTGAGAGG +CAGGGGCGTGTGTGGGGGGGGGCGTGTGTGAGGGGGGGGCGTGTGTGAGAGGGAGGGGGC +GTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTG +TGTGAGAGGCAGGGGCGTGTGTGGGGGGGGCGTGTGTGAGGGGGGCGTGTGAGAGGGAGG +GGCGTGTGTGGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGT +GTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAAGGGAGGGGTGTGTGT +GAGAGTGGGGGCGTGTGTGAGAGTTAGGGGCGTGAGAGGTAGGGGCGTGTGTGAGAGGGA +GGGGCGTGTGTGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGG +CGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGCGTG +TGCGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGGGAGGGGGCGTGTGT +GAGAGGGAGGGGCGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGTGA +GGGAGGGGCGTGAGAGGGAGGGGCGTGTGTGAGGGGGGGCGTGTGTGAGAGGTAGGGGCG +TGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGT +GTGTGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGT +GAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTG +AAGGGAGGGGCGTGTGTGAGAGTGGGGGCGTGTGTGAGAGGGGCGTGAGAGGTAGGGGCG +TGTGTGAGAGGGAGGGGGCGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTG +AGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGAGA +GGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAAGGGGCGTGTGAGAGGG +AGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGG +GGGTGTGTGTGAGACCGAGGGGGCGTGTAAGGGAGGGGGTGTGTGTGAGAGGGAAGCGTG +TGCACACACCAGCCCTAACCATGATCACTCTCTGGCCACCAAGATTTGGAACAGCAACTT +CTGTCACATTTGAATGTTTTTAAAGCAGGTGCCACTTTGTTGCCATAAACCAAACCGTAG +TCTGT +>p:HG002_1_chr20:63948414-63948859 +ACAGAACACAGGTGCGGACAGGGAACGGCATCCTCAGAGCATGGTCAGGGGAGAAAAGCA 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+GGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGG +GAGGGGCGTGTGTGAAGGGAGGGGCGTGTGTGAGAGTGGGGGCGTGTGTGAGTTAGGGGC +GTGAGAGGTAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGAGA +GGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGG +AGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAG +GGGCGTGTGTGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGAGAGGGAGGGGCGT +GTGTGAGAGGGAGGGGCGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTG +AGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGAGAGGGAGGGGGCGTGTGTGAGGGAG +GGGCGTGTGTGAGAGGGAGGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAG +GGGGTGTGTGTGAGACCGAGGGGGCGTGTAAGGGAGGGGGTGTGTGTGAGAGGGAAGCGT +GTGCACACACCAGCCCTAACCATGATCACTCTCTGGCCACCAAGATTTGGAACAGCAACT +TCTGTCACATTTGAATGTTTTTAAAGCAGGTGCCACTTTGTTGCCATAAACCAAACCGTA +GTCTGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/haps.fa.ref.fa new file mode 100644 index 00000000..2636ea7d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63948414-63948859 +ACAGAACACAGGTGCGGACAGGGAACGGCATCCTCAGAGCATGGTCAGGGGAGAAAAGCAAGCTGGAAGGAGAGATGATTCCATCTGTATAAAATCCAGGAAACGAAGGACGCTCACCGCCATGCGCCTCGGTGTGAGGAGGGAGGCGTGTGTGAGAGGGAGGGGATGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGTGTGTGTGAGACCGAGGGGGCGTGTAAGGGAGGGGGTGTGTGTGAGAGGGAAGCGTGTGCACACACCAGCCCTAACCATGATCACTCTCTGGCCACCAAGATTTGGAACAGCAACTTCTGTCACATTTGAATGTTTTTAAAGCAGGTGCCACTTTGTTGCCATAAACCAAACCGTAGTCTGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/msa.fa new file mode 100644 index 00000000..c2c10901 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/msa.fa @@ -0,0 +1,205 @@ +>ref_chr20_63948414_63948859 +acagaacacaggtgcggacagggaacggcatcctcagagcatggtcaggggagaaaagca +agctggaaggagagatgattccatctgtataaaatccaggaaacgaaggacgctcaccgc +catgcgcctcg------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--gtgtgaggagggaggcgtgtgtgagagggaggggatgtgt---------------gtg +agagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaaggggcgtgtgtga +ga---gggaggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgtaa +gggagggggtgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcactc +tctggccaccaagatttggaacagcaacttctgtcacatttgaatgtttttaaagcaggt +gccactttgttgccataaaccaaaccgtagtctgt +>syndip_1_chr20:63948414-63948859 +acagaacacaggtgcggacagggaacggcatcctcagagcatggtcaggggagaaaagca +agctggaaggagagatgattccatctgtataaaatccaggaaacgaaggacgctcaccgc +catgcgcctcggtgtgaggagggaggcgtgtgtgagagggaggggcgtgtgtgagaggga +-ggggcgtgtgtgagagggaggggcgtgtgtgagggaggggtgtgtgtgagagggagggg +cgtgtgtgagagggagggggcgtgtgtgagaggcagggg-gcgtgtgtgtgaggggcgtg +tgtgagagggaggggcgtgtgtgagagggagggg-gcgtgtgtgagggggggcgtgtgtg +agaggtaggggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagag +gg-----------------aggggcgtgtgtgtgagggaggggcgtgtgagag-ggaggg +ggcgtgtgtgagaggcaggggcgtgtgtgtgagggaggggcgtgagagggaggggcgtgt +gtgagagggagggggcgtgtgtgagggggggcgtgtgtgagaggtaggggcgtgtgt--- +-gggagggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgaga +cggaggggcgtgtgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgagagg +gaggggcgtgtgtgagggagggg---gcgtgtgagagggaggggcgtgtgtgagagggag +ggggcgtgtgtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagggaggggg +cgtgtgtgagagggaggggcgtgtgagaggg-aggggcgtgtgtgagagg---------- +gagggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgaaggga +ggggcgtgtgtgagagggagggggcgtgagagggaggggcgtgtgtgagagggaggggcg +tgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtg +tgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtga +gag--------ggagggggcgtgtgagagggagggggcgtgtgtgagagggagaggcgtg +tgtgagaggga-ggggcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtg +agagggagggggcgtgtgtgagagggagggggcgtgt-------------gtgagaggga +gaggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagagggagagg +cgtgtgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgagagggaggggcg +tgtgtgagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgt +gtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtg +agagggaggggcgtgtgtgagagggag--------------ggggcgtgtgtgagaggga +ggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagaggga-g +gggcgtgtgtgagagggaggggcgtgtgtgaagggaggggcgtgtgtgagagtgggggcg +tgtgtgagttaggggcgtgagaggtaggggcgtgtgtgagagggaggggcgtgtgtgaga +gggagggggcgtg-----agagggaggggcgtgtgtgagagggaggggcgtgtgtgagag +ggaggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagaggg +aggggcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtgagagggagggg +-gcgtgtgagagggaggggcgtgtgtgagagggaggggc--gtgtgagagggaggggcgt +gtgtgagaggga-ggggcgtgtgtgagagggagggg-cgtgtgtgagagggaggggcgtg +agagggagggggcgtgtgt--gagggaggggcgtgtgtgagaggga-ggggggcgtgtgt +gagagggagggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgtaa +gggagggggtgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcactc +tctggccaccaagatttggaacagcaacttctgtcacatttgaatgtttttaaagcaggt +gccactttgttgccataaaccaaaccgtagtctgt +>syndip_2_chr20:63948414-63948859 +acagaacacaggtgcggacagggaacggcatcctcagagcatggtcaggggagaaaagca +agctggaaggagagatgattccatctgtataaaatccaggaaacgaaggacgctcaccgc +catgcgcctcggtgtgaggagggaggcgtgtgtgagagggaggggcgtgtgtgagaggga +gggggcgtgtgtgagagggaggggcgtgtgtgagggaggggtgtgtgtgagagggagggg +cgtgtgtgagagggagggggcgtgtgtgaaagggaggggcgtgtgtgagggaggggcgtg +tgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtgagggagggggcgtgtgtg +agagggaggggcgtgtgtgagaggcaggggcgtgtgtgagagtgggggcgtgtgtgaggg +ggggcgtgtgtgagagggagggggcgtgtgtgagaggtaggggcgtgtgtgagagggagg +ggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtggggggggcgtgt +gtgag-gggggggcgtgtgtgagagggagggggcgtgtgagagggaggggcgtgtgtgag +agggagggggcgtgtgtgtgaggga-ggggcgtgtgtgagagggaggggcgtgtgtga-- +-agggaggggtgtgtgtgagagtgggggcgtgtgtgagaggg--------gcgtgagagg +taggggcgtgtgtgagagggaggggtgtgtgtgagagggaggggcgtgtgtgagaggga- +ggggcgtgtgtgag-ggagggggcgtgtgtgagagggaggggcgtgtgtgagggaggggg +cgtgtgtgagagggaggggcgtgtgtgagagtgggggcgtgtgtgggggggcgtgtgtga +gggggggcgtgtgtgagaggta-ggggcgtgtgtgagagggaggggcgtgtgtg-aggga +ggggcgtgtgtgagaggcaggggcgtgtgtgggggggggcgtgtgt--gaggggggggcg +tgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtg +tgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtggggggggcgtgtgtgagg +ggggcgtgtgagagggaggggcgtgtgtggggaggggcgtgtgtgagagggaggggcgtg +tgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtg +tgaagggaggggtgtgtgtgagagtgggggcgtgtgtgagagttaggggcgtgagaggta +ggggcgtgtgtgagagggaggggcgtgtgtgaggga-ggggcgtgtgtgagagggagggg +cgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcg +tgtgtgagggagggggcgtgtgcgagagggaggggcgtgtgtgagagggagggggcgtgt +gtgag-ggagggggcgtgtgtgagagggaggggcgtgtgagag-ggagggggcgtgtgtg +agaggcaggggcgtgtgtgtgagggaggggcgtgagagggaggggcgtgtgtga---ggg +ggggcgtgtgtgagaggtaggggcgtgtgtgagagggagggggcgtgtgtgagagggagg +gggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgt--------------- +----------------gtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgaga +gggagggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtga-ag +ggaggggcgtgtgtgagagtgggggcgtgtgtgagaggg----------gcgtgagaggt +aggggcgtgtgtgagagggagggg-gcgtgagagggaggggcgtgtgtgagagggagggg +cgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgt +gtgtgagagggagggggcgtgtgtgagagggagggg-cgtgt---------------gtg +agagggaaggggcgtgtga--gagggaggggcgtgtgtgagaggga-ggggcgtgtgtga +ga---gggaggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgtaa +gggagggggtgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcactc +tctggccaccaagatttggaacagcaacttctgtcacatttgaatgtttttaaagcaggt +gccactttgttgccataaaccaaaccgtagtctgt +>p:HG002_1_chr20:63948414-63948859 +acagaacacaggtgcggacagggaacggcatcctcagagcatggtcaggggagaaaagca +agctggaaggagagatgattccatctgtataaaatccaggaaacgaaggacgctcaccgc +catgcgcctcggtgtgaggagggaggcgtgtgtgagagggaggggcgtgtgtgagaggga +gggggcgtgtgtgagagggaggggcgtgtgtgagggaggggtgtgtgtgagagggagggg +cgtgtgtgagagggagggggcgtgtgtgaaagggaggggcgtgtgtgagggaggggcgtg +tgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtgagggagggggcgtgtgtg +agagggaggggcgtgtgtgagaggcaggggcgtgtgtgagagtgggggcgtgtgtgaggg +ggggcgtgtgtgagagggagggggcgtgtgtgagaggtaggggcgtgtgtgagagggagg +ggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtggggggggcgtgt +gtgag-gggggggcgtgtgtgagagggagggggcgtgtgagagggaggggcgtgtgtgag +agggagggggcgtgtgtgtgaggga-ggggcgtgtgtgagagggaggggcgtgtgtga-- +-agggaggggtgtgtgtgagagtgggggcgtgtgtgagaggg--------gcgtgagagg +taggggcgtgtgtgagagggaggggtgtgtgtgagagggaggggcgtgtgtgagaggga- +ggggcgtgtgtgag-ggagggggcgtgtgtgagagggaggggcgtgtgtgagggaggggg +cgtgtgtgagagggaggggcgtgtgtgagagtgggggcgtgtgtgggggggcgtgtgtga +gggggggcgtgtgtgagaggta-ggggcgtgtgtgagagggaggggcgtgtgtg-aggga +ggggcgtgtgtgagaggcaggggcgtgtgtgggggggggcgtgtgt--gaggggggggcg +tgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtg +tgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtggggggggcgtgtgtgagg +ggggcgtgtgagagggaggggcgtgtgtggggaggggcgtgtgtgagagggaggggcgtg +tgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtg +tgaagggaggggtgtgtgtgagagtgggggcgtgtgtgagagttaggggcgtgagaggta +ggggcgtgtgtgagagggaggggcgtgtgtgaggga-ggggcgtgtgtgagagggagggg +cgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcg +tgtgtgagggagggggcgtgtgcgagagggaggggcgtgtgtgagagggagggggcgtgt +gtgag-ggagggggcgtgtgtgagagggaggggcgtgtgagag-ggagggggcgtgtgtg +agaggcaggggcgtgtgtgtgagggaggggcgtgagagggaggggcgtgtgtga---ggg +ggggcgtgtgtgagaggtaggggcgtgtgtgagagggagggggcgtgtgtgagagggagg +gggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgt--------------- +----------------gtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgaga +gggagggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtga-ag +ggaggggcgtgtgtgagagtgggggcgtgtgtgagaggg----------gcgtgagaggt +aggggcgtgtgtgagagggagggg-gcgtgagagggaggggcgtgtgtgagagggagggg +cgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgt +gtgtgagagggagggggcgtgtgtgagagggagggg-cgtgt---------------gtg +agagggaaggggcgtgtga--gagggaggggcgtgtgtgagaggga-ggggcgtgtgtga +ga---gggaggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgtaa +gggagggggtgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcactc +tctggccaccaagatttggaacagcaacttctgtcacatttgaatgtttttaaagcaggt +gccactttgttgccataaaccaaaccgtagtctgt +>p:HG002_2_chr20:63948414-63948859 +acagaacacaggtgcggacagggaacggcatcctcagagcatggtcaggggagaaaagca +agctggaaggagagatgattccatctgtataaaatccaggaaacgaaggacgctcaccgc +catgcgcctcggtgtgaggagggaggcgtgtgtgagagggaggggcgtgtgtgagaggga +-ggggcgtgtgtgagagggaggggcgtgtgtgagggaggggtgtgtgtgagagggagggg +cgtgtgtgagagggagggggcgtgtgtgagaggcagggg-gcgtgtgtgtgaggggcgtg +tgtgagagggaggggcgtgtgtgagagggagggg-gcgtgtgtgagggggggcgtgtgtg +agaggtaggggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagag +gg-----------------aggggcgtgtgtgtgagggaggggcgtgtgagag-ggaggg +ggcgtgtgtgagaggcaggggcgtgtgtgtgagggaggggcgtgagagggaggggcgtgt +gtgagagggagggggcgtgtgtgagggggggcgtgtgtgagaggtaggggcgtgtgt--- +-gggagggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgaga +cggaggggcgtgtgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgagagg +gaggggcgtgtgtgagggagggg---gcgtgtgagagggaggggcgtgtgtgagagggag +ggggcgtgtgtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagggaggggg +cgtgtgtgagagggaggggcgtgtgagaggg-aggggcgtgtgtgagagg---------- +gagggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgaaggga +ggggcgtgtgtgagagggagggggcgtgagagggaggggcgtgtgtgagagggaggggcg +tgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtg +tgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtga +gag--------ggagggggcgtgtgagagggagggggcgtgtgtgagagggagaggcgtg +tgtgagaggga-ggggcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtg +agagggagggggcgtgtgtgagagggagggggcgtgt-------------gtgagaggga +gaggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagagggagagg +cgtgtgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgagagggaggggcg +tgtgtgagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgt +gtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtg +agagggaggggcgtgtgtgagagggag--------------ggggcgtgtgtgagaggga +ggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagaggga-g +gggcgtgtgtgagagggaggggcgtgtgtgaagggaggggcgtgtgtgagagtgggggcg +tgtgtgagttaggggcgtgagaggtaggggcgtgtgtgagagggaggggcgtgtgtgaga +gggagggggcgtg-----agagggaggggcgtgtgtgagagggaggggcgtgtgtgagag +ggaggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagaggg +aggggcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtgagagggagggg +-gcgtgtgagagggaggggcgtgtgtgagagggaggggc--gtgtgagagggaggggcgt +gtgtgagaggga-ggggcgtgtgtgagagggagggg-cgtgtgtgagagggaggggcgtg +agagggagggggcgtgtgt--gagggaggggcgtgtgtgagaggga-ggggggcgtgtgt +gagagggagggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgtaa +gggagggggtgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcactc +tctggccaccaagatttggaacagcaacttctgtcacatttgaatgtttttaaagcaggt +gccactttgttgccataaaccaaaccgtagtctgt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/msa.fa.fai new file mode 100644 index 00000000..6d36ac49 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63948414_63948859 2375 29 60 61 +syndip_1_chr20:63948414-63948859 2375 2478 60 61 +syndip_2_chr20:63948414-63948859 2375 4927 60 61 +p:HG002_1_chr20:63948414-63948859 2375 7377 60 61 +p:HG002_2_chr20:63948414-63948859 2375 9827 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/output.vcf.gz new file mode 100644 index 00000000..51ef938b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/output.vcf.gz.tbi new file mode 100644 index 00000000..c6d72bc0 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63948514-63948759/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/base.vcf.gz new file mode 100644 index 00000000..2b3a8900 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/base.vcf.gz.tbi new file mode 100644 index 00000000..cfc1b064 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/comp.vcf.gz new file mode 100644 index 00000000..cf78afa2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/comp.vcf.gz.tbi new file mode 100644 index 00000000..55686939 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/haps.fa new file mode 100644 index 00000000..b3d7f313 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/haps.fa @@ -0,0 +1,106 @@ +>ref_chr20_63964668_63966718 +CCTGGCCTGCTTGGGTGGAATTGGGCAGGTGTCCAGGCTGTCCGCAGCCCTGCAGGGAGCAGGTGAGGTGAGGGCCAGGAGGGCCTAACTGTGGGCCCCATTACCCCCAGGCCGTGGCCGAGGAGCACCCTGACCTGGAACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACAAGCCCCCATACCTTTTCTTACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGAACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCCAACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCTGTGGCACGAGGTGCTTTGTTCTCCGACCTGGTCAGCAGCACCATTTTGCAGGGCGGTGTGTGTCTGCTGATAGCAATGGGCCTGCTGACTGTCACCGGCTTGCTGACCACAATGGGCCTGCTGACTGTCACTGGCTTGGTGACCGGCACGGGTTTCGTAACTGTCACAAGCTTTGTTACCGTAATGGGTTTGGTGACAGGTACGGGTTTGGTGACCGGCACAGACTTGGTGACTGTGATGGGTTTGGTGACCGGCATGGCCTTGGTGACGGGCATGGGCCTGCTGACTGTGACAGGTTTGGTGACTGGCACGGGCCTAGTGACCGGGATGGCCTTGGTGACTGGCATGGGTCTGCCGACCGAGACTGGCTTGCTGATGCCAATGGGTTTGCTGACACCCACAGGTTTGCCAATAGTGACAGGTTTGCTCACTCCGATGGGCTTGCTGACCCCAACAGGCCGGCTGATGGTGACCGGCCTGCTGATGGGCCCAGGCTTGGAGGCAGGCAGGGGTCGGTCCATGTGGTTCCAGATCCGGTGTTTCTCCAGCTGGGT +>syndip_1_chr20:63964668-63966718 +CCTGGCCTGCTTGGGTGGAATTGGGCAGGTGTCCAGGCTGTCCGCAGCCCTGCAGGGAGC +AGGTGAGGTGAGGGCCAGGAGGGCCTAACTGTGGGCCCCATTACCCCCAGGCCGTGGCCG +AGGAGCACCCTGACCTGGAACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTG +GGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCAT +ACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTG +TTCCTCCCTGTGGCACGAGGTGCTTTGTTCTCCGACCTGGTCAGCAGCACCATTTTGCAG +GGCGGTGTGTGTCTGCTGATAGCAATGGGCCTGCTGACTGTCACCGGCTTGCTGACCACA +ATGGGCCTGCTGACTGTCACTGGCTTGGTGACCGGCACGGGTTTCGTAACTGTCACAAGC +TTTGTTACCGTAATGGGTTTGGTGACAGGTACGGGTTTGGTGACCGGCACAGACTTGGTG +ACTGTGATGGGTTTGGTGACCGGCATGGCCTTGGTGACGGGCATGGGCCTGCTGACTGTG +ACAGGTTTGGTGACTGGCACGGGCCTAGTGACCGGGATGGCCTTGGTGACTGGCATGGGT +CTGCCGACCGAGACTGGCTTGCTGATGCCAATGGGTTTGCTGACACCCACAGGTTTGCCA +ATAGTGACAGGTTTGCTCACTCCGATGGGCTTGCTGACCCCAACAGGCCGGCTGATGGTG +ACCGGCCTGCTGATGGGCCCAGGCTTGGAGGCAGGCAGGGGTCGGTCCATGTGGTTCCAG +ATCCGGTGTTTCTCCAGCTGGGT +>syndip_2_chr20:63964668-63966718 +CCTGGCCTGCTTGGGTGGAATTGGGCAGGTGTCCAGGCTGTCCGCAGCCCTGCAGGGAGC +AGGTGAGGTGAGGGCCAGGAGGGCCTAACTGTGGGCCCCATTACCCCCAGGCCGTGGCCG +AGGAGCACCCTGACCTGGAACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTG +GGACAAGCCCCCATACCTTTTCTTACCACTGTTCCCTGACCTGGGACGAGCCCCCATACC +TTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTC +CCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGC +CCCCATACCTTTTCTCACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTC +TCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGA +CCTGGAACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCA +TACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACT +GTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGAC +GAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTT +CTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCG +ACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCCCGACCTGGGACGAGCCCCC +ATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTAC +CACTGTTCCTCCCCAACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCC +GACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCC +CATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTA +CCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCC +CGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCCCGACCTGGGACGAGCCC +CCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTTACC +ACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCCGACC +TGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATA +CCTTTTCTTACCACTGTTCCTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTTACCAC +TGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCTGTG +GCACGAGGTGCTTTGTTCTCCGACCTGGTCAGCAGCACCATTTTGCAGGGCGGTGTGTGT +CTGCTGATAGCAATGGGCCTGCTGACTGTCACCGGCTTGCTGACCACAATGGGCCTGCTG +ACTGTCACTGGCTTGGTGACCGGCACGGGTTTCGTAACTGTCACAAGCTTTGTTACCGTA +ATGGGTTTGGTGACAGGTACGGGTTTGGTGACCGGCACAGACTTGGTGACTGTGATGGGT +TTGGTGACCGGCATGGCCTTGGTGACGGGCATGGGCCTGCTGACTGTGACAGGTTTGGTG +ACTGGCACGGGCCTAGTGACCGGGATGGCCTTGGTGACTGGCATGGGTCTGCCGACCGAG +ACTGGCTTGCTGATGCCAATGGGTTTGCTGACACCCACAGGTTTGCCAATAGTGACAGGT +TTGCTCACTCCGATGGGCTTGCTGACCCCAACAGGCCGGCTGATGGTGACCGGCCTGCTG +ATGGGCCCAGGCTTGGAGGCAGGCAGGGGTCGGTCCATGTGGTTCCAGATCCGGTGTTTC +TCCAGCTGGGT +>p:HG002_1_chr20:63964668-63966718 +CCTGGCCTGCTTGGGTGGAATTGGGCAGGTGTCCAGGCTGTCCGCAGCCCTGCAGGGAGC +AGGTGAGGTGAGGGCCAGGAGGGCCTAACTGTGGGCCCCATTACCCCCAGGCCGTGGCCG +AGGAGCACCCTGACCTGGAACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTG +GGACAAGCCCCCATACCTTTTCTTACCACTGTTCCCTGACCTGGGACGAGCCCCCATACC +TTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTC +CCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGC +CCCCATACCTTTTCTCACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTC +TCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGA +CCTGGAACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCA +TACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACT +GTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGAC +GAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTT +CTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCG +ACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCCCGACCTGGGACGAGCCCCC +ATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTAC +CACTGTTCCTCCCCAACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCC +GACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCC +CATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTA +CCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCC +CGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCCCGACCTGGGACGAGCCC +CCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTTACC +ACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCCGACC +TGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATA +CCTTTTCTTACCACTGTTCCTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTTACCAC +TGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCTGTG +GCACGAGGTGCTTTGTTCTCCGACCTGGTCAGCAGCACCATTTTGCAGGGCGGTGTGTGT +CTGCTGATAGCAATGGGCCTGCTGACTGTCACCGGCTTGCTGACCACAATGGGCCTGCTG +ACTGTCACTGGCTTGGTGACCGGCACGGGTTTCGTAACTGTCACAAGCTTTGTTACCGTA +ATGGGTTTGGTGACAGGTACGGGTTTGGTGACCGGCACAGACTTGGTGACTGTGATGGGT +TTGGTGACCGGCATGGCCTTGGTGACGGGCATGGGCCTGCTGACTGTGACAGGTTTGGTG +ACTGGCACGGGCCTAGTGACCGGGATGGCCTTGGTGACTGGCATGGGTCTGCCGACCGAG +ACTGGCTTGCTGATGCCAATGGGTTTGCTGACACCCACAGGTTTGCCAATAGTGACAGGT +TTGCTCACTCCGATGGGCTTGCTGACCCCAACAGGCCGGCTGATGGTGACCGGCCTGCTG +ATGGGCCCAGGCTTGGAGGCAGGCAGGGGTCGGTCCATGTGGTTCCAGATCCGGTGTTTC +TCCAGCTGGGT +>p:HG002_2_chr20:63964668-63966718 +CCTGGCCTGCTTGGGTGGAATTGGGCAGGTGTCCAGGCTGTCCGCAGCCCTGCAGGGAGC +AGGTGAGGTGAGGGCCAGGAGGGCCTAACTGTGGGCCCCATTACCCCCAGGCCGTGGCCG +AGGAGCACCCTGACCTGGAACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTG +GGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCAT +ACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTG +TTCCTCCCTGTGGCACGAGGTGCTTTGTTCTCCGACCTGGTCAGCAGCACCATTTTGCAG +GGCGGTGTGTGTCTGCTGATAGCAATGGGCCTGCTGACTGTCACCGGCTTGCTGACCACA +ATGGGCCTGCTGACTGTCACTGGCTTGGTGACCGGCACGGGTTTCGTAACTGTCACAAGC +TTTGTGACCGTAATGGGTTTGGTGACAGGTACGGGTTTGGTGACCGGCACAGACTTGGTG +ACTGTGATGGGTTTGGTGACCGGCATGGCCTTGGTGACGGGCATGGGCCTGCTGACTGTG +ACAGGTTTGGTGACTGGCACGGGCCTAGTGACCGGGATGGCCTTGGTGACTGGCATGGGT +CTGCCGACCGAGACTGGCTTGCTGATGCCAATGGGTTTGCTGACACCCACAGGTTTGCCA +ATAGTGACAGGTTTGCTCACTCCGATGGGCTTGCTGACCCCAACAGGCCGGCTGATGGTG +ACCGGCCTGCTGATGGGCCCAGGCTTGGAGGCAGGCAGGGGTCGGTCCATGTGGTTCCAG +ATCCGGTGTTTCTCCAGCTGGGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/haps.fa.ref.fa new file mode 100644 index 00000000..16bd4f6b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63964668-63966718 +CCTGGCCTGCTTGGGTGGAATTGGGCAGGTGTCCAGGCTGTCCGCAGCCCTGCAGGGAGCAGGTGAGGTGAGGGCCAGGAGGGCCTAACTGTGGGCCCCATTACCCCCAGGCCGTGGCCGAGGAGCACCCTGACCTGGAACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACAAGCCCCCATACCTTTTCTTACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGAACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCCAACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTCACCACTGTTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCTGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCCGACCTGGGACGAGCCCCCATACCTTTTCTTACCACTGTTCCTCCCTGTGGCACGAGGTGCTTTGTTCTCCGACCTGGTCAGCAGCACCATTTTGCAGGGCGGTGTGTGTCTGCTGATAGCAATGGGCCTGCTGACTGTCACCGGCTTGCTGACCACAATGGGCCTGCTGACTGTCACTGGCTTGGTGACCGGCACGGGTTTCGTAACTGTCACAAGCTTTGTTACCGTAATGGGTTTGGTGACAGGTACGGGTTTGGTGACCGGCACAGACTTGGTGACTGTGATGGGTTTGGTGACCGGCATGGCCTTGGTGACGGGCATGGGCCTGCTGACTGTGACAGGTTTGGTGACTGGCACGGGCCTAGTGACCGGGATGGCCTTGGTGACTGGCATGGGTCTGCCGACCGAGACTGGCTTGCTGATGCCAATGGGTTTGCTGACACCCACAGGTTTGCCAATAGTGACAGGTTTGCTCACTCCGATGGGCTTGCTGACCCCAACAGGCCGGCTGATGGTGACCGGCCTGCTGATGGGCCCAGGCTTGGAGGCAGGCAGGGGTCGGTCCATGTGGTTCCAGATCCGGTGTTTCTCCAGCTGGGT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/msa.fa new file mode 100644 index 00000000..b5374e1a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/msa.fa @@ -0,0 +1,180 @@ +>ref_chr20_63964668_63966718 +cctggcctgcttgggtggaattgggcaggtgtccaggctgtccgcagccctgcagggagc +aggtgaggtgagggccaggagggcctaactgtgggccccattacccccaggccgtggccg +aggagcaccctgacctggaacgagcccccataccttttctcaccactgttccccgacctg +ggacaagcccccataccttttcttaccactgttccctgacctgggacgagcccccatacc +ttttctcaccactgttccctgacctgggacgagcccccataccttttctcaccactgttc +cccgacctgggacgagcccccataccttttctcaccactgttccctgacctgggacgagc +ccccataccttttctcaccactgttcctccccgacctgggacgagcccccataccttttc +tcaccactgttccccgacctgggacgagcccccataccttttctcaccactgttccctga +cctggaacgagcccccataccttttctcaccactgttccccgacctgggacgagccccca +taccttttctcaccactgttccccgacctgggacgagcccccataccttttctcaccact +gttccccgacctgggacgagcccccataccttttctcaccactgttccccgacctgggac +gagcccccataccttttctcaccactgttccccgacctgggacgagcccccatacctttt +ctcaccactgttccctgacctgggacgagcccccataccttttctcaccactgttccccg +acctgggacgagcccccataccttttcttaccactgttccccgacctgggacgagccccc +ataccttttcttaccactgttcctccccgacctgggacgagcccccataccttttctcac +cactgttcctccccaacctgggacgagcccccataccttttctcaccactgttcctcccc +gacctgggacgagcccccataccttttctcaccactgttccctgacctgggacgagcccc +cataccttttcttaccactgttcctccccgacctgggacgagcccccataccttttctta +ccactgttcctccccgacctgggacgagcccccataccttttcttaccactgttcctccc +cgacctgggacgagcccccataccttttcttaccactgttccccgacctgggacgagccc +ccataccttttctcaccactgttccctgacctgggacgagcccccataccttttcttacc +actgttccctgacctgggacgagcccccataccttttctcaccactgttcctccccgacc +tgggacgagcccccataccttttctcaccactgttccccgacctgggacgagcccccata +ccttttcttaccactgttcctccctgacctgggacgagcccccataccttttcttaccac +tgttcctccccgacctgggacgagcccccataccttttcttaccactgttcctccctgtg +gcacgaggtgctttgttctccgacctggtcagcagcaccattttgcagggcggtgtgtgt +ctgctgatagcaatgggcctgctgactgtcaccggcttgctgaccacaatgggcctgctg +actgtcactggcttggtgaccggcacgggtttcgtaactgtcacaagctttgttaccgta +atgggtttggtgacaggtacgggtttggtgaccggcacagacttggtgactgtgatgggt +ttggtgaccggcatggccttggtgacgggcatgggcctgctgactgtgacaggtttggtg +actggcacgggcctagtgaccgggatggccttggtgactggcatgggtctgccgaccgag +actggcttgctgatgccaatgggtttgctgacacccacaggtttgccaatagtgacaggt +ttgctcactccgatgggcttgctgaccccaacaggccggctgatggtgaccggcctgctg +atgggcccaggcttggaggcaggcaggggtcggtccatgtggttccagatccggtgtttc +tccagctgggt +>syndip_1_chr20:63964668-63966718 +cctggcctgcttgggtggaattgggcaggtgtccaggctgtccgcagccctgcagggagc +aggtgaggtgagggccaggagggcctaactgtgggccccattacccccaggccgtggccg +aggag------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------------------caccctgacc +tggaacgagcccccataccttttctcaccactgttccctgacctgggacgagcccccata +ccttttctcaccactgttcctccccgacctgggacgagcccccataccttttctcaccac +tgt---tccctgacctgggacgagcccccataccttttcttaccactgttcctccctgtg +gcacgaggtgctttgttctccgacctggtcagcagcaccattttgcagggcggtgtgtgt +ctgctgatagcaatgggcctgctgactgtcaccggcttgctgaccacaatgggcctgctg +actgtcactggcttggtgaccggcacgggtttcgtaactgtcacaagctttgttaccgta +atgggtttggtgacaggtacgggtttggtgaccggcacagacttggtgactgtgatgggt +ttggtgaccggcatggccttggtgacgggcatgggcctgctgactgtgacaggtttggtg +actggcacgggcctagtgaccgggatggccttggtgactggcatgggtctgccgaccgag +actggcttgctgatgccaatgggtttgctgacacccacaggtttgccaatagtgacaggt +ttgctcactccgatgggcttgctgaccccaacaggccggctgatggtgaccggcctgctg +atgggcccaggcttggaggcaggcaggggtcggtccatgtggttccagatccggtgtttc +tccagctgggt +>syndip_2_chr20:63964668-63966718 +cctggcctgcttgggtggaattgggcaggtgtccaggctgtccgcagccctgcagggagc +aggtgaggtgagggccaggagggcctaactgtgggccccattacccccaggccgtggccg +aggagcaccctgacctggaacgagcccccataccttttctcaccactgttccccgacctg +ggacaagcccccataccttttcttaccactgttccctgacctgggacgagcccccatacc +ttttctcaccactgttccctgacctgggacgagcccccataccttttctcaccactgttc +cccgacctgggacgagcccccataccttttctcaccactgttccctgacctgggacgagc +ccccataccttttctcaccactgttcctccccgacctgggacgagcccccataccttttc +tcaccactgttccccgacctgggacgagcccccataccttttctcaccactgttccctga +cctggaacgagcccccataccttttctcaccactgttccccgacctgggacgagccccca +taccttttctcaccactgttccccgacctgggacgagcccccataccttttctcaccact +gttccccgacctgggacgagcccccataccttttctcaccactgttccccgacctgggac +gagcccccataccttttctcaccactgttccccgacctgggacgagcccccatacctttt +ctcaccactgttccctgacctgggacgagcccccataccttttctcaccactgttccccg +acctgggacgagcccccataccttttcttaccactgttccccgacctgggacgagccccc +ataccttttcttaccactgttcctccccgacctgggacgagcccccataccttttcttac +cactgttcctccccaacctgggacgagcccccataccttttctcaccactgttcctcccc +gacctgggacgagcccccataccttttctcaccactgttccctgacctgggacgagcccc +cataccttttcttaccactgttcctccccgacctgggacgagcccccataccttttctta +ccactgttcctccccgacctgggacgagcccccataccttttcttaccactgttcctccc +cgacctgggacgagcccccataccttttcttaccactgttccccgacctgggacgagccc +ccataccttttctcaccactgttccctgacctgggacgagcccccataccttttcttacc +actgttccctgacctgggacgagcccccataccttttctcaccactgttcctccccgacc +tgggacgagcccccataccttttctcaccactgttccccgacctgggacgagcccccata +ccttttcttaccactgttcctccctgacctgggacgagcccccataccttttcttaccac +tgttcctccccgacctgggacgagcccccataccttttcttaccactgttcctccctgtg +gcacgaggtgctttgttctccgacctggtcagcagcaccattttgcagggcggtgtgtgt +ctgctgatagcaatgggcctgctgactgtcaccggcttgctgaccacaatgggcctgctg +actgtcactggcttggtgaccggcacgggtttcgtaactgtcacaagctttgttaccgta +atgggtttggtgacaggtacgggtttggtgaccggcacagacttggtgactgtgatgggt +ttggtgaccggcatggccttggtgacgggcatgggcctgctgactgtgacaggtttggtg +actggcacgggcctagtgaccgggatggccttggtgactggcatgggtctgccgaccgag +actggcttgctgatgccaatgggtttgctgacacccacaggtttgccaatagtgacaggt +ttgctcactccgatgggcttgctgaccccaacaggccggctgatggtgaccggcctgctg +atgggcccaggcttggaggcaggcaggggtcggtccatgtggttccagatccggtgtttc +tccagctgggt +>p:HG002_1_chr20:63964668-63966718 +cctggcctgcttgggtggaattgggcaggtgtccaggctgtccgcagccctgcagggagc +aggtgaggtgagggccaggagggcctaactgtgggccccattacccccaggccgtggccg +aggagcaccctgacctggaacgagcccccataccttttctcaccactgttccccgacctg +ggacaagcccccataccttttcttaccactgttccctgacctgggacgagcccccatacc +ttttctcaccactgttccctgacctgggacgagcccccataccttttctcaccactgttc +cccgacctgggacgagcccccataccttttctcaccactgttccctgacctgggacgagc +ccccataccttttctcaccactgttcctccccgacctgggacgagcccccataccttttc +tcaccactgttccccgacctgggacgagcccccataccttttctcaccactgttccctga +cctggaacgagcccccataccttttctcaccactgttccccgacctgggacgagccccca +taccttttctcaccactgttccccgacctgggacgagcccccataccttttctcaccact +gttccccgacctgggacgagcccccataccttttctcaccactgttccccgacctgggac +gagcccccataccttttctcaccactgttccccgacctgggacgagcccccatacctttt +ctcaccactgttccctgacctgggacgagcccccataccttttctcaccactgttccccg +acctgggacgagcccccataccttttcttaccactgttccccgacctgggacgagccccc +ataccttttcttaccactgttcctccccgacctgggacgagcccccataccttttcttac +cactgttcctccccaacctgggacgagcccccataccttttctcaccactgttcctcccc +gacctgggacgagcccccataccttttctcaccactgttccctgacctgggacgagcccc +cataccttttcttaccactgttcctccccgacctgggacgagcccccataccttttctta +ccactgttcctccccgacctgggacgagcccccataccttttcttaccactgttcctccc +cgacctgggacgagcccccataccttttcttaccactgttccccgacctgggacgagccc +ccataccttttctcaccactgttccctgacctgggacgagcccccataccttttcttacc +actgttccctgacctgggacgagcccccataccttttctcaccactgttcctccccgacc +tgggacgagcccccataccttttctcaccactgttccccgacctgggacgagcccccata +ccttttcttaccactgttcctccctgacctgggacgagcccccataccttttcttaccac +tgttcctccccgacctgggacgagcccccataccttttcttaccactgttcctccctgtg +gcacgaggtgctttgttctccgacctggtcagcagcaccattttgcagggcggtgtgtgt +ctgctgatagcaatgggcctgctgactgtcaccggcttgctgaccacaatgggcctgctg +actgtcactggcttggtgaccggcacgggtttcgtaactgtcacaagctttgttaccgta +atgggtttggtgacaggtacgggtttggtgaccggcacagacttggtgactgtgatgggt +ttggtgaccggcatggccttggtgacgggcatgggcctgctgactgtgacaggtttggtg +actggcacgggcctagtgaccgggatggccttggtgactggcatgggtctgccgaccgag +actggcttgctgatgccaatgggtttgctgacacccacaggtttgccaatagtgacaggt +ttgctcactccgatgggcttgctgaccccaacaggccggctgatggtgaccggcctgctg +atgggcccaggcttggaggcaggcaggggtcggtccatgtggttccagatccggtgtttc +tccagctgggt +>p:HG002_2_chr20:63964668-63966718 +cctggcctgcttgggtggaattgggcaggtgtccaggctgtccgcagccctgcagggagc +aggtgaggtgagggccaggagggcctaactgtgggccccattacccccaggccgtggccg +aggag------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------------------caccctgacc +tggaacgagcccccataccttttctcaccactgttccctgacctgggacgagcccccata +ccttttctcaccactgttcctccccgacctgggacgagcccccataccttttctcaccac +tgt---tccctgacctgggacgagcccccataccttttcttaccactgttcctccctgtg +gcacgaggtgctttgttctccgacctggtcagcagcaccattttgcagggcggtgtgtgt +ctgctgatagcaatgggcctgctgactgtcaccggcttgctgaccacaatgggcctgctg +actgtcactggcttggtgaccggcacgggtttcgtaactgtcacaagctttgtgaccgta +atgggtttggtgacaggtacgggtttggtgaccggcacagacttggtgactgtgatgggt +ttggtgaccggcatggccttggtgacgggcatgggcctgctgactgtgacaggtttggtg +actggcacgggcctagtgaccgggatggccttggtgactggcatgggtctgccgaccgag +actggcttgctgatgccaatgggtttgctgacacccacaggtttgccaatagtgacaggt +ttgctcactccgatgggcttgctgaccccaacaggccggctgatggtgaccggcctgctg +atgggcccaggcttggaggcaggcaggggtcggtccatgtggttccagatccggtgtttc +tccagctgggt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/msa.fa.fai new file mode 100644 index 00000000..c1cd88c9 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63964668_63966718 2051 29 60 61 +syndip_1_chr20:63964668-63966718 2051 2149 60 61 +syndip_2_chr20:63964668-63966718 2051 4269 60 61 +p:HG002_1_chr20:63964668-63966718 2051 6390 60 61 +p:HG002_2_chr20:63964668-63966718 2051 8511 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/output.vcf.gz new file mode 100644 index 00000000..1bf2cdb5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/output.vcf.gz.tbi new file mode 100644 index 00000000..74315506 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:63964768-63966618/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/base.vcf.gz new file mode 100644 index 00000000..07b10eee Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/base.vcf.gz.tbi new file mode 100644 index 00000000..bb297398 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/comp.vcf.gz new file mode 100644 index 00000000..ce2849b0 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/comp.vcf.gz.tbi new file mode 100644 index 00000000..c72ceeb8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/haps.fa new file mode 100644 index 00000000..097dac20 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/haps.fa @@ -0,0 +1,31 @@ +>ref_chr20_64065753_64066112 +TGGAACAGTCCAGGCGAGGGGTGCTGGCCTGCTTGGGGGCAACTCAGAGGCCTGGAGGATAGATGAGGAGGGGGGCTGTGGGCCTTGTAGGTGTTGGCTGTGGCCGTGCCTGGAGTGGAGGGACCCTTGAAAGTTTGGCCTCAGCTCGGGACACTGATGTTCCCGGGTTGGCCCTTCATGAGAGTTTGGCCTCAGCTCGGGACACTGATGTTCCTGGGTTGGCCCTTCACAGCTGGTGGGCGGGGGGTGCTTTGGGGAGAGGCTGCCCTGCGCATCAGGGCATCAAGACACAGGGGAGTGAATGAACCTGGGGCTGCAGTTTCACCTGGGTGTGGCCCTGGCTGCTGGGGAGGGGCCGTG +>syndip_1_chr20:64065753-64066112 +TGGAACAGTCCAGGCGAGGGGTGCTGGCCTGCTTGGGGGCAACTCAGAGGCCTGGAGGAT +AGATGAGGAGGGGGGCTGTGGGCCTTGTAGGTGTTGGCTGTGGCCGTGCCTGGAGTGGAG +GGACCCTTGAAAGTTTGGCCTCAGCTCGGGACACTGATGTTCCCGGGTTGGCCCTTCATG +AGAGTTTGGCCTCAGCTCGGGACACTGATGTTCCTGGGTTGGCCCTTCACAGCTGGTGGG +CGGGGGGTGCTTTGGGGAGAGGCTGCCCTGCGCATCAGGGCATCAAGACACAGGGGAGTG +AATGAACCTGGGGCTGCAGTTTCACCTGGGTGTGGCCCTGGCTGCTGGGGAGGGGCCGTG +>syndip_2_chr20:64065753-64066112 +TGGAACAGTCCAGGCGAGGGGTGCTGGCCTGCTTGGGGGCAACTCAGAGGCCTGGAGGAT +AGATGAGGAGGGGGGCTGTGGGCCTTGTAGGTGTTGGCTGTGGCCGTGCCTGGAGTGGAG +GGACCCTTGAAAGTTTGGCCTCAGCTCGGGACACTGATGTTCCCGGGTTGGCCCTTCATG +AGAGTTTGGCCTCAGCTCGGGACACTGATGTTCCTGGGTTGGCCCTTCACAGCTGGTGGG +CGGGGGGTGCTTTGGGGAGAGGCTGCCCTGCGCATCAGGGCATCAAGACACAGGGGAGTG +AATGAACCTGGGGCTGCAGTTTCACCTGGGTGTGGCCCTGGCTGCTGGGGAGGGGCCGTG +>p:HG002_1_chr20:64065753-64066112 +TGGAACAGTCCAGGCGAGGGGTGCTGGCCTGCTTGGGGGCAACTCAGAGGCCTGGAGGAT +AGATGAGGAGGGGGGCTGTGGGCCTTGTAGGTGTTGGCTGTGGCCGTGCCTGGAGTGGAG +GGACCCTTGAAAGTTTGGCCTCAGCTCGGGACACTGATGTTCCCGGGTTGGCCCTTCATG +AGAGTTTGGCCTCAGCTCGGGACACTGATGTTCCTGGGTTGGCCCTTCACAGCTGGTGGG +CGGGGGGTGCTTTGGGGAGAGGCTGCCCTGCGCATCAGGGCATCAAGACACAGGGGAGTG +AATGAACCTGGGGCTGCAGTTTCACCTGGGTGTGGCCCTGGCTGCTGGGGAGGGGCCGTG +>p:HG002_2_chr20:64065753-64066112 +TGGAACAGTCCAGGCGAGGGGTGCTGGCCTGCTTGGGGGCAACTCAGAGGCCTGGAGGAT +AGATGAGGAGGGGGGCTGTGGGCCTTGTAGGTGTTGGCTGTGGCCGTGCCTGGAGTGGAG +GGACCCTTGAAAGTTTGGCCTCAGCTCGGGACACTGATGTTCCCGGGTTGGCCCTTCATG +AGAGTTTGGCCTCAGCTCGGGACACTGATGTTCCCGGGTTGGCCCTTCATGAGAGTTTGG +CCTCAGCTCGGGACACTGATGTTCCTGGGTTGGCCCTTCACAGCTGGTGGGCGGGGGGTG +CTTTGGGGAGAGGCTGCCCTGCGCATCAGGGCATCAAGACACAGGGGAGTGAATGAACCT +GGGGCTGCAGTTTCACCTGGGTGTGGCCCTGGCTGCTGGGGAGGGGCCGTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/haps.fa.ref.fa new file mode 100644 index 00000000..db9de780 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:64065753-64066112 +TGGAACAGTCCAGGCGAGGGGTGCTGGCCTGCTTGGGGGCAACTCAGAGGCCTGGAGGATAGATGAGGAGGGGGGCTGTGGGCCTTGTAGGTGTTGGCTGTGGCCGTGCCTGGAGTGGAGGGACCCTTGAAAGTTTGGCCTCAGCTCGGGACACTGATGTTCCCGGGTTGGCCCTTCATGAGAGTTTGGCCTCAGCTCGGGACACTGATGTTCCTGGGTTGGCCCTTCACAGCTGGTGGGCGGGGGGTGCTTTGGGGAGAGGCTGCCCTGCGCATCAGGGCATCAAGACACAGGGGAGTGAATGAACCTGGGGCTGCAGTTTCACCTGGGTGTGGCCCTGGCTGCTGGGGAGGGGCCGTG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/msa.fa new file mode 100644 index 00000000..5c88c05c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/msa.fa @@ -0,0 +1,40 @@ +>ref_chr20_64065753_64066112 +tggaacagtccaggcgaggggtgctggcctgcttgggggcaactcagaggcctggaggat +agatgaggaggggggctgtgggccttgtaggtgttggctgtggccgtgcctggagtggag +ggacccttgaa------------------------------------------------- +--agtttggcctcagctcgggacactgatgttcccgggttggcccttcatgagagtttgg +cctcagctcgggacactgatgttcctgggttggcccttcacagctggtgggcggggggtg +ctttggggagaggctgccctgcgcatcagggcatcaagacacaggggagtgaatgaacct +ggggctgcagtttcacctgggtgtggccctggctgctggggaggggccgtg +>syndip_1_chr20:64065753-64066112 +tggaacagtccaggcgaggggtgctggcctgcttgggggcaactcagaggcctggaggat +agatgaggaggggggctgtgggccttgtaggtgttggctgtggccgtgcctggagtggag +ggacccttgaa------------------------------------------------- +--agtttggcctcagctcgggacactgatgttcccgggttggcccttcatgagagtttgg +cctcagctcgggacactgatgttcctgggttggcccttcacagctggtgggcggggggtg +ctttggggagaggctgccctgcgcatcagggcatcaagacacaggggagtgaatgaacct +ggggctgcagtttcacctgggtgtggccctggctgctggggaggggccgtg +>syndip_2_chr20:64065753-64066112 +tggaacagtccaggcgaggggtgctggcctgcttgggggcaactcagaggcctggaggat +agatgaggaggggggctgtgggccttgtaggtgttggctgtggccgtgcctggagtggag +ggacccttgaa------------------------------------------------- +--agtttggcctcagctcgggacactgatgttcccgggttggcccttcatgagagtttgg +cctcagctcgggacactgatgttcctgggttggcccttcacagctggtgggcggggggtg +ctttggggagaggctgccctgcgcatcagggcatcaagacacaggggagtgaatgaacct +ggggctgcagtttcacctgggtgtggccctggctgctggggaggggccgtg +>p:HG002_1_chr20:64065753-64066112 +tggaacagtccaggcgaggggtgctggcctgcttgggggcaactcagaggcctggaggat +agatgaggaggggggctgtgggccttgtaggtgttggctgtggccgtgcctggagtggag +ggacccttgaa------------------------------------------------- +--agtttggcctcagctcgggacactgatgttcccgggttggcccttcatgagagtttgg +cctcagctcgggacactgatgttcctgggttggcccttcacagctggtgggcggggggtg +ctttggggagaggctgccctgcgcatcagggcatcaagacacaggggagtgaatgaacct +ggggctgcagtttcacctgggtgtggccctggctgctggggaggggccgtg +>p:HG002_2_chr20:64065753-64066112 +tggaacagtccaggcgaggggtgctggcctgcttgggggcaactcagaggcctggaggat +agatgaggaggggggctgtgggccttgtaggtgttggctgtggccgtgcctggagtggag +ggacccttgaaagtttggcctcagctcgggacactgatgttcccgggttggcccttcatg +agagtttggcctcagctcgggacactgatgttcccgggttggcccttcatgagagtttgg +cctcagctcgggacactgatgttcctgggttggcccttcacagctggtgggcggggggtg +ctttggggagaggctgccctgcgcatcagggcatcaagacacaggggagtgaatgaacct +ggggctgcagtttcacctgggtgtggccctggctgctggggaggggccgtg diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/msa.fa.fai new file mode 100644 index 00000000..a31283db --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_64065753_64066112 411 29 60 61 +syndip_1_chr20:64065753-64066112 411 481 60 61 +syndip_2_chr20:64065753-64066112 411 933 60 61 +p:HG002_1_chr20:64065753-64066112 411 1386 60 61 +p:HG002_2_chr20:64065753-64066112 411 1839 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/output.vcf.gz new file mode 100644 index 00000000..0e4af5b9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/output.vcf.gz.tbi new file mode 100644 index 00000000..0806a63f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64065853-64066012/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/base.vcf.gz new file mode 100644 index 00000000..b5cd6af9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/base.vcf.gz.tbi new file mode 100644 index 00000000..bb297398 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/comp.vcf.gz new file mode 100644 index 00000000..7d398031 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/comp.vcf.gz.tbi new file mode 100644 index 00000000..0a4dbd9b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/haps.fa new file mode 100644 index 00000000..e898806d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/haps.fa @@ -0,0 +1,58 @@ +>ref_chr20_64090604_64091490 +ACAGCCTTGACCTGTGACCTTTCATCTCAGTGGATCAGGCATGGGACCCCCGTGCTGAGAAGGAGGCAACTCTGAAGGGGCCATTCAGCTGTGTGGGTGCCAGGGGCCTGTCTGCAGGAGTGATGCTCAGCCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGGGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGGGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGGGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCGTGTCTCCAAGTGACGAACAGACCCGGGTTTCACCCCGTCTCTGCCACTGTGACAGGTGGCCTCACACCTCTGAGGCTTCGTGCTCTCAGCAGTGGCCGGGTATGGTGGGGGTGACTGAGCTCCAGGAGCA +>syndip_1_chr20:64090604-64091490 +ACAGCCTTGACCTGTGACCTTTCATCTCAGTGGATCAGGCATGGGACCCCCGTGCTGAGA +AGGAGGCAACTCTGAAGGGGCCATTCAGCTGTGTGGGTGCCAGGGGCCTGTCTGCAGGAG +TGATGCTCAGCCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTG +GGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGT +GCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGG +CCCAGCTGTGGCAGGGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCC +CTGGGCACTGATCTGGGGCCCAGCTGTGGCAGGGGTGCCCTGGGCACTGATCTGGGGCCC +AGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTG +GGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGC +TGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGC +ACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGT +GGCAGGGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACT +GATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCGTGTCTCCAAGTGACGAACAGACC +CGGGTTTCACCCCGTCTCTGCCACTGTGACAGGTGGCCTCACACCTCTGAGGCTTCGTGC +TCTCAGCAGTGGCCGGGTATGGTGGGGGTGACTGAGCTCCAGGAGCA +>syndip_2_chr20:64090604-64091490 +ACAGCCTTGACCTGTGACCTTTCATCTCAGTGGATCAGGCATGGGACCCCCGTGCTGAGA +AGGAGGCAACTCTGAAGGGGCCATTCAGCTGTGTGGGTGCCAGGGGCCTGTCTGCAGGAG +TGATGCTCAGCCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTG +GGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGT +GCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGG +CCCAGCTGTGGCAGGGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCC +CTGGGCACTGATCTGGGGCCCAGCTGTGGCAGGGGTGCCCTGGGCACTGATCTGGGGCCC +AGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTG +GGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGC +TGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGC +ACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGT +GGCAGGGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACT +GATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCGTGTCTCCAAGTGACGAACAGACC +CGGGTTTCACCCCGTCTCTGCCACTGTGACAGGTGGCCTCACACCTCTGAGGCTTCGTGC +TCTCAGCAGTGGCCGGGTATGGTGGGGGTGACTGAGCTCCAGGAGCA +>p:HG002_1_chr20:64090604-64091490 +ACAGCCTTGACCTGTGACCTTTCATCTCAGTGGATCAGGCATGGGACCCCCGTGCTGAGA +AGGAGGCAACTCTGAAGGGGCCATTCAGCTGTGTGGGTGCCAGGGGCCTGTCTGCAGGAG +TGATGCTCAGCCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTG +GGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGT +GCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGG +CCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCC +CTGGGCACTGATCTGGGGCCCAGCTGTGGCAGGGGTGCCCTGGGCACTGATCTGGGGCCC +AGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTG +GACGTGTCTCCAAGTGACGAACAGACCCGGGTTTCACCCCGTCTCTGCCACTGTGACAGG +TGGCCTCACACCTCTGAGGCTTCGTGCTCTCAGCAGTGGCCGGGTATGGTGGGGGTGACT +GAGCTCCAGGAGCA +>p:HG002_2_chr20:64090604-64091490 +ACAGCCTTGACCTGTGACCTTTCATCTCAGTGGATCAGGCATGGGACCCCCGTGCTGAGA +AGGAGGCAACTCTGAAGGGGCCATTCAGCTGTGTGGGTGCCAGGGGCCTGTCTGCAGGAG +TGATGCTCAGCCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTG +GGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGT +GCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGG +CCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCC +CTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCC +AGCTGTGGCAGGGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTG +GGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGACGTGTCTCCAAGTGACGAA +CAGACCCGGGTTTCACCCCGTCTCTGCCACTGTGACAGGTGGCCTCACACCTCTGAGGCT +TCGTGCTCTCAGCAGTGGCCGGGTATGGTGGGGGTGACTGAGCTCCAGGAGCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/haps.fa.ref.fa new file mode 100644 index 00000000..2ef1df38 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:64090604-64091490 +ACAGCCTTGACCTGTGACCTTTCATCTCAGTGGATCAGGCATGGGACCCCCGTGCTGAGAAGGAGGCAACTCTGAAGGGGCCATTCAGCTGTGTGGGTGCCAGGGGCCTGTCTGCAGGAGTGATGCTCAGCCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGGGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGGGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGGGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCACTGATCTGGGGCCCAGCTGTGGCAGAGGTGCCCTGGGCGTGTCTCCAAGTGACGAACAGACCCGGGTTTCACCCCGTCTCTGCCACTGTGACAGGTGGCCTCACACCTCTGAGGCTTCGTGCTCTCAGCAGTGGCCGGGTATGGTGGGGGTGACTGAGCTCCAGGAGCA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/msa.fa new file mode 100644 index 00000000..c62ab1dd --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/msa.fa @@ -0,0 +1,80 @@ +>ref_chr20_64090604_64091490 +acagccttgacctgtgacctttcatctcagtggatcaggcatgggacccccgtgctgaga +aggaggcaactctgaaggggccattcagctgtgtgggtgccaggggcctgtctgcaggag +tgatgctcagccactgatctggggcccagctgtggcagaggtgccctgggcactgatctg +gggcccagctgtggcagaggtgccctgggcactgatctggggcccagctgtggcagaggt +gccctgggcactgatctggggcccagctgtggcagaggtgccctgggcactgatctgggg +cccagctgtggcaggggtgccctgggcactgatctggggcccagctgtggcagaggtgcc +ctgggcactgatctggggcccagctgtggcaggggtgccctgggcactgatctggggccc +agctgtggcagaggtgccctgggcactgatctggggcccagctgtggcagaggtgccctg +ggcactgatctggggcccagctgtggcagaggtgccctgggcactgatctggggcccagc +tgtggcagaggtgccctgggcactgatctggggcccagctgtggcagaggtgccctgggc +actgatctggggcccagctgtggcagaggtgccctgggcactgatctggggcccagctgt +ggcaggggtgccctgggcactgatctggggcccagctgtggcagaggtgccctgggcact +gatctggggcccagctgtggcagaggtgccctgggcgtgtctccaagtgacgaacagacc +cgggtttcaccccgtctctgccactgtgacaggtggcctcacacctctgaggcttcgtgc +tctcagcagtggccgggtatggtgggggtgactgagctccaggagca +>syndip_1_chr20:64090604-64091490 +acagccttgacctgtgacctttcatctcagtggatcaggcatgggacccccgtgctgaga +aggaggcaactctgaaggggccattcagctgtgtgggtgccaggggcctgtctgcaggag +tgatgctcagccactgatctggggcccagctgtggcagaggtgccctgggcactgatctg +gggcccagctgtggcagaggtgccctgggcactgatctggggcccagctgtggcagaggt +gccctgggcactgatctggggcccagctgtggcagaggtgccctgggcactgatctgggg +cccagctgtggcaggggtgccctgggcactgatctggggcccagctgtggcagaggtgcc +ctgggcactgatctggggcccagctgtggcaggggtgccctgggcactgatctggggccc +agctgtggcagaggtgccctgggcactgatctggggcccagctgtggcagaggtgccctg +ggcactgatctggggcccagctgtggcagaggtgccctgggcactgatctggggcccagc +tgtggcagaggtgccctgggcactgatctggggcccagctgtggcagaggtgccctgggc +actgatctggggcccagctgtggcagaggtgccctgggcactgatctggggcccagctgt +ggcaggggtgccctgggcactgatctggggcccagctgtggcagaggtgccctgggcact +gatctggggcccagctgtggcagaggtgccctgggcgtgtctccaagtgacgaacagacc +cgggtttcaccccgtctctgccactgtgacaggtggcctcacacctctgaggcttcgtgc +tctcagcagtggccgggtatggtgggggtgactgagctccaggagca +>syndip_2_chr20:64090604-64091490 +acagccttgacctgtgacctttcatctcagtggatcaggcatgggacccccgtgctgaga +aggaggcaactctgaaggggccattcagctgtgtgggtgccaggggcctgtctgcaggag +tgatgctcagccactgatctggggcccagctgtggcagaggtgccctgggcactgatctg +gggcccagctgtggcagaggtgccctgggcactgatctggggcccagctgtggcagaggt +gccctgggcactgatctggggcccagctgtggcagaggtgccctgggcactgatctgggg +cccagctgtggcaggggtgccctgggcactgatctggggcccagctgtggcagaggtgcc +ctgggcactgatctggggcccagctgtggcaggggtgccctgggcactgatctggggccc +agctgtggcagaggtgccctgggcactgatctggggcccagctgtggcagaggtgccctg +ggcactgatctggggcccagctgtggcagaggtgccctgggcactgatctggggcccagc +tgtggcagaggtgccctgggcactgatctggggcccagctgtggcagaggtgccctgggc +actgatctggggcccagctgtggcagaggtgccctgggcactgatctggggcccagctgt +ggcaggggtgccctgggcactgatctggggcccagctgtggcagaggtgccctgggcact +gatctggggcccagctgtggcagaggtgccctgggcgtgtctccaagtgacgaacagacc +cgggtttcaccccgtctctgccactgtgacaggtggcctcacacctctgaggcttcgtgc +tctcagcagtggccgggtatggtgggggtgactgagctccaggagca +>p:HG002_1_chr20:64090604-64091490 +acagccttgacctgtgacctttcatctcagtggatcaggcatgggacccccgtgctgaga +aggaggcaactctgaaggggccattcagctgtgtgggtgccaggggcctgtctgcaggag +tgatgctcagc------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------------cactgatctggggccc +agctgtggcagaggtgccctgggcactgatctggggcccagctgtggcagaggtgccctg +ggcactgatctggggcccagctgtggcagaggtgccctgggcactgatctggggcccagc +tgtggcagaggtgccctgggcactgatctggggcccagctgtggcagaggtgccctgggc +actgatctggggcccagctgtggcagaggtgccctgggcactgatctggggcccagctgt +ggcaggggtgccctgggcactgatctggggcccagctgtggcagaggtgccctgggcact +gatctggggcccagctgtggcagaggtgccctggacgtgtctccaagtgacgaacagacc +cgggtttcaccccgtctctgccactgtgacaggtggcctcacacctctgaggcttcgtgc +tctcagcagtggccgggtatggtgggggtgactgagctccaggagca +>p:HG002_2_chr20:64090604-64091490 +acagccttgacctgtgacctttcatctcagtggatcaggcatgggacccccgtgctgaga +aggaggcaactctgaaggggccattcagctgtgtgggtgccaggggcctgtctgcaggag +tgatgctcagccactgatctggggcccagctgtggcaga--------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------ggtgccctgggcactgatctggggccc +agctgtggcagaggtgccctgggcactgatctggggcccagctgtggcagaggtgccctg +ggcactgatctggggcccagctgtggcagaggtgccctgggcactgatctggggcccagc +tgtggcagaggtgccctgggcactgatctggggcccagctgtggcagaggtgccctgggc +actgatctggggcccagctgtggcagaggtgccctgggcactgatctggggcccagctgt +ggcaggggtgccctgggcactgatctggggcccagctgtggcagaggtgccctgggcact +gatctggggcccagctgtggcagaggtgccctggacgtgtctccaagtgacgaacagacc +cgggtttcaccccgtctctgccactgtgacaggtggcctcacacctctgaggcttcgtgc +tctcagcagtggccgggtatggtgggggtgactgagctccaggagca diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/msa.fa.fai new file mode 100644 index 00000000..657f3e5d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_64090604_64091490 887 29 60 61 +syndip_1_chr20:64090604-64091490 887 965 60 61 +syndip_2_chr20:64090604-64091490 887 1901 60 61 +p:HG002_1_chr20:64090604-64091490 887 2838 60 61 +p:HG002_2_chr20:64090604-64091490 887 3775 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/output.vcf.gz new file mode 100644 index 00000000..d275ec6e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/output.vcf.gz.tbi new file mode 100644 index 00000000..abec3b04 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64090704-64091390/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/base.vcf.gz new file mode 100644 index 00000000..629124a3 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/base.vcf.gz.tbi new file mode 100644 index 00000000..bb297398 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/comp.vcf.gz new file mode 100644 index 00000000..432ac091 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/comp.vcf.gz.tbi new file mode 100644 index 00000000..1c210477 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/haps.fa new file mode 100644 index 00000000..366641f0 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/haps.fa @@ -0,0 +1,88 @@ +>ref_chr20_64096558_64097265 +ATTGCGGCCTCTTTGTGCTTATTCATAATCCCTCTCTAACAGGCAGAATGGAGCCCCATATTTCCTCACGGCAGCTACACTGACACAGAATAGTGTCATCTTGGGTGCTGCTGCCACTGCCAATATCGCCGCCACCATCATCATCACAATCATCACCATCACCACCATCATCACCACTATCATCATCACCACTATCACCACCACCAGCACCTTCATTATCACATTCACCATCCTCACCATCCTCACCACCACCATCACCACCATCATCACCATCATCATCATGACCATCACCACCATCACCACTATCACCACCACCACCATCATTACCATCATCATCACGACCATCACCACCATCATCACCATCACCACTATCACCACCACCACCATCATTACCATCATCATCACGACCATCACCACCATCATCACCATCACCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCATCACCATCATCACCATCATCATCATCACCACTACCATCACGCTCACAGTCATCACCATCACCACCATGATCACTGCCATCATCACCACCACCATCACCACCATAATCCCCCCCAACTATTACAACCATTAACTTATTTAACAAAAATTTATTAATCACCAACGATTTTCCCAGCCCTTTCCAGCACCATTTCAGGTGCTTGGATACACTCATACCTTATTAGCATCCCT +>syndip_1_chr20:64096558-64097265 +ATTGCGGCCTCTTTGTGCTTATTCATAATCCCTCTCTAACAGGCAGAATGGAGCCCCATA +TTTCCTCACGGCAGCTACACTGACACAGAATAGTGTCATCTTGGGTGCTGCTGCCACTGC +CAATATCGCCGCCACCATCATCATCACAATCATCACCATCACCACCATCATCACCACTAT +CATCATCACCACTATCACCACCACCAGCACCTTCATTATCACATTCACCATCCTCACCAT +CCTCACCACCACCATCACCACCATCATCACCATCATCATCATGACCATCACCACCATCAC +CACTATCACCACCACCACCATCATTACCATCATCATCACGACCATCACCACCATCATCAC +CATCACCACTATCACCACCACCACCATCATTACCATCATCATCACGACCATCACCACCAT +CATCACCATCACCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCAT +CACCATCATCACCATCATCATCATCACCACTACCATCACGCTCACAGTCATCACCATCAC +CACCATGATCACTGCCATCATCACCACCACCATCACCACCATAATCCCCCCCAACTATTA +CAACCATTAACTTATTTAACAAAAATTTATTAATCACCAACGATTTTCCCAGCCCTTTCC +AGCACCATTTCAGGTGCTTGGATACACTCATACCTTATTAGCATCCCT +>syndip_2_chr20:64096558-64097265 +ATTGCGGCCTCTTTGTGCTTATTCATAATCCCTCTCTAACAGGCAGAATGGAGCCCCATA +TTTCCTCACGGCAGCTACACTGACACAGAATAGTGTCATCTTGGGTGCTGCTGCCACTGC +CAATATCGCCGCCACCATCATCATCACAATCATCACCATCACCACCATCATCACCACTAT +CATCATCACCACTATCACCACCACCAGCACCTTCATTATCACATTCACCATCCTCACCAT +CCTCACCACCACCATCACCACCATCATCACCATCATCATCATGACCATCACCACCATCAC +CACTATCACCACCACCACCATCATTACCATCATCATCACGACCATCACCACCATCATCAC +CATCACCACTATCACCACCACCACCATCATTACCATCATCATCACGACCATCACCACCAT +CATCACCATCACCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCAT +CACCATCATCACCATCATCATCATCACCACTACCATCACGCTCACAGTCATCACCATCAC +CACCATGATCACTGCCATCATCACCACCACCATCACCACCATAATCCCCCCCAACTATTA +CAACCATTAACTTATTTAACAAAAATTTATTAATCACCAACGATTTTCCCAGCCCTTTCC +AGCACCATTTCAGGTGCTTGGATACACTCATACCTTATTAGCATCCCT +>p:HG002_1_chr20:64096558-64097265 +ATTGCGGCCTCTTTGTGCTTATTCATAATCCCTCTCTAACAGGCAGAATGGAGCCCCATA +TTTCCTCACGGCAGCTACACTGACACAGAATAGTGTCATCTTGGGTGCTGCTGCCACTGC +CAATATCGCTGCCACCATCATCATCACAATCATCACCATCACCACCATCATCACCACTAT +CATCATCACCACTATCACCACCACCAGCACCTTATCACATTCACCATCCTCACCATCCTC +ACCACCACCATCACCACCATCATCACCATCATCATCATGACCATCACCACCATCACCACT +ATCACCACCACCACCATCATTACCATCATCATCACGACCATCACCACCATCATCACCATC +ACCACTATCACCACCACCACCATCATTACCATCATCATCACGACCATCACCACCATCATC +ACCATCACCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCATCACT +GTCACCATCATCACCATCCTCACTATCACCACCACCACCATCATCACCATCACCATCATC +ACAGTCATCACCGTCACCATCATCACCATCCTCACTATCACCACCACCACCATCATCACC +ATCACCATCATCACAGTCATCACCGTCACCATCATCACCATCCTCACTATCACCACCACC +ACCATCATCACCATCACCATCATCACAGTCATCACCGTCACCATCATCACCATCCTCACT +ATCACCACCACCACCATCATCACCATCACCATCATCACAGTCATCACCGTCACCATCATC +ACCATCCTCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCATCACC +GTCACCATCATCACCATCCTCACTATCACCACCACCACCATCACCATCACCATCATCACA +GTCATCACCGTCACCATCATCACCATCCTCACTATCACCACCACCATCATCACCATCACC +ATCATCACAGTCATCACCGTCACCATCATCACCATCCTCACTATCACCACCACCACCATC +ATCACCATCACCATCATCACAGTCATCACCGTCACCATCATCACCATCCTCACTATCACC +ACCACCATCATCACCATCACCATCATCACAGTCATCACCGTCACCATCATCACCATCCTC +ACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCATCACCGTCACCATC +ATCACCATCCTCACTATCACCACCACCACCATCATCACCATCACCATCATCACAATCATC +ACCGTCACCATCATCACCATCCTCACTATCACCACCACCACCATCATCACCATCACTATC +ATCACAGTCATCACCGTCACCATCATCACCATCCTCACTATCACCACCACTACCATCATC +ATCACATTCATCATCACTATTACCATCATCATCACCACCATCACCATCACTATCACCACC +ATCATTACATTTGTCACCATCACCACCATTATCACCATCACCGCTATCACCACCACCACC +GTCATCATCACCATCATCATCATCACCACTACCATCACGCTCACAGTCATCACCATCACC +ACCATGATCACTGCCATCATCACCACCACCATCACCACCATAATCCCCCCCAACTATTAC +AACCATTAACTTATTTAACAAAAATTTATTAATCACCAACGATTTTCCCAGCCCTTTCCA +GCACCATTTCAGGTGCTTGGATACACTCATACCTTATTAGCATCCCT +>p:HG002_2_chr20:64096558-64097265 +ATTGCGGCCTCTTTGTGCTTATTCATAATCCCTCTCTAACAGGCAGAATGGAGCCCCATA +TTTCCTCACGGCAGCTACACTGACACAGAATAGTGTCATCTTGGGTGCTGCTGCCACTGC +CAATATCGCCGCCACCATCATCATCACAATCATCACCATCACCACCATCATCACCACTAT +CATCATCACCACTATCACCACCACCAGCACCTTCATTATCACATTCACCATCCTCACCAT +CCTCACCACCACCATCACCACCATCATCACCACCATCACCACTATCACCACCACCACCAT +CATTACCATCATCATCACGACCATCACCACCATCATCACCATCACCACTATCACCACCAC +CACCATCATTACCATCATCATCACGACCATCACCACCATCATCACCATCACCACTATCAC +CACCACCACCATCATCACCATCACCATCATCACAGTCATCACTGTCACCATCATCACCAT +CCTCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCATCACCGTCAC +CATCATCACCATCCTCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGT +CATCACCGTCACCATCATCACCATCCTCACTATCACCACCACCACCATCATCACCATCAC +CATCATCACAGTCATCACCGTCACCATCATCACCATCCTCACTATCACCACCACCACCAT +CATCACCATCACCATCATCACAGTCATCACCATCACCATCATCACCATCCTCACTATCAC +CACCACCACCATCATCACCATCACCATCATCACAGTCATCACCGTCACCATCATCACCAT +CCTCACTATCACCACCACCACCATCACCATCACCATCATCACAGTCATCACCGTCACCAT +CATCACCATCCTCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCAT +CACCGTCACCATCATCACCATCCTCACTATCACCACCACCACCATCATCACCATCACCAT +CATCACAGTCATCACCGTCACCATCATCACCATCCTCACTATCACCACCACCATCATCAC +CATCACCATCATCACAGTCATCACCGTCACCATCATCACCATCCTCACTATCACCACCAC +CACCATCATTACCATCACCATCATCACAGTCATCACCGTCACCATCATCACCATCCTCAC +TATCACCACCACCACCATCATCACCATCACCATCATCACAATCATCACTGTCACCATCAT +CACCATCCTCACTATCACCACCACCACCATCATTACCATCACTATCATCACAGTCATCAC +CGTCACCATCATCACCATCCTCACTATCACCACCACTACCATCATCATCACATTCATCAT +CACTATTACCATCATCATCACCACCATCACCATCACTATCACCACCATCATTACATTTGT +CACCATCACCACCATTATCACCATCACCGCTATCACCACCACCACCGTCATCATCACCAT +CATCATCATCACCACTACCATCACGCTCACAGTCATCACCATCACCACCATGATCACTGC +CATCATCACCACCACCATCACCACCATAATCCCCCCCAACTATTACAACCATTAACTTAT +TTAACAAAAATTTATTAATCACCAACGATTTTCCCAGCCCTTTCCAGCACCATTTCAGGT +GCTTGGATACACTCATACCTTATTAGCATCCCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/haps.fa.ref.fa new file mode 100644 index 00000000..066111f8 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:64096558-64097265 +ATTGCGGCCTCTTTGTGCTTATTCATAATCCCTCTCTAACAGGCAGAATGGAGCCCCATATTTCCTCACGGCAGCTACACTGACACAGAATAGTGTCATCTTGGGTGCTGCTGCCACTGCCAATATCGCCGCCACCATCATCATCACAATCATCACCATCACCACCATCATCACCACTATCATCATCACCACTATCACCACCACCAGCACCTTCATTATCACATTCACCATCCTCACCATCCTCACCACCACCATCACCACCATCATCACCATCATCATCATGACCATCACCACCATCACCACTATCACCACCACCACCATCATTACCATCATCATCACGACCATCACCACCATCATCACCATCACCACTATCACCACCACCACCATCATTACCATCATCATCACGACCATCACCACCATCATCACCATCACCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCATCACCATCATCACCATCATCATCATCACCACTACCATCACGCTCACAGTCATCACCATCACCACCATGATCACTGCCATCATCACCACCACCATCACCACCATAATCCCCCCCAACTATTACAACCATTAACTTATTTAACAAAAATTTATTAATCACCAACGATTTTCCCAGCCCTTTCCAGCACCATTTCAGGTGCTTGGATACACTCATACCTTATTAGCATCCCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/msa.fa new file mode 100644 index 00000000..c76087a2 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/msa.fa @@ -0,0 +1,150 @@ +>ref_chr20_64096558_64097265 +attgcggcctctttgtgcttattcataatccctctctaacaggcagaatggagccccata +tttcctcacggcagctacactgacacagaatagtgtcatcttgggtgctgctgccactgc +caatatcgccgccaccatcatcatcacaatcatcaccatcaccaccatcatcaccactat +catcatcaccactatcaccaccaccagcaccttcattatcacattcaccatcctcaccat +cctcaccaccaccatcaccaccatcatcaccatcatcatcatgaccatcaccaccatcac +cactatcaccaccaccaccatcattaccatcatcatcacgaccatcaccaccatcatcac +catcaccactatcaccaccaccaccatcattaccatcatcatcacgaccatcaccaccat +catcaccatcaccactatcaccaccaccaccatcatcaccatcaccatcatcacagtcat +caccatcatcaccatcatcatcatcaccactaccatcacgctcacagtcatcaccatcac +caccatgatcactgccatcatcaccaccaccatcaccaccataatcccccccaactatta +caaccattaacttatttaacaaaaatttattaatcacca--acgattttcccagcccttt +ccagcaccatttcaggtgcttggatacactcataccttattagcatc------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------------------cct +>syndip_1_chr20:64096558-64097265 +attgcggcctctttgtgcttattcataatccctctctaacaggcagaatggagccccata +tttcctcacggcagctacactgacacagaatagtgtcatcttgggtgctgctgccactgc +caatatcgccgccaccatcatcatcacaatcatcaccatcaccaccatcatcaccactat +catcatcaccactatcaccaccaccagcaccttcattatcacattcaccatcctcaccat +cctcaccaccaccatcaccaccatcatcaccatcatcatcatgaccatcaccaccatcac +cactatcaccaccaccaccatcattaccatcatcatcacgaccatcaccaccatcatcac +catcaccactatcaccaccaccaccatcattaccatcatcatcacgaccatcaccaccat +catcaccatcaccactatcaccaccaccaccatcatcaccatcaccatcatcacagtcat +caccatcatcaccatcatcatcatcaccactaccatcacgctcacagtcatcaccatcac +caccatgatcactgccatcatcaccaccaccatcaccaccataatcccccccaactatta +caaccattaacttatttaacaaaaatttattaatcacca--acgattttcccagcccttt +ccagcaccatttcaggtgcttggatacactcataccttattagcatc------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------------------cct +>syndip_2_chr20:64096558-64097265 +attgcggcctctttgtgcttattcataatccctctctaacaggcagaatggagccccata +tttcctcacggcagctacactgacacagaatagtgtcatcttgggtgctgctgccactgc +caatatcgccgccaccatcatcatcacaatcatcaccatcaccaccatcatcaccactat +catcatcaccactatcaccaccaccagcaccttcattatcacattcaccatcctcaccat +cctcaccaccaccatcaccaccatcatcaccatcatcatcatgaccatcaccaccatcac +cactatcaccaccaccaccatcattaccatcatcatcacgaccatcaccaccatcatcac +catcaccactatcaccaccaccaccatcattaccatcatcatcacgaccatcaccaccat +catcaccatcaccactatcaccaccaccaccatcatcaccatcaccatcatcacagtcat +caccatcatcaccatcatcatcatcaccactaccatcacgctcacagtcatcaccatcac +caccatgatcactgccatcatcaccaccaccatcaccaccataatcccccccaactatta +caaccattaacttatttaacaaaaatttattaatcacca--acgattttcccagcccttt +ccagcaccatttcaggtgcttggatacactcataccttattagcatc------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------------------cct +>p:HG002_1_chr20:64096558-64097265 +attgcggcctctttgtgcttattcataatccctctctaacaggcagaatggagccccata +tttcctcacggcagctacactgacacagaatagtgtcatcttgggtgctgctgccactgc +caatatcgctgccaccatcatcatcacaatcatcaccatcaccaccatcatcaccactat +catcatcaccactatcaccaccaccagcacc----ttatcacattcaccatcctcaccat +cctcaccaccaccatcaccaccatcatcaccatcatcatcatgaccatcaccaccatcac +cactatcaccaccaccaccatcattaccatcatcatcacgaccatcaccaccatcatcac +catcaccactatcaccaccaccaccatcattaccatcatcatcacgaccatcaccaccat +catcaccatcaccactatcaccaccaccaccatcatcaccatcaccatcatcacagtcat +cactgtcaccatcatcaccatcctcactatcaccaccaccaccatcatcaccatcaccat +catcacagtcatcaccgtcaccatcatcaccatcctcactatcaccaccacc-accatca +tcaccatcaccatcatcacagtcatcaccgtcaccatcatcaccatcctcactatcacca +ccaccaccatcatcaccatcaccatcatcacagtcatcaccgtcaccatcatcaccatcc +tcactatcaccaccaccaccatcatcaccatcaccatcatcacagtcatcaccgtcacca +tcatcaccatcctcactatcaccaccaccaccatcatcaccatcaccatcatcacagtca +tcaccgtcaccatcatcaccatcctcactatcaccaccaccaccatcaccatcaccatca +tcacagtcatcaccgtcaccatcatcaccatcctcactat---caccaccaccatcatca +ccatcaccatcatcacagtcatcaccgtcaccatcatcaccatcctcactatcaccacca +ccaccatcatcaccatcaccatcatcacagtcatcaccgtcaccatcatcaccatcctca +ctatcaccaccaccatcatcaccatcaccatcatcacagtcatcaccgtcaccatcatca +ccatcctcactatcaccaccaccaccatcatcaccatcaccatcatcacagtcatcaccg +tcaccatcatcaccatcctcactatcaccaccaccaccatcatcaccatcaccatcatca +caatcatcaccgtcaccatcatcaccatcctcactatcaccaccaccaccatcatcacca +tcactatcatcacagtcatcaccgtcaccatcatcaccatcctcactatcaccaccacta +ccatcatcatcacattcatcatcactattaccatcatcatcaccaccatcaccatcacta +tcaccaccatcattacatttgtcaccatcaccaccattatcaccatcaccgctatcacca +ccaccaccgtcatcatcaccatcatcatcatcaccactaccatcacgctcacagtcatca +ccatcaccaccatgatcactgccatcatcaccaccaccatcaccaccataatccccccca +actattacaaccattaacttatttaacaaaaatttattaatcaccaacgattttcccagc +cctttccagcaccatttcaggtgcttggatacactcataccttattagcatccct +>p:HG002_2_chr20:64096558-64097265 +attgcggcctctttgtgcttattcataatccctctctaacaggcagaatggagccccata +tttcctcacggcagctacactgacacagaatagtgtcatcttgggtgctgctgccactgc +caatatcgccgccaccatcatcatcacaatcatcaccatcaccaccatcatcaccactat +catcatcaccactatcaccaccaccagcaccttcattatcacattcaccatcctcaccat +cctcaccaccaccatcaccaccat---------------------catcaccaccatcac +cactatcaccaccaccaccatcattaccatcatcatcacgaccatcaccaccatcatcac +catcaccactatcaccaccaccaccatcattaccatcatcatcacgaccatcaccaccat +catcaccatcaccactatcaccaccaccaccatcatcaccatcaccatcatcacagtcat +cactgtcaccatcatcaccatcctcactatcaccaccaccaccatcatcaccatcaccat +catcacagtcatcaccgtcaccatcatcaccatcctcactatcaccaccacc-accatca +tcaccatcaccatcatcacagtcatcaccgtcaccatcatcaccatcctcactatcacca +ccaccaccatcatcaccatcaccatcatcacagtcatcaccgtcaccatcatcaccatcc +tcactatcaccaccaccaccatcatcaccatcaccatcatcacagtcatcaccatcacca +tcatcaccatcctcactatcaccaccaccaccatcatcaccatcaccatcatcacagtca +tcaccgtcaccatcatcaccatcctcactatcaccaccaccaccatcaccatcaccatca +tcacagtcatcaccgtcaccatcatcaccatcctcactatcaccaccaccaccatcatca +ccatcaccatcatcacagtcatcaccgtcaccatcatcaccatcctcactatcaccacca +ccaccatcatcaccatcaccatcatcacagtcatcaccgtcaccatcatcaccatcctca +ctatcaccaccaccatcatcaccatcaccatcatcacagtcatcaccgtcaccatcatca +ccatcctcactatcaccaccaccaccatcattaccatcaccatcatcacagtcatcaccg +tcaccatcatcaccatcctcactatcaccaccaccaccatcatcaccatcaccatcatca +caatcatcactgtcaccatcatcaccatcctcactatcaccaccaccaccatcattacca +tcactatcatcacagtcatcaccgtcaccatcatcaccatcctcactatcaccaccacta +ccatcatcatcacattcatcatcactattaccatcatcatcaccaccatcaccatcacta +tcaccaccatcattacatttgtcaccatcaccaccattatcaccatcaccgctatcacca +ccaccaccgtcatcatcaccatcatcatcatcaccactaccatcacgctcacagtcatca +ccatcaccaccatgatcactgccatcatcaccaccaccatcaccaccataatccccccca +actattacaaccattaacttatttaacaaaaatttattaatcaccaacgattttcccagc +cctttccagcaccatttcaggtgcttggatacactcataccttattagcatccct diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/msa.fa.fai new file mode 100644 index 00000000..c47b575d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_64096558_64097265 1735 29 60 61 +syndip_1_chr20:64096558-64097265 1735 1827 60 61 +syndip_2_chr20:64096558-64097265 1735 3625 60 61 +p:HG002_1_chr20:64096558-64097265 1735 5424 60 61 +p:HG002_2_chr20:64096558-64097265 1735 7223 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/output.vcf.gz new file mode 100644 index 00000000..7f57002f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/output.vcf.gz.tbi new file mode 100644 index 00000000..0ba207cc Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64096658-64097165/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/base.vcf.gz new file mode 100644 index 00000000..bbc8058c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/base.vcf.gz.tbi new file mode 100644 index 00000000..68c755fe Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/comp.vcf.gz new file mode 100644 index 00000000..3595d2f1 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/comp.vcf.gz.tbi new file mode 100644 index 00000000..7a12c1d5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/haps.fa new file mode 100644 index 00000000..d1205380 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/haps.fa @@ -0,0 +1,174 @@ +>ref_chr20_64125009_64128075 +ATTACAGGTGTGCACCACCACACCCAGCTAATTTTTTTGTATTTTCAGTAGAGATGAGGTTTCACTGTGTTAGCCAGGATGGTCTCGATTTCCTGACCTCATGATCCACCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGCGCCCGGACACACTTTGCTAGTTTTTTTTTTTTGTTTTGTTTTTTTAGTAGCAGTGCTGGGATTACAGGTGTCAGCCACCATGCCTGGCTCAAATACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACTACACCATCTTGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTCAAATACCACACCGTCTTGATTACCAAAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATAACACACCGTCTTGATTACCACAGCTTTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTCCTATAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATACCACCCTGTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTCAAATACTACTGTCCTGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACTATCTTGATTACTACAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATAACACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTCAAATACCACACTGTCTTGATTACCACAGCTGTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACGCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACTACACTGTCTTGATTAACACAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTAACACAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTGTACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACTACACTGTCTTGATTAACACAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCTGTTTTGAGGTCAGGTAGTGTCAGTCCCTCTAACTTCATTTTTCAAAGTTGTTAGGGGATTATAGGTTCTTTGCAAATTTCTATGCAAATTTTGGAATCAGTTTGTTAATTTCCAGAAAAAAGCCTCTTGC +>syndip_1_chr20:64125009-64128075 +ATTACAGGTGTGCACCACCACACCCAGCTAATTTTTTTGTATTTTCAGTAGAGATGAGGT +TTCACTGTGTTAGCCAGGATGGTCTCGATTTCCTGACCTCATGATCCACCCACCTTGGCC +TCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGCGCCCGGACACACTTTGCTAGTTTT +TTTTTTTTGTTTTGTTTTTTTAGTAGCAGTGCTGGGATTACAGGTGTCAGCCACCATGCC +TGGCTCAAATACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACTACACCATCT +TGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTC +AAATACCACACCGTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTA +CCAAAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATAA +CACACCGTCTTGATTACCACAGCTTTATACTCAAATACTACACCGTCTTGATTACCACAG +CTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACT +GTCTTGATTCCTATAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTAT +ACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTG +ATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAA +TACCACCCTGTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTACCA +CAGCTGTATACTCAAATACTACACCGTCTTGATTACCACAGCTGTATACTCAAATACTAC +ACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACCGCTT +TATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTC +TGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTC +AAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTAC +TACAGCTTTATACTCAAATACCACACTATCTTGATTACTACAGCTTTATACTCAAATACT +ACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCT +TTATACTCAAATACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACCGT +CTTGATTACCACAGCTGTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATAC +TCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGAT +TACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATA +CCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTGATTACTACAG +CTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACT +GTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTAT +ACTCAAATACCACACTGTCTTGATTACCACAGCTGTATACTCAAATACCACACTGTCTTG +ATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACGCAA +ATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACT +ACAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACTA +CACTGTCTTGATTAACACAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCT +TTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGT +CTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATAC +TCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGAT +TACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAAT +ACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACTAT +AGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCTGTTTTGAGG +TCAGGTAGTGTCAGTCCCTCTAACTTCATTTTTCAAAGTTGTTAGGGGATTATAGGTTCT +TTGCAAATTTCTATGCAAATTTTGGAATCAGTTTGTTAATTTCCAGAAAAAAGCCTCTTG +C +>syndip_2_chr20:64125009-64128075 +ATTACAGGTGTGCACCACCACACCCAGCTAATTTTTTTGTATTTTCAGTAGAGATGAGGT +TTCACTGTGTTAGCCAGGATGGTCTCGATTTCCTGACCTCATGATCCACCCACCTTGGCC +TCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGCGCCCGGACACACTTTGCTAGTTTT +TTTTTTTTGTTTTGTTTTTTTAGTAGCAGTGCTGGGATTACAGGTGTCAGCCACCATGCC +TGGCTCAAATACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACTACACCATCT +TGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTC +AAATACCACACCGTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTA +CCAAAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATAA +CACACCGTCTTGATTACCACAGCTTTATACTCAAATACTACACCGTCTTGATTACCACAG +CTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACT +GTCTTGATTCCTATAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTAT +ACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTG +ATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAA +TACCACCCTGTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTACCA +CAGCTGTATACTCAAATACTACACCGTCTTGATTACCACAGCTGTATACTCAAATACTAC +ACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACCGCTT +TATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTC +TGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTC +AAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTAC +TACAGCTTTATACTCAAATACCACACTATCTTGATTACTACAGCTTTATACTCAAATACT +ACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCT +TTATACTCAAATACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACCGT +CTTGATTACCACAGCTGTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATAC +TCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGAT +TACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATA +CCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTGATTACTACAG +CTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACT +GTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTAT +ACTCAAATACCACACTGTCTTGATTACCACAGCTGTATACTCAAATACCACACTGTCTTG +ATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACGCAA +ATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACT +ACAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACTA +CACTGTCTTGATTAACACAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCT +TTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGT +CTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATAC +TCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGAT +TACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAAT +ACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACTAT +AGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCTGTTTTGAGG +TCAGGTAGTGTCAGTCCCTCTAACTTCATTTTTCAAAGTTGTTAGGGGATTATAGGTTCT +TTGCAAATTTCTATGCAAATTTTGGAATCAGTTTGTTAATTTCCAGAAAAAAGCCTCTTG +C +>p:HG002_1_chr20:64125009-64128075 +ATTACAGGTGTGCACCACCACACCCAGCTAATTTTTTTGTATTTTCAGTAGAGATGAGGT +TTCACTGTGTTAGCCAGGATGGTCTCGATTTCCTGACCTCATGATCCACCCACCTTGGCC +TCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGCGCCCGGACACACTTTGCTAGTTTT +TTTTTTTTGTTTTGTTTTTTTAGTAGCAGTGCTGGGATTACAGGTGTCAGCCACCATGCC +TGGCTCAAATACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACTACACCATCT +TGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTC +AAATACCACACCGTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTA +CCAAAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATAA +CACACCGTCTTGATTACCACAGCTTTATACTCAAATACTACACCGTCTTGATTACCACAG +CTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACT +GTCTTGATTCCTATAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTAT +ACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTG +ATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAA +TACCACCCTGTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTACCA +CAGCTGTATACTCAAATACTACACCGTCTTGATTACCACAGCTGTATACTCAAATACTAC +ACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACCGCTT +TATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTC +TGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTC +AAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTAC +TACAGCTTTATACTCAAATACCACACTATCTTGATTACTACAGCTTTATACTCAAATACT +ACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCT +TTATACTCAAATACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACCGT +CTTGATTACCACAGCTGTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATAC +TCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGAT +TACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATA +CCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTGATTACTACAG +CTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACT +GTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTAT +ACTCAAATACCACACTGTCTTGATTACCACAGCTGTATACTCAAATACCACACTGTCTTG +ATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACGCAA +ATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACT +ACAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACTA +CACTGTCTTGATTAACACAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCT +TTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGT +CTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATAC +TCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGAT +TACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAAT +ACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACTAT +AGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCTGTTTTGAGG +TCAGGTAGTGTCAGTCCCTCTAACTTCATTTTTCAAAGTTGTTAGGGGATTATAGGTTCT +TTGCAAATTTCTATGCAAATTTTGGAATCAGTTTGTTAATTTCCAGAAAAAAGCCTCTTG +C +>p:HG002_2_chr20:64125009-64128075 +ATTACAGGTGTGCACCACCACACCCAGCTAATTTTTTTGTATTTTCAGTAGAGATGAGGT +TTCACTGTGTTAGCCAGGATGGTCTCGATTTCCTGACCTCATGATCCACCCACCTTGGCC +TCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGCGCCCGGACACACTTTGCTAGTTTT +TTTTTTTTGTTTTGTTTTTTTAGTAGCAGTGCTGGGATTACAGGTGTCAGCCACCATGCC +TGGCTCAAATACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACTACACCATCT +TGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTC +AAATACCACACCGTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTA +CCAAAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATAA +CACACCGTCTTGATTACCACAGCTTTATACTCAAATACTACACCGTCTTGATTACCACAG +CTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACT +GTCTTGATTCCTATAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTAT +ACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTG +ATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAA +TACCACCCTGTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTACCA +CAGCTGTATACTCAAATACTACACCGTCTTGATTACCACAGCTGTATACTCAAATACTAC +ACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACCGCTT +TATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTC +TGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTC +AAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTAC +TACAGCTTTATACTCAAATACCACACTATCTTGATTACTACAGCTTTATACTCAAATACT +ACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCT +TTATACTCAAATACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACCGT +CTTGATTACCACAGCTGTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATAC +TCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGAT +TACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATA +CCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTGATTACTACAG +CTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACT +GTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTAT +ACTCAAATACCACACTGTCTTGATTACCACAGCTGTATACTCAAATACCACACTGTCTTG +ATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACGCAA +ATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACT +ACAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACTA +CACTGTCTTGATTAACACAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCT +TTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGT +CTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATAC +TCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGAT +TACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAAT +ACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACTAT +AGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCTGTTTTGAGG +TCAGGTAGTGTCAGTCCCTCTAACTTCATTTTTCAAAGTTGTTAGGGGATTATAGGTTCT +TTGCAAATTTCTATGCAAATTTTGGAATCAGTTTGTTAATTTCCAGAAAAAAGCCTCTTG +C diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/haps.fa.ref.fa new file mode 100644 index 00000000..ef619193 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:64125009-64128075 +ATTACAGGTGTGCACCACCACACCCAGCTAATTTTTTTGTATTTTCAGTAGAGATGAGGTTTCACTGTGTTAGCCAGGATGGTCTCGATTTCCTGACCTCATGATCCACCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGCGCCCGGACACACTTTGCTAGTTTTTTTTTTTTGTTTTGTTTTTTTAGTAGCAGTGCTGGGATTACAGGTGTCAGCCACCATGCCTGGCTCAAATACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACTACACCATCTTGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTCAAATACCACACCGTCTTGATTACCAAAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATAACACACCGTCTTGATTACCACAGCTTTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTCCTATAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATACCACCCTGTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTCAAATACTACTGTCCTGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACTATCTTGATTACTACAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATACTACACCGTCTTGATTACCACAGCTTTATACTCAAATAACACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACCGTCTTGATTACCACAGCTGTATACTCAAATACCACACTGTCTTGATTACCACAGCTGTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACGCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACTACACTGTCTTGATTAACACAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTAACACAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTGTACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACCACAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACCACACTGTCTTGATTACTACAGCTTTATACTCAAATACTACACTGTCTTGATTAACACAGCTTTATACTCAAATACTACACTGTCTTGATTACCACAGCTTTATACTCAAATACTACACTGTCTTGATTACTATAGCTTTATACTCAAATACCACACTGTCTTGATTACTATAGCTTTATACTCTGTTTTGAGGTCAGGTAGTGTCAGTCCCTCTAACTTCATTTTTCAAAGTTGTTAGGGGATTATAGGTTCTTTGCAAATTTCTATGCAAATTTTGGAATCAGTTTGTTAATTTCCAGAAAAAAGCCTCTTGC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/msa.fa new file mode 100644 index 00000000..c309b2ea --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/msa.fa @@ -0,0 +1,280 @@ +>ref_chr20_64125009_64128075 +attacaggtgtgcaccaccacacccagctaatttttttgtattttcagtagagatgaggt +ttcactgtgttagccaggatggtctcgatttcctgacctcatgatccacccaccttggcc +tcccaaagtgctgggattacaggtgtgagccactgcgcccggacacactttgctagtttt +ttttttttgttttgtttttttagtagcagtgctgggattacaggtgtcagccaccatgcc +tggctcaaatactacactgtcttgattactacagctttatactcaaatactacaccatct +tgattactacagctt--------------------------------------tatactc +aaataccacaccgtcttgattaccacagctgtatactcaaataccacaccgtcttgatta +ccaaagctttatactcaaataccacactgtcttgattaccacagct-------------- +-----------------ttatactcaaataacacaccgtcttgattaccacagctttata +ctcaaatactacaccgtcttgattaccacagctttatactcaaataccacactgtcttga +ttaccacagctttatactcaaatactacactgtcttgattcctatagc------------ +-------------------tttatactcaaataccacactgtcttgattaccacagcttt +atactcaaatactacactgtcttgattactatagctttatactcaaatactacactgtct +tgattactatagctttatactcaaatactacactgtctgattactacagctttatactca +aataccaccctgtcttgattaccacagctttatactcaaataccacaccgtcttgattac +cacagctgtatactcaaatactactgtcctgattactacagctttatactcaaataccac +accgtcttgattaccacagctgtatactcaaatactacaccgtcttgattaccacagctt +tatactcaaatactacaccgtcttgattaccacagctttatactcaaataccacactgtc +ttgattactatagctttatactcaaatactacactgtctgattactacagctttatactc +aaataccacactgtcttgattaccacagctttatactcaaatactacactgtcttgatta +ctatagctttatactcaaatactacactgtctgattactacagctttatactcaaatacc +acactatcttgattactacagctttatactcaaatactacactgtctgattactacagct +ttatactcaaataccacaccgtcttgattaccacagctttatactcaaatactacactgt +cttgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatac +tcaaatactacaccgtcttgattaccacagctttatactcaaatactacaccgtcttgat +taccacagctttatactcaaataacacactgtcttgattactatagctttatactcaaat +actacactgtctgattactacagctttatactcaaataccacactgtcttgattaccaca +gctttatactcaaatactacactgtctgattactacagctttatactcaaataccacact +gtcttgattaccacagctttatactcaaatactacactgtcttgattaccacagctttat +actcaaataccacaccgtcttgattaccacagctgtatactcaaataccacactgtcttg +attaccacagctgtatactcaaataccacactgtcttgattaccacagctttatactcaa +ataccacactgtcttgattactatagctttatactcaaataccacactgtcttgattacc +acagctttatacgcaaataccacactgtcttgattactatagctttatactcaaatacca +cactgtcttgattactacagctttatactcaaataccacactgtcttgattactacagct +ttatactcaaatactacactgtcttgattaacacagctttatactcaaatactacactgt +cttgattaccacagctttatactcaaatactacactgtcttgattactatagctttatac +tcaaataccacactgtcttgattactatagctttatactcaaatactacactgtcttgat +taccacagctttatactcaaatactacactgtcttgattact------------------ +--------------------atagctttatactcaaataccacactgtcttgattaccac +--------------------------------------agctttatactcaaataccaca +ctgtcttgattaccacagctttatactcaaataccacactgtcttgattaccacagcttt +atactcaaataccacactgtcttgattactatagctttatactcaaataccacactgtct +tgattactacagctttatactcaaataccacactgtcttgattaacacagctttatactc +aaatactacactgtcttgattaccacagctttatactcaaatactacactgtcttgatta +ctatagctttatactcaaataccacactgtcttgattactatagctttatactcaaatac +tacactgtcttgattaccacagctttatactcaaatactacactgtcttgattactatag +ctttgtactcaaataccacactgtcttgattaccacagctttatactcaaataccacact +gtcttgattaccacagctttatactcaaataccacactgtcttgattactatagctttat +actcaaataccacactgtcttgattactacagctttatactcaaataccacactgtcttg +attactacagctttatactcaaatactacactgtcttgattaacacagctttatactcaa +atactacactgtcttgattaccacagctttatactcaaatactacactgtcttgattact +atagctttatactcaaataccacactgtcttgattactatagctttatactctgttttga +ggtcaggtagtgtcagtccctctaacttcatttttcaaagttgttaggggattataggtt +ctttgcaaatttctatgcaaattttggaatcagtttgttaatttccagaaaaaagcctct +tgc +>syndip_1_chr20:64125009-64128075 +attacaggtgtgcaccaccacacccagctaatttttttgtattttcagtagagatgaggt +ttcactgtgttagccaggatggtctcgatttcctgacctcatgatccacccaccttggcc +tcccaaagtgctgggattacaggtgtgagccactgcgcccggacacactttgctagtttt +ttttttttgttttgtttttttagtagcagtgctgggattacaggtgtcagccaccatgcc +tggctcaaatactacactgtcttgattactacagctttatactcaaatactacaccatct +tgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatactc +aaataccacaccgtcttgattaccacagctttatactcaaataccacaccgtcttgatta +ccaaagctttata-------------------------------ctcaaataccacactg +tcttgattaccacagctttatactcaaataacacaccgtcttgattaccacagctttata +ctcaaatactacaccgtcttgattaccacagctttatactcaaataccacactgtcttga +ttaccacagctttata-------------------------------ctcaaataccaca +ctgtcttgattcctatagctttatactcaaataccacactgtcttgattaccacagcttt +atactcaaatactacactgtcttgattactatagctttatactcaaatactacactgtct +tgattactatagctttatactcaaatactacactgtctgattactacagctttatactca +aataccaccctgtcttgattaccacagctttatactcaaataccacaccgtcttgattac +cacagctgtatactcaaatact------------------------------------ac +accgtcttgattaccacagctgtatactcaaatactacactgtcttgattaccacagctt +tatactcaaataccacactgtcttgattaccaccgctttatactcaaataccacactgtc +ttgattactatagctttatactcaaatactacactgtctgattactacagctttatactc +aaataccacactgtcttgattaccacagctttatactcaaatactacactgtcttgatta +ctatagctttatactcaaatactacactgtctgattactacagctttatactcaaatacc +acactatcttgattactacagctttatactcaaatactacactgtctgattactacagct +ttatactcaaataccacaccgtcttgattaccacagctttatactcaaatactacactgt +cttgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatac +tcaaatactacaccgtcttgattaccacagctttatactcaaatactacaccgtcttgat +taccacagctttatactcaaataccacactgtcttgattactatagctttatactcaaat +actacactgtctgattactacagctttatactcaaataccacactgtcttgattaccaca +gctttatactcaaatactacactgtctgattactacagctttatactcaaataccacact +gtcttgattaccacagctttatactcaaatactacactgtcttgattaccacagctttat +actcaaataccacaccgtcttgattaccacagctgtatactcaaataccacactgtcttg +attaccacagctgtatactcaaataccacactgtcttgattaccacagctttatactcaa +atacc------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------acactgtcttgattaccacagctttatac +gcaaataccacactgtcttgattactatagctttatactcaaataccacactgtcttgat +tactacagctttatactcaaataccacactgtcttgattactacagctttatactcaaat +actacactgtcttgattaacacagctttatactcaaatactacactgtcttgattaccac +agctttatactcaaatactacactgtcttgattactatagctttatactcaaataccaca +ctgtcttgattactatagctttatactcaaatactacactgtcttgattaccacagcttt +atactcaaatactacactgtcttgattactatagctttatactcaaataccacactgtct +tgattaccac-------------------------------------------------- +------------------------------------------------------------ +----agctttatactcaaataccacactgtcttgattaccacagctttatactcaaatac +tacactgtcttgattactac---------------------------------------- +------------------------------------agctttatactcaaatacc----- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------acactgtcttgattact +atagctttatactcaaataccacactgtcttgattactatagctttatactctgttttga +ggtcaggtagtgtcagtccctctaacttcatttttcaaagttgttaggggattataggtt +ctttgcaaatttctatgcaaattttggaatcagtttgttaatttccagaaaaaagcctct +tgc +>syndip_2_chr20:64125009-64128075 +attacaggtgtgcaccaccacacccagctaatttttttgtattttcagtagagatgaggt +ttcactgtgttagccaggatggtctcgatttcctgacctcatgatccacccaccttggcc +tcccaaagtgctgggattacaggtgtgagccactgcgcccggacacactttgctagtttt +ttttttttgttttgtttttttagtagcagtgctgggattacaggtgtcagccaccatgcc +tggctcaaatactacactgtcttgattactacagctttatactcaaatactacaccatct +tgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatactc +aaataccacaccgtcttgattaccacagctttatactcaaataccacaccgtcttgatta +ccaaagctttata-------------------------------ctcaaataccacactg +tcttgattaccacagctttatactcaaataacacaccgtcttgattaccacagctttata +ctcaaatactacaccgtcttgattaccacagctttatactcaaataccacactgtcttga +ttaccacagctttata-------------------------------ctcaaataccaca +ctgtcttgattcctatagctttatactcaaataccacactgtcttgattaccacagcttt +atactcaaatactacactgtcttgattactatagctttatactcaaatactacactgtct +tgattactatagctttatactcaaatactacactgtctgattactacagctttatactca +aataccaccctgtcttgattaccacagctttatactcaaataccacaccgtcttgattac +cacagctgtatactcaaatact------------------------------------ac +accgtcttgattaccacagctgtatactcaaatactacactgtcttgattaccacagctt +tatactcaaataccacactgtcttgattaccaccgctttatactcaaataccacactgtc +ttgattactatagctttatactcaaatactacactgtctgattactacagctttatactc +aaataccacactgtcttgattaccacagctttatactcaaatactacactgtcttgatta +ctatagctttatactcaaatactacactgtctgattactacagctttatactcaaatacc +acactatcttgattactacagctttatactcaaatactacactgtctgattactacagct +ttatactcaaataccacaccgtcttgattaccacagctttatactcaaatactacactgt +cttgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatac +tcaaatactacaccgtcttgattaccacagctttatactcaaatactacaccgtcttgat +taccacagctttatactcaaataccacactgtcttgattactatagctttatactcaaat +actacactgtctgattactacagctttatactcaaataccacactgtcttgattaccaca +gctttatactcaaatactacactgtctgattactacagctttatactcaaataccacact +gtcttgattaccacagctttatactcaaatactacactgtcttgattaccacagctttat +actcaaataccacaccgtcttgattaccacagctgtatactcaaataccacactgtcttg +attaccacagctgtatactcaaataccacactgtcttgattaccacagctttatactcaa +atacc------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------acactgtcttgattaccacagctttatac +gcaaataccacactgtcttgattactatagctttatactcaaataccacactgtcttgat +tactacagctttatactcaaataccacactgtcttgattactacagctttatactcaaat +actacactgtcttgattaacacagctttatactcaaatactacactgtcttgattaccac +agctttatactcaaatactacactgtcttgattactatagctttatactcaaataccaca +ctgtcttgattactatagctttatactcaaatactacactgtcttgattaccacagcttt +atactcaaatactacactgtcttgattactatagctttatactcaaataccacactgtct +tgattaccac-------------------------------------------------- +------------------------------------------------------------ +----agctttatactcaaataccacactgtcttgattaccacagctttatactcaaatac +cacactgtcttgattactac---------------------------------------- +------------------------------------agctttatactcaaatacc----- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------acactgtcttgattact +atagctttatactcaaataccacactgtcttgattactatagctttatactctgttttga +ggtcaggtagtgtcagtccctctaacttcatttttcaaagttgttaggggattataggtt +ctttgcaaatttctatgcaaattttggaatcagtttgttaatttccagaaaaaagcctct +tgc +>p:HG002_1_chr20:64125009-64128075 +attacaggtgtgcaccaccacacccagctaatttttttgtattttcagtagagatgaggt +ttcactgtgttagccaggatggtctcgatttcctgacctcatgatccacccaccttggcc +tcccaaagtgctgggattacaggtgtgagccactgcgcccggacacactttgctagtttt +ttttttttgttttgtttttttagtagcagtgctgggattacaggtgtcagccaccatgcc +tggctcaaatactacactgtcttgattactacagctttatactcaaatactacaccatct +tgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatactc +aaataccacaccgtcttgattaccacagctttatactcaaataccacaccgtcttgatta +ccaaagctttata-------------------------------ctcaaataccacactg +tcttgattaccacagctttatactcaaataacacaccgtcttgattaccacagctttata +ctcaaatactacaccgtcttgattaccacagctttatactcaaataccacactgtcttga +ttaccacagctttata-------------------------------ctcaaataccaca +ctgtcttgattcctatagctttatactcaaataccacactgtcttgattaccacagcttt +atactcaaatactacactgtcttgattactatagctttatactcaaatactacactgtct +tgattactatagctttatactcaaatactacactgtctgattactacagctttatactca +aataccaccctgtcttgattaccacagctttatactcaaataccacaccgtcttgattac +cacagctgtatactcaaatact------------------------------------ac +accgtcttgattaccacagctgtatactcaaatactacactgtcttgattaccacagctt +tatactcaaataccacactgtcttgattaccaccgctttatactcaaataccacactgtc +ttgattactatagctttatactcaaatactacactgtctgattactacagctttatactc +aaataccacactgtcttgattaccacagctttatactcaaatactacactgtcttgatta +ctatagctttatactcaaatactacactgtctgattactacagctttatactcaaatacc +acactatcttgattactacagctttatactcaaatactacactgtctgattactacagct +ttatactcaaataccacaccgtcttgattaccacagctttatactcaaatactacactgt +cttgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatac +tcaaatactacaccgtcttgattaccacagctttatactcaaatactacaccgtcttgat +taccacagctttatactcaaataccacactgtcttgattactatagctttatactcaaat +actacactgtctgattactacagctttatactcaaataccacactgtcttgattaccaca +gctttatactcaaatactacactgtctgattactacagctttatactcaaataccacact +gtcttgattaccacagctttatactcaaatactacactgtcttgattaccacagctttat +actcaaataccacaccgtcttgattaccacagctgtatactcaaataccacactgtcttg +attaccacagctgtatactcaaataccacactgtcttgattaccacagctttatactcaa +atacc------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------acactgtcttgattaccacagctttatac +gcaaataccacactgtcttgattactatagctttatactcaaataccacactgtcttgat +tactacagctttatactcaaataccacactgtcttgattactacagctttatactcaaat +actacactgtcttgattaacacagctttatactcaaatactacactgtcttgattaccac +agctttatactcaaatactacactgtcttgattactatagctttatactcaaataccaca +ctgtcttgattactatagctttatactcaaatactacactgtcttgattaccacagcttt +atactcaaatactacactgtcttgattactatagctttatactcaaataccacactgtct +tgattaccac-------------------------------------------------- +------------------------------------------------------------ +----agctttatactcaaataccacactgtcttgattaccacagctttatactcaaatac +cacactgtcttgattactac---------------------------------------- +------------------------------------agctttatactcaaatacc----- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------acactgtcttgattact +atagctttatactcaaataccacactgtcttgattactatagctttatactctgttttga +ggtcaggtagtgtcagtccctctaacttcatttttcaaagttgttaggggattataggtt +ctttgcaaatttctatgcaaattttggaatcagtttgttaatttccagaaaaaagcctct +tgc +>p:HG002_2_chr20:64125009-64128075 +attacaggtgtgcaccaccacacccagctaatttttttgtattttcagtagagatgaggt +ttcactgtgttagccaggatggtctcgatttcctgacctcatgatccacccaccttggcc +tcccaaagtgctgggattacaggtgtgagccactgcgcccggacacactttgctagtttt +ttttttttgttttgtttttttagtagcagtgctgggattacaggtgtcagccaccatgcc +tggctcaaatactacactgtcttgattactacagctttatactcaaatactacaccatct +tgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatactc +aaataccacaccgtcttgattaccacagctttatactcaaataccacaccgtcttgatta +ccaaagctttata-------------------------------ctcaaataccacactg +tcttgattaccacagctttatactcaaataacacaccgtcttgattaccacagctttata +ctcaaatactacaccgtcttgattaccacagctttatactcaaataccacactgtcttga +ttaccacagctttata-------------------------------ctcaaataccaca +ctgtcttgattcctatagctttatactcaaataccacactgtcttgattaccacagcttt +atactcaaatactacactgtcttgattactatagctttatactcaaatactacactgtct +tgattactatagctttatactcaaatactacactgtctgattactacagctttatactca +aataccaccctgtcttgattaccacagctttatactcaaataccacaccgtcttgattac +cacagctgtatactcaaatact------------------------------------ac +accgtcttgattaccacagctgtatactcaaatactacactgtcttgattaccacagctt +tatactcaaataccacactgtcttgattaccaccgctttatactcaaataccacactgtc +ttgattactatagctttatactcaaatactacactgtctgattactacagctttatactc +aaataccacactgtcttgattaccacagctttatactcaaatactacactgtcttgatta +ctatagctttatactcaaatactacactgtctgattactacagctttatactcaaatacc +acactatcttgattactacagctttatactcaaatactacactgtctgattactacagct +ttatactcaaataccacaccgtcttgattaccacagctttatactcaaatactacactgt +cttgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatac +tcaaatactacaccgtcttgattaccacagctttatactcaaatactacaccgtcttgat +taccacagctttatactcaaataccacactgtcttgattactatagctttatactcaaat +actacactgtctgattactacagctttatactcaaataccacactgtcttgattaccaca +gctttatactcaaatactacactgtctgattactacagctttatactcaaataccacact +gtcttgattaccacagctttatactcaaatactacactgtcttgattaccacagctttat +actcaaataccacaccgtcttgattaccacagctgtatactcaaataccacactgtcttg +attaccacagctgtatactcaaataccacactgtcttgattaccacagctttatactcaa +atacc------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------acactgtcttgattaccacagctttatac +gcaaataccacactgtcttgattactatagctttatactcaaataccacactgtcttgat +tactacagctttatactcaaataccacactgtcttgattactacagctttatactcaaat +actacactgtcttgattaacacagctttatactcaaatactacactgtcttgattaccac +agctttatactcaaatactacactgtcttgattactatagctttatactcaaataccaca +ctgtcttgattactatagctttatactcaaatactacactgtcttgattaccacagcttt +atactcaaatactacactgtcttgattactatagctttatactcaaataccacactgtct +tgattaccac-------------------------------------------------- +------------------------------------------------------------ +----agctttatactcaaataccacactgtcttgattaccacagctttatactcaaatac +tacactgtcttgattactac---------------------------------------- +------------------------------------agctttatactcaaatacc----- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------acactgtcttgattact +atagctttatactcaaataccacactgtcttgattactatagctttatactctgttttga +ggtcaggtagtgtcagtccctctaacttcatttttcaaagttgttaggggattataggtt +ctttgcaaatttctatgcaaattttggaatcagtttgttaatttccagaaaaaagcctct +tgc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/msa.fa.fai new file mode 100644 index 00000000..8e2fb2e7 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_64125009_64128075 3243 29 60 61 +syndip_1_chr20:64125009-64128075 3243 3361 60 61 +syndip_2_chr20:64125009-64128075 3243 6693 60 61 +p:HG002_1_chr20:64125009-64128075 3243 10026 60 61 +p:HG002_2_chr20:64125009-64128075 3243 13359 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/output.vcf.gz new file mode 100644 index 00000000..7a978db9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/output.vcf.gz.tbi new file mode 100644 index 00000000..87896cdb Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64125109-64127975/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/base.vcf.gz new file mode 100644 index 00000000..47e9b791 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/base.vcf.gz.tbi new file mode 100644 index 00000000..b7e2f661 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/comp.vcf.gz new file mode 100644 index 00000000..d3bbfffa Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/comp.vcf.gz.tbi new file mode 100644 index 00000000..0e0c05e5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/haps.fa new file mode 100644 index 00000000..3057221c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/haps.fa @@ -0,0 +1,246 @@ +>ref_chr20_64131704_64134056 +AGGCTGTTGTAGGTGGGCCAGGAGGGGCTGGGCAGCCCATGAGGGTGAGGCTGAGACTCCACACTGAGCCCAGGTTTAGGGGACCTGGTGGGGGTCACAGCCTCCCCTGTCCCAGACTTCTCCTGGCCTCTCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCACTCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACTCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATGAGACCCCCTCACTGTCCACTCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCGCCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCGCCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACTCTCATGTCCTATGAGACCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCAACTCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCAAAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCAAAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCAAAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCATATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCATATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCAGGACCCTCTGCATTTGCTCCTTGGGTTCCCGGAACTTGAGCTTGGGTCTTGGTCCACAGCAGCTTTGGGAAGGGCCCTCGGCTGCTTTTTGCTTCAGCAGCTGGGGAGCAGTTAACTTTCAGACCCGGCCC +>syndip_1_chr20:64131704-64134056 +AGGCTGTTGTAGGTGGGCCAGGAGGGGCTGGGCAGCCCATGAGGGTGAGGCTGAGACTCC +ACACTGAGCCCAGGTTTAGGGGACCTGGTGGGGGTCACAGCCTCCCCTGTCCCAGACTTC +TCCTGGCCTCTCTCATGTCCTATGAGACCCCCTCACTGTCCACTCTCATGGCCTGTAGAG +ACCCCCTCACTGTCAACTCTCATGTCCTATAGAGACCCCCTCACTGTCAACTCTCATGTC +CTATGAGACCCCCTCACTGTCCACTCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCC +TCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACT +GTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCC +CCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATA +GAGACCCCCTCACTGTCCACTCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCAT +GTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCA +CCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTC +ACTGTCCACTCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGA +CCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCC +TGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACTCT +CATGTCCTATGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGT +CCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCC +CTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATG +AGACCCCCTCACTGTCCACTCTCATGTCCTATGAGACCCCCTCACTGTCCACTCTCATGG +CCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCAC +CCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCA +CTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGAC +CCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCT +GTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACTCT +CATGTCCTATAGAGACCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGT +CCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCC +CTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACTCTCATGTCCTATGA +GACCCCCTCACTGTCCACTCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGT +CCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCACC +CTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCAC +TGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACC +CCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCGTGTCCTA +TAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTC +ATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTC +CACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCC +TCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGA +GACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCAACTCTCATGT +CCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATGAGACCCCCTCACTGTCCACC +CTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCAC +TGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACC +CCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCAACTCTCATGTCCTA +TAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTCTCCACCCTC +ATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGT +CCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCC +TCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGA +GACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGT +CCTATAGAGACCCCCTCACTCTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCAC +CCTCGTGTCCTATAGAGACCCCCTCACTCTCCACCCTCATGGCCTATAGAGACCCCCTCA +CTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACTCTCATGTCCTATGAGAC +CCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCT +ATGAGACCCCCTCACTGTCCACTCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCA +TGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCC +ACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTC +ACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACTCTCATGTCCTATGAGA +CCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGGCCT +ATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTC +ATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGT +CCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACTCTCATGGCCTGTAGAGACCCC +CTCACTGTCCACCCATATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCAGGACCCTCT +GCATTTGCTCCTTGGGTTCCCGGAACTTGAGCTTGGGTCTTGGTCCACAGCAGCTTTGGG +AAGGGCCCTCGGCTGCTTTTTGCTTCAGCAGCTGGGGAGCAGTTAACTTTCAGACCCGGC +CC +>syndip_2_chr20:64131704-64134056 +AGGCTGTTGTAGGTGGGCCAGGAGGGGCTGGGCAGCCCATGAGGGTGAGGCTGAGACTCC +ACACTGAGCCCAGGTTTAGGGGACCTGGTGGGGGTCACAGCCTCCCCTGTCCCAGACTTC +TCCTGGCCTCTCTCATGTCCTATGAGACCCCCTCACTGTCCACTCTCATGGCCTGTAGAG +ACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGC +CTATGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCC +TCATGTCCTATAGAGACCCCTCACTGTCCACCCTCATGGCCTATGAGACCCCCTCACTGT +CCACTCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCC +CTCACTGTCCACCCTCATGTCCTATAGAGACCCCTCACTGTCCACCCTCATGGCCTATGA +GACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGT +CCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACC +CTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACT +GTCCACTCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACC +CCCTCACTGTCCACCCTCGTGTCCTATGAGACCCCCTCACTGTCCACCCTCGTGTCCTAT +AGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCA +TGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCC +ACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCT +CACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGA +GACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGG +CCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCAC +CCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCAC +TGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACC +CCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTA +TAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCA +TGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTC +CACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCC +TCACTGTCCACCCTCGTGTCCTATGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGA +GACCCCCTCACTGTCCACCCTCATGGCCTATGAGACCCCCTCACTGTCCACCCTCGTGTC +CTATGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCC +TCATGGCCTATGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTG +TCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCC +CCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTAT +GAGACCCCCTCACTGTCCACTCTCATGTCCTATAGAGACCCCTCACTGTCCACCCTCATG +GCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCA +CCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTC +ACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAG +ACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTC +CTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACC +CTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCAC +TGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACC +CCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTA +TAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTC +GTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGT +CCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCC +CTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATG +AGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATG +TCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCA +CCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTC +ACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATGAGA +CCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCC +TATAGAGACCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCT +CGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGT +CCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCC +TCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAG +AGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATG +TCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCA +CCCATATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTC +ACTGTCCACCCTCAGGACCCTCTGCATTTGCTCCTTGGGTTCCCGGAACTTGAGCTTGGG +TCTTGGTCCACAGCAGCTTTGGGAAGGGCCCTCGGCTGCTTTTTGCTTCAGCAGCTGGGG +AGCAGTTAACTTTCAGACCCGGCCC +>p:HG002_1_chr20:64131704-64134056 +AGGCTGTTGTAGGTGGGCCAGGAGGGGCTGGGCAGCCCATGAGGGTGAGGCTGAGACTCC +ACACTGAGCCCAGGTTTAGGGGACCTGGTGGGGGTCACAGCCTCCCCTGTCCCAGACTTC +TCCTGGCCTCTCTCATGTCCTATGAGACCCCCTCACTGTCCACTCTCATGGCCTGTAGAG +ACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGC +CTATGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCC +TCATGTCCTATAGAGACCCCTCACTGTCCACCCTCATGGCCTATGAGACCCCCTCACTGT +CCACTCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCC +CTCACTGTCCACCCTCATGTCCTATAGAGACCCCTCACTGTCCACCCTCATGGCCTATGA +GACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGT +CCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACC +CTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACT +GTCCACTCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACC +CCCTCACTGTCCACCCTCGTGTCCTATGAGACCCCCTCACTGTCCACCCTCGTGTCCTAT +AGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCA +TGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCC +ACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCT +CACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGA +GACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGG +CCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCAC +CCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCAC +TGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACC +CCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTA +TAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCA +TGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTC +CACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCC +TCACTGTCCACCCTCGTGTCCTATGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGA +GACCCCCTCACTGTCCACCCTCATGGCCTATGAGACCCCCTCACTGTCCACCCTCGTGTC +CTATGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCC +TCATGGCCTATGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTG +TCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCC +CCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTAT +GAGACCCCCTCACTGTCCACTCTCATGTCCTATAGAGACCCCTCACTGTCCACCCTCATG +GCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCA +CCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTC +ACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAG +ACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTC +CTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACC +CTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCAC +TGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACC +CCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTA +TAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTC +GTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGT +CCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCC +CTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATG +AGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATG +TCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCA +CCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTC +ACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATGAGA +CCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCC +TATAGAGACCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCT +CGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGT +CCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCC +TCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAG +AGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATG +TCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCA +CCCATATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTC +ACTGTCCACCCTCAGGACCCTCTGCATTTGCTCCTTGGGTTCCCGGAACTTGAGCTTGGG +TCTTGGTCCACAGCAGCTTTGGGAAGGGCCCTCGGCTGCTTTTTGCTTCAGCAGCTGGGG +AGCAGTTAACTTTCAGACCCGGCCC +>p:HG002_2_chr20:64131704-64134056 +AGGCTGTTGTAGGTGGGCCAGGAGGGGCTGGGCAGCCCATGAGGGTGAGGCTGAGACTCC +ACACTGAGCCCAGGTTTAGGGGACCTGGTGGGGGTCACAGCCTCCCCTGTCCCAGACTTC +TCCTGGCCTCTCTCATGTCCTATGAGACCCCCTCACTGTCCACTCTCATGGCCTGTAGAG +ACCCCCTCACTGTCAACTCTCATGTCCTATAGAGACCCCCTCACTGTCAACTCTCATGTC +CTATGAGACCCCCTCACTGTCCACTCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCC +TCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACT +GTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCC +CCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATA +GAGACCCCCTCACTGTCCACTCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCAT +GTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCA +CCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTC +ACTGTCCACTCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGA +CCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCC +TGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACTCT +CATGTCCTATGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGT +CCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCC +CTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATG +AGACCCCCTCACTGTCCACTCTCATGTCCTATGAGACCCCCTCACTGTCCACTCTCATGG +CCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCAC +CCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCA +CTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGAC +CCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCT +GTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACTCT +CATGTCCTATAGAGACCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGT +CCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCC +CTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACTCTCATGTCCTATGA +GACCCCCTCACTGTCCACTCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGT +CCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCACC +CTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCAC +TGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACC +CCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCGTGTCCTA +TAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTC +ATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTC +CACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCC +TCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGA +GACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCAACTCTCATGT +CCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATGAGACCCCCTCACTGTCCACC +CTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCAC +TGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACC +CCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCAACTCTCATGTCCTA +TAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTCTCCACCCTC +ATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGT +CCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCC +TCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGA +GACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGT +CCTATAGAGACCCCCTCACTCTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCAC +CCTCGTGTCCTATAGAGACCCCCTCACTCTCCACCCTCATGGCCTATAGAGACCCCCTCA +CTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACTCTCATGTCCTATGAGAC +CCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCT +ATGAGACCCCCTCACTGTCCACTCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCA +TGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCC +ACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTC +ACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACTCTCATGTCCTATGAGA +CCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGGCCT +ATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTC +ATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGT +CCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACTCTCATGGCCTGTAGAGACCCC +CTCACTGTCCACCCATATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCAGGACCCTCT +GCATTTGCTCCTTGGGTTCCCGGAACTTGAGCTTGGGTCTTGGTCCACAGCAGCTTTGGG +AAGGGCCCTCGGCTGCTTTTTGCTTCAGCAGCTGGGGAGCAGTTAACTTTCAGACCCGGC +CC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/haps.fa.ref.fa new file mode 100644 index 00000000..1dca2959 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:64131704-64134056 +AGGCTGTTGTAGGTGGGCCAGGAGGGGCTGGGCAGCCCATGAGGGTGAGGCTGAGACTCCACACTGAGCCCAGGTTTAGGGGACCTGGTGGGGGTCACAGCCTCCCCTGTCCCAGACTTCTCCTGGCCTCTCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCACTCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACTCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATGAGACCCCCTCACTGTCCACTCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCGCCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCGCCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACTCTCATGTCCTATGAGACCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCAACTCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCAAAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCAAAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCAAAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCATATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCATATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCAGGACCCTCTGCATTTGCTCCTTGGGTTCCCGGAACTTGAGCTTGGGTCTTGGTCCACAGCAGCTTTGGGAAGGGCCCTCGGCTGCTTTTTGCTTCAGCAGCTGGGGAGCAGTTAACTTTCAGACCCGGCCC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/msa.fa new file mode 100644 index 00000000..0c7d1060 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/msa.fa @@ -0,0 +1,330 @@ +>ref_chr20_64131704_64134056 +aggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactcc +acactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagacttc +tcctggcctctctcatgtcctat------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------gagaccccctcactgtccaccctcatgtcctgtagagaccccctcactgtcc +actctcatggcctatagagaccccctcactgtccaccctcatggcctgtagagaccccct +cactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctataga +gaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgt +cctatgagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccacc +ctcatgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcac +tgtccaccctca----------------------------------tgtcctgtagagac +cccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcgtgtccta +tagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctc +atgtcctat-gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgt +ccactctcatgtcctatagagaccccctcactgtccaccctcatggcctatgagaccccc +tcactgtccactctcatggcctatagagaccccctcactgtccaccctcatggcctatag +agaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatg +tcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtcca +ccctcatggcctat---------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----gagaccccctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccc +tcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccccctcact +gtccaccctcatgtcctatagagaccccctcactgtccgccctcatgtcctatgagaccc +cctcactgtccaccctcatgt--------------------------------------- +-----------------------------cctatagagaccccctcactgtccaccctca +tggcctgtagagaccccctcactgtccgccctcatgtcctat------------------ +-----------------gagaccccctcactgtccaccctcatgtcctgtagagaccccc +tcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctat-- +------------------------------------------------------------ +------------------------------------------------------------ +---------------gagaccccctcactgtccaccctcatgtcctat-gagaccccctc +actgtccaccctcatgtcctatgaga---------------------------------- +--cccctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccctcatgtc +ctat-----------------------------------gagaccccctcactgtccact +ctcatgtcctatgaga--cccctcactgtccaccctcatgtcctatagagaccccctcac +tgtccaccctcatggcctgtagagaccccctcactgtcaactctcatgtcctatgagacc +ccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcc-- +------------------------------------------------------------ +------------------------------------------------------------ +--------------aaagagaccccctcactgtccaccctcatggcctgtagagaccccc +tcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctatag +agaccccctcactgtccaccctcatgtccaaagagaccccctcactgtccaccctcatgg +cctgtagagac---------------------------------cccctcactgtccacc +ctcatggcctgta----------------------------------------------- +-------------------gagaccccctcactgtccaccctcatgtcctatagagaccc +cctcactgtccaccctcatgtccaaagagaccccctcactgtccaccctcatggcctgta +------------------------------------------------------------ +------gagaccccctcactgtccacccatatggcctgtagagaccccctcactgtccac +cctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctca +ctgtccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctgtagaga +ccccctcactgtccaccctcatggcctgtagagaccccctcactgtccacccatatggcc +tgtagagaccccctcactgtccaccctcaggaccctctgcatttgctccttgggttcccg +gaacttgagcttgggtcttggtccacagcagctttgggaagggccctcggctgctttttg +cttcagcagctggggagcagttaactttcagacccggccc +>syndip_1_chr20:64131704-64134056 +aggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactcc +acactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagacttc +tcctggcctctctcatgtcctatgagaccccctcactgtccactctcatggcctgtagag +accccctcactgtcaactctcatgtcctatagagaccccctcactgtcaactctcatgtc +ctatgagaccccctcactgtccactctcatggcctgtagagaccccctcactgtccaccc +tcatgt------------------------------------------------------ +------------------------------------------------------------ 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+tggcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactctc +caccctcatggcctatagagaccccctcactgtccaccctcgtgtcctatagagaccccc +tcactctccaccctcatggcctatagagaccccctcactgtccaccctcatggcctatag +agaccccctcactgtccactctcatgtcctatgagaccccctcactgtccaccctcatgg +cctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccact +ctcatgtcctatgagaccccctcactgtccaccctcatggcctgtagagaccccctcact +gtccaccctcatgtcctatgagaccccctcactgtccaccctcgtgtcctatagagaccc +cctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctata +gagaccccctcactgtccactctcatgtcctatgagaccccctcactgtccaccctcatg +tcctatgagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccac +cctcatgtcctat-gagaccccctcactgtccaccctcatgtcctatagagaccccctca +ctgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatagaga +ccccctcactgtccactctcatggcctgtagagaccccctcactgtccacccatatggcc +tgtagagaccccctcactgtccaccctcaggaccctctgcatttgctccttgggttcccg +gaacttgagcttgggtcttggtccacagcagctttgggaagggccctcggctgctttttg +cttcagcagctggggagcagttaactttcagacccggccc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/msa.fa.fai new file mode 100644 index 00000000..0a959bfc --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_64131704_64134056 3880 29 60 61 +syndip_1_chr20:64131704-64134056 3880 4008 60 61 +syndip_2_chr20:64131704-64134056 3880 7987 60 61 +p:HG002_1_chr20:64131704-64134056 3880 11967 60 61 +p:HG002_2_chr20:64131704-64134056 3880 15947 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/output.vcf.gz new file mode 100644 index 00000000..788005db Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/output.vcf.gz.tbi new file mode 100644 index 00000000..2f243634 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64131804-64133956/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/base.vcf.gz new file mode 100644 index 00000000..28d3209e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/base.vcf.gz.tbi new file mode 100644 index 00000000..dd81a1ac Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/comp.vcf.gz new file mode 100644 index 00000000..11438d43 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/comp.vcf.gz.tbi new file mode 100644 index 00000000..6fcf0afb Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/haps.fa new file mode 100644 index 00000000..a2cd290f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/haps.fa @@ -0,0 +1,112 @@ +>ref_chr20_64134783_64136487 +AGCATTAGGTGTATCTCCTAATGCTATCCCTCCCCTCTCCCCGCACCCCACAAAAGTCCCCGGTGTGTGATGTTCCCCTTGAAAAGGAGGCGTTTCTGCTTCTCCTCTTTCCGGTCCTTGACAGTGATTCCGTGCATCACAAACACACACGCTCCCTCAGTTACACGAATCACAAACACACGCTCCCTCAGTTTTGTGCATCACAAACGCACACGCTCCCTCAGTTTTGTGCGTCACACACACGCTCCCTCAGTTTTGTGCGCCACAAACACGCGCACTCCCTCAGTTATGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACACACACGCTCCCTCAGTTTTGTGTGTCACAAACACACACGCTCCTTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTTTGTGCATCACACACACATTCCCTCAGTTTTGTGCGCCACAAACACGCGCGCTCCCTCAGTTTTGTGCATCACAAACGCACATGCTCCCTCAGTTTTGGGCATCACAAACACATTCCCTCAGTTTTGTGCATCACAAACGCACACGCTCCCTCAGTTTTGTGCGTCACAAACACACACGCTACCTCAGTTTTGTGTGTTACAAACACACACGCTCCCTCAGTTTCGTGCATCCCAAACATGCTCCCTCAGTTATGTGCGTCACAAACACGCTCCCTCAGTTTTGTGTGTCACAAACACACACGCTCCCTCAGTTTTGTGCATCACAAACACACACATTCCCTCAGTTTTGTGCGTCACAAACACGCGTGCTCTCTCAGTTATGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACACACACGCTCCCTCAGCTTTGTGCTTCACAAACACACACGCTCCCTCAGTTTTGTGTGTTACAAACACACACGCTCCCTCAGTTTCGTGCATCCCAAAGACGATTCCTCAGTTTTGTGCATCACAAACACATATGCTCCCTCAGTTTTGTGCGTCACAAACGCGCGCTCCCTCAGTTATGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACACACACGCTCCCTCAGTTTTGTGTGTCACAAACACACACGCTCCCTCAGTTTTGCGCATCACAAACACACACGCTCCCTCAGTTGTCAGGGGACTTTGCACTGTGCCTTTGCATGAAACACCATGGCTTGAAGAGGTCCCGCATCGTTAGGGCCCCCTTGCCCATGGTGTGGCGTCCCCTGACCGATTTAGCCGTTATTGAGGGACATCGAGGTT +>syndip_1_chr20:64134783-64136487 +AGCATTAGGTGTATCTCCTAATGCTATCCCTCCCCTCTCCCCGCACCCCACAAAAGTCCC +CGGTGTGTGATGTTCCCCTTGAAAAGGAGGCGTTTCTGCTTCTCCTCTTTCCGGTCCTTG +ACAGTGATTCCGTGCATCACAAACACACACGCTCCCTCAGTTACACGAATCACAAACACA +CGCTCCCTCAGTTTTGTGCATCACAAACGCACACGCTCCCTCAGTTTTGTGCGTCACACA +CACGCTCCCTCAGTTTTGTGCGTCACACACACGCTCCCTCAGTTTTGTGCGCCACAAACA +CGCGCACTCCCTCAGTTATGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCA +CAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGT +GCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAG +TTTTGTGCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTC +CCTCAGTTTTGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACACACACGC +TCCCTCAGTTTTGTGTGTCACAAACACACACGCTCCTTCAGTTTTGTGCTTCACAAACAC +ACACGCTCCCTCAGTTTTGTGCATCACACACACATTCCCTCAGTTTTGTGCGCCACAAAC +ACGCGCGCTCCCTCAGTTTTGTGCATCACAAACGCACATGCTCCCTCAGTTTTGGGCATC +ACAAACACATTCCCTCAGTTTTGTGCATCACAAACGCACACGCTCCCTCAGTTTTGTGCG +TCACAAACACACACGCTACCTCAGTTTTGTGTGTTACAAACACACACGCTCCCTCAGTTT +CGTGCATCCCAAACATGCTCCCTCAGTTATGTGCGTCACAAACACGCTCCCTCAGTTTTG +TGTGTCACAAACACACACGCTCCCTCAGTTTTGTGCATCACAAACACACACATTCCCTCA +GTTTTGTGCGTCACAAACACGCGTGCTCTCTCAGTTATGTGCGTCACAAACACAGACGCT +CCCTCAGTTTTGCGCATCACACACACGCTCCCTCAGCTTTGTGCTTCACAAACACACACG +CTCCCTCAGTTTTGTGTGTTACAAACACACACGCTCCCTCAGTTTCGTGCATCCCAAAGA +CGATTCCTCAGTTTTGTGCATCACAAACACATATGCTCCCTCAGTTTTGTGCGTCACAAA +CGCGCGCTCCCTCAGTTATGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCA +CACACACGCTCCCTCAGTTTTGTGTGTCACAAACACACACGCTCCCTCAGTTGTCAGGGG +ACTTTGCACTGTGCCTTTGCATGAAACACCATGGCTTGAAGAGGTCCCGCATCGTTAGGG +CCCCCTTGCCCATGGTGTGGCGTCCCCTGACCGATTTAGCCGTTATTGAGGGACATCGAG +GTT +>syndip_2_chr20:64134783-64136487 +AGCATTAGGTGTATCTCCTAATGCTATCCCTCCCCTCTCCCCGCACCCCACAAAAGTCCC +CGGTGTGTGATGTTCCCCTTGAAAAGGAGGCGTTTCTGCTTCTCCTCTTTCCGGTCCTTG +ACAGTGATTCCGTGCATCACAAACACACACGCTCCCTCAGTTACACGAATCACAAACACA +CGCTCCCTCAGTTTTGTGCATCACAAACGCACACGCTCCCTCAGTTTTGTGCGTCACACA +CACGCTCCCTCAGTTTTGTGCGCCACAAACACGCGCACTCCCTCAGTTATGTGCGTCACA +AACACAGACGCTCCCTCAGTTTTGCGCATCACAAACACACACGCTCCCTCAGTTATGGAC +ATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTT +ATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCC +TCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACAC +GCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCGTCACAAAC +ACAGACGCTCCCTCAGTTTTGCGCATCACACACACGCTCCCTCAGTTTTGTGTGTCACAA +ACACACACGCTCCTTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTTTGTGCA +TCACACACACATTCCCTCAGTTTTGTGCGCCACAAACACGCGCGCTCCCTCAGTTTTGTG +CATCACAAACGCACATGCTCCCTCAGTTTTGGGCATCACAAACACATTCCCTCAGTTTTG +TGCATCACAAACGCACACGCTCCCTCAGTTTTGTGCGTCACAAACACACACGCTACCTCA +GTTTTGTGTGTTACAAACACACACGCTCCCTCAGTTTCGTGCATCCCAAACATGCTCCCT +CAGTTATGTGCGTCACAAACACGCTCCCTCAGTTTTGTGTGTCACAAACACACACGCTCC +CTCAGTTTTGTGCATCACAAACACACACATTCCCTCAGTTTTGTGCGTCACAAACACGCG +TGCTCTCTCAGTTATGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACACA +CACGCTCCCTCAGCTTTGTGCTTCACAAACACACACGCTCCCTCAGTTTTGTGTGTTACA +AACACACACGCTCCCTCAGTTTCGTGCATCCCAAAGACGATTCCTCAGTTTTGTGCATCA +CAAACACATATGCTCCCTCAGTTTTGTGCGTCACAAACGCGCGCTCCCTCAGTTATGTGC +GTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACACACACGCTCCCTCAGTTTTGT +GTGTCACAAACACACACGCTCCCTCAGTTTTGCGCATCACAAACACACACGCTCCCTCAG +TTGTCAGGGGACTTTGCACTGTGCCTTTGCATGAAACACCATGGCTTGAAGAGGTCCCGC +ATCGTTAGGGCCCCCTTGCCCATGGTGTGGCGTCCCCTGACCGATTTAGCCGTTATTGAG +GGACATCGAGGTT +>p:HG002_1_chr20:64134783-64136487 +AGCATTAGGTGTATCTCCTAATGCTATCCCTCCCCTCTCCCCGCACCCCACAAAAGTCCC +CGGTGTGTGATGTTCCCCTTGAAAAGGAGGCGTTTCTGCTTCTCCTCTTTCCGGTCCTTG +ACAGTGATTCCGTGCATCACAAACACACACGCTCCCTCAGTTACACGAATCACAAACACA +CGCTCCCTCAGTTTTGTGCATCACAAACGCACACGCTCCCTCAGTTTTGTGCGTCACACA +CACGCTCCCTCAGTTTTGTGCGCCACAAACACGCGCACTCCCTCAGTTATGTGCGTCACA +AACACAGACGCTCCCTCAGTTTTGCGCATCACAAACACACACGCTCCCTCAGTTATGGAC +ATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTT +ATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCC +TCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACAC +GCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCGTCACAAAC +ACAGACGCTCCCTCAGTTTTGCGCATCACACACACGCTCCCTCAGTTTTGTGTGTCACAA +ACACACACGCTCCTTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTTTGTGCA +TCACACACACATTCCCTCAGTTTTGTGCGCCACAAACACGCGCGCTCCCTCAGTTTTGTG +CATCACAAACGCACATGCTCCCTCAGTTTTGGGCATCACAAACACATTCCCTCAGTTTTG +TGCATCACAAACGCACACGCTCCCTCAGTTTTGTGCGTCACAAACACACACGCTACCTCA +GTTTTGTGTGTTACAAACACACACGCTCCCTCAGTTTCGTGCATCCCAAACATGCTCCCT +CAGTTATGTGCGTCACAAACACGCTCCCTCAGTTTTGTGTGTCACAAACACACACGCTCC +CTCAGTTTTGTGCATCACAAACACACACATTCCCTCAGTTTTGTGCGTCACAAACACGCG +TGCTCTCTCAGTTATGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACACA +CACGCTCCCTCAGCTTTGTGCTTCACAAACACACACGCTCCCTCAGTTTTGTGTGTTACA +AACACACACGCTCCCTCAGTTTCGTGCATCCCAAAGACGATTCCTCAGTTTTGTGCATCA +CAAACACATATGCTCCCTCAGTTTTGTGCGTCACAAACGCGCGCTCCCTCAGTTATGTGC +GTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACACACACGCTCCCTCAGTTTTGT +GTGTCACAAACACACACGCTCCCTCAGTTTTGCGCATCACAAACACACACGCTCCCTCAG +TTGTCAGGGGACTTTGCACTGTGCCTTTGCATGAAACACCATGGCTTGAAGAGGTCCCGC +ATCGTTAGGGCCCCCTTGCCCATGGTGTGGCGTCCCCTGACCGATTTAGCCGTTATTGAG +GGACATCGAGGTT +>p:HG002_2_chr20:64134783-64136487 +AGCATTAGGTGTATCTCCTAATGCTATCCCTCCCCTCTCCCCGCACCCCACAAAAGTCCC +CGGTGTGTGATGTTCCCCTTGAAAAGGAGGCGTTTCTGCTTCTCCTCTTTCCGGTCCTTG +ACAGTGATTCCGTGCATCACAAACACACACGCTCCCTCAGTTACACGAATCACAAACACA +CGCTCCCTCAGTTTTGTGCATCACAAACGCACACGCTCCCTCAGTTTTGTGCGTCACACA +CACGCTCCCTCAGTTTTGTGCGTCACACACACGCTCCCTCAGTTTTGTGCGCCACAAACA +CGCGCACTCCCTCAGTTATGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCA +CAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGT +GCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAG +TTTTGTGCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTC +CCTCAGTTTTGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACACACACGC +TCCCTCAGTTTTGTGTGTCACAAACACACACGCTCCTTCAGTTTTGTGCTTCACAAACAC +ACACGCTCCCTCAGTTTTGTGCATCACACACACATTCCCTCAGTTTTGTGCGCCACAAAC +ACGCGCGCTCCCTCAGTTTTGTGCATCACAAACGCACATGCTCCCTCAGTTTTGGGCATC +ACAAACACATTCCCTCAGTTTTGTGCATCACAAACGCACACGCTCCCTCAGTTTTGTGCG +TCACAAACACACACGCTACCTCAGTTTTGTGTGTTACAAACACACACGCTCCCTCAGTTT +CGTGCATCCCAAACATGCTCCCTCAGTTATGTGCGTCACAAACACGCTCCCTCAGTTTTG +TGTGTCACAAACACACACGCTCCCTCAGTTTTGTGCATCACAAACACACACATTCCCTCA +GTTTTGTGCGTCACAAACACGCGTGCTCTCTCAGTTATGTGCGTCACAAACACAGACGCT +CCCTCAGTTTTGCGCATCACACACACGCTCCCTCAGCTTTGTGCTTCACAAACACACACG +CTCCCTCAGTTTTGTGTGTTACAAACACACACGCTCCCTCAGTTTCGTGCATCCCAAAGA +CGATTCCTCAGTTTTGTGCATCACAAACACATATGCTCCCTCAGTTTTGTGCGTCACAAA +CGCGCGCTCCCTCAGTTATGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCA +CACACACGCTCCCTCAGTTTTGTGTGTCACAAACACACACGCTCCCTCAGTTGTCAGGGG +ACTTTGCACTGTGCCTTTGCATGAAACACCATGGCTTGAAGAGGTCCCGCATCGTTAGGG +CCCCCTTGCCCATGGTGTGGCGTCCCCTGACCGATTTAGCCGTTATTGAGGGACATCGAG +GTT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/haps.fa.ref.fa new file mode 100644 index 00000000..52e034fb --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:64134783-64136487 +AGCATTAGGTGTATCTCCTAATGCTATCCCTCCCCTCTCCCCGCACCCCACAAAAGTCCCCGGTGTGTGATGTTCCCCTTGAAAAGGAGGCGTTTCTGCTTCTCCTCTTTCCGGTCCTTGACAGTGATTCCGTGCATCACAAACACACACGCTCCCTCAGTTACACGAATCACAAACACACGCTCCCTCAGTTTTGTGCATCACAAACGCACACGCTCCCTCAGTTTTGTGCGTCACACACACGCTCCCTCAGTTTTGTGCGCCACAAACACGCGCACTCCCTCAGTTATGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTATGGACATCACAAACACACACGCTCCCTCAGTTTTGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACACACACGCTCCCTCAGTTTTGTGTGTCACAAACACACACGCTCCTTCAGTTTTGTGCTTCACAAACACACACGCTCCCTCAGTTTTGTGCATCACACACACATTCCCTCAGTTTTGTGCGCCACAAACACGCGCGCTCCCTCAGTTTTGTGCATCACAAACGCACATGCTCCCTCAGTTTTGGGCATCACAAACACATTCCCTCAGTTTTGTGCATCACAAACGCACACGCTCCCTCAGTTTTGTGCGTCACAAACACACACGCTACCTCAGTTTTGTGTGTTACAAACACACACGCTCCCTCAGTTTCGTGCATCCCAAACATGCTCCCTCAGTTATGTGCGTCACAAACACGCTCCCTCAGTTTTGTGTGTCACAAACACACACGCTCCCTCAGTTTTGTGCATCACAAACACACACATTCCCTCAGTTTTGTGCGTCACAAACACGCGTGCTCTCTCAGTTATGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACACACACGCTCCCTCAGCTTTGTGCTTCACAAACACACACGCTCCCTCAGTTTTGTGTGTTACAAACACACACGCTCCCTCAGTTTCGTGCATCCCAAAGACGATTCCTCAGTTTTGTGCATCACAAACACATATGCTCCCTCAGTTTTGTGCGTCACAAACGCGCGCTCCCTCAGTTATGTGCGTCACAAACACAGACGCTCCCTCAGTTTTGCGCATCACACACACGCTCCCTCAGTTTTGTGTGTCACAAACACACACGCTCCCTCAGTTTTGCGCATCACAAACACACACGCTCCCTCAGTTGTCAGGGGACTTTGCACTGTGCCTTTGCATGAAACACCATGGCTTGAAGAGGTCCCGCATCGTTAGGGCCCCCTTGCCCATGGTGTGGCGTCCCCTGACCGATTTAGCCGTTATTGAGGGACATCGAGGTT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/msa.fa new file mode 100644 index 00000000..d562f23e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/msa.fa @@ -0,0 +1,150 @@ +>ref_chr20_64134783_64136487 +agcattaggtgtatctcctaatgctatccctcccctctccccgcaccccacaaaagtccc +cggtgtgtgatgttccccttgaaaaggaggcgtttctgcttctcctctttccggtccttg +acagtgattccgtgcatcacaaacacacacgctccctcagttacacgaatcacaaacaca +cgctccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaca +cacgctccctcagttttgtgcgccacaaacacgcgcactccctcagttatgtgcgtcaca +aacacagacgctccctcagttttgcgcatcacaaacacacacgctccctcagttatggac +atcacaaacacacacgctccctcagttttgtgcttcacaaacacacacgctccctcagtt +atggacatcacaaacacacacgctccctcagttttgtgcttcacaaacacacacgctccc +tcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaacacacac +gctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaac +acacacgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttc +acaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcagttttg +tgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctccctcagttt +tgtgtgtcacaaacacacacgctccttcagttttgtgcttcacaaacacacacgctccct +cagttttgtgcatcacacacacattccctcagttttgtgcgccacaaacacgcgcgctcc +ctcagttttgtgcatcacaaacgcacatgctccctcagttttgggcatcacaaacacatt +ccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaaacaca +cacgctacctcagttttgtgtgttacaaacacacacgctccctcagtttcgtgcatccca +aacatgctccctcagttatgtgcgtcacaaacacgctccctcagttttgtgtgtcacaaa +cacacacgctccctcagttttgtgcatcacaaacacacacattccctcagttttgtgcgt +cacaaacacgcgtgctctctcagttatgtgcgtcacaaacacagacgctccctcagtttt +gcgcatcacacacacgctccctcagctttgtgcttcacaaacacacacgctccctcagtt +ttgtgtgttacaaacacacacgctccctcagtttcgtgcatcccaaagacgattcctcag +ttttgtgcatcacaaacacatatgctccctcagttttgtgcgtcacaaacgcgcgctccc +tcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctc +cctcagttttgtgtgtcacaaacacacacgctccctcagttttgcgcatcacaaacacac +acgctccctcagttgtcaggggactttgcactgtgcctttgcatgaaacaccatggcttg +aagaggtcccgcatcgttagggcccccttgcccatggtgtggcgtcccctgaccgattta +gccgttattgagggacatcgaggtt +>syndip_1_chr20:64134783-64136487 +agcattaggtgtatctcctaatgctatccctcccctctccccgcaccccacaaaagtccc +cggtgtgtgatgttccccttgaaaaggaggcgtttctgcttctcctctttccggtccttg +acagtgattccgtgcatcacaaacacacacgctccctcagttacacgaatcacaaacaca +cgctccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaca +cacgctccctcagttttgtgcgtc------------------------------------ +-acacacacgctccctcagttttgtgcg-------------------------------- +------------------------------------------------------------ +----------------------------------------ccacaaacacgcgcactccc +tcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacaaacacacac +gctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaac +acacacgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttc +acaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcagttttg +tgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctccctcagttt +tgtgtgtcacaaacacacacgctccttcagttttgtgcttcacaaacacacacgctccct +cagttttgtgcatcacacacacattccctcagttttgtgcgccacaaacacgcgcgctcc +ctcagttttgtgcatcacaaacgcacatgctccctcagttttgggcatcacaaacacatt +ccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaaacaca +cacgctacctcagttttgtgtgttacaaacacacacgctccctcagtttcgtgcatccca +aacatgctccctcagttatgtgcgtcacaaacacgctccctcagttttgtgtgtcacaaa +cacacacgctccctcagttttgtgcatcacaaacacacacattccctcagttttgtgcgt +cacaaacacgcgtgctctctcagttatgtgcgtcacaaacacagacgctccctcagtttt +gcgcatcacacacacgctccctcagctttgtgcttcacaaacacacacgctccctcagtt +ttgtgtgttacaaacacacacgctccctcagtttcgtgcatcccaaagacgattcctcag +ttttgtgcatcacaaacacatatgctccctcagttttgtgcgtcacaaacgcgcgctccc +tcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctc +cctcagttttgtgtg---------------------------------tcacaaacacac +acgctccctcagttgtcaggggactttgcactgtgcctttgcatgaaacaccatggcttg +aagaggtcccgcatcgttagggcccccttgcccatggtgtggcgtcccctgaccgattta +gccgttattgagggacatcgaggtt +>syndip_2_chr20:64134783-64136487 +agcattaggtgtatctcctaatgctatccctcccctctccccgcaccccacaaaagtccc +cggtgtgtgatgttccccttgaaaaggaggcgtttctgcttctcctctttccggtccttg +acagtgattccgtgcatcacaaacacacacgctccctcagttacacgaatcacaaacaca +cgctccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaca +cacgctccctcagttttgtgcgccacaaacacgcgcactccctcagttatgtgcgtcaca +aacacagacgctccctcagttttgcgca-------------------------------- +------------------------------------------------------------ +----------------------------------------tcacaaacacacacgctccc +tcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaacacacac +gctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaac +acacacgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttc +acaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcagttttg +tgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctccctcagttt +tgtgtgtcacaaacacacacgctccttcagttttgtgcttcacaaacacacacgctccct +cagttttgtgcatcacacacacattccctcagttttgtgcgccacaaacacgcgcgctcc +ctcagttttgtgcatcacaaacgcacatgctccctcagttttgggcatcacaaacacatt +ccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaaacaca +cacgctacctcagttttgtgtgttacaaacacacacgctccctcagtttcgtgcatccca +aacatgctccctcagttatgtgcgtcacaaacacgctccctcagttttgtgtgtcacaaa +cacacacgctccctcagttttgtgcatcacaaacacacacattccctcagttttgtgcgt +cacaaacacgcgtgctctctcagttatgtgcgtcacaaacacagacgctccctcagtttt +gcgcatcacacacacgctccctcagctttgtgcttcacaaacacacacgctccctcagtt +ttgtgtgttacaaacacacacgctccctcagtttcgtgcatcccaaagacgattcctcag +ttttgtgcatcacaaacacatatgctccctcagttttgtgcgtcacaaacgcgcgctccc +tcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctc +cctcagttttgtgtgtcacaaacacacacgctccctcagttttgcgcatcacaaacacac +acgctccctcagttgtcaggggactttgcactgtgcctttgcatgaaacaccatggcttg +aagaggtcccgcatcgttagggcccccttgcccatggtgtggcgtcccctgaccgattta +gccgttattgagggacatcgaggtt +>p:HG002_1_chr20:64134783-64136487 +agcattaggtgtatctcctaatgctatccctcccctctccccgcaccccacaaaagtccc +cggtgtgtgatgttccccttgaaaaggaggcgtttctgcttctcctctttccggtccttg +acagtgattccgtgcatcacaaacacacacgctccctcagttacacgaatcacaaacaca +cgctccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaca +cacgctccctcagttttgtgcgccacaaacacgcgcactccctcagttatgtgcgtcaca +aacacagacgctccctcagttttgcgca-------------------------------- +------------------------------------------------------------ +----------------------------------------tcacaaacacacacgctccc +tcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaacacacac +gctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaac +acacacgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttc +acaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcagttttg +tgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctccctcagttt +tgtgtgtcacaaacacacacgctccttcagttttgtgcttcacaaacacacacgctccct +cagttttgtgcatcacacacacattccctcagttttgtgcgccacaaacacgcgcgctcc +ctcagttttgtgcatcacaaacgcacatgctccctcagttttgggcatcacaaacacatt +ccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaaacaca +cacgctacctcagttttgtgtgttacaaacacacacgctccctcagtttcgtgcatccca +aacatgctccctcagttatgtgcgtcacaaacacgctccctcagttttgtgtgtcacaaa +cacacacgctccctcagttttgtgcatcacaaacacacacattccctcagttttgtgcgt +cacaaacacgcgtgctctctcagttatgtgcgtcacaaacacagacgctccctcagtttt +gcgcatcacacacacgctccctcagctttgtgcttcacaaacacacacgctccctcagtt +ttgtgtgttacaaacacacacgctccctcagtttcgtgcatcccaaagacgattcctcag +ttttgtgcatcacaaacacatatgctccctcagttttgtgcgtcacaaacgcgcgctccc +tcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctc +cctcagttttgtgtgtcacaaacacacacgctccctcagttttgcgcatcacaaacacac +acgctccctcagttgtcaggggactttgcactgtgcctttgcatgaaacaccatggcttg +aagaggtcccgcatcgttagggcccccttgcccatggtgtggcgtcccctgaccgattta +gccgttattgagggacatcgaggtt +>p:HG002_2_chr20:64134783-64136487 +agcattaggtgtatctcctaatgctatccctcccctctccccgcaccccacaaaagtccc +cggtgtgtgatgttccccttgaaaaggaggcgtttctgcttctcctctttccggtccttg +acagtgattccgtgcatcacaaacacacacgctccctcagttacacgaatcacaaacaca +cgctccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaca +cacgctccctcagttttgtgcgtc------------------------------------ +-acacacacgctccctcagttttgtgcg-------------------------------- +------------------------------------------------------------ +----------------------------------------ccacaaacacgcgcactccc +tcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacaaacacacac +gctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaac +acacacgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttc +acaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcagttttg +tgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctccctcagttt +tgtgtgtcacaaacacacacgctccttcagttttgtgcttcacaaacacacacgctccct +cagttttgtgcatcacacacacattccctcagttttgtgcgccacaaacacgcgcgctcc +ctcagttttgtgcatcacaaacgcacatgctccctcagttttgggcatcacaaacacatt +ccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaaacaca +cacgctacctcagttttgtgtgttacaaacacacacgctccctcagtttcgtgcatccca +aacatgctccctcagttatgtgcgtcacaaacacgctccctcagttttgtgtgtcacaaa +cacacacgctccctcagttttgtgcatcacaaacacacacattccctcagttttgtgcgt +cacaaacacgcgtgctctctcagttatgtgcgtcacaaacacagacgctccctcagtttt +gcgcatcacacacacgctccctcagctttgtgcttcacaaacacacacgctccctcagtt +ttgtgtgttacaaacacacacgctccctcagtttcgtgcatcccaaagacgattcctcag +ttttgtgcatcacaaacacatatgctccctcagttttgtgcgtcacaaacgcgcgctccc +tcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctc +cctcagttttgtgtg---------------------------------tcacaaacacac +acgctccctcagttgtcaggggactttgcactgtgcctttgcatgaaacaccatggcttg +aagaggtcccgcatcgttagggcccccttgcccatggtgtggcgtcccctgaccgattta +gccgttattgagggacatcgaggtt diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/msa.fa.fai new file mode 100644 index 00000000..ed542de2 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_64134783_64136487 1705 29 60 61 +syndip_1_chr20:64134783-64136487 1705 1797 60 61 +syndip_2_chr20:64134783-64136487 1705 3565 60 61 +p:HG002_1_chr20:64134783-64136487 1705 5334 60 61 +p:HG002_2_chr20:64134783-64136487 1705 7103 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/output.vcf.gz new file mode 100644 index 00000000..95a03832 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/output.vcf.gz.tbi new file mode 100644 index 00000000..dee6e3a7 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64134883-64136387/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/base.vcf.gz new file mode 100644 index 00000000..659c19cd Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/base.vcf.gz.tbi new file mode 100644 index 00000000..c1da5b04 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/comp.vcf.gz new file mode 100644 index 00000000..30fb7b7b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/comp.vcf.gz.tbi new file mode 100644 index 00000000..c4234266 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/haps.fa new file mode 100644 index 00000000..38724929 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/haps.fa @@ -0,0 +1,217 @@ +>ref_chr20_64173309_64176630 +CAGAGGTGGGCTGTTGGACAGGTGCGGCTGATAGAGTGGGTGTCTTTTGTGGGCTTCTCCCCAGCCTGTGGCCTGGCCTAGTCAGTAGAGATGGTCAGGGGAGCAGGAGGGAGCCCATACCCCAGTGCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTCCCTTTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTCCCTTTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCTTCTAGCATCTTTCCTGCTCCCTGGTAGCCTCTTGGGAGCCACCTATTTCTGGAGGTCCCCACTCTGGGTTCCTTGTCCTGGGTGTGGGGCGAATGTGCTGGACTGGGGTCACAGCATTGAACCCCACTTGGAGCTGAGGA +>syndip_1_chr20:64173309-64176630 +CAGAGGTGGGCTGTTGGACAGGTGCGGCTGATAGAGTGGGTGTCTTTTGTGGGCTTCTCC +CCAGCCTGTGGCCTGGCCTAGTCAGTAGAGATGGTCAGGGGAGCAGGAGGGAGCCCATAC +CCCAGTGCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTC +CCTTTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTAGTTG +TGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCAT +TTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCC +TGACTTCTCCTCCTGCAGCATCCTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTC +TCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCT +GCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCAT +CTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGT +AGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCC +ATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTC +CCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCT +CCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCAT +CTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGT +AGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCC +ATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTC +CCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCT +CCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTT +TCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGT +GTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCAACTTTCCTAGTTGTGTCCATTTCCCCT +CCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCC +TGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCT +TTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTG +TAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCAT +TTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTCCCCCTCCCTGG +CTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTGCAGC +ATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTA +GTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTT +CCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCT +TCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAG +CATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCC +TGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCC +ATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTC +CCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCT +CCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCCTGCAG +CATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGT +AGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTG +TCCATTCCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTT +CCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCC +CTGGCTTCTCCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGACTT +CTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCC +TGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCT +TTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAG +TTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCAT +TTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCC +TGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTC +TCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTGCAGCA +TCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAG +TTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCAT +TTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCC +TGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCC +TGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCT +TTCCCTGTAGTTGTGTTCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAG +TTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCAT +TTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCC +TGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCC +TGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCT +TTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCTTCTAGCATCTTTCCTGC +TCCCTGGTAGCCTCTTGGGAGCCACCTATTTCTGGAGGTCCCCACTCTGGGTTCCTTGTC +CTGGGTGTGGGGCGAATGTGCTGGACTGGGGTCACAGCATTGAACCCCACTTGGAGCTGA +GGA +>syndip_2_chr20:64173309-64176630 +CAGAGGTGGGCTGTTGGACAGGTGCGGCTGATAGAGTGGGTGTCTTTTGTGGGCTTCTCC +CCAGCCTGTGGCCTGGCCTAGTCAGTAGAGATGGTCAGGGGAGCAGGAGGGAGCCCATAC +CCCAGTGCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTC +CCTTTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTAGTTG +TGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCAT +TTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCC +TGACTTCTCCTCCTGCAGCATCCTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTC +TCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCT +GCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCAT +CTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGT +AGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCC +ATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCC +CTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTG +GCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTG +CAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTT +CCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTT +GTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCC +CTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCT +CCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCAT +CTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGT +TGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCC +CCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGC +TTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCA +GCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTACAGCATCTTTCC +CTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTC +CATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCT +CCCTGGCTTCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCC +TGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTC +CTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGT +CCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCC +TCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTC +CTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATC +TTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTA +GTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCTAGTTGTGTCCA +TTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCC +CTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTT +CTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGC +AGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTC +CCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTG +TGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTC +CCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGG +CTTCTCCTCTTCTAGCATCTTTCCTGCTCCCTGGTAGCCTCTTGGGAGCCACCTATTTCT +GGAGGTCCCCACTCTGGGTTCCTTGTCCTGGGTGTGGGGCGAATGTGCTGGACTGGGGTC +ACAGCATTGAACCCCACTTGGAGCTGAGGA +>p:HG002_1_chr20:64173309-64176630 +CAGAGGTGGGCTGTTGGACAGGTGCGGCTGATAGAGTGGGTGTCTTTTGTGGGCTTCTCC +CCAGCCTGTGGCCTGGCCTAGTCAGTAGAGATGGTCAGGGGAGCAGGAGGGAGCCCATAC +CCCAGTGCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTC +CCTTTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTAGTTG +TGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCAT +TTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCC +TGACTTCTCCTCCTGCAGCATCCTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTC +TCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCT +GCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCAT +CTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGT +AGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCC +ATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCC +CTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTG +GCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTG +CAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTT +CCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTT +GTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCC +CTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCT +CCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCAT +CTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGT +TGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCC +CCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGC +TTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCA +GCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTACAGCATCTTTCC +CTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTC +CATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCT +CCCTGGCTTCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCC +TGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTC +CTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGT +CCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCC +TCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTC +CTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATC +TTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTA +GTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCTAGTTGTGTCCA +TTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCC +CTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTT +CTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGC +AGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTC +CCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTG +TGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTC +CCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGG +CTTCTCCTCTTCTAGCATCTTTCCTGCTCCCTGGTAGCCTCTTGGGAGCCACCTATTTCT +GGAGGTCCCCACTCTGGGTTCCTTGTCCTGGGTGTGGGGCGAATGTGCTGGACTGGGGTC +ACAGCATTGAACCCCACTTGGAGCTGAGGA +>p:HG002_2_chr20:64173309-64176630 +CAGAGGTGGGCTGTTGGACAGGTGCGGCTGATAGAGTGGGTGTCTTTTGTGGGCTTCTCC +CCAGCCTGTGGCCTGGCCTAGTCAGTAGAGATGGTCAGGGGAGCAGGAGGGAGCCCATAC +CCCAGTGCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTC +CCTTTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTAGTTG +TGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCAT +TTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCC +TGACTTCTCCTCCTGCAGCATCCTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTC +TCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCT +GCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCAT +CTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGT +AGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCC +ATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTC +CCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCT +CCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCAT +CTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGT +AGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCC +ATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTC +CCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCT +CCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTT +TCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGT +GTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCAACTTTCCTAGTTGTGTCCATTTCCCCT +CCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCC +TGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCT +TTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAG +TTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTC +CCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTCCCCCTCCCTGGCTT +CTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTGCAGCATC +TTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTT +GTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCC +CTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCT +CCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCAT +CTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGT +AGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATT +TCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCT +GGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCT +GTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCCTGCAGCAT +CTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGT +TGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCC +ATTCCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCC +CTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTG +GCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTC +CTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGC +AGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTC +CCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTG +TGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTC +CCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGG +CTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCC +TCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTGCAGCATCT +TTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTG +TGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTC +CCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGG +CTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGC +AGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTC +CCTGTAGTTGTGTTCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTG +TGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTC +CCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGG +CTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGC +AGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTC +CCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCTTCTAGCATCTTTCCTGCTCC +CTGGTAGCCTCTTGGGAGCCACCTATTTCTGGAGGTCCCCACTCTGGGTTCCTTGTCCTG +GGTGTGGGGCGAATGTGCTGGACTGGGGTCACAGCATTGAACCCCACTTGGAGCTGAGGA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/haps.fa.ref.fa new file mode 100644 index 00000000..296e951e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:64173309-64176630 +CAGAGGTGGGCTGTTGGACAGGTGCGGCTGATAGAGTGGGTGTCTTTTGTGGGCTTCTCCCCAGCCTGTGGCCTGGCCTAGTCAGTAGAGATGGTCAGGGGAGCAGGAGGGAGCCCATACCCCAGTGCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTCCCTTTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTCCCTTTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCTTCTAGCATCTTTCCTGCTCCCTGGTAGCCTCTTGGGAGCCACCTATTTCTGGAGGTCCCCACTCTGGGTTCCTTGTCCTGGGTGTGGGGCGAATGTGCTGGACTGGGGTCACAGCATTGAACCCCACTTGGAGCTGAGGA diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/msa.fa new file mode 100644 index 00000000..06fc06ba --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/msa.fa @@ -0,0 +1,365 @@ +>ref_chr20_64173309_64176630 +cagaggtgggctgttggacaggtgcggctgatagagtgggtgtcttttgtgggcttctcc +ccagcctgtggcctggcctagtcagtagagatggtcaggggagcaggagggagcccatac +cccagtgcctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatccttc +cctt--------------------------------------------------tagttg +tgtccatttcccctccctgacttctcctcctgcagcatccttccctttagttgtgtccat +ttcccctccctgacttctcctcctgcagcatctttcctagttgtgtccatttcccctccc +tgacttctcctcctgcagcatctttccttgtagttgtgtccatttcccctccctggcttc +tcctcctgcag------------------------------------------------- +----catctttccttgtagttgtgtccatttcccctccctgacttctcctcctgc----- +---------------------------------------------agcatccttccctgt +agttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcc +atttcccctccctggctt---ctcctgcagcatctttccctgtagttgtgtccatttccc +ctccctggctt---ctcctgcagcatctttccctgtagttgtgtccatttcccctccctg +gcttctcctgtagcatctttccctgtagttgtgtccattccccctccctggcttctcctg +tagcatctttcc---tagttgtgtccatttcccctccctggcttctcctgc--------- +-----------------------------------------agcatctttccctgtagtt +gtgtccatttcccctccctggcttctcctg------------------------------ +--------------------tagcatctttcc---tagttgtgtccatttcccctccctg +gcttctcctcctgcagcatctttccctgtagttgtgtccattccccctccctggcttctc +ctgtagcatctttcc---tagttgtgtccatttcccctccctggcttctcctgtagcatc +tttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagtt +gtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccattt +cccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctg +gcttctcctgtagcatctttccctgtagttgtgtccattccccctccctgacttctcctc +ctgcagcatctttccctgtagttgtgtccatttcccctccctggcgtctcctcctgcagc +atctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcc-- +-tagttgtgtccatttcccctccctggcttctc--------------------------- +------------------------------------------------------------ +----ctcctgcagcatctttccctgtagttgtgtccattccccctccctggcttctcctg +tagcatctttcc-----------------------------------------------t +agttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtccatt +tcccctccctggcttctcctgcagcatctttccc-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +-tgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgt +gtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcc +cctccctgg--------------------------------------------------- +------------------------------------------------------------ +---------------------------------------------cttctcctgcagcat +ctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgt +agttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtcc +atttcccctccctggcttctcctgcagcatctttccctg--------------------- +-----------------------------tagttgtgtccatttcccctccctggcttct +cctgtagcatctttccctgtagttgtgtccattccccctccctggcgtctcctcctgcag +catctttccctgtagttgtgtccattccccctccctggctt------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------ctcctgcagcatctttccctgtagttgtgtccatttcccctccc +tggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcc +tgtagcatctttcc---tagttgtgtccatttcccctccctggcttctcctgcagcatct +ttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtag +ttgtgtccattccccctccctgacttctcctcctgcagcatctttccctgtagttgtgtc +catttcccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccatttcc +cctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttc +tcctcctgcagcatctttccctgtagttgtgtccattccccctccctggcttctcctgta +gcatctttcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcc--- +tagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtc +catttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccct +ccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctccctggcttc +tcctgcagcatctttcc---tagttgtgtccatttcccctccctggcttctcctgcagca +tctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttccctg +tagttgtgtccattccccctccctggcgtctcctcctgcagcatctttccctgtagttgt +gtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcc +cctccctggcttctcctgtagcatctttccctgtagttgtgtccattccccctccctggc +gtctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcct +cctgcagcatctttccctgtagttgtgtccattccccctccctggcttctcctcctgcag +catctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccc +tgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtg +tccatttcccctccctggcttctcctcttctagcatctttcctgctccctggtagcctct +tgggagccacctatttctggaggtccccactctgggttccttgtcctgggtgtggggcga +atgtgctggactggggtcacagcattgaaccccacttggagctgagga +>syndip_1_chr20:64173309-64176630 +cagaggtgggctgttggacaggtgcggctgatagagtgggtgtcttttgtgggcttctcc +ccagcctgtggcctggcctagtcagtagagatggtcaggggagcaggagggagcccatac +cccagtgcctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatccttc +cctttagttgtgtccatttcccctccctgacttctcctcctgcagcatctttcctagttg +tgtccatttcccctccctgacttctcctcctgcagcatctttccttgtagttgtgtccat +ttcccctccctggcttctcctcctgcagcatctttcctagttgtgtccatttcccctccc +tgacttctcctcctgcagcatccttccctgtagttgtgtccatttcccctccctgacttc +tcctcctgcagcatctttccctgtagttgtgtccatttcccctccctgacttctcctcct +gcagcatctttccttgtagttgtgtccatttcccctccctggcttctcctcctgcagcat +ctttccctgtagttgtgtccattccccctccctggcttctcctgtagcatctttccctgt +agttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcc +atttcccctccctggctt---ctcctgcagcatctttccctgtagttgtgtccatttccc +ctccctggctt---ctcctgcagcatctttccctgtagttgtgtccatttcccctccctg +gcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctg +cagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatcttt +ccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagtt +gtgtccatttcccctccctggcttctcctg------------------------------ +--------------------cagcatctttccctgtagttgtgtccatttcccctccctg +gctt---ctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc +ctgtagcatctttcc---tagttgtgtccatttcccctccctggcttctcctgtagcatc +tttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagtt +gtgtccatttcccctccctggcttctcctgtagcaactttcc---tagttgtgtccattt +cccctccctggcttctcctgtagcatctttcc---tagttgtgtccatttcccctccctg +gcttctcctgtagcatctttccctgtagttgtgtccatttcccctccctggctt---ctc +ctgcagcatctttccctgtagttgtgtccatttcccctccctggcgtctcctcctgcagc +atctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcc-- +-tagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtcca +ttccccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctcc +ctggcttctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctg +tagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcct +agttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtccatt +tcccctccctggcttctcctgcagcatctttccc-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +-tgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgt +gtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcc +cctccctgg--------------------------------------------------- +------------------------------------------------------------ +---------------------------------------------cttctcctgtagcat +ctttcc---tagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgt +agttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcc +atttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctc +cctggcgtctcctcctgcagcatctttcctagttgtgtccatttcccctccctggcttct +cctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctcctgcag +catctttccctgtagttgtgtccattccccctccctggcttctcctcctgcagcatcttt +ccctgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgta +gttgtgtccattccccctccctggcttctcctcctgtagcatctttccctgtagttgtgt +ccattccccctccctgacttctcctcctgcagcatctttccctgtagttgtgtccatttc +ccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatttcccctccc +tggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcc +tgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatct +ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag +ttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtc +cattccccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatttcc +cctccctggctt------------------------------------------------ +-----ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgta +gcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctg +tagttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtc +catttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccct +ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc +tcctgtagcatctttccctgtagttgtgttcatttcccctccctggcttctcctgcagca +tctttccctgtagttgtgtccatttcccctccctggctt--------------------- +--------------------------------ctcctgcagcatctttccctgtagttgt +gtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcc +cctccctggctt------------------------------------------------ +------------------------------------------------------------ +---------------------------------------------------ctcctgcag +catctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccc +tgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtg +tccatttcccctccctggcttctcctcttctagcatctttcctgctccctggtagcctct +tgggagccacctatttctggaggtccccactctgggttccttgtcctgggtgtggggcga +atgtgctggactggggtcacagcattgaaccccacttggagctgagga +>syndip_2_chr20:64173309-64176630 +cagaggtgggctgttggacaggtgcggctgatagagtgggtgtcttttgtgggcttctcc +ccagcctgtggcctggcctagtcagtagagatggtcaggggagcaggagggagcccatac +cccagtgcctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatccttc +cctttagttgtgtccatttcccctccctgacttctcctcctgcagcatctttcctagttg +tgtccatttcccctccctgacttctcctcctgcagcatctttccttgtagttgtgtccat +ttcccctccctggcttctcctcctgcagcatctttcctagttgtgtccatttcccctccc +tgacttctcctcctgcagcatccttccctgtagttgtgtccatttcccctccctgacttc +tcctcctgcagcatctttccctgtagttgtgtccatttcccctccctgacttctcctcct +gcagcatctttccttgtagttgtgtccatttcccctccctggcttctcctcctgcagcat +ctttccctgtagttgtgtccattccccctccctggcttctcctgtagcatctttccctgt +agttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcc +atttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatttccc +ctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctg +gcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctg +cagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatcttt +ccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagtt +gtgtccatttcccctccctggcttctcctgtagcatctttcc---tagttgtgtccattt +cccctccctggcttctcctgtagcatctttcc---tagttgtgtccatttcccctccctg +gctt---ctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc +ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatc +tttcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcc---tagtt +gtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccattt +cccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctg +gcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggctt---ctc +ctacagcatctttccctgtagttgtgtccatttcccctccctgg---cttctcctgtagc +atctttcc---tagttgtgtccatttcccctccctggcttctcctgtagcatctttccct +gtagttgtgtccatttcccctccctgg--------------------------------- +------------------------------------------------------------ +----cttctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctg +tagcatctttcc-----------------------------------------------t +agttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtccatt +tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct +ggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcct +gtagcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttcc +ctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgt +gtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcc +cctccctggcgtctcctcctgcagcatctttcctagttgtgtccatttcccctccctggc +ttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctcct +gcagcatctttccctgtagttgtgtccattccccctccctggcttctcctcctgcagcat +ctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgt +agttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtcc +atttcccctccctggcttctcctgcagcatctttccctg--------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------tagttgtgtccatttcccctccctggcttctcctgcagca +tctttccctgtagttgtgt----------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------ccatttcccctccctggcttctcctgcagcatctttccctgtagttgtg +tccatttcccctccctggcttctcctcttctagcatctttcctgctccctggtagcctct +tgggagccacctatttctggaggtccccactctgggttccttgtcctgggtgtggggcga +atgtgctggactggggtcacagcattgaaccccacttggagctgagga +>p:HG002_1_chr20:64173309-64176630 +cagaggtgggctgttggacaggtgcggctgatagagtgggtgtcttttgtgggcttctcc +ccagcctgtggcctggcctagtcagtagagatggtcaggggagcaggagggagcccatac +cccagtgcctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatccttc +cctttagttgtgtccatttcccctccctgacttctcctcctgcagcatctttcctagttg +tgtccatttcccctccctgacttctcctcctgcagcatctttccttgtagttgtgtccat +ttcccctccctggcttctcctcctgcagcatctttcctagttgtgtccatttcccctccc +tgacttctcctcctgcagcatccttccctgtagttgtgtccatttcccctccctgacttc +tcctcctgcagcatctttccctgtagttgtgtccatttcccctccctgacttctcctcct +gcagcatctttccttgtagttgtgtccatttcccctccctggcttctcctcctgcagcat +ctttccctgtagttgtgtccattccccctccctggcttctcctgtagcatctttccctgt +agttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcc +atttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatttccc +ctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctg +gcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctg +cagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatcttt +ccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagtt +gtgtccatttcccctccctggcttctcctgtagcatctttcc---tagttgtgtccattt +cccctccctggcttctcctgtagcatctttcc---tagttgtgtccatttcccctccctg +gctt---ctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc +ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatc +tttcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcc---tagtt +gtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccattt +cccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctg +gcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggctt---ctc +ctacagcatctttccctgtagttgtgtccatttcccctccctgg---cttctcctgtagc +atctttcc---tagttgtgtccatttcccctccctggcttctcctgtagcatctttccct +gtagttgtgtccatttcccctccctgg--------------------------------- +------------------------------------------------------------ +----cttctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctg +tagcatctttcc-----------------------------------------------t +agttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtccatt +tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct +ggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcct +gtagcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttcc +ctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgt +gtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcc +cctccctggcgtctcctcctgcagcatctttcctagttgtgtccatttcccctccctggc +ttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctcct +gcagcatctttccctgtagttgtgtccattccccctccctggcttctcctcctgcagcat +ctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgt +agttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtcc +atttcccctccctggcttctcctgcagcatctttccctg--------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------tagttgtgtccatttcccctccctggcttctcctgcagca +tctttccctgtagttgtgt----------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------ccatttcccctccctggcttctcctgcagcatctttccctgtagttgtg +tccatttcccctccctggcttctcctcttctagcatctttcctgctccctggtagcctct +tgggagccacctatttctggaggtccccactctgggttccttgtcctgggtgtggggcga +atgtgctggactggggtcacagcattgaaccccacttggagctgagga +>p:HG002_2_chr20:64173309-64176630 +cagaggtgggctgttggacaggtgcggctgatagagtgggtgtcttttgtgggcttctcc +ccagcctgtggcctggcctagtcagtagagatggtcaggggagcaggagggagcccatac +cccagtgcctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatccttc +cctttagttgtgtccatttcccctccctgacttctcctcctgcagcatctttcctagttg +tgtccatttcccctccctgacttctcctcctgcagcatctttccttgtagttgtgtccat +ttcccctccctggcttctcctcctgcagcatctttcctagttgtgtccatttcccctccc +tgacttctcctcctgcagcatccttccctgtagttgtgtccatttcccctccctgacttc +tcctcctgcagcatctttccctgtagttgtgtccatttcccctccctgacttctcctcct +gcagcatctttccttgtagttgtgtccatttcccctccctggcttctcctcctgcagcat +ctttccctgtagttgtgtccattccccctccctggcttctcctgtagcatctttccctgt +agttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcc +atttcccctccctggctt---ctcctgcagcatctttccctgtagttgtgtccatttccc +ctccctggctt---ctcctgcagcatctttccctgtagttgtgtccatttcccctccctg +gcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctg +cagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgt--------- +-----------------------------------------agcatctttccctgtagtt +gtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccattt +cccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctg +gctt---ctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc +ctgtagcatctttcc---tagttgtgtccatttcccctccctggcttctcctgtagcatc +tttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagtt +gtgtccatttcccctccctggcttctcctgtagcaactttcc---tagttgtgtccattt +cccctccctggcttctcctgtagcatctttcc---tagttgtgtccatttcccctccctg +gcttctcctgtagcatctttccctgtagttgtgtccatttcccctccctggctt---ctc +ctgcagcatctttccctgtagttgtgtccatttcccctccctgg---cttctcctgcagc +atctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcc-- +-tagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtcca +ttccccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctcc +ctggcttctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctg +tagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcct +agttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtccatt +tcccctccctggcttctcctgcagcatctttccc-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +-tgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgt +gtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcc +cctccctgg--------------------------------------------------- +------------------------------------------------------------ +---------------------------------------------cttctcctgtagcat +ctttcc---tagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgt +agttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcc +atttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctc +cctggcgtctcctcctgcagcatctttcctagttgtgtccatttcccctccctggcttct +cctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctcctgcag +catctttccctgtagttgtgtccattccccctccctggcttctcctcctgcagcatcttt +ccctgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgta +gttgtgtccattccccctccctggcttctcctcctgcagcatctttccctgtagttgtgt +ccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatttc +ccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatttcccctccc +tggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcc +tgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatct +ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag +ttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtc +cattccccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatttcc +cctccctggctt------------------------------------------------ +-----ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgta +gcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctg +tagttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtc +catttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccct +ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc +tcctgtagcatctttccctgtagttgtgttcatttcccctccctggcttctcctgcagca +tctttccctgtagttgtgtccatttcccctccctggctt--------------------- +--------------------------------ctcctgcagcatctttccctgtagttgt +gtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcc +cctccctggctt------------------------------------------------ +------------------------------------------------------------ +---------------------------------------------------ctcctgcag +catctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccc +tgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtg +tccatttcccctccctggcttctcctcttctagcatctttcctgctccctggtagcctct +tgggagccacctatttctggaggtccccactctgggttccttgtcctgggtgtggggcga +atgtgctggactggggtcacagcattgaaccccacttggagctgagga diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/msa.fa.fai new file mode 100644 index 00000000..dbcf6bde --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_64173309_64176630 4308 29 60 61 +syndip_1_chr20:64173309-64176630 4308 4443 60 61 +syndip_2_chr20:64173309-64176630 4308 8857 60 61 +p:HG002_1_chr20:64173309-64176630 4308 13272 60 61 +p:HG002_2_chr20:64173309-64176630 4308 17687 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/output.vcf.gz new file mode 100644 index 00000000..2313b80b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/output.vcf.gz.tbi new file mode 100644 index 00000000..867cc8e8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:64173409-64176530/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/base.vcf.gz new file mode 100644 index 00000000..996f963d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/base.vcf.gz.tbi new file mode 100644 index 00000000..4d6c0b66 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/comp.vcf.gz new file mode 100644 index 00000000..89e6f920 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/comp.vcf.gz.tbi new file mode 100644 index 00000000..d1e70d42 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/haps.fa new file mode 100644 index 00000000..aeab0df0 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/haps.fa @@ -0,0 +1,98 @@ +>ref_chr20_641736_642566 +ATCATCCGGTGACAGGGATCATCATCCCTGCCTGGCATAGAAACCCGGACATCGGACCCTGCCCTCCCGCTGCTTCCGCAGGGACAGGGGGCAGCCAGCAGAGCCTCCCTCTGGGGGTGCCCCCCAATCTGGTTGCCTGGGACGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCAGCGGGGGTGAAGTTGCCTGGGGGGGGCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCAGCGGGGGTGGAGCACCCTGGACGGCCCCGCGGAGCCCCCTGCGGGAGGCGAGGGCGGCCCTCGGGCTCTGGAAGGGGCCGCGCGGCCTGGAAGACATTACACGGCTGTCGGGCGGGGGGCGGCGCTCGCAGTTCCGGAGGGGG +>syndip_1_chr20:641736-642566 +ATCATCCGGTGACAGGGATCATCATCCCTGCCTGGCATAGAAACCCGGACATCGGACCCT +GCCCTCCCGCTGCTTCCGCAGGGACAGGGGGCAGCCAGCAGAGCCTCCCTCTGGGGGTGC +CCCCCAATCTGGTTGCCTGGGAGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGG +GCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGG +GGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCT +GGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGT +TGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGG +TGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGC +GGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCC +AGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCC +AGCGGGGGTGGAGTTGCCTGGGGGGGGCCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGC +CCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGG +CCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCCAGCGGGGGTGGAGTTGCCTGGGGGGG +GGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGG +GGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCC +TGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTT +GCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGT +TGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGA +GTTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGT +GGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGCACCCTGGACGGCCCCGCGGAGCCC +CCTGCGGGAGGCGAGGGCGGCCCTCGGGCTCTGGAAGGGGCCGCGCGGCCTGGAAGACAT +TACACGGCTGTCGGGCGGGGGGCGGCGCTCGCAGTTCCGGAGGGGG +>syndip_2_chr20:641736-642566 +ATCATCCGGTGACAGGGATCATCATCCCTGCCTGGCATAGAAACCCGGACATCGGACCCT +GCCCTCCCGCTGCTTCCGCAGGGACAGGGGGCAGCCAGCAGAGCCTCCCTCTGGGGGTGC +CCCCCAATCTGGTTGCCTGGGACGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGG +CCCAGCGGGGGTGGAGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGG +GGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGC +CTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGT +TGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGG +AGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCG +GGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGC +GGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCC +AGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGG +GGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGG +GGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCAGGGGTGGAGTTGCCTG +GGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGC +CTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTG +CCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGT +TGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAG +TTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGT +GGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCG +GGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCC +AGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCC +AGCGGGGGTGGAGCACCCTGGACGGCCCCGCGGAGCCCCCTGCGGGAGGCGAGGGCGGCC +CTCGGGCTCTGGAAGGGGCCGCGCGGCCTGGAAGACATTACACGGCTGTCGGGCGGGGGG +CGGCGCTCGCAGTTCCGGAGGGGG +>p:HG002_1_chr20:641736-642566 +ATCATCCGGTGACAGGGATCATCATCCCTGCCTGGCATAGAAACCCGGACATCGGACCCT +GCCCTCCCGCTGCTTCCGCAGGGACAGGGGGCAGCCAGCAGAGCCTCCCTCTGGGGGTGC +CCCCCAATCTGGTTGCCTGGGACGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGG +CCCAGCGGGGGTGGAGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGG +GGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGC +CTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGT +TGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGG +AGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCG +GGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGC +GGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCC +AGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGG +GGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGG +GGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCAGGGGTGGAGTTGCCTG +GGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGC +CTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTG +CCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGT +TGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAG +TTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGT +GGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCG +GGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCC +AGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCC +AGCGGGGGTGGAGCACCCTGGACGGCCCCGCGGAGCCCCCTGCGGGAGGCGAGGGCGGCC +CTCGGGCTCTGGAAGGGGCCGCGCGGCCTGGAAGACATTACACGGCTGTCGGGCGGGGGG +CGGCGCTCGCAGTTCCGGAGGGGG +>p:HG002_2_chr20:641736-642566 +ATCATCCGGTGACAGGGATCATCATCCCTGCCTGGCATAGAAACCCGGACATCGGACCCT +GCCCTCCCGCTGCTTCCGCAGGGACAGGGGGCAGCCAGCAGAGCCTCCCTCTGGGGGTGC +CCCCCAATCTGGTTGCCTGGGAGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGG +GCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGG +GGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCT +GGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGT +TGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGG +TGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGC +GGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCC +AGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCC +AGCGGGGGTGGAGTTGCCTGGGGGGGGCCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGC +CCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGG +CCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCCAGCGGGGGTGGAGTTGCCTGGGGGGG +GGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGG +GGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCC +TGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTT +GCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGT +TGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGA +GTTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGT +GGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGCACCCTGGACGGCCCCGCGGAGCCC +CCTGCGGGAGGCGAGGGCGGCCCTCGGGCTCTGGAAGGGGCCGCGCGGCCTGGAAGACAT +TACACGGCTGTCGGGCGGGGGGCGGCGCTCGCAGTTCCGGAGGGGG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/haps.fa.ref.fa new file mode 100644 index 00000000..09538986 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:641736-642566 +ATCATCCGGTGACAGGGATCATCATCCCTGCCTGGCATAGAAACCCGGACATCGGACCCTGCCCTCCCGCTGCTTCCGCAGGGACAGGGGGCAGCCAGCAGAGCCTCCCTCTGGGGGTGCCCCCCAATCTGGTTGCCTGGGACGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCAGCGGGGGTGAAGTTGCCTGGGGGGGGCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCAGCGGGGGTGGAGCACCCTGGACGGCCCCGCGGAGCCCCCTGCGGGAGGCGAGGGCGGCCCTCGGGCTCTGGAAGGGGCCGCGCGGCCTGGAAGACATTACACGGCTGTCGGGCGGGGGGCGGCGCTCGCAGTTCCGGAGGGGG diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/msa.fa new file mode 100644 index 00000000..12cccca8 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/msa.fa @@ -0,0 +1,125 @@ +>ref_chr20_641736_642566 +atcatccggtgacagggatcatcatccctgcctggcatagaaacccggacatcggaccct +gccctcccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtgc +cccccaatctggttgcctgggacgggggcccagcgggggtggagttgcct-ggggggggg +gcccagcgggggtggagttgcctggggggggaggcccagcgggggtggagttgcctgggg +gggggaggcccagcgggggtggagttgcctgggggggggtgcccagcgggggtggagttg +cctggggggggcccagcgggggtggagttgcctgtggggggaggcccagcgggggtggag +ttgcct-ggggggggcccagcgggggtggggttgcctggggggggaggcccagcgggggt +ggagttgcctgggggggggaggcccagcgggggtggagttgcctgggggggggtgcccag +cgggggtggagttgcct------------------------------------------- +--------------------gggggg-------------------------------ggc +ccagcgggggtggagttgcctgtggtggg---gggccagcgggggtgaagttgcctgggg +gggg----ccagcgggggtggagttgcctgggggggggccagcgggggtggagttgcctg +tgggggggggccagcgggggtggagttgcctgggggggg----ccagcgggggtggagtt +gcctgggggggg----ccagcgggggtggagcaccctggacggcccc--------gcgga +gccccctgcgggaggcgagggcggccctcgggctctggaaggggccgcgcggcctggaag +acattacacggctgtcgggcggggggcggcgctcgcagttccggaggggg---------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------ +>syndip_1_chr20:641736-642566 +atcatccggtgacagggatcatcatccctgcctggcatagaaacccggacatcggaccct +gccctcccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtgc +cccccaatctggttgcctgggaggggggcccagcgggggtggagttgcctgggggggggg +gcccagcgggggtggagttgcctgggggggg-ggcccagcgggggtggagttgcctgggg +gggggaggcccagcgggggtggagttgcctgggggggg--gcccagcgggggtggagttg +cctggg-----------------------------ggggggaggcccagcgggggtggag +ttgcctgggggggggcccagcgggggtggagttgcctgggggggg-ggcccagcgggggt +ggagttgcctgggggggggaggcccagcgggggtggagttgcctgggggggg--gcccag +cgggggtggagttgcctgggg---------------------------gggggaggccca +gcgggggtggagttgcctgggggggg-------------------------------ggc +ccagcgggggtggagttgcctg-gggggg---ggcccagcgggggtggagttgcctgggg +gggg---cccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcctg +-gggggggccccagcgggggtggagttgcctgggggggg--gcccagcgggggtggagtt +gcctgggggggg--gcccagcgggggtggagttgcctggggggggcccagcgggggtgga +gttgcctggggggggccccagcgggggtggagttgcctgggggggggcccagcgggggtg +gagttgcctggggggggggcccagcgggggtggagttgcctggggggggggcccagcggg +ggtggagttgcctgggggggggggcccagcgggggtggagttgcctgggggggggcccag +cgggggtggagttgcctg-gggggggggcccagcgggggtggagttgcct-ggggggggc +ccagcgggggtggagttgcct-gggggggggcccagcgggggtggagttgcctg-ggggg +ggggcccagcgggggtggagttgcctg-gggggggcccagcgggggtggagttgcctgtg +ggggggggcccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcct +gggggggggcccagcgggggtggagcaccctggacggccccgcggagccccctgcgggag +gcgagggcggccctcgggctctggaaggggccgcgcggcctggaagacattacacggctg +tcgggcggggggcggcgctcgcagttccggaggggg +>syndip_2_chr20:641736-642566 +atcatccggtgacagggatcatcatccctgcctggcatagaaacccggacatcggaccct +gccctcccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtgc +cccccaatctggttgcctgggacgggggcccagcgggggtggagttgcct-ggggggggg +gcccagcgggggtggagttgcctggggggggaggcccagcgggggtggagttgcctgggg +gggggaggcccagcgggggtggagttgcctgggggggggtgcccagcgggggtggagttg +cctggggggggcccagcgggggtggagttgcctgtggggggaggcccagcgggggtggag +ttgcct-ggggggggcccagcgggggtggggttgcctggggggggaggcccagcgggggt +ggagttgcctgggggggggaggcccagcgggggtggagttgcctgggggggggtgcccag +cgggggtggagttgcctgggggggggcccagcgggggtggagttgcctggggggggccca +gcgggggtggggttgcctggggggggcccagcgggggtggggttgcctggggggggaggc +ccagcgggggtggagttgcctg-ggggggggaggcccagcgggggtggagttgcctgggg +gggggtgcccagcgggggtggagttgcctggggggggcccagcgggggtggggttgcctg +-ggggggg-cccagcgggggtggggttgcctggggggggaggcccagcaggggtggagtt +gcctgggggggggtgcccagcgggggtggagttgcctggggggggcccagcgggggtgga +gttgcctgggggggg-cccagcgggggtggagttgcctgggggggggcccagcggggatg +gggttgcct-gggggggggcccagcgggggtggggttgcct-gggggggggcccagcggg +ggtggagttgcct--gggggggggcccagcgggggtggagttgcct-ggggggggcccag +cgggggtggagttgcctgtgggggggggcccagcgggggtggagttgcctgggggggggc +ccagcgggggtggagttgcctggggggggggcccagcgggggtggagttgcctgtggtgg +ggggcccagcgggggtggagttgcctgtgggggggcccagcgggggtggagttgcctgtg +ggggggggcccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcct +-ggggggggcccagcgggggtggagcaccctggacggccccgcggagccccctgcgggag +gcgagggcggccctcgggctctggaaggggccgcgcggcctggaagacattacacggctg +tcgggcggggggcggcgctcgcagttccggaggggg +>p:HG002_1_chr20:641736-642566 +atcatccggtgacagggatcatcatccctgcctggcatagaaacccggacatcggaccct +gccctcccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtgc +cccccaatctggttgcctgggacgggggcccagcgggggtggagttgcct-ggggggggg +gcccagcgggggtggagttgcctggggggggaggcccagcgggggtggagttgcctgggg +gggggaggcccagcgggggtggagttgcctgggggggggtgcccagcgggggtggagttg +cctggggggggcccagcgggggtggagttgcctgtggggggaggcccagcgggggtggag +ttgcct-ggggggggcccagcgggggtggggttgcctggggggggaggcccagcgggggt +ggagttgcctgggggggggaggcccagcgggggtggagttgcctgggggggggtgcccag +cgggggtggagttgcctgggggggggcccagcgggggtggagttgcctggggggggccca +gcgggggtggggttgcctggggggggcccagcgggggtggggttgcctggggggggaggc +ccagcgggggtggagttgcctg-ggggggggaggcccagcgggggtggagttgcctgggg +gggggtgcccagcgggggtggagttgcctggggggggcccagcgggggtggggttgcctg +-ggggggg-cccagcgggggtggggttgcctggggggggaggcccagcaggggtggagtt +gcctgggggggggtgcccagcgggggtggagttgcctggggggggcccagcgggggtgga +gttgcctgggggggg-cccagcgggggtggagttgcctgggggggggcccagcggggatg +gggttgcct-gggggggggcccagcgggggtggggttgcct-gggggggggcccagcggg +ggtggagttgcct--gggggggggcccagcgggggtggagttgcct-ggggggggcccag +cgggggtggagttgcctgtgggggggggcccagcgggggtggagttgcctgggggggggc +ccagcgggggtggagttgcctggggggggggcccagcgggggtggagttgcctgtggtgg +ggggcccagcgggggtggagttgcctgtgggggggcccagcgggggtggagttgcctgtg +ggggggggcccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcct +-ggggggggcccagcgggggtggagcaccctggacggccccgcggagccccctgcgggag +gcgagggcggccctcgggctctggaaggggccgcgcggcctggaagacattacacggctg +tcgggcggggggcggcgctcgcagttccggaggggg +>p:HG002_2_chr20:641736-642566 +atcatccggtgacagggatcatcatccctgcctggcatagaaacccggacatcggaccct +gccctcccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtgc +cccccaatctggttgcctgggaggggggcccagcgggggtggagttgcctgggggggggg +gcccagcgggggtggagttgcctgggggggg-ggcccagcgggggtggagttgcctgggg +gggggaggcccagcgggggtggagttgcctgggggggg--gcccagcgggggtggagttg +cctggg-----------------------------ggggggaggcccagcgggggtggag +ttgcctgggggggggcccagcgggggtggagttgcctgggggggg-ggcccagcgggggt +ggagttgcctgggggggggaggcccagcgggggtggagttgcctgggggggg--gcccag +cgggggtggagttgcctgggg---------------------------gggggaggccca +gcgggggtggagttgcctgggggggg-------------------------------ggc +ccagcgggggtggagttgcctg-gggggg---ggcccagcgggggtggagttgcctgggg +gggg---cccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcctg +-gggggggccccagcgggggtggagttgcctgggggggg--gcccagcgggggtggagtt +gcctgggggggg--gcccagcgggggtggagttgcctggggggggcccagcgggggtgga +gttgcctggggggggccccagcgggggtggagttgcctgggggggggcccagcgggggtg +gagttgcctggggggggggcccagcgggggtggagttgcctggggggggggcccagcggg +ggtggagttgcctgggggggggggcccagcgggggtggagttgcctgggggggggcccag +cgggggtggagttgcctg-gggggggggcccagcgggggtggagttgcct-ggggggggc +ccagcgggggtggagttgcct-gggggggggcccagcgggggtggagttgcctg-ggggg +ggggcccagcgggggtggagttgcctg-gggggggcccagcgggggtggagttgcctgtg +ggggggggcccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcct +gggggggggcccagcgggggtggagcaccctggacggccccgcggagccccctgcgggag +gcgagggcggccctcgggctctggaaggggccgcgcggcctggaagacattacacggctg +tcgggcggggggcggcgctcgcagttccggaggggg diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/msa.fa.fai new file mode 100644 index 00000000..c265ec0c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_641736_642566 1416 25 60 61 +syndip_1_chr20:641736-642566 1416 1495 60 61 +syndip_2_chr20:641736-642566 1416 2965 60 61 +p:HG002_1_chr20:641736-642566 1416 4436 60 61 +p:HG002_2_chr20:641736-642566 1416 5907 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/output.vcf.gz new file mode 100644 index 00000000..65742123 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/output.vcf.gz.tbi new file mode 100644 index 00000000..92dc985e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:641836-642466/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/base.vcf.gz new file mode 100644 index 00000000..2b902ecf Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/base.vcf.gz.tbi new file mode 100644 index 00000000..b096be60 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/comp.vcf.gz new file mode 100644 index 00000000..13a5c5a1 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/comp.vcf.gz.tbi new file mode 100644 index 00000000..cd202e07 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/haps.fa new file mode 100644 index 00000000..7dd3b59a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/haps.fa @@ -0,0 +1,26 @@ +>ref_chr20_7720811_7721104 +TCACACATTTAAGATACAATTCCTTTCCCCACCCCAACTCTCCAGGTTTCCTGAATTAATTGGAAGGAAACTGTTATATTTCCTTAATTCCTGAAGTGGGAGTTAAATCTAAATCTAACAAATGACATTTTCTTTTTCTTTTCTTTTCTTTCTTTTTTTTTTTTTTTTTGGGATGGAGTTCCACTCTTGTTGCCCAGGCTGGACAGGCTGGAATACAATGGCGTGATCTTGGCTCTCTGCAACCTCCGACTCCCAGGTTCAAGTGATTCTCCTGCCTCAGCCTCCCAACTAGCT +>syndip_1_chr20:7720811-7721104 +TCACACATTTAAGATACAATTCCTTTCCCCACCCCAACTCTCCAGGTTTCCTGAATTAAT +TGGAAGGAAACTGTTATATTTCCTTAATTCCTGAAGTGGGAGTTAAATCTAAATCTAACA +AATGAC*TTTTCTTTTTCTTTT*TTTTTTTTTTTGGGATGGAGTTCCACTCTTGTTGCCC +AGGCTGGACAGGCTGGAATACAATGGCGTGATCTTGGCTCTCTGCAACCTCCGACTCCCA +GGTTCAAGTGATTCTCCTGCCTCAGCCTCCCAACTAGCT +>syndip_2_chr20:7720811-7721104 +TCACACATTTAAGATACAATTCCTTTCCCCACCCCAACTCTCCAGGTTTCCTGAATTAAT +TGGAAGGAAACTGTTATATTTCCTTAATTCCTGAAGTGGGAGTTAAATCTAAATCTAACA +AATGACGTTTTCTTTTTCTTTTCTTTTTTTTTTTGGGATGGAGTTCCACTCTTGTTGCCC +AGGCTGGACAGGCTGGAATACAATGGCGTGATCTTGGCTCTCTGCAACCTCCGACTCCCA +GGTTCAAGTGATTCTCCTGCCTCAGCCTCCCAACTAGCT +>p:HG002_1_chr20:7720811-7721104 +TCACACATTTAAGATACAATTCCTTTCCCCACCCCAACTCTCCAGGTTTCCTGAATTAAT +TGGAAGGAAACTGTTATATTTCCTTAATTCCTGAAGTGGGAGTTAAATCTAAATCTAACA +AATGACGTTTTCTTTTTCTTTTCTTTTTTTTTTTGGGATGGAGTTCCACTCTTGTTGCCC +AGGCTGGACAGGCTGGAATACAATGGCGTGATCTTGGCTCTCTGCAACCTCCGACTCCCA +GGTTCAAGTGATTCTCCTGCCTCAGCCTCCCAACTAGCT +>p:HG002_2_chr20:7720811-7721104 +TCACACATTTAAGATACAATTCCTTTCCCCACCCCAACTCTCCAGGTTTCCTGAATTAAT +TGGAAGGAAACTGTTATATTTCCTTAATTCCTGAAGTGGGAGTTAAATCTAAATCTAACA +AATGACATTTTCTTTTTCTTTTCTTTTCTTTCTTTTTTTTTTTTTTTTTGGGATGGAGTT +CCACTCTTGTTGCCCAGGCTGGACAGGCTGGAATACAATGGCGTGATCTTGGCTCTCTGC +AACCTCCGACTCCCAGGTTCAAGTGATTCTCCTGCCTCAGCCTCCCAACTAGCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/haps.fa.ref.fa new file mode 100644 index 00000000..3e29a118 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:7720811-7721104 +TCACACATTTAAGATACAATTCCTTTCCCCACCCCAACTCTCCAGGTTTCCTGAATTAATTGGAAGGAAACTGTTATATTTCCTTAATTCCTGAAGTGGGAGTTAAATCTAAATCTAACAAATGACATTTTCTTTTTCTTTTCTTTTCTTTCTTTTTTTTTTTTTTTTTGGGATGGAGTTCCACTCTTGTTGCCCAGGCTGGACAGGCTGGAATACAATGGCGTGATCTTGGCTCTCTGCAACCTCCGACTCCCAGGTTCAAGTGATTCTCCTGCCTCAGCCTCCCAACTAGCT diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/msa.fa new file mode 100644 index 00000000..44437053 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/msa.fa @@ -0,0 +1,30 @@ +>ref_chr20_7720811_7721104 +tcacacatttaagatacaattcctttccccaccccaactctccaggtttcctgaattaat +tggaaggaaactgttatatttccttaattcctgaagtgggagttaaatctaaatctaaca +aatgacattttctttttcttttcttttctttctttttttttttttttttgggatggagtt +ccactcttgttgcccaggctggacaggctggaatacaatggcgtgatcttggctctctgc +aacctccgactcccaggttcaagtgattctcctgcctcagcctcccaactagct +>syndip_1_chr20:7720811-7721104 +tcacacatttaagatacaattcctttccccaccccaactctccaggtttcctgaattaat +tggaaggaaactgttatatttccttaattcctgaagtgggagttaaatctaaatctaaca +aatgac--ttttctttttctttt---------------tttttttttttgggatggagtt +ccactcttgttgcccaggctggacaggctggaatacaatggcgtgatcttggctctctgc +aacctccgactcccaggttcaagtgattctcctgcctcagcctcccaactagct +>syndip_2_chr20:7720811-7721104 +tcacacatttaagatacaattcctttccccaccccaactctccaggtttcctgaattaat +tggaaggaaactgttatatttccttaattcctgaagtgggagttaaatctaaatctaaca +aatgacgttttctttttcttttc---------------tttttttttttgggatggagtt +ccactcttgttgcccaggctggacaggctggaatacaatggcgtgatcttggctctctgc +aacctccgactcccaggttcaagtgattctcctgcctcagcctcccaactagct +>p:HG002_1_chr20:7720811-7721104 +tcacacatttaagatacaattcctttccccaccccaactctccaggtttcctgaattaat +tggaaggaaactgttatatttccttaattcctgaagtgggagttaaatctaaatctaaca +aatgacgttttctttttcttttc---------------tttttttttttgggatggagtt +ccactcttgttgcccaggctggacaggctggaatacaatggcgtgatcttggctctctgc +aacctccgactcccaggttcaagtgattctcctgcctcagcctcccaactagct +>p:HG002_2_chr20:7720811-7721104 +tcacacatttaagatacaattcctttccccaccccaactctccaggtttcctgaattaat +tggaaggaaactgttatatttccttaattcctgaagtgggagttaaatctaaatctaaca +aatgacattttctttttcttttcttttctttctttttttttttttttttgggatggagtt +ccactcttgttgcccaggctggacaggctggaatacaatggcgtgatcttggctctctgc +aacctccgactcccaggttcaagtgattctcctgcctcagcctcccaactagct diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/msa.fa.fai new file mode 100644 index 00000000..8651713c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_7720811_7721104 294 27 60 61 +syndip_1_chr20:7720811-7721104 294 358 60 61 +syndip_2_chr20:7720811-7721104 294 689 60 61 +p:HG002_1_chr20:7720811-7721104 294 1021 60 61 +p:HG002_2_chr20:7720811-7721104 294 1353 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/output.vcf.gz new file mode 100644 index 00000000..929eb374 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/output.vcf.gz.tbi new file mode 100644 index 00000000..5ae7585a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:7720911-7721004/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/base.vcf.gz new file mode 100644 index 00000000..7531adaa Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/base.vcf.gz.tbi new file mode 100644 index 00000000..0a44f543 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/comp.vcf.gz new file mode 100644 index 00000000..63c4b927 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/comp.vcf.gz.tbi new file mode 100644 index 00000000..e08b08df Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/haps.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/haps.fa new file mode 100644 index 00000000..c52bda1e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/haps.fa @@ -0,0 +1,128 @@ +>ref_chr20_8661811_8662758 +GCCAACCTACGTTAAGTAATTCATAACTTCAGTATTTAATAAATCTTCAGTGAAAGGCAAGAGGCTACACACAGTGACAGACCCAGAGATAAACCCTGTGCCCCTAGAGATTTGCACTCCTCTTAAAAGTGTATATATATATAATTATATAATTATTTATTATATAATTATATATAATTATATAATTATTTATTATATAATTATATATAATATACAATTATTTATTATATAATTATATATAATTATATATTTATTATATTTATTATACAGTTATATAATAAATAATTATATAATTATATATAATTATATATTATTTATTATCTAATTCTATATTAAATATAATTATTTATTATCTAATTCTATATTATATATAATTATTTATTATATAATTCTATATTATATATAATTATTATATAATTCTATATATAATTATTTATTATATAATTCTATACATAAGTATTTATTATATAATTATGTATATAATTATTTATTATATAATTATGTATAATATGTAATTATTTATTATATAATTATGTATAATATGTAATTATTTATTATATAATTATGTATAATATATAATTATTTATTATATAATTATGTATAATATATAATTATTTATTATATAATTATGTGTTATGTATAATTATTATATAATTATGTATAATATATATATAATTTTTTATTATATAATTATGTATAATATATAATTTTTTATAATTATGTGTAATATATAATTATTTATCATATAATTACAATATATATTATTAACATAATATCTAAATATATTAATAATCTAATATCTATAATTAATATAATATATAAATATTACTTCTTGAAATCCAACGTGCACCTGAATCACCTGAGCCGTTGTTAAAATGCAGATTCGAGATCCTGCATTTCTAACAAGTTACTGGGTGAGGCAGAAGATGCTTAGCAAAGGCCCACACC +>syndip_1_chr20:8661811-8662758 +GCCAACCTACGTTAAGTAATTCATAACTTCAGTATTTAATAAATCTTCAGTGAAAGGCAA +GAGGCTACACACAGTGACAGACCCAGAGATAAACCCTGTGCCCCTAGAGATTTGCACTCC +TCTTAAAAGTGTATATATATATAATTATATAATTATTTATTATATAATTATATATAATTA +TATAATTATTTATTATATAATTATATATAATTATATAATTATTTATTATATAATTATATA +TAATATACAATTATTTATTATATAATTATATATAATTATATATTTATTATATTTATTATA +CAGTTATATAATAAATAATTATATAATTATATATAATTATATATATATAATTATATATAA +TTATATATAATTATATAATTATATATAATTGTATATAATTATTTATTATATAATTATATA +TTATTTATTATATAATTATATAATTATATATTATTTATTATATATTATATAATTATATAA +TTATATATTATTTATTATATAATATATAATTATATATTATTTATTATATAATTATATATT +ATTTATTATATATATTATTTATTATATAATTATATATTATGTATTATATAATTATATAAT +TATATATTATGTATTATATAATTATATATTATGTATTATATAATTATATAATTATATATT +ATGTATTATATAATTATATATTATTTATTATATAATTATATAATTATATATTATTTATTA +TATAATTATATAATTATATATTATTTATTATATAATTATATAATTATATATTATTTATTA +TATAATTATATAATTATATATTATTTATTATATAATTATATATTATTTATTATATAATTA +TATATTATTTATTACATAAATATATATTATTTATTACATAAGTATATATCACTTATTATA +TAATTGCATATAATTATTTATTATATAATTGCATATAATTATTATATAATTGTATATAGT +TATTTATTATATAATTGTATATAGTTATTTATTATATAATTCTATATAATTATTTATTAT +CTAATTCTATATTAAATATAATTATTTATTATCTAATTCTATATTATATATAATTATTTA +TTATATAATTCTATATTATATATAATTATTATATAATTCTATATATAATTATTTATTATA +TAATTCTATACATAAGTATTTATTATATAATTATGTATATAATTATTTATTATATAATTA +TGTATAATATGTAATTATTTATTATATAATTATGTATAATATGTAATTATTTATTATATA +ATTATGTATAATATATAATTATTTATTATATAATTATGTATAATATATAATTATTTATTA +TATAATTATGTGTTATGTATAATTATTATATAATTATGTATAATATATATATAATTTTTT +ATTATATAATTATGTATAATATATAATTTTTTATAATTATGTGTAATATATAATTATTTA +TCATATAATTACAATATATATTATTAACATAATATCTAAATATATTAATAATCTAATATC +TATAATTAATATAATATATAAATATTACTTCTTGAAATCCAACGTGCACCTGAATCACCT +GAGCCGTTGTTAAAATGCAGATTCGAGATCCTGCATTTCTAACAAGTTACTGGGTGAGGC +AGAAGATGCTTAGCAAAGGCCCACACC +>syndip_2_chr20:8661811-8662758 +GCCAACCTACGTTAAGTAATTCATAACTTCAGTATTTAATAAATCTTCAGTGAAAGGCAA +GAGGCTACACACAGTGACAGACCCAGAGATAAACCCTGTGCCCCTAGAGATTTGCACTCC +TCTTAAAAGTGTATATATATATAATTATATAATTATTTATTATATAATGATATATAATTA +TATAATTATTTATTATATAATGATATATAATTATATAATTATTTATTATATAATTATATA +TAATTATATAATTATTTATTATATAATTATATATAATTATATAATTATTTATTATATAAT +TATATATAATTATATAATTATTTATTATATAATTATATATAATTATATAATTATTTATTA +TATAATTATATATAATTATATAATTATTTATTATATAATTATATATAATTATATAATTAT +TTATTATATAATTATATATAATTATATAATTATTTATTATATAATTATATATAATTATAT +AATTATTTATTATATAATTATATATAATATACAATTATTTATTATATAATTATATATAAT +ATACAATTATTTATTATATAATTATATATAATTATATATTTATTATATTTATTATACAGT +TATATAATAAATATATAATTATATATAAATATATAATTATATATAATTATATATATATAA +TTATATGTAATTATATATAATTATATAATTATTATATAATTGTATATAATATATAATTAT +ATAATTATATATTATTTATTATATAATATATAATTATATAATTATATATTATTTATTATA +TAATATATAATTATATAATTATATATTATTTATTATATAATTATATATTATTTATTATAT +ATATTATTTATTATATAATTATATAATTATATATTATTTATTATATAATTATATATTATT +TATTATATAATATATAATTATATATTATTTATTATATAATATATAATTATATATTATTTA +TTATATAATTATATATTATGTATTATATAATATATAATTATATATTATGTATTATATAAT +TATATAATTATATATTATTTATTATATAATTATATAATTATATATTATTTATTACATAAT +TATATATTATTTATTACATAAGTATATATTATTTATTACATAAGTATATATCACTTATTA +TATAATTGTATATAATTATTTATTATATAATTGCATATAATTATTTATTATATAATTGTA +TATAGTTATTTATTATATAATTCTATATAGTTATTTATTATATAATTCTATATAATTATT +TATTATCTAATTCTATATTATATATAATTATTTATTATCTAATTCTATATTATATATAAT +TATTTATTATATAATTCTATATTATATATAATTATTTATTATATAATTCTATATTATATA +TAATTATTATATAATTCTATATATAATTATTTATTATATAATTCTATACATAAGTATTTA +TTATATAATTATGTATATAATTATTTATTATATAATTATGTATAATATGTAATTATTTAT +TATATAATTATGTATAATATATAATTGTTTATTATATAATTATGTATAATATATAATTAT +TTATTATATAATTATGTATAATATATAATTATTTATTATATAATTATGTGTTATGTATAA +TTATTTATTATATAATTATGTATAATATATATATAATTTTTTATTATATAATTATGTATA +ATATATAATTTTTTATAATTATGTGTAATATATAATTATTTATCATATAATTACAATATA +TATTATTAACATAATATCTAAATATATTAATAATCTAATATCTATAATTAATATAATATA +TAAATATTACTTCTTGAAATCCAACGTGCACCTGAATCACCTGAGCCGTTGTTAAAATGC +AGATTCGAGATCCTGCATTTCTAACAAGTTACTGGGTGAGGCAGAAGATGCTTAGCAAAG +GCCCACACC +>p:HG002_1_chr20:8661811-8662758 +GCCAACCTACGTTAAGTAATTCATAACTTCAGTATTTAATAAATCTTCAGTGAAAGGCAA +GAGGCTACACACAGTGACAGACCCAGAGATAAACCCTGTGCCCCTAGAGATTTGCACTCC +TCTTAAAAGTGTATATATATATAATTATATAATTATTTATTATATAATGATATATAATTA +TATAATTATTTATTATATAATGATATATAATTATATAATTATTTATTATATAATTATATA +TAATTATATAATTATTTATTATATAATTATATATAATTATATAATTATTTATTATATAAT +TATATATAATTATATAATTATTTATTATATAATTATATATAATTATATAATTATTTATTA +TATAATTATATATAATTATATAATTATTTATTATATAATTATATATAATTATATAATTAT +TTATTATATAATTATATATAATTATATAATTATTTATTATATAATTATATATAATTATAT +AATTATTTATTATATAATTATATATAATATACAATTATTTATTATATAATTATATATAAT +ATACAATTATTTATTATATAATTATATATAATTATATATTTATTATATTTATTATACAGT +TATATAATAAATATATAATTATATATAAATATATAATTATATATAATTATATATATATAA +TTATATGTAATTATATATAATTATATAATTATTATATAATTGTATATAATATATAATTAT +ATAATTATATATTATTTATTATATAATATATAATTATATAATTATATATTATTTATTATA +TAATATATAATTATATAATTATATATTATTTATTATATAATTATATATTATTTATTATAT +ATATTATTTATTATATAATTATATAATTATATATTATTTATTATATAATTATATATTATT +TATTATATAATATATAATTATATATTATTTATTATATAATATATAATTATATATTATTTA +TTATATAATTATATATTATGTATTATATAATATATAATTATATATTATGTATTATATAAT +TATATAATTATATATTATTTATTATATAATTATATAATTATATATTATTTATTACATAAT +TATATATTATTTATTACATAAGTATATATTATTTATTACATAAGTATATATCACTTATTA +TATAATTGTATATAATTATTTATTATATAATTGCATATAATTATTTATTATATAATTGTA +TATAGTTATTTATTATATAATTCTATATAGTTATTTATTATATAATTCTATATAATTATT +TATTATCTAATTCTATATTATATATAATTATTTATTATCTAATTCTATATTATATATAAT +TATTTATTATATAATTCTATATTATATATAATTATTTATTATATAATTCTATATTATATA +TAATTATTATATAATTCTATATATAATTATTTATTATATAATTCTATACATAAGTATTTA +TTATATAATTATGTATATAATTATTTATTATATAATTATGTATAATATGTAATTATTTAT +TATATAATTATGTATAATATATAATTGTTTATTATATAATTATGTATAATATATAATTAT +TTATTATATAATTATGTATAATATATAATTATTTATTATATAATTATGTGTTATGTATAA +TTATTTATTATATAATTATGTATAATATATATATAATTTTTTATTATATAATTATGTATA +ATATATAATTTTTTATAATTATGTGTAATATATAATTATTTATCATATAATTACAATATA +TATTATTAACATAATATCTAAATATATTAATAATCTAATATCTATAATTAATATAATATA +TAAATATTACTTCTTGAAATCCAACGTGCACCTGAATCACCTGAGCCGTTGTTAAAATGC +AGATTCGAGATCCTGCATTTCTAACAAGTTACTGGGTGAGGCAGAAGATGCTTAGCAAAG +GCCCACACC +>p:HG002_2_chr20:8661811-8662758 +GCCAACCTACGTTAAGTAATTCATAACTTCAGTATTTAATAAATCTTCAGTGAAAGGCAA +GAGGCTACACACAGTGACAGACCCAGAGATAAACCCTGTGCCCCTAGAGATTTGCACTCC +TCTTAAAAGTGTATATATATATAATTATATAATTATTTATTATATAATTATATATAATTA +TATAATTATTTATTATATAATTATATATAATTATATAATTATTTATTATATAATTATATA +TAATATACAATTATTTATTATATAATTATATATAATTATATATTTATTATATTTATTATA +CAGTTATATAATAAATAATTATATAATTATATATAATTATATATATATAATTATATATAA +TTATATATAATTATATAATTATATATAATTGTATATAATTATTTATTATATAATTATATA +TTATTTATTATATAATTATATAATTATATATTATTTATTATATATTATATAATTATATAA +TTATATATTATTTATTATATAATATATAATTATATATTATTTATTATATAATTATATATT +ATTTATTATATATATTATTTATTATATAATTATATATTATGTATTATATAATTATATAAT +TATATATTATGTATTATATAATTATATATTATGTATTATATAATTATATAATTATATATT +ATGTATTATATAATTATATATTATTTATTATATAATTATATAATTATATATTATTTATTA +TATAATTATATAATTATATATTATTTATTATATAATTATATAATTATATATTATTTATTA +TATAATTATATAATTATATATTATTTATTATATAATTATATATTATTTATTATATAATTA +TATATTATTTATTACATAAATATATATTATTTATTACATAAGTATATATCACTTATTATA +TAATTGCATATAATTATTTATTATATAATTGCATATAATTATTATATAATTGTATATAGT +TATTTATTATATAATTGTATATAGTTATTTATTATATAATTCTATATAATTATTTATTAT +CTAATTCTATATTAAATATAATTATTTATTATCTAATTCTATATTATATATAATTATTTA +TTATATAATTCTATATTATATATAATTATTATATAATTCTATATATAATTATTTATTATA +TAATTCTATACATAAGTATTTATTATATAATTATGTATATAATTATTTATTATATAATTA +TGTATAATATGTAATTATTTATTATATAATTATGTATAATATGTAATTATTTATTATATA +ATTATGTATAATATATAATTATTTATTATATAATTATGTATAATATATAATTATTTATTA +TATAATTATGTGTTATGTATAATTATTATATAATTATGTATAATATATATATAATTTTTT +ATTATATAATTATGTATAATATATAATTTTTTATAATTATGTGTAATATATAATTATTTA +TCATATAATTACAATATATATTATTAACATAATATCTAAATATATTAATAATCTAATATC +TATAATTAATATAATATATAAATATTACTTCTTGAAATCCAACGTGCACCTGAATCACCT +GAGCCGTTGTTAAAATGCAGATTCGAGATCCTGCATTTCTAACAAGTTACTGGGTGAGGC +AGAAGATGCTTAGCAAAGGCCCACACC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/haps.fa.ref.fa new file mode 100644 index 00000000..b5e952ab --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:8661811-8662758 +GCCAACCTACGTTAAGTAATTCATAACTTCAGTATTTAATAAATCTTCAGTGAAAGGCAAGAGGCTACACACAGTGACAGACCCAGAGATAAACCCTGTGCCCCTAGAGATTTGCACTCCTCTTAAAAGTGTATATATATATAATTATATAATTATTTATTATATAATTATATATAATTATATAATTATTTATTATATAATTATATATAATATACAATTATTTATTATATAATTATATATAATTATATATTTATTATATTTATTATACAGTTATATAATAAATAATTATATAATTATATATAATTATATATTATTTATTATCTAATTCTATATTAAATATAATTATTTATTATCTAATTCTATATTATATATAATTATTTATTATATAATTCTATATTATATATAATTATTATATAATTCTATATATAATTATTTATTATATAATTCTATACATAAGTATTTATTATATAATTATGTATATAATTATTTATTATATAATTATGTATAATATGTAATTATTTATTATATAATTATGTATAATATGTAATTATTTATTATATAATTATGTATAATATATAATTATTTATTATATAATTATGTATAATATATAATTATTTATTATATAATTATGTGTTATGTATAATTATTATATAATTATGTATAATATATATATAATTTTTTATTATATAATTATGTATAATATATAATTTTTTATAATTATGTGTAATATATAATTATTTATCATATAATTACAATATATATTATTAACATAATATCTAAATATATTAATAATCTAATATCTATAATTAATATAATATATAAATATTACTTCTTGAAATCCAACGTGCACCTGAATCACCTGAGCCGTTGTTAAAATGCAGATTCGAGATCCTGCATTTCTAACAAGTTACTGGGTGAGGCAGAAGATGCTTAGCAAAGGCCCACACC diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/msa.fa b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/msa.fa new file mode 100644 index 00000000..3286542a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/msa.fa @@ -0,0 +1,170 @@ +>ref_chr20_8661811_8662758 +gccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggcaa +gaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactcc +tcttaaaag--------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------tgtata +tatatataattatataattattt--------attatataattatatataattatata--- +--------attatttattatataattatatataatatac------------aattattta +ttatataattatatataattatat--------atttattatat----ttattatacagt- +-tatataataaataattatataattatatataattatat------------------att +atttattatctaattctatattaaatataattatttattatc------------------ +--------------taattctatattatatataattatttattatataattctatattat +atataattattatataattctatatataattatttattatataattctatacataagtat +ttattatataattatgtatataattatttattatataattatgtataatatgtaattatt +tattatataattatgtataatatgtaattatttattatataattatgtataatatataat +tatttattatataattatgtataatatataattatttattatataattatgtgttatgta +taa----ttattatataattatgtataatatatatataattttttattatataattatgt +ataatatataattttttataattatgtgtaatatataattatttatcatataattacaat +atatattattaacataatatctaaatatattaataatctaatatctataattaatataat +atataaatattacttcttgaaatccaacgtgcacctgaatcacctgagccgttgttaaaa +tgcagattcgagatcctgcatttctaacaagttactgggtgaggcagaagatgcttagca +aaggcccacacc +>syndip_1_chr20:8661811-8662758 +gccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggcaa +gaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactcc +tcttaaaagtgtatatatatataattatataattatttattatataattatatataatta +tataattatttattatataattatatataattatataattatttattatataattatata +taa-tatacaattatttattatataattatatataattatatatttattatatttat--- +--tatacagttatataataaataattatataattatatataattatata---------ta +tataattatatataattatata-----taattatataattatatataattg--------- +----------------------tatataattatttattatataattatat---------- +-attatttattatataattatata----------------attatat------------- +-----attatttattatata---------------------------------------- +--------------------ttatataattatataattatatattatttattatata--- +--atatataattatatat-------tatttattatataattatatattatttatta---- +-----tatatattatttattatata----------------------attatatattatg +tattatataattatataattatatattatgtattatataat----------------tat +atattatgtattatataattatataattatatattatgtattatataattatatattatt +tattatataattatataattatatattatttattatataattatataattatatattatt +tattatataat---------------------tatataattatatattatttattatata +attatataattatat-attattt--------attatataattatatattatttattatat +aattatatattatttattacataaatatatattatttattacataagtatatatcactta +ttatataattgcatataattatttattatataattgcatataa----ttattatataatt +gtatatagttatttattatataattgtatatagttatttattatataattctatataatt +atttattatctaattctatattaaatataattatttattatc------------------ +--------------taattctatattatatataattatttattatataattctatattat +atataattattatataattctatatataattatttattatataattctatacataagtat +ttattatataattatgtatataattatttattatataattatgtataatatgtaattatt +tattatataattatgtataatatgtaattatttattatataattatgtataatatataat +tatttattatataattatgtataatatataattatttattatataattatgtgttatgta +taa----ttattatataattatgtataatatatatataattttttattatataattatgt +ataatatataattttttataattatgtgtaatatataattatttatcatataattacaat +atatattattaacataatatctaaatatattaataatctaatatctataattaatataat +atataaatattacttcttgaaatccaacgtgcacctgaatcacctgagccgttgttaaaa +tgcagattcgagatcctgcatttctaacaagttactgggtgaggcagaagatgcttagca +aaggcccacacc +>syndip_2_chr20:8661811-8662758 +gccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggcaa +gaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactcc +tcttaaaagtgtatatatatataattatataattatttattatataatgatatataatta +tataattatttattatataatgatatataattatataattatttattatataattatata +taattatataattatttattatataattatatataattatataattatttattatataat +tatatataattatataattatttattatataattatatataattatataattatttatta +tataattatatataattatataattatttattatataattatatataattatataattat +ttattatataattatatataattatataattatttattatataattatatataattatat +aattatttattatataattatatataatatacaattatttattatataattatatataat +atacaattatttattatataattatatataattatatatttattatatttattatacagt +tatataataaatatataattatatataaatatataattatatataattatatatatataa +ttatatgtaattatatataattatataattattatataattgtatataatatataattat +ataattatatattatttattatataatatataattatataattatatattatttattata +taatatataattatataattatatattatttattatataattatatattatttattatat +atattatttattatataattatataattatatattatttattatataattatatattatt +tattatataa-tatataattatatattatttattatataa-tatataattatatattatt +tattatataattatatattatgtattatataatatataattatatattatgtattatata +attatataattatat-attatttattatataattatataattatatattatttattacat +aattatatattatttattacataagtatatattatttattacataagtatatatcactta +ttatataattgtatataattatttattatataattgcatataattatttattatataatt +gtatatagttatttattatataattctatatagttatttattatataattctatataatt +atttattatctaattctatattatatataattatttattatctaattctatattatatat +aattatttattatataattctatattatatataattatttattatataattctatattat +atataattattatataattctatatataattatttattatataattctatacataagtat +ttattatataattatgtatataattatttattatataattatgtataatatgtaattatt +tattatataattatgtataatatataattgtttattatataattatgtataatatataat +tatttattatataattatgtataatatataattatttattatataattatgtgttatgta +taattatttattatataattatgtataatatatatataattttttattatataattatgt +ataatatataattttttataattatgtgtaatatataattatttatcatataattacaat +atatattattaacataatatctaaatatattaataatctaatatctataattaatataat +atataaatattacttcttgaaatccaacgtgcacctgaatcacctgagccgttgttaaaa +tgcagattcgagatcctgcatttctaacaagttactgggtgaggcagaagatgcttagca +aaggcccacacc +>p:HG002_1_chr20:8661811-8662758 +gccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggcaa +gaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactcc +tcttaaaagtgtatatatatataattatataattatttattatataatgatatataatta +tataattatttattatataatgatatataattatataattatttattatataattatata +taattatataattatttattatataattatatataattatataattatttattatataat +tatatataattatataattatttattatataattatatataattatataattatttatta +tataattatatataattatataattatttattatataattatatataattatataattat +ttattatataattatatataattatataattatttattatataattatatataattatat +aattatttattatataattatatataatatacaattatttattatataattatatataat +atacaattatttattatataattatatataattatatatttattatatttattatacagt +tatataataaatatataattatatataaatatataattatatataattatatatatataa +ttatatgtaattatatataattatataattattatataattgtatataatatataattat +ataattatatattatttattatataatatataattatataattatatattatttattata +taatatataattatataattatatattatttattatataattatatattatttattatat +atattatttattatataattatataattatatattatttattatataattatatattatt +tattatataa-tatataattatatattatttattatataa-tatataattatatattatt +tattatataattatatattatgtattatataatatataattatatattatgtattatata +attatataattatat-attatttattatataattatataattatatattatttattacat +aattatatattatttattacataagtatatattatttattacataagtatatatcactta +ttatataattgtatataattatttattatataattgcatataattatttattatataatt +gtatatagttatttattatataattctatatagttatttattatataattctatataatt +atttattatctaattctatattatatataattatttattatctaattctatattatatat +aattatttattatataattctatattatatataattatttattatataattctatattat +atataattattatataattctatatataattatttattatataattctatacataagtat +ttattatataattatgtatataattatttattatataattatgtataatatgtaattatt +tattatataattatgtataatatataattgtttattatataattatgtataatatataat +tatttattatataattatgtataatatataattatttattatataattatgtgttatgta +taattatttattatataattatgtataatatatatataattttttattatataattatgt +ataatatataattttttataattatgtgtaatatataattatttatcatataattacaat +atatattattaacataatatctaaatatattaataatctaatatctataattaatataat +atataaatattacttcttgaaatccaacgtgcacctgaatcacctgagccgttgttaaaa +tgcagattcgagatcctgcatttctaacaagttactgggtgaggcagaagatgcttagca +aaggcccacacc +>p:HG002_2_chr20:8661811-8662758 +gccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggcaa +gaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactcc +tcttaaaagtgtatatatatataattatataattatttattatataattatatataatta +tataattatttattatataattatatataattatataattatttattatataattatata +taa-tatacaattatttattatataattatatataattatatatttattatatttat--- +--tatacagttatataataaataattatataattatatataattatata---------ta +tataattatatataattatata-----taattatataattatatataattg--------- +----------------------tatataattatttattatataattatat---------- +-attatttattatataattatata----------------attatat------------- +-----attatttattatata---------------------------------------- +--------------------ttatataattatataattatatattatttattatata--- +--atatataattatatat-------tatttattatataattatatattatttatta---- +-----tatatattatttattatata----------------------attatatattatg +tattatataattatataattatatattatgtattatataat----------------tat +atattatgtattatataattatataattatatattatgtattatataattatatattatt +tattatataattatataattatatattatttattatataattatataattatatattatt +tattatataat---------------------tatataattatatattatttattatata +attatataattatat-attattt--------attatataattatatattatttattatat +aattatatattatttattacataaatatatattatttattacataagtatatatcactta +ttatataattgcatataattatttattatataattgcatataa----ttattatataatt +gtatatagttatttattatataattgtatatagttatttattatataattctatataatt +atttattatctaattctatattaaatataattatttattatc------------------ +--------------taattctatattatatataattatttattatataattctatattat +atataattattatataattctatatataattatttattatataattctatacataagtat +ttattatataattatgtatataattatttattatataattatgtataatatgtaattatt +tattatataattatgtataatatgtaattatttattatataattatgtataatatataat +tatttattatataattatgtataatatataattatttattatataattatgtgttatgta +taa----ttattatataattatgtataatatatatataattttttattatataattatgt +ataatatataattttttataattatgtgtaatatataattatttatcatataattacaat +atatattattaacataatatctaaatatattaataatctaatatctataattaatataat +atataaatattacttcttgaaatccaacgtgcacctgaatcacctgagccgttgttaaaa +tgcagattcgagatcctgcatttctaacaagttactgggtgaggcagaagatgcttagca +aaggcccacacc diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/msa.fa.fai new file mode 100644 index 00000000..1face17a --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_8661811_8662758 1932 27 60 61 +syndip_1_chr20:8661811-8662758 1932 2024 60 61 +syndip_2_chr20:8661811-8662758 1932 4021 60 61 +p:HG002_1_chr20:8661811-8662758 1932 6019 60 61 +p:HG002_2_chr20:8661811-8662758 1932 8017 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/output.vcf.gz new file mode 100644 index 00000000..e0c6ee9f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/output.vcf.gz.tbi new file mode 100644 index 00000000..6201d41b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab/phab/chr20/chr20:8661911-8662658/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/fn.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab_bench/fn.vcf.gz new file mode 100644 index 00000000..3ae7538f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab_bench/fn.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/fn.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab_bench/fn.vcf.gz.tbi new file mode 100644 index 00000000..7256b59b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab_bench/fn.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/fp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab_bench/fp.vcf.gz new file mode 100644 index 00000000..1b1c7158 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab_bench/fp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/fp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab_bench/fp.vcf.gz.tbi new file mode 100644 index 00000000..b320ff9e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab_bench/fp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/params.json b/repo_utils/answer_key/refine/refine_output_one/phab_bench/params.json new file mode 100644 index 00000000..8f42ddc8 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab_bench/params.json @@ -0,0 +1 @@ +{"base": "test_results/refine_output_one/phab.output.vcf.gz", "comp": "test_results/refine_output_one/phab.output.vcf.gz", "output": "test_results/refine_output_one/phab_bench", "includebed": "/tmp/r6w1i688.bed", "extend": 0, "debug": false, "reference": null, "refdist": 500, "pctseq": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "chunksize": 1000, "bSample": "syndip", "cSample": "p:HG002", "dup_to_ins": false, "sizemin": 5, "sizefilt": 5, "sizemax": 50000, "passonly": false, "no_ref": "a", "pick": "single"} \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/phab_bench/fn.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab_bench/phab_bench/fn.vcf.gz new file mode 100644 index 00000000..ac21f8d9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab_bench/phab_bench/fn.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/phab_bench/fn.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab_bench/phab_bench/fn.vcf.gz.tbi new file mode 100644 index 00000000..67bd5499 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab_bench/phab_bench/fn.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/phab_bench/fp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab_bench/phab_bench/fp.vcf.gz new file mode 100644 index 00000000..dd019151 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab_bench/phab_bench/fp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/phab_bench/fp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab_bench/phab_bench/fp.vcf.gz.tbi new file mode 100644 index 00000000..ba98850f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab_bench/phab_bench/fp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/phab_bench/params.json b/repo_utils/answer_key/refine/refine_output_one/phab_bench/phab_bench/params.json new file mode 100644 index 00000000..0cbf4b82 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab_bench/phab_bench/params.json @@ -0,0 +1 @@ +{"base": "test_results/refine_output_one/phab.output.vcf.gz", "comp": "test_results/refine_output_one/phab.output.vcf.gz", "output": "test_results/refine_output_one/phab_bench", "includebed": "/tmp/q0h1fc4a.bed", "extend": 0, "debug": false, "reference": null, "refdist": 500, "pctseq": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "chunksize": 1000, "bSample": "syndip", "cSample": "p:HG002", "dup_to_ins": false, "sizemin": 5, "sizefilt": 5, "sizemax": 50000, "passonly": false, "no_ref": "a", "pick": "single"} \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/phab_bench/summary.json b/repo_utils/answer_key/refine/refine_output_one/phab_bench/phab_bench/summary.json new file mode 100644 index 00000000..f526e62c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab_bench/phab_bench/summary.json @@ -0,0 +1,28 @@ +{ + "TP-base": 386, + "TP-comp": 386, + "FP": 15, + "FN": 2, + "precision": 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files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab_bench/phab_bench/tp-base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/phab_bench/tp-comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab_bench/phab_bench/tp-comp.vcf.gz new file mode 100644 index 00000000..2909054d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab_bench/phab_bench/tp-comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/phab_bench/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab_bench/phab_bench/tp-comp.vcf.gz.tbi new file mode 100644 index 00000000..f7b1ae10 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab_bench/phab_bench/tp-comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/summary.json b/repo_utils/answer_key/refine/refine_output_one/phab_bench/summary.json new file mode 100644 index 00000000..6b821bdf --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/phab_bench/summary.json @@ -0,0 +1,27 @@ +{ + "TP-base": 380, + "TP-comp": 380, + "FP": 15, + "FN": 2, + "precision": 0.9620253164556962, + "recall": 0.9947643979057592, + "f1": 0.9781209781209782, + "base cnt": 382, + "comp cnt": 395, + "TP-comp_TP-gt": 380, + "TP-comp_FP-gt": 0, + "TP-base_TP-gt": 380, + "TP-base_FP-gt": 0, + "gt_concordance": 1.0, + "gt_matrix": { + "(0, 1)": { + "(1, 0)": 146 + }, + "(1, 0)": { + "(0, 1)": 184 + }, + "(1, 1)": { + "(1, 1)": 50 + } + } +} \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-base.vcf.gz new file mode 100644 index 00000000..6e1b7b0d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-base.vcf.gz.tbi new file mode 100644 index 00000000..1adf0ecc Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-comp.vcf.gz new file mode 100644 index 00000000..fecb99d7 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-comp.vcf.gz.tbi new file mode 100644 index 00000000..2cc487c4 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/refine.region_summary.json b/repo_utils/answer_key/refine/refine_output_one/refine.region_summary.json new file mode 100644 index 00000000..62264fdd --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/refine.region_summary.json @@ -0,0 +1,18 @@ +{ + "TP": 197, + "TN": 15, + "FP": 11, + "FN": 2, + "base P": 201, + "base N": 24, + "comp P": 210, + "comp N": 15, + "PPV": 0.9380952380952381, + "TPR": 0.9800995024875622, + "TNR": 0.625, + "NPV": 1.0, + "ACC": 0.9422222222222222, + "BA": 0.8025497512437811, + "F1": 0.9586374695863747, + "UND": 0 +} \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_one/refine.regions.txt b/repo_utils/answer_key/refine/refine_output_one/refine.regions.txt new file mode 100644 index 00000000..9afda13e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/refine.regions.txt @@ -0,0 +1,226 @@ +chrom start end in_tpbase in_tp in_fn in_fp refined out_tpbase out_tp out_fn out_fp state +chr20 29401872 29402284 0 0 0 0 False 0 0 0 0 TN +chr20 64065853 64066012 0 0 0 1 True 0 0 0 1 FP +chr20 38194533 38194667 2 2 0 0 False 2 2 0 0 TP +chr20 17081216 17081411 2 2 1 0 True 2 2 0 0 TP +chr20 55532159 55533379 1 1 0 0 False 1 1 0 0 TP +chr20 44763896 44764286 2 2 1 0 True 2 2 0 0 TP +chr20 63535674 63536246 1 1 2 0 True 1 1 0 0 TP +chr20 23942431 23942956 1 1 0 0 False 1 1 0 0 TP +chr20 25067059 25068113 3 3 0 0 False 3 3 0 0 TP +chr20 1149807 1150221 2 2 0 0 False 2 2 0 0 TP +chr20 24836081 24836385 2 2 0 0 False 2 2 0 0 TP +chr20 38462931 38464784 2 2 2 0 True 4 4 0 0 TP +chr20 56710555 56711194 2 2 0 0 False 2 2 0 0 TP +chr20 61331528 61331754 2 2 0 0 False 2 2 0 0 TP +chr20 1257933 1260529 2 2 0 0 False 2 2 0 0 TP +chr20 22882702 22882831 2 2 0 0 False 2 2 0 0 TP +chr20 53415642 53415861 2 2 0 0 False 2 2 0 0 TP +chr20 25781636 25781927 0 0 0 1 True 0 0 0 1 FP +chr20 5041857 5042710 1 1 1 1 True 2 2 0 1 FP +chr20 61282506 61283670 4 4 2 0 True 6 6 0 0 TP +chr20 53203987 53204474 2 2 2 1 True 4 4 0 0 TP +chr20 61919676 61921375 2 2 0 0 False 2 2 0 0 TP +chr20 62830612 62830839 2 2 1 1 True 2 2 0 0 TP +chr20 63049033 63049413 3 3 1 0 True 2 2 0 0 TP +chr20 30404513 30406202 0 0 0 0 False 0 0 0 0 TN +chr20 61201683 61202475 2 2 4 1 True 8 8 0 0 TP +chr20 51952483 51954893 0 0 0 1 True 0 0 0 1 FP +chr20 20458640 20458938 2 2 0 0 False 2 2 0 0 TP +chr20 48811479 48811776 1 1 0 0 False 1 1 0 0 TP +chr20 51061050 51061259 2 2 0 0 False 2 2 0 0 TP +chr20 64090704 64091390 0 0 0 2 True 0 0 0 2 FP +chr20 63028876 63029403 2 2 0 1 True 2 2 0 0 TP +chr20 61475406 61475727 2 2 0 0 False 2 2 0 0 TP +chr20 63167387 63167628 2 2 1 0 True 3 3 0 0 TP +chr20 21120212 21120540 2 2 1 0 True 1 1 0 0 TP +chr20 64096658 64097165 0 0 0 2 True 0 0 0 1 FP +chr20 709729 709976 2 2 0 0 False 2 2 0 0 TP +chr20 45773743 45774080 1 1 0 0 False 1 1 0 0 TP +chr20 61337205 61337591 2 2 0 0 False 2 2 0 0 TP +chr20 14861937 14862742 5 5 5 1 True 15 15 0 0 TP +chr20 63553294 63553758 1 1 0 0 False 1 1 0 0 TP +chr20 23560883 23561192 1 1 2 2 True 3 3 0 0 TP +chr20 20337200 20337708 1 1 6 2 True 3 3 0 0 TP +chr20 24681988 24682278 2 2 1 0 True 1 1 0 1 FP +chr20 8661911 8662658 1 1 3 1 True 9 9 0 0 TP +chr20 19080758 19080828 0 0 0 0 False 0 0 0 0 TN +chr20 57350808 57350988 1 1 1 0 True 3 3 0 0 TP +chr20 10802676 10802959 1 1 1 0 True 2 2 0 0 TP +chr20 62321031 62321874 2 2 3 0 True 5 5 0 0 TP +chr20 63747282 63747608 2 2 0 0 False 2 2 0 0 TP +chr20 21721174 21721736 2 2 1 0 True 3 3 0 0 TP +chr20 57780734 57781507 2 2 0 0 False 2 2 0 0 TP +chr20 58694862 58695412 2 2 0 0 False 2 2 0 0 TP +chr20 38313618 38315070 3 3 0 0 False 3 3 0 0 TP +chr20 23267965 23268088 2 2 0 0 False 2 2 0 0 TP +chr20 4482585 4482735 2 2 0 0 False 2 2 0 0 TP +chr20 63103249 63103493 1 1 0 0 False 1 1 0 0 TP +chr20 34235750 34236214 0 0 2 1 True 2 2 0 0 TP +chr20 61744188 61744655 2 2 1 0 True 2 2 0 0 TP +chr20 2842574 2842998 2 2 0 0 False 2 2 0 0 TP +chr20 63372065 63372692 2 2 1 0 True 2 2 0 0 TP +chr20 62504279 62504615 2 2 0 0 False 2 2 0 0 TP +chr20 64125109 64127975 3 3 3 0 True 12 12 0 0 TP +chr20 19663366 19663527 2 2 0 0 False 2 2 0 0 TP +chr20 63824631 63825145 2 2 0 0 False 2 2 0 0 TP +chr20 63158183 63158727 2 2 0 0 False 2 2 0 0 TP +chr20 50775544 50776024 1 1 2 1 True 4 4 0 0 TP +chr20 63546436 63546843 1 1 0 0 False 1 1 0 0 TP +chr20 54690771 54690874 2 2 0 0 False 2 2 0 0 TP +chr20 62825034 62825240 2 2 0 0 False 2 2 0 0 TP +chr20 63068409 63068800 2 2 0 0 False 2 2 0 0 TP +chr20 1301599 1302668 2 2 0 0 False 2 2 0 0 TP +chr20 63294079 63294267 2 2 0 0 False 2 2 0 0 TP +chr20 51890756 51891015 1 1 0 0 False 1 1 0 0 TP +chr20 56280422 56282115 3 3 6 2 True 10 10 0 0 TP +chr20 18675650 18675916 2 2 0 0 False 2 2 0 0 TP +chr20 61723833 61724245 1 1 0 0 False 1 1 0 0 TP +chr20 60600107 60600321 1 1 0 0 False 1 1 0 0 TP +chr20 57974804 57975203 2 2 0 0 False 2 2 0 0 TP +chr20 64201854 64202099 3 3 0 0 False 3 3 0 0 TP +chr20 62270279 62271095 1 1 3 1 True 5 5 0 0 TP +chr20 64173409 64176530 4 4 7 3 True 18 18 0 0 TP +chr20 63491589 63493065 1 1 3 1 True 4 4 0 0 TP +chr20 62622308 62622508 1 1 0 0 False 1 1 0 0 TP +chr20 63948514 63948759 2 2 1 1 True 3 3 0 0 TP +chr20 53913028 53913353 2 2 0 0 False 2 2 0 0 TP +chr20 63693325 63693885 1 1 6 1 True 10 10 0 0 TP +chr20 22081961 22084123 4 4 3 1 True 9 9 0 0 TP +chr20 278900 279187 3 3 1 0 True 4 4 0 0 TP +chr20 2240925 2241727 1 1 5 1 True 7 7 0 0 TP +chr20 46788807 46789531 2 2 0 0 False 2 2 0 0 TP +chr20 48449705 48450462 4 4 2 0 True 6 6 0 0 TP +chr20 17303131 17303610 1 1 0 0 False 1 1 0 0 TP +chr20 49834109 49834559 2 2 1 0 True 3 3 0 0 TP +chr20 18209097 18210728 3 3 2 1 True 5 5 0 0 TP +chr20 63303655 63304859 2 2 0 0 False 2 2 0 0 TP +chr20 63156767 63157326 2 2 0 0 False 2 2 0 0 TP +chr20 16257741 16259346 2 2 2 0 True 4 4 1 0 FN +chr20 61176725 61176975 2 2 0 0 False 2 2 0 0 TP +chr20 7720911 7721004 1 1 1 0 True 1 1 1 0 FN +chr20 50300450 50301562 2 2 0 0 False 2 2 0 0 TP +chr20 45600569 45600747 2 2 2 0 True 2 2 0 0 TP +chr20 58196700 58196937 2 2 0 0 False 2 2 0 0 TP +chr20 22471831 22472130 2 2 0 0 False 2 2 0 0 TP +chr20 40982703 40982943 2 2 0 0 False 2 2 0 0 TP +chr20 62417424 62418063 3 3 0 0 False 3 3 0 0 TP +chr20 63226486 63226653 1 1 0 0 False 1 1 0 0 TP +chr20 57090672 57091412 1 1 2 0 True 4 4 0 0 TP +chr20 41196210 41196649 3 3 1 0 True 4 4 0 0 TP +chr20 7719330 7719415 1 1 0 0 False 1 1 0 0 TP +chr20 56284258 56284408 2 2 0 0 False 2 2 0 0 TP +chr20 63221480 63221877 1 1 2 1 True 2 2 0 0 TP +chr20 24982027 24982424 1 1 0 0 False 1 1 0 0 TP +chr20 63450491 63450614 2 2 0 0 False 2 2 0 0 TP +chr20 29799755 29799979 0 0 0 0 False 0 0 0 0 TN +chr20 62975788 62976225 1 1 0 0 False 1 1 0 0 TP +chr20 13848164 13848650 3 3 1 0 True 3 3 0 0 TP +chr20 59383804 59385236 3 3 2 0 True 4 4 0 0 TP +chr20 62422444 62422792 2 2 0 0 False 2 2 0 0 TP +chr20 24956961 24957199 2 2 0 0 False 2 2 0 0 TP +chr20 38895736 38896616 1 1 0 0 False 1 1 0 0 TP +chr20 63770912 63771104 0 0 0 2 True 0 0 0 2 FP +chr20 32724927 32725000 0 0 0 0 False 0 0 0 0 TN +chr20 59442036 59442274 2 2 0 0 False 2 2 0 0 TP +chr20 32723469 32724638 0 0 0 0 False 0 0 0 0 TN +chr20 25561369 25562322 2 2 0 0 False 2 2 0 0 TP +chr20 57189946 57190541 0 0 3 1 True 1 1 0 0 TP +chr20 63234103 63234417 1 1 0 0 False 1 1 0 0 TP +chr20 62317837 62318460 2 2 0 0 False 2 2 0 0 TP +chr20 36642142 36642223 1 1 0 0 False 1 1 0 0 TP +chr20 57417271 57418235 2 2 0 0 False 2 2 0 0 TP +chr20 63027997 63028167 2 2 1 0 True 4 4 0 0 TP +chr20 63220180 63220560 1 1 0 0 False 1 1 0 0 TP +chr20 57948798 57949491 1 1 4 1 True 5 5 0 0 TP +chr20 63235329 63235451 2 2 0 0 False 2 2 0 0 TP +chr20 63401702 63402320 1 1 0 0 False 1 1 0 0 TP +chr20 63879305 63880535 1 1 0 0 False 1 1 0 0 TP +chr20 64157894 64158977 2 2 0 0 False 2 2 0 0 TP +chr20 63250583 63250645 0 0 0 0 False 0 0 0 0 TN +chr20 63853670 63854027 1 1 0 0 False 1 1 0 0 TP +chr20 34205619 34205961 1 1 0 0 False 1 1 0 0 TP +chr20 62057573 62059140 1 1 3 1 True 7 7 0 0 TP +chr20 64011722 64013002 2 2 0 0 False 2 2 0 0 TP +chr20 35539120 35539725 4 4 1 0 True 4 4 0 0 TP +chr20 63486763 63487417 2 2 0 0 False 2 2 0 0 TP +chr20 57110212 57110786 2 2 1 0 True 2 2 0 0 TP +chr20 55943919 55945808 2 2 2 1 True 5 5 0 0 TP +chr20 9188445 9189563 2 2 0 0 False 2 2 0 0 TP +chr20 61045927 61046288 1 1 0 0 False 1 1 0 0 TP +chr20 7435215 7435750 2 2 0 0 False 2 2 0 0 TP +chr20 61229587 61229718 2 2 0 0 False 2 2 0 0 TP +chr20 63964768 63966618 1 1 1 0 True 1 1 0 0 TP +chr20 41278322 41278385 0 0 0 0 False 0 0 0 0 TN +chr20 64233048 64233546 2 2 0 0 False 2 2 0 0 TP +chr20 62212844 62213875 4 4 0 0 False 4 4 0 0 TP +chr20 63641779 63642136 1 1 2 1 True 2 2 0 0 TP +chr20 17197123 17197242 2 2 0 0 False 2 2 0 0 TP +chr20 55624482 55625808 6 6 6 0 True 11 11 0 0 TP +chr20 61329258 61329578 0 0 0 2 True 0 0 0 2 FP +chr20 41278746 41278816 0 0 0 0 False 0 0 0 0 TN +chr20 51500592 51500881 2 2 0 0 False 2 2 0 0 TP +chr20 61399095 61399169 0 0 0 0 False 0 0 0 0 TN +chr20 61289625 61290556 1 1 2 1 True 2 2 0 0 TP +chr20 64134883 64136387 3 3 1 0 True 4 4 0 0 TP +chr20 9015548 9016040 1 1 0 0 False 1 1 0 0 TP +chr20 60702942 60703116 2 2 2 1 True 3 3 0 0 TP +chr20 23155504 23155976 3 3 2 2 True 5 5 0 0 TP +chr20 420555 420771 2 2 0 0 False 2 2 0 0 TP +chr20 24407983 24408998 3 3 1 0 True 2 2 0 0 TP +chr20 61653427 61654068 1 1 0 0 False 1 1 0 0 TP +chr20 55627344 55628451 7 7 4 0 True 8 8 0 0 TP +chr20 32722424 32723213 0 0 1 0 True 0 0 0 0 TN +chr20 16395149 16395422 3 3 1 0 True 3 3 0 0 TP +chr20 48959359 48959653 2 2 0 0 False 2 2 0 0 TP +chr20 20295955 20296566 2 2 2 1 True 3 3 0 0 TP +chr20 64042716 64043062 1 1 0 0 False 1 1 0 0 TP +chr20 61561920 61562504 0 0 2 1 True 2 2 0 0 TP +chr20 2442966 2443944 2 2 0 0 False 2 2 0 0 TP +chr20 60314330 60315021 2 2 2 0 True 6 6 0 0 TP +chr20 50258450 50258552 2 2 0 0 False 2 2 0 0 TP +chr20 58309423 58309813 1 1 0 0 False 1 1 0 0 TP +chr20 62360190 62360713 0 0 8 2 True 5 5 0 0 TP +chr20 52526077 52526295 1 1 0 0 False 1 1 0 0 TP +chr20 16226954 16228488 3 3 0 0 False 3 3 0 0 TP +chr20 35580013 35580887 1 1 2 1 True 7 7 0 0 TP +chr20 20320285 20320580 1 1 2 1 True 1 1 0 0 TP +chr20 60087391 60087966 2 2 0 0 False 2 2 0 0 TP +chr20 641836 642466 3 3 2 0 True 5 5 0 0 TP +chr20 63392592 63392813 1 1 0 0 False 1 1 0 0 TP +chr20 58519902 58520373 2 2 0 0 False 2 2 0 0 TP +chr20 60764031 60764635 2 2 0 0 False 2 2 0 0 TP +chr20 63731238 63731792 1 1 0 0 False 1 1 0 0 TP +chr20 37361752 37362059 2 2 1 0 True 2 2 0 0 TP +chr20 10977797 10977978 2 2 0 0 False 2 2 0 0 TP +chr20 14485671 14485749 0 0 0 0 False 0 0 0 0 TN +chr20 63361274 63361472 2 2 0 0 False 2 2 0 0 TP +chr20 4844738 4844907 2 2 0 0 False 2 2 0 0 TP +chr20 5039949 5040500 0 0 0 2 True 0 0 0 2 FP +chr20 41257574 41258204 0 0 0 1 True 0 0 0 1 FP +chr20 63669579 63670497 2 2 0 0 False 2 2 0 0 TP +chr20 61100792 61102688 1 1 4 1 True 3 3 0 0 TP +chr20 63154585 63154996 1 1 1 0 True 2 2 0 0 TP +chr20 5554104 5554186 0 0 0 0 False 0 0 0 0 TN +chr20 61783403 61784840 3 3 1 0 True 4 4 0 0 TP +chr20 64131804 64133956 5 5 8 1 True 26 26 0 0 TP +chr20 50853639 50853929 2 2 0 0 False 2 2 0 0 TP +chr20 63334892 63335505 2 2 0 0 False 2 2 0 0 TP +chr20 4811159 4811230 1 1 0 0 False 1 1 0 0 TP +chr20 50666148 50666894 2 2 0 0 False 2 2 0 0 TP +chr20 7721059 7721320 0 0 0 0 False 0 0 0 0 TN +chr20 62349612 62349933 1 1 5 1 True 6 6 0 0 TP +chr20 47225524 47225646 2 2 0 0 False 2 2 0 0 TP +chr20 48390898 48391232 2 2 0 0 False 2 2 0 0 TP +chr20 51651107 51651510 3 3 0 0 False 3 3 0 0 TP +chr20 31689079 31689528 2 2 0 0 False 2 2 0 0 TP +chr20 47894414 47899006 3 3 0 0 False 3 3 0 0 TP +chr20 62875172 62875557 2 2 3 0 True 3 3 0 0 TP +chr20 63559288 63559964 1 1 4 1 True 4 4 0 0 TP +chr20 63793629 63793788 1 1 0 0 False 1 1 0 0 TP +chr20 16894360 16894436 1 1 0 0 False 1 1 0 0 TP +chr20 62986310 62986806 2 2 0 0 False 2 2 0 0 TP +chr20 38123590 38124706 2 2 1 4 True 7 7 0 0 TP +chr20 4032219 4033602 2 2 2 1 True 4 4 0 0 TP +chr20 5962327 5962411 0 0 0 0 False 0 0 0 0 TN +chr20 20354570 20358324 7 7 9 1 True 14 14 0 0 TP diff --git a/repo_utils/answer_key/refine/refine_output_one/refine.variant_summary.json b/repo_utils/answer_key/refine/refine_output_one/refine.variant_summary.json new file mode 100644 index 00000000..5fe37b92 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/refine.variant_summary.json @@ -0,0 +1,17 @@ +{ + "TP-base": 598, + "TP-comp": 598, + "FP": 15, + "FN": 2, + "precision": 0.9755301794453507, + "recall": 0.9966666666666667, + "f1": 0.9859851607584501, + "base cnt": 600, + "comp cnt": 613, + "TP-comp_TP-gt": 0, + "TP-comp_FP-gt": 0, + "TP-base_TP-gt": 0, + "TP-base_FP-gt": 0, + "gt_concordance": 0, + "gt_matrix": {} +} \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_one/summary.json b/repo_utils/answer_key/refine/refine_output_one/summary.json new file mode 100644 index 00000000..5e91bbcb --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_one/summary.json @@ -0,0 +1,32 @@ +{ + "TP-base": 386, + "TP-comp": 386, + "FP": 65, + "FN": 201, + "precision": 0.8558758314855875, + "recall": 0.6575809199318569, + "f1": 0.7437379576107899, + "base cnt": 587, + "comp cnt": 451, + "TP-comp_TP-gt": 381, + "TP-comp_FP-gt": 5, + "TP-base_TP-gt": 381, + "TP-base_FP-gt": 5, + "gt_concordance": 0.9870466321243523, + "gt_matrix": { + "(1, 0)": { + "(0, 1)": 202, + "(1, 0)": 14, + "(1, 1)": 1 + }, + "(0, 1)": { + "(1, 0)": 144, + "(0, 1)": 12 + }, + "(1, 1)": { + "(1, 1)": 9, + "(1, 0)": 2, + "(0, 1)": 2 + } + } +} \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_one/tp-base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/tp-base.vcf.gz new file mode 100644 index 00000000..da7dfb8e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/tp-base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/tp-base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/tp-base.vcf.gz.tbi new file mode 100644 index 00000000..893b883b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/tp-base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/tp-comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/tp-comp.vcf.gz new file mode 100644 index 00000000..54f11a78 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/tp-comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/tp-comp.vcf.gz.tbi new file mode 100644 index 00000000..5cc5c220 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_one/tp-comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/fn.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/fn.vcf.gz new file mode 100644 index 00000000..d3385bcf Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/fn.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/fn.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/fn.vcf.gz.tbi new file mode 100644 index 00000000..e7b65a6a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/fn.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/fp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/fp.vcf.gz new file mode 100644 index 00000000..1fc24349 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/fp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/fp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/fp.vcf.gz.tbi new file mode 100644 index 00000000..eea428cf Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/fp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/log.txt b/repo_utils/answer_key/refine/refine_output_two/log.txt new file mode 100644 index 00000000..77b52b8d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/log.txt @@ -0,0 +1,64 @@ +2023-03-04 00:10:25,303 [INFO] Truvari v4.0.0.dev0+detached +2023-03-04 00:10:25,304 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/refine_data/hg002_base.vcf.gz -c repo_utils/test_files/refine_data/hg002_comp.vcf.gz --includebed repo_utils/test_files/refine_data/h1_hc_tr_hg002.bed -s 5 -o test_results/refine_output_two +2023-03-04 00:10:25,305 [INFO] Params: +{ + "base": "/data/repo_utils/test_files/refine_data/hg002_base.vcf.gz", + "comp": "/data/repo_utils/test_files/refine_data/hg002_comp.vcf.gz", + "output": "test_results/refine_output_two", + "includebed": "/data/repo_utils/test_files/refine_data/h1_hc_tr_hg002.bed", + "extend": 0, + "debug": false, + "reference": null, + "refdist": 500, + "pctseq": 0.7, + "minhaplen": 50, + "pctsize": 0.7, + "pctovl": 0.0, + "typeignore": false, + "chunksize": 1000, + "bSample": "syndip", + "cSample": "HG002", + "dup_to_ins": false, + "sizemin": 5, + "sizefilt": 5, + "sizemax": 50000, + "passonly": false, + "no_ref": false, + "pick": "single" +} +2023-03-04 00:10:25,376 [INFO] Including 225 bed regions +2023-03-04 00:10:26,816 [INFO] Zipped 7158 variants Counter({'comp': 5303, 'base': 1855}) +2023-03-04 00:10:26,817 [INFO] 212 chunks of 7158 variants Counter({'__filtered': 6120, 'base': 587, 'comp': 451}) +2023-03-04 00:10:26,987 [INFO] Stats: { + "TP-base": 386, + "TP-comp": 386, + "FP": 65, + "FN": 201, + "precision": 0.8558758314855875, + "recall": 0.6575809199318569, + "f1": 0.7437379576107899, + "base cnt": 587, + "comp cnt": 451, + "TP-comp_TP-gt": 381, + "TP-comp_FP-gt": 5, + "TP-base_TP-gt": 381, + "TP-base_FP-gt": 5, + "gt_concordance": 0.9870466321243523, + "gt_matrix": { + "(1, 0)": { + "(0, 1)": 202, + "(1, 0)": 14, + "(1, 1)": 1 + }, + "(0, 1)": { + "(1, 0)": 144, + "(0, 1)": 12 + }, + "(1, 1)": { + "(1, 1)": 9, + "(1, 0)": 2, + "(0, 1)": 2 + } + } +} +2023-03-04 00:10:26,987 [INFO] Finished bench diff --git a/repo_utils/answer_key/refine/refine_output_two/params.json b/repo_utils/answer_key/refine/refine_output_two/params.json new file mode 100644 index 00000000..f2b33015 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/params.json @@ -0,0 +1 @@ +{"base": "/data/repo_utils/test_files/refine_data/hg002_base.vcf.gz", "comp": "/data/repo_utils/test_files/refine_data/hg002_comp.vcf.gz", "output": "test_results/refine_output_two", "includebed": "/data/repo_utils/test_files/refine_data/h1_hc_tr_hg002.bed", "extend": 0, "debug": false, "reference": null, "refdist": 500, "pctseq": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "chunksize": 1000, "bSample": "syndip", "cSample": "HG002", "dup_to_ins": false, "sizemin": 5, "sizefilt": 5, "sizemax": 50000, "passonly": false, "no_ref": false, "pick": "single"} \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_two/phab.output.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab.output.vcf.gz new file mode 100644 index 00000000..b31d20ca Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab.output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab.output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab.output.vcf.gz.tbi new file mode 100644 index 00000000..665a4db4 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab.output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/base.vcf.gz new file mode 100644 index 00000000..9c596fdb Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/base.vcf.gz.tbi new file mode 100644 index 00000000..96900b14 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/comp.vcf.gz new file mode 100644 index 00000000..e2030ab3 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/comp.vcf.gz.tbi new file mode 100644 index 00000000..cf351cd5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/haps.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/haps.fa new file mode 100644 index 00000000..e4dd3885 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/haps.fa @@ -0,0 +1,110 @@ +>ref_chr20_14861837_14862842 +GCTCTCCTGCTGCTGGCCAAGCAGGACCCCAAGGTCCACTGGGATGTACATACTTATGGTATTATGCTCTGCAATACTTGTGGGGGCTGTGGAATGCACACTTCCAAAGTGAAATAGGACATTGGAGGTTTTATATATAAATATATATATATATATTTATATATATATTTATATATATATATTTATATATATTTATATATATTTATATATATATTTATATATATATAAATATATATAAATATATAAATATATATAAATATATATTTATACATAAATATATAAATATATAATATATATAAATATATATTATACATAAATATATAAATATATATAAATATATATAAATATATATTTATACATAAATATATAAATATATATATATATAAATATATATAAATATATATTTATATATTAATATATATAAATATATTACTATGTATATTTATATATATTTATATAAATATATATAAATATATGTAAATATATATATAAAAATATATATTAATATATAAAAATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATAAATATAAATATATATAAATATATAAAAATATATATATAAATATAAATATATATAAATATATATGTATAAATATATATATAAATATAAATATATATAAATATATATATATAAATATATATATAAATATATATATATAAATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATATATTTTTTTTTAATAGAGAGGATGAAGACCAAAGCAGTGAGTTCCACCTAAGCTGGCCCTTGCCTTTTGTCTAACAGGAAACCCAGTCCTTCCTAATGGGCACAGAATTTTCAGAGAAGAGAGCAGAAG +>syndip_1_chr20:14861837-14862842 +GCTCTCCTGCTGCTGGCCAAGCAGGACCCCAAGGTCCACTGGGATGTACATACTTATGGT +ATTATGCTCTGCAATACTTGTGGGGGCTGTGGAATGCACACTTCCAAAGTGAAATAGGAC +ATTGGAGGTTTTATATATAAATATATATATATATATTTATATATATATTTATATATATAT +ATTTATATATATTTATATATATTTATATATATATTTATATATATATTTATATATATATTT +ATATATATATTTATATATATATTTATATATATATTTATATATATATTTATATATATTTAT +ATATATTTATATATATTTTTATATATTTTTATATATATAAATATATAAAAATATATATAA +ATATATAAAAATATATAAAAATATATAAATATATATAAATATATAAATATATATAAATAT +ATATAAATATATATTTATATATAAATATATATAAATATATATTTATACATAAATATATAT +AAATATATATTTATACATAAATATATAAATATATATAATATATATAAATATATATTATAC +ATATATATATAAATATATATTATACATAAATATATAAATATATATAAATATATATAAATA +TATATTTATACATAAATATATAAATATATATATAAATATATATAAATATATATAAATATA +TATATAAATATATATATAAATATATATAAATATATATATAAATATATATATAAATATATA +TAAATATATATAAATATATATATAAATATATATAAATATATATAAATATATATTTATATA +TTAATATATAAATATATATAAATATATATTTATATATTAATATATAAATATATATATATT +AATATATATAAATATATATAAATATATATTTATATATTAATATATATATATTAATATATA +TATATTTATATATTAATATATATATTTATATATTAATATATATAAATATATTACTATGTA +TATTTATATATATTTATATAAATATATATAAATATATGTAAATATATATATAAAAATATA +TATTAATATATAAAAATATATATATAAATATATATAAATATATATATAAATATATATAAA +TATATATATATAAATATATATAAATAAATATATAAATATATATAAATATATATATAAATA +TATATAAATATATATAAATATATATAAAAATATATATAAATATATATATAAATATATATA +AATATATATATAAATATATATATAAATATATATATAAATATATATAAATATATATATAAA +TATATATAAATATATATATAATTATATATAAATATATATAAATATATATAAATATATATA +TAAATATATATAAATATATATAAATATATATAAATATATATATAAATATATATAAATATA +TATATATAAATATATATAAATATATATATAAATATATATAAATATATATATAAATATAAA +TATATATAAATATATAAAAATATATATATAAATATAAATATATATAAATATATATGTATA +AATATATATATAAATATAAATATATATATATAAATATATATATAAATATATATATATAAA +TATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATATATT +TTTTTTTAATAGAGAGGATGAAGACCAAAGCAGTGAGTTCCACCTAAGCTGGCCCTTGCC +TTTTGTCTAACAGGAAACCCAGTCCTTCCTAATGGGCACAGAATTTTCAGAGAAGAGAGC +AGAAG +>syndip_2_chr20:14861837-14862842 +GCTCTCCTGCTGCTGGCCAAGCAGGACCCCAAGGTCCACTGGGATGTACATACTTATGGT +ATTATGCTCTGCAATACTTGTGGGGGCTGTGGAATGCACACTTCCAAAGTGAAATAGGAC +ATTGGAGGTTTTATATATAAATATATATATATATATTTATATATATATTTATATATATAT +ATTTATATATATTTATATATATTTATATATATATTTATATATATATTTATATATATTTAT +ATATTTATATATATTTATATATATTTTTATATATATAAATATATAAAAATATATAAATAT +ATATAAATATATAAATATATATAAATATATATTTATACATAAATATATAAATATATATAA +TATATATAAATATATATTATACATATATATATAAATATATATTATACATAAATATATAAA +TATATATAAATATATATAAATATATATTTATACATAAATATATAAATATATATATATATA +AATATATATAAATATATATTTATATATTAATATATATAAATATATTACTATGTATATTTA +TATATATTTATATAAATATATATAAATATATGTAAATATATATATAAAAATATATATTAA +TATATAAAAATATATATATAAATATATATATAAATATATATAAATAAATATATATAAATA +TATATATAAATATATATAAATATATATAAATATATATATAAATATATATAAATATATATA +AATATATATATAAATATATATATAAATATATATAAATATATATAAATAAATATATAAATA +TATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATAAATATA +TATAAATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATA +TAAATATATATAAATATATATATAAATATATATAAATATATATATAAATATAAATATATA +TAAATATATAAAAATATATATATAAATATAAATATATATAAATATATATGTATAAATATA +TATATAAATATAAATATATATAAATATATATATATAAATATATATATAAATATATATAAA +TATATATAAAAATATATATAAATATATATATAAATATATATATAAATATATATAAATATA +TATATAAATATATATAAATATATATATATATATTTTTTTTTAATAGAGAGGATGAAGACC +AAAGCAGTGAGTTCCACCTAAGCTGGCCCTTGCCTTTTGTCTAACAGGAAACCCAGTCCT +TCCTAATGGGCACAGAATTTTCAGAGAAGAGAGCAGAAG +>p:HG002_1_chr20:14861837-14862842 +GCTCTCCTGCTGCTGGCCAAGCAGGACCCCAAGGTCCACTGGGATGTACATACTTATGGT +ATTATGCTCTGCAATACTTGTGGGGGCTGTGGAATGCACACTTCCAAAGTGAAATAGGAC +ATTGGAGGTTTTATATATAAATATATATATATATATTTATATATATATTTATATATATAT +ATTTATATATATTTATATATATTTATATATATATTTATATATATATTTATATATATTTAT +ATATTTATATATATTTATATATATTTTTATATATATAAATATATAAAAATATATAAATAT +ATATAAATATATAAATATATATAAATATATATTTATACATAAATATATAAATATATATAA +TATATATAAATATATATTATACATATATATATAAATATATATTATACATAAATATATAAA +TATATATAAATATATATAAATATATATTTATACATAAATATATAAATATATATATATATA +AATATATATAAATATATATTTATATATTAATATATATAAATATATTACTATGTATATTTA +TATATATTTATATAAATATATATAAATATATGTAAATATATATATAAAAATATATATTAA +TATATAAAAATATATATATAAATATATATAAATATATATATAAATAAATATATATAAATA +TATATATAAATATATATAAATATATATAAATATATATATAAATATATATAAATATATATA +AATATATATATAAATATATATATAAATATATATAAATATATATAAATAAATATATAAATA +TATATATAAATATATATAAATATATATATAAATATATAAATATATATATATAAATATATA +TAAATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATA +AATATATATAAATATATATATAAATATATATAAATATATATATAAATATAAATATATATA +AATATATAAAAATATATATATAAATATAAATATATATAAATATATATGTATAAATATATA +TATAAATATAAATATATATAAATATATATATATAAATATATATATAAATATATATAAATA +TATATAAAAATATATATAAATATATATATAAATATATATATAAATATATATAAATATATA +TATAAATATATATAAATATATATATATATATTTTTTTTTAATAGAGAGGATGAAGACCAA +AGCAGTGAGTTCCACCTAAGCTGGCCCTTGCCTTTTGTCTAACAGGAAACCCAGTCCTTC +CTAATGGGCACAGAATTTTCAGAGAAGAGAGCAGAAG +>p:HG002_2_chr20:14861837-14862842 +GCTCTCCTGCTGCTGGCCAAGCAGGACCCCAAGGTCCACTGGGATGTACATACTTATGGT +ATTATGCTCTGCAATACTTGTGGGGGCTGTGGAATGCACACTTCCAAAGTGAAATAGGAC +ATTGGAGGTTTTATATATAAATATATATATATATATTTATATATATATTTATATATATAT +ATTTATATATATTTATATATATTTATATATATATTTATATATATATAAATATATATAAAT +ATATAAATATATATAAATATATATTTATACATAAATATATAAATATATTTATATATATTT +ATATATATTTATATATATTTTTATATATTTTTATATATATAAATATATAAAAATATATAT +AAATATATAAAAATATATAAAAATATATAAATATATATAAATATATAAATATATATAAAT +ATATATAAATATATATTTATATATAAATATATATAAATATATATTTATACATAAATATAT +ATAAATATATATTTATACATAAATATATAAATATATATAATATATATAAATATATATTAT +ACATAAATATATAAATATATATTATACATAAATATATAAATATATATAAATATATATAAA +TATATATTTATACATAAATATATAAATATATATATAAATATATATAAATATATATAAATA +TATATATAAATATATATATAAATATATATAAATATATATATAAATATATATATAAATATA +TATAAATATATATAAATATATATATAAATATATATAAATATATATAAATATATATTTATA +TATTAATATATAAATATATATAAATATATATTTATATATTAATATATAAATATATATATA +TTAATATATATAAATATATATAAATATATATTTATATATTAATATATATATATTAATATA +TATATATTTATATATTAATATATATATTTATATATTAATATATATAAATATATTACTATG +TATATTTATATATATTTATATAAATATATATAAATATATGTAAATATATATATAAAAATA +TATATTAATATATAAAATATATATAAATATATATTATACATAAATATATAAATATATATA +AATATATATAAATATATATTTATACATAAATATATAAATATATATATATATAAATATATA +TAAATATATATTTATATATTAATATATATAAATATATTACTATGTATATTTATATATATT +TATATAAATATATATAAATATATGTAAATATATATATAAAAATATATATTAATATATAAA +AATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATAAA +TATATATAAATATATATATAAATATATATAAATATATATATAAATATATATAAATATATA +TATATAAATATATATAAATATATATATAAATATATATAAATATATATATAAATATAAATA +TATATAAATATATAAAAATATATATATAAATATAAATATATATAAATATATATGTATAAA +TATATATATAAATATAAATATATATATATAAATATATATATAAATATATATATATAAATA +TATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATATATTTT +TTTTTAATAGAGAGGATGAAGACCAAAGCAGTGAGTTCCACCTAAGCTGGCCCTTGCCTT +TTGTCTAACAGGAAACCCAGTCCTTCCTAATGGGCACAGAATTTTCAGAGAAGAGAGCAG +AAG diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/haps.fa.ref.fa new file mode 100644 index 00000000..235ee6a4 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:14861837-14862842 +GCTCTCCTGCTGCTGGCCAAGCAGGACCCCAAGGTCCACTGGGATGTACATACTTATGGTATTATGCTCTGCAATACTTGTGGGGGCTGTGGAATGCACACTTCCAAAGTGAAATAGGACATTGGAGGTTTTATATATAAATATATATATATATATTTATATATATATTTATATATATATATTTATATATATTTATATATATTTATATATATATTTATATATATATAAATATATATAAATATATAAATATATATAAATATATATTTATACATAAATATATAAATATATAATATATATAAATATATATTATACATAAATATATAAATATATATAAATATATATAAATATATATTTATACATAAATATATAAATATATATATATATAAATATATATAAATATATATTTATATATTAATATATATAAATATATTACTATGTATATTTATATATATTTATATAAATATATATAAATATATGTAAATATATATATAAAAATATATATTAATATATAAAAATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATAAATATAAATATATATAAATATATAAAAATATATATATAAATATAAATATATATAAATATATATGTATAAATATATATATAAATATAAATATATATAAATATATATATATAAATATATATATAAATATATATATATAAATATATATATAAATATATATAAATATATATATAAATATATATAAATATATATATATATATTTTTTTTTAATAGAGAGGATGAAGACCAAAGCAGTGAGTTCCACCTAAGCTGGCCCTTGCCTTTTGTCTAACAGGAAACCCAGTCCTTCCTAATGGGCACAGAATTTTCAGAGAAGAGAGCAGAAG diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/msa.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/msa.fa new file mode 100644 index 00000000..fa6db6c9 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/msa.fa @@ -0,0 +1,155 @@ +>ref_chr20_14861837_14862842 +gctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggt +attatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggac +attggaggttttatatataaatatatatatatatatttatatatatatttatatatatat +atttatatatatttatatatatttatatatatatttatat-------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------atatataaatatatataaatatataaatatat +ataaatatatatttatacataaatatataaatatata----------------------- +----atatatataaatatatattatacataaatatataaatatatataaatatatataaa +tatatatttatacataaatatataaatatat------atatatataaatatatataa--- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------atatatatttatatattaatatatataaatatattactatg +tatatttatatatatttatataaatatatataaatatatgtaaatatatatataaaaata +tatattaatatataaaaatatatatataaatata-------------tataaatatatat +ataaat------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------------------------atat +ataaatatatatatataaatatatataaatatatatataaatatatataaatatatatat +aaatatatataaatat------atatatataaatatatataaatatatatataaatatat +ataaatatat--------atataaatataaatatatataaatatataaaaatatatatat +aaatataaatatatataaatatatatgtataaatatatatataaatataaatatatataa +atatatatatataaatatatatataaat-------------------------------- +atatatatataaatatatatataaatatatataaatatatatataaatatatataaatat +atatatatatatttttttttaatagagaggatgaagaccaaagcagtgagttccacctaa +gctggcccttgccttttgtctaacaggaaacccagtccttcctaatgggcacagaatttt +cagagaagagagcagaag +>syndip_1_chr20:14861837-14862842 +gctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggt +attatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggac +attggaggttttatatataaatatatatatatatatttatatatatatttatatatatat +atttatatatatttatatatatttatatatatatttatatatatat--ttatatatatat +ttatatatatatttatatatatatttatatatatatttatatatatatttatatatattt +atatatatttatatatatttttatatatttttatatatataaatatataaaaatatatat +aaatatataaaaatatataaaaatatataaatatatataaatatataaatatatataaat +atatataaatatatatttatatataaatatatataaatatatatttatacataaatatat +ataaatatatatttatacataaatatataaatatatataatatatataaatatatattat +acatatatatataaatatatattatacataaatatataaatatatataaatatatataaa +tatatatttatacataaatatataaatatatatataaatatatataaatatatataaata 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+atatatatatatttttttttaatagagaggatgaagaccaaagcagtgagttccacctaa +gctggcccttgccttttgtctaacaggaaacccagtccttcctaatgggcacagaatttt +cagagaagagagcagaag +>syndip_2_chr20:14861837-14862842 +gctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggt +attatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggac +attggaggttttatatataaatatatatatatatatttatatatatatttatatatatat +atttatatatatttatatatatttatatatatatttatatatatat--ttatatata--- +-----------------------------------------------------------t +ttatatatttatatatatttatatatatttttatatatataaatatataaaa-------- +------------------------------------------------------------ +----------------------------atatataaatatatataaatatataaatatat +ataaatatatatttatacataaatatataaatatatataatatatataaatatatattat +acatatatatataaatatatattatacataaatatataaatatatataaatatatataaa +tatatatttatacataaatatataaatatat------atatatataaatatatataa--- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------atatatatttatatattaatatatataaatatattactatg +tatatttatatatatttatataaatatatataaatatatgtaaatatatatataaaaata +tatattaatatataaaaatatatatataaatata-------------tatataaatatat +ataaataaatatatataaatatatatataaatatatataaatatatataaatat--atat +ataaatatatataaatatatataaatatatatataaatatatatataaatatatataaat +atatataaataaatatataaatatatatataaatatatataaatatatatataaatatat +ataaatatatatatataaatatatataaatatatatataaatatatataaatatatatat +aaatatatataaatat------atatatataaatatatataaatatatatataaatatat +ataaatatat--------atataaatataaatatatataaatatataaaaatatatatat +aaatataaatatatataaatatatatgtataaatatatatataaatataaatatatataa +atatatatatataaatatatatataaatatatataaatatatataaaaatatatataa-- +atatatatataaatatatatataaatatatataaatatatatataaatatatataaatat +atatatatatatttttttttaatagagaggatgaagaccaaagcagtgagttccacctaa +gctggcccttgccttttgtctaacaggaaacccagtccttcctaatgggcacagaatttt +cagagaagagagcagaag +>p:HG002_1_chr20:14861837-14862842 +gctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggt +attatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggac +attggaggttttatatataaatatatatatatatatttatatatatatttatatatatat +atttatatatatttatatatatttatatatatatttatatatatat--ttatatata--- +-----------------------------------------------------------t +ttatatatttatatatatttatatatatttttatatatataaatatataaaa-------- +------------------------------------------------------------ +----------------------------atatataaatatatataaatatataaatatat +ataaatatatatttatacataaatatataaatatatataatatatataaatatatattat +acatatatatataaatatatattatacataaatatataaatatatataaatatatataaa +tatatatttatacataaatatataaatatat------atatatataaatatatataa--- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------atatatatttatatattaatatatataaatatattactatg +tatatttatatatatttatataaatatatataaatatatgtaaatatatatataaaaata +tatattaatatataaaaatatatatataaatata-------------tataaatatatat +ataaataaatatatataaatatatatataaatatatataaatatatataaatat--atat +ataaatatatataaatatatataaatatatatataaatatatatataaatatatataaat +atatataaataaatatataaatatatatataaatatatataaatatatatataa--atat +ataaatatatatatataaatatatataaatatatatataaatatatataaatatatatat +aaatatatataaatat------atatatataaatatatataaatatatatataaatatat +ataaatatat--------atataaatataaatatatataaatatataaaaatatatatat +aaatataaatatatataaatatatatgtataaatatatatataaatataaatatatataa +atatatatatataaatatatatataaatatatataaatatatataaaaatatatataa-- +atatatatataaatatatatataaatatatataaatatatatataaatatatataaatat +atatatatatatttttttttaatagagaggatgaagaccaaagcagtgagttccacctaa +gctggcccttgccttttgtctaacaggaaacccagtccttcctaatgggcacagaatttt +cagagaagagagcagaag +>p:HG002_2_chr20:14861837-14862842 +gctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggt +attatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggac +attggaggttttatatataaatatatatatatatatttatatatatatttatatatatat +atttatatatatttatatatatttatatatatatttatatatatataaatatatataaat +atataaatatatataaatatatatttatacataaatatataaatatatttatatatattt +atatatatttatatatatttttatatatttttatatatataaatatataaaaatatatat +aaatatataaaaatatataaaaatatataaatatatataaatatataaatatatataaat +atatataaatatatatttatatataaatatatataaatatatatttatacataaatatat +ataaatatatatttatacataaatatataaatatatataatatatataaatatatattat +acataaatatataaatatatattatacataaatatataaatatatataaatatatataaa +tatatatttatacataaatatataaatatatatataaatatatataaatatatataaata +tatatataaatatatatataaatatatataaatatatatataaatatatatataaatata +tataaatatatataaatatatatataaatatatataaatatatataaatatatatttata +tattaatatataaatatatataaatatatatttatatattaatatataaatatatatata +ttaatatatataaatatatataaatatatatttatatattaatatatatatattaatata +tatatatttatatattaatatatatatttatatattaatatatataaatatattactatg +tatatttatatatatttatataaatatatataaatatatgtaaatatatatataaaaata +tatattaatatataaa---atatatataaatatatattatacataaatatataaatatat +ataaatatatataaatatatatttatacataaatatataaatatatatatatataaatat +atataaatatatatttatatattaatatatataaatatattactatgtatatttatatat +atttatataaatatatataaatatatgtaaatatatatataaaaatatatatta--atat +ataaaaatatatatataaatatatataaatatatatataaatatatataaatat------ +atatatataaatatatataaatatatatataaatatatataaatatatatataaatatat +ataaatatatatatataaatatatataaatatatatataaatatatataaatatatatat +aaatataaatatatataaatata----taaaaatatatatataaatataaatatatataa +atatatatgtataaatatatatataaatataaatatatatatataaatatatatataaat +atatatatataaatatatatataaatatatataaatatatatataaatatatataaatat +atatatatatatttttttttaatagagaggatgaagaccaaagcagtgagttccacctaa +gctggcccttgccttttgtctaacaggaaacccagtccttcctaatgggcacagaatttt +cagagaagagagcagaag diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/msa.fa.fai new file mode 100644 index 00000000..d303b4fe --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_14861837_14862842 1758 29 60 61 +syndip_1_chr20:14861837-14862842 1758 1851 60 61 +syndip_2_chr20:14861837-14862842 1758 3673 60 61 +p:HG002_1_chr20:14861837-14862842 1758 5496 60 61 +p:HG002_2_chr20:14861837-14862842 1758 7319 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/output.vcf.gz new file mode 100644 index 00000000..5d7b560d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:14861937-14862742/output.vcf.gz.tbi new 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a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:18209097-18210728/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:18209097-18210728/comp.vcf.gz new file mode 100644 index 00000000..7a0a5f47 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:18209097-18210728/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:18209097-18210728/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:18209097-18210728/comp.vcf.gz.tbi new file mode 100644 index 00000000..0b33bba0 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:18209097-18210728/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:18209097-18210728/haps.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:18209097-18210728/haps.fa new file mode 100644 index 00000000..5c498c19 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:18209097-18210728/haps.fa @@ -0,0 +1,148 @@ +>ref_chr20_18208997_18210828 +GTATTCTTTGTACTGTTTTTATTTTTGCAACTTTTCTGTGTTTACAGTTATTTCCAAATAAAAAATAAGCAGAAAGGAAAAGCTAATCATCTCCCCCTATTCCAGTCCCCCAGGCATGTATCCTTCCGTAGCTTCTCCACACCTACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCATTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTCCACACCCACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCTAGACGATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCAGACCTTCTCCACACCCACACAGACCTAGACGATTCCTTCCACACCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTGTGCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTGCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAAACGATTCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGACAATTCCTTGCACACCTTCTCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGACAATTCCTTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGATGATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCCTAACACCCACACGAACCTAGAGAATTCCTTCCACACCTTCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAAATTCTTATACACTTAAAATGGGATTTTGTTGTTTTATTAAAATGCAGTCATTCTCTATGCATTAATTATTGTGCAGCTTGATTTTTCTCCTTTTTTTTTGTTAAATCTTCCTCCGTCATCCAGGCTGGAGTGCAG +>syndip_1_chr20:18208997-18210828 +GTATTCTTTGTACTGTTTTTATTTTTGCAACTTTTCTGTGTTTACAGTTATTTCCAAATA +AAAAATAAGCAGAAAGGAAAAGCTAATCATCTCCCCCTATTCCAGTCCCCCAGGCATGTA +TCCTTCCGTAGCTTCTCCACACCTACACGAACCTAGACGATTCCTTCCACACCTTCCCCA +CACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGAT +GAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTC +CCCACACCCATTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTCCACACCC +ACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCTAGACGATT +CCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCAGACCTTCTCCA +CACCCACACAGACCTAGACGATTCCTTCCACACCTCCACACCCACACGAACCTAGACGAA +TTCCTTCCACACCTTGTGCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTC +CACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTA +GACGATTCCTTCCACACTTTCCCCACACCCACACGAACCTAGACGATTCCTTCCACACCT +CCACACCCACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCT +AGACGATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAATTCCTTCCACACA +CACATGAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACATGAACCTAGACGAT +TCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCACACCTTCCCC +ACACCCACACAGACCTAGACGAATTCCTTGCACACCTTCTCCACACCCACACGAACCTAG +ACGAATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTCCACACCT +TCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACGAAC +CTAAACGATTCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCAC +ACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACA +CGAACCTAGACGATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTT +CCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCCCCACACCC +ACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACAATT +CCTTGCACACCTTCTCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCTCCAC +ACCCACACAAACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGAC +GATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTC +TCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCT +AGACAATTCCTTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACC +TTCTCCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGA +ACCTAGATGATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCC +ACACCTTCCTAACACCCACACGAACCTAGAGAATTCCTTCCACACCTTCACACCCACACA +AACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAAATTCTTA +TACACTTAAAATGGGATTTTGTTGTTTTATTAAAATGCAGTCATTCTCTATGCATTAATT +ATTGTGCAGCTTGATTTTTCTCCTTTTTTTTTGTTAAATCTTCCTCCGTCATCCAGGCTG +GAGTGCAG +>syndip_2_chr20:18208997-18210828 +GTATTCTTTGTACTGTTTTTATTTTTGCAACTTTTCTGTGTTTACAGTTATTTCCAAATA +AAAAATAAGCAGAAAGGAAAAGCTAATCATCTCCCCCTATTCCAGTCCCCCAGGCATGTA +TCCTTCCGTAGCTTCTCCACACCTACACGAACCTAGACGATTCCTTCCACACCTTCCCCA +CACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGAT +GAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTC +CCCACACCCATTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTCCACACCC +ACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCTAGACGATT +CCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCAGACCTTCTCCA +CACCCACACAGACCTAGACGATTCCTTCCACACCTCCACACCCACACGAACCTAGACGAA +TTCCTTCCACACCTTGTGCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTC +CACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTA +GACGATTCCTTCCACACTTTCCCCACACCCACAAGAACCTAGACGATTCCTTCCACACCT +CCACACCCACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCT +AGACGATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAATTCCTTCCACACA +CACATGAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACATGAACCTAGACGAT +TCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCACACCTTCCCC +ACACCCACACAGACCTAGACGAATTCCTTGCACACCTTCTCCACACCCACACGAACCTAG +ACGAATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTCCACACCT +TCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACGAAC +CTAAACGATTCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCAC +ACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACA +CGAACCTAGACGATTCCTTCCACACCACACGAACCTAGACAATTCCTTCCACACCTTCTC +ACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAGACCTAG +ACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACAATTCCTTGCACACCT +TCTCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACAAAC +CTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGACGATTCCTTCCAC +ACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACA +CGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGACAATTCCTT +CCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCC +ACACAAACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGATGATT +CCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCCTAA +CACCCACACGAACCTAGAGAATTCCTTCCACACCTTCACACCCACACAAACCTAGACGAA +TTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAAATTCTTATACACTTAAAAT +GGGATTTTGTTGTTTTATTAAAATGCAGTCATTCTCTATGCATTAATTATTGTGCAGCTT +GATTTTTCTCCTTTTTTTTTGTTAAATCTTCCTCCGTCATCCAGGCTGGAGTGCAG +>p:HG002_1_chr20:18208997-18210828 +GTATTCTTTGTACTGTTTTTATTTTTGCAACTTTTCTGTGTTTACAGTTATTTCCAAATA +AAAAATAAGCAGAAAGGAAAAGCTAATCATCTCCCCCTATTCCAGTCCCCCAGGCATGTA +TCCTTCCGTAGCTTCTCCACACCTACACGAACCTAGACGATTCCTTCCACACCTTCCCCA +CACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGAT +GAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTC +CCCACACCCATTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTCCACACCC +ACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCTAGACGATT +CCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCAGACCTTCTCCA +CACCCACACAGACCTAGACGATTCCTTCCACACCTCCACACCCACACGAACCTAGACGAA +TTCCTTCCACACCTTGTGCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTC +CACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTA +GACGATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTGCACACC +TTCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCATACCCACACGA +ACCTAGACAATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAATTCCTTCCA +CACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAAA +CGATTCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCACACCTT +CCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAAC +CTAGACGATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTCCACA +CCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACG +AACCTAAACGATTCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTC +CACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCC +ACACGAACCTAGACGATTCCTTCCACACCACACGAACCTAGACAATTCCTTCCACACCTT +CCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACC +TAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGACAATTCCTTGCACAC +CTTCTCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACAA +ACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGACGATTCCTTCC +ACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCA +CACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGACAATTCC +TTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACAC +CCACACAAACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGATGA +TTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCCT +AACACCCACACGAACCTAGAGAATTCCTTCCACACCTTCACACCCACACAAACCTAGACG +AATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAAATTCTTATACACTTAAA +ATGGGATTTTGTTGTTTTATTAAAATGCAGTCATTCTCTATGCATTAATTATTGTGCAGC +TTGATTTTTCTCCTTTTTTTTTGTTAAATCTTCCTCCGTCATCCAGGCTGGAGTGCAG +>p:HG002_2_chr20:18208997-18210828 +GTATTCTTTGTACTGTTTTTATTTTTGCAACTTTTCTGTGTTTACAGTTATTTCCAAATA +AAAAATAAGCAGAAAGGAAAAGCTAATCATCTCCCCCTATTCCAGTCCCCCAGGCATGTA +TCCTTCCGTAGCTTCTCCACACCTACACGAACCTAGACGATTCCTTCCACACCTTCCCCA +CACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGAT +GAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTC +CCCACACCCATTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTCCACACCC +ACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCTAGACGATT +CCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCAGACCTTCTCCA +CACCCACACAGACCTAGACGATTCCTTCCACACCTCCACACCCACACGAACCTAGACGAA +TTCCTTCCACACCTTGTGCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTC +CACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTA +GACGATTCCTTCCACACTTTCCCCACACCCACACGAACCTAGACGATTCCTTCCACACCT +CCACACCCACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCT +AGACGATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAATTCCTTCCACACA +CACATGAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACATGAACCTAGACGAT +TCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTGCACACCTTCTCC +ACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCATACCCACACGAACCTAG +ACAATTCCTTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTT +CTCCACACCCACACGAACCTAAACGATTCCTTCCACACCTTCTCCACACCCACACACACC +TAGATGAATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCAC +ACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCTCCATACCCACAC +GAACCTAGACAATTCCTTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTC +CACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCC +ACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGACAATTC +CTTGCACACCTTCTCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCTCCACA +CCCACACAAACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGACG +ATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCT +CCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTA +GACAATTCCTTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCT +TCTCCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAA +CCTAGATGATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCA +CACCTTCCTAACACCCACACGAACCTAGAGAATTCCTTCCACACCTTCACACCCACACAA +ACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAAATTCTTAT +ACACTTAAAATGGGATTTTGTTGTTTTATTAAAATGCAGTCATTCTCTATGCATTAATTA +TTGTGCAGCTTGATTTTTCTCCTTTTTTTTTGTTAAATCTTCCTCCGTCATCCAGGCTGG +AGTGCAG diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:18209097-18210728/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:18209097-18210728/haps.fa.ref.fa new file mode 100644 index 00000000..48f827cd --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:18209097-18210728/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:18208997-18210828 +GTATTCTTTGTACTGTTTTTATTTTTGCAACTTTTCTGTGTTTACAGTTATTTCCAAATAAAAAATAAGCAGAAAGGAAAAGCTAATCATCTCCCCCTATTCCAGTCCCCCAGGCATGTATCCTTCCGTAGCTTCTCCACACCTACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCATTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTCCACACCCACACGAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAAACCTAGACGATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCAGACCTTCTCCACACCCACACAGACCTAGACGATTCCTTCCACACCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTGTGCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTGCACACCTTCTCCACACCCACACGAACCTAGACGAATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAAACGATTCCTTCCACACCTTCTCCACACCCACACACACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCTCCATACCCACACGAACCTAGACAATTCCTTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGACAATTCCTTGCACACCTTCTCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACGAACCTAGACGATTCCTTCCACACCTTCCCCACACCCACACGAACCTAGACAATTCCTTCCACACCTTCTCACACCCACACAAACCTAGATGAATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCCTCACACCCACACGAACCTAGATGATTCCTTCCACACCTTCCCCACACCCACACAGACCTAGACGAATTCCTTCCACACCTTCCTAACACCCACACGAACCTAGAGAATTCCTTCCACACCTTCACACCCACACAAACCTAGACGAATTCCTTCCACACCTTCTCCACACCCACACAAACCTAGACAAATTCTTATACACTTAAAATGGGATTTTGTTGTTTTATTAAAATGCAGTCATTCTCTATGCATTAATTATTGTGCAGCTTGATTTTTCTCCTTTTTTTTTGTTAAATCTTCCTCCGTCATCCAGGCTGGAGTGCAG diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:18209097-18210728/msa.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:18209097-18210728/msa.fa new file mode 100644 index 00000000..84c385b9 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:18209097-18210728/msa.fa @@ -0,0 +1,185 @@ +>ref_chr20_18208997_18210828 +gtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatttccaaata +aaaaataagcagaaaggaaaagctaatcatctccccctattccagtcccccaggcatgta +tccttccgtagcttctccacacct------------------------------------ +-----acacgaacctagacgattccttccacaccttccccacacccacacgaacctagat +gaattccttccacaccttctccacacccacacgaacctagacgattccttccacaccttc +cccacacccattctccacacccacacgaacctagacgattccttccacacctccacaccc +acacgaacctagatgaattccttccacaccttccccacacccacacaaacctagacgatt +ccttccacaccttctccacacccacacgaacctagacgaattccttccagaccttctcca +cacccacacagacctagacgattccttccacacctccacacccacacgaacctagacgaa +ttccttccacaccttgtgcacacccacacgaacctagacgaattccttccacaccttctc +cacacccacacgaacctagacgaattccttccacaccttctccacacccacacgaaccta +gacgattccttccacaccttccccacacccacacagacctagacgaattccttgcacacc +ttctccacacccacacgaacctagacgaattccttccacaccttctccatacccacacga +acctagacaattccttccacaccttct-------------------------------ca +cacccacacaaacctagatgaattccttccacaccttctccacacccacacgaacctaaa +cgattccttccacaccttctccacacccacacacacctagatgaattccttccacacctt +ccccacacccacacagacctagacgaattccttccacaccttctccacacccacacgaac +ctagacg-attccttccacaccttctccatacccacacgaacctagacaattccttccac +accttctcacacccacacaa---------------------------------------- +-------------------------------------------acctagatgaattcctt +ccacaccttccccacacccacacagacctagacgaattccttccacaccttctccacacc +cacacgaacctagacg-------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +-attccttccacaccttccccacacccacacgaacctagacaattccttgcacaccttct +cacacccacacaaacctagacgaattccttccacaccttctccacacccacacaaaccta +gacgaattccttccacaccttcctcacacccacacgaacctagacgattccttccacacc +ttccccacacccacacagacctagacgaattccttccacaccttctccacacccacacga +acctagacgattccttccacaccttccccacacccacacgaacctagacaattccttcca +caccttctcacacccacacaaacctagatgaattccttccacaccttctccacacccaca +caaacctagacgaattccttccacaccttcctcacacccacacgaacctagatgattcct +tccacaccttccccacacccacacagacctagacgaattccttccacaccttcctaacac +ccacacgaacctagagaattccttccacaccttcacacccacacaaacctagacgaattc +cttccacaccttctccacacccacacaaacctagacaaattcttatacacttaaaatggg +attttgttgttttattaaaatgcagtcattctctatgcattaattattgtgcagcttgat +ttttctcctttttttttgttaaatcttcctccgtcatccaggctggagtgcag +>syndip_1_chr20:18208997-18210828 +gtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatttccaaata +aaaaataagcagaaaggaaaagctaatcatctccccctattccagtcccccaggcatgta +tccttccgtagcttctccacacctacacgaacctagacgattccttccacaccttcccca +cacccacacgaacctagacgattccttccacaccttccccacacccacacgaacctagat +gaattccttccacaccttctccacacccacacgaacctagacgattccttccacaccttc +cccacacccattctccacacccacacgaacctagacgattccttccacacctccacaccc +acacgaacctagatgaattccttccacaccttccccacacccacacaaacctagacgatt +ccttccacaccttctccacacccacacgaacctagacgaattccttccagaccttctcca +cacccacacagacctagacgattccttccacacctccacacccacacgaacctagacgaa +ttccttccacaccttgtgcacacccacacgaacctagacgaattccttccacaccttctc +cacacccacacgaacctagacgaattccttccacaccttctccacacccacacgaaccta +gacgattccttccacactttccccacacccacacgaacctagacg-attccttccacac- +--ctccacacccacacgaacctagatgaattccttccacaccttccccacacccacacaa +acctagacgattccttccacaccttctccacacccacacaaacctagacaattccttcca +cacacacatgaacctagatgaattccttccacaccttctccacacccacatgaacctaga +cgattccttccacaccttctccacacccacacacacctagatgaattccttccacacctt +ccccacacccacacagacctagacgaattccttgcacaccttctccacacccacacgaac +ctagacgaattccttccacaccttctccatacccacacgaacctagacaattccttccac +accttctcacacccacacaaacctagatgaattccttccacaccttctccacacccacac +gaacctaaacgattccttccacaccttctccacacccacacacacctagatgaattcctt +ccacaccttccccacacccacacagacctagacgaattccttccacaccttctccacacc +cacacgaacctagacgattccttccacaccttctccatacccacacgaacctagacaatt +ccttccacaccttctcacacccacacaaacctagatgaattccttccacaccttccccac +acccacacagacctagacga---------------------------------------- +-attccttccacaccttctccacacccacacgaacctagacaattccttgcacaccttct +cacacccacacaaacctagacgaattccttccacaccttctccacacccacacaaaccta +gacgaattccttccacaccttcctcacacccacacgaacctagacgattccttccacacc +ttccccacacccacacagacctagacgaattccttccacaccttctccacacccacacga +acctagacgattccttccacaccttccccacacccacacgaacctagacaattccttcca +caccttctcacacccacacaaacctagatgaattccttccacaccttctccacacccaca +caaacctagacgaattccttccacaccttcctcacacccacacgaacctagatgattcct +tccacaccttccccacacccacacagacctagacgaattccttccacaccttcctaacac +ccacacgaacctagagaattccttccacaccttcacacccacacaaacctagacgaattc +cttccacaccttctccacacccacacaaacctagacaaattcttatacacttaaaatggg +attttgttgttttattaaaatgcagtcattctctatgcattaattattgtgcagcttgat +ttttctcctttttttttgttaaatcttcctccgtcatccaggctggagtgcag +>syndip_2_chr20:18208997-18210828 +gtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatttccaaata +aaaaataagcagaaaggaaaagctaatcatctccccctattccagtcccccaggcatgta +tccttccgtagcttctccacacctacacgaacctagacgattccttccacaccttcccca +cacccacacgaacctagacgattccttccacaccttccccacacccacacgaacctagat +gaattccttccacaccttctccacacccacacgaacctagacgattccttccacaccttc +cccacacccattctccacacccacacgaacctagacgattccttccacacctccacaccc +acacgaacctagatgaattccttccacaccttccccacacccacacaaacctagacgatt +ccttccacaccttctccacacccacacgaacctagacgaattccttccagaccttctcca +cacccacacagacctagacgattccttccacacctccacacccacacgaacctagacgaa +ttccttccacaccttgtgcacacccacacgaacctagacgaattccttccacaccttctc +cacacccacacgaacctagacgaattccttccacaccttctccacacccacacgaaccta +gacgattccttccacactttccccacacccacaagaacctagacg-attccttccacac- +--ctccacacccacacgaacctagatgaattccttccacaccttccccacacccacacaa +acctagacgattccttccacaccttctccacacccacacaaacctagacaattccttcca +cacacacatgaacctagatgaattccttccacaccttctccacacccacatgaacctaga 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a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:18209097-18210728/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:18209097-18210728/msa.fa.fai new file mode 100644 index 00000000..3b7a95ce --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:18209097-18210728/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_18208997_18210828 2153 29 60 61 +syndip_1_chr20:18208997-18210828 2153 2252 60 61 +syndip_2_chr20:18208997-18210828 2153 4475 60 61 +p:HG002_1_chr20:18208997-18210828 2153 6699 60 61 +p:HG002_2_chr20:18208997-18210828 2153 8923 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:18209097-18210728/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:18209097-18210728/output.vcf.gz new file mode 100644 index 00000000..6997065d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:18209097-18210728/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:18209097-18210728/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:18209097-18210728/output.vcf.gz.tbi new file mode 100644 index 00000000..36a63799 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:18209097-18210728/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/base.vcf.gz new file mode 100644 index 00000000..b742512f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/base.vcf.gz.tbi new file mode 100644 index 00000000..87a4c7e6 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/comp.vcf.gz new file mode 100644 index 00000000..3279b421 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/comp.vcf.gz.tbi new file mode 100644 index 00000000..56ea59ce Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/haps.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/haps.fa new file mode 100644 index 00000000..3682baaa --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/haps.fa @@ -0,0 +1,144 @@ +>ref_chr20_20337100_20337808 +TACGTGGAAGCATAGGGAAGGAAGGGATGTTTGTTGAGGGGTGGTGTGATGCAGCAGAGGAAGAGGACCAGAGGAAAGCAGCCACTGGAAATAAGGAAACAGGGTTTAGGAAGGCCTCACTAGACCTGTTAGGATGGATGCATGGATGGATGGATGGATGGACAGAATGGGTGGGTGGATGGATGGATGGATAGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGATGGATAAATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGGTGGATGGATGGATGGATGGATAGATGGGTGGGTGGGTGGATGGATGGATGGATGGATAGAATAAAAAAGAAAGCTAGGACATGGTTCTAGTGTTCTTAGCAGACGTCCCACCATGGAAGAGGTCATGGAGCACAGGGGCTTTGGGAAAGGTGTTTACAATCCTGCCTGCCTCTCACCCAGACCTCTTG +>syndip_1_chr20:20337100-20337808 +TACGTGGAAGCATAGGGAAGGAAGGGATGTTTGTTGAGGGGTGGTGTGATGCAGCAGAGG +AAGAGGACCAGAGGAAAGCAGCCACTGGAAATAAGGAAACAGGGTTTAGGAAGGCCTCAC +TAGACCTGTTAGGATGGATGCATGGATGGATGGATGGATGGACAGAATGGGTGGGTGGAT +GGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGAT +GGGTGGATGGATAGATGGGTGGATGGATAAATGGATGGATGGATGGATGGATAGATGGGT +GGGTAGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGT +GGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGT +GGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATAGATGGGTGGATGGATAAATGGATGGATGGATGGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATAGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGAT +GGGTGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGT +GGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGAT +GGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGT +GGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATAGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +GGATGGATGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGT +GGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGGT +GGATGGATGGATGGATGGATAGAATAAAAAAGAAAGCTAGGACATGGTTCTAGTGTTCTT +AGCAGACGTCCCACCATGGAAGAGGTCATGGAGCACAGGGGCTTTGGGAAAGGTGTTTAC +AATCCTGCCTGCCTCTCACCCAGACCTCTTG +>syndip_2_chr20:20337100-20337808 +TACGTGGAAGCATAGGGAAGGAAGGGATGTTTGTTGAGGGGTGGTGTGATGCAGCAGAGG +AAGAGGACCAGAGGAAAGCAGCCACTGGAAATAAGGAAACAGGGTTTAGGAAGGCCTCAC +TAGACCTGTTAGGATGGATGCATGGATGGATGGATGGATGGACAGAATGGGTGGGTGGAT +GGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGATGGATAAATGGATGGATGGATGGATGGATAGATGGGTGGGTAGATGGAT +GGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGGTGGAT +GGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGT +GGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGGTGGATGGATAAATGGATGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGT +GGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGATGGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGAT +GGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGAT +GGATGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGATAGATGGGT +GGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGAT +GGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGGTGGGTGGGTGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGAT +AGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGAT +GGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGGTGGATGGATGGAT +GGATGGATAGAATAAAAAAGAAAGCTAGGACATGGTTCTAGTGTTCTTAGCAGACGTCCC +ACCATGGAAGAGGTCATGGAGCACAGGGGCTTTGGGAAAGGTGTTTACAATCCTGCCTGC 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+TACGTGGAAGCATAGGGAAGGAAGGGATGTTTGTTGAGGGGTGGTGTGATGCAGCAGAGGAAGAGGACCAGAGGAAAGCAGCCACTGGAAATAAGGAAACAGGGTTTAGGAAGGCCTCACTAGACCTGTTAGGATGGATGCATGGATGGATGGATGGATGGACAGAATGGGTGGGTGGATGGATGGATGGATAGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATAGATGGGTGGATGGATAAATGGATGGATGGATGGATGGATAGATGGGTGGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATGTGGGTGGATGGATGGATGGATAGATGGGTGGGTGGGTGGATGGATGGATGGATGGATAGATGGGTGGGTGGGTGGATGGATGGATGGATGGATAGAATAAAAAAGAAAGCTAGGACATGGTTCTAGTGTTCTTAGCAGACGTCCCACCATGGAAGAGGTCATGGAGCACAGGGGCTTTGGGAAAGGTGTTTACAATCCTGCCTGCCTCTCACCCAGACCTCTTG diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/msa.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/msa.fa new file mode 100644 index 00000000..234cf394 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/msa.fa @@ -0,0 +1,190 @@ +>ref_chr20_20337100_20337808 +tacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagagg +aagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctcac +tagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtggat +ggatggatggatagatggatggatggatggatggatggatggatggatggatggatggat +agatgggtgggtgggtggatggatggatggatggatggatggatggatggatgga----t +ggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggat +ggatggatagatgggtgggtggatggatggatggatagatgggtggatggataaatggat +ggatggatggatggatagatgggtgggtggatggatggatggatggatggatggatggat +ggatagat----------------------gtgggtggatggatggatggatagatgggt +gggtgggtggatggatggatggatggatagatgggtgggtgggtggatggatggatggat +gg---------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------atagaataaaaaagaaagctaggacatggttctagtgttctt +agcagacgtcccaccatggaagaggtcatggagcacaggggctttgggaaaggtgtttac +aatcctgcctgcctctcacccagacctcttg +>syndip_1_chr20:20337100-20337808 +tacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagagg +aagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctcac +tagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtggat +ggatggatggatggatggatggatggatagatgggtgggtggatggatggatggatagat +gggtggatggatagatgggtggatggataaatggatggatggatggatggatagatgggt +gggtagatggatggatggatggatggatggatggatggatggatggatggatagatgggt +gggtgggtggatggatggatggatggatggatggatggatggatagatgggtgggtggat +ggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggt 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+ggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt +gggtggatggatggatggatagatgggtgggtggatggatggatggatggatggatagat +ggatagatgggtgggtggatggatggatggatagatgggtgggtggatagatggatggat +ggatggatggatggatggatggatggatggatggatagatgggtgggtgggtggatggat +ggatggatggatggatggatggatggatggatggatagatgggtgggtggatggatggat +ggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggat +ggatggatagatgggtggatggataaatggatggatggatggatggatagatgggtgggt +ggatggatggatggatggatggatggatggatggatagatagatgggtgggtggatggat +ggatggatagatgggtgggtgggtggatggatggatggatggatagatgggtgggtgggt +ggatggatggatggatggatagaataaaaaagaaagctaggacatggttctagtgttctt +agcagacgtcccaccatggaagaggtcatggagcacaggggctttgggaaaggtgtttac +aatcctgcctgcctctcacccagacctcttg diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/msa.fa.fai new file mode 100644 index 00000000..971882d3 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_20337100_20337808 2191 29 60 61 +syndip_1_chr20:20337100-20337808 2191 2291 60 61 +syndip_2_chr20:20337100-20337808 2191 4553 60 61 +p:HG002_1_chr20:20337100-20337808 2191 6816 60 61 +p:HG002_2_chr20:20337100-20337808 2191 9079 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/output.vcf.gz new file mode 100644 index 00000000..910a3e88 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/output.vcf.gz.tbi new file mode 100644 index 00000000..efe8ad17 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20337200-20337708/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/base.vcf.gz new file mode 100644 index 00000000..1d09e6c8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/base.vcf.gz.tbi new file mode 100644 index 00000000..a990e137 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/comp.vcf.gz new file mode 100644 index 00000000..9a108aba Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/comp.vcf.gz.tbi new file mode 100644 index 00000000..5c7fc669 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/haps.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/haps.fa new file mode 100644 index 00000000..bdff3850 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/haps.fa @@ -0,0 +1,356 @@ +>ref_chr20_20354470_20358424 +TCCAGTCTGGGTGACAGAGAGAGACCTTGTCTCAAAAAAAAAAAAAAAAAATCAGGTACAGAAAGGTAAATACTGCACGATCTCACTTACATGTGGAATCTAAAGAAGTTGAATTCATAAGGGTAATGAGGGGAGGAAGGGGTGGTCATACTGTGTGAAGGGAGATAGTCACACTGAGGGAAGGTGGTCACACTGTGAGAAGGGAGGTAGTCACATTGTGAGAGAAAAAGTGATCACACTGTGTGAGGGGAGGTGGTCACACTGTGAGAGAAAAAGTAATCATACTGTGAAAGGGAGGTGGTCACGCTGAGAGGGGAGGTGGTCACACTGTGTCAGGGGAGGTGGTCACACTGTGAGAGAAAAAGTAATCACACTGTGAGGGGATGTGGTCACACTGAGAGGGGAGGTGGTCAGACTGTGTCAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAGATGGTCACACTGCAAGAGGGGAGGTGATCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACATTGTGAGAGGGAAGGGGGTCACTGTGAGAGGGGAGAAGGTCACACTAAGGGGAGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAGGAGGTGGTCACACTGTGAGGGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACTATGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGGGGTCACACTGTGAGGGGGAAGGTGGTCACACTGTGAGAGGGGAGAAGGTCACACTAAGGGGAGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAGGAGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACTATGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTAAGGGGAGGTGATCACACTGTGAGGGGACGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGACCACACAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGGGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGCTAGTCACACTGAGGGGAGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGCGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGCGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGAAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGGCACACTGTGAGGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTCACACTGTGAAAGAAGATGATCACAGTATGAGAGGTCATCCTTCAAGAGGCAAGTGCCCAAAAATCTGTTTATAATCTAGAGCAATATTTGCCTGAAATAAACTTTAAAAGTGGTTTTACGCTATTTAACCCAGTGTCAGA +>syndip_1_chr20:20354470-20358424 +TCCAGTCTGGGTGACAGAGAGAGACCTTGTCTCAAAAAAAAAAAAAAAAAATCAGGTACA +GAAAGGTAAATACTGCACGATCTCACTTACATGTGGAATCTAAAGAAGTTGAATTCATAA +GGGTAATGAGGGGAGGAAGGGGTGGTCATACTGTGTGAAGGGAGATAGTCACACTGAGGG +AAGGTGGTCACACTGTGAGAAGGGAGGTAGTCACATTGTGAGAGAAAAAGTGATCACACT +GTGTGAGGGGAGGTGGTCACACTGTGAGAGAAAAAGTAATCATACTGTGAAAGGGAGGTG +GTCACGCTGAGAGGGGAGGTGGTCACACTGTGTCAGGGGAGGTGGTCACACTGTGAGAGA +AAAAGTAATCACACTGTGAGGGGATGTGGTCACACTGAGAGGGGAGGTGGTCAGACTGTG +TCAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCAGA +CTCTGTCAGAGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAAGTGG +TCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAGATGGTCACACTGCAAGAGGGGA +GGTGATCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGAGA +GGGAAGGTGGTCACACTGTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACAT +TGTGAGAGGGAAGGGGGTCACTGTGAGAGGGGAGAAGGTCACACTAAGGGGAGGTAGTCA +CACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAGGAGGTGGTC +ACACTGTGAGGGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACT +ATGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACAC +TGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTACTCACA +CTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGAC +ACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGGGGTCACACTGTGAGGGGGAAGGTG +GTCACACTGTGAGAGGGGAGAAGGTCACACTAAGGGGAGGTAGTCACACTGTGAGGGGAG +GTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAGGAGGTGGTCACACTGTGAGGGGA +GGTCACACTGAGGGGAGGTAGTGACACTATGAGCAGAGATGGTCACACTGTGAGGGGAGG +TGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAG +GTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGA +GGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGG +AGGGGGTCACACTGTGAGGGGGAAGGTGGTCACACTGTGAGAGGGGAGAAGGTCACACTA +AGGGGAGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGT +GAGAGGAGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACTATGA +GCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTG +AGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTCACACTGT +GAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTG +TGAGCAGAGATGGTCACACTGTAAGGGGAGGTGATCACACTGTGAGGGGACGTCACACTG +TGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGACCACACAGGGGAGGTGGTCACACT +GAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACAC +TGAGGGGAGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGA +GGGGGGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGCTAGTCACACTG +AGGGGAGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTG +AGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGA +GGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAG +GGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGG +GGAGGTGGTCACAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGTGTGAG +GGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGG +AGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGA +AGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAG +GTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAG +TGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGT +GGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTG +GTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGAGGAGGTGGTC +ACACTGAGGGGAGGTGGTCATACTGTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTA +GTCACACTGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGT +AGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGT +CATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGG +TCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGT +CACACTGAGGGGAGGTGGTCACAGTGTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTC +ACAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGT +CACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTC +ACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCA +CAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTC +ACACTGAGGGGAGGTGGTCACAGTGTGCGGGGAGGTGGTCATACTGAGGGGAGGTGGTCA +CACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTC +ACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGGGGTCATA +CTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCAC +ACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACA +CTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAC +TGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGT +GTGCGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACAC +TGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACT +GAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTG +TGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGT +GAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTG +AGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGA +GGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACAGTGTG +AGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGA +GGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGTG +AGGGGAGGTGGTCACATTGAGGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGA +GGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAG +GAGAGGTGGTCATAGTGTGCGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGG +GGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAG +GGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGG +GAAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCATAGTGTGAG +GGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGTGA +GGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGGCACACTGTG +AGGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGG +GGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTCACACTGAGGGG +AAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTCACACTGTGAAAGA +AGATGATCACAGTATGAGAGGTCATCCTTCAAGAGGCAAGTGCCCAAAAATCTGTTTATA +ATCTAGAGCAATATTTGCCTGAAATAAACTTTAAAAGTGGTTTTACGCTATTTAACCCAG +TGTCAGA +>syndip_2_chr20:20354470-20358424 +TCCAGTCTGGGTGACAGAGAGAGACCTTGTCTCAAAAAAAAAAAAAAAAAATCAGGTACA +GAAAGGTAAATACTGCACGATCTCACTTACATGTGGAATCTAAAGAAGTTGAATTCATAA +GGGTAATGAGGGGAGGAAGGGGTGGTCATACTGTGTGAAGGGAGATAGTCACACTGAGGG +AAGGTGGTCACACTGTGAGAAGGGAGGTAGTCACATTGTGAGAGAAAAAGTGATCACACT +GTGTGAGGGGAGGTGGTCACACTGTGAGAGAAAAAGTAATCATACTGTGAAAGGGAGGTG +GTCACGCTGAGAGGGGAGGTGGTCACACTGTGTCAGGGGAGGTGGTCACACTGTGAGAGA +AAAAGTAATCACACTGTGAGGGGATGTGGTCACACTGAGAGGGGAGGTGGTCAGACTGTG +TCAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCAGA +CTCTGTCAGAGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAAGTGG +TCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAGATGGTCACACTGCAAGAGGGGA +GGTGATCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGAGA +GGGAAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGTGAGGGGAGGTGGTCAC +ACTGTGAGGGGAGGTGGTCACATTGTGAGAGGGAAGGGGGTCACTGTGAGAGGGGAGAAG +GTCACACTAAGGGGAGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGG +TCACACTGTGAGAGGAGGTGGTCACACTGTGAGGGGTGGTCACACTGTGAGGGGAGGTCA +CACTGAGGGGAGGTAGTGACACTATGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTC +ACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGT +CACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGG +TCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGGG +GTCACACTGTGAGGGGGAAGGTGGTCACACTGTGAGAGGGGAGAAGGTCACACTAAGGGG +AGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAG +GAGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACTATGAGCAGA +GATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAG +AGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTCACACTGTGAGGG +GAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGC +AGAGATGGTCACACTGTAAGGGGAGGTGATCACACTGTGAGGGGACGTCACACTGTGAGG +GGAGGTGGTCACACTGTGAGAGGGGAGGTGACCACACAGGGGAGGTGGTCACACTGAGGG +GAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGG +GGAGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGG +GGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGCTAGTCACACTGAGGGG +AGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGG +AGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGA +AGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAG +GTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGG +TGGTCACAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAG +GTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGG +TGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGG +TCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGT +CACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCAC +ACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACT +GTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTG +AGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGG +GGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAG +AGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGG +AGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAAGTGGTCACACTGAGGG +GAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGG +GGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAG +AGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGG +GGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGG +GAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGG +AGGTGGTCACAGTGTGCGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACAGTGTGAGGG +GAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGG +AGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGA +GGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGG +AAGTAGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGG +TGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAGGGGGTCATACTGCGAGTGG +AGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGA +AGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAG +GTGGTCATAGTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGA +GGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGG +AAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAG +GAGGTAGTCACACTGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAG +GGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGA +GGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGG +AGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGA +GGTGGTCACAGTGTGCGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACAGTGTGAGGGG +AGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGCGGGGAGGTGGTCACACTGAGGGGA +GGTGGTCATAGTGTGAGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACACTGTGAGGGG +AGGTGGTCACACTGAGGAGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGAGA +GGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAG +GTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGTGAGGGGA +GGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAG +GTGGTGACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGG +TGGTCACACTGTGAGGGGAGGTGGTCACATTGAGGAGAGGTGGTCATAGTGTGAGGGGAG +GTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGG +TGGTCACACTGAGGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGT +GGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACAGTGTGAGGGGAGG +TGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGT +GGTCACACTGAGGGAAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTG +GTCATAGTGTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGAGAGGT +GGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGG +TGGGCACACTGTGAGGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGT +GGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGG +TCACACTGAGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTC +ACACTGTGAAAGAAGATGATCACAGTATGAGAGGTCATCCTTCAAGAGGCAAGTGCCCAA +AAATCTGTTTATAATCTAGAGCAATATTTGCCTGAAATAAACTTTAAAAGTGGTTTTACG +CTATTTAACCCAGTGTCAGA +>p:HG002_1_chr20:20354470-20358424 +TCCAGTCTGGGTGACAGAGAGAGACCTTGTCTCAAAAAAAAAAAAAAAAAATCAGGTACA +GAAAGGTAAATACTGCACGATCTCACTTACATGTGGAATCTAAAGAAGTTGAATTCATAA +GGGTAATGAGGGGAGGAAGGGGTGGTCATACTGTGTGAAGGGAGATAGTCACACTGAGGG +AAGGTGGTCACACTGTGAGAAGGGAGGTAGTCACATTGTGAGAGAAAAAGTGATCACACT +GTGTGAGGGGAGGTGGTCACACTGTGAGAGAAAAAGTAATCATACTGTGAAAGGGAGGTG +GTCACGCTGAGAGGGGAGGTGGTCACACTGTGTCAGGGGAGGTGGTCACACTGTGAGAGA +AAAAGTAATCACACTGTGAGGGGATGTGGTCACACTGAGAGGGGAGGTGGTCAGACTGTG +TCAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCACA +CTGAGGGGAAGTGGTCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAGATGGTCAC +ACTGCAAGAGGGGAGGTGATCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTG +ATCACACTGAGGGAAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGTGAGGGG +AGGTGGTCACACTGTGAGGGGAGGTGGTCACATTGTGAGAGGGAAGGGGGTCACTGTGAG +AGGGGAGAAGGTCACACTAAGGGGAGGTAGTCACACTGTGAGGGGAGGTGATCACACTAA +GGGGAGGTGGTCACACTGTGAGAGGAGGTGGTCACACTGTGAGGGGTGGTCACACTGTGA +GGGGAGGTCACACTGAGGGGAGGTAGTGACACTATGAGCAGAGATGGTCACACTGTGAGG +GGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAG +GGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGG +GGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAG +GGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGGGGTCACACTGT +GAGGGGGAAGGTGGTCACACTGTGAGAGGGGAGAAGGTCACACTAAGGGGAGGTAGTCAC +ACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAGGAGGTGGTCA +CACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACTATGAGCAGAGATGGTCACA +CTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCAC +ACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTCACACTGTGAGGGGAGGTGGTCA +CACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTC +ACACTGTAAGGGGAGGTGATCACACTGTGAGGGGACGTCACACTGTGAGGGGAGGTGGTC +ACACTGTGAGAGGGGAGGTGACCACACAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGA +CACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTC +ACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGGGGTGGTCACA +CTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGCTAGTCACACTGAGGGGAGGGGTCATA +CTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCAC +ACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACA +CTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAC +TGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGT +GTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCATAG +TGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACT +GAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTG +AGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGA +GGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGA +GGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAG +GTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTG +GTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTC +ACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGT +CACACTGAGGGGAAGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCAT +ACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCA +CACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAGGGGGTC +ATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGT +CACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTC +ACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCA +CAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCAC +AGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCA +CACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCAC +ACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACA +CTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAAGTAGTCAC +ACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATACT +GTGAGTGAGGAGGTAGTCACACTGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCAC +ACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACA +CTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAG +TGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACA +CTGAGGGGAGGTGGTCATACTGTGTGCGGGGAGGTGGTCATACTGAGGGGAGGTGGTCAC +ACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCA +CACTGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTC +ACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATA +CTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCAC +ACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACA +GTGTGCGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCAC +ACTGAGGGGAGGTGGTCACAGTGTGCGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATA +GTGTGAGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCAC +ACTGAGGAGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATA +GTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAG +TGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACA +CTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTGACAC +TGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACT +GTGAGGGGAGGTGGTCACATTGAGGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACAC +TGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACT +GAGGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTG +AGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACT +GAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTG +AGGGAAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCATAGTGT +GAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTG +TGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGGCACACT +GTGAGGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTG +AGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTCACACTGAG +GGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTCACACTGTGAA +AGAAGATGATCACAGTATGAGAGGTCATCCTTCAAGAGGCAAGTGCCCAAAAATCTGTTT +ATAATCTAGAGCAATATTTGCCTGAAATAAACTTTAAAAGTGGTTTTACGCTATTTAACC +CAGTGTCAGA +>p:HG002_2_chr20:20354470-20358424 +TCCAGTCTGGGTGACAGAGAGAGACCTTGTCTCAAAAAAAAAAAAAAAAAATCAGGTACA +GAAAGGTAAATACTGCACGATCTCACTTACATGTGGAATCTAAAGAAGTTGAATTCATAA +GGGTAATGAGGGGAGGAAGGGGTGGTCATACTGTGTGAAGGGAGATAGTCACACTGAGGG +AAGGTGGTCACACTGTGAGAAGGGAGGTAGTCACATTGTGAGAGAAAAAGTGATCACACT +GTGTGAGGGGAGGTGGTCACACTGTGAGAGAAAAAGTAATCATACTGTGAAAGGGAGGTG +GTCACGCTGAGAGGGGAGGTGGTCACACTGTGTCAGGGGAGGTGGTCACACTGTGAGAGA +AAAAGTAATCACACTGTGAGGGGATGTGGTCACACTGAGAGGGGAGGTGGTCAGACTGTG +TCAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCAGA +CTCTGTCAGAGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAAGTGG +TCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAGATGGTCACACTGCAAGAGGGGA +GGTGATCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGAGA +GGGAAGGTGGTCACACTGTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACAT +TGTGAGAGGGAAGGGGGTCACTGTGAGAGGGGAGAAGGTCACACTAAGGGGAGGTAGTCA +CACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAGGAGGTGGTC +ACACTGTGAGGGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACT +ATGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACAC +TGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTACTCACA +CTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGAC +ACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGGGGTCACACTGTGAGGGGGAAGGTG +GTCACACTGTGAGAGGGGAGAAGGTCACACTAAGGGGAGGTAGTCACACTGTGAGGGGAG +GTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAGGAGGTGGTCACACTGTGAGGGGA +GGTCACACTGAGGGGAGGTAGTGACACTATGAGCAGAGATGGTCACACTGTGAGGGGAGG +TGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAG +GTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGA +GGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGG +AGGGGGTCACACTGTGAGGGGGAAGGTGGTCACACTGTGAGAGGGGAGAAGGTCACACTA +AGGGGAGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGT +GAGAGGAGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACTATGA +GCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTG +AGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTCACACTGT +GAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTG +TGAGCAGAGATGGTCACACTGTAAGGGGAGGTGATCACACTGTGAGGGGACGTCACACTG +TGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGACCACACAGGGGAGGTGGTCACACT +GAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACAC +TGAGGGGAGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGA +GGGGGGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGCTAGTCACACTG +AGGGGAGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTG +AGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGA +GGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAG +GGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGG +GGAGGTGGTCACAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGTGTGAG +GGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGG +AGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGA +AGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGT +GGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTG +GTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGG +TCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCA +CACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAG +TGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCA +CACTGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTC +ACACTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACA +CTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACAC +TGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACA +CTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTG +TGAGTGAGGAGGTAGTCACACTGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACA +CTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACAC +TGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGT +GTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACAC +TGAGGGGAGGTGGTCACAGTGTGCGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACACT +GAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACAC +TGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACA +CTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTG +TGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACT +GAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTG +AGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGT +ACGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTG +AGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGA +GGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGTG +AGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGTGA +GGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAG +GGGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGG +GGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACAGTGTGAG +GGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGG +GGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGTGAG +GGGAGGTGGTCACATTGAGGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGG +GGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGA +GAGGTGGTCATAGTGTGCGGGGAGGTGGTCACACTGCGGGGAGGTGGTCATACTGAGGGG +AGGTGGTCACAGTGTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGG +GAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGA +AGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCATAGTGTGAGGG +GAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGTGAGG +GGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGGCACACTGTGAG +GGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGG +AAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTCACACTGAGGGGAA +GTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTCACACTGTGAAAGAAG +ATGATCACAGTATGAGAGGTCATCCTTCAAGAGGCAAGTGCCCAAAAATCTGTTTATAAT +CTAGAGCAATATTTGCCTGAAATAAACTTTAAAAGTGGTTTTACGCTATTTAACCCAGTG +TCAGA diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/haps.fa.ref.fa new file mode 100644 index 00000000..53b76a9d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:20354470-20358424 +TCCAGTCTGGGTGACAGAGAGAGACCTTGTCTCAAAAAAAAAAAAAAAAAATCAGGTACAGAAAGGTAAATACTGCACGATCTCACTTACATGTGGAATCTAAAGAAGTTGAATTCATAAGGGTAATGAGGGGAGGAAGGGGTGGTCATACTGTGTGAAGGGAGATAGTCACACTGAGGGAAGGTGGTCACACTGTGAGAAGGGAGGTAGTCACATTGTGAGAGAAAAAGTGATCACACTGTGTGAGGGGAGGTGGTCACACTGTGAGAGAAAAAGTAATCATACTGTGAAAGGGAGGTGGTCACGCTGAGAGGGGAGGTGGTCACACTGTGTCAGGGGAGGTGGTCACACTGTGAGAGAAAAAGTAATCACACTGTGAGGGGATGTGGTCACACTGAGAGGGGAGGTGGTCAGACTGTGTCAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGTGAGAGGGGAGGTGGTCACACTGAGGGGAGATGGTCACACTGCAAGAGGGGAGGTGATCACACTGAGGGGAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGAGAGGGAAGGTGGTCACACTGTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACATTGTGAGAGGGAAGGGGGTCACTGTGAGAGGGGAGAAGGTCACACTAAGGGGAGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAGGAGGTGGTCACACTGTGAGGGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACTATGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGGGGTCACACTGTGAGGGGGAAGGTGGTCACACTGTGAGAGGGGAGAAGGTCACACTAAGGGGAGGTAGTCACACTGTGAGGGGAGGTGATCACACTAAGGGGAGGTGGTCACACTGTGAGAGGAGGTGGTCACACTGTGAGGGGAGGTCACACTGAGGGGAGGTAGTGACACTATGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTAAGGGGAGGTGATCACACTGTGAGGGGACGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGAGGGGAGGTGACCACACAGGGGAGGTGGTCACACTGAGGGGAGGTAGTGACACTGTGAGCAGAGATGGTCACACTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGGGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGCTAGTCACACTGAGGGGAGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGATGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGCGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGTGAGGAGGTAGTCACACTGAGGGGAGGGGGTCATACTGCGAGTGGAGGTAGTCACACTGTGAAGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATACTGTGAGGGGAAGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACAGTGTGCGGGGAGGTGGTCATACTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGAAGGTGGTCACACTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACAGTGTGAGGGGAGGTGGTCACACTGAGGAGAGGTGGTCATAGTGTGAGGGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGTGAGGGGAGGTGGGCACACTGTGAGGGGTGGTAGTCACACTGAGAGGAGGTGGTCACACTGAGGGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTCACACTGAGGGGAAGTGGTCACACTGAGGGGAATGGTCATACTGTGAGGGGAGGTGGTCACACTGTGAAAGAAGATGATCACAGTATGAGAGGTCATCCTTCAAGAGGCAAGTGCCCAAAAATCTGTTTATAATCTAGAGCAATATTTGCCTGAAATAAACTTTAAAAGTGGTTTTACGCTATTTAACCCAGTGTCAGA diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/msa.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/msa.fa new file mode 100644 index 00000000..e227e981 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/msa.fa @@ -0,0 +1,490 @@ +>ref_chr20_20354470_20358424 +tccagtctgggtgacagagagagaccttgtctcaaaaaaaaaaaaaaaaaatcaggtaca +gaaaggtaaatactgcacgatctcacttacatgtggaatctaaagaagttgaattcataa +gggtaatgaggggaggaaggggtggtcatactgtgtgaagggagatagtcacactgaggg +aaggtggtcacactgtgagaagggaggtagtcacattgtgagagaaaaagtgatcacact +gtgtgaggggaggtggtcacactgtgagagaaaaagtaatcatactgtgaaagggaggtg +gtcacgctgagaggggaggtggtcacactgtgtcaggggaggtggtcacactgtgagaga +aaaagtaatcacactgtgaggggatgtggtcacactgagaggggaggtggtcagactgtg +tcagaggaggtggtcacactgagg------------------------------------ +----------ggaggtggtcacactgtgagaggggaggtggtcacactgaggggaagtgg 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+--------------------------------------tgaggggaggtggtcacactga +ggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactgag +gggaggtggtcatagtgtgaggggaggtggtcacactgtgaggggaggtggtcacattga +ggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactgag +gggaggtggtcatagtgtgaggggaggtggtcacactgaggagaggtggtcatagtgtgc +ggggaggtggtcacactgcggggaggtggtcatactgaggggaggtggtcacagtgtgag +gggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcatagtgtga +ggggaggtggtcacactgaggggaggtggtcacactgagggaaggtggtcacactgaggg +gaggtggtcatagtgtgaggggaggtggtcatagtgtgaggggaggtggtcacagtgtga +ggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcacactgag +gggaggtggtcacactgtgaggggaggtgggcacactgtgaggggtggtagtcacactga +gaggaggtggtcacactgaggggaggtggtcacactgaggggaagtggtcacactgaggg +gaatggtcatactgtgaggggaggtggtcacactgaggggaagtggtcacactgagggga +atggtcatactgtgaggggaggtggtcacactgtgaaagaagatgatcacagtatgagag +gtcatccttcaagaggcaagtgcccaaaaatctgtttataatctagagcaatatttgcct +gaaataaactttaaaagtggttttacgctatttaacccagtgtcaga diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/msa.fa.fai new file mode 100644 index 00000000..4d7ae930 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_20354470_20358424 5807 29 60 61 +syndip_1_chr20:20354470-20358424 5807 5967 60 61 +syndip_2_chr20:20354470-20358424 5807 11905 60 61 +p:HG002_1_chr20:20354470-20358424 5807 17844 60 61 +p:HG002_2_chr20:20354470-20358424 5807 23783 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/output.vcf.gz new file mode 100644 index 00000000..d59eaf3a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/output.vcf.gz.tbi new file mode 100644 index 00000000..5f33b14f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:20354570-20358324/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/base.vcf.gz new file mode 100644 index 00000000..c756ec7c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/base.vcf.gz.tbi new file mode 100644 index 00000000..19ab6d40 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/comp.vcf.gz new file mode 100644 index 00000000..fe7d594b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/comp.vcf.gz.tbi new file mode 100644 index 00000000..cd4392fa Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/haps.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/haps.fa new file mode 100644 index 00000000..8fa5013b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/haps.fa @@ -0,0 +1,68 @@ +>ref_chr20_23155404_23156076 +GGGAAAGACACAGAGGTAGAATCTGCGTTAGGAATAAAAACCGCTACTCTCCGTTGTTCTGTGTGCTTTTGCAGTCATGATTGATGCAGGCAGCACCCTTCTGCAGAAGTAAATTTTGCCCTGCAGCACAAAAGAGGAAGGAAAGCAAGGGAAGGGAAGGGGAGGGGAGGAAGGGAAGGAAAAGAGAGAGAAAGAGAAAGAGAGAAAGAGAGGAAGGAAGGAAGGAAGGAGAGAGAGAAAGAAAGAAGGAAAGAGGAAGGAAGGAAGAAAGAAAAGAAAGAAAGAAAAAAGAAAGAAAGGAAGGAGAGAAAGAAATGAAAGAGAAAGAAAGAAAGAAAGAAAGAAAGGAGAGAAAAAGGAAAAACAAAGAAAGAGAAAAGAAGGAGAGAAGGAAAGGAAAAAGAAAGAAAGAAGGAAAGAAAGAAAAAAGAAGGAAAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAAAGAGAAAGGAAGGAAGGAAGGAAGGTCTTAACACCTTGGTAATTTTTGTGCTCTTCCCTGGACTTTGGACTTTGCAGCCTTAGGGAGACAGAGCTCTTTAATGTACACTTTCCCATCAGGCACTGCATGGCCAAGAACCTGCCTGCAAAGCCCCCA +>syndip_1_chr20:23155404-23156076 +GGGAAAGACACAGAGGTAGAATCTGCGTTAGGAATAAAAACCGCTACTCTCCGTTGTTCT +GTGTGCTTTTGCAGTCATGATTGATGCAGGCAGCACCCTTCTGCAGAAGTAAATTTTGCC +CTGCAGCACAAAAGAGGAAGGAAAGCAAGGGAAGGGAAGGGGAGGGGAGGAAGGGAAGGG +GAGGGGAGGAAGGGAAGGGGAGGGGAGGAAGGCGAGGTGAGGGGAGGAGAGGTGAGGGGA +GGGGGGGAGGGGAGGGGAGGGAGAGTGAGGAAGAGAGAGAGAAAGGGAGAGAGGAAGGAA +AGAAGAAAGGAAGGAAGGAAAGAAGGAAGGAAGGGAGGGAGGGAGGGAGGAAAGAAGGAA +GGAAAGGAGGGAGGAAGGGAGGGAAAGAGAGAGAGAGGAAAAGAGAGAGAAAGAGAAAGA +GAGAAAGAGAGGAAGGAAGGAAGGAAGGAGAGAGAGAAAGAAAGAAGGAAAGAGGAAGGA +AGGAAGAAAGAAAAGAAAGAAAGAAAAAAGAAAGAAAGGAAGGAGAGAAAGAAATGAAAG +AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGGAGAGAAAAAGGAAAAACAAAGAAAG +AGAAAAGAAGGAGAGAAGGAAAGGAAAAAGAAAGAAAGAAGGAAAGAAAGAAAAAAGAAG +GAAAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG +AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAAAGAGAAAGGAAGGAAGGAAGGAAG +GTCTTAACACCTTGGTAATTTTTGTGCTCTTCCCTGGACTTTGGACTTTGCAGCCTTAGG +GAGACAGAGCTCTTTAATGTACACTTTCCCATCAGGCACTGCATGGCCAAGAACCTGCCT +GCAAAGCCCCCA +>syndip_2_chr20:23155404-23156076 +GGGAAAGACACAGAGGTAGAATCTGCGTTAGGAATAAAAACCGCTACTCTCCGTTGTTCT +GTGTGCTTTTGCAGTCATGATTGATGCAGGCAGCACCCTTCTGCAGAAGTAAATTTTGCC +CTGCAGCACAAAAGAGGAAGGAAAGCAAGGGAAGGGAAGGGGAGGGGAGGAAGGGAAGGG +GAGGGGAGGAAGGCGAGGTGAGGGGAGGAGAGGTGAGGGGAGGGGGGGAGGGGAGGGGAG +GGAGAGTGAGGAAGAGAGAGAGAAAGGGAGAGAGGAAGGAAAGAAGAAAGGAAGGAAGGA +AAGAAGGAAGGAAGGGAGGGAGGGAGGGAGGAAAGAAGGAAGGAAAGGAGGGAGGAAGGG +AGGGAAAGAGAGAGAGAGGAAAAGAGAGAGAAAGAGAAAGAGAGAAAGAGAGGAAGGAAG +GAAGGAAGGAGAGAGAGAAAGAAAGAAGGAAAGAGGAAGGAAGGAAGAAAGAAAAGAAAG +AAAGAAAAAAGAAAGAAAGGAAGGAGAGAAAGAAATGAAAGAGAAAGAAAGAAAGAAAGA +AAGAAAGGAGAGAAAAAGGAAAAACAAAGAAAGAGAAAAGAAGGAGAGAAGGAAAGGAAA +AAGAAAGAAAGAAGGAAAGAAAGAAAAAAGAAGGAAAGAAAGAAGAAAGAAAGAAAGAAA +GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAAAGAGAAAGGAAGGAA +GGAAGGAAGGTCTTAACACCTTGGTAATTTTTGTGCTCTTCCCTGGACTTTGGACTTTGC +AGCCTTAGGGAGACAGAGCTCTTTAATGTACACTTTCCCATCAGGCACTGCATGGCCAAG +AACCTGCCTGCAAAGCCCCCA +>p:HG002_1_chr20:23155404-23156076 +GGGAAAGACACAGAGGTAGAATCTGCGTTAGGAATAAAAACCGCTACTCTCCGTTGTTCT +GTGTGCTTTTGCAGTCATGATTGATGCAGGCAGCACCCTTCTGCAGAAGTAAATTTTGCC +CTGCAGCACAAAAGAGGAAGGAAAGCAAGGGAAGGGAAGGGGAGGGGAGGAAGGGAAGGG +GAGGGGAGGAAGGCGAGGTGAGGGGAGGAGAGGTGAGGGGAGGGGGGGAGGGGAGGGGAG +GGAGAGTGAGGAAGAGAGAGAGAAAGGGAGAGAGGAAGGAAAGAAGAAAGGAAGGAAGGA +AAGAAGGAAGGAAGGGAGGGAGGGAGGGAGGAAAGAAGGAAGGAAAGGAGGGAGGAAGGG +AGGGAAAGAGAGAGAGAGGAAAAGAGAGAGAAAGAGAAAGAGAGAAAGAGAGGAAGGAAG +GAAGGAAGGAGAGAGAGAAAGAAAGAAGGAAAGAGGAAGGAAGGAAGAAAGAAAAGAAAG +AAAGAAAAAAGAAAGAAAGGAAGGAGAGAAAGAAATGAAAGAGAAAGAAAGAAAGAAAGA +AAGAAAGGAGAGAAAAAGGAAAAACAAAGAAAGAGAAAAGAAGGAGAGAAGGAAAGGAAA +AAGAAAGAAAGAAGGAAAGAAAGAAAAAAGAAGGAAAGAAAGAAGAAAGAAAGAAAGAAA +GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAAAGAGAAAGGAA +GGAAGGAAGGAAGGTCTTAACACCTTGGTAATTTTTGTGCTCTTCCCTGGACTTTGGACT +TTGCAGCCTTAGGGAGACAGAGCTCTTTAATGTACACTTTCCCATCAGGCACTGCATGGC +CAAGAACCTGCCTGCAAAGCCCCCA +>p:HG002_2_chr20:23155404-23156076 +GGGAAAGACACAGAGGTAGAATCTGCGTTAGGAATAAAAACCGCTACTCTCCGTTGTTCT +GTGTGCTTTTGCAGTCATGATTGATGCAGGCAGCACCCTTCTGCAGAAGTAAATTTTGCC +CTGCAGCACAAAAGAGGAAGGAAAGCAAGGGAAGGGAAGGGGAGGGGAGGAAGGGAAGGG +GAGGGGAGGAAGGGAAGGGGAGGGGAGGAAGGCGAGGTGAGGGGAGGAGAGGTGAGGGGA +GGGGGGGAGGGGAGGGGAGGGAGAGTGAGGAAGAGAGAGAGAAAGGGAGAGAGGAAGGAA +AGAAGAAAGGAAGGAAGGAAAGAAGGAAGGAAGGGAGGGAGGGAGGGAGGAAAGAAGGAA +GGAAAGGAGGGAGGAAGGGAGGGAAAGAGAGAGAGAGGAAAAGAGAGAGAAAGAGAAAGA +GAGAAAGAGAGGAAGGAAGGAAGGAAGGAGAGAGAGAAAGAAAGAAGGAAAGAGGAAGGA +AGGAAGAAAGAAAAGAAAGAAAGAAAAAAGAAAGAAAGGAAGGAGAGAAAGAAATGAAAG +AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGGAGAGAAAAAGGAAAAACAAAGAAAG +AGAAAAGAAGGAGAGAAGGAAAGGAAAAAGAAAGAAAGAAGGAAAGAAAGAAAAAAGAAG +GAAAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG +AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAAAGAGAAAGGAAGGAAGGAAGGAAG +GTCTTAACACCTTGGTAATTTTTGTGCTCTTCCCTGGACTTTGGACTTTGCAGCCTTAGG +GAGACAGAGCTCTTTAATGTACACTTTCCCATCAGGCACTGCATGGCCAAGAACCTGCCT +GCAAAGCCCCCA diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/haps.fa.ref.fa new file mode 100644 index 00000000..74c4f4f3 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:23155404-23156076 +GGGAAAGACACAGAGGTAGAATCTGCGTTAGGAATAAAAACCGCTACTCTCCGTTGTTCTGTGTGCTTTTGCAGTCATGATTGATGCAGGCAGCACCCTTCTGCAGAAGTAAATTTTGCCCTGCAGCACAAAAGAGGAAGGAAAGCAAGGGAAGGGAAGGGGAGGGGAGGAAGGGAAGGAAAAGAGAGAGAAAGAGAAAGAGAGAAAGAGAGGAAGGAAGGAAGGAAGGAGAGAGAGAAAGAAAGAAGGAAAGAGGAAGGAAGGAAGAAAGAAAAGAAAGAAAGAAAAAAGAAAGAAAGGAAGGAGAGAAAGAAATGAAAGAGAAAGAAAGAAAGAAAGAAAGAAAGGAGAGAAAAAGGAAAAACAAAGAAAGAGAAAAGAAGGAGAGAAGGAAAGGAAAAAGAAAGAAAGAAGGAAAGAAAGAAAAAAGAAGGAAAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAAAGAGAAAGGAAGGAAGGAAGGAAGGTCTTAACACCTTGGTAATTTTTGTGCTCTTCCCTGGACTTTGGACTTTGCAGCCTTAGGGAGACAGAGCTCTTTAATGTACACTTTCCCATCAGGCACTGCATGGCCAAGAACCTGCCTGCAAAGCCCCCA diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/msa.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/msa.fa new file mode 100644 index 00000000..1aeba093 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/msa.fa @@ -0,0 +1,85 @@ +>ref_chr20_23155404_23156076 +gggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttct +gtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgcc +ctgcagcacaaaagaggaaggaaagcaag-------------------ggaagggaaggg +gaggggaggaaggga--------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------aggaaaagagagagaaagagaaaga +gagaaagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaagga +aggaagaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag +--------agaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaag +agaaaagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaag +gaaagaaag------------aagaaagaaagaaagaaagaaagaaagaaagaaagaaag +aaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaag +gtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttagg +gagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcct +gcaaagccccca +>syndip_1_chr20:23155404-23156076 +gggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttct +gtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgcc +ctgcagcacaaaagaggaaggaaagcaagggaagggaaggggaggggaggaagggaaggg +gaggggaggaagggaaggggaggggaggaaggcgaggtgaggggaggagaggtgagggga +gggggggaggggaggggagggagagtgaggaagagagagagaaagggagagaggaaggaa +agaagaaaggaaggaaggaaagaaggaaggaagggagggagggagggaggaaagaaggaa +ggaaaggagggaggaagggagggaaagagagagagaggaaaagagagagaaagagaaaga +gagaaagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaagga +aggaagaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag +agaaagaaagaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaag +agaaaagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaag +gaaagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag +aaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaag +gtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttagg +gagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcct +gcaaagccccca +>syndip_2_chr20:23155404-23156076 +gggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttct +gtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgcc +ctgcagcacaaaagaggaaggaaagcaag-------------------ggaagggaaggg +gaggggaggaagggaaggggaggggaggaaggcgaggtgaggggaggagaggtgagggga +gggggggaggggaggggagggagagtgaggaagagagagagaaagggagagaggaaggaa +agaagaaaggaaggaaggaaagaaggaaggaagggagggagggagggaggaaagaaggaa +ggaaaggagggaggaagggagggaaagagagagagaggaaaagagagagaaagagaaaga +gagaaagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaagga +aggaagaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag +--------agaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaag +agaaaagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaag +gaaagaaag------------------------aagaaagaaagaaagaaagaaagaaag +aaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaag +gtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttagg +gagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcct +gcaaagccccca +>p:HG002_1_chr20:23155404-23156076 +gggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttct +gtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgcc +ctgcagcacaaaagaggaaggaaagcaag-------------------ggaagggaaggg +gaggggaggaagggaaggggaggggaggaaggcgaggtgaggggaggagaggtgagggga +gggggggaggggaggggagggagagtgaggaagagagagagaaagggagagaggaaggaa +agaagaaaggaaggaaggaaagaaggaaggaagggagggagggagggaggaaagaaggaa +ggaaaggagggaggaagggagggaaagagagagagaggaaaagagagagaaagagaaaga +gagaaagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaagga +aggaagaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag +--------agaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaag +agaaaagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaag +gaaagaaag--------------------aagaaagaaagaaagaaagaaagaaagaaag +aaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaag +gtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttagg +gagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcct +gcaaagccccca +>p:HG002_2_chr20:23155404-23156076 +gggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttct +gtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgcc +ctgcagcacaaaagaggaaggaaagcaagggaagggaaggggaggggaggaagggaaggg +gaggggaggaagggaaggggaggggaggaaggcgaggtgaggggaggagaggtgagggga +gggggggaggggaggggagggagagtgaggaagagagagagaaagggagagaggaaggaa +agaagaaaggaaggaaggaaagaaggaaggaagggagggagggagggaggaaagaaggaa +ggaaaggagggaggaagggagggaaagagagagagaggaaaagagagagaaagagaaaga +gagaaagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaagga +aggaagaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag +agaaagaaagaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaag +agaaaagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaag +gaaagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag +aaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaag +gtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttagg +gagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcct +gcaaagccccca diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/msa.fa.fai new file mode 100644 index 00000000..bc806fd7 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_23155404_23156076 912 29 60 61 +syndip_1_chr20:23155404-23156076 912 991 60 61 +syndip_2_chr20:23155404-23156076 912 1953 60 61 +p:HG002_1_chr20:23155404-23156076 912 2916 60 61 +p:HG002_2_chr20:23155404-23156076 912 3879 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/output.vcf.gz new file mode 100644 index 00000000..cf51a4cb Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/output.vcf.gz.tbi new file mode 100644 index 00000000..df98dc3f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:23155504-23155976/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/base.vcf.gz new file mode 100644 index 00000000..2a714015 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/base.vcf.gz.tbi new file mode 100644 index 00000000..d5a41b41 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/comp.vcf.gz new file mode 100644 index 00000000..51535172 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/comp.vcf.gz.tbi new file mode 100644 index 00000000..91d9c94a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/haps.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/haps.fa new file mode 100644 index 00000000..5298e2a6 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/haps.fa @@ -0,0 +1,58 @@ +>ref_chr20_34235650_34236314 +AGCGCATGCCTGTGGCCCCTACTACTCAGGAGGCAGGGGTGGGAGGATTGCTAGAGCCCAGGAAGTCGTGGCTGAAGTGGGCTCATGATAATGCCACTGCACTCCAGCCTGTGTGACAGAGTGAGACTCTGAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAGGAAGGAAGGAAGGAAGGAAGGAAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGAAGGAAGGAAGGAGGGAGGGAGGGAAGAAGGAAAGAAGGAAGGAAGGAGAAAGAGAGAAAGAGAGAGAGAAGAAGAAAGAGAAAGAAACAGAAAAGGAAGGAAGGAGAGAGAGAAAGAAAGAGAAAGAGAAGGAAGGAAGGAAGGAGAAAGAAAGGAAAGGAAAGGAGTGGAAAGGAAAGGAGAGGAAAGGAGAAAGGAGGGAGGGAGGGAAAAGAAAGAAAGAAAGAAAAGGCTAAACCTGACTATGATATTGAATTTACTGCTAGCTCTAGGTGGTTTAAATGATTCAAGAATCATGGCCATGGCTGGGCGCAGTGGCTCACGCCTATAATCCCAGCACTTTGGGAGGCCGAAGCGGGC +>syndip_1_chr20:34235650-34236314 +AGCGCATGCCTGTGGCCCCTACTACTCAGGAGGCAGGGGTGGGAGGATTGCTAGAGCCCA +GGAAGTCGTGGCTGAAGTGGGCTCATGATAATGCCACTGCACTCCAGCCTGTGTGACAGA +GTGAGACTCTGAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG +AAAGAAAGAAAGAAGGAAGGAAGGAAGGAAGGAAGGAAAGGAAGGAAGGAAGGAAGGAAG +GAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGAAGGAGGAGGGAGGGAAGAAT +GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGA +AGGAAGGAAGGAGGGAGGGAGGGAAGAAGGAAGGAGGAGGGAGGGAGGGAAGCAGGAAAG +AAGGAAGGAAGGAGAAAGAGAGAAAGAGAGAGAGAAGAAGAAAGAGAAAGAAACAGAAAA +GGAAGGAAGGAGAGAGAGAAAGAAAGAGAAAGAGAAGGAAGGAAGGAAGGAGAAAGAAAG +GAAAGGAAAGGAGTGGAAAGGAAAGGAGAGGAAAGGAGAAAGGAGGGAGGGAGGGAAAAG +AAAGAAAGAAAGAAAAGGCTAAACCTGACTATGATATTGAATTTACTGCTAGCTCTAGGT +GGTTTAAATGATTCAAGAATCATGGCCATGGCTGGGCGCAGTGGCTCACGCCTATAATCC +CAGCACTTTGGGAGGCCGAAGCGGGC +>syndip_2_chr20:34235650-34236314 +AGCGCATGCCTGTGGCCCCTACTACTCAGGAGGCAGGGGTGGGAGGATTGCTAGAGCCCA +GGAAGTCGTGGCTGAAGTGGGCTCATGATAATGCCACTGCACTCCAGCCTGTGTGACAGA +GTGAGACTCTGAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG +AAAGAAAGAAAGAAGGAAGGAAGGAAGGAAGGAAGGAAAGGAAGGAAGGAAGGAAGGAAG +GAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGAAGGAGGAGGGAGGGAAGAAT +GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGA +AGGAAGGAAGGAGGGAGGGAGGGAAGAAGGAAGGAGGAGGGAGGGAGGGAAGCAGGAAAG +AAGGAAGGAAGGAGAAAGAGAGAAAGAGAGAGAGAAGAAGAAAGAGAAAGAAACAGAAAA +GGAAGGAAGGAGAGAGAGAAAGAAAGAGAAAGAGAAGGAAGGAAGGAAGGAGAAAGAAAG +GAAAGGAAAGGAGTGGAAAGGAAAGGAGAGGAAAGGAGAAAGGAGGGAGGGAGGGAAAAG +AAAGAAAGAAAGAAAAGGCTAAACCTGACTATGATATTGAATTTACTGCTAGCTCTAGGT +GGTTTAAATGATTCAAGAATCATGGCCATGGCTGGGCGCAGTGGCTCACGCCTATAATCC +CAGCACTTTGGGAGGCCGAAGCGGGC +>p:HG002_1_chr20:34235650-34236314 +AGCGCATGCCTGTGGCCCCTACTACTCAGGAGGCAGGGGTGGGAGGATTGCTAGAGCCCA +GGAAGTCGTGGCTGAAGTGGGCTCATGATAATGCCACTGCACTCCAGCCTGTGTGACAGA +GTGAGACTCTGAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG +AAAGAAAGAAAGAAGGAAGGAAGGAAGGAAGGAAGGAAAGGAAGGAAGGAAGGAAGGAAG +GAAGGAAGGAAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGG +AAGGAAGGAAGGAAGGAGGGAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGAA +GGAAGGAAGGAGGGAGGGAGGGAAGAAGGAAGGAGGAGGGAGGGAGGGAAGAAGGAAAGA +AGGAAGGAAGGAGAAAGAGAGAAAGAGAGAGAGAAGAAGAAAGAGAAAGAAACAGAAAAG +GAAGGAAGGAGAGAGAGAAAGAAAGAGAAAGAGAAGGAAGGAAGGAAGGAGAAAGAAAGG +AAAGGAAAGGAGTGGAAAGGAAAGGAGAGGAAAGGAGAAAGGAGGGAGGGAGGGAAAAGA +AAGAAAGAAAGAAAAGGCTAAACCTGACTATGATATTGAATTTACTGCTAGCTCTAGGTG +GTTTAAATGATTCAAGAATCATGGCCATGGCTGGGCGCAGTGGCTCACGCCTATAATCCC +AGCACTTTGGGAGGCCGAAGCGGGC +>p:HG002_2_chr20:34235650-34236314 +AGCGCATGCCTGTGGCCCCTACTACTCAGGAGGCAGGGGTGGGAGGATTGCTAGAGCCCA +GGAAGTCGTGGCTGAAGTGGGCTCATGATAATGCCACTGCACTCCAGCCTGTGTGACAGA +GTGAGACTCTGAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG +AAAGAAAGAAAGAAGGAAGGAAGGAAGGAAGGAAGGAAAGGAAGGAAGGAAGGAAGGAAG +GAAGGAAGGAAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGG +AAGGAAGGAAGGAAGGAGGGAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGAA +GGAAGGAAGGAGGGAGGGAGGGAAGAAGGAAGGAGGAGGGAGGGAGGGAAGAAGGAAAGA +AGGAAGGAAGGAGAAAGAGAGAAAGAGAGAGAGAAGAAGAAAGAGAAAGAAACAGAAAAG +GAAGGAAGGAGAGAGAGAAAGAAAGAGAAAGAGAAGGAAGGAAGGAAGGAGAAAGAAAGG +AAAGGAAAGGAGTGGAAAGGAAAGGAGAGGAAAGGAGAAAGGAGGGAGGGAGGGAAAAGA +AAGAAAGAAAGAAAAGGCTAAACCTGACTATGATATTGAATTTACTGCTAGCTCTAGGTG +GTTTAAATGATTCAAGAATCATGGCCATGGCTGGGCGCAGTGGCTCACGCCTATAATCCC +AGCACTTTGGGAGGCCGAAGCGGGC diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/haps.fa.ref.fa new file mode 100644 index 00000000..83fe6093 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:34235650-34236314 +AGCGCATGCCTGTGGCCCCTACTACTCAGGAGGCAGGGGTGGGAGGATTGCTAGAGCCCAGGAAGTCGTGGCTGAAGTGGGCTCATGATAATGCCACTGCACTCCAGCCTGTGTGACAGAGTGAGACTCTGAGAAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAGGAAGGAAGGAAGGAAGGAAGGAAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGCGGGAGGGAGGGAAGAAGGAAGGAAGGAAGGAAGGAGGGAGGGAGGGAAGAAGGAAAGAAGGAAGGAAGGAGAAAGAGAGAAAGAGAGAGAGAAGAAGAAAGAGAAAGAAACAGAAAAGGAAGGAAGGAGAGAGAGAAAGAAAGAGAAAGAGAAGGAAGGAAGGAAGGAGAAAGAAAGGAAAGGAAAGGAGTGGAAAGGAAAGGAGAGGAAAGGAGAAAGGAGGGAGGGAGGGAAAAGAAAGAAAGAAAGAAAAGGCTAAACCTGACTATGATATTGAATTTACTGCTAGCTCTAGGTGGTTTAAATGATTCAAGAATCATGGCCATGGCTGGGCGCAGTGGCTCACGCCTATAATCCCAGCACTTTGGGAGGCCGAAGCGGGC diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/msa.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/msa.fa new file mode 100644 index 00000000..59c13257 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/msa.fa @@ -0,0 +1,70 @@ +>ref_chr20_34235650_34236314 +agcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccca +ggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacaga +gtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag +aaagaaagaaagaaggaaggaaggaaggaaggaaggaaaggaaggaaggaaggaaggaag +gaaggaaggaaaggaa-------------------------------------------- +-----------ggaaggaaggaaggaaggaaggaagcgggagggagggaagaaggaagga +aggaaggaaggagggagggagggaaga--------------------------aggaaag +aaggaaggaaggagaaagagagaaagagagagagaagaagaaagagaaagaaacagaaaa +ggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggaaggagaaagaaag +gaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaaaag +aaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctctaggt +ggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataatcc +cagcactttgggaggccgaagcgggc +>syndip_1_chr20:34235650-34236314 +agcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccca +ggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacaga +gtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag +aaagaaagaaagaaggaaggaaggaaggaaggaaggaaaggaaggaaggaaggaaggaag +gaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaggagggagggaagaat +gaaggaaggaaggaaggaaggaaggaaggaaggaagcgggagggagggaagaaggaagga +aggaaggaaggagggagggagggaagaaggaaggaggagggagggagggaagcaggaaag +aaggaaggaaggagaaagagagaaagagagagagaagaagaaagagaaagaaacagaaaa +ggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggaaggagaaagaaag +gaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaaaag +aaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctctaggt +ggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataatcc +cagcactttgggaggccgaagcgggc +>syndip_2_chr20:34235650-34236314 +agcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccca +ggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacaga +gtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag +aaagaaagaaagaaggaaggaaggaaggaaggaaggaaaggaaggaaggaaggaaggaag +gaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaggagggagggaagaat +gaaggaaggaaggaaggaaggaaggaaggaaggaagcgggagggagggaagaaggaagga +aggaaggaaggagggagggagggaagaaggaaggaggagggagggagggaagcaggaaag +aaggaaggaaggagaaagagagaaagagagagagaagaagaaagagaaagaaacagaaaa +ggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggaaggagaaagaaag +gaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaaaag +aaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctctaggt +ggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataatcc +cagcactttgggaggccgaagcgggc +>p:HG002_1_chr20:34235650-34236314 +agcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccca +ggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacaga +gtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag +aaagaaagaaagaaggaaggaaggaaggaaggaaggaaaggaaggaaggaaggaaggaag +gaaggaaggaaaggaa-ggaaggaaggaaggaaggaaggaagcgggagggagggaagaag +gaaggaaggaaggaaggagggaaggaaggaaggaagcgggagggagggaagaaggaagga +aggaaggaaggagggagggagggaagaaggaaggaggagggagggagggaagaaggaaag +aaggaaggaaggagaaagagagaaagagagagagaagaagaaagagaaagaaacagaaaa +ggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggaaggagaaagaaag +gaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaaaag +aaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctctaggt +ggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataatcc +cagcactttgggaggccgaagcgggc +>p:HG002_2_chr20:34235650-34236314 +agcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccca +ggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacaga +gtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag +aaagaaagaaagaaggaaggaaggaaggaaggaaggaaaggaaggaaggaaggaaggaag +gaaggaaggaaaggaa-ggaaggaaggaaggaaggaaggaagcgggagggagggaagaag +gaaggaaggaaggaaggagggaaggaaggaaggaagcgggagggagggaagaaggaagga +aggaaggaaggagggagggagggaagaaggaaggaggagggagggagggaagaaggaaag +aaggaaggaaggagaaagagagaaagagagagagaagaagaaagagaaagaaacagaaaa +ggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggaaggagaaagaaag +gaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaaaag +aaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctctaggt +ggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataatcc +cagcactttgggaggccgaagcgggc diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/msa.fa.fai new file mode 100644 index 00000000..483d93f0 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_34235650_34236314 746 29 60 61 +syndip_1_chr20:34235650-34236314 746 822 60 61 +syndip_2_chr20:34235650-34236314 746 1615 60 61 +p:HG002_1_chr20:34235650-34236314 746 2409 60 61 +p:HG002_2_chr20:34235650-34236314 746 3203 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/output.vcf.gz new file mode 100644 index 00000000..27c4a340 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/output.vcf.gz.tbi new file mode 100644 index 00000000..9c09f117 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:34235750-34236214/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/base.vcf.gz new file mode 100644 index 00000000..a1c31ba7 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/base.vcf.gz.tbi new file mode 100644 index 00000000..5768be8d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/comp.vcf.gz new file mode 100644 index 00000000..89a3ed16 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/comp.vcf.gz.tbi new file mode 100644 index 00000000..95762d70 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/haps.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/haps.fa new file mode 100644 index 00000000..e8a42173 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/haps.fa @@ -0,0 +1,146 @@ +>ref_chr20_38123490_38124806 +TTTTAAGTCCACAGCCTGTGACCAATGGCAACAGAGCAGAAGGTTAGAGCAATTACTGTGGATGGAGCTTGCCCAGTAGGCCTCCTAGCTCCATTTTCTAGCTTTGTGATCTCAGGCCTGTCCTGTAACCTCTCTGGGCCTCAGAAACCTCTCTCTCTCTCTATATATATATATATATAATAATATATAATAATAATATATAATATGTATAATAATAATATATAATATTTATAATAATAATATATATAATATGTATATATAATATACATATACCTATTATATATAATATACCTATTATATATAATATACATAAACCTATTATATATAATATACCTATTATATATAAGATACCTATTATATATAATATACCTATTATATATAAGATACCTATTATATATAATATACATATACCTATTATATATATAATATACCTATTATATATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTATATATAATACACATTATATATAATATATAACACACATTATATATAATATATAACACACATTATATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACACATTATATATTATATATAATACACATTATATATAATATATAATACACATTATATATAATACTTATTATATATTATACATAATATACATATTATATATAATACATAATATACGTATATTATATAATATACATATTATATATAATACATAATATACGTATATTATATAATATACATATTATATATATTATACTATATATAATACTCATATATATACATATTATATATACATATTATATATAATACTCATATTATATGTACATATTATACATACATATTATATATAATACACATATATACATATTATATATAATACACACACACATTATATATGTCTTATATATAATATACATATTATATATGTATTATATTATTATAGATATAATATACATATTATATCTATATATAAAATATATATGTAGAGAGAGAGAGACAGGGTCTCATTTTGTCTCCCAGGCTGGAGTGCAGTGGTGCAATCTTGGCTCACTACAACCTCCACCTCCCAGGCTCAAGGGATCCTCCAGCTTCAGCCCCCCGAGTACCTGGGACTACAGGAACGCGTCACCATGCCTGGCTAATTTTTTTTTATTTTTTGTAGAGATGGGGTTTCGCCATGTTGCCGAGGCTGGTGTCAA +>syndip_1_chr20:38123490-38124806 +TTTTAAGTCCACAGCCTGTGACCAATGGCAACAGAGCAGAAGGTTAGAGCAATTACTGTG +GATGGAGCTTGCCCAGTAGGCCTCCTAGCTCCATTTTCTAGCTTTGTGATCTCAGGCCTG +TCCTGTAACCTCTCTGGGCCTCAGAAACCTCTCTCTCTCTCTATATATATATATATATAA +TAATATATAATAATAATATATAATATGTATAATAATAATATATAATATTTATAATAATAA +TATATATAATATGTATATATAATATACATATACCTATTATATATAATATACCTATTATAT +ATAATATACATATACCTATTATATATAATATACCTATTATATATAAGATACCTATTATAT +ATAATATACATATACCTATTATATATATAATATACCTATTATATATATATAATATACCTA +TTATATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTA +TTATATATATAATATACCTATTATATATAATATACCTATTATATATAAAATATACCTATT +ATATATAATATACCTATTATATACATTATATATAATATACCTATTATATGCATTATATAT +AATATACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATA +CCTATTATATGCATTATATATAATATACCTATTATATGCATTATATAATATATTATATAT +AATATGCATATTATATGTATTATATATTATATATTATATATATAATATACATATTATATG +TATTATATATTATATATTATATATATAATATACATATTATATGTATTATATATTATATAT +AATATACATATTATATATTATATATTATATACATATTATATATTATATATTATATACATA +TTATATATTATATACATATTATATATTATATATTATATACATATTATACATTATATATAT +CTAAAATATATAATACACATTATATATTATATAATACACATTATATATAATATATAATAC +ACATTATATATTATATATAATACACATTATATATTATATATAATACACATTATATATTAT +ATAATACACATTATATATTATATATAATACACATTATATATTATATATAATACACATTAT +ATATTATATATAATACACATTATATATTATATAATACACATTATATATTATATATAATAC +ACATTATATATATAATACACATTATATATTATATATAATACATAATACACATTATATATT +ATATATAATACACATTATATATAATATATAACACACATTATATATAATATATAACACACA +TTATATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAA +TACACATTATATATTATATATAATACACATATATTATATATAATACACATTATATATTAT +ATATAATACACATTATATATAATATATAATACACATTATATATAATACTTATTATATATT +ATACATAATATACATATTATATATAATACATAATATACGTATATTATATAATATACATAT +TATATATAATACATAATATACGTATATTATATAATATACATATTATATATATTATACTAT +ATATAATACTCATATATATACATATTATATATACATATTATATATAATACTCATATTATA +TGTACATATTATACATACATATTATATATAATACACATATATACATATTATATATAATAC +ACACACACATTATATATGTCTTATATATAATATACATATTATATATGTATTATATTATTA +TAGATATAATATACATATTATATCTATATATAAAATATATATGTAGAGAGAGAGAGACAG +GGTCTCATTTTGTCTCCCAGGCTGGAGTGCAGTGGTGCAATCTTGGCTCACTACAACCTC +CACCTCCCAGGCTCAAGGGATCCTCCAGCTTCAGCCCCCCGAGTACCTGGGACTACAGGA +ACGCGTCACCATGCCTGGCTAATTTTTTTTTATTTTTTGTAGAGATGGGGTTTCGCCATG +TTGCCGAGGCTGGTGTCAA +>syndip_2_chr20:38123490-38124806 +TTTTAAGTCCACAGCCTGTGACCAATGGCAACAGAGCAGAAGGTTAGAGCAATTACTGTG +GATGGAGCTTGCCCAGTAGGCCTCCTAGCTCCATTTTCTAGCTTTGTGATCTCAGGCCTG +TCCTGTAACCTCTCTGGGCCTCAGAAACCTCTCTCTCTCTCTATATATATATATATATAA +TAATATATAATAATAATATATAATATGTATAATAATAATATATAATATTTATAATAATAA +TATATATAATATGTATATATAATATACATATACCTATTATATATAATATACCTATTATAT +ATAATATACATATACCTATTATATATAATATACCTATTATATATAAGATACCTATTATAT +ATAATATACATATACCTATTATATATATAATATACCTATTATATATATATAATATACCTA +TTATATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTA +TTATATATATAATATACCTATTATATATAATATACCTATTATATATAAAATATACCTATT +ATATATAATATACCTATTATATACATTATATATAATATACCTATTATATGCATTATATAT +AATATACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATA +CCTATTATATGCATTATATAATATATTATATATAATATGCATATTATATGTATTATATAT +TATATATTATATATATAATATACATATTATATGTATTATATATTATATATTATATATATA +ATATACATATTATATGTATTATATATTATATATAATATACATATTATATATTATATATTA +TATACATATTATATATTATATATTATATACATATTATATATTATATACATATTATATATT +ATATATTATATACATATTATACATTATATATATCTAAAATATATAATACACATTATATAT +TATATAATACACATTATATATAATATATAATACACATTATATATTATATATAATACACAT +TATATATTATATATAATACACATTATATATTATATAATACACATTATATATTATATATAA +TACACATTATATATTATATATAATACACATTATATATTATATATAATACACATTATATAT +TATATATAATACACATTATATATTATATAATACACATTATATATTATATATAATACACAT +TATATATATAATACACATTATATATTATATATAATACATAATACACATTATATATTATAT +ATAATACACATTATATATAATATATAACACACATTATATATAATATATAACACACATTAT +ATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACA +CATTATATATTATATATAATACACATATATTATATATAATACACATTATATATTATATAT +AATACACATTATATATAATATATAATACACATTATATATAATACTTATTATATATTATAC +ATAATATACATATTATATATAATACATAATATACGTATATTATATAATATACATATTATA +TATAATACATAATATACGTATATTATATAATATACATATTATATATATTATACTATATAT +AATACTCATATATATACATATTATATATACATATTATATATAATACTCATATTATATGTA +CATATTATACATACATATTATATATAATACACATATATACATATTATATATAATACACAC +ACACATTATATATGTCTTATATATAATATACATATTATATATGTATTATATTATTATAGA +TATAATATACATATTATATCTATATATAAAATATATATGTAGAGAGAGAGAGACAGGGTC +TCATTTTGTCTCCCAGGCTGGAGTGCAGTGGTGCAATCTTGGCTCACTACAACCTCCACC +TCCCAGGCTCAAGGGATCCTCCAGCTTCAGCCCCCCGAGTACCTGGGACTACAGGAACGC +GTCACCATGCCTGGCTAATTTTTTTTTATTTTTTGTAGAGATGGGGTTTCGCCATGTTGC +CGAGGCTGGTGTCAA +>p:HG002_1_chr20:38123490-38124806 +TTTTAAGTCCACAGCCTGTGACCAATGGCAACAGAGCAGAAGGTTAGAGCAATTACTGTG +GATGGAGCTTGCCCAGTAGGCCTCCTAGCTCCATTTTCTAGCTTTGTGATCTCAGGCCTG +TCCTGTAACCTCTCTGGGCCTCAGAAACCTCTCTCTCTCTCTATATATATATATATATAA +TAATATATAATAATAATATATAATATGTATAATAATAATATATAATATTTATAATAATAA +TATATATAATATGTATATATAATATACATATACCTATTATATATAATATACCTATTATAT +ATAATATACATAAACCTATTATATATAATATACCTATTATATATAAGATACCTATTATAT +ATAATATACCTATACCTATTATATATATAAGATACCTATTATATATAATATACATACCTA +TTACCTATTATATATATAATATACCTATTATATATATATAATATACCTATTATATATATA +ATATACCTATTATACCTATTATATATAATATACCTATTATATATATAATATACCTATTAT +ATATAATATACCTATTATATACATTATATATAATATACCTATTATATGCATTATATATAA +TATACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATACC +TATTATATGCATTATATAATATATTATATATAATATGCATATTATATGTATTATATATTA +TATATTATATATATAATATACATATTATATGTATTATATATTATATATTATATATATAAT +ATACATATTATATGTATTATATATTATATATAATATACATATTATATATTATATATTATA +TACATATTATATATTATATATTATATACATATTATATATTATATACATATTATATATTAT +ATATTATATACATATTATACATTATATATATCTAAAATATATAATACACATTATATATTA +TATAATACACATTATATATAATATATAATACACATTATATATTATATATAATACACATTA +TATATTATATATAATACACATTATATATTATATAATACACATTATATATTATATATAATA +CACATTATATATTATATATAATACACATTATATATTATATATAATACACATTATATATTA +TATATAATACACATTATATATTATATAATACACATTATATATTATATATAATACACATTA +TATATATAATACACATTATATATTATATATAATACATAATACACATTATATATTATATAT +AATACACATTATATATAATATATAACACACATTATATATAATATATAACACACATTATAT +ATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACACA +TTATATATTATATATAATACACATATATTATATATAATACACATTATATATTATATATAA +TACACATTATATATAATATATAATACACATTATATATAATACTTATTATATATTATACAT +AATATACATATTATATATAATACATAATATACGTATATTATATAATATACATATTATATA +TAATACATAATATACGTATATTATATAATATACATATTATATATATTATACTATATATAA +TACTCATATATATACATATTATATATACATATTATATATAATACTCATATTATATGTACA +TATTATACATACATATTATATATAATACACATATATACATATTATATATAATACACACAC +ACATTATATATGTCTTATATATAATATACATATTATATATGTATTATATTATTATAGATA +TAATATACATATTATATCTATATATAAAATATATATGTAGAGAGAGAGAGACAGGGTCTC +ATTTTGTCTCCCAGGCTGGAGTGCAGTGGTGCAATCTTGGCTCACTACAACCTCCACCTC +CCAGGCTCAAGGGATCCTCCAGCTTCAGCCCCCCGAGTACCTGGGACTACAGGAACGCGT +CACCATGCCTGGCTAATTTTTTTTTATTTTTTGTAGAGATGGGGTTTCGCCATGTTGCCG +AGGCTGGTGTCAA +>p:HG002_2_chr20:38123490-38124806 +TTTTAAGTCCACAGCCTGTGACCAATGGCAACAGAGCAGAAGGTTAGAGCAATTACTGTG +GATGGAGCTTGCCCAGTAGGCCTCCTAGCTCCATTTTCTAGCTTTGTGATCTCAGGCCTG +TCCTGTAACCTCTCTGGGCCTCAGAAACCTCTCTCTCTCTCTATATATATATATATATAA +TAATATATAATAATAATATATAATATGTATAATAATAATATATAATATTTATAATAATAA +TATATATAATATGTATATATAATATACATATACCTATTATATATAATATACCTATTATAT +ATAATATACATAAACCTATTATATATAATATACCTATTATATATAAGATACCTATTATAT +ATAATATACCTATACCTATTATATATATAATATACCTTATATATAAGATACCTATTATAT +ATAATATACATATACCTATTATATATATAATATACCTATTATATATATATAATATACCTA +TTATATATATAATATACCTATTATATATATAATATACCTATTATATATATAATACCTATT +ATATATAATATACCTATTATATACATTATATATAATATACCTATTATATGCATTATATAT +AATATACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATA +CCTATTATATGCATTATATATAATATACCTATTATATGCATTATATAATATATTATATAT +AATATGCATATTATATGTATTATATATTATATATTATATATATAATATACATATTATATG +TATTATATATTATATATTATATATATAATATACATATTATATGTATTATATATTATATAT +AATATACATATTATATATTATATATTATATACATATTATATATTATATATTATATACATA +TTATATATTATATACATATTATATATTATATATTATATACATATTATACATTATATATAT +CTAAAATATATAATACACATTATATATTATATAATACACATTATATATAATATATAATAC +ACATTATATATTATATATAATACACATTATATATTATATATAATACACATTATATATTAT +ATAATACACATTATATATTATATATAATACACATTATATATTATATATAATACACATTAT +ATATTATATATAATACACATTATATATTATATAATACACATTATATATTATATATAATAC +ACATTATATATATAATACACATTATATATTATATATAATACATAATACACATTACCTATT +ATATATAATACACATTATATATAATATATAACACACATTATATATAATATATAACACACA +TTATATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAA +TACACATTATATATTATATATAATACACATATATTATATATAATACACATTATATATTAT +ATATAATACACATTATATATAATATATAATACACATTATATATAATACTTATTATATATT +ATACATAATATACATATTATATATAATACATAATATACGTATATTATATAATATACATAT +TATATATAATACATAATATACGTATATTATATAATATACATATTATATATATTATACTAT +ATATAATACTCATATATATACATATTATATATACATATTATATATAATACTCATATTATA +TGTACATATTATACATACATATTATATATAATACACATATATACATATTATATATAATAC +ACACACACATTATATATGTCTTATATATAATATACATATTATATATGTATTATATTATTA +TAGATATAATATACATATTATATCTATATATAAAATATATATGTAGAGAGAGAGAGACAG +GGTCTCATTTTGTCTCCCAGGCTGGAGTGCAGTGGTGCAATCTTGGCTCACTACAACCTC +CACCTCCCAGGCTCAAGGGATCCTCCAGCTTCAGCCCCCCGAGTACCTGGGACTACAGGA +ACGCGTCACCATGCCTGGCTAATTTTTTTTTATTTTTTGTAGAGATGGGGTTTCGCCATG +TTGCCGAGGCTGGTGTCAA diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/haps.fa.ref.fa new file mode 100644 index 00000000..5cab64c6 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:38123490-38124806 +TTTTAAGTCCACAGCCTGTGACCAATGGCAACAGAGCAGAAGGTTAGAGCAATTACTGTGGATGGAGCTTGCCCAGTAGGCCTCCTAGCTCCATTTTCTAGCTTTGTGATCTCAGGCCTGTCCTGTAACCTCTCTGGGCCTCAGAAACCTCTCTCTCTCTCTATATATATATATATATAATAATATATAATAATAATATATAATATGTATAATAATAATATATAATATTTATAATAATAATATATATAATATGTATATATAATATACATATACCTATTATATATAATATACCTATTATATATAATATACATAAACCTATTATATATAATATACCTATTATATATAAGATACCTATTATATATAATATACCTATTATATATAAGATACCTATTATATATAATATACATATACCTATTATATATATAATATACCTATTATATATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTATATATAATACACATTATATATAATATATAACACACATTATATATAATATATAACACACATTATATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACACATTATATATTATATATAATACACATTATATATAATATATAATACACATTATATATAATACTTATTATATATTATACATAATATACATATTATATATAATACATAATATACGTATATTATATAATATACATATTATATATAATACATAATATACGTATATTATATAATATACATATTATATATATTATACTATATATAATACTCATATATATACATATTATATATACATATTATATATAATACTCATATTATATGTACATATTATACATACATATTATATATAATACACATATATACATATTATATATAATACACACACACATTATATATGTCTTATATATAATATACATATTATATATGTATTATATTATTATAGATATAATATACATATTATATCTATATATAAAATATATATGTAGAGAGAGAGAGACAGGGTCTCATTTTGTCTCCCAGGCTGGAGTGCAGTGGTGCAATCTTGGCTCACTACAACCTCCACCTCCCAGGCTCAAGGGATCCTCCAGCTTCAGCCCCCCGAGTACCTGGGACTACAGGAACGCGTCACCATGCCTGGCTAATTTTTTTTTATTTTTTGTAGAGATGGGGTTTCGCCATGTTGCCGAGGCTGGTGTCAA diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/msa.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/msa.fa new file mode 100644 index 00000000..16f18f58 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/msa.fa @@ -0,0 +1,185 @@ +>ref_chr20_38123490_38124806 +ttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgtg +gatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcctg +tcctgtaacctctctgggcctcagaaacctctctctctctctatatatatatatatataa +taatatataataataatatataatatgtataataataatatataatatttataataataa +tatatataatatgtatatataatatacatatacctattatatataatatacctattatat +ataatatacataaacctattatatataatatacctattatatataagatacctattatat +ataatatacctat--------tatatataagatacct----------------attatat +ataatatacata------------------tacctattatatatataatatacctattat +atatatataatatacctattatatatataatatacctatta------------------- +------------------------------------------------------------ +-------------tatatataatatacctattatatatataata---------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------tacctattatatataatacacatta +tatataatatataacacacattatatataatatataacacacattatatattatatataa +tacacattatatattatatataatacacatatattatatataatacacattatatattat +atataatacacatatattatatataatacacattatatattatatataatacacattata +tataatatataatacacattatatataatacttattatatattatacataatatacatat +tatatataatacataatatacgtatattatataatatacatattatatataatacataat +atacgtatattatataatatacatattatatatattatactatatataatactcatatat +atacatattatatatacatattatatataatactcatattatatgtacatattatacata +catattatatataatacacatatatacatattatatataatacacacacacattatatat +gtcttatatataatatacatattatatatgtattatattattatagatataatatacata +ttatatctatatataaaatatatatgtagagagagagagacagggtctcattttgtctcc +caggctggagtgcagtggtgcaatcttggctcactacaacctccacctcccaggctcaag +ggatcctccagcttcagccccccgagtacctgggactacaggaacgcgtcaccatgcctg +gctaatttttttttattttttgtagagatggggtttcgccatgttgccgaggctggtgtc +aa +>syndip_1_chr20:38123490-38124806 +ttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgtg +gatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcctg +tcctgtaacctctctgggcctcagaaacctctctctctctctatatatatatatatataa +taatatataataataatatataatatgtataataataatatataatatttataataataa +tatatataatatgtatatataatatacatatacctattatatataatatacctattatat +ataatatacatatacctattatatataatatacctattatatataagatacctattatat +ataatatacatatacctattatatatataatatacct----------------attatat +atatataatatacctattatatatataatatacctattatatatataatatacctat--t +atatatataatatacctattatatatataatatacctattatatata--atatacctatt +atatataaaatatacctattatatataatatacctattatatacattatatataatatac +ctattatatgcattatatataatatacctattatatgcattatatataatatacctatta +tatgcattatatataatatacctattatatgcattatatataatatacctattatatgca +ttatataatatattatatataatatgcatattatatgtattatatattatatattatata +tataatatacatattatatgtattatatattatatattatatatataatatacatattat +atgtattatatattatatataatatacatattatatattatatattatatacatattata +tattatatattatatacatattatatattatatacatattatatattatatattatatac +atattatacattatatatatctaaaatatataatacacattatatattatataatacaca +ttatatataatatataatacacattatatattatatataatacacattatatattatata +taatacacattatatat-----------------------tatataatacacattatata +ttatatataatacacattatatattatatataatacacattatatattatatataataca +cattatatattatataatacacattatatattatatataatacacattatatatataata +cacattatatattatatataatacataatacacattatatattatatataatacacatta +tatataatatataacacacattatatataatatataacacacattatatattatatataa +tacacattatatattatatataatacacatatattatatataatacacattatatattat +atataatacacatatattatatataatacacattatatattatatataatacacattata +tataatatataatacacattatatataatacttattatatattatacataatatacatat +tatatataatacataatatacgtatattatataatatacatattatatataatacataat +atacgtatattatataatatacatattatatatattatactatatataatactcatatat +atacatattatatatacatattatatataatactcatattatatgtacatattatacata +catattatatataatacacatatatacatattatatataatacacacacacattatatat +gtcttatatataatatacatattatatatgtattatattattatagatataatatacata +ttatatctatatataaaatatatatgtagagagagagagacagggtctcattttgtctcc +caggctggagtgcagtggtgcaatcttggctcactacaacctccacctcccaggctcaag +ggatcctccagcttcagccccccgagtacctgggactacaggaacgcgtcaccatgcctg +gctaatttttttttattttttgtagagatggggtttcgccatgttgccgaggctggtgtc +aa +>syndip_2_chr20:38123490-38124806 +ttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgtg 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+ggatcctccagcttcagccccccgagtacctgggactacaggaacgcgtcaccatgcctg +gctaatttttttttattttttgtagagatggggtttcgccatgttgccgaggctggtgtc +aa +>p:HG002_1_chr20:38123490-38124806 +ttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgtg +gatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcctg +tcctgtaacctctctgggcctcagaaacctctctctctctctatatatatatatatataa +taatatataataataatatataatatgtataataataatatataatatttataataataa +tatatataatatgtatatataatatacatatacctattatatataatatacctattatat +ataatatacataaacctattatatataatatacctattatatataagatacctattatat +ataatatacctatacctattatatatataagatacct----------------attatat +ataatatacatacctat-------------tacctattatatatataatatacctattat +atatatataatatacctattatatatataatatacctat-----------tatacctatt +atatataatatacctattatatatataatatacct---------attatatataatatac +ctattatatacattatatataatatacctattatatgcattatatataatatacctatta +tatgcattatatataatatacctattatatgcattatatataatatacctattatatgca +ttatataatatattatatataatatgcatattatatgtattatatattatatattatata 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+catattatatataatacacatatatacatattatatataatacacacacacattatatat +gtcttatatataatatacatattatatatgtattatattattatagatataatatacata +ttatatctatatataaaatatatatgtagagagagagagacagggtctcattttgtctcc +caggctggagtgcagtggtgcaatcttggctcactacaacctccacctcccaggctcaag +ggatcctccagcttcagccccccgagtacctgggactacaggaacgcgtcaccatgcctg +gctaatttttttttattttttgtagagatggggtttcgccatgttgccgaggctggtgtc +aa +>p:HG002_2_chr20:38123490-38124806 +ttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgtg +gatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcctg +tcctgtaacctctctgggcctcagaaacctctctctctctctatatatatatatatataa +taatatataataataatatataatatgtataataataatatataatatttataataataa +tatatataatatgtatatataatatacatatacctattatatataatatacctattatat +ataatatacataaacctattatatataatatacctattatatataagatacctattatat +ataatatacctatacctattatatatataatataccttatatataagatacctattatat +ataatatacata------------------tacctattatatatataatatacctattat +atatatataatatacctattatatatataatatacctattatatatataatatacctatt +atatatataatacctattatatata--atatacctattatatacattatatataatatac +ctattatatgcattatatataatatacctattatatgcattatatataatatacctatta +tatgcattatatataatatacctattatatgcattatatataatatacctattatatgca +ttatataatatattatatataatatgcatattatatgtattatatattatatattatata +tataatatacatattatatgtattatatattatatattatatatataatatacatattat +atgtattatatattatatataatatacatattatatattatatattatatacatattata +tattatatattatatacatattatatattatatacatattatatattatatattatatac +atattatacattatatatatctaaaatatataatacacattatatattatataatacaca +ttatatataatatataatacacattatatattatatataatacacattatatattatata +taatacacattatatat-----------------------tatataatacacattatata +ttatatataatacacattatatattatatataatacacattatatattatatataataca +cattatatattatataatacacattatatattatatataatacacattatatatataata +cacattatatattatatataatacataatacacattacctattatatataatacacatta +tatataatatataacacacattatatataatatataacacacattatatattatatataa +tacacattatatattatatataatacacatatattatatataatacacattatatattat +atataatacacatatattatatataatacacattatatattatatataatacacattata +tataatatataatacacattatatataatacttattatatattatacataatatacatat +tatatataatacataatatacgtatattatataatatacatattatatataatacataat +atacgtatattatataatatacatattatatatattatactatatataatactcatatat +atacatattatatatacatattatatataatactcatattatatgtacatattatacata +catattatatataatacacatatatacatattatatataatacacacacacattatatat +gtcttatatataatatacatattatatatgtattatattattatagatataatatacata +ttatatctatatataaaatatatatgtagagagagagagacagggtctcattttgtctcc +caggctggagtgcagtggtgcaatcttggctcactacaacctccacctcccaggctcaag +ggatcctccagcttcagccccccgagtacctgggactacaggaacgcgtcaccatgcctg +gctaatttttttttattttttgtagagatggggtttcgccatgttgccgaggctggtgtc +aa diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/msa.fa.fai new file mode 100644 index 00000000..fa727735 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_38123490_38124806 2102 29 60 61 +syndip_1_chr20:38123490-38124806 2102 2201 60 61 +syndip_2_chr20:38123490-38124806 2102 4373 60 61 +p:HG002_1_chr20:38123490-38124806 2102 6546 60 61 +p:HG002_2_chr20:38123490-38124806 2102 8719 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/output.vcf.gz new file mode 100644 index 00000000..3629252f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/output.vcf.gz.tbi new file mode 100644 index 00000000..f2b28444 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:38123590-38124706/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/base.vcf.gz new file mode 100644 index 00000000..e18db582 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/base.vcf.gz.tbi new file mode 100644 index 00000000..195b9d7b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/comp.vcf.gz new file mode 100644 index 00000000..23f911e4 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/comp.vcf.gz.tbi new file mode 100644 index 00000000..b7f9c9ff Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/haps.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/haps.fa new file mode 100644 index 00000000..28c26a64 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/haps.fa @@ -0,0 +1,132 @@ +>ref_chr20_4032119_4033702 +CGGGATTGCAGATGAAGTCTCGTTCACTCAGTGCTCAGTGGTGTCCAGGCTGGAGTGCAGCGGCGTGATCTCGGCTCGCTACAACCACCTCCCAGCCGCCTGCCTTGGCCTCCCAAAGAGCCGAGATTGCAGCCTCTGCCCGGCCGCCACCCCGTCTGGGAAGTGAGGAGCGTCTCTGCTTGGCCACCCATCGTCTGGGATATGAGGAGCCCCTCTGCCTGGCTGCCCAGTCTGGAAAGTGAGGAGCGTCTCTGCCCGGCCGCCATCCCATCTAGGAAGCGAGGAGCGTCTCTGCCCGGCCGCCATCCCATCTAGGAAGCGAGGAGCGCCTCTTCCCGGCTGCCATCCCATCTAGGAACTGAGGAGCGTCTCTGCCCGGCCGCCCATCGTCTGAGATGTGGGGAGCACCTCTGCCCCACCGCCCTGTCTGGGATGTGAGGAGCGCCTCTGCTGGGCCGCAACCCTGTCTGGGAGGTGAGGAGCGTCTCTGCCCCGCCGCTCCGTCTGAGAAGTGAGGAAACCCTCTGCCTGGCAACCGCCCCGTCTGAGAAGTGAGGAGCCCCTCCGTCCGGCAACCACCCCGTCTGGGAAGTGAGGAGCGTCTCCGCCCGGCAGCCACCCCGTCCGGGAGGGAGGTGGGGGGGGGGGTCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCGGCCGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCGGCTGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCTGCCCCGCCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCTGGCCAGCCGCCCCATCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGGGGGAGGGGGGGTCAGCCCCCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGGGGTCAGCCCCCTTTCCGGCCGCCGCCTGTCCGGGAGGTGAGGGGCGCCTCTGCCTGGCCGCCCCTACTGGGAAGTGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGACAGCCCCCCGCCCGGCCAGCCGCCCTATCCAGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCTGGCCAGCCGCCCCGTCCGGGAGGGTAGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCATCCGGGAGGTGAGGGGCGCTTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCACGACCCCGTCTGGGAGGTGTGCCCAGCGGCTCATTGGGGATGGGCCATGATGACAATGGCGGTTTTGTGGAATAGAAAGGCGGGAAGGGTGGGGAAAAAATTGAGAAATCGGATGGTTGCCGGGTCTGTGTGGATGGAAGTAGACATG +>syndip_1_chr20:4032119-4033702 +CGGGATTGCAGATGAAGTCTCGTTCACTCAGTGCTCAGTGGTGTCCAGGCTGGAGTGCAG +CGGCGTGATCTCGGCTCGCTACAACCACCTCCCAGCCGCCTGCCTTGGCCTCCCAAAGAG +CCGAGATTGCAGCCTCTGCCCGGCCGCCACCCCGTCTGGGAAGTGAGGAGCGTCTCTGCT +TGGCCACCCATCGTCTGGGATATGAGGAGCCCCTCTGCCTGGCTGCCCAGTCTGGAAAGT +GAGGAGCGTCTCTGCCCGGCCGCCATCCCATCTAGGAAGCGAGGAGCGCCTCTTCCCGGC +TGCCATCCCATCTAGGAACTGAGGAGCGTCTCTGCCCGGCCGCCCATCGTCTGAGATGTG +GGGAGCACCTCTGCCCCACCGCCCTGTCTGGGATGTGAGGAGCGCCTCTGCTGGGCCGCA +ACCCTGTCTGGGAGGTGAGGAGCGTCTCTGCCCCGCCGCTCCGTCTGAGAAGTGAGGAAA +CCCTCTGCCTGGCAACCGCCCCGTCTGAGAAGTGAGGAGCCCCTCCGTCCGGCAACCACC +CCGTCTGGGAAGTGAGGAGCGTCTCCGCCCGGCAGCCACCCCGTCCGGGAGGGAGGTGGG +GGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGTGAGGGGCTCCTCTGCCC +GGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGG +GAGGCGGGGGGGGGGGTCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCC +CCCGCCCGGCCGGCCGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTAC +TGGGAAGTGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGT +CAGCCCCCCGCCCGGCCGGCTGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGC +CCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCTGCCCCGCCCGGGAGGGAGGTG +GGGGGGTCAGCCCCCCGCCTGGCCAGCCGCCCCATCCGGGAGGGAGGTGGGGGGGTCAGC +CCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGGGGGAGGGGGGGTCAGCCCCCTGCCCGG +CCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCC +CCGTCCGGGAGGGAGGTGGGGGGATCAGCCCCCCGCCTGGCCAGCCGCCCCGTCCGGGAG +GTGAGGGGCGCCTCTGCCCGGCCACCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCC +AGCCGCCCCGTCCGGGAGGGAGGCGGGGGGGGGGGTCGGCCAGCCGCCCCGTCCGGGAGG +GAGGTGGGGGGGTCAGCCCCCTTTCCGGCCGCCGCCTGTCCGGGAGGTGAGGGGCGCCTC +TGCCTGGCCGCCCCTACTGGGAAGTGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCCGG +GAGGGAGGTGGGGGGGACAGCCCCCCGCCCGGCCAGCCGCCCTATCCAGGAGGTGAGGGG +CGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCTGGCCAGCCGCCC +CGTCCGGGAGGGTAGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCATCCGGGAGG +TGAGGGGCGCTTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCA +CGACCCCGTCTGGGAGGTGTGCCCAGCGGCTCATTGGGGATGGGCCATGATGACAATGGC +GGTTTTGTGGAATAGAAAGGCGGGAAGGGTGGGGAAAAAATTGAGAAATCGGATGGTTGC +CGGGTCTGTGTGGATGGAAGTAGACATG +>syndip_2_chr20:4032119-4033702 +CGGGATTGCAGATGAAGTCTCGTTCACTCAGTGCTCAGTGGTGTCCAGGCTGGAGTGCAG +CGGCGTGATCTCGGCTCGCTACAACCACCTCCCAGCCGCCTGCCTTGGCCTCCCAAAGAG +CCGAGATTGCAGCCTCTGCCCGGCCGCCACCCCGTCTGGGAAGTGAGGAGCGTCTCTGCT +TGGCCACCCATCGTCTGGGATATGAGGAGCCCCTCTGCCTGGCTGCCCAGTCTGGAAAGT +GAGGAGCGTCTCTGCCCGGCCGCCATCCCATCTAGGAAGCGAGGAGCGTCTCTGCCCGGC +CGCCATCCCATCTAGGAAGCGAGGAGCGCCTCTTCCCGGCTGCCATCCCATCTAGGAACT +GAGGAGCGTCTCTGCCCGGCCGCCCATCGTCTGAGATGTGGGGAGCACCTCTGCCCCACC +GCCCTGTCTGGGATGTGAGGAGCGCCTCTGCTGGGCCGCAACCCTGTCTGGGAGGTGAGG +AGCGTCTCTGCCCCGCCGCTCCGTCTGAGAAGTGAGGAAACCCTCTGCCTGGCAACCGCC +CCGTCTGAGAAGTGAGGAGCCCCTCCGTCCGGCAACCACCCCGTCTGGGAAGTGAGGAGC +GTCTCCGCCCGGCAGCCACCCCGTCCGGGAGGGAGGTGGGGGGGGGGGTCGGCCAGCCGC +CCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCGGCCGCCCCGTCCGGGA +GGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGACCCCTCTGCCCGGCC +AGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCGGCTGCCCCGT +CCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTG +CCCGGCCAGCTGCCCCGCCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCTGGCCAGCC +GCCCCATCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGG +GAGGGGGGAGGGGGGGTCAGCCCCCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGG +GGGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGATC +AGCCCCCCGCCTGGCCAGCCGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCACC +CCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGCGG +GGGGGGGGGTCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCTTTCC +GGCCGCCGCCTGTCCGGGAGGTGAGGGGCGCCTCTGCCTGGCCGCCCCTACTGGGAAGTG +AGGACCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGACAGCCCCCC +GCCCGGCCAGCCGCCCTATCCAGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGG +GAAGTGAGGAGCCCCTCTGCCTGGCCAGCCGCCCCGTCCGGGAGGGTAGTGGGGGGGTCA +GCCCCCCGCCCGGCCAGCCGCCCCATCCGGGAGGTGAGGGGCGCTTCTGCCCGGCCGCCC +CTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCACGACCCCGTCTGGGAGGTGTGCCCAG +CGGCTCATTGGGGATGGGCCATGATGACAATGGCGGTTTTGTGGAATAGAAAGGCGGGAA +GGGTGGGGAAAAAATTGAGAAATCGGATGGTTGCCGGGTCTGTGTGGATGGAAGTAGACA +TG +>p:HG002_1_chr20:4032119-4033702 +CGGGATTGCAGATGAAGTCTCGTTCACTCAGTGCTCAGTGGTGTCCAGGCTGGAGTGCAG +CGGCGTGATCTCGGCTCGCTACAACCACCTCCCAGCCGCCTGCCTTGGCCTCCCAAAGAG +CCGAGATTGCAGCCTCTGCCCGGCCGCCACCCCGTCTGGGAAGTGAGGAGCGTCTCTGCT +TGGCCACCCATCGTCTGGGATATGAGGAGCCCCTCTGCCTGGCTGCCCAGTCTGGAAAGT +GAGGAGCGTCTCTGCCCGGCCGCCATCCCATCTAGGAAGCGAGGAGCGTCTCTGCCCGGC +CGCCATCCCATCTAGGAAGCGAGGAGCGCCTCTTCCCGGCTGCCATCCCATCTAGGAACT +GAGGAGCGTCTCTGCCCGGCCGCCCATCGTCTGAGATGTGGGGAGCACCTCTGCCCCACC +GCCCTGTCTGGGATGTGAGGAGCGCCTCTGCTGGGCCGCAACCCTGTCTGGGAGGTGAGG +AGCGTCTCTGCCCCGCCGCTCCGTCTGAGAAGTGAGGAAACCCTCTGCCTGGCAACCGCC +CCGTCTGAGAAGTGAGGAGCCCCTCCGTCCGGCAACCACCCCGTCTGGGAAGTGAGGAGC +GTCTCCGCCCGGCAGCCACCCCGTCCGGGAGGGAGGTGGGGGGGGGGGTCGGCCAGCCGC +CCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCGGCCGCCCCGTCCGGGA +GGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGACCCCTCTGCCCGGCC +AGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCGGCTGCCCCGT +CCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTG +CCCGGCCAGCTGCCCCGCCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCTGGCCAGCC +GCCCCATCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGG +GAGGGGGGAGGGGGGGTCAGCCCCCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGG +GGGGGGGGTCAGCCCCCTTTCCGGCCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGATC +AGCCCCCCGCCTGGCCAGCCGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCACC +CCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGCGG +GGGGGGGGGTCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCTTCC +GGCCGGGCCGCCTGTCCGGGAGGTGAGGGGCGCCTCTGCCTGGCCGCCCCTACTGGGAAG +TGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGACAGCCCC +CCGCCCGGCCAGCCGCCCTATCCAGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACT +GGGAAGTGAGGAGCCCCTCTGCCTGGCCAGCCGCCCCGTCCGGGAGGGTAGTGGGGGGGT +CAGCCCCCCGCCCGGCCAGCCGCCCCATCCGGGAGGTGAGGGGCGCTTCTGCCCGGCCGC +CCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCACGACCCCGTCTGGGAGGTGTGCCC +AGCGGCTCATTGGGGATGGGCCATGATGACAATGGCGGTTTTGTGGAATAGAAAGGCGGG +AAGGGTGGGGAAAAAATTGAGAAATCGGATGGTTGCCGGGTCTGTGTGGATGGAAGTAGA +CATG +>p:HG002_2_chr20:4032119-4033702 +CGGGATTGCAGATGAAGTCTCGTTCACTCAGTGCTCAGTGGTGTCCAGGCTGGAGTGCAG +CGGCGTGATCTCGGCTCGCTACAACCACCTCCCAGCCGCCTGCCTTGGCCTCCCAAAGAG +CCGAGATTGCAGCCTCTGCCCGGCCGCCACCCCGTCTGGGAAGTGAGGAGCGTCTCTGCT +TGGCCACCCATCGTCTGGGATATGAGGAGCCCCTCTGCCTGGCTGCCCAGTCTGGAAAGT +GAGGAGCGTCTCTGCCCGGCCGCCATCCCATCTAGGAAGCGAGGAGCGTCTCTGCCCGGC +CGCCATCCCATCTAGGAAGCGAGGAGCGCCTCTTCCCGGCTGCCATCCCATCTAGGAACT +GAGGAGCGTCTCTGCCCGGCCGCCCATCGTCTGAGATGTGGGGAGCACCTCTGCCCCACC +GCCCTGTCTGGGATGTGAGGAGCGCCTCTGCTGGGCCGCAACCCTGTCTGGGAGGTGAGG +AGCGTCTCTGCCCCGCCGCTCCGTCTGAGAAGTGAGGAAACCCTCTGCCTGGCAACCGCC +CCGTCTGAGAAGTGAGGAGCCCCTCCGTCCGGCAACCACCCCGTCCGGGAGGGAGGTGGG +GGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGTGAGGGGCTCCTCTGCCC +GGCCGCCCCTACTGGGAAGTGAGGAGCGTCTCCGCCCGGCAGCCACCCCGTCCGGGAGGG +AGGTGGGGGGGGGGGTCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCC +CCGCCCGGCCGGCCGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACT +GGGAAGTGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTC +AGCCCCCCGCCCGGCCGGCTGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCC +CCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCTGCCCCGCCCGGGAGGGAGGTGG +GGGGGTCAGCCCCCCGCCTGGCCAGCCGCCCCATCCGGGAGGGAGGTGGGGGGGTCAGCC +CCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGGGGGAGGGGGGGTCAGCCCCCTGCCCGGC +CAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGGGGTCAGCCCCCTTTCCGGCCGCCGCCC +CGTCCGGGAGGGAGGTGGGGGGATCAGCCCCCCGCCTGGCCAGCCGCCCCGTCCGGGAGG +TGAGGGGCGCCTCTGCCCGGCCACCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCA +GCCGCCCCGTCCGGGAGGGAGGCGGGGGGGGGGGTCGGCCAGCCGCCCCGTCCGGGAGGG +AGGTGGGGGGGTCAGCCCCCCTTCCGGCCGGCCGCCCTGTCCGGGAGGTGAGGGGCGCCT +CTGCCTGGCCGCCCCTACTGGGAAGTGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCCG +GGAGGGAGGTGGGGGGGACAGCCCCCCGCCCGGCCAGCCGCCCTATCCAGGAGGTGAGGG +GCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCTGGCCAGCCGCC +CCGTCCGGGAGGGTAGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCATCCGGGAG +GTGAGGGGCGCTTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCC +ACGACCCCGTCTGGGAGGTGTGCCCAGCGGCTCATTGGGGATGGGCCATGATGACAATGG +CGGTTTTGTGGAATAGAAAGGCGGGAAGGGTGGGGAAAAAATTGAGAAATCGGATGGTTG +CCGGGTCTGTGTGGATGGAAGTAGACATG diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/haps.fa.ref.fa new file mode 100644 index 00000000..5d92d772 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:4032119-4033702 +CGGGATTGCAGATGAAGTCTCGTTCACTCAGTGCTCAGTGGTGTCCAGGCTGGAGTGCAGCGGCGTGATCTCGGCTCGCTACAACCACCTCCCAGCCGCCTGCCTTGGCCTCCCAAAGAGCCGAGATTGCAGCCTCTGCCCGGCCGCCACCCCGTCTGGGAAGTGAGGAGCGTCTCTGCTTGGCCACCCATCGTCTGGGATATGAGGAGCCCCTCTGCCTGGCTGCCCAGTCTGGAAAGTGAGGAGCGTCTCTGCCCGGCCGCCATCCCATCTAGGAAGCGAGGAGCGTCTCTGCCCGGCCGCCATCCCATCTAGGAAGCGAGGAGCGCCTCTTCCCGGCTGCCATCCCATCTAGGAACTGAGGAGCGTCTCTGCCCGGCCGCCCATCGTCTGAGATGTGGGGAGCACCTCTGCCCCACCGCCCTGTCTGGGATGTGAGGAGCGCCTCTGCTGGGCCGCAACCCTGTCTGGGAGGTGAGGAGCGTCTCTGCCCCGCCGCTCCGTCTGAGAAGTGAGGAAACCCTCTGCCTGGCAACCGCCCCGTCTGAGAAGTGAGGAGCCCCTCCGTCCGGCAACCACCCCGTCTGGGAAGTGAGGAGCGTCTCCGCCCGGCAGCCACCCCGTCCGGGAGGGAGGTGGGGGGGGGGGTCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCGGCCGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCGGCTGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCAGCTGCCCCGCCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCTGGCCAGCCGCCCCATCCGGGAGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGGGGGAGGGGGGGTCAGCCCCCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGGGGTCAGCCCCCTTTCCGGCCGCCGCCTGTCCGGGAGGTGAGGGGCGCCTCTGCCTGGCCGCCCCTACTGGGAAGTGAGGACCCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGGAGGTGGGGGGGACAGCCCCCCGCCCGGCCAGCCGCCCTATCCAGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCTGGCCAGCCGCCCCGTCCGGGAGGGTAGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCATCCGGGAGGTGAGGGGCGCTTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCACGACCCCGTCTGGGAGGTGTGCCCAGCGGCTCATTGGGGATGGGCCATGATGACAATGGCGGTTTTGTGGAATAGAAAGGCGGGAAGGGTGGGGAAAAAATTGAGAAATCGGATGGTTGCCGGGTCTGTGTGGATGGAAGTAGACATG diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/msa.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/msa.fa new file mode 100644 index 00000000..971318f7 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/msa.fa @@ -0,0 +1,175 @@ +>ref_chr20_4032119_4033702 +cgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgcag +cggcgtgatctcggctcgctacaaccacctcccagccgcctgccttggcctcccaaagag +ccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctctgct +tggccacccatcgtctgggatatgaggagcccctctgcctggctgcccagtctggaaagt +gaggagcgtctctgcccggccgccatcccatctaggaagcgaggagcgtctctgcccggc +cgccatcccatctaggaagcgaggagcgcctcttcccggctgccatcccatctaggaact +gaggagcgtctctgcccggccgcccatcgtctgagatgtggggagcacctctgccccacc +gccctgtctgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggtgagg +agcgtctctgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaaccgcc +ccgtctgagaagtgaggagcccctccgtccggcaaccaccccgt---------------- +------------------------------------------------------------ +-----------ctgggaagtgaggagcgtctccgcccggcagccaccccgtccgggaggg +aggt-------------------------------------------------------- +------------------------------------------------------------ +------------gggggggggggtcggccagccgccccgtccgggagggaggtggggggg +tcagccccccgcccggccggccgccccgtccgggaggtgaggggcgcctctgcccggccg +cccctactgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtg +ggggggtcagccccccgcccggccggctgccccgtccgggaggtgaggggcgcctctgcc +cggccgcccctactgggaagtgaggagcccctctgcccggccagctgccccgcccgggag +ggaggtgggggggtcagccccccgcctggccagccgccccatccgggagggaggtggggg +ggtcagccccccgcccggccagccgccccgtccgggaggggggagggggggtcagccccc +tgcccggccagccgccccgtccgggagggaggtggggggggg------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------gtcagccccctttccggcc--gccgcctgtccgggaggtg +aggggcgcctctgcctggccgcccctactgggaagtgaggacccctctgcccggccagcc +gccccgtccgggagggaggtgggggggacagccccccgcccggccagccgccctatccag +gaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggagcccctctgcctg +gccagccgccccgtccgggagggtagtgggggggtcagccccccgcccggccagccgccc +catccgggaggtgaggggcgcttctgcccggccgcccctactgggaagtgaggagcccct +ctgcccggccacgaccccgtctgggaggtgtgcccagcggctcattggggatgggccatg +atgacaatggcggttttgtggaatagaaaggcgggaagggtggggaaaaaattgagaaat +cggatggttgccgggtctgtgtggatggaagtagacatg +>syndip_1_chr20:4032119-4033702 +cgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgcag +cggcgtgatctcggctcgctacaaccacctcccagccgcctgccttggcctcccaaagag +ccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctctgct +tggccacccatcgtctgggatatgaggagcccctctgcctggctgcccagtctggaaagt +----------------------------------------gaggagcgtctctgcccggc +cgccatcccatctaggaagcgaggagcgcctcttcccggctgccatcccatctaggaact +gaggagcgtctctgcccggccgcccatcgtctgagatgtggggagcacctctgccccacc +gccctgtctgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggtgagg +agcgtctctgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaaccgcc +ccgtctgagaagtgaggagcccctccgtccggcaaccaccccgt---------------- +------------------------------------------------------------ +-----------ctgggaagtgaggagcgtctccgcccggcagccaccccgtccgggaggg +aggtggggggggtcagccccccgcccggccagccgccccgtccgggaggtgaggggctcc +tctgcccggccgcccctactgggaagtgaggagcccctctgcccggccagccgccccgtc +cgggagggaggcgggggggggggtcggccagccgccccgtccgggagggaggtggggggg +tcagccccccgcccggccggccgccccgtccgggaggtgaggggcgcctctgcccggccg +cccctactgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtg +ggggggtcagccccccgcccggccggctgccccgtccgggaggtgaggggcgcctctgcc +cggccgcccctactgggaagtgaggagcccctctgcccggccagctgccccgcccgggag +ggaggtgggggggtcagccccccgcctggccagccgccccatccgggagggaggtggggg +ggtcagccccccgcccggccagccgccccgtccgggaggggggagggggggtcagccccc +tgcccggccagccgccccgtccgggagggaggtggggggggg--tcagccccccgcccgg +ccagccgccccgtccgggagggaggtggggggatcagccccccgcctggccagccgcccc +gtccgggaggtgaggggcgcctctgcccggccacccctactgggaagtgaggagcccctc +tgcccggccagccgccccgtccgggagggaggcgggggggggggtcggccagccgccccg +tccgggagggaggtgggggggtcagccccctttccggcc--gccgcctgtccgggaggtg +aggggcgcctctgcctggccgcccctactgggaagtgaggacccctctgcccggccagcc +gccccgtccgggagggaggtgggggggacagccccccgcccggccagccgccctatccag +gaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggagcccctctgcctg +gccagccgccccgtccgggagggtagtgggggggtcagccccccgcccggccagccgccc +catccgggaggtgaggggcgcttctgcccggccgcccctactgggaagtgaggagcccct +ctgcccggccacgaccccgtctgggaggtgtgcccagcggctcattggggatgggccatg +atgacaatggcggttttgtggaatagaaaggcgggaagggtggggaaaaaattgagaaat +cggatggttgccgggtctgtgtggatggaagtagacatg +>syndip_2_chr20:4032119-4033702 +cgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgcag +cggcgtgatctcggctcgctacaaccacctcccagccgcctgccttggcctcccaaagag +ccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctctgct +tggccacccatcgtctgggatatgaggagcccctctgcctggctgcccagtctggaaagt +gaggagcgtctctgcccggccgccatcccatctaggaagcgaggagcgtctctgcccggc +cgccatcccatctaggaagcgaggagcgcctcttcccggctgccatcccatctaggaact +gaggagcgtctctgcccggccgcccatcgtctgagatgtggggagcacctctgccccacc +gccctgtctgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggtgagg +agcgtctctgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaaccgcc +ccgtctgagaagtgaggagcccctccgtccggcaaccaccccgt---------------- +------------------------------------------------------------ +-----------ctgggaagtgaggagcgtctccgcccggcagccaccccgtccgggaggg +aggt-------------------------------------------------------- +------------------------------------------------------------ +------------gggggggggggtcggccagccgccccgtccgggagggaggtggggggg +tcagccccccgcccggccggccgccccgtccgggaggtgaggggcgcctctgcccggccg +cccctactgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtg +ggggggtcagccccccgcccggccggctgccccgtccgggaggtgaggggcgcctctgcc +cggccgcccctactgggaagtgaggagcccctctgcccggccagctgccccgcccgggag +ggaggtgggggggtcagccccccgcctggccagccgccccatccgggagggaggtggggg +ggtcagccccccgcccggccagccgccccgtccgggaggggggagggggggtcagccccc +tgcccggccagccgccccgtccgggagggaggtgggggggggggtcagccccccgcccgg +ccagccgccccgtccgggagggaggtggggggatcagccccccgcctggccagccgcccc +gtccgggaggtgaggggcgcctctgcccggccacccctactgggaagtgaggagcccctc +tgcccggccagccgccccgtccgggagggaggcgggggggggggtcggccagccgccccg +tccgggagggaggtgggggggtcagccccctttccggcc--gccgcctgtccgggaggtg +aggggcgcctctgcctggccgcccctactgggaagtgaggacccctctgcccggccagcc +gccccgtccgggagggaggtgggggggacagccccccgcccggccagccgccctatccag +gaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggagcccctctgcctg +gccagccgccccgtccgggagggtagtgggggggtcagccccccgcccggccagccgccc +catccgggaggtgaggggcgcttctgcccggccgcccctactgggaagtgaggagcccct +ctgcccggccacgaccccgtctgggaggtgtgcccagcggctcattggggatgggccatg +atgacaatggcggttttgtggaatagaaaggcgggaagggtggggaaaaaattgagaaat +cggatggttgccgggtctgtgtggatggaagtagacatg +>p:HG002_1_chr20:4032119-4033702 +cgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgcag +cggcgtgatctcggctcgctacaaccacctcccagccgcctgccttggcctcccaaagag +ccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctctgct +tggccacccatcgtctgggatatgaggagcccctctgcctggctgcccagtctggaaagt +gaggagcgtctctgcccggccgccatcccatctaggaagcgaggagcgtctctgcccggc +cgccatcccatctaggaagcgaggagcgcctcttcccggctgccatcccatctaggaact +gaggagcgtctctgcccggccgcccatcgtctgagatgtggggagcacctctgccccacc +gccctgtctgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggtgagg +agcgtctctgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaaccgcc +ccgtctgagaagtgaggagcccctccgtccggcaaccaccccgt---------------- +------------------------------------------------------------ +-----------ctgggaagtgaggagcgtctccgcccggcagccaccccgtccgggaggg +aggt-------------------------------------------------------- +------------------------------------------------------------ +------------gggggggggggtcggccagccgccccgtccgggagggaggtggggggg +tcagccccccgcccggccggccgccccgtccgggaggtgaggggcgcctctgcccggccg +cccctactgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtg +ggggggtcagccccccgcccggccggctgccccgtccgggaggtgaggggcgcctctgcc +cggccgcccctactgggaagtgaggagcccctctgcccggccagctgccccgcccgggag +ggaggtgggggggtcagccccccgcctggccagccgccccatccgggagggaggtggggg +ggtcagccccccgcccggccagccgccccgtccgggaggggggagggggggtcagccccc +tgcccggccagccgccccgtccgggagggaggtggggggggggtcagccccctttccggc +ccagccgccccgtccgggagggaggtggggggatcagccccccgcctggccagccgcccc +gtccgggaggtgaggggcgcctctgcccggccacccctactgggaagtgaggagcccctc +tgcccggccagccgccccgtccgggagggaggcgggggggggggtcggccagccgccccg +tccgggagggaggtgggggggtcagccccccttccggccgggccgcctgtccgggaggtg +aggggcgcctctgcctggccgcccctactgggaagtgaggacccctctgcccggccagcc +gccccgtccgggagggaggtgggggggacagccccccgcccggccagccgccctatccag +gaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggagcccctctgcctg +gccagccgccccgtccgggagggtagtgggggggtcagccccccgcccggccagccgccc +catccgggaggtgaggggcgcttctgcccggccgcccctactgggaagtgaggagcccct +ctgcccggccacgaccccgtctgggaggtgtgcccagcggctcattggggatgggccatg +atgacaatggcggttttgtggaatagaaaggcgggaagggtggggaaaaaattgagaaat +cggatggttgccgggtctgtgtggatggaagtagacatg +>p:HG002_2_chr20:4032119-4033702 +cgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgcag +cggcgtgatctcggctcgctacaaccacctcccagccgcctgccttggcctcccaaagag +ccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctctgct +tggccacccatcgtctgggatatgaggagcccctctgcctggctgcccagtctggaaagt +gaggagcgtctctgcccggccgccatcccatctaggaagcgaggagcgtctctgcccggc +cgccatcccatctaggaagcgaggagcgcctcttcccggctgccatcccatctaggaact +gaggagcgtctctgcccggccgcccatcgtctgagatgtggggagcacctctgccccacc +gccctgtctgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggtgagg +agcgtctctgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaaccgcc +ccgtctgagaagtgaggagcccctccgtccggcaaccaccccgtccgggagggaggtggg +gggggtcagccccccgcccggccagccgccccgtccgggaggtgaggggctcctctgccc +ggccgcccctactgggaagtgaggagcgtctccgcccggcagccaccccgtccgggaggg +aggt-------------------------------------------------------- +------------------------------------------------------------ +------------gggggggggggtcggccagccgccccgtccgggagggaggtggggggg +tcagccccccgcccggccggccgccccgtccgggaggtgaggggcgcctctgcccggccg +cccctactgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtg +ggggggtcagccccccgcccggccggctgccccgtccgggaggtgaggggcgcctctgcc +cggccgcccctactgggaagtgaggagcccctctgcccggccagctgccccgcccgggag +ggaggtgggggggtcagccccccgcctggccagccgccccatccgggagggaggtggggg +ggtcagccccccgcccggccagccgccccgtccgggaggggggagggggggtcagccccc +tgcccggccagccgccccgtccgggagggaggtggggggggggtcagccccctttccggc +c--gccgccccgtccgggagggaggtggggggatcagccccccgcctggccagccgcccc +gtccgggaggtgaggggcgcctctgcccggccacccctactgggaagtgaggagcccctc +tgcccggccagccgccccgtccgggagggaggcgggggggggggtcggccagccgccccg +tccgggagggaggtgggggggtcagccccccttccggccggccgccctgtccgggaggtg +aggggcgcctctgcctggccgcccctactgggaagtgaggacccctctgcccggccagcc +gccccgtccgggagggaggtgggggggacagccccccgcccggccagccgccctatccag +gaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggagcccctctgcctg +gccagccgccccgtccgggagggtagtgggggggtcagccccccgcccggccagccgccc +catccgggaggtgaggggcgcttctgcccggccgcccctactgggaagtgaggagcccct +ctgcccggccacgaccccgtctgggaggtgtgcccagcggctcattggggatgggccatg +atgacaatggcggttttgtggaatagaaaggcgggaagggtggggaaaaaattgagaaat +cggatggttgccgggtctgtgtggatggaagtagacatg diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/msa.fa.fai new file mode 100644 index 00000000..680e4d65 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_4032119_4033702 2019 27 60 61 +syndip_1_chr20:4032119-4033702 2019 2112 60 61 +syndip_2_chr20:4032119-4033702 2019 4197 60 61 +p:HG002_1_chr20:4032119-4033702 2019 6283 60 61 +p:HG002_2_chr20:4032119-4033702 2019 8369 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/output.vcf.gz new file mode 100644 index 00000000..3db53c0e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/output.vcf.gz.tbi new file mode 100644 index 00000000..9030cb83 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:4032219-4033602/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/base.vcf.gz new file mode 100644 index 00000000..e1aa2591 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/base.vcf.gz.tbi new file mode 100644 index 00000000..8cb2f510 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/comp.vcf.gz new file mode 100644 index 00000000..5d61eef3 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/comp.vcf.gz.tbi new file mode 100644 index 00000000..8754ab7b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/haps.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/haps.fa new file mode 100644 index 00000000..fa3389c7 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/haps.fa @@ -0,0 +1,102 @@ +>ref_chr20_53203887_53204574 +CATACCACATGGGGCTACTAAGCCCTTCAAATGTGACTGGTCCAAATTAAAATATACTGTAAGTATAAAACACACTGAACTTGAAAGGCTTAGTCCAAAAACCGTAGTGCACAATATCTCCTTCATTTTTATAATATGATACTATTATATCATAATTTTATAATATACTATTATATCATATTATATGATACTATTTATATCATCATATGATGATATGATATACTATATCATCATATGATGATATGATATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATTATATCATAATATGATATAATATTTTGGACATACTAGGTTAAATAAGATATAGTTATATAAATCAATTTCACTTATTTCTTTCTCATTCTTTAATGTGACTACTGAAGCATATGAAATTCCATGCATAGCTGACATTCTACTTCTATTG +>syndip_1_chr20:53203887-53204574 +CATACCACATGGGGCTACTAAGCCCTTCAAATGTGACTGGTCCAAATTAAAATATACTGT +AAGTATAAAACACACTGAACTTGAAAGGCTTAGTCCAAAAACCGTAGTGCACAATATCTC +CTTCATTTTTATAATATGATACTATTATATCATAATTTTATAATATACTATTATATCATA +TTATATGATACTATTTATATCATCATATGATGATATACTATTATATCATCATATGATGAT +ATACTATTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACT +ATATCATCATATGATGATATACTATATCATCATATGATGATATGATATACTATATCATCA +TATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGA +TATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATAC +TATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCAT +CATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGAT +GATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGAT +ACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATC +ATCACATGATGATATGATACTATATCATCACATGATGATATGATACTATATCATCACATG +ATGATATGATACTATATCATCACATGATGATATGATACTATATCATCACATGATGATATG +ATACTATATCATCACATGATGATATGATACTATATCATCACATGATGATATGATACTATA +TCATCACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCA +TCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATAT +CATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTAT +ATCATCATATAACATGATGATATGATACTATTATATCATAATATGATATAATATTTTGGA +CATACTAGGTTAAATAAGATATAGTTATATAAATCAATTTCACTTATTTCTTTCTCATTC +TTTAATGTGACTACTGAAGCATATGAAATTCCATGCATAGCTGACATTCTACTTCTATTG +>syndip_2_chr20:53203887-53204574 +CATACCACATGGGGCTACTAAGCCCTTCAAATGTGACTGGTCCAAATTAAAATATACTGT +AAGTATAAAACACACTGAACTTGAAAGGCTTAGTCCAAAAACCGTAGTGCACAATATCTC +CTTCATTTTTATAATATGATACTATTATATCATAATTTTATAATATACTATTATATCATA +TTATATGATACTATTTATATCATCATATGATGATATGATATTATATCATCATATGATGAT +ATGATACTATATCATCATATGATGATATGATATACTATATCATCATATGATGATATGATA +CTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCA +TCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGA +TGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGA +TACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATAT +CATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATAT +GATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATAT +GATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTAT +ATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCAT +ATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGAT +ATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACT +ATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATC +ATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATG +ATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATA +CTATATCATAACATGATGATATGATACTATATCATAACATGATGATATGATACTATATCA +TCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATAT +CATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTAT +ATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACT +ATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATA +CTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGA +TACTATTATATCATAATATGATATAATATTTTGGACATACTAGGTTAAATAAGATATAGT +TATATAAATCAATTTCACTTATTTCTTTCTCATTCTTTAATGTGACTACTGAAGCATATG +AAATTCCATGCATAGCTGACATTCTACTTCTATTG +>p:HG002_1_chr20:53203887-53204574 +CATACCACATGGGGCTACTAAGCCCTTCAAATGTGACTGGTCCAAATTAAAATATACTGT +AAGTATAAAACACACTGAACTTGAAAGGCTTAGTCCAAAAACCGTAGTGCACAATATCTC +CTTCATTTTTATAATATGATACTATTATATCATAATTTTATAATATACTATTATATCATA +TTATATGATACTATTTATATCATCATATGATGATATGATATACTATATCATCATATGATG +ATATGATATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGA +TACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATAT +CATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATAT +GATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATAT +GATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTAT +ATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCAT +ATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGAT +ATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACT +ATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATC +ATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATG +ATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATA +CTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCA +TCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGA +TGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGA +TACTATATCATAACATGATGATATGATACTATATCATAACATGATGATATGATACTATAT +CATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTAT +ATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACT +ATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATA +CTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGA +TACTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATAT +GATACTATTATATCATAATATGATATAATATTTTGGACATACTAGGTTAAATAAGATATA +GTTATATAAATCAATTTCACTTATTTCTTTCTCATTCTTTAATGTGACTACTGAAGCATA +TGAAATTCCATGCATAGCTGACATTCTACTTCTATTG +>p:HG002_2_chr20:53203887-53204574 +CATACCACATGGGGCTACTAAGCCCTTCAAATGTGACTGGTCCAAATTAAAATATACTGT +AAGTATAAAACACACTGAACTTGAAAGGCTTAGTCCAAAAACCGTAGTGCACAATATCTC +CTTCATTTTTATAATATGATACTATTATATCATAATTTTATAATATACTATTATATCATA +TTATATGATACTATTTATATCATCATATGATGATATGATATACTATATCATCATATGATG +ATATGATTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACT +ATATCATCATATGATGATATACTATATCATCATATGATGATATGATACTATATCATCATA +TGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATA +TGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTA +TATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCA +TATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGA +TATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATAC +TATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCAT +CACATGATGATATGATACTATATCATCACATGATGATATGATACTATATCATCACATGAT +GATATGATACTATATCATCACATGATGATATGATACTATATCATCATATGATGATATGAT +ACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATC +ATCATATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATC +ATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCA +TCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATAT +CATCATATAACATGATGATATGATACTATTATATCATAATATGATATAATATTTTGGACA +TACTAGGTTAAATAAGATATAGTTATATAAATCAATTTCACTTATTTCTTTCTCATTCTT +TAATGTGACTACTGAAGCATATGAAATTCCATGCATAGCTGACATTCTACTTCTATTG diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/haps.fa.ref.fa new file mode 100644 index 00000000..72153792 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:53203887-53204574 +CATACCACATGGGGCTACTAAGCCCTTCAAATGTGACTGGTCCAAATTAAAATATACTGTAAGTATAAAACACACTGAACTTGAAAGGCTTAGTCCAAAAACCGTAGTGCACAATATCTCCTTCATTTTTATAATATGATACTATTATATCATAATTTTATAATATACTATTATATCATATTATATGATACTATTTATATCATCATATGATGATATGATATACTATATCATCATATGATGATATGATATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATATCATCATATAACATGATGATATGATACTATTATATCATAATATGATATAATATTTTGGACATACTAGGTTAAATAAGATATAGTTATATAAATCAATTTCACTTATTTCTTTCTCATTCTTTAATGTGACTACTGAAGCATATGAAATTCCATGCATAGCTGACATTCTACTTCTATTG diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/msa.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/msa.fa new file mode 100644 index 00000000..3a138c17 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/msa.fa @@ -0,0 +1,140 @@ +>ref_chr20_53203887_53204574 +cataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgt +aagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctc +cttcatttttataatatgatactattatatcataattttataatatactattatatcata +ttatatgatactatttatatcatcatatgatgatatgatat------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------------actatatcatcatat +gatgatatgatatactatatcatcatatgatgatatgatactatatcatcatatgatgat +atgatactatatcatcatatgatgatatgatactatatcatc------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------atatgatgatat +gatactatatcatcat-----atgatgatatgatactatatcatcatataacatgatgat +atgatactatatcatcatataacatgatgatatgatactatatcatcatataacatgatg +atatgatactatatcatcatataacatgatgatatgatactatatcatcatataacatga +tgatatgatactattatatcataatatgatataatattttggacatactaggttaaataa +gatatagttatataaatcaatttcacttatttctttctcattctttaatgtgactactga +agcatatgaaattccatgcatagctgacattctacttctattg +>syndip_1_chr20:53203887-53204574 +cataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgt +aagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctc +cttcatttttataatatgatactattatatcataattttataatatactattatatcata +ttatatgatactatttatatcatcatatgatgatatactat--tatatcatcatatgatg +atata------------------------------ctattatatcatcatatgatgatat +gatactatatcatcatatgatgatatgatactatatcatcatatgatgat---atactat +atcatcatatgatgatatgatatactatatcatcatatgatgatatgatactatatcatc +atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg +atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata +ctatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatca +tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga +tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga +tactatatcatcatatgatgatatgatactatatcatcacatgatgatatgatactatat +catcacatgatgatatgatactatatcatcacatgatgatatgatactatatcatcacat +gatgatatg--atactatatcatcacatgatgatatgatactatatcatcacatgatgat +atgatactatatcatcacatgatgatatgatactatatcatc------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------acatgatgatat +gatactatatcatcatataacatgatgatatgatactatatcatcatataacatgatgat +atgatactatatcatcatataacatgatgatatgatactatatcatcatataacatgatg +atatgatactatatcatcatataacatgatgatatgatactatatcatcatataacatga +tgatatgatactattatatcataatatgatataatattttggacatactaggttaaataa +gatatagttatataaatcaatttcacttatttctttctcattctttaatgtgactactga +agcatatgaaattccatgcatagctgacattctacttctattg +>syndip_2_chr20:53203887-53204574 +cataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgt +aagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctc +cttcatttttataatatgatactattatatcataattttataatatactattatatcata +ttatatgatactatttatatcatcatatgatgatatgatat--tatatcatcatatgatg +atatg--atactatatcatcatatgatgatatgatatactatatcatcatatgatgatat +gatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactat +atcatcatatgatgatatg--atactatatcatcatatgatgatatgatactatatcatc +atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg +atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata +ctatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatca +tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga +tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga +tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat +catcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatat +gatgatatg--atactatatcatcatatgatgatatgatactatatcatcatatgatgat +atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact +atatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatc +atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg +atatgatactatatcataacatgatgatatgatactatatcataacatgatgatatgata +ctatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatga +tactatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatat +gatactatatcatcatataacatgatgatatgatactatatcatcatataacatgatgat +atgatactatatcatcatataacatgatgatatgatactatatcatcatataacatgatg +atatgatactatatcatcatataacatgatgatatgatactatatcatcatataacatga +tgatatgatactattatatcataatatgatataatattttggacatactaggttaaataa +gatatagttatataaatcaatttcacttatttctttctcattctttaatgtgactactga +agcatatgaaattccatgcatagctgacattctacttctattg +>p:HG002_1_chr20:53203887-53204574 +cataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgt +aagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctc +cttcatttttataatatgatactattatatcataattttataatatactattatatcata +ttatatgatactatttatatcatcatatgatgatatgatatactatatcatcatatgatg +atatgatatactatatcatcatatgatgatatg--atactatatcatcatatgatgatat +gatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactat +atcatcatatgatgatatg--atactatatcatcatatgatgatatgatactatatcatc +atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg +atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata +ctatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatca +tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga +tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga +tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat +catcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatat +gatgatatg--atactatatcatcatatgatgatatgatactatatcatcatatgatgat +atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact +atatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatc +atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg +atatgatactatatcataacatgatgatatgatactatatcataacatgatgatatgata +ctatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatga +tactatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatat +gatactatatcatcatataacatgatgatatgatactatatcatcatataacatgatgat +atgatactatatcatcatataacatgatgatatgatactatatcatcatataacatgatg +atatgatactatatcatcatataacatgatgatatgatactatatcatcatataacatga +tgatatgatactattatatcataatatgatataatattttggacatactaggttaaataa +gatatagttatataaatcaatttcacttatttctttctcattctttaatgtgactactga +agcatatgaaattccatgcatagctgacattctacttctattg +>p:HG002_2_chr20:53203887-53204574 +cataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgt +aagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctc +cttcatttttataatatgatactattatatcataattttataatatactattatatcata +ttatatgatactatttatatcatcatatgatgatatgatatactatatcatcatatgatg +atatg--------------------------------attatatcatcatatgatgatat +gatactatatcatcatatgatgatatgatactatatcatcatatgatgat---atactat +atcatcatatgatgatatg--atactatatcatcatatgatgatatgatactatatcatc +atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg +atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata +ctatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatca +tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga +tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga +tactatatcatcatatgatgatatgatactatatcatcacatgatgatatgatactatat +catcacatgatgatatgatactatatcatcacatgatgatatgatactatatcatcacat +gatgatatg--atactatatcatcatatgatgatatgatactatatcatcatatgatgat +atgatactatatcatcatatgatgatatgatactatatcatc------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------atatgatgatat +gatactatatcatcatataacatgatgatatgatactatatcatcatataacatgatgat +atgatactatatcatcatataacatgatgatatgatactatatcatcatataacatgatg +atatgatactatatcatcatataacatgatgatatgatactatatcatcatataacatga +tgatatgatactattatatcataatatgatataatattttggacatactaggttaaataa +gatatagttatataaatcaatttcacttatttctttctcattctttaatgtgactactga +agcatatgaaattccatgcatagctgacattctacttctattg diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/msa.fa.fai new file mode 100644 index 00000000..247b5864 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_53203887_53204574 1603 29 60 61 +syndip_1_chr20:53203887-53204574 1603 1693 60 61 +syndip_2_chr20:53203887-53204574 1603 3357 60 61 +p:HG002_1_chr20:53203887-53204574 1603 5022 60 61 +p:HG002_2_chr20:53203887-53204574 1603 6687 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/output.vcf.gz new file mode 100644 index 00000000..66c8c225 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/output.vcf.gz.tbi new file mode 100644 index 00000000..cab6bf8a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:53203987-53204474/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/base.vcf.gz new file mode 100644 index 00000000..5ee6c1be Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/base.vcf.gz.tbi new file mode 100644 index 00000000..d4b52b85 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/comp.vcf.gz new file mode 100644 index 00000000..5e44c7d6 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/comp.vcf.gz.tbi new file mode 100644 index 00000000..22ee7d24 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/haps.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/haps.fa new file mode 100644 index 00000000..7861c3a4 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/haps.fa @@ -0,0 +1,148 @@ +>ref_chr20_55943819_55945908 +GTGCTGGGTACTGTCCCAGTCCTCCTACCTGTTTACCTCACTTCCACCCTTGCCTCCTTCCAAGTCAATCCCATGGGAACCAGCATTTTCTGAAACTCAATAAAATTAGCTAGCATTTCAGCCAGGTGCAGTGGCTCAAGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGTGGATCACTTGAGGTTAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCTCGCCTCTACTAAAAATACAAAAATTAGCTGGGCATGCTGGCATGTGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAACTGCTTGAGCCTGGGAGGCAGAGGTTGCAGTGAGCTGAGATGGCACCACTGCATTCCAGCTGGGCAACAGAGAGAGACTCTTTCTTAAATATATATATTTTATATATATATAGATACACACACACACACACACACACACACATATATATATATATATATATATATATATATATATGCATGCATGCCAGATGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGAGAGGCCAAGGTGGGCAGATCATCTGAGGTCAGGAGTTCCAGACCAGCCTAGCCAACATGGTGAAACTCCATCTCTACTAAAAATACAAAATTAGCTGGCTGTGGTGGCTCATGCTGGTAATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTGAACCTGGGAGGTGGAGGTTGCAGTGAGCCGAGATCACACCACTGCACTCCAGCCTGGATGACAGAGCGAGACTCCATTAAAAAAATATATCTATATCTATAGATATCTATAGATATATATCTAGATATAGATCTATGAGTATATATCTATAGATATCTAGATATATATTTATAGATAGATATATCTATAGATATCTATATATTTCTATCGATAGAGATATCTATAGATATCTATCAATATATCTATAGATTTCTAGAGATATGTATCTAGATATAAATCTATAGACATAGATATAGATATATAGATATTTAACTGCCAATGTCCTAAACACTTTATACTCAACACATTTTTTATAAAAAAAAATAGATATCGGTCTAGATAGTATCTATCTAGATATCGGTCTAGATAGTATCTATCTAGATATCTGTGTAGATGTCTAGATATCTATCTAGATATTATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTAGATAGTATCTGTCGCTATCTAGATATCTAGATAGTATCTGTCTAGATAGCTATCTAGATAGTATCTGTCTAGATAGCTATCTAGATAGTATCTGTCCAGATATCTGTAGCTATCTAGATTGTATCTGTCTAGATATCTGTAGATATCTAGATATCTATATCTATCTGGATATCTATAGATATTTAACTGCCGGGCAATGTCCTAAACCCTTTACACTCAACACATTTCATTTTATAACAAAATATGAGGTAGATATTATTATTTCCCTCAACTCACAGAGAAGAAAAAAATGAAGCATATGGAGCCCATGGGC +>syndip_1_chr20:55943819-55945908 +GTGCTGGGTACTGTCCCAGTCCTCCTACCTGTTTACCTCACTTCCACCCTTGCCTCCTTC +CAAGTCAATCCCATGGGAACCAGCATTTTCTGAAACTCAATAAAATTAGCTAGCATTTCA +GCCAGGTGCAGTGGCTCAAGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGTGGAT +CACTTGAGGTTAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCTCGCCTCTACTA +AAAATACAAAAATTAGCTGGGCATGCTGGCATGTGCCTGTAATCCCAGCTACTCAGGAGG +CTGAGGCAGGAGAACTGCTTGAGCCTGGGAGGCAGAGGTTGCAGTGAGCTGAGATGGCAC +CACTGCATTCCAGCTGGGCAACAGAGAGAGACTCTTTCTTAAATATATATATTTTATATA +TATATAGATACACACACACACACACACACACACACATATATATATATATATATATATATA +TATATATATGCATGCATGCCAGATGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGAGA +GGCCAAGGTGGGCAGATCATCTGAGGTCAGGAGTTCCAGACCAGCCTAGCCAACATGGTG +AAACTCCATCTCTACTAAAAATACAAAATTAGCTGGCTGTGGTGGCTCATGCTGGTAATC +CCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTGAACCTGGGAGGTGGAGGTTGCAG +TGAGCCGAGATCACACCACTGCACTCCAGCCTGGATGACAGAGCGAGACTCCATTAAAAA +AATATATCTATATCTATAGATATCTATAGATATATATCTAGATATAGATCTATGAGTATA +TATCTATAGATATCTAGATATATATTTATAGATAGATATATCTATAGATATCTATATATT +TCTATCGATAGAGATATCTATAGATATCTATCAATATATCTATAGATTTCTAGAGATATG +TATCTAGATATAAATCTATAGACATAGATATAGATATATAGATATTTAACTGCCAATGTC +CTAAACACTTTATACTCAACACATTTTTTATAAAAAAAAATAGATATCGGTCTAGATAGT +ATCTATCTAGATATCGGTCTAGATAGTATCTATCTAGATATCTGTGTAGATGTCTAGATA +TCTATCTAGATATTATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATCT +GTCGCTATCTAGATATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATAGTA +TCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAG +ATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCT +ATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAG +ATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCT +ATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCT +GTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATA +GTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATC +TAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATA +TCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATC +TAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTC +GCTATCTAGATATCTAGATAGTATCTGTCGCTATCTAGATATCTAGATAGTATCTGTCTA +GATAGCTATCTAGATAGTATCTGTCTAGATAGCTATCTAGATAGTATCTGTCCAGATATC +TGTAGCTATCTAGATTGTATCTGTCTAGATATCTGTAGATATCTAGATATCTATATCTAT +CTGGATATCTATAGATATTTAACTGCCGGGCAATGTCCTAAACCCTTTACACTCAACACA +TTTCATTTTATAACAAAATATGAGGTAGATATTATTATTTCCCTCAACTCACAGAGAAGA +AAAAAATGAAGCATATGGAGCCCATGGGC +>syndip_2_chr20:55943819-55945908 +GTGCTGGGTACTGTCCCAGTCCTCCTACCTGTTTACCTCACTTCCACCCTTGCCTCCTTC +CAAGTCAATCCCATGGGAACCAGCATTTTCTGAAACTCAATAAAATTAGCTAGCATTTCA +GCCAGGTGCAGTGGCTCAAGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGTGGAT +CACTTGAGGTTAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCTCGCCTCTACTA +AAAATACAAAAATTAGCTGGGCATGCTGGCATGTGCCTGTAATCCCAGCTACTCAGGAGG +CTGAGGCAGGAGAACTGCTTGAGCCTGGGAGGCAGAGGTTGCAGTGAGCTGAGATGGCAC +CACTGCATTCCAGCTGGGCAACAGAGAGAGACTCTTTCTTAAATATATATATTTTATATA +TATATAGATACACACACACACACACACACACACACACACACACACACACACACACATATA +TATATATATATATATATATATATATATATATATATATATATATGCATGCATGCCAGATGC +AGTGGCTCACGCCTGTAATCCCAGCACTTTGAGAGGCCAAGGTGGGCAGATCATCTGAGG +TCAGGAGTTCCAGACCAGCCTAGCCAACATGGTGAAACTCCATCTCTACTAAAAATACAA +AATTAGCTGGCTGTGGTGGCTCATGCTGGTAATCCCAGCTACTTGGGAGGCTGAGGCAGG +AGAATCACTTGAACCTGGGAGGTGGAGGTTGCAGTGAGCCGAGATCACACCACTGCACTC +CAGCCTGGATGACAGAGCGAGACTCCATTAAAAAAATATATCTATATCTATAGATATCTA +TAGATATATATCTAGATATAGATCTATGAGTATATATCTATAGATATCTAGATATATATT +TATAGATAGATATATCTATAGATATCTATATATTTCTATCGATAGAGATATCTATAGATA +TCTATCAATATATCTATAGATTTCTAGAGATATGTATCTAGATATAAATCTATAGACATA +GATATAGATATATAGATATTTAACTGCCAATGTCCTAAACACTTTATACTCAACACATTT +TTTATAAAAAAAAATAGATATCGGTCTAGATAGTATCTATCTAGATATCGGTCTAGATAG +TATCTATCTAGATATCGGTCTAGATAGTATCTATCTAGATATCTGTGTAGATGTCTAGAT +ATCTATCTAGATATTATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATC +TGTCGCTATCTAGATATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATAGT +ATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTA +GATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATC +TATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTA +GATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGC +TATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATC +TGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGAT +AGTATCTGTCGCTATCTAGATATCTAGATAGTATCTGTCGCTATCTAGATATCTAGATAG +TATCTGTCTAGATAGCTATCTAGATAGTATCTGTCTAGATAGCTATCTAGATAGTATCTG +TCCAGATATCTGTAGCTATCTAGATTGTATCTGTCTAGATATCTGTAGATATCTAGATAT +CTATATCTATCTGGATATCTATAGATATTTAACTGCCGGGCAATGTCCTAAACCCTTTAC +ACTCAACACATTTCATTTTATAACAAAATATGAGGTAGATATTATTATTTCCCTCAACTC +ACAGAGAAGAAAAAAATGAAGCATATGGAGCCCATGGGC +>p:HG002_1_chr20:55943819-55945908 +GTGCTGGGTACTGTCCCAGTCCTCCTACCTGTTTACCTCACTTCCACCCTTGCCTCCTTC +CAAGTCAATCCCATGGGAACCAGCATTTTCTGAAACTCAATAAAATTAGCTAGCATTTCA +GCCAGGTGCAGTGGCTCAAGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGTGGAT +CACTTGAGGTTAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCTCGCCTCTACTA +AAAATACAAAAATTAGCTGGGCATGCTGGCATGTGCCTGTAATCCCAGCTACTCAGGAGG +CTGAGGCAGGAGAACTGCTTGAGCCTGGGAGGCAGAGGTTGCAGTGAGCTGAGATGGCAC +CACTGCATTCCAGCTGGGCAACAGAGAGAGACTCTTTCTTAAATATATATATTTTATATA +TATATAGATACACACACACACACACACACACACACACACACACACACACACACACATATA +TATATATATATATATATATATATATATATATATATATATATATGCATGCATGCCAGATGC +AGTGGCTCACGCCTGTAATCCCAGCACTTTGAGAGGCCAAGGTGGGCAGATCATCTGAGG +TCAGGAGTTCCAGACCAGCCTAGCCAACATGGTGAAACTCCATCTCTACTAAAAATACAA +AATTAGCTGGCTGTGGTGGCTCATGCTGGTAATCCCAGCTACTTGGGAGGCTGAGGCAGG +AGAATCACTTGAACCTGGGAGGTGGAGGTTGCAGTGAGCCGAGATCACACCACTGCACTC +CAGCCTGGATGACAGAGCGAGACTCCATTAAAAAAATATATCTATATCTATAGATATCTA +TAGATATATATCTAGATATAGATCTATGAGTATATATCTATAGATATCTAGATATATATT +TATAGATAGATATATCTATAGATATCTATATATTTCTATCGATAGAGATATCTATAGATA +TCTATCAATATATCTATAGATTTCTAGAGATATGTATCTAGATATAAATCTATAGACATA +GATATAGATATATAGATATTTAACTGCCAATGTCCTAAACACTTTATACTCAACACATTT +TTTATAAAAAAAAATAGATATCGGTCTAGATAGTATCTATCTAGATATCGGTCTAGATAG +TATCTATCTAGATATCTGTGTAGATGTCTAGATATCTATCTAGATATTATCTATCTAGAT +ATCTGTCGCTATCTAGATATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGAT +ATCTGTCGCTATCTAGATATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGAT +AGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTAT +CTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGAT +ATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTAT +CTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGT +CGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGT +ATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTA +GATAGTATCTGTCGCTATCTAGATATCTAGATAGTATCTGTCGCTATCTAGATATCTAGA +TAGTATCTGTCTAGATAGCTATCTAGATAGTATCTGTCTAGATAGCTATCTAGATAGTAT +CTGTCCAGATATCTGTAGCTATCTAGATTGTATCTGTCTAGATATCTGTAGATATCTAGA +TATCTATATCTATCTGGATATCTATAGATATTTAACTGCCGGGCAATGTCCTAAACCCTT +TACACTCAACACATTTCATTTTATAACAAAATATGAGGTAGATATTATTATTTCCCTCAA +CTCACAGAGAAGAAAAAAATGAAGCATATGGAGCCCATGGGC +>p:HG002_2_chr20:55943819-55945908 +GTGCTGGGTACTGTCCCAGTCCTCCTACCTGTTTACCTCACTTCCACCCTTGCCTCCTTC +CAAGTCAATCCCATGGGAACCAGCATTTTCTGAAACTCAATAAAATTAGCTAGCATTTCA +GCCAGGTGCAGTGGCTCAAGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGTGGAT +CACTTGAGGTTAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCTCGCCTCTACTA +AAAATACAAAAATTAGCTGGGCATGCTGGCATGTGCCTGTAATCCCAGCTACTCAGGAGG +CTGAGGCAGGAGAACTGCTTGAGCCTGGGAGGCAGAGGTTGCAGTGAGCTGAGATGGCAC +CACTGCATTCCAGCTGGGCAACAGAGAGAGACTCTTTCTTAAATATATATATTTTATATA +TATATAGATACACACACACACACACACACACACACATATATATATATATATATATATATA +TATATATATGCATGCATGCCAGATGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGAGA +GGCCAAGGTGGGCAGATCATCTGAGGTCAGGAGTTCCAGACCAGCCTAGCCAACATGGTG +AAACTCCATCTCTACTAAAAATACAAAATTAGCTGGCTGTGGTGGCTCATGCTGGTAATC +CCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTGAACCTGGGAGGTGGAGGTTGCAG +TGAGCCGAGATCACACCACTGCACTCCAGCCTGGATGACAGAGCGAGACTCCATTAAAAA +AATATATCTATATCTATAGATATCTATAGATATATATCTAGATATAGATCTATGAGTATA +TATCTATAGATATCTAGATATATATTTATAGATAGATATATCTATAGATATCTATATATT +TCTATCGATAGAGATATCTATAGATATCTATCAATATATCTATAGATTTCTAGAGATATG +TATCTAGATATAAATCTATAGACATAGATATAGATATATAGATATTTAACTGCCAATGTC +CTAAACACTTTATACTCAACACATTTTTTATAAAAAAAAATAGATATCGGTCTAGATAGT +ATCTATCTAGATATCGGTCTAGATAGTATCTATCTAGATATCTGTGTAGATGTCTAGATA +TCTATCTAGATATTATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATCT +GTCGCTATCTAGATATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATAGTA +TCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAG +ATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCT +ATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAG +ATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCT +ATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCT +GTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATA +GTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATC +TAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATA +TCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATC +TAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTC +GCTATCTAGATATCTAGATAGTATCTGTCGCTATCTAGATATCTAGATAGTATCTGTCTA +GATAGCTATCTAGATAGTATCTGTCTAGATAGCTATCTAGATAGTATCTGTCCAGATATC +TGTAGCTATCTAGATTGTATCTGTCTAGATATCTGTAGATATCTAGATATCTATATCTAT +CTGGATATCTATAGATATTTAACTGCCGGGCAATGTCCTAAACCCTTTACACTCAACACA +TTTCATTTTATAACAAAATATGAGGTAGATATTATTATTTCCCTCAACTCACAGAGAAGA +AAAAAATGAAGCATATGGAGCCCATGGGC diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/haps.fa.ref.fa new file mode 100644 index 00000000..5336576f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:55943819-55945908 +GTGCTGGGTACTGTCCCAGTCCTCCTACCTGTTTACCTCACTTCCACCCTTGCCTCCTTCCAAGTCAATCCCATGGGAACCAGCATTTTCTGAAACTCAATAAAATTAGCTAGCATTTCAGCCAGGTGCAGTGGCTCAAGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGTGGATCACTTGAGGTTAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCTCGCCTCTACTAAAAATACAAAAATTAGCTGGGCATGCTGGCATGTGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAACTGCTTGAGCCTGGGAGGCAGAGGTTGCAGTGAGCTGAGATGGCACCACTGCATTCCAGCTGGGCAACAGAGAGAGACTCTTTCTTAAATATATATATTTTATATATATATAGATACACACACACACACACACACACACACATATATATATATATATATATATATATATATATATGCATGCATGCCAGATGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGAGAGGCCAAGGTGGGCAGATCATCTGAGGTCAGGAGTTCCAGACCAGCCTAGCCAACATGGTGAAACTCCATCTCTACTAAAAATACAAAATTAGCTGGCTGTGGTGGCTCATGCTGGTAATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTGAACCTGGGAGGTGGAGGTTGCAGTGAGCCGAGATCACACCACTGCACTCCAGCCTGGATGACAGAGCGAGACTCCATTAAAAAAATATATCTATATCTATAGATATCTATAGATATATATCTAGATATAGATCTATGAGTATATATCTATAGATATCTAGATATATATTTATAGATAGATATATCTATAGATATCTATATATTTCTATCGATAGAGATATCTATAGATATCTATCAATATATCTATAGATTTCTAGAGATATGTATCTAGATATAAATCTATAGACATAGATATAGATATATAGATATTTAACTGCCAATGTCCTAAACACTTTATACTCAACACATTTTTTATAAAAAAAAATAGATATCGGTCTAGATAGTATCTATCTAGATATCGGTCTAGATAGTATCTATCTAGATATCTGTGTAGATGTCTAGATATCTATCTAGATATTATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTATCTAGATAGTATCTGTCGCTATCTAGATATCTAGATAGTATCTGTCGCTATCTAGATATCTAGATAGTATCTGTCTAGATAGCTATCTAGATAGTATCTGTCTAGATAGCTATCTAGATAGTATCTGTCCAGATATCTGTAGCTATCTAGATTGTATCTGTCTAGATATCTGTAGATATCTAGATATCTATATCTATCTGGATATCTATAGATATTTAACTGCCGGGCAATGTCCTAAACCCTTTACACTCAACACATTTCATTTTATAACAAAATATGAGGTAGATATTATTATTTCCCTCAACTCACAGAGAAGAAAAAAATGAAGCATATGGAGCCCATGGGC diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/msa.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/msa.fa new file mode 100644 index 00000000..d643e135 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/msa.fa @@ -0,0 +1,195 @@ +>ref_chr20_55943819_55945908 +gtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctccttc +caagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttca +gccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtggat +cacttgaggttaggagtttgagaccagcctggccaacatggtgaaacctcgcctctacta +aaaatacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggagg +ctgaggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggcac +cactgcattccagctgggcaacagagagagactctttcttaaatatatatattttatata +tatatagatacacacacacacacacacacacacac------------------------- +---------atatatatatatatatatatatatatatatatatgcatgcatgccagatgc +agtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgagg +tcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaatacaa +aattagctggctgtggtggctcatgctggtaatcccagctacttgggaggctgaggcagg +agaatcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcactc +cagcctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatcta +tagatatatatctagatatagatctatgagtatatatctatagatatctagatatatatt +tatagatagatatatctatagatatctatatatttctatcgatagagatatctatagata +tctatcaatatatctatagatttctagagatatgtatctagatataaatctatagacata +gatatagatatatagatatttaactgccaatgtcctaaacactttatactcaacacattt +tttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagatag +tatctatctagatatctgtgtagatgtctagatatctatctagatat-----tatctatc +tagatatctgtcgctatctagatatctatctagatatctgtcgctatctagatatctatc +taga-------------------------------------------------------- +-------------------------------------------tatctgtcgctatctag +atatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgct +atctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatct +gtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagata +gtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatc +tagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagata +tctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatc +tagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtc +gctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagta +tctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctagatag +tatctgtcgctatctagatatctagatagtatctgtctagatagctatctagatagtatc +tgtctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatc +tgtctagatatctgtagatatctagatatctatatctatctggatatctatagatattta +actgccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatat +gaggtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagc +ccatgggc +>syndip_1_chr20:55943819-55945908 +gtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctccttc +caagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttca +gccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtggat +cacttgaggttaggagtttgagaccagcctggccaacatggtgaaacctcgcctctacta +aaaatacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggagg +ctgaggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggcac +cactgcattccagctgggcaacagagagagactctttcttaaatatatatattttatata +tatatagatacacacacacacacacacacacacac------------------------- +---------atatatatatatatatatatatatatatatatatgcatgcatgccagatgc +agtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgagg +tcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaatacaa +aattagctggctgtggtggctcatgctggtaatcccagctacttgggaggctgaggcagg +agaatcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcactc +cagcctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatcta +tagatatatatctagatatagatctatgagtatatatctatagatatctagatatatatt +tatagatagatatatctatagatatctatatatttctatcgatagagatatctatagata +tctatcaatatatctatagatttctagagatatgtatctagatataaatctatagacata +gatatagatatatagatatttaactgccaatgtcctaaacactttatactcaacacattt +tttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagatag +tatctatctagatatctgtgtagatgtctagatatctatctagatat-----tatctatc +tagatatctgtcgctatctagatatctatctagatatctgtcgctatctagatatctatc +tagatatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatct +atctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctag +atatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgct +atctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatct +gtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagata +gtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatc +tagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagata +tctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatc +tagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtc +gctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagta +tctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctagatag +tatctgtcgctatctagatatctagatagtatctgtctagatagctatctagatagtatc +tgtctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatc +tgtctagatatctgtagatatctagatatctatatctatctggatatctatagatattta +actgccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatat +gaggtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagc +ccatgggc +>syndip_2_chr20:55943819-55945908 +gtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctccttc +caagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttca +gccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtggat +cacttgaggttaggagtttgagaccagcctggccaacatggtgaaacctcgcctctacta +aaaatacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggagg +ctgaggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggcac +cactgcattccagctgggcaacagagagagactctttcttaaatatatatattttatata +tatatagatacacacacacacacacacacacacacacacacacacacacacacacatata +tatatatatatatatatatatatatatatatatatatatatatgcatgcatgccagatgc +agtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgagg +tcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaatacaa +aattagctggctgtggtggctcatgctggtaatcccagctacttgggaggctgaggcagg +agaatcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcactc +cagcctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatcta +tagatatatatctagatatagatctatgagtatatatctatagatatctagatatatatt +tatagatagatatatctatagatatctatatatttctatcgatagagatatctatagata +tctatcaatatatctatagatttctagagatatgtatctagatataaatctatagacata +gatatagatatatagatatttaactgccaatgtcctaaacactttatactcaacacattt +tttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagatag +tatctatctagatatcggtctagat-----agtatctatctagatatctgtgtagatgtc +tagatatctatctagatat---tatctatctagatatctgtcgctatctagatatctatc +taga-------------------------------------------------------- +-------------------------------------------tatctgtcgctatctag +atatctatctaga----------------------------------------------- +-------------------------------------------------------tatct +gtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagata +gtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatc +tagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagata +tctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatc +tagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtc +gctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagta +tctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctagatag +tatctgtcgctatctagatatctagatagtatctgtctagatagctatctagatagtatc +tgtctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatc +tgtctagatatctgtagatatctagatatctatatctatctggatatctatagatattta +actgccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatat +gaggtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagc +ccatgggc +>p:HG002_1_chr20:55943819-55945908 +gtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctccttc +caagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttca +gccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtggat +cacttgaggttaggagtttgagaccagcctggccaacatggtgaaacctcgcctctacta +aaaatacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggagg +ctgaggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggcac +cactgcattccagctgggcaacagagagagactctttcttaaatatatatattttatata +tatatagatacacacacacacacacacacacacacacacacacacacacacacacatata +tatatatatatatatatatatatatatatatatatatatatatgcatgcatgccagatgc +agtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgagg +tcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaatacaa +aattagctggctgtggtggctcatgctggtaatcccagctacttgggaggctgaggcagg +agaatcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcactc +cagcctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatcta +tagatatatatctagatatagatctatgagtatatatctatagatatctagatatatatt +tatagatagatatatctatagatatctatatatttctatcgatagagatatctatagata +tctatcaatatatctatagatttctagagatatgtatctagatataaatctatagacata +gatatagatatatagatatttaactgccaatgtcctaaacactttatactcaacacattt +tttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagatag +tatctatctagatatctgtgtagatgtctagatatctatctagatat-----tatctatc +tagatatctgtcgctatctagatatctatctagatatctgtcgctatctagatatctatc +taga-------------------------------------------------------- +-------------------------------------------tatctgtcgctatctag +atatctatctaga----------------------------------------------- +-------------------------------------------------------tatct +gtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagata +gtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatc +tagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagata +tctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatc +tagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtc +gctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagta +tctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctagatag +tatctgtcgctatctagatatctagatagtatctgtctagatagctatctagatagtatc +tgtctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatc +tgtctagatatctgtagatatctagatatctatatctatctggatatctatagatattta +actgccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatat +gaggtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagc +ccatgggc +>p:HG002_2_chr20:55943819-55945908 +gtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctccttc +caagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttca +gccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtggat +cacttgaggttaggagtttgagaccagcctggccaacatggtgaaacctcgcctctacta +aaaatacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggagg +ctgaggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggcac +cactgcattccagctgggcaacagagagagactctttcttaaatatatatattttatata +tatatagatacacacacacacacacacacacacac------------------------- +---------atatatatatatatatatatatatatatatatatgcatgcatgccagatgc +agtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgagg +tcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaatacaa +aattagctggctgtggtggctcatgctggtaatcccagctacttgggaggctgaggcagg +agaatcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcactc +cagcctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatcta +tagatatatatctagatatagatctatgagtatatatctatagatatctagatatatatt +tatagatagatatatctatagatatctatatatttctatcgatagagatatctatagata +tctatcaatatatctatagatttctagagatatgtatctagatataaatctatagacata +gatatagatatatagatatttaactgccaatgtcctaaacactttatactcaacacattt +tttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagatag +tatctatctagatatctgtgtagatgtctagatatctatctagatat-----tatctatc +tagatatctgtcgctatctagatatctatctagatatctgtcgctatctagatatctatc +tagatatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatct +atctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctag +atatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgct +atctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatct +gtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagata +gtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatc +tagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagata +tctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatc +tagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtc +gctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagta +tctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctagatag +tatctgtcgctatctagatatctagatagtatctgtctagatagctatctagatagtatc +tgtctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatc +tgtctagatatctgtagatatctagatatctatatctatctggatatctatagatattta +actgccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatat +gaggtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagc +ccatgggc diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/msa.fa.fai new file mode 100644 index 00000000..26e58832 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_55943819_55945908 2228 29 60 61 +syndip_1_chr20:55943819-55945908 2228 2329 60 61 +syndip_2_chr20:55943819-55945908 2228 4629 60 61 +p:HG002_1_chr20:55943819-55945908 2228 6930 60 61 +p:HG002_2_chr20:55943819-55945908 2228 9231 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/output.vcf.gz new file mode 100644 index 00000000..6f89793d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/output.vcf.gz.tbi new file mode 100644 index 00000000..f5134ca6 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:55943919-55945808/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/base.vcf.gz new file mode 100644 index 00000000..b47ff7bc Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/base.vcf.gz.tbi new file mode 100644 index 00000000..2619cd93 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/comp.vcf.gz new file mode 100644 index 00000000..ea2b05ae Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/comp.vcf.gz.tbi new file mode 100644 index 00000000..7a9f6bbe Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/haps.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/haps.fa new file mode 100644 index 00000000..5d4b84e0 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/haps.fa @@ -0,0 +1,130 @@ +>ref_chr20_61201583_61202575 +AATACAGCATATCAAAATGTATGGGATGCAGCTAAAGCAGTGCTCAGAGGACAATCTATACTACTAGAGGCTTATATTAGAAAAAAAAATTTAAATCAATAACCTAAGCTTTCACCATTAGAGAAGGAATTTCCTCACTCAGGACCCTCTGCGGATGTCGCCTCCATCCTCATCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCATGGTGTCACCTCCATCCTTACTCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTCCATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTCCATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCGTGAGTGCCAGCTCTGTCTACCCTCGGGACCCTCCATGAGTGTCTCCTCTATCTACCCTCAGGACCCTCTGTGAATGTCCTCGCCATCCATACTCCCCCCTCTTAGACCCAGACTGTTTCAGGGTTGGACACTGAGCTGTGGCCCCTGAGCCTAGCTCTTCTCCGAGCTTCTCTTGGGCACCTCTCTCTCAGACTAGGCT +>syndip_1_chr20:61201583-61202575 +AATACAGCATATCAAAATGTATGGGATGCAGCTAAAGCAGTGCTCAGAGGACAATCTATA +CTACTAGAGGCTTATATTAGAAAAAAAAATTTAAATCAATAACCTAAGCTTTCACCATTA +GAGAAGGAATTTCCTCACTCAGGACCCTCTGCGGATGTCGCCTCCATCCTCATCAGGACC +CTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCATGGTGTCACCTCCATCCTTAC +TCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTC +CATCCTCACTCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGGT +GTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTCCATCCTCACCAGGATCC +CCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAG +GACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCGCCATC +CTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCA +CCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACCAGGACCCTCCAT +GAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGG +ACCCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCGCCATCC +TCACTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCA +CCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACCAGGATCCCCTGT +AAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGG +ACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATAGTGCCACCTCCATCCT +CACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACC +TCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATG +GTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGAC +CCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTC +ACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCA +TCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGT +CACCTCCATCCTCACTCAGGACCCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCT +CCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTC +AGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCGTGAGTGCCAGCTCTG +TCTACCCTCGGGACCCTCCATGAGTGTCTCCTCTATCTACCCTCAGGACCCTCTGTGAAT +GTCCTCGCCATCCATACTCCCCCCTCTTAGACCCAGACTGTTTCAGGGTTGGACACTGAG +CTGTGGCCCCTGAGCCTAGCTCTTCTCCGAGCTTCTCTTGGGCACCTCTCTCTCAGACTA +GGCT +>syndip_2_chr20:61201583-61202575 +AATACAGCATATCAAAATGTATGGGATGCAGCTAAAGCAGTGCTCAGAGGACAATCTATA +CTACTAGAGGCTTATATTAGAAAAAAAAATTTAAATCAATAACCTAAGCTTTCACCATTA +GAGAAGGAATTTCCTCACTCAGGACCCTCTGCGGATGTCGCCTCCATCCTCATCAGGACC +CTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCATGGTGTCACCTCCATCCTTAC +TCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTC +CATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGT +GTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCC +TCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGGTGTCACCTCCATCCTCAC +TCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCGC +CATCCTCACTCAGGACCCTCCATGAGTGCCACCTCCATCCTCACCAGGATCCCCTGTAAG +TGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAGGACCCTCC +ATGAGTGTCACCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGA +CCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTC +ACTCAGGACCCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGAGTGTCAC +CTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGT +GTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCC +TCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCATGGTGTCACCTCCATCCTTACT +CAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTCC +ATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGAGT +GTCACCTCCATCCTCAGGACCCTCCATGGTGTCACCTCCATCCTCAGGACCCTCCATGAG +TGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACC +CTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGGTGTCACCTCCATCCTC +ACTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACC +TCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCATG +GTGTCACCTCCATCCTTACTCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGAC +CCTCCATGAGTGCCACCTCCATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTC +ACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCT +CCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCGTGA +GTGCCAGCTCTGTCTACCCTCGGGACCCTCCATGAGTGTCTCCTCTATCTACCCTCAGGA +CCCTCTGTGAATGTCCTCGCCATCCATACTCCCCCCTCTTAGACCCAGACTGTTTCAGGG +TTGGACACTGAGCTGTGGCCCCTGAGCCTAGCTCTTCTCCGAGCTTCTCTTGGGCACCTC +TCTCTCAGACTAGGCT +>p:HG002_1_chr20:61201583-61202575 +AATACAGCATATCAAAATGTATGGGATGCAGCTAAAGCAGTGCTCAGAGGACAATCTATA +CTACTAGAGGCTTATATTAGAAAAAAAAATTTAAATCAATAACCTAAGCTTTCACCATTA +GAGAAGGAATTTCCTCACTCAGGACCCTCTGCGGATGTCGCCTCCATCCTCATCAGGACC +CTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCATGGTGTCACCTCCATCCTTAC +TCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTC +CATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGT +GTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCC +TCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGGTGTCACCTCCATCCTCAC +TCAGGACCCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGGTGTCACCT +CCATCCTCACTCAGGACCCTCCATGGGTGCCACCTCCATCCTCACCAGGATCCCCTGTAA +GTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAGGACCCTC +CATGAGTGTCACCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGG +ACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCT +CACTCAGGACCCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGAGTGTCA +CCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGG +TGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACC +CTCCATGGTGTCACCTCCATCCTCACTCGGACCCTCCATGAGTGTCACCTCCATCCTCAC +TCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTC +CATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGT +GTCACCTCCATCCTCAGGACCCTCCATGGTGTCACCTCCATCCTCAGGACCCTCCATGAG +TGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACC +CTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGGTGTCACCTCCATCCTC +ACTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACC +TCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCATA +GTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGAC +CCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGGTGTCACCTCCATCCTC +ACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCT +CCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCGTGA +GTGCCAGCTCTGTCTACCCTCGGGACCCTCCATGAGTGTCTCCTCTATCTACCCTCAGGA +CCCTCTGTGAATGTCCTCGCCATCCATACTCCCCCCTCTTAGACCCAGACTGTTTCAGGG +TTGGACACTGAGCTGTGGCCCCTGAGCCTAGCTCTTCTCCGAGCTTCTCTTGGGCACCTC +TCTCTCAGACTAGGCT +>p:HG002_2_chr20:61201583-61202575 +AATACAGCATATCAAAATGTATGGGATGCAGCTAAAGCAGTGCTCAGAGGACAATCTATA +CTACTAGAGGCTTATATTAGAAAAAAAAATTTAAATCAATAACCTAAGCTTTCACCATTA +GAGAAGGAATTTCCTCACTCAGGACCCTCTGCGGATGTCGCCTCCATCCTCATCAGGACC +CTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCATGGTGTCACCTCCATCCTTAC +TCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTC +CATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGT +GTCACCTCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTCCATCCTCACCAGGATCC +CCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAG +GACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATC +CTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCA +CCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACCAGGACCCTCCAT +GAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGG +ACCCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCGCCATCC +TCACTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCA +CCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACCAGGATCCCCTGT +AAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGG +ACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCT +CACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACC +TCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCGGACCCTCCATGA +GTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGAC +CCTCCATGAGTGCCACCTCCATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTC +ACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCA +TCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGT +CACCTCCATCCTCACTCAGGACCCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCT +CCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTC +AGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCGTGAGTGCCAGCTCTG +TCTACCCTCGGGACCCTCCATGAGTGTCTCCTCTATCTACCCTCAGGACCCTCTGTGAAT +GTCCTCGCCATCCATACTCCCCCCTCTTAGACCCAGACTGTTTCAGGGTTGGACACTGAG +CTGTGGCCCCTGAGCCTAGCTCTTCTCCGAGCTTCTCTTGGGCACCTCTCTCTCAGACTA +GGCT diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/haps.fa.ref.fa new file mode 100644 index 00000000..1cfaf0a4 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:61201583-61202575 +AATACAGCATATCAAAATGTATGGGATGCAGCTAAAGCAGTGCTCAGAGGACAATCTATACTACTAGAGGCTTATATTAGAAAAAAAAATTTAAATCAATAACCTAAGCTTTCACCATTAGAGAAGGAATTTCCTCACTCAGGACCCTCTGCGGATGTCGCCTCCATCCTCATCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACACTCCATGGTGTCACCTCCATCCTTACTCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTCCATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCGCCATCCTCACTCAGGACCCTCCATGAGTGCCACCTCCATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCGTGAGTGCCAGCTCTGTCTACCCTCGGGACCCTCCATGAGTGTCTCCTCTATCTACCCTCAGGACCCTCTGTGAATGTCCTCGCCATCCATACTCCCCCCTCTTAGACCCAGACTGTTTCAGGGTTGGACACTGAGCTGTGGCCCCTGAGCCTAGCTCTTCTCCGAGCTTCTCTTGGGCACCTCTCTCTCAGACTAGGCT diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/msa.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/msa.fa new file mode 100644 index 00000000..d2b596e4 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/msa.fa @@ -0,0 +1,165 @@ +>ref_chr20_61201583_61202575 +aatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctata +ctactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccatta +gagaaggaatttcctcactcaggaccctctgcggatgtcgcctccatcctcatcaggacc +ctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatccttac +tcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccacctc +catcctcac-caggatcccctgtaagtgtcacctccatcctcaccaggaccctccatg-- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------agtgtcacctccatcctca---gga +ccctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcaccgccatcct +cactcaggaccctccatgagtgccacctccatcctcac-caggatcccctgtaagtgtca +cctccatcctcac-caggaccctccatgagtgtcacctccatc----ctcaggaccctcc +atg--------------------------------------------------------- +----------agtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcc +tcactcaggaccctccatg-gtgtcacctccatcctcactcaggaccctccatgggtgtc +acctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctcc +atggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcag +gaccctccgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctat +ctaccctcaggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccag +actgtttcagggttggacactgagctgtggcccctgagcctagctcttctccgagcttct +cttgggcacctctctctcagactaggct +>syndip_1_chr20:61201583-61202575 +aatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctata +ctactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccatta +gagaaggaatttcctcactcaggaccctctgcggatgtcgcctccatcctcatcaggacc +ctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatccttac +tcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccacctc +catcctcactcaggatcccctgtaagtgtcacctccatcctcaccaggaccctccatg-g +tgtcaccgccatcctcactcaggaccctccatgagtgccacctccatcctcaccaggatc +ccctgtaagtgtcacctccatcctcac-caggaccctccatgagtgtcacctccatc--- +-ctcaggaccctccatgagtgtcacctccatcctcactcaggaccctccat-ggtgtcac +cgccatcctcactcaggaccctccatg-gtgtcacctccatcctcactcaggaccctcca +tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctca------ +----------------------ccaggaccctccatgagtgtcacctccatcctcactca +ggaccctccatggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccat +cctcactcaggaccctccat-ggtgtcaccgccatcctca-------------------- +-----------ctcaggaccctccatgagtgtcacctccatcctcactcaggaccctcca +tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcaccagga +tcccctgtaagtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcct +cactcaggaccctccatggtgtcacctccatcctcactcaggaccctccat-agtgccac +ctccatcctcaccaggatcccctgtaagtgtcacctccatcctcac-caggaccctccat +gagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcagg +accctccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcct +cactcaggaccctccatgggtgtcacctccatcctcac-tcaggaccctccatggtgtca +cctccatcctcac-caggaccctccatgagtgtcacctccatc----ctcaggaccctcc +atg--------------------------------------------------------- +----------agtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcc +tcactcaggaccctccatg-gtgtcacctccatcctcactcaggaccctccatgggtgtc +acctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctcc +atggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcag +gaccctccgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctat +ctaccctcaggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccag +actgtttcagggttggacactgagctgtggcccctgagcctagctcttctccgagcttct +cttgggcacctctctctcagactaggct +>syndip_2_chr20:61201583-61202575 +aatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctata +ctactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccatta +gagaaggaatttcctcactcaggaccctctgcggatgtcgcctccatcctcatcaggacc +ctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatccttac +tcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccacctc +catcctcac-caggatcccctgtaagtgtcacctccatcctcaccaggaccctccatgag +tgtcacctccatcctcactcaggaccctccatg-gtgtcacctccatcctcactcaggac +cctccatggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctc +actcaggaccctccatgagtgtcacctccatcctcactcaggaccctccat-ggtgtcac +cgccatcctcactcaggaccctccatgagtgccacctccatcctcaccaggatcccctgt +aagtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcctcaggaccc +tccatgagtgtcacctccatcctcaggaccctccatgagtgtcacctccatcctcactca +ggaccctccatggtgtcacctccatcctcactcaggaccctccat-ggtgtcacctccat +cctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccatgagtg +tcacctccatcctcaggaccctccatgagtgtcacctccatcctcactcaggaccctcca +tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcagg +accctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatcct +tactcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccac +ctccatcctcaccaggatcccctgtaagtgtcacctccatcctcactcaggaccctccat +gagtgtcacctccatcctca----ggaccctccatggtgtcacctccatcctca---gga +ccctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcct +cactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccatgggtgtca +cctccatcctcactcaggaccctccatgagtgtcacctccatcctcactcaggaccctcc +atggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcag +gacactccatggtgtcacctccatccttactcaggaccctccatggtgtcaccgccatcc +tcactcaggaccctccatgagtgccacctccatcctcac-caggatcccctgtaagtgtc +acctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctcc +atggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcag +gaccctccgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctat +ctaccctcaggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccag +actgtttcagggttggacactgagctgtggcccctgagcctagctcttctccgagcttct +cttgggcacctctctctcagactaggct +>p:HG002_1_chr20:61201583-61202575 +aatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctata +ctactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccatta +gagaaggaatttcctcactcaggaccctctgcggatgtcgcctccatcctcatcaggacc +ctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatccttac +tcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccacctc +catcctcac-caggatcccctgtaagtgtcacctccatcctcaccaggaccctccatgag +tgtcacctccatcctcactcaggaccctccatg-gtgtcacctccatcctcactcaggac +cctccatggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctc +actcaggaccctccatgggtgtcacctccatcctcactcaggaccctccatgggtgtcac +ctccatcctcactcaggaccctccatgggtgccacctccatcctcaccaggatcccctgt +aagtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcctcaggaccc +tccatgagtgtcacctccatcctcaggaccctccatgagtgtcacctccatcctcactca +ggaccctccatggtgtcacctccatcctcactcaggaccctccat-ggtgtcacctccat +cctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccatgagtg +tcacctccatcctcaggaccctccatgagtgtcacctccatcctcactcaggaccctcca +tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcagg +accctccatggtgtcacctccatcctcactcggaccctccatgagtgtcacctccatcct +cactcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccac +ctccatcctcaccaggatcccctgtaagtgtcacctccatcctcac-caggaccctccat +gagtgtcacctccatcctca----ggaccctccatggtgtcacctccatcctca---gga +ccctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcct +cactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccatgggtgtca +cctccatcctcactcaggaccctccatgagtgtcacctccatcctcactcaggaccctcc +atggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcag +gacactccatagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcc +tcactcaggaccctccatg-gtgtcacctccatcctcactcaggaccctccatgggtgtc +acctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctcc +atggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcag +gaccctccgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctat +ctaccctcaggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccag +actgtttcagggttggacactgagctgtggcccctgagcctagctcttctccgagcttct +cttgggcacctctctctcagactaggct +>p:HG002_2_chr20:61201583-61202575 +aatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctata +ctactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccatta +gagaaggaatttcctcactcaggaccctctgcggatgtcgcctccatcctcatcaggacc +ctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatccttac +tcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccacctc +catcctcac-caggatcccctgtaagtgtcacctccatcctcaccaggaccctccatgag +tgtcacctccatcctcactcaggaccctccatgagtgccacctccatcctcaccaggatc +ccctgtaagtgtcacctccatcctcac-caggaccctccatgagtgtcacctccatc--- +-ctcaggaccctccatgagtgtcacctccatcctcactcaggaccctccat-ggtgtcac +ctccatcctcactcaggaccctccatg-gtgtcacctccatcctcactcaggaccctcca +tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctca------ +----------------------ccaggaccctccatgagtgtcacctccatcctcactca +ggaccctccatggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccat +cctcactcaggaccctccat-ggtgtcaccgccatcctca-------------------- +-----------ctcaggaccctccatgagtgtcacctccatcctcactcaggaccctcca +tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcaccagga +tcccctgtaagtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcct +cactcaggaccctccatggtgtcacctccatcctcactcaggaccctccat-ggtgtcac +ctccatcctcaccaggatcccctgtaagtgtcacctccatcctcac-caggaccctccat +gagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcgga +ccctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcaccgccatcct +cactcaggaccctccatgagtgccacctccatcctcac-caggatcccctgtaagtgtca +cctccatcctcac-caggaccctccatgagtgtcacctccatc----ctcaggaccctcc +atg--------------------------------------------------------- +----------agtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcc +tcactcaggaccctccatg-gtgtcacctccatcctcactcaggaccctccatgggtgtc +acctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctcc +atggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcag +gaccctccgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctat +ctaccctcaggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccag +actgtttcagggttggacactgagctgtggcccctgagcctagctcttctccgagcttct +cttgggcacctctctctcagactaggct diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/msa.fa.fai new file mode 100644 index 00000000..1282a813 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_61201583_61202575 1888 29 60 61 +syndip_1_chr20:61201583-61202575 1888 1983 60 61 +syndip_2_chr20:61201583-61202575 1888 3937 60 61 +p:HG002_1_chr20:61201583-61202575 1888 5892 60 61 +p:HG002_2_chr20:61201583-61202575 1888 7847 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/output.vcf.gz new file mode 100644 index 00000000..d787c537 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/output.vcf.gz.tbi new file mode 100644 index 00000000..4be73317 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:61201683-61202475/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/base.vcf.gz new file mode 100644 index 00000000..3cb780c8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/base.vcf.gz.tbi new file mode 100644 index 00000000..9fe5d9c7 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/comp.vcf.gz new file mode 100644 index 00000000..918c5c76 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/comp.vcf.gz.tbi new file mode 100644 index 00000000..bf4dba02 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/haps.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/haps.fa new file mode 100644 index 00000000..c30c0eef --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/haps.fa @@ -0,0 +1,148 @@ +>ref_chr20_62057473_62059240 +TCCAAGATCCATGTACCCCAACACCACCCTACCTGGCTACGCTCCTCTCACAACTTTGAGATCAAGATGCCACGTGTGCCTTCCTCACATCGGCGCTTTCCAGTGATGCCCAGTGGGGGACACAAAGGGCCCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCTCCAGTCCCCAAACACAGTCCCCAACAGACAACTTCTCCTGTCCCCACATGCGGCTCCCAACAAACAATTTCTCCTGCCCTCACACGCGGTTCCCAACGACAACTTCTGCTCCACAACATGACACCCACGGTGGGAGAAGCTGGGGGCACTTCACTACATCATCCTGCACACTGCAGCATGGCCTGCTCCAGGCAGAAGGCAGGCCTGGAGAAGAGCCTGGGACCACCGCGGACTGACC +>syndip_1_chr20:62057473-62059240 +TCCAAGATCCATGTACCCCAACACCACCCTACCTGGCTACGCTCCTCTCACAACTTTGAG +ATCAAGATGCCACGTGTGCCTTCCTCACATCGGCGCTTTCCAGTGATGCCCAGTGGGGGA +CACAAAGGGCCCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAG +ACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTAC +ACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACG +GACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGA +CCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCC +AACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATG +GGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCA +GGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACA +GGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAG +GAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTC +AGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTC +GGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACA +GACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTA +CACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGAC +GGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAG +ACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGG +CCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAA +TGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACC +AGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACAC +AGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCA +GGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACC +TCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGC +TCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCA +CAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCT +ACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGA +CGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAG +ACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGG +CCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAA +TGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACAC +CAGGCCACAGACAGTGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGAC +ACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTC +AGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAAC +CTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGG +CTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGC +CACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGT +CTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAA +GGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAG +CAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGG +GGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGA +CAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACA +CACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGG +ACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACC +TCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAA +CCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGG +GCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGG +CCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAG +GTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGA +AGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAG +CAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGG +GGGGCCAACCTCTCCAGTCCCCAAACACAGTCCCCAACAGACAACTTCTCCTGTCCCCAC +ATGCGGCTCCCAACAAACAATTTCTCCTGCCCTCACACGCGGTTCCCAACGACAACTTCT +GCTCCACAACATGACACCCACGGTGGGAGAAGCTGGGGGCACTTCACTACATCATCCTGC +ACACTGCAGCATGGCCTGCTCCAGGCAGAAGGCAGGCCTGGAGAAGAGCCTGGGACCACC +GCGGACTGACC +>syndip_2_chr20:62057473-62059240 +TCCAAGATCCATGTACCCCAACACCACCCTACCTGGCTACGCTCCTCTCACAACTTTGAG +ATCAAGATGCCACGTGTGCCTTCCTCACATCGGCGCTTTCCAGTGATGCCCAGTGGGGGA +CACAAAGGGCCCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAG +ACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACA +CACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGG +ACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACC +TCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAA +CCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGG +GCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGC +CACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGT +CTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCTCCAGTCCCCAAACAC +AGTCCCCAACAGACAACTTCTCCTGTCCCCACATGCGGCTCCCAACAAACAATTTCTCCT +GCCCTCACACGCGGTTCCCAACGACAACTTCTGCTCCACAACATGACACCCACGGTGGGA +GAAGCTGGGGGCACTTCACTACATCATCCTGCACACTGCAGCATGGCCTGCTCCAGGCAG +AAGGCAGGCCTGGAGAAGAGCCTGGGACCACCGCGGACTGACC +>p:HG002_1_chr20:62057473-62059240 +TCCAAGATCCATGTACCCCAACACCACCCTACCTGGCTACGCTCCTCTCACAACTTTGAG +ATCAAGATGCCACGTGTGCCTTCCTCACATCGGCGCTTTCCAGTGATGCCCAGTGGGGGA +CACAAAGGGCCCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAG +ACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACA +CACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACG +GACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGA +CCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCC +AACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATG +GGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAG +GCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAG +GTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCTCCAGTCCCCAAAC +ACAGTCCCCAACAGACAACTTCTCCTGTCCCCACATGCGGCTCCCAACAAACAATTTCTC +CTGCCCTCACACGCGGTTCCCAACGACAACTTCTGCTCCACAACATGACACCCACGGTGG +GAGAAGCTGGGGGCACTTCACTACATCATCCTGCACACTGCAGCATGGCCTGCTCCAGGC +AGAAGGCAGGCCTGGAGAAGAGCCTGGGACCACCGCGGACTGACC +>p:HG002_2_chr20:62057473-62059240 +TCCAAGATCCATGTACCCCAACACCACCCTACCTGGCTACGCTCCTCTCACAACTTTGAG +ATCAAGATGCCACGTGTGCCTTCCTCACATCGGCGCTTTCCAGTGATGCCCAGTGGGGGA +CACAAAGGGCCCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAG +ACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTAC +ACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACG +GACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGA +CCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCC +AACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATG +GGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCA +GGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACA +GGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAG +GAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTC +AGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTC +GGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACA +GACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTA +CACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGAC +GGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAG +ACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGG +CCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAA +TGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACC +AGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACAC +AGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCA +GGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACC +TCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGC +TCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCA +CAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCT +ACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGA +CGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAG +ACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGG +CCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAA +TGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACAC +CAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGAC +ACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTC +AGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAAC +CTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGG +CTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCC +ACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTC +TACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAG +GACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCA +AGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGG +GGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGAC +AATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACAC +ACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGA +CACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCT +CAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAA +CCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGG +GCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGG +CCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGG +TCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAA +GGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGC +AAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGG +GGGCCAACCTCTCCAGTCCCCAAACACAGTCCCCAACAGACAACTTCTCCTGTCCCCACA +TGCGGCTCCCAACAAACAATTTCTCCTGCCCTCACACGCGGTTCCCAACGACAACTTCTG +CTCCACAACATGACACCCACGGTGGGAGAAGCTGGGGGCACTTCACTACATCATCCTGCA +CACTGCAGCATGGCCTGCTCCAGGCAGAAGGCAGGCCTGGAGAAGAGCCTGGGACCACCG +CGGACTGACC diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/haps.fa.ref.fa new file mode 100644 index 00000000..eee96022 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:62057473-62059240 +TCCAAGATCCATGTACCCCAACACCACCCTACCTGGCTACGCTCCTCTCACAACTTTGAGATCAAGATGCCACGTGTGCCTTCCTCACATCGGCGCTTTCCAGTGATGCCCAGTGGGGGACACAAAGGGCCCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGCCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGCCAACCTCAGCAAGACCTCAGGAAGGACGGACACAGGTCTACACACCAGGCCACAGACAATGGGGCTCGGGGGGCCAACCTCTCCAGTCCCCAAACACAGTCCCCAACAGACAACTTCTCCTGTCCCCACATGCGGCTCCCAACAAACAATTTCTCCTGCCCTCACACGCGGTTCCCAACGACAACTTCTGCTCCACAACATGACACCCACGGTGGGAGAAGCTGGGGGCACTTCACTACATCATCCTGCACACTGCAGCATGGCCTGCTCCAGGCAGAAGGCAGGCCTGGAGAAGAGCCTGGGACCACCGCGGACTGACC diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/msa.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/msa.fa new file mode 100644 index 00000000..b89f9652 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/msa.fa @@ -0,0 +1,290 @@ +>ref_chr20_62057473_62059240 +tccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttgag +atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga +cacaaagggcccagcaagacctcaggaaggacggacacaggcctacacaccaggccacag +acaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctac +acaccaggccacagacaatggggctcg--------------------------------- +------------------------------------------------------------ +-----------------------------------------------------gggggcc +aacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatg +gggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacca +ggccacagacaatggggctc---------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------------gggggccaacctcagcaag +acctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggg +ccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaa +tggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacc +aggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacac +aggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctca +ggaaggacggacacaggc------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------------------------ct +acacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagga +cggacacaggtctacacaccaggccacagacaatggggctcg------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------gggggccaacctcagcaagacctc +aggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggccaac +ctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatgggg +ctc-gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggc +cacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggt +ctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaa +ggacggacacaggcctacacaccaggccacagacaatggggctc---------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------ggggggccaacctcagcaagacctcaggaaggacggacaca +ggcctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagg +aaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctca +gcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcg +ggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacag +acaatggggctcggggggccaacctctccagtccccaaacacagtccccaacagacaact +tctcctgtccccacatgcggctcccaacaaacaatttctcctgccctcacacgcggttcc +caacgacaacttctgctccacaacatgacacccacggtgggagaagctgggggcacttca +ctacatcatcctgcacactgcagcatggcctgctccaggcagaaggcaggcctggagaag +agcctgggaccaccgcggactgacc +>syndip_1_chr20:62057473-62059240 +tccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttgag +atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga +cacaaagggcccagcaagacctcaggaaggacggacacaggcctacacaccaggccacag +acaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctac +acaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacg +gacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaaga +cctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggcc +aacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatg +gggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacca +ggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacaca +ggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcag +gaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacctc +agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc +gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccaca +gacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggccta +cacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggac +ggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaag +acctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggg +ccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaa +tggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacc +aggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacac +aggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctca +ggaaggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacc +tcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggc +tcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggcca +cagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtct +acacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagga +cggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaag +acctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggg +ccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaa +tggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacac +caggccacagacagtggggctcggggggccaacctcagcaagacctcaggaaggacggac +acaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctc +aggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggccaac +ctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatgggg +ctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggc +cacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggt +ctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaa +ggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcag +caagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgg +gggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacaga +caatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctaca +caccaggccacagacaatggggctc-gggggccaacctcagcaagacctcaggaaggacg +gacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagac +ctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggcca +acctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatgg +ggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccag +gccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacaca +ggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagg +aaggacggacacaggtctacacac------------------------------------ +-------------------------------------caggccacagacaatggggctcg +ggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacag +acaatggggctcggggggccaacctctccagtccccaaacacagtccccaacagacaact +tctcctgtccccacatgcggctcccaacaaacaatttctcctgccctcacacgcggttcc +caacgacaacttctgctccacaacatgacacccacggtgggagaagctgggggcacttca +ctacatcatcctgcacactgcagcatggcctgctccaggcagaaggcaggcctggagaag +agcctgggaccaccgcggactgacc +>syndip_2_chr20:62057473-62059240 +tccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttgag +atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga +cacaaagggcc------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------cagcaagacctcaggaaggacggacacaggtctacacacc +aggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacac +aggtctacacaccaggccacagacaatggggctc-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------------------gggggccaac +ctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatgggg +ctc-gggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggc +cacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggt +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---ctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagg +aaggacggacacaggtctacacac------------------------------------ +-------------------------------------caggccacagacaatggggctcg +ggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacag +acaatggggctcggggggccaacctctccagtccccaaacacagtccccaacagacaact +tctcctgtccccacatgcggctcccaacaaacaatttctcctgccctcacacgcggttcc +caacgacaacttctgctccacaacatgacacccacggtgggagaagctgggggcacttca +ctacatcatcctgcacactgcagcatggcctgctccaggcagaaggcaggcctggagaag +agcctgggaccaccgcggactgacc +>p:HG002_1_chr20:62057473-62059240 +tccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttgag +atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga +cacaaagggcc------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------cagcaagacctcaggaaggacggacacaggtctacacacc +aggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacac +aggtctacacaccaggccacagacaatggggctc-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------------ggggggccaac +ctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatgggg +ctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggc +cacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggt +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---ctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagg +aaggacggacacaggtctacacac------------------------------------ +-------------------------------------caggccacagacaatggggctcg +ggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacag +acaatggggctcggggggccaacctctccagtccccaaacacagtccccaacagacaact +tctcctgtccccacatgcggctcccaacaaacaatttctcctgccctcacacgcggttcc +caacgacaacttctgctccacaacatgacacccacggtgggagaagctgggggcacttca +ctacatcatcctgcacactgcagcatggcctgctccaggcagaaggcaggcctggagaag +agcctgggaccaccgcggactgacc +>p:HG002_2_chr20:62057473-62059240 +tccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttgag +atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga +cacaaagggcccagcaagacctcaggaaggacggacacaggtctacacaccaggccacag +acaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctac +acaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacg +gacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaaga +cctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggcc +aacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatg +gggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacca +ggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacaca +ggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcag +gaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacctc +agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc +gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccaca +gacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggccta +cacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggac +ggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaag +acctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggg +ccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaa +tggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacc +aggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacac +aggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctca +ggaaggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacc +tcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggc +tcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggcca +cagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtct +acacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagga +cggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaag +acctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggg +ccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaa +tggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacac +caggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggac +acaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctc +aggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggccaac +ctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatgggg +ctc-gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggc +cacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggt +ctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaa +ggacggacacaggcctacacaccaggccacagacaatggggctc---------------- +----------------------------------------------------------gg +gggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacaga +caatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctaca +caccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacg +gacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagac +ctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggcca +acctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatgg +ggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccag +gccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacaca +ggcctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagg +aaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctca +gcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcg +ggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacag +acaatggggctcggggggccaacctctccagtccccaaacacagtccccaacagacaact +tctcctgtccccacatgcggctcccaacaaacaatttctcctgccctcacacgcggttcc +caacgacaacttctgctccacaacatgacacccacggtgggagaagctgggggcacttca +ctacatcatcctgcacactgcagcatggcctgctccaggcagaaggcaggcctggagaag +agcctgggaccaccgcggactgacc diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/msa.fa.fai new file mode 100644 index 00000000..aa42074e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_62057473_62059240 3385 29 60 61 +syndip_1_chr20:62057473-62059240 3385 3505 60 61 +syndip_2_chr20:62057473-62059240 3385 6981 60 61 +p:HG002_1_chr20:62057473-62059240 3385 10458 60 61 +p:HG002_2_chr20:62057473-62059240 3385 13935 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/output.vcf.gz new file mode 100644 index 00000000..6ed8e759 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/output.vcf.gz.tbi new file mode 100644 index 00000000..63b1d379 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62057573-62059140/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/base.vcf.gz new file mode 100644 index 00000000..7b8f7754 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/base.vcf.gz.tbi new file mode 100644 index 00000000..cce7ab7c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/comp.vcf.gz new file mode 100644 index 00000000..45b1d46f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/comp.vcf.gz.tbi new file mode 100644 index 00000000..585db4aa Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/haps.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/haps.fa new file mode 100644 index 00000000..f1c24c1c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/haps.fa @@ -0,0 +1,70 @@ +>ref_chr20_62270179_62271195 +CGTCCTAGTCCCTGGTGCAGACGAGGAGCCTGAGAGGCTTAGCAGCTCATGTGTGTGTCAGCTGGGAACCCACAGCAAGTGGATTCCAAAGCCTGCCATGTCCCTGTTGCCACTAGCACCTCCTCCTCCACTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCCCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTTTCCTTGTCCCTTTCTGGTCTCTCTGGTCCTCTCCTTCTCTCCTTGTCCCTCTCCCTCTGCCTCTGCTTTGCCCACCCCAGACCCTGCTCCTTCCTGAAGAGCCTGCCCTGAGGTGACAGCTGTGTTTCCCTGGAATGCCTACTGCCCTTGGGATCCCTTTCCTGGAAGCCCGGTGGGAA +>syndip_1_chr20:62270179-62271195 +CGTCCTAGTCCCTGGTGCAGACGAGGAGCCTGAGAGGCTTAGCAGCTCATGTGTGTGTCA +GCTGGGAACCCACAGCAAGTGGATTCCAAAGCCTGCCATGTCCCTGTTGCCACTAGCACC +TCCTCCTCCACTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCCTGGCCTCTCTG +GGTCCTCTCCTTGTCCCTCCCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTC +TCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGG +GTCCTCTCCTTGTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTC +TCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCTGACCTCTCTGAGTCCTCTCCTTGTC +CCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCT +CTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGG +TCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTC +TCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTT +GTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCT +CCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTG +TCCCTCTCTGGCCTCTCTGGGTCCTTTCCTTGTCCCTTTCTGGTCTCTCTGGTCCTCTCC +TTCTCTCCTTGTCCCTCTCCCTCTGCCTCTGCTTTGCCCACCCCAGACCCTGCTCCTTCC +TGAAGAGCCTGCCCTGAGGTGACAGCTGTGTTTCCCTGGAATGCCTACTGCCCTTGGGAT +CCCTTTCCTGGAAGCCCGGTGGGAA +>syndip_2_chr20:62270179-62271195 +CGTCCTAGTCCCTGGTGCAGACGAGGAGCCTGAGAGGCTTAGCAGCTCATGTGTGTGTCA +GCTGGGAACCCACAGCAAGTGGATTCCAAAGCCTGCCATGTCCCTGTTGCCACTAGCACC +TCCTCCTCCACTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCCTGGCCTCTCTG +GGTCCTCTCCTTGTCCCTCCCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTC +TCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGG +GTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCT +CTCCTTGTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTT +GTCCCTCTCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCC +TCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCT +GGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTC +CTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTG +GGTCCTTTCCTTGTCCCTTTCTGGTCTCTCTGGTCCTCTCCTTCTCTCCTTGTCCCTCTC +CCTCTGCCTCTGCTTTGCCCACCCCAGACCCTGCTCCTTCCTGAAGAGCCTGCCCTGAGG +TGACAGCTGTGTTTCCCTGGAATGCCTACTGCCCTTGGGATCCCTTTCCTGGAAGCCCGG +TGGGAA +>p:HG002_1_chr20:62270179-62271195 +CGTCCTAGTCCCTGGTGCAGACGAGGAGCCTGAGAGGCTTAGCAGCTCATGTGTGTGTCA +GCTGGGAACCCACAGCAAGTGGATTCCAAAGCCTGCCATGTCCCTGTTGCCACTAGCACC +TCCTCCTCCACTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCCTGGCCTCTCTG +GGTCCTCTCCTTGTCCCTCCCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTC +TCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGG +GTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCT +CTCCTTGTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTT +GTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCC +TCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCT +GGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTC +CTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTG +GGTCCTTTCCTTGTCCCTTTCTGGTCTCTCTGGTCCTCTCCTTCTCTCCTTGTCCCTCTC +CCTCTGCCTCTGCTTTGCCCACCCCAGACCCTGCTCCTTCCTGAAGAGCCTGCCCTGAGG +TGACAGCTGTGTTTCCCTGGAATGCCTACTGCCCTTGGGATCCCTTTCCTGGAAGCCCGG +TGGGAA +>p:HG002_2_chr20:62270179-62271195 +CGTCCTAGTCCCTGGTGCAGACGAGGAGCCTGAGAGGCTTAGCAGCTCATGTGTGTGTCA +GCTGGGAACCCACAGCAAGTGGATTCCAAAGCCTGCCATGTCCCTGTTGCCACTAGCACC +TCCTCCTCCACTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCCTGGCCTCTCTG +GGTCCTCTCCTTGTCCCTCCCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTC +TCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGG +GTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCT +CTCCTTGTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTT +GTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGT +CCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCT +GGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTC +CTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTC +CTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCC +TCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCC +TTGTCCCTCTCTGGCCTCTCTGGGTCCTTTCCTTGTCCCTTTCTGGTCTCTCTGGTCCTC +TCCTTCTCTCCTTGTCCCTCTCCCTCTGCCTCTGCTTTGCCCACCCCAGACCCTGCTCCT +TCCTGAAGAGCCTGCCCTGAGGTGACAGCTGTGTTTCCCTGGAATGCCTACTGCCCTTGG +GATCCCTTTCCTGGAAGCCCGGTGGGAA diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/haps.fa.ref.fa new file mode 100644 index 00000000..232094ce --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:62270179-62271195 +CGTCCTAGTCCCTGGTGCAGACGAGGAGCCTGAGAGGCTTAGCAGCTCATGTGTGTGTCAGCTGGGAACCCACAGCAAGTGGATTCCAAAGCCTGCCATGTCCCTGTTGCCACTAGCACCTCCTCCTCCACTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCCCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCTGACCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTCTCCTTGTCCCTCTCTGGCCTCTCTGGGTCCTTTCCTTGTCCCTTTCTGGTCTCTCTGGTCCTCTCCTTCTCTCCTTGTCCCTCTCCCTCTGCCTCTGCTTTGCCCACCCCAGACCCTGCTCCTTCCTGAAGAGCCTGCCCTGAGGTGACAGCTGTGTTTCCCTGGAATGCCTACTGCCCTTGGGATCCCTTTCCTGGAAGCCCGGTGGGAA diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/msa.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/msa.fa new file mode 100644 index 00000000..c0057c01 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/msa.fa @@ -0,0 +1,90 @@ +>ref_chr20_62270179_62271195 +cgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtca +gctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcacc +tcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctg +ggtcctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcctc +tctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgg +gtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcct +ctccttgtccctc-ctggcctctctgggtcctctccttgtccctctctgggtcctctcct +tgtccctctctggcctctctgggtcctctctgacctctctgggtcctctccttgtccctc +tctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgg +gtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcct +ctccttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctggg +tcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctc +tccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcctt +gtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtccttt +ccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgcc +tctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagct +gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgggaa +>syndip_1_chr20:62270179-62271195 +cgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtca +gctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcacc +tcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctg +ggtcctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcctc +tctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgg +gtcctctccttgtccctc-ctggcctctctgggtcctctccttgtccctctctgggtcct +ctccttgtccctctctggcctctctgggtcctctct---gacctctctgagtcctctcct +tgtc-----------------------------cctctctgggtcctctccttgtccctc +tctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgg +gtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcct +ctccttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctggg +tcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctc +tccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcctt +gtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtccttt +ccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgcc +tctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagct +gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgggaa +>syndip_2_chr20:62270179-62271195 +cgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtca +gctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcacc +tcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctg +ggtcctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcctc +tctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgg +gtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcct +ctccttgtccctc-ctggcctctctgggtcctctccttgtccctctctgggtcctctcct +tgtc-----------------------------cctctctga--------------cctc +tctgggtcctctc----------------------------------------------- +------------------------------------------------------------ +---------------------cttgtccctctctgggtcctctccttgtccctctctggg +tcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctc +tccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcctt +gtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtccttt +ccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgcc +tctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagct +gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgggaa +>p:HG002_1_chr20:62270179-62271195 +cgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtca +gctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcacc +tcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctg +ggtcctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcctc +tctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgg +gtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcct +ctccttgtccctc-ctggcctctctgggtcctctccttgtccctctctgggtcctctcct +tgtc-----------------------------cctctctgg--------------cctc +tctgggtcctctc----------------------------------------------- +------------------------------------------------------------ +---------------------ctctgggtcctctccttgtccctctctggcctctctggg +tcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctc +tccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcctt +gtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtccttt +ccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgcc +tctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagct +gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgggaa +>p:HG002_2_chr20:62270179-62271195 +cgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtca +gctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcacc +tcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctg +ggtcctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcctc +tctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgg +gtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcct +ctccttgtccctc-ctggcctctctgggtcctctccttgtccctctctgggtcctctcct +tgtc-----------------------------cctctctgggtcctctccttgtccctc +tctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgg +gtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcct +ctccttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctggg +tcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctc +tccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcctt +gtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtccttt +ccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgcc +tctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagct +gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgggaa diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/msa.fa.fai new file mode 100644 index 00000000..a994a053 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_62270179_62271195 1018 29 60 61 +syndip_1_chr20:62270179-62271195 1018 1098 60 61 +syndip_2_chr20:62270179-62271195 1018 2167 60 61 +p:HG002_1_chr20:62270179-62271195 1018 3237 60 61 +p:HG002_2_chr20:62270179-62271195 1018 4307 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/output.vcf.gz new file mode 100644 index 00000000..60eb2ef2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/output.vcf.gz.tbi new file mode 100644 index 00000000..031ae0ac Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62270279-62271095/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/base.vcf.gz new file mode 100644 index 00000000..20a67750 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/base.vcf.gz.tbi new file mode 100644 index 00000000..3f54a83f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/comp.vcf.gz new file mode 100644 index 00000000..65641dbf Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/comp.vcf.gz.tbi new file mode 100644 index 00000000..63c0569b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/haps.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/haps.fa new file mode 100644 index 00000000..26dc345c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/haps.fa @@ -0,0 +1,102 @@ +>ref_chr20_62349512_62350033 +GAATCCTACAGTCAGCTCAACTATCATTCAAGAGGGAGGACAAAACAGCCGTTTTCAGACAATTCCGGATAGACTGTCATGGAATAGAAAAACTACAGGGTGCATTTCAGGAAGGAGGAAGCAGCAACCCAGGGGATGGGGATGGGGATGGGGATGGTGGGGGTGATGGGGGTGATGATGGTGATGGTGATGGTGATGGTGATGGTGATGGTGATGGTGGGGGTGGTGATGGGTGGGGGTGATGACGGTGGGAGTGGGGGTGATGACGGTGATGGTGGGGGTGATGACGGTGATGGTGGGGGTGATGACGGTGATGGTGGGGGTGATGATGGTGGGAGTGGGCTGGTAGTGGGGGTGATGGTTTGGGTGGGAGTAAGGTGATGGTGGAGGTAAAGAGGCAGAAAATTGCTGGCTGATGACATGGAGCCCCCTTCCCTGGAGGAGAGGTGGGGTGGCGGGTAAAGGGTGCAGGGAGAACATGGGCAGGCTAATGTTTTGGGACACTGGTGGGTGACCAGGTCC +>syndip_1_chr20:62349512-62350033 +GAATCCTACAGTCAGCTCAACTATCATTCAAGAGGGAGGACAAAACAGCCGTTTTCAGAC +AATTCCGGATAGACTGTCATGGAATAGAAAAACTACAGGGTGCATTTCAGGAAGGAGGAA +GCAGCAACCCAGGGGATGGGGATGGGGATGGGGATGGGGATGGTGGGGGTGATGGGGGTG +ATGATGGTGATGGTGATGGTGATGGTGATGGTGATGGTGATGGTGGGGGTGGTGATGGTG +GGGGTGGGGGTGGTGATGGTGGGGGTGGGGGTGATGATGGTGATGGTGGGGGTGATGACG +GTGGGGCTGGGGGTGATGATGGTGGGGGTGATGACGGTGATGATGGGGGTGGAGGGGTGA +TGACGGTGATGATGGGGGTGGGGGGGTGATGACGGTGATGTGGGGGTGATGACGGTGGGG +GTGGGGGTGATGACGGTGATGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTG +GGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGATG +GTGATGGTGGGGGTGATGATGGTGGGGGTGGGGGTGATGATGGTGAGGGTGATGATGGTG +GGGGTAATGACGGTGGGGTGGGGGTGATGACGGTGGGAGTGGGGGTGATGACGGTGATGG +TGGGGGTGATGACGGTGATGGTGGGGGTGATGACGGTGATGGCGGTGGGGGTGATGACGG +TGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGA +CGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGA +TGACGGTGGGGGTGGGGGTGATGACGGTGATGGTAGAGGTGATGATGGTGGGGGTGATGG +TGGGGGTGGGGGTGGGGGTGGGGGTGATGATGGTGATGGTGGGGGTGATGATGGTGAGGG +TGATGATGGTGGGGGTGATGGTGGGGGTGGGGGTGGGGGTGGGGGTGATGACGGTGATGG +TGGGGGTGATGATGGTGGGAGTGGGCTGGTAGTGGGGGTGATGGTTTGGGTGGGAGTAAG +GTGATGGTGGAGGTAAAGAGGCAGAAAATTGCTGGCTGATGACATGGAGCCCCCTTCCCT +GGAGGAGAGGTGGGGTGGCGGGTAAAGGGTGCAGGGAGAACATGGGCAGGCTAATGTTTT +GGGACACTGGTGGGTGACCAGGTCC +>syndip_2_chr20:62349512-62350033 +GAATCCTACAGTCAGCTCAACTATCATTCAAGAGGGAGGACAAAACAGCCGTTTTCAGAC +AATTCCGGATAGACTGTCATGGAATAGAAAAACTACAGGGTGCATTTCAGGAAGGAGGAA +GCAGCAACCCAGGGGATGGGGATGGGGATGGGGATGGGGATGGTGGGGGTGATGGGGGTG +ATGATGGTGATGGTGGGGGTGATGATGGTGATGGTGATGGTGATGGTGATGGTGGGGGTG +GTGATGGTGGGGGTGGGGGTGATGATGGTGATGGTGGGGGTGATGACGGTGGGGCTGGGG +GTGATGATGGTGGGGGTGATGACGGTGATGATGGGGGTGGAGGGGTGATGACGGTGATGA +TGGGGGTGGGGGGGTGATGACGGTGATGTGGGGGTGATGACGGTGGGGGTGGGGGTGATG +ACGGTGATGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTG +ATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGG +GTGATGATGGTGATGGTGGGGGTGATGATGGTGGGGGTGGGGGTGATGATGGTGAGGGTG +ATGATGGTGGGGGTAATGACGGTGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGA +CGGTGATGGTGGGGGTGATGACGATGATGGTGGGGGTGATGACGGTGATGGCGGTGGGGG +TGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGG +GGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGG +TGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGATGGTAGAGGTGATGATGGTGG +GGGTGGGGGTGGGGGTGGGGGTGAGGGTGATGATGGTGGGGGTGATGATGGTGATGGTGG +GGGTGATGATGGTGAGGGTGATGATGGTGGGGGTGATGGTGGGGGTGGGGGTGGGGGTAA +TGACGGTGGGGTGGGGGTAATGACGGTGGGGGTGGGGGTGATGACGGTGGGAGTGGGGGT +GATGACGGTGATGGTGGGGGTGATGACGGTGATGGTGGGGGTGATGACGGTGATGGCGGT +GGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGG +GGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGT +GATGGTAGAGGTGATGATGGTGGGGGTGATGGTGGGGGTGGGGGTGGGGGTGGGGGTGAT +GATGGTGATGGTGGGGGTGATGATGGTGAGGGTGATGATGGTGGGGGTGATGGTGGGGGT +GGGGGTGGGGGTGGGGGTGATGATGGTGGGAGTGGGCTGGTAGTGGGGGTGATGGTTTGG +GTGGGAGTAAGGTGATGGTGGAGGTAAAGAGGCAGAAAATTGCTGGCTGATGACATGGAG +CCCCCTTCCCTGGAGGAGAGGTGGGGTGGCGGGTAAAGGGTGCAGGGAGAACATGGGCAG +GCTAATGTTTTGGGACACTGGTGGGTGACCAGGTCC +>p:HG002_1_chr20:62349512-62350033 +GAATCCTACAGTCAGCTCAACTATCATTCAAGAGGGAGGACAAAACAGCCGTTTTCAGAC +AATTCCGGATAGACTGTCATGGAATAGAAAAACTACAGGGTGCATTTCAGGAAGGAGGAA +GCAGCAACCCAGGGGATGGGGATGGGGATGGGGATGGTGGGGGTGATGGGGGTGATGATG +GTGATGGTGATGGTGATGGTGATGGTGATGGTGATGGTGGGGGTGGTGATGGGTGGGGGT +GATGACGGTGGGAGTGGGGGTGATGACGGTGATGGTGGGGGTGATGACGGTGATGGTGGG +GGTGATGATGGTGGGGGTGATGACGGTGATGATGGGGGTGGAGGGGTGATGACGGTGATG +ATGGGGGTGGGGGGGTGATGACGGTGATGTGGGGGTGATGACGGTGGGGGTGGGGGTGAT +GACGGTGATGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGT +GATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGG +GGTGATGATGGTGATGGTGGGGGTGATGATGGTGGGGGTGGGGGTGATGATGGTGAGGGT +GATGATGGTGGGGGTAATGACGGTGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATG +ACGGTGATGGTGGGGGTGATGACGATGATGGTGGGGGTGATGACGGTGATGGCGGTGGGG +GTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTG +GGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGG +GTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGATGGTAGAGGTGATGATGGTG +GGGGTGGGGGTGGGGGTGGGGGTGAGGGTGATGATGGTGGGGGTGATGATGGTGATGGTG +GGGGTGATGATGGTGAGGGTGATGATGGTGGGGGTGATGGTGGGGGTGGGGGTGGGGGTA +ATGACGGTGGGGTGGGGGTAATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGG +TGATGACGGTGATGGTGGGGGTGATGACGATGATGGTGGGGGTGATGACGGTGATGGCGG +TGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGG +GGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGG +TGATGGTAGAGGTGATGATGGTGGGGGTGATGGTGGGGGTGGGGGTGGGGGTGGGGGTGA +TGATGGTGATGGTGGGGGTGATGATGGTGAGGGTGATGATGGTGGGGGTGATGGTGGGGG +TGGCGGTGATGGTGGGGGTGATGATGGTGGGAGTGGGCTGGTAGTGGGGGTGATGGTTTG +GGTGGGAGTAAGGTGATGGTGGAGGTAAAGAGGCAGAAAATTGCTGGCTGATGACATGGA +GCCCCCTTCCCTGGAGGAGAGGTGGGGTGGCGGGTAAAGGGTGCAGGGAGAACATGGGCA +GGCTAATGTTTTGGGACACTGGTGGGTGACCAGGTCC +>p:HG002_2_chr20:62349512-62350033 +GAATCCTACAGTCAGCTCAACTATCATTCAAGAGGGAGGACAAAACAGCCGTTTTCAGAC +AATTCCGGATAGACTGTCATGGAATAGAAAAACTACAGGGTGCATTTCAGGAAGGAGGAA +GCAGCAACCCAGGGGATGGGGATGGGGATGGGGATGGTGGGGGTGATGGGGGTGATGATG +GTGATGGTGATGGTGATGGTGATGGTGATGGTGATGGTGGGGGTGGTGATGGTGGTGATG +GTGGGGGTGGGGGTGGTGATGGTGGGGGTGGGGGTGATGATGGTGATGGTGGGGGTGATG +ACGGTGGGGCTGGGGGTGATGATGGTGGGGGTGATGACGGTGATGATGGGGGTGGAGGGG +TGATGACGGTGATGATGGGGGTGGGGGGGTGATGACGGTGATGTGGGGGTGATGACGGTG +GGGGTGGGGGTGATGACGGTGATGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACG +GTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATG +ATGGTGATGGTGGGGGTGATGATGGTGGGGGTGGGGGTGATGATGGTGAGGGTGATGATG +GTGGGGGTAATGACGGTGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGA +TGGTGGGGGTGATGACGATGATGGTGGGGGTGATGACGGTGATGGCGGTGGGGGTGATGA +CGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGA +TGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGGTGATGACGGTGGGGGTGGGGG +TGATGACGGTGGGGGTGGGGGTGATGACGGTGATGGTAGAGGTGATGATGGTGGGGGTGA +TGGTGGGGGTGGGGGTGGGGGTGGGGGTGATGATGGTGGTGGGGGTGATGACGGTGGGAG +TGGGGGTGATGACGGTGATGGTGGGGGTGATGACGGTGATGGTGGGGGTGATGACGGTGA +TGGTGGGGGTGATGATGGTGGGAGTGGGCTGGTAGTGGGGGTGATGGTTTGGGTGGGAGT +AAGGTGATGGTGGAGGTAAAGAGGCAGAAAATTGCTGGCTGATGACATGGAGCCCCCTTC +CCTGGAGGAGAGGTGGGGTGGCGGGTAAAGGGTGCAGGGAGAACATGGGCAGGCTAATGT +TTTGGGACACTGGTGGGTGACCAGGTCC diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/haps.fa.ref.fa new file mode 100644 index 00000000..8f32fa6f --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:62349512-62350033 +GAATCCTACAGTCAGCTCAACTATCATTCAAGAGGGAGGACAAAACAGCCGTTTTCAGACAATTCCGGATAGACTGTCATGGAATAGAAAAACTACAGGGTGCATTTCAGGAAGGAGGAAGCAGCAACCCAGGGGATGGGGATGGGGATGGGGATGGTGGGGGTGATGGGGGTGATGATGGTGATGGTGATGGTGATGGTGATGGTGATGGTGATGGTGGGGGTGGTGATGGGTGGGGGTGATGACGGTGGGAGTGGGGGTGATGACGGTGATGGTGGGGGTGATGACGGTGATGGTGGGGGTGATGACGGTGATGGTGGGGGTGATGATGGTGGGAGTGGGCTGGTAGTGGGGGTGATGGTTTGGGTGGGAGTAAGGTGATGGTGGAGGTAAAGAGGCAGAAAATTGCTGGCTGATGACATGGAGCCCCCTTCCCTGGAGGAGAGGTGGGGTGGCGGGTAAAGGGTGCAGGGAGAACATGGGCAGGCTAATGTTTTGGGACACTGGTGGGTGACCAGGTCC diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/msa.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/msa.fa new file mode 100644 index 00000000..d7f97116 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/msa.fa @@ -0,0 +1,140 @@ +>ref_chr20_62349512_62350033 +gaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcagac +aattccggatagactgtcatggaatagaaaaactacagggtgcatttcaggaaggaggaa +gcagcaaccca------ggggatggggatggggatggggatggtgggggtgatgggggtg +atgatggtgatggtgatggtgatggtgatggtgatggtgatggtggg---------ggtg +gtgat-----gggtgggggtgatgacggtgggagtgggggtgatgacggtgatggtgggg +gtgatgacggtgatggtgggggtgatgac------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------ggtgatggtgggggtgatgatggtgggagtgggctg +gtagtgggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaa +ttgctggctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagg +gtgcagggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtcc +>syndip_1_chr20:62349512-62350033 +gaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcagac +aattccggatagactgtcatggaatagaaaaactacagggtgcatttcaggaaggaggaa +gcagcaacccaggggatggggatggggatggggatggggatggtgggggtgatgggggtg +atgatggtgatggtgatggtgatggtgatggtgatggtgatggtggg---------ggtg +gtgatggtgggggtgggggtggtgatggtgggggtgggggtgatgatggtgatggtgggg +gtgatgacggtggggctgggggtgatgatggtgggggtgatgacggtgatgatgggggtg +gaggggtgatgacggtgatgatgggggtgggggggtgatgacggtgatgtgggggtgatg +acggtgggggtgggggtgatgacggtgat---------------------ggtgggggtg +atgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggg +gtgatgacggtgggggtgggggtgatgatggtgatggtgggggtgatgatggtgggggtg +ggggtgatgatggtgagggtgatgatggtgggggtaatgacggtggggtgggggtgatga +cggtgggagtgggggtgatgacggtgatggtgggggtgatgacggtgatggtgggggtga +tgacggtgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgg +gggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtggggg +tgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtga +tggtagaggtgatgatggtgggggtgatggtgggggtgggggtggg---------ggtgg +gggtgatgatggt----------------------------------------------- +---------------------------------------------------gatggtggg +ggtgatgatggtgagggtgatgatggtgggggtgatggtgggggtgggggtgggggtggg +ggtgatgac--------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------ggtgatggtgggggtgatgatggtgggagtgggctg +gtagtgggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaa +ttgctggctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagg +gtgcagggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtcc +>syndip_2_chr20:62349512-62350033 +gaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcagac +aattccggatagactgtcatggaatagaaaaactacagggtgcatttcaggaaggaggaa +gcagcaaccca------ggggatggggatggggatggggatggggatggtgggggtgatg +ggggtgatgatggtgatggtgggggtgatgatggtgatggtgatggt---------gatg +gtgat------ggtgggggtggtgatggtgggggtgggggtgatgatggtgatggtgggg +gtgatgacggtggggctgggggtgatgatggtgggggtgatgacggtgatgatgggggtg +gaggggtgatgacggtgatgatgggggtgggggggtgatgacggtgatgtgggggtgatg +acggtgggggtgggggtgatgacggtgatggtgggggtgatgacggtgggggtgggggtg +atgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggg +gtgatgacggtgggggtgggggtgatgatggtgatggtgggggtgatgatggtgggggtg +ggggtgatgatggtgagggtgatgatggtgggggtaatgacggtggggtgggggtgatga +cggtgggggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtga +tgacggtgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgg +gggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtggggg +tgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtga +tggtagaggtgatgatggtgggggtgggggtgggggtgggggtgagggtgatgatggtgg +gggtgatgatggtgatggtgggggtgatgatggtgagggtgatgatggtgggggtgatgg +tgggggtgggggtgggggtaatgacggtggggtgggggtaatgacggtgggggtgggggt +gatgacggtgggagtgggggtgatgacggtgatggtgggggtgatgacggtgatggtggg +ggtgatgacggtgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtggg +ggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggt +gggggtgggggtgatgacggtgatggtagaggtgatgatggtgggggtgatggtgggggt +gggggtgggggtgggggtgatgatggtgatggtgggggtgatgatggtgagggtgatgat +ggtgggggtgatggtgggggtgggggtgggggtgggggtgatgatggtgggagtgggctg +gtagtgggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaa +ttgctggctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagg +gtgcagggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtcc +>p:HG002_1_chr20:62349512-62350033 +gaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcagac +aattccggatagactgtcatggaatagaaaaactacagggtgcatttcaggaaggaggaa +gcagcaaccca------ggggatggggatggggatggggatggtgggggtgatgggggtg +atgatggtgatggtgatggtgatggtgatggtgatggtgatggtggg---------ggtg +gtgat-----gggtgggggtgatgacggtgggagtgggggtgatgacggtgatggtgggg +gtgatgacggtgatggtgggggtgatgatggtgggggtgatgacggtgatgatgggggtg +gaggggtgatgacggtgatgatgggggtgggggggtgatgacggtgatgtgggggtgatg +acggtgggggtgggggtgatgacggtgatggtgggggtgatgacggtgggggtgggggtg +atgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggg +gtgatgacggtgggggtgggggtgatgatggtgatggtgggggtgatgatggtgggggtg +ggggtgatgatggtgagggtgatgatggtgggggtaatgacggtggggtgggggtgatga +cggtgggggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtga +tgacggtgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgg +gggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtggggg +tgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtga +tggtagaggtgatgatggtgggggtgggggtgggggtgggggtgagggtgatgatggtgg +gggtgatgatggtgatggtgggggtgatgatggtgagggtgatgatggtgggggtgatgg +tgggggtgggggtgggggtaatgacggtggggtgggggtaatgacggtgggggtgggggt +gatgacggtgggggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtggg +ggtgatgacggtgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtggg +ggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggt +gggggtgggggtgatgacggtgatggtagaggtgatgatggtgggggtgatggtgggggt +gggggtgggggtgggggtgatgatggtgatggtgggggtgatgatggtgagggtgatgat +ggtgggggtgatggtgggggtggcggtgatggtgggggtgatgatggtgggagtgggctg +gtagtgggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaa +ttgctggctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagg +gtgcagggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtcc +>p:HG002_2_chr20:62349512-62350033 +gaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcagac +aattccggatagactgtcatggaatagaaaaactacagggtgcatttcaggaaggaggaa +gcagcaaccca------ggggatggggatggggatggggatggtgggggtgatgggggtg +atgatggtgatggtgatggtgatggtgatggtgatggtgatggtgggggtggtgatggtg +gtgatggtgggggtgggggtggtgatggtgggggtgggggtgatgatggtgatggtgggg +gtgatgacggtggggctgggggtgatgatggtgggggtgatgacggtgatgatgggggtg +gaggggtgatgacggtgatgatgggggtgggggggtgatgacggtgatgtgggggtgatg +acggtgggggtgggggtgatgacggtgat---------------------ggtgggggtg +atgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggg +gtgatgacggtgggggtgggggtgatgatggtgatggtgggggtgatgatggtgggggtg +ggggtgatgatggtgagggtgatgatggtgggggtaatgacggtggggtgggggtgatga +cggtgggggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtga +tgacggtgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgg +gggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtggggg +tgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtga +tggtagaggtgatgatggtgggggtgatggtgggggtgggggtggg---------ggtgg +gggtgatgatggt----------------------------------------------- +---------------------------------------------------ggtgggggt +gatgacggtgggagtgggggtgatgacggtgatggtgggggtgatgacggtgatggtggg +ggtgatgac--------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------ggtgatggtgggggtgatgatggtgggagtgggctg +gtagtgggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaa +ttgctggctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagg +gtgcagggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtcc diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/msa.fa.fai new file mode 100644 index 00000000..4c939f99 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_62349512_62350033 1617 29 60 61 +syndip_1_chr20:62349512-62350033 1617 1707 60 61 +syndip_2_chr20:62349512-62350033 1617 3385 60 61 +p:HG002_1_chr20:62349512-62350033 1617 5064 60 61 +p:HG002_2_chr20:62349512-62350033 1617 6743 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/output.vcf.gz new file mode 100644 index 00000000..5c28bcda Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/output.vcf.gz.tbi new file mode 100644 index 00000000..f931a30b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62349612-62349933/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/base.vcf.gz new file mode 100644 index 00000000..913e2678 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/base.vcf.gz.tbi new file mode 100644 index 00000000..4c63a0c5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/comp.vcf.gz new file mode 100644 index 00000000..799b6de6 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/comp.vcf.gz.tbi new file mode 100644 index 00000000..59fca592 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/haps.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/haps.fa new file mode 100644 index 00000000..5f276114 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/haps.fa @@ -0,0 +1,52 @@ +>ref_chr20_62830512_62830939 +CCCAGGGCCAGAAGGGCAGCATGGGAGACCCCGGCCTTCCAGGCCCCCAGGGCCTCCGAGGTGACGTGGGCGACCGGGTAAGTGGCCCTCTCAGCAGGAAGCTCCCCTGCACCCCCTCTACCCATGTACCACAGTCCCCCACCCCCATGACAGTCCCCCAACCCCCACCACAGTCCCCCAACCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCACCCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCTACCACAATCCCCCACCCCCCACCACAGTCCCCTGGGACGCAGACAGGGAGAGGCCCTTGCAGCTCCCAGTGGGAAATCTGGCCATGGGCAGTGTCTCCCTGCGTGGCGGAGGCAGTGGCATCAGGGCCCCGACTGTGGCGCCTTTGGCCCCTCTGACCTTCCA +>syndip_1_chr20:62830512-62830939 +CCCAGGGCCAGAAGGGCAGCATGGGAGACCCCGGCCTTCCAGGCCCCCAGGGCCTCCGAG +GTGACGTGGGCGACCGGGTAAGTGGCCCTCTCAGCAGGAAGCTCCCCTGCACCCCCTCTA +CCCATGTACCACAGTCCCCCACCCCCCACCGTGCTCCACCCCCCACCACAGTCCCCCACC +CCCCACCCCAGTCCCCAAACCCCTACCACAGTCCCCCAACCCCACCACAGTCCCCCACCC +CCTACCACAGTCCCCCACCCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCC +CCACCACAGTCCGCCAACCCCCATGACAGTCCCTCAACCCCCACCACAGTCCCCCAACCC +CCATGACAGTCCCCCAACCCCCACCACAGTCCCCCAACCCCCACCACAGTCCCCACCCCC +TACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCTACCACAATCCCCCACCCCC +CACCACAGTCCCCTGGGACGCAGACAGGGAGAGGCCCTTGCAGCTCCCAGTGGGAAATCT +GGCCATGGGCAGTGTCTCCCTGCGTGGCGGAGGCAGTGGCATCAGGGCCCCGACTGTGGC +GCCTTTGGCCCCTCTGACCTTCCA +>syndip_2_chr20:62830512-62830939 +CCCAGGGCCAGAAGGGCAGCATGGGAGACCCCGGCCTTCCAGGCCCCCAGGGCCTCCGAG +GTGACGTGGGCGACCGGGTAAGTGGCCCTCTCAGCAGGAAGCTCCCCTGCACCCCCTCTA +CCCATGTACCACAGTCCCCCACCCCCCACCACAGTCCCCCACCCCCCACCCCAGTCCCCA +AACCCCTACCACAGTCCCCCAACCCCACCACAGTCCCCCACCCCCTACCACAGTCCCCCA +ACCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCACCACAGTCCGCCAA +CCCCCATGACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCACCACAGTCCGCCAAC +CCCCATGACAGTCCCCCAACCCCCACCACAGTCCCCCAACCCCCATGACAGTCCCCCAAC +CCCCACCACAGTCCCCCAACCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCACCC +CCTACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCTACCACAATCCCCCACCC +CCCACCACAGTCCCCTGGGACGCAGACAGGGAGAGGCCCTTGCAGCTCCCAGTGGGAAAT +CTGGCCATGGGCAGTGTCTCCCTGCGTGGCGGAGGCAGTGGCATCAGGGCCCCGACTGTG +GCGCCTTTGGCCCCTCTGACCTTCCA +>p:HG002_1_chr20:62830512-62830939 +CCCAGGGCCAGAAGGGCAGCATGGGAGACCCCGGCCTTCCAGGCCCCCAGGGCCTCCGAG +GTGACGTGGGCGACCGGGTAAGTGGCCCTCTCAGCAGGAAGCTCCCCTGCACCCCCTCTA +CCCATGTACCACAGTCCCCCACCCCCCACCACAGTCCCCCACCCCCCACCCCAGTCCCCA +AACCCCTACCACAGTCCCCCAACCCCACCACAGTCCCCCACCCCCTACCACAGTCCCCCA +ACCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCACCACAGTCCGCCAA +CCCCCATGACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCACCACAGTCCGCCAAC +CCCCATGACAGTCCCCCAACCCCCACCACAGTCCCCCAACCCCCATGACAGTCCCCCAAC +CCCCACCACAGTCCCCCAACCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCACCC +CCTACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCTACCACAATCCCCCACCC +CCCACCACAGTCCCCTGGGACGCAGACAGGGAGAGGCCCTTGCAGCTCCCAGTGGGAAAT +CTGGCCATGGGCAGTGTCTCCCTGCGTGGCGGAGGCAGTGGCATCAGGGCCCCGACTGTG +GCGCCTTTGGCCCCTCTGACCTTCCA +>p:HG002_2_chr20:62830512-62830939 +CCCAGGGCCAGAAGGGCAGCATGGGAGACCCCGGCCTTCCAGGCCCCCAGGGCCTCCGAG +GTGACGTGGGCGACCGGGTAAGTGGCCCTCTCAGCAGGAAGCTCCCCTGCACCCCCTCTA +CCCATGTACCACAGTCCCCCACCCCCCACCGTGCTCCACCCCCCACCACAGTCCCCCACC +CCCCACCCCAGTCCCCAAACCCCTACCACAGTCCCCCAACCCCACCACAGTCCCCCACCC +CCTACCACAGTCCCCCACCCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCC +CCACCACAGTCCGCCAACCCCCATGACAGTCCCCCAACCCCCACCACAGTCCCCCAACCC +CCATGACAGTCCCCCAACCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCACCCCC +TACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCTACCACAATCCCCCACCCCC +CACCACAGTCCCCTGGGACGCAGACAGGGAGAGGCCCTTGCAGCTCCCAGTGGGAAATCT +GGCCATGGGCAGTGTCTCCCTGCGTGGCGGAGGCAGTGGCATCAGGGCCCCGACTGTGGC +GCCTTTGGCCCCTCTGACCTTCCA diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/haps.fa.ref.fa new file mode 100644 index 00000000..df37a9a0 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:62830512-62830939 +CCCAGGGCCAGAAGGGCAGCATGGGAGACCCCGGCCTTCCAGGCCCCCAGGGCCTCCGAGGTGACGTGGGCGACCGGGTAAGTGGCCCTCTCAGCAGGAAGCTCCCCTGCACCCCCTCTACCCATGTACCACAGTCCCCCACCCCCATGACAGTCCCCCAACCCCCACCACAGTCCCCCAACCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCACCCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCTACCACAATCCCCCACCCCCCACCACAGTCCCCTGGGACGCAGACAGGGAGAGGCCCTTGCAGCTCCCAGTGGGAAATCTGGCCATGGGCAGTGTCTCCCTGCGTGGCGGAGGCAGTGGCATCAGGGCCCCGACTGTGGCGCCTTTGGCCCCTCTGACCTTCCA diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/msa.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/msa.fa new file mode 100644 index 00000000..eab0a7e0 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/msa.fa @@ -0,0 +1,65 @@ +>ref_chr20_62830512_62830939 +cccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccgag +gtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctcta +cccatgtaccacagtccccc---------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------acccccatgacagtcccccaa +cccccaccacagtcccccaacccctaccacagtcccccaacccccaccacagtccccacc +ccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatcccccacc +ccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaaa +tctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactgt +ggcgcctttggcccctctgaccttcca +>syndip_1_chr20:62830512-62830939 +cccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccgag +gtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctcta +cccatgtaccacagtcccccaccccccaccgtgctccacc-------------------- +----------------------ccccaccacagtcccccaccccccaccccagtccccaa +acccctaccacagtcccccaa-ccccaccacagtcccccaccccctaccacagtccccca +ccccctaccacagtcccccaacccccaccacagtcccccacccccaccacagtccgccaa +cccccatgacagtccctca--------------------acccccaccacagtcccccaa +cccccatgacagtcccccaacccccaccacagtcccccaacccccaccacagtccccacc +ccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatcccccacc +ccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaaa +tctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactgt +ggcgcctttggcccctctgaccttcca +>syndip_2_chr20:62830512-62830939 +cccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccgag +gtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctcta +cccatgtaccacagtcccccaccccccaccacagtcccccaccccccaccccagtcccca +aacccctaccacagtcccccaaccccaccacagtcccccaccccctaccacagtccccca +acccctaccacagtcccccaacccccaccacagtcccccaccccc-accacagtccgcca +acccccatgacagtcccccaacccccaccacagtcccccacccccaccacagtccgccaa +cccccatgacagtcccccaacccccaccacagtcccccaacccccatgacagtcccccaa +cccccaccacagtcccccaacccctaccacagtcccccaacccccaccacagtccccacc +ccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatcccccacc +ccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaaa +tctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactgt +ggcgcctttggcccctctgaccttcca +>p:HG002_1_chr20:62830512-62830939 +cccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccgag +gtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctcta +cccatgtaccacagtcccccaccccccaccacagtcccccaccccccaccccagtcccca +aacccctaccacagtcccccaaccccaccacagtcccccaccccctaccacagtccccca +acccctaccacagtcccccaacccccaccacagtcccccaccccc-accacagtccgcca +acccccatgacagtcccccaacccccaccacagtcccccacccccaccacagtccgccaa +cccccatgacagtcccccaacccccaccacagtcccccaacccccatgacagtcccccaa +cccccaccacagtcccccaacccctaccacagtcccccaacccccaccacagtccccacc +ccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatcccccacc +ccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaaa +tctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactgt +ggcgcctttggcccctctgaccttcca +>p:HG002_2_chr20:62830512-62830939 +cccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccgag +gtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctcta +cccatgtaccacagtcccccaccccccaccgtgctccacc-------------------- +----------------------ccccaccacagtcccccaccccccaccccagtccccaa +acccctaccacagtcccccaa-ccccaccacagtcccccaccccctaccacagtccccca +ccccctaccacagtcccccaacccccaccacagtcccccacccccaccacagtccgccaa +cccccatgacagtccccca--------------------acccccaccacagtcccccaa +cccccatgacagtcccccaacccctaccacagtcccccaacccccaccacagtccccacc +ccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatcccccacc +ccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaaa +tctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactgt +ggcgcctttggcccctctgaccttcca diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/msa.fa.fai new file mode 100644 index 00000000..dcf5fc89 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_62830512_62830939 687 29 60 61 +syndip_1_chr20:62830512-62830939 687 762 60 61 +syndip_2_chr20:62830512-62830939 687 1495 60 61 +p:HG002_1_chr20:62830512-62830939 687 2229 60 61 +p:HG002_2_chr20:62830512-62830939 687 2963 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/output.vcf.gz new file mode 100644 index 00000000..3226bba8 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/output.vcf.gz.tbi new file mode 100644 index 00000000..ba42378a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:62830612-62830839/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/base.vcf.gz new file mode 100644 index 00000000..a7ffe7e5 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/base.vcf.gz.tbi new file mode 100644 index 00000000..acf47b4d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/comp.vcf.gz new file mode 100644 index 00000000..1b3c4724 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/comp.vcf.gz.tbi new file mode 100644 index 00000000..191b6680 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/haps.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/haps.fa new file mode 100644 index 00000000..380fba4b --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/haps.fa @@ -0,0 +1,58 @@ +>ref_chr20_63221380_63221977 +TCCCACTGCAGAGAACTGTCATCTGCCTGTAAGTACCAGTGCCAGGTGCTCTGGGGCCGATGTCTCCGTTAGCCCCAAGGTGGAGGCTCAGGGAGCAGATGTGAGCGTGCCTTGCTCATCGCAGTAGCTTCGGACTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGACTGCATTGCTCTTGCAGCACCACCCGCCTCCGTGGACACCTTCAGCAGTGAGACAATGCAGGCTCTGCTACAAGAGGTGCTTACTGGGCTCTGCTCTGGTGAGGAGAGGCCTCGCCTGGCAGCCAGACAGAGTCCCAGCAGGGCAAGATGAAAATTCGGGGCCCTCGTTCAAACAGCAAGAGAAGGCTCTTTCCTTCCTTCCAGCGCCCCTCCCTGCACCT +>syndip_1_chr20:63221380-63221977 +TCCCACTGCAGAGAACTGTCATCTGCCTGTAAGTACCAGTGCCAGGTGCTCTGGGGCCGA +TGTCTCCGTTAGCCCCAAGGTGGAGGCTCAGGGAGCAGATGTGAGCGTGCCTTGCTCATC +GCAGTAGCTTCGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGAC +TGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGACTGCATT +GCTCTTGCAGCACCACCCGCCTCCGTGGACACCTTCAGCAGTGAGACAATGCAGGCTCTG +CTACAAGAGGTGCTTACTGGGCTCTGCTCTGGTGAGGAGAGGCCTCGCCTGGCAGCCAGA +CAGAGTCCCAGCAGGGCAAGATGAAAATTCGGGGCCCTCGTTCAAACAGCAAGAGAAGGC +TCTTTCCTTCCTTCCAGCGCCCCTCCCTGCACCT +>syndip_2_chr20:63221380-63221977 +TCCCACTGCAGAGAACTGTCATCTGCCTGTAAGTACCAGTGCCAGGTGCTCTGGGGCCGA +TGTCTCCGTTAGCCCCAAGGTGGAGGCTCAGGGAGCAGATGTGAGCGTGCCTTGCTCATC +GCAGTAGCTTCGGACTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGAG +TGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGG +GACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGATTGC +AGGGATTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGAC +TGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGACTGCAGG +GATTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGACTGC +AGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGAC +TGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGG +GACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGC +AGGGATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGAT +TGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGG +GATTGCAGGGACTGCAGGGACTGCATTGCTCTTGCAGCACCACCCGCCTCCGTGGACACC +TTCAGCAGTGAGACAATGCAGGCTCTGCTACAAGAGGTGCTTACTGGGCTCTGCTCTGGT +GAGGAGAGGCCTCGCCTGGCAGCCAGACAGAGTCCCAGCAGGGCAAGATGAAAATTCGGG +GCCCTCGTTCAAACAGCAAGAGAAGGCTCTTTCCTTCCTTCCAGCGCCCCTCCCTGCACC +T +>p:HG002_1_chr20:63221380-63221977 +TCCCACTGCAGAGAACTGTCATCTGCCTGTAAGTACCAGTGCCAGGTGCTCTGGGGCCGA +TGTCTCCGTTAGCCCCAAGGTGGAGGCTCAGGGAGCAGATGTGAGCGTGCCTTGCTCATC +GCAGTAGCTTCGGACTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGAT +TGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGCAGG +GACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGATTGC +AGGGATTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGAC +TGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGG +GATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGC +AGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGAC +TGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGG +GACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGATTGC +AGGGATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGAC +TGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGG +GATTGCAGGGACTGCAGGGACTGCATTGCTCTTGCAGCACCACCCGCCTCCGTGGACACC +TTCAGCAGTGAGACAATGCAGGCTCTGCTACAAGAGGTGCTTACTGGGCTCTGCTCTGGT +GAGGAGAGGCCTCGCCTGGCAGCCAGACAGAGTCCCAGCAGGGCAAGATGAAAATTCGGG +GCCCTCGTTCAAACAGCAAGAGAAGGCTCTTTCCTTCCTTCCAGCGCCCCTCCCTGCACC +T +>p:HG002_2_chr20:63221380-63221977 +TCCCACTGCAGAGAACTGTCATCTGCCTGTAAGTACCAGTGCCAGGTGCTCTGGGGCCGA +TGTCTCCGTTAGCCCCAAGGTGGAGGCTCAGGGAGCAGATGTGAGCGTGCCTTGCTCATC +GCAGTAGCTTCGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGAC +TGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGACTGCATT +GCTCTTGCAGCACCACCCGCCTCCGTGGACACCTTCAGCAGTGAGACAATGCAGGCTCTG +CTACAAGAGGTGCTTACTGGGCTCTGCTCTGGTGAGGAGAGGCCTCGCCTGGCAGCCAGA +CAGAGTCCCAGCAGGGCAAGATGAAAATTCGGGGCCCTCGTTCAAACAGCAAGAGAAGGC +TCTTTCCTTCCTTCCAGCGCCCCTCCCTGCACCT diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/haps.fa.ref.fa new file mode 100644 index 00000000..39d1febb --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63221380-63221977 +TCCCACTGCAGAGAACTGTCATCTGCCTGTAAGTACCAGTGCCAGGTGCTCTGGGGCCGATGTCTCCGTTAGCCCCAAGGTGGAGGCTCAGGGAGCAGATGTGAGCGTGCCTTGCTCATCGCAGTAGCTTCGGACTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGACTGCAGGGACTGCAGGGACTGCAGGGATTGCAGGGATTGCAGGGACTGCAGGGACTGCATTGCTCTTGCAGCACCACCCGCCTCCGTGGACACCTTCAGCAGTGAGACAATGCAGGCTCTGCTACAAGAGGTGCTTACTGGGCTCTGCTCTGGTGAGGAGAGGCCTCGCCTGGCAGCCAGACAGAGTCCCAGCAGGGCAAGATGAAAATTCGGGGCCCTCGTTCAAACAGCAAGAGAAGGCTCTTTCCTTCCTTCCAGCGCCCCTCCCTGCACCT diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/msa.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/msa.fa new file mode 100644 index 00000000..c5e22900 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/msa.fa @@ -0,0 +1,95 @@ +>ref_chr20_63221380_63221977 +tcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccga +tgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcatc +gcagtagcttc------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------ggactgcagggattgcagggactgcagggattgcagggattgcagg +gattgcagggactgcagggattgcagggactgcagggactgcagggactgcagggactgc +agggactgcagggattgcagggattgcagggattgcagggactgcagggattgcagggac +tgcagggactgcagggattgcagggactgcagggactgcagggactgcagggattgcagg +gattgcagggactgcagggactgcattgctcttgcagcaccacccgcctccgtggacacc +ttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctggt +gaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcggg +gccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcacc +t +>syndip_1_chr20:63221380-63221977 +tcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccga +tgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcatc +gcagtagcttc------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------ggactgcagggattgcagggac +tgcagggactgcagggattgcagggactgcagggactgcagggactgcagggattgcagg +gattgcagggactgcagggactgcattgctcttgcagcaccacccgcctccgtggacacc +ttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctggt +gaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcggg +gccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcacc +t +>syndip_2_chr20:63221380-63221977 +tcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccga +tgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcatc +gcagtagcttcggactgcagggattgcagggactgcagggattgcagggattgcagggag +tgcagggactgcagggactgcagggattgcagggactgcagggactgcagggactgcagg +gactgcagggactgcagggactgcagggattgcagggactgcagggactgcagggattgc +agggattgcagggattgcagggactgcagggattgcagggactgcagggactgcagggac +tgcagggactgcagggactgcagggattgcagggattgcagggattgcagggactgcagg +gattgcagggactgcagggactgcagggattgcagggactgcagggactgcagggactgc +agggattgcagggattgcagggattgcagggattgcagggattgcagggactgcagggac +tgcagggactgcagggactgcagggattgcagggattgcagggattgcagggattgcagg +gactgcagggactgcagggattgcagggattgcagggattgcagggattgcagggattgc +agggattgcagggactgcagggactgcagggactgcagggattgcagggattgcagggat +tgcagggattgcagggactgcagggactgcagggattgcagggattgcagggattgcagg +gattgcagggactgcagggactgcattgctcttgcagcaccacccgcctccgtggacacc +ttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctggt +gaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcggg +gccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcacc +t +>p:HG002_1_chr20:63221380-63221977 +tcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccga +tgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcatc +gcagtagcttcggactgcagggattgcagggactgcagggattgcagggattgcagggat +tgcagggactgcagggattgcagggactgcagggactgcagggactgcagggactgcagg +gactgcagggattgcagggattgcagggattgcagggactgcagggactgcagggattgc +agggattgcagggactgcagggactgcagggattgcagggactgcagggactgcagggac +tgcagggactgcagggactgcagggactgcagggattgcagggattgcagggattgcagg +gattgcagggactgcagggactgcagggactgcagggactgcagggactgcagggactgc +agggattgcagggattgcagggattgcagggattgcagggattgcagggactgcagggac +tgcagggactgcagggactgcagggattgcagggattgcagggattgcagggattgcagg +gactgcagggactgcagggattgcagggattgcagggattgcagggattgcagggattgc +agggattgcagggactgcagggactgcagggactgcagggattgcagggattgcagggac +tgcagggactgcagggattgcagggactgcagggactgcagggactgcagggattgcagg +gattgcagggactgcagggactgcattgctcttgcagcaccacccgcctccgtggacacc +ttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctggt +gaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcggg +gccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcacc +t +>p:HG002_2_chr20:63221380-63221977 +tcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccga +tgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcatc +gcagtagcttc------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------ggactgcagggattgcagggac +tgcagggactgcagggattgcagggactgcagggactgcagggactgcagggattgcagg +gattgcagggactgcagggactgcattgctcttgcagcaccacccgcctccgtggacacc +ttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctggt +gaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcggg +gccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcacc +t diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/msa.fa.fai new file mode 100644 index 00000000..8fe1fa2d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63221380_63221977 1021 29 60 61 +syndip_1_chr20:63221380-63221977 1021 1102 60 61 +syndip_2_chr20:63221380-63221977 1021 2175 60 61 +p:HG002_1_chr20:63221380-63221977 1021 3249 60 61 +p:HG002_2_chr20:63221380-63221977 1021 4323 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/output.vcf.gz new file mode 100644 index 00000000..66ac122a Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/output.vcf.gz.tbi new file mode 100644 index 00000000..12079a1f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63221480-63221877/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/base.vcf.gz new file mode 100644 index 00000000..462ffff4 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/base.vcf.gz.tbi new file mode 100644 index 00000000..2c80c27e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/comp.vcf.gz new file mode 100644 index 00000000..9d458a94 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/comp.vcf.gz.tbi new file mode 100644 index 00000000..4db79b7f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/haps.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/haps.fa new file mode 100644 index 00000000..e5295545 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/haps.fa @@ -0,0 +1,202 @@ +>ref_chr20_63491489_63493165 +GTGAGCATGATGCCCCCACAGTGCACACAGAGATGCCTGCAACATCTTTGGCTGCAGCCCACTGGCTGGGGGTCTCCTATCAGTGCCCTTCTCTAGGGTCTCAGATTTGTTTATGGTTTCTCTTCTTGGTGGGATGGATGGATGGATGGACGGATGGATGGGGAGGTGGGTGGATGGATGGATGGATGTATGAATGGGGTGGTAGATGGATGGGGAGGTGGATGGACAGAAGGATGGGTGGGGAGATGGATGAGTAGGGAGATGGATGGATGGATTGGTGGATGGATGGATGGATGGATGGATGAGGAGGTAGATGAGTGGATGGACAGAAGGATGGATGGGTAGGAAGGTGGGTGGATGAATGGATGGATGGGGAGGTGGATGGATAGATGGATGGATGGATGGATGGATGGATGGATGGATGGGGGGATAGATGGATGGATGGATGGATGGACGGACGGATGGGGAGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGAGGAGATGAACGGATGGATGAGATGGATGGATGGATGATGGAGGGAAGGATGGCTGGGTGGGGAGATGGATGGATAGAGAGGTGGATGGGTGGATGGGGAGATGGATGGATGGATGGATGGATGGGGAAGTGGATGGATGGGGAGGTGGATGGATGGATGTATGGGTGGGTAGGTGGGTGGATAGATGGATGGATGGATGGATGGATAAATGGATGGATGGAAGGATGGATGGATAGGTAGGTGGGTGGATGGATGGATGGATGGATGTACAGAAGGATGGATGGGTGGGTAGGTGGGTGAGTGGATGAATGGATGGATGGATAGATAGAAGGATGGATGGGTGGGTCAATAGATGGATGGATAGAGAGAAGGATGGATGGGTGGGTAGATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGTTGAGACAATGGATGGATGGATGGATGGATGGAGAGATGGATGGATGGATGGATGGACAGAAGGATGGATGGGTGGGGAGGTGGATGGATGGATGGAAGGATGGATGGATGGATAGAGAGAAGGATGGATGGGTGGGACAATGGATGGATGGATGCATGGATGGATGGATGGAGGGATAGAGAGAAGGATGGATGGGTGGGACAATCAATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGGTGGGGAGATGGATGGATGGATGGAGAGGTGGATGGATGGATGGATGGATGGATTGATGGACAGAAGGATGGATGGGTGGGGAGGTGGATAGATGGAGAGATGGAGGGATGGTTCGATAGAGAGAAGGATGGATGGGACAATGGATGGATGGATGGATGGAGTGAAGGATGGATGGGTGGGGAGATGGATGGATCGATGGATGGATGGATGGATAGATAGATGGATGGAGAGGTGGATAGATGGATGGGTGGATGGATGGACAGAGGATGGATGGGTGGGGAGGTGGGTGGATGGATGGATGGATGTGGGATGGACTGTCCCACAGAAAGTGTGTGGTAAGGGGAGAGATTGGAGACAGCCCAGTCTTGAGATGCCTTGTAGGGGCCCCTGGTCTAGGGCAGGCAGAGCTGGCCAGGCAGGAGCTCCAGCACAGCGCCCTTGCTCACCGCCAATCTTGTACACGTCCTGCAGCGGC +>syndip_1_chr20:63491489-63493165 +GTGAGCATGATGCCCCCACAGTGCACACAGAGATGCCTGCAACATCTTTGGCTGCAGCCC +ACTGGCTGGGGGTCTCCTATCAGTGCCCTTCTCTAGGGTCTCAGATTTGTTTATGGTTTC +TCTTCTTGGTGGGATGGATGGATGGATGGACGGATGGATGGGGAGGTGGGTGGATGGATG +GATGGATGTATGAATGGGGTGGTAGATGGATGGGGAGGTGGATGGACAGAAGGATGGGTG +GGGAGATGGATGAGTAGGGAGATGGATGGATGGATTGGTGGATGGATGGATGGATGGATG +GATGAGGAGGTAGATGAGTGGATGGACAGAAGGATGGATGGGTAGGAAGGTGGGTGGATG +AATGGATGGATGGGGAGGTGGATGGATAGATGGATGGATGGATGGATGGATGGATGGATG +GATGGGGGGATAGATGGATGGATGGATGGATGGACGGACGGATGGGGAGGTGGATGGATG +GATGGATGGATGGATGGATGGATGGATGAGGAGATGAACGGATGGATGAGATGGATGGAT +GGATGATGGAGGGAAGGATGGCTGGGTGGGGAGATGGATGGATAGAGAGGTGGATGGGTG +GATGGGGAGATGGATGGATGGATGGATGGATGGGGAAGTGGATGGATGGGGAGGTGGATG +GATGGATAGGTGGATGGGTGGATGGACAGAAGGATGAATGGGTAGGGAGATGGATGGATG +GATGGATGGGGAGGGATGGATGGATGGATGGATGGATGGGTGGATGGATAGAAGGATGGA +TGGGTGGGGAGGTGGGTGGGTGGGTGGATGGATGGAGAGATGGATAGATGGATAGATGGA +TGGATGGATGGATGGATGGAGAGAAGGATGGATGGGTGGGGAGGTGGGTGGGTGGGTGGA +TGGGTGGATGGATGGATGGGTGGGGAGGTGGGCGGGTGGATGGATGGATGGATGCAGAGG +TGGGTGGATGGATGGATGGAGAGAAGGATGGATGGGTGGGGAGGTGGGTGGGTGGATGGA +TGGATGAGTGGGGAGGTGGGTGGGTGGGTGGATGGATGGATGGATGGATGCATGGATGGA +TGGATGGAGAGGTGGGTGGACGGATGGATGGATTGGGAGGTGGGTAGATGGGTGGATGGA +CAGAAGGATGGATGGGTGGGGAGGTGGGTGGGTGGGTGGATGGATGGATGGGGAGGTGGA +TGGATGGATGGTTAGATGGGGAGGTGGGTGGATGGGTGGATGGACAGAAGGATGGATGGG +TAGGGAGGTAGGTGAGTGGATGGATGGATGGGGAGATGGATGGATGGATAGAGAGAAGGA +TGGATGGGTGGGACAATGGATGGATGGATGGATAGAAGGATGGACGGGTGGGGAGATGGA +TGGATGGATGGATGGATGGATGGATGGATGGACAGAAGGATGTATGGGTGGGTAGGTGGG +TGGATAGATGGATGGATGGATGGATGGATAAATGGATGGATGGAAGGATGGATGGATAGG +TAGGTGGGTGGATGGATGGATGGATGGATGTACAGAAGGATGGATGGGTGGGTAGGTGGG +TGAGTGGATGAATGGATGGATGGATAGATAGAAGGATGGATGGGTGGGTCAATAGATGGA +TGGATAGAGAGAAGGATGGATGGGTGGGGAGATGGATGGATGGATGGATGGATGGATGGA +TGGATGGATGGATAGAGAGAAGGATGGATGGTTGAGACAATGGATGGATGGATGGATGGA +GAGATGGATGGATGGACGGATGGACAGAAGGATGGATGGGTGGGGAGGTGGATGGATGGA +TTGAAGGATGGATGGGTGGGGACATGGATGGATGGATGGATGGATGGATGGATGGATGGA +CAGAAGGATGTATGGGTGGGGAGGTGGGTGGATAGATGGATGGATGGGGAAATGGATGGA +TGGAAGGATGGATGGATAGGGAGGTGGGTGGATGGATGGATGGATGGATGTACAGAAGGA +TGGATGGGTGGGGAGGTGGGTGAGTGGATGAATGGATGGATGGATAGATAGAAGGATGGA +TGGGTGGGACAATAGATGGATGGATAGAGAGAAGGATGGATGGGTGGGGAGATAGATGGA +TGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGTTGAGACAATGGATGGATGGA +TGGATGGATGGAGAGATGGATGGATGGATGGATGGACAGAAGGATGGATGGGTGGGGAGG +TGGATGGATGGATGGAAGGATGGATGGATGGATAGAGAGAAGGATGGATGGGTGGGACAA +TGGATGGATGGATGCATGGATGGATGGATGGAGGGATAGAGAGAAGGATGGATGGGTGGG +ACAATCAATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGGTGGGGAGA +TGGATGGATGGATGGAGAGGTGGATGGATGGATGGATGGATGGATTGATGGACAGAAGGA +TGGATGGGTGGGGAGGTGGATAGATGGAGAGATGGAGGGATGGTTCGATAGAGAGAAGGA +TGGATGGGACAATGGATGGATGGATGGATGGAGTGAAGGATGGATGGGTGGGGAGATGGA +TGGATCGATGGATGGATGGATGGATAGATAGATGGATGGAGAGGTGGATAGATGGATGGG +TGGATGGATGGACAGAGGATGGATGGGTGGGGAGGTGGGTGGATGGATGGATGGATGTGG +GATGGACTGTCCCACAGAAAGTGTGTGGTAAGGGGAGAGATTGGAGACAGCCCAGTCTTG +AGATGCCTTGTAGGGGCCCCTGGTCTAGGGCAGGCAGAGCTGGCCAGGCAGGAGCTCCAG +CACAGCGCCCTTGCTCACCGCCAATCTTGTACACGTCCTGCAGCGGC +>syndip_2_chr20:63491489-63493165 +GTGAGCATGATGCCCCCACAGTGCACACAGAGATGCCTGCAACATCTTTGGCTGCAGCCC +ACTGGCTGGGGGTCTCCTATCAGTGCCCTTCTCTAGGGTCTCAGATTTGTTTATGGTTTC +TCTTCTTGGTGGGATGGATGGATGGATGGACGGATGGATGGGGAGGTGGGTGGATGGATG +GATGGATGTATGAATGGGGTGGTAGATGGATGGGGAGGTGGATGGACAGAAGGATGGGTG +GGGAGATGGATGAGTAGGGAGATGGATGGATGGATTGGTGGATGGATGGATGGATGGATG +GATGAGGAGGTAGATGAGTGGATGGACAGAAGGATGGATGGGTAGGAAGGTGGGTGGATG +AATGGATGGATGGGGAGGTGGATGGATAGATGGATGGATGGATGGATGGATGGATGGATG +GATGGGGGGATAGATGGATGGATGGATGGATGGACGGACGGATGGGGAGGTGGATGGATG +GATGGATGGATGGATGGATGGATGGATGGATGGATGAGGAGATGAACGGATGGATGAGAT +GGATGGATGGATGATGGAGGGAAGGATGGCTGGGTGGGGAGATGGATGGATAGAGAGGTG +GATGGGTGGATGGGGAGATGGATGGATGGATGGATGGATGGGGAAGTGGATGGATGGGGA +GGTGGATGGATGGATAGGTGGATGGGTGGATGGACAGAAGGATGAATGGGTAGGGAGATG +GATGGATGGATGGATGCGGAGGGATGGATGGATGGATGGATGGATGGGTGGATGGATAGA +AGGATGGATGGGTGGGGAGGTGGGTGGGTGGGTGCGTGGATGGATGGAGAGATGGATAGA +TGGATAGATGGATGGATGGATGGATGGATGGATGGAGAGAAGGATGGATGGGTGGGGAGG +TGGGTGGGTGGGTGGATGGGTGGATGGATGGATGGGTGGGGAGGTGGGCGGGTGGATGGA +TGGATGGATGCAGAGGTGGGTGGATGGATGGATGGAGAGAAGGATGGATGGGTGGGGAGG +TGGGTGGGTGGATGGATGGATGAGTGGGGAGGTGGGTGGGTGGATGGATGGATGGATGGA +TGCATGGATGGATGGATGGAGAGGTGGGTGGATGGGTGGATGGACAGAAGGATGGATGGG +TGGGGAGGTGGGTGAGTGGGTGGATGGATGAATGGGGAGGTGGATGGATGGATGGATGGA +TGAAGGATGGATGGGTGGGGAGGTGGGTGGACGGATGGATGGATTGGGAGGTGGGTAGAT +GGGTGGATGGACAGAAGGATGGATGGGTGGGGAGGTGGGTGGGTGGGTGGATGGATGGAT +GGGGAGGTGGATGGATGGATGGTTAGATGGGGAGGTGGGTGGATGGGTGGATGGACAGAA +GGATGGATGGGTAGGGAGGTAGGTGAGTGGATGGATGGATGGGGAGATGGATGGATGGAT +AGAGAGAAGGATGGATGGGTGGGACAATGGATGGATGGATGGATAGAAGGATGGACGGGT +GGGGAGATGGATGGATGGATGGATGGATGGATGGATGGACAGAAGGATGTATGGGTGGGG +AGGTGGGTGGATAGATGGATGGATGGATGGATGGGGAAATGGATGGATGGAAGGATGGAT +GGATAGGGAGGTGGGTGGATGGATGGATGGATGGATGTACAGAAGGATGGATGGGTGGGG +AGGTGGGTGAGTGGATGAATGGATGGATGGATAGATAGAAGGATGGATGGGTGGGACAAT +AGATGGATGGATAGAGAGAAGGATGGATGGGTGGGGAGATGGATGGATGGATGGATGGAT +GGATGGATGGATAGAGAGAAGGATGGATGGTTGAGACAATGGATGGATGGATGGATGGAT +GGAGAGATGGATGGATGGATGGATGGACAGAAGGATGGATGGGTGGGGAGGTGGATGGAT +GGATTGAAGGATGGACGGGTGGGGAGATGGATGGATGGATGGATGGATGGATGGATGGAT +GGATGGACAGAAGGATGTATGGGTGGGTAGGTGGGTGGATAGATGGATGGATGGATGGAT +GGATAAATGGATGGATGGAAGGATGGATGGATAGGTAGGTGGGTGGATGGATGGATGGAT +GGATGTACAGAAGGATGGATGGGTGGGTAGGTGGGTGAGTGGATGAATGGATGGATGGAT +AGATAGAAGGATGGATGGGTGGGTCAATAGATGGATGGATAGAGAGAAGGATGGATGGGT +GGGTAGATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGTTGAGACAAT +GGATGGATGGATGGATGGATGGAGAGATGGATGGATGGATGGATGGACAGAAGGATGGAT +GGGTGGGGAGGTGGATGGATGGATGGAAGGATGGATGGATGGATAGAGAGAAGGATGGAT +GGGTGGGACAATGGATGGATGGATGCATGGATGGATGGATGGAGGGATAGAGAGAAGGAT +GGATGGGTGGGACAATCAATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGAT +GGGTGGGGAGATGGATGGATGGATGGAGAGGTGGATGGATGGATGGATGGATGGATTGAT +GGACAGAAGGATGGATGGGTGGGGAGGTGGATAGATGGAGAGATGGAGGGATGGTTCGAT +AGAGAGAAGGATGGATGGGACAATGGATGGATGGATGGATGGAGTGAAGGATGGATGGGT +GGGGAGATGGATGGATCGATGGATGGATGGATGGATAGATAGATGGATGGAGAGGTGGAT +AGATGGATGGGTGGATGGATGGACAGAGGATGGATGGGTGGGGAGGTGGGTGGATGGATG +GATGGATGTGGGATGGACTGTCCCACAGAAAGTGTGTGGTAAGGGGAGAGATTGGAGACA +GCCCAGTCTTGAGATGCCTTGTAGGGGCCCCTGGTCTAGGGCAGGCAGAGCTGGCCAGGC +AGGAGCTCCAGCACAGCGCCCTTGCTCACCGCCAATCTTGTACACGTCCTGCAGCGGC +>p:HG002_1_chr20:63491489-63493165 +GTGAGCATGATGCCCCCACAGTGCACACAGAGATGCCTGCAACATCTTTGGCTGCAGCCC +ACTGGCTGGGGGTCTCCTATCAGTGCCCTTCTCTAGGGTCTCAGATTTGTTTATGGTTTC +TCTTCTTGGTGGGATGGATGGATGGATGGACGGATGGATGGGGAGGTGGGTGGATGGATG +GATGGATGTATGAATGGGGTGGTAGATGGATGGGGAGGTGGATGGACAGAAGGATGGGTG +GGGAGATGGATGAGTAGGGAGATGGATGGATGGATTGGTGGATGGATGGATGGATGGATG +GATGAGGAGGTAGATGAGTGGATGGACAGAAGGATGGATGGGTAGGAAGGTGGGTGGATG +AATGGATGGATGGGGAGGTGGATGGATAGATGGATGGATGGATGGATGGATGGATGGATG +GATGGGGGGATAGATGGATGGATGGATGGATGGACGGACGGATGGGGAGGTGGATGGATG +GATGGATGGATGGATGGATGGATGGATGGATGGATGAGGAGATGAACGGATGGATGAGAT +GGATGGATGGATGATGGAGGGAAGGATGGCTGGGTGGGGAGATGGATGGATAGAGAGGTG +GATGGGTGGATGGGGAGATGGATGGATGGATGGATGGATGGGGAAGTGGATGGATGGGGA +GGTGGATGGATGGATAGGTGGATGGGTGGATGGACAGAAGGATGAATGGGTAGGGAGATG +GATGGATGGATGGATGCGGAGGGATGGATGGATGGATGGATGGATGGGTGGATGGATAGA +AGGATGGATGGGTGGGGAGGTGGGTGGGTGGGTGCGTGGATGGATGGAGAGATGGATAGA +TGGATAGATGGATGGATGGATGGATGGATGGATGGAGAGAAGGATGGATGGGTGGGGAGG +TGGGTGGGTGGGTGGATGGGTGGATGGATGGATGGGTGGGGAGGTGGGCGGGTGGATGGA +TGGATGGATGCAGAGGTGGGTGGATGGATGGATGGAGAGAAGGATGGATGGGTGGGGAGG +TGGGTGGGTGGATGGATGGATGAGTGGGGAGGTGGGTGGGTGGATGGATGGATGGATGGA +TGCATGGATGGATGGATGGAGAGGTGGGTGGATGGGTGGATGGACAGAAGGATGGATGGG +TGGGGAGGTGGGTGAGTGGGTGGATGGATGAATGGGGAGGTGGATGGATGGATGGATGGA +TGAAGGATGGATGGGTGGGGAGGTGGGTGGACGGATGGATGGATTGGGAGGTGGGTAGAT +GGGTGGATGGACAGAAGGATGGATGGGTGGGGAGGTGGGTGGGTGGGTGGATGGATGGAT +GGGGAGGTGGATGGATGGATGGTTAGATGGGGAGGTGGGTGGATGGGTGGATGGACAGAA +GGATGGATGGGTAGGGAGGTAGGTGAGTGGATGGATGGATGGGGAGATGGATGGATGGAT +AGAGAGAAGGATGGATGGGTGGGACAATGGATGGATGGATGGATAGAAGGATGGACGGGT +GGGGAGATGGATGGATGGATGGATGGATGGATGGATGGACAGAAGGATGTATGGGTGGGG +AGGTGGGTGGATAGATGGATGGATGGATGGATGGGGAAATGGATGGATGGAAGGATGGAT +GGATAGGGAGGTGGGTGGATGGATGGATGGATGGATGTACAGAAGGATGGATGGGTGGGG +AGGTGGGTGAGTGGATGAATGGATGGATGGATAGATAGAAGGATGGATGGGTGGGACAAT +AGATGGATGGATAGAGAGAAGGATGGATGGGTGGGGAGATGGATGGATGGATGGATGGAT +GGATGGATGGATAGAGAGAAGGATGGATGGTTGAGACAATGGATGGATGGATGGATGGAT +GGAGAGATGGATGGATGGATGGATGGACAGAAGGATGGATGGGTGGGGAGGTGGATGGAT +GGATTGAAGGATGGACGGGTGGGGAGATGGATGGATGGATGGATGGATGGATGGATGGAT +GGATGGACAGAAGGATGTATGGGTGGGTAGGTGGGTGGATAGATGGATGGATGGATGGAT +GGATAAATGGATGGATGGAAGGATGGATGGATAGGTAGGTGGGTGGATGGATGGATGGAT +GGATGTACAGAAGGATGGATGGGTGGGTAGGTGGGTGAGTGGATGAATGGATGGATGGAT +AGATAGAAGGATGGATGGGTGGGTCAATAGATGGATGGATAGAGAGAAGGATGGATGGGT +GGGTAGATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGTTGAGACAAT +GGATGGATGGATGGATGGATGGAGAGATGGATGGATGGATGGATGGACAGAAGGATGGAT +GGGTGGGGAGGTGGATGGATGGATGGAAGGATGGATGGATGGATAGAGAGAAGGATGGAT +GGGTGGGACAATGGATGGATGGATGCATGGATGGATGGATGGAGGGATAGAGAGAAGGAT +GGATGGGTGGGACAATCAATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGAT +GGGTGGGGAGATGGATGGATGGATGGAGAGGTGGATGGATGGATGGATGGATGGATTGAT +GGACAGAAGGATGGATGGGTGGGGAGGTGGATAGATGGAGAGATGGAGGGATGGTTCGAT +AGAGAGAAGGATGGATGGGACAATGGATGGATGGATGGATGGAGTGAAGGATGGATGGGT +GGGGAGATGGATGGATCGATGGATGGATGGATGGATAGATAGATGGATGGAGAGGTGGAT +AGATGGATGGGTGGATGGATGGACAGAGGATGGATGGGTGGGGAGGTGGGTGGATGGATG +GATGGATGTGGGATGGACTGTCCCACAGAAAGTGTGTGGTAAGGGGAGAGATTGGAGACA +GCCCAGTCTTGAGATGCCTTGTAGGGGCCCCTGGTCTAGGGCAGGCAGAGCTGGCCAGGC +AGGAGCTCCAGCACAGCGCCCTTGCTCACCGCCAATCTTGTACACGTCCTGCAGCGGC +>p:HG002_2_chr20:63491489-63493165 +GTGAGCATGATGCCCCCACAGTGCACACAGAGATGCCTGCAACATCTTTGGCTGCAGCCC +ACTGGCTGGGGGTCTCCTATCAGTGCCCTTCTCTAGGGTCTCAGATTTGTTTATGGTTTC +TCTTCTTGGTGGGATGGATGGATGGATGGACGGATGGATGGGGAGGTGGGTGGATGGATG +GATGGATGTATGAATGGGGTGGTAGATGGATGGGGAGGTGGATGGACAGAAGGATGGGTG +GGGAGATGGATGAGTAGGGAGATGGATGGATGGATTGGTGGATGGATGGATGGATGGATG +GATGAGGAGGTAGATGAGTGGATGGACAGAAGGATGGATGGGTAGGAAGGTGGGTGGATG +AATGGATGGATGGGGAGGTGGATGGATAGATGGATGGATGGATGGATGGATGGATGGATG +GATGGGGGGATAGATGGATGGATGGATGGATGGACGGACGGATGGGGAGGTGGATGGATG +GATGGATGGATGGATGGATGGATGGATGGATGGATGAGGAGATGAACGGATGGATGAGAT +GGATGGATGGATGATGGAGGGAAGGATGGCTGGGTGGGGAGATGGATGGATAGAGAGGTG +GATGGGTGGATGGGGAGATGGATGGATGGATGGATGGATGGGGAAGTGGATGGATGGGGA +GGTGGATGGATGGATGTATGGGTGGGTGGATGGACAGAAGGATGAATGGGTAGGGAGATG +GATGGATGGATGGATGGGGAGGGATGGATGGATGGATGGATGGATGGGTGGATGGATAGA +AGGATGGATGGGTGGGGAGGTGGGTGGGTGGGTGGATGGATGGAGAGATGGATAGATGGA +TAGATGGATGGATGGATGGATGGATGGAGAGAAGGATGGATGGGTGGGGAGGTGGGTGGG +TGGGTGGATGGGTGGATGGATGGATGGGTGGGGAGGTGGGCGGGTGGATGGATGGATGGA +TGCAGAGGTGGGTGGATGGATGGATGGAGAGAAGGATGGATGGGTGGGGAGGTGGGTGGG +TGGATGGATGGATGAGTGGGGAGGTGGGTGGGTGGGTGGATGGATGGATGGATGGATGCA +TGGATGGATGGATGGAGAGGTGGGTGGACGGATGGATGGATTGGGAGGTGGGTAGATGGG +TGGATGGACAGAAGGATGGATGGGTGGGGAGGTGGGTGGGTGGGTGGATGGATGGATGGG +GAGGTGGATGGATGGATGGTTAGATGGGGAGGTGGGTGGATGGGTGGATGGACAGAAGGA +TGGATGGGTAGGGAGGTAGGTGAGTGGATGGATGGATGGGGAGATGGATGGATGGATAGA +GAGAAGGATGGATGGGTGGGACAATGGATGGATGGATGGATAGAAGGATGGACGGGTGGG +GAGATGGATGGATGGATGGATGGATGGATGGATGGATGGACAGAAGGATGTATGGGTGGG +GAGGTGGGTGGATAGATGGATGGATGGATGGATGGGGAAATGGATGGATGGAAGGATGGA +TGGATAGGGAGGTGGGTGGATGGATGGATGGATGGATGTACAGAAGGATGGATGGGTGGG +GAGGTGGGTGAGTGGATGAATGGATGGATGGATAGATAGAAGGATGGATGGGTGGGACAA +TAGATGGATGGATAGAGAGAAGGATGGATGGGTGGGGAGATGGATGGATGGATGGATGGA +TGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGTTGAGACAATGGATGGATGGA +TGGATGGAGAGATGGATGGATGGACGGATGGACAGAAGGATGGATGGGTGGGGAGGTGGA +TGGATGGATTGAAGGATGGATGGGTGGGGACATGGATGGATGGATGGATGGATGGATGGA +TGGATGGACAGAAGGATGTATAGGTGGGTGGATAGATGGATGGATGGATGGATGGATAAA +TGGATGGATGGAAGGATGGATGGATAGGTAGGTGGGTGGATGGATGGATGGATGGATGTA +CAGAAGGATGGATGGGTGGGTAGGTGGGTGAGTGGATGAATGGATGGATGGATAGATAGA +AGGATGGATGGGTGGGTCAATAGATGGATGGATAGAGAGAAGGATGGATGGGTGGGTAGA +TGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGTTGAGACAATGGATGGA +TGGATGGATGGATGGAGAGATGGATGGATGGATGGATGGACAGAAGGATGGATGGGTGGG +GAGGTGGATGGATGGATGGAAGGATGGATGGATGGATAGAGAGAAGGATGGATGGGTGGG +ACAATGGATGGATGGATGCATGGATGGATGGATGGAGGGATAGAGAGAAGGATGGATGGG +TGGGACAATCAATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGGTGGG +GAGATGGATGGATGGATGGAGAGGTGGATGGATGGATGGATGGATGGATTGATGGACAGA +AGGATGGATGGGTGGGGAGGTGGATAGATGGAGAGATGGAGGGATGGTTCGATAGAGAGA +AGGATGGATGGGACAATGGATGGATGGATGGATGGAGTGAAGGATGGATGGGTGGGGAGA +TGGATGGATCGATGGATGGATGGATGGATAGATAGATGGATGGAGAGGTGGATAGATGGA +TGGGTGGATGGATGGACAGAGGATGGATGGGTGGGGAGGTGGGTGGATGGATGGATGGAT +GTGGGATGGACTGTCCCACAGAAAGTGTGTGGTAAGGGGAGAGATTGGAGACAGCCCAGT +CTTGAGATGCCTTGTAGGGGCCCCTGGTCTAGGGCAGGCAGAGCTGGCCAGGCAGGAGCT +CCAGCACAGCGCCCTTGCTCACCGCCAATCTTGTACACGTCCTGCAGCGGC diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/haps.fa.ref.fa new file mode 100644 index 00000000..ebd054e8 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63491489-63493165 +GTGAGCATGATGCCCCCACAGTGCACACAGAGATGCCTGCAACATCTTTGGCTGCAGCCCACTGGCTGGGGGTCTCCTATCAGTGCCCTTCTCTAGGGTCTCAGATTTGTTTATGGTTTCTCTTCTTGGTGGGATGGATGGATGGATGGACGGATGGATGGGGAGGTGGGTGGATGGATGGATGGATGTATGAATGGGGTGGTAGATGGATGGGGAGGTGGATGGACAGAAGGATGGGTGGGGAGATGGATGAGTAGGGAGATGGATGGATGGATTGGTGGATGGATGGATGGATGGATGGATGAGGAGGTAGATGAGTGGATGGACAGAAGGATGGATGGGTAGGAAGGTGGGTGGATGAATGGATGGATGGGGAGGTGGATGGATAGATGGATGGATGGATGGATGGATGGATGGATGGATGGGGGGATAGATGGATGGATGGATGGATGGACGGACGGATGGGGAGGTGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGAGGAGATGAACGGATGGATGAGATGGATGGATGGATGATGGAGGGAAGGATGGCTGGGTGGGGAGATGGATGGATAGAGAGGTGGATGGGTGGATGGGGAGATGGATGGATGGATGGATGGATGGGGAAGTGGATGGATGGGGAGGTGGATGGATGGATGTATGGGTGGGTAGGTGGGTGGATAGATGGATGGATGGATGGATGGATAAATGGATGGATGGAAGGATGGATGGATAGGTAGGTGGGTGGATGGATGGATGGATGGATGTACAGAAGGATGGATGGGTGGGTAGGTGGGTGAGTGGATGAATGGATGGATGGATAGATAGAAGGATGGATGGGTGGGTCAATAGATGGATGGATAGAGAGAAGGATGGATGGGTGGGTAGATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGTTGAGACAATGGATGGATGGATGGATGGATGGAGAGATGGATGGATGGATGGATGGACAGAAGGATGGATGGGTGGGGAGGTGGATGGATGGATGGAAGGATGGATGGATGGATAGAGAGAAGGATGGATGGGTGGGACAATGGATGGATGGATGCATGGATGGATGGATGGAGGGATAGAGAGAAGGATGGATGGGTGGGACAATCAATGGATGGATGGATGGATGGATGGATAGAGAGAAGGATGGATGGGTGGGGAGATGGATGGATGGATGGAGAGGTGGATGGATGGATGGATGGATGGATTGATGGACAGAAGGATGGATGGGTGGGGAGGTGGATAGATGGAGAGATGGAGGGATGGTTCGATAGAGAGAAGGATGGATGGGACAATGGATGGATGGATGGATGGAGTGAAGGATGGATGGGTGGGGAGATGGATGGATCGATGGATGGATGGATGGATAGATAGATGGATGGAGAGGTGGATAGATGGATGGGTGGATGGATGGACAGAGGATGGATGGGTGGGGAGGTGGGTGGATGGATGGATGGATGTGGGATGGACTGTCCCACAGAAAGTGTGTGGTAAGGGGAGAGATTGGAGACAGCCCAGTCTTGAGATGCCTTGTAGGGGCCCCTGGTCTAGGGCAGGCAGAGCTGGCCAGGCAGGAGCTCCAGCACAGCGCCCTTGCTCACCGCCAATCTTGTACACGTCCTGCAGCGGC diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/msa.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/msa.fa new file mode 100644 index 00000000..b991f8f6 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/msa.fa @@ -0,0 +1,260 @@ +>ref_chr20_63491489_63493165 +gtgagcatgatgcccccacagtgcacacagagatgcctgcaacatctttggctgcagccc +actggctgggggtctcctatcagtgcccttctctagggtctcagatttgtttatggtttc +tcttct------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------tggtgggatggatggatggatggacggatggat +ggggaggtgggtggatgg--------atggatggatgtatgaatggggtggtagatggat +ggggaggtggatggacagaaggatgggtggggagatggatgagtagggagatggatggat +ggattggtggatggatggatggatggatggatgaggaggtagatgagtggatggacagaa +ggatggatgggtaggaaggtgggtggatgaatggatgga--------------------t +ggggaggtggatggatagatggatggatggatggatggatggatggatggatggggggat +agatggatggatggatggatggacggacggatggggaggtggatggatggatggatggat +ggatggatggatggatggatggatgaggagatgaacggatggatgagatg----gatgga +tggatgatggagggaaggatggctgggtggggagatggatggatagagaggtggatgggt +ggatggggagatggatggatggatggatggatgggga----agtggatggatggggaggt +ggatggatggatgtatgggtgg----------------gtaggtgggtggatagatggat +ggatggatggatggataaatggatggatggaaggatggatggataggtaggtgggtggat +ggatggatggatggatgtacagaaggatggatgggtgggtaggtgggtgagtggatgaat +ggatggatggatagatagaaggatggatgggtgggtcaatagatggatggatagagagaa +ggatggatgggtggg----tagatggatggatggatggatggatggatagagagaaggat +ggatggttgagacaatggatggatggatggatggatggagagatggatggatggatggat +ggacagaaggatggatgggtggggaggtggatggatggatggaaggatggatggatggat +agagagaaggatggatgggtgggacaatggatggatggatgcatggatggatggatggag +ggatagagagaaggatggatgggtgggacaatcaatggatggatggatggatggatggat +agagagaaggatggatgggtggggagatggatggatggatggagaggtggatggatggat +ggatggatggattgatggacagaaggatggatgggtggggaggtggatagatggagagat +ggagggatggttcgatagagagaaggatggatgggacaatggatggatggatggatggag +tgaaggatggatgggtggggagatggatggatcgatggatggatggatggatagatagat +ggatggagaggtggatagatggatgggtggatggatggacagaggatggatgggtgggga +ggtgggtggatggatggatggatgtgggatggactgtcccacagaaagtgtgtggtaagg +ggagagattggagacagcccagtcttgagatgccttgtaggggcccctggtctagggcag +gcagagctggccaggcaggagctccagcacagcgcccttgctcaccgccaatcttgtaca +cgtcctgcagcggc +>syndip_1_chr20:63491489-63493165 +gtgagcatgatgcccccacagtgcacacagagatgcctgcaacatctttggctgcagccc +actggctgggggtctcctatcagtgcccttctctagggtctcagatttgtttatggtttc +tcttcttggtgggatggatggatggatggacggatggatggggaggtgggtggatggatg +gatggatgtatgaatggggtggtagatggatggggaggtggatggacagaaggatgggtg +gggagatggatgagtagggagatggatggatggattggtggatggatggatggatggatg +gatgaggaggtagatgagtggatggacagaaggatggatgggtaggaaggtgggtggatg +aatggatggatggggaggtggatggatagatggatggatggatggatggatggatggatg +gatggggggatagatggatggatggatggatggacggacggatggggagg--------tg +gatggatggatggatggatggatggatggatggatgaggagatgaacggatggatgagat +ggatggatggatgatggagggaaggatggctgggtggggagatggatggatagagaggtg +gatgggtggatggggagatggatggatggatggatggatggggaagtggatggatgggga +ggtggatggatggataggtggatgggtggatggacagaaggatgaatgggtagggagatg +gatggatggatggatggggagggatggatggatggatggatggatgggtggatggataga +aggatggatgggtggggaggtgggtgggtgg----gtggatggatggagagatggataga +tggata----gatggatggatggatggatggatggagagaaggatggatgggtggggagg +tgggtgggtgggtggatgggtggatggatggatgggtggggaggtgggcgggtggatgga +tggatggatgcagaggtgggtggatggatggatggagagaaggatggatgggtggggagg +tgggtgggtggatggatggatgagtggggaggtgggtgggtgggtggatggatggatgga +tggatgcatggatggatgga---------------------------------------- +------------------------------------------------------------ +---------------tggagaggtgggtggacggatggatggattgggaggtgggtagat +gggtggatggacagaaggatggatgggtggggaggtgggtgggtgggtggatggatggat +ggggaggtggatggatggatggttagatggggaggtgggtggatgggtggatggacagaa +ggatggatgggtagggaggtaggtgagtggatggatggatggggagatggatggatggat +agagagaaggatggatgggtgggacaatggatggatggatggatagaaggatggacgggt +ggggagatggatggatggatggatggatggatggatggatggacagaaggatgtatgggt +gggtaggtgggtggatagatggatggatggatggatggataaatggatggatggaaggat +ggatggataggtaggtgggtggatggatggatggatggatgtacagaaggatggatgggt +gggtaggtgggtgagtggatgaatggatggatggatagatagaaggatggatgggtgggt +caatagatggatggatagagagaaggatggatgggtggggagatggatggatggatggat +ggatggatggatggatggatggatagagagaaggatggatggttgagaca----atggat +ggatggatggatggagagatggatggatggacggatggacagaaggatggatgggtgggg +aggtggatggatggattgaaggatggatgggtgggga----catggatggatggatggat +ggatggatggatggatggacagaaggatgt--------atgggtggggaggtgggtggat +agatggatggatggggaaatggatggatggaaggatggatggatagggaggtgggtggat +ggatggatggatggatgtacagaaggatggatgggtggggaggtgggtgagtggatgaat +ggatggatggatagatagaaggatggatgggtgggacaatagatggatggatagagagaa +ggatggatgggtggggagatagatggatggatggatggatggatggatagagagaaggat +ggatggttgagacaatggatggatggatggatggatggagagatggatggatggatggat +ggacagaaggatggatgggtggggaggtggatggatggatggaaggatggatggatggat +agagagaaggatggatgggtgggacaatggatggatggatgcatggatggatggatggag +ggatagagagaaggatggatgggtgggacaatcaatggatggatggatggatggatggat +agagagaaggatggatgggtggggagatggatggatggatggagaggtggatggatggat +ggatggatggattgatggacagaaggatggatgggtggggaggtggatagatggagagat +ggagggatggttcgatagagagaaggatggatgggacaatggatggatggatggatggag +tgaaggatggatgggtggggagatggatggatcgatggatggatggatggatagatagat +ggatggagaggtggatagatggatgggtggatggatggacagaggatggatgggtgggga +ggtgggtggatggatggatggatgtgggatggactgtcccacagaaagtgtgtggtaagg +ggagagattggagacagcccagtcttgagatgccttgtaggggcccctggtctagggcag +gcagagctggccaggcaggagctccagcacagcgcccttgctcaccgccaatcttgtaca +cgtcctgcagcggc +>syndip_2_chr20:63491489-63493165 +gtgagcatgatgcccccacagtgcacacagagatgcctgcaacatctttggctgcagccc +actggctgggggtctcctatcagtgcccttctctagggtctcagatttgtttatggtttc +tcttcttggtgggatggatggatggatggacggatggatggggaggtgggtggatggatg +gatggatgtatgaatggggtggtagatggatggggaggtggatggacagaaggatgggtg +gggagatggatgagtagggagatggatggatggattggtggatggatggatggatggatg +gatgaggaggtagatgagtggatggacagaaggatggatgggtaggaaggtgggtggatg +aatggatggatggggaggtggatggatagatggatggatggatggatggatggatggatg +gatggggggatagatggatggatggatggatggacggacggatggggaggtggatggatg +gatggatggatggatggatggatggatggatggatgaggagatgaacggatggatgagat +ggatggatggatgatggagggaaggatggctgggtggggagatggatggatagagaggtg +gatgggtggatggggagatggatggatggatggatggatggggaagtggatggatgggga +ggtggatggatggataggtggatgggtggatggacagaaggatgaatgggtagggagatg +gatggatggatggatgcggagggatggatggatggatggatggatgggtggatggataga +aggatggatgggtggggaggtgggtgggtgggtgcgtggatggatggagagatggataga +tggatagatggatggatggatggatggatggatggagagaaggatggatgggtggggagg +tgggtgggtgggtggatgggtggatggatggatgggtggggaggtgggcgggtggatgga +tggatggatgcagaggtgggtggatggatggatggagagaaggatggatgggtggggagg +tgggtgggtggatggatggatgagtggggaggtgggtgggtggatggatggatggatgga +tgcatggatggatggatggagaggtgggtggatgggtggatggacagaaggatggatggg +tggggaggtgggtgagtgggtggatggatgaatggggaggtggatggatggatggatgga +tgaaggatggatgggtggggaggtgggtggacggatggatggattgggaggtgggtagat +gggtggatggacagaaggatggatgggtggggaggtgggtgggtgggtggatggatggat +ggggaggtggatggatggatggttagatggggaggtgggtggatgggtggatggacagaa +ggatggatgggtagggaggtaggtgagtggatggatggatggggagatggatggatggat +agagagaaggatggatgggtgggacaatggatggatggatggatagaaggatggacgggt +gggga----gatggatggatggatggatggatggatggatggacagaaggatgtatgggt +ggggaggtgggtggatagatggatggatggatggatggggaaatggatggatggaaggat +ggatggatagggaggtgggtggatggatggatggatggatgtacagaaggatggatgggt +ggggaggtgggtgagtggatgaatggatggatggatagatagaaggatggatgggtggga +caatagatggatggatagagagaaggatggatgggtgggga--------gatggatggat +ggatggatggatggatggatggatagagagaaggatggatggttgagacaatggatggat +ggatggatggatggagagatggatggatggatggatggacagaaggatggatgggtgggg +aggtggatggatggattgaaggatggacgggtggggagatggatggatggatggatggat +ggatggatggatggatggacagaaggatgtatgggtgggtaggtgggtggatagatggat +ggatggatggatggataaatggatggatggaaggatggatggataggtaggtgggtggat +ggatggatggatggatgtacagaaggatggatgggtgggtaggtgggtgagtggatgaat +ggatggatggatagatagaaggatggatgggtgggtcaatagatggatggatagagagaa +ggatggatgggtggg----tagatggatggatggatggatggatggatagagagaaggat +ggatggttgagacaatggatggatggatggatggatggagagatggatggatggatggat +ggacagaaggatggatgggtggggaggtggatggatggatggaaggatggatggatggat +agagagaaggatggatgggtgggacaatggatggatggatgcatggatggatggatggag +ggatagagagaaggatggatgggtgggacaatcaatggatggatggatggatggatggat +agagagaaggatggatgggtggggagatggatggatggatggagaggtggatggatggat +ggatggatggattgatggacagaaggatggatgggtggggaggtggatagatggagagat +ggagggatggttcgatagagagaaggatggatgggacaatggatggatggatggatggag +tgaaggatggatgggtggggagatggatggatcgatggatggatggatggatagatagat +ggatggagaggtggatagatggatgggtggatggatggacagaggatggatgggtgggga +ggtgggtggatggatggatggatgtgggatggactgtcccacagaaagtgtgtggtaagg +ggagagattggagacagcccagtcttgagatgccttgtaggggcccctggtctagggcag +gcagagctggccaggcaggagctccagcacagcgcccttgctcaccgccaatcttgtaca +cgtcctgcagcggc +>p:HG002_1_chr20:63491489-63493165 +gtgagcatgatgcccccacagtgcacacagagatgcctgcaacatctttggctgcagccc +actggctgggggtctcctatcagtgcccttctctagggtctcagatttgtttatggtttc +tcttcttggtgggatggatggatggatggacggatggatggggaggtgggtggatggatg +gatggatgtatgaatggggtggtagatggatggggaggtggatggacagaaggatgggtg +gggagatggatgagtagggagatggatggatggattggtggatggatggatggatggatg +gatgaggaggtagatgagtggatggacagaaggatggatgggtaggaaggtgggtggatg +aatggatggatggggaggtggatggatagatggatggatggatggatggatggatggatg +gatggggggatagatggatggatggatggatggacggacggatggggaggtggatggatg +gatggatggatggatggatggatggatggatggatgaggagatgaacggatggatgagat +ggatggatggatgatggagggaaggatggctgggtggggagatggatggatagagaggtg +gatgggtggatggggagatggatggatggatggatggatggggaagtggatggatgggga +ggtggatggatggataggtggatgggtggatggacagaaggatgaatgggtagggagatg +gatggatggatggatgcggagggatggatggatggatggatggatgggtggatggataga +aggatggatgggtggggaggtgggtgggtgggtgcgtggatggatggagagatggataga +tggatagatggatggatggatggatggatggatggagagaaggatggatgggtggggagg +tgggtgggtgggtggatgggtggatggatggatgggtggggaggtgggcgggtggatgga +tggatggatgcagaggtgggtggatggatggatggagagaaggatggatgggtggggagg +tgggtgggtggatggatggatgagtggggaggtgggtgggtggatggatggatggatgga +tgcatggatggatggatggagaggtgggtggatgggtggatggacagaaggatggatggg +tggggaggtgggtgagtgggtggatggatgaatggggaggtggatggatggatggatgga +tgaaggatggatgggtggggaggtgggtggacggatggatggattgggaggtgggtagat +gggtggatggacagaaggatggatgggtggggaggtgggtgggtgggtggatggatggat +ggggaggtggatggatggatggttagatggggaggtgggtggatgggtggatggacagaa +ggatggatgggtagggaggtaggtgagtggatggatggatggggagatggatggatggat +agagagaaggatggatgggtgggacaatggatggatggatggatagaaggatggacgggt +gggga----gatggatggatggatggatggatggatggatggacagaaggatgtatgggt +ggggaggtgggtggatagatggatggatggatggatggggaaatggatggatggaaggat +ggatggatagggaggtgggtggatggatggatggatggatgtacagaaggatggatgggt +ggggaggtgggtgagtggatgaatggatggatggatagatagaaggatggatgggtggga +caatagatggatggatagagagaaggatggatgggtgggga--------gatggatggat +ggatggatggatggatggatggatagagagaaggatggatggttgagacaatggatggat +ggatggatggatggagagatggatggatggatggatggacagaaggatggatgggtgggg +aggtggatggatggattgaaggatggacgggtggggagatggatggatggatggatggat +ggatggatggatggatggacagaaggatgtatgggtgggtaggtgggtggatagatggat +ggatggatggatggataaatggatggatggaaggatggatggataggtaggtgggtggat +ggatggatggatggatgtacagaaggatggatgggtgggtaggtgggtgagtggatgaat +ggatggatggatagatagaaggatggatgggtgggtcaatagatggatggatagagagaa +ggatggatgggtggg----tagatggatggatggatggatggatggatagagagaaggat +ggatggttgagacaatggatggatggatggatggatggagagatggatggatggatggat +ggacagaaggatggatgggtggggaggtggatggatggatggaaggatggatggatggat +agagagaaggatggatgggtgggacaatggatggatggatgcatggatggatggatggag +ggatagagagaaggatggatgggtgggacaatcaatggatggatggatggatggatggat +agagagaaggatggatgggtggggagatggatggatggatggagaggtggatggatggat +ggatggatggattgatggacagaaggatggatgggtggggaggtggatagatggagagat +ggagggatggttcgatagagagaaggatggatgggacaatggatggatggatggatggag +tgaaggatggatgggtggggagatggatggatcgatggatggatggatggatagatagat +ggatggagaggtggatagatggatgggtggatggatggacagaggatggatgggtgggga +ggtgggtggatggatggatggatgtgggatggactgtcccacagaaagtgtgtggtaagg +ggagagattggagacagcccagtcttgagatgccttgtaggggcccctggtctagggcag +gcagagctggccaggcaggagctccagcacagcgcccttgctcaccgccaatcttgtaca +cgtcctgcagcggc +>p:HG002_2_chr20:63491489-63493165 +gtgagcatgatgcccccacagtgcacacagagatgcctgcaacatctttggctgcagccc +actggctgggggtctcctatcagtgcccttctctagggtctcagatttgtttatggtttc +tcttcttggtgggatggatggatggatggacggatggatggggaggtgggtggatggatg +gatggatgtatgaatggggtggtagatggatggggaggtggatggacagaaggatgggtg +gggagatggatgagtagggagatggatggatggattggtggatggatggatggatggatg +gatgaggaggtagatgagtggatggacagaaggatggatgggtaggaaggtgggtggatg +aatggatggatggggaggtggatggatagatggatggatggatggatggatggatggatg +gatggggggatagatggatggatggatggatggacggacggatggggaggtggatggatg +gatggatggatggatggatggatggatggatggatgaggagatgaacggatggatgagat +ggatggatggatgatggagggaaggatggctgggtggggagatggatggatagagaggtg +gatgggtggatggggagatggatggatggatggatggatggggaagtggatggatgggga +ggtggatggatggatgtatgggtgggtggatggacagaaggatgaatgggtagggagatg +gatggatggatggatggggagggatggatggatggatggatggatgggtggatggataga +aggatggatgggtggggaggtgggtgggtgg----gtggatggatggagagatggataga +tggata----gatggatggatggatggatggatggagagaaggatggatgggtggggagg +tgggtgggtgggtggatgggtggatggatggatgggtggggaggtgggcgggtggatgga +tggatggatgcagaggtgggtggatggatggatggagagaaggatggatgggtggggagg +tgggtgggtggatggatggatgagtggggaggtgggtgggtgggtggatggatggatgga +tggatgcatggatggatgga---------------------------------------- +------------------------------------------------------------ +---------------tggagaggtgggtggacggatggatggattgggaggtgggtagat +gggtggatggacagaaggatggatgggtggggaggtgggtgggtgggtggatggatggat +ggggaggtggatggatggatggttagatggggaggtgggtggatgggtggatggacagaa +ggatggatgggtagggaggtaggtgagtggatggatggatggggagatggatggatggat +agagagaaggatggatgggtgggacaatggatggatggatggatagaaggatggacgggt +ggggagatggatggatggatggatggatggatggatggatggacagaaggatgtatgggt +ggggaggtgggtggatagatggatggatggatggatggggaaatggatggatggaaggat +ggatggatagggaggtgggtggatggatggatggatggatgtacagaaggatggatgggt +ggggaggtgggtgagtggatgaatggatggatggatagatagaaggatggatgggtggga +caatagatggatggatagagagaaggatggatgggtggggagatggatggatggatggat +ggatggatggatggatggatggatagagagaaggatggatggttgagaca----atggat +ggatggatggatggagagatggatggatggacggatggacagaaggatggatgggtgggg +aggtggatggatggattgaaggatggatgggtgggga----catggatggatggatggat +ggatggatggatggatggacagaaggatgt--------ataggtgggtggatagatggat +ggatggatggatggataaatggatggatggaaggatggatggataggtaggtgggtggat +ggatggatggatggatgtacagaaggatggatgggtgggtaggtgggtgagtggatgaat +ggatggatggatagatagaaggatggatgggtgggtcaatagatggatggatagagagaa +ggatggatgggtggg----tagatggatggatggatggatggatggatagagagaaggat +ggatggttgagacaatggatggatggatggatggatggagagatggatggatggatggat +ggacagaaggatggatgggtggggaggtggatggatggatggaaggatggatggatggat +agagagaaggatggatgggtgggacaatggatggatggatgcatggatggatggatggag +ggatagagagaaggatggatgggtgggacaatcaatggatggatggatggatggatggat +agagagaaggatggatgggtggggagatggatggatggatggagaggtggatggatggat +ggatggatggattgatggacagaaggatggatgggtggggaggtggatagatggagagat +ggagggatggttcgatagagagaaggatggatgggacaatggatggatggatggatggag +tgaaggatggatgggtggggagatggatggatcgatggatggatggatggatagatagat +ggatggagaggtggatagatggatgggtggatggatggacagaggatggatgggtgggga +ggtgggtggatggatggatggatgtgggatggactgtcccacagaaagtgtgtggtaagg +ggagagattggagacagcccagtcttgagatgccttgtaggggcccctggtctagggcag +gcagagctggccaggcaggagctccagcacagcgcccttgctcaccgccaatcttgtaca +cgtcctgcagcggc diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/msa.fa.fai new file mode 100644 index 00000000..4cd7541c --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63491489_63493165 3014 29 60 61 +syndip_1_chr20:63491489-63493165 3014 3128 60 61 +syndip_2_chr20:63491489-63493165 3014 6227 60 61 +p:HG002_1_chr20:63491489-63493165 3014 9327 60 61 +p:HG002_2_chr20:63491489-63493165 3014 12427 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/output.vcf.gz new file mode 100644 index 00000000..6c87860e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/output.vcf.gz.tbi new file mode 100644 index 00000000..b0eb76f7 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63491589-63493065/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/base.vcf.gz new file mode 100644 index 00000000..ae437b06 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/base.vcf.gz.tbi new file mode 100644 index 00000000..684e9ec7 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/comp.vcf.gz new file mode 100644 index 00000000..f976e260 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/comp.vcf.gz.tbi new file mode 100644 index 00000000..783c43dc Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/haps.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/haps.fa new file mode 100644 index 00000000..70e23aa5 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/haps.fa @@ -0,0 +1,54 @@ +>ref_chr20_63559188_63560064 +TGGGGGGGCCCTGGACTTTCCCTCCCAGTCCTGGCACCTTGCAGGTGGAGAGGGCTCTTCAGGAAGGCATAGTTGGCCTCCTGCAGACGCGCACCTGGCCGGCAGGCACGAGGGTCTGCTGAGCCTCGCAGAAGTCCAGGAGGCTACGCCAGAGGGGGCAGCAGCGCAGAAGGAGGTGGTCTCCTGTGAGGGTGGGAGTCAGATGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGAGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGAGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGAGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTCAGGCAGGAGTCGGCAGCTCCCTAGCCCAGCCCTGGCCTCACCTGTGTTCCCACCCTGGAAGAGCCCAGCCCCGCCCTCACCGATCAGGCAGAGCCCCTCCTGGGCCCGCGTGACAGCCACATTCACTTGGTTGGGGTCCACAACGAAGCCCAGAAACTTCTTGAGCCAGCTCTTGGTGGGCCGCTGGTCCAGGTCGCTCTTGGCACAGGTGCGGACG +>syndip_1_chr20:63559188-63560064 +TGGGGGGGCCCTGGACTTTCCCTCCCAGTCCTGGCACCTTGCAGGTGGAGAGGGCTCTTC +AGGAAGGCATAGTTGGCCTCCTGCAGACGCGCACCTGGCCGGCAGGCACGAGGGTCTGCT +GAGCCTCGCAGAAGTCCAGGAGGCTACGCCAGAGGGGGCAGCAGCGCAGAAGGAGGTGGT +CTCCTGTGAGGGTGGGAGTCAGATGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGT +CAGGTGGGAGGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGA +GTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGG +GTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGAGTCAGGTGGGAGGAGTCAG +GGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCA +GAGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGG +TCAGGCAGGAGTCGGCAGCTCCCTAGCCCAGCCCTGGCCTCACCTGTGTTCCCACCCTGG +AAGAGCCCAGCCCCGCCCTCACCGATCAGGCAGAGCCCCTCCTGGGCCCGCGTGACAGCC +ACATTCACTTGGTTGGGGTCCACAACGAAGCCCAGAAACTTCTTGAGCCAGCTCTTGGTG +GGCCGCTGGTCCAGGTCGCTCTTGGCACAGGTGCGGACG +>syndip_2_chr20:63559188-63560064 +TGGGGGGGCCCTGGACTTTCCCTCCCAGTCCTGGCACCTTGCAGGTGGAGAGGGCTCTTC +AGGAAGGCATAGTTGGCCTCCTGCAGACGCGCACCTGGCCGGCAGGCACGAGGGTCTGCT +GAGCCTCGCAGAAGTCCAGGAGGCTACGCCAGAGGGGGCAGCAGCGCAGAAGGAGGTGGT +CTCCTGTGAGGGTGGGAGTCAGATGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGT +CAGGTGGGAGGAGTCAGGGTCAGGTGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGG +TCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGAGTCAGGTGGGAGGAGTCAGG +GTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTCAGGCAGGAGTCGGCAGCTCC +CTAGCCCAGCCCTGGCCTCACCTGTGTTCCCACCCTGGAAGAGCCCAGCCCCGCCCTCAC +CGATCAGGCAGAGCCCCTCCTGGGCCCGCGTGACAGCCACATTCACTTGGTTGGGGTCCA +CAACGAAGCCCAGAAACTTCTTGAGCCAGCTCTTGGTGGGCCGCTGGTCCAGGTCGCTCT +TGGCACAGGTGCGGACG +>p:HG002_1_chr20:63559188-63560064 +TGGGGGGGCCCTGGACTTTCCCTCCCAGTCCTGGCACCTTGCAGGTGGAGAGGGCTCTTC +AGGAAGGCATAGTTGGCCTCCTGCAGACGCGCACCTGGCCGGCAGGCACGAGGGTCTGCT +GAGCCTCGCAGAAGTCCAGGAGGCTACGCCAGAGGGGGCAGCAGCGCAGAAGGAGGTGGT +CTCCTGTGAGGGTGGGAGTCAGATGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGT +CAGGTGGGAGGAGTCAGGGTCAGGTGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGG +TCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGAGTCAGGTGGGAGGAGTCAGG +GTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTCAGGCAGGAGTCGGCAGCTCC +CTAGCCCAGCCCTGGCCTCACCTGTGTTCCCACCCTGGAAGAGCCCAGCCCCGCCCTCAC +CGATCAGGCAGAGCCCCTCCTGGGCCCGCGTGACAGCCACATTCACTTGGTTGGGGTCCA +CAACGAAGCCCAGAAACTTCTTGAGCCAGCTCTTGGTGGGCCGCTGGTCCAGGTCGCTCT +TGGCACAGGTGCGGACG +>p:HG002_2_chr20:63559188-63560064 +TGGGGGGGCCCTGGACTTTCCCTCCCAGTCCTGGCACCTTGCAGGTGGAGAGGGCTCTTC +AGGAAGGCATAGTTGGCCTCCTGCAGACGCGCACCTGGCCGGCAGGCACGAGGGTCTGCT +GAGCCTCGCAGAAGTCCAGGAGGCTACGCCAGAGGGGGCAGCAGCGCAGAAGGAGGTGGT +CTCCTGTGAGGGTGGGAGTCAGATGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGT +CAGGTGGGAGGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGG +TCAGATGGGAGTCAGTCAGAGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGG +GTCAGGTCGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGTCAGTCAGGGT +CAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGAG +TCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTCA +GGCAGGAGTCGGCAGCTCCCTAGCCCAGCCCTGGCCTCACCTGTGTTCCCACCCTGGAAG +AGCCCAGCCCCGCCCTCACCGATCAGGCAGAGCCCCTCCTGGGCCCGCGTGACAGCCACA +TTCACTTGGTTGGGGTCCACAACGAAGCCCAGAAACTTCTTGAGCCAGCTCTTGGTGGGC +CGCTGGTCCAGGTCGCTCTTGGCACAGGTGCGGACG diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/haps.fa.ref.fa new file mode 100644 index 00000000..8f47a2fb --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63559188-63560064 +TGGGGGGGCCCTGGACTTTCCCTCCCAGTCCTGGCACCTTGCAGGTGGAGAGGGCTCTTCAGGAAGGCATAGTTGGCCTCCTGCAGACGCGCACCTGGCCGGCAGGCACGAGGGTCTGCTGAGCCTCGCAGAAGTCCAGGAGGCTACGCCAGAGGGGGCAGCAGCGCAGAAGGAGGTGGTCTCCTGTGAGGGTGGGAGTCAGATGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGAGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGAGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGTCAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGATGGGAGTCAGTCAGAGTCAGGTGGGAGGAGTCAGGGTCAGGTGGGAGGAGTCAGGGTCAGGTCGGAGTCAGGGTCAGGCAGGAGTCGGCAGCTCCCTAGCCCAGCCCTGGCCTCACCTGTGTTCCCACCCTGGAAGAGCCCAGCCCCGCCCTCACCGATCAGGCAGAGCCCCTCCTGGGCCCGCGTGACAGCCACATTCACTTGGTTGGGGTCCACAACGAAGCCCAGAAACTTCTTGAGCCAGCTCTTGGTGGGCCGCTGGTCCAGGTCGCTCTTGGCACAGGTGCGGACG diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/msa.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/msa.fa new file mode 100644 index 00000000..9a4bce11 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/msa.fa @@ -0,0 +1,80 @@ +>ref_chr20_63559188_63560064 +tgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctcttc +aggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgct +gagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggt +ctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcagggt +caggtgggaggagtcagggtcaggtgggagtcagtcagggtcaggtgggaggagtcaggg +tcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtcagg +gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtgggag-gagtcag +ggtcagatgggagtcagtcagagtcaggtgggaggagtcagggtcaggtgggaggagtca +gggtcaggt---cggagtcagggtcaggtgggag-gagtcagggtcaggtgggagtcagt +cagggtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcag +tcagagtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtca +gggtcaggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccc +tggaagagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgaca +gccacattcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttg +gtgggccgctggtccaggtcgctcttggcacaggtgcggacg +>syndip_1_chr20:63559188-63560064 +tgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctcttc +aggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgct +gagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggt +ctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcagggt +caggtgggag-------------------------------------------------- +------------------------------------------------------------ +-----------ggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcag +agtcaggtgggag-gagtcagggtcaggtgggaggagtcagggtcaggtgggaggagtca +gggtcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggag-gagt +cagggtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcag +tcagagtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtca +gggtcaggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccc +tggaagagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgaca +gccacattcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttg +gtgggccgctggtccaggtcgctcttggcacaggtgcggacg +>syndip_2_chr20:63559188-63560064 +tgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctcttc +aggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgct +gagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggt +ctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtggga----------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------ggagtcagggtcaggtgggag-gagtcagggtcaggtgggagtcagt +cagggtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcag +tcagagtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtca +gggtcaggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccc +tggaagagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgaca +gccacattcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttg +gtgggccgctggtccaggtcgctcttggcacaggtgcggacg +>p:HG002_1_chr20:63559188-63560064 +tgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctcttc +aggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgct +gagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggt +ctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtggga----------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------ggagtcagggtcaggtgggag-gagtcagggtcaggtgggagtcagt +cagggtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcag +tcagagtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtca +gggtcaggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccc +tggaagagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgaca +gccacattcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttg +gtgggccgctggtccaggtcgctcttggcacaggtgcggacg +>p:HG002_2_chr20:63559188-63560064 +tgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctcttc +aggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgct +gagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggt +ctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcagggt +caggtgggag-------------------------------------------------- +------------------------------------------------------------ +-----------ggagtcagggtcaggtgggaggagtcagggtcaggtgggag-gagtcag +ggtcagatgggagtcagtcagagtcaggtgggaggagtcagggtcaggtgggaggagtca +gggtcaggt---cggagtcagggtcaggtgggag-gagtcagggtcaggtgggagtcagt +cagggtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcag +tcagagtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtca +gggtcaggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccc +tggaagagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgaca +gccacattcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttg +gtgggccgctggtccaggtcgctcttggcacaggtgcggacg diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/msa.fa.fai new file mode 100644 index 00000000..2a8de5a0 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63559188_63560064 882 29 60 61 +syndip_1_chr20:63559188-63560064 882 960 60 61 +syndip_2_chr20:63559188-63560064 882 1891 60 61 +p:HG002_1_chr20:63559188-63560064 882 2823 60 61 +p:HG002_2_chr20:63559188-63560064 882 3755 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/output.vcf.gz new file mode 100644 index 00000000..a52b6f6f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/output.vcf.gz.tbi new file mode 100644 index 00000000..c9ec3693 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63559288-63559964/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/base.vcf.gz new file mode 100644 index 00000000..3d60d8af Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/base.vcf.gz.tbi new file mode 100644 index 00000000..ad97ee51 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/comp.vcf.gz new file mode 100644 index 00000000..f1759fcd Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/comp.vcf.gz.tbi new file mode 100644 index 00000000..8f7ade10 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/haps.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/haps.fa new file mode 100644 index 00000000..2d2aea6d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/haps.fa @@ -0,0 +1,62 @@ +>ref_chr20_63641679_63642236 +TCTATTACTGCGGCTAGTTACTGTCCCGCCAGGACCAGACTCTGGACCTGCCTCGTGCGCTGCTGGGGACGCCCAGTAAACACGGGAGGAGCCCCCGACCCCCACCCCAGCTCAGCGCCTCGGAGTCCCCGGCCCCGCTCTGCGCCCCTCCGAGCTCCGCCCTAGCCCCGCCCCCGCCCAGTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCTGGCCCCGCCCCCGCCCAGTGCCCCGCCCCCTGACTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTTCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCGGCCCCGCCCCCGCACCTTCTCGCGCAGCCGCTCGCGCAGTGCGGCCAGGTGTGCCTCGCGGATCTCCTTGCTGAGCTCCATCTTGTAGTTGAGCTTCTCCTCCGCCTGGCGGCTGAAGTTGTTATTCTCCTCCAGCGCCTTGTG +>syndip_1_chr20:63641679-63642236 +TCTATTACTGCGGCTAGTTACTGTCCCGCCAGGACCAGACTCTGGACCTGCCTCGTGCGC +TGCTGGGGACGCCCAGTAAACACGGGAGGAGCCCCCGACCCCCACCCCAGCTCAGCGCCT +CGGAGTCCCCGGCCCCGCTCTGCGCCCCTCCGAGCTCCGCCCTAGCCCCGCCCCCGCCCA +GTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAG +CTCCGCCCTGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCTGGCCCCGCCCCC +CGCCCAGTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGC +TCCGAGCTCCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCTGGCCCC +GCCCCCGCCCAGTGCCCCGCCCCCTGACTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTG +CCCGCTCCGAGCTCCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCG +GCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTTCGCCCCGGCCCCGCCCCGGCCCCTGCCC +GCTCCGAGCTCCGCCCCGGCCCCGCCCCCGCACCTTCTCGCGCAGCCGCTCGCGCAGTGC +GGCCAGGTGTGCCTCGCGGATCTCCTTGCTGAGCTCCATCTTGTAGTTGAGCTTCTCCTC +CGCCTGGCGGCTGAAGTTGTTATTCTCCTCCAGCGCCTTGTG +>syndip_2_chr20:63641679-63642236 +TCTATTACTGCGGCTAGTTACTGTCCCGCCAGGACCAGACTCTGGACCTGCCTCGTGCGC +TGCTGGGGACGCCCAGTAAACACGGGAGGAGCCCCCGACCCCCACCCCAGCTCAGCGCCT +CGGAGTCCCCGGCCCCGCTCTGCGCCCCTCCGAGCTCCGCCCTAGCCCCGCCCCCGCCCA +GTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAG +CTCCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCTGGCCCCGCCCCC +GCCCAGTGCCCCGCCCCCTGACTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCT +CCGAGCTCCACCCTGGCCCCGCCCCCGCCCAGTGCCCCGCCCCCTGCCTGCTGCTTGCCC +TGCCCCCTCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCGGCCCCGCCCCGGCCCAGTG +CCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTC +CGCCCTGGCCCCGCCCCCGCCCAGTGCCCCGCCCCCTGCCTGCTGCTTGCCCTGCCCCCT +CCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCGGCCTCGCCCCGGCCCCTGCCCGCTCCG +AGCTTCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTTCGCCCCGGCCCCGCCC +CGGCCCCTGCCCGCTCCGAGCTCCGCCCCGGCCCCGCCCCCGCACCTTCTCGCGCAGCCG +CTCGCGCAGTGCGGCCAGGTGTGCCTCGCGGATCTCCTTGCTGAGCTCCATCTTGTAGTT +GAGCTTCTCCTCCGCCTGGCGGCTGAAGTTGTTATTCTCCTCCAGCGCCTTGTG +>p:HG002_1_chr20:63641679-63642236 +TCTATTACTGCGGCTAGTTACTGTCCCGCCAGGACCAGACTCTGGACCTGCCTCGTGCGC +TGCTGGGGACGCCCAGTAAACACGGGAGGAGCCCCCGACCCCCACCCCAGCTCAGCGCCT +CGGAGTCCCCGGCCCCGCTCTGCGCCCCTCCGAGCTCCGCCCTAGCCCCGCCCCCGCCCA +GTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAG +CTCCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCTGGCCCCGCCCCC +GCCCAGTGCCCCGCCCCCTGACTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCT +CCGAGCTCCACCCTGGCCCCGCCCCCGCCCAGTGCCCCGCCCCCTGCCTGCTGCTTGCCC +TGCCCCCTCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCGGCCCCGCCCCGGCCCAGTG +CCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTC +CGCCCTGGCCCCGCCCCCGCCCAGTGCCCCGCCCCCTGCCTGCTGCTTGCCCTGCCCCCT +CCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCGGCCTCGCCCCGGCCCCTGCCCGCTCCG +AGCTTCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTTCGCCCCGGCCCCGCCC +CGGCCCCTGCCCGCTCCGAGCTCCGCCCCGGCCCCGCCCCCGCACCTTCTCGCGCAGCCG +CTCGCGCAGTGCGGCCAGGTGTGCCTCGCGGATCTCCTTGCTGAGCTCCATCTTGTAGTT +GAGCTTCTCCTCCGCCTGGCGGCTGAAGTTGTTATTCTCCTCCAGCGCCTTGTG +>p:HG002_2_chr20:63641679-63642236 +TCTATTACTGCGGCTAGTTACTGTCCCGCCAGGACCAGACTCTGGACCTGCCTCGTGCGC +TGCTGGGGACGCCCAGTAAACACGGGAGGAGCCCCCGACCCCCACCCCAGCTCAGCGCCT +CGGAGTCCCCGGCCCCGCTCTGCGCCCCTCCGAGCTCCGCCCTAGCCCCGCCCCCGCCCA +GTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAG +CTCCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCTGGCCCCGCCCCC +GCCCAGTGCCCCGCCCCCTGACTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCT +CCGAGCTCCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCTGGCCCCG +CCCCCGCCCAGTGCCCCGCCCCCTGACTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGC +CCGCTCCGAGCTCCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCGG +CCCCGCCCCGGCCCCTGCCCGCTCCGAGCTTCGCCCCGGCCCCGCCCCGGCCCCTGCCCG +CTCCGAGCTCCGCCCCGGCCCCGCCCCCGCACCTTCTCGCGCAGCCGCTCGCGCAGTGCG +GCCAGGTGTGCCTCGCGGATCTCCTTGCTGAGCTCCATCTTGTAGTTGAGCTTCTCCTCC +GCCTGGCGGCTGAAGTTGTTATTCTCCTCCAGCGCCTTGTG diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/haps.fa.ref.fa new file mode 100644 index 00000000..423b8813 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63641679-63642236 +TCTATTACTGCGGCTAGTTACTGTCCCGCCAGGACCAGACTCTGGACCTGCCTCGTGCGCTGCTGGGGACGCCCAGTAAACACGGGAGGAGCCCCCGACCCCCACCCCAGCTCAGCGCCTCGGAGTCCCCGGCCCCGCTCTGCGCCCCTCCGAGCTCCGCCCTAGCCCCGCCCCCGCCCAGTGCCCCGCCCCCTGCCTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCTGGCCCCGCCCCCGCCCAGTGCCCCGCCCCCTGACTGCTGCTAGCCCTGCCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTTCGCCCCGGCCCCGCCCCGGCCCCTGCCCGCTCCGAGCTCCGCCCCGGCCCCGCCCCCGCACCTTCTCGCGCAGCCGCTCGCGCAGTGCGGCCAGGTGTGCCTCGCGGATCTCCTTGCTGAGCTCCATCTTGTAGTTGAGCTTCTCCTCCGCCTGGCGGCTGAAGTTGTTATTCTCCTCCAGCGCCTTGTG diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/msa.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/msa.fa new file mode 100644 index 00000000..deab91fd --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/msa.fa @@ -0,0 +1,80 @@ +>ref_chr20_63641679_63642236 +tctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcgc +tgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcct +cggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccca +gtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgag +ctccgccccggccccgccccggcccctgcccgctccgagctccgccctggccccg-cccc +cgcccagtgccccgccccctgactgctgctagccctgc---------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------ccccgccccggcccctgcccgctccgagcttcgccccggccccgcc +ccggcccctgcccgctccgagctccgccccggccccgcccccgcaccttctcgcgcagcc +gctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtagt +tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgtg +>syndip_1_chr20:63641679-63642236 +tctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcgc +tgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcct +cggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccca +gtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgag +ctccgccctggccccgccccggcccctgcccgctccgagctccgccctggccccgccccc +cgcccagtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgc +tccgagctccgccccgg------------------------------------------- +------------------------------------------------------------ +------------------------------ccccgccccggcccctgcccgctccgagct +ccgccctggccccgcccccgcccagtgccccgccccctgactgctgctagccctgccccc +gccccggcccctgcccgctccgagctccgccccggccccgccccggcccctgcccgctcc +gagctccgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgcc +ccggcccctgcccgctccgagctccgccccggccccgcccccgcaccttctcgcgcagcc +gctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtagt +tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgtg +>syndip_2_chr20:63641679-63642236 +tctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcgc +tgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcct +cggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccca +gtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgag +ctccgccccggccccgccccggcccctgcccgctccgagctccgccctggccccg-cccc +cgcccagtgccccgccccctgactgctgctagccctgcccccgccccggcccctgcccgc +tccgagctccaccctggccccgcccccgcccagtgccccgccccctgcctgctgcttgcc +ctgccccctccccggcccctgcccgctccgagctccgccccggccccgccccggcccagt +gccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgagct +ccgccctggccccgcccccgcccagtgccccgccccctgcctgctgcttgccctgccccc +tccccggcccctgcccgctccgagctccgccccggcctcgccccggcccctgcccgctcc +gagcttcgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgcc +ccggcccctgcccgctccgagctccgccccggccccgcccccgcaccttctcgcgcagcc +gctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtagt +tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgtg +>p:HG002_1_chr20:63641679-63642236 +tctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcgc +tgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcct +cggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccca +gtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgag +ctccgccccggccccgccccggcccctgcccgctccgagctccgccctggccccg-cccc +cgcccagtgccccgccccctgactgctgctagccctgcccccgccccggcccctgcccgc +tccgagctccaccctggccccgcccccgcccagtgccccgccccctgcctgctgcttgcc +ctgccccctccccggcccctgcccgctccgagctccgccccggccccgccccggcccagt +gccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgagct +ccgccctggccccgcccccgcccagtgccccgccccctgcctgctgcttgccctgccccc +tccccggcccctgcccgctccgagctccgccccggcctcgccccggcccctgcccgctcc +gagcttcgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgcc +ccggcccctgcccgctccgagctccgccccggccccgcccccgcaccttctcgcgcagcc +gctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtagt +tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgtg +>p:HG002_2_chr20:63641679-63642236 +tctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcgc +tgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcct +cggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccca +gtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgag +ctccgccccggccccgccccggcccctgcccgctccgagctccgccctggccccg-cccc +cgcccagtgccccgccccctgactgctgctagccctgcccccgccccggcccctgcccgc +tccgagctccgccccgg------------------------------------------- +------------------------------------------------------------ +------------------------------ccccgccccggcccctgcccgctccgagct +ccgccctggccccgcccccgcccagtgccccgccccctgactgctgctagccctgccccc +gccccggcccctgcccgctccgagctccgccccggccccgccccggcccctgcccgctcc +gagctccgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgcc +ccggcccctgcccgctccgagctccgccccggccccgcccccgcaccttctcgcgcagcc +gctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtagt +tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgtg diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/msa.fa.fai new file mode 100644 index 00000000..d35f8cb1 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63641679_63642236 895 29 60 61 +syndip_1_chr20:63641679-63642236 895 973 60 61 +syndip_2_chr20:63641679-63642236 895 1917 60 61 +p:HG002_1_chr20:63641679-63642236 895 2862 60 61 +p:HG002_2_chr20:63641679-63642236 895 3807 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/output.vcf.gz new file mode 100644 index 00000000..174783ad Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/output.vcf.gz.tbi new file mode 100644 index 00000000..0b0b0500 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63641779-63642136/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63693325-63693885/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63693325-63693885/base.vcf.gz new file mode 100644 index 00000000..75f4e621 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63693325-63693885/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63693325-63693885/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63693325-63693885/base.vcf.gz.tbi new file mode 100644 index 00000000..fd4c9400 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63693325-63693885/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63693325-63693885/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63693325-63693885/comp.vcf.gz new file mode 100644 index 00000000..0d0bcf09 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63693325-63693885/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63693325-63693885/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63693325-63693885/comp.vcf.gz.tbi new file mode 100644 index 00000000..da90a64e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63693325-63693885/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63693325-63693885/haps.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63693325-63693885/haps.fa new file mode 100644 index 00000000..f5f368c3 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63693325-63693885/haps.fa @@ -0,0 +1,432 @@ +>ref_chr20_63693225_63693985 +TCGGCCTGAGCACAGCATTCCCCGAAGGCAGCGGGCACAGCCGGTCCTGGACCCCACTGGTAAATGGGGCCCCAGGTGGGACCCTCAGACTCCTGCGTGGAAGGCAGTGTGGGCCAGAGTCCTGGGCTGCTTGGGGTGGGCATCCTCGGGCCCTGCTTGGCCCCGCCTCTCTGTTCCCCTATGGGAGTGATGGGGGCCTCCACCTCCACCACCAGCACCAGCAGCACCACCTCCACCTCCACCTCCACCTCCACCTCCACCACCACCTCCACCTCCACCACCACCTCCTCCACCACCACCACCTCCACCACCACCACCACCACCACCACCTCCACCTCCACCACCTCCACCTCCACCACCACCACCTCCACCTCCACCACCACCACCTCCACCTCCACCACCACCTCCACCACCACCACCTCCACCTCCACCACCACCTCCACCACCACCACCACCACCACCACCACCACCACCACCACCTCCACCACCACCACCTGCACCACCACCTCCACCTCCACCACCACCACCACCTCCACCTCCACCAGCAGCAGCATCACTTGTTGGGGAGACCCTGTGCAACTCCATGCACAGCCCTGTCCCTGCCATAGCCCCGACCCCTAAGCACAGCCCTGTCCAACTGCCACACGTCCCCTGCCTCCCATGCATGGTCCTGGGGGGTCAACTGCACACGCCAGGGTCCTAGGGTCCTAGACCCCTGTCCTCCCTGTTTCTGCCTCTGTTTGGGGTGGAGTCCAAGTCTC +>syndip_1_chr20:63693225-63693985 +TCGGCCTGAGCACAGCATTCCCCGAAGGCAGCGGGCACAGCCGGTCCTGGACCCCACTGG +TAAATGGGGCCCCAGGTGGGACCCTCAGACTCCTGCGTGGAAGGCAGTGTGGGCCAGAGT +CCTGGGCTGCTTGGGGTGGGCATCCTCGGGCCCTGCTTGGCCCCGCCTCTCTGTTCCCCT +ATGGGAGTGATGGGGGCCTCCACCTCCACCACCAGCACCAGCAGCACCACCTCCACCTTC +ACCACCACCACCTCCACCACCACCTCCACCACCTCCACCTCCACCACCTCCACCACCTCC +ACCACCACCACCTCCACCACCACCACCTCCACCACCACCACCACCACCACCTCCACCACC +ACCACCACCACCACCACCTCCACCTCCACCACCTCCACCACCACCTCCACCTCCACCACC +ACCTCCACCTCCACCTCCACCACCACCACCTCCACCACCTCCACCACCTCCACCTCCACC +ACCACCTCCACCTCCACCACCACCTCCACCTCCACCTCCACCTCCACCTCCACCACCACC +ACCTCCACCACCTCCACCACCTCCACCTCCACCACCACCACCTCCACCTCCACCTCCACC +ACCTCCACCTCCACCACCTCCACCTCCACCACCTCCACCACCACCACCACCACCACCACC +ACCTCCACCACCACCACCACCACCACCTCCACCACCTCCACCTCCACCACCTCCACCACC +ACCACCTCCACCACCACCTCCACCACCACCTCCACCTCCACCACCTCCACCTCCACCACC +TCCACCTCCACCTCCACCACCACCTCCACCACCTCCACCACCACCTCCACCACCTCCACC +TCCACCACCACCACCTCCACCACCACCACCACCACCACCTCCACCACCTCCACCTCCACC +ACCTCCACCACCACCACCTCCACCACCACCTCCACCACCACCTCCACCTCCACCACCTCC +ACCTCCACCACCTCCACCTCCACCTCCACCACCACCTCCACCACCTCCACCACCACCTCC +ACCACCTCCACCACCTCCACCACCACCTCCACCACCTCCACCTCCACCACCACCACCTCC +ACCTCCACCACCACCACCTCCACCACCACCTCCACCTCCACCACCACCACCTCCACCTCC +ACCACCACCACCTCCACCACCACCTCCACCACCACCACCACCACCACCACCTCCACCTCC +ACCACCTCCACCACCACCACCACCACCTCCACCTCCACCACCTCCACCACCTCCACCACC +ACCACCACCACCTCCACCACCTCCACCACCACCTCCACCACCTCCACCTCCACCACCACC +ACCTCCACCACCACCACCTCCACCTCCACCTCCACCTCCACCTCCACCACCACCTCCACC +TCCACCACCACCTCCACCACCACCTCCACCTCCACCACCTCCACCTCCACCTCCACCACC +TCCACCACCACCACCACCACCACCACCACCACCACCACCTCCACCACCTCCACCTCCACC +TCCACCACCACCACCACCACCTCCACCACCACCACCACCACCTCCACCACCTCCACCACC +ACCTCCACCACCACCACCACCACCACCACCACCACCTCCACCACCTCCACCTCCACCTCC +ACCTCCACCACCTCCACCACCTCCACCACCACCTCCACCACCACCACCACCACCTCCACC +ACCACCTCCACCTCCACCACCACCTCCACCACCACCTCCACCTCCACCACCTCCACCTCC +ACCACCTCCACCACCTCCACCTCCACCACCTCCACCTCCACCTCCACCACCTCCACCACC +ACCACCACCACCACCACCACCACCACCACCTCCACCACCACCACCTCCACCACCACCTCC +ACCACCTCCACCACCACCTCCACCACCACCACCACCACCACCACCACCACCACCACCTCC +ACCACCACCTCCACCTCCACCACCACCTCCACCACCACCTCCACCTCCACCACCTCCACC +TCCACCACCTCCACCACCTCCACCACCACCACCACCACCTCCACCACCACCTCCACCTCC +ACCACCACCACCACCACCACCACCTCCACCACCACCACCTCCACCACCACCTCCACCACC +TCCACCACCACCTCCACCTCCACCACCTCCACCACCACCTCCACCACCACCTCCACCACC +ACCACCTCCACCACCACCTCCACCACCTCCACCACCACCTCCACCTCCACCACCTCCACC +ACCACCTCCACCACCACCTCCACCACCACCACCTCCACCACCACCTCCACCACCTCCACC +ACCACCTCCACCTCCACCACCTCCACCTCCACCTCCACCACCTCCACCACCACCACCACC +ACCACCACCACCACCACCACCACCACCACCACCACCTCCACCTCCACCTCCACCACCTCC +ACCTCCACCACCTCCACCACCACCTCCACCTCCACCACCTCCACCTCCACCTCCACCACC +TCCACCTCCACCACCTCCACCTCCACCTCCACCACCTCCACCACCACCACCTCCACCACC +ACCTCCACCACCTCCACCACCACCTCCACCTCCACCACCTCCACCACCACCTCCACCACC +ACCTCCACCACCACCACCTCCACCACCACCTCCACCACCTCCACCACCACCTCCACCTCC +ACCACCTCCACCTCCACCTCCACCACCTCCACCACCACCACCACCACCACCACCACCACC +ACCACCTCCACCACCACCACCTCCACCACCACCTCCACCACCACCACCACCACCTCCACC +ACCACCACCACCACCTCCACCACCACCTCCACCACCTCCACCACCACCACCACCACCACC +ACCACCTCCACCACCACCTCCACCACCACCACCACCACCACCACCACCTCCACCACCTCC +ACCTCCACCACCACCACCACCTCCACCACCACCACCACCACCACCTCCACCTCCACCACC +ACCACCTCCACCACCACCACCACCTCCACCACCACCTCCACCACCACCACCACCACCACC +ACCACCACCTCCACCACCTCCACCACCTCCACCACCACCTCCACCACCTCCACCACCACC +ACCACCACCTCCACCACCACCTCCACCACCACCACCACCACCACCACCTCCACCTCCACC +TCCACCACCTCCACCTCCACCACCTCCACCTCCACCACCTCCACCTCCACCTCCACCTCC +ACCACCACCTCCACCTCCACCACCACCTCCTCCACCACCACCACCTCCACCACCACCACC +ACCACCACCACCTCCACCTCCACCACCTCCACCTCCACCACCACCACCTCCACCTCCACC +ACCACCACCTCCACCACCTCCACCACCACCTCCACCACCTCCACCTCCACCACCACCACC +TCCACCACCACCACCTCCACCTCCACCACCACCACCACCACCACCTCCACCTCCACCACC +ACCTCCACCACCACCTCCACCTCCACCTCCACCACCTCCACCACCACCTCCACCACCTCC +ACCACCTCCACCTCCACCACCACCACCACCTCCACCACCACCACCACCACCTCTACCACC +TCTACCACCACCACCACCACCTCCACCACCACCACCACCACCTCCACCACCACCACCACC +ACCACCTCCACCACCACCTCCACCACCTCCACCACCACCACCACCACCTCTACCACCTCC +ACCTCCACCACCACCACCACCTCTACCACCACCACCACCACCTCCACCACCACCACCACC +TCCACCACCACCACCACCTCCACCACCACCTCCACCACCACCTCCACCACCTCCACCACC +ACCACCACCTCCACCTCCACCACCTCCACCACCACCTCCACCACCACCACCACCACCACC +TCCACCACCACCTCCACCACCTCCACCACCACCACCACCACCTCTACCACCTCCACCTCC +ACCACCACCACCACCTCCACCTCCACCACCACCACCACCACCACCACCACCACCACCTCC +ACCACCACCACCACCACCACCTCTACCACCACCACCACCACCTCCACCACCACCACCACC 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+ACCACCACCACCACCACCTCCACCACCTCCACCACCTCCACCACCACCACCACCACCTCC +ACCTCCACCTCCACCACCTCCACCACCACCACCTCCACCACCACCACCACCACCACCACC +ACCTCCACCTCCACCTCCACCACCTCCACCTCCACCACCACCACCACCACCACCACCACC +ACCACCACCTCCACCTCCACCTCCACCACCTCCACCACCACCACCTCCACCACCACCACC +TCCACCTCCACCACCTCCACCACCACCTCCACCACCACCACCTCCACCTCCACCACCACC +ACCTCCACCACCACCACCTCCACCTCCACCACCACCACCTCCACCACCTCCACCACCACC +TCCACCACCACCACCTCCACCTCCACCACCACCACCTCCACCACCTCCACCACCACCACC +TCCACCACCACCACCTCCACCACCTCCACCACCACCACCACCACCTCCACCACCTCCACC +ACCTCCACCACCACCACCACCACCTCCACCTCCACCTCCACCACCTCCACCACCACCACC +TCCACCACCACCACCACCACCACCTCCACCACCTCCACCACCACCACCACCACCTCCACC +TCCACCTCCACCACCTCCACCACCACCACCTCCACCACCACCACCACCACCACCACCACC +ACCTCCACCTCCACCTCCACCACCTCCACCTCCACCACCACCACCACCACCACCACCTCC +ACCACCACCTCCACCTCCACCTCCACCACCTCCACCTCCACCACCACCACCACCACCACC +ACCACCACCACCACCTCCACCTCCACCTCCACCACCACCACCTCTACCACCACCTCCACC +ACCACCACCACCACCACCACCACCACCTCCACCACCTCCACCACCACCACCTCCACCACC +ACCACCTCCACCTCCACCACCACCACCACCTCCACCACCTCCACCACCACCTCCACCTCC +ACCTCCACCACCTCCACCACCACCACCTCCACCACCACCACCACCACCACCACCTCCACC +ACCTCCACCACCACCACCTCCACCACCACCACCTCCACCTCCACCACCTCCACCACCTCC +ACCACCACCACCACCTCCACCACCACCACCACCACCACCTCCACCTCCACCACCTCTACC +ACCACCTCCACCACCACCACCACCACCACCTCCACCTCCACCACCTCCACCTCCACCACC +TCTACCACCACCTCCACCACCACCACCTCCACCTCCACCTCCACCACCACCACCTCCACC +TCCACCTCCACCACCACCACCACCACCACCACCTCCACCACCACCACCACCACCACCACC +ACCACCTCCACCTCCACCACCACCACCTCCACCACCACCACCTCCACCACCTCCACCACC +ACCTCCACCTCCACCACCACCACCTCCACCTCCACCTCCACCACCACCACCACCACCTCC +ACCACCACCACCTCCACCACCAACACCTCCACCTCCACCTCCACCACCACCACCACCACC +TCCACCTCCACCACCACCTCCACCACCACCACCTCCACCTCCACCACCACCACCTCCACC +ACCACCTCCACCACCTCCACCACCACCACCTCCACCACCACCTCCACCACCACCACCACC +ACCACCTCCACCTCCACCTCCACCACCACCACCTCTACCACCACCTCCACCACCACCACC +ACCACCACCACCACCACCTCCACCTCCACCTCCACCACCTCCACCTCCACCACCACCACC +ACCACCACCACCTCCACCACCACCTCCACCTCCACCTCCACCACCTCCACCTCCACCACC +ACCACCACCACCACCACCACCACCACCACCTCCACCTCCACCTCCACCACCACCACCTCT +ACCACCACCTCCACCACCACCACCACCACCACCACCACCACCTCCACCACCACCACCTCC +ACCTCCACCACCACCACCTCCACCTCCACCACCACCACCTCCACCTCCACCACCACCACC +ACCACCACCACCTCCACCACCACCACCTCCACCACCTCCACCACCACCTCCACCACCACC +ACCTCCACCACCTCCACCACCACCTCCACCTCCACCACCACCACCTCCACCACCACCACC +TCCACCTCCACCACCACCACCTCCACCTCCACCTCCACCACCTCCACCTCCACCACCTCC +ACCACCACCACCTCCACCACCTCCACCACCACCTCCACCTCCACCACCACCACCTCCACC +ACCACCACCTCCACCACCTCCACCACCACCTCCACCTCCACCACCACCACCTCCACCTCC +ACCTCCACCACCACCACCACCACCTCCACTACCACCACCTCCACCTCCACCACCACCACC +TCCACCACCAACACCTCCACCTCCACCTCCACCTCCACCACCACCACCTCCACCTCCACC +ACCACCACCTCCACCACCACCACCTCCACCACCTCCACCTCCACCACCACCACCTCCACC +ACCACCTCCACCACCACCACCACCTCCACCACCACCACCTCCACCACCACCTCCACCACC +ACCACCTCCACCACCACCTCCACCACCACCTCCACCTCCACCACCACCACCTGCACCACC +ACCTCCACCTCCACCACCACCACCACCTCCACCTCCACCAGCAGCAGCATCACTTGTTGG +GGAGACCCTGTGCAACTCCATGCACAGCCCTGTCCCTGCCATAGCCCCGACCCCTAAGCA +CAGCCCTGTCCAACTGCCACACGTCCCCTGCCTCCCATGCATGGTCCTGGGGGGTCAACT +GCACACGCCAGGGTCCTAGGGTCCTAGACCCCTGTCCTCCCTGTTTCTGCCTCTGTTTGG +GGTGGAGTCCAAGTCTC +>syndip_2_chr20:63693225-63693985 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00000000..64949e0d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63693325-63693885/msa.fa @@ -0,0 +1,660 @@ +>ref_chr20_63693225_63693985 +tcggcctgagcacagcattccccgaaggcagcgggcacagccggtcctggaccccactgg +taaatggggccccaggtgggaccctcagactcctgcgtggaaggcagtgtgggccagagt +cctgggctgcttggggtgggcatcctcgggccctgcttggccccgcctctctgttcccct +atgggagtgatgggggcctccacctccaccaccagcaccagcagcaccacctccacctcc +acctccacctccacctccaccaccacctccacctccaccaccacctcctccaccacc--- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ 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b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63948514-63948759/base.vcf.gz.tbi new file mode 100644 index 00000000..1e5323ef Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63948514-63948759/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63948514-63948759/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63948514-63948759/comp.vcf.gz new file mode 100644 index 00000000..90ce9961 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63948514-63948759/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63948514-63948759/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63948514-63948759/comp.vcf.gz.tbi new file mode 100644 index 00000000..601c8aa2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63948514-63948759/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63948514-63948759/haps.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63948514-63948759/haps.fa new file mode 100644 index 00000000..077e6ccb --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63948514-63948759/haps.fa @@ -0,0 +1,162 @@ +>ref_chr20_63948414_63948859 +ACAGAACACAGGTGCGGACAGGGAACGGCATCCTCAGAGCATGGTCAGGGGAGAAAAGCAAGCTGGAAGGAGAGATGATTCCATCTGTATAAAATCCAGGAAACGAAGGACGCTCACCGCCATGCGCCTCGGTGTGAGGAGGGAGGCGTGTGTGAGAGGGAGGGGATGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGTGTGTGTGAGACCGAGGGGGCGTGTAAGGGAGGGGGTGTGTGTGAGAGGGAAGCGTGTGCACACACCAGCCCTAACCATGATCACTCTCTGGCCACCAAGATTTGGAACAGCAACTTCTGTCACATTTGAATGTTTTTAAAGCAGGTGCCACTTTGTTGCCATAAACCAAACCGTAGTCTGT +>syndip_1_chr20:63948414-63948859 +ACAGAACACAGGTGCGGACAGGGAACGGCATCCTCAGAGCATGGTCAGGGGAGAAAAGCA +AGCTGGAAGGAGAGATGATTCCATCTGTATAAAATCCAGGAAACGAAGGACGCTCACCGC +CATGCGCCTCGGTGTGAGGAGGGAGGCGTGTGTGAGAGGGAGGGGATGTGTGTGAGAGGG +AGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGTGTGTGTGAGAGGGAGGGG +CGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGCAGGGGGCGTGTGTGTGAGGGGCGTGT +GTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGGGGGGGCGTGTGTGAG +AGGTAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGCGTGTGTGAGAGGG +AGGGGCGTGTGTGTGAGGGAGGGGCGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGCAGGG +GCGTGTGTGTGAGGGAGGGGCGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGT +GTGAGGGGGGGCGTGTGTGAGAGGTAGGGGCGTGTGTGGGAGGGGGCGTGTGTGAGAGGG +AGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGACGGAGGGGCGTGTGTGAGAGGGAG +GGGGCGTGTGTGAGAGGGAGAGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGG +CGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGAGGCGTG +TGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGAG +AGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGA +GGGAGGGGCGTGTGTGAAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGAGAGGGAGGG +GCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGC +GTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTG +TGTGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGAGAGGGAGGGGGCGTGTGTGA +GAGGGAGAGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGAGGG +AGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGA +GAGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGCGTGTGTGAGAGGGAGAGG +CGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGAGGCGTGTGTGAGAGGGAGGGGCG +TGTGTGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGT +GTGAGAGGGAGAGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTG +AGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAG +AGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAG +GGAGGGGCGTGTGTGAAGGGAGGGGCGTGTGTGAGAGTGGGGGCGTGTGTGAGTTAGGGG +CGTGAGAGGTAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGAG +AGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGG +GAAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGCA +GGGGCGTGTGTGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGAGAGGGAGGGGCG +TGTGTGAGAGGGAGGGGCGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGT +GAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGAGAGGGAGGGGGCGTGTGTGAGGGA +GGGGCGTGTGTGAGAGGGAGGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGA +GGGGGTGTGTGTGAGACCGAGGGGGCGTGTAAGGGAGGGGGTGTGTGTGAGAGGGAAGCG +TGTGCACACACCAGCCCTAACCATGATCACTCTCTGGCCACCAAGATTTGGAACAGCAAC +TTCTGTCACATTTGAATGTTTTTAAAGCAGGTGCCACTTTGTTGCCATAAACCAAACCGT +AGTCTGT +>syndip_2_chr20:63948414-63948859 +ACAGAACACAGGTGCGGACAGGGAACGGCATCCTCAGAGCATGGTCAGGGGAGAAAAGCA +AGCTGGAAGGAGAGATGATTCCATCTGTATAAAATCCAGGAAACGAAGGACGCTCACCGC +CATGCGCCTCGGTGTGAGGAGGGAGGCGTGTGTGAGAGGGAGGGGATGTGTGTGAGAGGG +AGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGAGGGGTGTGTGTGAGAGGGAGGG +GCGTGTGTGAGAGGGAGGGGGCGTGTGTGAAAGGGAGGGGCGTGTGTGAGGGAGGGGCGT +GTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGAGGGAGGGGGCGTGTGT +GAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGAGAGTGGGGGCGTGTGTGAGG +GGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGTAGGGGCGTGTGTGAGAGGGAG +GGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGGGGGGGGCGTG +TGTGAGGGGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGAGAGGGAGGGGCGTGTGTGAG +AGGGAGGGGGCGTGTGTGTGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAAGG +GAGGGGTGTGTGTGAGAGTGGGGGCGTGTGTGAGAGGGGCGTGAGAGGTAGGGGCGTGTG +TGAGAGGGAGGGGTGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGA +GGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGCGTGTGTGAGAGGG +AGGGGCGTGTGTGAGAGTGGGGGCGTGTGTGGGGGGGCGTGTGTGAGGGGGGGCGTGTGT +GAGAGGTAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGCGTGTGTGAGAG +GCAGGGGCGTGTGTGGGGGGGGGCGTGTGTGAGGGGGGGGCGTGTGTGAGAGGGAGGGGG +CGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGT +GTGTGAGAGGCAGGGGCGTGTGTGGGGGGGGCGTGTGTGAGGGGGGCGTGTGAGAGGGAG +GGGCGTGTGTGGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCG +TGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAAGGGAGGGGTGTGTG +TGAGAGTGGGGGCGTGTGTGAGAGTTAGGGGCGTGAGAGGTAGGGGCGTGTGTGAGAGGG +AGGGGCGTGTGTGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGG +GCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGCGT +GTGCGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGGGAGGGGGCGTGTG +TGAGAGGGAGGGGCGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGTG +AGGGAGGGGCGTGAGAGGGAGGGGCGTGTGTGAGGGGGGGCGTGTGTGAGAGGTAGGGGC +GTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCG +TGTGTGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTG +TGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGT +GAAGGGAGGGGCGTGTGTGAGAGTGGGGGCGTGTGTGAGAGGGGCGTGAGAGGTAGGGGC +GTGTGTGAGAGGGAGGGGGCGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGT +GAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGAG +AGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAAGGGGCGTGTGAGAGG +GAGGGGCGTGTGTGAGAGGAAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAG +GGGGTGTGTGTGAGACCGAGGGGGCGTGTAAGGGAGGGGGTGTGTGTGAGAGGGAAGCGT +GTGCACACACCAGCCCTAACCATGATCACTCTCTGGCCACCAAGATTTGGAACAGCAACT +TCTGTCACATTTGAATGTTTTTAAAGCAGGTGCCACTTTGTTGCCATAAACCAAACCGTA +GTCTGT +>p:HG002_1_chr20:63948414-63948859 +ACAGAACACAGGTGCGGACAGGGAACGGCATCCTCAGAGCATGGTCAGGGGAGAAAAGCA +AGCTGGAAGGAGAGATGATTCCATCTGTATAAAATCCAGGAAACGAAGGACGCTCACCGC +CATGCGCCTCGGTGTGAGGAGGGAGGCGTGTGTGAGAGGGAGGGGATGTGTGTGAGAGGG +AGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGAGGGGTGTGTGTGAGAGGGAGGG +GCGTGTGTGAGAGGGAGGGGGCGTGTGTGAAAGGGAGGGGCGTGTGTGAGGGAGGGGCGT +GTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGAGGGAGGGGGCGTGTGT +GAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGAGAGTGGGGGCGTGTGTGAGG +GGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGTAGGGGCGTGTGTGAGAGGGAG +GGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGGGGGGGGCGTG +TGTGAGGGGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGAGAGGGAGGGGCGTGTGTGAG +AGGGAGGGGGCGTGTGTGTGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAAGG +GAGGGGTGTGTGTGAGAGTGGGGGCGTGTGTGAGAGGGGCGTGAGAGGTAGGGGCGTGTG +TGAGAGGGAGGGGTGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGA +GGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGCGTGTGTGAGAGGG +AGGGGCGTGTGTGAGAGTGGGGGCGTGTGTGGGGGGGCGTGTGTGAGGGGGGGCGTGTGT +GAGAGGTAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGCGTGTGTGAGAG +GCAGGGGCGTGTGTGGGGGGGGGCGTGTGTGAGGGGGGGGCGTGTGTGAGAGGGAGGGGG +CGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGT +GTGTGAGAGGCAGGGGCGTGTGTGGGGGGGGCGTGTGTGAGGGGGGCGTGTGAGAGGGAG +GGGCGTGTGTGGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCG +TGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAAGGGAGGGGTGTGTG +TGAGAGTGGGGGCGTGTGTGAGAGTTAGGGGCGTGAGAGGTAGGGGCGTGTGTGAGAGGG +AGGGGCGTGTGTGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGG +GCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGCGT +GTGCGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGGGAGGGGGCGTGTG +TGAGAGGGAGGGGCGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGTG +AGGGAGGGGCGTGAGAGGGAGGGGCGTGTGTGAGGGGGGGCGTGTGTGAGAGGTAGGGGC +GTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCG +TGTGTGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTG +TGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGT +GAAGGGAGGGGCGTGTGTGAGAGTGGGGGCGTGTGTGAGAGGGGCGTGAGAGGTAGGGGC +GTGTGTGAGAGGGAGGGGGCGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGT +GAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGAG +AGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAAGGGGCGTGTGAGAGG +GAGGGGCGTGTGTGAGAGGAAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAG +GGGGTGTGTGTGAGACCGAGGGGGCGTGTAAGGGAGGGGGTGTGTGTGAGAGGGAAGCGT +GTGCACACACCAGCCCTAACCATGATCACTCTCTGGCCACCAAGATTTGGAACAGCAACT +TCTGTCACATTTGAATGTTTTTAAAGCAGGTGCCACTTTGTTGCCATAAACCAAACCGTA +GTCTGT +>p:HG002_2_chr20:63948414-63948859 +ACAGAACACAGGTGCGGACAGGGAACGGCATCCTCAGAGCATGGTCAGGGGAGAAAAGCA +AGCTGGAAGGAGAGATGATTCCATCTGTATAAAATCCAGGAAACGAAGGACGCTCACCGC +CATGCGCCTCGGTGTGAGGAGGGAGGCGTGTGTGAGAGGGAGGGGATGTGTGTGAGAGGG +AGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGGTGTGTGTGAGAGGGAGGGGC +GTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGCAGGGGGCGTGTGTGTGAGGGGCGTGTG +TGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGGGGGGGCGTGTGTGAGA +GGTAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGCGTGTGTGAGAGGGA +GGGGCGTGTGTGTGAGGGAGGGGCGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGCAGGGG +CGTGTGTGTGAGGGAGGGGCGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTG +TGAGGGGGGGCGTGTGTGAGAGGTAGGGGCGTGTGTGGGAGGGGGCGTGTGTGAGAGGGA +GGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGACGGAGGGGCGTGTGTGAGAGGGAGG +GGGCGTGTGTGAGAGGGAGAGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGC +GTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGAGGCGTGT +GTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGAGA +GGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAG +GGAGGGGCGTGTGTGAAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGAGAGGGAGGGG +CGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCG +TGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGT +GTGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGAGAGGGAGGGGGCGTGTGTGAG +AGGGAGAGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAGGGGCGTGTGTGAGGGA +GGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAG +AGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGGGAGGGGGCGTGTGTGAGAGGGAGAGGC +GTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGAGGCGTGTGTGAGAGGGAGGGGCGT +GTGTGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTG +TGAGAGGGAGAGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGA +GAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGA +GGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGG +GAGGGGCGTGTGTGAAGGGAGGGGCGTGTGTGAGAGTGGGGGCGTGTGTGAGTTAGGGGC +GTGAGAGGTAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGAGA +GGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGG +AGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGCAG +GGGCGTGTGTGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGAGAGGGAGGGGCGT +GTGTGAGAGGGAGGGGCGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTG +AGAGGGAGGGGCGTGTGTGAGAGGGAGGGGCGTGAGAGGGAGGGGGCGTGTGTGAGGAAG +GGGCGTGTGTGAGAGGGAGGGGGGCGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAG +GGGGTGTGTGTGAGACCGAGGGGGCGTGTAAGGGAGGGGGTGTGTGTGAGAGGGAAGCGT +GTGCACACACCAGCCCTAACCATGATCACTCTCTGGCCACCAAGATTTGGAACAGCAACT +TCTGTCACATTTGAATGTTTTTAAAGCAGGTGCCACTTTGTTGCCATAAACCAAACCGTA +GTCTGT diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63948514-63948759/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63948514-63948759/haps.fa.ref.fa new file mode 100644 index 00000000..2636ea7d --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63948514-63948759/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:63948414-63948859 +ACAGAACACAGGTGCGGACAGGGAACGGCATCCTCAGAGCATGGTCAGGGGAGAAAAGCAAGCTGGAAGGAGAGATGATTCCATCTGTATAAAATCCAGGAAACGAAGGACGCTCACCGCCATGCGCCTCGGTGTGAGGAGGGAGGCGTGTGTGAGAGGGAGGGGATGTGTGTGAGAGGGAGGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAAGGGGCGTGTGTGAGAGGGAGGGGCGTGTGTGAGAGGGAGGGGGTGTGTGTGAGACCGAGGGGGCGTGTAAGGGAGGGGGTGTGTGTGAGAGGGAAGCGTGTGCACACACCAGCCCTAACCATGATCACTCTCTGGCCACCAAGATTTGGAACAGCAACTTCTGTCACATTTGAATGTTTTTAAAGCAGGTGCCACTTTGTTGCCATAAACCAAACCGTAGTCTGT diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63948514-63948759/msa.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63948514-63948759/msa.fa new file mode 100644 index 00000000..36e34a97 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63948514-63948759/msa.fa @@ -0,0 +1,205 @@ +>ref_chr20_63948414_63948859 +acagaacacaggtgcggacagggaacggcatcctcagagcatggtcaggggagaaaagca +agctggaaggagagatgattccatctgtataaaatccaggaaacgaaggacgctcaccgc +catgcgcctcggtgtgaggagggaggcgtgtgtgagagggaggggatgtgtgtgagaggg +agggggcgtgtgtgagagggaggggcgtgtgtgagagggaaggggcgtgtgtgagaggga +ggggcgtgtgtgagagggagggggtgtgtgtgaga------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------------ccgagggggcgtgtaa +gggagggggtgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcactc +tctggccaccaagatttggaacagcaacttctgtcacatttgaatgtttttaaagcaggt +gccactttgttgccataaaccaaaccgtagtctgt +>syndip_1_chr20:63948414-63948859 +acagaacacaggtgcggacagggaacggcatcctcagagcatggtcaggggagaaaagca +agctggaaggagagatgattccatctgtataaaatccaggaaacgaaggacgctcaccgc +catgcgcctcggtgtgaggagggaggcgtgtgtgagagggaggggatgtgtgtgagaggg +a-ggggcgtgtgtgagagggaggggcgtgtgtgag---ggaggggtgtgtgtgagaggga +ggggcgtgtgtgagagggagggggcgtgtgtgagaggcagggg-gcgtgtgtgtgagggg +cgtgtgtgagagggaggggcgtgtgtgagagggagggg-gcgtgtgtgagggggggcgtg +tgtgagaggtaggggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtg +agaggg-----------------aggggcgtgtgtgtgagggaggggcgtgtgagag-gg +agggggcgtgtgtgagaggcaggggcgtgtgtgtgagggaggggcgtgagagggaggggc +gtgtgtgagagggagggggcgtgtgtgagggggggcgtgtgtgagaggtaggggcgtgtg +t----gggagggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgt +gagacggaggggcgtgtgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtga +gagggaggggcgtgtgtgagggagggg---gcgtgtgagagggaggggcgtgtgtgagag +ggagggggcgtgtgtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagggag +ggggcgtgtgtgagagggaggggcgtgtgagaggg-aggggcgtgtgtgagagg------ +----gagggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgaa +gggaggggcgtgtgtgagagggagggggcgtgagagggaggggcgtgtgtgagagggagg +ggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggagggg +cgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgt +gtgagag--------ggagggggcgtgtgagagggagggggcgtgtgtgagagggagagg +cgtgtgtgagaggga-ggggcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtg +tgtgagagggagggggcgtgtgtgagagggagggggcgtgt-------------gtgaga +gggagaggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagaggga +gaggcgtgtgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgagagggagg +ggcgtgtgtgagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggc +gtgtgtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtg +tgtgagagggaggggcgtgtgtgagagggag--------------ggggcgtgtgtgaga +gggaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagagg +ga-ggggcgtgtgtgagagggaggggcgtgtgtgaagggaggggcgtgtgtgagagtggg +ggcgtgtgtgagttaggggcgtgagaggtaggggcgtgtgtgagagggaggggcgtgtgt +gagagggagggggcgtg-----agagggaggggcgtgtgtgagagggaggggcgtgtgtg +agagggaggggcgtgtgtgagagggaaggggcgtgtgtgagagggaggggcgtgtgtgag +agggaggggcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtgagaggga +gggg-gcgtgtgagagggaggggcgtgtgtgagagggaggggc--gtgtgagagggaggg +gcgtgtgtgagaggga-ggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggc +gtgagagggagggggcgtgtgtgagggaggggcgtgtgtgagagggaggggggcgtgtgt +gagagggagggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgtaa +gggagggggtgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcactc +tctggccaccaagatttggaacagcaacttctgtcacatttgaatgtttttaaagcaggt +gccactttgttgccataaaccaaaccgtagtctgt +>syndip_2_chr20:63948414-63948859 +acagaacacaggtgcggacagggaacggcatcctcagagcatggtcaggggagaaaagca +agctggaaggagagatgattccatctgtataaaatccaggaaacgaaggacgctcaccgc +catgcgcctcggtgtgaggagggaggcgtgtgtgagagggaggggatgtgtgtgagaggg +agggggcgtgtgtgagagggaggggcgtgtgtgag---agaggggtgtgtgtgagaggga +ggggcgtgtgtgagagggagggggcgtgtgtgaaagggaggggcgtgtgtgagggagggg +cgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtgagggagggggcgtg +tgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtgagagtgggggcgtgtgtg +agggggggcgtgtgtgagagggagggggcgtgtgtgagaggtaggggcgtgtgtgagagg +gaggggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtggggggggc +gtgtgtgag-gggggggcgtgtgtgagagggagggggcgtgtgagagggaggggcgtgtg +tgagagggagggggcgtgtgtgtgaggga-ggggcgtgtgtgagagggaggggcgtgtgt +ga---agggaggggtgtgtgtgagagtgggggcgtgtgtgagaggg--------gcgtga +gaggtaggggcgtgtgtgagagggaggggtgtgtgtgagagggaggggcgtgtgtgagag +gga-ggggcgtgtgtgag-ggagggggcgtgtgtgagagggaggggcgtgtgtgagggag 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+tgtgtgaagggaggggtgtgtgtgagagtgggggcgtgtgtgagagttaggggcgtgaga +ggtaggggcgtgtgtgagagggaggggcgtgtgtgaggga-ggggcgtgtgtgagaggga +ggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggagg +ggcgtgtgtgagggagggggcgtgtgcgagagggaggggcgtgtgtgagagggagggggc +gtgtgtgag-ggagggggcgtgtgtgagagggaggggcgtgtgagag-ggagggggcgtg +tgtgagaggcaggggcgtgtgtgtgagggaggggcgtgagagggaggggcgtgtgtga-- +-gggggggcgtgtgtgagaggtaggggcgtgtgtgagagggagggggcgtgtgtgagagg +gagggggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgt----------- +--------------------gtgagagggaggggcgtgtgtgagagggaggggcgtgtgt +gagagggagggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtg +a-agggaggggcgtgtgtgagagtg--ggggcgtgtgtgagaggg--------gcgtgag +aggtaggggcgtgtgtgagagggagggg-gcgtgagagggaggggcgtgtgtgagaggga +ggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagaggcaggg +gcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgt--------------- +gtgagagggaaggggcgtgtgagagggaggggcgtgtgtgagaggaaggggcgtgtgtga +ga---gggaggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgtaa 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b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63948514-63948759/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_63948414_63948859 2375 29 60 61 +syndip_1_chr20:63948414-63948859 2375 2478 60 61 +syndip_2_chr20:63948414-63948859 2375 4927 60 61 +p:HG002_1_chr20:63948414-63948859 2375 7377 60 61 +p:HG002_2_chr20:63948414-63948859 2375 9827 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63948514-63948759/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63948514-63948759/output.vcf.gz new file mode 100644 index 00000000..f81cefed Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63948514-63948759/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63948514-63948759/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:63948514-63948759/output.vcf.gz.tbi new file mode 100644 index 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a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64131804-64133956/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64131804-64133956/comp.vcf.gz new file mode 100644 index 00000000..6bbc6134 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64131804-64133956/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64131804-64133956/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64131804-64133956/comp.vcf.gz.tbi new file mode 100644 index 00000000..7a8ad9d1 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64131804-64133956/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64131804-64133956/haps.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64131804-64133956/haps.fa new file mode 100644 index 00000000..5709c8fa --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64131804-64133956/haps.fa @@ -0,0 +1,245 @@ +>ref_chr20_64131704_64134056 +AGGCTGTTGTAGGTGGGCCAGGAGGGGCTGGGCAGCCCATGAGGGTGAGGCTGAGACTCCACACTGAGCCCAGGTTTAGGGGACCTGGTGGGGGTCACAGCCTCCCCTGTCCCAGACTTCTCCTGGCCTCTCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCACTCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACTCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATGAGACCCCCTCACTGTCCACTCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCGCCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCGCCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACTCTCATGTCCTATGAGACCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCAACTCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCAAAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCAAAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCAAAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCATATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCATATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCAGGACCCTCTGCATTTGCTCCTTGGGTTCCCGGAACTTGAGCTTGGGTCTTGGTCCACAGCAGCTTTGGGAAGGGCCCTCGGCTGCTTTTTGCTTCAGCAGCTGGGGAGCAGTTAACTTTCAGACCCGGCCC 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a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64131804-64133956/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64131804-64133956/haps.fa.ref.fa new file mode 100644 index 00000000..1dca2959 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64131804-64133956/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:64131704-64134056 +AGGCTGTTGTAGGTGGGCCAGGAGGGGCTGGGCAGCCCATGAGGGTGAGGCTGAGACTCCACACTGAGCCCAGGTTTAGGGGACCTGGTGGGGGTCACAGCCTCCCCTGTCCCAGACTTCTCCTGGCCTCTCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCACTCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACTCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATGAGACCCCCTCACTGTCCACTCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCGTGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCGCCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCGCCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATGAGACCCCCTCACTGTCCACTCTCATGTCCTATGAGACCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCAACTCTCATGTCCTATGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCAAAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCAAAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCAAAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCATATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACCCATATGGCCTGTAGAGACCCCCTCACTGTCCACCCTCAGGACCCTCTGCATTTGCTCCTTGGGTTCCCGGAACTTGAGCTTGGGTCTTGGTCCACAGCAGCTTTGGGAAGGGCCCTCGGCTGCTTTTTGCTTCAGCAGCTGGGGAGCAGTTAACTTTCAGACCCGGCCC diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64131804-64133956/msa.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64131804-64133956/msa.fa new file mode 100644 index 00000000..ceae29cd --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64131804-64133956/msa.fa @@ -0,0 +1,400 @@ +>ref_chr20_64131704_64134056 +aggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactcc +acactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagacttc +tcctggcctctctcatgtcctatgagaccccctcactgtccaccctcatgtcctgtagag +accccctcactgtccactctcatggcctatagagaccccctcactgtccaccctcatggc +ctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccacc +ctcatgt----------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------cctatagagaccccctcactgtccaccctcatg +gcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccac +cctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctca +ctgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctgtagaga +ccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcgtgtcct +atagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccct +catgtcctat-gagaccccctcactgtccaccctcatgtcctatagagaccccctcactg +tccactctcatgtcctatagagaccccctcactgtccaccctcatggcctat-------- +---------------------------gagaccccctcactgtccactctcatggcctat +agagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctca +tggcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtc +caccctcatggcctgtagagaccccctcactgtccaccctcatggcctatgagaccccct +cactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctatagag +accccctcactgtccaccctcgtgtccta------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------tagagaccccctcactgtccaccctcatgtcctatagagacc +ccctcactgtccgccctcatgtcctatgagaccccctcactgtccaccctcatgtcctat +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------------------agaga +ccccctcactgtccaccctcatggcctgtagagaccccctcactgtccgccctcatgtcc +tat--------------------------------------------------------- +------------gagaccccctcactgtccaccctcatgtcctgtagagaccccctcact +gtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccc +cctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctat +-gaga-cccctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccctca +tgtcctat-gagaccccctcactgtccactctcatgtcctatgaga-------------- +--------------------------------------------------------cccc +tcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctgtag +agaccccctcactgtcaactctcatgtcctatgagaccccctcactgtccaccctcatgt +cctatagagaccccctcactgtccaccctcatgtccaaagagaccccctcactgtccacc +ctcatggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcac +tgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtcc--------- +-------------------------aaagagaccccctcactgtccaccctcatggcctg +tagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctc +atgtcctatagagaccccctcactgtccaccctcatgtccaaagagaccccctcactgtc +caccctcatggcctgtagagaccccctcactgtccacccatatggcctgtagagaccccc +tcactgtccaccctcatgtcctata----------------------------------- +-------------------------------gagaccccctcactgtccaccctcatggc +ctgtagagaccccctcactgtccaccctcatggcctgt---------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------agagaccccctcactgtccaccctcatggcctgtagagaccc +cctcactgtccaccctcatggcctgtagagaccccctcactgtccacccatatggcctgt +agagaccccctcactgtccaccctcaggaccctctgcatttgctccttgggttcccggaa +cttgagcttgggtcttggtccacagcagctttgggaagggccctcggctgctttttgctt +cagcagctggggagcagttaactttcagacccggccc +>syndip_1_chr20:64131704-64134056 +aggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactcc +acactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagacttc +tcctggcctctctcatgtcctatgagaccccctcactgtccaccctcatgtcctgtagag +accccctcactgtccactctcatggcctatagagaccccctcactgtcaactctcatgtc +ctat-gagaccccctcactgtccactctcatggcctgtagagaccccctcactgtccacc +ctcatgt----------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------cctatagagaccccctcactgtccaccctcatg +gcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccac +cctcatggcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctca +ctgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagaga +ccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcgtgtcct +atagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccct +catgtcctatagagaccccctcactgtccaccctcatgtcctgtagagaccccctcactg +tccaccctcatgtcctat------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtc +caccctcatggcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccct +cactgtccactctcatgtcctatgagaccccctcactgtccaccctcgtgtcctatagag +accccctcactgtccaccctcatgtcctat------------------------------ +------------------------------------------------------------ +---------------------------------------------agagaccccctcact +gtccaccctcatggcctgtagagaccccctcactgtccaccctcgtgtcctatagagacc +ccctcactgtccaccctcatgtcctatgagaccccctcactgtccactctcatgtcctat +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------------------------gaga +ccccctcactgtccactctcatggcctgtagagaccccctcactgtccaccctcatgtcc +tgt--------------------------------------------------------- +-----------agagaccccctcactgtccaccctcgtgtcctatagagaccccctcact +gtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccc +cctcactgtccaccctcatgtcctatagagaccccctcactgtccactctcatgtcctat +agagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctca +tggcctgtagagaccccctcactgtccactctcatggcctatagagaccccctcactgtc +caccctcatggcctatagagaccccctcactgtccaccctcatggcctgtagagaccccc +tcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctgtag +agaccccctcactgtccaccctcatggcctatgagaccccctcactgtccactctcatgg +cctgtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccacc +ctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccccctcac +tgtccaccctcatgtcctatagagaccccctcactgtccgccctcatgtcctatgagacc +ccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctg +tagagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctc +atgtcctatagagaccccctcactgtccgccctcatgtcctatgagaccccctcactgtc +caccctcatgtcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccc +tcactgtccaccctcatgtcctatg-agaccccctcactgtccaccctcatgtcctatga +gaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcgtgtc +ctatagagaccccctcactgtcaactctcatgtcctatagagaccccctcactgtccacc +ctcgtgtcctatgagaccccctcactgtccaccctcatgtcctatagagaccccctcact +gtccaccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctat-gagacc +ccctcactgtccactctcatgtcctatgagaccccctcactgtccaccctcgtgtcctat +agagaccccctcactgtcaactctcatgtcctatagagaccccctcactgtccaccctcg +tgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtc +caccctcatggcctgtagagaccccctcactgtcaactctcatgtcctatgagaccccct +cactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtccaa-aga +gaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgg +cctgtagagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccac +cctcat-gtccaaagagaccccctcactgtccaccctcatggcctgtagagaccccctca +ctgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctatagaga +ccccctcactgtccaccctcatgtccaaagagaccccctcactgtccaccctcatggcct +gtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccactctc +atgtcctatgagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtc +caccctcatgtcctatgagaccccctcactgtccaccctcgtgtcctatagagaccccct +cactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctatagag +accccctcactgtccactctcatgtcctatgagaccccctcactgtccaccctcatgtcc +tatgagaccccctcactgtccacccatatggcctgtagagaccccctcactgtccaccct +catgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactg +tccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccc +cctcactgtccaccctcatggcctgtagagaccccctcactgtccacccatatggcctgt +agagaccccctcactgtccaccctcaggaccctctgcatttgctccttgggttcccggaa +cttgagcttgggtcttggtccacagcagctttgggaagggccctcggctgctttttgctt +cagcagctggggagcagttaactttcagacccggccc +>syndip_2_chr20:64131704-64134056 +aggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactcc +acactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagacttc +tcctggcctctctcatgtcctatgagaccccctcactgtccaccctcatgtcctgtagag +accccctcactgtccactctcatggcctatagagaccccctcactgtccaccctcatggc +ctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccacc +ctcatgtcctatagagacccctcactgtccaccctcatggcctatgagaccccctcactg +tccactctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccc +cctcactgtccaccctcatgtcctatagagacccctcactgtccaccctcatggcctatg +agaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatg +gcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccac +cctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctca +ctgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctgtagaga +ccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcgtgtcct +atagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccct +catgtcctat-gagaccccctcactgtccaccctcatgtcctatagagaccccctcactg +tccactctcatgtcctatagagaccccctcactgtccaccctcatggcctatagagaccc +cctcactgtccaccctcatggcctgtagagaccccctcactgtccactctcatggcctat +agagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctca +tggcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtc +caccctcatggcctgtagagaccccctcactgtccaccctcatggcctatgagaccccct +cactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctatagag +accccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtc +ctatagagaccccctcactgtccgccctcatgtcctatgagaccccctcactgtccaccc +tcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcact +gtccaccctcatgtcctgtagagaccccctcactgtccaccctcatgtcctatagagacc +ccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctat +gagaccccctcactgtccaccctcatgtcctatgagacccctcactgtccaccctcatgt +cctatgagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccactc +tcatgtcctatgagaccccctcactgtccaccctcatggcctgtagagaccccctcactg +tccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccc +cctcactgtccaccctcatggcctgtagagaccccctcactgtcaactctcatgtcctat +gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcat +gtccaaagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtcca +ccctcatggcctgtagagaccccctcactgtccaccctcatggcctatagagaccccctc +actgtccaccctcatgtccaaagagaccccctcactgtccaccctcatggcctgtagaga +ccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcc +tatagagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccc +tcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccccctcact +gtccaccctcatggcctatagagaccccctcactgtccaccctcatgtcctatgagaccc +cctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctat +agagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcg +tgtcctatagagaccccctcactgtccaccctcatggcctatagag-------------- +------------------------------------------------------accccc +tcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcctat-- +-------------------------------agagaccccctcactgtccaccctcatgg +cctatagagaccccctcactgtccaccctcatgtccaaagagaccccctcactgtccacc +ctcatggcctgtagagaccccctcactgtccacccatatggcctgtagagaccccctcac +tgtccaccctcatgtcct------------------------------------------ +-------------------------atagagaccccctcactgtccaccctcatggcctg +tagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctc +atggcctgtagagaccccctcactgtccaccctcatggcctatgagaccccctcactgtc +caccctcatggcctgtagagaccccctcactgtccaccctcatgtcctatagaga-cccc +tcactgtccaccctcatgtcctata----------------------------------- +-------------------------------gagaccccctcactgtccaccctcgtgtc +ctatagagaccccctcactgtccaccctcatgtcctat---------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------gagaccccctcactgtccaccctcatgtcctatagag +accccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcc +ta---------------------------------tagagaccccctcactgtccaccct +catgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactg +tccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccc +cctcactgtccacccatatggcctgtagagaccccctcactgtccacccatatggcctgt +agagaccccctcactgtccaccctcaggaccctctgcatttgctccttgggttcccggaa +cttgagcttgggtcttggtccacagcagctttgggaagggccctcggctgctttttgctt +cagcagctggggagcagttaactttcagacccggccc +>p:HG002_1_chr20:64131704-64134056 +aggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactcc +acactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagacttc +tcctggcctctctcatgtcctatgagaccccctcactgtccaccctcatgtcctgtagag +accccctcactgtccactctcatggcctatagagaccccctcactgtccaccctcatggc +ctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccacc +ctcatgtcctatagagacccctcactgtccaccctcatggcctatgagaccccctcactg +tccactctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccc +cctcactgtccaccctcatgtcctatagagacccctcactgtccaccctcatggcctatg +agaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatg +gcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccac +cctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctca +ctgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctgtagaga +ccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcgtgtcct +atagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccct +catgtcctat-gagaccccctcactgtccaccctcatgtcctatagagaccccctcactg +tccactctcatgtcctatagagaccccctcactgtccaccctcatggcctat-------- +---------------------------gagaccccctcactgtccactctcatggcctat +agagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctca +tggcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtc +caccctcatggcctgtagagaccccctcactgtccaccctcatggcctatgagaccccct +cactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctatagag +accccctcactgtccaccctcgtgtccta------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------tagagaccccctcactgtccaccctcatgtcctatagagacc +ccctcactgtccgccctcatgtcctatgagaccccctcactgtccaccctcatgtcctat +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------------------agaga +ccccctcactgtccaccctcatggcctgtagagaccccctcactgtccgccctcatgtcc +tat--------------------------------------------------------- +------------gagaccccctcactgtccaccctcatgtcctgtagagaccccctcact +gtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccc +cctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctat +-gaga-cccctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccctca +tgtcctat-gagaccccctcactgtccactctcatgtcctatgaga-------------- +--------------------------------------------------------cccc +tcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctgtag +agaccccctcactgtcaactctcatgtcctatgagaccccctcactgtccaccctcatgt +cctatagagaccccctcactgtccaccctcatgtccaaagagaccccctcactgtccacc +ctcatggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcac +tgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtcc--------- +-------------------------aaagagaccccctcactgtccaccctcatggcctg +tagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctc +atgtcctatagagaccccctcactgtccaccctcatgtccaaagagaccccctcactgtc +caccctcatggcctgtagagaccccctcactgtccacccatatggcctgtagagaccccc +tcactgtccaccctcatgtcctata----------------------------------- +-------------------------------gagaccccctcactgtccaccctcatggc +ctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccacc +ctcatgtcctatgagaccccctcactgtccaccctcatgtcctatagagaccccctcact +gtccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcctat------- +--------------------------agagaccccctcactgtccaccctcgtgtcctat +agagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctca +tgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtc +caccctcatggcctatagagaccccctcactgtccaccctcatgtcctatgagaccccct +cactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctataga +gaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatg- +------------------------------------------------------------ +-----------------------------------------tcctatagagaccccctca +ctgtccaccctcatgtcctgtagagaccccctcactgtccaccctcatggcctatagaga +ccccctcactgtccaccctcatggcctatgagaccccctcactgtccaccctcatggcct +gtagagaccccctcactgtccaccctcatgtcctatagagacccctcactgtccaccctc +atgtcctata-------------------------------------------------- +----------------gagaccccctcactgtccaccctcgtgtcctatagagaccccct +cactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctatagag +accccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcc +ta---------------------------------tagagaccccctcactgtccaccct +catgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactg +tccaccctcatgtcctatagagaccccctcactgtccaccctcgtggcctgtagagaccc +cctcactgtccaccctcatggcctgtagagaccccctcactgtccacccatatggcctgt +agagaccccctcactgtccaccctcaggaccctctgcatttgctccttgggttcccggaa +cttgagcttgggtcttggtccacagcagctttgggaagggccctcggctgctttttgctt +cagcagctggggagcagttaactttcagacccggccc +>p:HG002_2_chr20:64131704-64134056 +aggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactcc +acactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagacttc +tcctggcctctctcatgtcctatgagaccccctcactgtccaccctcatgtcctgtagag +accccctcactgtccactctcatggcctatagagaccccctcactgtccaccctcatggc +ctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccacc +ctcatgt----------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------cctatagagaccccctcactgtccaccctcatg +gcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccac +cctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctca +ctgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctgtagaga +ccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcgtgtcct +atagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccct +catgtcctat-gagaccccctcactgtccaccctcatgtcctatagagaccccctcactg +tccaccctcatgtcctat------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtc +caccctcatggcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccct +cactgtccactctcatgtcctatgagaccccctcactgtccaccctcgtgtcctatagag +accccctcactgtccaccctcatgtcctat------------------------------ +------------------------------------------------------------ +---------------------------------------------agagaccccctcact +gtccaccctcatggcctgtagagaccccctcactgtccaccctcgtgtcctatagagacc +ccctcactgtccaccctcatgtcctatgagaccccctcactgtccactctcatgtcctat +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------------------------gaga +ccccctcactgtccactctcatggcctgtagagaccccctcactgtccaccctcatgtcc +tgt--------------------------------------------------------- +-----------agagaccccctcactgtccaccctcgtgtcctatagagaccccctcact +gtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccc +cctcactgtccactctcatgtcctatagagaccccctcactgtccaccctcatggcctat +-gagaccccctcactgtccactctcatggcctatagagaccccctcactgtccaccctca +tggcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtc +caccctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccc +tcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtcctat-g +agaccccctcactgtccactctcatgtcctatgagaccccctcactgtccactctcatgg +cctgtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccacc +ctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccccctcac +tgtccaccctcatgtcctatagagaccccctcactgtccgccctcatgtcctatgagacc +ccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctg +tagagaccccctcactgtccgccctcatgtcctatagagaccccctcactgtccaccctc +atgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtc +caccctcatgtcctatagagaccccctcactgtccaccctcatgtcctgtagagaccccc +tcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatga +gaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtc +ctatgaga--cccctcactgtccaccctcatgtcctat-gagaccccctcactgtccacc +ctcatgtcctatgagaccccctcactgtccactctcatgtcctatgaga--cccctcact +gtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagacc +ccctcactgtcaactctcatgtcctatgagaccccctcactgtccaccctcatgtcctat +agagaccccctcactgtccaccctcatgtcc-aaagagaccccctcactgtccaccctca +tggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtc +caccctcatggcctatagagaccccctcactgtccaccctcatgtccaaagagaccccct +cactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctgtaga +gaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatg- +tccaaagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccac +ccatatggcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctca +ctgtccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctatagaga +ccccctcactgtccactctcatgtcctatgagaccccctcactgtccaccctcatggcct +atagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccactctc +atgtcctatgagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtc +caccctcatgtcctatgagaccccctcactgtccaccctcgtgtcctatagagaccccct +cactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctatagag +accccctcactgtccactctcatgtcctatgagaccccctcactgtccaccctcatgtcc +tatgagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccct +catgtcctat-gagaccccctcactgtccaccctcatgtcctatagagaccccctcactg +tccaccctcatgtcctgtagagaccccctcactgtccaccctcatggcctgtagagaccc +cctcactgtccaccctcatggcctgtagagaccccctcactgtccacccatatggcctgt +agagaccccctcactgtccaccctcaggaccctctgcatttgctccttgggttcccggaa +cttgagcttgggtcttggtccacagcagctttgggaagggccctcggctgctttttgctt +cagcagctggggagcagttaactttcagacccggccc diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64131804-64133956/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64131804-64133956/msa.fa.fai new file mode 100644 index 00000000..de2c70e6 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64131804-64133956/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_64131704_64134056 4717 29 60 61 +syndip_1_chr20:64131704-64134056 4717 4859 60 61 +syndip_2_chr20:64131704-64134056 4717 9689 60 61 +p:HG002_1_chr20:64131704-64134056 4717 14520 60 61 +p:HG002_2_chr20:64131704-64134056 4717 19351 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64131804-64133956/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64131804-64133956/output.vcf.gz new file mode 100644 index 00000000..c8c019c9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64131804-64133956/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64131804-64133956/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64131804-64133956/output.vcf.gz.tbi new file mode 100644 index 00000000..896125fe Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64131804-64133956/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/base.vcf.gz new file mode 100644 index 00000000..5bcf67e9 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/base.vcf.gz.tbi new file mode 100644 index 00000000..6092728c Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/comp.vcf.gz new file mode 100644 index 00000000..3d42a7b6 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/comp.vcf.gz.tbi new file mode 100644 index 00000000..69c81368 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/haps.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/haps.fa new file mode 100644 index 00000000..a21829fb --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/haps.fa @@ -0,0 +1,218 @@ +>ref_chr20_64173309_64176630 +CAGAGGTGGGCTGTTGGACAGGTGCGGCTGATAGAGTGGGTGTCTTTTGTGGGCTTCTCCCCAGCCTGTGGCCTGGCCTAGTCAGTAGAGATGGTCAGGGGAGCAGGAGGGAGCCCATACCCCAGTGCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTCCCTTTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTCCCTTTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCTTCTAGCATCTTTCCTGCTCCCTGGTAGCCTCTTGGGAGCCACCTATTTCTGGAGGTCCCCACTCTGGGTTCCTTGTCCTGGGTGTGGGGCGAATGTGCTGGACTGGGGTCACAGCATTGAACCCCACTTGGAGCTGAGGA +>syndip_1_chr20:64173309-64176630 +CAGAGGTGGGCTGTTGGACAGGTGCGGCTGATAGAGTGGGTGTCTTTTGTGGGCTTCTCC +CCAGCCTGTGGCCTGGCCTAGTCAGTAGAGATGGTCAGGGGAGCAGGAGGGAGCCCATAC +CCCAGTGCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTC +CCTTTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTCCCTTTAG +TTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTC +CATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCTAGTTGTGTCCATTTCCCCT +CCCTGACTTCTCCTCCTGCAGCATCCTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGAC +TTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCT +CCTGCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAG +CATCCTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCC +TGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTG +TCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCC +CTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCT +TCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCAT +CTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGT +TGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATT +TCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCT +GGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCT +GTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCC +TAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTC +CATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCT +CCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTC +TCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGACTTCTCCTCCTGCA +GCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTT +TCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGT +GTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTCCCCCT +CCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTCC +TGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCT +TTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGT +CCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCC +TCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTT +CTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGC +ATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCT +GTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGT +CCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCC +TCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCGT +CTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGC +AGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTC +CCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGT +CCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCC +TCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGACTT +CTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCC +TGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCT +TTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAG +TTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTC +CCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTT +CTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGC +ATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCT +GTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCTAGTTGTGTCCA +TTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCC +CTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCGTCTC +CTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGC +ATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCT +GTAGTTGTGTCCATTCCCCCTCCCTGGCGTCTCCTGCAGCATCTTTCCCTGTAGTTGTGT +CCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCC +TCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGG +CTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCC +TGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCT +TTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCTTCTAGCATCTTTCCTGC +TCCCTGGTAGCCTCTTGGGAGCCACCTATTTCTGGAGGTCCCCACTCTGGGTTCCTTGTC +CTGGGTGTGGGGCGAATGTGCTGGACTGGGGTCACAGCATTGAACCCCACTTGGAGCTGA +GGA +>syndip_2_chr20:64173309-64176630 +CAGAGGTGGGCTGTTGGACAGGTGCGGCTGATAGAGTGGGTGTCTTTTGTGGGCTTCTCC +CCAGCCTGTGGCCTGGCCTAGTCAGTAGAGATGGTCAGGGGAGCAGGAGGGAGCCCATAC +CCCAGTGCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTC +CCTTTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTAGTTG +TGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCAT +TTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCT +CCCTGACTTCTCCTCCTGCAGCATCCTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGC +TTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCA +GCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCC +CTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGT +GTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCT +CCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTC +TCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCA +GCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCC +CTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGT +GTCCATTCCCCCTCCCTGACTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCC +CCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTC +TCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCT +TTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAG +TTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTC +CCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGG +CTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGC +AGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTC +CCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTG +TGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCC +TCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTT +CTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCCTGCAGC +ATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTA +GTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGT +CCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCC +CTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTG +CAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTT +CCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTT +GTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCTAGTTGTGTCCATTTCCC +CTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCT +TCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCGTCTCCTCCTG +CAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTT +CCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTT +GTGTCCATTCCCCCTCCCTGGCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTT +CCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTG +GCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTC +TTCTAGCATCTTTCCTGCTCCCTGGTAGCCTCTTGGGAGCCACCTATTTCTGGAGGTCCC +CACTCTGGGTTCCTTGTCCTGGGTGTGGGGCGAATGTGCTGGACTGGGGTCACAGCATTG +AACCCCACTTGGAGCTGAGGA +>p:HG002_1_chr20:64173309-64176630 +CAGAGGTGGGCTGTTGGACAGGTGCGGCTGATAGAGTGGGTGTCTTTTGTGGGCTTCTCC +CCAGCCTGTGGCCTGGCCTAGTCAGTAGAGATGGTCAGGGGAGCAGGAGGGAGCCCATAC +CCCAGTGCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTC +CCTTTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTAGTTG +TGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCAT +TTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCT +CCCTGACTTCTCCTCCTGCAGCATCCTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGC +TTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCA +GCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCC +CTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGT +GTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCC +CCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGC +TTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGACTTCTCCTCCT +GCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCCTGCAGCAT +CTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGT +TGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCC +ATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCT +GGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCA +GCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCC +CTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGT +GTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCC +CCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGC +TTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCA +GCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCC +CTGTAGTTGTGTCCATTCCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGT +TGTGTCCATTCCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATT +TCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCT +GGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCA +GCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCC +CTGTAGTTGTGTCCATTCCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTAGTTGT +GTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCT +CCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTC +TCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCA +TCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCTAG +TTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCAT +TTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCC +TGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTC +TCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCA +TCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTCCTCCTGCAGCATCTTTCCCTG +TAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTC +CATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCT +CCCTGGCTTCTCCTCTTCTAGCATCTTTCCTGCTCCCTGGTAGCCTCTTGGGAGCCACCT +ATTTCTGGAGGTCCCCACTCTGGGTTCCTTGTCCTGGGTGTGGGGCGAATGTGCTGGACT +GGGGTCACAGCATTGAACCCCACTTGGAGCTGAGGA +>p:HG002_2_chr20:64173309-64176630 +CAGAGGTGGGCTGTTGGACAGGTGCGGCTGATAGAGTGGGTGTCTTTTGTGGGCTTCTCC +CCAGCCTGTGGCCTGGCCTAGTCAGTAGAGATGGTCAGGGGAGCAGGAGGGAGCCCATAC +CCCAGTGCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTC +CCTTTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTCCCTTTAG +TTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTAGTTGTGTCCAT +TTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCT +CCCTGGCTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCTCCCTGAC +TTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCT +CCTGCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAG +CATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCC +TGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCCTTCCCTGTAGTTGTG +TCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCC +CTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCT +TCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAG +CATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCT +AGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCC +ATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCT +GGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCT +CCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTT +TCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGT +GTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCC +CCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGC +TTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGACTTCTCCTCCT +GCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCCTGCAGCAT +CTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGT +TGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTCCC +CCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGC +TCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCA +TCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTG +TGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTC +CCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGG +CTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGC +AGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTC +CCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTG +TGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTC +CCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGG +CGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCC +TGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCT +TTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTG +TGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTC +CCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGA +CTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCGTCTCC +TCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCA +TCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTG +TAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCAT +TTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGG +CTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGC +AGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTC +CCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCTAGTTGTGT +CCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCC +TCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCGT +CTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGC +AGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTC +CCTGTAGTTGTGTCCATTCCCCCTCCCTGGCGTCTCCTGCAGCATCTTTCCCTGTAGTTG +TGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTC +CCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCC +TGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTC +TCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCA +TCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCTTCTAGCATCTTTCC +TGCTCCCTGGTAGCCTCTTGGGAGCCACCTATTTCTGGAGGTCCCCACTCTGGGTTCCTT +GTCCTGGGTGTGGGGCGAATGTGCTGGACTGGGGTCACAGCATTGAACCCCACTTGGAGC +TGAGGA diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/haps.fa.ref.fa new file mode 100644 index 00000000..296e951e --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:64173309-64176630 +CAGAGGTGGGCTGTTGGACAGGTGCGGCTGATAGAGTGGGTGTCTTTTGTGGGCTTCTCCCCAGCCTGTGGCCTGGCCTAGTCAGTAGAGATGGTCAGGGGAGCAGGAGGGAGCCCATACCCCAGTGCCTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTCCCTTTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTCCCTTTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCTTGTAGTTGTGTCCATTTCCCCTCCCTGACTTCTCCTCCTGCAGCATCCTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGACTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGTAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCGTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTCCCCCTCCCTGGCTTCTCCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTGCAGCATCTTTCCCTGTAGTTGTGTCCATTTCCCCTCCCTGGCTTCTCCTCTTCTAGCATCTTTCCTGCTCCCTGGTAGCCTCTTGGGAGCCACCTATTTCTGGAGGTCCCCACTCTGGGTTCCTTGTCCTGGGTGTGGGGCGAATGTGCTGGACTGGGGTCACAGCATTGAACCCCACTTGGAGCTGAGGA diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/msa.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/msa.fa new file mode 100644 index 00000000..a985dea5 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/msa.fa @@ -0,0 +1,420 @@ +>ref_chr20_64173309_64176630 +cagaggtgggctgttggacaggtgcggctgatagagtgggtgtcttttgtgggcttctcc +ccagcctgtggcctggcctagtcagtagagatggtcaggggagcaggagggagcccatac +cccagtgcctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatccttc +cctttagttgtgtccatttcccctccctgacttctcctcctgcagcatccttccctttag +ttgtgtccatttcccctccctgacttctcctcctgcagcatctttcc---tagttgtgtc +catttcccctccctgacttctcctcctgcagcatctttccttgtagttgtgtccatttcc +cctccctggcttctcctcctgcagcatctttccttgtagttgtgtccatttcccctccct +gacttctc---------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------ctcctgcagcatccttccctgtagtt +gtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccattt +cccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctg +gcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctg +tagcatctttccctgtagttgtgtccattccccctccctggcttctcctgtagcatcttt +cctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtg +tccatttcccctccctggcttctcctgtagcatctttcc---tagttgtgtccatttccc +ctccctggcttctcctcctgcagcatctttccctgtagttgtgtccattccccctccctg +gcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtag +catctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgt +agttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcc +atttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctc +cctggcttctcctgtagcatctttccctgtagttgtgtccattccccctccctgacttct +cctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcgtctcctcctg +cagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatcttt +cctagttgtgtccatttcccctccctggcttctc-------------------------- +------------------------------------------------------------ +-----ctcctgcagcatctttccctgtagttgtgtccattccccctccctggcttctcct +gtagcatctttcc---tagttgtgtccatttcccctccctggcttctcctgtagcatctt +tcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgt +gtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcc +cctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctccctggc +ttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgc- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +agcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttc +cctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttg +tgtcca--------------------------------------------------tttc +ccctccctggcttctcctgtagcatctttccctgtagttgtgtccattccccctccctgg +cgtctcctcctgcagcatctttccctgtagttgtgtccattccccctccctgg---cttc +tcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagca +tctttccctg-------------------------------------------------- +-----------------------------------------------tagttgtgtccat +ttcccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctgg +cttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgt +agcatctttccctgtagttgtgtccattccccctccctgacttctc-------------- +------------------------------------------------------------ +-----------------------ctcctgcagcatctttccctgtagttgtgtccatttc +ccctccctggcgtctc-------------------------------------------- +---ctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgt +agcatctttcc---tagttgtgtccatttcccctccctggcttctcctcctgcagcatct +ttccctgtagttgtgtccattccccctccctggcttctcctgtagcatctttcc------ +-----------------------------------------------tagttgtgtccat +ttcccctccctggcttctcctgtagcatctttcct------------------------- +-------------------------agttgtgtccatttcccctccctggcttctcctgc +agcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttc +cctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttg +tgtccatttcccctccctggcttctcctgcagcatctttcc---tagttgtgtccatttc +ccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctgg +---cttctcctgtagcatctttccctgtagttgtgtccattccccctccctggcgtctcc +tcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagca 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+------------------------------------------------------------ +------------------------------------------------------------ +agcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttc +cctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttg +tgtcca--------------------------------------------------tttc +ccctccctggcttctcctgtagcatctttccctgtagttgtgtccattccccctccctgg +cgtctcctcctgcagcatctttccctgtagttgtgtccattccccctccctgg---cttc +tcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagca +tctttccctg-------------------------------------------------- +-----------------------------------------------tagttgtgtccat +ttcccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctgg +cttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgt +agcatctttccctgtagttgtgtccattccccctccctgacttctc-------------- +------------------------------------------------------------ +-----------------------ctcctgcagcatctttccctgtagttgtgtccatttc +ccctccctggcgtctc-------------------------------------------- +---ctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgt +agcatctttcc---tagttgtgtccatttcccctccctggcttctcctcctgcagcatct +ttccctgtagttgtgtccattccccctccctggcttctcctgtagcatctttcc------ +-----------------------------------------------tagttgtgtccat +ttcccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctgg +cttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgc +agcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttc +cctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttcc---tagttg +tgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttc +ccctccctggcttctcctgtagcatctttccctgtagttgtgtccattccccctccctgg +cgtctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctgg---cttc +tcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagca +tctttccctgtagttgtgtccattccccctccctggcgtctcctgcagcatctttccctg +tagttgtgtccatttcccctccctgg---cttctcctgcagcatctttccctgtagttgt +gtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatt +ccccctccctggctt--------------------------------------------- +--ctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcct +gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctt +tccctgtagttgtgtccatttcccctccctggcttctcctcttctagcatctttcctgct +ccctggtagcctcttgggagccacctatttctggaggtccccactctgggttccttgtcc +tgggtgtggggcgaatgtgctggactggggtcacagcattgaaccccacttggagctgag +ga diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/msa.fa.fai new file mode 100644 index 00000000..94215b41 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_64173309_64176630 4922 29 60 61 +syndip_1_chr20:64173309-64176630 4922 5068 60 61 +syndip_2_chr20:64173309-64176630 4922 10107 60 61 +p:HG002_1_chr20:64173309-64176630 4922 15147 60 61 +p:HG002_2_chr20:64173309-64176630 4922 20187 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/output.vcf.gz new file mode 100644 index 00000000..fa755225 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/output.vcf.gz.tbi new file mode 100644 index 00000000..b3e0327d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:64173409-64176530/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/base.vcf.gz new file mode 100644 index 00000000..ba21ddad Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/base.vcf.gz.tbi new file mode 100644 index 00000000..1611cbcc Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/comp.vcf.gz new file mode 100644 index 00000000..f56b72ce Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/comp.vcf.gz.tbi new file mode 100644 index 00000000..ea1f0489 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/haps.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/haps.fa new file mode 100644 index 00000000..2cc212bc --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/haps.fa @@ -0,0 +1,128 @@ +>ref_chr20_8661811_8662758 +GCCAACCTACGTTAAGTAATTCATAACTTCAGTATTTAATAAATCTTCAGTGAAAGGCAAGAGGCTACACACAGTGACAGACCCAGAGATAAACCCTGTGCCCCTAGAGATTTGCACTCCTCTTAAAAGTGTATATATATATAATTATATAATTATTTATTATATAATTATATATAATTATATAATTATTTATTATATAATTATATATAATATACAATTATTTATTATATAATTATATATAATTATATATTTATTATATTTATTATACAGTTATATAATAAATAATTATATAATTATATATAATTATATATTATTTATTATCTAATTCTATATTAAATATAATTATTTATTATCTAATTCTATATTATATATAATTATTTATTATATAATTCTATATTATATATAATTATTATATAATTCTATATATAATTATTTATTATATAATTCTATACATAAGTATTTATTATATAATTATGTATATAATTATTTATTATATAATTATGTATAATATGTAATTATTTATTATATAATTATGTATAATATGTAATTATTTATTATATAATTATGTATAATATATAATTATTTATTATATAATTATGTATAATATATAATTATTTATTATATAATTATGTGTTATGTATAATTATTATATAATTATGTATAATATATATATAATTTTTTATTATATAATTATGTATAATATATAATTTTTTATAATTATGTGTAATATATAATTATTTATCATATAATTACAATATATATTATTAACATAATATCTAAATATATTAATAATCTAATATCTATAATTAATATAATATATAAATATTACTTCTTGAAATCCAACGTGCACCTGAATCACCTGAGCCGTTGTTAAAATGCAGATTCGAGATCCTGCATTTCTAACAAGTTACTGGGTGAGGCAGAAGATGCTTAGCAAAGGCCCACACC +>syndip_1_chr20:8661811-8662758 +GCCAACCTACGTTAAGTAATTCATAACTTCAGTATTTAATAAATCTTCAGTGAAAGGCAA +GAGGCTACACACAGTGACAGACCCAGAGATAAACCCTGTGCCCCTAGAGATTTGCACTCC +TCTTAAAAGTGTATATATATATAATTATATAATTATTTATTATATAATTATATATAATTA +TATAATTATTTATTATATAATTATATATAATTATATAATTATTTATTATATAATTATATA +TAATATACAATTATTTATTATATAATTATATATAATTATATATTTATTATATTTATTATA +CAGTTATATAATAAATAATTATATAATTATATATAATTATATATATATAATTATATATAA +TTATATATAATTATATAATTATATATAATTGTATATAATTATTTATTATATAATTATATA +TTATTTATTATATAATTATATAATTATATATTATTTATTATATATTATATAATTATATAA +TTATATATTATTTATTATATAATATATAATTATATATTATTTATTATATAATTATATATT +ATTTATTATATATATTATTTATTATATAATTATATATTATGTATTATATAATTATATAAT +TATATATTATGTATTATATAATTATATATTATGTATTATATAATTATATAATTATATATT +ATGTATTATATAATTATATATTATTTATTATATAATTATATAATTATATATTATTTATTA +TATAATTATATAATTATATATTATTTATTATATAATTATATAATTATATATTATTTATTA +TATAATTATATAATTATATATTATTTATTATATAATTATATATTATTTATTATATAATTA +TATATTATTTATTACATAAATATATATTATTTATTACATAAGTATATATCACTTATTATA +TAATTGCATATAATTATTTATTATATAATTGCATATAATTATTATATAATTGTATATAGT +TATTTATTATATAATTGTATATAGTTATTTATTATATAATTCTATATAATTATTTATTAT +CTAATTCTATATTAAATATAATTATTTATTATCTAATTCTATATTATATATAATTATTTA +TTATATAATTCTATATTATATATAATTATTATATAATTCTATATATAATTATTTATTATA +TAATTCTATACATAAGTATTTATTATATAATTATGTATATAATTATTTATTATATAATTA +TGTATAATATGTAATTATTTATTATATAATTATGTATAATATGTAATTATTTATTATATA +ATTATGTATAATATATAATTATTTATTATATAATTATGTATAATATATAATTATTTATTA +TATAATTATGTGTTATGTATAATTATTATATAATTATGTATAATATATATATAATTTTTT +ATTATATAATTATGTATAATATATAATTTTTTATAATTATGTGTAATATATAATTATTTA +TCATATAATTACAATATATATTATTAACATAATATCTAAATATATTAATAATCTAATATC +TATAATTAATATAATATATAAATATTACTTCTTGAAATCCAACGTGCACCTGAATCACCT +GAGCCGTTGTTAAAATGCAGATTCGAGATCCTGCATTTCTAACAAGTTACTGGGTGAGGC +AGAAGATGCTTAGCAAAGGCCCACACC +>syndip_2_chr20:8661811-8662758 +GCCAACCTACGTTAAGTAATTCATAACTTCAGTATTTAATAAATCTTCAGTGAAAGGCAA +GAGGCTACACACAGTGACAGACCCAGAGATAAACCCTGTGCCCCTAGAGATTTGCACTCC +TCTTAAAAGTGTATATATATATAATTATATAATTATTTATTATATAATTATATATAATTA +TATAATTATTTATTATATAATGATATATAATTATATAATTATTTATTATATAATTATATA +TAATTATATAATTATTTATTATATAATTATATATAATTATATAATTATTTATTATATAAT +TATATATAATTATATAATTATTTATTATATAATTATATATAATTATATAATTATTTATTA +TATAATTATATATAATTATATAATTATTTATTATATAATTATATATAATTATATAATTAT +TTATTATATAATTATATATAATTATATAATTATTTATTATATAATTATATATAATTATAT +AATTATTTATTATATAATTATATATAATATACAATTATTTATTATATAATTATATATAAT +ATACAATTATTTATTATATAATTATATATAATTATATATTTATTATATTTATTATACAGT +TATATAATAAATAATTATATAATTATATATAATTATATAATTATATATAATTATATATAT +ATAATTATATGTAATTATATATAATTATATAATTATTATATAATTGTATATAATATATAA +TTATATAATTATATATTATTTATTATATAATATATAATTATATAATTATATATTATTTAT +TATATAATATATAATTATATAATTATATATTATTTATTATATAATTATATATTATTTATT +ATATATATTATTTATTATATAATTATATAATTATATATTATTTATTATATAATTATATAT +TATTTATTATATAATATATAATTATATATTATTTATTATATAATATATAATTATATATTA +TTTATTATATAATTATATATTATGTATTATATAATATATAATTATATATTATGTATTATA +TAATTATATAATTATATATTATTTATTATATAATTATATAATTATATATTATTTATTACA +TAATTATATATTATTTATTACATAAGTATATATTATTTATTACATAAGTATATATCACTT +ATTATATAATTGTATATAATTATTTATTATATAATTGCATATAATTATTTATTATATAAT +TGTATATAGTTATTTATTATATAATTCTATATAGTTATTTATTATATAATTCTATATAAT +TATTTATTATCTAATTCTATATTATATATAATTATTTATTATCTAATTCTATATTAAATA +TAATTATTTATTATCTAATTCTATATTATATATAATTATTTATTATATAATTCTATATTA +TATATAATTATTATATAATTCTATATATAATTATTTATTATATAATTCTATACATAAGTA +TTTATTATATAATTATGTATATAATTATTTATTATATAATTATGTATAATATGTAATTAT +TTATTATATAATTATGTATAATATGTAATTATTTATTATATAATTATGTATAATATATAA +TTATTTATTATATAATTATGTATAATATATAATTATTTATTATATAATTATGTGTTATGT +ATAATTATTATATAATTATGTATAATATATATATAATTTTTTATTATATAATTATGTATA +ATATATAATTTTTTATAATTATGTGTAATATATAATTATTTATCATATAATTACAATATA +TATTATTAACATAATATCTAAATATATTAATAATCTAATATCTATAATTAATATAATATA +TAAATATTACTTCTTGAAATCCAACGTGCACCTGAATCACCTGAGCCGTTGTTAAAATGC +AGATTCGAGATCCTGCATTTCTAACAAGTTACTGGGTGAGGCAGAAGATGCTTAGCAAAG +GCCCACACC +>p:HG002_1_chr20:8661811-8662758 +GCCAACCTACGTTAAGTAATTCATAACTTCAGTATTTAATAAATCTTCAGTGAAAGGCAA +GAGGCTACACACAGTGACAGACCCAGAGATAAACCCTGTGCCCCTAGAGATTTGCACTCC +TCTTAAAAGTGTATATATATATAATTATATAATTATTTATTATATAATTATATATAATTA +TATAATTATTTATTATATAATTATATATAATATACAATTATTTATTATATAATTATATAT +AATTATATATTTATTTATTATATAATTATATATAATTATATAATTATTTATTATATAATT +ATATATAATTATATAATTATTTATTATATAATTATATATAATTATATAATTATTTATTAT +ATAATTATATATAATTATATAATTATTTATTATATAATTATATATAATTATATAATTATT +TATTATATAATTATATATAATTATATAATTATTTATTATATAATTATATATAATTATATA +ATTATTTATTATATAATTATATATAATATACAATTATTTATTATATAATTATATATAATA +TACAATTATTTATTATATAATTATATATAATTATATATTTATTATATTTATTATACAGTT +ATATAATAAATATATAATTATATATAAATATATAATTATATATAATTATATATATATAAT +TATATGTAATTATATATAATTATATAATTATTATATAATTGTATATAATATATAATTATA +TAATTATATATTATTTATTATATAATATATAATTATATAATTATATATTATTTATTATAT +AATATATAATTATATAATTATATATTATTTATTATATAATTATATATTATTTATTATATA +TATTATTTATTATATAATTATATAATTATATATTATTTATTATATAATTATATATTATTT +ATTATATAATATATAATTATATATTATTTATTATATAATATATAATTATATATTATTTAT +TATATAATTATATATTATGTATTATATAATATATAATTATATATTATGTATTATATAATT +ATATAATTATATATTATTTATTATATAATTATATAATTATATATTATTTATTACATAATT +ATATATTATTTATTACATAAGTATATATTATTTATTACATAAGTATATATCACTTATTAT +ATAATTGTATATAATTATTTATTATATAATTGCATATAATTATTTATTATATAATTGTAT +ATAGTTATTTATTATATAATTCTATATAGTTATATTTATTATACAGTTATATAATAAATA +ATTATATAATTATATATAATTATATATTATTTATTATCTAATTCTATATTAAATATAATT +ATTTATTATCTAATTCTATATTATATATAATTATTTATTATATAATTCTATATTATATAT +AATTATTATATAATTCTATATATAATTATTTATTATATAATTCTATACATAAGTATTTAT +TATATAATTATGTATATAATTATTTATTATATAATTATGTATAATATGTAATTATTTATT +ATATAATTATGTATAATATGTAATTATTTATTATATAATTATGTATAATATATAATTATT +TATTATATAATTATGTATAATATATAATTATTTATTATATAATTATGTGTTATGTATAAT +TATTATATAATTATGTATAATATATATATAATTTTTTATTATATAATTATGTATAATATA +TAATTTTTTATAATTATGTGTAATATATAATTATTTATCATATAATTACAATATATATTA +TTAACATAATATCTAAATATATTAATAATCTAATATCTATAATTAATATAATATATAAAT +ATTACTTCTTGAAATCCAACGTGCACCTGAATCACCTGAGCCGTTGTTAAAATGCAGATT +CGAGATCCTGCATTTCTAACAAGTTACTGGGTGAGGCAGAAGATGCTTAGCAAAGGCCCA +CACC +>p:HG002_2_chr20:8661811-8662758 +GCCAACCTACGTTAAGTAATTCATAACTTCAGTATTTAATAAATCTTCAGTGAAAGGCAA +GAGGCTACACACAGTGACAGACCCAGAGATAAACCCTGTGCCCCTAGAGATTTGCACTCC +TCTTAAAAGTGTATATATATATAATTATATAATTATTTATTATATAATTATATATAATTA +TATAATTATTTATTATATAATTATATATAATATACAATTATTTATTATATAATTATATAT +AATATACAATTATTTATTATATAATTATATATAATTATATATTTATTATATTTATTATAC +AGTTATATAATAAATAATTATATAATTATATATAATTATATATATATAATTATATATAAT +TATATATAATTATATAATTATATATAATTGTATATAATTATTTATTATATAATTATATAT +TATTTATTATATAATTATATAATTATATATTATTTATTATATATTATATAATTATATAAT +TATATATTATTTATTATATAATATATAATTATATATTATTTATTATATAATTATATATTA +TTTATTATATATATTATTTATTATATAATTATATATTATGTATTATATAATTATATAATT +ATATATTATGTATTATATAATTATATATTATGTATTATATAATTATATAATTATATATTA +TGTATTATATAATTATATATTATTTATTATATAATTATATAATTATATATTATTTATTAT +ATAATTATATAATTATATATTATTTATTATATAATTATATAATTATATATTATTTATTAT +ATAATTATATAATTATATATTATTTATTATATAATTATATATTATTTATTATATAATTAT +ATATTATTTATTACATAAATATATATTATTTATTACATAAGTATATATCACTTATTATAT +AATTGCATATAATTATTTATTATATAATTGCATATAATTATTATATATTTATTATATTTA +TTATACAGTTATATAATAAATAATTATATAATTATATATAATTATATATTATTTATTATC +TAATTCTATATTAAATATAATTATTTATTATCTAATTCTATATTATATATAATTATTTAT +TATATAATTCTATATTATATATAATTATTATATAATTCTATATATAATTATTTATTATAT +AATTCTATACATAAGTATTTATTATATAATTATGTATATAATTATTTATTATATAATTAT +GTATAATATGTAATTATTTATTATATAATTATGTATAATATGTAATTATTTATTATATAA +TTATGTATAATATATAATTATTTATTATATAATTATGTATAATATATAATTATTTATTAT +ATAATTATGTGTTATGTATAATTATTATATAATTATGTATAATATATATATAATTTTTTA +TTATATAATTATGTATAATATATAATTTTTTATAATTATGTGTAATATATAATTATTTAT +CATATAATTACAATATATATTATTAACATAATATCTAAATATATTAATAATCTAATATCT +ATAATTAATATAATATATAAATATTACTTCTTGAAATCCAACGTGCACCTGAATCACCTG +AGCCGTTGTTAAAATGCAGATTCGAGATCCTGCATTTCTAACAAGTTACTGGGTGAGGCA +GAAGATGCTTAGCAAAGGCCCACACC diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/haps.fa.ref.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/haps.fa.ref.fa new file mode 100644 index 00000000..b5e952ab --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/haps.fa.ref.fa @@ -0,0 +1,2 @@ +>chr20:8661811-8662758 +GCCAACCTACGTTAAGTAATTCATAACTTCAGTATTTAATAAATCTTCAGTGAAAGGCAAGAGGCTACACACAGTGACAGACCCAGAGATAAACCCTGTGCCCCTAGAGATTTGCACTCCTCTTAAAAGTGTATATATATATAATTATATAATTATTTATTATATAATTATATATAATTATATAATTATTTATTATATAATTATATATAATATACAATTATTTATTATATAATTATATATAATTATATATTTATTATATTTATTATACAGTTATATAATAAATAATTATATAATTATATATAATTATATATTATTTATTATCTAATTCTATATTAAATATAATTATTTATTATCTAATTCTATATTATATATAATTATTTATTATATAATTCTATATTATATATAATTATTATATAATTCTATATATAATTATTTATTATATAATTCTATACATAAGTATTTATTATATAATTATGTATATAATTATTTATTATATAATTATGTATAATATGTAATTATTTATTATATAATTATGTATAATATGTAATTATTTATTATATAATTATGTATAATATATAATTATTTATTATATAATTATGTATAATATATAATTATTTATTATATAATTATGTGTTATGTATAATTATTATATAATTATGTATAATATATATATAATTTTTTATTATATAATTATGTATAATATATAATTTTTTATAATTATGTGTAATATATAATTATTTATCATATAATTACAATATATATTATTAACATAATATCTAAATATATTAATAATCTAATATCTATAATTAATATAATATATAAATATTACTTCTTGAAATCCAACGTGCACCTGAATCACCTGAGCCGTTGTTAAAATGCAGATTCGAGATCCTGCATTTCTAACAAGTTACTGGGTGAGGCAGAAGATGCTTAGCAAAGGCCCACACC diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/msa.fa b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/msa.fa new file mode 100644 index 00000000..2cba7a82 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/msa.fa @@ -0,0 +1,170 @@ +>ref_chr20_8661811_8662758 +gccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggcaa +gaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactcc +tc---------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------ttaaaagtgtatatata +tataattatataattatttattatataattatatataatt--atataattatttattata +taattatatataatatacaattatttattatataattatatataattatatatttattat +atttattatacagttatataataaataattatataattatatataattatatattattta +ttatctaattctatattaaatataattatttattatctaattctatattatatataatta +tttattatataattctatattatatataattattatataattctatatataattatttat +tatataattctatacataagtatttattatataattatgtatataattatttattatata +attatgtataatatgtaattatttattatataattatgtataatatgtaattatttatta +tataattatgtataatatataattatttattatataattatgtataatatataattattt +attatataattatgtgttatgtataattattatataattatgtataatatatatataatt +ttttattatataattatgtataatatataattttttataattatgtgtaatatataatta +tttatcatataattacaatatatattattaacataatatctaaatatattaataatctaa +tatctataattaatataatatataaatattacttcttgaaatccaacgtgcacctgaatc +acctgagccgttgttaaaatgcagattcgagatcctgcatttctaacaagttactgggtg +aggcagaagatgcttagcaaaggcccacacc +>syndip_1_chr20:8661811-8662758 +gccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggcaa +gaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactcc +tcttaaaagtgtatatatatataattatataattatttattatataattatatataatta +tataattatttattatataattatatataattatataattatttattatataattatata +taa----------------------------------tatacaattatttattatataat +tatatataattatatatttattatatttat-----tatacagttatataataaataatta +tataattatatataattatata---------tatataattatatataattatata----- +taattatataattatatataattgtatataattatttattatataattatat-------- +---attatttattatataattatata----------------attatat----------- +-------attatttattatata-------------------------------------- +--------------------------ttatataattatataattatatattatttattat +ata-----atatataattatatat-------tatttattatataattatatattatttat +ta---------tatatattatttattatata----------------------attatat +attatgtattatataattatataattatatattatgtattatataat------------- +---tatatattatgtattatataattatataattatatattatgtattatataattatat +attatttattatataattatataattatatattatttattatataattatataattatat +attatttattatataat---------------------tatataattatatattatttat +tatataattatataattatatattattt--------attatataattatatattatttat +tatataattatatattatttattacataaatatatattatttattacataagtatatatc +acttattatataattgcatataattatttattatataattgcatataa----ttattata +taattgtatat-------agttatttattatataattg---------------------- +--------------tatatagttatttattatataattctatata-------attattta +ttatctaattctatattaaatataattatttattatctaattctatattatatataatta +tttattatataattctatattatatataattattatataattctatatataattatttat +tatataattctatacataagtatttattatataattatgtatataattatttattatata +attatgtataatatgtaattatttattatataattatgtataatatgtaattatttatta +tataattatgtataatatataattatttattatataattatgtataatatataattattt +attatataattatgtgttatgtataattattatataattatgtataatatatatataatt +ttttattatataattatgtataatatataattttttataattatgtgtaatatataatta +tttatcatataattacaatatatattattaacataatatctaaatatattaataatctaa +tatctataattaatataatatataaatattacttcttgaaatccaacgtgcacctgaatc +acctgagccgttgttaaaatgcagattcgagatcctgcatttctaacaagttactgggtg +aggcagaagatgcttagcaaaggcccacacc +>syndip_2_chr20:8661811-8662758 +gccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggcaa +gaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactcc +tcttaaaagtgtatatatatataattatataattatttattatataattatatataatta +tataattatttattatataatgatatataattatataattatttattatataattatata +taattatataattatttattatataattatatataattatataattatttattatataat +tatatataattatataattatttattatataattatatataattatataattatttatta +tataattatatataattatataattatttattatataattatatataattatataattat +ttattatataattatatataat--tatataattatttattatataattatatataattat +ataattatttattatataattatatataatatacaattatttattatataattatatata +atatacaattatttattatataattatatataattatatatttattatatttattataca +gttatataataaataattatataattatatataattatataattatatataattatatat +atataattatatgtaattatatataattatataattattatataattgtatataatatat +aattatataattatatattatttattatataatatataattatataattatatattattt +attatataatatataattatataattatatattatttattatataattatatattattta +ttatatatattatttattatataattatataattatatattatttattatataattatat +attatttattatataa-tatataattatatattatttattatataa-tatataattatat +attatttattatataattatatattatgtattatataatatataattatatattatgtat +tatataattatataattatatattatttattatataattatataattatatattatttat +tacataattatatattatttattacataagtatatattatttattacataagtatatatc +acttattatataattgtatataattatttattatataattgcatataattatttattata +taattgtatat-------agttatttattatataattctatata-----------gttat +ttattatataattctatataattatttattatctaattctatattatatataattattta +ttatctaattctatattaaatataattatttattatctaattctatattatatataatta +tttattatataattctatattatatataattattatataattctatatataattatttat +tatataattctatacataagtatttattatataattatgtatataattatttattatata +attatgtataatatgtaattatttattatataattatgtataatatgtaattatttatta +tataattatgtataatatataattatttattatataattatgtataatatataattattt +attatataattatgtgttatgtataattattatataattatgtataatatatatataatt +ttttattatataattatgtataatatataattttttataattatgtgtaatatataatta +tttatcatataattacaatatatattattaacataatatctaaatatattaataatctaa +tatctataattaatataatatataaatattacttcttgaaatccaacgtgcacctgaatc +acctgagccgttgttaaaatgcagattcgagatcctgcatttctaacaagttactgggtg +aggcagaagatgcttagcaaaggcccacacc +>p:HG002_1_chr20:8661811-8662758 +gccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggcaa +gaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactcc +tcttaaaagtgtatatatatataattatataattatttattatataattatatataatta +tataattatttattatataattatatataa-tatacaattatttattatataattatata +taattatatatttatttattatataattatatataattatataattatttattatataat +tatatataattatataattatttattatataattatatataattatataattatttatta +tataattatatataattatataattatttattatataattatatataattatataattat +ttattatataattatatataat--tatataattatttattatataattatatataattat +ataattatttattatataattatatataatatacaattatttattatataattatatata +atatacaattatttattatataattatatataattatatatttattatatttattataca +gttatataataaa----tatataattatatataaatatataattatatataattatatat +atataattatatgtaattatatataattatataattattatataattgtatataatatat +aattatataattatatattatttattatataatatataattatataattatatattattt +attatataatatataattatataattatatattatttattatataattatatattattta +ttatatatattatttattatataattatataattatatattatttattatataattatat +attatttattatataa-tatataattatatattatttattatataa-tatataattatat +attatttattatataattatatattatgtattatataatatataattatatattatgtat +tatataattatataattatatattatttattatataattatataattatatattatttat +tacataattatatattatttattacataagtatatattatttattacataagtatatatc +acttattatataattgtatataattatttattatataattgcatataattatttattata +taattgtatat-------agttatttattatataattctatata-----------gttat +atttattatacagttatataataaataattatataattatatataattatatattattta +ttatctaattctatattaaatataattatttattatctaattctatattatatataatta +tttattatataattctatattatatataattattatataattctatatataattatttat +tatataattctatacataagtatttattatataattatgtatataattatttattatata +attatgtataatatgtaattatttattatataattatgtataatatgtaattatttatta +tataattatgtataatatataattatttattatataattatgtataatatataattattt +attatataattatgtgttatgtataattattatataattatgtataatatatatataatt +ttttattatataattatgtataatatataattttttataattatgtgtaatatataatta +tttatcatataattacaatatatattattaacataatatctaaatatattaataatctaa +tatctataattaatataatatataaatattacttcttgaaatccaacgtgcacctgaatc +acctgagccgttgttaaaatgcagattcgagatcctgcatttctaacaagttactgggtg +aggcagaagatgcttagcaaaggcccacacc +>p:HG002_2_chr20:8661811-8662758 +gccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggcaa +gaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactcc +tcttaaaagtgtatatatatataattatataattatttattatataattatatataatta +tataattatttattatataattatatataa-tatacaattatttattatataattatata +taa----------------------------------tatacaattatttattatataat +tatatataattatatatttattatatttat-----tatacagttatataataaataatta +tataattatatataattatata---------tatataattatatataattatata----- +taattatataattatatataattgtatataattatttattatataattatat-------- +---attatttattatataattatata----------------attatat----------- +-------attatttattatata-------------------------------------- +--------------------------ttatataattatataattatatattatttattat +ata-----atatataattatatat-------tatttattatataattatatattatttat +ta---------tatatattatttattatata----------------------attatat +attatgtattatataattatataattatatattatgtattatataat------------- +---tatatattatgtattatataattatataattatatattatgtattatataattatat +attatttattatataattatataattatatattatttattatataattatataattatat +attatttattatataat---------------------tatataattatatattatttat +tatataattatataattatatattattt--------attatataattatatattatttat +tatataattatatattatttattacataaatatatattatttattacataagtatatatc +acttattatataattgcatataattatttattatataattgcatataa----ttattata +tatttat------------tatatttattatacagt------------------------ +--------------tatataataaataattatataattatatataattatatattattta +ttatctaattctatattaaatataattatttattatctaattctatattatatataatta +tttattatataattctatattatatataattattatataattctatatataattatttat +tatataattctatacataagtatttattatataattatgtatataattatttattatata +attatgtataatatgtaattatttattatataattatgtataatatgtaattatttatta +tataattatgtataatatataattatttattatataattatgtataatatataattattt +attatataattatgtgttatgtataattattatataattatgtataatatatatataatt +ttttattatataattatgtataatatataattttttataattatgtgtaatatataatta +tttatcatataattacaatatatattattaacataatatctaaatatattaataatctaa +tatctataattaatataatatataaatattacttcttgaaatccaacgtgcacctgaatc +acctgagccgttgttaaaatgcagattcgagatcctgcatttctaacaagttactgggtg +aggcagaagatgcttagcaaaggcccacacc diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/msa.fa.fai b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/msa.fa.fai new file mode 100644 index 00000000..5fe00dfa --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/msa.fa.fai @@ -0,0 +1,5 @@ +ref_chr20_8661811_8662758 1951 27 60 61 +syndip_1_chr20:8661811-8662758 1951 2043 60 61 +syndip_2_chr20:8661811-8662758 1951 4059 60 61 +p:HG002_1_chr20:8661811-8662758 1951 6076 60 61 +p:HG002_2_chr20:8661811-8662758 1951 8093 60 61 diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/output.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/output.vcf.gz new file mode 100644 index 00000000..5007034b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/output.vcf.gz.tbi new file mode 100644 index 00000000..6f00faaf Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab/chr20/chr20:8661911-8662658/output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/fn.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab_bench/fn.vcf.gz new file mode 100644 index 00000000..fef5be0f Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab_bench/fn.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/fn.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab_bench/fn.vcf.gz.tbi new file mode 100644 index 00000000..0500e75b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab_bench/fn.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/fp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab_bench/fp.vcf.gz new file mode 100644 index 00000000..762d97f2 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab_bench/fp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/fp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab_bench/fp.vcf.gz.tbi new file mode 100644 index 00000000..be67484b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab_bench/fp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/params.json b/repo_utils/answer_key/refine/refine_output_two/phab_bench/params.json new file mode 100644 index 00000000..50a777c7 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab_bench/params.json @@ -0,0 +1 @@ +{"base": "test_results/refine_output_two/phab.output.vcf.gz", "comp": "test_results/refine_output_two/phab.output.vcf.gz", "output": "test_results/refine_output_two/phab_bench", "includebed": "/tmp/mpxcw45p.bed", "extend": 0, "debug": false, "reference": null, "refdist": 500, "pctseq": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "chunksize": 1000, "bSample": "syndip", "cSample": "p:HG002", "dup_to_ins": false, "sizemin": 5, "sizefilt": 5, "sizemax": 50000, "passonly": false, "no_ref": "a", "pick": "single"} \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/summary.json b/repo_utils/answer_key/refine/refine_output_two/phab_bench/summary.json new file mode 100644 index 00000000..877330ee --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/phab_bench/summary.json @@ -0,0 +1,31 @@ +{ + "TP-base": 111, + "TP-comp": 111, + "FP": 20, + "FN": 31, + "precision": 0.8473282442748091, + "recall": 0.7816901408450704, + "f1": 0.8131868131868132, + "base cnt": 142, + "comp cnt": 131, + "TP-comp_TP-gt": 106, + "TP-comp_FP-gt": 5, + "TP-base_TP-gt": 106, + "TP-base_FP-gt": 5, + "gt_concordance": 0.954954954954955, + "gt_matrix": { + "(0, 1)": { + "(1, 0)": 42 + }, + "(1, 0)": { + "(0, 1)": 50, + "(1, 1)": 1, + "(1, 0)": 1 + }, + "(1, 1)": { + "(1, 0)": 3, + "(1, 1)": 13, + "(0, 1)": 1 + } + } +} \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-base.vcf.gz new file mode 100644 index 00000000..50623581 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-base.vcf.gz.tbi new file mode 100644 index 00000000..96bd2423 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-comp.vcf.gz new file mode 100644 index 00000000..01306c1e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-comp.vcf.gz.tbi new file mode 100644 index 00000000..8550e98d Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/refine.region_summary.json b/repo_utils/answer_key/refine/refine_output_two/refine.region_summary.json new file mode 100644 index 00000000..8eed70c4 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/refine.region_summary.json @@ -0,0 +1,18 @@ +{ + "TP": 81, + "TN": 2, + "FP": 17, + "FN": 37, + "base P": 122, + "base N": 7, + "comp P": 126, + "comp N": 3, + "PPV": 0.6428571428571429, + "TPR": 0.6639344262295082, + "TNR": 0.2857142857142857, + "NPV": 0.6666666666666666, + "ACC": 0.6434108527131783, + "BA": 0.4748243559718969, + "F1": 0.6532258064516129, + "UND": 0 +} \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_two/refine.regions.txt b/repo_utils/answer_key/refine/refine_output_two/refine.regions.txt new file mode 100644 index 00000000..446aefd7 --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/refine.regions.txt @@ -0,0 +1,130 @@ +chrom start end in_tpbase in_tp in_fn in_fp refined out_tpbase out_tp out_fn out_fp state +chr20 38194533 38194667 2 2 0 0 False 2 2 0 0 TP +chr20 17081216 17081411 2 2 1 0 False 2 2 1 0 FN +chr20 44763896 44764286 2 2 1 0 False 2 2 1 0 FN +chr20 23942431 23942956 1 1 0 0 False 1 1 0 0 TP +chr20 25067059 25068113 3 3 0 0 False 3 3 0 0 TP +chr20 1149807 1150221 2 2 0 0 False 2 2 0 0 TP +chr20 24836081 24836385 2 2 0 0 False 2 2 0 0 TP +chr20 56710555 56711194 2 2 0 0 False 2 2 0 0 TP +chr20 61331528 61331754 2 2 0 0 False 2 2 0 0 TP +chr20 1257933 1260529 2 2 0 0 False 2 2 0 0 TP +chr20 22882702 22882831 2 2 0 0 False 2 2 0 0 TP +chr20 53415642 53415861 2 2 0 0 False 2 2 0 0 TP +chr20 61282506 61283670 4 4 2 0 False 4 4 2 0 FN +chr20 53203987 53204474 2 2 2 1 True 4 4 0 0 TP +chr20 61919676 61921375 2 2 0 0 False 2 2 0 0 TP +chr20 62830612 62830839 2 2 1 1 True 2 2 0 0 TP +chr20 63049033 63049413 3 3 1 0 False 3 3 1 0 FN +chr20 61201683 61202475 2 2 4 1 True 3 3 2 0 FN +chr20 20458640 20458938 2 2 0 0 False 2 2 0 0 TP +chr20 64090704 64091390 0 0 0 2 False 0 0 0 2 FP +chr20 63028876 63029403 2 2 0 1 False 2 2 0 1 FP +chr20 61475406 61475727 2 2 0 0 False 2 2 0 0 TP +chr20 63167387 63167628 2 2 1 0 False 2 2 1 0 FN +chr20 21120212 21120540 2 2 1 0 False 2 2 1 0 FN +chr20 64096658 64097165 0 0 0 2 False 0 0 0 2 FP +chr20 709729 709976 2 2 0 0 False 2 2 0 0 TP +chr20 61337205 61337591 2 2 0 0 False 2 2 0 0 TP +chr20 14861937 14862742 5 5 5 1 True 12 12 0 1 FP +chr20 20337200 20337708 1 1 6 2 True 3 3 0 0 TP +chr20 24681988 24682278 2 2 1 0 False 2 2 1 0 FN +chr20 8661911 8662658 1 1 3 1 True 5 5 1 1 FN,FP +chr20 21721174 21721736 2 2 1 0 False 2 2 1 0 FN +chr20 58694862 58695412 2 2 0 0 False 2 2 0 0 TP +chr20 23267965 23268088 2 2 0 0 False 2 2 0 0 TP +chr20 4482585 4482735 2 2 0 0 False 2 2 0 0 TP +chr20 63103249 63103493 1 1 0 0 False 1 1 0 0 TP +chr20 34235750 34236214 0 0 2 1 True 2 2 0 0 TP +chr20 61744188 61744655 2 2 1 0 False 2 2 1 0 FN +chr20 63372065 63372692 2 2 1 0 False 2 2 1 0 FN +chr20 64125109 64127975 3 3 3 0 False 3 3 3 0 FN +chr20 62504279 62504615 2 2 0 0 False 2 2 0 0 TP +chr20 19663366 19663527 2 2 0 0 False 2 2 0 0 TP +chr20 63824631 63825145 2 2 0 0 False 2 2 0 0 TP +chr20 63158183 63158727 2 2 0 0 False 2 2 0 0 TP +chr20 63068409 63068800 2 2 0 0 False 2 2 0 0 TP +chr20 1301599 1302668 2 2 0 0 False 2 2 0 0 TP +chr20 63294079 63294267 2 2 0 0 False 2 2 0 0 TP +chr20 18675650 18675916 2 2 0 0 False 2 2 0 0 TP +chr20 57974804 57975203 2 2 0 0 False 2 2 0 0 TP +chr20 62270279 62271095 1 1 3 1 True 3 3 3 0 FN +chr20 64173409 64176530 4 4 7 3 True 5 5 5 9 FN,FP +chr20 63491589 63493065 1 1 3 1 True 9 9 0 0 TP +chr20 63948514 63948759 2 2 1 1 True 2 2 0 1 FP +chr20 63693325 63693885 1 1 6 1 True 6 6 0 0 TP +chr20 278900 279187 3 3 1 0 False 3 3 1 0 FN +chr20 48449705 48450462 4 4 2 0 False 4 4 2 0 FN +chr20 46788807 46789531 2 2 0 0 False 2 2 0 0 TP +chr20 63303655 63304859 2 2 0 0 False 2 2 0 0 TP +chr20 18209097 18210728 3 3 2 1 True 5 5 0 1 FP +chr20 63156767 63157326 2 2 0 0 False 2 2 0 0 TP +chr20 61176725 61176975 2 2 0 0 False 2 2 0 0 TP +chr20 58196700 58196937 2 2 0 0 False 2 2 0 0 TP +chr20 45600569 45600747 2 2 2 0 False 2 2 2 0 FN +chr20 22471831 22472130 2 2 0 0 False 2 2 0 0 TP +chr20 62417424 62418063 3 3 0 0 False 3 3 0 0 TP +chr20 41196210 41196649 3 3 1 0 False 3 3 1 0 FN +chr20 56284258 56284408 2 2 0 0 False 2 2 0 0 TP +chr20 63221480 63221877 1 1 2 1 True 2 2 0 0 TP +chr20 63450491 63450614 2 2 0 0 False 2 2 0 0 TP +chr20 13848164 13848650 3 3 1 0 False 3 3 1 0 FN +chr20 62422444 62422792 2 2 0 0 False 2 2 0 0 TP +chr20 24956961 24957199 2 2 0 0 False 2 2 0 0 TP +chr20 63770912 63771104 0 0 0 2 False 0 0 0 2 FP +chr20 32724927 32725000 0 0 0 0 False 0 0 0 0 TN +chr20 59442036 59442274 2 2 0 0 False 2 2 0 0 TP +chr20 32723469 32724638 0 0 0 0 False 0 0 0 0 TN +chr20 25561369 25562322 2 2 0 0 False 2 2 0 0 TP +chr20 62317837 62318460 2 2 0 0 False 2 2 0 0 TP +chr20 36642142 36642223 1 1 0 0 False 1 1 0 0 TP +chr20 57417271 57418235 2 2 0 0 False 2 2 0 0 TP +chr20 63027997 63028167 2 2 1 0 False 2 2 1 0 FN +chr20 63235329 63235451 2 2 0 0 False 2 2 0 0 TP +chr20 34205619 34205961 1 1 0 0 False 1 1 0 0 TP +chr20 62057573 62059140 1 1 3 1 True 9 9 0 0 TP +chr20 63486763 63487417 2 2 0 0 False 2 2 0 0 TP +chr20 57110212 57110786 2 2 1 0 False 2 2 1 0 FN +chr20 55943919 55945808 2 2 2 1 True 3 3 2 0 FN +chr20 7435215 7435750 2 2 0 0 False 2 2 0 0 TP +chr20 64233048 64233546 2 2 0 0 False 2 2 0 0 TP +chr20 62212844 62213875 4 4 0 0 False 4 4 0 0 TP +chr20 63641779 63642136 1 1 2 1 True 2 2 0 0 TP +chr20 17197123 17197242 2 2 0 0 False 2 2 0 0 TP +chr20 61329258 61329578 0 0 0 2 False 0 0 0 2 FP +chr20 51500592 51500881 2 2 0 0 False 2 2 0 0 TP +chr20 64134883 64136387 3 3 1 0 False 3 3 1 0 FN +chr20 23155504 23155976 3 3 2 2 True 4 4 1 1 FN,FP +chr20 420555 420771 2 2 0 0 False 2 2 0 0 TP +chr20 55627344 55628451 7 7 4 0 False 7 7 4 0 FN +chr20 32722424 32723213 0 0 1 0 False 0 0 1 0 FN +chr20 16395149 16395422 3 3 1 0 False 3 3 1 0 FN +chr20 48959359 48959653 2 2 0 0 False 2 2 0 0 TP +chr20 2442966 2443944 2 2 0 0 False 2 2 0 0 TP +chr20 60314330 60315021 2 2 2 0 False 2 2 2 0 FN +chr20 50258450 50258552 2 2 0 0 False 2 2 0 0 TP +chr20 16226954 16228488 3 3 0 0 False 3 3 0 0 TP +chr20 60087391 60087966 2 2 0 0 False 2 2 0 0 TP +chr20 641836 642466 3 3 2 0 False 3 3 2 0 FN +chr20 58519902 58520373 2 2 0 0 False 2 2 0 0 TP +chr20 60764031 60764635 2 2 0 0 False 2 2 0 0 TP +chr20 10977797 10977978 2 2 0 0 False 2 2 0 0 TP +chr20 63361274 63361472 2 2 0 0 False 2 2 0 0 TP +chr20 4844738 4844907 2 2 0 0 False 2 2 0 0 TP +chr20 5039949 5040500 0 0 0 2 False 0 0 0 2 FP +chr20 63669579 63670497 2 2 0 0 False 2 2 0 0 TP +chr20 61783403 61784840 3 3 1 0 False 3 3 1 0 FN +chr20 64131804 64133956 5 5 8 1 True 7 7 8 2 FN,FP +chr20 50853639 50853929 2 2 0 0 False 2 2 0 0 TP +chr20 63334892 63335505 2 2 0 0 False 2 2 0 0 TP +chr20 50666148 50666894 2 2 0 0 False 2 2 0 0 TP +chr20 62349612 62349933 1 1 5 1 True 3 3 1 1 FN,FP +chr20 47225524 47225646 2 2 0 0 False 2 2 0 0 TP +chr20 48390898 48391232 2 2 0 0 False 2 2 0 0 TP +chr20 31689079 31689528 2 2 0 0 False 2 2 0 0 TP +chr20 62875172 62875557 2 2 3 0 False 2 2 3 0 FN +chr20 63559288 63559964 1 1 4 1 True 2 2 0 0 TP +chr20 62986310 62986806 2 2 0 0 False 2 2 0 0 TP +chr20 38123590 38124706 2 2 1 4 True 6 6 2 1 FN,FP +chr20 4032219 4033602 2 2 2 1 True 2 2 2 1 FN,FP +chr20 20354570 20358324 7 7 9 1 True 10 10 4 1 FN,FP diff --git a/repo_utils/answer_key/refine/refine_output_two/refine.variant_summary.json b/repo_utils/answer_key/refine/refine_output_two/refine.variant_summary.json new file mode 100644 index 00000000..b3389dcf --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/refine.variant_summary.json @@ -0,0 +1,17 @@ +{ + "TP-base": 324, + "TP-comp": 324, + "FP": 31, + "FN": 69, + "precision": 0.9126760563380282, + "recall": 0.8244274809160306, + "f1": 0.8663101604278075, + "base cnt": 393, + "comp cnt": 355, + "TP-comp_TP-gt": 0, + "TP-comp_FP-gt": 0, + "TP-base_TP-gt": 0, + "TP-base_FP-gt": 0, + "gt_concordance": 0, + "gt_matrix": {} +} \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_two/summary.json b/repo_utils/answer_key/refine/refine_output_two/summary.json new file mode 100644 index 00000000..5e91bbcb --- /dev/null +++ b/repo_utils/answer_key/refine/refine_output_two/summary.json @@ -0,0 +1,32 @@ +{ + "TP-base": 386, + "TP-comp": 386, + "FP": 65, + "FN": 201, + "precision": 0.8558758314855875, + "recall": 0.6575809199318569, + "f1": 0.7437379576107899, + "base cnt": 587, + "comp cnt": 451, + "TP-comp_TP-gt": 381, + "TP-comp_FP-gt": 5, + "TP-base_TP-gt": 381, + "TP-base_FP-gt": 5, + "gt_concordance": 0.9870466321243523, + "gt_matrix": { + "(1, 0)": { + "(0, 1)": 202, + "(1, 0)": 14, + "(1, 1)": 1 + }, + "(0, 1)": { + "(1, 0)": 144, + "(0, 1)": 12 + }, + "(1, 1)": { + "(1, 1)": 9, + "(1, 0)": 2, + "(0, 1)": 2 + } + } +} \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_two/tp-base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/tp-base.vcf.gz new file mode 100644 index 00000000..da7dfb8e Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/tp-base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/tp-base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/tp-base.vcf.gz.tbi new file mode 100644 index 00000000..893b883b Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/tp-base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/tp-comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/tp-comp.vcf.gz new file mode 100644 index 00000000..54f11a78 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/tp-comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/tp-comp.vcf.gz.tbi new file mode 100644 index 00000000..5cc5c220 Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/tp-comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/segment/segment.vcf b/repo_utils/answer_key/segment/segment.vcf new file mode 100644 index 00000000..cf3158c4 --- /dev/null +++ b/repo_utils/answer_key/segment/segment.vcf @@ -0,0 +1,3566 @@ +##fileformat=VCFv4.1 +##FILTER= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##INFO= +##INFO= +##INFO= +##FORMAT= +##bcftools_mergeVersion=1.10.2+htslib-1.10.2 +##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 +##INFO= +##INFO= +##bcftools_viewVersion=1.12+htslib-1.12 +##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 +##bcftools_mergeVersion=1.12+htslib-1.12 +##bcftools_mergeCommand=merge -O z -f x -m none input1.vcf.gz input2.vcf.gz input3.vcf.gz; Date=Mon Aug 16 18:05:13 2021 +##FORMAT= +##FORMAT= +##INFO= +##FORMAT= ploidy)"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 +chr20 64506 . C CTCCAT 60 . QNAME=cluster19_000000F;QSTART=25698398;QSTRAND=- GT:DP:AD ./.:35:13,22 1|0:30:14,16 ./.:21:12,9 +chr20 66235 . C CGACTCCACTCCATT 60 . QNAME=HG002-S9-H1-000001F;QSTART=45138;QSTRAND=+ GT:DP:AD 1|1:42:20,22 1|1:27:5,22 1|1:33:22,11 +chr20 66369 . C T 60 . QNAME=cluster19_000000F;QSTART=25696521;QSTRAND=- GT:DP:AD ./.:34:21,13 1|0:30:21,9 ./.:41:16,25 +chr20 67373 . G GAAATGTGAT 60 . QNAME=cluster23_scaffold_2;QSTART=25629267;QSTRAND=- GT:DP:AD ./.:38:18,20 ./.:37:20,17 0|1:29:20,9 +chr20 68303 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=47219;QSTRAND=+ GT:DP:AD 1|1:41:18,23 0|1:43:18,25 1|1:29:15,14 +chr20 72450 . G A 60 . QNAME=cluster19_000000F;QSTART=25690440;QSTRAND=- GT:DP:AD ./.:16:6,10 1|0:23:10,13 ./.:33:15,18 +chr20 72765 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=51682;QSTRAND=+ GT:DP:AD 1|1:14:9,5 0|1:33:10,23 1|0:36:18,18 +chr20 72765 . T TAA 60 . QNAME=cluster23_scaffold_2;QSTART=25623873;QSTRAND=- GT:DP:AD ./.:43:18,25 ./.:15:6,9 0|1:31:13,18 +chr20 72982 . A C 60 . QNAME=cluster19_000000F;QSTART=25689909;QSTRAND=- GT:DP:AD ./.:43:18,25 1|0:32:23,9 ./.:17:6,11 +chr20 73765 . C A 60 . QNAME=cluster19_000000F;QSTART=25689126;QSTRAND=- GT:DP:AD ./.:26:6,20 1|0:22:9,13 ./.:14:8,6 +chr20 75250 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25621388;QSTRAND=- GT:DP:AD ./.:19:8,11 ./.:16:5,11 0|1:18:11,7 +chr20 76709 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25635256;QSTRAND=- GT:DP:AD ./.:27:7,20 ./.:37:25,12 1|0:43:25,18 +chr20 77005 . A G 60 . QNAME=cluster19_000000F;QSTART=25685886;QSTRAND=- GT:DP:AD ./.:27:7,20 1|0:14:6,8 ./.:32:13,19 +chr20 77736 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25618901;QSTRAND=- GT:DP:AD ./.:47:23,24 ./.:28:13,15 0|1:36:17,19 +chr20 78705 . A T 60 . QNAME=cluster19_000000F;QSTART=25684187;QSTRAND=- GT:DP:AD ./.:38:14,24 1|0:45:22,23 ./.:45:21,24 +chr20 80457 . C T 60 . QNAME=cluster19_000000F;QSTART=25682435;QSTRAND=- GT:DP:AD ./.:30:18,12 1|0:33:12,21 ./.:41:17,24 +chr20 80497 . C CT 60 . QNAME=cluster19_000000F;QSTART=25682394;QSTRAND=- GT:DP:AD ./.:37:13,24 1|0:32:20,12 ./.:26:16,10 +chr20 81154 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=60071;QSTRAND=+ GT:DP:AD 1|1:11:5,6 0|1:36:16,20 1|1:27:16,11 +chr20 82603 . A C 60 . QNAME=cluster19_000000F;QSTART=25680288;QSTRAND=- GT:DP:AD ./.:19:6,13 1|0:24:11,13 ./.:24:12,12 +chr20 83158 . C T 60 . QNAME=cluster19_000000F;QSTART=25679733;QSTRAND=- GT:DP:AD ./.:25:8,17 1|0:31:11,20 ./.:32:10,22 +chr20 85259 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=64176;QSTRAND=+ GT:DP:AD 1|1:24:11,13 0|1:38:19,19 1|1:31:19,12 +chr20 85729 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=64646;QSTRAND=+ GT:DP:AD 1|1:25:17,8 0|1:30:16,14 1|1:31:14,17 +chr20 86079 . C A 60 . QNAME=cluster19_000000F;QSTART=45136;QSTRAND=+ GT:DP:AD ./.:15:7,8 0|1:34:14,20 ./.:29:15,14 +chr20 86859 . T TTGGTATCTAG 60 . QNAME=HG002-S9-H1-000001F;QSTART=65777;QSTRAND=+ GT:DP:AD 1|1:34:25,9 0|1:36:19,17 1|1:38:17,21 +chr20 88108 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=67035;QSTRAND=+ GT:DP:AD 1|1:20:7,13 1|1:40:24,16 1|1:33:11,22 +chr20 88453 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25623502;QSTRAND=- GT:DP:AD ./.:24:12,12 ./.:24:10,14 1|0:33:22,11 +chr20 88865 . G GACACAC 60 . QNAME=cluster19_000000F;QSTART=47933;QSTRAND=+ GT:DP:AD ./.:18:9,9 0|1:30:12,18 1|0:38:17,21 +chr20 88865 . G GACAC 60 . QNAME=cluster19_000000F;QSTART=25674022;QSTRAND=- GT:DP:AD ./.:44:23,21 1|0:32:21,11 ./.:45:23,22 +chr20 90339 . G A 60 . QNAME=cluster19_000000F;QSTART=25672552;QSTRAND=- GT:DP:AD ./.:32:20,12 1|0:30:15,15 ./.:25:18,7 +chr20 92251 . G A 60 . QNAME=cluster19_000000F;QSTART=25670641;QSTRAND=- GT:DP:AD ./.:37:18,19 1|0:41:25,16 ./.:36:12,24 +chr20 92395 . C CT 60 . QNAME=cluster19_000000F;QSTART=25670496;QSTRAND=- GT:DP:AD ./.:15:8,7 1|0:24:19,5 ./.:35:17,18 +chr20 92969 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25618979;QSTRAND=- GT:DP:AD ./.:32:12,20 ./.:28:13,15 1|0:30:17,13 +chr20 93706 . G A 60 . QNAME=cluster19_000000F;QSTART=52778;QSTRAND=+ GT:DP:AD ./.:31:21,10 0|1:31:21,10 ./.:38:18,20 +chr20 94088 . G GT 60 . QNAME=HG002-S9-H1-000001F;QSTART=73013;QSTRAND=+ GT:DP:AD 1|1:27:20,7 1|0:26:8,18 ./.:39:21,18 +chr20 94613 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=73538;QSTRAND=+ GT:DP:AD 1|1:27:21,6 ./.:21:15,6 ./.:20:13,7 +chr20 96130 . C T 60 . QNAME=cluster19_000000F;QSTART=25666761;QSTRAND=- GT:DP:AD ./.:39:14,25 1|0:34:22,12 ./.:32:7,25 +chr20 96321 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=75246;QSTRAND=+ GT:DP:AD 1|1:35:19,16 1|1:28:12,16 ./.:33:23,10 +chr20 97324 . G GT 60 . QNAME=HG002-S9-H1-000001F;QSTART=76250;QSTRAND=+ GT:DP:AD 1|1:20:15,5 ./.:33:8,25 ./.:24:12,12 +chr20 98593 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=77519;QSTRAND=+ GT:DP:AD 1|1:27:14,13 1|0:30:9,21 ./.:26:8,18 +chr20 99430 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=78356;QSTRAND=+ GT:DP:AD 1|1:37:17,20 ./.:49:24,25 ./.:31:17,14 +chr20 99840 . G C 60 . QNAME=cluster19_000000F;QSTART=25663051;QSTRAND=- GT:DP:AD ./.:37:19,18 1|0:41:19,22 ./.:24:5,19 +chr20 100014 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=78940;QSTRAND=+ GT:DP:AD 1|1:21:11,10 1|1:32:10,22 1|1:11:5,6 +chr20 101338 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=54816;QSTRAND=+ GT:DP:AD 0|1:21:5,16 ./.:16:7,9 ./.:14:6,8 +chr20 101341 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25610607;QSTRAND=- GT:DP:AD ./.:46:25,21 ./.:48:25,23 1|0:31:6,25 +chr20 101371 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=80297;QSTRAND=+ GT:DP:AD 1|0:14:6,8 0|1:34:17,17 ./.:28:8,20 +chr20 101433 . A C 60 . QNAME=cluster19_000000F;QSTART=25661458;QSTRAND=- GT:DP:AD ./.:36:14,22 1|1:30:12,18 ./.:24:11,13 +chr20 101438 . G A 60 . QNAME=cluster19_000000F;QSTART=25661453;QSTRAND=- GT:DP:AD ./.:30:22,8 1|1:47:22,25 ./.:27:8,19 +chr20 101498 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25610450;QSTRAND=- GT:DP:AD ./.:21:6,15 ./.:36:21,15 1|0:25:9,16 +chr20 101505 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=54983;QSTRAND=+ GT:DP:AD 0|1:47:25,22 ./.:31:7,24 1|0:36:25,11 +chr20 101576 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=80502;QSTRAND=+ GT:DP:AD 1|1:19:10,9 1|1:30:10,20 0|1:18:6,12 +chr20 102609 . C CTGTG 60 . QNAME=cluster23_scaffold_2;QSTART=25594014;QSTRAND=- GT:DP:AD ./.:19:5,14 ./.:21:6,15 0|1:30:14,16 +chr20 102613 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=56089;QSTRAND=+ GT:DP:AD 0|1:25:14,11 ./.:39:20,19 ./.:35:11,24 +chr20 102619 . G C 60 . QNAME=cluster19_000000F;QSTART=25660280;QSTRAND=- GT:DP:AD ./.:41:21,20 1|1:40:16,24 1|0:29:18,11 +chr20 102621 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25609335;QSTRAND=- GT:DP:AD ./.:49:25,24 ./.:37:22,15 1|0:28:15,13 +chr20 102623 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25609333;QSTRAND=- GT:DP:AD ./.:30:15,15 ./.:38:23,15 1|0:34:16,18 +chr20 102633 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=81537;QSTRAND=+ GT:DP:AD 1|0:45:25,20 ./.:14:6,8 ./.:23:12,11 +chr20 102634 . T C 60 . QNAME=cluster19_000000F;QSTART=25660265;QSTRAND=- GT:DP:AD ./.:24:7,17 1|1:31:22,9 ./.:13:7,6 +chr20 105364 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25591258;QSTRAND=- GT:DP:AD ./.:39:16,23 ./.:28:16,12 0|1:24:8,16 +chr20 106471 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=85374;QSTRAND=+ GT:DP:AD 1|1:40:18,22 ./.:31:8,23 ./.:27:5,22 +chr20 106775 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=85678;QSTRAND=+ GT:DP:AD 1|1:20:7,13 ./.:41:19,22 0|1:20:15,5 +chr20 107149 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25589473;QSTRAND=- GT:DP:AD ./.:23:11,12 ./.:22:12,10 0|1:28:22,6 +chr20 107514 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25589108;QSTRAND=- GT:DP:AD ./.:36:19,17 ./.:38:15,23 0|1:15:10,5 +chr20 109367 . C A 60 . QNAME=cluster19_000000F;QSTART=25653532;QSTRAND=- GT:DP:AD ./.:35:11,24 1|1:38:23,15 ./.:12:6,6 +chr20 110447 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=89350;QSTRAND=+ GT:DP:AD 1|1:30:5,25 1|1:20:6,14 0|1:31:23,8 +chr20 110867 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=89770;QSTRAND=+ GT:DP:AD 1|1:26:18,8 1|1:29:9,20 0|1:24:15,9 +chr20 111066 . C T 60 . QNAME=cluster19_000000F;QSTART=70130;QSTRAND=+ GT:DP:AD ./.:33:11,22 0|1:37:14,23 ./.:43:24,19 +chr20 111725 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=90628;QSTRAND=+ GT:DP:AD 1|1:18:6,12 ./.:22:17,5 ./.:32:7,25 +chr20 111886 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=90789;QSTRAND=+ GT:DP:AD 1|1:45:24,21 1|1:36:11,25 0|1:32:14,18 +chr20 112799 . A G 60 . QNAME=cluster19_000000F;QSTART=25650100;QSTRAND=- GT:DP:AD ./.:19:5,14 1|0:31:7,24 ./.:47:22,25 +chr20 113005 . C CT 60 . QNAME=cluster19_000000F;QSTART=25649893;QSTRAND=- GT:DP:AD ./.:24:13,11 1|0:19:14,5 ./.:35:11,24 +chr20 113290 . G A 60 . QNAME=cluster19_000000F;QSTART=25649608;QSTRAND=- GT:DP:AD ./.:19:10,9 1|0:27:21,6 ./.:29:9,20 +chr20 115856 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=25580766;QSTRAND=- GT:DP:AD ./.:33:20,13 ./.:25:16,9 0|1:46:21,25 +chr20 120058 . C T 60 . QNAME=cluster19_000000F;QSTART=25642840;QSTRAND=- GT:DP:AD ./.:25:10,15 1|0:32:22,10 ./.:21:16,5 +chr20 120721 . G A 60 . QNAME=cluster19_000000F;QSTART=79785;QSTRAND=+ GT:DP:AD ./.:36:12,24 0|1:15:6,9 ./.:40:24,16 +chr20 121264 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=74739;QSTRAND=+ GT:DP:AD 0|1:32:20,12 ./.:19:9,10 ./.:34:16,18 +chr20 121540 . T C 60 . QNAME=cluster19_000000F;QSTART=25641358;QSTRAND=- GT:DP:AD ./.:26:11,15 1|0:28:5,23 ./.:32:18,14 +chr20 122158 . G A 60 . QNAME=cluster19_000000F;QSTART=25640740;QSTRAND=- GT:DP:AD ./.:20:7,13 1|0:27:20,7 ./.:26:7,19 +chr20 122876 . A T 60 . QNAME=cluster19_000000F;QSTART=25640022;QSTRAND=- GT:DP:AD ./.:26:21,5 1|0:30:19,11 ./.:34:9,25 +chr20 124258 . C T 60 . QNAME=cluster19_000000F;QSTART=25638640;QSTRAND=- GT:DP:AD ./.:37:13,24 1|0:33:21,12 ./.:39:19,20 +chr20 125994 . G A 60 . QNAME=cluster19_000000F;QSTART=25636904;QSTRAND=- GT:DP:AD ./.:47:23,24 1|0:13:8,5 ./.:36:11,25 +chr20 126062 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=104949;QSTRAND=+ GT:DP:AD 1|0:41:25,16 0|1:33:20,13 1|1:45:24,21 +chr20 126062 . C CTTT 60 . QNAME=cluster19_000000F;QSTART=25636833;QSTRAND=- GT:DP:AD ./.:45:24,21 1|0:29:9,20 ./.:31:18,13 +chr20 127645 . T G 60 . QNAME=cluster19_000000F;QSTART=25635250;QSTRAND=- GT:DP:AD ./.:28:19,9 1|0:33:15,18 ./.:47:25,22 +chr20 127687 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=106574;QSTRAND=+ GT:DP:AD 1|1:32:17,15 1|1:31:8,23 0|1:32:11,21 +chr20 128317 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=107204;QSTRAND=+ GT:DP:AD 1|1:39:15,24 ./.:41:18,23 ./.:13:6,7 +chr20 128517 . C CAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=107405;QSTRAND=+ GT:DP:AD 1|0:18:8,10 ./.:48:25,23 1|0:38:22,16 +chr20 128517 . C CA 60 . QNAME=HG002-S9-H2-000001F;QSTART=81976;QSTRAND=+ GT:DP:AD 0|1:31:12,19 0|1:21:6,15 ./.:41:16,25 +chr20 129417 . G C 60 . QNAME=cluster19_000000F;QSTART=25633479;QSTRAND=- GT:DP:AD ./.:31:6,25 1|0:38:19,19 ./.:32:13,19 +chr20 129457 . A G 60 . QNAME=cluster19_000000F;QSTART=25633439;QSTRAND=- GT:DP:AD ./.:34:15,19 1|0:41:24,17 ./.:31:10,21 +chr20 130061 . C T 60 . QNAME=cluster19_000000F;QSTART=25632835;QSTRAND=- GT:DP:AD ./.:17:10,7 1|0:36:17,19 ./.:27:13,14 +chr20 130282 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=83741;QSTRAND=+ GT:DP:AD 0|1:32:14,18 ./.:36:19,17 ./.:24:10,14 +chr20 130329 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=109218;QSTRAND=+ GT:DP:AD 1|1:27:7,20 ./.:47:24,23 ./.:35:16,19 +chr20 130338 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=109227;QSTRAND=+ GT:DP:AD 1|1:21:7,14 0|1:48:23,25 0|1:34:24,10 +chr20 130338 . A G 60 . QNAME=cluster19_000000F;QSTART=25632558;QSTRAND=- GT:DP:AD ./.:35:19,16 1|0:25:17,8 ./.:20:5,15 +chr20 130339 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=109228;QSTRAND=+ GT:DP:AD 1|1:34:14,20 0|1:41:22,19 0|1:44:19,25 +chr20 130636 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25565985;QSTRAND=- GT:DP:AD ./.:39:16,23 ./.:42:20,22 0|1:24:13,11 +chr20 130736 . A C 60 . QNAME=cluster19_000000F;QSTART=25632160;QSTRAND=- GT:DP:AD ./.:20:8,12 1|0:21:10,11 ./.:40:24,16 +chr20 130742 . T C 60 . QNAME=cluster19_000000F;QSTART=25632154;QSTRAND=- GT:DP:AD ./.:38:25,13 1|0:21:12,9 ./.:37:23,14 +chr20 131163 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=110052;QSTRAND=+ GT:DP:AD 1|1:28:13,15 ./.:39:25,14 ./.:27:22,5 +chr20 131230 . A G 60 . QNAME=cluster19_000000F;QSTART=25631666;QSTRAND=- GT:DP:AD ./.:35:14,21 1|0:30:9,21 ./.:35:21,14 +chr20 131374 . G A 60 . QNAME=cluster19_000000F;QSTART=25631522;QSTRAND=- GT:DP:AD ./.:13:6,7 1|0:38:16,22 ./.:21:6,15 +chr20 132236 . C T 60 . QNAME=cluster19_000000F;QSTART=91302;QSTRAND=+ GT:DP:AD ./.:32:7,25 0|1:29:23,6 ./.:36:20,16 +chr20 133539 . T C 60 . QNAME=cluster19_000000F;QSTART=25629357;QSTRAND=- GT:DP:AD ./.:23:8,15 1|0:35:21,14 ./.:47:25,22 +chr20 133631 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25562990;QSTRAND=- GT:DP:AD ./.:32:16,16 ./.:37:23,14 0|1:44:19,25 +chr20 133700 . C A 60 . QNAME=cluster19_000000F;QSTART=25629196;QSTRAND=- GT:DP:AD ./.:28:16,12 1|0:35:12,23 ./.:35:17,18 +chr20 134275 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25562346;QSTRAND=- GT:DP:AD ./.:27:19,8 ./.:29:11,18 0|1:27:20,7 +chr20 134452 . A C 60 . QNAME=cluster19_000000F;QSTART=25628444;QSTRAND=- GT:DP:AD ./.:19:12,7 1|0:25:15,10 ./.:22:10,12 +chr20 134675 . C CA 60 . QNAME=cluster19_000000F;QSTART=25628220;QSTRAND=- GT:DP:AD ./.:16:5,11 1|0:24:6,18 ./.:36:23,13 +chr20 134915 . G A 60 . QNAME=cluster19_000000F;QSTART=25627980;QSTRAND=- GT:DP:AD ./.:17:6,11 1|0:37:15,22 ./.:36:13,23 +chr20 135005 . T C 60 . QNAME=cluster19_000000F;QSTART=25627890;QSTRAND=- GT:DP:AD ./.:43:20,23 1|0:22:17,5 ./.:27:19,8 +chr20 135211 . C CA 60 . QNAME=cluster19_000000F;QSTART=25627683;QSTRAND=- GT:DP:AD ./.:31:23,8 1|0:40:19,21 ./.:23:5,18 +chr20 135293 . C G 60 . QNAME=cluster19_000000F;QSTART=25627601;QSTRAND=- GT:DP:AD ./.:15:5,10 1|0:30:5,25 ./.:35:13,22 +chr20 135387 . G A 60 . QNAME=cluster19_000000F;QSTART=94453;QSTRAND=+ GT:DP:AD ./.:24:16,8 0|1:28:23,5 ./.:30:22,8 +chr20 135595 . A G 60 . QNAME=cluster19_000000F;QSTART=25627299;QSTRAND=- GT:DP:AD ./.:40:25,15 1|0:28:13,15 ./.:29:7,22 +chr20 135764 . G A 60 . QNAME=cluster19_000000F;QSTART=25627130;QSTRAND=- GT:DP:AD ./.:45:24,21 1|0:34:23,11 ./.:28:11,17 +chr20 135904 . G A 60 . QNAME=cluster19_000000F;QSTART=25626990;QSTRAND=- GT:DP:AD ./.:36:25,11 1|0:36:24,12 ./.:17:10,7 +chr20 136146 . A G 60 . QNAME=cluster19_000000F;QSTART=25626748;QSTRAND=- GT:DP:AD ./.:31:13,18 1|0:20:12,8 ./.:30:11,19 +chr20 136216 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=89675;QSTRAND=+ GT:DP:AD 0|1:42:23,19 ./.:27:20,7 ./.:27:5,22 +chr20 136668 . G GCAGGATTTCAT 60 . QNAME=cluster19_000000F;QSTART=25626215;QSTRAND=- GT:DP:AD ./.:22:7,15 1|0:24:7,17 ./.:32:10,22 +chr20 139004 . G GT 60 . QNAME=cluster19_000000F;QSTART=25623878;QSTRAND=- GT:DP:AD ./.:19:8,11 1|1:41:21,20 ./.:23:7,16 +chr20 139481 . A AAG 60 . QNAME=HG002-S9-H1-000001F;QSTART=118371;QSTRAND=+ GT:DP:AD 1|1:29:23,6 1|1:31:17,14 0|1:28:8,20 +chr20 139830 . A G 60 . QNAME=cluster19_000000F;QSTART=25623050;QSTRAND=- GT:DP:AD ./.:32:12,20 1|0:20:9,11 ./.:33:13,20 +chr20 140109 . C CAATT 60 . QNAME=HG002-S9-H1-000001F;QSTART=119001;QSTRAND=+ GT:DP:AD 1|1:35:15,20 1|1:28:17,11 0|1:31:7,24 +chr20 140669 . A C 60 . QNAME=cluster19_000000F;QSTART=25622207;QSTRAND=- GT:DP:AD ./.:41:20,21 1|0:32:15,17 ./.:31:19,12 +chr20 140837 . C A 60 . QNAME=cluster19_000000F;QSTART=25622039;QSTRAND=- GT:DP:AD ./.:24:16,8 1|0:45:20,25 ./.:36:17,19 +chr20 140838 . G GT 60 . QNAME=cluster23_scaffold_3;QSTART=25571114;QSTRAND=- GT:DP:AD ./.:36:20,16 ./.:38:16,22 1|0:24:16,8 +chr20 140859 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25571092;QSTRAND=- GT:DP:AD ./.:44:21,23 ./.:29:6,23 1|1:33:15,18 +chr20 141183 . C T 60 . QNAME=cluster19_000000F;QSTART=25621694;QSTRAND=- GT:DP:AD ./.:40:24,16 1|0:14:9,5 ./.:39:19,20 +chr20 141335 . G A 60 . QNAME=cluster19_000000F;QSTART=25621542;QSTRAND=- GT:DP:AD ./.:21:6,15 1|0:32:14,18 ./.:29:22,7 +chr20 141867 . G A 60 . QNAME=cluster19_000000F;QSTART=25621011;QSTRAND=- GT:DP:AD ./.:36:12,24 1|0:37:12,25 ./.:34:24,10 +chr20 142165 . T TTA 60 . QNAME=cluster19_000000F;QSTART=25620711;QSTRAND=- GT:DP:AD ./.:20:11,9 1|0:26:15,11 ./.:26:7,19 +chr20 143010 . G GT 60 . QNAME=cluster19_000000F;QSTART=102084;QSTRAND=+ GT:DP:AD ./.:33:21,12 0|1:21:13,8 0|1:28:18,10 +chr20 143661 . A C 60 . QNAME=cluster19_000000F;QSTART=25619215;QSTRAND=- GT:DP:AD ./.:33:22,11 1|0:34:12,22 ./.:28:9,19 +chr20 143771 . C T 60 . QNAME=cluster19_000000F;QSTART=25619105;QSTRAND=- GT:DP:AD ./.:28:5,23 1|0:13:7,6 ./.:23:18,5 +chr20 144480 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=123375;QSTRAND=+ GT:DP:AD 1|1:33:11,22 ./.:17:10,7 ./.:29:13,16 +chr20 144897 . G C 60 . QNAME=cluster19_000000F;QSTART=25617979;QSTRAND=- GT:DP:AD ./.:27:8,19 1|0:31:7,24 ./.:33:13,20 +chr20 145888 . G A 60 . QNAME=cluster19_000000F;QSTART=25616994;QSTRAND=- GT:DP:AD ./.:22:15,7 1|1:26:5,21 ./.:25:6,19 +chr20 145959 . C A 60 . QNAME=cluster19_000000F;QSTART=25616923;QSTRAND=- GT:DP:AD ./.:35:25,10 1|1:34:10,24 ./.:37:20,17 +chr20 145973 . T C 60 . QNAME=cluster19_000000F;QSTART=25616909;QSTRAND=- GT:DP:AD ./.:32:11,21 1|1:13:7,6 ./.:29:18,11 +chr20 146089 . C T 60 . QNAME=cluster19_000000F;QSTART=25616793;QSTRAND=- GT:DP:AD ./.:22:6,16 1|1:38:18,20 ./.:30:24,6 +chr20 146119 . C T 60 . QNAME=cluster19_000000F;QSTART=25616763;QSTRAND=- GT:DP:AD ./.:25:17,8 1|1:24:19,5 ./.:29:18,11 +chr20 146282 . C A 60 . QNAME=cluster19_000000F;QSTART=25616600;QSTRAND=- GT:DP:AD ./.:28:13,15 1|1:22:6,16 ./.:23:7,16 +chr20 146289 . A T 60 . QNAME=cluster19_000000F;QSTART=25616593;QSTRAND=- GT:DP:AD ./.:30:17,13 1|1:45:22,23 ./.:39:25,14 +chr20 147079 . A C 60 . QNAME=cluster19_000000F;QSTART=25615803;QSTRAND=- GT:DP:AD ./.:35:11,24 1|1:24:16,8 ./.:20:14,6 +chr20 147311 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25564642;QSTRAND=- GT:DP:AD ./.:45:21,24 ./.:17:7,10 1|1:36:18,18 +chr20 148061 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=101523;QSTRAND=+ GT:DP:AD 0|1:33:25,8 ./.:27:19,8 ./.:21:16,5 +chr20 148072 . C G 60 . QNAME=cluster19_000000F;QSTART=25614810;QSTRAND=- GT:DP:AD ./.:33:24,9 1|1:31:23,8 ./.:24:10,14 +chr20 148222 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25563731;QSTRAND=- GT:DP:AD ./.:40:18,22 ./.:41:16,25 1|1:42:22,20 +chr20 148422 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25563531;QSTRAND=- GT:DP:AD ./.:42:24,18 ./.:44:19,25 1|1:20:6,14 +chr20 148972 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=127865;QSTRAND=+ GT:DP:AD 1|1:23:9,14 1|1:33:15,18 1|1:23:16,7 +chr20 148994 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=127887;QSTRAND=+ GT:DP:AD 1|1:20:12,8 ./.:39:24,15 ./.:26:5,21 +chr20 149013 . A ACCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=127907;QSTRAND=+;SVTYPE=INS;SVLEN=69 GT:DP:AD 1/1:35:19,16 ./.:31:21,10 1/0:17:8,9 +chr20 149073 . G GAATCCTGACCCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCA 60 . QNAME=cluster23_scaffold_2;QSTART=25547471;QSTRAND=-;SVTYPE=INS;SVLEN=69 GT:DP:AD ./.:44:25,19 ./.:36:12,24 0/1:27:20,7 +chr20 149095 . G GGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGACCCATATTTGGGAA 60 . QNAME=cluster19_000000F;QSTART=25613718;QSTRAND=-;SVTYPE=INS;SVLEN=69 GT:DP:AD ./.:36:13,23 1/1:14:7,7 ./.:40:19,21 +chr20 149223 . C T 60 . QNAME=cluster19_000000F;QSTART=25613590;QSTRAND=- GT:DP:AD ./.:26:5,21 1|1:42:19,23 ./.:38:21,17 +chr20 150418 . T A 60 . QNAME=cluster23_scaffold_2;QSTART=25546126;QSTRAND=- GT:DP:AD ./.:22:14,8 ./.:28:18,10 0|1:35:25,10 +chr20 150492 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25561392;QSTRAND=- GT:DP:AD ./.:39:17,22 ./.:37:20,17 1|0:29:9,20 +chr20 150721 . C T 60 . QNAME=cluster19_000000F;QSTART=25612092;QSTRAND=- GT:DP:AD ./.:30:24,6 1|1:14:5,9 ./.:33:17,16 +chr20 150854 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=129816;QSTRAND=+ GT:DP:AD 1|1:41:20,21 1|1:31:13,18 1|1:29:16,13 +chr20 151016 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=129978;QSTRAND=+ GT:DP:AD 1|1:25:5,20 1|1:40:18,22 1|1:42:17,25 +chr20 151307 . C CCA 60 . QNAME=cluster19_000000F;QSTART=25611507;QSTRAND=- GT:DP:AD ./.:21:11,10 1|1:22:17,5 ./.:31:10,21 +chr20 151898 . A T 60 . QNAME=cluster23_scaffold_2;QSTART=25544647;QSTRAND=- GT:DP:AD ./.:30:25,5 ./.:25:13,12 0|1:37:20,17 +chr20 152134 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=131095;QSTRAND=+ GT:DP:AD 1|1:37:20,17 ./.:34:24,10 ./.:43:18,25 +chr20 152450 . C CA 60 . QNAME=cluster19_000000F;QSTART=25610364;QSTRAND=- GT:DP:AD ./.:50:25,25 1|1:30:23,7 ./.:33:15,18 +chr20 152517 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=131475;QSTRAND=+ GT:DP:AD 1|1:14:8,6 1|1:33:19,14 1|1:16:7,9 +chr20 152792 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=131750;QSTRAND=+ GT:DP:AD 1|0:25:5,20 ./.:32:17,15 1|1:21:11,10 +chr20 153098 . G GT 60 . QNAME=HG002-S9-H1-000001F;QSTART=132057;QSTRAND=+ GT:DP:AD 1|0:49:24,25 ./.:27:21,6 1|1:39:23,16 +chr20 153259 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=132218;QSTRAND=+ GT:DP:AD 1|0:31:15,16 ./.:26:12,14 1|1:32:18,14 +chr20 153376 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=106903;QSTRAND=+ GT:DP:AD 0|1:23:12,11 1|1:27:6,21 ./.:38:23,15 +chr20 153555 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25558332;QSTRAND=- GT:DP:AD ./.:35:17,18 ./.:26:5,21 1|1:45:22,23 +chr20 153640 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25558247;QSTRAND=- GT:DP:AD ./.:25:20,5 ./.:32:25,7 1|1:49:24,25 +chr20 153643 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=132602;QSTRAND=+ GT:DP:AD 1|1:45:20,25 1|1:16:6,10 1|1:25:14,11 +chr20 153725 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=132684;QSTRAND=+ GT:DP:AD 1|1:35:11,24 1|1:25:6,19 1|1:15:5,10 +chr20 153759 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=132718;QSTRAND=+ GT:DP:AD 1|0:33:17,16 ./.:32:14,18 1|0:36:23,13 +chr20 153780 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=132739;QSTRAND=+ GT:DP:AD 1|1:26:19,7 1|1:31:6,25 1|1:29:5,24 +chr20 153835 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=132785;QSTRAND=+ GT:DP:AD 1|1:21:15,6 1|1:30:9,21 1|1:14:7,7 +chr20 153898 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=132848;QSTRAND=+ GT:DP:AD 1|0:20:13,7 ./.:30:25,5 1|0:36:16,20 +chr20 154002 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=132952;QSTRAND=+ GT:DP:AD 1|1:38:17,21 1|1:27:9,18 1|1:40:25,15 +chr20 154128 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=133079;QSTRAND=+ GT:DP:AD 1|0:25:6,19 ./.:33:16,17 1|1:22:17,5 +chr20 154203 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=133154;QSTRAND=+ GT:DP:AD 1|1:26:12,14 1|1:37:13,24 1|1:27:6,21 +chr20 154290 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=133241;QSTRAND=+ GT:DP:AD 1|1:29:6,23 1|1:33:10,23 1|1:37:17,20 +chr20 154474 . G GTTTGCATTCACAGGAAGACTATAAATAAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=133426;QSTRAND=+;SVTYPE=INS;SVLEN=29 GT:DP:AD 1/1:24:18,6 1/1:18:11,7 1/1:19:9,10 +chr20 154847 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=133823;QSTRAND=+ GT:DP:AD 1|1:35:14,21 1|1:27:9,18 1|1:22:7,15 +chr20 155384 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=134360;QSTRAND=+ GT:DP:AD 1|0:24:13,11 ./.:25:12,13 1|1:17:7,10 +chr20 155733 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=134709;QSTRAND=+ GT:DP:AD 1|0:17:10,7 ./.:25:13,12 1|1:36:24,12 +chr20 155813 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=134789;QSTRAND=+ GT:DP:AD 1|0:37:15,22 ./.:27:11,16 1|1:23:5,18 +chr20 156080 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=135056;QSTRAND=+ GT:DP:AD 1|0:26:12,14 ./.:21:15,6 1|1:28:21,7 +chr20 156287 . G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=135264;QSTRAND=+ GT:DP:AD 1|0:31:12,19 ./.:49:25,24 1|1:20:8,12 +chr20 156473 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=135450;QSTRAND=+ GT:DP:AD 1|0:30:13,17 ./.:41:25,16 1|1:35:10,25 +chr20 156486 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=110029;QSTRAND=+ GT:DP:AD 0|1:31:9,22 1|1:31:8,23 ./.:31:19,12 +chr20 156669 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=135646;QSTRAND=+ GT:DP:AD 1|0:37:25,12 ./.:32:17,15 1|1:21:14,7 +chr20 156813 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=135790;QSTRAND=+ GT:DP:AD 1|0:19:9,10 ./.:25:14,11 1|1:36:13,23 +chr20 156881 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=135856;QSTRAND=+ GT:DP:AD 1|0:50:25,25 ./.:35:14,21 1|1:33:9,24 +chr20 157033 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=110574;QSTRAND=+ GT:DP:AD 0|1:15:6,9 1|1:34:19,15 ./.:38:17,21 +chr20 157259 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=136234;QSTRAND=+ GT:DP:AD 1|0:25:6,19 ./.:25:14,11 1|1:34:21,13 +chr20 157292 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=136267;QSTRAND=+ GT:DP:AD 1|1:30:11,19 1|1:21:14,7 1|1:35:25,10 +chr20 157363 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=136338;QSTRAND=+ GT:DP:AD 1|1:18:9,9 1|1:20:12,8 1|1:33:24,9 +chr20 157484 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=136459;QSTRAND=+ GT:DP:AD 1|0:25:19,6 ./.:25:7,18 1|1:21:6,15 +chr20 157507 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=136482;QSTRAND=+ GT:DP:AD 1|0:29:17,12 ./.:44:22,22 1|1:27:6,21 +chr20 157819 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=136794;QSTRAND=+ GT:DP:AD 1|0:32:10,22 ./.:17:10,7 1|1:26:13,13 +chr20 157914 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=136889;QSTRAND=+ GT:DP:AD 1|0:31:10,21 ./.:35:23,12 1|1:16:8,8 +chr20 157960 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=111492;QSTRAND=+ GT:DP:AD 0|1:26:9,17 1|1:24:10,14 ./.:32:20,12 +chr20 157962 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=111494;QSTRAND=+ GT:DP:AD 0|1:32:15,17 1|1:30:18,12 ./.:35:24,11 +chr20 157965 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=136932;QSTRAND=+ GT:DP:AD 1|0:13:8,5 ./.:38:21,17 1|1:27:17,10 +chr20 157974 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=136941;QSTRAND=+ GT:DP:AD 1|0:31:25,6 ./.:33:21,12 1|1:30:14,16 +chr20 157979 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=136946;QSTRAND=+ GT:DP:AD 1|0:39:25,14 ./.:46:21,25 1|1:15:7,8 +chr20 158513 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=137480;QSTRAND=+ GT:DP:AD 1|0:31:8,23 ./.:22:5,17 1|1:44:23,21 +chr20 158532 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=137499;QSTRAND=+ GT:DP:AD 1|0:27:18,9 ./.:49:24,25 1|0:33:22,11 +chr20 158721 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=112253;QSTRAND=+ GT:DP:AD 0|1:30:17,13 1|1:14:6,8 ./.:43:20,23 +chr20 158768 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=137735;QSTRAND=+ GT:DP:AD 1|0:36:24,12 ./.:26:15,11 1|1:31:8,23 +chr20 158815 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=137782;QSTRAND=+ GT:DP:AD 1|0:38:17,21 ./.:25:13,12 1|1:39:16,23 +chr20 158935 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=137902;QSTRAND=+ GT:DP:AD 1|0:19:14,5 ./.:36:23,13 1|1:41:25,16 +chr20 159104 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=138071;QSTRAND=+ GT:DP:AD 1|1:35:25,10 1|1:24:6,18 1|1:19:6,13 +chr20 159197 . A T 60 . QNAME=cluster23_scaffold_2;QSTART=25537337;QSTRAND=- GT:DP:AD ./.:24:10,14 ./.:26:17,9 0|1:28:22,6 +chr20 159200 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=112732;QSTRAND=+ GT:DP:AD 0|1:26:6,20 1|1:44:24,20 ./.:31:22,9 +chr20 159274 . T TAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=138242;QSTRAND=+ GT:DP:AD 1|0:24:13,11 ./.:23:6,17 1|1:19:13,6 +chr20 159274 . T TAA 60 . QNAME=HG002-S9-H2-000001F;QSTART=112807;QSTRAND=+ GT:DP:AD 0|1:21:6,15 1|1:31:11,20 ./.:31:23,8 +chr20 159286 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=138259;QSTRAND=+ GT:DP:AD 1|0:28:13,15 ./.:25:15,10 1|1:29:18,11 +chr20 159445 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=112979;QSTRAND=+ GT:DP:AD 0|1:26:5,21 1|1:35:15,20 ./.:31:17,14 +chr20 159495 . G GAATGGCATAAACT 60 . QNAME=HG002-S9-H1-000001F;QSTART=138469;QSTRAND=+ GT:DP:AD 1|0:25:6,19 ./.:27:14,13 1|1:26:13,13 +chr20 159530 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=138516;QSTRAND=+ GT:DP:AD 1|0:39:22,17 ./.:24:15,9 1|1:37:12,25 +chr20 159639 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=113173;QSTRAND=+ GT:DP:AD 0|1:44:21,23 1|1:22:6,16 ./.:32:16,16 +chr20 159864 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=138847;QSTRAND=+ GT:DP:AD 1|0:21:15,6 ./.:41:18,23 1|1:34:16,18 +chr20 159865 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=138848;QSTRAND=+ GT:DP:AD 1|0:21:13,8 ./.:37:16,21 1|1:39:16,23 +chr20 160054 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=139036;QSTRAND=+ GT:DP:AD 1|0:24:19,5 ./.:48:23,25 1|1:19:11,8 +chr20 160212 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=139194;QSTRAND=+ GT:DP:AD 1|0:30:9,21 ./.:42:20,22 1|1:25:16,9 +chr20 160282 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=139264;QSTRAND=+ GT:DP:AD 1|0:32:14,18 ./.:41:17,24 1|1:24:17,7 +chr20 160312 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=139294;QSTRAND=+ GT:DP:AD 1|0:30:14,16 ./.:33:20,13 1|1:28:10,18 +chr20 160384 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=139366;QSTRAND=+ GT:DP:AD 1|0:34:19,15 ./.:30:10,20 1|1:22:17,5 +chr20 160388 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=139370;QSTRAND=+ GT:DP:AD 1|0:29:24,5 ./.:31:20,11 1|1:22:15,7 +chr20 160408 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=139390;QSTRAND=+ GT:DP:AD 1|0:35:16,19 ./.:20:12,8 1|1:35:10,25 +chr20 160413 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=139395;QSTRAND=+ GT:DP:AD 1|0:14:8,6 ./.:26:10,16 1|1:20:6,14 +chr20 160433 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=139415;QSTRAND=+ GT:DP:AD 1|0:37:16,21 ./.:18:9,9 1|1:32:11,21 +chr20 160558 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=139540;QSTRAND=+ GT:DP:AD 1|0:42:24,18 ./.:29:12,17 1|0:36:25,11 +chr20 160625 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=139607;QSTRAND=+ GT:DP:AD 1|0:22:7,15 ./.:35:11,24 1|1:34:10,24 +chr20 160727 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=139709;QSTRAND=+ GT:DP:AD 1|0:46:25,21 ./.:24:14,10 1|1:27:21,6 +chr20 160731 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=139713;QSTRAND=+ GT:DP:AD 1|0:31:9,22 ./.:40:22,18 1|1:18:8,10 +chr20 160873 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=139855;QSTRAND=+ GT:DP:AD 1|0:28:19,9 ./.:29:9,20 1|1:23:5,18 +chr20 160889 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=139871;QSTRAND=+ GT:DP:AD 1|0:29:13,16 ./.:20:12,8 1|1:31:10,21 +chr20 160956 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=139938;QSTRAND=+ GT:DP:AD 1|0:19:11,8 ./.:28:19,9 1|1:32:18,14 +chr20 160967 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=139949;QSTRAND=+ GT:DP:AD 1|0:29:20,9 ./.:38:22,16 1|1:17:10,7 +chr20 161128 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140110;QSTRAND=+ GT:DP:AD 1|0:30:12,18 ./.:28:11,17 1|1:20:10,10 +chr20 161181 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140163;QSTRAND=+ GT:DP:AD 1|0:17:8,9 ./.:41:24,17 1|1:32:7,25 +chr20 161221 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140203;QSTRAND=+ GT:DP:AD 1|0:32:16,16 ./.:15:7,8 1|1:19:14,5 +chr20 161380 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=140362;QSTRAND=+ GT:DP:AD 1|1:15:8,7 1|1:36:17,19 1|1:23:18,5 +chr20 161451 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=140433;QSTRAND=+ GT:DP:AD 1|0:30:9,21 ./.:25:13,12 1|1:32:16,16 +chr20 161571 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=140553;QSTRAND=+ GT:DP:AD 1|0:22:12,10 ./.:17:8,9 1|1:26:20,6 +chr20 161588 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140570;QSTRAND=+ GT:DP:AD 1|1:18:5,13 1|1:45:22,23 1|1:39:19,20 +chr20 161621 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=140603;QSTRAND=+ GT:DP:AD 1|0:27:6,21 ./.:15:9,6 1|1:29:9,20 +chr20 161638 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=140620;QSTRAND=+ GT:DP:AD 1|1:34:12,22 1|1:37:13,24 1|1:33:25,8 +chr20 161698 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140680;QSTRAND=+ GT:DP:AD 1|0:43:18,25 ./.:34:18,16 1|1:38:17,21 +chr20 161730 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=140712;QSTRAND=+ GT:DP:AD 1|0:32:11,21 ./.:35:15,20 1|1:28:16,12 +chr20 161734 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=140716;QSTRAND=+ GT:DP:AD 1|0:45:20,25 ./.:31:21,10 1|1:26:12,14 +chr20 161770 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140752;QSTRAND=+ GT:DP:AD 1|0:19:7,12 ./.:39:16,23 1|1:29:12,17 +chr20 161914 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=140896;QSTRAND=+ GT:DP:AD 1|0:32:12,20 ./.:25:20,5 1|1:20:7,13 +chr20 161918 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=115449;QSTRAND=+ GT:DP:AD 0|1:25:5,20 1|1:27:16,11 ./.:40:17,23 +chr20 161991 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140973;QSTRAND=+ GT:DP:AD 1|0:28:22,6 ./.:29:16,13 1|1:32:21,11 +chr20 162151 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=141133;QSTRAND=+ GT:DP:AD 1|1:40:19,21 1|1:25:8,17 1|1:32:8,24 +chr20 162224 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=141206;QSTRAND=+ GT:DP:AD 1|0:34:15,19 ./.:21:16,5 1|1:30:12,18 +chr20 162225 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=141207;QSTRAND=+ GT:DP:AD 1|0:42:17,25 ./.:28:13,15 1|1:23:10,13 +chr20 162228 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=141210;QSTRAND=+ GT:DP:AD 1|0:26:10,16 ./.:27:5,22 1|1:41:21,20 +chr20 162268 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=141250;QSTRAND=+ GT:DP:AD 1|0:37:19,18 ./.:44:25,19 1|1:42:23,19 +chr20 162455 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=141437;QSTRAND=+ GT:DP:AD 1|0:15:7,8 ./.:39:20,19 1|1:18:6,12 +chr20 162806 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=116337;QSTRAND=+ GT:DP:AD 0|1:48:24,24 1|1:31:12,19 ./.:30:24,6 +chr20 162854 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=141836;QSTRAND=+ GT:DP:AD 1|0:44:25,19 ./.:24:14,10 1|1:23:11,12 +chr20 162932 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=141914;QSTRAND=+ GT:DP:AD 1|0:19:14,5 ./.:39:25,14 1|1:36:11,25 +chr20 163082 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=142064;QSTRAND=+ GT:DP:AD 1|0:45:22,23 ./.:16:8,8 1|1:28:10,18 +chr20 163113 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=142095;QSTRAND=+ GT:DP:AD 1|0:14:7,7 ./.:29:11,18 1|1:24:12,12 +chr20 163277 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=142259;QSTRAND=+ GT:DP:AD 1|1:15:9,6 1|1:49:25,24 1|1:46:24,22 +chr20 163741 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=117272;QSTRAND=+ GT:DP:AD 0|1:23:9,14 1|1:26:7,19 ./.:28:10,18 +chr20 163894 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=117425;QSTRAND=+ GT:DP:AD 0|1:30:18,12 1|1:26:18,8 ./.:17:6,11 +chr20 163919 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=117450;QSTRAND=+ GT:DP:AD 0|1:45:22,23 1|1:22:14,8 ./.:35:15,20 +chr20 163929 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=117460;QSTRAND=+ GT:DP:AD 0|1:35:14,21 1|1:34:25,9 ./.:31:21,10 +chr20 164191 . C CT 60 . QNAME=HG002-S9-H2-000001F;QSTART=117723;QSTRAND=+ GT:DP:AD 0|1:35:19,16 1|1:25:18,7 ./.:36:17,19 +chr20 164258 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=117787;QSTRAND=+ GT:DP:AD 0|1:28:21,7 1|1:26:20,6 ./.:26:5,21 +chr20 164569 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=143551;QSTRAND=+ GT:DP:AD 1|1:37:22,15 1|1:37:20,17 1|1:30:21,9 +chr20 164616 . G GC 60 . QNAME=HG002-S9-H2-000001F;QSTART=118146;QSTRAND=+ GT:DP:AD 0|1:17:5,12 1|1:25:11,14 ./.:23:11,12 +chr20 164772 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=118302;QSTRAND=+ GT:DP:AD 0|1:44:21,23 1|1:20:13,7 ./.:40:20,20 +chr20 165108 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=118638;QSTRAND=+ GT:DP:AD 0|1:30:20,10 1|1:22:12,10 ./.:26:9,17 +chr20 165108 . C CAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=144091;QSTRAND=+ GT:DP:AD 1|0:27:9,18 ./.:26:9,17 ./.:24:9,15 +chr20 165108 . C CACAT 60 . QNAME=cluster23_scaffold_3;QSTART=25546750;QSTRAND=- GT:DP:AD ./.:31:19,12 ./.:39:20,19 1|1:35:16,19 +chr20 165212 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=144196;QSTRAND=+ GT:DP:AD 1|0:23:12,11 ./.:43:24,19 1|1:26:16,10 +chr20 166310 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=145294;QSTRAND=+ GT:DP:AD 1|0:41:16,25 ./.:45:25,20 1|1:14:6,8 +chr20 166354 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=119884;QSTRAND=+ GT:DP:AD 0|1:40:15,25 1|1:29:20,9 ./.:37:13,24 +chr20 166856 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=145840;QSTRAND=+ GT:DP:AD 1|0:30:9,21 ./.:33:25,8 1|1:44:23,21 +chr20 167044 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=146027;QSTRAND=+ GT:DP:AD 1|0:17:10,7 ./.:33:15,18 1|1:42:23,19 +chr20 167104 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25529412;QSTRAND=- GT:DP:AD ./.:42:18,24 ./.:33:25,8 0|1:15:10,5 +chr20 167274 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=146257;QSTRAND=+ GT:DP:AD 1|0:29:16,13 ./.:36:21,15 1|1:36:22,14 +chr20 167276 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=146259;QSTRAND=+ GT:DP:AD 1|0:35:10,25 ./.:38:15,23 1|1:25:12,13 +chr20 167443 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=146426;QSTRAND=+ GT:DP:AD 1|1:20:14,6 1|1:15:6,9 1|1:35:12,23 +chr20 167839 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=146822;QSTRAND=+ GT:DP:AD 1|1:21:7,14 1|1:26:5,21 1|1:23:10,13 +chr20 168062 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=147045;QSTRAND=+ GT:DP:AD 1|0:30:8,22 ./.:25:14,11 1|1:26:16,10 +chr20 168766 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=122296;QSTRAND=+ GT:DP:AD 0|1:29:18,11 1|1:29:19,10 ./.:30:13,17 +chr20 169334 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=122864;QSTRAND=+ GT:DP:AD 0|1:20:8,12 1|1:36:17,19 ./.:25:15,10 +chr20 170689 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=124219;QSTRAND=+ GT:DP:AD 0|1:27:9,18 1|1:25:10,15 ./.:27:18,9 +chr20 171892 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=125422;QSTRAND=+ GT:DP:AD 0|1:29:6,23 1|1:22:8,14 ./.:40:17,23 +chr20 171929 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=125459;QSTRAND=+ GT:DP:AD 0|1:36:22,14 1|1:39:15,24 0|1:36:11,25 +chr20 172156 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=125686;QSTRAND=+ GT:DP:AD 0|1:20:8,12 1|0:28:20,8 ./.:21:8,13 +chr20 172258 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=25539602;QSTRAND=- GT:DP:AD ./.:35:19,16 ./.:31:9,22 1|0:36:23,13 +chr20 172331 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=125861;QSTRAND=+ GT:DP:AD 0|1:26:13,13 1|1:42:23,19 0|1:19:13,6 +chr20 172351 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=125881;QSTRAND=+ GT:DP:AD 0|1:41:16,25 1|1:32:7,25 0|1:27:19,8 +chr20 172626 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=126156;QSTRAND=+ GT:DP:AD 0|1:27:22,5 1|1:16:5,11 0|1:34:24,10 +chr20 172657 . T TTC 60 . QNAME=HG002-S9-H2-000001F;QSTART=126188;QSTRAND=+ GT:DP:AD 0|1:40:25,15 1|1:38:16,22 0|1:19:5,14 +chr20 172752 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=126284;QSTRAND=+ GT:DP:AD 0|1:37:22,15 1|1:36:11,25 ./.:41:24,17 +chr20 172789 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=25523730;QSTRAND=- GT:DP:AD ./.:29:11,18 ./.:38:20,18 0|1:36:25,11 +chr20 173036 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25523483;QSTRAND=- GT:DP:AD ./.:46:24,22 ./.:17:12,5 0|1:36:22,14 +chr20 173050 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=126582;QSTRAND=+ GT:DP:AD 0|1:32:13,19 1|1:16:6,10 ./.:32:12,20 +chr20 173133 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25523386;QSTRAND=- GT:DP:AD ./.:28:12,16 ./.:40:24,16 0|1:38:14,24 +chr20 173215 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=152197;QSTRAND=+ GT:DP:AD 1|0:29:12,17 ./.:15:10,5 ./.:34:12,22 +chr20 173973 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=127505;QSTRAND=+ GT:DP:AD 0|1:35:24,11 1|1:42:17,25 ./.:35:11,24 +chr20 174069 . G A 60 . QNAME=cluster19_000000F;QSTART=133216;QSTRAND=+ GT:DP:AD ./.:36:16,20 0|1:19:12,7 ./.:49:24,25 +chr20 174280 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25522243;QSTRAND=- GT:DP:AD ./.:23:18,5 ./.:31:7,24 0|1:45:24,21 +chr20 174737 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25521786;QSTRAND=- GT:DP:AD ./.:34:10,24 ./.:18:5,13 0|1:31:7,24 +chr20 174986 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25521537;QSTRAND=- GT:DP:AD ./.:32:20,12 ./.:48:23,25 0|1:44:24,20 +chr20 175210 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25521313;QSTRAND=- GT:DP:AD ./.:24:11,13 ./.:38:16,22 0|1:23:11,12 +chr20 175239 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25521284;QSTRAND=- GT:DP:AD ./.:23:17,6 ./.:25:8,17 0|1:41:16,25 +chr20 175269 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=128801;QSTRAND=+ GT:DP:AD 0|1:28:8,20 1|1:23:13,10 0|1:36:12,24 +chr20 175314 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=128846;QSTRAND=+ GT:DP:AD 0|1:28:18,10 1|1:19:13,6 ./.:42:17,25 +chr20 175375 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25521148;QSTRAND=- GT:DP:AD ./.:30:14,16 ./.:26:15,11 0|1:38:21,17 +chr20 175501 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25521022;QSTRAND=- GT:DP:AD ./.:27:10,17 ./.:31:19,12 0|1:18:7,11 +chr20 175524 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=129056;QSTRAND=+ GT:DP:AD 0|1:30:23,7 1|1:21:13,8 0|1:25:16,9 +chr20 175532 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=129064;QSTRAND=+ GT:DP:AD 0|1:43:25,18 1|1:36:21,15 0|1:28:17,11 +chr20 175563 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25520960;QSTRAND=- GT:DP:AD ./.:14:5,9 ./.:29:6,23 0|1:18:5,13 +chr20 175565 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25520958;QSTRAND=- GT:DP:AD ./.:15:8,7 ./.:29:20,9 0|1:37:24,13 +chr20 175595 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25520928;QSTRAND=- GT:DP:AD ./.:26:15,11 ./.:35:21,14 0|1:30:17,13 +chr20 175658 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25520865;QSTRAND=- GT:DP:AD ./.:32:25,7 ./.:16:10,6 0|1:47:25,22 +chr20 175659 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25520864;QSTRAND=- GT:DP:AD ./.:18:10,8 ./.:33:12,21 0|1:29:19,10 +chr20 175676 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25520847;QSTRAND=- GT:DP:AD ./.:26:18,8 ./.:38:15,23 0|1:35:14,21 +chr20 175688 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=129220;QSTRAND=+ GT:DP:AD 0|1:30:13,17 1|1:38:17,21 0|1:24:18,6 +chr20 175689 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=129221;QSTRAND=+ GT:DP:AD 0|1:28:7,21 1|1:31:13,18 0|1:27:5,22 +chr20 175813 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25520710;QSTRAND=- GT:DP:AD ./.:30:25,5 ./.:35:18,17 0|1:26:17,9 +chr20 175893 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=129425;QSTRAND=+ GT:DP:AD 0|1:38:19,19 1|1:34:14,20 0|1:23:17,6 +chr20 175897 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=129429;QSTRAND=+ GT:DP:AD 0|1:20:11,9 1|1:31:11,20 0|1:46:25,21 +chr20 176011 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=129543;QSTRAND=+ GT:DP:AD 0|1:35:25,10 1|1:40:16,24 ./.:42:21,21 +chr20 176015 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=129547;QSTRAND=+ GT:DP:AD 0|1:29:22,7 1|1:26:10,16 ./.:30:18,12 +chr20 176015 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25520508;QSTRAND=- GT:DP:AD ./.:25:10,15 ./.:36:18,18 0|1:38:19,19 +chr20 176128 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=25520395;QSTRAND=- GT:DP:AD ./.:28:12,16 ./.:18:5,13 0|1:41:17,24 +chr20 176156 . A T 60 . QNAME=cluster23_scaffold_2;QSTART=25520367;QSTRAND=- GT:DP:AD ./.:25:20,5 ./.:31:17,14 0|1:37:24,13 +chr20 176325 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25520198;QSTRAND=- GT:DP:AD ./.:27:14,13 ./.:29:9,20 0|1:39:23,16 +chr20 176400 . G GCCC 60 . QNAME=cluster23_scaffold_2;QSTART=25520120;QSTRAND=- GT:DP:AD ./.:42:25,17 ./.:19:10,9 0|1:20:7,13 +chr20 176406 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25520114;QSTRAND=- GT:DP:AD ./.:31:10,21 ./.:21:5,16 0|1:25:9,16 +chr20 176516 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=130048;QSTRAND=+ GT:DP:AD 0|1:36:14,22 1|1:35:19,16 0|1:23:12,11 +chr20 176631 . C T 60 . QNAME=cluster19_000000F;QSTART=135778;QSTRAND=+ GT:DP:AD ./.:36:20,16 0|1:29:24,5 ./.:25:8,17 +chr20 176881 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=130413;QSTRAND=+ GT:DP:AD 0|1:24:13,11 1|0:31:23,8 ./.:39:14,25 +chr20 177105 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=130637;QSTRAND=+ GT:DP:AD 0|1:26:6,20 1|1:17:6,11 0|1:18:9,9 +chr20 177210 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25519310;QSTRAND=- GT:DP:AD ./.:25:20,5 ./.:23:18,5 0|1:40:19,21 +chr20 177334 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25519186;QSTRAND=- GT:DP:AD ./.:33:15,18 ./.:47:24,23 0|1:23:5,18 +chr20 177335 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=130867;QSTRAND=+ GT:DP:AD 0|1:27:16,11 1|1:18:9,9 0|1:18:13,5 +chr20 177343 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25519177;QSTRAND=- GT:DP:AD ./.:38:22,16 ./.:28:7,21 0|1:29:14,15 +chr20 177473 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=131005;QSTRAND=+ GT:DP:AD 0|1:37:17,20 1|1:43:18,25 0|1:29:23,6 +chr20 177674 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=131206;QSTRAND=+ GT:DP:AD 0|1:37:17,20 1|1:20:9,11 ./.:25:19,6 +chr20 177749 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25518771;QSTRAND=- GT:DP:AD ./.:26:21,5 ./.:23:7,16 0|1:20:5,15 +chr20 177793 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=131325;QSTRAND=+ GT:DP:AD 0|1:34:20,14 1|1:25:14,11 ./.:32:7,25 +chr20 177854 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=131386;QSTRAND=+ GT:DP:AD 0|1:35:12,23 1|1:31:19,12 0|1:20:11,9 +chr20 178043 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25518477;QSTRAND=- GT:DP:AD ./.:20:15,5 ./.:29:19,10 0|1:27:14,13 +chr20 178049 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25518471;QSTRAND=- GT:DP:AD ./.:22:5,17 ./.:35:16,19 0|1:28:15,13 +chr20 178343 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25518177;QSTRAND=- GT:DP:AD ./.:28:15,13 ./.:26:16,10 0|1:43:21,22 +chr20 178456 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25518064;QSTRAND=- GT:DP:AD ./.:29:7,22 ./.:42:20,22 0|1:28:11,17 +chr20 178604 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25517916;QSTRAND=- GT:DP:AD ./.:22:7,15 ./.:40:24,16 0|1:40:17,23 +chr20 178648 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=132180;QSTRAND=+ GT:DP:AD 0|1:20:5,15 1|1:27:12,15 ./.:27:6,21 +chr20 178883 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25517637;QSTRAND=- GT:DP:AD ./.:33:19,14 ./.:21:9,12 0|1:22:16,6 +chr20 179104 . A C 60 . QNAME=cluster23_scaffold_2;QSTART=25517416;QSTRAND=- GT:DP:AD ./.:33:11,22 ./.:28:6,22 0|1:37:16,21 +chr20 179470 . A AT 60 . QNAME=HG002-S9-H2-000001F;QSTART=133003;QSTRAND=+ GT:DP:AD 0|1:25:8,17 1|1:27:5,22 0|1:42:25,17 +chr20 179567 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=133100;QSTRAND=+ GT:DP:AD 0|1:26:8,18 1|1:24:11,13 0|1:27:20,7 +chr20 179575 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25516944;QSTRAND=- GT:DP:AD ./.:41:16,25 ./.:23:9,14 0|1:38:20,18 +chr20 179892 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=133425;QSTRAND=+ GT:DP:AD 0|1:33:16,17 1|1:29:21,8 ./.:26:6,20 +chr20 179910 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=133443;QSTRAND=+ GT:DP:AD 0|1:22:17,5 1|1:30:20,10 0|1:44:20,24 +chr20 180809 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=134342;QSTRAND=+ GT:DP:AD 0|1:33:25,8 1|1:46:24,22 0|1:49:25,24 +chr20 180861 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25515658;QSTRAND=- GT:DP:AD ./.:28:7,21 ./.:41:17,24 0|1:33:25,8 +chr20 180945 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25515574;QSTRAND=- GT:DP:AD ./.:21:16,5 ./.:28:8,20 0|1:23:7,16 +chr20 181095 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25515424;QSTRAND=- GT:DP:AD ./.:19:12,7 ./.:27:17,10 0|1:12:7,5 +chr20 181461 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25515058;QSTRAND=- GT:DP:AD ./.:28:7,21 ./.:15:6,9 0|1:31:8,23 +chr20 181576 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25514943;QSTRAND=- GT:DP:AD ./.:40:15,25 ./.:19:9,10 0|1:35:20,15 +chr20 181650 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25514869;QSTRAND=- GT:DP:AD ./.:32:15,17 ./.:23:13,10 0|1:17:10,7 +chr20 181651 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25514868;QSTRAND=- GT:DP:AD ./.:38:16,22 ./.:16:7,9 0|1:28:21,7 +chr20 182042 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=135575;QSTRAND=+ GT:DP:AD 0|1:36:22,14 1|1:38:15,23 ./.:27:11,16 +chr20 182056 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=25514467;QSTRAND=- GT:DP:AD ./.:34:21,13 ./.:36:13,23 0|1:32:13,19 +chr20 182966 . A AAT 60 . QNAME=HG002-S9-H2-000001F;QSTART=136500;QSTRAND=+ GT:DP:AD 0|1:22:7,15 1|1:33:25,8 0|1:39:14,25 +chr20 182982 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25513539;QSTRAND=- GT:DP:AD ./.:50:25,25 ./.:31:8,23 0|1:35:18,17 +chr20 183100 . T TACACAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=136636;QSTRAND=+ GT:DP:AD 0|1:46:22,24 1|1:24:19,5 ./.:23:14,9 +chr20 183100 . T TAC 60 . QNAME=cluster23_scaffold_2;QSTART=25513419;QSTRAND=- GT:DP:AD ./.:43:22,21 ./.:22:6,16 0|1:26:20,6 +chr20 183442 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25513077;QSTRAND=- GT:DP:AD ./.:42:20,22 ./.:26:11,15 0|1:32:22,10 +chr20 183617 . G GGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAA 60 . QNAME=cluster23_scaffold_2;QSTART=25512867;QSTRAND=-;SVTYPE=INS;SVLEN=35 GT:DP:AD ./.:35:16,19 ./.:32:20,12 0/1:24:11,13 +chr20 183638 . G GAAAAC 60 . QNAME=cluster19_000000F;QSTART=142795;QSTRAND=+ GT:DP:AD ./.:30:6,24 0|1:45:25,20 ./.:40:19,21 +chr20 183643 . G C 60 . QNAME=cluster19_000000F;QSTART=142804;QSTRAND=+ GT:DP:AD ./.:37:17,20 0|1:33:24,9 ./.:27:12,15 +chr20 183643 . G GAAAAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=137185;QSTRAND=+ GT:DP:AD 0|1:41:22,19 1|0:40:25,15 ./.:30:17,13 +chr20 183699 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=137245;QSTRAND=+ GT:DP:AD 0|1:31:23,8 1|1:37:21,16 ./.:47:24,23 +chr20 183795 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25512689;QSTRAND=- GT:DP:AD ./.:23:18,5 ./.:31:7,24 0|1:49:24,25 +chr20 184483 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25512001;QSTRAND=- GT:DP:AD ./.:32:10,22 ./.:43:23,20 0|1:30:19,11 +chr20 184792 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25511692;QSTRAND=- GT:DP:AD ./.:18:9,9 ./.:23:7,16 0|1:38:13,25 +chr20 184838 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25511646;QSTRAND=- GT:DP:AD ./.:42:25,17 ./.:28:15,13 0|1:17:7,10 +chr20 185161 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=25511323;QSTRAND=- GT:DP:AD ./.:29:13,16 ./.:21:11,10 0|1:31:11,20 +chr20 185267 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=138813;QSTRAND=+ GT:DP:AD 0|1:31:22,9 1|1:49:24,25 0|1:44:19,25 +chr20 185522 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25510962;QSTRAND=- GT:DP:AD ./.:41:24,17 ./.:47:24,23 0|1:23:7,16 +chr20 185547 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25510937;QSTRAND=- GT:DP:AD ./.:23:11,12 ./.:48:24,24 0|1:30:22,8 +chr20 185835 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25510648;QSTRAND=- GT:DP:AD ./.:33:20,13 ./.:19:6,13 0|1:37:18,19 +chr20 186086 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=139632;QSTRAND=+ GT:DP:AD 0|1:24:18,6 1|1:43:22,21 ./.:30:15,15 +chr20 186099 . C CAA 60 . QNAME=cluster23_scaffold_2;QSTART=25510382;QSTRAND=- GT:DP:AD ./.:22:6,16 ./.:21:14,7 0|1:41:25,16 +chr20 186183 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=139729;QSTRAND=+ GT:DP:AD 0|1:34:18,16 1|1:25:7,18 ./.:24:7,17 +chr20 186577 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25509904;QSTRAND=- GT:DP:AD ./.:20:12,8 ./.:18:7,11 0|1:23:7,16 +chr20 186669 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=140215;QSTRAND=+ GT:DP:AD 0|1:40:23,17 1|1:29:21,8 ./.:31:14,17 +chr20 186684 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=25509797;QSTRAND=- GT:DP:AD ./.:24:17,7 ./.:28:9,19 0|1:28:15,13 +chr20 186790 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=140336;QSTRAND=+ GT:DP:AD 0|1:28:18,10 1|1:10:5,5 0|1:23:10,13 +chr20 186800 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25509681;QSTRAND=- GT:DP:AD ./.:28:19,9 ./.:19:13,6 0|1:31:8,23 +chr20 186814 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25509667;QSTRAND=- GT:DP:AD ./.:24:17,7 ./.:46:21,25 0|1:39:21,18 +chr20 187006 . T A 60 . QNAME=cluster23_scaffold_2;QSTART=25509475;QSTRAND=- GT:DP:AD ./.:41:16,25 ./.:33:25,8 0|1:35:22,13 +chr20 187133 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25509348;QSTRAND=- GT:DP:AD ./.:30:17,13 ./.:41:24,17 0|1:46:23,23 +chr20 187259 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=25509222;QSTRAND=- GT:DP:AD ./.:32:18,14 ./.:28:13,15 0|1:34:22,12 +chr20 187379 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25509102;QSTRAND=- GT:DP:AD ./.:34:15,19 ./.:28:13,15 0|1:22:9,13 +chr20 187439 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=140985;QSTRAND=+ GT:DP:AD 0|1:33:14,19 1|1:26:15,11 ./.:24:13,11 +chr20 187498 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25508983;QSTRAND=- GT:DP:AD ./.:20:5,15 ./.:18:13,5 0|1:35:21,14 +chr20 187600 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25508881;QSTRAND=- GT:DP:AD ./.:15:7,8 ./.:36:18,18 0|1:23:10,13 +chr20 187825 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=141371;QSTRAND=+ GT:DP:AD 0|1:31:12,19 1|1:16:8,8 ./.:41:24,17 +chr20 188087 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=141633;QSTRAND=+ GT:DP:AD 0|1:20:13,7 1|1:41:23,18 0|1:25:15,10 +chr20 188490 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25507991;QSTRAND=- GT:DP:AD ./.:18:7,11 ./.:18:7,11 0|1:26:21,5 +chr20 189060 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=142606;QSTRAND=+ GT:DP:AD 0|1:14:8,6 1|1:42:18,24 ./.:30:6,24 +chr20 189354 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=142900;QSTRAND=+ GT:DP:AD 0|1:24:9,15 1|1:21:11,10 0|1:34:21,13 +chr20 189473 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25507008;QSTRAND=- GT:DP:AD ./.:33:17,16 ./.:34:23,11 0|1:48:25,23 +chr20 189948 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=143494;QSTRAND=+ GT:DP:AD 0|1:23:6,17 1|1:40:19,21 0|1:26:21,5 +chr20 190001 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=143547;QSTRAND=+ GT:DP:AD 0|1:14:6,8 1|1:44:20,24 0|1:29:10,19 +chr20 190548 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=144094;QSTRAND=+ GT:DP:AD 0|1:34:13,21 1|1:41:18,23 ./.:37:19,18 +chr20 190675 . C CTT 60 . QNAME=HG002-S9-H2-000001F;QSTART=144222;QSTRAND=+ GT:DP:AD 0|1:23:7,16 1|1:36:25,11 ./.:45:20,25 +chr20 190675 . C CT 60 . QNAME=cluster23_scaffold_2;QSTART=25505805;QSTRAND=- GT:DP:AD ./.:26:6,20 ./.:27:9,18 0|1:24:11,13 +chr20 190950 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=144498;QSTRAND=+ GT:DP:AD 0|1:26:8,18 1|1:28:20,8 ./.:45:24,21 +chr20 190986 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=144534;QSTRAND=+ GT:DP:AD 0|1:37:24,13 1|1:42:21,21 ./.:33:23,10 +chr20 191069 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25505411;QSTRAND=- GT:DP:AD ./.:35:24,11 ./.:24:13,11 0|1:24:5,19 +chr20 191221 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=170203;QSTRAND=+ GT:DP:AD 1|0:43:20,23 ./.:25:7,18 ./.:44:21,23 +chr20 191726 . C CTT 60 . QNAME=cluster23_scaffold_3;QSTART=25520132;QSTRAND=- GT:DP:AD ./.:32:18,14 ./.:17:5,12 1|0:23:15,8 +chr20 191877 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=145424;QSTRAND=+ GT:DP:AD 0|1:38:25,13 1|1:48:25,23 0|1:40:16,24 +chr20 192100 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=145647;QSTRAND=+ GT:DP:AD 0|1:21:8,13 1|1:23:17,6 0|1:32:16,16 +chr20 193110 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=146657;QSTRAND=+ GT:DP:AD 0|1:30:23,7 1|1:12:5,7 0|1:22:16,6 +chr20 193428 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=146975;QSTRAND=+ GT:DP:AD 0|1:35:16,19 1|1:30:19,11 0|1:27:19,8 +chr20 193735 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25502747;QSTRAND=- GT:DP:AD ./.:17:8,9 ./.:29:23,6 0|1:39:19,20 +chr20 193942 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=25502540;QSTRAND=- GT:DP:AD ./.:26:18,8 ./.:19:10,9 0|1:20:8,12 +chr20 193996 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25502486;QSTRAND=- GT:DP:AD ./.:37:23,14 ./.:43:22,21 0|1:39:17,22 +chr20 194746 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=148293;QSTRAND=+ GT:DP:AD 0|1:24:11,13 1|1:38:19,19 0|1:27:12,15 +chr20 195745 . C CGT 60 . QNAME=cluster23_scaffold_2;QSTART=25500735;QSTRAND=- GT:DP:AD ./.:41:19,22 ./.:25:8,17 0|1:26:12,14 +chr20 195977 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25500503;QSTRAND=- GT:DP:AD ./.:20:8,12 ./.:39:25,14 0|1:45:22,23 +chr20 196106 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25515756;QSTRAND=- GT:DP:AD ./.:18:7,11 ./.:35:23,12 1|0:28:16,12 +chr20 196584 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=175566;QSTRAND=+ GT:DP:AD 1|0:29:19,10 ./.:23:17,6 1|1:20:7,13 +chr20 196609 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=175591;QSTRAND=+ GT:DP:AD 1|0:20:13,7 ./.:20:14,6 1|0:20:15,5 +chr20 198088 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25513774;QSTRAND=- GT:DP:AD ./.:40:24,16 ./.:34:23,11 1|0:45:23,22 +chr20 198171 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=177153;QSTRAND=+ GT:DP:AD 1|0:27:19,8 ./.:38:17,21 1|1:23:18,5 +chr20 198174 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=177156;QSTRAND=+ GT:DP:AD 1|0:34:11,23 ./.:42:22,20 1|0:14:8,6 +chr20 198215 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=177197;QSTRAND=+ GT:DP:AD 1|0:33:20,13 ./.:31:13,18 1|1:33:9,24 +chr20 198433 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25498047;QSTRAND=- GT:DP:AD ./.:31:7,24 ./.:27:20,7 0|1:25:14,11 +chr20 198814 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=177796;QSTRAND=+ GT:DP:AD 1|0:31:18,13 ./.:17:7,10 1|0:21:9,12 +chr20 198921 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=177903;QSTRAND=+ GT:DP:AD 1|0:15:9,6 ./.:12:5,7 1|1:31:8,23 +chr20 199123 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=178105;QSTRAND=+ GT:DP:AD 1|0:34:18,16 ./.:33:19,14 1|0:36:18,18 +chr20 199139 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=178122;QSTRAND=+ GT:DP:AD 1|0:20:12,8 ./.:48:24,24 ./.:24:9,15 +chr20 199139 . C CTT 60 . QNAME=cluster23_scaffold_3;QSTART=25512721;QSTRAND=- GT:DP:AD ./.:18:5,13 ./.:33:9,24 1|1:44:19,25 +chr20 199741 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25496737;QSTRAND=- GT:DP:AD ./.:44:20,24 ./.:34:9,25 0|1:15:10,5 +chr20 200997 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=179980;QSTRAND=+ GT:DP:AD 1|0:28:10,18 ./.:34:12,22 1|0:26:12,14 +chr20 201076 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25510784;QSTRAND=- GT:DP:AD ./.:27:20,7 ./.:33:18,15 1|0:35:12,23 +chr20 201326 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=180309;QSTRAND=+ GT:DP:AD 1|0:36:14,22 ./.:25:20,5 1|0:36:17,19 +chr20 201372 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=180355;QSTRAND=+ GT:DP:AD 1|0:39:20,19 ./.:20:11,9 1|1:41:23,18 +chr20 201418 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=180401;QSTRAND=+ GT:DP:AD 1|0:28:17,11 ./.:38:18,20 1|0:31:24,7 +chr20 201525 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25494953;QSTRAND=- GT:DP:AD ./.:36:16,20 ./.:15:10,5 0|1:43:21,22 +chr20 201908 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25494570;QSTRAND=- GT:DP:AD ./.:19:6,13 ./.:27:20,7 0|1:17:12,5 +chr20 201932 . C CAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=180916;QSTRAND=+ GT:DP:AD 1|0:31:17,14 ./.:28:9,19 1|0:34:16,18 +chr20 201932 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25494545;QSTRAND=- GT:DP:AD ./.:17:10,7 ./.:30:16,14 0|1:21:10,11 +chr20 202581 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=181568;QSTRAND=+ GT:DP:AD 1|0:24:14,10 ./.:39:24,15 1|0:21:8,13 +chr20 203580 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=182567;QSTRAND=+ GT:DP:AD 1|0:34:13,21 ./.:13:7,6 1|0:37:22,15 +chr20 203602 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=182589;QSTRAND=+ GT:DP:AD 1|0:32:18,14 ./.:24:8,16 ./.:36:24,12 +chr20 203847 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=182827;QSTRAND=+ GT:DP:AD 1|0:26:18,8 ./.:34:15,19 1|0:48:24,24 +chr20 204090 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=183070;QSTRAND=+ GT:DP:AD 1|0:21:6,15 ./.:15:10,5 1|0:30:13,17 +chr20 205285 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=184265;QSTRAND=+ GT:DP:AD 1|0:44:23,21 ./.:46:23,23 1|0:42:21,21 +chr20 205764 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=184744;QSTRAND=+ GT:DP:AD 1|0:22:6,16 ./.:38:15,23 1|1:22:17,5 +chr20 206102 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25490375;QSTRAND=- GT:DP:AD ./.:18:6,12 ./.:49:25,24 0|1:29:18,11 +chr20 206175 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=185156;QSTRAND=+ GT:DP:AD 1|0:40:24,16 ./.:13:5,8 ./.:28:10,18 +chr20 206197 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25490284;QSTRAND=- GT:DP:AD ./.:37:15,22 ./.:16:9,7 0|1:33:21,12 +chr20 206446 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25490035;QSTRAND=- GT:DP:AD ./.:12:5,7 ./.:21:7,14 0|1:40:19,21 +chr20 207202 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=186184;QSTRAND=+ GT:DP:AD 1|0:36:11,25 ./.:25:17,8 1|1:34:21,13 +chr20 207307 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25489173;QSTRAND=- GT:DP:AD ./.:25:10,15 ./.:39:22,17 0|1:25:12,13 +chr20 207389 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=186371;QSTRAND=+ GT:DP:AD 1|0:37:19,18 ./.:33:18,15 1|1:32:19,13 +chr20 207466 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25489014;QSTRAND=- GT:DP:AD ./.:36:14,22 ./.:31:12,19 0|1:21:14,7 +chr20 209694 . A C 60 . QNAME=cluster23_scaffold_2;QSTART=25486787;QSTRAND=- GT:DP:AD ./.:43:21,22 ./.:25:7,18 0|1:40:21,19 +chr20 210024 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25486457;QSTRAND=- GT:DP:AD ./.:27:22,5 ./.:29:6,23 0|1:44:22,22 +chr20 211156 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=190137;QSTRAND=+ GT:DP:AD 1|0:13:5,8 ./.:24:7,17 1|1:28:19,9 +chr20 211168 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=190149;QSTRAND=+ GT:DP:AD 1|0:26:10,16 ./.:25:19,6 1|1:27:12,15 +chr20 211428 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=190409;QSTRAND=+ GT:DP:AD 1|0:43:22,21 ./.:22:7,15 1|1:31:7,24 +chr20 212994 . A AT 60 . QNAME=HG002-S9-H2-000001F;QSTART=166535;QSTRAND=+ GT:DP:AD 0|1:36:16,20 ./.:47:25,22 0|1:24:15,9 +chr20 213120 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25483361;QSTRAND=- GT:DP:AD ./.:37:15,22 ./.:32:7,25 0|1:38:15,23 +chr20 213126 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25483355;QSTRAND=- GT:DP:AD ./.:36:25,11 ./.:16:5,11 0|1:35:19,16 +chr20 213223 . G C 60 . QNAME=cluster23_scaffold_2;QSTART=25483258;QSTRAND=- GT:DP:AD ./.:27:7,20 ./.:31:6,25 0|1:20:13,7 +chr20 213244 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25483237;QSTRAND=- GT:DP:AD ./.:30:17,13 ./.:17:5,12 0|1:21:5,16 +chr20 213641 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25498222;QSTRAND=- GT:DP:AD ./.:42:22,20 ./.:39:20,19 1|0:43:18,25 +chr20 213649 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=192630;QSTRAND=+ GT:DP:AD 1|0:35:21,14 ./.:12:6,6 ./.:12:6,6 +chr20 213886 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=192867;QSTRAND=+ GT:DP:AD 1|0:23:11,12 ./.:26:16,10 ./.:27:20,7 +chr20 214444 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=193425;QSTRAND=+ GT:DP:AD 1|0:42:20,22 ./.:25:12,13 ./.:28:15,13 +chr20 214461 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=193442;QSTRAND=+ GT:DP:AD 1|0:35:14,21 ./.:40:20,20 ./.:35:16,19 +chr20 214646 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=193627;QSTRAND=+ GT:DP:AD 1|0:40:21,19 ./.:17:5,12 ./.:31:24,7 +chr20 214824 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=193804;QSTRAND=+ GT:DP:AD 1|0:33:8,25 ./.:34:14,20 ./.:23:16,7 +chr20 214879 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=193859;QSTRAND=+ GT:DP:AD 1|0:22:8,14 ./.:40:25,15 ./.:30:21,9 +chr20 214962 . A AT 60 . QNAME=cluster23_scaffold_2;QSTART=25481518;QSTRAND=- GT:DP:AD ./.:30:19,11 ./.:32:20,12 0|1:17:6,11 +chr20 215031 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25496832;QSTRAND=- GT:DP:AD ./.:30:17,13 ./.:26:18,8 1|0:29:6,23 +chr20 215055 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=194035;QSTRAND=+ GT:DP:AD 1|0:30:12,18 ./.:42:17,25 1|1:43:20,23 +chr20 215963 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=194943;QSTRAND=+ GT:DP:AD 1|0:20:13,7 ./.:17:8,9 ./.:27:16,11 +chr20 217163 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25479317;QSTRAND=- GT:DP:AD ./.:37:13,24 ./.:25:20,5 0|1:44:22,22 +chr20 217754 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=196734;QSTRAND=+ GT:DP:AD 1|1:37:21,16 1|1:31:18,13 0|1:18:9,9 +chr20 217756 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25494107;QSTRAND=- GT:DP:AD ./.:25:11,14 ./.:27:7,20 1|0:41:20,21 +chr20 219501 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=198481;QSTRAND=+ GT:DP:AD 1|0:26:15,11 ./.:32:20,12 0|1:27:6,21 +chr20 224189 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=203169;QSTRAND=+ GT:DP:AD 1|0:32:9,23 ./.:41:16,25 0|1:26:12,14 +chr20 225761 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=204741;QSTRAND=+ GT:DP:AD 1|0:22:5,17 ./.:35:16,19 0|1:33:14,19 +chr20 225955 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=204935;QSTRAND=+ GT:DP:AD 1|1:28:22,6 1|1:31:19,12 1|1:37:25,12 +chr20 226775 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=205755;QSTRAND=+ GT:DP:AD 1|0:25:12,13 ./.:36:22,14 0|1:46:23,23 +chr20 227248 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=206228;QSTRAND=+ GT:DP:AD 1|0:14:9,5 ./.:17:11,6 ./.:38:16,22 +chr20 227262 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25484605;QSTRAND=- GT:DP:AD ./.:33:15,18 ./.:25:9,16 1|0:16:11,5 +chr20 227527 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=206507;QSTRAND=+ GT:DP:AD 1|0:41:20,21 ./.:44:23,21 1|1:23:17,6 +chr20 227692 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=25484175;QSTRAND=- GT:DP:AD ./.:28:15,13 ./.:38:19,19 1|0:32:14,18 +chr20 227704 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=206684;QSTRAND=+ GT:DP:AD 1|0:31:6,25 ./.:29:22,7 1|1:29:7,22 +chr20 227705 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25484162;QSTRAND=- GT:DP:AD ./.:27:14,13 ./.:26:17,9 1|0:35:23,12 +chr20 227706 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25484161;QSTRAND=- GT:DP:AD ./.:21:5,16 ./.:27:11,16 1|0:12:5,7 +chr20 227707 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25484160;QSTRAND=- GT:DP:AD ./.:29:13,16 ./.:25:7,18 1|0:24:5,19 +chr20 227909 . T G 60 . QNAME=cluster23_scaffold_3;QSTART=25483958;QSTRAND=- GT:DP:AD ./.:13:6,7 ./.:32:19,13 1|0:22:8,14 +chr20 228044 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25483823;QSTRAND=- GT:DP:AD ./.:28:14,14 ./.:20:8,12 1|0:38:17,21 +chr20 228763 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25467743;QSTRAND=- GT:DP:AD ./.:39:20,19 ./.:38:17,21 0|1:24:7,17 +chr20 229210 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25482657;QSTRAND=- GT:DP:AD ./.:39:23,16 ./.:27:5,22 1|0:27:10,17 +chr20 229265 . T TCTC 60 . QNAME=cluster23_scaffold_3;QSTART=25482599;QSTRAND=- GT:DP:AD ./.:33:14,19 ./.:29:9,20 1|0:38:25,13 +chr20 229420 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=208400;QSTRAND=+ GT:DP:AD 1|0:33:17,16 ./.:24:9,15 ./.:38:24,14 +chr20 229665 . C G 60 . QNAME=cluster23_scaffold_3;QSTART=25482199;QSTRAND=- GT:DP:AD ./.:15:7,8 ./.:37:18,19 1|1:38:17,21 +chr20 229898 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25481966;QSTRAND=- GT:DP:AD ./.:30:19,11 ./.:36:14,22 1|0:32:13,19 +chr20 229993 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25481871;QSTRAND=- GT:DP:AD ./.:26:8,18 ./.:31:22,9 1|0:47:24,23 +chr20 230118 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25466388;QSTRAND=- GT:DP:AD ./.:33:22,11 ./.:18:7,11 0|1:22:8,14 +chr20 230234 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=209214;QSTRAND=+ GT:DP:AD 1|0:27:9,18 ./.:42:18,24 ./.:29:20,9 +chr20 230273 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25481591;QSTRAND=- GT:DP:AD ./.:47:22,25 ./.:28:17,11 1|0:32:9,23 +chr20 230354 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25481510;QSTRAND=- GT:DP:AD ./.:27:21,6 ./.:38:15,23 1|0:38:18,20 +chr20 230514 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25481350;QSTRAND=- GT:DP:AD ./.:32:18,14 ./.:20:14,6 1|0:31:23,8 +chr20 230790 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25481074;QSTRAND=- GT:DP:AD ./.:27:9,18 ./.:44:21,23 1|0:18:9,9 +chr20 230868 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=209848;QSTRAND=+ GT:DP:AD 1|0:31:7,24 ./.:25:20,5 0|1:22:16,6 +chr20 230923 . T C 60 . QNAME=cluster19_000000F;QSTART=190079;QSTRAND=+ GT:DP:AD ./.:33:12,21 0|1:20:13,7 ./.:41:20,21 +chr20 231070 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=210050;QSTRAND=+ GT:DP:AD 1|0:39:23,16 ./.:27:6,21 0|1:28:10,18 +chr20 231318 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=210298;QSTRAND=+ GT:DP:AD 1|0:26:9,17 ./.:27:13,14 ./.:28:5,23 +chr20 231710 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=210690;QSTRAND=+ GT:DP:AD 1|0:32:10,22 ./.:46:24,22 1|1:22:16,6 +chr20 231898 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=185439;QSTRAND=+ GT:DP:AD 0|1:29:6,23 1|1:39:17,22 1|0:44:24,20 +chr20 231900 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=185441;QSTRAND=+ GT:DP:AD 0|1:23:10,13 1|1:40:19,21 1|0:34:17,17 +chr20 232009 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25479855;QSTRAND=- GT:DP:AD ./.:27:10,17 ./.:23:16,7 1|0:42:24,18 +chr20 232033 . A AAAATAAAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=211014;QSTRAND=+ GT:DP:AD 1|1:33:15,18 ./.:22:14,8 ./.:19:12,7 +chr20 232033 . A AAAATAAATAAAT 60 . QNAME=cluster19_000000F;QSTART=25530755;QSTRAND=- GT:DP:AD ./.:26:10,16 1|0:26:11,15 1|0:39:16,23 +chr20 232033 . A AAAAT 60 . QNAME=cluster19_000000F;QSTART=191190;QSTRAND=+ GT:DP:AD ./.:24:12,12 0|1:28:12,16 0|1:39:16,23 +chr20 232468 . C CTT 60 . QNAME=cluster23_scaffold_3;QSTART=25479382;QSTRAND=- GT:DP:AD ./.:36:23,13 ./.:33:19,14 1|0:44:23,21 +chr20 232614 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25479237;QSTRAND=- GT:DP:AD ./.:38:14,24 ./.:19:5,14 1|0:34:24,10 +chr20 232882 . A C 60 . QNAME=cluster23_scaffold_3;QSTART=25478969;QSTRAND=- GT:DP:AD ./.:18:6,12 ./.:29:12,17 1|0:32:19,13 +chr20 233213 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25478643;QSTRAND=- GT:DP:AD ./.:32:15,17 ./.:28:9,19 1|0:34:23,11 +chr20 233246 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25478610;QSTRAND=- GT:DP:AD ./.:17:12,5 ./.:36:13,23 1|0:26:14,12 +chr20 233732 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=212720;QSTRAND=+ GT:DP:AD 1|1:13:8,5 1|0:26:15,11 1|1:31:25,6 +chr20 234020 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25477836;QSTRAND=- GT:DP:AD ./.:33:22,11 ./.:25:16,9 1|0:26:8,18 +chr20 234023 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=25477833;QSTRAND=- GT:DP:AD ./.:36:24,12 ./.:36:18,18 1|0:26:11,15 +chr20 234239 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=213226;QSTRAND=+ GT:DP:AD 1|0:26:15,11 ./.:27:22,5 ./.:37:16,21 +chr20 234441 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=213428;QSTRAND=+ GT:DP:AD 1|1:21:16,5 1|0:20:11,9 ./.:37:22,15 +chr20 234630 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25477230;QSTRAND=- GT:DP:AD ./.:36:25,11 ./.:22:17,5 1|0:44:23,21 +chr20 234736 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25477124;QSTRAND=- GT:DP:AD ./.:20:6,14 ./.:17:12,5 1|0:37:19,18 +chr20 234758 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25477102;QSTRAND=- GT:DP:AD ./.:31:22,9 ./.:26:10,16 1|0:39:15,24 +chr20 234803 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=25477057;QSTRAND=- GT:DP:AD ./.:20:8,12 ./.:32:18,14 1|0:43:22,21 +chr20 234949 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25476911;QSTRAND=- GT:DP:AD ./.:34:10,24 ./.:23:6,17 1|0:20:7,13 +chr20 235000 . T G 60 . QNAME=cluster23_scaffold_3;QSTART=25476860;QSTRAND=- GT:DP:AD ./.:41:16,25 ./.:25:9,16 1|0:32:14,18 +chr20 235023 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25476837;QSTRAND=- GT:DP:AD ./.:30:9,21 ./.:30:21,9 1|0:31:14,17 +chr20 235274 . T G 60 . QNAME=cluster23_scaffold_2;QSTART=25461228;QSTRAND=- GT:DP:AD ./.:21:13,8 ./.:27:20,7 0|1:49:25,24 +chr20 235380 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=25476480;QSTRAND=- GT:DP:AD ./.:32:18,14 ./.:20:9,11 1|0:23:10,13 +chr20 235457 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25476403;QSTRAND=- GT:DP:AD ./.:21:12,9 ./.:34:16,18 1|1:25:18,7 +chr20 235579 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25476281;QSTRAND=- GT:DP:AD ./.:40:24,16 ./.:21:11,10 1|0:28:16,12 +chr20 235581 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25476279;QSTRAND=- GT:DP:AD ./.:45:23,22 ./.:16:5,11 1|0:34:9,25 +chr20 235682 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25476178;QSTRAND=- GT:DP:AD ./.:37:12,25 ./.:29:22,7 1|0:32:12,20 +chr20 236006 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25475854;QSTRAND=- GT:DP:AD ./.:31:6,25 ./.:29:18,11 1|0:29:15,14 +chr20 236109 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=215096;QSTRAND=+ GT:DP:AD 1|1:16:7,9 1|1:38:17,21 1|1:18:11,7 +chr20 236170 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=215157;QSTRAND=+ GT:DP:AD 1|1:34:22,12 1|0:23:16,7 1|1:26:8,18 +chr20 236433 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=215420;QSTRAND=+ GT:DP:AD 1|1:41:22,19 1|0:29:19,10 0|1:39:25,14 +chr20 236640 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=215627;QSTRAND=+ GT:DP:AD 1|1:29:7,22 1|0:43:23,20 0|1:28:14,14 +chr20 236959 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=215947;QSTRAND=+ GT:DP:AD 1|1:44:19,25 1|0:15:7,8 ./.:31:25,6 +chr20 237090 . A C 60 . QNAME=cluster23_scaffold_3;QSTART=25474776;QSTRAND=- GT:DP:AD ./.:33:14,19 ./.:37:12,25 1|0:26:12,14 +chr20 237210 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=216198;QSTRAND=+ GT:DP:AD 1|1:29:21,8 1|1:25:15,10 1|1:26:19,7 +chr20 237614 . A AG 60 . QNAME=HG002-S9-H1-000001F;QSTART=216603;QSTRAND=+ GT:DP:AD 1|1:23:13,10 1|0:18:5,13 1|0:18:13,5 +chr20 238142 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25473723;QSTRAND=- GT:DP:AD ./.:31:19,12 ./.:29:8,21 1|1:27:17,10 +chr20 238370 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=217359;QSTRAND=+ GT:DP:AD 1|1:41:20,21 1|0:19:7,12 1|1:25:9,16 +chr20 238458 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=217447;QSTRAND=+ GT:DP:AD 1|1:19:14,5 1|0:19:8,11 ./.:20:6,14 +chr20 238634 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=25473237;QSTRAND=- GT:DP:AD ./.:31:19,12 ./.:26:18,8 1|1:37:20,17 +chr20 238645 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=25473226;QSTRAND=- GT:DP:AD ./.:33:20,13 ./.:28:19,9 1|1:29:20,9 +chr20 238721 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=217710;QSTRAND=+ GT:DP:AD 1|1:49:25,24 1|0:22:6,16 ./.:38:18,20 +chr20 238845 . G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=217835;QSTRAND=+ GT:DP:AD 1|1:14:5,9 1|0:29:13,16 1|1:49:25,24 +chr20 239021 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25472849;QSTRAND=- GT:DP:AD ./.:40:22,18 ./.:43:19,24 1|1:36:17,19 +chr20 239041 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25457466;QSTRAND=- GT:DP:AD ./.:16:8,8 ./.:41:18,23 0|1:30:16,14 +chr20 239418 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=218408;QSTRAND=+ GT:DP:AD 1|1:41:21,20 1|0:25:6,19 ./.:25:9,16 +chr20 239441 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25457065;QSTRAND=- GT:DP:AD ./.:18:10,8 ./.:33:21,12 0|1:33:11,22 +chr20 239444 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=218434;QSTRAND=+ GT:DP:AD 1|1:10:5,5 1|0:24:16,8 ./.:24:18,6 +chr20 239451 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=218441;QSTRAND=+ GT:DP:AD 1|1:18:5,13 1|0:12:6,6 ./.:38:13,25 +chr20 239556 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=218546;QSTRAND=+ GT:DP:AD 1|1:20:7,13 1|0:29:11,18 1|1:29:15,14 +chr20 239563 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=218553;QSTRAND=+ GT:DP:AD 1|1:48:24,24 1|0:21:11,10 1|1:33:25,8 +chr20 239613 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25456893;QSTRAND=- GT:DP:AD ./.:26:19,7 ./.:35:19,16 0|1:15:7,8 +chr20 239649 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25472221;QSTRAND=- GT:DP:AD ./.:17:12,5 ./.:39:16,23 1|1:31:25,6 +chr20 239662 . A C 60 . QNAME=cluster23_scaffold_3;QSTART=25472208;QSTRAND=- GT:DP:AD ./.:16:6,10 ./.:32:22,10 1|1:20:12,8 +chr20 239803 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=218793;QSTRAND=+ GT:DP:AD 1|1:40:23,17 1|0:26:10,16 ./.:29:21,8 +chr20 239945 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25471925;QSTRAND=- GT:DP:AD ./.:10:5,5 ./.:28:8,20 1|0:38:19,19 +chr20 239951 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=25471919;QSTRAND=- GT:DP:AD ./.:29:21,8 ./.:31:24,7 1|1:24:12,12 +chr20 240008 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25471862;QSTRAND=- GT:DP:AD ./.:24:10,14 ./.:24:16,8 1|1:39:20,19 +chr20 240075 . C CAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=219066;QSTRAND=+ GT:DP:AD 1|1:34:25,9 1|0:24:8,16 ./.:40:22,18 +chr20 240075 . C CAA 60 . QNAME=cluster23_scaffold_3;QSTART=25471793;QSTRAND=- GT:DP:AD ./.:17:8,9 ./.:32:19,13 1|1:39:22,17 +chr20 240116 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25471752;QSTRAND=- GT:DP:AD ./.:49:24,25 ./.:33:8,25 1|1:39:18,21 +chr20 240166 . T G 60 . QNAME=cluster23_scaffold_3;QSTART=25471702;QSTRAND=- GT:DP:AD ./.:45:23,22 ./.:15:5,10 1|1:24:18,6 +chr20 240377 . T G 60 . QNAME=cluster23_scaffold_3;QSTART=25471491;QSTRAND=- GT:DP:AD ./.:24:6,18 ./.:32:21,11 1|1:16:8,8 +chr20 240458 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25471410;QSTRAND=- GT:DP:AD ./.:28:11,17 ./.:39:23,16 1|1:25:7,18 +chr20 240477 . G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=219471;QSTRAND=+ GT:DP:AD 1|1:48:25,23 1|0:25:10,15 ./.:38:21,17 +chr20 240477 . G GAA 60 . QNAME=cluster23_scaffold_3;QSTART=25471389;QSTRAND=- GT:DP:AD ./.:40:18,22 ./.:17:11,6 1|0:37:16,21 +chr20 240477 . G GAAA 60 . QNAME=cluster23_scaffold_2;QSTART=25456024;QSTRAND=- GT:DP:AD ./.:28:8,20 ./.:23:9,14 0|1:30:6,24 +chr20 240872 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25470994;QSTRAND=- GT:DP:AD ./.:26:12,14 ./.:34:23,11 1|1:36:25,11 +chr20 241191 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25470675;QSTRAND=- GT:DP:AD ./.:31:13,18 ./.:28:12,16 1|1:35:19,16 +chr20 241301 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=220295;QSTRAND=+ GT:DP:AD 1|1:23:11,12 1|0:31:17,14 1|1:30:24,6 +chr20 241898 . C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=220893;QSTRAND=+ GT:DP:AD 1|1:22:6,16 1|0:36:18,18 ./.:16:8,8 +chr20 241991 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25469875;QSTRAND=- GT:DP:AD ./.:39:14,25 ./.:32:17,15 1|1:38:20,18 +chr20 242033 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=221028;QSTRAND=+ GT:DP:AD 1|1:26:14,12 1|0:44:23,21 ./.:36:20,16 +chr20 242067 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=221062;QSTRAND=+ GT:DP:AD 1|1:40:25,15 1|0:39:21,18 ./.:40:20,20 +chr20 242195 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=221190;QSTRAND=+ GT:DP:AD 1|1:37:18,19 1|0:30:12,18 1|1:28:9,19 +chr20 242353 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=221348;QSTRAND=+ GT:DP:AD 1|1:23:6,17 1|0:22:9,13 ./.:29:18,11 +chr20 242531 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=221526;QSTRAND=+ GT:DP:AD 1|1:26:13,13 1|0:19:11,8 ./.:27:21,6 +chr20 242614 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=221609;QSTRAND=+ GT:DP:AD 1|1:26:15,11 1|0:39:22,17 ./.:30:13,17 +chr20 242798 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=221793;QSTRAND=+ GT:DP:AD 1|1:25:15,10 1|0:24:13,11 ./.:27:9,18 +chr20 242897 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=221892;QSTRAND=+ GT:DP:AD 1|1:36:25,11 1|0:39:17,22 1|1:33:16,17 +chr20 243066 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25468800;QSTRAND=- GT:DP:AD ./.:21:15,6 ./.:26:6,20 1|1:38:16,22 +chr20 243217 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=222212;QSTRAND=+ GT:DP:AD 1|1:33:15,18 1|0:24:19,5 1|1:41:25,16 +chr20 243487 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=222482;QSTRAND=+ GT:DP:AD 1|1:25:15,10 1|0:33:13,20 ./.:25:8,17 +chr20 243532 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=222527;QSTRAND=+ GT:DP:AD 1|1:29:5,24 1|0:19:11,8 1|1:23:13,10 +chr20 243960 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=222954;QSTRAND=+ GT:DP:AD 1|1:45:25,20 1|0:25:10,15 ./.:30:11,19 +chr20 244300 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=223293;QSTRAND=+ GT:DP:AD 1|1:13:5,8 1|0:27:10,17 1|1:32:17,15 +chr20 244330 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=223323;QSTRAND=+ GT:DP:AD 1|1:32:13,19 1|0:41:21,20 1|1:17:9,8 +chr20 244417 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=223410;QSTRAND=+ GT:DP:AD 1|1:31:15,16 1|0:29:19,10 1|1:17:5,12 +chr20 244771 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=223764;QSTRAND=+ GT:DP:AD 1|1:43:23,20 1|0:46:22,24 ./.:17:10,7 +chr20 244773 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25467095;QSTRAND=- GT:DP:AD ./.:20:8,12 ./.:20:8,12 1|1:33:14,19 +chr20 244803 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=223796;QSTRAND=+ GT:DP:AD 1|1:27:13,14 1|0:40:21,19 ./.:29:5,24 +chr20 244964 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25466904;QSTRAND=- GT:DP:AD ./.:30:6,24 ./.:21:7,14 1|1:21:15,6 +chr20 244981 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25466887;QSTRAND=- GT:DP:AD ./.:33:12,21 ./.:34:14,20 1|1:30:11,19 +chr20 245127 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=224120;QSTRAND=+ GT:DP:AD 1|1:36:15,21 1|0:17:6,11 ./.:19:8,11 +chr20 245425 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25466443;QSTRAND=- GT:DP:AD ./.:20:13,7 ./.:27:8,19 1|1:36:21,15 +chr20 245470 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=224461;QSTRAND=+ GT:DP:AD 1|0:30:8,22 ./.:26:19,7 ./.:38:23,15 +chr20 245472 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=224463;QSTRAND=+ GT:DP:AD 1|0:35:20,15 ./.:14:6,8 1|0:26:9,17 +chr20 245474 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=199028;QSTRAND=+ GT:DP:AD 0|1:28:9,19 ./.:17:8,9 ./.:16:8,8 +chr20 245512 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25466366;QSTRAND=- GT:DP:AD ./.:31:20,11 ./.:30:18,12 1|1:32:25,7 +chr20 245789 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25466089;QSTRAND=- GT:DP:AD ./.:31:25,6 ./.:42:20,22 1|1:20:12,8 +chr20 245803 . A G 60 . QNAME=cluster19_000000F;QSTART=204954;QSTRAND=+ GT:DP:AD ./.:45:20,25 0|1:39:23,16 ./.:24:11,13 +chr20 245877 . G A 60 . QNAME=cluster19_000000F;QSTART=205028;QSTRAND=+ GT:DP:AD ./.:27:5,22 0|1:49:24,25 ./.:31:9,22 +chr20 245928 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25465950;QSTRAND=- GT:DP:AD ./.:34:9,25 ./.:26:17,9 1|1:30:22,8 +chr20 246148 . T A 60 . QNAME=cluster19_000000F;QSTART=205299;QSTRAND=+ GT:DP:AD ./.:36:21,15 0|1:24:13,11 1|1:29:20,9 +chr20 246383 . G A 60 . QNAME=cluster19_000000F;QSTART=205534;QSTRAND=+ GT:DP:AD ./.:20:10,10 0|1:22:9,13 ./.:33:23,10 +chr20 246501 . G T 60 . QNAME=cluster19_000000F;QSTART=205652;QSTRAND=+ GT:DP:AD ./.:36:22,14 0|1:18:9,9 ./.:35:22,13 +chr20 246605 . A G 60 . QNAME=cluster19_000000F;QSTART=205756;QSTRAND=+ GT:DP:AD ./.:22:6,16 0|1:48:23,25 1|1:24:9,15 +chr20 246926 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25449587;QSTRAND=- GT:DP:AD ./.:35:25,10 ./.:45:22,23 0|1:24:14,10 +chr20 246986 . G GCACA 60 . QNAME=cluster23_scaffold_3;QSTART=25464888;QSTRAND=- GT:DP:AD ./.:25:8,17 ./.:32:13,19 1|1:33:13,20 +chr20 247326 . G A 60 . QNAME=cluster19_000000F;QSTART=206477;QSTRAND=+ GT:DP:AD ./.:40:16,24 0|1:26:5,21 1|1:39:16,23 +chr20 247512 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25448999;QSTRAND=- GT:DP:AD ./.:22:16,6 ./.:29:8,21 0|1:14:7,7 +chr20 247516 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25448995;QSTRAND=- GT:DP:AD ./.:26:14,12 ./.:27:9,18 0|1:14:9,5 +chr20 247565 . A C 60 . QNAME=cluster19_000000F;QSTART=206708;QSTRAND=+ GT:DP:AD ./.:32:17,15 0|1:27:9,18 1|1:27:15,12 +chr20 247714 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25464170;QSTRAND=- GT:DP:AD ./.:29:12,17 ./.:30:25,5 1|1:27:11,16 +chr20 247936 . G A 60 . QNAME=cluster19_000000F;QSTART=207079;QSTRAND=+ GT:DP:AD ./.:32:16,16 0|1:13:6,7 1|1:21:10,11 +chr20 248065 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25463819;QSTRAND=- GT:DP:AD ./.:46:22,24 ./.:30:9,21 1|1:19:13,6 +chr20 248099 . T A 60 . QNAME=cluster23_scaffold_3;QSTART=25463785;QSTRAND=- GT:DP:AD ./.:33:19,14 ./.:16:11,5 1|1:34:16,18 +chr20 248173 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25463711;QSTRAND=- GT:DP:AD ./.:32:19,13 ./.:29:11,18 1|1:11:5,6 +chr20 248248 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=25463636;QSTRAND=- GT:DP:AD ./.:14:7,7 ./.:36:16,20 1|1:18:12,6 +chr20 248357 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25463527;QSTRAND=- GT:DP:AD ./.:31:22,9 ./.:28:15,13 1|1:38:24,14 +chr20 248371 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25463513;QSTRAND=- GT:DP:AD ./.:25:5,20 ./.:20:14,6 1|1:22:11,11 +chr20 248716 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25447795;QSTRAND=- GT:DP:AD ./.:42:21,21 ./.:33:12,21 0|1:48:25,23 +chr20 248740 . C CA 60 . QNAME=cluster19_000000F;QSTART=207884;QSTRAND=+ GT:DP:AD ./.:48:24,24 0|1:35:16,19 ./.:21:6,15 +chr20 248815 . G A 60 . QNAME=cluster19_000000F;QSTART=207959;QSTRAND=+ GT:DP:AD ./.:35:13,22 0|1:17:7,10 ./.:35:14,21 +chr20 248838 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25463047;QSTRAND=- GT:DP:AD ./.:25:15,10 ./.:18:12,6 1|0:45:24,21 +chr20 248854 . T C 60 . QNAME=cluster19_000000F;QSTART=207998;QSTRAND=+ GT:DP:AD ./.:37:24,13 0|1:47:25,22 1|1:22:17,5 +chr20 249081 . T C 60 . QNAME=cluster19_000000F;QSTART=208225;QSTRAND=+ GT:DP:AD ./.:23:18,5 0|1:39:18,21 1|1:34:17,17 +chr20 249089 . C CAA 60 . QNAME=cluster19_000000F;QSTART=208234;QSTRAND=+ GT:DP:AD ./.:24:19,5 0|1:48:24,24 0|1:27:11,16 +chr20 249089 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25462795;QSTRAND=- GT:DP:AD ./.:36:12,24 ./.:20:7,13 1|0:35:20,15 +chr20 249337 . G C 60 . QNAME=cluster19_000000F;QSTART=208483;QSTRAND=+ GT:DP:AD ./.:25:11,14 0|1:25:6,19 ./.:26:12,14 +chr20 249412 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=202962;QSTRAND=+ GT:DP:AD 0|1:24:11,13 1|0:29:9,20 ./.:40:22,18 +chr20 249536 . A T 60 . QNAME=cluster19_000000F;QSTART=208680;QSTRAND=+ GT:DP:AD ./.:27:20,7 0|1:41:25,16 ./.:20:9,11 +chr20 249875 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=228862;QSTRAND=+ GT:DP:AD 1|0:21:6,15 0|1:30:7,23 1|1:31:12,19 +chr20 249900 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=228887;QSTRAND=+ GT:DP:AD 1|0:26:12,14 0|1:32:23,9 1|1:24:18,6 +chr20 250218 . C T 60 . QNAME=cluster19_000000F;QSTART=209362;QSTRAND=+ GT:DP:AD ./.:26:9,17 0|1:21:12,9 ./.:19:8,11 +chr20 250342 . C T 60 . QNAME=cluster19_000000F;QSTART=209486;QSTRAND=+ GT:DP:AD ./.:25:9,16 0|1:30:8,22 ./.:17:11,6 +chr20 250449 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=229436;QSTRAND=+ GT:DP:AD 1|0:26:7,19 0|1:28:13,15 1|1:33:19,14 +chr20 250472 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=229459;QSTRAND=+ GT:DP:AD 1|0:27:9,18 ./.:26:14,12 1|1:28:13,15 +chr20 250554 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=229541;QSTRAND=+ GT:DP:AD 1|0:35:19,16 ./.:25:20,5 1|1:29:14,15 +chr20 250671 . A C 60 . QNAME=cluster19_000000F;QSTART=209815;QSTRAND=+ GT:DP:AD ./.:28:8,20 0|1:19:9,10 ./.:40:24,16 +chr20 250864 . G A 60 . QNAME=cluster19_000000F;QSTART=210008;QSTRAND=+ GT:DP:AD ./.:27:9,18 0|1:38:25,13 ./.:38:19,19 +chr20 251035 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=230022;QSTRAND=+ GT:DP:AD 1|0:40:23,17 ./.:33:23,10 1|1:35:10,25 +chr20 251370 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=230357;QSTRAND=+ GT:DP:AD 1|0:39:20,19 ./.:45:21,24 1|0:36:17,19 +chr20 251466 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=230453;QSTRAND=+ GT:DP:AD 1|0:24:10,14 0|1:16:5,11 1|1:35:10,25 +chr20 251699 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=230686;QSTRAND=+ GT:DP:AD 1|0:37:15,22 ./.:35:15,20 1|1:28:19,9 +chr20 251939 . G C 60 . QNAME=cluster19_000000F;QSTART=211083;QSTRAND=+ GT:DP:AD ./.:45:25,20 0|1:18:7,11 ./.:34:24,10 +chr20 251993 . T TACACACACACACACAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=230981;QSTRAND=+ GT:DP:AD 1|0:41:17,24 ./.:28:9,19 ./.:23:8,15 +chr20 251993 . T TACACAC 60 . QNAME=cluster19_000000F;QSTART=211138;QSTRAND=+ GT:DP:AD ./.:32:12,20 0|1:30:5,25 ./.:42:22,20 +chr20 251993 . T TACACACACAC 60 . QNAME=cluster23_scaffold_3;QSTART=25459884;QSTRAND=- GT:DP:AD ./.:16:10,6 ./.:31:10,21 1|0:38:25,13 +chr20 251993 . T TACACACACACACAC 60 . QNAME=cluster23_scaffold_2;QSTART=25444505;QSTRAND=- GT:DP:AD ./.:18:6,12 ./.:20:8,12 0|1:28:18,10 +chr20 252833 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=231836;QSTRAND=+ GT:DP:AD 1|0:32:8,24 ./.:40:20,20 1|1:16:10,6 +chr20 252834 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=231837;QSTRAND=+ GT:DP:AD 1|0:42:18,24 ./.:29:12,17 1|1:30:10,20 +chr20 252982 . A T 60 . QNAME=cluster19_000000F;QSTART=212132;QSTRAND=+ GT:DP:AD ./.:36:25,11 0|1:28:12,16 ./.:37:24,13 +chr20 253238 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=232240;QSTRAND=+ GT:DP:AD 1|1:42:18,24 1|1:44:20,24 1|1:36:17,19 +chr20 253538 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=232540;QSTRAND=+ GT:DP:AD 1|0:48:23,25 0|1:35:24,11 1|1:34:22,12 +chr20 253719 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=232721;QSTRAND=+ GT:DP:AD 1|0:15:7,8 0|1:28:15,13 1|1:39:24,15 +chr20 253968 . A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25457909;QSTRAND=- GT:DP:AD ./.:23:13,10 ./.:45:21,24 1|0:24:14,10 +chr20 254466 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=233468;QSTRAND=+ GT:DP:AD 1|0:16:6,10 0|1:30:21,9 1|1:27:16,11 +chr20 255081 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=234083;QSTRAND=+ GT:DP:AD 1|0:24:10,14 0|1:27:18,9 1|1:16:10,6 +chr20 255329 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=234331;QSTRAND=+ GT:DP:AD 1|0:26:17,9 0|1:42:17,25 1|1:30:25,5 +chr20 255356 . C CAAAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=234359;QSTRAND=+ GT:DP:AD 1|0:37:19,18 0|1:36:21,15 ./.:25:11,14 +chr20 255356 . C CAAAAAAAAA 60 . QNAME=cluster23_scaffold_3;QSTART=25456512;QSTRAND=- GT:DP:AD ./.:27:15,12 ./.:13:6,7 1|1:39:21,18 +chr20 255447 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=234457;QSTRAND=+ GT:DP:AD 1|0:23:12,11 0|1:30:6,24 1|1:34:11,23 +chr20 255527 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=234537;QSTRAND=+ GT:DP:AD 1|0:33:14,19 0|1:35:23,12 1|1:43:19,24 +chr20 255597 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=234607;QSTRAND=+ GT:DP:AD 1|0:36:21,15 0|1:22:16,6 1|1:24:12,12 +chr20 255645 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=234655;QSTRAND=+ GT:DP:AD 1|0:44:22,22 0|1:27:18,9 1|1:17:12,5 +chr20 255687 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=234697;QSTRAND=+ GT:DP:AD 1|0:38:17,21 0|1:32:11,21 1|1:36:19,17 +chr20 255778 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=234788;QSTRAND=+ GT:DP:AD 1|0:38:21,17 0|1:36:25,11 1|1:43:18,25 +chr20 255818 . G GAT 60 . QNAME=cluster19_000000F;QSTART=25506967;QSTRAND=- GT:DP:AD ./.:32:7,25 1|0:24:15,9 ./.:39:18,21 +chr20 256161 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=235169;QSTRAND=+ GT:DP:AD 1|0:46:25,21 0|1:18:7,11 1|1:32:16,16 +chr20 256351 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=235359;QSTRAND=+ GT:DP:AD 1|0:21:5,16 0|1:16:7,9 1|1:37:14,23 +chr20 256411 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=235419;QSTRAND=+ GT:DP:AD 1|0:45:23,22 0|1:30:12,18 1|1:25:18,7 +chr20 256777 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=235785;QSTRAND=+ GT:DP:AD 1|0:28:17,11 0|1:33:15,18 1|1:19:7,12 +chr20 256856 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=235864;QSTRAND=+ GT:DP:AD 1|0:34:15,19 0|1:27:13,14 1|1:25:8,17 +chr20 256904 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=235912;QSTRAND=+ GT:DP:AD 1|0:22:10,12 0|1:18:11,7 1|1:36:12,24 +chr20 256928 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=235936;QSTRAND=+ GT:DP:AD 1|0:18:6,12 0|1:19:6,13 1|1:22:10,12 +chr20 256977 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=235985;QSTRAND=+ GT:DP:AD 1|0:18:7,11 0|1:21:13,8 1|1:12:6,6 +chr20 257036 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=236040;QSTRAND=+ GT:DP:AD 1|0:33:20,13 0|1:36:19,17 1|1:35:25,10 +chr20 257175 . A AT 60 . QNAME=HG002-S9-H1-000001F;QSTART=236180;QSTRAND=+ GT:DP:AD 1|0:37:24,13 0|1:23:9,14 1|1:31:22,9 +chr20 257379 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=236384;QSTRAND=+ GT:DP:AD 1|0:27:22,5 0|1:19:6,13 1|1:39:18,21 +chr20 257866 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=236865;QSTRAND=+ GT:DP:AD 1|0:20:13,7 0|1:29:14,15 1|1:22:6,16 +chr20 257889 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=236888;QSTRAND=+ GT:DP:AD 1|0:36:12,24 0|1:24:7,17 1|1:36:14,22 +chr20 257899 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=236898;QSTRAND=+ GT:DP:AD 1|0:28:21,7 0|1:11:5,6 1|1:47:23,24 +chr20 258096 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=237095;QSTRAND=+ GT:DP:AD 1|0:33:8,25 0|1:23:18,5 1|1:17:9,8 +chr20 258653 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=237652;QSTRAND=+ GT:DP:AD 1|0:28:7,21 0|1:16:10,6 1|1:24:18,6 +chr20 258767 . A ACTGTGAAGACCTGGTCCCCACCCCCGTTTTTAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=237767;QSTRAND=+;SVTYPE=INS;SVLEN=33 GT:DP:AD 1/0:20:13,7 0/1:41:19,22 1/1:25:12,13 +chr20 258770 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=237802;QSTRAND=+ GT:DP:AD 1|0:24:12,12 0|1:48:25,23 1|1:32:7,25 +chr20 259023 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=238055;QSTRAND=+ GT:DP:AD 1|0:39:24,15 0|1:20:5,15 1|1:31:22,9 +chr20 259047 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=238079;QSTRAND=+ GT:DP:AD 1|0:27:20,7 0|1:15:9,6 1|1:34:10,24 +chr20 259056 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=238088;QSTRAND=+ GT:DP:AD 1|0:43:20,23 0|1:21:6,15 1|1:29:7,22 +chr20 260063 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=239095;QSTRAND=+ GT:DP:AD 1|0:44:21,23 0|1:38:17,21 1|1:42:21,21 +chr20 260065 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=239097;QSTRAND=+ GT:DP:AD 1|0:35:20,15 0|1:28:11,17 1|1:31:18,13 +chr20 260593 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=239625;QSTRAND=+ GT:DP:AD 1|0:42:19,23 0|1:37:15,22 1|1:36:22,14 +chr20 260725 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=239757;QSTRAND=+ GT:DP:AD 1|0:19:5,14 0|1:18:7,11 1|1:25:19,6 +chr20 260755 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=239787;QSTRAND=+ GT:DP:AD 1|0:46:21,25 ./.:14:6,8 1|1:18:7,11 +chr20 260997 . G A 60 . QNAME=cluster19_000000F;QSTART=220179;QSTRAND=+ GT:DP:AD ./.:29:7,22 0|1:38:25,13 ./.:46:21,25 +chr20 261768 . G A 60 . QNAME=cluster19_000000F;QSTART=220950;QSTRAND=+ GT:DP:AD ./.:34:10,24 0|1:35:14,21 ./.:19:14,5 +chr20 261944 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=240972;QSTRAND=+ GT:DP:AD 1|0:20:12,8 ./.:34:19,15 1|1:26:11,15 +chr20 261974 . G T 60 . QNAME=cluster19_000000F;QSTART=221156;QSTRAND=+ GT:DP:AD ./.:16:11,5 0|1:32:22,10 ./.:32:25,7 +chr20 262044 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=241072;QSTRAND=+ GT:DP:AD 1|0:31:8,23 0|1:40:19,21 1|1:40:25,15 +chr20 262053 . T C 60 . QNAME=cluster19_000000F;QSTART=221235;QSTRAND=+ GT:DP:AD ./.:39:19,20 0|1:37:12,25 ./.:30:16,14 +chr20 262157 . C T 60 . QNAME=cluster19_000000F;QSTART=221339;QSTRAND=+ GT:DP:AD ./.:48:23,25 0|1:21:11,10 ./.:33:14,19 +chr20 262198 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25434273;QSTRAND=- GT:DP:AD ./.:16:6,10 ./.:28:11,17 0|1:29:15,14 +chr20 262582 . C CT 60 . QNAME=cluster19_000000F;QSTART=221765;QSTRAND=+ GT:DP:AD ./.:30:25,5 0|1:27:16,11 ./.:22:10,12 +chr20 262711 . G T 60 . QNAME=cluster19_000000F;QSTART=221894;QSTRAND=+ GT:DP:AD ./.:24:7,17 0|1:29:9,20 ./.:45:22,23 +chr20 262757 . G C 60 . QNAME=cluster19_000000F;QSTART=221940;QSTRAND=+ GT:DP:AD ./.:11:5,6 0|1:39:21,18 ./.:37:13,24 +chr20 263038 . A C 60 . QNAME=cluster19_000000F;QSTART=222221;QSTRAND=+ GT:DP:AD ./.:19:11,8 0|1:28:20,8 ./.:44:19,25 +chr20 263283 . C A 60 . QNAME=cluster19_000000F;QSTART=222466;QSTRAND=+ GT:DP:AD ./.:31:16,15 0|1:30:9,21 ./.:15:7,8 +chr20 263451 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=242479;QSTRAND=+ GT:DP:AD 1|0:33:13,20 0|1:43:23,20 1|1:31:24,7 +chr20 263479 . G GGT 60 . QNAME=cluster19_000000F;QSTART=222663;QSTRAND=+ GT:DP:AD ./.:24:9,15 0|1:23:6,17 ./.:33:10,23 +chr20 263505 . C T 60 . QNAME=cluster19_000000F;QSTART=222690;QSTRAND=+ GT:DP:AD ./.:25:15,10 0|1:22:7,15 ./.:18:13,5 +chr20 263692 . A G 60 . QNAME=cluster19_000000F;QSTART=222877;QSTRAND=+ GT:DP:AD ./.:25:18,7 0|1:18:9,9 ./.:22:8,14 +chr20 263732 . C T 60 . QNAME=cluster19_000000F;QSTART=222917;QSTRAND=+ GT:DP:AD ./.:27:22,5 0|1:26:11,15 ./.:26:21,5 +chr20 263776 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=242796;QSTRAND=+ GT:DP:AD 1|0:39:14,25 ./.:12:5,7 1|1:29:7,22 +chr20 264344 . G A 60 . QNAME=cluster19_000000F;QSTART=223529;QSTRAND=+ GT:DP:AD ./.:32:21,11 0|1:30:7,23 ./.:39:14,25 +chr20 264825 . T G 60 . QNAME=cluster19_000000F;QSTART=224010;QSTRAND=+ GT:DP:AD ./.:29:9,20 0|1:41:21,20 ./.:38:16,22 +chr20 265021 . G T 60 . QNAME=cluster19_000000F;QSTART=224206;QSTRAND=+ GT:DP:AD ./.:24:8,16 0|1:41:20,21 ./.:26:17,9 +chr20 265021 . G GT 60 . QNAME=HG002-S9-H2-000001F;QSTART=218568;QSTRAND=+ GT:DP:AD 0|1:18:13,5 1|0:24:9,15 0|1:48:24,24 +chr20 265024 . T G 60 . QNAME=cluster19_000000F;QSTART=224209;QSTRAND=+ GT:DP:AD ./.:36:13,23 0|1:36:20,16 ./.:47:25,22 +chr20 265028 . T G 60 . QNAME=cluster19_000000F;QSTART=224213;QSTRAND=+ GT:DP:AD ./.:31:20,11 0|1:36:12,24 ./.:12:6,6 +chr20 265032 . T G 60 . QNAME=cluster19_000000F;QSTART=224217;QSTRAND=+ GT:DP:AD ./.:35:25,10 0|1:27:6,21 ./.:22:8,14 +chr20 265049 . C T 60 . QNAME=cluster19_000000F;QSTART=224234;QSTRAND=+ GT:DP:AD ./.:41:24,17 0|1:28:12,16 ./.:19:9,10 +chr20 265294 . G T 60 . QNAME=cluster19_000000F;QSTART=224479;QSTRAND=+ GT:DP:AD ./.:21:15,6 0|1:27:19,8 ./.:39:17,22 +chr20 265614 . C T 60 . QNAME=cluster19_000000F;QSTART=224799;QSTRAND=+ GT:DP:AD ./.:27:22,5 0|1:16:8,8 ./.:31:8,23 +chr20 265842 . T TTAAA 60 . QNAME=cluster19_000000F;QSTART=225028;QSTRAND=+ GT:DP:AD ./.:27:6,21 0|1:20:5,15 1|1:42:20,22 +chr20 267423 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25429056;QSTRAND=- GT:DP:AD ./.:32:20,12 ./.:34:19,15 0|1:35:10,25 +chr20 268285 . C A 60 . QNAME=cluster23_scaffold_2;QSTART=25428194;QSTRAND=- GT:DP:AD ./.:20:5,15 ./.:27:9,18 0|1:37:21,16 +chr20 268294 . A T 60 . QNAME=cluster23_scaffold_2;QSTART=25428185;QSTRAND=- GT:DP:AD ./.:28:17,11 ./.:21:8,13 0|1:23:12,11 +chr20 268599 . T A 60 . QNAME=cluster23_scaffold_3;QSTART=25443260;QSTRAND=- GT:DP:AD ./.:32:9,23 ./.:24:13,11 1|1:29:8,21 +chr20 269435 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25442424;QSTRAND=- GT:DP:AD ./.:38:25,13 ./.:41:22,19 1|1:28:5,23 +chr20 269844 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=223390;QSTRAND=+ GT:DP:AD 0|1:34:11,23 ./.:11:6,5 ./.:30:20,10 +chr20 271443 . T TAC 60 . QNAME=cluster23_scaffold_2;QSTART=25425034;QSTRAND=- GT:DP:AD ./.:31:21,10 ./.:13:6,7 0|1:25:13,12 +chr20 271455 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=25440416;QSTRAND=- GT:DP:AD ./.:49:25,24 ./.:46:21,25 1|0:30:23,7 +chr20 271524 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25440347;QSTRAND=- GT:DP:AD ./.:21:14,7 ./.:36:19,17 1|0:33:9,24 +chr20 271615 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25440256;QSTRAND=- GT:DP:AD ./.:34:22,12 ./.:22:13,9 1|0:18:10,8 +chr20 272116 . A AC 60 . QNAME=cluster23_scaffold_3;QSTART=25439754;QSTRAND=- GT:DP:AD ./.:27:21,6 ./.:42:23,19 1|0:36:15,21 +chr20 272348 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25439523;QSTRAND=- GT:DP:AD ./.:28:9,19 ./.:21:7,14 1|0:40:16,24 +chr20 272493 . C A 60 . QNAME=cluster23_scaffold_2;QSTART=25423984;QSTRAND=- GT:DP:AD ./.:26:20,6 ./.:15:6,9 0|1:25:13,12 +chr20 273372 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=252388;QSTRAND=+ GT:DP:AD 1|0:26:11,15 ./.:35:19,16 1|0:36:16,20 +chr20 273876 . C CAAGAA 60 . QNAME=cluster23_scaffold_3;QSTART=25437990;QSTRAND=- GT:DP:AD ./.:24:12,12 ./.:23:16,7 1|0:31:20,11 +chr20 273894 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25437972;QSTRAND=- GT:DP:AD ./.:22:13,9 ./.:30:24,6 1|0:47:24,23 +chr20 273903 . A AAGGGAGGG 60 . QNAME=HG002-S9-H2-000001F;QSTART=227450;QSTRAND=+ GT:DP:AD 0|1:41:24,17 1|1:19:5,14 ./.:34:19,15 +chr20 274125 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=253141;QSTRAND=+ GT:DP:AD 1|0:16:9,7 ./.:12:6,6 ./.:36:20,16 +chr20 274210 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=253226;QSTRAND=+ GT:DP:AD 1|0:22:7,15 ./.:27:14,13 1|0:18:11,7 +chr20 274599 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=253615;QSTRAND=+ GT:DP:AD 1|0:17:11,6 ./.:39:16,23 ./.:26:16,10 +chr20 274829 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25437045;QSTRAND=- GT:DP:AD ./.:47:25,22 ./.:41:22,19 1|0:38:13,25 +chr20 274893 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25436981;QSTRAND=- GT:DP:AD ./.:24:6,18 ./.:27:7,20 1|0:28:6,22 +chr20 275122 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=25436752;QSTRAND=- GT:DP:AD ./.:33:17,16 ./.:41:20,21 1|0:21:5,16 +chr20 275241 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=254256;QSTRAND=+ GT:DP:AD 1|0:35:17,18 ./.:36:13,23 1|0:39:18,21 +chr20 275322 . C CG 60 . QNAME=cluster23_scaffold_3;QSTART=25436551;QSTRAND=- GT:DP:AD ./.:26:19,7 ./.:13:7,6 1|0:35:22,13 +chr20 275361 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25436512;QSTRAND=- GT:DP:AD ./.:25:16,9 ./.:49:24,25 1|0:28:11,17 +chr20 275466 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=254481;QSTRAND=+ GT:DP:AD 1|0:31:7,24 ./.:34:12,22 ./.:32:19,13 +chr20 275606 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25436267;QSTRAND=- GT:DP:AD ./.:25:12,13 ./.:34:11,23 1|0:32:22,10 +chr20 275918 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25435955;QSTRAND=- GT:DP:AD ./.:42:22,20 ./.:37:12,25 1|0:30:17,13 +chr20 275932 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=254947;QSTRAND=+ GT:DP:AD 1|0:25:6,19 ./.:43:23,20 1|0:29:21,8 +chr20 276086 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=255101;QSTRAND=+ GT:DP:AD 1|0:21:9,12 ./.:26:10,16 1|0:29:6,23 +chr20 276119 . G GA 60 . QNAME=cluster23_scaffold_3;QSTART=25435753;QSTRAND=- GT:DP:AD ./.:22:6,16 ./.:31:6,25 1|0:33:23,10 +chr20 276122 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25435750;QSTRAND=- GT:DP:AD ./.:42:24,18 ./.:39:18,21 1|0:39:25,14 +chr20 276225 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=255240;QSTRAND=+ GT:DP:AD 1|0:34:12,22 ./.:35:17,18 1|0:32:14,18 +chr20 276245 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=255260;QSTRAND=+ GT:DP:AD 1|0:30:5,25 ./.:14:5,9 ./.:24:18,6 +chr20 276351 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=255366;QSTRAND=+ GT:DP:AD 1|0:30:13,17 ./.:33:14,19 1|0:41:17,24 +chr20 276391 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=255406;QSTRAND=+ GT:DP:AD 1|0:25:6,19 ./.:40:15,25 1|0:39:19,20 +chr20 276679 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=255694;QSTRAND=+ GT:DP:AD 1|0:27:21,6 ./.:32:11,21 1|0:32:15,17 +chr20 277092 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=256107;QSTRAND=+ GT:DP:AD 1|0:22:9,13 ./.:37:23,14 1|0:32:14,18 +chr20 277162 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=256177;QSTRAND=+ GT:DP:AD 1|0:21:15,6 ./.:45:23,22 ./.:30:23,7 +chr20 277171 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=256186;QSTRAND=+ GT:DP:AD 1|1:15:7,8 ./.:19:13,6 1|0:28:9,19 +chr20 277550 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=256565;QSTRAND=+ GT:DP:AD 1|0:14:5,9 ./.:28:22,6 1|0:31:20,11 +chr20 277574 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=256589;QSTRAND=+ GT:DP:AD 1|0:30:21,9 ./.:21:6,15 1|0:35:23,12 +chr20 277654 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=256669;QSTRAND=+ GT:DP:AD 1|0:20:13,7 ./.:18:7,11 1|0:24:10,14 +chr20 277664 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=256679;QSTRAND=+ GT:DP:AD 1|0:31:7,24 ./.:26:10,16 1|0:43:18,25 +chr20 277800 . C CAG 60 . QNAME=HG002-S9-H1-000001F;QSTART=256816;QSTRAND=+ GT:DP:AD 1|0:29:21,8 ./.:21:11,10 1|0:43:20,23 +chr20 277808 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=256825;QSTRAND=+ GT:DP:AD 1|0:34:15,19 ./.:21:14,7 1|0:23:13,10 +chr20 277915 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=256932;QSTRAND=+ GT:DP:AD 1|0:35:16,19 ./.:32:22,10 1|0:33:12,21 +chr20 278070 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=257087;QSTRAND=+ GT:DP:AD 1|0:19:9,10 ./.:23:10,13 1|0:42:22,20 +chr20 278107 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25433763;QSTRAND=- GT:DP:AD ./.:31:8,23 ./.:30:25,5 1|0:30:14,16 +chr20 278224 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=257241;QSTRAND=+ GT:DP:AD 1|0:46:25,21 ./.:30:25,5 1|0:21:6,15 +chr20 278515 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=257532;QSTRAND=+ GT:DP:AD 1|0:29:16,13 ./.:29:24,5 ./.:33:13,20 +chr20 278561 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25433309;QSTRAND=- GT:DP:AD ./.:34:18,16 ./.:13:7,6 1|0:39:18,21 +chr20 278930 . C CGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAG 60 . QNAME=HG002-S9-H2-000001F;QSTART=232485;QSTRAND=+;SVTYPE=INS;SVLEN=184 GT:DP:AD 0/1:29:9,20 ./.:22:16,6 ./.:24:5,19 +chr20 278930 . C CGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGCGGGAG 60 . QNAME=cluster23_scaffold_2;QSTART=25417363;QSTRAND=-;SVTYPE=INS;SVLEN=188 GT:DP:AD ./.:19:11,8 ./.:33:12,21 0/1:36:12,24 +chr20 278962 . G GGGAGGGAGGGACGGAGGGAGGAAGGGCGGGAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=257980;QSTRAND=+;SVTYPE=INS;SVLEN=32 GT:DP:AD 1/0:42:17,25 ./.:17:10,7 ./.:20:9,11 +chr20 278966 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=258015;QSTRAND=+ GT:DP:AD 1|0:15:5,10 ./.:38:13,25 ./.:42:17,25 +chr20 278977 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=258026;QSTRAND=+ GT:DP:AD 1|0:28:5,23 ./.:26:12,14 ./.:12:7,5 +chr20 279062 . G GGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGTGGGAGGGAGGGAGGGAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=258112;QSTRAND=+;SVTYPE=INS;SVLEN=139 GT:DP:AD 1/0:29:6,23 ./.:40:23,17 ./.:32:9,23 +chr20 279069 . A AGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGCGGGACGGAGGGAGGGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=232808;QSTRAND=+;SVTYPE=INS;SVLEN=438 GT:DP:AD 0/1:26:5,21 ./.:30:8,22 ./.:38:15,23 +chr20 279069 . A AGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGC 60 . QNAME=cluster19_000000F;QSTART=25483168;QSTRAND=-;SVTYPE=INS;SVLEN=543 GT:DP:AD ./.:37:13,24 1/1:24:6,18 ./.:42:19,23 +chr20 279069 . A AGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGCGGGACGGAGGGAGGGC 60 . QNAME=cluster23_scaffold_2;QSTART=25416710;QSTRAND=-;SVTYPE=INS;SVLEN=514 GT:DP:AD ./.:39:23,16 ./.:26:5,21 0/1:21:11,10 +chr20 279098 . G GGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGCGGGACGGAGGGAGGGACGGAGGGCGGGACGGAGGGAC 60 . QNAME=cluster23_scaffold_3;QSTART=25432493;QSTRAND=-;SVTYPE=INS;SVLEN=179 GT:DP:AD ./.:25:20,5 ./.:28:17,11 1/0:23:13,10 +chr20 279102 . C G 60 . QNAME=cluster23_scaffold_3;QSTART=25432489;QSTRAND=- GT:DP:AD ./.:40:22,18 ./.:29:22,7 1|0:42:19,23 +chr20 279177 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=258365;QSTRAND=+ GT:DP:AD 1|1:30:10,20 ./.:29:6,23 0|1:32:15,17 +chr20 279328 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=258516;QSTRAND=+ GT:DP:AD 1|0:14:6,8 ./.:17:8,9 1|0:12:5,7 +chr20 279759 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=258947;QSTRAND=+ GT:DP:AD 1|0:33:13,20 ./.:47:25,22 1|0:35:19,16 +chr20 279880 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=259068;QSTRAND=+ GT:DP:AD 1|0:33:13,20 ./.:37:23,14 1|0:21:9,12 +chr20 280083 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=25431508;QSTRAND=- GT:DP:AD ./.:29:15,14 ./.:30:13,17 1|0:25:18,7 +chr20 280230 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=259418;QSTRAND=+ GT:DP:AD 1|0:28:7,21 ./.:32:11,21 ./.:15:5,10 +chr20 280339 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=259527;QSTRAND=+ GT:DP:AD 1|0:47:22,25 ./.:25:17,8 ./.:35:23,12 +chr20 280418 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25431240;QSTRAND=- GT:DP:AD ./.:41:25,16 ./.:18:5,13 1|0:42:25,17 +chr20 280635 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25431023;QSTRAND=- GT:DP:AD ./.:41:18,23 ./.:29:21,8 1|0:34:10,24 +chr20 281010 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=260198;QSTRAND=+ GT:DP:AD 1|0:45:23,22 ./.:44:20,24 ./.:28:10,18 +chr20 281470 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=260658;QSTRAND=+ GT:DP:AD 1|0:27:7,20 ./.:38:23,15 1|0:26:8,18 +chr20 281585 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25430073;QSTRAND=- GT:DP:AD ./.:45:24,21 ./.:31:6,25 1|0:20:15,5 +chr20 281929 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=261117;QSTRAND=+ GT:DP:AD 1|0:29:16,13 ./.:43:20,23 1|0:32:14,18 +chr20 282596 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=261784;QSTRAND=+ GT:DP:AD 1|0:13:5,8 ./.:44:23,21 ./.:27:22,5 +chr20 282775 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=261963;QSTRAND=+ GT:DP:AD 1|0:35:24,11 ./.:35:12,23 ./.:26:8,18 +chr20 283019 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=262207;QSTRAND=+ GT:DP:AD 1|0:39:19,20 ./.:17:8,9 ./.:20:10,10 +chr20 283328 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=262516;QSTRAND=+ GT:DP:AD 1|0:29:6,23 ./.:19:5,14 ./.:30:20,10 +chr20 283411 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=262599;QSTRAND=+ GT:DP:AD 1|0:14:6,8 ./.:32:18,14 ./.:37:21,16 +chr20 283535 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=262723;QSTRAND=+ GT:DP:AD 1|0:18:7,11 ./.:37:17,20 ./.:28:7,21 +chr20 283694 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=262883;QSTRAND=+ GT:DP:AD 1|0:31:21,10 ./.:37:20,17 ./.:26:5,21 +chr20 283724 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=262913;QSTRAND=+ GT:DP:AD 1|0:19:13,6 ./.:24:5,19 ./.:26:14,12 +chr20 283802 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25427856;QSTRAND=- GT:DP:AD ./.:37:14,23 ./.:27:16,11 1|0:35:18,17 +chr20 283857 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=263046;QSTRAND=+ GT:DP:AD 1|0:30:25,5 ./.:22:14,8 ./.:29:7,22 +chr20 284338 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=263527;QSTRAND=+ GT:DP:AD 1|0:37:12,25 ./.:45:24,21 ./.:22:8,14 +chr20 284356 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=263545;QSTRAND=+ GT:DP:AD 1|0:28:12,16 ./.:29:5,24 ./.:35:11,24 +chr20 284597 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=263786;QSTRAND=+ GT:DP:AD 1|0:17:11,6 ./.:30:17,13 1|0:39:20,19 +chr20 284724 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=263913;QSTRAND=+ GT:DP:AD 1|0:32:18,14 ./.:25:13,12 1|0:28:15,13 +chr20 284881 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=264070;QSTRAND=+ GT:DP:AD 1|0:41:16,25 ./.:42:23,19 1|0:17:9,8 +chr20 285327 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=264516;QSTRAND=+ GT:DP:AD 1|0:30:12,18 ./.:43:19,24 1|0:26:15,11 +chr20 285600 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=264789;QSTRAND=+ GT:DP:AD 1|0:35:12,23 ./.:38:17,21 1|0:26:18,8 +chr20 285621 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=264810;QSTRAND=+ GT:DP:AD 1|0:39:21,18 ./.:22:15,7 1|0:39:21,18 +chr20 285738 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=264927;QSTRAND=+ GT:DP:AD 1|0:37:16,21 ./.:40:21,19 ./.:40:24,16 +chr20 286151 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=265340;QSTRAND=+ GT:DP:AD 1|0:11:5,6 ./.:39:23,16 ./.:20:8,12 +chr20 286710 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=265898;QSTRAND=+ GT:DP:AD 1|0:14:8,6 ./.:21:12,9 1|0:28:5,23 +chr20 286812 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=266000;QSTRAND=+ GT:DP:AD 1|0:29:19,10 ./.:28:7,21 1|0:43:21,22 +chr20 287237 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=266425;QSTRAND=+ GT:DP:AD 1|0:25:20,5 ./.:36:17,19 1|0:37:24,13 +chr20 287305 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=266493;QSTRAND=+ GT:DP:AD 1|0:37:19,18 ./.:30:14,16 1|0:33:23,10 +chr20 287629 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=266817;QSTRAND=+ GT:DP:AD 1|0:18:8,10 ./.:36:23,13 1|0:39:14,25 +chr20 287833 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=267021;QSTRAND=+ GT:DP:AD 1|0:14:8,6 ./.:27:6,21 1|0:30:16,14 +chr20 287837 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=267025;QSTRAND=+ GT:DP:AD 1|0:19:6,13 ./.:32:13,19 ./.:31:20,11 +chr20 287876 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=267064;QSTRAND=+ GT:DP:AD 1|0:24:15,9 ./.:26:15,11 1|0:20:14,6 +chr20 287908 . C CAAAAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=267097;QSTRAND=+ GT:DP:AD 1|0:26:10,16 ./.:30:17,13 ./.:44:21,23 +chr20 287908 . C CAAAAAAAA 60 . QNAME=cluster23_scaffold_3;QSTART=25423742;QSTRAND=- GT:DP:AD ./.:40:18,22 ./.:38:21,17 1|0:29:24,5 +chr20 287932 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=267129;QSTRAND=+ GT:DP:AD 1|0:32:15,17 ./.:27:14,13 ./.:23:14,9 +chr20 288158 . C CTTTCTTTTTCTT 60 . QNAME=HG002-S9-H1-000001F;QSTART=267356;QSTRAND=+ GT:DP:AD 1|0:36:16,20 ./.:34:16,18 ./.:30:5,25 +chr20 288174 . C CTTTTTCTTTTTCTT 60 . QNAME=cluster23_scaffold_3;QSTART=25423462;QSTRAND=- GT:DP:AD ./.:27:11,16 ./.:31:8,23 1|0:41:16,25 +chr20 288174 . C CT 60 . QNAME=cluster23_scaffold_2;QSTART=25407604;QSTRAND=- GT:DP:AD ./.:23:6,17 ./.:33:11,22 0|1:46:25,21 +chr20 288365 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=267574;QSTRAND=+ GT:DP:AD 1|0:32:7,25 ./.:44:21,23 1|0:39:18,21 +chr20 288516 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=267725;QSTRAND=+ GT:DP:AD 1|0:18:13,5 ./.:25:9,16 1|0:32:16,16 +chr20 289049 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=268258;QSTRAND=+ GT:DP:AD 1|0:22:5,17 ./.:39:16,23 1|0:24:14,10 +chr20 289196 . A ACC 60 . QNAME=HG002-S9-H1-000001F;QSTART=268406;QSTRAND=+ GT:DP:AD 1|0:37:12,25 ./.:27:19,8 ./.:28:23,5 +chr20 289196 . A ACCC 60 . QNAME=cluster23_scaffold_3;QSTART=25422437;QSTRAND=- GT:DP:AD ./.:28:5,23 ./.:28:15,13 1|0:44:21,23 +chr20 289787 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=268997;QSTRAND=+ GT:DP:AD 1|0:34:22,12 ./.:27:17,10 1|0:30:18,12 +chr20 289993 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=269203;QSTRAND=+ GT:DP:AD 1|0:43:25,18 ./.:29:6,23 1|0:41:23,18 +chr20 290134 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=269344;QSTRAND=+ GT:DP:AD 1|0:46:23,23 ./.:48:24,24 1|0:18:13,5 +chr20 290494 . G GC 60 . QNAME=HG002-S9-H2-000001F;QSTART=244671;QSTRAND=+ GT:DP:AD 0|1:18:12,6 1|1:47:22,25 0|1:30:5,25 +chr20 290563 . A ATT 60 . QNAME=cluster23_scaffold_2;QSTART=25405212;QSTRAND=- GT:DP:AD ./.:40:20,20 ./.:33:10,23 0|1:27:15,12 +chr20 290584 . T TTA 60 . QNAME=HG002-S9-H1-000001F;QSTART=269795;QSTRAND=+ GT:DP:AD 1|0:16:10,6 ./.:32:16,16 ./.:18:10,8 +chr20 290584 . T TTTA 60 . QNAME=cluster23_scaffold_3;QSTART=25421047;QSTRAND=- GT:DP:AD ./.:44:24,20 ./.:23:10,13 1|0:27:17,10 +chr20 291796 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=271004;QSTRAND=+ GT:DP:AD 1|0:30:23,7 ./.:11:6,5 1|0:27:14,13 +chr20 291952 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=271160;QSTRAND=+ GT:DP:AD 1|1:25:15,10 1|1:23:5,18 1|1:37:23,14 +chr20 293331 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25418305;QSTRAND=- GT:DP:AD ./.:45:25,20 ./.:44:24,20 1|0:20:15,5 +chr20 293692 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=272898;QSTRAND=+ GT:DP:AD 1|0:35:25,10 ./.:29:8,21 1|0:17:5,12 +chr20 296976 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=251153;QSTRAND=+ GT:DP:AD 0|1:33:17,16 1|1:21:16,5 0|1:25:8,17 +chr20 297051 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=251228;QSTRAND=+ GT:DP:AD 0|1:24:6,18 1|1:26:10,16 0|1:25:15,10 +chr20 297191 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=251368;QSTRAND=+ GT:DP:AD 0|1:43:24,19 1|1:32:10,22 0|1:30:9,21 +chr20 297874 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=252051;QSTRAND=+ GT:DP:AD 0|1:18:13,5 1|1:44:23,21 0|1:23:6,17 +chr20 298162 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=277366;QSTRAND=+ GT:DP:AD 1|0:24:19,5 ./.:25:8,17 0|1:36:25,11 +chr20 298541 . C T 60 . QNAME=cluster19_000000F;QSTART=258279;QSTRAND=+ GT:DP:AD ./.:30:6,24 0|1:40:23,17 ./.:21:5,16 +chr20 298839 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=278043;QSTRAND=+ GT:DP:AD 1|0:33:9,24 ./.:44:19,25 1|0:26:15,11 +chr20 299130 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=278334;QSTRAND=+ GT:DP:AD 1|0:36:15,21 ./.:50:25,25 1|0:40:20,20 +chr20 301074 . G C 60 . QNAME=cluster23_scaffold_2;QSTART=25394701;QSTRAND=- GT:DP:AD ./.:35:20,15 ./.:19:5,14 0|1:25:5,20 +chr20 301778 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=280982;QSTRAND=+ GT:DP:AD 1|0:22:17,5 ./.:32:25,7 1|0:32:25,7 +chr20 302639 . T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=281844;QSTRAND=+ GT:DP:AD 1|0:26:20,6 ./.:40:21,19 1|0:30:24,6 +chr20 302891 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=282096;QSTRAND=+ GT:DP:AD 1|1:36:12,24 1|1:41:21,20 1|1:20:6,14 +chr20 303233 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=282438;QSTRAND=+ GT:DP:AD 1|1:26:18,8 1|1:47:22,25 1|1:26:12,14 +chr20 303404 . C A 60 . QNAME=cluster19_000000F;QSTART=263142;QSTRAND=+ GT:DP:AD ./.:24:17,7 0|1:39:22,17 ./.:28:18,10 +chr20 303430 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=282635;QSTRAND=+ GT:DP:AD 1|1:25:16,9 1|0:22:9,13 1|1:43:18,25 +chr20 304111 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=283316;QSTRAND=+ GT:DP:AD 1|1:27:17,10 1|0:30:7,23 1|1:46:25,21 +chr20 304170 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=283375;QSTRAND=+ GT:DP:AD 1|1:29:6,23 1|1:16:7,9 1|1:26:14,12 +chr20 304190 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=283395;QSTRAND=+ GT:DP:AD 1|1:43:23,20 ./.:25:7,18 1|1:14:7,7 +chr20 304257 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=258434;QSTRAND=+ GT:DP:AD 0|1:37:22,15 1|0:20:5,15 0|1:17:12,5 +chr20 304335 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=258512;QSTRAND=+ GT:DP:AD 0|1:33:12,21 1|0:34:15,19 0|1:28:23,5 +chr20 304365 . G C 60 . QNAME=cluster19_000000F;QSTART=264103;QSTRAND=+ GT:DP:AD ./.:39:19,20 0|1:32:12,20 ./.:24:7,17 +chr20 304375 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25391400;QSTRAND=- GT:DP:AD ./.:20:6,14 ./.:29:7,22 0|1:40:21,19 +chr20 304376 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=258553;QSTRAND=+ GT:DP:AD 0|1:39:16,23 1|1:33:15,18 ./.:36:24,12 +chr20 304377 . G C 60 . QNAME=cluster23_scaffold_2;QSTART=25391398;QSTRAND=- GT:DP:AD ./.:23:10,13 ./.:28:5,23 0|1:28:22,6 +chr20 304450 . T C 60 . QNAME=cluster19_000000F;QSTART=264188;QSTRAND=+ GT:DP:AD ./.:37:18,19 0|1:23:14,9 ./.:31:25,6 +chr20 304460 . T C 60 . QNAME=cluster19_000000F;QSTART=264198;QSTRAND=+ GT:DP:AD ./.:34:15,19 0|1:33:19,14 ./.:36:13,23 +chr20 304461 . T C 60 . QNAME=cluster19_000000F;QSTART=264199;QSTRAND=+ GT:DP:AD ./.:35:22,13 0|1:32:18,14 ./.:24:7,17 +chr20 304463 . A T 60 . QNAME=cluster19_000000F;QSTART=264201;QSTRAND=+ GT:DP:AD ./.:29:13,16 0|1:49:24,25 ./.:17:12,5 +chr20 304679 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=283884;QSTRAND=+ GT:DP:AD 1|0:32:8,24 ./.:42:23,19 1|0:26:5,21 +chr20 304705 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=258881;QSTRAND=+ GT:DP:AD 0|1:28:8,20 1|1:31:25,6 0|1:15:9,6 +chr20 305012 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=284217;QSTRAND=+ GT:DP:AD 1|1:35:15,20 1|1:20:6,14 1|1:33:12,21 +chr20 305384 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=284589;QSTRAND=+ GT:DP:AD 1|0:29:19,10 0|1:21:14,7 1|0:35:23,12 +chr20 305403 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=284608;QSTRAND=+ GT:DP:AD 1|1:35:11,24 1|1:21:7,14 1|1:43:23,20 +chr20 305843 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=260019;QSTRAND=+ GT:DP:AD 0|1:29:20,9 1|0:30:17,13 0|1:38:15,23 +chr20 305871 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=260047;QSTRAND=+ GT:DP:AD 0|1:39:20,19 1|1:44:23,21 0|1:24:12,12 +chr20 305882 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=260058;QSTRAND=+ GT:DP:AD 0|1:21:10,11 1|1:48:25,23 0|1:29:19,10 +chr20 305943 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=285148;QSTRAND=+ GT:DP:AD 1|1:43:19,24 1|1:34:16,18 1|1:22:13,9 +chr20 306194 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=285399;QSTRAND=+ GT:DP:AD 1|1:32:18,14 1|1:41:17,24 1|1:39:23,16 +chr20 306232 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=285438;QSTRAND=+ GT:DP:AD 1|0:29:12,17 0|1:23:6,17 1|0:23:5,18 +chr20 306268 . A ACCAGGCTGGAGTGCAGTGGCTCACTGCGTGGCTCGCTACAGCCTACAACTCCTGGGCTCCAGCAATCCTGCTGCCCCAGCCTCCTGTGTAACTGAGACTACAGGCACGCACCACCACACCCAGCTAATTTTTTCTTTCTTTTTTTTTTTTTTGAGATGAACTCTCACTCTGTTGC 60 . QNAME=HG002-S9-H1-000001F;QSTART=285475;QSTRAND=+;SVTYPE=INS;SVLEN=175 GT:DP:AD 1/1:34:18,16 ./.:32:19,13 1/1:25:13,12 +chr20 306268 . A ACCAGGCTGGAGTGCAGTGGCTCACTGCGTGGCTCGCTACAGCCTACAACTCCTGGGCTCCAGCAATCCTGCTGCCCCAGCCTCCTGTGTAACTGAGACTACAGGCACGCACCACCACACCCAGCTAATGTTTTCTTTCTTTTTTTTTTTTTTGAGATGAACTCTCACTCTGTTGC 60 . QNAME=cluster19_000000F;QSTART=25455794;QSTRAND=-;SVTYPE=INS;SVLEN=175 GT:DP:AD ./.:33:15,18 1/1:35:11,24 ./.:34:9,25 +chr20 306413 . T TC 60 . QNAME=cluster23_scaffold_2;QSTART=25389187;QSTRAND=- GT:DP:AD ./.:32:25,7 ./.:21:7,14 0|1:26:11,15 +chr20 306414 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=260765;QSTRAND=+ GT:DP:AD 0|1:37:21,16 1|0:46:25,21 ./.:36:11,25 +chr20 306535 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=260886;QSTRAND=+ GT:DP:AD 0|1:36:22,14 1|0:37:14,23 0|1:16:11,5 +chr20 306582 . A G 60 . QNAME=cluster19_000000F;QSTART=266491;QSTRAND=+ GT:DP:AD ./.:33:9,24 0|1:22:12,10 ./.:20:11,9 +chr20 306627 . T G 60 . QNAME=cluster19_000000F;QSTART=25455435;QSTRAND=- GT:DP:AD ./.:33:15,18 1|0:30:22,8 ./.:24:13,11 +chr20 306642 . T C 60 . QNAME=cluster19_000000F;QSTART=25455420;QSTRAND=- GT:DP:AD ./.:32:10,22 1|1:27:15,12 ./.:29:12,17 +chr20 306653 . C T 60 . QNAME=cluster19_000000F;QSTART=25455409;QSTRAND=- GT:DP:AD ./.:49:24,25 1|0:33:13,20 ./.:19:6,13 +chr20 306667 . T C 60 . QNAME=cluster19_000000F;QSTART=25455395;QSTRAND=- GT:DP:AD ./.:28:5,23 1|0:45:22,23 ./.:35:21,14 +chr20 306742 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=261093;QSTRAND=+ GT:DP:AD 0|1:25:15,10 ./.:32:9,23 0|1:14:6,8 +chr20 306776 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=286157;QSTRAND=+ GT:DP:AD 1|0:33:23,10 ./.:21:11,10 1|0:33:13,20 +chr20 306885 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=286266;QSTRAND=+ GT:DP:AD 1|1:27:9,18 1|1:31:23,8 1|1:31:17,14 +chr20 306993 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=286374;QSTRAND=+ GT:DP:AD 1|0:30:25,5 1|1:25:18,7 1|0:27:18,9 +chr20 307589 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=286970;QSTRAND=+ GT:DP:AD 1|1:32:12,20 1|0:31:16,15 1|1:26:16,10 +chr20 307693 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=262044;QSTRAND=+ GT:DP:AD 0|1:34:25,9 ./.:19:13,6 ./.:33:10,23 +chr20 308128 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=262479;QSTRAND=+ GT:DP:AD 0|1:18:11,7 0|1:40:25,15 ./.:41:18,23 +chr20 308132 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=287513;QSTRAND=+ GT:DP:AD 1|1:43:21,22 1|1:24:8,16 1|1:29:13,16 +chr20 308261 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=262612;QSTRAND=+ GT:DP:AD 0|1:25:9,16 0|1:30:5,25 ./.:37:25,12 +chr20 308278 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=262629;QSTRAND=+ GT:DP:AD 0|1:24:12,12 1|1:32:10,22 0|1:45:22,23 +chr20 308352 . T C 60 . QNAME=cluster19_000000F;QSTART=25453711;QSTRAND=- GT:DP:AD ./.:16:8,8 1|0:33:13,20 0|1:27:22,5 +chr20 308718 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=263069;QSTRAND=+ GT:DP:AD 0|1:23:15,8 1|1:23:17,6 0|1:24:7,17 +chr20 308968 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=288349;QSTRAND=+ GT:DP:AD 1|1:23:7,16 1|1:17:6,11 1|1:11:6,5 +chr20 309141 . A G 60 . QNAME=cluster19_000000F;QSTART=25452922;QSTRAND=- GT:DP:AD ./.:27:10,17 1|0:37:12,25 0|1:33:14,19 +chr20 309613 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=263964;QSTRAND=+ GT:DP:AD 0|1:38:22,16 ./.:22:16,6 ./.:34:22,12 +chr20 309637 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=289018;QSTRAND=+ GT:DP:AD 1|1:29:24,5 ./.:12:7,5 1|0:39:24,15 +chr20 309639 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=289020;QSTRAND=+ GT:DP:AD 1|1:36:18,18 ./.:25:9,16 1|0:41:21,20 +chr20 309653 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=289034;QSTRAND=+ GT:DP:AD 1|1:46:24,22 ./.:15:8,7 1|0:32:23,9 +chr20 309674 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=289055;QSTRAND=+ GT:DP:AD 1|1:39:16,23 1|1:35:14,21 1|1:37:25,12 +chr20 310521 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=289902;QSTRAND=+ GT:DP:AD 1|1:21:6,15 1|0:34:20,14 0|1:13:7,6 +chr20 310522 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=289903;QSTRAND=+ GT:DP:AD 1|1:19:9,10 1|0:29:8,21 0|1:42:21,21 +chr20 310523 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=289904;QSTRAND=+ GT:DP:AD 1|1:27:20,7 1|0:21:13,8 0|1:23:18,5 +chr20 310719 . A AT 60 . QNAME=HG002-S9-H1-000001F;QSTART=290101;QSTRAND=+ GT:DP:AD 1|1:35:20,15 1|0:31:6,25 0|1:45:24,21 +chr20 311107 . C G 60 . QNAME=cluster19_000000F;QSTART=271016;QSTRAND=+ GT:DP:AD ./.:35:22,13 0|1:32:12,20 1|0:38:25,13 +chr20 311145 . T G 60 . QNAME=cluster19_000000F;QSTART=271054;QSTRAND=+ GT:DP:AD ./.:33:10,23 0|1:32:13,19 1|0:30:7,23 +chr20 311237 . C T 60 . QNAME=cluster19_000000F;QSTART=271146;QSTRAND=+ GT:DP:AD ./.:39:21,18 0|1:28:8,20 1|0:25:8,17 +chr20 311327 . G C 60 . QNAME=cluster19_000000F;QSTART=271236;QSTRAND=+ GT:DP:AD ./.:31:24,7 0|1:30:10,20 1|0:34:21,13 +chr20 311347 . C CATTATT 60 . QNAME=cluster19_000000F;QSTART=271257;QSTRAND=+ GT:DP:AD ./.:21:11,10 0|1:32:12,20 1|0:19:8,11 +chr20 311683 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=291065;QSTRAND=+ GT:DP:AD 1|0:39:20,19 1|0:46:22,24 0|1:40:16,24 +chr20 311774 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=291156;QSTRAND=+ GT:DP:AD 1|0:29:21,8 1|1:16:7,9 0|1:18:12,6 +chr20 311791 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=291173;QSTRAND=+ GT:DP:AD 1|1:32:17,15 1|1:22:14,8 1|1:34:17,17 +chr20 312718 . A AT 60 . QNAME=cluster23_scaffold_2;QSTART=25382881;QSTRAND=- GT:DP:AD ./.:46:21,25 ./.:18:10,8 0|1:25:15,10 +chr20 314417 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=293799;QSTRAND=+ GT:DP:AD 1|0:18:7,11 ./.:16:9,7 ./.:43:19,24 +chr20 314431 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=293813;QSTRAND=+ GT:DP:AD 1|0:48:23,25 ./.:40:23,17 ./.:25:16,9 +chr20 314495 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=268847;QSTRAND=+ GT:DP:AD 0|1:31:6,25 ./.:34:24,10 ./.:38:22,16 +chr20 314567 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25381032;QSTRAND=- GT:DP:AD ./.:21:7,14 ./.:41:18,23 0|1:18:9,9 +chr20 314595 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=268947;QSTRAND=+ GT:DP:AD 0|1:30:15,15 ./.:36:15,21 1|0:27:12,15 +chr20 314668 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=269020;QSTRAND=+ GT:DP:AD 0|1:40:19,21 ./.:27:7,20 1|0:33:11,22 +chr20 314877 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=269229;QSTRAND=+ GT:DP:AD 0|1:21:13,8 ./.:15:6,9 1|0:37:25,12 +chr20 314905 . C CTT 60 . QNAME=cluster23_scaffold_2;QSTART=25380692;QSTRAND=- GT:DP:AD ./.:37:25,12 ./.:21:14,7 0|1:30:22,8 +chr20 315222 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=269573;QSTRAND=+ GT:DP:AD 0|1:47:25,22 ./.:35:23,12 1|0:26:6,20 +chr20 315528 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=269879;QSTRAND=+ GT:DP:AD 0|1:30:20,10 ./.:28:14,14 1|0:32:7,25 +chr20 315724 . G GTATTAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=270076;QSTRAND=+ GT:DP:AD 0|1:40:23,17 ./.:35:14,21 1|0:28:16,12 +chr20 316587 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=295969;QSTRAND=+ GT:DP:AD 1|0:39:14,25 ./.:23:5,18 ./.:37:17,20 +chr20 316724 . G GT 60 . QNAME=cluster23_scaffold_2;QSTART=25378872;QSTRAND=- GT:DP:AD ./.:17:5,12 ./.:34:11,23 0|1:34:12,22 +chr20 318091 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=272445;QSTRAND=+ GT:DP:AD 0|1:35:17,18 ./.:30:16,14 1|0:31:18,13 +chr20 318388 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=272742;QSTRAND=+ GT:DP:AD 0|1:26:5,21 ./.:18:11,7 1|0:16:11,5 +chr20 318854 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=273208;QSTRAND=+ GT:DP:AD 0|1:17:10,7 1|1:26:10,16 1|1:15:9,6 +chr20 318943 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=273296;QSTRAND=+ GT:DP:AD 0|1:44:23,21 1|1:22:16,6 1|1:29:16,13 +chr20 318971 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=298353;QSTRAND=+ GT:DP:AD 1|1:43:19,24 1|1:38:21,17 1|0:31:10,21 +chr20 319115 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=273468;QSTRAND=+ GT:DP:AD 0|1:41:22,19 1|1:29:12,17 1|0:16:5,11 +chr20 319367 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=298749;QSTRAND=+ GT:DP:AD 1|0:33:11,22 ./.:28:7,21 ./.:30:17,13 +chr20 319623 . G C 60 . QNAME=cluster19_000000F;QSTART=25442440;QSTRAND=- GT:DP:AD ./.:37:23,14 1|0:24:5,19 ./.:27:5,22 +chr20 319838 . G A 60 . QNAME=cluster19_000000F;QSTART=25442225;QSTRAND=- GT:DP:AD ./.:16:9,7 1|0:37:15,22 ./.:29:12,17 +chr20 321250 . A G 60 . QNAME=cluster19_000000F;QSTART=25440813;QSTRAND=- GT:DP:AD ./.:32:11,21 1|0:31:15,16 ./.:37:23,14 +chr20 326089 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=305469;QSTRAND=+ GT:DP:AD 1|0:33:14,19 0|1:44:19,25 ./.:31:20,11 +chr20 328569 . G GA 60 . QNAME=cluster23_scaffold_3;QSTART=25382887;QSTRAND=- GT:DP:AD ./.:38:15,23 ./.:39:21,18 1|0:31:7,24 +chr20 328717 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25382739;QSTRAND=- GT:DP:AD ./.:32:24,8 ./.:37:24,13 1|0:37:21,16 +chr20 336200 . C CTCTTCT 60 . QNAME=HG002-S9-H1-000001F;QSTART=315579;QSTRAND=+ GT:DP:AD 1|0:34:11,23 0|1:25:14,11 ./.:46:21,25 +chr20 336200 . C CTCT 60 . QNAME=cluster23_scaffold_3;QSTART=25375253;QSTRAND=- GT:DP:AD ./.:37:25,12 ./.:34:23,11 1|0:26:17,9 +chr20 336336 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25375132;QSTRAND=- GT:DP:AD ./.:31:24,7 ./.:26:16,10 1|0:37:13,24 +chr20 338577 . A ATG 60 . QNAME=HG002-S9-H1-000001F;QSTART=317950;QSTRAND=+ GT:DP:AD 1|0:48:24,24 0|1:33:16,17 1|1:37:17,20 +chr20 340763 . C T 60 . QNAME=cluster19_000000F;QSTART=25421304;QSTRAND=- GT:DP:AD ./.:30:11,19 1|0:24:16,8 ./.:34:16,18 +chr20 340858 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=295186;QSTRAND=+ GT:DP:AD 0|1:18:11,7 ./.:32:15,17 ./.:16:10,6 +chr20 340865 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=295193;QSTRAND=+ GT:DP:AD 0|1:25:7,18 ./.:38:13,25 ./.:36:21,15 +chr20 341112 . T TCACACA 60 . QNAME=HG002-S9-H2-000001F;QSTART=295441;QSTRAND=+ GT:DP:AD 0|1:38:21,17 ./.:29:15,14 ./.:20:11,9 +chr20 341968 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=296297;QSTRAND=+ GT:DP:AD 0|1:15:5,10 1|0:34:19,15 ./.:32:11,21 +chr20 342602 . C CTTT 60 . QNAME=HG002-S9-H1-000001F;QSTART=321976;QSTRAND=+ GT:DP:AD 1|0:26:9,17 ./.:30:5,25 ./.:30:21,9 +chr20 342602 . C CTTTTT 60 . QNAME=cluster19_000000F;QSTART=302510;QSTRAND=+ GT:DP:AD ./.:30:9,21 0|1:44:19,25 ./.:46:21,25 +chr20 342602 . C CTTTTTTTT 60 . QNAME=cluster23_scaffold_3;QSTART=25368856;QSTRAND=- GT:DP:AD ./.:22:15,7 ./.:19:10,9 1|0:31:25,6 +chr20 342602 . C CTTTTTTT 60 . QNAME=cluster23_scaffold_2;QSTART=25353008;QSTRAND=- GT:DP:AD ./.:32:14,18 ./.:45:25,20 0|1:26:5,21 +chr20 342621 . T TTTC 60 . QNAME=cluster19_000000F;QSTART=25419443;QSTRAND=- GT:DP:AD ./.:44:19,25 1|0:35:16,19 ./.:24:7,17 +chr20 342641 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=296962;QSTRAND=+ GT:DP:AD 0|1:29:8,21 ./.:41:21,20 ./.:32:8,24 +chr20 342664 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=296985;QSTRAND=+ GT:DP:AD 0|1:46:24,22 ./.:33:18,15 ./.:29:16,13 +chr20 342939 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=297260;QSTRAND=+ GT:DP:AD 0|1:36:22,14 ./.:42:25,17 ./.:39:21,18 +chr20 343326 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=297647;QSTRAND=+ GT:DP:AD 0|1:36:16,20 ./.:34:9,25 ./.:46:25,21 +chr20 343479 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=297800;QSTRAND=+ GT:DP:AD 0|1:42:23,19 ./.:26:11,15 ./.:26:5,21 +chr20 343825 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=298146;QSTRAND=+ GT:DP:AD 0|1:46:23,23 ./.:34:24,10 ./.:45:22,23 +chr20 343865 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=298186;QSTRAND=+ GT:DP:AD 0|1:17:12,5 ./.:15:8,7 ./.:36:22,14 +chr20 343893 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=298214;QSTRAND=+ GT:DP:AD 0|1:36:21,15 ./.:27:15,12 ./.:17:10,7 +chr20 344097 . C CAA 60 . QNAME=HG002-S9-H2-000001F;QSTART=298419;QSTRAND=+ GT:DP:AD 0|1:39:24,15 ./.:29:6,23 ./.:42:17,25 +chr20 344097 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25367360;QSTRAND=- GT:DP:AD ./.:37:19,18 ./.:37:23,14 1|0:34:20,14 +chr20 344354 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=298677;QSTRAND=+ GT:DP:AD 0|1:33:10,23 ./.:22:6,16 ./.:32:10,22 +chr20 344458 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=298781;QSTRAND=+ GT:DP:AD 0|1:40:22,18 ./.:30:17,13 ./.:43:22,21 +chr20 344798 . T G 60 . QNAME=cluster23_scaffold_3;QSTART=25366659;QSTRAND=- GT:DP:AD ./.:25:9,16 ./.:32:13,19 1|0:21:14,7 +chr20 345372 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=299695;QSTRAND=+ GT:DP:AD 0|1:34:15,19 ./.:19:9,10 ./.:31:22,9 +chr20 345506 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=299829;QSTRAND=+ GT:DP:AD 0|1:23:6,17 ./.:29:23,6 ./.:36:15,21 +chr20 345647 . T TACAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=299971;QSTRAND=+ GT:DP:AD 0|1:22:5,17 ./.:19:14,5 ./.:44:23,21 +chr20 348484 . C CGTGTGTGTGT 60 . QNAME=HG002-S9-H1-000001F;QSTART=327861;QSTRAND=+ GT:DP:AD 1|0:34:21,13 ./.:25:5,20 1|0:26:6,20 +chr20 348484 . C CGTGTGTGTGTGT 60 . QNAME=cluster19_000000F;QSTART=308397;QSTRAND=+ GT:DP:AD ./.:34:21,13 0|1:26:15,11 0|1:16:5,11 +chr20 349198 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=303519;QSTRAND=+ GT:DP:AD 0|1:35:14,21 ./.:31:20,11 ./.:17:6,11 +chr20 350477 . T TA 60 . QNAME=cluster23_scaffold_3;QSTART=25360969;QSTRAND=- GT:DP:AD ./.:30:9,21 ./.:28:11,17 1|0:31:22,9 +chr20 350646 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25360799;QSTRAND=- GT:DP:AD ./.:30:15,15 ./.:12:7,5 1|0:27:7,20 +chr20 351164 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=305467;QSTRAND=+ GT:DP:AD 0|1:36:13,23 ./.:43:23,20 ./.:29:21,8 +chr20 352819 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=332204;QSTRAND=+ GT:DP:AD 1|0:42:19,23 1|1:38:23,15 1|1:22:12,10 +chr20 354581 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=308884;QSTRAND=+ GT:DP:AD 0|1:35:16,19 ./.:14:8,6 ./.:24:18,6 +chr20 355283 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=309586;QSTRAND=+ GT:DP:AD 0|1:20:5,15 ./.:41:25,16 ./.:32:19,13 +chr20 356924 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=336307;QSTRAND=+ GT:DP:AD 1|1:30:8,22 1|1:14:9,5 1|1:18:10,8 +chr20 358585 . T C 60 . QNAME=cluster19_000000F;QSTART=25403485;QSTRAND=- GT:DP:AD ./.:11:6,5 1|0:26:10,16 ./.:25:19,6 +chr20 358586 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=312887;QSTRAND=+ GT:DP:AD 0|1:35:24,11 ./.:34:9,25 ./.:44:20,24 +chr20 358841 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=338223;QSTRAND=+ GT:DP:AD 1|0:16:10,6 0|1:28:8,20 1|1:26:5,21 +chr20 359869 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=314170;QSTRAND=+ GT:DP:AD 0|1:24:14,10 1|0:41:16,25 ./.:17:10,7 +chr20 359913 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=314214;QSTRAND=+ GT:DP:AD 0|1:43:19,24 1|0:36:23,13 ./.:31:7,24 +chr20 359914 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=314215;QSTRAND=+ GT:DP:AD 0|1:21:12,9 1|0:34:19,15 ./.:20:12,8 +chr20 359916 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=314217;QSTRAND=+ GT:DP:AD 0|1:22:14,8 1|0:37:21,16 ./.:42:22,20 +chr20 359924 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=314225;QSTRAND=+ GT:DP:AD 0|1:30:22,8 1|0:28:5,23 ./.:24:11,13 +chr20 359930 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=314231;QSTRAND=+ GT:DP:AD 0|1:37:20,17 1|0:37:18,19 ./.:28:17,11 +chr20 359931 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=314232;QSTRAND=+ GT:DP:AD 0|1:18:10,8 1|0:25:13,12 ./.:34:22,12 +chr20 359947 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=314248;QSTRAND=+ GT:DP:AD 0|1:22:7,15 1|0:43:23,20 ./.:12:5,7 +chr20 359953 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=314254;QSTRAND=+ GT:DP:AD 0|1:11:6,5 1|0:26:16,10 ./.:30:20,10 +chr20 359954 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=314255;QSTRAND=+ GT:DP:AD 0|1:40:22,18 1|0:44:19,25 ./.:26:19,7 +chr20 359955 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=314256;QSTRAND=+ GT:DP:AD 0|1:30:15,15 1|0:26:9,17 ./.:31:16,15 +chr20 359960 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=314261;QSTRAND=+ GT:DP:AD 0|1:32:7,25 1|0:31:25,6 ./.:42:22,20 +chr20 359969 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=314270;QSTRAND=+ GT:DP:AD 0|1:27:8,19 1|0:31:21,10 ./.:39:15,24 +chr20 359998 . C CA 60 . QNAME=HG002-S9-H2-000001F;QSTART=314300;QSTRAND=+ GT:DP:AD 0|1:40:23,17 ./.:35:17,18 1|0:31:14,17 +chr20 360554 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=314856;QSTRAND=+ GT:DP:AD 0|1:26:9,17 1|0:32:13,19 ./.:28:15,13 +chr20 360556 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=314858;QSTRAND=+ GT:DP:AD 0|1:38:20,18 1|0:36:18,18 ./.:24:15,9 +chr20 360622 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=314924;QSTRAND=+ GT:DP:AD 0|1:11:6,5 1|0:32:20,12 ./.:29:15,14 +chr20 361302 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=315604;QSTRAND=+ GT:DP:AD 0|1:48:23,25 1|0:34:25,9 ./.:24:15,9 +chr20 362051 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=316353;QSTRAND=+ GT:DP:AD 0|1:33:11,22 1|0:38:18,20 ./.:29:16,13 +chr20 362052 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=316354;QSTRAND=+ GT:DP:AD 0|1:40:24,16 1|0:34:14,20 ./.:29:8,21 +chr20 362185 . G GA 60 . QNAME=cluster23_scaffold_3;QSTART=25349263;QSTRAND=- GT:DP:AD ./.:37:17,20 ./.:31:12,19 1|0:26:12,14 +chr20 362679 . A ATG 60 . QNAME=HG002-S9-H2-000001F;QSTART=316982;QSTRAND=+ GT:DP:AD 0|1:19:8,11 1|0:21:15,6 ./.:39:24,15 +chr20 363003 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=317307;QSTRAND=+ GT:DP:AD 0|1:28:10,18 1|0:41:21,20 ./.:15:5,10 +chr20 363114 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=317418;QSTRAND=+ GT:DP:AD 0|1:32:7,25 1|0:32:7,25 ./.:40:16,24 +chr20 363119 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=317423;QSTRAND=+ GT:DP:AD 0|1:34:21,13 1|0:36:22,14 ./.:35:12,23 +chr20 363245 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=342624;QSTRAND=+ GT:DP:AD 1|0:23:15,8 0|1:41:19,22 1|0:23:8,15 +chr20 363435 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=317739;QSTRAND=+ GT:DP:AD 0|1:24:14,10 1|0:22:7,15 ./.:38:17,21 +chr20 363987 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=318291;QSTRAND=+ GT:DP:AD 0|1:38:13,25 1|0:11:6,5 ./.:41:18,23 +chr20 364755 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=319059;QSTRAND=+ GT:DP:AD 0|1:11:5,6 1|0:35:23,12 ./.:34:20,14 +chr20 364763 . C CAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=344143;QSTRAND=+ GT:DP:AD 1|1:17:11,6 1|1:29:10,19 1|1:35:10,25 +chr20 365042 . G A 60 . QNAME=cluster19_000000F;QSTART=25397024;QSTRAND=- GT:DP:AD ./.:30:12,18 1|0:32:25,7 ./.:21:6,15 +chr20 365220 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=344601;QSTRAND=+ GT:DP:AD 1|1:22:5,17 1|1:33:25,8 1|1:35:17,18 +chr20 366032 . C T 60 . QNAME=cluster19_000000F;QSTART=25396036;QSTRAND=- GT:DP:AD ./.:24:5,19 1|0:28:9,19 ./.:13:8,5 +chr20 366107 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=345487;QSTRAND=+ GT:DP:AD 1|1:12:6,6 1|1:42:23,19 1|1:31:25,6 +chr20 366279 . C T 60 . QNAME=cluster19_000000F;QSTART=25395803;QSTRAND=- GT:DP:AD ./.:45:24,21 1|0:43:21,22 ./.:34:14,20 +chr20 366317 . A G 60 . QNAME=cluster19_000000F;QSTART=25395765;QSTRAND=- GT:DP:AD ./.:40:22,18 1|0:46:22,24 ./.:33:16,17 +chr20 366341 . A G 60 . QNAME=cluster19_000000F;QSTART=25395741;QSTRAND=- GT:DP:AD ./.:40:19,21 1|0:33:14,19 ./.:14:7,7 +chr20 366365 . C A 60 . QNAME=cluster19_000000F;QSTART=25395717;QSTRAND=- GT:DP:AD ./.:18:12,6 1|0:30:12,18 ./.:31:13,18 +chr20 366711 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=346091;QSTRAND=+ GT:DP:AD 1|0:25:11,14 ./.:23:8,15 1|1:29:18,11 +chr20 367006 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=346386;QSTRAND=+ GT:DP:AD 1|1:29:17,12 1|0:44:22,22 1|1:37:23,14 +chr20 367079 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=346459;QSTRAND=+ GT:DP:AD 1|0:45:23,22 ./.:26:15,11 1|1:11:5,6 +chr20 367082 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=346462;QSTRAND=+ GT:DP:AD 1|0:44:25,19 ./.:32:16,16 1|1:31:20,11 +chr20 367106 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=346486;QSTRAND=+ GT:DP:AD 1|0:36:24,12 ./.:25:9,16 1|1:34:13,21 +chr20 367141 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=346521;QSTRAND=+ GT:DP:AD 1|0:33:16,17 1|0:20:14,6 1|1:48:24,24 +chr20 367176 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=346552;QSTRAND=+ GT:DP:AD 1|0:26:14,12 ./.:42:17,25 1|1:36:14,22 +chr20 367226 . A C 60 . QNAME=cluster19_000000F;QSTART=25394856;QSTRAND=- GT:DP:AD ./.:30:20,10 1|0:43:21,22 ./.:44:20,24 +chr20 367234 . A AAAAC 60 . QNAME=cluster19_000000F;QSTART=25394844;QSTRAND=- GT:DP:AD ./.:29:8,21 1|0:36:24,12 ./.:28:17,11 +chr20 367235 . C A 60 . QNAME=cluster19_000000F;QSTART=25394843;QSTRAND=- GT:DP:AD ./.:21:12,9 1|0:41:21,20 ./.:29:13,16 +chr20 367252 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=346617;QSTRAND=+ GT:DP:AD 1|0:46:22,24 ./.:31:20,11 1|1:37:20,17 +chr20 367264 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=321569;QSTRAND=+ GT:DP:AD 0|1:36:12,24 1|1:17:7,10 ./.:34:10,24 +chr20 367521 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=346886;QSTRAND=+ GT:DP:AD 1|0:35:25,10 0|1:38:17,21 ./.:11:6,5 +chr20 367522 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=346887;QSTRAND=+ GT:DP:AD 1|0:24:18,6 ./.:15:5,10 ./.:38:16,22 +chr20 367522 . G C 60 . QNAME=cluster19_000000F;QSTART=327442;QSTRAND=+ GT:DP:AD ./.:23:15,8 0|1:17:9,8 ./.:35:18,17 +chr20 367544 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=321849;QSTRAND=+ GT:DP:AD 0|1:40:23,17 ./.:34:14,20 1|0:20:8,12 +chr20 367675 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=347040;QSTRAND=+ GT:DP:AD 1|0:18:12,6 ./.:45:21,24 0|1:34:19,15 +chr20 367690 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=321995;QSTRAND=+ GT:DP:AD 0|1:20:10,10 ./.:30:10,20 0|1:35:14,21 +chr20 367721 . G GT 60 . QNAME=HG002-S9-H1-000001F;QSTART=347087;QSTRAND=+ GT:DP:AD 1|0:37:15,22 0|1:34:25,9 1|0:28:19,9 +chr20 367877 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=347243;QSTRAND=+ GT:DP:AD 1|0:22:11,11 ./.:37:17,20 ./.:30:24,6 +chr20 368132 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=322437;QSTRAND=+ GT:DP:AD 0|1:23:11,12 1|0:19:9,10 ./.:32:14,18 +chr20 368260 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=322565;QSTRAND=+ GT:DP:AD 0|1:13:7,6 1|0:20:11,9 ./.:28:6,22 +chr20 368410 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=322713;QSTRAND=+ GT:DP:AD 0|1:18:5,13 1|0:41:23,18 ./.:29:23,6 +chr20 368474 . C T 60 . QNAME=cluster19_000000F;QSTART=328395;QSTRAND=+ GT:DP:AD ./.:22:14,8 0|1:40:21,19 1|0:40:17,23 +chr20 368491 . G A 60 . QNAME=cluster19_000000F;QSTART=328412;QSTRAND=+ GT:DP:AD ./.:25:7,18 0|1:21:8,13 ./.:26:10,16 +chr20 368580 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=322883;QSTRAND=+ GT:DP:AD 0|1:26:7,19 1|0:29:22,7 ./.:33:13,20 +chr20 368662 . G C 60 . QNAME=cluster19_000000F;QSTART=25393418;QSTRAND=- GT:DP:AD ./.:46:21,25 1|0:29:15,14 ./.:36:11,25 +chr20 369093 . T C 60 . QNAME=cluster19_000000F;QSTART=25392989;QSTRAND=- GT:DP:AD ./.:17:7,10 1|0:32:19,13 ./.:38:25,13 +chr20 369284 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25342176;QSTRAND=- GT:DP:AD ./.:46:25,21 ./.:19:7,12 1|0:27:16,11 +chr20 369514 . G A 60 . QNAME=cluster19_000000F;QSTART=25392568;QSTRAND=- GT:DP:AD ./.:37:12,25 1|0:26:11,15 ./.:25:20,5 +chr20 369594 . T A 60 . QNAME=cluster23_scaffold_3;QSTART=25341866;QSTRAND=- GT:DP:AD ./.:27:6,21 ./.:32:21,11 1|0:37:18,19 +chr20 369657 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25341802;QSTRAND=- GT:DP:AD ./.:37:20,17 ./.:13:8,5 1|1:31:11,20 +chr20 369846 . T C 60 . QNAME=cluster19_000000F;QSTART=25392242;QSTRAND=- GT:DP:AD ./.:31:11,20 1|0:32:9,23 1|0:33:25,8 +chr20 369998 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=349364;QSTRAND=+ GT:DP:AD 1|0:28:7,21 ./.:31:11,20 ./.:48:25,23 +chr20 370237 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=349603;QSTRAND=+ GT:DP:AD 1|0:28:18,10 0|1:31:8,23 ./.:38:16,22 +chr20 370371 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=349737;QSTRAND=+ GT:DP:AD 1|0:30:5,25 1|1:20:12,8 ./.:18:13,5 +chr20 371300 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=350666;QSTRAND=+ GT:DP:AD 1|0:31:10,21 0|1:35:22,13 ./.:39:19,20 +chr20 371526 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=350892;QSTRAND=+ GT:DP:AD 1|0:33:8,25 1|1:25:16,9 ./.:16:7,9 +chr20 372007 . T C 60 . QNAME=cluster19_000000F;QSTART=25390081;QSTRAND=- GT:DP:AD ./.:25:8,17 1|0:42:18,24 ./.:29:12,17 +chr20 372073 . A G 60 . QNAME=cluster19_000000F;QSTART=25390015;QSTRAND=- GT:DP:AD ./.:24:8,16 1|0:28:19,9 ./.:16:8,8 +chr20 372441 . A G 60 . QNAME=cluster19_000000F;QSTART=25389647;QSTRAND=- GT:DP:AD ./.:26:12,14 1|0:23:16,7 ./.:20:12,8 +chr20 372564 . A C 60 . QNAME=cluster19_000000F;QSTART=25389524;QSTRAND=- GT:DP:AD ./.:48:23,25 1|0:31:17,14 ./.:28:14,14 +chr20 372676 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=352042;QSTRAND=+ GT:DP:AD 1|0:35:19,16 1|1:37:25,12 ./.:12:7,5 +chr20 372735 . G T 60 . QNAME=cluster19_000000F;QSTART=25389353;QSTRAND=- GT:DP:AD ./.:30:6,24 1|0:31:18,13 ./.:44:20,24 +chr20 373053 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=352419;QSTRAND=+ GT:DP:AD 1|0:23:6,17 1|1:28:10,18 ./.:22:12,10 +chr20 373694 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=353060;QSTRAND=+ GT:DP:AD 1|0:29:20,9 0|1:13:5,8 ./.:22:5,17 +chr20 373749 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=353115;QSTRAND=+ GT:DP:AD 1|0:28:22,6 0|1:38:15,23 ./.:26:11,15 +chr20 374221 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=353587;QSTRAND=+ GT:DP:AD 1|0:27:21,6 0|1:32:13,19 ./.:31:23,8 +chr20 374323 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=353689;QSTRAND=+ GT:DP:AD 1|0:18:11,7 1|1:25:6,19 ./.:27:17,10 +chr20 374523 . A G 60 . QNAME=cluster19_000000F;QSTART=25387565;QSTRAND=- GT:DP:AD ./.:35:20,15 1|0:47:23,24 ./.:36:21,15 +chr20 374580 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=353946;QSTRAND=+ GT:DP:AD 1|0:22:6,16 0|1:30:13,17 ./.:20:15,5 +chr20 374601 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=353967;QSTRAND=+ GT:DP:AD 1|0:28:17,11 0|1:29:21,8 ./.:34:20,14 +chr20 374675 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=354041;QSTRAND=+ GT:DP:AD 1|0:31:19,12 1|1:42:17,25 ./.:35:17,18 +chr20 374716 . C T 60 . QNAME=cluster19_000000F;QSTART=334637;QSTRAND=+ GT:DP:AD ./.:31:18,13 0|1:23:8,15 ./.:32:23,9 +chr20 374726 . C T 60 . QNAME=cluster19_000000F;QSTART=334647;QSTRAND=+ GT:DP:AD ./.:19:10,9 0|1:42:23,19 ./.:39:19,20 +chr20 374740 . G GGT 60 . QNAME=HG002-S9-H1-000001F;QSTART=354107;QSTRAND=+ GT:DP:AD 1|0:30:11,19 0|1:36:22,14 ./.:15:8,7 +chr20 374743 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=354111;QSTRAND=+ GT:DP:AD 1|0:17:9,8 0|1:33:14,19 ./.:29:14,15 +chr20 374744 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=354112;QSTRAND=+ GT:DP:AD 1|0:19:11,8 0|1:10:5,5 ./.:27:10,17 +chr20 374747 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=354115;QSTRAND=+ GT:DP:AD 1|0:30:25,5 0|1:34:19,15 ./.:12:7,5 +chr20 374754 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=354122;QSTRAND=+ GT:DP:AD 1|0:36:17,19 0|1:31:19,12 ./.:28:5,23 +chr20 374836 . T C 60 . QNAME=cluster19_000000F;QSTART=25387252;QSTRAND=- GT:DP:AD ./.:34:22,12 1|0:20:7,13 ./.:24:14,10 +chr20 374900 . C G 60 . QNAME=cluster19_000000F;QSTART=25387188;QSTRAND=- GT:DP:AD ./.:16:7,9 1|0:24:19,5 ./.:26:17,9 +chr20 374905 . A AC 60 . QNAME=HG002-S9-H1-000001F;QSTART=354274;QSTRAND=+ GT:DP:AD 1|0:23:10,13 1|1:39:19,20 ./.:27:5,22 +chr20 375120 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=354489;QSTRAND=+ GT:DP:AD 1|0:29:23,6 1|1:41:22,19 ./.:23:13,10 +chr20 375218 . G GA 60 . QNAME=cluster19_000000F;QSTART=335143;QSTRAND=+ GT:DP:AD ./.:29:19,10 0|1:29:12,17 ./.:22:14,8 +chr20 375359 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=354727;QSTRAND=+ GT:DP:AD 1|0:28:20,8 1|1:34:18,16 ./.:48:23,25 +chr20 375590 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=354958;QSTRAND=+ GT:DP:AD 1|0:34:14,20 0|1:41:17,24 ./.:36:25,11 +chr20 376026 . T TCAAA 60 . QNAME=cluster19_000000F;QSTART=25386057;QSTRAND=- GT:DP:AD ./.:26:18,8 1|0:32:17,15 ./.:21:14,7 +chr20 376031 . A C 60 . QNAME=cluster19_000000F;QSTART=25386052;QSTRAND=- GT:DP:AD ./.:18:9,9 1|0:44:21,23 ./.:32:19,13 +chr20 376031 . A AAAAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=355400;QSTRAND=+ GT:DP:AD 1|0:42:25,17 0|1:20:7,13 ./.:32:23,9 +chr20 376141 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=355513;QSTRAND=+ GT:DP:AD 1|0:18:7,11 1|1:36:17,19 ./.:24:9,15 +chr20 376217 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=355589;QSTRAND=+ GT:DP:AD 1|0:24:7,17 1|1:43:25,18 ./.:29:20,9 +chr20 376406 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=355778;QSTRAND=+ GT:DP:AD 1|0:47:22,25 1|1:18:7,11 ./.:27:20,7 +chr20 376484 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=355856;QSTRAND=+ GT:DP:AD 1|0:38:24,14 1|1:36:14,22 ./.:25:6,19 +chr20 376926 . T C 60 . QNAME=cluster19_000000F;QSTART=25385157;QSTRAND=- GT:DP:AD ./.:28:8,20 1|0:12:7,5 ./.:21:10,11 +chr20 376988 . C T 60 . QNAME=cluster19_000000F;QSTART=25385095;QSTRAND=- GT:DP:AD ./.:41:16,25 1|0:31:14,17 ./.:23:10,13 +chr20 377035 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=356407;QSTRAND=+ GT:DP:AD 1|0:27:14,13 1|1:32:23,9 ./.:47:24,23 +chr20 377056 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=356428;QSTRAND=+ GT:DP:AD 1|0:16:9,7 1|1:34:17,17 ./.:28:6,22 +chr20 377184 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=356556;QSTRAND=+ GT:DP:AD 1|0:24:12,12 1|1:35:11,24 ./.:27:9,18 +chr20 377366 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=356738;QSTRAND=+ GT:DP:AD 1|0:43:22,21 1|1:25:7,18 ./.:33:24,9 +chr20 377680 . G GT 60 . QNAME=cluster23_scaffold_2;QSTART=25317935;QSTRAND=- GT:DP:AD ./.:42:19,23 ./.:30:16,14 0|1:19:10,9 +chr20 377737 . T C 60 . QNAME=cluster19_000000F;QSTART=25384354;QSTRAND=- GT:DP:AD ./.:26:9,17 1|1:26:10,16 ./.:48:25,23 +chr20 377922 . G A 60 . QNAME=cluster19_000000F;QSTART=25384169;QSTRAND=- GT:DP:AD ./.:25:6,19 1|1:35:17,18 ./.:31:14,17 +chr20 377975 . A G 60 . QNAME=cluster19_000000F;QSTART=25384116;QSTRAND=- GT:DP:AD ./.:25:13,12 1|1:14:9,5 ./.:37:12,25 +chr20 378291 . C T 60 . QNAME=cluster19_000000F;QSTART=25383800;QSTRAND=- GT:DP:AD ./.:25:8,17 1|1:25:14,11 ./.:31:12,19 +chr20 378907 . T A 60 . QNAME=cluster19_000000F;QSTART=338834;QSTRAND=+ GT:DP:AD ./.:24:18,6 0|1:47:24,23 ./.:44:21,23 +chr20 379030 . C T 60 . QNAME=cluster19_000000F;QSTART=25383061;QSTRAND=- GT:DP:AD ./.:21:7,14 1|1:49:24,25 ./.:27:10,17 +chr20 379398 . G A 60 . QNAME=cluster19_000000F;QSTART=25382693;QSTRAND=- GT:DP:AD ./.:37:15,22 1|1:25:13,12 ./.:32:14,18 +chr20 379418 . T C 60 . QNAME=cluster19_000000F;QSTART=25382673;QSTRAND=- GT:DP:AD ./.:24:13,11 1|0:41:16,25 ./.:41:21,20 +chr20 379468 . G A 60 . QNAME=cluster19_000000F;QSTART=25382623;QSTRAND=- GT:DP:AD ./.:23:5,18 1|1:36:17,19 ./.:43:22,21 +chr20 379581 . A C 60 . QNAME=cluster19_000000F;QSTART=25382510;QSTRAND=- GT:DP:AD ./.:31:9,22 1|0:35:24,11 ./.:32:16,16 +chr20 379662 . T C 60 . QNAME=cluster19_000000F;QSTART=25382429;QSTRAND=- GT:DP:AD ./.:36:12,24 1|1:39:18,21 ./.:29:20,9 +chr20 379675 . G GA 60 . QNAME=cluster19_000000F;QSTART=339603;QSTRAND=+ GT:DP:AD ./.:27:10,17 0|1:21:15,6 ./.:29:5,24 +chr20 379699 . G C 60 . QNAME=cluster19_000000F;QSTART=25382392;QSTRAND=- GT:DP:AD ./.:24:13,11 1|1:16:5,11 ./.:39:22,17 +chr20 379759 . T C 60 . QNAME=cluster19_000000F;QSTART=25382332;QSTRAND=- GT:DP:AD ./.:36:20,16 1|1:45:20,25 ./.:25:13,12 +chr20 379794 . T C 60 . QNAME=cluster19_000000F;QSTART=25382297;QSTRAND=- GT:DP:AD ./.:19:13,6 1|1:16:7,9 ./.:32:19,13 +chr20 379816 . C T 60 . QNAME=cluster19_000000F;QSTART=25382275;QSTRAND=- GT:DP:AD ./.:37:12,25 1|1:31:6,25 ./.:39:16,23 +chr20 379966 . G T 60 . QNAME=cluster19_000000F;QSTART=25382125;QSTRAND=- GT:DP:AD ./.:37:22,15 1|1:40:15,25 ./.:32:18,14 +chr20 380070 . G C 60 . QNAME=cluster19_000000F;QSTART=25382021;QSTRAND=- GT:DP:AD ./.:39:17,22 1|1:34:18,16 ./.:22:16,6 +chr20 380078 . G C 60 . QNAME=cluster19_000000F;QSTART=25382013;QSTRAND=- GT:DP:AD ./.:32:21,11 1|1:38:13,25 ./.:22:8,14 +chr20 380145 . T C 60 . QNAME=cluster19_000000F;QSTART=340073;QSTRAND=+ GT:DP:AD ./.:38:24,14 0|1:25:18,7 ./.:37:19,18 +chr20 380289 . A C 60 . QNAME=cluster19_000000F;QSTART=25381804;QSTRAND=- GT:DP:AD ./.:31:20,11 1|1:17:8,9 ./.:28:21,7 +chr20 380548 . T C 60 . QNAME=cluster19_000000F;QSTART=25381545;QSTRAND=- GT:DP:AD ./.:25:13,12 1|1:24:17,7 ./.:23:7,16 +chr20 380662 . G A 60 . QNAME=cluster19_000000F;QSTART=25381431;QSTRAND=- GT:DP:AD ./.:24:8,16 1|1:43:22,21 1|0:15:6,9 +chr20 380663 . C A 60 . QNAME=cluster19_000000F;QSTART=25381430;QSTRAND=- GT:DP:AD ./.:22:9,13 1|1:40:16,24 1|0:23:7,16 +chr20 380672 . A G 60 . QNAME=cluster19_000000F;QSTART=25381421;QSTRAND=- GT:DP:AD ./.:22:8,14 1|1:17:5,12 1|0:27:12,15 +chr20 380679 . T C 60 . QNAME=cluster19_000000F;QSTART=25381414;QSTRAND=- GT:DP:AD ./.:32:10,22 1|1:34:24,10 1|0:23:18,5 +chr20 380684 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25330774;QSTRAND=- GT:DP:AD ./.:42:25,17 ./.:28:9,19 1|0:38:25,13 +chr20 380878 . T TGATTAGCTCCGGTTTGCATCACCCGGACCGGGGGATTAGCTCCGGTTTGCATCACCCGGACCGGGG 60 . QNAME=cluster19_000000F;QSTART=25381150;QSTRAND=-;SVTYPE=INS;SVLEN=66 GT:DP:AD ./.:21:9,12 1/0:15:8,7 ./.:25:20,5 +chr20 381233 . G A 60 . QNAME=cluster19_000000F;QSTART=25380795;QSTRAND=- GT:DP:AD ./.:43:23,20 1|0:24:7,17 ./.:34:10,24 +chr20 381358 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=360727;QSTRAND=+ GT:DP:AD 1|0:28:17,11 ./.:23:6,17 ./.:31:23,8 +chr20 381423 . C G 60 . QNAME=cluster23_scaffold_3;QSTART=25330068;QSTRAND=- GT:DP:AD ./.:26:6,20 ./.:36:14,22 1|0:40:19,21 +chr20 381637 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=361006;QSTRAND=+ GT:DP:AD 1|0:41:21,20 1|1:36:16,20 0|1:26:13,13 +chr20 381684 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=361053;QSTRAND=+ GT:DP:AD 1|0:29:11,18 0|1:31:10,21 1|0:34:25,9 +chr20 381742 . T TG 60 . QNAME=HG002-S9-H2-000001F;QSTART=336041;QSTRAND=+ GT:DP:AD 0|1:35:16,19 1|0:28:6,22 1|0:20:15,5 +chr20 381797 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=336096;QSTRAND=+ GT:DP:AD 0|1:28:23,5 0|1:32:8,24 1|0:33:8,25 +chr20 382099 . C CTG 60 . QNAME=cluster19_000000F;QSTART=25379926;QSTRAND=- GT:DP:AD ./.:39:24,15 1|0:19:12,7 ./.:39:18,21 +chr20 382099 . C CTGTGTGTG 60 . QNAME=cluster23_scaffold_3;QSTART=25329384;QSTRAND=- GT:DP:AD ./.:26:20,6 ./.:26:8,18 1|0:40:16,24 +chr20 383089 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25328394;QSTRAND=- GT:DP:AD ./.:31:14,17 ./.:14:7,7 1|0:36:15,21 +chr20 383651 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=363020;QSTRAND=+ GT:DP:AD 1|0:44:20,24 1|0:34:13,21 0|1:30:16,14 +chr20 384031 . A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25327451;QSTRAND=- GT:DP:AD ./.:14:9,5 ./.:29:15,14 1|0:21:16,5 +chr20 384050 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25311569;QSTRAND=- GT:DP:AD ./.:42:23,19 ./.:33:12,21 0|1:29:16,13 +chr20 384103 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=25327379;QSTRAND=- GT:DP:AD ./.:38:22,16 ./.:20:11,9 1|0:44:23,21 +chr20 385860 . A AT 60 . QNAME=cluster23_scaffold_2;QSTART=25309758;QSTRAND=- GT:DP:AD ./.:45:22,23 ./.:43:20,23 0|1:25:10,15 +chr20 385969 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=365338;QSTRAND=+ GT:DP:AD 1|0:17:7,10 ./.:19:5,14 0|1:41:18,23 +chr20 386036 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=365405;QSTRAND=+ GT:DP:AD 1|0:25:16,9 1|1:50:25,25 1|1:48:24,24 +chr20 386320 . T C 60 . QNAME=cluster19_000000F;QSTART=346244;QSTRAND=+ GT:DP:AD ./.:24:5,19 0|1:35:25,10 1|0:25:7,18 +chr20 391001 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25320481;QSTRAND=- GT:DP:AD ./.:29:17,12 ./.:26:19,7 1|0:31:19,12 +chr20 391003 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=345301;QSTRAND=+ GT:DP:AD 0|1:46:24,22 1|0:40:19,21 0|1:36:24,12 +chr20 391137 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=345435;QSTRAND=+ GT:DP:AD 0|1:39:18,21 1|0:28:23,5 0|1:46:25,21 +chr20 391138 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=345436;QSTRAND=+ GT:DP:AD 0|1:32:25,7 1|0:42:17,25 0|1:40:24,16 +chr20 391328 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=345626;QSTRAND=+ GT:DP:AD 0|1:36:24,12 1|0:39:23,16 0|1:18:6,12 +chr20 392557 . A AT 60 . QNAME=HG002-S9-H2-000001F;QSTART=346855;QSTRAND=+ GT:DP:AD 0|1:26:15,11 1|0:29:12,17 1|1:26:21,5 +chr20 393192 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=347407;QSTRAND=+ GT:DP:AD 0|1:13:6,7 1|0:35:20,15 0|1:13:8,5 +chr20 393417 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=347631;QSTRAND=+ GT:DP:AD 0|1:21:12,9 1|0:38:16,22 0|1:28:11,17 +chr20 393740 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=347954;QSTRAND=+ GT:DP:AD 0|1:13:5,8 1|0:44:21,23 0|1:23:14,9 +chr20 393795 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=348009;QSTRAND=+ GT:DP:AD 0|1:17:9,8 1|0:40:19,21 0|1:39:17,22 +chr20 394032 . C CT 60 . QNAME=HG002-S9-H2-000001F;QSTART=348247;QSTRAND=+ GT:DP:AD 0|1:39:18,21 1|0:30:12,18 0|1:15:8,7 +chr20 394119 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=348334;QSTRAND=+ GT:DP:AD 0|1:33:8,25 1|0:31:15,16 0|1:26:18,8 +chr20 394301 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=348516;QSTRAND=+ GT:DP:AD 0|1:11:5,6 ./.:28:17,11 0|1:31:6,25 +chr20 394462 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=348677;QSTRAND=+ GT:DP:AD 0|1:14:8,6 1|1:44:21,23 0|1:21:14,7 +chr20 394799 . G GA 60 . QNAME=cluster23_scaffold_3;QSTART=25316682;QSTRAND=- GT:DP:AD ./.:37:17,20 ./.:46:23,23 1|0:35:10,25 +chr20 394955 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=349170;QSTRAND=+ GT:DP:AD 0|1:25:11,14 ./.:31:22,9 0|1:24:14,10 +chr20 396582 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=350797;QSTRAND=+ GT:DP:AD 0|1:16:10,6 1|0:30:13,17 0|1:50:25,25 +chr20 397598 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=351813;QSTRAND=+ GT:DP:AD 0|1:38:24,14 1|0:43:21,22 0|1:21:14,7 +chr20 397600 . T A 60 . QNAME=cluster23_scaffold_2;QSTART=25298101;QSTRAND=- GT:DP:AD ./.:30:25,5 ./.:39:24,15 0|1:14:8,6 +chr20 397886 . A AC 60 . QNAME=cluster23_scaffold_3;QSTART=25313594;QSTRAND=- GT:DP:AD ./.:23:13,10 ./.:41:16,25 1|0:23:10,13 +chr20 398287 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=352502;QSTRAND=+ GT:DP:AD 0|1:44:20,24 1|0:28:5,23 0|1:33:24,9 +chr20 398312 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=352527;QSTRAND=+ GT:DP:AD 0|1:46:23,23 1|0:32:13,19 0|1:24:14,10 +chr20 398313 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=352528;QSTRAND=+ GT:DP:AD 0|1:33:24,9 1|0:32:18,14 0|1:14:6,8 +chr20 398315 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=352530;QSTRAND=+ GT:DP:AD 0|1:31:21,10 1|0:13:7,6 0|1:28:13,15 +chr20 398320 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=352535;QSTRAND=+ GT:DP:AD 0|1:41:20,21 1|0:25:20,5 0|1:35:19,16 +chr20 398324 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=352539;QSTRAND=+ GT:DP:AD 0|1:35:13,22 1|0:39:16,23 0|1:36:23,13 +chr20 398327 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=352542;QSTRAND=+ GT:DP:AD 0|1:29:24,5 1|0:31:21,10 0|1:40:19,21 +chr20 398334 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=352549;QSTRAND=+ GT:DP:AD 0|1:36:21,15 1|0:16:11,5 0|1:31:22,9 +chr20 398897 . C T 60 . QNAME=cluster19_000000F;QSTART=25363212;QSTRAND=- GT:DP:AD ./.:22:13,9 1|0:20:8,12 ./.:16:5,11 +chr20 399283 . A G 60 . QNAME=cluster19_000000F;QSTART=25362826;QSTRAND=- GT:DP:AD ./.:29:8,21 1|1:36:14,22 1|1:27:13,14 +chr20 399958 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=379327;QSTRAND=+ GT:DP:AD 1|0:30:7,23 1|0:48:25,23 ./.:23:6,17 +chr20 400146 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=379516;QSTRAND=+ GT:DP:AD 1|0:18:5,13 1|1:30:7,23 1|0:19:12,7 +chr20 400336 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=379706;QSTRAND=+ GT:DP:AD 1|0:22:7,15 1|1:41:25,16 1|0:20:12,8 +chr20 400547 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=379917;QSTRAND=+ GT:DP:AD 1|0:44:25,19 1|1:14:6,8 1|0:36:20,16 +chr20 400677 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=380047;QSTRAND=+ GT:DP:AD 1|0:31:17,14 1|1:32:25,7 1|0:27:6,21 +chr20 400755 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=380125;QSTRAND=+ GT:DP:AD 1|0:32:7,25 1|0:24:15,9 ./.:22:17,5 +chr20 400797 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=380167;QSTRAND=+ GT:DP:AD 1|0:23:10,13 1|1:23:9,14 1|0:34:10,24 +chr20 400887 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=380257;QSTRAND=+ GT:DP:AD 1|0:32:25,7 1|1:38:16,22 1|0:18:5,13 +chr20 401685 . C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=381056;QSTRAND=+ GT:DP:AD 1|0:34:24,10 1|1:23:18,5 ./.:38:25,13 +chr20 401685 . C CAA 60 . QNAME=cluster23_scaffold_3;QSTART=25309792;QSTRAND=- GT:DP:AD ./.:27:19,8 ./.:28:12,16 1|0:19:11,8 +chr20 401702 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=381073;QSTRAND=+ GT:DP:AD 1|0:38:23,15 1|1:26:14,12 1|0:47:25,22 +chr20 401915 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=381286;QSTRAND=+ GT:DP:AD 1|0:35:20,15 1|1:42:19,23 1|0:44:25,19 +chr20 401983 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=381354;QSTRAND=+ GT:DP:AD 1|0:40:22,18 1|1:20:11,9 1|0:25:17,8 +chr20 402232 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=381603;QSTRAND=+ GT:DP:AD 1|0:43:19,24 1|1:35:20,15 1|0:39:14,25 +chr20 402478 . C CAA 60 . QNAME=HG002-S9-H2-000001F;QSTART=356694;QSTRAND=+ GT:DP:AD 0|1:28:13,15 ./.:32:12,20 ./.:25:13,12 +chr20 402478 . C CAAA 60 . QNAME=cluster23_scaffold_2;QSTART=25293220;QSTRAND=- GT:DP:AD ./.:41:24,17 ./.:38:17,21 0|1:35:18,17 +chr20 402492 . A AT 60 . QNAME=cluster19_000000F;QSTART=362418;QSTRAND=+ GT:DP:AD ./.:36:15,21 0|1:14:5,9 1|0:16:6,10 +chr20 402498 . A T 60 . QNAME=cluster19_000000F;QSTART=362424;QSTRAND=+ GT:DP:AD ./.:39:20,19 0|1:43:18,25 1|0:23:5,18 +chr20 402504 . A T 60 . QNAME=cluster19_000000F;QSTART=362430;QSTRAND=+ GT:DP:AD ./.:28:12,16 0|1:30:15,15 1|0:34:24,10 +chr20 402509 . A T 60 . QNAME=cluster19_000000F;QSTART=362435;QSTRAND=+ GT:DP:AD ./.:19:14,5 0|1:32:11,21 1|0:28:22,6 +chr20 403076 . C T 60 . QNAME=cluster19_000000F;QSTART=363002;QSTRAND=+ GT:DP:AD ./.:22:16,6 0|1:38:15,23 1|0:38:16,22 +chr20 403697 . A G 60 . QNAME=cluster19_000000F;QSTART=363623;QSTRAND=+ GT:DP:AD ./.:39:17,22 0|1:17:8,9 1|0:13:8,5 +chr20 403859 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=383222;QSTRAND=+ GT:DP:AD 1|0:38:18,20 1|0:45:24,21 ./.:20:6,14 +chr20 404000 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=383363;QSTRAND=+ GT:DP:AD 1|0:14:7,7 1|1:30:11,19 1|0:25:19,6 +chr20 404254 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=383617;QSTRAND=+ GT:DP:AD 1|0:21:7,14 1|0:34:11,23 ./.:25:12,13 +chr20 404408 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=383771;QSTRAND=+ GT:DP:AD 1|0:35:24,11 1|1:16:10,6 1|0:38:22,16 +chr20 404596 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=383959;QSTRAND=+ GT:DP:AD 1|1:37:12,25 1|1:40:21,19 1|1:20:15,5 +chr20 405155 . T TCACA 60 . QNAME=cluster19_000000F;QSTART=365082;QSTRAND=+ GT:DP:AD ./.:29:16,13 0|1:33:21,12 1|0:17:11,6 +chr20 405220 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=384583;QSTRAND=+ GT:DP:AD 1|0:27:14,13 1|1:28:16,12 1|0:33:11,22 +chr20 405345 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=384709;QSTRAND=+ GT:DP:AD 1|0:27:11,16 1|0:38:20,18 ./.:23:5,18 +chr20 405478 . C T 60 . QNAME=cluster19_000000F;QSTART=365408;QSTRAND=+ GT:DP:AD ./.:31:13,18 0|1:30:16,14 1|0:22:12,10 +chr20 405820 . A G 60 . QNAME=cluster19_000000F;QSTART=365750;QSTRAND=+ GT:DP:AD ./.:33:17,16 0|1:46:22,24 1|0:31:15,16 +chr20 406708 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25288989;QSTRAND=- GT:DP:AD ./.:21:6,15 ./.:45:21,24 0|1:16:6,10 +chr20 406732 . A AAAAAAAAAAAAG 60 . QNAME=HG002-S9-H1-000001F;QSTART=386097;QSTRAND=+ GT:DP:AD 1|0:14:8,6 ./.:37:20,17 ./.:34:24,10 +chr20 406732 . A AAAAAAAAAAG 60 . QNAME=cluster19_000000F;QSTART=25355374;QSTRAND=- GT:DP:AD ./.:45:21,24 1|0:30:23,7 ./.:36:12,24 +chr20 407013 . G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=386390;QSTRAND=+ GT:DP:AD 1|0:39:24,15 1|1:36:14,22 1|0:29:12,17 +chr20 407083 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=386460;QSTRAND=+ GT:DP:AD 1|0:24:10,14 1|0:41:17,24 ./.:34:9,25 +chr20 407113 . A G 60 . QNAME=cluster19_000000F;QSTART=367037;QSTRAND=+ GT:DP:AD ./.:41:20,21 0|1:33:8,25 1|0:36:14,22 +chr20 407171 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=386548;QSTRAND=+ GT:DP:AD 1|0:33:24,9 1|0:39:20,19 ./.:21:6,15 +chr20 407872 . C T 60 . QNAME=cluster19_000000F;QSTART=367796;QSTRAND=+ GT:DP:AD ./.:33:23,10 0|1:33:8,25 1|0:18:11,7 +chr20 408028 . G GGCCCCGCCC 60 . QNAME=HG002-S9-H2-000001F;QSTART=362274;QSTRAND=+ GT:DP:AD 0|1:18:11,7 ./.:31:18,13 0|1:35:22,13 +chr20 408029 . G GCCCCGCCCA 60 . QNAME=cluster19_000000F;QSTART=367992;QSTRAND=+ GT:DP:AD ./.:12:6,6 0|1:20:9,11 1|0:25:9,16 +chr20 408057 . T TC 60 . QNAME=HG002-S9-H1-000001F;QSTART=387432;QSTRAND=+ GT:DP:AD 1|1:23:13,10 1|1:34:24,10 1|1:24:15,9 +chr20 408812 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=363067;QSTRAND=+ GT:DP:AD 0|1:33:15,18 0|1:50:25,25 1|1:24:18,6 +chr20 409237 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=363492;QSTRAND=+ GT:DP:AD 0|1:30:22,8 0|1:19:5,14 1|1:42:18,24 +chr20 409340 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=363594;QSTRAND=+ GT:DP:AD 0|1:34:23,11 0|1:27:13,14 1|1:47:24,23 +chr20 410526 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=364779;QSTRAND=+ GT:DP:AD 0|1:26:10,16 0|1:39:16,23 1|1:23:5,18 +chr20 413334 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=367586;QSTRAND=+ GT:DP:AD 0|1:40:15,25 0|1:17:12,5 1|1:34:19,15 +chr20 413941 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=368192;QSTRAND=+ GT:DP:AD 0|1:26:12,14 0|1:27:20,7 1|1:22:13,9 +chr20 414091 . C CA 60 . QNAME=HG002-S9-H2-000001F;QSTART=368343;QSTRAND=+ GT:DP:AD 0|1:31:21,10 0|1:39:21,18 1|1:13:6,7 +chr20 414317 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=368569;QSTRAND=+ GT:DP:AD 0|1:27:15,12 0|1:19:12,7 1|1:20:12,8 +chr20 415178 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=369430;QSTRAND=+ GT:DP:AD 0|1:29:24,5 0|1:29:23,6 1|1:22:14,8 +chr20 415379 . A AAAAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=394754;QSTRAND=+ GT:DP:AD 1|1:24:5,19 1|1:32:20,12 1|1:17:6,11 +chr20 415512 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=394890;QSTRAND=+ GT:DP:AD 1|0:15:9,6 1|0:20:8,12 ./.:28:15,13 +chr20 416154 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25295271;QSTRAND=- GT:DP:AD ./.:40:15,25 ./.:30:21,9 1|0:25:19,6 +chr20 416334 . G T 60 . QNAME=cluster19_000000F;QSTART=376310;QSTRAND=+ GT:DP:AD ./.:44:20,24 0|1:22:12,10 1|0:41:21,20 +chr20 417284 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=396662;QSTRAND=+ GT:DP:AD 1|1:43:21,22 1|1:40:18,22 1|1:34:17,17 +chr20 417395 . T TTG 60 . QNAME=cluster23_scaffold_3;QSTART=25294028;QSTRAND=- GT:DP:AD ./.:24:16,8 ./.:32:21,11 1|1:38:13,25 +chr20 417634 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=397012;QSTRAND=+ GT:DP:AD 1|0:41:16,25 1|0:40:20,20 ./.:28:18,10 +chr20 418430 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=397808;QSTRAND=+ GT:DP:AD 1|0:36:22,14 1|0:31:9,22 ./.:39:16,23 +chr20 418432 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=397810;QSTRAND=+ GT:DP:AD 1|0:15:6,9 1|0:31:24,7 ./.:28:9,19 +chr20 418579 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=372835;QSTRAND=+ GT:DP:AD 0|1:27:15,12 ./.:18:12,6 1|1:28:14,14 +chr20 418601 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=372857;QSTRAND=+ GT:DP:AD 0|1:37:25,12 ./.:35:24,11 1|1:49:24,25 +chr20 418603 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=372859;QSTRAND=+ GT:DP:AD 0|1:36:17,19 ./.:36:21,15 1|1:16:9,7 +chr20 418658 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=372914;QSTRAND=+ GT:DP:AD 0|1:35:24,11 ./.:40:17,23 1|1:15:9,6 +chr20 419117 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=398495;QSTRAND=+ GT:DP:AD 1|1:25:10,15 1|0:35:25,10 1|1:27:8,19 +chr20 420228 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=374466;QSTRAND=+ GT:DP:AD 0|1:36:17,19 ./.:25:11,14 1|1:29:10,19 +chr20 420465 . A AG 60 . QNAME=HG002-S9-H2-000001F;QSTART=374704;QSTRAND=+ GT:DP:AD 0|1:19:11,8 ./.:22:8,14 1|1:24:5,19 +chr20 420561 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=399939;QSTRAND=+ GT:DP:AD 1|1:31:17,14 1|0:37:21,16 1|1:47:25,22 +chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCATCCCCCGTCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 60 . QNAME=HG002-S9-H1-000001F;QSTART=400044;QSTRAND=+;SVTYPE=INS;SVLEN=226 GT:DP:AD 1/0:45:21,24 1/1:27:20,7 ./.:31:15,16 +chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCCATCCCCCGTCCGCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 61 . QNAME=HG002-S9-H2-000001F;QSTART=374905;QSTRAND=+;SVTYPE=INS;SVLEN=227 GT:DP:AD 0/1:27:19,8 ./.:40:20,20 1/1:23:7,16 +chr20 421409 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=401013;QSTRAND=+ GT:DP:AD 1|1:29:23,6 1|0:33:15,18 1|1:17:6,11 +chr20 421527 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=375993;QSTRAND=+ GT:DP:AD 0|1:29:24,5 ./.:36:17,19 1|1:37:13,24 +chr20 422066 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=401670;QSTRAND=+ GT:DP:AD 1|1:31:24,7 1|0:40:16,24 1|1:30:23,7 +chr20 422277 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=376743;QSTRAND=+ GT:DP:AD 0|1:44:23,21 ./.:42:22,20 1|1:29:14,15 +chr20 422548 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=402151;QSTRAND=+ GT:DP:AD 1|0:26:8,18 1|0:30:22,8 ./.:34:19,15 +chr20 422567 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=402170;QSTRAND=+ GT:DP:AD 1|0:26:11,15 1|0:38:15,23 ./.:32:13,19 +chr20 423009 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=402612;QSTRAND=+ GT:DP:AD 1|1:40:21,19 1|0:26:20,6 1|1:31:20,11 +chr20 423705 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=403308;QSTRAND=+ GT:DP:AD 1|1:22:17,5 1|0:38:15,23 1|1:43:22,21 +chr20 423763 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=403366;QSTRAND=+ GT:DP:AD 1|1:40:20,20 1|0:30:25,5 1|1:17:7,10 +chr20 424272 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=403875;QSTRAND=+ GT:DP:AD 1|1:34:17,17 1|0:47:25,22 1|1:26:17,9 +chr20 424413 . A AC 60 . QNAME=HG002-S9-H1-000001F;QSTART=404017;QSTRAND=+ GT:DP:AD 1|0:38:17,21 1|0:21:6,15 1|0:31:19,12 +chr20 426816 . C CT 60 . QNAME=cluster19_000000F;QSTART=25335060;QSTRAND=- GT:DP:AD ./.:16:9,7 1|0:27:22,5 1|0:40:22,18 +chr20 429226 . A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25281985;QSTRAND=- GT:DP:AD ./.:31:23,8 ./.:34:24,10 1|1:31:10,21 +chr20 429249 . G A 60 . QNAME=cluster19_000000F;QSTART=389451;QSTRAND=+ GT:DP:AD ./.:36:17,19 0|1:30:10,20 ./.:17:9,8 +chr20 431198 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=410801;QSTRAND=+ GT:DP:AD 1|1:33:8,25 1|0:34:24,10 1|1:36:13,23 +chr20 433902 . T C 60 . QNAME=cluster19_000000F;QSTART=25327992;QSTRAND=- GT:DP:AD ./.:46:25,21 1|0:27:9,18 ./.:15:8,7 +chr20 434000 . G GT 60 . QNAME=cluster23_scaffold_3;QSTART=25277228;QSTRAND=- GT:DP:AD ./.:14:5,9 ./.:15:9,6 1|1:20:8,12 +chr20 434001 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=413586;QSTRAND=+ GT:DP:AD 1|1:16:9,7 1|0:36:12,24 1|1:28:12,16 +chr20 434561 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=414146;QSTRAND=+ GT:DP:AD 1|1:49:24,25 1|0:39:23,16 1|1:13:8,5 +chr20 435505 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=415090;QSTRAND=+ GT:DP:AD 1|1:30:10,20 1|0:25:18,7 1|1:45:20,25 +chr20 436968 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=416553;QSTRAND=+ GT:DP:AD 1|1:25:19,6 1|0:28:19,9 1|1:13:5,8 +chr20 437555 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=417140;QSTRAND=+ GT:DP:AD 1|1:43:21,22 1|0:38:17,21 1|1:26:19,7 +chr20 438423 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=418008;QSTRAND=+ GT:DP:AD 1|1:32:25,7 1|0:39:22,17 ./.:38:24,14 +chr20 439461 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=419046;QSTRAND=+ GT:DP:AD 1|1:41:22,19 1|0:36:25,11 ./.:30:18,12 +chr20 441161 . T TCCA 60 . QNAME=HG002-S9-H1-000001F;QSTART=420747;QSTRAND=+ GT:DP:AD 1|1:32:17,15 1|0:31:18,13 ./.:12:6,6 +chr20 443554 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=423142;QSTRAND=+ GT:DP:AD 1|0:28:18,10 1|0:36:16,20 ./.:38:24,14 +chr20 443921 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=423509;QSTRAND=+ GT:DP:AD 1|0:27:17,10 1|0:19:9,10 ./.:36:11,25 +chr20 444453 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=424041;QSTRAND=+ GT:DP:AD 1|0:48:25,23 1|0:18:13,5 ./.:27:17,10 +chr20 444790 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=424374;QSTRAND=+ GT:DP:AD 1|0:30:20,10 1|0:45:23,22 ./.:29:16,13 +chr20 444962 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=424546;QSTRAND=+ GT:DP:AD 1|0:40:20,20 1|0:21:11,10 ./.:34:17,17 +chr20 445789 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=425373;QSTRAND=+ GT:DP:AD 1|0:42:22,20 1|0:35:17,18 ./.:20:7,13 +chr20 446426 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=426010;QSTRAND=+ GT:DP:AD 1|0:17:8,9 1|0:39:24,15 ./.:26:17,9 +chr20 446529 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=426113;QSTRAND=+ GT:DP:AD 1|0:21:8,13 1|0:17:6,11 ./.:26:18,8 +chr20 446943 . A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25264284;QSTRAND=- GT:DP:AD ./.:17:9,8 ./.:40:20,20 1|1:36:22,14 +chr20 447123 . A AT 60 . QNAME=cluster23_scaffold_2;QSTART=25248333;QSTRAND=- GT:DP:AD ./.:23:16,7 ./.:40:20,20 0|1:15:8,7 +chr20 447395 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=426978;QSTRAND=+ GT:DP:AD 1|0:28:8,20 1|0:22:17,5 ./.:31:17,14 +chr20 448123 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=427706;QSTRAND=+ GT:DP:AD 1|0:36:13,23 1|0:24:12,12 ./.:39:22,17 +chr20 448284 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=427867;QSTRAND=+ GT:DP:AD 1|0:26:8,18 1|0:29:7,22 ./.:21:11,10 +chr20 448552 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=428135;QSTRAND=+ GT:DP:AD 1|0:22:7,15 1|0:22:11,11 ./.:24:7,17 +chr20 448689 . G GA 60 . QNAME=cluster19_000000F;QSTART=25313206;QSTRAND=- GT:DP:AD ./.:31:7,24 1|0:47:25,22 1|0:41:17,24 +chr20 448841 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25262384;QSTRAND=- GT:DP:AD ./.:38:13,25 ./.:28:21,7 1|0:37:18,19 +chr20 449078 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=428660;QSTRAND=+ GT:DP:AD 1|0:36:21,15 1|0:30:15,15 ./.:37:21,16 +chr20 449153 . C CTT 60 . QNAME=HG002-S9-H1-000001F;QSTART=428736;QSTRAND=+ GT:DP:AD 1|0:32:25,7 1|0:27:18,9 ./.:31:15,16 +chr20 449266 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=428850;QSTRAND=+ GT:DP:AD 1|0:35:11,24 1|0:25:9,16 ./.:34:25,9 +chr20 449285 . T TAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=428870;QSTRAND=+ GT:DP:AD 1|0:26:18,8 1|0:21:7,14 ./.:20:8,12 +chr20 449285 . T TA 60 . QNAME=cluster19_000000F;QSTART=409488;QSTRAND=+ GT:DP:AD ./.:21:9,12 0|1:23:7,16 ./.:33:18,15 +chr20 449362 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25261863;QSTRAND=- GT:DP:AD ./.:38:20,18 ./.:28:15,13 1|0:39:21,18 +chr20 450092 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=429681;QSTRAND=+ GT:DP:AD 1|0:40:24,16 1|0:44:24,20 ./.:24:9,15 +chr20 450315 . A AT 60 . QNAME=cluster23_scaffold_2;QSTART=25245141;QSTRAND=- GT:DP:AD ./.:29:6,23 ./.:34:25,9 0|1:34:23,11 +chr20 450858 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=430447;QSTRAND=+ GT:DP:AD 1|0:39:18,21 1|0:49:24,25 ./.:28:18,10 +chr20 452042 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=431631;QSTRAND=+ GT:DP:AD 1|0:17:12,5 1|0:33:11,22 ./.:32:7,25 +chr20 452135 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=431724;QSTRAND=+ GT:DP:AD 1|0:20:7,13 1|0:44:25,19 ./.:22:17,5 +chr20 453153 . C CAA 60 . QNAME=cluster23_scaffold_3;QSTART=25258071;QSTRAND=- GT:DP:AD ./.:29:20,9 ./.:10:5,5 1|0:28:20,8 +chr20 453153 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25242302;QSTRAND=- GT:DP:AD ./.:40:24,16 ./.:33:17,16 0|1:39:23,16 +chr20 453460 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=433040;QSTRAND=+ GT:DP:AD 1|0:44:21,23 1|0:13:6,7 ./.:30:19,11 +chr20 453539 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=433120;QSTRAND=+ GT:DP:AD 1|0:50:25,25 1|0:29:19,10 ./.:26:19,7 +chr20 453540 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=433121;QSTRAND=+ GT:DP:AD 1|0:36:16,20 1|0:21:12,9 ./.:30:18,12 +chr20 453540 . A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25257683;QSTRAND=- GT:DP:AD ./.:42:17,25 ./.:32:15,17 1|1:32:14,18 +chr20 453995 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=433576;QSTRAND=+ GT:DP:AD 1|0:35:11,24 1|0:15:6,9 ./.:44:24,20 +chr20 454087 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=433668;QSTRAND=+ GT:DP:AD 1|0:32:17,15 1|0:21:6,15 ./.:16:9,7 +chr20 454295 . G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=433874;QSTRAND=+ GT:DP:AD 1|0:33:15,18 1|0:24:11,13 ./.:20:12,8 +chr20 454614 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=434193;QSTRAND=+ GT:DP:AD 1|0:20:9,11 1|0:37:20,17 ./.:35:22,13 +chr20 454650 . C CATTATT 60 . QNAME=HG002-S9-H1-000001F;QSTART=434230;QSTRAND=+ GT:DP:AD 1|0:29:12,17 1|0:21:7,14 ./.:33:22,11 +chr20 454798 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=434383;QSTRAND=+ GT:DP:AD 1|0:14:5,9 1|0:20:10,10 ./.:25:20,5 +chr20 456053 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=435638;QSTRAND=+ GT:DP:AD 1|0:38:19,19 1|0:25:18,7 ./.:15:10,5 +chr20 456603 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=436180;QSTRAND=+ GT:DP:AD 1|0:32:12,20 ./.:20:14,6 ./.:29:6,23 +chr20 456818 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=436395;QSTRAND=+ GT:DP:AD 1|0:12:5,7 1|0:42:17,25 ./.:24:18,6 +chr20 458314 . A AT 60 . QNAME=cluster23_scaffold_2;QSTART=25237142;QSTRAND=- GT:DP:AD ./.:41:18,23 ./.:35:25,10 0|1:25:15,10 +chr20 458331 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=412772;QSTRAND=+ GT:DP:AD 0|1:38:20,18 0|1:28:5,23 1|1:26:16,10 +chr20 458461 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=412902;QSTRAND=+ GT:DP:AD 0|1:46:22,24 0|1:24:13,11 1|1:35:16,19 +chr20 459799 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=414240;QSTRAND=+ GT:DP:AD 0|1:33:11,22 0|1:45:21,24 1|1:32:19,13 +chr20 460464 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=414902;QSTRAND=+ GT:DP:AD 0|1:33:11,22 0|1:23:11,12 1|1:24:12,12 +chr20 461679 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=416117;QSTRAND=+ GT:DP:AD 0|1:28:18,10 0|1:31:18,13 1|1:22:9,13 +chr20 462293 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=416731;QSTRAND=+ GT:DP:AD 0|1:42:18,24 0|1:28:7,21 1|1:44:24,20 +chr20 463154 . A G 60 . QNAME=cluster19_000000F;QSTART=423351;QSTRAND=+ GT:DP:AD ./.:21:16,5 0|1:36:13,23 1|1:47:25,22 +chr20 463252 . C G 60 . QNAME=cluster19_000000F;QSTART=423449;QSTRAND=+ GT:DP:AD ./.:41:18,23 0|1:35:13,22 1|1:36:13,23 +chr20 463841 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=418279;QSTRAND=+ GT:DP:AD 0|1:34:11,23 ./.:37:24,13 ./.:26:12,14 +chr20 465665 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=445241;QSTRAND=+ GT:DP:AD 1|1:35:18,17 1|1:41:24,17 1|1:38:23,15 +chr20 466029 . A AAAAT 60 . QNAME=HG002-S9-H2-000001F;QSTART=420467;QSTRAND=+ GT:DP:AD 0|1:22:14,8 ./.:15:10,5 ./.:47:23,24 +chr20 466637 . G GTGTATATATA 60 . QNAME=HG002-S9-H2-000001F;QSTART=421079;QSTRAND=+ GT:DP:AD 0|1:47:23,24 ./.:28:22,6 ./.:31:23,8 +chr20 466637 . G GTATA 60 . QNAME=cluster19_000000F;QSTART=426834;QSTRAND=+ GT:DP:AD ./.:28:7,21 0|1:22:14,8 1|0:19:14,5 +chr20 466637 . G GTA 60 . QNAME=cluster23_scaffold_2;QSTART=25228821;QSTRAND=- GT:DP:AD ./.:21:15,6 ./.:16:10,6 0|1:22:15,7 +chr20 467024 . C CT 60 . QNAME=cluster23_scaffold_2;QSTART=25228433;QSTRAND=- GT:DP:AD ./.:36:15,21 ./.:32:23,9 0|1:43:24,19 +chr20 468015 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=447588;QSTRAND=+ GT:DP:AD 1|1:28:14,14 1|1:32:19,13 1|1:26:10,16 +chr20 468269 . C A 60 . QNAME=cluster19_000000F;QSTART=428469;QSTRAND=+ GT:DP:AD ./.:25:8,17 0|1:39:14,25 1|1:40:15,25 +chr20 469249 . G A 60 . QNAME=cluster19_000000F;QSTART=429449;QSTRAND=+ GT:DP:AD ./.:26:7,19 0|1:30:21,9 1|1:28:17,11 +chr20 469257 . A T 60 . QNAME=cluster19_000000F;QSTART=429457;QSTRAND=+ GT:DP:AD ./.:27:8,19 0|1:37:25,12 1|1:33:19,14 +chr20 470060 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=424511;QSTRAND=+ GT:DP:AD 0|1:18:7,11 ./.:30:24,6 ./.:27:18,9 +chr20 471168 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=425619;QSTRAND=+ GT:DP:AD 0|1:22:10,12 ./.:38:23,15 ./.:17:9,8 +chr20 472424 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=451997;QSTRAND=+ GT:DP:AD 1|0:37:18,19 ./.:17:7,10 ./.:44:25,19 +chr20 472457 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=452030;QSTRAND=+ GT:DP:AD 1|1:22:8,14 1|1:28:8,20 1|1:22:8,14 +chr20 477729 . C T 60 . QNAME=cluster19_000000F;QSTART=25284173;QSTRAND=- GT:DP:AD ./.:35:17,18 1|0:24:14,10 1|1:29:15,14 +chr20 480234 . T G 60 . QNAME=cluster23_scaffold_3;QSTART=25230992;QSTRAND=- GT:DP:AD ./.:25:15,10 ./.:28:23,5 1|0:25:6,19 +chr20 484694 . T TTG 60 . QNAME=cluster19_000000F;QSTART=25277206;QSTRAND=- GT:DP:AD ./.:41:22,19 1|0:23:12,11 ./.:24:19,5 +chr20 484991 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=464564;QSTRAND=+ GT:DP:AD 1|0:25:13,12 ./.:44:20,24 ./.:35:17,18 +chr20 485103 . A ATATATATATAT 60 . QNAME=cluster23_scaffold_2;QSTART=25210343;QSTRAND=- GT:DP:AD ./.:32:7,25 ./.:26:9,17 0|1:19:7,12 +chr20 485105 . A T 60 . QNAME=cluster23_scaffold_2;QSTART=25210341;QSTRAND=- GT:DP:AD ./.:36:20,16 ./.:44:24,20 0|1:26:18,8 +chr20 485105 . A ATAATATATATATAT 60 . QNAME=HG002-S9-H2-000001F;QSTART=439555;QSTRAND=+ GT:DP:AD 0|1:31:16,15 ./.:16:9,7 ./.:16:5,11 +chr20 485105 . A ATATATATATAT 60 . QNAME=cluster19_000000F;QSTART=25276784;QSTRAND=- GT:DP:AD ./.:32:13,19 1|0:26:11,15 ./.:23:7,16 +chr20 485107 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=439570;QSTRAND=+ GT:DP:AD 0|1:15:8,7 1|0:46:23,23 1|1:21:15,6 +chr20 485109 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=439572;QSTRAND=+ GT:DP:AD 0|1:23:7,16 1|0:28:19,9 1|1:22:7,15 +chr20 485115 . T A 60 . QNAME=cluster19_000000F;QSTART=445307;QSTRAND=+ GT:DP:AD ./.:16:7,9 0|1:32:13,19 ./.:13:6,7 +chr20 485117 . T A 60 . QNAME=cluster19_000000F;QSTART=445309;QSTRAND=+ GT:DP:AD ./.:49:25,24 0|1:18:10,8 ./.:18:12,6 +chr20 485138 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=439601;QSTRAND=+ GT:DP:AD 0|1:35:14,21 ./.:40:17,23 ./.:31:21,10 +chr20 485139 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=439602;QSTRAND=+ GT:DP:AD 0|1:32:23,9 ./.:31:25,6 ./.:37:15,22 +chr20 487542 . G A 60 . QNAME=cluster19_000000F;QSTART=447734;QSTRAND=+ GT:DP:AD ./.:38:19,19 0|1:33:14,19 ./.:13:5,8 +chr20 488040 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25223189;QSTRAND=- GT:DP:AD ./.:41:23,18 ./.:36:17,19 1|1:29:14,15 +chr20 490335 . C CT 60 . QNAME=cluster19_000000F;QSTART=25271553;QSTRAND=- GT:DP:AD ./.:38:19,19 1|0:33:12,21 ./.:29:5,24 +chr20 490909 . A C 60 . QNAME=cluster19_000000F;QSTART=25270979;QSTRAND=- GT:DP:AD ./.:31:18,13 1|0:17:11,6 ./.:32:25,7 +chr20 493202 . A T 60 . QNAME=cluster19_000000F;QSTART=25268686;QSTRAND=- GT:DP:AD ./.:43:20,23 1|0:42:24,18 1|1:36:22,14 +chr20 494543 . T C 60 . QNAME=cluster19_000000F;QSTART=25267345;QSTRAND=- GT:DP:AD ./.:33:16,17 1|0:43:21,22 ./.:37:17,20 +chr20 498335 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25212893;QSTRAND=- GT:DP:AD ./.:28:10,18 ./.:30:15,15 1|1:16:7,9 +chr20 498901 . T C 60 . QNAME=cluster19_000000F;QSTART=459093;QSTRAND=+ GT:DP:AD ./.:20:6,14 0|1:31:12,19 ./.:28:19,9 +chr20 499958 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25195485;QSTRAND=- GT:DP:AD ./.:31:17,14 ./.:19:5,14 0|1:26:15,11 +chr20 500634 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25210593;QSTRAND=- GT:DP:AD ./.:25:17,8 ./.:39:20,19 1|0:41:19,22 +chr20 501285 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=480825;QSTRAND=+ GT:DP:AD 1|0:19:5,14 ./.:17:11,6 ./.:29:17,12 +chr20 504037 . G GC 60 . QNAME=HG002-S9-H2-000001F;QSTART=458500;QSTRAND=+ GT:DP:AD 0|1:29:17,12 ./.:21:9,12 ./.:31:19,12 +chr20 505351 . G GT 60 . QNAME=cluster19_000000F;QSTART=25256536;QSTRAND=- GT:DP:AD ./.:25:18,7 1|0:29:21,8 1|0:38:19,19 +chr20 505587 . C G 60 . QNAME=cluster19_000000F;QSTART=465779;QSTRAND=+ GT:DP:AD ./.:44:22,22 0|1:11:6,5 ./.:26:15,11 +chr20 505869 . A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25205356;QSTRAND=- GT:DP:AD ./.:37:20,17 ./.:31:25,6 1|0:37:21,16 +chr20 505905 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25205320;QSTRAND=- GT:DP:AD ./.:32:14,18 ./.:14:8,6 1|0:38:17,21 +chr20 506070 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=485609;QSTRAND=+ GT:DP:AD 1|0:29:8,21 ./.:33:16,17 0|1:44:25,19 +chr20 506079 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=485618;QSTRAND=+ GT:DP:AD 1|0:17:11,6 ./.:32:9,23 0|1:29:14,15 +chr20 506080 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=485619;QSTRAND=+ GT:DP:AD 1|0:35:15,20 ./.:18:11,7 0|1:37:18,19 +chr20 506097 . C T 60 . QNAME=cluster19_000000F;QSTART=25255790;QSTRAND=- GT:DP:AD ./.:25:10,15 1|0:45:20,25 1|0:15:9,6 +chr20 506098 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=485637;QSTRAND=+ GT:DP:AD 1|0:16:8,8 ./.:20:10,10 0|1:33:13,20 +chr20 506127 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25205098;QSTRAND=- GT:DP:AD ./.:27:20,7 ./.:26:14,12 1|0:32:12,20 +chr20 507967 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=487506;QSTRAND=+ GT:DP:AD 1|1:35:14,21 1|1:29:21,8 1|1:37:13,24 +chr20 508286 . C T 60 . QNAME=cluster19_000000F;QSTART=25253601;QSTRAND=- GT:DP:AD ./.:33:22,11 1|0:33:20,13 1|1:35:21,14 +chr20 508793 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25186650;QSTRAND=- GT:DP:AD ./.:22:16,6 ./.:39:19,20 0|1:34:24,10 +chr20 511703 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=466166;QSTRAND=+ GT:DP:AD 0|1:16:8,8 ./.:27:6,21 ./.:45:22,23 +chr20 511705 . C T 60 . QNAME=cluster19_000000F;QSTART=25250182;QSTRAND=- GT:DP:AD ./.:46:24,22 1|0:41:25,16 1|1:15:5,10 +chr20 512561 . G T 60 . QNAME=cluster19_000000F;QSTART=25249326;QSTRAND=- GT:DP:AD ./.:16:7,9 1|0:30:14,16 1|1:18:7,11 +chr20 512965 . T C 60 . QNAME=cluster19_000000F;QSTART=25248922;QSTRAND=- GT:DP:AD ./.:25:18,7 1|0:35:16,19 ./.:37:18,19 +chr20 514164 . C T 60 . QNAME=cluster19_000000F;QSTART=25247723;QSTRAND=- GT:DP:AD ./.:45:24,21 1|0:20:8,12 1|1:24:5,19 +chr20 518933 . C CT 60 . QNAME=cluster23_scaffold_2;QSTART=25176511;QSTRAND=- GT:DP:AD ./.:15:7,8 ./.:28:22,6 0|1:28:18,10 +chr20 522293 . C T 60 . QNAME=cluster19_000000F;QSTART=25239596;QSTRAND=- GT:DP:AD ./.:19:14,5 1|0:31:12,19 1|1:37:18,19 +chr20 523858 . C CA 60 . QNAME=cluster19_000000F;QSTART=25238030;QSTRAND=- GT:DP:AD ./.:37:22,15 1|0:48:24,24 0|1:31:7,24 +chr20 523869 . A C 60 . QNAME=cluster19_000000F;QSTART=484060;QSTRAND=+ GT:DP:AD ./.:19:5,14 0|1:21:15,6 ./.:33:13,20 +chr20 524145 . C T 60 . QNAME=cluster19_000000F;QSTART=25237743;QSTRAND=- GT:DP:AD ./.:32:23,9 1|1:33:8,25 1|1:26:12,14 +chr20 524654 . T C 60 . QNAME=cluster19_000000F;QSTART=25237234;QSTRAND=- GT:DP:AD ./.:31:6,25 1|0:37:23,14 ./.:29:21,8 +chr20 525133 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=504669;QSTRAND=+ GT:DP:AD 1|0:34:11,23 ./.:32:24,8 ./.:45:21,24 +chr20 525391 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=504927;QSTRAND=+ GT:DP:AD 1|0:37:12,25 ./.:21:6,15 ./.:20:13,7 +chr20 525836 . T TA 60 . QNAME=cluster23_scaffold_2;QSTART=25169607;QSTRAND=- GT:DP:AD ./.:45:22,23 ./.:40:24,16 0|1:33:21,12 +chr20 526238 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=505772;QSTRAND=+ GT:DP:AD 1|0:29:23,6 1|0:39:15,24 1|1:36:15,21 +chr20 526685 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=506219;QSTRAND=+ GT:DP:AD 1|0:34:12,22 ./.:27:14,13 ./.:33:21,12 +chr20 527001 . C CAGAGAGAGAG 60 . QNAME=cluster19_000000F;QSTART=25234878;QSTRAND=- GT:DP:AD ./.:41:17,24 1|0:34:19,15 ./.:23:6,17 +chr20 527001 . C CAGAG 60 . QNAME=cluster23_scaffold_3;QSTART=25184221;QSTRAND=- GT:DP:AD ./.:30:19,11 ./.:23:6,17 1|0:35:20,15 +chr20 527001 . C CAG 60 . QNAME=cluster23_scaffold_2;QSTART=25168440;QSTRAND=- GT:DP:AD ./.:25:13,12 ./.:23:14,9 0|1:26:16,10 +chr20 527003 . G GAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=506537;QSTRAND=+ GT:DP:AD 1|0:33:21,12 ./.:39:14,25 ./.:32:22,10 +chr20 527729 . G A 60 . QNAME=cluster19_000000F;QSTART=487918;QSTRAND=+ GT:DP:AD ./.:47:22,25 0|1:23:14,9 ./.:35:13,22 +chr20 527782 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=507317;QSTRAND=+ GT:DP:AD 1|0:21:12,9 ./.:29:12,17 ./.:37:20,17 +chr20 528449 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=507984;QSTRAND=+ GT:DP:AD 1|0:35:13,22 ./.:26:21,5 ./.:28:6,22 +chr20 529190 . A AT 60 . QNAME=cluster19_000000F;QSTART=25232688;QSTRAND=- GT:DP:AD ./.:43:24,19 1|0:18:5,13 1|1:32:14,18 +chr20 530468 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=510003;QSTRAND=+ GT:DP:AD 1|0:33:10,23 ./.:26:13,13 ./.:35:12,23 +chr20 531253 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=510788;QSTRAND=+ GT:DP:AD 1|0:21:10,11 ./.:32:16,16 ./.:44:21,23 +chr20 532352 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=511885;QSTRAND=+ GT:DP:AD 1|0:25:12,13 ./.:14:9,5 ./.:31:14,17 +chr20 533815 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=513348;QSTRAND=+ GT:DP:AD 1|0:42:19,23 ./.:36:15,21 ./.:26:5,21 +chr20 535034 . C CA 60 . QNAME=cluster19_000000F;QSTART=495224;QSTRAND=+ GT:DP:AD ./.:30:7,23 0|1:20:13,7 ./.:24:18,6 +chr20 535629 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=515160;QSTRAND=+ GT:DP:AD 1|0:34:16,18 ./.:48:24,24 ./.:29:12,17 +chr20 535685 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=515216;QSTRAND=+ GT:DP:AD 1|0:29:19,10 ./.:24:6,18 ./.:33:19,14 +chr20 537243 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=516773;QSTRAND=+ GT:DP:AD 1|0:34:21,13 ./.:29:24,5 ./.:17:6,11 +chr20 537496 . G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=517027;QSTRAND=+ GT:DP:AD 1|0:27:8,19 ./.:24:14,10 ./.:29:13,16 +chr20 537963 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=517495;QSTRAND=+ GT:DP:AD 1|0:45:20,25 ./.:13:8,5 ./.:34:16,18 +chr20 538108 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=517640;QSTRAND=+ GT:DP:AD 1|0:47:25,22 1|0:17:5,12 1|1:30:13,17 +chr20 539053 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=518585;QSTRAND=+ GT:DP:AD 1|0:42:22,20 ./.:21:9,12 ./.:33:8,25 +chr20 539493 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25155947;QSTRAND=- GT:DP:AD ./.:26:12,14 ./.:16:11,5 0|1:24:9,15 +chr20 541244 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=520776;QSTRAND=+ GT:DP:AD 1|0:39:16,23 ./.:16:10,6 ./.:16:7,9 +chr20 541502 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=521034;QSTRAND=+ GT:DP:AD 1|0:37:25,12 ./.:27:12,15 ./.:39:25,14 +chr20 542623 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=522155;QSTRAND=+ GT:DP:AD 1|0:47:22,25 ./.:24:18,6 ./.:22:11,11 +chr20 544402 . G GT 60 . QNAME=cluster19_000000F;QSTART=25217475;QSTRAND=- GT:DP:AD ./.:42:22,20 1|0:25:12,13 1|1:23:10,13 +chr20 545973 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=525505;QSTRAND=+ GT:DP:AD 1|0:25:20,5 ./.:40:15,25 ./.:35:19,16 +chr20 546122 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25149317;QSTRAND=- GT:DP:AD ./.:14:8,6 ./.:29:9,20 0|1:17:11,6 +chr20 547548 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=527078;QSTRAND=+ GT:DP:AD 1|0:32:15,17 ./.:21:9,12 ./.:30:23,7 +chr20 548222 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=527752;QSTRAND=+ GT:DP:AD 1|0:29:16,13 0|1:37:25,12 ./.:19:6,13 +chr20 548577 . A AT 60 . QNAME=cluster19_000000F;QSTART=25213299;QSTRAND=- GT:DP:AD ./.:26:9,17 1|0:18:11,7 0|1:16:9,7 +chr20 548577 . A ATT 60 . QNAME=cluster23_scaffold_3;QSTART=25162641;QSTRAND=- GT:DP:AD ./.:27:16,11 ./.:24:18,6 1|0:17:8,9 +chr20 548971 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=528495;QSTRAND=+ GT:DP:AD 1|0:27:9,18 ./.:27:8,19 ./.:29:15,14 +chr20 549092 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=528616;QSTRAND=+ GT:DP:AD 1|0:46:23,23 ./.:17:12,5 ./.:31:11,20 +chr20 549227 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=528751;QSTRAND=+ GT:DP:AD 1|0:37:20,17 ./.:14:9,5 ./.:33:12,21 +chr20 549670 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=529190;QSTRAND=+ GT:DP:AD 1|0:39:20,19 ./.:30:20,10 ./.:18:12,6 +chr20 550104 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=529624;QSTRAND=+ GT:DP:AD 1|0:42:25,17 ./.:19:13,6 ./.:35:12,23 +chr20 550577 . C T 60 . QNAME=cluster19_000000F;QSTART=25211299;QSTRAND=- GT:DP:AD ./.:31:8,23 1|0:23:8,15 1|1:35:22,13 +chr20 551334 . C A 60 . QNAME=cluster19_000000F;QSTART=25210542;QSTRAND=- GT:DP:AD ./.:13:6,7 1|0:42:18,24 1|1:22:7,15 +chr20 551415 . T A 60 . QNAME=cluster19_000000F;QSTART=25210461;QSTRAND=- GT:DP:AD ./.:32:14,18 1|0:32:22,10 1|1:33:25,8 +chr20 551424 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=530944;QSTRAND=+ GT:DP:AD 1|0:30:24,6 1|0:36:11,25 1|1:24:17,7 +chr20 551459 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=530979;QSTRAND=+ GT:DP:AD 1|0:29:5,24 1|0:18:9,9 1|1:23:15,8 +chr20 552161 . G A 60 . QNAME=cluster19_000000F;QSTART=25209715;QSTRAND=- GT:DP:AD ./.:28:18,10 1|0:26:16,10 1|1:35:14,21 +chr20 552253 . C T 60 . QNAME=cluster19_000000F;QSTART=25209623;QSTRAND=- GT:DP:AD ./.:39:16,23 1|0:42:18,24 1|1:32:22,10 +chr20 552281 . A G 60 . QNAME=cluster19_000000F;QSTART=25209595;QSTRAND=- GT:DP:AD ./.:38:19,19 1|0:24:16,8 1|1:29:11,18 +chr20 553245 . C G 60 . QNAME=cluster19_000000F;QSTART=25208632;QSTRAND=- GT:DP:AD ./.:33:24,9 1|0:48:23,25 1|1:25:13,12 +chr20 553335 . C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=532856;QSTRAND=+ GT:DP:AD 1|0:25:15,10 ./.:23:17,6 ./.:40:25,15 +chr20 553335 . C CAAA 60 . QNAME=cluster19_000000F;QSTART=25208539;QSTRAND=- GT:DP:AD ./.:27:11,16 1|0:25:14,11 1|1:26:5,21 +chr20 553919 . C T 60 . QNAME=cluster19_000000F;QSTART=25207955;QSTRAND=- GT:DP:AD ./.:32:15,17 1|0:37:22,15 1|1:23:7,16 +chr20 554853 . T A 60 . QNAME=cluster19_000000F;QSTART=25207021;QSTRAND=- GT:DP:AD ./.:33:19,14 1|0:19:14,5 1|1:32:11,21 +chr20 555892 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=535413;QSTRAND=+ GT:DP:AD 1|1:40:17,23 1|1:37:18,19 1|1:22:8,14 +chr20 556119 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=535640;QSTRAND=+ GT:DP:AD 1|0:22:6,16 0|1:17:12,5 1|1:22:15,7 +chr20 556141 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=535662;QSTRAND=+ GT:DP:AD 1|1:22:6,16 1|1:34:21,13 1|1:28:6,22 +chr20 556215 . G A 60 . QNAME=cluster19_000000F;QSTART=516405;QSTRAND=+ GT:DP:AD ./.:16:10,6 0|1:41:21,20 1|1:20:9,11 +chr20 556356 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=535877;QSTRAND=+ GT:DP:AD 1|0:22:17,5 ./.:22:15,7 ./.:32:10,22 +chr20 556431 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=510889;QSTRAND=+ GT:DP:AD 0|1:16:11,5 1|0:34:17,17 ./.:33:9,24 +chr20 556435 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=535956;QSTRAND=+ GT:DP:AD 1|0:34:15,19 0|1:39:20,19 1|1:43:22,21 +chr20 556632 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=536153;QSTRAND=+ GT:DP:AD 1|1:39:17,22 1|1:38:13,25 1|1:20:9,11 +chr20 556794 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=536315;QSTRAND=+ GT:DP:AD 1|1:25:18,7 1|1:32:10,22 1|1:48:25,23 +chr20 556861 . C A 60 . QNAME=cluster19_000000F;QSTART=517051;QSTRAND=+ GT:DP:AD ./.:20:9,11 0|1:28:19,9 1|1:44:25,19 +chr20 556869 . C CAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=536391;QSTRAND=+ GT:DP:AD 1|1:50:25,25 1|0:27:5,22 ./.:46:25,21 +chr20 556869 . C CAAAAAA 60 . QNAME=cluster23_scaffold_3;QSTART=25154341;QSTRAND=- GT:DP:AD ./.:35:23,12 ./.:42:25,17 1|0:36:13,23 +chr20 556869 . C CAAAAA 60 . QNAME=cluster23_scaffold_2;QSTART=25138562;QSTRAND=- GT:DP:AD ./.:32:15,17 ./.:44:25,19 0|1:15:6,9 +chr20 556881 . A AAAAAAT 60 . QNAME=cluster19_000000F;QSTART=517072;QSTRAND=+ GT:DP:AD ./.:28:9,19 0|1:33:16,17 ./.:16:11,5 +chr20 556883 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=536407;QSTRAND=+ GT:DP:AD 1|1:26:6,20 1|0:29:5,24 ./.:33:17,16 +chr20 556885 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=536409;QSTRAND=+ GT:DP:AD 1|1:21:14,7 1|0:11:6,5 ./.:17:8,9 +chr20 556887 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=536411;QSTRAND=+ GT:DP:AD 1|1:29:13,16 1|0:38:25,13 ./.:16:5,11 +chr20 557034 . T C 60 . QNAME=cluster19_000000F;QSTART=517230;QSTRAND=+ GT:DP:AD ./.:14:9,5 0|1:28:13,15 1|1:41:22,19 +chr20 557559 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=537083;QSTRAND=+ GT:DP:AD 1|1:37:14,23 1|0:23:14,9 ./.:35:18,17 +chr20 557586 . C T 60 . QNAME=cluster19_000000F;QSTART=517782;QSTRAND=+ GT:DP:AD ./.:11:5,6 0|1:18:6,12 1|1:28:21,7 +chr20 557591 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=537115;QSTRAND=+ GT:DP:AD 1|1:47:22,25 1|1:14:8,6 1|1:41:24,17 +chr20 557603 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=537127;QSTRAND=+ GT:DP:AD 1|1:20:14,6 1|0:21:14,7 ./.:24:14,10 +chr20 557995 . C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=537520;QSTRAND=+ GT:DP:AD 1|1:43:25,18 1|1:45:22,23 1|1:23:18,5 +chr20 558185 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=537710;QSTRAND=+ GT:DP:AD 1|1:46:22,24 1|0:21:8,13 ./.:41:25,16 +chr20 558374 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=537899;QSTRAND=+ GT:DP:AD 1|1:14:8,6 1|0:20:14,6 ./.:28:22,6 +chr20 558479 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=538004;QSTRAND=+ GT:DP:AD 1|1:37:14,23 1|0:31:11,20 ./.:25:12,13 +chr20 558719 . G A 60 . QNAME=cluster19_000000F;QSTART=518916;QSTRAND=+ GT:DP:AD ./.:21:11,10 0|1:16:9,7 1|1:39:15,24 +chr20 558928 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=538449;QSTRAND=+ GT:DP:AD 1|1:42:24,18 1|0:34:24,10 ./.:33:22,11 +chr20 559006 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=538527;QSTRAND=+ GT:DP:AD 1|1:29:16,13 1|1:35:15,20 1|1:35:12,23 +chr20 559112 . G GT 60 . QNAME=HG002-S9-H1-000001F;QSTART=538634;QSTRAND=+ GT:DP:AD 1|1:38:25,13 1|0:21:9,12 ./.:39:25,14 +chr20 559189 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=538711;QSTRAND=+ GT:DP:AD 1|1:37:22,15 1|1:34:10,24 1|1:28:21,7 +chr20 559234 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=538756;QSTRAND=+ GT:DP:AD 1|1:36:23,13 1|0:38:20,18 1|0:15:10,5 +chr20 559282 . G T 60 . QNAME=cluster19_000000F;QSTART=519479;QSTRAND=+ GT:DP:AD ./.:42:21,21 0|1:34:19,15 0|1:36:16,20 +chr20 559554 . T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=539077;QSTRAND=+ GT:DP:AD 1|1:17:10,7 1|1:35:15,20 1|1:30:9,21 +chr20 560063 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=539586;QSTRAND=+ GT:DP:AD 1|0:33:21,12 1|0:18:12,6 ./.:28:6,22 +chr20 560086 . C G 60 . QNAME=cluster19_000000F;QSTART=520282;QSTRAND=+ GT:DP:AD ./.:31:10,21 0|1:31:20,11 1|1:29:20,9 +chr20 560087 . A C 60 . QNAME=cluster19_000000F;QSTART=520283;QSTRAND=+ GT:DP:AD ./.:35:17,18 0|1:29:21,8 1|1:33:25,8 +chr20 560103 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=539625;QSTRAND=+ GT:DP:AD 1|1:39:18,21 1|1:28:10,18 1|1:17:5,12 +chr20 560343 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=514801;QSTRAND=+ GT:DP:AD 0|1:25:7,18 1|0:39:25,14 ./.:20:14,6 +chr20 560618 . G T 60 . QNAME=cluster19_000000F;QSTART=520814;QSTRAND=+ GT:DP:AD ./.:39:19,20 0|1:22:7,15 1|1:37:16,21 +chr20 560691 . G A 60 . QNAME=cluster19_000000F;QSTART=520887;QSTRAND=+ GT:DP:AD ./.:28:9,19 0|1:32:23,9 1|1:28:22,6 +chr20 560945 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=540467;QSTRAND=+ GT:DP:AD 1|1:28:9,19 1|0:27:16,11 ./.:15:5,10 +chr20 561211 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=540733;QSTRAND=+ GT:DP:AD 1|1:26:14,12 1|1:20:10,10 1|1:21:14,7 +chr20 562030 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=541552;QSTRAND=+ GT:DP:AD 1|1:16:11,5 1|1:38:23,15 1|1:34:22,12 +chr20 562133 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=541655;QSTRAND=+ GT:DP:AD 1|1:22:12,10 1|1:31:23,8 1|1:43:21,22 +chr20 562219 . A G 60 . QNAME=cluster19_000000F;QSTART=522415;QSTRAND=+ GT:DP:AD ./.:31:14,17 0|1:33:24,9 1|1:27:11,16 +chr20 562642 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=542164;QSTRAND=+ GT:DP:AD 1|1:23:9,14 1|1:23:11,12 1|1:33:17,16 +chr20 562657 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=542179;QSTRAND=+ GT:DP:AD 1|1:29:22,7 1|1:45:20,25 1|1:36:18,18 +chr20 562994 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=542516;QSTRAND=+ GT:DP:AD 1|1:32:11,21 1|1:26:5,21 1|1:36:17,19 +chr20 563100 . C T 60 . QNAME=cluster19_000000F;QSTART=523296;QSTRAND=+ GT:DP:AD ./.:34:23,11 0|1:25:14,11 1|1:33:16,17 +chr20 563396 . C T 60 . QNAME=cluster19_000000F;QSTART=25198477;QSTRAND=- GT:DP:AD ./.:17:6,11 1|0:25:14,11 ./.:29:13,16 +chr20 563773 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=543295;QSTRAND=+ GT:DP:AD 1|1:32:25,7 1|0:22:10,12 ./.:32:9,23 +chr20 564270 . G A 60 . QNAME=cluster19_000000F;QSTART=25197603;QSTRAND=- GT:DP:AD ./.:24:19,5 1|1:29:12,17 1|1:28:9,19 +chr20 564271 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=543793;QSTRAND=+ GT:DP:AD 1|1:28:9,19 ./.:27:16,11 ./.:20:14,6 +chr20 564553 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=519011;QSTRAND=+ GT:DP:AD 0|1:30:16,14 1|1:21:6,15 1|1:32:15,17 +chr20 564629 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25130802;QSTRAND=- GT:DP:AD ./.:24:19,5 ./.:23:17,6 0|1:25:11,14 +chr20 565205 . A AT 60 . QNAME=cluster19_000000F;QSTART=25196667;QSTRAND=- GT:DP:AD ./.:37:14,23 1|1:33:8,25 1|1:30:25,5 +chr20 565232 . C T 60 . QNAME=cluster19_000000F;QSTART=25196640;QSTRAND=- GT:DP:AD ./.:27:6,21 1|1:47:22,25 1|0:39:24,15 +chr20 565534 . T A 60 . QNAME=cluster19_000000F;QSTART=25196338;QSTRAND=- GT:DP:AD ./.:23:18,5 1|1:23:15,8 1|1:25:5,20 +chr20 565902 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=545424;QSTRAND=+ GT:DP:AD 1|0:29:8,21 ./.:16:5,11 ./.:21:6,15 +chr20 565980 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=545502;QSTRAND=+ GT:DP:AD 1|1:30:24,6 ./.:26:6,20 ./.:33:9,24 +chr20 566018 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25145195;QSTRAND=- GT:DP:AD ./.:21:5,16 ./.:31:21,10 1|0:44:24,20 +chr20 566096 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=545618;QSTRAND=+ GT:DP:AD 1|1:31:25,6 ./.:25:18,7 ./.:34:11,23 +chr20 567105 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=546621;QSTRAND=+ GT:DP:AD 1|0:35:15,20 ./.:32:24,8 ./.:23:17,6 +chr20 568286 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=522738;QSTRAND=+ GT:DP:AD 0|1:38:21,17 ./.:18:13,5 ./.:40:22,18 +chr20 568720 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=523172;QSTRAND=+ GT:DP:AD 0|1:35:14,21 ./.:34:17,17 ./.:24:17,7 +chr20 568936 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25142277;QSTRAND=- GT:DP:AD ./.:19:6,13 ./.:38:16,22 1|0:40:18,22 +chr20 569261 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=523713;QSTRAND=+ GT:DP:AD 0|1:32:13,19 ./.:36:18,18 ./.:28:17,11 +chr20 569263 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=548779;QSTRAND=+ GT:DP:AD 1|0:24:12,12 ./.:16:6,10 ./.:16:11,5 +chr20 569274 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=523726;QSTRAND=+ GT:DP:AD 0|1:32:21,11 ./.:40:21,19 ./.:35:16,19 +chr20 569446 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=523898;QSTRAND=+ GT:DP:AD 0|1:28:6,22 1|0:31:23,8 ./.:31:8,23 +chr20 569520 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=523972;QSTRAND=+ GT:DP:AD 0|1:36:22,14 1|1:32:21,11 1|1:36:15,21 +chr20 569616 . A C 60 . QNAME=cluster19_000000F;QSTART=25192256;QSTRAND=- GT:DP:AD ./.:25:15,10 1|1:42:24,18 1|1:28:7,21 +chr20 569956 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=524408;QSTRAND=+ GT:DP:AD 0|1:32:17,15 ./.:26:15,11 ./.:24:11,13 +chr20 570171 . A C 60 . QNAME=cluster19_000000F;QSTART=25191701;QSTRAND=- GT:DP:AD ./.:36:24,12 1|1:15:5,10 1|1:23:11,12 +chr20 570174 . T C 60 . QNAME=cluster19_000000F;QSTART=25191698;QSTRAND=- GT:DP:AD ./.:27:9,18 1|1:37:15,22 1|1:26:21,5 +chr20 570223 . C CT 60 . QNAME=cluster19_000000F;QSTART=25191648;QSTRAND=- GT:DP:AD ./.:44:24,20 1|1:24:11,13 0|1:44:20,24 +chr20 570223 . C CTT 60 . QNAME=cluster23_scaffold_3;QSTART=25140988;QSTRAND=- GT:DP:AD ./.:24:7,17 ./.:28:16,12 1|0:36:12,24 +chr20 570243 . G A 60 . QNAME=cluster19_000000F;QSTART=25191628;QSTRAND=- GT:DP:AD ./.:28:17,11 1|1:41:22,19 1|1:37:19,18 +chr20 570390 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=524842;QSTRAND=+ GT:DP:AD 0|1:27:19,8 1|1:26:16,10 1|1:29:8,21 +chr20 570410 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=524862;QSTRAND=+ GT:DP:AD 0|1:43:18,25 ./.:38:16,22 ./.:28:7,21 +chr20 570752 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=525204;QSTRAND=+ GT:DP:AD 0|1:38:18,20 1|1:33:18,15 1|1:38:20,18 +chr20 571051 . C CT 60 . QNAME=HG002-S9-H2-000001F;QSTART=525504;QSTRAND=+ GT:DP:AD 0|1:21:15,6 1|1:31:9,22 1|1:34:15,19 +chr20 571277 . T C 60 . QNAME=cluster19_000000F;QSTART=25190593;QSTRAND=- GT:DP:AD ./.:21:13,8 1|1:19:14,5 1|1:34:23,11 +chr20 571843 . G A 60 . QNAME=cluster19_000000F;QSTART=25190027;QSTRAND=- GT:DP:AD ./.:36:24,12 1|0:36:22,14 ./.:12:6,6 +chr20 573141 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=552656;QSTRAND=+ GT:DP:AD 1|0:43:21,22 ./.:44:25,19 ./.:29:11,18 +chr20 574599 . C CT 60 . QNAME=cluster19_000000F;QSTART=25187270;QSTRAND=- GT:DP:AD ./.:25:12,13 1|0:29:14,15 ./.:29:19,10 +chr20 574632 . G A 60 . QNAME=cluster19_000000F;QSTART=25187237;QSTRAND=- GT:DP:AD ./.:37:12,25 1|0:30:12,18 ./.:31:7,24 +chr20 574708 . G A 60 . QNAME=cluster19_000000F;QSTART=25187161;QSTRAND=- GT:DP:AD ./.:24:7,17 1|1:38:16,22 ./.:43:19,24 +chr20 577333 . G A 60 . QNAME=cluster19_000000F;QSTART=537532;QSTRAND=+ GT:DP:AD ./.:36:19,17 0|1:30:8,22 ./.:32:19,13 +chr20 578654 . T TAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=533107;QSTRAND=+ GT:DP:AD 0|1:31:14,17 ./.:32:23,9 1|1:25:8,17 +chr20 578790 . T C 60 . QNAME=cluster19_000000F;QSTART=25183083;QSTRAND=- GT:DP:AD ./.:31:15,16 1|1:32:8,24 ./.:28:22,6 +chr20 580481 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=559995;QSTRAND=+ GT:DP:AD 1|1:32:16,16 1|1:36:12,24 0|1:42:24,18 +chr20 580899 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=560413;QSTRAND=+ GT:DP:AD 1|0:35:17,18 1|1:25:8,17 ./.:31:20,11 +chr20 581272 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=560786;QSTRAND=+ GT:DP:AD 1|0:22:9,13 1|0:28:13,15 ./.:33:14,19 +chr20 581577 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=536031;QSTRAND=+ GT:DP:AD 0|1:46:22,24 ./.:40:24,16 ./.:35:21,14 +chr20 581670 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=561184;QSTRAND=+ GT:DP:AD 1|1:20:11,9 1|1:36:18,18 ./.:18:5,13 +chr20 581801 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=561315;QSTRAND=+ GT:DP:AD 1|1:27:17,10 1|1:28:17,11 1|0:26:9,17 +chr20 582041 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=536494;QSTRAND=+ GT:DP:AD 0|1:20:12,8 ./.:10:5,5 0|1:46:22,24 +chr20 582389 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=536842;QSTRAND=+ GT:DP:AD 0|1:38:20,18 ./.:20:10,10 0|1:28:11,17 +chr20 583353 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=562864;QSTRAND=+ GT:DP:AD 1|0:20:7,13 1|1:26:15,11 ./.:26:21,5 +chr20 583466 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=537919;QSTRAND=+ GT:DP:AD 0|1:29:14,15 ./.:40:18,22 0|1:39:21,18 +chr20 583895 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=538348;QSTRAND=+ GT:DP:AD 0|1:29:9,20 ./.:31:14,17 0|1:36:20,16 +chr20 584249 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=563760;QSTRAND=+ GT:DP:AD 1|1:17:8,9 1|1:39:22,17 0|1:30:17,13 +chr20 584433 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=538886;QSTRAND=+ GT:DP:AD 0|1:37:22,15 ./.:19:10,9 0|1:22:6,16 +chr20 584664 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=539117;QSTRAND=+ GT:DP:AD 0|1:45:23,22 ./.:33:21,12 0|1:38:19,19 +chr20 584861 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=539314;QSTRAND=+ GT:DP:AD 0|1:23:5,18 ./.:30:11,19 0|1:16:9,7 +chr20 585289 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=564800;QSTRAND=+ GT:DP:AD 1|1:42:21,21 1|1:21:9,12 0|1:24:13,11 +chr20 585341 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=539794;QSTRAND=+ GT:DP:AD 0|1:42:17,25 ./.:11:6,5 0|1:33:14,19 +chr20 585726 . A ATATATGTATATGTACG 60 . QNAME=HG002-S9-H2-000001F;QSTART=540180;QSTRAND=+ GT:DP:AD 0|1:17:11,6 ./.:35:12,23 0|1:15:9,6 +chr20 585739 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=540208;QSTRAND=+ GT:DP:AD 0|1:28:16,12 ./.:34:20,14 0|1:27:12,15 +chr20 585749 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=540218;QSTRAND=+ GT:DP:AD 0|1:24:18,6 ./.:22:5,17 0|1:38:17,21 +chr20 586045 . C CT 60 . QNAME=cluster19_000000F;QSTART=25175829;QSTRAND=- GT:DP:AD ./.:33:13,20 1|1:33:10,23 1|0:11:6,5 +chr20 586124 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=540590;QSTRAND=+ GT:DP:AD 0|1:30:17,13 ./.:32:18,14 0|1:20:7,13 +chr20 586280 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=565791;QSTRAND=+ GT:DP:AD 1|0:32:15,17 1|1:41:16,25 ./.:25:18,7 +chr20 586536 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=541002;QSTRAND=+ GT:DP:AD 0|1:31:8,23 ./.:19:8,11 0|1:38:21,17 +chr20 588052 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=542518;QSTRAND=+ GT:DP:AD 0|1:32:7,25 ./.:39:15,24 0|1:15:7,8 +chr20 588077 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=542543;QSTRAND=+ GT:DP:AD 0|1:32:12,20 ./.:44:19,25 0|1:40:16,24 +chr20 588283 . A ATT 60 . QNAME=HG002-S9-H2-000001F;QSTART=542750;QSTRAND=+ GT:DP:AD 0|1:33:24,9 ./.:24:15,9 0|1:25:7,18 +chr20 588283 . A AT 60 . QNAME=cluster19_000000F;QSTART=25173590;QSTRAND=- GT:DP:AD ./.:28:11,17 1|1:44:20,24 ./.:39:17,22 +chr20 590301 . A AAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=569813;QSTRAND=+ GT:DP:AD 1|0:46:21,25 ./.:29:24,5 ./.:34:13,21 +chr20 590301 . A AACAC 60 . QNAME=cluster19_000000F;QSTART=25171568;QSTRAND=- GT:DP:AD ./.:35:12,23 1|1:11:6,5 ./.:21:5,16 +chr20 590927 . G C 60 . QNAME=cluster23_scaffold_2;QSTART=25104488;QSTRAND=- GT:DP:AD ./.:28:23,5 ./.:49:25,24 0|1:31:6,25 +chr20 592228 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=546693;QSTRAND=+ GT:DP:AD 0|1:32:10,22 ./.:34:19,15 0|1:33:10,23 +chr20 592392 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=546857;QSTRAND=+ GT:DP:AD 0|1:27:6,21 ./.:14:6,8 0|1:23:7,16 +chr20 593097 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=547562;QSTRAND=+ GT:DP:AD 0|1:30:6,24 ./.:18:11,7 0|1:13:7,6 +chr20 593103 . T TTA 60 . QNAME=cluster19_000000F;QSTART=25168764;QSTRAND=- GT:DP:AD ./.:20:6,14 1|0:20:12,8 ./.:34:16,18 +chr20 593121 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25118087;QSTRAND=- GT:DP:AD ./.:20:8,12 ./.:36:13,23 1|0:31:16,15 +chr20 593121 . A ATATATATTTTT 60 . QNAME=HG002-S9-H2-000001F;QSTART=547587;QSTRAND=+ GT:DP:AD 0|1:34:23,11 ./.:36:22,14 ./.:29:16,13 +chr20 593121 . A ATATATTTTTTT 60 . QNAME=cluster23_scaffold_2;QSTART=25102283;QSTRAND=- GT:DP:AD ./.:13:6,7 ./.:47:22,25 0|1:38:16,22 +chr20 593122 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=572636;QSTRAND=+ GT:DP:AD 1|0:31:18,13 0|1:34:22,12 ./.:40:16,24 +chr20 593123 . T A 60 . QNAME=cluster19_000000F;QSTART=25168744;QSTRAND=- GT:DP:AD ./.:27:7,20 1|0:36:21,15 ./.:27:10,17 +chr20 593638 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=548114;QSTRAND=+ GT:DP:AD 0|1:39:18,21 ./.:30:24,6 0|1:21:14,7 +chr20 593664 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=548140;QSTRAND=+ GT:DP:AD 0|1:26:9,17 ./.:29:9,20 0|1:11:6,5 +chr20 594618 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25100785;QSTRAND=- GT:DP:AD ./.:30:9,21 ./.:24:15,9 0|1:25:8,17 +chr20 595643 . T TTTA 60 . QNAME=HG002-S9-H1-000001F;QSTART=575151;QSTRAND=+ GT:DP:AD 1|0:19:6,13 1|1:30:19,11 ./.:46:22,24 +chr20 596470 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25114738;QSTRAND=- GT:DP:AD ./.:31:9,22 ./.:43:25,18 1|0:36:13,23 +chr20 596536 . G GAAAACA 60 . QNAME=cluster23_scaffold_3;QSTART=25114666;QSTRAND=- GT:DP:AD ./.:26:8,18 ./.:10:5,5 1|0:46:24,22 +chr20 596656 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=576166;QSTRAND=+ GT:DP:AD 1|0:30:22,8 1|1:40:15,25 ./.:38:14,24 +chr20 596715 . C T 60 . QNAME=cluster19_000000F;QSTART=556911;QSTRAND=+ GT:DP:AD ./.:10:5,5 0|1:36:22,14 ./.:38:22,16 +chr20 597212 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=576722;QSTRAND=+ GT:DP:AD 1|0:33:24,9 1|1:24:17,7 ./.:32:8,24 +chr20 597374 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=576884;QSTRAND=+ GT:DP:AD 1|0:36:19,17 1|1:25:18,7 ./.:23:5,18 +chr20 597779 . C T 60 . QNAME=cluster19_000000F;QSTART=557975;QSTRAND=+ GT:DP:AD ./.:47:22,25 0|1:42:22,20 ./.:29:6,23 +chr20 598186 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25113016;QSTRAND=- GT:DP:AD ./.:21:14,7 ./.:36:15,21 1|0:17:7,10 +chr20 598263 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=552737;QSTRAND=+ GT:DP:AD 0|1:28:22,6 ./.:17:6,11 0|1:24:10,14 +chr20 598702 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25112500;QSTRAND=- GT:DP:AD ./.:30:7,23 ./.:15:6,9 1|0:24:15,9 +chr20 599013 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=578523;QSTRAND=+ GT:DP:AD 1|0:26:14,12 1|1:30:14,16 1|1:30:19,11 +chr20 599421 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=578929;QSTRAND=+ GT:DP:AD 1|0:18:8,10 1|1:34:10,24 ./.:22:7,15 +chr20 600604 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=580112;QSTRAND=+ GT:DP:AD 1|1:23:15,8 1|1:42:18,24 1|1:34:14,20 +chr20 600839 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=580347;QSTRAND=+ GT:DP:AD 1|0:22:17,5 1|1:32:16,16 ./.:15:5,10 +chr20 600991 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=580499;QSTRAND=+ GT:DP:AD 1|0:44:19,25 1|1:33:14,19 ./.:18:13,5 +chr20 601642 . G A 60 . QNAME=cluster19_000000F;QSTART=25160230;QSTRAND=- GT:DP:AD ./.:23:13,10 1|0:37:15,22 ./.:29:5,24 +chr20 601683 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=581192;QSTRAND=+ GT:DP:AD 1|0:44:25,19 1|1:44:22,22 0|1:42:22,20 +chr20 601683 . T TAA 60 . QNAME=cluster23_scaffold_3;QSTART=25109518;QSTRAND=- GT:DP:AD ./.:45:25,20 ./.:40:21,19 1|0:14:9,5 +chr20 602460 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=581969;QSTRAND=+ GT:DP:AD 1|0:12:6,6 1|1:33:22,11 ./.:25:5,20 +chr20 602943 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25108259;QSTRAND=- GT:DP:AD ./.:44:21,23 ./.:30:12,18 1|1:28:15,13 +chr20 606311 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=585820;QSTRAND=+ GT:DP:AD 1|1:28:13,15 1|1:42:25,17 1|1:23:13,10 +chr20 606780 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=586289;QSTRAND=+ GT:DP:AD 1|0:25:17,8 ./.:22:9,13 1|1:24:9,15 +chr20 607272 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=561745;QSTRAND=+ GT:DP:AD 0|1:38:17,21 ./.:14:5,9 ./.:28:10,18 +chr20 607445 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=586954;QSTRAND=+ GT:DP:AD 1|1:37:18,19 ./.:31:25,6 1|1:37:19,18 +chr20 607522 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=587031;QSTRAND=+ GT:DP:AD 1|0:37:13,24 ./.:40:17,23 1|1:15:5,10 +chr20 607633 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=562106;QSTRAND=+ GT:DP:AD 0|1:39:14,25 ./.:29:17,12 ./.:29:22,7 +chr20 607790 . A C 60 . QNAME=cluster19_000000F;QSTART=567986;QSTRAND=+ GT:DP:AD ./.:20:10,10 0|1:23:9,14 ./.:25:12,13 +chr20 608989 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=588498;QSTRAND=+ GT:DP:AD 1|0:33:14,19 ./.:33:14,19 1|1:12:5,7 +chr20 609812 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=589321;QSTRAND=+ GT:DP:AD 1|1:28:9,19 ./.:26:6,20 1|1:31:10,21 +chr20 609898 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=589407;QSTRAND=+ GT:DP:AD 1|1:16:11,5 1|1:28:17,11 1|1:39:25,14 +chr20 609899 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=589408;QSTRAND=+ GT:DP:AD 1|1:19:5,14 1|1:19:8,11 1|1:22:16,6 +chr20 610256 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=589765;QSTRAND=+ GT:DP:AD 1|1:20:7,13 ./.:38:15,23 1|1:28:6,22 +chr20 610966 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=590475;QSTRAND=+ GT:DP:AD 1|0:29:20,9 ./.:35:23,12 1|1:18:13,5 +chr20 611394 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=590903;QSTRAND=+ GT:DP:AD 1|1:42:23,19 ./.:25:13,12 1|1:32:15,17 +chr20 611826 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=566299;QSTRAND=+ GT:DP:AD 0|1:45:20,25 ./.:31:23,8 ./.:37:17,20 +chr20 611881 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=591390;QSTRAND=+ GT:DP:AD 1|1:13:6,7 ./.:39:20,19 1|1:35:17,18 +chr20 612157 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=591666;QSTRAND=+ GT:DP:AD 1|1:24:8,16 ./.:22:6,16 1|1:32:19,13 +chr20 612432 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=591941;QSTRAND=+ GT:DP:AD 1|1:41:21,20 ./.:27:22,5 1|1:25:20,5 +chr20 612664 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=592173;QSTRAND=+ GT:DP:AD 1|1:31:23,8 ./.:25:19,6 1|1:40:18,22 +chr20 612674 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=592183;QSTRAND=+ GT:DP:AD 1|0:20:12,8 ./.:21:12,9 1|1:29:19,10 +chr20 614136 . T C 60 . QNAME=cluster19_000000F;QSTART=574332;QSTRAND=+ GT:DP:AD ./.:33:9,24 0|1:39:15,24 ./.:35:23,12 +chr20 614408 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=568827;QSTRAND=+ GT:DP:AD 0|1:31:6,25 ./.:27:10,17 ./.:39:18,21 +chr20 614473 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=593924;QSTRAND=+ GT:DP:AD 1|0:18:8,10 ./.:15:5,10 ./.:33:10,23 +chr20 614475 . A C 60 . QNAME=cluster19_000000F;QSTART=574671;QSTRAND=+ GT:DP:AD ./.:16:11,5 0|1:45:21,24 ./.:28:15,13 +chr20 614477 . A C 60 . QNAME=cluster19_000000F;QSTART=574673;QSTRAND=+ GT:DP:AD ./.:25:8,17 0|1:40:17,23 ./.:25:9,16 +chr20 614492 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=593943;QSTRAND=+ GT:DP:AD 1|0:34:16,18 ./.:47:25,22 1|1:22:15,7 +chr20 614492 . T TAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=568912;QSTRAND=+ GT:DP:AD 0|1:18:10,8 ./.:18:5,13 ./.:29:16,13 +chr20 614494 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=593945;QSTRAND=+ GT:DP:AD 1|0:29:14,15 ./.:30:16,14 1|1:42:19,23 +chr20 614496 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=568917;QSTRAND=+ GT:DP:AD 0|1:22:7,15 ./.:16:7,9 ./.:30:23,7 +chr20 614517 . G GTA 60 . QNAME=cluster23_scaffold_3;QSTART=25096741;QSTRAND=- GT:DP:AD ./.:27:12,15 ./.:35:17,18 1|1:41:22,19 +chr20 614555 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=594006;QSTRAND=+ GT:DP:AD 1|0:38:23,15 ./.:19:6,13 1|1:23:9,14 +chr20 614561 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=594012;QSTRAND=+ GT:DP:AD 1|0:44:24,20 ./.:36:21,15 1|1:20:6,14 +chr20 614710 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=594161;QSTRAND=+ GT:DP:AD 1|0:45:25,20 ./.:34:18,16 1|1:15:6,9 +chr20 615045 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=569466;QSTRAND=+ GT:DP:AD 0|1:39:19,20 ./.:23:5,18 ./.:25:18,7 +chr20 615409 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=594860;QSTRAND=+ GT:DP:AD 1|0:18:5,13 ./.:28:6,22 1|1:28:7,21 +chr20 615455 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=569876;QSTRAND=+ GT:DP:AD 0|1:31:6,25 ./.:31:13,18 ./.:33:24,9 +chr20 615471 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=594922;QSTRAND=+ GT:DP:AD 1|1:16:7,9 ./.:32:7,25 1|1:27:17,10 +chr20 615863 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=570284;QSTRAND=+ GT:DP:AD 0|1:29:14,15 ./.:26:20,6 ./.:50:25,25 +chr20 616031 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=570452;QSTRAND=+ GT:DP:AD 0|1:32:16,16 ./.:44:20,24 ./.:35:19,16 +chr20 616321 . G GT 60 . QNAME=HG002-S9-H1-000001F;QSTART=595773;QSTRAND=+ GT:DP:AD 1|0:26:16,10 ./.:41:20,21 1|1:17:11,6 +chr20 616321 . G GTT 60 . QNAME=HG002-S9-H2-000001F;QSTART=570743;QSTRAND=+ GT:DP:AD 0|1:40:18,22 ./.:34:11,23 ./.:31:23,8 +chr20 616559 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=570982;QSTRAND=+ GT:DP:AD 0|1:28:17,11 ./.:36:11,25 ./.:34:24,10 +chr20 616743 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=571166;QSTRAND=+ GT:DP:AD 0|1:28:22,6 ./.:35:14,21 ./.:30:5,25 +chr20 617022 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=571445;QSTRAND=+ GT:DP:AD 0|1:24:9,15 ./.:31:21,10 ./.:23:10,13 +chr20 617094 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=596546;QSTRAND=+ GT:DP:AD 1|1:35:14,21 ./.:33:18,15 1|1:25:11,14 +chr20 617427 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=571850;QSTRAND=+ GT:DP:AD 0|1:34:11,23 ./.:26:6,20 ./.:10:5,5 +chr20 617634 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=597086;QSTRAND=+ GT:DP:AD 1|0:34:18,16 ./.:37:22,15 1|1:11:5,6 +chr20 617892 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=597344;QSTRAND=+ GT:DP:AD 1|1:25:13,12 ./.:22:16,6 1|1:27:8,19 +chr20 618050 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=597502;QSTRAND=+ GT:DP:AD 1|0:38:21,17 ./.:32:19,13 1|1:35:15,20 +chr20 618051 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=572474;QSTRAND=+ GT:DP:AD 0|1:42:20,22 ./.:20:10,10 ./.:39:18,21 +chr20 619223 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=573646;QSTRAND=+ GT:DP:AD 0|1:23:13,10 ./.:36:16,20 ./.:43:23,20 +chr20 620320 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=599772;QSTRAND=+ GT:DP:AD 1|1:46:24,22 ./.:32:9,23 1|1:33:20,13 +chr20 620391 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=599843;QSTRAND=+ GT:DP:AD 1|1:40:24,16 ./.:26:13,13 1|1:31:15,16 +chr20 621742 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=576165;QSTRAND=+ GT:DP:AD 0|1:38:25,13 ./.:41:22,19 ./.:29:10,19 +chr20 622380 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=601832;QSTRAND=+ GT:DP:AD 1|0:41:25,16 ./.:29:8,21 1|1:38:21,17 +chr20 622562 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=576985;QSTRAND=+ GT:DP:AD 0|1:26:5,21 ./.:10:5,5 ./.:26:8,18 +chr20 622615 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=602067;QSTRAND=+ GT:DP:AD 1|1:38:23,15 ./.:28:11,17 1|1:36:17,19 +chr20 622976 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=577399;QSTRAND=+ GT:DP:AD 0|1:25:18,7 ./.:11:5,6 0|1:23:13,10 +chr20 624131 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=578554;QSTRAND=+ GT:DP:AD 0|1:17:5,12 ./.:34:24,10 ./.:35:11,24 +chr20 624618 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=579041;QSTRAND=+ GT:DP:AD 0|1:31:23,8 ./.:37:14,23 ./.:41:16,25 +chr20 624679 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=604131;QSTRAND=+ GT:DP:AD 1|1:44:21,23 ./.:25:16,9 1|1:31:9,22 +chr20 625245 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=604697;QSTRAND=+ GT:DP:AD 1|0:39:19,20 ./.:30:16,14 1|1:44:24,20 +chr20 625293 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=604745;QSTRAND=+ GT:DP:AD 1|1:28:12,16 ./.:34:25,9 1|1:29:5,24 +chr20 626070 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=580493;QSTRAND=+ GT:DP:AD 0|1:18:10,8 1|1:36:12,24 ./.:38:20,18 +chr20 626301 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=605753;QSTRAND=+ GT:DP:AD 1|0:29:23,6 ./.:41:25,16 1|1:20:6,14 +chr20 626305 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=605757;QSTRAND=+ GT:DP:AD 1|0:43:22,21 ./.:25:7,18 1|1:28:5,23 +chr20 626441 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=605893;QSTRAND=+ GT:DP:AD 1|0:36:20,16 ./.:34:13,21 1|1:22:10,12 +chr20 626569 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=580992;QSTRAND=+ GT:DP:AD 0|1:34:23,11 ./.:37:16,21 ./.:32:23,9 +chr20 626821 . A AC 60 . QNAME=HG002-S9-H1-000001F;QSTART=606274;QSTRAND=+ GT:DP:AD 1|0:31:13,18 ./.:33:20,13 1|0:17:12,5 +chr20 626950 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=606403;QSTRAND=+ GT:DP:AD 1|0:34:19,15 ./.:44:20,24 1|0:36:13,23 +chr20 627161 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=606614;QSTRAND=+ GT:DP:AD 1|0:24:17,7 ./.:33:14,19 1|1:29:18,11 +chr20 627348 . A G 60 . QNAME=cluster19_000000F;QSTART=25134578;QSTRAND=- GT:DP:AD ./.:28:14,14 1|0:31:9,22 ./.:29:17,12 +chr20 628116 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=607569;QSTRAND=+ GT:DP:AD 1|0:32:25,7 ./.:19:7,12 1|0:31:6,25 +chr20 628203 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=607656;QSTRAND=+ GT:DP:AD 1|1:43:19,24 ./.:33:14,19 1|1:43:25,18 +chr20 628339 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=607792;QSTRAND=+ GT:DP:AD 1|1:30:24,6 ./.:40:22,18 1|1:37:22,15 +chr20 628481 . G C 60 . QNAME=cluster23_scaffold_2;QSTART=25066979;QSTRAND=- GT:DP:AD ./.:30:16,14 ./.:37:19,18 0|1:41:25,16 +chr20 628698 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=608151;QSTRAND=+ GT:DP:AD 1|0:26:12,14 ./.:31:15,16 1|0:41:17,24 +chr20 628723 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=608176;QSTRAND=+ GT:DP:AD 1|0:10:5,5 ./.:35:19,16 1|0:25:17,8 +chr20 628961 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=608414;QSTRAND=+ GT:DP:AD 1|0:26:11,15 ./.:31:18,13 1|1:17:11,6 +chr20 629302 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=608755;QSTRAND=+ GT:DP:AD 1|0:25:17,8 ./.:38:15,23 1|1:26:11,15 +chr20 629494 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=608947;QSTRAND=+ GT:DP:AD 1|0:25:19,6 ./.:27:19,8 ./.:32:16,16 +chr20 629610 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25065850;QSTRAND=- GT:DP:AD ./.:19:8,11 ./.:32:25,7 0|1:31:15,16 +chr20 629678 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=609131;QSTRAND=+ GT:DP:AD 1|0:36:20,16 ./.:23:5,18 1|1:42:19,23 +chr20 629911 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=609364;QSTRAND=+ GT:DP:AD 1|0:31:11,20 ./.:30:14,16 1|1:27:18,9 +chr20 629941 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=609394;QSTRAND=+ GT:DP:AD 1|0:34:13,21 ./.:27:15,12 1|1:21:15,6 +chr20 630017 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=609470;QSTRAND=+ GT:DP:AD 1|0:36:12,24 ./.:13:7,6 1|1:32:10,22 +chr20 630420 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=609873;QSTRAND=+ GT:DP:AD 1|0:17:11,6 ./.:37:14,23 ./.:27:21,6 +chr20 630708 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=610158;QSTRAND=+ GT:DP:AD 1|0:21:6,15 ./.:25:14,11 1|1:20:5,15 +chr20 631945 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=611395;QSTRAND=+ GT:DP:AD 1|0:40:25,15 ./.:43:19,24 ./.:28:8,20 +chr20 632007 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=611457;QSTRAND=+ GT:DP:AD 1|0:17:6,11 ./.:36:25,11 ./.:23:18,5 +chr20 632024 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=611474;QSTRAND=+ GT:DP:AD 1|0:21:14,7 ./.:23:15,8 ./.:33:11,22 +chr20 632038 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=611488;QSTRAND=+ GT:DP:AD 1|0:24:7,17 ./.:28:8,20 ./.:35:17,18 +chr20 632119 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=611569;QSTRAND=+ GT:DP:AD 1|0:37:19,18 ./.:33:25,8 ./.:31:15,16 +chr20 633319 . A G 60 . QNAME=cluster19_000000F;QSTART=25128607;QSTRAND=- GT:DP:AD ./.:24:12,12 1|0:26:14,12 0|1:17:9,8 +chr20 633850 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=613300;QSTRAND=+ GT:DP:AD 1|0:38:13,25 ./.:32:14,18 ./.:17:10,7 +chr20 634306 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=613756;QSTRAND=+ GT:DP:AD 1|0:23:16,7 ./.:33:22,11 ./.:37:13,24 +chr20 634343 . C T 60 . QNAME=cluster19_000000F;QSTART=25127583;QSTRAND=- GT:DP:AD ./.:24:6,18 1|0:26:16,10 0|1:27:21,6 +chr20 634367 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=613817;QSTRAND=+ GT:DP:AD 1|0:40:15,25 1|0:36:11,25 0|1:35:25,10 +chr20 634490 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=613940;QSTRAND=+ GT:DP:AD 1|0:46:24,22 ./.:44:19,25 ./.:23:18,5 +chr20 634534 . G A 60 . QNAME=cluster19_000000F;QSTART=25127392;QSTRAND=- GT:DP:AD ./.:25:12,13 1|0:31:15,16 0|1:28:15,13 +chr20 634915 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=614365;QSTRAND=+ GT:DP:AD 1|0:19:9,10 ./.:25:10,15 ./.:30:23,7 +chr20 637164 . T C 60 . QNAME=cluster19_000000F;QSTART=25124762;QSTRAND=- GT:DP:AD ./.:13:8,5 1|0:45:22,23 ./.:23:12,11 +chr20 637615 . T C 60 . QNAME=cluster19_000000F;QSTART=25124311;QSTRAND=- GT:DP:AD ./.:46:24,22 1|0:27:5,22 ./.:31:19,12 +chr20 638468 . T TA 60 . QNAME=cluster23_scaffold_3;QSTART=25072790;QSTRAND=- GT:DP:AD ./.:32:14,18 ./.:35:13,22 1|1:21:5,16 +chr20 638748 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=618198;QSTRAND=+ GT:DP:AD 1|0:26:20,6 1|0:23:10,13 ./.:39:16,23 +chr20 638918 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=618368;QSTRAND=+ GT:DP:AD 1|0:31:11,20 ./.:34:15,19 ./.:16:8,8 +chr20 639104 . A AT 60 . QNAME=HG002-S9-H1-000001F;QSTART=618555;QSTRAND=+ GT:DP:AD 1|0:35:12,23 ./.:18:9,9 1|1:35:18,17 +chr20 639255 . T C 60 . QNAME=cluster19_000000F;QSTART=25122672;QSTRAND=- GT:DP:AD ./.:39:24,15 1|0:33:16,17 ./.:15:9,6 +chr20 639552 . T C 60 . QNAME=cluster19_000000F;QSTART=25122375;QSTRAND=- GT:DP:AD ./.:10:5,5 1|0:28:22,6 0|1:33:13,20 +chr20 639866 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25055593;QSTRAND=- GT:DP:AD ./.:40:25,15 ./.:22:6,16 0|1:16:5,11 +chr20 640046 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=619497;QSTRAND=+ GT:DP:AD 1|0:10:5,5 ./.:33:15,18 ./.:32:22,10 +chr20 640049 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=619500;QSTRAND=+ GT:DP:AD 1|1:28:12,16 ./.:29:5,24 1|0:31:19,12 +chr20 640284 . T TC 60 . QNAME=cluster23_scaffold_2;QSTART=25055174;QSTRAND=- GT:DP:AD ./.:19:8,11 ./.:48:23,25 0|1:34:25,9 +chr20 641878 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621329;QSTRAND=+ GT:DP:AD 1|0:17:11,6 ./.:15:9,6 0|1:33:12,21 +chr20 641905 . T TG 60 . QNAME=cluster23_scaffold_3;QSTART=25069351;QSTRAND=- GT:DP:AD ./.:29:5,24 ./.:18:8,10 1|0:18:7,11 +chr20 641906 . G GGCGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCT 60 . QNAME=cluster23_scaffold_2;QSTART=25053389;QSTRAND=-;SVTYPE=INS;SVLEN=163 GT:DP:AD ./.:13:6,7 ./.:34:21,13 0/1:27:16,11 +chr20 641913 . G GGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGA 60 . QNAME=HG002-S9-H1-000001F;QSTART=621365;QSTRAND=+;SVTYPE=INS;SVLEN=66 GT:DP:AD 1/0:34:18,16 ./.:32:17,15 ./.:36:16,20 +chr20 641930 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25053365;QSTRAND=- GT:DP:AD ./.:33:16,17 ./.:15:6,9 0|1:27:13,14 +chr20 641970 . T TG 60 . QNAME=cluster23_scaffold_2;QSTART=25053324;QSTRAND=- GT:DP:AD ./.:30:14,16 ./.:26:16,10 0|1:31:12,19 +chr20 641977 . G T 60 . QNAME=cluster19_000000F;QSTART=25119950;QSTRAND=- GT:DP:AD ./.:34:16,18 1|0:24:7,17 ./.:28:20,8 +chr20 642037 . T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=621551;QSTRAND=+ GT:DP:AD 1|0:41:18,23 ./.:44:19,25 ./.:35:18,17 +chr20 642067 . T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=621582;QSTRAND=+ GT:DP:AD 1|0:25:9,16 ./.:38:22,16 ./.:27:21,6 +chr20 642068 . G GTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCC 60 . QNAME=cluster23_scaffold_2;QSTART=25053097;QSTRAND=-;SVTYPE=INS;SVLEN=129 GT:DP:AD ./.:34:24,10 ./.:30:19,11 0/1:18:11,7 +chr20 642069 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621584;QSTRAND=+ GT:DP:AD 1|0:33:20,13 ./.:15:10,5 ./.:27:19,8 +chr20 642076 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25053089;QSTRAND=- GT:DP:AD ./.:31:22,9 ./.:36:21,15 0|1:29:21,8 +chr20 642100 . T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=621616;QSTRAND=+ GT:DP:AD 1|0:30:22,8 ./.:39:21,18 ./.:45:25,20 +chr20 642123 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=621639;QSTRAND=+ GT:DP:AD 1|0:46:23,23 ./.:21:6,15 0|1:42:20,22 +chr20 642130 . T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=621647;QSTRAND=+ GT:DP:AD 1|0:34:15,19 ./.:16:8,8 ./.:23:8,15 +chr20 642132 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=25053033;QSTRAND=- GT:DP:AD ./.:13:6,7 ./.:30:7,23 0|1:35:13,22 +chr20 642207 . T TGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGG 60 . QNAME=HG002-S9-H2-000001F;QSTART=596630;QSTRAND=+;SVTYPE=INS;SVLEN=501 GT:DP:AD 0/1:27:12,15 ./.:20:10,10 ./.:22:17,5 +chr20 642207 . T TGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGG 60 . QNAME=cluster19_000000F;QSTART=602404;QSTRAND=+;SVTYPE=INS;SVLEN=630 GT:DP:AD ./.:28:16,12 0/1:27:13,14 ./.:24:18,6 +chr20 642230 . T TGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTG 60 . QNAME=cluster19_000000F;QSTART=25119065;QSTRAND=-;SVTYPE=INS;SVLEN=632 GT:DP:AD ./.:35:18,17 1/0:33:10,23 ./.:44:25,19 +chr20 642230 . T TG 60 . QNAME=cluster23_scaffold_3;QSTART=25069025;QSTRAND=- GT:DP:AD ./.:25:9,16 ./.:21:6,15 1|1:42:23,19 +chr20 642265 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621776;QSTRAND=+ GT:DP:AD 1|1:37:12,25 0|1:27:9,18 ./.:36:22,14 +chr20 642271 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=621782;QSTRAND=+ GT:DP:AD 1|0:34:25,9 ./.:27:11,16 ./.:40:24,16 +chr20 642271 . G GC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597195;QSTRAND=+ GT:DP:AD 0|1:17:6,11 1|1:22:17,5 0|1:22:17,5 +chr20 642271 . G GGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGC 60 . QNAME=cluster23_scaffold_3;QSTART=25068731;QSTRAND=-;SVTYPE=INS;SVLEN=257 GT:DP:AD ./.:36:19,17 ./.:28:5,23 1/0:27:18,9 +chr20 642277 . G A 60 . QNAME=cluster19_000000F;QSTART=603104;QSTRAND=+ GT:DP:AD ./.:25:6,19 0|1:46:25,21 ./.:25:18,7 +chr20 642284 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621795;QSTRAND=+ GT:DP:AD 1|1:16:5,11 1|1:24:8,16 1|1:25:16,9 +chr20 642300 . G GGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597225;QSTRAND=+ GT:DP:AD 0|1:27:11,16 0|1:40:18,22 1|1:15:6,9 +chr20 642300 . G GCCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGC 60 . QNAME=HG002-S9-H1-000001F;QSTART=621812;QSTRAND=+;SVTYPE=INS;SVLEN=408 GT:DP:AD 1/0:44:19,25 ./.:35:12,23 ./.:42:17,25 +chr20 642300 . G GC 60 . QNAME=cluster19_000000F;QSTART=25118993;QSTRAND=- GT:DP:AD ./.:31:7,24 1|0:45:25,20 ./.:37:25,12 +chr20 642330 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=622249;QSTRAND=+ GT:DP:AD 1|0:34:14,20 ./.:33:15,18 1|0:21:13,8 +chr20 642330 . G GGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597257;QSTRAND=+;SVTYPE=INS;SVLEN=66 GT:DP:AD 0/1:18:11,7 ./.:23:10,13 ./.:25:12,13 +chr20 642330 . G GC 60 . QNAME=cluster19_000000F;QSTART=25118962;QSTRAND=- GT:DP:AD ./.:30:14,16 1|1:45:20,25 ./.:24:18,6 +chr20 642330 . G GCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGGGC 60 . QNAME=cluster23_scaffold_2;QSTART=25052609;QSTRAND=-;SVTYPE=INS;SVLEN=226 GT:DP:AD ./.:41:21,20 ./.:28:9,19 0/1:18:12,6 +chr20 642353 . T G 60 . QNAME=cluster23_scaffold_2;QSTART=25052586;QSTRAND=- GT:DP:AD ./.:23:15,8 ./.:16:6,10 0|1:24:17,7 +chr20 642362 . G C 60 . QNAME=cluster23_scaffold_2;QSTART=25052577;QSTRAND=- GT:DP:AD ./.:48:24,24 ./.:26:12,14 0|1:12:7,5 +chr20 642362 . G GC 60 . QNAME=HG002-S9-H1-000001F;QSTART=622282;QSTRAND=+ GT:DP:AD 1|1:25:14,11 1|1:32:16,16 1|0:30:7,23 +chr20 642391 . G GC 60 . QNAME=HG002-S9-H1-000001F;QSTART=622312;QSTRAND=+ GT:DP:AD 1|1:27:9,18 1|1:16:9,7 0|1:20:15,5 +chr20 642391 . G GGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGGC 60 . QNAME=cluster23_scaffold_3;QSTART=25068286;QSTRAND=-;SVTYPE=INS;SVLEN=322 GT:DP:AD ./.:21:9,12 ./.:41:25,16 1/0:14:6,8 +chr20 642420 . G GC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597415;QSTRAND=+ GT:DP:AD 0|1:14:9,5 1|1:39:25,14 1|0:28:11,17 +chr20 642420 . G GGC 60 . QNAME=HG002-S9-H1-000001F;QSTART=622342;QSTRAND=+ GT:DP:AD 1|0:36:19,17 ./.:30:25,5 ./.:34:25,9 +chr20 642420 . G GGGC 60 . QNAME=cluster23_scaffold_2;QSTART=25052515;QSTRAND=- GT:DP:AD ./.:30:22,8 ./.:36:25,11 0|1:39:16,23 +chr20 642746 . C CGGGGTGCGGGT 60 . QNAME=cluster19_000000F;QSTART=603580;QSTRAND=+ GT:DP:AD ./.:43:22,21 0|1:42:23,19 ./.:20:13,7 +chr20 642746 . C CGGGGGTGCGGGT 60 . QNAME=cluster23_scaffold_2;QSTART=25052177;QSTRAND=- GT:DP:AD ./.:24:12,12 ./.:23:6,17 0|1:23:11,12 +chr20 642861 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=622784;QSTRAND=+ GT:DP:AD 1|0:50:25,25 ./.:32:14,18 ./.:33:22,11 +chr20 643742 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25051181;QSTRAND=- GT:DP:AD ./.:45:22,23 ./.:40:19,21 0|1:32:8,24 +chr20 643827 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=623747;QSTRAND=+ GT:DP:AD 1|0:30:24,6 ./.:47:23,24 ./.:38:15,23 +chr20 644129 . T A 60 . QNAME=cluster23_scaffold_2;QSTART=25050794;QSTRAND=- GT:DP:AD ./.:16:7,9 ./.:22:14,8 0|1:27:14,13 +chr20 644423 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=624343;QSTRAND=+ GT:DP:AD 1|0:33:20,13 ./.:30:25,5 ./.:37:12,25 +chr20 644731 . T TA 60 . QNAME=cluster23_scaffold_2;QSTART=25050192;QSTRAND=- GT:DP:AD ./.:25:13,12 ./.:27:18,9 0|1:26:20,6 +chr20 645244 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25049678;QSTRAND=- GT:DP:AD ./.:22:9,13 ./.:27:7,20 0|1:30:25,5 +chr20 645246 . A AT 60 . QNAME=HG002-S9-H1-000001F;QSTART=625167;QSTRAND=+ GT:DP:AD 1|0:41:19,22 ./.:36:22,14 ./.:26:6,20 +chr20 645378 . A AG 60 . QNAME=HG002-S9-H1-000001F;QSTART=625300;QSTRAND=+ GT:DP:AD 1|1:23:13,10 ./.:36:17,19 1|1:13:8,5 +chr20 645437 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=625359;QSTRAND=+ GT:DP:AD 1|0:26:12,14 ./.:18:8,10 1|0:12:7,5 +chr20 645520 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=625442;QSTRAND=+ GT:DP:AD 1|1:27:18,9 ./.:23:14,9 1|0:36:19,17 +chr20 645645 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=625567;QSTRAND=+ GT:DP:AD 1|0:15:9,6 ./.:31:20,11 ./.:33:18,15 +chr20 646133 . T TCTA 60 . QNAME=HG002-S9-H1-000001F;QSTART=626056;QSTRAND=+ GT:DP:AD 1|1:33:11,22 ./.:35:10,25 1|1:43:21,22 +chr20 646134 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=626059;QSTRAND=+ GT:DP:AD 1|1:25:13,12 ./.:18:9,9 1|1:22:15,7 +chr20 646331 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=626256;QSTRAND=+ GT:DP:AD 1|0:20:8,12 ./.:33:14,19 1|0:44:24,20 +chr20 646515 . C CAAAAAAAAAAAAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=626441;QSTRAND=+ GT:DP:AD 1|0:34:24,10 ./.:40:21,19 ./.:31:20,11 +chr20 646515 . C CAAAAAAAAAAAAAAAA 60 . QNAME=HG002-S9-H2-000001F;QSTART=601515;QSTRAND=+ GT:DP:AD 0|1:30:16,14 ./.:34:14,20 ./.:32:10,22 +chr20 646515 . C CA 60 . QNAME=cluster19_000000F;QSTART=25114773;QSTRAND=- GT:DP:AD ./.:33:21,12 1|0:16:6,10 ./.:35:18,17 +chr20 646515 . C CAAAAAAAAAAAAAAAAAA 60 . QNAME=cluster23_scaffold_3;QSTART=25064139;QSTRAND=- GT:DP:AD ./.:34:14,20 ./.:44:21,23 1|1:31:12,19 +chr20 646526 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=626468;QSTRAND=+ GT:DP:AD 1|0:30:11,19 ./.:31:6,25 1|0:21:10,11 +chr20 646770 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25048130;QSTRAND=- GT:DP:AD ./.:29:6,23 ./.:36:18,18 0|1:25:9,16 +chr20 648246 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=628188;QSTRAND=+ GT:DP:AD 1|1:32:24,8 ./.:18:10,8 1|0:27:14,13 +chr20 648569 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=628511;QSTRAND=+ GT:DP:AD 1|1:40:22,18 ./.:26:17,9 1|0:29:19,10 +chr20 649005 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=628947;QSTRAND=+ GT:DP:AD 1|0:28:12,16 ./.:31:8,23 1|0:25:17,8 +chr20 649182 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=604196;QSTRAND=+ GT:DP:AD 0|1:30:10,20 ./.:31:8,23 ./.:28:18,10 +chr20 649716 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=604730;QSTRAND=+ GT:DP:AD 0|1:38:23,15 ./.:13:8,5 ./.:45:24,21 +chr20 649983 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=629923;QSTRAND=+ GT:DP:AD 1|0:39:14,25 ./.:27:19,8 1|0:37:15,22 +chr20 650241 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25044659;QSTRAND=- GT:DP:AD ./.:28:16,12 ./.:19:9,10 0|1:30:15,15 +chr20 650254 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=605268;QSTRAND=+ GT:DP:AD 0|1:32:22,10 ./.:34:14,20 0|1:17:5,12 +chr20 650326 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=630266;QSTRAND=+ GT:DP:AD 1|1:17:8,9 ./.:25:10,15 1|1:29:16,13 +chr20 650473 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=630413;QSTRAND=+ GT:DP:AD 1|0:17:8,9 ./.:30:11,19 1|0:26:20,6 +chr20 650495 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25044405;QSTRAND=- GT:DP:AD ./.:41:18,23 ./.:22:9,13 0|1:48:24,24 +chr20 650525 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=605539;QSTRAND=+ GT:DP:AD 0|1:24:12,12 ./.:27:16,11 ./.:38:15,23 +chr20 650651 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=605665;QSTRAND=+ GT:DP:AD 0|1:19:8,11 ./.:20:7,13 ./.:30:21,9 +chr20 650723 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=605737;QSTRAND=+ GT:DP:AD 0|1:36:17,19 ./.:26:9,17 ./.:20:11,9 +chr20 650781 . C A 60 . QNAME=cluster19_000000F;QSTART=25110507;QSTRAND=- GT:DP:AD ./.:12:6,6 1|0:30:7,23 ./.:22:5,17 +chr20 651264 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=631204;QSTRAND=+ GT:DP:AD 1|1:33:12,21 ./.:27:21,6 1|1:32:15,17 +chr20 651860 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=606874;QSTRAND=+ GT:DP:AD 0|1:23:13,10 ./.:38:19,19 0|1:41:18,23 +chr20 651923 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=25042977;QSTRAND=- GT:DP:AD ./.:31:25,6 ./.:11:6,5 0|1:38:14,24 +chr20 652315 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=632254;QSTRAND=+ GT:DP:AD 1|0:28:16,12 ./.:31:13,18 1|1:39:25,14 +chr20 652505 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=632444;QSTRAND=+ GT:DP:AD 1|0:38:14,24 ./.:32:21,11 1|1:29:23,6 +chr20 653265 . G GT 60 . QNAME=cluster23_scaffold_2;QSTART=25041634;QSTRAND=- GT:DP:AD ./.:41:18,23 ./.:26:10,16 0|1:41:21,20 +chr20 653266 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=25041633;QSTRAND=- GT:DP:AD ./.:30:8,22 ./.:21:10,11 0|1:22:8,14 +chr20 653324 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=633245;QSTRAND=+ GT:DP:AD 1|0:33:10,23 ./.:33:8,25 1|1:32:19,13 +chr20 653378 . C T 60 . QNAME=cluster19_000000F;QSTART=25107910;QSTRAND=- GT:DP:AD ./.:19:6,13 1|0:29:21,8 0|1:25:10,15 +chr20 653790 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=633711;QSTRAND=+ GT:DP:AD 1|1:37:13,24 ./.:19:12,7 1|0:22:12,10 +chr20 653820 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=633741;QSTRAND=+ GT:DP:AD 1|1:34:12,22 ./.:25:19,6 ./.:34:25,9 +chr20 653977 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=608974;QSTRAND=+ GT:DP:AD 0|1:19:14,5 ./.:13:5,8 ./.:24:17,7 +chr20 654666 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=609663;QSTRAND=+ GT:DP:AD 0|1:19:12,7 ./.:28:7,21 ./.:42:21,21 +chr20 655173 . C CAGAAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=635095;QSTRAND=+ GT:DP:AD 1|1:26:19,7 1|1:21:7,14 1|1:30:19,11 +chr20 656194 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=636124;QSTRAND=+ GT:DP:AD 1|0:38:22,16 ./.:37:19,18 ./.:22:15,7 +chr20 658219 . G A 60 . QNAME=cluster19_000000F;QSTART=25103060;QSTRAND=- GT:DP:AD ./.:29:16,13 1|0:42:23,19 1|0:43:23,20 +chr20 658277 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=613283;QSTRAND=+ GT:DP:AD 0|1:17:7,10 ./.:32:19,13 ./.:29:10,19 +chr20 659380 . T TGGAG 60 . QNAME=HG002-S9-H2-000001F;QSTART=614387;QSTRAND=+ GT:DP:AD 0|1:18:10,8 ./.:27:19,8 ./.:38:13,25 +chr20 659768 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=639698;QSTRAND=+ GT:DP:AD 1|0:40:21,19 ./.:45:20,25 ./.:15:10,5 +chr20 659929 . C T 60 . QNAME=cluster19_000000F;QSTART=25101350;QSTRAND=- GT:DP:AD ./.:19:7,12 1|0:36:17,19 1|0:26:16,10 +chr20 660098 . C A 60 . QNAME=cluster19_000000F;QSTART=620951;QSTRAND=+ GT:DP:AD ./.:47:23,24 0|1:12:6,6 ./.:21:11,10 +chr20 660145 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=640075;QSTRAND=+ GT:DP:AD 1|1:35:13,22 1|1:22:13,9 1|0:17:11,6 +chr20 660346 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=640276;QSTRAND=+ GT:DP:AD 1|0:35:15,20 0|1:34:10,24 ./.:20:14,6 +chr20 660450 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25050195;QSTRAND=- GT:DP:AD ./.:28:10,18 ./.:35:16,19 1|0:32:13,19 +chr20 660628 . C CAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=640559;QSTRAND=+ GT:DP:AD 1|0:44:20,24 ./.:23:7,16 ./.:21:12,9 +chr20 660628 . C CA 60 . QNAME=cluster19_000000F;QSTART=621482;QSTRAND=+ GT:DP:AD ./.:33:19,14 0|1:29:19,10 ./.:14:6,8 +chr20 660640 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=640572;QSTRAND=+ GT:DP:AD 1|1:33:25,8 0|1:21:14,7 ./.:28:20,8 +chr20 660909 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=615919;QSTRAND=+ GT:DP:AD 0|1:16:7,9 ./.:33:25,8 ./.:38:16,22 +chr20 661249 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=641181;QSTRAND=+ GT:DP:AD 1|1:29:11,18 1|1:15:9,6 1|0:49:25,24 +chr20 662494 . C CG 60 . QNAME=cluster23_scaffold_2;QSTART=25032395;QSTRAND=- GT:DP:AD ./.:36:18,18 ./.:32:14,18 0|1:31:10,21 +chr20 663033 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=642965;QSTRAND=+ GT:DP:AD 1|0:26:20,6 0|1:29:22,7 1|1:31:6,25 +chr20 663218 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25047427;QSTRAND=- GT:DP:AD ./.:29:20,9 ./.:29:24,5 1|0:42:24,18 +chr20 663275 . T C 60 . QNAME=cluster19_000000F;QSTART=624129;QSTRAND=+ GT:DP:AD ./.:28:6,22 0|1:43:18,25 0|1:36:16,20 +chr20 663449 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25047196;QSTRAND=- GT:DP:AD ./.:39:17,22 ./.:20:8,12 1|0:47:24,23 +chr20 663558 . A C 60 . QNAME=cluster19_000000F;QSTART=624412;QSTRAND=+ GT:DP:AD ./.:21:16,5 0|1:23:6,17 ./.:11:6,5 +chr20 664220 . G GC 60 . QNAME=cluster23_scaffold_2;QSTART=25030668;QSTRAND=- GT:DP:AD ./.:10:5,5 ./.:42:17,25 0|1:21:10,11 +chr20 665209 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=645141;QSTRAND=+ GT:DP:AD 1|1:35:21,14 1|1:26:13,13 1|1:32:8,24 +chr20 665270 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=645202;QSTRAND=+ GT:DP:AD 1|0:35:17,18 ./.:34:23,11 ./.:33:23,10 +chr20 665483 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=645415;QSTRAND=+ GT:DP:AD 1|1:12:7,5 1|1:22:12,10 0|1:26:14,12 +chr20 666690 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=646622;QSTRAND=+ GT:DP:AD 1|0:22:11,11 ./.:38:14,24 ./.:37:25,12 +chr20 667092 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=647024;QSTRAND=+ GT:DP:AD 1|1:31:15,16 1|1:27:7,20 1|1:29:23,6 +chr20 667181 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=647113;QSTRAND=+ GT:DP:AD 1|0:29:14,15 ./.:40:21,19 ./.:45:20,25 +chr20 667787 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=647719;QSTRAND=+ GT:DP:AD 1|0:24:19,5 ./.:29:9,20 ./.:18:7,11 +chr20 668165 . A ATTG 60 . QNAME=HG002-S9-H1-000001F;QSTART=648098;QSTRAND=+ GT:DP:AD 1|0:44:25,19 ./.:22:7,15 1|1:37:13,24 +chr20 668172 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=648107;QSTRAND=+ GT:DP:AD 1|0:27:12,15 ./.:24:12,12 1|1:30:19,11 +chr20 668176 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=648111;QSTRAND=+ GT:DP:AD 1|0:18:13,5 ./.:46:22,24 1|1:40:17,23 +chr20 668345 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=648280;QSTRAND=+ GT:DP:AD 1|0:42:17,25 ./.:25:5,20 1|1:27:22,5 +chr20 669291 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=649226;QSTRAND=+ GT:DP:AD 1|0:21:10,11 ./.:18:11,7 1|1:19:14,5 +chr20 670996 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=650931;QSTRAND=+ GT:DP:AD 1|0:37:20,17 ./.:37:22,15 1|1:30:19,11 +chr20 671453 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=651388;QSTRAND=+ GT:DP:AD 1|0:33:18,15 ./.:14:5,9 1|1:31:9,22 +chr20 671595 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=651530;QSTRAND=+ GT:DP:AD 1|0:34:22,12 ./.:36:17,19 1|1:25:9,16 +chr20 672290 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=652225;QSTRAND=+ GT:DP:AD 1|0:35:19,16 ./.:50:25,25 1|1:32:25,7 +chr20 672422 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=652355;QSTRAND=+ GT:DP:AD 1|0:48:24,24 ./.:19:10,9 1|1:34:10,24 +chr20 672619 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=652552;QSTRAND=+ GT:DP:AD 1|0:31:19,12 ./.:27:7,20 1|1:38:18,20 +chr20 673008 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=652941;QSTRAND=+ GT:DP:AD 1|0:40:21,19 ./.:32:22,10 1|1:20:14,6 +chr20 673547 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=653480;QSTRAND=+ GT:DP:AD 1|0:24:9,15 ./.:37:20,17 1|1:42:22,20 +chr20 674405 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=654334;QSTRAND=+ GT:DP:AD 1|0:26:12,14 ./.:40:18,22 0|1:28:14,14 +chr20 674407 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=654336;QSTRAND=+ GT:DP:AD 1|0:18:9,9 ./.:34:18,16 1|1:26:10,16 +chr20 674409 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=654338;QSTRAND=+ GT:DP:AD 1|0:21:14,7 ./.:42:18,24 1|1:39:18,21 +chr20 674411 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=654340;QSTRAND=+ GT:DP:AD 1|0:48:24,24 ./.:25:19,6 1|1:34:17,17 +chr20 674413 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=654342;QSTRAND=+ GT:DP:AD 1|0:22:12,10 ./.:24:17,7 1|0:38:14,24 +chr20 674688 . A AGT 60 . QNAME=HG002-S9-H2-000001F;QSTART=629699;QSTRAND=+ GT:DP:AD 0|1:37:20,17 1|1:37:23,14 ./.:36:11,25 +chr20 675537 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25019374;QSTRAND=- GT:DP:AD ./.:29:16,13 ./.:20:6,14 0|1:21:7,14 +chr20 675763 . T TGGC 60 . QNAME=cluster19_000000F;QSTART=25085511;QSTRAND=- GT:DP:AD ./.:16:11,5 1|1:40:21,19 ./.:23:15,8 +chr20 676166 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=656075;QSTRAND=+ GT:DP:AD 1|0:19:10,9 ./.:39:17,22 1|1:31:23,8 +chr20 676254 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25034416;QSTRAND=- GT:DP:AD ./.:20:5,15 ./.:35:21,14 1|1:19:11,8 +chr20 677116 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25033554;QSTRAND=- GT:DP:AD ./.:16:10,6 ./.:34:12,22 1|1:34:13,21 +chr20 677219 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=632231;QSTRAND=+ GT:DP:AD 0|1:40:20,20 ./.:20:11,9 1|1:27:20,7 +chr20 677478 . G A 60 . QNAME=cluster19_000000F;QSTART=638336;QSTRAND=+ GT:DP:AD ./.:33:17,16 0|1:27:6,21 ./.:16:8,8 +chr20 677582 . A AAATAATAAT 60 . QNAME=HG002-S9-H2-000001F;QSTART=632593;QSTRAND=+ GT:DP:AD 0|1:24:14,10 ./.:29:18,11 ./.:20:9,11 +chr20 677689 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25032982;QSTRAND=- GT:DP:AD ./.:14:9,5 ./.:26:7,19 1|1:35:25,10 +chr20 677734 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25032937;QSTRAND=- GT:DP:AD ./.:43:20,23 ./.:38:14,24 1|1:28:6,22 +chr20 677799 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=25032872;QSTRAND=- GT:DP:AD ./.:37:17,20 ./.:32:19,13 1|1:43:24,19 +chr20 677892 . A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25032778;QSTRAND=- GT:DP:AD ./.:20:7,13 ./.:27:8,19 1|1:17:12,5 +chr20 678014 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25032656;QSTRAND=- GT:DP:AD ./.:28:11,17 ./.:45:25,20 1|1:29:14,15 +chr20 678015 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25032655;QSTRAND=- GT:DP:AD ./.:18:9,9 ./.:28:16,12 1|1:18:10,8 +chr20 678191 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=658098;QSTRAND=+ GT:DP:AD 1|1:34:15,19 1|1:47:22,25 1|1:27:11,16 +chr20 678230 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=633249;QSTRAND=+ GT:DP:AD 0|1:23:16,7 ./.:26:16,10 1|1:30:6,24 +chr20 678305 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=633324;QSTRAND=+ GT:DP:AD 0|1:32:8,24 ./.:18:8,10 ./.:18:6,12 +chr20 678433 . C G 60 . QNAME=cluster23_scaffold_3;QSTART=25032237;QSTRAND=- GT:DP:AD ./.:31:11,20 ./.:41:23,18 1|1:39:22,17 +chr20 678642 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25032028;QSTRAND=- GT:DP:AD ./.:38:13,25 ./.:37:24,13 1|1:23:17,6 +chr20 678678 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25031992;QSTRAND=- GT:DP:AD ./.:31:16,15 ./.:28:5,23 1|1:12:6,6 +chr20 678706 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25031964;QSTRAND=- GT:DP:AD ./.:24:18,6 ./.:34:15,19 1|1:19:7,12 +chr20 678778 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25031892;QSTRAND=- GT:DP:AD ./.:13:6,7 ./.:16:8,8 1|1:23:9,14 +chr20 678797 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25031873;QSTRAND=- GT:DP:AD ./.:30:22,8 ./.:44:20,24 1|1:31:13,18 +chr20 678839 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=633858;QSTRAND=+ GT:DP:AD 0|1:31:23,8 ./.:29:24,5 1|1:27:13,14 +chr20 679151 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25031519;QSTRAND=- GT:DP:AD ./.:41:20,21 ./.:37:20,17 1|1:48:24,24 +chr20 679482 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=634501;QSTRAND=+ GT:DP:AD 0|1:11:6,5 ./.:30:5,25 1|1:31:13,18 +chr20 679483 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=634502;QSTRAND=+ GT:DP:AD 0|1:15:5,10 ./.:34:9,25 1|1:34:14,20 +chr20 680009 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25030661;QSTRAND=- GT:DP:AD ./.:29:7,22 ./.:25:5,20 1|1:24:5,19 +chr20 680029 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25030641;QSTRAND=- GT:DP:AD ./.:33:8,25 ./.:33:10,23 1|1:21:5,16 +chr20 680047 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=635066;QSTRAND=+ GT:DP:AD 0|1:18:13,5 ./.:26:19,7 ./.:26:5,21 +chr20 680149 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25030521;QSTRAND=- GT:DP:AD ./.:34:12,22 ./.:45:21,24 1|1:28:8,20 +chr20 680216 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25014695;QSTRAND=- GT:DP:AD ./.:41:25,16 ./.:21:5,16 0|1:27:20,7 +chr20 680257 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25030413;QSTRAND=- GT:DP:AD ./.:28:16,12 ./.:34:20,14 1|1:44:20,24 +chr20 680491 . G GA 60 . QNAME=cluster23_scaffold_3;QSTART=25030178;QSTRAND=- GT:DP:AD ./.:38:15,23 ./.:45:24,21 1|1:24:5,19 +chr20 680625 . T A 60 . QNAME=cluster23_scaffold_3;QSTART=25030044;QSTRAND=- GT:DP:AD ./.:32:14,18 ./.:27:16,11 1|1:17:10,7 +chr20 680841 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25029828;QSTRAND=- GT:DP:AD ./.:37:24,13 ./.:25:11,14 1|1:44:24,20 +chr20 681789 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25028880;QSTRAND=- GT:DP:AD ./.:24:11,13 ./.:24:6,18 1|1:29:15,14 +chr20 681958 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25028711;QSTRAND=- GT:DP:AD ./.:25:16,9 ./.:26:15,11 1|1:27:15,12 +chr20 682463 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=637482;QSTRAND=+ GT:DP:AD 0|1:48:24,24 ./.:45:25,20 1|1:34:18,16 +chr20 682684 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25027985;QSTRAND=- GT:DP:AD ./.:15:10,5 ./.:25:16,9 1|1:26:6,20 +chr20 683486 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25027183;QSTRAND=- GT:DP:AD ./.:27:22,5 ./.:37:20,17 1|1:34:15,19 +chr20 683498 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=638517;QSTRAND=+ GT:DP:AD 0|1:38:19,19 0|1:43:18,25 1|1:16:6,10 +chr20 683582 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25027087;QSTRAND=- GT:DP:AD ./.:26:12,14 ./.:15:7,8 1|1:41:21,20 +chr20 684734 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=639753;QSTRAND=+ GT:DP:AD 0|1:22:7,15 ./.:24:14,10 1|1:42:22,20 +chr20 684907 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=639926;QSTRAND=+ GT:DP:AD 0|1:22:13,9 ./.:33:20,13 ./.:24:13,11 +chr20 685089 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25025580;QSTRAND=- GT:DP:AD ./.:29:23,6 ./.:20:13,7 1|1:34:12,22 +chr20 685645 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25025024;QSTRAND=- GT:DP:AD ./.:32:8,24 ./.:26:18,8 1|1:22:13,9 +chr20 686394 . C T 60 . QNAME=cluster19_000000F;QSTART=25074886;QSTRAND=- GT:DP:AD ./.:29:9,20 1|0:36:22,14 ./.:35:19,16 +chr20 686439 . C CAAAAAAAAAAAAAA 60 . QNAME=HG002-S9-H2-000001F;QSTART=641447;QSTRAND=+ GT:DP:AD 0|1:25:10,15 ./.:31:18,13 ./.:37:18,19 +chr20 686455 . A AAAAAAAAAAAAAAAAAAAAAAAAAAT 60 . QNAME=cluster23_scaffold_3;QSTART=25024197;QSTRAND=-;SVTYPE=INS;SVLEN=26 GT:DP:AD ./.:33:22,11 ./.:29:7,22 1/0:41:25,16 +chr20 686455 . A AAAAAAAAAAAAAAAAAAAAAAAAAT 60 . QNAME=cluster23_scaffold_2;QSTART=25008439;QSTRAND=-;SVTYPE=INS;SVLEN=25 GT:DP:AD ./.:31:13,18 ./.:34:16,18 0/1:16:5,11 +chr20 686794 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=641815;QSTRAND=+ GT:DP:AD 0|1:34:23,11 0|1:29:22,7 1|1:34:11,23 +chr20 687380 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=642401;QSTRAND=+ GT:DP:AD 0|1:16:11,5 ./.:23:6,17 ./.:43:19,24 +chr20 687915 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=667816;QSTRAND=+ GT:DP:AD 1|1:14:7,7 1|1:41:20,21 ./.:27:13,14 +chr20 688002 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=667903;QSTRAND=+ GT:DP:AD 1|1:39:20,19 1|1:21:15,6 ./.:37:15,22 +chr20 688657 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25006237;QSTRAND=- GT:DP:AD ./.:16:11,5 ./.:22:7,15 0|1:37:16,21 +chr20 688666 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=25006228;QSTRAND=- GT:DP:AD ./.:33:12,21 ./.:33:24,9 0|1:42:19,23 +chr20 689007 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=668908;QSTRAND=+ GT:DP:AD 1|0:23:13,10 1|1:43:18,25 0|1:37:20,17 +chr20 689613 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=669514;QSTRAND=+ GT:DP:AD 1|0:34:17,17 1|1:45:22,23 0|1:22:7,15 +chr20 689671 . G A 60 . QNAME=cluster19_000000F;QSTART=650517;QSTRAND=+ GT:DP:AD ./.:24:16,8 0|1:31:22,9 ./.:26:10,16 +chr20 690105 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=670006;QSTRAND=+ GT:DP:AD 1|0:27:17,10 1|1:40:18,22 0|1:39:15,24 +chr20 690819 . A AGT 60 . QNAME=HG002-S9-H2-000001F;QSTART=645841;QSTRAND=+ GT:DP:AD 0|1:23:7,16 ./.:20:13,7 1|0:30:14,16 +chr20 690853 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=670750;QSTRAND=+ GT:DP:AD 1|0:30:12,18 1|1:35:18,17 ./.:40:19,21 +chr20 690931 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25003967;QSTRAND=- GT:DP:AD ./.:47:25,22 ./.:29:6,23 0|1:26:10,16 +chr20 690947 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=670844;QSTRAND=+ GT:DP:AD 1|0:34:16,18 1|1:21:7,14 ./.:21:6,15 +chr20 691419 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25003479;QSTRAND=- GT:DP:AD ./.:31:7,24 ./.:27:7,20 0|1:42:25,17 +chr20 691923 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=671820;QSTRAND=+ GT:DP:AD 1|0:32:18,14 0|1:41:17,24 ./.:26:17,9 +chr20 692698 . C CTT 60 . QNAME=HG002-S9-H1-000001F;QSTART=672596;QSTRAND=+ GT:DP:AD 1|0:26:20,6 0|1:31:22,9 ./.:30:16,14 +chr20 692996 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=672895;QSTRAND=+ GT:DP:AD 1|0:23:15,8 1|1:23:8,15 0|1:33:24,9 +chr20 693104 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=673003;QSTRAND=+ GT:DP:AD 1|0:19:12,7 1|1:28:22,6 0|1:26:6,20 +chr20 693463 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=673362;QSTRAND=+ GT:DP:AD 1|0:18:11,7 1|1:41:22,19 0|1:30:21,9 +chr20 694203 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=649226;QSTRAND=+ GT:DP:AD 0|1:41:16,25 ./.:34:25,9 ./.:31:19,12 +chr20 694318 . A G 60 . QNAME=cluster19_000000F;QSTART=25066966;QSTRAND=- GT:DP:AD ./.:11:5,6 1|0:48:25,23 0|1:19:7,12 +chr20 694678 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=674577;QSTRAND=+ GT:DP:AD 1|0:37:20,17 0|1:43:19,24 ./.:41:19,22 +chr20 695001 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=674900;QSTRAND=+ GT:DP:AD 1|0:41:21,20 1|1:35:20,15 0|1:21:15,6 +chr20 695004 . G C 60 . QNAME=cluster19_000000F;QSTART=25066280;QSTRAND=- GT:DP:AD ./.:26:14,12 1|0:33:10,23 0|1:35:19,16 +chr20 695155 . G GTA 60 . QNAME=cluster19_000000F;QSTART=656000;QSTRAND=+ GT:DP:AD ./.:37:23,14 0|1:43:24,19 ./.:47:24,23 +chr20 695259 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=675158;QSTRAND=+ GT:DP:AD 1|0:18:12,6 1|1:37:17,20 0|1:35:10,25 +chr20 695798 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=675697;QSTRAND=+ GT:DP:AD 1|0:13:5,8 0|1:24:19,5 ./.:42:23,19 +chr20 695931 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=675830;QSTRAND=+ GT:DP:AD 1|0:23:16,7 1|1:27:14,13 0|1:35:11,24 +chr20 696160 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=676059;QSTRAND=+ GT:DP:AD 1|0:35:10,25 0|1:29:13,16 ./.:16:6,10 +chr20 697221 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=677120;QSTRAND=+ GT:DP:AD 1|0:29:20,9 0|1:32:17,15 ./.:42:20,22 +chr20 697409 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=677308;QSTRAND=+ GT:DP:AD 1|0:45:24,21 0|1:19:12,7 ./.:18:13,5 +chr20 697409 . G T 60 . QNAME=cluster19_000000F;QSTART=25063875;QSTRAND=- GT:DP:AD ./.:21:6,15 1|0:25:12,13 0|1:41:19,22 +chr20 697934 . C G 60 . QNAME=cluster19_000000F;QSTART=25063350;QSTRAND=- GT:DP:AD ./.:26:21,5 1|0:22:13,9 0|1:26:10,16 +chr20 698083 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=677982;QSTRAND=+ GT:DP:AD 1|0:15:5,10 ./.:30:5,25 ./.:39:18,21 +chr20 698123 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=678022;QSTRAND=+ GT:DP:AD 1|0:20:9,11 1|1:27:8,19 0|1:49:25,24 +chr20 698533 . C T 60 . QNAME=cluster19_000000F;QSTART=659379;QSTRAND=+ GT:DP:AD ./.:35:21,14 0|1:22:13,9 ./.:19:14,5 +chr20 698627 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=653650;QSTRAND=+ GT:DP:AD 0|1:33:11,22 1|0:33:24,9 0|1:32:8,24 +chr20 698723 . G A 60 . QNAME=cluster19_000000F;QSTART=25062561;QSTRAND=- GT:DP:AD ./.:46:25,21 1|0:28:21,7 0|1:28:16,12 +chr20 699085 . C T 60 . QNAME=cluster19_000000F;QSTART=25062199;QSTRAND=- GT:DP:AD ./.:41:22,19 1|0:30:25,5 0|1:38:21,17 +chr20 699214 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25011435;QSTRAND=- GT:DP:AD ./.:30:25,5 ./.:30:12,18 1|0:19:12,7 +chr20 700520 . C T 60 . QNAME=cluster19_000000F;QSTART=25060764;QSTRAND=- GT:DP:AD ./.:24:10,14 1|0:31:8,23 0|1:23:6,17 +chr20 700649 . C CT 60 . QNAME=cluster19_000000F;QSTART=25060634;QSTRAND=- GT:DP:AD ./.:23:15,8 1|0:29:14,15 0|1:34:10,24 +chr20 701307 . A G 60 . QNAME=cluster19_000000F;QSTART=25059976;QSTRAND=- GT:DP:AD ./.:24:18,6 1|0:20:10,10 0|1:16:6,10 +chr20 701558 . C T 60 . QNAME=cluster19_000000F;QSTART=25059725;QSTRAND=- GT:DP:AD ./.:48:23,25 1|0:26:18,8 0|1:17:12,5 +chr20 702627 . G A 60 . QNAME=cluster19_000000F;QSTART=25058656;QSTRAND=- GT:DP:AD ./.:45:23,22 1|0:42:22,20 0|1:46:23,23 +chr20 702901 . T C 60 . QNAME=cluster19_000000F;QSTART=25058382;QSTRAND=- GT:DP:AD ./.:17:8,9 1|0:28:9,19 0|1:19:6,13 +chr20 702972 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=682868;QSTRAND=+ GT:DP:AD 1|0:33:10,23 0|1:30:7,23 ./.:20:12,8 +chr20 704472 . A G 60 . QNAME=cluster19_000000F;QSTART=25056811;QSTRAND=- GT:DP:AD ./.:39:17,22 1|0:19:10,9 0|1:24:17,7 +chr20 704662 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=659683;QSTRAND=+ GT:DP:AD 0|1:26:18,8 ./.:35:23,12 ./.:27:10,17 +chr20 704704 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=684600;QSTRAND=+ GT:DP:AD 1|0:32:10,22 1|1:27:9,18 1|0:34:14,20 +chr20 705070 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=684966;QSTRAND=+ GT:DP:AD 1|0:20:12,8 1|1:33:15,18 ./.:39:22,17 +chr20 705212 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=660233;QSTRAND=+ GT:DP:AD 0|1:23:12,11 ./.:39:17,22 1|0:27:9,18 +chr20 705650 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=685546;QSTRAND=+ GT:DP:AD 1|0:40:24,16 1|0:41:21,20 ./.:49:24,25 +chr20 706757 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=661778;QSTRAND=+ GT:DP:AD 0|1:22:13,9 ./.:45:25,20 1|0:20:10,10 +chr20 707000 . T TAA 60 . QNAME=cluster23_scaffold_2;QSTART=24987895;QSTRAND=- GT:DP:AD ./.:44:24,20 ./.:33:8,25 0|1:21:8,13 +chr20 707128 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=687024;QSTRAND=+ GT:DP:AD 1|1:32:10,22 1|0:40:16,24 1|1:19:5,14 +chr20 707704 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=662725;QSTRAND=+ GT:DP:AD 0|1:33:8,25 ./.:24:12,12 1|0:26:21,5 +chr20 708199 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=688095;QSTRAND=+ GT:DP:AD 1|0:29:22,7 1|0:26:11,15 0|1:48:24,24 +chr20 708250 . C CTTTTGT 60 . QNAME=cluster19_000000F;QSTART=669097;QSTRAND=+ GT:DP:AD ./.:38:18,20 0|1:40:21,19 ./.:31:21,10 +chr20 708422 . A ATT 60 . QNAME=HG002-S9-H2-000001F;QSTART=663444;QSTRAND=+ GT:DP:AD 0|1:31:14,17 ./.:17:11,6 1|0:18:11,7 +chr20 708747 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=688642;QSTRAND=+ GT:DP:AD 1|0:37:12,25 1|0:21:10,11 ./.:23:13,10 +chr20 708784 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=688679;QSTRAND=+ GT:DP:AD 1|0:37:24,13 1|0:13:5,8 ./.:22:16,6 +chr20 709830 . G GACACTGCTCGGTCCTCCGCTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCGCTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGAACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGA 60 . QNAME=HG002-S9-H1-000001F;QSTART=689726;QSTRAND=+;SVTYPE=INS;SVLEN=465 GT:DP:AD 1/0:41:16,25 ./.:30:18,12 ./.:21:10,11 +chr20 709916 . T TG 60 . QNAME=cluster19_000000F;QSTART=670769;QSTRAND=+ GT:DP:AD ./.:37:21,16 0|1:33:16,17 ./.:18:10,8 +chr20 710119 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24984870;QSTRAND=- GT:DP:AD ./.:45:23,22 ./.:20:10,10 0|1:21:12,9 +chr20 710584 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24984405;QSTRAND=- GT:DP:AD ./.:42:24,18 ./.:15:10,5 0|1:18:6,12 +chr20 710789 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=691149;QSTRAND=+ GT:DP:AD 1|0:39:24,15 1|1:26:15,11 1|1:30:10,20 +chr20 710948 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=691308;QSTRAND=+ GT:DP:AD 1|0:29:13,16 0|1:44:25,19 1|0:15:5,10 +chr20 711068 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24983921;QSTRAND=- GT:DP:AD ./.:37:17,20 ./.:46:22,24 0|1:41:18,23 +chr20 711120 . G GGT 60 . QNAME=HG002-S9-H2-000001F;QSTART=666051;QSTRAND=+ GT:DP:AD 0|1:26:10,16 ./.:32:11,21 ./.:26:18,8 +chr20 711120 . G GGTGT 60 . QNAME=cluster23_scaffold_2;QSTART=24983865;QSTRAND=- GT:DP:AD ./.:41:16,25 ./.:35:19,16 0|1:33:9,24 +chr20 711177 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=691537;QSTRAND=+ GT:DP:AD 1|0:41:21,20 1|1:38:19,19 1|1:28:19,9 +chr20 711562 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=691922;QSTRAND=+ GT:DP:AD 1|1:27:12,15 1|1:22:13,9 1|0:34:12,22 +chr20 711631 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=691991;QSTRAND=+ GT:DP:AD 1|1:27:9,18 1|1:20:11,9 1|1:28:19,9 +chr20 712536 . C T 60 . QNAME=cluster19_000000F;QSTART=25048841;QSTRAND=- GT:DP:AD ./.:37:14,23 1|0:36:19,17 ./.:42:20,22 +chr20 712711 . C CT 60 . QNAME=cluster19_000000F;QSTART=25048665;QSTRAND=- GT:DP:AD ./.:40:25,15 1|0:45:20,25 ./.:32:7,25 +chr20 712944 . T C 60 . QNAME=cluster19_000000F;QSTART=25048432;QSTRAND=- GT:DP:AD ./.:41:21,20 1|0:35:22,13 ./.:26:6,20 +chr20 712978 . G A 60 . QNAME=cluster19_000000F;QSTART=25048398;QSTRAND=- GT:DP:AD ./.:29:7,22 1|0:32:7,25 ./.:18:13,5 +chr20 713101 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=693459;QSTRAND=+ GT:DP:AD 1|1:41:24,17 ./.:32:16,16 ./.:27:16,11 +chr20 713206 . T A 60 . QNAME=cluster19_000000F;QSTART=25048170;QSTRAND=- GT:DP:AD ./.:14:7,7 1|0:35:14,21 ./.:24:12,12 +chr20 713207 . T A 60 . QNAME=cluster19_000000F;QSTART=25048169;QSTRAND=- GT:DP:AD ./.:28:20,8 1|0:20:14,6 ./.:39:19,20 +chr20 713208 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=693566;QSTRAND=+ GT:DP:AD 1|1:21:11,10 1|0:30:21,9 ./.:31:17,14 +chr20 713417 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=693775;QSTRAND=+ GT:DP:AD 1|1:14:6,8 1|1:16:10,6 1|0:26:11,15 +chr20 713874 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24981111;QSTRAND=- GT:DP:AD ./.:24:15,9 ./.:33:17,16 0|1:16:9,7 +chr20 713943 . T C 60 . QNAME=cluster19_000000F;QSTART=25047433;QSTRAND=- GT:DP:AD ./.:23:7,16 1|0:34:19,15 ./.:25:7,18 +chr20 713965 . G A 60 . QNAME=cluster19_000000F;QSTART=25047411;QSTRAND=- GT:DP:AD ./.:19:5,14 1|0:27:16,11 ./.:35:13,22 +chr20 714250 . T C 60 . QNAME=cluster19_000000F;QSTART=25047126;QSTRAND=- GT:DP:AD ./.:36:25,11 1|0:34:11,23 ./.:29:8,21 +chr20 714816 . A G 60 . QNAME=cluster19_000000F;QSTART=675669;QSTRAND=+ GT:DP:AD ./.:24:15,9 0|1:26:5,21 1|0:28:22,6 +chr20 715026 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=695384;QSTRAND=+ GT:DP:AD 1|1:25:17,8 0|1:45:23,22 1|0:39:20,19 +chr20 715559 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=695917;QSTRAND=+ GT:DP:AD 1|1:33:10,23 1|1:42:18,24 1|0:27:14,13 +chr20 715567 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=695925;QSTRAND=+ GT:DP:AD 1|1:29:23,6 1|1:37:18,19 1|0:23:15,8 +chr20 715736 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24979249;QSTRAND=- GT:DP:AD ./.:46:21,25 ./.:27:16,11 0|1:16:11,5 +chr20 715825 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=24994915;QSTRAND=- GT:DP:AD ./.:41:20,21 ./.:49:24,25 1|0:15:5,10 +chr20 715836 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=696194;QSTRAND=+ GT:DP:AD 1|1:36:20,16 1|0:25:8,17 1|0:34:24,10 +chr20 716956 . T C 60 . QNAME=cluster19_000000F;QSTART=677809;QSTRAND=+ GT:DP:AD ./.:34:15,19 0|1:30:6,24 1|0:24:8,16 +chr20 717272 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=697630;QSTRAND=+ GT:DP:AD 1|0:28:18,10 ./.:38:20,18 0|1:19:6,13 +chr20 717541 . C T 60 . QNAME=cluster19_000000F;QSTART=678392;QSTRAND=+ GT:DP:AD ./.:19:6,13 0|1:17:9,8 ./.:32:9,23 +chr20 717932 . G C 60 . QNAME=cluster19_000000F;QSTART=25043444;QSTRAND=- GT:DP:AD ./.:34:11,23 1|0:37:16,21 ./.:22:8,14 +chr20 718343 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=698701;QSTRAND=+ GT:DP:AD 1|0:30:16,14 ./.:37:23,14 0|1:18:6,12 +chr20 718374 . C G 60 . QNAME=cluster19_000000F;QSTART=25043002;QSTRAND=- GT:DP:AD ./.:23:12,11 1|1:28:14,14 ./.:29:16,13 +chr20 718391 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=698749;QSTRAND=+ GT:DP:AD 1|0:29:21,8 1|1:37:25,12 0|1:44:24,20 +chr20 718820 . T A 60 . QNAME=cluster19_000000F;QSTART=679671;QSTRAND=+ GT:DP:AD ./.:26:7,19 0|1:28:9,19 ./.:39:21,18 +chr20 719274 . C T 60 . QNAME=cluster19_000000F;QSTART=680125;QSTRAND=+ GT:DP:AD ./.:26:15,11 0|1:22:8,14 ./.:37:13,24 +chr20 719464 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=699822;QSTRAND=+ GT:DP:AD 1|0:24:13,11 1|1:36:15,21 1|1:36:20,16 +chr20 719532 . T C 60 . QNAME=cluster19_000000F;QSTART=25041844;QSTRAND=- GT:DP:AD ./.:19:11,8 1|0:28:7,21 ./.:37:20,17 +chr20 720367 . C G 60 . QNAME=cluster19_000000F;QSTART=681218;QSTRAND=+ GT:DP:AD ./.:23:11,12 0|1:18:8,10 ./.:41:23,18 +chr20 720501 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=700859;QSTRAND=+ GT:DP:AD 1|0:39:21,18 1|1:35:17,18 0|1:31:16,15 +chr20 720677 . C G 60 . QNAME=cluster19_000000F;QSTART=25040699;QSTRAND=- GT:DP:AD ./.:24:14,10 1|1:32:11,21 ./.:44:20,24 +chr20 720868 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=701226;QSTRAND=+ GT:DP:AD 1|0:35:16,19 0|1:29:6,23 0|1:26:19,7 +chr20 720953 . A G 60 . QNAME=cluster19_000000F;QSTART=25040423;QSTRAND=- GT:DP:AD ./.:35:24,11 1|1:27:13,14 ./.:37:15,22 +chr20 720987 . T C 60 . QNAME=cluster19_000000F;QSTART=25040389;QSTRAND=- GT:DP:AD ./.:34:10,24 1|1:28:11,17 ./.:41:25,16 +chr20 721070 . T C 60 . QNAME=cluster19_000000F;QSTART=25040306;QSTRAND=- GT:DP:AD ./.:28:7,21 1|0:39:22,17 ./.:44:19,25 +chr20 721315 . A T 60 . QNAME=cluster19_000000F;QSTART=25040061;QSTRAND=- GT:DP:AD ./.:36:11,25 1|1:16:10,6 ./.:26:16,10 +chr20 721448 . C T 60 . QNAME=cluster19_000000F;QSTART=25039928;QSTRAND=- GT:DP:AD ./.:33:25,8 1|1:36:17,19 ./.:21:15,6 +chr20 721653 . G A 60 . QNAME=cluster19_000000F;QSTART=25039723;QSTRAND=- GT:DP:AD ./.:22:13,9 1|1:28:12,16 ./.:31:19,12 +chr20 721675 . G C 60 . QNAME=cluster19_000000F;QSTART=25039701;QSTRAND=- GT:DP:AD ./.:33:8,25 1|1:23:10,13 ./.:14:7,7 +chr20 721926 . C T 60 . QNAME=cluster19_000000F;QSTART=25039450;QSTRAND=- GT:DP:AD ./.:35:21,14 1|1:30:15,15 ./.:34:10,24 +chr20 722151 . T C 60 . QNAME=cluster19_000000F;QSTART=683002;QSTRAND=+ GT:DP:AD ./.:25:11,14 0|1:42:23,19 ./.:30:12,18 +chr20 722203 . T C 60 . QNAME=cluster19_000000F;QSTART=25039173;QSTRAND=- GT:DP:AD ./.:21:6,15 1|1:25:7,18 ./.:18:9,9 +chr20 722204 . G A 60 . QNAME=cluster19_000000F;QSTART=683055;QSTRAND=+ GT:DP:AD ./.:30:22,8 0|1:22:9,13 ./.:33:8,25 +chr20 722214 . G T 60 . QNAME=cluster19_000000F;QSTART=25039162;QSTRAND=- GT:DP:AD ./.:22:9,13 1|1:28:7,21 ./.:22:5,17 +chr20 722255 . T C 60 . QNAME=cluster19_000000F;QSTART=25039121;QSTRAND=- GT:DP:AD ./.:41:18,23 1|1:33:14,19 ./.:27:17,10 +chr20 722277 . C T 60 . QNAME=cluster19_000000F;QSTART=25039099;QSTRAND=- GT:DP:AD ./.:41:20,21 1|1:36:24,12 ./.:17:9,8 +chr20 722412 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=702770;QSTRAND=+ GT:DP:AD 1|0:23:6,17 ./.:28:22,6 0|1:21:6,15 +chr20 723134 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=703492;QSTRAND=+ GT:DP:AD 1|0:22:8,14 ./.:21:16,5 0|1:33:25,8 +chr20 723311 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=703669;QSTRAND=+ GT:DP:AD 1|1:33:24,9 1|1:36:18,18 1|1:20:10,10 +chr20 723467 . C CTTTCT 60 . QNAME=cluster19_000000F;QSTART=684316;QSTRAND=+ GT:DP:AD ./.:23:16,7 0|1:33:20,13 ./.:35:11,24 +chr20 723709 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=704067;QSTRAND=+ GT:DP:AD 1|0:32:22,10 0|1:23:6,17 0|1:17:7,10 +chr20 723727 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=704085;QSTRAND=+ GT:DP:AD 1|0:27:18,9 ./.:31:10,21 0|1:19:10,9 +chr20 723799 . G A 60 . QNAME=cluster19_000000F;QSTART=25037577;QSTRAND=- GT:DP:AD ./.:20:12,8 1|0:41:20,21 ./.:17:12,5 +chr20 723808 . G A 60 . QNAME=cluster19_000000F;QSTART=684661;QSTRAND=+ GT:DP:AD ./.:44:22,22 0|1:22:13,9 ./.:36:19,17 +chr20 723875 . G A 60 . QNAME=cluster19_000000F;QSTART=684728;QSTRAND=+ GT:DP:AD ./.:26:13,13 0|1:38:20,18 ./.:42:17,25 +chr20 723915 . A G 60 . QNAME=cluster19_000000F;QSTART=25037461;QSTRAND=- GT:DP:AD ./.:19:13,6 1|0:35:25,10 ./.:28:20,8 +chr20 724055 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=704413;QSTRAND=+ GT:DP:AD 1|0:22:6,16 0|1:13:8,5 0|1:27:18,9 +chr20 724660 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=705019;QSTRAND=+ GT:DP:AD 1|0:40:15,25 ./.:31:17,14 0|1:19:12,7 +chr20 725763 . T G 60 . QNAME=cluster19_000000F;QSTART=686616;QSTRAND=+ GT:DP:AD ./.:34:9,25 0|1:31:18,13 ./.:14:7,7 +chr20 726010 . C CA 60 . QNAME=HG002-S9-H2-000001F;QSTART=680942;QSTRAND=+ GT:DP:AD 0|1:12:6,6 1|0:33:12,21 ./.:29:13,16 +chr20 726010 . C CAAAAAAA 60 . QNAME=cluster19_000000F;QSTART=686864;QSTRAND=+ GT:DP:AD ./.:41:18,23 0|1:23:16,7 ./.:29:6,23 +chr20 726075 . G A 60 . QNAME=cluster19_000000F;QSTART=686935;QSTRAND=+ GT:DP:AD ./.:34:16,18 0|1:33:20,13 ./.:19:11,8 +chr20 726115 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=706466;QSTRAND=+ GT:DP:AD 1|0:31:23,8 0|1:27:16,11 0|1:44:20,24 +chr20 726166 . T C 60 . QNAME=cluster19_000000F;QSTART=687026;QSTRAND=+ GT:DP:AD ./.:32:11,21 0|1:28:6,22 ./.:26:18,8 +chr20 726847 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=707198;QSTRAND=+ GT:DP:AD 1|0:25:5,20 ./.:30:5,25 0|1:34:20,14 +chr20 727050 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=707401;QSTRAND=+ GT:DP:AD 1|0:41:19,22 ./.:18:7,11 0|1:18:11,7 +chr20 727183 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=707534;QSTRAND=+ GT:DP:AD 1|0:36:11,25 ./.:48:24,24 0|1:30:14,16 +chr20 727236 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=707587;QSTRAND=+ GT:DP:AD 1|0:36:23,13 ./.:39:19,20 0|1:34:18,16 +chr20 727293 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=24983447;QSTRAND=- GT:DP:AD ./.:22:13,9 ./.:37:15,22 1|0:35:19,16 +chr20 727295 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=707646;QSTRAND=+ GT:DP:AD 1|0:30:7,23 ./.:37:17,20 ./.:20:15,5 +chr20 727600 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=24983174;QSTRAND=- GT:DP:AD ./.:32:21,11 ./.:42:25,17 1|0:33:12,21 +chr20 727602 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=24983172;QSTRAND=- GT:DP:AD ./.:42:23,19 ./.:29:22,7 1|0:32:13,19 +chr20 727613 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=707964;QSTRAND=+ GT:DP:AD 1|0:35:21,14 1|1:33:25,8 0|1:14:7,7 +chr20 727615 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=707966;QSTRAND=+ GT:DP:AD 1|0:35:11,24 1|1:25:16,9 0|1:38:24,14 +chr20 727615 . C CGA 60 . QNAME=HG002-S9-H2-000001F;QSTART=682514;QSTRAND=+ GT:DP:AD 0|1:35:11,24 ./.:38:16,22 ./.:19:7,12 +chr20 727774 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=682674;QSTRAND=+ GT:DP:AD 0|1:13:7,6 1|1:45:21,24 ./.:28:11,17 +chr20 727926 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=708277;QSTRAND=+ GT:DP:AD 1|0:17:12,5 1|0:35:11,24 ./.:36:15,21 +chr20 728062 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=708413;QSTRAND=+ GT:DP:AD 1|1:37:25,12 1|1:37:21,16 0|1:29:10,19 +chr20 728326 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=708677;QSTRAND=+ GT:DP:AD 1|0:26:10,16 0|1:24:13,11 ./.:34:25,9 +chr20 728330 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=708681;QSTRAND=+ GT:DP:AD 1|0:37:13,24 0|1:35:18,17 ./.:36:11,25 +chr20 728371 . G A 60 . QNAME=cluster19_000000F;QSTART=689183;QSTRAND=+ GT:DP:AD ./.:33:16,17 0|1:13:8,5 ./.:20:7,13 +chr20 728488 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=683386;QSTRAND=+ GT:DP:AD 0|1:41:17,24 1|0:33:20,13 0|1:31:19,12 +chr20 728626 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=24966366;QSTRAND=- GT:DP:AD ./.:26:21,5 ./.:31:12,19 0|1:38:17,21 +chr20 728679 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=709030;QSTRAND=+ GT:DP:AD 1|1:37:13,24 1|0:18:8,10 1|1:45:24,21 +chr20 728689 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=709040;QSTRAND=+ GT:DP:AD 1|1:34:16,18 1|0:34:19,15 0|1:20:15,5 +chr20 728722 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=709073;QSTRAND=+ GT:DP:AD 1|1:37:19,18 1|0:47:24,23 1|1:20:9,11 +chr20 728924 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=709275;QSTRAND=+ GT:DP:AD 1|1:33:19,14 1|0:32:12,20 0|1:39:22,17 +chr20 729045 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=709396;QSTRAND=+ GT:DP:AD 1|1:18:11,7 1|0:42:23,19 1|1:39:21,18 +chr20 729328 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=709679;QSTRAND=+ GT:DP:AD 1|1:34:14,20 1|0:27:8,19 1|1:15:8,7 +chr20 729751 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=684649;QSTRAND=+ GT:DP:AD 0|1:32:10,22 1|0:38:21,17 0|1:44:24,20 +chr20 729893 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=684791;QSTRAND=+ GT:DP:AD 0|1:43:20,23 1|0:25:11,14 0|1:40:24,16 +chr20 730190 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=710541;QSTRAND=+ GT:DP:AD 1|0:27:14,13 ./.:47:23,24 1|0:50:25,25 +chr20 730755 . A AG 60 . QNAME=HG002-S9-H1-000001F;QSTART=711107;QSTRAND=+ GT:DP:AD 1|1:23:15,8 1|1:40:17,23 1|1:23:12,11 +chr20 731406 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=686305;QSTRAND=+ GT:DP:AD 0|1:18:6,12 1|0:33:20,13 0|1:30:18,12 +chr20 731541 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=711893;QSTRAND=+ GT:DP:AD 1|1:41:21,20 1|0:31:6,25 1|1:35:19,16 +chr20 732158 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=687057;QSTRAND=+ GT:DP:AD 0|1:26:8,18 1|0:30:12,18 0|1:16:10,6 +chr20 732263 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=687162;QSTRAND=+ GT:DP:AD 0|1:39:21,18 1|0:27:10,17 0|1:37:15,22 +chr20 732533 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=712885;QSTRAND=+ GT:DP:AD 1|1:38:16,22 1|0:32:20,12 1|1:33:13,20 +chr20 733181 . T TTATG 60 . QNAME=HG002-S9-H1-000001F;QSTART=713534;QSTRAND=+ GT:DP:AD 1|0:32:13,19 ./.:40:23,17 ./.:30:25,5 +chr20 733364 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=713720;QSTRAND=+ GT:DP:AD 1|1:34:25,9 1|0:28:5,23 1|1:34:16,18 +chr20 733573 . A AAAAACAAAAC 60 . QNAME=cluster23_scaffold_3;QSTART=24977194;QSTRAND=- GT:DP:AD ./.:25:12,13 ./.:47:24,23 1|0:15:8,7 +chr20 733617 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=713967;QSTRAND=+ GT:DP:AD 1|0:22:5,17 ./.:22:6,16 1|0:32:7,25 +chr20 733672 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=714022;QSTRAND=+ GT:DP:AD 1|0:15:5,10 ./.:26:12,14 ./.:33:24,9 +chr20 733818 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=714168;QSTRAND=+ GT:DP:AD 1|1:23:6,17 1|1:29:18,11 1|1:29:20,9 +chr20 733903 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24976864;QSTRAND=- GT:DP:AD ./.:44:24,20 ./.:22:13,9 1|0:27:7,20 +chr20 734373 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=714723;QSTRAND=+ GT:DP:AD 1|0:21:6,15 ./.:36:23,13 ./.:35:22,13 +chr20 734383 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=714733;QSTRAND=+ GT:DP:AD 1|0:14:6,8 ./.:16:11,5 ./.:23:16,7 +chr20 734531 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=714881;QSTRAND=+ GT:DP:AD 1|1:43:21,22 1|0:28:9,19 1|1:23:14,9 +chr20 734610 . G GGTGTGT 60 . QNAME=HG002-S9-H1-000001F;QSTART=714961;QSTRAND=+ GT:DP:AD 1|0:29:17,12 1|0:36:12,24 1|1:33:15,18 +chr20 734610 . G GGTGTGTGT 60 . QNAME=HG002-S9-H2-000001F;QSTART=689509;QSTRAND=+ GT:DP:AD 0|1:33:14,19 ./.:13:6,7 ./.:25:15,10 +chr20 734610 . G GGT 60 . QNAME=cluster19_000000F;QSTART=695423;QSTRAND=+ GT:DP:AD ./.:49:24,25 0|1:35:13,22 ./.:23:17,6 +chr20 734650 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=24976111;QSTRAND=- GT:DP:AD ./.:28:23,5 ./.:29:16,13 1|0:13:8,5 +chr20 735203 . C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=715560;QSTRAND=+ GT:DP:AD 1|1:33:11,22 1|1:28:19,9 1|1:30:18,12 +chr20 735555 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=715912;QSTRAND=+ GT:DP:AD 1|1:32:20,12 1|0:33:19,14 1|1:30:23,7 +chr20 735589 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=690496;QSTRAND=+ GT:DP:AD 0|1:26:5,21 1|0:26:18,8 1|1:26:7,19 +chr20 736154 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24974606;QSTRAND=- GT:DP:AD ./.:23:15,8 ./.:47:24,23 1|0:31:11,20 +chr20 736400 . A C 60 . QNAME=cluster23_scaffold_3;QSTART=24974360;QSTRAND=- GT:DP:AD ./.:27:8,19 ./.:34:10,24 1|0:30:21,9 +chr20 736444 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=716801;QSTRAND=+ GT:DP:AD 1|1:30:20,10 1|0:47:23,24 1|1:35:10,25 +chr20 736925 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=691830;QSTRAND=+ GT:DP:AD 0|1:37:17,20 1|0:29:19,10 0|1:40:15,25 +chr20 737005 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=691910;QSTRAND=+ GT:DP:AD 0|1:34:10,24 1|0:24:13,11 0|1:32:11,21 +chr20 737174 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=717531;QSTRAND=+ GT:DP:AD 1|1:16:10,6 1|1:46:21,25 1|1:20:14,6 +chr20 737624 . A AAAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=717982;QSTRAND=+ GT:DP:AD 1|0:38:15,23 ./.:20:7,13 ./.:21:8,13 +chr20 737624 . A AAATAAT 60 . QNAME=cluster19_000000F;QSTART=698439;QSTRAND=+ GT:DP:AD ./.:33:21,12 0|1:29:18,11 ./.:36:25,11 +chr20 737898 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=718258;QSTRAND=+ GT:DP:AD 1|0:44:25,19 ./.:32:25,7 ./.:35:10,25 +chr20 738059 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=718419;QSTRAND=+ GT:DP:AD 1|1:24:11,13 1|1:30:25,5 1|1:26:6,20 +chr20 738091 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=718451;QSTRAND=+ GT:DP:AD 1|1:44:23,21 1|1:16:5,11 1|1:30:18,12 +chr20 738584 . C CA 60 . QNAME=cluster19_000000F;QSTART=699405;QSTRAND=+ GT:DP:AD ./.:23:9,14 0|1:32:9,23 ./.:26:16,10 +chr20 738739 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=693644;QSTRAND=+ GT:DP:AD 0|1:25:17,8 1|0:32:12,20 0|1:38:22,16 +chr20 739096 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=719456;QSTRAND=+ GT:DP:AD 1|1:15:6,9 1|0:38:25,13 1|1:30:6,24 +chr20 739210 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=719570;QSTRAND=+ GT:DP:AD 1|1:42:20,22 1|0:22:15,7 1|1:32:18,14 +chr20 739239 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=719599;QSTRAND=+ GT:DP:AD 1|1:40:24,16 1|0:35:10,25 1|1:35:16,19 +chr20 740272 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=695177;QSTRAND=+ GT:DP:AD 0|1:29:18,11 1|0:33:14,19 0|1:28:11,17 +chr20 740467 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=720827;QSTRAND=+ GT:DP:AD 1|1:38:17,21 1|1:29:7,22 1|1:20:9,11 +chr20 741153 . T G 60 . QNAME=cluster23_scaffold_3;QSTART=24969615;QSTRAND=- GT:DP:AD ./.:17:12,5 ./.:13:6,7 1|0:44:23,21 +chr20 741453 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=721813;QSTRAND=+ GT:DP:AD 1|0:24:12,12 ./.:39:21,18 ./.:32:22,10 +chr20 741767 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=696672;QSTRAND=+ GT:DP:AD 0|1:20:5,15 1|0:42:18,24 0|1:24:17,7 +chr20 741939 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=696844;QSTRAND=+ GT:DP:AD 0|1:30:6,24 1|0:15:7,8 1|1:35:23,12 +chr20 742416 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=24968352;QSTRAND=- GT:DP:AD ./.:33:17,16 ./.:29:15,14 1|0:32:9,23 +chr20 742511 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=722871;QSTRAND=+ GT:DP:AD 1|0:41:17,24 ./.:34:25,9 ./.:34:9,25 +chr20 742657 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=24968111;QSTRAND=- GT:DP:AD ./.:31:14,17 ./.:30:16,14 1|0:42:22,20 +chr20 743121 . G GTCTCTCTCTC 60 . QNAME=cluster19_000000F;QSTART=703943;QSTRAND=+ GT:DP:AD ./.:23:14,9 0|1:47:22,25 ./.:25:13,12 +chr20 743153 . C CACACACACACACA 60 . QNAME=HG002-S9-H1-000001F;QSTART=723514;QSTRAND=+ GT:DP:AD 1|0:28:18,10 ./.:23:7,16 ./.:12:5,7 +chr20 743160 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=698057;QSTRAND=+ GT:DP:AD 0|1:28:15,13 ./.:31:9,22 ./.:27:12,15 +chr20 743160 . T TCACACA 60 . QNAME=cluster23_scaffold_3;QSTART=24967602;QSTRAND=- GT:DP:AD ./.:36:24,12 ./.:31:16,15 1|0:31:14,17 +chr20 743162 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=698059;QSTRAND=+ GT:DP:AD 0|1:36:17,19 1|0:22:16,6 1|0:19:5,14 +chr20 743162 . T TCA 60 . QNAME=cluster23_scaffold_2;QSTART=24951823;QSTRAND=- GT:DP:AD ./.:27:6,21 ./.:27:14,13 0|1:35:11,24 +chr20 743164 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=698061;QSTRAND=+ GT:DP:AD 0|1:30:15,15 1|0:39:25,14 1|1:29:24,5 +chr20 743734 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=724096;QSTRAND=+ GT:DP:AD 1|0:36:18,18 ./.:31:11,20 ./.:29:22,7 +chr20 743803 . A AG 60 . QNAME=HG002-S9-H1-000001F;QSTART=724166;QSTRAND=+ GT:DP:AD 1|1:39:14,25 1|0:31:7,24 1|1:47:23,24 +chr20 743934 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=24966827;QSTRAND=- GT:DP:AD ./.:34:13,21 ./.:37:15,22 1|0:28:18,10 +chr20 744816 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=725179;QSTRAND=+ GT:DP:AD 1|1:34:9,25 1|1:25:11,14 1|1:31:9,22 +chr20 745347 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=725710;QSTRAND=+ GT:DP:AD 1|1:16:9,7 1|0:37:14,23 1|1:27:21,6 +chr20 745642 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=726005;QSTRAND=+ GT:DP:AD 1|0:38:22,16 ./.:30:14,16 ./.:33:20,13 +chr20 746583 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24964178;QSTRAND=- GT:DP:AD ./.:17:11,6 ./.:29:7,22 1|0:21:11,10 +chr20 746687 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=701585;QSTRAND=+ GT:DP:AD 0|1:37:19,18 1|1:26:15,11 0|1:27:7,20 +chr20 746832 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=701730;QSTRAND=+ GT:DP:AD 0|1:30:12,18 1|0:29:16,13 0|1:25:14,11 +chr20 746873 . C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=727237;QSTRAND=+ GT:DP:AD 1|0:30:14,16 ./.:20:5,15 ./.:30:15,15 +chr20 746937 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=24963825;QSTRAND=- GT:DP:AD ./.:41:18,23 ./.:13:5,8 1|0:44:25,19 +chr20 747249 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=702146;QSTRAND=+ GT:DP:AD 0|1:40:24,16 1|1:33:9,24 0|1:19:8,11 +chr20 747381 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=702278;QSTRAND=+ GT:DP:AD 0|1:27:19,8 1|1:29:16,13 0|1:38:15,23 +chr20 747855 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=702752;QSTRAND=+ GT:DP:AD 0|1:18:6,12 1|1:29:23,6 0|1:25:15,10 +chr20 748018 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=24962744;QSTRAND=- GT:DP:AD ./.:50:25,25 ./.:31:12,19 1|0:37:25,12 +chr20 748212 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=703108;QSTRAND=+ GT:DP:AD 0|1:25:18,7 1|1:31:22,9 0|1:32:15,17 +chr20 748431 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=703327;QSTRAND=+ GT:DP:AD 0|1:34:23,11 1|0:26:17,9 0|1:26:7,19 +chr20 748776 . G A 60 . QNAME=cluster19_000000F;QSTART=709602;QSTRAND=+ GT:DP:AD ./.:37:24,13 0|1:37:13,24 ./.:11:5,6 +chr20 749061 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24961702;QSTRAND=- GT:DP:AD ./.:38:23,15 ./.:17:6,11 1|0:28:20,8 +chr20 749346 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=704241;QSTRAND=+ GT:DP:AD 0|1:44:19,25 1|0:35:20,15 0|1:24:5,19 +chr20 749546 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=704441;QSTRAND=+ GT:DP:AD 0|1:26:9,17 1|0:23:6,17 0|1:30:10,20 +chr20 749854 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=730217;QSTRAND=+ GT:DP:AD 1|1:39:17,22 1|1:31:15,16 1|1:29:12,17 +chr20 750249 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=705144;QSTRAND=+ GT:DP:AD 0|1:39:21,18 1|0:30:24,6 0|1:30:19,11 +chr20 750361 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=705256;QSTRAND=+ GT:DP:AD 0|1:14:5,9 1|0:29:15,14 0|1:25:13,12 +chr20 750494 . C CA 60 . QNAME=cluster19_000000F;QSTART=25010915;QSTRAND=- GT:DP:AD ./.:19:6,13 1|0:35:15,20 1|1:16:8,8 +chr20 750546 . T G 60 . QNAME=cluster23_scaffold_3;QSTART=24960216;QSTRAND=- GT:DP:AD ./.:43:23,20 ./.:37:23,14 1|0:38:19,19 +chr20 750567 . C A 60 . QNAME=cluster19_000000F;QSTART=711393;QSTRAND=+ GT:DP:AD ./.:36:16,20 0|1:39:22,17 ./.:31:22,9 +chr20 751100 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=705995;QSTRAND=+ GT:DP:AD 0|1:29:6,23 1|0:32:11,21 0|1:27:10,17 +chr20 751283 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=706178;QSTRAND=+ GT:DP:AD 0|1:25:18,7 1|0:14:5,9 0|1:36:20,16 +chr20 751519 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=706389;QSTRAND=+ GT:DP:AD 0|1:39:24,15 1|0:39:20,19 0|1:20:15,5 +chr20 751627 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=706497;QSTRAND=+ GT:DP:AD 0|1:32:13,19 1|0:35:20,15 0|1:33:19,14 +chr20 751651 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=706521;QSTRAND=+ GT:DP:AD 0|1:43:18,25 1|0:30:6,24 0|1:34:13,21 +chr20 751755 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=706625;QSTRAND=+ GT:DP:AD 0|1:32:15,17 1|0:30:18,12 0|1:48:24,24 +chr20 752120 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=706990;QSTRAND=+ GT:DP:AD 0|1:36:15,21 1|0:18:11,7 0|1:29:13,16 +chr20 752235 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=707105;QSTRAND=+ GT:DP:AD 0|1:32:9,23 1|0:30:21,9 0|1:31:20,11 +chr20 752300 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=707170;QSTRAND=+ GT:DP:AD 0|1:19:14,5 1|0:29:6,23 0|1:14:5,9 +chr20 752450 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=732803;QSTRAND=+ GT:DP:AD 1|1:24:11,13 1|1:16:5,11 1|1:21:10,11 +chr20 752821 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=707691;QSTRAND=+ GT:DP:AD 0|1:20:8,12 1|0:28:8,20 0|1:44:25,19 +chr20 753097 . G GAAGAAAGAAAGAAAGAAAAGA 60 . QNAME=cluster19_000000F;QSTART=25008316;QSTRAND=- GT:DP:AD ./.:34:25,9 1|0:31:7,24 ./.:29:18,11 +chr20 753097 . G GAAGA 60 . QNAME=cluster23_scaffold_3;QSTART=24957670;QSTRAND=- GT:DP:AD ./.:34:20,14 ./.:42:24,18 1|0:38:23,15 +chr20 753109 . A AAAGAAAAGAAAGAAAGAAAGAAAAGAAAGAAAG 60 . QNAME=HG002-S9-H2-000001F;QSTART=707980;QSTRAND=+;SVTYPE=INS;SVLEN=33 GT:DP:AD 0/1:30:6,24 ./.:29:16,13 ./.:32:20,12 +chr20 753109 . A AAAGAAAAGAAAGAAAGAAAGAAAAG 60 . QNAME=cluster23_scaffold_2;QSTART=24941877;QSTRAND=-;SVTYPE=INS;SVLEN=25 GT:DP:AD ./.:45:25,20 ./.:22:10,12 0/1:42:24,18 +chr20 753112 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=733465;QSTRAND=+ GT:DP:AD 1|0:32:21,11 0|1:30:13,17 ./.:34:15,19 +chr20 753113 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=733466;QSTRAND=+ GT:DP:AD 1|0:25:15,10 0|1:28:13,15 ./.:19:7,12 +chr20 753148 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=708051;QSTRAND=+ GT:DP:AD 0|1:38:19,19 1|0:22:5,17 0|1:32:9,23 +chr20 753159 . A AAG 60 . QNAME=HG002-S9-H2-000001F;QSTART=708063;QSTRAND=+ GT:DP:AD 0|1:30:5,25 1|1:38:21,17 0|1:30:23,7 +chr20 753159 . A AAAGAAAG 60 . QNAME=cluster23_scaffold_3;QSTART=24957601;QSTRAND=- GT:DP:AD ./.:37:21,16 ./.:29:6,23 1|0:20:13,7 +chr20 753194 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=708099;QSTRAND=+ GT:DP:AD 0|1:30:16,14 1|0:30:10,20 0|1:40:17,23 +chr20 753319 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=708224;QSTRAND=+ GT:DP:AD 0|1:22:10,12 1|0:27:19,8 0|1:32:16,16 +chr20 753350 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24957410;QSTRAND=- GT:DP:AD ./.:36:19,17 ./.:16:5,11 1|0:37:12,25 +chr20 753848 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=24956912;QSTRAND=- GT:DP:AD ./.:32:7,25 ./.:22:5,17 1|0:48:24,24 +chr20 753849 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=24956911;QSTRAND=- GT:DP:AD ./.:27:16,11 ./.:34:20,14 1|0:37:20,17 +chr20 753973 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=708878;QSTRAND=+ GT:DP:AD 0|1:44:20,24 1|0:44:24,20 0|1:34:12,22 +chr20 754002 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=734337;QSTRAND=+ GT:DP:AD 1|0:28:16,12 ./.:26:8,18 ./.:17:12,5 +chr20 754073 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=24956687;QSTRAND=- GT:DP:AD ./.:48:23,25 ./.:32:9,23 1|0:41:21,20 +chr20 754124 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=734459;QSTRAND=+ GT:DP:AD 1|1:26:5,21 1|0:38:25,13 1|1:34:20,14 +chr20 754553 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=709458;QSTRAND=+ GT:DP:AD 0|1:47:22,25 1|0:36:22,14 0|1:23:15,8 +chr20 755158 . G T 60 . QNAME=cluster19_000000F;QSTART=25006253;QSTRAND=- GT:DP:AD ./.:31:6,25 1|0:16:6,10 ./.:24:6,18 +chr20 755213 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=735548;QSTRAND=+ GT:DP:AD 1|1:19:12,7 1|1:25:5,20 1|1:41:24,17 +chr20 755214 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=735549;QSTRAND=+ GT:DP:AD 1|0:12:5,7 ./.:28:12,16 ./.:16:7,9 +chr20 755269 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=735605;QSTRAND=+ GT:DP:AD 1|1:35:10,25 1|1:36:19,17 1|1:46:25,21 +chr20 755467 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=735803;QSTRAND=+ GT:DP:AD 1|0:28:22,6 ./.:37:21,16 ./.:35:16,19 +chr20 755545 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=24955214;QSTRAND=- GT:DP:AD ./.:18:8,10 ./.:37:21,16 1|0:34:25,9 +chr20 755581 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=710487;QSTRAND=+ GT:DP:AD 0|1:37:24,13 1|1:32:12,20 1|1:29:12,17 +chr20 755749 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=736085;QSTRAND=+ GT:DP:AD 1|0:35:10,25 ./.:15:6,9 ./.:33:22,11 +chr20 755803 . A G 60 . QNAME=cluster19_000000F;QSTART=716622;QSTRAND=+ GT:DP:AD ./.:31:11,20 0|1:25:14,11 ./.:30:22,8 +chr20 756000 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=736336;QSTRAND=+ GT:DP:AD 1|1:31:20,11 1|1:33:11,22 0|1:12:6,6 +chr20 756217 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=736553;QSTRAND=+ GT:DP:AD 1|0:20:15,5 ./.:19:11,8 ./.:46:23,23 +chr20 756388 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=24954371;QSTRAND=- GT:DP:AD ./.:39:17,22 ./.:36:16,20 1|0:20:14,6 +chr20 756408 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=736744;QSTRAND=+ GT:DP:AD 1|0:20:15,5 ./.:24:8,16 ./.:34:12,22 +chr20 756478 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=24954281;QSTRAND=- GT:DP:AD ./.:34:18,16 ./.:18:10,8 1|0:16:10,6 +chr20 756637 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=24954122;QSTRAND=- GT:DP:AD ./.:21:7,14 ./.:34:22,12 1|0:28:5,23 +chr20 756764 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=24953995;QSTRAND=- GT:DP:AD ./.:28:14,14 ./.:26:11,15 1|0:28:5,23 +chr20 756909 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=737243;QSTRAND=+ GT:DP:AD 1|1:21:11,10 1|1:49:24,25 1|1:15:5,10 +chr20 758241 . A AT 60 . QNAME=HG002-S9-H1-000001F;QSTART=738576;QSTRAND=+ GT:DP:AD 1|1:28:10,18 1|1:20:8,12 0|1:24:19,5 +chr20 758241 . A ATTT 60 . QNAME=cluster23_scaffold_3;QSTART=24952516;QSTRAND=- GT:DP:AD ./.:28:19,9 ./.:24:16,8 1|0:21:12,9 +chr20 758268 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=738603;QSTRAND=+ GT:DP:AD 1|0:33:14,19 ./.:28:9,19 ./.:20:8,12 +chr20 758339 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=738674;QSTRAND=+ GT:DP:AD 1|0:33:17,16 ./.:16:10,6 ./.:32:21,11 +chr20 758391 . A C 60 . QNAME=cluster23_scaffold_3;QSTART=24952366;QSTRAND=- GT:DP:AD ./.:14:5,9 ./.:19:12,7 1|0:18:5,13 +chr20 758562 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=24952195;QSTRAND=- GT:DP:AD ./.:32:21,11 ./.:25:5,20 1|0:27:16,11 +chr20 758620 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=713525;QSTRAND=+ GT:DP:AD 0|1:21:11,10 1|0:39:24,15 0|1:24:12,12 +chr20 758664 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=24952093;QSTRAND=- GT:DP:AD ./.:31:6,25 ./.:33:24,9 1|0:32:12,20 +chr20 758808 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=739143;QSTRAND=+ GT:DP:AD 1|1:28:14,14 1|1:30:12,18 1|1:19:9,10 +chr20 758874 . C G 60 . QNAME=cluster19_000000F;QSTART=719692;QSTRAND=+ GT:DP:AD ./.:38:16,22 0|1:34:10,24 ./.:33:18,15 +chr20 759464 . C CA 60 . QNAME=HG002-S9-H2-000001F;QSTART=714362;QSTRAND=+ GT:DP:AD 0|1:23:14,9 1|1:41:23,18 0|1:25:20,5 +chr20 760189 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=715087;QSTRAND=+ GT:DP:AD 0|1:32:18,14 1|0:26:19,7 0|1:18:8,10 +chr20 760275 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=740600;QSTRAND=+ GT:DP:AD 1|1:24:6,18 1|1:32:25,7 1|1:25:6,19 +chr20 761203 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=741528;QSTRAND=+ GT:DP:AD 1|1:38:16,22 0|1:24:13,11 1|1:38:19,19 +chr20 761573 . C G 60 . QNAME=cluster19_000000F;QSTART=24999845;QSTRAND=- GT:DP:AD ./.:43:24,19 1|0:32:17,15 1|0:46:24,22 +chr20 761593 . G A 60 . QNAME=cluster19_000000F;QSTART=24999825;QSTRAND=- GT:DP:AD ./.:12:6,6 1|1:23:11,12 ./.:25:10,15 +chr20 761595 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=741920;QSTRAND=+ GT:DP:AD 1|1:38:21,17 1|1:22:12,10 1|1:21:15,6 +chr20 761987 . A G 60 . QNAME=cluster19_000000F;QSTART=24999431;QSTRAND=- GT:DP:AD ./.:31:15,16 1|0:42:18,24 1|1:36:12,24 +chr20 762072 . A C 60 . QNAME=cluster23_scaffold_3;QSTART=24948690;QSTRAND=- GT:DP:AD ./.:30:22,8 ./.:31:23,8 1|0:26:12,14 +chr20 762187 . G T 60 . QNAME=cluster19_000000F;QSTART=24999231;QSTRAND=- GT:DP:AD ./.:18:9,9 1|0:34:17,17 1|0:36:11,25 +chr20 762374 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=742699;QSTRAND=+ GT:DP:AD 1|1:22:13,9 1|1:29:13,16 1|0:41:17,24 +chr20 762480 . C G 60 . QNAME=cluster19_000000F;QSTART=24998938;QSTRAND=- GT:DP:AD ./.:43:21,22 1|0:17:7,10 1|0:17:5,12 +chr20 762486 . C T 60 . QNAME=cluster19_000000F;QSTART=24998932;QSTRAND=- GT:DP:AD ./.:47:24,23 1|0:14:8,6 1|0:33:25,8 +chr20 762576 . T C 60 . QNAME=cluster19_000000F;QSTART=24998842;QSTRAND=- GT:DP:AD ./.:25:16,9 1|0:25:6,19 1|0:42:23,19 +chr20 762628 . C T 60 . QNAME=cluster19_000000F;QSTART=24998790;QSTRAND=- GT:DP:AD ./.:31:20,11 1|0:33:9,24 1|0:27:21,6 +chr20 763183 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=743508;QSTRAND=+ GT:DP:AD 1|1:19:12,7 1|1:17:10,7 1|0:16:7,9 +chr20 763406 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=743731;QSTRAND=+ GT:DP:AD 1|1:48:24,24 0|1:28:11,17 ./.:30:15,15 +chr20 763806 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=744131;QSTRAND=+ GT:DP:AD 1|1:33:23,10 1|1:26:21,5 1|0:36:17,19 +chr20 764018 . A ACAGGTCAAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=744344;QSTRAND=+ GT:DP:AD 1|1:22:16,6 0|1:27:5,22 ./.:35:10,25 +chr20 764203 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=744537;QSTRAND=+ GT:DP:AD 1|1:38:16,22 1|1:38:16,22 1|0:28:23,5 +chr20 764230 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=744564;QSTRAND=+ GT:DP:AD 1|1:20:5,15 1|1:36:22,14 1|0:22:14,8 +chr20 764442 . A AGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGG 60 . QNAME=cluster23_scaffold_3;QSTART=24946242;QSTRAND=-;SVTYPE=INS;SVLEN=78 GT:DP:AD ./.:30:19,11 ./.:35:14,21 1/0:46:22,24 +chr20 764537 . A AGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=744872;QSTRAND=+;SVTYPE=INS;SVLEN=117 GT:DP:AD 1/1:23:18,5 0/1:14:6,8 ./.:45:20,25 +chr20 764537 . A AGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAT 60 . QNAME=cluster19_000000F;QSTART=24996803;QSTRAND=-;SVTYPE=INS;SVLEN=78 GT:DP:AD ./.:25:14,11 1/0:43:20,23 ./.:30:22,8 +chr20 764800 . C A 60 . QNAME=cluster23_scaffold_2;QSTART=24930190;QSTRAND=- GT:DP:AD ./.:34:22,12 ./.:29:16,13 0|1:35:24,11 +chr20 765454 . G A 60 . QNAME=cluster19_000000F;QSTART=24995886;QSTRAND=- GT:DP:AD ./.:42:17,25 1|0:24:12,12 ./.:41:18,23 +chr20 765937 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=746389;QSTRAND=+ GT:DP:AD 1|1:40:25,15 0|1:13:5,8 ./.:23:11,12 +chr20 766211 . A AG 60 . QNAME=HG002-S9-H1-000001F;QSTART=746664;QSTRAND=+ GT:DP:AD 1|1:35:10,25 1|1:20:10,10 1|0:47:22,25 +chr20 766216 . G T 60 . QNAME=cluster19_000000F;QSTART=24995123;QSTRAND=- GT:DP:AD ./.:27:16,11 1|0:28:16,12 ./.:25:7,18 +chr20 766241 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=746694;QSTRAND=+ GT:DP:AD 1|1:33:22,11 1|1:24:12,12 1|0:34:22,12 +chr20 766308 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=746761;QSTRAND=+ GT:DP:AD 1|1:45:25,20 1|1:42:20,22 1|0:18:10,8 +chr20 766512 . C A 60 . QNAME=cluster19_000000F;QSTART=24994827;QSTRAND=- GT:DP:AD ./.:40:15,25 1|0:20:10,10 ./.:21:7,14 +chr20 766576 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=747029;QSTRAND=+ GT:DP:AD 1|1:22:10,12 1|1:32:11,21 1|1:32:18,14 +chr20 766899 . T TA 60 . QNAME=cluster23_scaffold_2;QSTART=24928090;QSTRAND=- GT:DP:AD ./.:24:10,14 ./.:26:16,10 0|1:43:21,22 +chr20 767023 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=747476;QSTRAND=+ GT:DP:AD 1|1:45:23,22 0|1:40:24,16 ./.:27:16,11 +chr20 767036 . A ATAG 60 . QNAME=cluster19_000000F;QSTART=24994300;QSTRAND=- GT:DP:AD ./.:27:18,9 1|0:34:19,15 ./.:30:24,6 +chr20 767191 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=747644;QSTRAND=+ GT:DP:AD 1|1:31:8,23 1|1:37:17,20 1|0:21:14,7 +chr20 767349 . C T 60 . QNAME=cluster19_000000F;QSTART=24993987;QSTRAND=- GT:DP:AD ./.:36:22,14 1|0:24:16,8 ./.:25:17,8 +chr20 767359 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=24943323;QSTRAND=- GT:DP:AD ./.:21:7,14 ./.:39:25,14 1|0:14:7,7 +chr20 767376 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=747829;QSTRAND=+ GT:DP:AD 1|1:35:12,23 1|1:39:24,15 1|0:19:11,8 +chr20 767966 . T C 60 . QNAME=cluster19_000000F;QSTART=24993370;QSTRAND=- GT:DP:AD ./.:48:24,24 1|0:32:11,21 ./.:26:12,14 +chr20 768267 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=748720;QSTRAND=+ GT:DP:AD 1|1:21:15,6 0|1:43:22,21 ./.:27:22,5 +chr20 768330 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=748783;QSTRAND=+ GT:DP:AD 1|1:23:14,9 1|1:22:16,6 1|0:27:5,22 +chr20 769651 . C G 60 . QNAME=cluster23_scaffold_3;QSTART=24941031;QSTRAND=- GT:DP:AD ./.:34:17,17 ./.:15:6,9 1|0:25:14,11 +chr20 769672 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=750125;QSTRAND=+ GT:DP:AD 1|1:42:17,25 0|1:22:17,5 ./.:19:14,5 +chr20 769904 . A C 60 . QNAME=cluster19_000000F;QSTART=730843;QSTRAND=+ GT:DP:AD ./.:23:15,8 0|1:35:14,21 ./.:26:16,10 +chr20 770094 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=750547;QSTRAND=+ GT:DP:AD 1|1:43:22,21 1|1:23:16,7 1|0:21:7,14 +chr20 770601 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24940081;QSTRAND=- GT:DP:AD ./.:34:15,19 ./.:45:20,25 1|0:36:15,21 +chr20 771027 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=751480;QSTRAND=+ GT:DP:AD 1|1:30:18,12 0|1:37:16,21 ./.:26:10,16 +chr20 771488 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=24939194;QSTRAND=- GT:DP:AD ./.:27:15,12 ./.:39:19,20 1|0:35:19,16 +chr20 771669 . G GAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=752121;QSTRAND=+ GT:DP:AD 1|1:28:11,17 ./.:23:6,17 ./.:32:23,9 +chr20 771669 . G GA 60 . QNAME=cluster19_000000F;QSTART=732609;QSTRAND=+ GT:DP:AD ./.:17:7,10 0|1:19:6,13 ./.:44:20,24 +chr20 771669 . G GAA 60 . QNAME=cluster23_scaffold_3;QSTART=24939011;QSTRAND=- GT:DP:AD ./.:42:17,25 ./.:23:16,7 1|0:34:20,14 +chr20 771724 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=752178;QSTRAND=+ GT:DP:AD 1|1:20:8,12 1|1:22:12,10 1|0:42:20,22 +chr20 771989 . T G 60 . QNAME=cluster19_000000F;QSTART=24989348;QSTRAND=- GT:DP:AD ./.:23:8,15 1|1:35:12,23 1|0:22:11,11 +chr20 772587 . G GT 60 . QNAME=cluster23_scaffold_3;QSTART=24938092;QSTRAND=- GT:DP:AD ./.:42:22,20 ./.:28:9,19 1|0:32:20,12 +chr20 772599 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=753053;QSTRAND=+ GT:DP:AD 1|0:34:10,24 1|1:30:24,6 ./.:27:20,7 +chr20 772666 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=24938013;QSTRAND=- GT:DP:AD ./.:25:10,15 ./.:23:7,16 1|0:27:16,11 +chr20 772719 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=753173;QSTRAND=+ GT:DP:AD 1|1:21:7,14 1|1:33:25,8 1|1:23:14,9 +chr20 772824 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=753278;QSTRAND=+ GT:DP:AD 1|1:40:16,24 1|1:39:15,24 1|0:24:6,18 +chr20 772843 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=753297;QSTRAND=+ GT:DP:AD 1|1:33:18,15 1|1:47:23,24 1|1:28:15,13 +chr20 772872 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=753326;QSTRAND=+ GT:DP:AD 1|1:41:25,16 0|1:34:16,18 1|0:28:13,15 +chr20 773095 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=753549;QSTRAND=+ GT:DP:AD 1|1:37:16,21 0|1:28:5,23 ./.:29:16,13 +chr20 773193 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24921798;QSTRAND=- GT:DP:AD ./.:24:11,13 ./.:23:14,9 0|1:36:16,20 +chr20 773273 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24921718;QSTRAND=- GT:DP:AD ./.:26:5,21 ./.:37:24,13 0|1:41:19,22 +chr20 773723 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=754177;QSTRAND=+ GT:DP:AD 1|1:42:25,17 1|1:22:11,11 1|1:23:12,11 +chr20 773737 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=754191;QSTRAND=+ GT:DP:AD 1|1:25:14,11 1|1:36:15,21 1|1:18:11,7 +chr20 774159 . G A 60 . QNAME=cluster19_000000F;QSTART=735098;QSTRAND=+ GT:DP:AD ./.:47:25,22 0|1:29:5,24 ./.:38:24,14 +chr20 774304 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=729331;QSTRAND=+ GT:DP:AD 0|1:38:13,25 ./.:46:23,23 ./.:42:19,23 +chr20 774383 . T C 60 . QNAME=cluster19_000000F;QSTART=735322;QSTRAND=+ GT:DP:AD ./.:33:14,19 0|1:32:16,16 ./.:38:17,21 +chr20 774574 . A G 60 . QNAME=cluster19_000000F;QSTART=735513;QSTRAND=+ GT:DP:AD ./.:30:10,20 0|1:33:15,18 ./.:49:25,24 +chr20 775431 . G A 60 . QNAME=cluster19_000000F;QSTART=24985918;QSTRAND=- GT:DP:AD ./.:16:6,10 1|0:38:20,18 1|1:38:17,21 +chr20 775463 . T C 60 . QNAME=cluster19_000000F;QSTART=24985886;QSTRAND=- GT:DP:AD ./.:42:19,23 1|1:27:18,9 1|1:36:16,20 +chr20 775534 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=755988;QSTRAND=+ GT:DP:AD 1|1:37:15,22 1|1:20:11,9 1|1:38:25,13 +chr20 775539 . A G 60 . QNAME=cluster19_000000F;QSTART=24985810;QSTRAND=- GT:DP:AD ./.:30:20,10 1|1:27:17,10 1|1:44:24,20 +chr20 775876 . A G 60 . QNAME=cluster19_000000F;QSTART=24985473;QSTRAND=- GT:DP:AD ./.:25:19,6 1|1:36:24,12 1|1:27:22,5 +chr20 775888 . A G 60 . QNAME=cluster19_000000F;QSTART=736819;QSTRAND=+ GT:DP:AD ./.:46:22,24 0|1:23:13,10 ./.:22:13,9 +chr20 776848 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=757302;QSTRAND=+ GT:DP:AD 1|0:40:25,15 0|1:28:16,12 ./.:32:11,21 +chr20 776855 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=757309;QSTRAND=+ GT:DP:AD 1|1:19:7,12 1|1:28:6,22 1|1:38:25,13 +chr20 776863 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=731890;QSTRAND=+ GT:DP:AD 0|1:40:23,17 ./.:27:14,13 ./.:21:7,14 +chr20 776921 . T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=757375;QSTRAND=+ GT:DP:AD 1|1:23:12,11 0|1:42:23,19 ./.:34:13,21 +chr20 777272 . C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=757727;QSTRAND=+ GT:DP:AD 1|1:22:9,13 1|0:45:20,25 1|1:14:9,5 +chr20 777276 . A AC 60 . QNAME=cluster19_000000F;QSTART=738209;QSTRAND=+ GT:DP:AD ./.:21:13,8 0|1:23:18,5 ./.:27:5,22 +chr20 777343 . A G 60 . QNAME=cluster19_000000F;QSTART=738276;QSTRAND=+ GT:DP:AD ./.:46:25,21 0|1:38:21,17 ./.:31:11,20 +chr20 777391 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=757846;QSTRAND=+ GT:DP:AD 1|1:36:21,15 ./.:24:19,5 ./.:30:17,13 +chr20 778013 . C CT 60 . QNAME=cluster23_scaffold_2;QSTART=24916988;QSTRAND=- GT:DP:AD ./.:24:8,16 ./.:41:23,18 0|1:44:25,19 +chr20 778339 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=758794;QSTRAND=+ GT:DP:AD 1|1:38:25,13 1|1:46:21,25 1|1:32:16,16 +chr20 778729 . C CT 60 . QNAME=cluster19_000000F;QSTART=24982619;QSTRAND=- GT:DP:AD ./.:30:15,15 1|0:44:20,24 ./.:27:12,15 +chr20 778749 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24916252;QSTRAND=- GT:DP:AD ./.:24:18,6 ./.:30:7,23 0|1:29:17,12 +chr20 778880 . A G 60 . QNAME=cluster19_000000F;QSTART=24982468;QSTRAND=- GT:DP:AD ./.:36:24,12 1|1:18:5,13 1|1:31:7,24 +chr20 779208 . T C 60 . QNAME=cluster19_000000F;QSTART=24982140;QSTRAND=- GT:DP:AD ./.:26:5,21 1|1:29:6,23 1|1:30:10,20 +chr20 779804 . T C 60 . QNAME=cluster19_000000F;QSTART=24981544;QSTRAND=- GT:DP:AD ./.:29:15,14 1|0:21:15,6 ./.:20:6,14 +chr20 780086 . G A 60 . QNAME=cluster19_000000F;QSTART=741018;QSTRAND=+ GT:DP:AD ./.:35:17,18 0|1:27:16,11 ./.:27:14,13 +chr20 780364 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=760819;QSTRAND=+ GT:DP:AD 1|1:30:17,13 ./.:28:21,7 ./.:39:16,23 +chr20 781143 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=761598;QSTRAND=+ GT:DP:AD 1|1:26:6,20 1|1:27:11,16 1|1:31:24,7 +chr20 781912 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=762367;QSTRAND=+ GT:DP:AD 1|1:19:6,13 1|1:19:12,7 1|1:33:22,11 +chr20 782053 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=762508;QSTRAND=+ GT:DP:AD 1|1:34:21,13 1|1:23:13,10 1|1:23:12,11 +chr20 782135 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=762590;QSTRAND=+ GT:DP:AD 1|1:30:11,19 1|1:43:18,25 1|1:33:25,8 +chr20 782243 . T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=762699;QSTRAND=+ GT:DP:AD 1|0:28:6,22 ./.:30:14,16 ./.:49:24,25 +chr20 782250 . G GA 60 . QNAME=HG002-S9-H2-000001F;QSTART=737280;QSTRAND=+ GT:DP:AD 0|1:35:25,10 1|1:30:10,20 1|1:19:13,6 +chr20 782334 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=762790;QSTRAND=+ GT:DP:AD 1|1:43:22,21 1|1:31:9,22 1|1:18:10,8 +chr20 782552 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=763008;QSTRAND=+ GT:DP:AD 1|1:41:21,20 1|1:24:16,8 1|1:19:13,6 +chr20 782748 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=763204;QSTRAND=+ GT:DP:AD 1|1:17:10,7 1|1:34:13,21 1|1:32:14,18 +chr20 782898 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=763354;QSTRAND=+ GT:DP:AD 1|1:28:21,7 1|1:31:12,19 1|1:33:14,19 +chr20 783008 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=763464;QSTRAND=+ GT:DP:AD 1|1:36:21,15 1|1:24:18,6 1|1:43:21,22 +chr20 783188 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=763644;QSTRAND=+ GT:DP:AD 1|1:35:20,15 1|1:15:5,10 1|1:21:16,5 +chr20 783194 . C T 60 . QNAME=cluster19_000000F;QSTART=24978153;QSTRAND=- GT:DP:AD ./.:30:5,25 1|0:45:21,24 1|1:30:22,8 +chr20 783195 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=763651;QSTRAND=+ GT:DP:AD 1|1:35:14,21 1|1:48:24,24 1|1:25:12,13 +chr20 783325 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=763781;QSTRAND=+ GT:DP:AD 1|1:27:7,20 1|1:11:6,5 1|1:40:15,25 +chr20 783424 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=763880;QSTRAND=+ GT:DP:AD 1|1:29:10,19 1|1:41:25,16 1|1:23:12,11 +chr20 783447 . A G 60 . QNAME=cluster19_000000F;QSTART=24977900;QSTRAND=- GT:DP:AD ./.:42:19,23 1|0:19:13,6 1|1:42:17,25 +chr20 783450 . C T 60 . QNAME=cluster19_000000F;QSTART=744383;QSTRAND=+ GT:DP:AD ./.:27:12,15 0|1:18:6,12 ./.:25:15,10 +chr20 783488 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=763944;QSTRAND=+ GT:DP:AD 1|1:24:15,9 ./.:28:8,20 ./.:25:14,11 +chr20 783520 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=763976;QSTRAND=+ GT:DP:AD 1|1:41:18,23 1|1:23:15,8 1|1:45:25,20 +chr20 783739 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=764195;QSTRAND=+ GT:DP:AD 1|1:36:22,14 1|1:28:23,5 1|1:19:12,7 +chr20 783834 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=764290;QSTRAND=+ GT:DP:AD 1|1:14:7,7 1|1:46:23,23 1|1:34:23,11 +chr20 783937 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=764393;QSTRAND=+ GT:DP:AD 1|1:39:23,16 1|1:41:22,19 1|1:33:15,18 +chr20 784114 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=764570;QSTRAND=+ GT:DP:AD 1|1:31:11,20 1|0:21:16,5 1|1:43:25,18 +chr20 784189 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=764645;QSTRAND=+ GT:DP:AD 1|1:18:9,9 1|1:35:23,12 1|1:43:25,18 +chr20 784244 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=764700;QSTRAND=+ GT:DP:AD 1|1:39:15,24 1|1:28:13,15 1|1:22:6,16 +chr20 784245 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=764701;QSTRAND=+ GT:DP:AD 1|1:15:5,10 1|1:33:18,15 1|1:35:21,14 +chr20 784337 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=764793;QSTRAND=+ GT:DP:AD 1|1:22:6,16 1|1:43:19,24 1|1:21:5,16 +chr20 784347 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=764803;QSTRAND=+ GT:DP:AD 1|1:46:23,23 1|1:31:16,15 1|1:29:23,6 +chr20 784686 . G T 60 . QNAME=cluster19_000000F;QSTART=24976661;QSTRAND=- GT:DP:AD ./.:31:24,7 1|0:19:14,5 1|1:35:21,14 +chr20 784695 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=765151;QSTRAND=+ GT:DP:AD 1|1:26:18,8 1|1:26:15,11 1|1:21:7,14 +chr20 784821 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=765277;QSTRAND=+ GT:DP:AD 1|1:21:7,14 1|1:25:7,18 1|1:24:15,9 +chr20 784842 . A G 60 . QNAME=cluster19_000000F;QSTART=745775;QSTRAND=+ GT:DP:AD ./.:35:18,17 0|1:20:13,7 ./.:14:9,5 +chr20 785145 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=765601;QSTRAND=+ GT:DP:AD 1|1:20:14,6 0|1:22:17,5 ./.:16:8,8 +chr20 785294 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=765750;QSTRAND=+ GT:DP:AD 1|1:43:23,20 1|1:35:19,16 1|1:41:24,17 +chr20 785303 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=765759;QSTRAND=+ GT:DP:AD 1|1:30:20,10 1|1:32:12,20 1|1:28:23,5 +chr20 785581 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=766037;QSTRAND=+ GT:DP:AD 1|1:13:6,7 1|1:32:18,14 1|1:18:13,5 +chr20 785647 . G A 60 . QNAME=cluster19_000000F;QSTART=24975700;QSTRAND=- GT:DP:AD ./.:24:8,16 1|0:27:6,21 1|1:36:17,19 +chr20 785693 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=766149;QSTRAND=+ GT:DP:AD 1|1:27:19,8 1|1:46:22,24 1|1:30:11,19 +chr20 785803 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=766259;QSTRAND=+ GT:DP:AD 1|1:47:24,23 1|1:24:13,11 1|1:15:9,6 +chr20 786660 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24924029;QSTRAND=- GT:DP:AD ./.:34:20,14 ./.:35:18,17 1|0:32:23,9 +chr20 787077 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=767533;QSTRAND=+ GT:DP:AD 1|1:33:15,18 1|1:46:22,24 1|1:23:16,7 +chr20 787930 . A T 60 . QNAME=cluster19_000000F;QSTART=24973418;QSTRAND=- GT:DP:AD ./.:23:17,6 1|0:46:25,21 1|1:35:10,25 +chr20 788431 . T C 60 . QNAME=cluster19_000000F;QSTART=24972917;QSTRAND=- GT:DP:AD ./.:23:5,18 1|0:41:21,20 1|1:33:8,25 +chr20 788945 . T C 60 . QNAME=cluster19_000000F;QSTART=24972403;QSTRAND=- GT:DP:AD ./.:36:18,18 1|0:45:24,21 1|1:41:21,20 +chr20 789027 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=769481;QSTRAND=+ GT:DP:AD 1|1:19:13,6 1|0:27:17,10 1|1:34:20,14 +chr20 789716 . G A 60 . QNAME=cluster19_000000F;QSTART=750648;QSTRAND=+ GT:DP:AD ./.:28:21,7 0|1:32:24,8 ./.:40:18,22 +chr20 789908 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=770362;QSTRAND=+ GT:DP:AD 1|1:22:14,8 1|1:39:24,15 1|1:39:18,21 +chr20 789995 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=770449;QSTRAND=+ GT:DP:AD 1|1:39:20,19 ./.:18:9,9 ./.:18:11,7 +chr20 790219 . T C 60 . QNAME=cluster19_000000F;QSTART=24971129;QSTRAND=- GT:DP:AD ./.:36:21,15 1|0:40:24,16 1|1:29:14,15 +chr20 790252 . G A 60 . QNAME=cluster19_000000F;QSTART=24971096;QSTRAND=- GT:DP:AD ./.:32:11,21 1|0:22:17,5 1|1:15:5,10 +chr20 790270 . C G 60 . QNAME=cluster19_000000F;QSTART=24971078;QSTRAND=- GT:DP:AD ./.:23:5,18 1|0:44:19,25 1|1:39:23,16 +chr20 790371 . C CAAAAAAAAAAAA 60 . QNAME=cluster19_000000F;QSTART=751304;QSTRAND=+ GT:DP:AD ./.:23:11,12 0|1:23:12,11 ./.:41:17,24 +chr20 790626 . T G 60 . QNAME=cluster19_000000F;QSTART=24970729;QSTRAND=- GT:DP:AD ./.:36:13,23 1|0:22:8,14 1|1:40:24,16 +chr20 790639 . C T 60 . QNAME=cluster19_000000F;QSTART=24970716;QSTRAND=- GT:DP:AD ./.:28:20,8 1|0:31:22,9 1|1:16:8,8 +chr20 791233 . A G 60 . QNAME=cluster19_000000F;QSTART=24970122;QSTRAND=- GT:DP:AD ./.:14:5,9 1|0:24:14,10 1|1:33:22,11 +chr20 791888 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=772334;QSTRAND=+ GT:DP:AD 1|1:34:13,21 ./.:30:10,20 ./.:29:6,23 +chr20 791971 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=772417;QSTRAND=+ GT:DP:AD 1|1:30:21,9 1|1:19:12,7 1|1:14:5,9 +chr20 792261 . T C 60 . QNAME=cluster19_000000F;QSTART=753205;QSTRAND=+ GT:DP:AD ./.:27:21,6 0|1:29:11,18 ./.:24:17,7 +chr20 792795 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=773241;QSTRAND=+ GT:DP:AD 1|1:30:20,10 1|1:42:17,25 1|1:29:19,10 +chr20 792866 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=773312;QSTRAND=+ GT:DP:AD 1|1:43:19,24 1|1:31:22,9 1|1:17:10,7 +chr20 792873 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=773319;QSTRAND=+ GT:DP:AD 1|1:40:24,16 1|1:23:6,17 1|1:20:11,9 +chr20 792876 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=773322;QSTRAND=+ GT:DP:AD 1|1:20:6,14 1|1:47:23,24 1|1:42:23,19 +chr20 792903 . A G 60 . QNAME=cluster19_000000F;QSTART=24968452;QSTRAND=- GT:DP:AD ./.:19:8,11 1|1:26:5,21 ./.:35:25,10 +chr20 793346 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24917353;QSTRAND=- GT:DP:AD ./.:25:19,6 ./.:32:21,11 1|0:15:8,7 +chr20 793395 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=773841;QSTRAND=+ GT:DP:AD 1|1:23:6,17 1|1:36:25,11 1|1:14:7,7 +chr20 793450 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=748471;QSTRAND=+ GT:DP:AD 0|1:27:13,14 ./.:33:23,10 ./.:17:7,10 +chr20 793500 . C T 60 . QNAME=cluster19_000000F;QSTART=24967855;QSTRAND=- GT:DP:AD ./.:34:21,13 1|0:21:14,7 ./.:11:5,6 +chr20 793560 . C CG 60 . QNAME=HG002-S9-H2-000001F;QSTART=748582;QSTRAND=+ GT:DP:AD 0|1:17:12,5 ./.:33:15,18 ./.:29:18,11 +chr20 793678 . C G 60 . QNAME=cluster19_000000F;QSTART=754621;QSTRAND=+ GT:DP:AD ./.:30:8,22 0|1:44:20,24 ./.:29:20,9 +chr20 793771 . T G 60 . QNAME=cluster19_000000F;QSTART=24967586;QSTRAND=- GT:DP:AD ./.:27:20,7 1|0:18:13,5 1|1:26:18,8 +chr20 794325 . T C 60 . QNAME=cluster19_000000F;QSTART=24967032;QSTRAND=- GT:DP:AD ./.:33:22,11 1|0:27:18,9 0|1:24:16,8 +chr20 794444 . A G 60 . QNAME=cluster19_000000F;QSTART=24966913;QSTRAND=- GT:DP:AD ./.:41:21,20 1|0:30:7,23 1|1:28:7,21 +chr20 794733 . T G 60 . QNAME=cluster19_000000F;QSTART=24966624;QSTRAND=- GT:DP:AD ./.:27:7,20 1|0:31:19,12 1|1:40:21,19 +chr20 795199 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24915502;QSTRAND=- GT:DP:AD ./.:30:9,21 ./.:26:6,20 1|0:17:6,11 +chr20 795434 . C A 60 . QNAME=cluster19_000000F;QSTART=24965923;QSTRAND=- GT:DP:AD ./.:30:9,21 1|0:32:17,15 1|1:35:19,16 +chr20 795539 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24915162;QSTRAND=- GT:DP:AD ./.:28:18,10 ./.:22:13,9 1|0:29:8,21 +chr20 795540 . C G 60 . QNAME=cluster23_scaffold_3;QSTART=24915161;QSTRAND=- GT:DP:AD ./.:24:18,6 ./.:14:9,5 1|0:34:25,9 +chr20 795731 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=750753;QSTRAND=+ GT:DP:AD 0|1:38:16,22 ./.:32:13,19 ./.:23:15,8 +chr20 795805 . G A 60 . QNAME=cluster19_000000F;QSTART=24965552;QSTRAND=- GT:DP:AD ./.:33:16,17 1|0:32:13,19 ./.:18:7,11 +chr20 795876 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=776322;QSTRAND=+ GT:DP:AD 1|1:33:18,15 ./.:22:5,17 1|0:15:9,6 +chr20 795985 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24899026;QSTRAND=- GT:DP:AD ./.:35:18,17 ./.:38:21,17 0|1:24:13,11 +chr20 796225 . T G 60 . QNAME=cluster19_000000F;QSTART=24965132;QSTRAND=- GT:DP:AD ./.:32:19,13 1|0:20:10,10 ./.:27:10,17 +chr20 796289 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=24898722;QSTRAND=- GT:DP:AD ./.:34:16,18 ./.:33:15,18 0|1:30:25,5 +chr20 796344 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=751366;QSTRAND=+ GT:DP:AD 0|1:42:25,17 1|1:35:19,16 ./.:17:7,10 +chr20 796564 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=751586;QSTRAND=+ GT:DP:AD 0|1:36:20,16 ./.:37:14,23 ./.:35:21,14 +chr20 797048 . A G 60 . QNAME=cluster19_000000F;QSTART=757991;QSTRAND=+ GT:DP:AD ./.:42:18,24 0|1:39:17,22 ./.:31:9,22 +chr20 797400 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=777846;QSTRAND=+ GT:DP:AD 1|0:20:8,12 ./.:34:10,24 ./.:17:10,7 +chr20 797739 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=778185;QSTRAND=+ GT:DP:AD 1|0:24:18,6 ./.:36:12,24 ./.:34:11,23 +chr20 797871 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=752893;QSTRAND=+ GT:DP:AD 0|1:34:16,18 0|1:31:6,25 ./.:43:22,21 +chr20 798053 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=753075;QSTRAND=+ GT:DP:AD 0|1:47:23,24 0|1:28:11,17 ./.:27:15,12 +chr20 798278 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=753300;QSTRAND=+ GT:DP:AD 0|1:19:12,7 0|1:26:8,18 ./.:24:5,19 +chr20 798467 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=753489;QSTRAND=+ GT:DP:AD 0|1:40:20,20 0|1:36:17,19 ./.:28:17,11 +chr20 798479 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=778925;QSTRAND=+ GT:DP:AD 1|1:22:11,11 0|1:31:16,15 ./.:19:9,10 +chr20 798594 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=753616;QSTRAND=+ GT:DP:AD 0|1:38:22,16 0|1:39:21,18 ./.:27:5,22 +chr20 798717 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=753739;QSTRAND=+ GT:DP:AD 0|1:36:15,21 ./.:34:22,12 ./.:22:6,16 +chr20 798853 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=779299;QSTRAND=+ GT:DP:AD 1|0:46:25,21 ./.:24:5,19 ./.:35:16,19 +chr20 799277 . C CAAAA 60 . QNAME=HG002-S9-H2-000001F;QSTART=754300;QSTRAND=+ GT:DP:AD 0|1:26:18,8 ./.:27:19,8 ./.:26:12,14 +chr20 799277 . C CAA 60 . QNAME=cluster19_000000F;QSTART=24962078;QSTRAND=- GT:DP:AD ./.:18:6,12 1|0:25:15,10 1|1:33:10,23 +chr20 799300 . C T 60 . QNAME=cluster19_000000F;QSTART=24962055;QSTRAND=- GT:DP:AD ./.:39:17,22 1|0:26:21,5 1|1:24:7,17 +chr20 799510 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=779956;QSTRAND=+ GT:DP:AD 1|1:31:16,15 1|0:30:25,5 1|1:28:6,22 +chr20 799644 . G A 60 . QNAME=cluster19_000000F;QSTART=24961711;QSTRAND=- GT:DP:AD ./.:26:19,7 1|0:33:9,24 1|1:43:20,23 +chr20 799744 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=780190;QSTRAND=+ GT:DP:AD 1|0:27:5,22 ./.:14:8,6 ./.:18:6,12 +chr20 800427 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=780873;QSTRAND=+ GT:DP:AD 1|0:29:23,6 ./.:24:11,13 ./.:13:5,8 +chr20 800604 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781050;QSTRAND=+ GT:DP:AD 1|0:39:25,14 ./.:32:25,7 ./.:34:19,15 +chr20 800640 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781086;QSTRAND=+ GT:DP:AD 1|0:27:17,10 ./.:32:20,12 ./.:39:16,23 +chr20 800707 . G A 60 . QNAME=cluster19_000000F;QSTART=24960676;QSTRAND=- GT:DP:AD ./.:31:15,16 1|0:35:10,25 1|1:12:7,5 +chr20 800818 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781252;QSTRAND=+ GT:DP:AD 1|1:19:14,5 1|0:30:21,9 1|1:17:7,10 +chr20 800884 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=781318;QSTRAND=+ GT:DP:AD 1|0:27:15,12 ./.:28:17,11 ./.:31:23,8 +chr20 800927 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=781361;QSTRAND=+ GT:DP:AD 1|0:22:12,10 ./.:32:12,20 ./.:22:13,9 +chr20 800955 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=781389;QSTRAND=+ GT:DP:AD 1|0:24:19,5 ./.:43:24,19 ./.:36:21,15 +chr20 801002 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781433;QSTRAND=+ GT:DP:AD 1|0:17:10,7 ./.:29:18,11 ./.:30:18,12 +chr20 801097 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781528;QSTRAND=+ GT:DP:AD 1|0:41:18,23 ./.:36:15,21 ./.:37:15,22 +chr20 801205 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781636;QSTRAND=+ GT:DP:AD 1|0:35:15,20 ./.:27:6,21 ./.:32:18,14 +chr20 801403 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=781834;QSTRAND=+ GT:DP:AD 1|0:23:7,16 ./.:41:22,19 ./.:21:13,8 +chr20 801427 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781858;QSTRAND=+ GT:DP:AD 1|0:21:7,14 ./.:27:8,19 ./.:23:7,16 +chr20 801488 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781919;QSTRAND=+ GT:DP:AD 1|0:18:13,5 1|0:35:13,22 1|1:23:7,16 +chr20 801793 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=782224;QSTRAND=+ GT:DP:AD 1|0:36:13,23 ./.:32:14,18 ./.:29:16,13 +chr20 801807 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=782238;QSTRAND=+ GT:DP:AD 1|0:35:20,15 ./.:46:22,24 ./.:36:25,11 +chr20 801893 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=782317;QSTRAND=+ GT:DP:AD 1|0:42:21,21 ./.:36:24,12 ./.:30:19,11 +chr20 802063 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=782487;QSTRAND=+ GT:DP:AD 1|0:20:6,14 ./.:23:7,16 ./.:23:7,16 +chr20 802155 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=757153;QSTRAND=+ GT:DP:AD 0|1:33:20,13 1|0:37:18,19 1|1:30:11,19 +chr20 802331 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=782755;QSTRAND=+ GT:DP:AD 1|1:26:15,11 1|0:29:8,21 ./.:46:21,25 +chr20 802369 . G A 60 . QNAME=cluster19_000000F;QSTART=763312;QSTRAND=+ GT:DP:AD ./.:22:6,16 0|1:37:18,19 ./.:23:9,14 +chr20 802531 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=757529;QSTRAND=+ GT:DP:AD 0|1:39:16,23 ./.:28:5,23 ./.:24:19,5 +chr20 802606 . C CA 60 . QNAME=HG002-S9-H2-000001F;QSTART=757605;QSTRAND=+ GT:DP:AD 0|1:43:24,19 ./.:38:20,18 0|1:24:12,12 +chr20 802739 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=757738;QSTRAND=+ GT:DP:AD 0|1:38:14,24 0|1:33:24,9 1|0:43:21,22 +chr20 803221 . C T 60 . QNAME=cluster19_000000F;QSTART=24958170;QSTRAND=- GT:DP:AD ./.:14:6,8 1|1:26:10,16 1|1:48:25,23 +chr20 803367 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=783791;QSTRAND=+ GT:DP:AD 1|1:30:14,16 1|1:28:10,18 1|1:17:9,8 +chr20 803419 . C T 60 . QNAME=cluster19_000000F;QSTART=24957972;QSTRAND=- GT:DP:AD ./.:21:13,8 1|1:29:5,24 1|1:34:22,12 +chr20 803499 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=783923;QSTRAND=+ GT:DP:AD 1|0:36:17,19 ./.:15:6,9 ./.:23:10,13 +chr20 803703 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=784127;QSTRAND=+ GT:DP:AD 1|1:27:13,14 1|1:25:5,20 1|1:16:11,5 +chr20 803760 . C T 60 . QNAME=cluster19_000000F;QSTART=24957631;QSTRAND=- GT:DP:AD ./.:37:15,22 1|1:34:15,19 1|1:21:13,8 +chr20 804087 . G A 60 . QNAME=cluster19_000000F;QSTART=24957304;QSTRAND=- GT:DP:AD ./.:30:15,15 1|1:16:6,10 1|1:41:20,21 +chr20 804255 . C T 60 . QNAME=cluster19_000000F;QSTART=24957136;QSTRAND=- GT:DP:AD ./.:29:6,23 1|1:30:9,21 1|1:29:21,8 +chr20 804315 . C G 60 . QNAME=cluster19_000000F;QSTART=24957076;QSTRAND=- GT:DP:AD ./.:47:22,25 1|1:29:10,19 1|1:33:25,8 +chr20 804381 . C T 60 . QNAME=cluster19_000000F;QSTART=24957010;QSTRAND=- GT:DP:AD ./.:43:20,23 1|1:48:24,24 1|1:39:16,23 +chr20 804444 . G A 60 . QNAME=cluster19_000000F;QSTART=24956947;QSTRAND=- GT:DP:AD ./.:22:9,13 1|1:37:12,25 1|1:33:25,8 +chr20 804465 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=784889;QSTRAND=+ GT:DP:AD 1|1:25:8,17 ./.:27:7,20 ./.:40:21,19 +chr20 804804 . A AT 60 . QNAME=HG002-S9-H1-000001F;QSTART=785229;QSTRAND=+ GT:DP:AD 1|0:27:22,5 ./.:33:17,16 ./.:23:11,12 +chr20 805255 . T C 60 . QNAME=cluster19_000000F;QSTART=24956137;QSTRAND=- GT:DP:AD ./.:46:25,21 1|1:30:19,11 1|1:23:5,18 +chr20 805274 . T C 60 . QNAME=cluster19_000000F;QSTART=24956118;QSTRAND=- GT:DP:AD ./.:27:13,14 1|1:16:7,9 1|1:43:23,20 +chr20 805356 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=785781;QSTRAND=+ GT:DP:AD 1|1:27:22,5 1|1:27:16,11 1|1:40:24,16 +chr20 805464 . C G 60 . QNAME=cluster19_000000F;QSTART=24955928;QSTRAND=- GT:DP:AD ./.:28:11,17 1|1:41:24,17 1|1:46:25,21 +chr20 805812 . C T 60 . QNAME=cluster19_000000F;QSTART=24955582;QSTRAND=- GT:DP:AD ./.:36:25,11 1|1:34:17,17 1|1:37:12,25 +chr20 806032 . T TA 60 . QNAME=cluster23_scaffold_2;QSTART=24889015;QSTRAND=- GT:DP:AD ./.:28:20,8 ./.:31:21,10 0|1:15:9,6 +chr20 806060 . A G 60 . QNAME=cluster19_000000F;QSTART=24955334;QSTRAND=- GT:DP:AD ./.:30:25,5 1|1:30:8,22 1|1:31:18,13 +chr20 806121 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=786547;QSTRAND=+ GT:DP:AD 1|1:35:11,24 1|1:30:6,24 1|1:35:21,14 +chr20 806416 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=786842;QSTRAND=+ GT:DP:AD 1|1:29:18,11 1|1:42:20,22 1|1:36:18,18 +chr20 806698 . A G 60 . QNAME=cluster19_000000F;QSTART=24954695;QSTRAND=- GT:DP:AD ./.:33:22,11 1|1:29:20,9 1|1:19:8,11 +chr20 806714 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24904019;QSTRAND=- GT:DP:AD ./.:32:21,11 ./.:29:10,19 1|0:19:8,11 +chr20 807227 . T TTTTATTTATTTATTTATTTA 60 . QNAME=cluster19_000000F;QSTART=24954146;QSTRAND=- GT:DP:AD ./.:36:21,15 1|1:40:20,20 1|1:27:12,15 +chr20 807315 . A G 60 . QNAME=cluster19_000000F;QSTART=24954058;QSTRAND=- GT:DP:AD ./.:40:18,22 1|1:38:16,22 1|1:24:11,13 +chr20 807395 . C T 60 . QNAME=cluster19_000000F;QSTART=24953978;QSTRAND=- GT:DP:AD ./.:28:6,22 1|1:42:23,19 1|1:46:23,23 +chr20 808070 . G A 60 . QNAME=cluster19_000000F;QSTART=24953303;QSTRAND=- GT:DP:AD ./.:46:25,21 1|1:34:24,10 1|1:15:6,9 +chr20 808486 . C T 60 . QNAME=cluster19_000000F;QSTART=24952887;QSTRAND=- GT:DP:AD ./.:25:10,15 1|1:39:16,23 1|1:41:21,20 +chr20 808747 . T C 60 . QNAME=cluster19_000000F;QSTART=24952626;QSTRAND=- GT:DP:AD ./.:50:25,25 1|1:35:19,16 1|1:46:23,23 +chr20 808798 . T TG 60 . QNAME=cluster23_scaffold_2;QSTART=24886230;QSTRAND=- GT:DP:AD ./.:40:20,20 ./.:29:15,14 0|1:20:14,6 +chr20 808973 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=789399;QSTRAND=+ GT:DP:AD 1|1:35:24,11 1|1:28:5,23 1|1:16:8,8 +chr20 809124 . T TA 60 . QNAME=cluster19_000000F;QSTART=24952248;QSTRAND=- GT:DP:AD ./.:31:11,20 1|1:31:9,22 1|0:26:5,21 +chr20 809124 . T TAA 60 . QNAME=cluster23_scaffold_2;QSTART=24885902;QSTRAND=- GT:DP:AD ./.:28:18,10 ./.:30:6,24 0|1:32:17,15 +chr20 809392 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=789818;QSTRAND=+ GT:DP:AD 1|1:14:8,6 1|1:45:25,20 1|1:34:22,12 +chr20 809449 . C A 60 . QNAME=cluster19_000000F;QSTART=24951923;QSTRAND=- GT:DP:AD ./.:22:8,14 1|1:13:6,7 1|1:18:5,13 +chr20 809476 . C T 60 . QNAME=cluster19_000000F;QSTART=24951896;QSTRAND=- GT:DP:AD ./.:26:15,11 1|1:31:12,19 1|1:23:13,10 +chr20 809653 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=790079;QSTRAND=+ GT:DP:AD 1|1:48:23,25 ./.:29:16,13 ./.:21:5,16 +chr20 809775 . T G 60 . QNAME=cluster19_000000F;QSTART=24951597;QSTRAND=- GT:DP:AD ./.:20:14,6 1|0:35:21,14 ./.:37:21,16 +chr20 810079 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=790505;QSTRAND=+ GT:DP:AD 1|1:25:16,9 1|1:33:8,25 1|1:43:21,22 +chr20 810083 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=790509;QSTRAND=+ GT:DP:AD 1|1:31:25,6 ./.:38:19,19 ./.:20:9,11 +chr20 810565 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=790991;QSTRAND=+ GT:DP:AD 1|1:42:22,20 1|1:27:11,16 1|1:33:17,16 +chr20 810659 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=791085;QSTRAND=+ GT:DP:AD 1|1:24:13,11 1|1:28:23,5 1|1:20:7,13 +chr20 810742 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=791168;QSTRAND=+ GT:DP:AD 1|1:20:14,6 ./.:28:23,5 ./.:24:7,17 +chr20 811032 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=791458;QSTRAND=+ GT:DP:AD 1|1:22:16,6 ./.:34:22,12 ./.:32:18,14 +chr20 811102 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=791528;QSTRAND=+ GT:DP:AD 1|1:20:12,8 ./.:30:9,21 ./.:42:25,17 +chr20 811314 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=791740;QSTRAND=+ GT:DP:AD 1|1:14:8,6 1|1:30:5,25 1|1:27:8,19 +chr20 811539 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=791965;QSTRAND=+ GT:DP:AD 1|1:37:14,23 ./.:26:19,7 ./.:25:6,19 +chr20 811587 . G A 60 . QNAME=cluster19_000000F;QSTART=24949785;QSTRAND=- GT:DP:AD ./.:12:5,7 1|1:36:12,24 1|1:46:22,24 +chr20 811839 . A AG 60 . QNAME=cluster23_scaffold_2;QSTART=24883186;QSTRAND=- GT:DP:AD ./.:34:12,22 ./.:11:6,5 0|1:30:6,24 +chr20 812140 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=792566;QSTRAND=+ GT:DP:AD 1|1:35:22,13 ./.:36:18,18 ./.:31:13,18 +chr20 812429 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=792855;QSTRAND=+ GT:DP:AD 1|1:25:8,17 ./.:28:15,13 ./.:37:23,14 +chr20 812492 . A C 60 . QNAME=cluster19_000000F;QSTART=24948880;QSTRAND=- GT:DP:AD ./.:30:20,10 1|1:14:9,5 1|1:50:25,25 +chr20 813255 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=793681;QSTRAND=+ GT:DP:AD 1|1:40:21,19 ./.:38:15,23 1|0:35:23,12 +chr20 813573 . C T 60 . QNAME=cluster19_000000F;QSTART=24947799;QSTRAND=- GT:DP:AD ./.:37:19,18 1|1:42:18,24 0|1:35:11,24 +chr20 813792 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=794218;QSTRAND=+ GT:DP:AD 1|1:22:13,9 ./.:20:14,6 1|0:25:20,5 +chr20 813863 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=794289;QSTRAND=+ GT:DP:AD 1|1:33:16,17 1|1:39:14,25 1|1:44:22,22 +chr20 814342 . T TG 60 . QNAME=cluster23_scaffold_2;QSTART=24880682;QSTRAND=- GT:DP:AD ./.:36:17,19 ./.:27:18,9 0|1:38:15,23 +chr20 814505 . T TTTTATTTA 60 . QNAME=HG002-S9-H1-000001F;QSTART=794932;QSTRAND=+ GT:DP:AD 1|1:40:15,25 ./.:25:12,13 1|0:33:24,9 +chr20 814505 . T TTTTA 60 . QNAME=cluster19_000000F;QSTART=24946863;QSTRAND=- GT:DP:AD ./.:24:15,9 1|1:15:10,5 0|1:42:23,19 +chr20 815073 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=795507;QSTRAND=+ GT:DP:AD 1|1:34:23,11 ./.:30:13,17 1|0:17:5,12 +chr20 815387 . A T 60 . QNAME=cluster19_000000F;QSTART=24945981;QSTRAND=- GT:DP:AD ./.:26:10,16 1|1:14:6,8 0|1:39:14,25 +chr20 815789 . C A 60 . QNAME=cluster19_000000F;QSTART=24945579;QSTRAND=- GT:DP:AD ./.:36:23,13 1|1:27:9,18 ./.:37:23,14 +chr20 816179 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=796613;QSTRAND=+ GT:DP:AD 1|1:38:19,19 ./.:17:11,6 1|0:27:14,13 +chr20 816728 . C CGTGT 60 . QNAME=cluster23_scaffold_2;QSTART=24878290;QSTRAND=- GT:DP:AD ./.:27:18,9 ./.:26:7,19 0|1:36:16,20 +chr20 816757 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=797184;QSTRAND=+ GT:DP:AD 1|0:33:16,17 ./.:19:5,14 1|0:14:8,6 +chr20 817397 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24877621;QSTRAND=- GT:DP:AD ./.:40:20,20 ./.:20:15,5 0|1:33:16,17 +chr20 817512 . A G 60 . QNAME=cluster19_000000F;QSTART=24943857;QSTRAND=- GT:DP:AD ./.:32:8,24 1|0:10:5,5 ./.:17:8,9 +chr20 817544 . G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=797972;QSTRAND=+ GT:DP:AD 1|0:35:25,10 ./.:27:12,15 1|0:27:6,21 +chr20 817584 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=798012;QSTRAND=+ GT:DP:AD 1|0:27:7,20 ./.:35:15,20 1|0:18:13,5 +chr20 817587 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=798015;QSTRAND=+ GT:DP:AD 1|0:34:13,21 ./.:37:15,22 1|0:19:8,11 +chr20 817664 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=798092;QSTRAND=+ GT:DP:AD 1|0:23:8,15 ./.:20:12,8 1|0:33:21,12 +chr20 817690 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=798118;QSTRAND=+ GT:DP:AD 1|0:27:12,15 1|1:32:21,11 1|1:26:8,18 +chr20 817718 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=798146;QSTRAND=+ GT:DP:AD 1|0:31:15,16 ./.:11:5,6 1|0:37:23,14 +chr20 817808 . T C 60 . QNAME=cluster19_000000F;QSTART=24943563;QSTRAND=- GT:DP:AD ./.:27:21,6 1|1:38:25,13 ./.:41:25,16 +chr20 817809 . T A 60 . QNAME=cluster19_000000F;QSTART=24943562;QSTRAND=- GT:DP:AD ./.:35:23,12 1|1:13:5,8 ./.:26:19,7 +chr20 817850 . G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=798279;QSTRAND=+ GT:DP:AD 1|0:41:22,19 ./.:17:8,9 ./.:41:22,19 +chr20 817871 . G GA 60 . QNAME=cluster23_scaffold_2;QSTART=24877148;QSTRAND=- GT:DP:AD ./.:24:18,6 ./.:37:14,23 0|1:26:13,13 +chr20 818023 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=798452;QSTRAND=+ GT:DP:AD 1|0:36:24,12 ./.:21:7,14 1|0:29:18,11 +chr20 818055 . T TG 60 . QNAME=cluster23_scaffold_2;QSTART=24876963;QSTRAND=- GT:DP:AD ./.:21:9,12 ./.:43:19,24 0|1:29:19,10 +chr20 818068 . T TG 60 . QNAME=cluster23_scaffold_2;QSTART=24876949;QSTRAND=- GT:DP:AD ./.:30:8,22 ./.:27:11,16 0|1:26:20,6 +chr20 818085 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=798514;QSTRAND=+ GT:DP:AD 1|0:31:14,17 ./.:17:11,6 1|0:28:9,19 +chr20 818112 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=798541;QSTRAND=+ GT:DP:AD 1|0:21:12,9 1|1:24:5,19 1|1:35:14,21 +chr20 818177 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24876840;QSTRAND=- GT:DP:AD ./.:25:12,13 ./.:18:13,5 0|1:40:24,16 +chr20 818388 . A AG 60 . QNAME=cluster23_scaffold_3;QSTART=24892321;QSTRAND=- GT:DP:AD ./.:48:24,24 ./.:36:14,22 1|0:48:23,25 +chr20 818488 . A ATT 60 . QNAME=HG002-S9-H1-000001F;QSTART=798918;QSTRAND=+ GT:DP:AD 1|0:14:9,5 ./.:27:21,6 ./.:28:10,18 +chr20 818488 . A AT 60 . QNAME=HG002-S9-H2-000001F;QSTART=773494;QSTRAND=+ GT:DP:AD 0|1:33:24,9 ./.:14:5,9 ./.:33:15,18 +chr20 818644 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=799075;QSTRAND=+ GT:DP:AD 1|1:23:11,12 ./.:32:16,16 1|0:45:25,20 +chr20 818794 . C CTT 60 . QNAME=HG002-S9-H1-000001F;QSTART=799226;QSTRAND=+ GT:DP:AD 1|1:21:11,10 ./.:30:10,20 1|0:19:9,10 +chr20 818839 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=24876179;QSTRAND=- GT:DP:AD ./.:19:13,6 ./.:44:20,24 0|1:36:14,22 +chr20 818891 . A G 60 . QNAME=cluster19_000000F;QSTART=24942480;QSTRAND=- GT:DP:AD ./.:34:9,25 1|1:26:20,6 ./.:20:7,13 +chr20 818898 . T TC 60 . QNAME=cluster23_scaffold_2;QSTART=24876119;QSTRAND=- GT:DP:AD ./.:21:9,12 ./.:44:21,23 0|1:33:10,23 +chr20 818940 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=799373;QSTRAND=+ GT:DP:AD 1|1:35:13,22 ./.:42:18,24 1|1:32:15,17 +chr20 818970 . G C 60 . QNAME=cluster19_000000F;QSTART=24942401;QSTRAND=- GT:DP:AD ./.:27:13,14 1|1:28:21,7 ./.:21:5,16 +chr20 819017 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=774025;QSTRAND=+ GT:DP:AD 0|1:29:14,15 ./.:31:25,6 ./.:27:15,12 +chr20 819249 . T C 60 . QNAME=cluster19_000000F;QSTART=780213;QSTRAND=+ GT:DP:AD ./.:24:7,17 0|1:25:5,20 ./.:28:5,23 +chr20 819251 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=774259;QSTRAND=+ GT:DP:AD 0|1:34:21,13 ./.:27:17,10 ./.:27:20,7 +chr20 820514 . T TTTC 60 . QNAME=HG002-S9-H1-000001F;QSTART=802126;QSTRAND=+ GT:DP:AD 1|1:23:14,9 1|1:36:23,13 1|1:25:9,16 +chr20 820545 . T TTC 60 . QNAME=cluster19_000000F;QSTART=24937541;QSTRAND=- GT:DP:AD ./.:17:10,7 1|1:29:10,19 ./.:23:15,8 +chr20 820587 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=802201;QSTRAND=+ GT:DP:AD 1|1:31:16,15 ./.:31:16,15 1|0:27:18,9 +chr20 820752 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=802366;QSTRAND=+ GT:DP:AD 1|1:39:24,15 ./.:40:24,16 1|0:37:20,17 +chr20 821376 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=24871732;QSTRAND=- GT:DP:AD ./.:28:20,8 ./.:16:5,11 0|1:22:17,5 +chr20 821480 . G T 60 . QNAME=cluster19_000000F;QSTART=24936606;QSTRAND=- GT:DP:AD ./.:35:17,18 1|1:41:18,23 0|1:17:10,7 +chr20 822153 . A AT 60 . QNAME=cluster23_scaffold_2;QSTART=24870954;QSTRAND=- GT:DP:AD ./.:41:23,18 ./.:36:23,13 0|1:23:12,11 +chr20 822622 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24870485;QSTRAND=- GT:DP:AD ./.:36:12,24 ./.:36:17,19 0|1:25:6,19 +chr20 823109 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=804719;QSTRAND=+ GT:DP:AD 1|1:38:15,23 1|1:39:16,23 1|1:28:9,19 +chr20 824454 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=806064;QSTRAND=+ GT:DP:AD 1|1:40:22,18 1|1:18:9,9 1|1:38:24,14 +chr20 825318 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=806928;QSTRAND=+ GT:DP:AD 1|1:16:10,6 ./.:33:23,10 1|0:24:17,7 +chr20 825338 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=806948;QSTRAND=+ GT:DP:AD 1|1:40:19,21 ./.:21:12,9 1|0:32:21,11 +chr20 825828 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=807438;QSTRAND=+ GT:DP:AD 1|1:34:23,11 1|1:27:5,22 1|1:39:14,25 +chr20 826034 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=807644;QSTRAND=+ GT:DP:AD 1|1:46:25,21 1|1:20:8,12 1|1:47:24,23 +chr20 826235 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=807845;QSTRAND=+ GT:DP:AD 1|1:35:15,20 1|1:48:23,25 1|1:40:17,23 +chr20 826944 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=808554;QSTRAND=+ GT:DP:AD 1|1:36:23,13 ./.:35:20,15 1|0:23:12,11 +chr20 827056 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=808666;QSTRAND=+ GT:DP:AD 1|1:41:22,19 ./.:19:11,8 1|0:29:24,5 +chr20 827617 . C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=809228;QSTRAND=+ GT:DP:AD 1|1:25:12,13 ./.:20:5,15 1|0:24:11,13 +chr20 827617 . C CAA 60 . QNAME=cluster19_000000F;QSTART=24930470;QSTRAND=- GT:DP:AD ./.:39:24,15 1|1:45:24,21 0|1:44:23,21 +chr20 827787 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=809398;QSTRAND=+ GT:DP:AD 1|1:40:16,24 1|1:48:23,25 1|1:34:20,14 +chr20 827840 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24865265;QSTRAND=- GT:DP:AD ./.:40:25,15 ./.:33:14,19 0|1:40:19,21 +chr20 827959 . G A 60 . QNAME=cluster19_000000F;QSTART=24930128;QSTRAND=- GT:DP:AD ./.:24:9,15 1|1:32:25,7 ./.:27:11,16 +chr20 828060 . G GAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=809672;QSTRAND=+ GT:DP:AD 1|1:25:6,19 1|1:39:17,22 0|1:32:19,13 +chr20 828060 . G GAAAAA 60 . QNAME=cluster23_scaffold_3;QSTART=24881385;QSTRAND=- GT:DP:AD ./.:26:11,15 ./.:31:16,15 1|0:24:9,15 +chr20 828725 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=810340;QSTRAND=+ GT:DP:AD 1|1:18:5,13 1|1:39:23,16 1|1:39:18,21 +chr20 828856 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=810471;QSTRAND=+ GT:DP:AD 1|1:33:21,12 1|1:28:13,15 1|1:37:23,14 +chr20 828857 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=810472;QSTRAND=+ GT:DP:AD 1|1:49:25,24 1|1:42:23,19 1|1:43:21,22 +chr20 828946 . C T 60 . QNAME=cluster19_000000F;QSTART=24929137;QSTRAND=- GT:DP:AD ./.:29:15,14 1|1:27:9,18 ./.:34:20,14 +chr20 829194 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24863907;QSTRAND=- GT:DP:AD ./.:29:13,16 ./.:26:15,11 0|1:49:24,25 +chr20 829287 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=810902;QSTRAND=+ GT:DP:AD 1|1:23:6,17 1|1:33:11,22 1|1:38:23,15 +chr20 830064 . A G 60 . QNAME=cluster19_000000F;QSTART=24928019;QSTRAND=- GT:DP:AD ./.:21:7,14 1|1:43:24,19 0|1:14:6,8 +chr20 830268 . C CTT 60 . QNAME=cluster23_scaffold_2;QSTART=24862831;QSTRAND=- GT:DP:AD ./.:37:12,25 ./.:29:21,8 0|1:38:15,23 +chr20 830270 . T C 60 . QNAME=cluster19_000000F;QSTART=24927813;QSTRAND=- GT:DP:AD ./.:33:12,21 1|1:36:20,16 ./.:16:8,8 +chr20 830311 . A G 60 . QNAME=cluster19_000000F;QSTART=24927772;QSTRAND=- GT:DP:AD ./.:24:13,11 1|1:48:25,23 0|1:17:12,5 +chr20 830449 . C CTT 60 . QNAME=cluster19_000000F;QSTART=24927632;QSTRAND=- GT:DP:AD ./.:37:23,14 1|1:28:6,22 0|1:33:13,20 +chr20 830787 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=812401;QSTRAND=+ GT:DP:AD 1|1:17:7,10 1|1:29:8,21 1|1:37:18,19 +chr20 830864 . G A 60 . QNAME=cluster19_000000F;QSTART=24927217;QSTRAND=- GT:DP:AD ./.:30:10,20 1|1:29:23,6 0|1:49:24,25 +chr20 831203 . G C 60 . QNAME=cluster19_000000F;QSTART=24926878;QSTRAND=- GT:DP:AD ./.:26:14,12 1|1:28:9,19 ./.:30:7,23 +chr20 831231 . T C 60 . QNAME=cluster19_000000F;QSTART=24926850;QSTRAND=- GT:DP:AD ./.:28:23,5 1|1:29:5,24 0|1:31:10,21 +chr20 831257 . C CA 60 . QNAME=cluster19_000000F;QSTART=795540;QSTRAND=+ GT:DP:AD ./.:24:12,12 0|1:45:22,23 1|1:45:22,23 +chr20 831332 . T C 60 . QNAME=cluster19_000000F;QSTART=24926749;QSTRAND=- GT:DP:AD ./.:20:7,13 1|1:31:25,6 0|1:29:9,20 +chr20 831358 . A T 60 . QNAME=cluster19_000000F;QSTART=24926723;QSTRAND=- GT:DP:AD ./.:33:13,20 1|1:33:22,11 0|1:39:14,25 +chr20 831366 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24861730;QSTRAND=- GT:DP:AD ./.:38:14,24 ./.:38:18,20 0|1:22:17,5 +chr20 832087 . A C 60 . QNAME=cluster19_000000F;QSTART=24925994;QSTRAND=- GT:DP:AD ./.:28:13,15 1|1:28:13,15 0|1:41:21,20 +chr20 833024 . A G 60 . QNAME=cluster19_000000F;QSTART=24925057;QSTRAND=- GT:DP:AD ./.:29:13,16 1|0:34:14,20 ./.:29:6,23 +chr20 833025 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=814639;QSTRAND=+ GT:DP:AD 1|1:29:14,15 0|1:23:7,16 0|1:24:9,15 +chr20 833026 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=814640;QSTRAND=+ GT:DP:AD 1|1:26:11,15 0|1:28:11,17 0|1:23:11,12 +chr20 833026 . G GA 60 . QNAME=cluster23_scaffold_3;QSTART=24876417;QSTRAND=- GT:DP:AD ./.:36:20,16 ./.:21:8,13 1|0:24:9,15 +chr20 833108 . C G 60 . QNAME=cluster19_000000F;QSTART=24924974;QSTRAND=- GT:DP:AD ./.:39:15,24 1|1:33:15,18 0|1:38:22,16 +chr20 835141 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24857955;QSTRAND=- GT:DP:AD ./.:23:10,13 ./.:29:19,10 0|1:34:14,20 +chr20 835164 . A ATC 60 . QNAME=HG002-S9-H1-000001F;QSTART=816779;QSTRAND=+ GT:DP:AD 1|1:37:21,16 ./.:41:17,24 ./.:24:7,17 +chr20 835200 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=24874243;QSTRAND=- GT:DP:AD ./.:36:12,24 ./.:37:22,15 1|0:37:19,18 +chr20 835200 . C CTCTATA 60 . QNAME=cluster23_scaffold_2;QSTART=24857890;QSTRAND=- GT:DP:AD ./.:19:6,13 ./.:38:18,20 0|1:33:24,9 +chr20 835202 . A C 60 . QNAME=cluster19_000000F;QSTART=24922880;QSTRAND=- GT:DP:AD ./.:21:7,14 1|1:21:5,16 ./.:40:18,22 +chr20 837045 . G GTT 60 . QNAME=cluster23_scaffold_2;QSTART=24856044;QSTRAND=- GT:DP:AD ./.:44:25,19 ./.:41:16,25 0|1:19:5,14 +chr20 838387 . G C 60 . QNAME=cluster23_scaffold_2;QSTART=24854702;QSTRAND=- GT:DP:AD ./.:25:19,6 ./.:21:9,12 0|1:29:24,5 +chr20 841266 . C T 60 . QNAME=cluster19_000000F;QSTART=805548;QSTRAND=+ GT:DP:AD ./.:30:19,11 0|1:21:11,10 0|1:21:6,15 +chr20 842793 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24850296;QSTRAND=- GT:DP:AD ./.:29:21,8 ./.:38:17,21 0|1:43:22,21 +chr20 842861 . T G 60 . QNAME=cluster23_scaffold_2;QSTART=24850228;QSTRAND=- GT:DP:AD ./.:36:17,19 ./.:19:6,13 0|1:12:6,6 +chr20 843131 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24849958;QSTRAND=- GT:DP:AD ./.:27:18,9 ./.:30:13,17 0|1:41:25,16 +chr20 843133 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24849956;QSTRAND=- GT:DP:AD ./.:35:22,13 ./.:29:17,12 0|1:44:22,22 +chr20 843148 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=824764;QSTRAND=+ GT:DP:AD 1|0:36:13,23 ./.:35:22,13 ./.:17:6,11 +chr20 843149 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=824765;QSTRAND=+ GT:DP:AD 1|0:32:12,20 ./.:38:22,16 ./.:38:21,17 +chr20 843779 . C A 60 . QNAME=cluster23_scaffold_2;QSTART=24849310;QSTRAND=- GT:DP:AD ./.:31:11,20 ./.:35:23,12 0|1:30:17,13 +chr20 843805 . T C 60 . QNAME=cluster19_000000F;QSTART=808087;QSTRAND=+ GT:DP:AD ./.:36:18,18 0|1:28:17,11 ./.:24:12,12 +chr20 843879 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=24849210;QSTRAND=- GT:DP:AD ./.:35:23,12 ./.:19:7,12 0|1:16:8,8 +chr20 844675 . C CT 60 . QNAME=HG002-S9-H2-000001F;QSTART=800823;QSTRAND=+ GT:DP:AD 0|1:39:22,17 0|1:26:5,21 1|1:35:15,20 +chr20 845035 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=826642;QSTRAND=+ GT:DP:AD 1|1:32:21,11 1|1:28:21,7 1|1:29:7,22 +chr20 845849 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=827456;QSTRAND=+ GT:DP:AD 1|1:36:24,12 ./.:21:10,11 1|1:42:19,23 +chr20 845870 . C G 60 . QNAME=cluster19_000000F;QSTART=810144;QSTRAND=+ GT:DP:AD ./.:13:7,6 0|1:34:12,22 ./.:36:17,19 +chr20 846023 . G T 60 . QNAME=cluster19_000000F;QSTART=24912069;QSTRAND=- GT:DP:AD ./.:41:19,22 1|0:25:13,12 ./.:19:12,7 +chr20 846067 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=827674;QSTRAND=+ GT:DP:AD 1|1:22:17,5 ./.:30:10,20 1|1:44:23,21 +chr20 846626 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=828233;QSTRAND=+ GT:DP:AD 1|1:26:21,5 ./.:28:6,22 1|1:26:18,8 +chr20 847610 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=829217;QSTRAND=+ GT:DP:AD 1|1:17:6,11 ./.:30:7,23 1|1:21:7,14 +chr20 847932 . C T 60 . QNAME=cluster19_000000F;QSTART=812206;QSTRAND=+ GT:DP:AD ./.:23:10,13 0|1:37:16,21 ./.:37:22,15 +chr20 847948 . C T 60 . QNAME=cluster19_000000F;QSTART=812222;QSTRAND=+ GT:DP:AD ./.:36:21,15 0|1:20:7,13 ./.:32:14,18 +chr20 848007 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=829614;QSTRAND=+ GT:DP:AD 1|1:43:22,21 ./.:11:5,6 1|1:34:13,21 +chr20 848148 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=829755;QSTRAND=+ GT:DP:AD 1|1:27:6,21 0|1:27:17,10 0|1:20:14,6 +chr20 848655 . G GCCC 60 . QNAME=cluster19_000000F;QSTART=812930;QSTRAND=+ GT:DP:AD ./.:21:7,14 0|1:20:15,5 ./.:13:6,7 +chr20 848655 . G GC 60 . QNAME=cluster23_scaffold_2;QSTART=24844441;QSTRAND=- GT:DP:AD ./.:31:15,16 ./.:29:24,5 0|1:45:24,21 +chr20 848966 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=830573;QSTRAND=+ GT:DP:AD 1|1:16:5,11 ./.:20:6,14 1|1:15:7,8 +chr20 849159 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=830766;QSTRAND=+ GT:DP:AD 1|1:29:18,11 ./.:22:17,5 1|1:21:11,10 +chr20 849210 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=830817;QSTRAND=+ GT:DP:AD 1|1:40:22,18 1|1:40:25,15 1|1:26:14,12 +chr20 849245 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=830852;QSTRAND=+ GT:DP:AD 1|1:40:17,23 ./.:47:23,24 1|1:13:8,5 +chr20 849509 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=831115;QSTRAND=+ GT:DP:AD 1|1:28:14,14 ./.:40:25,15 1|1:45:23,22 +chr20 849655 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=831261;QSTRAND=+ GT:DP:AD 1|1:37:24,13 ./.:29:21,8 1|1:16:10,6 +chr20 849665 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=831271;QSTRAND=+ GT:DP:AD 1|1:24:13,11 ./.:31:22,9 1|1:27:5,22 +chr20 849770 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=831376;QSTRAND=+ GT:DP:AD 1|1:25:17,8 ./.:28:19,9 1|1:17:8,9 +chr20 849895 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=831501;QSTRAND=+ GT:DP:AD 1|1:17:5,12 ./.:32:19,13 1|1:28:8,20 +chr20 850094 . T TACACAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=831701;QSTRAND=+ GT:DP:AD 1|0:34:11,23 ./.:35:14,21 0|1:30:5,25 +chr20 850094 . T TACACACACAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=806242;QSTRAND=+ GT:DP:AD 0|1:16:10,6 ./.:26:13,13 ./.:21:12,9 +chr20 850134 . C CACACAT 60 . QNAME=cluster19_000000F;QSTART=24907952;QSTRAND=- GT:DP:AD ./.:41:17,24 1|0:22:9,13 1|0:16:5,11 +chr20 850134 . C CACACACACACAT 60 . QNAME=cluster19_000000F;QSTART=814411;QSTRAND=+ GT:DP:AD ./.:43:25,18 0|1:34:24,10 ./.:33:16,17 +chr20 850182 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=831794;QSTRAND=+ GT:DP:AD 1|1:30:23,7 ./.:27:12,15 1|1:33:11,22 +chr20 850404 . C T 60 . QNAME=cluster19_000000F;QSTART=814692;QSTRAND=+ GT:DP:AD ./.:31:8,23 0|1:38:25,13 ./.:34:15,19 +chr20 850450 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=832062;QSTRAND=+ GT:DP:AD 1|1:40:20,20 0|1:28:14,14 1|1:26:6,20 +chr20 850608 . A G 60 . QNAME=cluster19_000000F;QSTART=814896;QSTRAND=+ GT:DP:AD ./.:31:17,14 0|1:33:18,15 ./.:30:8,22 +chr20 850762 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=832374;QSTRAND=+ GT:DP:AD 1|1:32:16,16 ./.:39:23,16 1|1:21:12,9 +chr20 850818 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=832430;QSTRAND=+ GT:DP:AD 1|1:30:12,18 0|1:37:19,18 1|1:43:22,21 +chr20 851565 . G A 60 . QNAME=cluster19_000000F;QSTART=815853;QSTRAND=+ GT:DP:AD ./.:31:7,24 0|1:22:9,13 ./.:30:22,8 +chr20 851698 . C T 60 . QNAME=cluster19_000000F;QSTART=24906388;QSTRAND=- GT:DP:AD ./.:32:18,14 1|0:42:17,25 ./.:38:24,14 +chr20 852010 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=833622;QSTRAND=+ GT:DP:AD 1|1:43:24,19 ./.:33:21,12 1|1:29:20,9 +chr20 852120 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=833732;QSTRAND=+ GT:DP:AD 1|1:44:23,21 ./.:29:7,22 1|1:39:14,25 +chr20 852153 . C T 60 . QNAME=cluster19_000000F;QSTART=816441;QSTRAND=+ GT:DP:AD ./.:42:19,23 0|1:44:20,24 ./.:40:22,18 +chr20 852155 . T C 60 . QNAME=cluster19_000000F;QSTART=816443;QSTRAND=+ GT:DP:AD ./.:32:25,7 0|1:16:10,6 ./.:37:15,22 +chr20 852165 . G A 60 . QNAME=cluster19_000000F;QSTART=816453;QSTRAND=+ GT:DP:AD ./.:33:11,22 0|1:34:11,23 ./.:29:14,15 +chr20 852714 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=834324;QSTRAND=+ GT:DP:AD 1|1:41:22,19 0|1:13:5,8 1|1:33:10,23 +chr20 852722 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=834332;QSTRAND=+ GT:DP:AD 1|1:30:17,13 ./.:42:19,23 1|1:37:12,25 +chr20 853509 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=835119;QSTRAND=+ GT:DP:AD 1|1:22:10,12 ./.:34:25,9 1|1:31:11,20 +chr20 853837 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=835447;QSTRAND=+ GT:DP:AD 1|1:41:24,17 ./.:35:14,21 1|1:27:6,21 +chr20 855703 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=837309;QSTRAND=+ GT:DP:AD 1|0:34:11,23 1|1:32:20,12 1|1:36:21,15 +chr20 855883 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=812032;QSTRAND=+ GT:DP:AD 0|1:42:18,24 ./.:46:24,22 ./.:16:7,9 +chr20 856057 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=837663;QSTRAND=+ GT:DP:AD 1|1:33:9,24 1|1:49:24,25 1|1:26:21,5 +chr20 856168 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=837774;QSTRAND=+ GT:DP:AD 1|0:24:10,14 0|1:31:7,24 ./.:23:11,12 +chr20 856433 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=838039;QSTRAND=+ GT:DP:AD 1|1:34:15,19 1|1:29:18,11 1|1:43:18,25 +chr20 856781 . G A 60 . QNAME=cluster19_000000F;QSTART=821063;QSTRAND=+ GT:DP:AD ./.:46:25,21 0|1:13:7,6 ./.:39:17,22 +chr20 857157 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=838763;QSTRAND=+ GT:DP:AD 1|1:17:6,11 1|1:25:13,12 1|1:27:21,6 +chr20 857179 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=838785;QSTRAND=+ GT:DP:AD 1|1:16:10,6 1|1:29:7,22 1|1:24:17,7 +chr20 857617 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=839223;QSTRAND=+ GT:DP:AD 1|1:40:17,23 1|1:22:11,11 1|1:33:22,11 +chr20 858872 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=840478;QSTRAND=+ GT:DP:AD 1|1:32:12,20 1|1:41:23,18 1|1:28:9,19 +chr20 858925 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=840531;QSTRAND=+ GT:DP:AD 1|1:26:13,13 1|1:29:22,7 1|1:35:15,20 +chr20 859762 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=841368;QSTRAND=+ GT:DP:AD 1|1:33:11,22 1|1:16:8,8 1|1:41:25,16 +chr20 860453 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=842059;QSTRAND=+ GT:DP:AD 1|0:23:10,13 0|1:30:22,8 ./.:18:5,13 +chr20 860488 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=816637;QSTRAND=+ GT:DP:AD 0|1:19:6,13 1|0:21:5,16 1|1:21:13,8 +chr20 861973 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=843579;QSTRAND=+ GT:DP:AD 1|1:42:23,19 1|1:35:15,20 1|1:32:19,13 +chr20 861975 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=843581;QSTRAND=+ GT:DP:AD 1|1:39:18,21 1|1:25:9,16 1|1:14:7,7 +chr20 862051 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=843657;QSTRAND=+ GT:DP:AD 1|1:15:10,5 1|1:29:8,21 1|1:37:20,17 +chr20 862053 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=843659;QSTRAND=+ GT:DP:AD 1|1:16:7,9 1|1:19:11,8 1|1:30:25,5 +chr20 862270 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=843876;QSTRAND=+ GT:DP:AD 1|1:42:24,18 1|0:45:24,21 1|1:44:19,25 +chr20 862270 . T TA 60 . QNAME=cluster19_000000F;QSTART=826553;QSTRAND=+ GT:DP:AD ./.:21:11,10 0|1:37:15,22 ./.:37:23,14 +chr20 862295 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=843901;QSTRAND=+ GT:DP:AD 1|1:31:6,25 1|1:32:15,17 1|1:27:5,22 +chr20 862400 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=818548;QSTRAND=+ GT:DP:AD 0|1:34:19,15 1|0:15:9,6 1|1:45:23,22 +chr20 863200 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=844806;QSTRAND=+ GT:DP:AD 1|0:31:8,23 0|1:35:22,13 ./.:37:15,22 +chr20 863302 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=819450;QSTRAND=+ GT:DP:AD 0|1:15:6,9 1|0:29:16,13 1|1:28:12,16 +chr20 864029 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=820176;QSTRAND=+ GT:DP:AD 0|1:31:17,14 1|0:39:21,18 1|1:24:8,16 +chr20 864049 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=820196;QSTRAND=+ GT:DP:AD 0|1:40:22,18 1|0:47:22,25 1|1:44:22,22 +chr20 864080 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=845685;QSTRAND=+ GT:DP:AD 1|1:30:9,21 1|1:13:6,7 1|1:24:12,12 +chr20 865868 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=847474;QSTRAND=+ GT:DP:AD 1|0:46:24,22 0|1:43:23,20 ./.:22:6,16 +chr20 866330 . A AC 60 . QNAME=HG002-S9-H1-000001F;QSTART=847937;QSTRAND=+ GT:DP:AD 1|0:26:10,16 0|1:32:13,19 ./.:40:18,22 +chr20 866340 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=847947;QSTRAND=+ GT:DP:AD 1|0:35:15,20 0|1:15:5,10 ./.:28:19,9 +chr20 866636 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=848243;QSTRAND=+ GT:DP:AD 1|0:28:10,18 0|1:42:22,20 ./.:39:23,16 +chr20 866712 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=848319;QSTRAND=+ GT:DP:AD 1|0:33:10,23 0|1:38:25,13 ./.:42:23,19 +chr20 866777 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=848384;QSTRAND=+ GT:DP:AD 1|0:34:11,23 0|1:45:24,21 ./.:24:15,9 +chr20 866852 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=848459;QSTRAND=+ GT:DP:AD 1|0:28:20,8 0|1:18:10,8 ./.:26:12,14 +chr20 867424 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=823571;QSTRAND=+ GT:DP:AD 0|1:37:14,23 ./.:27:5,22 1|0:41:18,23 +chr20 867469 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=849076;QSTRAND=+ GT:DP:AD 1|0:27:19,8 1|1:24:11,13 0|1:13:6,7 +chr20 867469 . T TGA 60 . QNAME=HG002-S9-H2-000001F;QSTART=823617;QSTRAND=+ GT:DP:AD 0|1:31:18,13 ./.:31:6,25 1|0:16:8,8 +chr20 867728 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=849335;QSTRAND=+ GT:DP:AD 1|0:19:12,7 0|1:41:23,18 ./.:37:24,13 +chr20 867974 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=824123;QSTRAND=+ GT:DP:AD 0|1:19:7,12 1|0:30:18,12 1|1:39:22,17 +chr20 868254 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=849861;QSTRAND=+ GT:DP:AD 1|1:10:5,5 1|1:44:22,22 1|1:42:21,21 +chr20 868526 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=850133;QSTRAND=+ GT:DP:AD 1|0:37:15,22 0|1:45:23,22 ./.:25:16,9 +chr20 868606 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=850213;QSTRAND=+ GT:DP:AD 1|0:30:14,16 0|1:48:23,25 ./.:40:22,18 +chr20 868745 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=824894;QSTRAND=+ GT:DP:AD 0|1:24:9,15 1|0:44:19,25 1|1:29:23,6 +chr20 868950 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=850558;QSTRAND=+ GT:DP:AD 1|0:30:5,25 0|1:28:12,16 ./.:24:19,5 +chr20 868956 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=850564;QSTRAND=+ GT:DP:AD 1|0:32:24,8 1|1:34:21,13 1|1:13:7,6 +chr20 869010 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=850618;QSTRAND=+ GT:DP:AD 1|1:24:15,9 1|1:37:12,25 1|1:42:18,24 +chr20 869733 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=851341;QSTRAND=+ GT:DP:AD 1|1:35:13,22 1|1:19:6,13 1|1:31:17,14 +chr20 869777 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=851385;QSTRAND=+ GT:DP:AD 1|1:29:24,5 1|1:29:17,12 1|1:33:12,21 +chr20 871966 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=828114;QSTRAND=+ GT:DP:AD 0|1:27:6,21 1|0:27:19,8 1|1:21:7,14 +chr20 871969 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=828117;QSTRAND=+ GT:DP:AD 0|1:31:23,8 1|0:28:6,22 1|1:38:23,15 +chr20 872450 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=828598;QSTRAND=+ GT:DP:AD 0|1:32:19,13 1|0:24:15,9 1|1:17:10,7 +chr20 872792 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=854400;QSTRAND=+ GT:DP:AD 1|1:39:19,20 1|1:24:13,11 1|1:32:17,15 +chr20 873491 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=855099;QSTRAND=+ GT:DP:AD 1|0:27:19,8 0|1:31:25,6 ./.:40:15,25 +chr20 873608 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=855216;QSTRAND=+ GT:DP:AD 1|0:41:22,19 0|1:25:19,6 ./.:35:25,10 +chr20 873920 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=855528;QSTRAND=+ GT:DP:AD 1|0:17:7,10 0|1:29:19,10 0|1:18:13,5 +chr20 873956 . C A 60 . QNAME=cluster19_000000F;QSTART=24884138;QSTRAND=- GT:DP:AD ./.:37:17,20 1|0:31:24,7 ./.:38:18,20 +chr20 874038 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=855646;QSTRAND=+ GT:DP:AD 1|0:36:22,14 0|1:33:12,21 0|1:18:6,12 +chr20 874111 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=855719;QSTRAND=+ GT:DP:AD 1|0:25:16,9 0|1:25:13,12 0|1:25:20,5 +chr20 874297 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=855905;QSTRAND=+ GT:DP:AD 1|0:22:15,7 0|1:34:13,21 0|1:32:11,21 +chr20 874696 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=856304;QSTRAND=+ GT:DP:AD 1|0:21:15,6 0|1:32:25,7 0|1:23:13,10 +chr20 875568 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=857175;QSTRAND=+ GT:DP:AD 1|0:46:22,24 0|1:14:9,5 ./.:24:5,19 +chr20 875568 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=24817550;QSTRAND=- GT:DP:AD ./.:24:13,11 ./.:19:14,5 0|1:27:17,10 +chr20 875920 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=857527;QSTRAND=+ GT:DP:AD 1|0:39:20,19 0|1:19:11,8 0|1:17:7,10 +chr20 876104 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=857711;QSTRAND=+ GT:DP:AD 1|0:23:12,11 0|1:38:24,14 0|1:45:21,24 +chr20 876144 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=24833309;QSTRAND=- GT:DP:AD ./.:30:9,21 ./.:28:19,9 1|0:16:7,9 +chr20 876194 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=857799;QSTRAND=+ GT:DP:AD 1|0:37:24,13 0|1:36:25,11 0|1:42:22,20 +chr20 876734 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24816386;QSTRAND=- GT:DP:AD ./.:46:24,22 ./.:24:14,10 0|1:24:18,6 +chr20 878979 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24814141;QSTRAND=- GT:DP:AD ./.:21:13,8 ./.:18:5,13 0|1:34:17,17 +chr20 879508 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=861113;QSTRAND=+ GT:DP:AD 1|0:15:7,8 0|1:27:17,10 ./.:21:10,11 +chr20 880111 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=861716;QSTRAND=+ GT:DP:AD 1|0:18:9,9 0|1:44:20,24 ./.:37:17,20 +chr20 880159 . G A 60 . QNAME=cluster19_000000F;QSTART=24877935;QSTRAND=- GT:DP:AD ./.:41:23,18 1|0:33:20,13 ./.:37:24,13 +chr20 880302 . A AG 60 . QNAME=HG002-S9-H1-000001F;QSTART=861908;QSTRAND=+ GT:DP:AD 1|0:30:8,22 0|1:35:10,25 ./.:28:18,10 +chr20 880463 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24812657;QSTRAND=- GT:DP:AD ./.:29:14,15 ./.:34:23,11 0|1:19:11,8 +chr20 880587 . C CA 60 . QNAME=cluster19_000000F;QSTART=24877506;QSTRAND=- GT:DP:AD ./.:19:13,6 1|0:23:17,6 ./.:14:5,9 +chr20 880743 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=862348;QSTRAND=+ GT:DP:AD 1|0:16:9,7 0|1:13:8,5 0|1:33:10,23 +chr20 881100 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=24812020;QSTRAND=- GT:DP:AD ./.:46:21,25 ./.:18:5,13 0|1:28:9,19 +chr20 881114 . G GGGAA 60 . QNAME=cluster23_scaffold_2;QSTART=24812002;QSTRAND=- GT:DP:AD ./.:25:20,5 ./.:32:11,21 0|1:27:5,22 +chr20 881524 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24811592;QSTRAND=- GT:DP:AD ./.:31:16,15 ./.:35:20,15 0|1:30:11,19 +chr20 881561 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24811555;QSTRAND=- GT:DP:AD ./.:29:17,12 ./.:30:15,15 0|1:40:17,23 +chr20 882074 . T G 60 . QNAME=cluster23_scaffold_2;QSTART=24811042;QSTRAND=- GT:DP:AD ./.:35:24,11 ./.:39:20,19 0|1:47:22,25 +chr20 882180 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24810936;QSTRAND=- GT:DP:AD ./.:11:5,6 ./.:24:14,10 0|1:40:22,18 +chr20 882348 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=863953;QSTRAND=+ GT:DP:AD 1|0:39:15,24 0|1:19:10,9 ./.:31:9,22 +chr20 882505 . C CTAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=864111;QSTRAND=+ GT:DP:AD 1|0:37:22,15 0|1:39:15,24 ./.:18:5,13 +chr20 882628 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=864236;QSTRAND=+ GT:DP:AD 1|0:45:25,20 0|1:36:17,19 ./.:28:8,20 +chr20 882865 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=864473;QSTRAND=+ GT:DP:AD 1|0:32:23,9 0|1:32:10,22 ./.:30:6,24 +chr20 883063 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=864671;QSTRAND=+ GT:DP:AD 1|0:39:20,19 0|1:31:23,8 0|1:28:20,8 +chr20 883101 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=864709;QSTRAND=+ GT:DP:AD 1|0:39:18,21 0|1:29:17,12 ./.:31:17,14 +chr20 883203 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24809913;QSTRAND=- GT:DP:AD ./.:24:19,5 ./.:23:16,7 0|1:26:21,5 +chr20 883230 . C T 60 . QNAME=cluster19_000000F;QSTART=24874863;QSTRAND=- GT:DP:AD ./.:27:13,14 1|0:30:25,5 ./.:13:5,8 +chr20 883431 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24809685;QSTRAND=- GT:DP:AD ./.:39:23,16 ./.:20:8,12 0|1:19:7,12 +chr20 883556 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=865164;QSTRAND=+ GT:DP:AD 1|0:15:10,5 0|1:42:21,21 ./.:32:13,19 +chr20 883658 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=24809458;QSTRAND=- GT:DP:AD ./.:37:25,12 ./.:33:10,23 0|1:41:18,23 +chr20 883812 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=865420;QSTRAND=+ GT:DP:AD 1|0:42:17,25 0|1:16:7,9 0|1:28:23,5 +chr20 883869 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=24809247;QSTRAND=- GT:DP:AD ./.:31:19,12 ./.:11:5,6 0|1:28:23,5 +chr20 883997 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=865605;QSTRAND=+ GT:DP:AD 1|0:19:14,5 0|1:41:21,20 0|1:28:11,17 +chr20 884017 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=865625;QSTRAND=+ GT:DP:AD 1|0:34:10,24 0|1:25:6,19 0|1:34:17,17 +chr20 884411 . G C 60 . QNAME=cluster23_scaffold_2;QSTART=24808705;QSTRAND=- GT:DP:AD ./.:17:8,9 ./.:18:5,13 0|1:46:25,21 +chr20 884723 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=866331;QSTRAND=+ GT:DP:AD 1|0:42:24,18 0|1:26:9,17 0|1:37:19,18 +chr20 884894 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24808222;QSTRAND=- GT:DP:AD ./.:26:21,5 ./.:37:19,18 0|1:37:21,16 +chr20 885587 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=867194;QSTRAND=+ GT:DP:AD 1|0:25:12,13 0|1:18:8,10 ./.:17:9,8 +chr20 885689 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=867296;QSTRAND=+ GT:DP:AD 1|0:32:16,16 0|1:23:9,14 ./.:36:16,20 +chr20 885707 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=867314;QSTRAND=+ GT:DP:AD 1|0:27:19,8 0|1:31:7,24 ./.:28:16,12 +chr20 885722 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=867329;QSTRAND=+ GT:DP:AD 1|0:18:6,12 0|1:15:8,7 ./.:16:11,5 +chr20 886620 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=868227;QSTRAND=+ GT:DP:AD 1|0:27:5,22 0|1:36:19,17 ./.:33:19,14 +chr20 886681 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=868288;QSTRAND=+ GT:DP:AD 1|0:36:23,13 0|1:41:19,22 0|1:42:21,21 +chr20 886694 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=868301;QSTRAND=+ GT:DP:AD 1|0:44:23,21 0|1:19:10,9 ./.:15:6,9 +chr20 887887 . G GAGGA 60 . QNAME=cluster23_scaffold_2;QSTART=24805229;QSTRAND=- GT:DP:AD ./.:42:22,20 ./.:32:10,22 0|1:22:11,11 +chr20 887996 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=869599;QSTRAND=+ GT:DP:AD 1|0:35:16,19 0|1:29:24,5 0|1:37:12,25 +chr20 888753 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=870356;QSTRAND=+ GT:DP:AD 1|0:23:14,9 0|1:39:21,18 ./.:34:22,12 +chr20 889503 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=871106;QSTRAND=+ GT:DP:AD 1|0:20:7,13 0|1:34:10,24 0|1:42:17,25 +chr20 889671 . C G 60 . QNAME=cluster23_scaffold_3;QSTART=24819782;QSTRAND=- GT:DP:AD ./.:32:10,22 ./.:39:14,25 1|0:22:9,13 +chr20 890514 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=872117;QSTRAND=+ GT:DP:AD 1|0:32:19,13 0|1:29:18,11 ./.:35:18,17 +chr20 890614 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=872217;QSTRAND=+ GT:DP:AD 1|0:46:23,23 ./.:40:15,25 ./.:30:18,12 +chr20 891187 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=872790;QSTRAND=+ GT:DP:AD 1|0:34:9,25 ./.:28:16,12 ./.:32:21,11 +chr20 891480 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=873083;QSTRAND=+ GT:DP:AD 1|0:39:15,24 ./.:27:22,5 ./.:35:24,11 +chr20 891653 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24801463;QSTRAND=- GT:DP:AD ./.:18:9,9 ./.:31:13,18 0|1:36:11,25 +chr20 892108 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=873711;QSTRAND=+ GT:DP:AD 1|0:31:15,16 ./.:48:24,24 ./.:44:24,20 +chr20 892511 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=874114;QSTRAND=+ GT:DP:AD 1|0:32:21,11 ./.:28:15,13 ./.:26:11,15 +chr20 892634 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=874237;QSTRAND=+ GT:DP:AD 1|0:25:20,5 ./.:29:10,19 ./.:33:12,21 +chr20 892840 . C T 60 . QNAME=cluster19_000000F;QSTART=24865254;QSTRAND=- GT:DP:AD ./.:42:19,23 1|0:35:10,25 ./.:32:8,24 +chr20 893106 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=874709;QSTRAND=+ GT:DP:AD 1|0:13:8,5 ./.:32:21,11 ./.:24:9,15 +chr20 893464 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=875067;QSTRAND=+ GT:DP:AD 1|0:40:15,25 ./.:28:23,5 ./.:13:7,6 +chr20 893483 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=875086;QSTRAND=+ GT:DP:AD 1|0:36:25,11 ./.:28:18,10 ./.:35:25,10 +chr20 894385 . C T 60 . QNAME=cluster19_000000F;QSTART=24863709;QSTRAND=- GT:DP:AD ./.:37:22,15 1|0:28:11,17 ./.:40:24,16 +chr20 895490 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=877093;QSTRAND=+ GT:DP:AD 1|0:42:25,17 ./.:39:25,14 ./.:39:24,15 +chr20 895600 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=877203;QSTRAND=+ GT:DP:AD 1|0:27:15,12 ./.:12:6,6 ./.:40:20,20 +chr20 896059 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=877662;QSTRAND=+ GT:DP:AD 1|0:18:6,12 ./.:19:10,9 ./.:29:14,15 +chr20 896562 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=878165;QSTRAND=+ GT:DP:AD 1|0:43:23,20 ./.:20:12,8 ./.:47:22,25 +chr20 896997 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=878600;QSTRAND=+ GT:DP:AD 1|0:37:13,24 ./.:29:11,18 ./.:32:18,14 +chr20 899093 . T C 60 . QNAME=cluster19_000000F;QSTART=24859001;QSTRAND=- GT:DP:AD ./.:32:23,9 1|0:28:6,22 ./.:34:9,25 +chr20 899180 . T A 60 . QNAME=cluster19_000000F;QSTART=24858914;QSTRAND=- GT:DP:AD ./.:25:6,19 1|0:32:23,9 ./.:20:11,9 +chr20 899195 . C G 60 . QNAME=cluster19_000000F;QSTART=24858899;QSTRAND=- GT:DP:AD ./.:19:11,8 1|0:29:10,19 ./.:32:19,13 +chr20 899252 . T A 60 . QNAME=cluster19_000000F;QSTART=24858842;QSTRAND=- GT:DP:AD ./.:35:16,19 1|0:28:8,20 ./.:39:22,17 +chr20 899447 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=881049;QSTRAND=+ GT:DP:AD 1|1:31:22,9 1|1:30:25,5 1|1:16:8,8 +chr20 899533 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=855679;QSTRAND=+ GT:DP:AD 0|1:32:23,9 ./.:16:8,8 ./.:40:17,23 +chr20 900321 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=856467;QSTRAND=+ GT:DP:AD 0|1:36:19,17 ./.:13:5,8 ./.:35:13,22 +chr20 900721 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=856867;QSTRAND=+ GT:DP:AD 0|1:31:25,6 ./.:36:25,11 ./.:36:25,11 +chr20 900932 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=857078;QSTRAND=+ GT:DP:AD 0|1:22:7,15 ./.:37:13,24 ./.:32:10,22 +chr20 900977 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=857123;QSTRAND=+ GT:DP:AD 0|1:29:13,16 ./.:22:5,17 ./.:21:8,13 +chr20 901001 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=857147;QSTRAND=+ GT:DP:AD 0|1:24:7,17 ./.:46:21,25 ./.:37:25,12 +chr20 901060 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=857206;QSTRAND=+ GT:DP:AD 0|1:48:25,23 ./.:33:24,9 ./.:18:12,6 +chr20 901437 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=857583;QSTRAND=+ GT:DP:AD 0|1:32:13,19 ./.:45:21,24 ./.:37:13,24 +chr20 901786 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=857932;QSTRAND=+ GT:DP:AD 0|1:41:16,25 0|1:19:9,10 ./.:38:24,14 +chr20 902160 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=858306;QSTRAND=+ GT:DP:AD 0|1:31:10,21 ./.:19:7,12 ./.:17:10,7 +chr20 902357 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=858503;QSTRAND=+ GT:DP:AD 0|1:33:16,17 ./.:33:21,12 ./.:32:25,7 +chr20 902728 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=858874;QSTRAND=+ GT:DP:AD 0|1:11:5,6 ./.:32:19,13 ./.:32:12,20 +chr20 903001 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=859147;QSTRAND=+ GT:DP:AD 0|1:33:12,21 ./.:15:10,5 ./.:25:16,9 +chr20 903427 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=859573;QSTRAND=+ GT:DP:AD 0|1:22:17,5 ./.:28:15,13 ./.:27:20,7 +chr20 903489 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=859635;QSTRAND=+ GT:DP:AD 0|1:34:12,22 ./.:38:14,24 ./.:31:18,13 +chr20 904502 . A AC 60 . QNAME=HG002-S9-H2-000001F;QSTART=860649;QSTRAND=+ GT:DP:AD 0|1:27:6,21 ./.:26:19,7 ./.:30:12,18 +chr20 905359 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=861506;QSTRAND=+ GT:DP:AD 0|1:25:14,11 ./.:32:8,24 ./.:15:5,10 +chr20 905407 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=861554;QSTRAND=+ GT:DP:AD 0|1:42:17,25 ./.:30:17,13 ./.:29:18,11 +chr20 905736 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=861883;QSTRAND=+ GT:DP:AD 0|1:24:8,16 ./.:29:22,7 ./.:23:6,17 +chr20 906213 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=862360;QSTRAND=+ GT:DP:AD 0|1:31:14,17 ./.:43:20,23 ./.:36:23,13 +chr20 906268 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=862415;QSTRAND=+ GT:DP:AD 0|1:17:7,10 ./.:25:17,8 ./.:21:7,14 +chr20 906812 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=862959;QSTRAND=+ GT:DP:AD 0|1:33:11,22 ./.:30:9,21 ./.:21:6,15 +chr20 906878 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=863025;QSTRAND=+ GT:DP:AD 0|1:28:23,5 ./.:24:7,17 ./.:22:17,5 +chr20 907157 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=863304;QSTRAND=+ GT:DP:AD 0|1:42:25,17 ./.:40:15,25 ./.:29:18,11 +chr20 907880 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=864027;QSTRAND=+ GT:DP:AD 0|1:37:17,20 ./.:37:15,22 0|1:26:15,11 +chr20 908674 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=864821;QSTRAND=+ GT:DP:AD 0|1:40:19,21 ./.:23:12,11 0|1:36:13,23 +chr20 909226 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24783890;QSTRAND=- GT:DP:AD ./.:25:14,11 ./.:13:5,8 0|1:35:20,15 +chr20 909261 . C A 60 . QNAME=cluster19_000000F;QSTART=873540;QSTRAND=+ GT:DP:AD ./.:32:9,23 0|1:24:11,13 ./.:36:11,25 +chr20 909371 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24783745;QSTRAND=- GT:DP:AD ./.:22:16,6 ./.:29:15,14 0|1:44:22,22 +chr20 909453 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=891055;QSTRAND=+ GT:DP:AD 1|0:37:14,23 ./.:33:23,10 ./.:39:14,25 +chr20 909635 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=24783481;QSTRAND=- GT:DP:AD ./.:36:23,13 ./.:30:6,24 0|1:39:23,16 +chr20 909706 . G C 60 . QNAME=cluster19_000000F;QSTART=873985;QSTRAND=+ GT:DP:AD ./.:21:5,16 0|1:46:21,25 ./.:38:21,17 +chr20 911795 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=893397;QSTRAND=+ GT:DP:AD 1|0:23:17,6 ./.:27:5,22 ./.:36:24,12 +chr20 912080 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=893662;QSTRAND=+ GT:DP:AD 1|0:19:8,11 ./.:25:5,20 ./.:41:23,18 +chr20 912305 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=893887;QSTRAND=+ GT:DP:AD 1|0:13:8,5 ./.:28:13,15 ./.:29:13,16 +chr20 913482 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=895064;QSTRAND=+ GT:DP:AD 1|0:32:20,12 ./.:31:8,23 ./.:25:12,13 +chr20 914079 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=895661;QSTRAND=+ GT:DP:AD 1|0:16:10,6 1|0:24:7,17 ./.:25:11,14 +chr20 914238 . A G 60 . QNAME=cluster19_000000F;QSTART=24843856;QSTRAND=- GT:DP:AD ./.:45:23,22 1|0:23:13,10 ./.:25:13,12 +chr20 914324 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=895906;QSTRAND=+ GT:DP:AD 1|1:37:14,23 1|1:32:18,14 1|0:24:14,10 +chr20 914682 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=896264;QSTRAND=+ GT:DP:AD 1|1:35:20,15 1|0:34:14,20 1|1:27:15,12 +chr20 914775 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=870922;QSTRAND=+ GT:DP:AD 0|1:25:16,9 ./.:27:10,17 1|0:17:9,8 +chr20 914780 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=896362;QSTRAND=+ GT:DP:AD 1|0:36:18,18 1|0:38:24,14 0|1:32:20,12 +chr20 914814 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=870961;QSTRAND=+ GT:DP:AD 0|1:26:15,11 ./.:16:6,10 1|0:29:19,10 +chr20 915350 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=896932;QSTRAND=+ GT:DP:AD 1|0:33:10,23 ./.:36:22,14 ./.:28:14,14 +chr20 915369 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=896951;QSTRAND=+ GT:DP:AD 1|1:37:14,23 1|0:14:8,6 1|0:18:5,13 +chr20 915656 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=897238;QSTRAND=+ GT:DP:AD 1|1:12:6,6 1|0:30:22,8 1|1:26:12,14 +chr20 916110 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=872257;QSTRAND=+ GT:DP:AD 0|1:23:8,15 ./.:40:15,25 ./.:35:15,20 +chr20 916419 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=898001;QSTRAND=+ GT:DP:AD 1|1:37:17,20 1|1:20:5,15 1|1:28:5,23 +chr20 916452 . A C 60 . QNAME=cluster19_000000F;QSTART=880731;QSTRAND=+ GT:DP:AD ./.:34:21,13 0|1:34:19,15 ./.:38:22,16 +chr20 916852 . C T 60 . QNAME=cluster19_000000F;QSTART=881131;QSTRAND=+ GT:DP:AD ./.:29:23,6 0|1:28:5,23 ./.:29:18,11 +chr20 916971 . C T 60 . QNAME=cluster19_000000F;QSTART=881250;QSTRAND=+ GT:DP:AD ./.:37:17,20 0|1:30:20,10 ./.:23:6,17 +chr20 917534 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=873681;QSTRAND=+ GT:DP:AD 0|1:22:11,11 ./.:23:8,15 ./.:27:14,13 +chr20 917575 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=899157;QSTRAND=+ GT:DP:AD 1|1:39:21,18 1|1:24:7,17 1|1:33:16,17 +chr20 917906 . T G 60 . QNAME=cluster19_000000F;QSTART=882185;QSTRAND=+ GT:DP:AD ./.:20:9,11 0|1:27:14,13 ./.:19:9,10 +chr20 918736 . G A 60 . QNAME=cluster19_000000F;QSTART=883015;QSTRAND=+ GT:DP:AD ./.:41:25,16 0|1:24:8,16 ./.:28:14,14 +chr20 919167 . C CTT 60 . QNAME=cluster23_scaffold_2;QSTART=24773947;QSTRAND=- GT:DP:AD ./.:33:9,24 ./.:13:7,6 0|1:28:13,15 +chr20 919371 . G C 60 . QNAME=cluster19_000000F;QSTART=883646;QSTRAND=+ GT:DP:AD ./.:38:18,20 0|1:32:8,24 ./.:31:9,22 +chr20 919994 . T C 60 . QNAME=cluster19_000000F;QSTART=24838101;QSTRAND=- GT:DP:AD ./.:39:25,14 1|0:35:12,23 ./.:46:24,22 +chr20 920055 . T TC 60 . QNAME=HG002-S9-H1-000001F;QSTART=901638;QSTRAND=+ GT:DP:AD 1|1:13:7,6 1|1:23:8,15 1|1:29:18,11 +chr20 920188 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=901771;QSTRAND=+ GT:DP:AD 1|0:32:11,21 1|0:41:25,16 ./.:24:8,16 +chr20 920292 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=901875;QSTRAND=+ GT:DP:AD 1|0:23:17,6 1|0:20:9,11 ./.:22:13,9 +chr20 920391 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=901974;QSTRAND=+ GT:DP:AD 1|0:16:10,6 ./.:25:12,13 ./.:21:11,10 +chr20 921033 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=902616;QSTRAND=+ GT:DP:AD 1|1:27:10,17 1|1:38:16,22 1|1:37:15,22 +chr20 921239 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=902822;QSTRAND=+ GT:DP:AD 1|1:38:20,18 1|1:16:6,10 1|1:11:6,5 +chr20 921288 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=902871;QSTRAND=+ GT:DP:AD 1|1:20:5,15 1|0:38:17,21 1|1:42:21,21 +chr20 921359 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=877507;QSTRAND=+ GT:DP:AD 0|1:17:8,9 ./.:21:14,7 ./.:35:10,25 +chr20 921417 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=877565;QSTRAND=+ GT:DP:AD 0|1:18:10,8 1|0:32:23,9 0|1:32:13,19 +chr20 921417 . T TG 60 . QNAME=cluster19_000000F;QSTART=885694;QSTRAND=+ GT:DP:AD ./.:38:17,21 0|1:28:7,21 ./.:31:23,8 +chr20 921667 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=903250;QSTRAND=+ GT:DP:AD 1|0:31:18,13 0|1:29:23,6 0|1:38:21,17 +chr20 922254 . C G 60 . QNAME=cluster19_000000F;QSTART=886531;QSTRAND=+ GT:DP:AD ./.:34:13,21 0|1:18:6,12 0|1:39:24,15 +chr20 922377 . G A 60 . QNAME=cluster19_000000F;QSTART=886654;QSTRAND=+ GT:DP:AD ./.:31:8,23 0|1:19:8,11 0|1:34:19,15 +chr20 923331 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=24769781;QSTRAND=- GT:DP:AD ./.:25:18,7 ./.:13:6,7 0|1:47:22,25 +chr20 923875 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=24769236;QSTRAND=- GT:DP:AD ./.:33:23,10 ./.:45:20,25 0|1:24:16,8 +chr20 924499 . C T 60 . QNAME=cluster19_000000F;QSTART=888776;QSTRAND=+ GT:DP:AD ./.:23:12,11 0|1:38:17,21 0|1:19:12,7 +chr20 928807 . G C 60 . QNAME=cluster19_000000F;QSTART=893084;QSTRAND=+ GT:DP:AD ./.:27:21,6 0|1:34:22,12 0|1:26:19,7 +chr20 929128 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=885275;QSTRAND=+ GT:DP:AD 0|1:48:24,24 1|1:19:11,8 0|1:38:13,25 +chr20 929177 . T C 60 . QNAME=cluster19_000000F;QSTART=893454;QSTRAND=+ GT:DP:AD ./.:41:19,22 0|1:37:18,19 ./.:44:20,24 +chr20 929220 . A T 60 . QNAME=cluster19_000000F;QSTART=893497;QSTRAND=+ GT:DP:AD ./.:38:18,20 0|1:18:13,5 ./.:25:6,19 +chr20 929491 . A C 60 . QNAME=cluster19_000000F;QSTART=24828605;QSTRAND=- GT:DP:AD ./.:22:9,13 1|1:29:17,12 ./.:24:9,15 +chr20 929623 . T C 60 . QNAME=cluster19_000000F;QSTART=24828473;QSTRAND=- GT:DP:AD ./.:25:14,11 1|1:38:18,20 ./.:44:24,20 +chr20 929701 . T G 60 . QNAME=cluster19_000000F;QSTART=24828395;QSTRAND=- GT:DP:AD ./.:36:11,25 1|1:25:6,19 ./.:36:11,25 +chr20 931616 . C T 60 . QNAME=cluster19_000000F;QSTART=24826480;QSTRAND=- GT:DP:AD ./.:40:22,18 1|1:18:10,8 ./.:33:11,22 +chr20 931983 . A G 60 . QNAME=cluster19_000000F;QSTART=24826113;QSTRAND=- GT:DP:AD ./.:39:21,18 1|1:16:8,8 ./.:26:14,12 +chr20 932022 . T C 60 . QNAME=cluster19_000000F;QSTART=24826074;QSTRAND=- GT:DP:AD ./.:30:21,9 1|1:36:17,19 ./.:45:24,21 +chr20 932357 . T C 60 . QNAME=cluster19_000000F;QSTART=24825739;QSTRAND=- GT:DP:AD ./.:27:7,20 1|1:42:18,24 ./.:20:11,9 +chr20 932610 . G A 60 . QNAME=cluster19_000000F;QSTART=24825486;QSTRAND=- GT:DP:AD ./.:29:10,19 1|1:30:21,9 ./.:21:15,6 +chr20 932660 . A AT 60 . QNAME=cluster19_000000F;QSTART=24825435;QSTRAND=- GT:DP:AD ./.:31:19,12 1|1:47:24,23 ./.:18:9,9 +chr20 932698 . G A 60 . QNAME=cluster19_000000F;QSTART=24825397;QSTRAND=- GT:DP:AD ./.:38:17,21 1|1:33:10,23 ./.:34:13,21 +chr20 932824 . G A 60 . QNAME=cluster19_000000F;QSTART=24825271;QSTRAND=- GT:DP:AD ./.:37:13,24 1|1:26:6,20 ./.:30:16,14 +chr20 933093 . C T 60 . QNAME=cluster19_000000F;QSTART=24825002;QSTRAND=- GT:DP:AD ./.:33:10,23 1|1:31:6,25 ./.:21:16,5 +chr20 933764 . G T 60 . QNAME=cluster19_000000F;QSTART=24824331;QSTRAND=- GT:DP:AD ./.:43:25,18 1|1:42:19,23 ./.:23:5,18 +chr20 933777 . T G 60 . QNAME=cluster19_000000F;QSTART=24824318;QSTRAND=- GT:DP:AD ./.:28:13,15 1|1:38:15,23 ./.:29:18,11 +chr20 934006 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=890153;QSTRAND=+ GT:DP:AD 0|1:31:22,9 ./.:43:25,18 ./.:43:18,25 +chr20 934616 . G A 60 . QNAME=cluster19_000000F;QSTART=24823479;QSTRAND=- GT:DP:AD ./.:23:17,6 1|1:33:11,22 ./.:24:8,16 +chr20 935220 . C A 60 . QNAME=cluster19_000000F;QSTART=24822875;QSTRAND=- GT:DP:AD ./.:29:24,5 1|1:20:14,6 ./.:23:7,16 +chr20 935920 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24757191;QSTRAND=- GT:DP:AD ./.:35:24,11 ./.:30:18,12 0|1:40:18,22 +chr20 936160 . A C 60 . QNAME=cluster19_000000F;QSTART=24821935;QSTRAND=- GT:DP:AD ./.:41:24,17 1|0:39:16,23 ./.:41:21,20 +chr20 937152 . A T 60 . QNAME=cluster19_000000F;QSTART=24820943;QSTRAND=- GT:DP:AD ./.:31:7,24 1|0:46:22,24 ./.:40:25,15 +chr20 937174 . C T 60 . QNAME=cluster19_000000F;QSTART=24820921;QSTRAND=- GT:DP:AD ./.:33:11,22 1|0:17:6,11 ./.:27:16,11 +chr20 937837 . T A 60 . QNAME=cluster19_000000F;QSTART=24820258;QSTRAND=- GT:DP:AD ./.:23:10,13 1|0:33:23,10 ./.:43:18,25 +chr20 937941 . A G 60 . QNAME=cluster19_000000F;QSTART=24820154;QSTRAND=- GT:DP:AD ./.:31:11,20 1|0:25:19,6 ./.:28:19,9 +chr20 938380 . G A 60 . QNAME=cluster19_000000F;QSTART=24819715;QSTRAND=- GT:DP:AD ./.:34:16,18 1|0:34:20,14 ./.:32:9,23 +chr20 940109 . A G 60 . QNAME=cluster19_000000F;QSTART=24817986;QSTRAND=- GT:DP:AD ./.:40:20,20 1|1:31:16,15 ./.:25:13,12 +chr20 940207 . G A 60 . QNAME=cluster19_000000F;QSTART=24817888;QSTRAND=- GT:DP:AD ./.:31:12,19 1|1:15:10,5 ./.:23:8,15 +chr20 941328 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=897475;QSTRAND=+ GT:DP:AD 0|1:27:9,18 1|1:22:16,6 0|1:31:10,21 +chr20 942095 . C CA 60 . QNAME=cluster19_000000F;QSTART=906369;QSTRAND=+ GT:DP:AD ./.:26:11,15 0|1:34:20,14 ./.:30:11,19 +chr20 942273 . A AT 60 . QNAME=HG002-S9-H2-000001F;QSTART=898421;QSTRAND=+ GT:DP:AD 0|1:33:8,25 1|1:34:12,22 0|1:21:11,10 +chr20 942277 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=898425;QSTRAND=+ GT:DP:AD 0|1:17:8,9 1|1:37:22,15 0|1:31:20,11 +chr20 942358 . C T 60 . QNAME=cluster19_000000F;QSTART=24815736;QSTRAND=- GT:DP:AD ./.:34:10,24 1|1:47:22,25 0|1:26:14,12 +chr20 942424 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=898572;QSTRAND=+ GT:DP:AD 0|1:25:9,16 ./.:26:13,13 ./.:20:9,11 +chr20 942563 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=898711;QSTRAND=+ GT:DP:AD 0|1:32:18,14 ./.:28:20,8 ./.:21:14,7 +chr20 942659 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=898807;QSTRAND=+ GT:DP:AD 0|1:21:12,9 1|1:37:24,13 0|1:32:13,19 +chr20 943015 . G A 60 . QNAME=cluster19_000000F;QSTART=24815079;QSTRAND=- GT:DP:AD ./.:36:11,25 1|1:39:16,23 0|1:31:16,15 +chr20 943016 . C A 60 . QNAME=cluster19_000000F;QSTART=24815078;QSTRAND=- GT:DP:AD ./.:28:16,12 1|1:14:8,6 0|1:46:24,22 +chr20 943950 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=900098;QSTRAND=+ GT:DP:AD 0|1:42:23,19 ./.:33:14,19 ./.:27:8,19 +chr20 943984 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=900132;QSTRAND=+ GT:DP:AD 0|1:34:25,9 1|1:32:17,15 0|1:41:18,23 +chr20 944029 . C CTT 60 . QNAME=cluster23_scaffold_3;QSTART=24765421;QSTRAND=- GT:DP:AD ./.:39:18,21 ./.:40:25,15 1|0:42:25,17 +chr20 944093 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24765357;QSTRAND=- GT:DP:AD ./.:27:18,9 ./.:36:21,15 1|0:25:16,9 +chr20 944094 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=24765356;QSTRAND=- GT:DP:AD ./.:13:6,7 ./.:19:10,9 1|0:26:15,11 +chr20 945682 . T C 60 . QNAME=cluster19_000000F;QSTART=909955;QSTRAND=+ GT:DP:AD ./.:25:7,18 0|1:45:20,25 0|1:22:5,17 +chr20 945711 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=901858;QSTRAND=+ GT:DP:AD 0|1:40:19,21 0|1:27:13,14 0|1:41:22,19 +chr20 945754 . G A 60 . QNAME=cluster19_000000F;QSTART=910027;QSTRAND=+ GT:DP:AD ./.:34:17,17 0|1:33:25,8 0|1:34:10,24 +chr20 945942 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=902089;QSTRAND=+ GT:DP:AD 0|1:31:8,23 0|1:15:8,7 0|1:27:13,14 +chr20 946505 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=928088;QSTRAND=+ GT:DP:AD 1|0:25:10,15 0|1:27:16,11 0|1:30:10,20 +chr20 946814 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=902961;QSTRAND=+ GT:DP:AD 0|1:18:13,5 ./.:44:22,22 1|0:32:24,8 +chr20 946899 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=903046;QSTRAND=+ GT:DP:AD 0|1:35:16,19 ./.:30:7,23 1|0:22:6,16 +chr20 947202 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=903349;QSTRAND=+ GT:DP:AD 0|1:36:21,15 ./.:18:7,11 1|0:26:17,9 +chr20 947218 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=903365;QSTRAND=+ GT:DP:AD 0|1:20:12,8 ./.:31:14,17 1|0:38:18,20 +chr20 947585 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=903732;QSTRAND=+ GT:DP:AD 0|1:23:16,7 ./.:18:7,11 1|0:30:23,7 +chr20 947624 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=903771;QSTRAND=+ GT:DP:AD 0|1:30:20,10 ./.:32:25,7 1|0:47:25,22 +chr20 947782 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=903929;QSTRAND=+ GT:DP:AD 0|1:35:15,20 ./.:26:7,19 1|0:28:23,5 +chr20 947795 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=903942;QSTRAND=+ GT:DP:AD 0|1:38:20,18 ./.:14:9,5 1|0:26:7,19 +chr20 947914 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=904061;QSTRAND=+ GT:DP:AD 0|1:22:8,14 ./.:36:16,20 1|0:20:5,15 +chr20 948357 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=904504;QSTRAND=+ GT:DP:AD 0|1:27:13,14 ./.:29:22,7 1|0:34:10,24 +chr20 948492 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=904639;QSTRAND=+ GT:DP:AD 0|1:16:8,8 ./.:33:24,9 1|0:19:9,10 +chr20 948493 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=904640;QSTRAND=+ GT:DP:AD 0|1:29:19,10 ./.:31:17,14 1|0:13:8,5 +chr20 948861 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=905008;QSTRAND=+ GT:DP:AD 0|1:36:19,17 ./.:37:19,18 1|0:33:23,10 +chr20 949016 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=905163;QSTRAND=+ GT:DP:AD 0|1:27:20,7 ./.:32:13,19 1|0:24:18,6 +chr20 949837 . C T 60 . QNAME=cluster19_000000F;QSTART=914110;QSTRAND=+ GT:DP:AD ./.:12:6,6 0|1:41:23,18 0|1:24:15,9 +chr20 949917 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=905960;QSTRAND=+ GT:DP:AD 0|1:40:25,15 ./.:31:9,22 1|0:38:18,20 +chr20 950840 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=906883;QSTRAND=+ GT:DP:AD 0|1:40:18,22 ./.:15:5,10 1|0:25:5,20 +chr20 950981 . A AAAATAAAT 60 . QNAME=HG002-S9-H2-000001F;QSTART=907025;QSTRAND=+ GT:DP:AD 0|1:40:25,15 ./.:30:22,8 1|0:32:9,23 +chr20 951023 . A AAAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=907075;QSTRAND=+ GT:DP:AD 0|1:25:7,18 ./.:29:16,13 1|0:40:19,21 +chr20 951100 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=907154;QSTRAND=+ GT:DP:AD 0|1:42:17,25 ./.:24:10,14 1|0:19:11,8 +chr20 951130 . A ATT 60 . QNAME=HG002-S9-H1-000001F;QSTART=932714;QSTRAND=+ GT:DP:AD 1|0:37:24,13 ./.:38:13,25 ./.:20:6,14 +chr20 951130 . A ATTT 60 . QNAME=cluster19_000000F;QSTART=915404;QSTRAND=+ GT:DP:AD ./.:39:17,22 0|1:40:15,25 ./.:36:18,18 +chr20 951130 . A ATTTTT 60 . QNAME=cluster23_scaffold_2;QSTART=24741977;QSTRAND=- GT:DP:AD ./.:15:9,6 ./.:31:25,6 0|1:24:9,15 +chr20 951172 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=907213;QSTRAND=+ GT:DP:AD 0|1:36:21,15 ./.:31:9,22 1|0:32:8,24 +chr20 951188 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=907229;QSTRAND=+ GT:DP:AD 0|1:20:13,7 ./.:27:6,21 1|0:24:7,17 +chr20 951376 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=932961;QSTRAND=+ GT:DP:AD 1|1:29:20,9 0|1:42:23,19 1|1:31:6,25 +chr20 951397 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=932982;QSTRAND=+ GT:DP:AD 1|0:39:21,18 ./.:37:18,19 ./.:28:22,6 +chr20 951428 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=933013;QSTRAND=+ GT:DP:AD 1|0:32:10,22 ./.:31:8,23 ./.:41:25,16 +chr20 951612 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=933197;QSTRAND=+ GT:DP:AD 1|0:34:15,19 ./.:32:10,22 ./.:31:11,20 +chr20 951687 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=933272;QSTRAND=+ GT:DP:AD 1|0:39:18,21 ./.:29:15,14 ./.:28:8,20 +chr20 951756 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=933341;QSTRAND=+ GT:DP:AD 1|0:30:25,5 ./.:28:13,15 ./.:36:25,11 +chr20 951868 . C T 60 . QNAME=cluster19_000000F;QSTART=916144;QSTRAND=+ GT:DP:AD ./.:15:6,9 0|1:25:11,14 1|1:27:19,8 +chr20 951870 . T C 60 . QNAME=cluster19_000000F;QSTART=916146;QSTRAND=+ GT:DP:AD ./.:19:12,7 0|1:15:8,7 1|1:34:25,9 +chr20 951975 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=908014;QSTRAND=+ GT:DP:AD 0|1:20:8,12 0|1:29:24,5 1|1:34:23,11 +chr20 952317 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=933902;QSTRAND=+ GT:DP:AD 1|0:22:12,10 ./.:42:23,19 ./.:27:5,22 +chr20 952372 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=933957;QSTRAND=+ GT:DP:AD 1|0:34:13,21 ./.:30:11,19 ./.:38:15,23 +chr20 952391 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=908430;QSTRAND=+ GT:DP:AD 0|1:17:9,8 0|1:22:8,14 1|1:16:7,9 +chr20 952475 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=934060;QSTRAND=+ GT:DP:AD 1|0:30:10,20 ./.:26:18,8 ./.:27:8,19 +chr20 952558 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=908597;QSTRAND=+ GT:DP:AD 0|1:21:16,5 0|1:40:25,15 1|1:47:24,23 +chr20 952594 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=934179;QSTRAND=+ GT:DP:AD 1|0:41:25,16 ./.:17:8,9 ./.:38:13,25 +chr20 952909 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=934494;QSTRAND=+ GT:DP:AD 1|0:35:14,21 ./.:33:24,9 ./.:12:7,5 +chr20 953115 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=909154;QSTRAND=+ GT:DP:AD 0|1:20:6,14 1|1:37:14,23 1|1:40:23,17 +chr20 953360 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=934941;QSTRAND=+ GT:DP:AD 1|0:31:24,7 ./.:31:6,25 ./.:20:12,8 +chr20 953456 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=935037;QSTRAND=+ GT:DP:AD 1|0:37:17,20 ./.:29:8,21 ./.:39:20,19 +chr20 953490 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=935071;QSTRAND=+ GT:DP:AD 1|1:32:19,13 1|1:30:21,9 1|1:30:7,23 +chr20 953507 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=935088;QSTRAND=+ GT:DP:AD 1|0:30:15,15 ./.:35:10,25 ./.:41:22,19 +chr20 953510 . A AT 60 . QNAME=HG002-S9-H2-000001F;QSTART=909546;QSTRAND=+ GT:DP:AD 0|1:30:8,22 1|1:32:11,21 1|1:35:17,18 +chr20 953670 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=909706;QSTRAND=+ GT:DP:AD 0|1:37:24,13 1|1:17:5,12 0|1:31:21,10 +chr20 953831 . T TC 60 . QNAME=HG002-S9-H1-000001F;QSTART=935412;QSTRAND=+ GT:DP:AD 1|0:26:15,11 ./.:23:13,10 ./.:32:21,11 +chr20 953857 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=935438;QSTRAND=+ GT:DP:AD 1|0:29:12,17 ./.:33:15,18 ./.:36:16,20 +chr20 953974 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=935554;QSTRAND=+ GT:DP:AD 1|0:43:20,23 ./.:21:16,5 ./.:38:22,16 +chr20 954305 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=935885;QSTRAND=+ GT:DP:AD 1|1:30:8,22 1|1:25:7,18 0|1:17:12,5 +chr20 954418 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=910454;QSTRAND=+ GT:DP:AD 0|1:27:12,15 1|1:37:16,21 0|1:44:20,24 +chr20 954610 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=24738500;QSTRAND=- GT:DP:AD ./.:24:6,18 ./.:32:12,20 0|1:39:25,14 +chr20 954684 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=936264;QSTRAND=+ GT:DP:AD 1|1:35:19,16 1|1:26:21,5 1|1:25:6,19 +chr20 954686 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=936266;QSTRAND=+ GT:DP:AD 1|1:17:5,12 1|1:45:25,20 0|1:46:22,24 +chr20 954688 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=936268;QSTRAND=+ GT:DP:AD 1|0:24:11,13 ./.:44:23,21 ./.:47:22,25 +chr20 955001 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=936579;QSTRAND=+ GT:DP:AD 1|0:44:22,22 ./.:28:12,16 ./.:42:21,21 +chr20 956302 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=937880;QSTRAND=+ GT:DP:AD 1|0:24:8,16 ./.:35:13,22 ./.:41:20,21 +chr20 956624 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=938202;QSTRAND=+ GT:DP:AD 1|1:24:8,16 1|1:42:21,21 1|1:31:12,19 +chr20 956630 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=938208;QSTRAND=+ GT:DP:AD 1|0:43:23,20 ./.:12:7,5 ./.:23:10,13 +chr20 957046 . C T 60 . QNAME=cluster19_000000F;QSTART=24801067;QSTRAND=- GT:DP:AD ./.:32:14,18 1|0:13:5,8 ./.:27:13,14 +chr20 957302 . G GTA 60 . QNAME=HG002-S9-H1-000001F;QSTART=938881;QSTRAND=+ GT:DP:AD 1|0:46:22,24 ./.:37:25,12 ./.:35:12,23 +chr20 957320 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=938900;QSTRAND=+ GT:DP:AD 1|0:26:6,20 ./.:46:22,24 ./.:38:14,24 +chr20 957322 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=938902;QSTRAND=+ GT:DP:AD 1|0:30:14,16 ./.:35:18,17 ./.:20:9,11 +chr20 957387 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=938967;QSTRAND=+ GT:DP:AD 1|1:24:19,5 1|1:39:19,20 0|1:43:21,22 +chr20 957642 . C CAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=939223;QSTRAND=+ GT:DP:AD 1|0:24:6,18 ./.:42:17,25 ./.:39:15,24 +chr20 957677 . T TAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=939264;QSTRAND=+ GT:DP:AD 1|0:28:8,20 ./.:13:5,8 ./.:45:22,23 +chr20 958217 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=939805;QSTRAND=+ GT:DP:AD 1|0:26:21,5 ./.:39:21,18 ./.:21:12,9 +chr20 958300 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=939888;QSTRAND=+ GT:DP:AD 1|0:32:14,18 ./.:34:11,23 ./.:27:15,12 +chr20 958487 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=940075;QSTRAND=+ GT:DP:AD 1|0:24:9,15 ./.:30:11,19 ./.:36:11,25 +chr20 958518 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=940106;QSTRAND=+ GT:DP:AD 1|0:42:17,25 ./.:21:11,10 ./.:30:6,24 +chr20 958523 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=940111;QSTRAND=+ GT:DP:AD 1|0:27:21,6 ./.:25:19,6 ./.:27:17,10 +chr20 958650 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24734462;QSTRAND=- GT:DP:AD ./.:46:24,22 ./.:23:7,16 0|1:28:5,23 +chr20 958880 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=940468;QSTRAND=+ GT:DP:AD 1|0:32:24,8 ./.:29:17,12 ./.:13:7,6 +chr20 959171 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=940737;QSTRAND=+ GT:DP:AD 1|0:16:11,5 ./.:35:22,13 ./.:44:22,22 +chr20 959315 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=940881;QSTRAND=+ GT:DP:AD 1|0:36:19,17 ./.:35:22,13 ./.:27:8,19 +chr20 959563 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=941129;QSTRAND=+ GT:DP:AD 1|0:21:11,10 ./.:27:7,20 ./.:34:15,19 +chr20 959871 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=941437;QSTRAND=+ GT:DP:AD 1|0:48:23,25 ./.:23:14,9 ./.:18:9,9 +chr20 960669 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=942235;QSTRAND=+ GT:DP:AD 1|0:20:5,15 ./.:30:20,10 ./.:50:25,25 +chr20 960776 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=942342;QSTRAND=+ GT:DP:AD 1|0:33:18,15 ./.:22:5,17 ./.:41:17,24 +chr20 960856 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=942422;QSTRAND=+ GT:DP:AD 1|0:39:22,17 ./.:42:21,21 ./.:25:5,20 +chr20 961022 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=942588;QSTRAND=+ GT:DP:AD 1|0:27:9,18 ./.:33:11,22 ./.:31:20,11 +chr20 961081 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=942647;QSTRAND=+ GT:DP:AD 1|1:31:21,10 1|1:32:14,18 1|1:37:17,20 +chr20 961455 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=943021;QSTRAND=+ GT:DP:AD 1|0:29:16,13 ./.:37:15,22 ./.:18:7,11 +chr20 961789 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=943355;QSTRAND=+ GT:DP:AD 1|0:40:19,21 ./.:30:15,15 ./.:36:20,16 +chr20 961809 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=943375;QSTRAND=+ GT:DP:AD 1|0:30:18,12 ./.:22:7,15 ./.:15:6,9 +chr20 962027 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=943593;QSTRAND=+ GT:DP:AD 1|0:10:5,5 ./.:17:7,10 ./.:16:5,11 +chr20 962140 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=943706;QSTRAND=+ GT:DP:AD 1|0:22:8,14 ./.:20:9,11 ./.:37:20,17 +chr20 962739 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=944305;QSTRAND=+ GT:DP:AD 1|0:32:8,24 ./.:21:5,16 ./.:24:14,10 +chr20 962818 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=944384;QSTRAND=+ GT:DP:AD 1|0:41:18,23 ./.:32:25,7 ./.:28:13,15 +chr20 964006 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=945572;QSTRAND=+ GT:DP:AD 1|0:31:19,12 ./.:35:25,10 ./.:35:19,16 +chr20 964368 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=945934;QSTRAND=+ GT:DP:AD 1|0:45:23,22 ./.:32:14,18 ./.:43:24,19 +chr20 964461 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=946027;QSTRAND=+ GT:DP:AD 1|0:28:8,20 ./.:32:17,15 ./.:27:8,19 +chr20 964587 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=946153;QSTRAND=+ GT:DP:AD 1|0:29:24,5 ./.:21:10,11 ./.:37:13,24 +chr20 964681 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=946247;QSTRAND=+ GT:DP:AD 1|0:26:12,14 ./.:20:11,9 ./.:35:13,22 +chr20 964763 . T TAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=946330;QSTRAND=+ GT:DP:AD 1|0:24:11,13 ./.:34:13,21 ./.:22:13,9 +chr20 964805 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=946373;QSTRAND=+ GT:DP:AD 1|0:25:18,7 ./.:30:16,14 ./.:30:10,20 +chr20 965654 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=947210;QSTRAND=+ GT:DP:AD 1|0:38:13,25 ./.:38:15,23 ./.:12:5,7 +chr20 965660 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=947216;QSTRAND=+ GT:DP:AD 1|0:19:6,13 ./.:37:22,15 ./.:45:20,25 +chr20 965819 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=947375;QSTRAND=+ GT:DP:AD 1|0:29:11,18 ./.:18:6,12 ./.:35:14,21 +chr20 965855 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=947411;QSTRAND=+ GT:DP:AD 1|0:31:15,16 ./.:31:24,7 ./.:40:22,18 +chr20 966123 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=947679;QSTRAND=+ GT:DP:AD 1|0:17:11,6 ./.:19:7,12 ./.:22:14,8 +chr20 966156 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=947712;QSTRAND=+ GT:DP:AD 1|0:26:5,21 ./.:34:14,20 ./.:43:22,21 +chr20 966449 . G GTC 60 . QNAME=HG002-S9-H1-000001F;QSTART=948006;QSTRAND=+ GT:DP:AD 1|0:30:13,17 ./.:33:21,12 ./.:24:5,19 +chr20 966507 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=948065;QSTRAND=+ GT:DP:AD 1|0:19:12,7 ./.:12:6,6 ./.:35:12,23 +chr20 966840 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=948398;QSTRAND=+ GT:DP:AD 1|0:28:10,18 ./.:19:9,10 ./.:47:24,23 +chr20 971192 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=952742;QSTRAND=+ GT:DP:AD 1|0:14:8,6 ./.:19:10,9 ./.:38:23,15 +chr20 971309 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=927343;QSTRAND=+ GT:DP:AD 0|1:34:15,19 ./.:18:7,11 ./.:30:9,21 +chr20 971575 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=927609;QSTRAND=+ GT:DP:AD 0|1:31:12,19 ./.:22:14,8 ./.:39:23,16 +chr20 972263 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=953813;QSTRAND=+ GT:DP:AD 1|1:28:11,17 ./.:40:18,22 ./.:40:24,16 +chr20 972407 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=953957;QSTRAND=+ GT:DP:AD 1|1:34:24,10 ./.:13:7,6 ./.:33:23,10 +chr20 972507 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=928541;QSTRAND=+ GT:DP:AD 0|1:21:10,11 ./.:14:8,6 ./.:24:5,19 +chr20 972633 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=954183;QSTRAND=+ GT:DP:AD 1|1:28:7,21 ./.:35:15,20 ./.:35:20,15 +chr20 972877 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=954427;QSTRAND=+ GT:DP:AD 1|1:13:8,5 ./.:29:22,7 ./.:44:22,22 +chr20 972959 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=954509;QSTRAND=+ GT:DP:AD 1|1:22:13,9 ./.:27:10,17 ./.:21:14,7 +chr20 973459 . A ATTGT 60 . QNAME=cluster19_000000F;QSTART=24784652;QSTRAND=- GT:DP:AD ./.:30:8,22 1|0:34:22,12 1|0:40:20,20 +chr20 973633 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=955179;QSTRAND=+ GT:DP:AD 1|1:33:13,20 ./.:27:8,19 ./.:22:8,14 +chr20 974110 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=930140;QSTRAND=+ GT:DP:AD 0|1:32:11,21 ./.:30:17,13 ./.:43:23,20 +chr20 974769 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=956315;QSTRAND=+ GT:DP:AD 1|1:31:18,13 ./.:35:20,15 ./.:36:14,22 +chr20 975693 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=957239;QSTRAND=+ GT:DP:AD 1|0:29:11,18 ./.:20:13,7 ./.:45:24,21 +chr20 976042 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=957588;QSTRAND=+ GT:DP:AD 1|1:47:24,23 ./.:30:12,18 1|0:34:15,19 +chr20 976694 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=958240;QSTRAND=+ GT:DP:AD 1|0:47:23,24 ./.:20:13,7 ./.:38:14,24 +chr20 977237 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=958783;QSTRAND=+ GT:DP:AD 1|0:16:9,7 ./.:22:11,11 ./.:22:12,10 +chr20 977764 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=959310;QSTRAND=+ GT:DP:AD 1|0:20:8,12 ./.:34:24,10 ./.:28:23,5 +chr20 978561 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=24714555;QSTRAND=- GT:DP:AD ./.:23:18,5 ./.:17:5,12 0|1:32:25,7 +chr20 978696 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=960242;QSTRAND=+ GT:DP:AD 1|0:33:18,15 ./.:42:18,24 ./.:32:7,25 +chr20 979248 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=960794;QSTRAND=+ GT:DP:AD 1|0:24:11,13 ./.:31:24,7 ./.:14:6,8 +chr20 980145 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=961691;QSTRAND=+ GT:DP:AD 1|0:39:16,23 ./.:29:17,12 ./.:36:18,18 +chr20 980577 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=936607;QSTRAND=+ GT:DP:AD 0|1:16:9,7 1|0:26:15,11 ./.:37:19,18 +chr20 980652 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=962198;QSTRAND=+ GT:DP:AD 1|0:27:14,13 ./.:46:21,25 ./.:26:6,20 +chr20 980884 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=962430;QSTRAND=+ GT:DP:AD 1|0:20:9,11 ./.:32:19,13 ./.:30:10,20 +chr20 981108 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=962654;QSTRAND=+ GT:DP:AD 1|0:38:17,21 ./.:25:13,12 ./.:23:7,16 +chr20 981138 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=962684;QSTRAND=+ GT:DP:AD 1|0:16:7,9 ./.:34:20,14 ./.:26:20,6 +chr20 984922 . C CCCAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=966469;QSTRAND=+ GT:DP:AD 1|0:33:12,21 ./.:18:5,13 0|1:34:25,9 +chr20 990421 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=971971;QSTRAND=+ GT:DP:AD 1|0:32:22,10 ./.:31:15,16 ./.:40:24,16 +chr20 991150 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=972700;QSTRAND=+ GT:DP:AD 1|0:29:19,10 ./.:30:13,17 ./.:29:7,22 +chr20 991319 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=972869;QSTRAND=+ GT:DP:AD 1|0:26:17,9 ./.:13:7,6 ./.:42:20,22 +chr20 991428 . A AT 60 . QNAME=cluster19_000000F;QSTART=955698;QSTRAND=+ GT:DP:AD ./.:24:18,6 0|1:32:21,11 ./.:33:10,23 +chr20 992032 . G GGGAC 60 . QNAME=cluster23_scaffold_3;QSTART=24717528;QSTRAND=- GT:DP:AD ./.:40:15,25 ./.:24:17,7 1|1:10:5,5 +chr20 992091 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=973641;QSTRAND=+ GT:DP:AD 1|0:39:14,25 ./.:26:21,5 ./.:31:8,23 +chr20 992263 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=24717296;QSTRAND=- GT:DP:AD ./.:44:21,23 ./.:22:11,11 1|0:34:9,25 +chr20 992288 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=973838;QSTRAND=+ GT:DP:AD 1|0:29:6,23 ./.:34:15,19 ./.:35:14,21 +chr20 992532 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=974082;QSTRAND=+ GT:DP:AD 1|0:26:20,6 ./.:31:15,16 ./.:40:21,19 +chr20 992797 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=974347;QSTRAND=+ GT:DP:AD 1|0:18:8,10 ./.:32:22,10 ./.:25:19,6 +chr20 993026 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=974576;QSTRAND=+ GT:DP:AD 1|0:26:16,10 ./.:30:22,8 ./.:36:18,18 +chr20 993059 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=974609;QSTRAND=+ GT:DP:AD 1|0:29:9,20 ./.:29:12,17 ./.:34:14,20 +chr20 993443 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=974993;QSTRAND=+ GT:DP:AD 1|0:26:17,9 ./.:31:16,15 ./.:27:21,6 +chr20 993795 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=975345;QSTRAND=+ GT:DP:AD 1|0:41:24,17 ./.:36:19,17 ./.:40:20,20 +chr20 993846 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=975396;QSTRAND=+ GT:DP:AD 1|0:41:16,25 ./.:40:19,21 ./.:32:25,7 +chr20 993854 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=975404;QSTRAND=+ GT:DP:AD 1|0:29:13,16 ./.:32:15,17 ./.:41:24,17 +chr20 993856 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=975406;QSTRAND=+ GT:DP:AD 1|0:22:6,16 ./.:20:14,6 ./.:24:5,19 +chr20 994379 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=975929;QSTRAND=+ GT:DP:AD 1|1:48:23,25 1|0:31:21,10 1|1:19:8,11 +chr20 994584 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=976134;QSTRAND=+ GT:DP:AD 1|0:32:25,7 ./.:19:6,13 ./.:30:7,23 +chr20 994605 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=976155;QSTRAND=+ GT:DP:AD 1|0:40:16,24 ./.:35:22,13 ./.:17:5,12 +chr20 996521 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=978071;QSTRAND=+ GT:DP:AD 1|0:17:10,7 ./.:39:24,15 ./.:26:14,12 +chr20 999077 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=980627;QSTRAND=+ GT:DP:AD 1|0:19:8,11 ./.:27:14,13 ./.:40:16,24 +chr20 63971 . TTCCATTCCAC T 60 . QNAME=cluster19_000000F;QSTART=25698928;QSTRAND=- GT:DP:AD ./.:17:12,5 1|0:42:24,18 ./.:33:14,19 +chr20 66141 . AATTCC A 60 . QNAME=cluster23_scaffold_3;QSTART=25645835;QSTRAND=- GT:DP:AD ./.:18:10,8 ./.:43:18,25 1|1:32:16,16 +chr20 72765 . TA T 60 . QNAME=cluster19_000000F;QSTART=25690125;QSTRAND=- GT:DP:AD ./.:39:16,23 1|0:48:24,24 ./.:24:15,9 +chr20 77736 . CA C 60 . QNAME=cluster19_000000F;QSTART=25685155;QSTRAND=- GT:DP:AD ./.:34:11,23 1|0:30:14,16 ./.:41:25,16 +chr20 89843 . CTCTT C 60 . QNAME=cluster19_000000F;QSTART=25673044;QSTRAND=- GT:DP:AD ./.:28:13,15 1|0:15:6,9 ./.:37:23,14 +chr20 91463 . TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=70391;QSTRAND=+ GT:DP:AD 1|1:38:15,23 1|0:37:25,12 ./.:23:10,13 +chr20 92969 . N . . END=92971;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 1/1:2 1/1:2 0/0:0 +chr20 92971 . N . . . SEGCNT=1 GT:SEG 1/1:2 0/0:0 0/0:0 +chr20 102609 . N . . END=102612;SVTYPE=DEL;SVLEN=3;SEGCNT=3 GT:SEG 1/1:2 1/1:2 0/1:1 +chr20 102612 . N . . END=102618;SVTYPE=DEL;SVLEN=6;SEGCNT=2 GT:SEG 0/1:1 1/1:2 0/1:1 +chr20 102618 . N . . END=102632;SVTYPE=DEL;SVLEN=14;SEGCNT=1 GT:SEG 0/1:1 0/0:0 0/0:0 +chr20 105364 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=84269;QSTRAND=+ GT:DP:AD 1|1:33:12,21 ./.:31:13,18 ./.:42:24,18 +chr20 121439 . TATTCTTCAGCTGTCAAA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=100343;QSTRAND=+ GT:DP:AD 1|1:36:18,18 ./.:32:8,24 ./.:39:14,25 +chr20 128517 . CA C 60 . QNAME=cluster19_000000F;QSTART=25634378;QSTRAND=- GT:DP:AD ./.:26:21,5 1|0:19:10,9 ./.:45:20,25 +chr20 140859 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=94325;QSTRAND=+ GT:DP:AD 0|1:27:6,21 1|0:23:18,5 ./.:29:11,18 +chr20 141634 . GA G 60 . QNAME=cluster19_000000F;QSTART=25621243;QSTRAND=- GT:DP:AD ./.:43:22,21 1|0:36:18,18 ./.:30:8,22 +chr20 145514 . GCAAA G 60 . QNAME=cluster19_000000F;QSTART=25617362;QSTRAND=- GT:DP:AD ./.:22:13,9 1|0:33:22,11 ./.:40:21,19 +chr20 145669 . ACC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=124565;QSTRAND=+ GT:DP:AD 1|1:31:20,11 1|0:32:17,15 1|0:19:10,9 +chr20 150864 . CTCT C 60 . QNAME=cluster19_000000F;QSTART=25611949;QSTRAND=- GT:DP:AD ./.:30:12,18 1|1:14:5,9 ./.:25:19,6 +chr20 151663 . TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=130626;QSTRAND=+ GT:DP:AD 1|1:32:14,18 1|1:31:9,22 1|1:29:24,5 +chr20 152450 . N . . END=152453;SVTYPE=DEL;SVLEN=3;SEGCNT=2 GT:SEG 1/1:2 0/0:0 1/1:2 +chr20 152453 . N . . . SEGCNT=1 GT:SEG 1/1:2 0/0:0 0/1:1 +chr20 153787 . CAAAAAAAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=132747;QSTRAND=+ GT:DP:AD 1|1:36:19,17 1|1:23:11,12 1|1:20:13,7 +chr20 154475 . TGCTC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=133456;QSTRAND=+ GT:DP:AD 1|1:33:8,25 1|1:36:21,15 1|1:28:20,8 +chr20 156877 . GTA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=135855;QSTRAND=+ GT:DP:AD 1|1:35:19,16 1|1:19:8,11 1|1:39:16,23 +chr20 157537 . GC G 60 . QNAME=HG002-S9-H2-000001F;QSTART=111079;QSTRAND=+ GT:DP:AD 0|1:39:15,24 1|1:15:7,8 ./.:41:22,19 +chr20 157922 . AATAT A 60 . QNAME=cluster23_scaffold_2;QSTART=25538608;QSTRAND=- GT:DP:AD ./.:19:12,7 ./.:33:17,16 0|1:27:5,22 +chr20 157927 . N . . END=157929;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 0/1:1 0/0:0 0/1:1 +chr20 157929 . N . . END=157934;SVTYPE=DEL;SVLEN=5;SEGCNT=3 GT:SEG 1/1:2 1/1:2 0/1:1 +chr20 157934 . N . . END=157936;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 1/1:2 1/1:2 0/0:0 +chr20 157936 . N . . END=157938;SVTYPE=DEL;SVLEN=2;SEGCNT=1 GT:SEG 0/1:1 1/1:2 0/0:0 +chr20 159755 . TTTG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=138742;QSTRAND=+ GT:DP:AD 1|1:29:17,12 1|1:24:7,17 1|1:38:18,20 +chr20 159952 . AG A 60 . QNAME=HG002-S9-H1-000001F;QSTART=138936;QSTRAND=+ GT:DP:AD 1|0:44:20,24 ./.:27:6,21 1|1:23:15,8 +chr20 164243 . CCTT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=117776;QSTRAND=+ GT:DP:AD 0|1:30:7,23 1|1:28:9,19 ./.:31:20,11 +chr20 166960 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=145945;QSTRAND=+ GT:DP:AD 1|0:40:20,20 ./.:30:15,15 1|1:46:21,25 +chr20 168478 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=147462;QSTRAND=+ GT:DP:AD 1|0:31:11,20 ./.:16:8,8 1|1:36:25,11 +chr20 170008 . CTACA C 60 . QNAME=cluster23_scaffold_2;QSTART=25526509;QSTRAND=- GT:DP:AD ./.:40:15,25 ./.:31:10,21 0|1:23:12,11 +chr20 173791 . CCTT C 60 . QNAME=cluster23_scaffold_2;QSTART=25522728;QSTRAND=- GT:DP:AD ./.:32:23,9 ./.:44:19,25 0|1:44:19,25 +chr20 174270 . TC T 60 . QNAME=cluster23_scaffold_2;QSTART=25522252;QSTRAND=- GT:DP:AD ./.:40:16,24 ./.:15:10,5 0|1:26:6,20 +chr20 181704 . AAAAT A 60 . QNAME=cluster23_scaffold_2;QSTART=25514815;QSTRAND=- GT:DP:AD ./.:37:24,13 ./.:38:17,21 0|1:38:25,13 +chr20 191726 . N . . END=191728;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 0/1:1 1/1:2 0/1:1 +chr20 191728 . N . . . SEGCNT=1 GT:SEG 0/0:0 0/0:0 0/1:1 +chr20 195745 . N . . END=195750;SVTYPE=DEL;SVLEN=5;SEGCNT=2 GT:SEG 0/1:1 1/1:2 0/1:1 +chr20 195750 . N . . END=195752;SVTYPE=DEL;SVLEN=2;SEGCNT=1 GT:SEG 0/1:1 1/1:2 0/0:0 +chr20 201932 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=155474;QSTRAND=+ GT:DP:AD 0|1:29:21,8 ./.:24:17,7 ./.:30:7,23 +chr20 203620 . TCCCTCCC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=182608;QSTRAND=+ GT:DP:AD 1|0:32:8,24 ./.:22:5,17 1|0:28:5,23 +chr20 206175 . TAAAA T 60 . QNAME=cluster23_scaffold_2;QSTART=25490302;QSTRAND=- GT:DP:AD ./.:39:23,16 ./.:28:19,9 0|1:39:21,18 +chr20 208792 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=187775;QSTRAND=+ GT:DP:AD 1|0:39:21,18 ./.:39:22,17 1|1:45:20,25 +chr20 212919 . AC A 60 . QNAME=cluster23_scaffold_2;QSTART=25483562;QSTRAND=- GT:DP:AD ./.:34:21,13 ./.:18:10,8 0|1:30:15,15 +chr20 214796 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=193778;QSTRAND=+ GT:DP:AD 1|0:34:14,20 ./.:30:21,9 ./.:24:10,14 +chr20 217714 . ATATG A 60 . QNAME=cluster23_scaffold_2;QSTART=25478766;QSTRAND=- GT:DP:AD ./.:14:8,6 ./.:16:7,9 0|1:24:5,19 +chr20 220972 . CTT C 60 . QNAME=cluster23_scaffold_2;QSTART=25475512;QSTRAND=- GT:DP:AD ./.:28:12,16 ./.:14:8,6 0|1:41:17,24 +chr20 221511 . GGGAA G 60 . QNAME=cluster23_scaffold_3;QSTART=25490352;QSTRAND=- GT:DP:AD ./.:19:10,9 ./.:18:5,13 1|1:37:12,25 +chr20 228258 . GCTTCTAATGTTTTTAT G 60 . QNAME=cluster23_scaffold_2;QSTART=25468232;QSTRAND=- GT:DP:AD ./.:49:25,24 ./.:19:12,7 0|1:28:5,23 +chr20 232484 . TG T 60 . QNAME=cluster23_scaffold_3;QSTART=25479366;QSTRAND=- GT:DP:AD ./.:43:25,18 ./.:32:7,25 1|0:26:11,15 +chr20 233198 . TGACGG T 60 . QNAME=cluster23_scaffold_3;QSTART=25478653;QSTRAND=- GT:DP:AD ./.:30:7,23 ./.:31:12,19 1|0:20:7,13 +chr20 234144 . N . . END=234146;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 1/1:2 1/1:2 0/1:1 +chr20 234146 . N . . END=234149;SVTYPE=DEL;SVLEN=3;SEGCNT=1 GT:SEG 0/0:0 0/0:0 0/1:1 +chr20 236273 . CTAAG C 60 . QNAME=cluster23_scaffold_3;QSTART=25475587;QSTRAND=- GT:DP:AD ./.:37:21,16 ./.:25:11,14 1|0:33:19,14 +chr20 236959 . CTT C 60 . QNAME=cluster23_scaffold_3;QSTART=25474905;QSTRAND=- GT:DP:AD ./.:23:8,15 ./.:38:15,23 1|0:38:24,14 +chr20 238622 . ACAAGGT A 60 . QNAME=cluster23_scaffold_3;QSTART=25473243;QSTRAND=- GT:DP:AD ./.:33:24,9 ./.:49:24,25 1|1:41:22,19 +chr20 243817 . N . . . SEGCNT=1 GT:SEG 0/0:0 0/0:0 1/1:2 +chr20 243818 . N . . END=243820;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 1/1:2 0/1:1 1/1:2 +chr20 244104 . GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=223099;QSTRAND=+ GT:DP:AD 1|1:17:8,9 1|0:18:6,12 ./.:24:19,5 +chr20 245437 . N . . END=245443;SVTYPE=DEL;SVLEN=6;SEGCNT=1 GT:SEG 0/0:0 0/0:0 1/1:2 +chr20 245443 . N . . END=245446;SVTYPE=DEL;SVLEN=3;SEGCNT=3 GT:SEG 0/1:1 0/1:1 1/1:2 +chr20 245446 . N . . END=245448;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 0/0:0 0/1:1 1/1:2 +chr20 245448 . N . . END=245452;SVTYPE=DEL;SVLEN=4;SEGCNT=1 GT:SEG 0/0:0 0/1:1 0/0:0 +chr20 247501 . N . . END=247505;SVTYPE=DEL;SVLEN=4;SEGCNT=1 GT:SEG 0/0:0 0/0:0 0/1:1 +chr20 247505 . N . . END=247508;SVTYPE=DEL;SVLEN=3;SEGCNT=2 GT:SEG 0/0:0 0/0:0 1/1:2 +chr20 247508 . N . . END=247512;SVTYPE=DEL;SVLEN=4;SEGCNT=1 GT:SEG 0/0:0 0/0:0 0/1:1 +chr20 247516 . N . . END=247521;SVTYPE=DEL;SVLEN=5;SEGCNT=2 GT:SEG 1/1:2 1/1:2 0/0:0 +chr20 247521 . N . . END=247525;SVTYPE=DEL;SVLEN=4;SEGCNT=1 GT:SEG 0/0:0 0/1:1 0/0:0 +chr20 248740 . CA C 60 . QNAME=cluster23_scaffold_3;QSTART=25463144;QSTRAND=- GT:DP:AD ./.:22:8,14 ./.:28:5,23 1|0:22:17,5 +chr20 249417 . N . . END=249420;SVTYPE=DEL;SVLEN=3;SEGCNT=2 GT:SEG 0/0:0 0/1:1 1/1:2 +chr20 249420 . N . . . SEGCNT=1 GT:SEG 0/0:0 0/0:0 1/1:2 +chr20 252881 . GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=231885;QSTRAND=+ GT:DP:AD 1|0:32:10,22 ./.:21:16,5 1|1:47:24,23 +chr20 255818 . GAT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=234829;QSTRAND=+ GT:DP:AD 1|0:30:6,24 ./.:25:9,16 1|1:26:13,13 +chr20 257008 . CAGAT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=236017;QSTRAND=+ GT:DP:AD 1|1:26:20,6 0|1:36:18,18 1|1:35:15,20 +chr20 257794 . CTGGTCT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=236800;QSTRAND=+ GT:DP:AD 1|0:28:21,7 0|1:43:19,24 1|1:36:20,16 +chr20 261185 . TTTTG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=240218;QSTRAND=+ GT:DP:AD 1|0:20:7,13 ./.:22:17,5 1|1:19:9,10 +chr20 263497 . TGTGTGTGC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=242526;QSTRAND=+ GT:DP:AD 1|0:40:24,16 ./.:31:24,7 1|1:26:7,19 +chr20 265021 . GT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=244042;QSTRAND=+ GT:DP:AD 1|0:20:9,11 ./.:41:21,20 ./.:23:16,7 +chr20 265390 . AAAG A 60 . QNAME=HG002-S9-H1-000001F;QSTART=244410;QSTRAND=+ GT:DP:AD 1|0:25:15,10 ./.:35:12,23 1|1:26:9,17 +chr20 266980 . CCT C 60 . QNAME=cluster23_scaffold_3;QSTART=25444877;QSTRAND=- GT:DP:AD ./.:32:23,9 ./.:22:8,14 1|1:29:12,17 +chr20 269686 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=223234;QSTRAND=+ GT:DP:AD 0|1:31:10,21 ./.:37:16,21 ./.:27:20,7 +chr20 270732 . ACTT A 60 . QNAME=cluster19_000000F;QSTART=229922;QSTRAND=+ GT:DP:AD ./.:24:17,7 0|1:25:19,6 ./.:30:11,19 +chr20 271440 . N . . END=271443;SVTYPE=DEL;SVLEN=3;SEGCNT=1 GT:SEG 0/0:0 0/0:0 0/1:1 +chr20 271443 . N . . END=271448;SVTYPE=DEL;SVLEN=5;SEGCNT=2 GT:SEG 0/0:0 0/1:1 0/1:1 +chr20 271448 . N . . END=271453;SVTYPE=DEL;SVLEN=5;SEGCNT=1 GT:SEG 0/0:0 0/0:0 0/1:1 +chr20 272200 . TA T 60 . QNAME=cluster23_scaffold_3;QSTART=25439670;QSTRAND=- GT:DP:AD ./.:23:12,11 ./.:27:12,15 1|0:46:21,25 +chr20 273903 . N . . END=273908;SVTYPE=DEL;SVLEN=5;SEGCNT=2 GT:SEG 0/0:0 0/0:0 1/1:2 +chr20 273908 . N . . END=273912;SVTYPE=DEL;SVLEN=4;SEGCNT=1 GT:SEG 0/0:0 0/0:0 0/1:1 +chr20 274820 . TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=253837;QSTRAND=+ GT:DP:AD 1|0:17:12,5 ./.:39:14,25 ./.:48:25,23 +chr20 280211 . CAACAACAACAATTGTACTTCCCTAAGGTTACACCCAGCAGGTGCATAAAACCTACAGTAACAAT C 60 . QNAME=cluster23_scaffold_3;QSTART=25431380;QSTRAND=-;SVTYPE=DEL;SVLEN=-64 GT:DP:AD ./.:42:24,18 ./.:45:20,25 1/0:39:24,15 +chr20 280403 . TAAC T 60 . QNAME=cluster23_scaffold_3;QSTART=25431252;QSTRAND=- GT:DP:AD ./.:20:15,5 ./.:31:23,8 1|0:39:16,23 +chr20 286163 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=265353;QSTRAND=+ GT:DP:AD 1|0:13:6,7 ./.:19:10,9 ./.:18:12,6 +chr20 289773 . TC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=268985;QSTRAND=+ GT:DP:AD 1|0:29:19,10 ./.:35:22,13 1|0:27:6,21 +chr20 291169 . TTCTC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=270382;QSTRAND=+ GT:DP:AD 1|0:41:25,16 ./.:27:21,6 1|0:30:13,17 +chr20 292806 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=272015;QSTRAND=+ GT:DP:AD 1|0:33:17,16 ./.:28:7,21 1|0:22:12,10 +chr20 293433 . GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=272641;QSTRAND=+ GT:DP:AD 1|0:36:16,20 ./.:22:17,5 ./.:32:25,7 +chr20 294073 . AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=273280;QSTRAND=+ GT:DP:AD 1|0:32:23,9 ./.:34:20,14 ./.:46:22,24 +chr20 297482 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=276688;QSTRAND=+ GT:DP:AD 1|0:23:7,16 ./.:29:23,6 1|0:40:16,24 +chr20 304504 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=258682;QSTRAND=+ GT:DP:AD 0|1:39:22,17 1|0:41:25,16 0|1:16:8,8 +chr20 306004 . TAAATA T 60 . QNAME=cluster19_000000F;QSTART=265743;QSTRAND=+ GT:DP:AD ./.:38:19,19 0|1:14:8,6 ./.:45:24,21 +chr20 307712 . CA C 60 . QNAME=cluster19_000000F;QSTART=25454350;QSTRAND=- GT:DP:AD ./.:36:20,16 1|0:33:9,24 0|1:21:13,8 +chr20 314905 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=269258;QSTRAND=+ GT:DP:AD 0|1:34:9,25 ./.:19:6,13 ./.:24:15,9 +chr20 316724 . N . . END=316727;SVTYPE=DEL;SVLEN=3;SEGCNT=2 GT:SEG 0/1:1 0/0:0 0/1:1 +chr20 316727 . N . . . SEGCNT=1 GT:SEG 0/0:0 0/0:0 0/1:1 +chr20 317772 . GA G 60 . QNAME=HG002-S9-H2-000001F;QSTART=272128;QSTRAND=+ GT:DP:AD 0|1:28:8,20 ./.:34:13,21 1|0:22:7,15 +chr20 318941 . AC A 60 . QNAME=HG002-S9-H2-000001F;QSTART=273296;QSTRAND=+ GT:DP:AD 0|1:35:15,20 1|1:21:15,6 1|1:31:8,23 +chr20 319633 . CCA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=299016;QSTRAND=+ GT:DP:AD 1|1:47:22,25 0|1:36:13,23 1|0:37:15,22 +chr20 320255 . CA C 60 . QNAME=cluster23_scaffold_2;QSTART=25375342;QSTRAND=- GT:DP:AD ./.:27:9,18 ./.:37:25,12 0|1:31:9,22 +chr20 328517 . N . . END=328519;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 1/1:2 1/1:2 1/1:2 +chr20 328519 . N . . . SEGCNT=1 GT:SEG 1/1:2 0/0:0 0/1:1 +chr20 328569 . GA G 60 . QNAME=cluster19_000000F;QSTART=25433495;QSTRAND=- GT:DP:AD ./.:17:9,8 1|0:46:25,21 ./.:28:21,7 +chr20 336200 . N . . END=336204;SVTYPE=DEL;SVLEN=4;SEGCNT=2 GT:SEG 0/1:1 0/0:0 0/1:1 +chr20 336204 . N . . END=336210;SVTYPE=DEL;SVLEN=6;SEGCNT=1 GT:SEG 0/1:1 0/0:0 0/0:0 +chr20 336263 . TTC T 60 . QNAME=cluster19_000000F;QSTART=25425802;QSTRAND=- GT:DP:AD ./.:27:20,7 1|0:34:18,16 ./.:29:11,18 +chr20 336308 . N . . END=336321;SVTYPE=DEL;SVLEN=13;SEGCNT=2 GT:SEG 1/1:2 0/1:1 1/1:2 +chr20 336321 . N . . END=336324;SVTYPE=DEL;SVLEN=3;SEGCNT=1 GT:SEG 0/0:0 0/0:0 0/1:1 +chr20 340238 . CTTTCT C 60 . QNAME=cluster23_scaffold_2;QSTART=25355374;QSTRAND=- GT:DP:AD ./.:34:24,10 ./.:35:18,17 0|1:16:7,9 +chr20 341505 . N . . END=341507;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 1/1:2 0/0:0 0/0:0 +chr20 341507 . N . . END=341511;SVTYPE=DEL;SVLEN=4;SEGCNT=1 GT:SEG 0/1:1 0/0:0 0/0:0 +chr20 342602 . CTTTTTTTT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=296932;QSTRAND=+ GT:DP:AD 0|1:20:15,5 ./.:39:25,14 ./.:25:12,13 +chr20 348484 . CGTGTGT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=302812;QSTRAND=+ GT:DP:AD 0|1:35:15,20 ./.:34:23,11 ./.:17:12,5 +chr20 350477 . TA T 60 . QNAME=HG002-S9-H2-000001F;QSTART=304799;QSTRAND=+ GT:DP:AD 0|1:21:14,7 ./.:34:10,24 ./.:39:14,25 +chr20 350646 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=330033;QSTRAND=+ GT:DP:AD 1|0:32:20,12 1|1:40:22,18 ./.:33:22,11 +chr20 350660 . AAAAAAAAAAAAAAAAAG A 60 . QNAME=HG002-S9-H2-000001F;QSTART=304981;QSTRAND=+ GT:DP:AD 0|1:17:5,12 ./.:21:9,12 ./.:26:17,9 +chr20 353673 . TC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=333059;QSTRAND=+ GT:DP:AD 1|0:31:16,15 1|1:40:18,22 1|1:44:19,25 +chr20 356342 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=335727;QSTRAND=+ GT:DP:AD 1|0:36:24,12 1|1:21:11,10 1|1:28:13,15 +chr20 356748 . ACC A 60 . QNAME=cluster19_000000F;QSTART=25405319;QSTRAND=- GT:DP:AD ./.:30:18,12 1|0:26:12,14 ./.:44:23,21 +chr20 358579 . N . . END=358581;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 1/1:2 0/1:1 0/0:0 +chr20 358581 . N . . . SEGCNT=1 GT:SEG 0/1:1 0/0:0 0/0:0 +chr20 359400 . GCAC G 60 . QNAME=HG002-S9-H1-000001F;QSTART=338783;QSTRAND=+ GT:DP:AD 1|0:25:8,17 0|1:32:14,18 1|1:31:13,18 +chr20 365798 . N . . END=365800;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 1/1:2 0/1:1 0/1:1 +chr20 365800 . N . . . SEGCNT=1 GT:SEG 0/0:0 0/1:1 0/0:0 +chr20 366058 . AGCCTCCCAAAGGAG A 60 . QNAME=cluster19_000000F;QSTART=25396010;QSTRAND=- GT:DP:AD ./.:12:5,7 1|0:13:8,5 ./.:32:23,9 +chr20 367164 . TCGCA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=346545;QSTRAND=+ GT:DP:AD 1|0:43:21,22 ./.:20:14,6 1|1:18:10,8 +chr20 367214 . AAAACAAAC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=346591;QSTRAND=+ GT:DP:AD 1|0:23:6,17 ./.:36:24,12 1|1:45:20,25 +chr20 367244 . AAAC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=346613;QSTRAND=+ GT:DP:AD 1|0:43:23,20 ./.:29:23,6 1|1:29:6,23 +chr20 368284 . CTT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=322590;QSTRAND=+ GT:DP:AD 0|1:38:17,21 1|0:36:21,15 ./.:20:12,8 +chr20 368677 . ACT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=322981;QSTRAND=+ GT:DP:AD 0|1:26:9,17 1|0:39:20,19 ./.:23:15,8 +chr20 369657 . CAAAAAA C 60 . QNAME=cluster19_000000F;QSTART=25392425;QSTRAND=- GT:DP:AD ./.:22:14,8 1|0:44:22,22 ./.:40:19,21 +chr20 375218 . GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=354588;QSTRAND=+ GT:DP:AD 1|0:26:18,8 ./.:43:21,22 ./.:24:10,14 +chr20 377153 . N . . END=377155;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 0/1:1 0/1:1 0/0:0 +chr20 377155 . N . . END=377160;SVTYPE=DEL;SVLEN=5;SEGCNT=1 GT:SEG 0/0:0 0/1:1 0/0:0 +chr20 377503 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=356876;QSTRAND=+ GT:DP:AD 1|0:19:5,14 1|1:24:6,18 ./.:34:25,9 +chr20 377680 . GT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=357052;QSTRAND=+ GT:DP:AD 1|1:42:25,17 1|1:17:7,10 ./.:24:16,8 +chr20 378708 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=333008;QSTRAND=+ GT:DP:AD 0|1:31:24,7 ./.:35:11,24 ./.:15:5,10 +chr20 380283 . TAA T 60 . QNAME=cluster19_000000F;QSTART=25381808;QSTRAND=- GT:DP:AD ./.:28:9,19 1|1:32:14,18 ./.:33:22,11 +chr20 380684 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=360055;QSTRAND=+ GT:DP:AD 1|0:15:10,5 1|1:31:9,22 ./.:24:14,10 +chr20 380878 . TGATTAGCTCCGGTTTGCATCACCCGGACCGGGG T 60 . QNAME=cluster23_scaffold_3;QSTART=25330580;QSTRAND=-;SVTYPE=DEL;SVLEN=-33 GT:DP:AD ./.:13:5,8 ./.:24:18,6 1/0:18:13,5 +chr20 381585 . AG A 60 . QNAME=cluster23_scaffold_3;QSTART=25329906;QSTRAND=- GT:DP:AD ./.:24:6,18 ./.:32:17,15 1|0:33:22,11 +chr20 382124 . TGTGC T 60 . QNAME=cluster23_scaffold_2;QSTART=25313491;QSTRAND=- GT:DP:AD ./.:22:6,16 ./.:35:12,23 0|1:26:8,18 +chr20 385414 . AT A 60 . QNAME=cluster19_000000F;QSTART=345340;QSTRAND=+ GT:DP:AD ./.:24:13,11 0|1:37:13,24 1|0:39:17,22 +chr20 387554 . GA G 60 . QNAME=cluster19_000000F;QSTART=347479;QSTRAND=+ GT:DP:AD ./.:44:21,23 0|1:24:6,18 ./.:24:13,11 +chr20 391001 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=345301;QSTRAND=+ GT:DP:AD 0|1:27:22,5 1|0:15:5,10 0|1:30:25,5 +chr20 392021 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=346320;QSTRAND=+ GT:DP:AD 0|1:40:17,23 ./.:27:22,5 ./.:17:5,12 +chr20 393337 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=347553;QSTRAND=+ GT:DP:AD 0|1:24:18,6 1|0:23:9,14 1|1:23:7,16 +chr20 395162 . CT C 60 . QNAME=cluster19_000000F;QSTART=25366946;QSTRAND=- GT:DP:AD ./.:21:10,11 1|0:22:8,14 ./.:41:22,19 +chr20 402478 . CAAAAAAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=381850;QSTRAND=+ GT:DP:AD 1|0:16:8,8 1|0:37:16,21 ./.:34:13,21 +chr20 405155 . TCA T 60 . QNAME=cluster19_000000F;QSTART=25356960;QSTRAND=- GT:DP:AD ./.:35:23,12 1|0:39:17,22 ./.:28:5,23 +chr20 405931 . GTTCT G 60 . QNAME=cluster19_000000F;QSTART=365862;QSTRAND=+ GT:DP:AD ./.:26:6,20 0|1:31:7,24 1|0:33:14,19 +chr20 405942 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=360160;QSTRAND=+ GT:DP:AD 0|1:16:6,10 ./.:30:19,11 ./.:24:19,5 +chr20 406708 . N . . END=406710;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 0/1:1 0/1:1 0/1:1 +chr20 406710 . N . . END=406712;SVTYPE=DEL;SVLEN=2;SEGCNT=1 GT:SEG 0/0:0 0/1:1 0/1:1 +chr20 407964 . CG C 60 . QNAME=HG002-S9-H1-000001F;QSTART=387342;QSTRAND=+ GT:DP:AD 1|0:40:24,16 1|0:12:5,7 ./.:30:8,22 +chr20 407977 . CG C 60 . QNAME=HG002-S9-H1-000001F;QSTART=387354;QSTRAND=+ GT:DP:AD 1|0:25:6,19 1|0:21:8,13 ./.:24:9,15 +chr20 408008 . GC G 60 . QNAME=HG002-S9-H1-000001F;QSTART=387384;QSTRAND=+ GT:DP:AD 1|0:30:16,14 ./.:19:6,13 ./.:33:8,25 +chr20 409291 . AT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=363547;QSTRAND=+ GT:DP:AD 0|1:42:22,20 ./.:29:24,5 ./.:19:14,5 +chr20 409466 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=363721;QSTRAND=+ GT:DP:AD 0|1:28:10,18 ./.:28:19,9 ./.:26:20,6 +chr20 412325 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=366579;QSTRAND=+ GT:DP:AD 0|1:17:11,6 ./.:42:17,25 ./.:31:23,8 +chr20 413917 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=368170;QSTRAND=+ GT:DP:AD 0|1:41:24,17 0|1:38:24,14 1|1:21:16,5 +chr20 414091 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=393467;QSTRAND=+ GT:DP:AD 1|0:40:15,25 ./.:37:12,25 ./.:37:19,18 +chr20 419860 . AGTGACCCTGCACCTGGCT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=374117;QSTRAND=+ GT:DP:AD 0|1:24:19,5 ./.:14:7,7 1|1:27:8,19 +chr20 422514 . GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=402119;QSTRAND=+ GT:DP:AD 1|0:42:17,25 1|0:50:25,25 ./.:20:5,15 +chr20 425626 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=405231;QSTRAND=+ GT:DP:AD 1|1:14:6,8 1|0:31:21,10 1|1:41:16,25 +chr20 429226 . AT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=383692;QSTRAND=+ GT:DP:AD 0|1:31:21,10 ./.:32:16,16 ./.:33:15,18 +chr20 433739 . AGGCTACCCACACTTCCTG A 60 . QNAME=HG002-S9-H1-000001F;QSTART=413343;QSTRAND=+ GT:DP:AD 1|1:46:21,25 1|0:32:15,17 1|1:43:23,20 +chr20 444562 . GTTTT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=424151;QSTRAND=+ GT:DP:AD 1|0:39:14,25 1|0:34:13,21 ./.:29:7,22 +chr20 446943 . AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=426528;QSTRAND=+ GT:DP:AD 1|1:35:19,16 1|0:25:8,17 ./.:16:9,7 +chr20 448689 . GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=428273;QSTRAND=+ GT:DP:AD 1|0:31:10,21 ./.:44:25,19 ./.:19:12,7 +chr20 449514 . GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=429105;QSTRAND=+ GT:DP:AD 1|1:30:11,19 1|0:18:5,13 1|1:29:10,19 +chr20 453153 . CAAAAAAAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=432743;QSTRAND=+ GT:DP:AD 1|0:30:17,13 1|0:30:21,9 ./.:30:18,12 +chr20 454236 . N . . END=454238;SVTYPE=DEL;SVLEN=2;SEGCNT=3 GT:SEG 1/1:2 0/1:1 0/0:0 +chr20 454238 . N . . . SEGCNT=2 GT:SEG 0/1:1 0/1:1 0/0:0 +chr20 454239 . N . . . SEGCNT=1 GT:SEG 0/1:1 0/0:0 0/0:0 +chr20 456337 . TTTCATCCA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=435923;QSTRAND=+ GT:DP:AD 1|0:45:23,22 1|0:29:10,19 ./.:28:23,5 +chr20 456571 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=411018;QSTRAND=+ GT:DP:AD 0|1:28:18,10 ./.:14:7,7 ./.:37:20,17 +chr20 456933 . N . . END=456935;SVTYPE=DEL;SVLEN=2;SEGCNT=3 GT:SEG 1/1:2 0/1:1 1/1:2 +chr20 456935 . N . . END=456937;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 0/1:1 0/1:1 1/1:2 +chr20 456937 . N . . . SEGCNT=1 GT:SEG 0/1:1 0/0:0 0/0:0 +chr20 460434 . CAAA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=414876;QSTRAND=+ GT:DP:AD 0|1:43:23,20 0|1:32:16,16 1|1:25:10,15 +chr20 465676 . GC G 60 . QNAME=HG002-S9-H1-000001F;QSTART=445253;QSTRAND=+ GT:DP:AD 1|1:27:17,10 1|1:27:6,21 1|1:23:6,17 +chr20 466637 . GTA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=446213;QSTRAND=+ GT:DP:AD 1|0:26:18,8 1|0:29:5,24 ./.:32:19,13 +chr20 475460 . N . . END=475462;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 0/1:1 0/1:1 0/0:0 +chr20 475462 . N . . END=475466;SVTYPE=DEL;SVLEN=4;SEGCNT=1 GT:SEG 0/0:0 0/1:1 0/0:0 +chr20 478540 . TC T 60 . QNAME=HG002-S9-H2-000001F;QSTART=432991;QSTRAND=+ GT:DP:AD 0|1:33:10,23 ./.:22:14,8 ./.:31:14,17 +chr20 485066 . CAAAA C 60 . QNAME=cluster23_scaffold_3;QSTART=25226160;QSTRAND=- GT:DP:AD ./.:21:10,11 ./.:27:20,7 1|0:22:12,10 +chr20 485088 . N . . END=485110;SVTYPE=DEL;SVLEN=22;SEGCNT=1 GT:SEG 0/1:1 0/0:0 0/0:0 +chr20 485110 . N . . END=485114;SVTYPE=DEL;SVLEN=4;SEGCNT=2 GT:SEG 0/1:1 0/1:1 0/0:0 +chr20 485114 . N . . END=485122;SVTYPE=DEL;SVLEN=8;SEGCNT=1 GT:SEG 0/1:1 0/0:0 0/0:0 +chr20 498335 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=452799;QSTRAND=+ GT:DP:AD 0|1:28:6,22 ./.:30:18,12 ./.:46:22,24 +chr20 505869 . AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=485410;QSTRAND=+ GT:DP:AD 1|0:19:5,14 ./.:20:5,15 ./.:22:12,10 +chr20 518713 . N . . END=518715;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 1/1:2 1/1:2 1/1:2 +chr20 518715 . N . . . SEGCNT=1 GT:SEG 0/1:1 0/1:1 0/1:1 +chr20 518933 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=473396;QSTRAND=+ GT:DP:AD 0|1:41:19,22 ./.:36:24,12 ./.:17:7,10 +chr20 524708 . N . . END=524710;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 1/1:2 1/1:2 0/1:1 +chr20 524710 . N . . . SEGCNT=1 GT:SEG 0/1:1 0/1:1 0/0:0 +chr20 525650 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=505187;QSTRAND=+ GT:DP:AD 1|0:29:13,16 ./.:27:11,16 ./.:35:13,22 +chr20 525836 . TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=505372;QSTRAND=+ GT:DP:AD 1|0:30:25,5 ./.:31:20,11 ./.:34:16,18 +chr20 526949 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=506484;QSTRAND=+ GT:DP:AD 1|0:37:21,16 ./.:49:25,24 ./.:41:24,17 +chr20 528594 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=508130;QSTRAND=+ GT:DP:AD 1|0:18:6,12 ./.:28:23,5 ./.:29:18,11 +chr20 532330 . ATT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=511866;QSTRAND=+ GT:DP:AD 1|0:21:10,11 ./.:17:10,7 ./.:17:6,11 +chr20 535034 . CAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=514568;QSTRAND=+ GT:DP:AD 1|0:12:6,6 ./.:22:13,9 ./.:39:16,23 +chr20 535739 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=515271;QSTRAND=+ GT:DP:AD 1|0:15:8,7 ./.:24:18,6 ./.:26:15,11 +chr20 546487 . ACT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=526020;QSTRAND=+ GT:DP:AD 1|0:34:13,21 ./.:26:21,5 ./.:19:13,6 +chr20 548575 . ATATTTT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=528106;QSTRAND=+ GT:DP:AD 1|0:20:14,6 ./.:26:19,7 ./.:41:21,20 +chr20 549649 . GGAAA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=529174;QSTRAND=+ GT:DP:AD 1|0:24:9,15 ./.:33:11,22 ./.:47:22,25 +chr20 552720 . CT C 60 . QNAME=cluster19_000000F;QSTART=25209156;QSTRAND=- GT:DP:AD ./.:38:23,15 1|0:25:12,13 1|1:39:24,15 +chr20 553335 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=507795;QSTRAND=+ GT:DP:AD 0|1:48:23,25 ./.:41:16,25 ./.:31:8,23 +chr20 558579 . ATTTT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=538105;QSTRAND=+ GT:DP:AD 1|1:23:18,5 1|0:22:10,12 ./.:42:19,23 +chr20 560062 . AC A 60 . QNAME=HG002-S9-H2-000001F;QSTART=514523;QSTRAND=+ GT:DP:AD 0|1:33:18,15 ./.:15:7,8 ./.:37:22,15 +chr20 560078 . CAA C 60 . QNAME=cluster19_000000F;QSTART=520277;QSTRAND=+ GT:DP:AD ./.:38:25,13 0|1:35:10,25 1|1:18:7,11 +chr20 560086 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=539610;QSTRAND=+ GT:DP:AD 1|1:24:8,16 1|0:38:19,19 ./.:35:23,12 +chr20 564560 . GTGTT G 60 . QNAME=cluster23_scaffold_3;QSTART=25146650;QSTRAND=- GT:DP:AD ./.:38:13,25 ./.:30:17,13 1|0:25:14,11 +chr20 566178 . AAAAAAT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=545701;QSTRAND=+ GT:DP:AD 1|1:22:9,13 ./.:27:14,13 ./.:34:22,12 +chr20 571992 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=551509;QSTRAND=+ GT:DP:AD 1|0:43:23,20 ./.:48:23,25 ./.:31:17,14 +chr20 577957 . N . . END=577959;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 1/1:2 1/1:2 0/1:1 +chr20 577959 . N . . . SEGCNT=1 GT:SEG 0/0:0 1/1:2 0/0:0 +chr20 578654 . TAC T 60 . QNAME=cluster19_000000F;QSTART=25183217;QSTRAND=- GT:DP:AD ./.:46:24,22 1|1:30:14,16 ./.:25:13,12 +chr20 581995 . N . . END=581997;SVTYPE=DEL;SVLEN=2;SEGCNT=3 GT:SEG 1/1:2 1/1:2 1/1:2 +chr20 581997 . N . . . SEGCNT=2 GT:SEG 0/1:1 1/1:2 0/0:0 +chr20 581998 . N . . . SEGCNT=1 GT:SEG 0/1:1 0/0:0 0/0:0 +chr20 585766 . GTA G 60 . QNAME=HG002-S9-H2-000001F;QSTART=540236;QSTRAND=+ GT:DP:AD 0|1:34:22,12 ./.:28:13,15 0|1:30:20,10 +chr20 586045 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=540513;QSTRAND=+ GT:DP:AD 0|1:26:16,10 ./.:28:13,15 0|1:50:25,25 +chr20 590301 . AAC A 60 . QNAME=HG002-S9-H2-000001F;QSTART=544770;QSTRAND=+ GT:DP:AD 0|1:21:8,13 ./.:13:7,6 0|1:21:13,8 +chr20 591644 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=546111;QSTRAND=+ GT:DP:AD 0|1:37:17,20 ./.:20:11,9 ./.:33:20,13 +chr20 593266 . CTTTTTTT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=572781;QSTRAND=+ GT:DP:AD 1|0:29:24,5 1|1:27:5,22 ./.:46:25,21 +chr20 594618 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=549095;QSTRAND=+ GT:DP:AD 0|1:34:25,9 ./.:33:9,24 ./.:25:19,6 +chr20 595396 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=549872;QSTRAND=+ GT:DP:AD 0|1:25:20,5 ./.:43:24,19 ./.:27:22,5 +chr20 599169 . N . . END=599171;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 1/1:2 1/1:2 1/1:2 +chr20 599171 . N . . . SEGCNT=1 GT:SEG 0/1:1 0/0:0 0/1:1 +chr20 601733 . GC G 60 . QNAME=cluster23_scaffold_3;QSTART=25109468;QSTRAND=- GT:DP:AD ./.:24:6,18 ./.:40:25,15 1|1:20:5,15 +chr20 612561 . AG A 60 . QNAME=cluster19_000000F;QSTART=25149310;QSTRAND=- GT:DP:AD ./.:33:17,16 1|0:18:13,5 ./.:27:18,9 +chr20 613783 . TGTGTGCTGAGTCCAGCTCAAGTCCCTTGGTTCCCACTGCTGCTAAGCATGCACG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=593293;QSTRAND=+;SVTYPE=DEL;SVLEN=-54 GT:DP:AD 1/1:46:24,22 1/0:29:14,15 1/1:43:19,24 +chr20 614449 . ATCTC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=593905;QSTRAND=+ GT:DP:AD 1|0:30:5,25 ./.:22:8,14 1|1:43:22,21 +chr20 630592 . N . . END=630594;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 1/1:2 0/0:0 1/1:2 +chr20 630594 . N . . END=630596;SVTYPE=DEL;SVLEN=2;SEGCNT=1 GT:SEG 0/1:1 0/0:0 0/1:1 +chr20 638468 . TA T 60 . QNAME=cluster19_000000F;QSTART=25123458;QSTRAND=- GT:DP:AD ./.:27:12,15 1|0:35:19,16 ./.:28:9,19 +chr20 641944 . GGA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621462;QSTRAND=+ GT:DP:AD 1|0:30:16,14 ./.:47:25,22 ./.:32:13,19 +chr20 642012 . GGT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621528;QSTRAND=+ GT:DP:AD 1|0:20:10,10 ./.:35:18,17 ./.:33:16,17 +chr20 642171 . GGA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621689;QSTRAND=+ GT:DP:AD 1|0:43:23,20 ./.:40:20,20 0|1:40:18,22 +chr20 642205 . GGT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621721;QSTRAND=+ GT:DP:AD 1|0:33:11,22 ./.:22:5,17 0|1:30:12,18 +chr20 642259 . N . . END=642261;SVTYPE=DEL;SVLEN=2;SEGCNT=1 GT:SEG 0/1:1 0/0:0 0/0:0 +chr20 642261 . N . . . SEGCNT=2 GT:SEG 0/1:1 0/0:0 0/1:1 +chr20 642262 . N . . END=642266;SVTYPE=DEL;SVLEN=4;SEGCNT=1 GT:SEG 0/0:0 0/0:0 0/1:1 +chr20 642893 . GTGA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=622817;QSTRAND=+ GT:DP:AD 1|0:18:8,10 ./.:40:15,25 ./.:39:22,17 +chr20 644264 . TA T 60 . QNAME=cluster23_scaffold_2;QSTART=25050659;QSTRAND=- GT:DP:AD ./.:40:21,19 ./.:24:16,8 0|1:26:18,8 +chr20 646614 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=601630;QSTRAND=+ GT:DP:AD 0|1:10:5,5 ./.:17:7,10 ./.:36:23,13 +chr20 649701 . N . . END=649703;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 0/1:1 0/0:0 0/1:1 +chr20 649703 . N . . . SEGCNT=1 GT:SEG 0/1:1 0/0:0 0/0:0 +chr20 651683 . TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=631624;QSTRAND=+ GT:DP:AD 1|0:42:17,25 ./.:48:23,25 ./.:43:25,18 +chr20 652904 . GACCTCCCTCCTCCGGCA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=632844;QSTRAND=+ GT:DP:AD 1|1:34:10,24 ./.:28:5,23 ./.:46:24,22 +chr20 653259 . CG C 60 . QNAME=HG002-S9-H1-000001F;QSTART=633182;QSTRAND=+ GT:DP:AD 1|0:32:19,13 ./.:33:23,10 ./.:28:13,15 +chr20 672388 . CGT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=652324;QSTRAND=+ GT:DP:AD 1|0:37:15,22 ./.:39:21,18 1|1:42:18,24 +chr20 674399 . N . . END=674404;SVTYPE=DEL;SVLEN=5;SEGCNT=2 GT:SEG 0/1:1 0/0:0 1/1:2 +chr20 674404 . N . . END=674406;SVTYPE=DEL;SVLEN=2;SEGCNT=1 GT:SEG 0/0:0 0/0:0 0/1:1 +chr20 674713 . GTGTGTGTGTGTGTGTGTGTA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=654643;QSTRAND=+ GT:DP:AD 1|0:33:14,19 ./.:36:15,21 1|1:36:14,22 +chr20 677414 . N . . END=677416;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 1/1:2 0/1:1 1/1:2 +chr20 677416 . N . . . SEGCNT=1 GT:SEG 0/1:1 0/0:0 0/0:0 +chr20 677892 . AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=657801;QSTRAND=+ GT:DP:AD 1|0:24:17,7 ./.:23:12,11 ./.:14:5,9 +chr20 685696 . N . . END=685703;SVTYPE=DEL;SVLEN=7;SEGCNT=3 GT:SEG 1/1:2 1/1:2 1/1:2 +chr20 685703 . N . . END=685706;SVTYPE=DEL;SVLEN=3;SEGCNT=2 GT:SEG 0/1:1 0/1:1 1/1:2 +chr20 685706 . N . . END=685709;SVTYPE=DEL;SVLEN=3;SEGCNT=1 GT:SEG 0/1:1 0/1:1 0/0:0 +chr20 690819 . AGTGT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=670721;QSTRAND=+ GT:DP:AD 1|0:17:9,8 1|1:41:23,18 0|1:25:18,7 +chr20 699214 . N . . END=699216;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 1/1:2 0/0:0 0/0:0 +chr20 699216 . N . . END=699218;SVTYPE=DEL;SVLEN=2;SEGCNT=1 GT:SEG 0/1:1 0/0:0 0/0:0 +chr20 700649 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=655672;QSTRAND=+ GT:DP:AD 0|1:14:7,7 ./.:38:20,18 ./.:30:10,20 +chr20 708422 . AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=688319;QSTRAND=+ GT:DP:AD 1|0:28:16,12 1|0:27:7,20 ./.:30:6,24 +chr20 709051 . TC T 60 . QNAME=cluster23_scaffold_2;QSTART=24985844;QSTRAND=- GT:DP:AD ./.:13:5,8 ./.:19:7,12 0|1:21:8,13 +chr20 709759 . AGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCC A 60 . QNAME=HG002-S9-H2-000001F;QSTART=664783;QSTRAND=+;SVTYPE=DEL;SVLEN=-93 GT:DP:AD 0/1:16:7,9 1/0:26:21,5 1/1:41:23,18 +chr20 712402 . GT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=692763;QSTRAND=+ GT:DP:AD 1|1:22:15,7 ./.:16:8,8 ./.:21:15,6 +chr20 712711 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=693071;QSTRAND=+ GT:DP:AD 1|0:33:13,20 ./.:15:10,5 ./.:22:8,14 +chr20 717158 . ATT A 60 . QNAME=cluster19_000000F;QSTART=678012;QSTRAND=+ GT:DP:AD ./.:36:18,18 0|1:30:23,7 ./.:47:24,23 +chr20 723429 . CTCT C 60 . QNAME=cluster19_000000F;QSTART=684281;QSTRAND=+ GT:DP:AD ./.:41:21,20 0|1:33:17,16 ./.:26:10,16 +chr20 726010 . CAAAAAAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=706370;QSTRAND=+ GT:DP:AD 1|0:33:15,18 ./.:36:17,19 0|1:33:8,25 +chr20 727508 . N . . END=727541;SVTYPE=DEL;SVLEN=33;SEGCNT=2 GT:SEG 0/0:0 1/1:2 0/0:0 +chr20 727541 . N . . END=727556;SVTYPE=DEL;SVLEN=15;SEGCNT=1 GT:SEG 0/0:0 0/1:1 0/0:0 +chr20 727556 . N . . . SEGCNT=2 GT:SEG 0/1:1 0/1:1 0/1:1 +chr20 727557 . N . . END=727591;SVTYPE=DEL;SVLEN=34;SEGCNT=1 GT:SEG 0/1:1 0/0:0 0/1:1 +chr20 727786 . N . . END=727788;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 0/1:1 0/1:1 0/1:1 +chr20 727788 . N . . . SEGCNT=1 GT:SEG 0/1:1 0/1:1 0/0:0 +chr20 727962 . GGC G 60 . QNAME=cluster23_scaffold_3;QSTART=24982813;QSTRAND=- GT:DP:AD ./.:41:24,17 ./.:26:18,8 1|0:42:25,17 +chr20 733492 . TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=713849;QSTRAND=+ GT:DP:AD 1|1:27:20,7 1|1:16:8,8 1|1:31:11,20 +chr20 733573 . AAAAAC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=713929;QSTRAND=+ GT:DP:AD 1|0:42:24,18 ./.:17:7,10 ./.:23:18,5 +chr20 736736 . N . . END=736738;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 0/1:1 1/1:2 1/1:2 +chr20 736738 . N . . . SEGCNT=1 GT:SEG 0/1:1 0/1:1 1/1:2 +chr20 737624 . AAATAAT A 60 . QNAME=cluster23_scaffold_3;QSTART=24973138;QSTRAND=- GT:DP:AD ./.:36:24,12 ./.:25:13,12 1|0:47:24,23 +chr20 743121 . N . . END=743126;SVTYPE=DEL;SVLEN=5;SEGCNT=2 GT:SEG 0/1:1 0/1:1 0/0:0 +chr20 743126 . N . . END=743130;SVTYPE=DEL;SVLEN=4;SEGCNT=1 GT:SEG 0/1:1 0/0:0 0/0:0 +chr20 743153 . CTCTCTCTCTCT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=723527;QSTRAND=+ GT:DP:AD 1|0:26:20,6 ./.:37:12,25 ./.:38:22,16 +chr20 745631 . CAGA C 60 . QNAME=cluster19_000000F;QSTART=706463;QSTRAND=+ GT:DP:AD ./.:12:6,6 0|1:29:12,17 ./.:31:7,24 +chr20 746873 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=701772;QSTRAND=+ GT:DP:AD 0|1:30:13,17 1|1:45:20,25 1|1:34:9,25 +chr20 748207 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=703105;QSTRAND=+ GT:DP:AD 0|1:39:17,22 1|0:27:14,13 0|1:43:24,19 +chr20 748246 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=728611;QSTRAND=+ GT:DP:AD 1|0:36:13,23 0|1:30:14,16 ./.:14:8,6 +chr20 748452 . AT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=703349;QSTRAND=+ GT:DP:AD 0|1:41:25,16 1|0:30:23,7 1|1:32:8,24 +chr20 751473 . N . . END=751479;SVTYPE=DEL;SVLEN=6;SEGCNT=3 GT:SEG 1/1:2 1/1:2 1/1:2 +chr20 751479 . N . . END=751484;SVTYPE=DEL;SVLEN=5;SEGCNT=2 GT:SEG 1/1:2 1/1:2 0/1:1 +chr20 751484 . N . . END=751499;SVTYPE=DEL;SVLEN=15;SEGCNT=1 GT:SEG 0/1:1 0/1:1 0/1:1 +chr20 752069 . ATCTT A 60 . QNAME=cluster23_scaffold_3;QSTART=24958698;QSTRAND=- GT:DP:AD ./.:44:19,25 ./.:29:7,22 1|0:43:21,22 +chr20 753141 . GAAAGAAAGAAAGAAAGAA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=733495;QSTRAND=+ GT:DP:AD 1|0:21:10,11 ./.:43:19,24 ./.:28:13,15 +chr20 756575 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=736912;QSTRAND=+ GT:DP:AD 1|1:21:16,5 1|1:23:14,9 0|1:35:18,17 +chr20 756872 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=737208;QSTRAND=+ GT:DP:AD 1|1:47:22,25 1|1:35:17,18 1|0:31:21,10 +chr20 758972 . N . . END=758977;SVTYPE=DEL;SVLEN=5;SEGCNT=3 GT:SEG 1/1:2 1/1:2 1/1:2 +chr20 758977 . N . . END=758981;SVTYPE=DEL;SVLEN=4;SEGCNT=2 GT:SEG 1/1:2 1/1:2 0/1:1 +chr20 758981 . N . . END=758983;SVTYPE=DEL;SVLEN=2;SEGCNT=1 GT:SEG 0/1:1 0/0:0 0/0:0 +chr20 759048 . AC A 60 . QNAME=cluster23_scaffold_3;QSTART=24951713;QSTRAND=- GT:DP:AD ./.:45:23,22 ./.:29:18,11 1|0:26:21,5 +chr20 771420 . CTT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=751874;QSTRAND=+ GT:DP:AD 1|1:33:20,13 ./.:32:19,13 ./.:39:22,17 +chr20 771669 . GA G 60 . QNAME=cluster19_000000F;QSTART=24989667;QSTRAND=- GT:DP:AD ./.:17:7,10 1|0:34:18,16 ./.:17:5,12 +chr20 772587 . N . . END=772589;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 0/0:0 1/1:2 0/1:1 +chr20 772589 . N . . . SEGCNT=1 GT:SEG 0/0:0 0/0:0 0/1:1 +chr20 775268 . N . . END=775277;SVTYPE=DEL;SVLEN=9;SEGCNT=2 GT:SEG 0/0:0 1/1:2 1/1:2 +chr20 775277 . N . . END=775280;SVTYPE=DEL;SVLEN=3;SEGCNT=1 GT:SEG 0/0:0 0/1:1 1/1:2 +chr20 776856 . TG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=757311;QSTRAND=+ GT:DP:AD 1|0:28:5,23 1|0:20:11,9 1|1:26:8,18 +chr20 778013 . CT C 60 . QNAME=cluster19_000000F;QSTART=738947;QSTRAND=+ GT:DP:AD ./.:26:15,11 0|1:28:13,15 ./.:22:16,6 +chr20 787239 . N . . END=787241;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 1/1:2 0/0:0 1/1:2 +chr20 787241 . N . . . SEGCNT=1 GT:SEG 0/0:0 0/0:0 0/1:1 +chr20 787512 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=767968;QSTRAND=+ GT:DP:AD 1|1:24:9,15 1|1:40:22,18 1|0:38:20,18 +chr20 790371 . N . . END=790379;SVTYPE=DEL;SVLEN=8;SEGCNT=2 GT:SEG 1/1:2 0/1:1 1/1:2 +chr20 790379 . N . . . SEGCNT=1 GT:SEG 0/1:1 0/0:0 0/1:1 +chr20 793560 . N . . END=793562;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 0/0:0 1/1:2 1/1:2 +chr20 793562 . N . . . SEGCNT=1 GT:SEG 0/0:0 0/1:1 1/1:2 +chr20 800494 . TCGATTACCTGCTCCACCCTGACTCACTC T 60 . QNAME=HG002-S9-H2-000001F;QSTART=755521;QSTRAND=+;SVTYPE=DEL;SVLEN=-28 GT:DP:AD 0/1:22:7,15 1/0:22:13,9 1/1:29:24,5 +chr20 800671 . GCACTCACCCCAT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=781118;QSTRAND=+ GT:DP:AD 1|0:25:17,8 ./.:39:24,15 ./.:15:7,8 +chr20 800960 . CCTT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781395;QSTRAND=+ GT:DP:AD 1|0:37:25,12 ./.:25:17,8 ./.:34:22,12 +chr20 801853 . N . . . SEGCNT=2 GT:SEG 0/0:0 0/1:1 1/1:2 +chr20 801854 . N . . END=801858;SVTYPE=DEL;SVLEN=4;SEGCNT=3 GT:SEG 0/1:1 0/1:1 1/1:2 +chr20 801858 . N . . END=801862;SVTYPE=DEL;SVLEN=4;SEGCNT=2 GT:SEG 0/1:1 0/1:1 0/1:1 +chr20 804804 . AT A 60 . QNAME=cluster19_000000F;QSTART=24956587;QSTRAND=- GT:DP:AD ./.:34:19,15 1|1:27:16,11 1|1:34:19,15 +chr20 805609 . AAG A 60 . QNAME=cluster19_000000F;QSTART=24955783;QSTRAND=- GT:DP:AD ./.:48:25,23 1|1:29:21,8 1|1:17:10,7 +chr20 805627 . AT A 60 . QNAME=cluster23_scaffold_2;QSTART=24889420;QSTRAND=- GT:DP:AD ./.:21:12,9 ./.:26:14,12 0|1:18:11,7 +chr20 806539 . CT C 60 . QNAME=cluster23_scaffold_2;QSTART=24888507;QSTRAND=- GT:DP:AD ./.:41:18,23 ./.:23:7,16 0|1:20:15,5 +chr20 807886 . CT C 60 . QNAME=cluster23_scaffold_2;QSTART=24887141;QSTRAND=- GT:DP:AD ./.:34:14,20 ./.:16:8,8 0|1:25:15,10 +chr20 808580 . CT C 60 . QNAME=cluster23_scaffold_2;QSTART=24886448;QSTRAND=- GT:DP:AD ./.:33:20,13 ./.:29:24,5 0|1:35:23,12 +chr20 814479 . AT A 60 . QNAME=cluster23_scaffold_2;QSTART=24880545;QSTRAND=- GT:DP:AD ./.:37:23,14 ./.:23:13,10 0|1:28:12,16 +chr20 816272 . CT C 60 . QNAME=cluster23_scaffold_2;QSTART=24878749;QSTRAND=- GT:DP:AD ./.:19:11,8 ./.:24:19,5 0|1:22:9,13 +chr20 816693 . GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=797128;QSTRAND=+ GT:DP:AD 1|0:17:7,10 1|1:23:15,8 1|0:28:17,11 +chr20 816723 . N . . END=816728;SVTYPE=DEL;SVLEN=5;SEGCNT=1 GT:SEG 0/1:1 0/0:0 0/1:1 +chr20 816728 . N . . END=816730;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 1/1:2 0/0:0 0/1:1 +chr20 816730 . N . . . SEGCNT=1 GT:SEG 0/1:1 0/0:0 0/0:0 +chr20 817544 . N . . END=817546;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 0/1:1 1/1:2 0/1:1 +chr20 817546 . N . . . SEGCNT=1 GT:SEG 0/0:0 0/1:1 0/1:1 +chr20 818794 . CT C 60 . QNAME=cluster23_scaffold_2;QSTART=24876223;QSTRAND=- GT:DP:AD ./.:17:10,7 ./.:31:13,18 0|1:34:14,20 +chr20 822153 . N . . END=822157;SVTYPE=DEL;SVLEN=4;SEGCNT=2 GT:SEG 1/1:2 1/1:2 0/1:1 +chr20 822157 . N . . . SEGCNT=1 GT:SEG 1/1:2 0/0:0 0/1:1 +chr20 830449 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=812065;QSTRAND=+ GT:DP:AD 1|0:30:7,23 ./.:36:16,20 ./.:21:10,11 +chr20 833025 . AG A 60 . QNAME=cluster19_000000F;QSTART=24925056;QSTRAND=- GT:DP:AD ./.:29:14,15 1|0:28:6,22 ./.:17:8,9 +chr20 836246 . TG T 60 . QNAME=cluster19_000000F;QSTART=24921836;QSTRAND=- GT:DP:AD ./.:36:12,24 1|1:31:12,19 0|1:32:20,12 +chr20 844439 . TGCCCAGGTC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=826056;QSTRAND=+ GT:DP:AD 1|1:26:11,15 1|1:28:12,16 1|1:29:14,15 +chr20 849258 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=830866;QSTRAND=+ GT:DP:AD 1|1:31:18,13 0|1:43:24,19 1|1:21:16,5 +chr20 852596 . ACT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=834209;QSTRAND=+ GT:DP:AD 1|1:20:11,9 0|1:28:5,23 1|1:42:20,22 +chr20 854857 . N . . END=854862;SVTYPE=DEL;SVLEN=5;SEGCNT=2 GT:SEG 1/1:2 1/1:2 1/1:2 +chr20 854862 . N . . END=854864;SVTYPE=DEL;SVLEN=2;SEGCNT=1 GT:SEG 0/1:1 0/0:0 1/1:2 +chr20 862244 . N . . END=862246;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 0/1:1 0/1:1 1/1:2 +chr20 862246 . N . . . SEGCNT=1 GT:SEG 0/0:0 0/0:0 0/1:1 +chr20 863798 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=845405;QSTRAND=+ GT:DP:AD 1|1:45:23,22 1|1:28:21,7 1|1:30:12,18 +chr20 865132 . AAGCAGAAAAGC A 60 . QNAME=cluster23_scaffold_2;QSTART=24827970;QSTRAND=- GT:DP:AD ./.:15:7,8 ./.:37:20,17 0|1:30:8,22 +chr20 867420 . N . . END=867422;SVTYPE=DEL;SVLEN=2;SEGCNT=1 GT:SEG 0/0:0 0/1:1 0/0:0 +chr20 867422 . N . . . SEGCNT=2 GT:SEG 0/0:0 0/1:1 0/1:1 +chr20 867423 . N . . . SEGCNT=1 GT:SEG 0/0:0 0/0:0 0/1:1 +chr20 867424 . N . . END=867427;SVTYPE=DEL;SVLEN=3;SEGCNT=2 GT:SEG 0/0:0 0/1:1 0/1:1 +chr20 868955 . TC T 60 . QNAME=HG002-S9-H2-000001F;QSTART=825105;QSTRAND=+ GT:DP:AD 0|1:37:21,16 ./.:31:17,14 ./.:28:18,10 +chr20 875035 . TC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=856644;QSTRAND=+ GT:DP:AD 1|0:40:24,16 0|1:42:17,25 0|1:29:6,23 +chr20 876144 . CAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=857752;QSTRAND=+ GT:DP:AD 1|0:32:13,19 0|1:22:14,8 0|1:24:8,16 +chr20 880587 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=862194;QSTRAND=+ GT:DP:AD 1|0:26:16,10 ./.:25:17,8 ./.:25:9,16 +chr20 885021 . TC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=866630;QSTRAND=+ GT:DP:AD 1|0:34:22,12 0|1:38:21,17 ./.:20:11,9 +chr20 886137 . AG A 60 . QNAME=cluster23_scaffold_2;QSTART=24806979;QSTRAND=- GT:DP:AD ./.:24:14,10 ./.:36:13,23 0|1:43:18,25 +chr20 887636 . N . . END=887638;SVTYPE=DEL;SVLEN=2;SEGCNT=3 GT:SEG 1/1:2 1/1:2 0/1:1 +chr20 887638 . N . . END=887640;SVTYPE=DEL;SVLEN=2;SEGCNT=2 GT:SEG 0/1:1 0/1:1 0/1:1 +chr20 887640 . N . . . SEGCNT=1 GT:SEG 0/1:1 0/1:1 0/0:0 +chr20 899251 . AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=880855;QSTRAND=+ GT:DP:AD 1|1:36:11,25 ./.:13:5,8 ./.:35:24,11 +chr20 911823 . AGACAGAGAGAGGGAGAGAGG A 60 . QNAME=HG002-S9-H1-000001F;QSTART=893426;QSTRAND=+ GT:DP:AD 1|0:26:6,20 ./.:21:13,8 ./.:30:18,12 +chr20 919146 . CTCTT C 60 . QNAME=cluster19_000000F;QSTART=883426;QSTRAND=+ GT:DP:AD ./.:46:22,24 0|1:34:25,9 ./.:21:9,12 +chr20 919990 . TG T 60 . QNAME=cluster19_000000F;QSTART=24838104;QSTRAND=- GT:DP:AD ./.:32:19,13 1|0:35:22,13 ./.:32:24,8 +chr20 925913 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=882062;QSTRAND=+ GT:DP:AD 0|1:47:22,25 ./.:31:16,15 ./.:32:24,8 +chr20 929302 . N . . END=929305;SVTYPE=DEL;SVLEN=3;SEGCNT=2 GT:SEG 0/0:0 1/1:2 0/0:0 +chr20 929305 . N . . END=929308;SVTYPE=DEL;SVLEN=3;SEGCNT=1 GT:SEG 0/0:0 0/1:1 0/0:0 +chr20 944018 . GCT G 60 . QNAME=cluster19_000000F;QSTART=24814076;QSTRAND=- GT:DP:AD ./.:14:8,6 1|1:21:10,11 0|1:21:13,8 +chr20 944028 . TC T 60 . QNAME=HG002-S9-H2-000001F;QSTART=900177;QSTRAND=+ GT:DP:AD 0|1:27:18,9 ./.:11:6,5 ./.:21:8,13 +chr20 949377 . GA G 60 . QNAME=HG002-S9-H2-000001F;QSTART=905525;QSTRAND=+ GT:DP:AD 0|1:45:20,25 ./.:20:15,5 1|0:15:7,8 +chr20 949516 . CTCTGAAGAGGTAACATTTGAACTGAGATGTAGAGGGAGAGAAGGAACTAGCCATGTGGAGATCTGGGGGAGGAGCATTCCAGGCAGAGGGGATAGCAAGTGCA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=905663;QSTRAND=+;SVTYPE=DEL;SVLEN=-103 GT:DP:AD 0/1:29:9,20 ./.:28:7,21 1/0:34:12,22 +chr20 951130 . N . . END=951143;SVTYPE=DEL;SVLEN=13;SEGCNT=2 GT:SEG 0/1:1 0/1:1 0/1:1 +chr20 951143 . N . . . SEGCNT=1 GT:SEG 0/1:1 0/0:0 0/0:0 +chr20 951868 . CGT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=907910;QSTRAND=+ GT:DP:AD 0|1:30:13,17 ./.:24:14,10 ./.:37:18,19 +chr20 953327 . GTTAT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=934913;QSTRAND=+ GT:DP:AD 1|1:35:16,19 1|1:22:6,16 1|1:34:11,23 +chr20 953787 . AC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=935369;QSTRAND=+ GT:DP:AD 1|0:10:5,5 ./.:39:21,18 ./.:23:8,15 +chr20 953954 . CG C 60 . QNAME=HG002-S9-H1-000001F;QSTART=935536;QSTRAND=+ GT:DP:AD 1|0:29:23,6 ./.:16:9,7 ./.:25:13,12 +chr20 954692 . CAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=936273;QSTRAND=+ GT:DP:AD 1|1:41:22,19 1|1:33:19,14 1|1:39:20,19 +chr20 959105 . GAGTGTGGTGGTGGGTGTGGGGC G 60 . QNAME=HG002-S9-H1-000001F;QSTART=940694;QSTRAND=+ GT:DP:AD 1|0:27:14,13 ./.:47:22,25 ./.:39:22,17 +chr20 964823 . N . . END=964827;SVTYPE=DEL;SVLEN=4;SEGCNT=1 GT:SEG 0/1:1 0/0:0 0/0:0 +chr20 964827 . N . . END=964831;SVTYPE=DEL;SVLEN=4;SEGCNT=2 GT:SEG 0/1:1 0/0:0 0/1:1 +chr20 964831 . N . . END=964834;SVTYPE=DEL;SVLEN=3;SEGCNT=3 GT:SEG 0/1:1 1/1:2 1/1:2 +chr20 964834 . N . . END=964836;SVTYPE=DEL;SVLEN=2;SEGCNT=1 GT:SEG 0/1:1 0/0:0 0/0:0 +chr20 966451 . CT C 60 . QNAME=cluster23_scaffold_2;QSTART=24726663;QSTRAND=- GT:DP:AD ./.:45:23,22 ./.:16:6,10 0|1:23:15,8 +chr20 966858 . AAAACAAGC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=948417;QSTRAND=+ GT:DP:AD 1|0:29:9,20 ./.:27:21,6 ./.:30:11,19 +chr20 970054 . TC T 60 . QNAME=cluster23_scaffold_2;QSTART=24723061;QSTRAND=- GT:DP:AD ./.:29:17,12 ./.:24:15,9 0|1:29:16,13 +chr20 973165 . TGG T 60 . QNAME=cluster23_scaffold_3;QSTART=24736401;QSTRAND=- GT:DP:AD ./.:28:11,17 ./.:22:17,5 1|0:32:23,9 +chr20 973459 . ATTGT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=955010;QSTRAND=+ GT:DP:AD 1|1:22:11,11 ./.:35:17,18 ./.:31:15,16 +chr20 995547 . GA G 60 . QNAME=cluster23_scaffold_2;QSTART=24697561;QSTRAND=- GT:DP:AD ./.:31:20,11 ./.:21:9,12 0|1:37:22,15 diff --git a/repo_utils/answer_key/stratify/stratify.txt b/repo_utils/answer_key/stratify/stratify.txt new file mode 100644 index 00000000..bf49e7d9 --- /dev/null +++ b/repo_utils/answer_key/stratify/stratify.txt @@ -0,0 +1,11 @@ +chr5 1234567 2345678 0 +chr21 10000000 20000000 0 +chr20 280300 280900 1 +chr20 100000 200000 253 +chr20 300000 620000 631 +chr20 642000 642350 19 +chr20 709000 709770 0 +chr20 709800 710000 1 +chr20 900000 1100000 225 +chr21 9000000 11000000 0 +chr19 1000000 1010000 0 diff --git a/repo_utils/answer_key/vcf2df/multi_vcf2df.jl b/repo_utils/answer_key/vcf2df/multi_vcf2df.jl new file mode 100644 index 00000000..3336392f Binary files /dev/null and b/repo_utils/answer_key/vcf2df/multi_vcf2df.jl differ diff --git a/repo_utils/answer_key/vcf2df/single_vcf2df.jl b/repo_utils/answer_key/vcf2df/single_vcf2df.jl new file mode 100644 index 00000000..3578d234 Binary files /dev/null and b/repo_utils/answer_key/vcf2df/single_vcf2df.jl differ diff --git a/repo_utils/answer_key/vcf2df/subset_vcf2df.jl b/repo_utils/answer_key/vcf2df/subset_vcf2df.jl new file mode 100644 index 00000000..aaec5cd5 Binary files /dev/null and b/repo_utils/answer_key/vcf2df/subset_vcf2df.jl differ diff --git a/repo_utils/answer_key/vcf2df/truv2df.jl b/repo_utils/answer_key/vcf2df/truv2df.jl new file mode 100644 index 00000000..330a3958 Binary files /dev/null and b/repo_utils/answer_key/vcf2df/truv2df.jl differ diff --git a/repo_utils/answer_key/vcf2df/vcf2df.jl b/repo_utils/answer_key/vcf2df/vcf2df.jl new file mode 100644 index 00000000..0b6af3d4 Binary files /dev/null and b/repo_utils/answer_key/vcf2df/vcf2df.jl differ diff --git a/repo_utils/answer_key/vcf2df/vcf2df_bare.jl b/repo_utils/answer_key/vcf2df/vcf2df_bare.jl new file mode 100644 index 00000000..b19c288e Binary files /dev/null and b/repo_utils/answer_key/vcf2df/vcf2df_bare.jl differ diff --git a/repo_utils/setup_test.sh b/repo_utils/setup_test.sh index 1e7bfc5d..67df8426 100644 --- a/repo_utils/setup_test.sh +++ b/repo_utils/setup_test.sh @@ -1,11 +1,13 @@ INDIR=repo_utils/test_files -ANSDIR=$INDIR/answer_key +ANSDIR=repo_utils/answer_key OD=test_results COVERAGE_RCFILE=.coveragerc # truvari in code coverage truv="coverage run --concurrency=multiprocessing,thread -p -m truvari.__main__" +# Fake MAFFT so we don't have to rely on it in github actions +export PATH=$INDIR/external/fake_mafft/:$PATH # ------------------------------------------------------------ # test helpers # ------------------------------------------------------------ @@ -29,7 +31,6 @@ info_tests() { infos=$3 python3 repo_utils/info_puller.py $base_vcf ${infos} | sort > $OD/answer.txt python3 repo_utils/info_puller.py $comp_vcf ${infos} | sort > $OD/result.txt - run test_infos_${name} assert_equal $(fn_md5 $OD/answer.txt) $(fn_md5 $OD/result.txt) } diff --git a/repo_utils/sub_tests/anno.sh b/repo_utils/sub_tests/anno.sh index a12c30e3..c9806d66 100644 --- a/repo_utils/sub_tests/anno.sh +++ b/repo_utils/sub_tests/anno.sh @@ -1,8 +1,8 @@ # ------------------------------------------------------------ # anno # ------------------------------------------------------------ -VCF=$INDIR/multi.vcf.gz -REF=$INDIR/reference.fa +VCF=$INDIR/variants/multi.vcf.gz +REF=$INDIR/references/reference.fa # hompct run test_anno_hompct \ @@ -54,17 +54,17 @@ fi # grm run test_anno_grm \ - $truv anno grm -i $INDIR/input2.vcf.gz -r $REF -o $OD/grm.jl + $truv anno grm -i $INDIR/variants/input2.vcf.gz -r $REF -o $OD/grm.jl if [ $test_anno_grm ]; then assert_exit_code 0 - df_check test_grm_result $ANSDIR/grm.jl $OD/grm.jl + df_check test_anno_grm $ANSDIR/anno/grm.jl $OD/grm.jl fi # trf run test_anno_trf \ - $truv anno trf -i $INDIR/multi.vcf.gz \ - -r $INDIR/repeats.adotto.bed.gz \ - -f $INDIR/reference.fa \ + $truv anno trf -i $INDIR/variants/multi.vcf.gz \ + -r $INDIR/beds/repeats.adotto.bed.gz \ + -f $INDIR/references/reference.fa \ -e $INDIR/external/trf \ -m 5 \ -o $OD/trf.vcf @@ -73,9 +73,9 @@ if [ $test_anno_trf ]; then fi run test_anno_trf_reg \ - $truv anno trf -i $INDIR/multi.vcf.gz \ - -r $INDIR/repeats.adotto.bed.gz \ - -f $INDIR/reference.fa \ + $truv anno trf -i $INDIR/variants/multi.vcf.gz \ + -r $INDIR/beds/repeats.adotto.bed.gz \ + -f $INDIR/references/reference.fa \ -e $INDIR/external/trf \ -m 5 -R \ -o $OD/trf.reg.vcf @@ -93,43 +93,42 @@ if [ $test_anno_badparam ]; then assert_exit_code 1 fi - -# TRF isn't deterministic for some reason, so it gives a different answer in action +# TRF isn't deterministic for some reason, so it can give a different answer in action? # run test_anno_trf_result # assert_equal $(fn_md5 $ANSDIR/trf.vcf) $(fn_md5 $OD/trf.vcf) # repmask run test_anno_repmask \ - $truv anno repmask -i $INDIR/multi.vcf.gz -o $OD/repmask.vcf -e $INDIR/external/fakeRM.py + $truv anno repmask -i $INDIR/variants/multi.vcf.gz -o $OD/repmask.vcf -e $INDIR/external/fakeRM.py if [ $test_anno_repmask ]; then assert_exit_code 0 - assert_equal $(fn_md5 $ANSDIR/repmask.vcf) $(fn_md5 $OD/repmask.vcf) + assert_equal $(fn_md5 $ANSDIR/anno/repmask.vcf) $(fn_md5 $OD/repmask.vcf) fi run test_anno_repmask_err \ - $truv anno repmask -i $INDIR/input1.vcf.gz -o $OD/repmask.vcf -e $INDIR/external/fakeRM.py + $truv anno repmask -i $INDIR/variants/input1.vcf.gz -o $OD/repmask.vcf -e $INDIR/external/fakeRM.py if [ $test_anno_repmask_err ]; then assert_exit_code 1 fi # bpovl run test_anno_bpovl \ - $truv anno bpovl $INDIR/input1.vcf.gz \ + $truv anno bpovl $INDIR/variants/input1.vcf.gz \ -o $OD/anno_bpovl.jl \ - -a $INDIR/anno.gtf.gz -p gff --sizemin 2 + -a $INDIR/misc/anno.gtf.gz -p gff --sizemin 2 if [ $test_anno_bpovl ]; then assert_exit_code 0 - df_check test_anno_bpovl_result $ANSDIR/anno_bpovl.jl $OD/anno_bpovl.jl + df_check test_anno_bpovl $ANSDIR/anno/anno_bpovl.jl $OD/anno_bpovl.jl fi # density -run truvari_anno_density \ - $truv anno density $INDIR/input3.vcf.gz \ +run test_anno_density \ + $truv anno density $INDIR/variants/input3.vcf.gz \ -o $OD/anno_density.jl \ - -g $INDIR/genome.bed -m $INDIR/mask.bed -if [ $truvari_anno_density ]; then + -g $INDIR/beds/genome.bed -m $INDIR/beds/mask.bed +if [ $test_anno_density ]; then assert_exit_code 0 - df_check test_anno_density_result $ANSDIR/anno_density.jl $OD/anno_density.jl + df_check test_anno_density $ANSDIR/anno/anno_density.jl $OD/anno_density.jl fi # dpcnt @@ -150,24 +149,32 @@ fi # grpaf run test_anno_grpaf \ - $truv anno grpaf $INDIR/grpaf.vcf.gz -l $INDIR/grpaf.labels.txt -o $OD/anno_grpaf.vcf + $truv anno grpaf $INDIR/variants/grpaf.vcf.gz -l $INDIR/misc/grpaf.labels.txt -o $OD/anno_grpaf.vcf if [ $test_anno_grpaf ]; then assert_exit_code 0 - assert_equal $(fn_md5 $ANSDIR/anno_grpaf.vcf) $(fn_md5 $OD/anno_grpaf.vcf) + assert_equal $(fn_md5 $ANSDIR/anno/anno_grpaf.vcf) $(fn_md5 $OD/anno_grpaf.vcf) fi run test_anno_grpaf_strict \ - $truv anno grpaf --strict $INDIR/grpaf.vcf.gz -l $INDIR/grpaf.labels.txt -o $OD/anno_grpaf.vcf + $truv anno grpaf --strict $INDIR/variants/grpaf.vcf.gz -l $INDIR/misc/grpaf.labels.txt -o $OD/anno_grpaf.vcf if [ $test_anno_grpaf_strict ]; then assert_exit_code 1 fi run test_anno_grpaf_subset \ $truv anno grpaf --tags AF,HWE,ExcHet \ - $INDIR/grpaf.vcf.gz \ - -l $INDIR/grpaf.labels.txt \ + $INDIR/variants/grpaf.vcf.gz \ + -l $INDIR/misc/grpaf.labels.txt \ -o $OD/anno_grpaf.subtags.vcf if [ $test_anno_grpaf_subset ]; then assert_exit_code 0 - assert_equal $(fn_md5 $ANSDIR/anno_grpaf.subtags.vcf) $(fn_md5 $OD/anno_grpaf.subtags.vcf) + assert_equal $(fn_md5 $ANSDIR/anno/anno_grpaf.subtags.vcf) $(fn_md5 $OD/anno_grpaf.subtags.vcf) +fi + +# +run test_anno_addid \ + $truv anno addid $INDIR/variants/multi.vcf.gz -o $OD/addid.vcf +if [ $test_anno_addid ]; then + assert_exit_code 0 + assert_equal $(fn_md5 $ANSDIR/anno/addid.vcf) $(fn_md5 $OD/addid.vcf) fi diff --git a/repo_utils/sub_tests/bench.sh b/repo_utils/sub_tests/bench.sh index 5ecf7587..79d399a9 100644 --- a/repo_utils/sub_tests/bench.sh +++ b/repo_utils/sub_tests/bench.sh @@ -7,25 +7,21 @@ bench() { f2=$2 k=$3 rm -rf $OD/bench${k} - $truv bench -b $INDIR/input${f1}.vcf.gz \ - -c $INDIR/input${f2}.vcf.gz \ - -f $INDIR/reference.fa \ + $truv bench -b $INDIR/variants/input${f1}.vcf.gz \ + -c $INDIR/variants/input${f2}.vcf.gz \ + -f $INDIR/references/reference.fa \ -o $OD/bench${k}/ ${4} } bench_assert() { k=$1 - if [ $name ]; then - assert_exit_code 0 - for i in $ANSDIR/bench${k}/*.vcf - do - bname=$(basename $i | sed 's/[\.|\-]/_/g') - result=$OD/bench${k}/$(basename $i) - sort_vcf $result - run test_bench${k}_${bname} - assert_equal $(fn_md5 $i) $(fn_md5 $result) - done - fi + assert_exit_code 0 + for i in $ANSDIR/bench/bench${k}/*.vcf.gz + do + bname=$(basename $i | sed 's/[\.|\-]/_/g') + result=$OD/bench${k}/$(basename $i) + assert_equal $(fn_md5 $i) $(fn_md5 $result) + done } run test_bench_12 bench 1 2 12 @@ -38,56 +34,46 @@ if [ $test_bench_13 ]; then bench_assert 13 fi -run test_bench_23 bench 2 3 23 --multimatch +run test_bench_23 bench 2 3 23 "--pick multi" if [ $test_bench_23 ]; then bench_assert 23 fi # Testing --includebed -run test_bench_13_includebed bench 1 3 13_includebed "--includebed $INDIR/include.bed" +run test_bench_13_includebed bench 1 3 13_includebed "--includebed $INDIR/beds/include.bed" if [ $test_bench_13_includebed ]; then bench_assert 13_includebed fi # Testing --extend -run test_bench_13_extend bench 1 3 13_extend "--includebed $INDIR/include.bed --extend 500" +run test_bench_13_extend bench 1 3 13_extend "--includebed $INDIR/beds/include.bed --extend 500" if [ $test_bench_13_extend ]; then bench_assert 13_extend fi # --unroll -rm -rf $OD/bench_unroll -run test_bench_unroll $truv bench -b $INDIR/real_small_base.vcf.gz \ - -c $INDIR/real_small_comp.vcf.gz \ +run test_bench_unroll $truv bench -b $INDIR/variants/real_small_base.vcf.gz \ + -c $INDIR/variants/real_small_comp.vcf.gz \ -o $OD/bench_unroll/ if [ $test_bench_unroll ]; then - assert_exit_code 0 - for i in $ANSDIR/bench_unroll/*.vcf - do - bname=$(basename $i | sed 's/[\.|\-]/_/g') - result=$OD/bench_unroll/$(basename $i) - sort_vcf $result - run test_bench_unroll_${bname} - assert_equal $(fn_md5 $i) $(fn_md5 $result) - done + bench_assert _unroll fi -# --giabreport -rm -rf $OD/bench_giab -run test_bench_giab $truv bench -b $INDIR/giab.vcf.gz \ - -c $INDIR/input1.vcf.gz \ - -f $INDIR/reference.fa \ - -o $OD/bench_giab/ \ - --includebed $INDIR/giab.bed \ - --multimatch \ - --giabreport \ - --prog -if [ $test_bench_giab ]; then - assert_exit_code 0 - assert_equal $(fn_md5 $ANSDIR/bench_giab_report.txt) $(fn_md5 $OD/bench_giab/giab_report.txt) +# --pick allele count +run test_bench_12_gtcomp bench 1 2 12_gtcomp "--pick ac" +if [ $test_bench_12_gtcomp ]; then + bench_assert 12_gtcomp fi +# --gtcomp edgecase +run test_bench_gtcomp_edgecase1 $truv bench -b $INDIR/variants/gtcomp_problem1_base.vcf.gz \ + -c $INDIR/variants/gtcomp_problem1_comp.vcf.gz \ + --pick ac \ + -o $OD/bench_gtcomp_edgecase1/ +if [ $test_bench_gtcomp_edgecase1 ]; then + bench_assert _gtcomp_edgecase1 +fi run test_bench_badparams $truv bench -b nofile.vcf -c nofile.aga -f notref.fa -o $OD if [ $test_bench_badparams ]; then assert_exit_code 100 diff --git a/repo_utils/sub_tests/collapse.sh b/repo_utils/sub_tests/collapse.sh index d952d71d..e927b31f 100644 --- a/repo_utils/sub_tests/collapse.sh +++ b/repo_utils/sub_tests/collapse.sh @@ -2,8 +2,8 @@ # collapse # ------------------------------------------------------------ collapse() { - $truv collapse -f $INDIR/reference.fa \ - -i $INDIR/input${1}.vcf.gz \ + $truv collapse -f $INDIR/references/reference.fa \ + -i $INDIR/variants/input${1}.vcf.gz \ -o $OD/input${1}_collapsed.vcf \ -c $OD/input${1}_removed.vcf \ ${2} @@ -15,18 +15,15 @@ collapse_assert() { assert_exit_code 0 - run test_collapse_${1}_collapsed - assert_equal $(fn_md5 $ANSDIR/input${1}_collapsed.vcf) $(fn_md5 $OD/input${1}_collapsed.vcf) - - run test_collapse_${1}_removed - assert_equal $(fn_md5 $ANSDIR/input${1}_removed.vcf) $(fn_md5 $OD/input${1}_removed.vcf) + assert_equal $(fn_md5 $ANSDIR/collapse/input${1}_collapsed.vcf) $(fn_md5 $OD/input${1}_collapsed.vcf) + assert_equal $(fn_md5 $ANSDIR/collapse/input${1}_removed.vcf) $(fn_md5 $OD/input${1}_removed.vcf) } collapse_multi() { # tests multi sample collapse with provided keep method keep=$1 - run test_collapse_multi_$keep $truv collapse -f $INDIR/reference.fa \ - -i $INDIR/multi.vcf.gz \ + run test_collapse_multi_$keep $truv collapse -f $INDIR/references/reference.fa \ + -i $INDIR/variants/multi.vcf.gz \ -o $OD/multi_collapsed_${keep}.vcf \ -c $OD/multi_removed_${keep}.vcf \ --keep $keep @@ -38,11 +35,8 @@ collapse_multi_assert() { sort_vcf $OD/multi_collapsed_${keep}.vcf sort_vcf $OD/multi_removed_${keep}.vcf - run test_collapse_multi_${keep}_collapsed - assert_equal $(fn_md5 $ANSDIR/multi_collapsed_${keep}.vcf) $(fn_md5 $OD/multi_collapsed_${keep}.vcf) - - run test_collapse_multi_${keep}_removed - assert_equal $(fn_md5 $ANSDIR/multi_removed_${keep}.vcf) $(fn_md5 $OD/multi_removed_${keep}.vcf) + assert_equal $(fn_md5 $ANSDIR/collapse/multi_collapsed_${keep}.vcf) $(fn_md5 $OD/multi_collapsed_${keep}.vcf) + assert_equal $(fn_md5 $ANSDIR/collapse/multi_removed_${keep}.vcf) $(fn_md5 $OD/multi_removed_${keep}.vcf) } run test_collapse_1 collapse 1 --null-consolidate=PL,DP diff --git a/repo_utils/sub_tests/consistency.sh b/repo_utils/sub_tests/consistency.sh index 5e566e38..0f150f21 100644 --- a/repo_utils/sub_tests/consistency.sh +++ b/repo_utils/sub_tests/consistency.sh @@ -1,17 +1,13 @@ # ------------------------------------------------------------ # consistency # ------------------------------------------------------------ -run test_consistency $truv consistency $INDIR/input*.vcf.gz -if [ $test_consistency ]; then - assert_exit_code 0 -fi -run test_consistency_results $truv consistency $INDIR/input*.vcf.gz -if [ $test_consistency_results ]; then - assert_equal $(fn_md5 $ANSDIR/consistency.txt) $(fn_md5 $STDOUT_FILE) +run test_consistency $truv consistency $INDIR/variants/input*.vcf.gz +if [ $test_consistency ]; then + assert_equal $(fn_md5 $ANSDIR/consistency/consistency.txt) $(fn_md5 $STDOUT_FILE) fi -run test_consistency_results_json $truv consistency --json $INDIR/input*.vcf.gz -if [ $test_consistency_results_json ]; then - assert_equal $(fn_md5 $ANSDIR/consistency.json) $(fn_md5 $STDOUT_FILE) +run test_consistency_json $truv consistency --json $INDIR/variants/input*.vcf.gz +if [ $test_consistency_json ]; then + assert_equal $(fn_md5 $ANSDIR/consistency/consistency.json) $(fn_md5 $STDOUT_FILE) fi diff --git a/repo_utils/sub_tests/divide.sh b/repo_utils/sub_tests/divide.sh index 1276e47d..030f7b15 100644 --- a/repo_utils/sub_tests/divide.sh +++ b/repo_utils/sub_tests/divide.sh @@ -1,12 +1,12 @@ # ------------------------------------------------------------ # divide # ------------------------------------------------------------ -run test_divide $truv divide $INDIR/multi.vcf.gz $OD/divided/ --no-compress +run test_divide $truv divide -m 100 $INDIR/variants/multi.vcf.gz $OD/divided/ if [ $test_divide ]; then assert_exit_code 0 run test_divide_result - for i in $ANSDIR/divided/*.vcf + for i in $ANSDIR/divide/divided/*.vcf.gz do assert_equal $(fn_md5 $i) $(fn_md5 $OD/divided/$(basename $i)) done diff --git a/repo_utils/sub_tests/phab.sh b/repo_utils/sub_tests/phab.sh index 811757ac..fbb8c4e9 100644 --- a/repo_utils/sub_tests/phab.sh +++ b/repo_utils/sub_tests/phab.sh @@ -1,12 +1,23 @@ # ------------------------------------------------------------ -# phab - disabled for now (tools) +# phab # ------------------------------------------------------------ -#run test_phab $truv phab -o $OD/phab_result \ -# -b $INDIR/phab_base.vcf.gz \ -# -c $INDIR/phab_comp.vcf.gz \ -# -f $INDIR/phab_ref.fa \ -# -r chr1:700-900 -#assert_exit_code 0 -# -#run test_phab_result -#assert_equal $(fn_md5 $ANSDIR/phab_result.vcf.gz) $(fn_md5 $OD/phab_result/output.vcf.gz) +run test_phab $truv phab -k $OD/phab_result \ + -o $OD/phab_result.vcf.gz \ + -b $INDIR/variants/phab_base.vcf.gz \ + -c $INDIR/variants/phab_comp.vcf.gz \ + -f $INDIR/references/phab_ref.fa \ + -r chr1:700-900 + +if [ $test_phab ]; then + assert_exit_code 0 + assert_equal $(fn_md5 $ANSDIR/phab/phab_result.vcf.gz) $(fn_md5 $OD/phab_result.vcf.gz) +fi + +run test_phab_badparams $truv phab -o $OD/phab_result\ + -b doesntexist.vcf \ + -c alsobad.vcf \ + -f noref \ + -r chrP:4802-99292 +if [ $test_phab_badparams ]; then + assert_exit_code 100 +fi diff --git a/repo_utils/sub_tests/refine.sh b/repo_utils/sub_tests/refine.sh new file mode 100644 index 00000000..c8224068 --- /dev/null +++ b/repo_utils/sub_tests/refine.sh @@ -0,0 +1,38 @@ +# ------------------------------------------------------------ +# refine +# ------------------------------------------------------------ +run test_refine_one $truv bench -b $INDIR/refine_data/hg002_base.vcf.gz \ + -c $INDIR/refine_data/hg002_comp.vcf.gz \ + --includebed $INDIR/refine_data/h1_hc_tr_hg002.bed \ + -s 5 -o $OD/refine_output_one + +run test_refine_one $truv refine -k -u -f $INDIR/refine_data/chr20.fa.gz $OD/refine_output_one + +if [ $test_refine_one ]; then + assert_exit_code 0 + assert_equal $(fn_md5 $ANSDIR/refine/refine_output_one/refine.regions.txt) \ + $(fn_md5 $OD/refine_output_one/refine.regions.txt) + assert_equal $(fn_md5 $ANSDIR/refine/refine_output_one/refine.variant_summary.json) \ + $(fn_md5 $OD/refine_output_one/refine.variant_summary.json) + assert_equal $(fn_md5 $ANSDIR/refine/refine_output_one/refine.region_summary.json) \ + $(fn_md5 $OD/refine_output_one/refine.region_summary.json) +fi + +run test_refine_two $truv bench -b $INDIR/refine_data/hg002_base.vcf.gz \ + -c $INDIR/refine_data/hg002_comp.vcf.gz \ + --includebed $INDIR/refine_data/h1_hc_tr_hg002.bed \ + -s 5 -o $OD/refine_output_two + +run test_refine_two $truv refine -k -I -r $INDIR/refine_data/h2_hc_tr_hg002.bed \ + -f $INDIR/refine_data/chr20.fa.gz \ + $OD/refine_output_two + +if [ $test_refine_two ]; then + assert_exit_code 0 + assert_equal $(fn_md5 $ANSDIR/refine/refine_output_two/refine.regions.txt) \ + $(fn_md5 $OD/refine_output_two/refine.regions.txt) + assert_equal $(fn_md5 $ANSDIR/refine/refine_output_two/refine.variant_summary.json) \ + $(fn_md5 $OD/refine_output_two/refine.variant_summary.json) + assert_equal $(fn_md5 $ANSDIR/refine/refine_output_two/refine.region_summary.json) \ + $(fn_md5 $OD/refine_output_two/refine.region_summary.json) +fi diff --git a/repo_utils/sub_tests/segment.sh b/repo_utils/sub_tests/segment.sh index 13e671a0..d1f42620 100644 --- a/repo_utils/sub_tests/segment.sh +++ b/repo_utils/sub_tests/segment.sh @@ -1,9 +1,8 @@ # ------------------------------------------------------------ # segment # ------------------------------------------------------------ -run test_segment $truv segment $ANSDIR/anno_answers.vcf.gz $OD/segment.vcf +run test_segment $truv segment --passonly $INDIR/variants/multi.vcf.gz -o $OD/segment.vcf if [ $test_segment ]; then assert_exit_code 0 - run test_segment_result - assert_equal $(fn_md5 $ANSDIR/segment.vcf) $(fn_md5 $OD/segment.vcf) + assert_equal $(fn_md5 $ANSDIR/segment/segment.vcf) $(fn_md5 $OD/segment.vcf) fi diff --git a/repo_utils/sub_tests/stratify.sh b/repo_utils/sub_tests/stratify.sh new file mode 100644 index 00000000..812f0a0c --- /dev/null +++ b/repo_utils/sub_tests/stratify.sh @@ -0,0 +1,11 @@ +# ------------------------------------------------------------ +# stratify +# ------------------------------------------------------------ +run test_stratify $truv stratify -w \ + $INDIR/beds/include.bed \ + $INDIR/variants/input1.vcf.gz \ + -o $OD/stratify.txt +if [ $test_stratify ]; then + assert_exit_code 0 + assert_equal $(fn_md5 $ANSDIR/stratify/stratify.txt) $(fn_md5 $OD/stratify.txt) +fi diff --git a/repo_utils/sub_tests/vcf2df.sh b/repo_utils/sub_tests/vcf2df.sh index 1549d74e..49a7ec80 100644 --- a/repo_utils/sub_tests/vcf2df.sh +++ b/repo_utils/sub_tests/vcf2df.sh @@ -1,38 +1,38 @@ # ------------------------------------------------------------ # vcf2df # ------------------------------------------------------------ -run test_vcf2df_bare $truv vcf2df -n $INDIR/input1.vcf.gz $OD/vcf2df_bare.jl +run test_vcf2df_bare $truv vcf2df -n $INDIR/variants/input1.vcf.gz $OD/vcf2df_bare.jl if [ $test_vcf2df_bare ]; then assert_exit_code 0 - df_check test_vcf2df_bare_result $ANSDIR/vcf2df_bare.jl $OD/vcf2df_bare.jl + df_check test_vcf2df_bare $ANSDIR/vcf2df/vcf2df_bare.jl $OD/vcf2df_bare.jl fi -run test_vcf2df $truv vcf2df -f -i -n $INDIR/input1.vcf.gz $OD/vcf2df.jl +run test_vcf2df $truv vcf2df -f -i -n $INDIR/variants/input1.vcf.gz $OD/vcf2df.jl if [ $test_vcf2df ]; then assert_exit_code 0 - df_check test_vcf2df_result $ANSDIR/vcf2df.jl $OD/vcf2df.jl + df_check test_vcf2df $ANSDIR/vcf2df/vcf2df.jl $OD/vcf2df.jl fi -run test_vcf2df_dir $truv vcf2df -f -i -b -n $OD/bench23/ $OD/truv2df.jl +run test_vcf2df_dir $truv vcf2df -f -i -b -n $ANSDIR/bench/bench23/ $OD/truv2df.jl if [ $test_vcf2df_dir ]; then assert_exit_code 0 - df_check test_vcf2df_dir_result $ANSDIR/truv2df.jl $OD/truv2df.jl + df_check test_vcf2df_dif $ANSDIR/vcf2df/truv2df.jl $OD/truv2df.jl fi -run test_vcf2df_single $truv vcf2df -f -i -s NA12878 $INDIR/input2.vcf.gz $OD/single_vcf2df.jl +run test_vcf2df_single $truv vcf2df -f -i -s NA12878 $INDIR/variants/input2.vcf.gz $OD/single_vcf2df.jl if [ $test_vcf2df_single ]; then assert_exit_code 0 - df_check test_vcf2df_single $ANSDIR/single_vcf2df.jl $OD/single_vcf2df.jl + df_check test_vcf2df_single $ANSDIR/vcf2df/single_vcf2df.jl $OD/single_vcf2df.jl fi -run test_vcf2df_subset $truv vcf2df -f -i -s HG00733,NA12878 $INDIR/multi.vcf.gz $OD/subset_vcf2df.jl +run test_vcf2df_subset $truv vcf2df -f -i -s HG00733,NA12878 $INDIR/variants/multi.vcf.gz $OD/subset_vcf2df.jl if [ $test_vcf2df_subset ]; then assert_exit_code 0 - df_check test_vcf2df_subset $ANSDIR/subset_vcf2df.jl $OD/subset_vcf2df.jl + df_check test_vcf2df_subset $ANSDIR/vcf2df/subset_vcf2df.jl $OD/subset_vcf2df.jl fi -run test_vcf2df_multi $truv vcf2df -f -i $INDIR/multi.vcf.gz $OD/multi_vcf2df.jl +run test_vcf2df_multi $truv vcf2df -f -i $INDIR/variants/multi.vcf.gz $OD/multi_vcf2df.jl if [ $test_vcf2df_multi ]; then assert_exit_code 0 - df_check test_vcf2df_multi $ANSDIR/multi_vcf2df.jl $OD/multi_vcf2df.jl + df_check test_vcf2df_multi $ANSDIR/vcf2df/multi_vcf2df.jl $OD/multi_vcf2df.jl fi diff --git a/repo_utils/test_files/answer_key/anno_bpovl.jl b/repo_utils/test_files/answer_key/anno_bpovl.jl deleted file mode 100644 index ce66202a..00000000 Binary files a/repo_utils/test_files/answer_key/anno_bpovl.jl and /dev/null differ diff --git a/repo_utils/test_files/answer_key/bench12/fn.vcf b/repo_utils/test_files/answer_key/bench12/fn.vcf deleted file mode 100644 index a7e8c1dd..00000000 --- a/repo_utils/test_files/answer_key/bench12/fn.vcf +++ /dev/null @@ -1,57 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 -chr20 278930 . C CGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAG 60 . QNAME=HG002-S9-H2-000001F;QSTART=232485;QSTRAND=+;SVTYPE=INS;SVLEN=184;PctSeqSimilarity=0.6435;PctSizeSimilarity=0.3389;PctRecOverlap=0.3407;SizeDiff=-359;StartDistance=-139;EndDistance=-139;TruScore=44;MatchId=3.0.0;Multi GT:PL:DP 0/1:7,9,6:23,9 -chr20 279062 . G GGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGTGGGAGGGAGGGAGGGAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=258112;QSTRAND=+;SVTYPE=INS;SVLEN=139;PctSeqSimilarity=0.4198;PctSizeSimilarity=0.256;PctRecOverlap=0.256;SizeDiff=-404;StartDistance=-7;EndDistance=-7;TruScore=31;MatchId=3.1.0;Multi GT:PL:DP 1/0:5,1,4:27,38 -chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCCATCCCCCGTCCGCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 61 . QNAME=HG002-S9-H2-000001F;QSTART=374905;QSTRAND=+;SVTYPE=INS;SVLEN=227;PctSeqSimilarity=0.9956;PctSizeSimilarity=0.9956;PctRecOverlap=1;SizeDiff=1;StartDistance=0;EndDistance=0;TruScore=99;MatchId=6.0.0;Multi GT:PL 0/1:. -chr20 641913 . G GGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGA 60 . QNAME=HG002-S9-H1-000001F;QSTART=621365;QSTRAND=+;SVTYPE=INS;SVLEN=66;PctSeqSimilarity=0.5614;PctSizeSimilarity=0.1048;PctRecOverlap=0.0872;SizeDiff=-564;StartDistance=-294;EndDistance=-294;GTMatch;TruScore=25;MatchId=8.0.0;Multi GT:PL:DP 1/0:7,5,7:34,13 -chr20 642300 . G GCCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGC 60 . QNAME=HG002-S9-H1-000001F;QSTART=621812;QSTRAND=+;SVTYPE=INS;SVLEN=408;PctSeqSimilarity=0.8071;PctSizeSimilarity=0.6456;PctRecOverlap=0.6461;SizeDiff=-224;StartDistance=70;EndDistance=70;GTMatch;TruScore=69;MatchId=8.2.1 GT:PL:DP 1/0:5,10,5:44,36 -chr20 642330 . G GGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597257;QSTRAND=+;SVTYPE=INS;SVLEN=66;PctSeqSimilarity=0.4025;PctSizeSimilarity=0.1048;PctRecOverlap=0.1062;SizeDiff=-564;StartDistance=123;EndDistance=123;GTMatch;TruScore=20;MatchId=8.3.0;Multi GT:PL:DP 0/1:6,1,9:20,25 -chr20 709830 . G GACACTGCTCGGTCCTCCGCTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCGCTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGAACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGA 60 . QNAME=HG002-S9-H1-000001F;QSTART=689726;QSTRAND=+;SVTYPE=INS;SVLEN=465;PctSeqSimilarity=0.152;PctSizeSimilarity=0.2;PctRecOverlap=0.2022;SizeDiff=372;StartDistance=71;EndDistance=-22;GTMatch;TruScore=18;MatchId=9.1.0;Multi GT:PL:DP 1/0:4,8,7:50,48 -chr20 949516 . CTCTGAAGAGGTAACATTTGAACTGAGATGTAGAGGGAGAGAAGGAACTAGCCATGTGGAGATCTGGGGGAGGAGCATTCCAGGCAGAGGGGATAGCAAGTGCA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=905663;QSTRAND=+;SVTYPE=DEL;SVLEN=-103;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=12.0._ GT:PL:DP 0/1:6,6,1:34,8 diff --git a/repo_utils/test_files/answer_key/bench12/fp.vcf b/repo_utils/test_files/answer_key/bench12/fp.vcf deleted file mode 100644 index 5c42d986..00000000 --- a/repo_utils/test_files/answer_key/bench12/fp.vcf +++ /dev/null @@ -1,52 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__v12_NA12878_giab_pbsq2-ccs_1000-pereg.h1-un.racon-p2.fasta.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__v12_NA12878_giab_pbsq2-ccs_1000-pereg.h2-un.racon-p2.fasta.gz.vcf.gz; Date=Thu Jul 22 20:43:36 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/unused_samples/grch38/NA12878/exact.vcf.gz; Date=Mon Aug 16 16:58:00 2021 -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 -chr20 380878 . T TGATTAGCTCCGGTTTGCATCACCCGGACCGGGGGATTAGCTCCGGTTTGCATCACCCGGACCGGGG 60 . QNAME=cluster19_000000F;QSTART=25381150;QSTRAND=-;SVTYPE=INS;SVLEN=66;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=5._.0 GT:PL:AD 1/0:8,3,9:38,14 -chr20 642230 . T TGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTG 60 . QNAME=cluster19_000000F;QSTART=25119065;QSTRAND=-;SVTYPE=INS;SVLEN=632;PctSeqSimilarity=0.8071;PctSizeSimilarity=0.6456;PctRecOverlap=0.6461;SizeDiff=-224;StartDistance=70;EndDistance=70;GTMatch;TruScore=69;MatchId=8.2.1 GT:PL:AD 1/0:7,5,6:16,7 -chr20 764537 . A AGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAT 60 . QNAME=cluster19_000000F;QSTART=24996803;QSTRAND=-;SVTYPE=INS;SVLEN=78;PctSeqSimilarity=0.802;PctSizeSimilarity=0.6667;PctRecOverlap=0.6752;SizeDiff=39;StartDistance=0;EndDistance=0;TruScore=71;MatchId=11.0.0;Multi GT:PL:AD 1/0:5,4,9:13,8 diff --git a/repo_utils/test_files/answer_key/bench12/log.txt b/repo_utils/test_files/answer_key/bench12/log.txt deleted file mode 100644 index aef3b289..00000000 --- a/repo_utils/test_files/answer_key/bench12/log.txt +++ /dev/null @@ -1,67 +0,0 @@ -2022-08-25 00:31:07,328 [INFO] Running /data/truvari/__main__.py bench -b repo_utils/test_files/input1.vcf.gz -c repo_utils/test_files/input2.vcf.gz -f repo_utils/test_files/reference.fa -o test_results/bench12/ -2022-08-25 00:31:07,329 [INFO] Params: -{ - "base": "repo_utils/test_files/input1.vcf.gz", - "comp": "repo_utils/test_files/input2.vcf.gz", - "output": "test_results/bench12/", - "reference": "repo_utils/test_files/reference.fa", - "giabreport": false, - "debug": false, - "prog": false, - "refdist": 500, - "unroll": false, - "pctsim": 0.7, - "minhaplen": 50, - "pctsize": 0.7, - "pctovl": 0.0, - "typeignore": false, - "dup_to_ins": false, - "use_lev": false, - "chunksize": 1000, - "gtcomp": false, - "bSample": null, - "cSample": null, - "sizemin": 50, - "sizefilt": 30, - "sizemax": 50000, - "passonly": false, - "no_ref": false, - "includebed": null, - "extend": 0, - "multimatch": false -} -2022-08-25 00:31:07,329 [INFO] Truvari version: 3.5.0-dev -2022-08-25 00:31:07,442 [INFO] Zipped 3934 variants Counter({'base': 2151, 'comp': 1783}) -2022-08-25 00:31:07,443 [INFO] 13 chunks of 3934 variants Counter({'__filtered': 3904, 'base': 16, 'comp': 14}) -2022-08-25 00:31:07,446 [INFO] Stats: { - "TP-base": 8, - "TP-call": 8, - "FP": 3, - "FN": 8, - "precision": 0.7272727272727273, - "recall": 0.5, - "f1": 0.5925925925925926, - "base cnt": 16, - "call cnt": 11, - "TP-call_TP-gt": 4, - "TP-call_FP-gt": 4, - "TP-base_TP-gt": 4, - "TP-base_FP-gt": 4, - "gt_concordance": 0.5, - "gt_matrix": { - "(1, 1)": { - "(1, 1)": 2, - "(1, 0)": 1, - "(0, 1)": 1 - }, - "(0, 1)": { - "(1, 1)": 1, - "(0, 1)": 1, - "(1, 0)": 1 - }, - "(1, 0)": { - "(1, 1)": 1 - } - } -} -2022-08-25 00:31:07,449 [INFO] Finished bench diff --git a/repo_utils/test_files/answer_key/bench12/summary.txt b/repo_utils/test_files/answer_key/bench12/summary.txt deleted file mode 100644 index 06a9df02..00000000 --- a/repo_utils/test_files/answer_key/bench12/summary.txt +++ /dev/null @@ -1,31 +0,0 @@ -{ - "TP-base": 8, - "TP-call": 8, - "FP": 3, - "FN": 8, - "precision": 0.7272727272727273, - "recall": 0.5, - "f1": 0.5925925925925926, - "base cnt": 16, - "call cnt": 11, - "TP-call_TP-gt": 4, - "TP-call_FP-gt": 4, - "TP-base_TP-gt": 4, - "TP-base_FP-gt": 4, - "gt_concordance": 0.5, - "gt_matrix": { - "(1, 1)": { - "(1, 1)": 2, - "(1, 0)": 1, - "(0, 1)": 1 - }, - "(0, 1)": { - "(1, 1)": 1, - "(0, 1)": 1, - "(1, 0)": 1 - }, - "(1, 0)": { - "(1, 1)": 1 - } - } -} \ No newline at end of file diff --git a/repo_utils/test_files/answer_key/bench12/tp-base.vcf b/repo_utils/test_files/answer_key/bench12/tp-base.vcf deleted file mode 100644 index a41c70bc..00000000 --- a/repo_utils/test_files/answer_key/bench12/tp-base.vcf +++ /dev/null @@ -1,57 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 -chr20 149013 . A ACCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=127907;QSTRAND=+;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=0.9967;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=-82;EndDistance=-82;GTMatch;TruScore=66;MatchId=1.0.0 GT:PL:DP 1/1:8,8,5:15,29 -chr20 279069 . A AGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGCGGGACGGAGGGAGGGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=232808;QSTRAND=+;SVTYPE=INS;SVLEN=438;PctSeqSimilarity=0.8739;PctSizeSimilarity=0.8066;PctRecOverlap=0.8085;SizeDiff=-105;StartDistance=0;EndDistance=0;TruScore=82;MatchId=3.2.0 GT:PL:DP 0/1:7,10,7:12,48 -chr20 306268 . A ACCAGGCTGGAGTGCAGTGGCTCACTGCGTGGCTCGCTACAGCCTACAACTCCTGGGCTCCAGCAATCCTGCTGCCCCAGCCTCCTGTGTAACTGAGACTACAGGCACGCACCACCACACCCAGCTAATTTTTTCTTTCTTTTTTTTTTTTTTGAGATGAACTCTCACTCTGTTGC 60 . QNAME=HG002-S9-H1-000001F;QSTART=285475;QSTRAND=+;SVTYPE=INS;SVLEN=175;PctSeqSimilarity=0.9972;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=99;MatchId=4.0.0 GT:PL:DP 1/1:2,7,2:17,31 -chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCATCCCCCGTCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 60 . QNAME=HG002-S9-H1-000001F;QSTART=400044;QSTRAND=+;SVTYPE=INS;SVLEN=226;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=6.1.0 GT:PL:DP 1/0:4,8,6:32,9 -chr20 613783 . TGTGTGCTGAGTCCAGCTCAAGTCCCTTGGTTCCCACTGCTGCTAAGCATGCACG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=593293;QSTRAND=+;SVTYPE=DEL;SVLEN=-54;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=7.0.0 GT:PL:DP 1/1:6,8,8:40,41 -chr20 642207 . T TGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGG 60 . QNAME=HG002-S9-H2-000001F;QSTART=596630;QSTRAND=+;SVTYPE=INS;SVLEN=501;PctSeqSimilarity=0.8817;PctSizeSimilarity=0.7952;PctRecOverlap=0.794;SizeDiff=-129;StartDistance=0;EndDistance=0;GTMatch;TruScore=82;MatchId=8.1.0 GT:PL:DP 0/1:5,9,1:7,43 -chr20 709759 . AGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCC A 60 . QNAME=HG002-S9-H2-000001F;QSTART=664783;QSTRAND=+;SVTYPE=DEL;SVLEN=-93;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=100;MatchId=9.0.0 GT:PL:DP 0/1:9,6,6:13,31 -chr20 764537 . A AGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=744872;QSTRAND=+;SVTYPE=INS;SVLEN=117;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=11.0.1 GT:PL:DP 1/1:2,1,5:40,30 diff --git a/repo_utils/test_files/answer_key/bench12/tp-call.vcf b/repo_utils/test_files/answer_key/bench12/tp-call.vcf deleted file mode 100644 index c15a05a7..00000000 --- a/repo_utils/test_files/answer_key/bench12/tp-call.vcf +++ /dev/null @@ -1,57 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__v12_NA12878_giab_pbsq2-ccs_1000-pereg.h1-un.racon-p2.fasta.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__v12_NA12878_giab_pbsq2-ccs_1000-pereg.h2-un.racon-p2.fasta.gz.vcf.gz; Date=Thu Jul 22 20:43:36 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/unused_samples/grch38/NA12878/exact.vcf.gz; Date=Mon Aug 16 16:58:00 2021 -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 -chr20 149095 . G GGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGACCCATATTTGGGAA 60 . QNAME=cluster19_000000F;QSTART=25613718;QSTRAND=-;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=0.9967;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=-82;EndDistance=-82;GTMatch;TruScore=66;MatchId=1.0.0 GT:PL:AD 1/1:10,5,10:30,43 -chr20 279069 . A AGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGC 60 . QNAME=cluster19_000000F;QSTART=25483168;QSTRAND=-;SVTYPE=INS;SVLEN=543;PctSeqSimilarity=0.8739;PctSizeSimilarity=0.8066;PctRecOverlap=0.8085;SizeDiff=-105;StartDistance=0;EndDistance=0;TruScore=82;MatchId=3.2.0 GT:PL:AD 1/1:8,1,10:40,42 -chr20 306268 . A ACCAGGCTGGAGTGCAGTGGCTCACTGCGTGGCTCGCTACAGCCTACAACTCCTGGGCTCCAGCAATCCTGCTGCCCCAGCCTCCTGTGTAACTGAGACTACAGGCACGCACCACCACACCCAGCTAATGTTTTCTTTCTTTTTTTTTTTTTTGAGATGAACTCTCACTCTGTTGC 60 . QNAME=cluster19_000000F;QSTART=25455794;QSTRAND=-;SVTYPE=INS;SVLEN=175;PctSeqSimilarity=0.9972;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=99;MatchId=4.0.0 GT:PL:AD 1/1:4,10,2:26,18 -chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCATCCCCCGTCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 60 . QNAME=cluster19_000000F;QSTART=25341211;QSTRAND=-;SVTYPE=INS;SVLEN=226;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=6.1.0 GT:PL:AD 1/1:7,10,5:44,42 -chr20 613783 . TGTGTGCTGAGTCCAGCTCAAGTCCCTTGGTTCCCACTGCTGCTAAGCATGCACG T 60 . QNAME=cluster19_000000F;QSTART=25148089;QSTRAND=-;SVTYPE=DEL;SVLEN=-54;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=7.0.0 GT:PL:AD 1/0:3,1,8:9,32 -chr20 642207 . T TGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGG 60 . QNAME=cluster19_000000F;QSTART=602404;QSTRAND=+;SVTYPE=INS;SVLEN=630;PctSeqSimilarity=0.8817;PctSizeSimilarity=0.7952;PctRecOverlap=0.794;SizeDiff=-129;StartDistance=0;EndDistance=0;GTMatch;TruScore=82;MatchId=8.1.0 GT:PL:AD 0/1:2,1,9:9,12 -chr20 709759 . AGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCC A 60 . QNAME=cluster19_000000F;QSTART=25051525;QSTRAND=-;SVTYPE=DEL;SVLEN=-93;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=100;MatchId=9.0.0 GT:PL:AD 1/0:8,10,9:32,27 -chr20 764537 . A AGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAT 60 . QNAME=cluster19_000000F;QSTART=725358;QSTRAND=+;SVTYPE=INS;SVLEN=117;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=11.0.1 GT:PL:AD 0/1:7,8,4:13,5 diff --git a/repo_utils/test_files/answer_key/bench13/fn.vcf b/repo_utils/test_files/answer_key/bench13/fn.vcf deleted file mode 100644 index 778116f9..00000000 --- a/repo_utils/test_files/answer_key/bench13/fn.vcf +++ /dev/null @@ -1,55 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 -chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCATCCCCCGTCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 60 . QNAME=HG002-S9-H1-000001F;QSTART=400044;QSTRAND=+;SVTYPE=INS;SVLEN=226;PctSeqSimilarity=0.9956;PctSizeSimilarity=0.9956;PctRecOverlap=1;SizeDiff=-1;StartDistance=0;EndDistance=0;TruScore=99;MatchId=8.1.0;Multi GT:PL:DP 1/0:4,8,6:32,9 -chr20 641913 . G GGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGA 60 . QNAME=HG002-S9-H1-000001F;QSTART=621365;QSTRAND=+;SVTYPE=INS;SVLEN=66;PctSeqSimilarity=0.6041;PctSizeSimilarity=0.4049;PctRecOverlap=0.411;SizeDiff=-97;StartDistance=7;EndDistance=7;GTMatch;TruScore=47;MatchId=10.0.0 GT:PL:DP 1/0:7,5,7:34,13 -chr20 642207 . T TGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGG 60 . QNAME=HG002-S9-H2-000001F;QSTART=596630;QSTRAND=+;SVTYPE=INS;SVLEN=501;PctSeqSimilarity=0.723;PctSizeSimilarity=0.513;PctRecOverlap=0.513;SizeDiff=244;StartDistance=-64;EndDistance=-64;GTMatch;TruScore=58;MatchId=10.1.2 GT:PL:DP 0/1:5,9,1:7,43 -chr20 642330 . G GGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597257;QSTRAND=+;SVTYPE=INS;SVLEN=66;PctSeqSimilarity=0.8835;PctSizeSimilarity=0.5116;PctRecOverlap=0;SizeDiff=-63;StartDistance=262;EndDistance=262;GTMatch;TruScore=46;MatchId=10.3.1 GT:PL:DP 0/1:6,1,9:20,25 -chr20 709830 . G GACACTGCTCGGTCCTCCGCTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCGCTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGAACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGA 60 . QNAME=HG002-S9-H1-000001F;QSTART=689726;QSTRAND=+;SVTYPE=INS;SVLEN=465;PctSeqSimilarity=0.152;PctSizeSimilarity=0.2;PctRecOverlap=0.2022;SizeDiff=372;StartDistance=71;EndDistance=-22;TruScore=18;MatchId=11.1.0;Multi GT:PL:DP 1/0:4,8,7:50,48 -chr20 764537 . A AGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=744872;QSTRAND=+;SVTYPE=INS;SVLEN=117;PctSeqSimilarity=0.8992;PctSizeSimilarity=0.6667;PctRecOverlap=0.0256;SizeDiff=39;StartDistance=95;EndDistance=95;TruScore=53;MatchId=13.0.0 GT:PL:DP 1/1:2,1,5:40,30 diff --git a/repo_utils/test_files/answer_key/bench13/fp.vcf b/repo_utils/test_files/answer_key/bench13/fp.vcf deleted file mode 100644 index 78ec88c6..00000000 --- a/repo_utils/test_files/answer_key/bench13/fp.vcf +++ /dev/null @@ -1,55 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__v12_HG00733_hgsvc_pbsq2-clr_1000-flye.h1-un.arrow-p1.fasta.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__v12_HG00733_hgsvc_pbsq2-clr_1000-flye.h2-un.arrow-p1.fasta.gz.vcf.gz; Date=Thu Jul 22 20:41:33 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/unused_samples/grch38/HG00733/exact.vcf.gz; Date=Mon Aug 16 16:57:27 2021 -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00733 -chr20 149073 . G GAATCCTGACCCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCA 60 . QNAME=cluster23_scaffold_2;QSTART=25547471;QSTRAND=-;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=0.9962;PctSizeSimilarity=1;PctRecOverlap=0.1304;SizeDiff=0;StartDistance=-60;EndDistance=-60;TruScore=70;MatchId=1.0.1;Multi GT 0/1 -chr20 280211 . CAACAACAACAATTGTACTTCCCTAAGGTTACACCCAGCAGGTGCATAAAACCTACAGTAACAAT C 60 . QNAME=cluster23_scaffold_3;QSTART=25431380;QSTRAND=-;SVTYPE=DEL;SVLEN=-64;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=5._.0 GT 1/0 -chr20 641906 . G GGCGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCT 60 . QNAME=cluster23_scaffold_2;QSTART=25053389;QSTRAND=-;SVTYPE=INS;SVLEN=163;PctSeqSimilarity=0.6041;PctSizeSimilarity=0.4049;PctRecOverlap=0.411;SizeDiff=-97;StartDistance=7;EndDistance=7;GTMatch;TruScore=47;MatchId=10.0.0 GT 0/1 -chr20 642068 . G GTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCC 60 . QNAME=cluster23_scaffold_2;QSTART=25053097;QSTRAND=-;SVTYPE=INS;SVLEN=129;PctSeqSimilarity=0.8835;PctSizeSimilarity=0.5116;PctRecOverlap=0;SizeDiff=-63;StartDistance=262;EndDistance=262;GTMatch;TruScore=46;MatchId=10.3.1 GT 0/1 -chr20 642271 . G GGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGC 60 . QNAME=cluster23_scaffold_3;QSTART=25068731;QSTRAND=-;SVTYPE=INS;SVLEN=257;PctSeqSimilarity=0.723;PctSizeSimilarity=0.513;PctRecOverlap=0.513;SizeDiff=244;StartDistance=-64;EndDistance=-64;GTMatch;TruScore=58;MatchId=10.1.2 GT 1/0 -chr20 642330 . G GCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGGGC 60 . QNAME=cluster23_scaffold_2;QSTART=25052609;QSTRAND=-;SVTYPE=INS;SVLEN=226;PctSeqSimilarity=0.8475;PctSizeSimilarity=0.292;PctRecOverlap=0;SizeDiff=-160;StartDistance=-417;EndDistance=-417;GTMatch;TruScore=37;MatchId=10.0.3;Multi GT 0/1 -chr20 764442 . A AGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGG 60 . QNAME=cluster23_scaffold_3;QSTART=24946242;QSTRAND=-;SVTYPE=INS;SVLEN=78;PctSeqSimilarity=0.8992;PctSizeSimilarity=0.6667;PctRecOverlap=0.0256;SizeDiff=39;StartDistance=95;EndDistance=95;TruScore=53;MatchId=13.0.0 GT 1/0 diff --git a/repo_utils/test_files/answer_key/bench13/log.txt b/repo_utils/test_files/answer_key/bench13/log.txt deleted file mode 100644 index 37088de3..00000000 --- a/repo_utils/test_files/answer_key/bench13/log.txt +++ /dev/null @@ -1,66 +0,0 @@ -2022-08-25 00:31:09,784 [INFO] Running /data/truvari/__main__.py bench -b repo_utils/test_files/input1.vcf.gz -c repo_utils/test_files/input3.vcf.gz -f repo_utils/test_files/reference.fa -o test_results/bench13/ -2022-08-25 00:31:09,786 [INFO] Params: -{ - "base": "repo_utils/test_files/input1.vcf.gz", - "comp": "repo_utils/test_files/input3.vcf.gz", - "output": "test_results/bench13/", - "reference": "repo_utils/test_files/reference.fa", - "giabreport": false, - "debug": false, - "prog": false, - "refdist": 500, - "unroll": false, - "pctsim": 0.7, - "minhaplen": 50, - "pctsize": 0.7, - "pctovl": 0.0, - "typeignore": false, - "dup_to_ins": false, - "use_lev": false, - "chunksize": 1000, - "gtcomp": false, - "bSample": null, - "cSample": null, - "sizemin": 50, - "sizefilt": 30, - "sizemax": 50000, - "passonly": false, - "no_ref": false, - "includebed": null, - "extend": 0, - "multimatch": false -} -2022-08-25 00:31:09,786 [INFO] Truvari version: 3.5.0-dev -2022-08-25 00:31:09,899 [INFO] Zipped 4216 variants Counter({'base': 2151, 'comp': 2065}) -2022-08-25 00:31:09,900 [INFO] 15 chunks of 4216 variants Counter({'__filtered': 4179, 'comp': 21, 'base': 16}) -2022-08-25 00:31:09,904 [INFO] Stats: { - "TP-base": 10, - "TP-call": 10, - "FP": 7, - "FN": 6, - "precision": 0.5882352941176471, - "recall": 0.625, - "f1": 0.6060606060606061, - "base cnt": 16, - "call cnt": 17, - "TP-call_TP-gt": 7, - "TP-call_FP-gt": 3, - "TP-base_TP-gt": 7, - "TP-base_FP-gt": 3, - "gt_concordance": 0.7, - "gt_matrix": { - "(1, 1)": { - "(1, 0)": 1, - "(1, 1)": 2 - }, - "(0, 1)": { - "(0, 1)": 2, - "(1, 1)": 2, - "(1, 0)": 1 - }, - "(1, 0)": { - "(1, 0)": 2 - } - } -} -2022-08-25 00:31:09,907 [INFO] Finished bench diff --git a/repo_utils/test_files/answer_key/bench13/summary.txt b/repo_utils/test_files/answer_key/bench13/summary.txt deleted file mode 100644 index 57913453..00000000 --- a/repo_utils/test_files/answer_key/bench13/summary.txt +++ /dev/null @@ -1,30 +0,0 @@ -{ - "TP-base": 10, - "TP-call": 10, - "FP": 7, - "FN": 6, - "precision": 0.5882352941176471, - "recall": 0.625, - "f1": 0.6060606060606061, - "base cnt": 16, - "call cnt": 17, - "TP-call_TP-gt": 7, - "TP-call_FP-gt": 3, - "TP-base_TP-gt": 7, - "TP-base_FP-gt": 3, - "gt_concordance": 0.7, - "gt_matrix": { - "(1, 1)": { - "(1, 0)": 1, - "(1, 1)": 2 - }, - "(0, 1)": { - "(0, 1)": 2, - "(1, 1)": 2, - "(1, 0)": 1 - }, - "(1, 0)": { - "(1, 0)": 2 - } - } -} \ No newline at end of file diff --git a/repo_utils/test_files/answer_key/bench13/tp-base.vcf b/repo_utils/test_files/answer_key/bench13/tp-base.vcf deleted file mode 100644 index a92cd211..00000000 --- a/repo_utils/test_files/answer_key/bench13/tp-base.vcf +++ /dev/null @@ -1,59 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 -chr20 149013 . A ACCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=127907;QSTRAND=+;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=1.0.0 GT:PL:DP 1/1:8,8,5:15,29 -chr20 278930 . C CGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAG 60 . QNAME=HG002-S9-H2-000001F;QSTART=232485;QSTRAND=+;SVTYPE=INS;SVLEN=184;PctSeqSimilarity=0.9866;PctSizeSimilarity=0.9787;PctRecOverlap=0.9788;SizeDiff=-4;StartDistance=0;EndDistance=0;GTMatch;TruScore=98;MatchId=4.0.0 GT:PL:DP 0/1:7,9,6:23,9 -chr20 279062 . G GGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGTGGGAGGGAGGGAGGGAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=258112;QSTRAND=+;SVTYPE=INS;SVLEN=139;PctSeqSimilarity=0.8801;PctSizeSimilarity=0.7765;PctRecOverlap=0.6872;SizeDiff=-40;StartDistance=-36;EndDistance=-36;GTMatch;TruScore=78;MatchId=4.1.2 GT:PL:DP 1/0:5,1,4:27,38 -chr20 279069 . A AGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGCGGGACGGAGGGAGGGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=232808;QSTRAND=+;SVTYPE=INS;SVLEN=438;PctSeqSimilarity=0.9203;PctSizeSimilarity=0.8521;PctRecOverlap=0.8524;SizeDiff=-76;StartDistance=0;EndDistance=0;GTMatch;TruScore=87;MatchId=4.2.1 GT:PL:DP 0/1:7,10,7:12,48 -chr20 306268 . A ACCAGGCTGGAGTGCAGTGGCTCACTGCGTGGCTCGCTACAGCCTACAACTCCTGGGCTCCAGCAATCCTGCTGCCCCAGCCTCCTGTGTAACTGAGACTACAGGCACGCACCACCACACCCAGCTAATTTTTTCTTTCTTTTTTTTTTTTTTGAGATGAACTCTCACTCTGTTGC 60 . QNAME=HG002-S9-H1-000001F;QSTART=285475;QSTRAND=+;SVTYPE=INS;SVLEN=175;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=100;MatchId=6.0.0 GT:PL:DP 1/1:2,7,2:17,31 -chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCCATCCCCCGTCCGCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 61 . QNAME=HG002-S9-H2-000001F;QSTART=374905;QSTRAND=+;SVTYPE=INS;SVLEN=227;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=8.0.0 GT:PL 0/1:. -chr20 613783 . TGTGTGCTGAGTCCAGCTCAAGTCCCTTGGTTCCCACTGCTGCTAAGCATGCACG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=593293;QSTRAND=+;SVTYPE=DEL;SVLEN=-54;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=100;MatchId=9.0.0 GT:PL:DP 1/1:6,8,8:40,41 -chr20 642300 . G GCCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGC 60 . QNAME=HG002-S9-H1-000001F;QSTART=621812;QSTRAND=+;SVTYPE=INS;SVLEN=408;PctSeqSimilarity=0.8906;PctSizeSimilarity=0.7892;PctRecOverlap=0.6724;SizeDiff=86;StartDistance=-91;EndDistance=-91;GTMatch;TruScore=78;MatchId=10.2.4 GT:PL:DP 1/0:5,10,5:44,36 -chr20 709759 . AGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCC A 60 . QNAME=HG002-S9-H2-000001F;QSTART=664783;QSTRAND=+;SVTYPE=DEL;SVLEN=-93;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=11.0.0 GT:PL:DP 0/1:9,6,6:13,31 -chr20 949516 . CTCTGAAGAGGTAACATTTGAACTGAGATGTAGAGGGAGAGAAGGAACTAGCCATGTGGAGATCTGGGGGAGGAGCATTCCAGGCAGAGGGGATAGCAAGTGCA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=905663;QSTRAND=+;SVTYPE=DEL;SVLEN=-103;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=100;MatchId=14.0.0 GT:PL:DP 0/1:6,6,1:34,8 diff --git a/repo_utils/test_files/answer_key/bench13/tp-call.vcf b/repo_utils/test_files/answer_key/bench13/tp-call.vcf deleted file mode 100644 index 5566492c..00000000 --- a/repo_utils/test_files/answer_key/bench13/tp-call.vcf +++ /dev/null @@ -1,58 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__v12_HG00733_hgsvc_pbsq2-clr_1000-flye.h1-un.arrow-p1.fasta.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__v12_HG00733_hgsvc_pbsq2-clr_1000-flye.h2-un.arrow-p1.fasta.gz.vcf.gz; Date=Thu Jul 22 20:41:33 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/unused_samples/grch38/HG00733/exact.vcf.gz; Date=Mon Aug 16 16:57:27 2021 -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00733 -chr20 149013 . A ACCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGAC 60 . QNAME=cluster23_scaffold_3;QSTART=25562871;QSTRAND=-;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=1.0.0 GT 1/0 -chr20 278930 . C CGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGCGGGAG 60 . QNAME=cluster23_scaffold_2;QSTART=25417363;QSTRAND=-;SVTYPE=INS;SVLEN=188;PctSeqSimilarity=0.9866;PctSizeSimilarity=0.9787;PctRecOverlap=0.9788;SizeDiff=-4;StartDistance=0;EndDistance=0;GTMatch;TruScore=98;MatchId=4.0.0 GT 0/1 -chr20 279069 . A AGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGCGGGACGGAGGGAGGGC 60 . QNAME=cluster23_scaffold_2;QSTART=25416710;QSTRAND=-;SVTYPE=INS;SVLEN=514;PctSeqSimilarity=0.9203;PctSizeSimilarity=0.8521;PctRecOverlap=0.8524;SizeDiff=-76;StartDistance=0;EndDistance=0;GTMatch;TruScore=87;MatchId=4.2.1 GT 0/1 -chr20 279098 . G GGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGCGGGACGGAGGGAGGGACGGAGGGCGGGACGGAGGGAC 60 . QNAME=cluster23_scaffold_3;QSTART=25432493;QSTRAND=-;SVTYPE=INS;SVLEN=179;PctSeqSimilarity=0.8801;PctSizeSimilarity=0.7765;PctRecOverlap=0.6872;SizeDiff=-40;StartDistance=-36;EndDistance=-36;GTMatch;TruScore=78;MatchId=4.1.2 GT 1/0 -chr20 306268 . A ACCAGGCTGGAGTGCAGTGGCTCACTGCGTGGCTCGCTACAGCCTACAACTCCTGGGCTCCAGCAATCCTGCTGCCCCAGCCTCCTGTGTAACTGAGACTACAGGCACGCACCACCACACCCAGCTAATTTTTTCTTTCTTTTTTTTTTTTTTGAGATGAACTCTCACTCTGTTGC 60 . QNAME=cluster23_scaffold_3;QSTART=25405192;QSTRAND=-;SVTYPE=INS;SVLEN=175;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=100;MatchId=6.0.0 GT 1/1 -chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCCATCCCCCGTCCGCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 60 . QNAME=cluster23_scaffold_3;QSTART=25290548;QSTRAND=-;SVTYPE=INS;SVLEN=227;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=8.0.0 GT 1/1 -chr20 613783 . TGTGTGCTGAGTCCAGCTCAAGTCCCTTGGTTCCCACTGCTGCTAAGCATGCACG T 60 . QNAME=cluster23_scaffold_3;QSTART=25097419;QSTRAND=-;SVTYPE=DEL;SVLEN=-54;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=100;MatchId=9.0.0 GT 1/1 -chr20 642391 . G GGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGGC 60 . QNAME=cluster23_scaffold_3;QSTART=25068286;QSTRAND=-;SVTYPE=INS;SVLEN=322;PctSeqSimilarity=0.8906;PctSizeSimilarity=0.7892;PctRecOverlap=0.6724;SizeDiff=86;StartDistance=-91;EndDistance=-91;GTMatch;TruScore=78;MatchId=10.2.4 GT 1/0 -chr20 709759 . AGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCC A 60 . QNAME=cluster23_scaffold_3;QSTART=25000888;QSTRAND=-;SVTYPE=DEL;SVLEN=-93;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=11.0.0 GT 1/1 -chr20 949516 . CTCTGAAGAGGTAACATTTGAACTGAGATGTAGAGGGAGAGAAGGAACTAGCCATGTGGAGATCTGGGGGAGGAGCATTCCAGGCAGAGGGGATAGCAAGTGCA C 60 . QNAME=cluster23_scaffold_3;QSTART=24759935;QSTRAND=-;SVTYPE=DEL;SVLEN=-103;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=100;MatchId=14.0.0 GT 1/0 diff --git a/repo_utils/test_files/answer_key/bench13_extend/fn.vcf b/repo_utils/test_files/answer_key/bench13_extend/fn.vcf deleted file mode 100644 index 4595deff..00000000 --- a/repo_utils/test_files/answer_key/bench13_extend/fn.vcf +++ /dev/null @@ -1,53 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 -chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCATCCCCCGTCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 60 . QNAME=HG002-S9-H1-000001F;QSTART=400044;QSTRAND=+;SVTYPE=INS;SVLEN=226;PctSeqSimilarity=0.9956;PctSizeSimilarity=0.9956;PctRecOverlap=1;SizeDiff=-1;StartDistance=0;EndDistance=0;TruScore=99;MatchId=6.1.0;Multi GT:PL:DP 1/0:4,8,6:32,9 -chr20 642207 . T TGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGG 60 . QNAME=HG002-S9-H2-000001F;QSTART=596630;QSTRAND=+;SVTYPE=INS;SVLEN=501;PctSeqSimilarity=0.723;PctSizeSimilarity=0.513;PctRecOverlap=0.513;SizeDiff=244;StartDistance=-64;EndDistance=-64;GTMatch;TruScore=58;MatchId=8.0.2 GT:PL:DP 0/1:5,9,1:7,43 -chr20 642330 . G GGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597257;QSTRAND=+;SVTYPE=INS;SVLEN=66;PctSeqSimilarity=0.8835;PctSizeSimilarity=0.5116;PctRecOverlap=0;SizeDiff=-63;StartDistance=262;EndDistance=262;GTMatch;TruScore=46;MatchId=8.2.1 GT:PL:DP 0/1:6,1,9:20,25 -chr20 709830 . G GACACTGCTCGGTCCTCCGCTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCGCTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGAACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGA 60 . QNAME=HG002-S9-H1-000001F;QSTART=689726;QSTRAND=+;SVTYPE=INS;SVLEN=465;PctSeqSimilarity=0.152;PctSizeSimilarity=0.2;PctRecOverlap=0.2022;SizeDiff=372;StartDistance=71;EndDistance=-22;TruScore=18;MatchId=9.0.0 GT:PL:DP 1/0:4,8,7:50,48 diff --git a/repo_utils/test_files/answer_key/bench13_extend/fp.vcf b/repo_utils/test_files/answer_key/bench13_extend/fp.vcf deleted file mode 100644 index 222a5ca9..00000000 --- a/repo_utils/test_files/answer_key/bench13_extend/fp.vcf +++ /dev/null @@ -1,52 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__v12_HG00733_hgsvc_pbsq2-clr_1000-flye.h1-un.arrow-p1.fasta.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__v12_HG00733_hgsvc_pbsq2-clr_1000-flye.h2-un.arrow-p1.fasta.gz.vcf.gz; Date=Thu Jul 22 20:41:33 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/unused_samples/grch38/HG00733/exact.vcf.gz; Date=Mon Aug 16 16:57:27 2021 -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00733 -chr20 149073 . G GAATCCTGACCCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCA 60 . QNAME=cluster23_scaffold_2;QSTART=25547471;QSTRAND=-;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=0.9962;PctSizeSimilarity=1;PctRecOverlap=0.1304;SizeDiff=0;StartDistance=-60;EndDistance=-60;TruScore=70;MatchId=1.0.1;Multi GT 0/1 -chr20 642068 . G GTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCC 60 . QNAME=cluster23_scaffold_2;QSTART=25053097;QSTRAND=-;SVTYPE=INS;SVLEN=129;PctSeqSimilarity=0.8835;PctSizeSimilarity=0.5116;PctRecOverlap=0;SizeDiff=-63;StartDistance=262;EndDistance=262;GTMatch;TruScore=46;MatchId=8.2.1 GT 0/1 -chr20 642271 . G GGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGC 60 . QNAME=cluster23_scaffold_3;QSTART=25068731;QSTRAND=-;SVTYPE=INS;SVLEN=257;PctSeqSimilarity=0.723;PctSizeSimilarity=0.513;PctRecOverlap=0.513;SizeDiff=244;StartDistance=-64;EndDistance=-64;GTMatch;TruScore=58;MatchId=8.0.2 GT 1/0 -chr20 642330 . G GCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGGGC 60 . QNAME=cluster23_scaffold_2;QSTART=25052609;QSTRAND=-;SVTYPE=INS;SVLEN=226;PctSeqSimilarity=0.4558;PctSizeSimilarity=0.292;PctRecOverlap=0.2952;SizeDiff=-160;StartDistance=0;EndDistance=0;GTMatch;TruScore=34;MatchId=8.2.3;Multi GT 0/1 diff --git a/repo_utils/test_files/answer_key/bench13_extend/log.txt b/repo_utils/test_files/answer_key/bench13_extend/log.txt deleted file mode 100644 index 3905f98d..00000000 --- a/repo_utils/test_files/answer_key/bench13_extend/log.txt +++ /dev/null @@ -1,69 +0,0 @@ -2022-08-25 00:31:16,780 [INFO] Running /data/truvari/__main__.py bench -b repo_utils/test_files/input1.vcf.gz -c repo_utils/test_files/input3.vcf.gz -f repo_utils/test_files/reference.fa -o test_results/bench13_extend/ --includebed repo_utils/test_files/include.bed --extend 500 -2022-08-25 00:31:16,781 [INFO] Params: -{ - "base": "repo_utils/test_files/input1.vcf.gz", - "comp": "repo_utils/test_files/input3.vcf.gz", - "output": "test_results/bench13_extend/", - "reference": "repo_utils/test_files/reference.fa", - "giabreport": false, - "debug": false, - "prog": false, - "refdist": 500, - "unroll": false, - "pctsim": 0.7, - "minhaplen": 50, - "pctsize": 0.7, - "pctovl": 0.0, - "typeignore": false, - "dup_to_ins": false, - "use_lev": false, - "chunksize": 1000, - "gtcomp": false, - "bSample": null, - "cSample": null, - "sizemin": 50, - "sizefilt": 30, - "sizemax": 50000, - "passonly": false, - "no_ref": false, - "includebed": "repo_utils/test_files/include.bed", - "extend": 500, - "multimatch": false -} -2022-08-25 00:31:16,781 [INFO] Truvari version: 3.5.0-dev -2022-08-25 00:31:16,803 [INFO] Including 11 bed regions -2022-08-25 00:31:16,805 [INFO] Found 1 chromosomes with overlapping regions -2022-08-25 00:31:16,805 [INFO] Extending the regions by 500 bases -2022-08-25 00:31:16,807 [INFO] Found 1 chromosomes with overlapping regions -2022-08-25 00:31:16,947 [INFO] Zipped 2050 variants Counter({'base': 1130, 'comp': 920}) -2022-08-25 00:31:16,948 [INFO] 11 chunks of 2050 variants Counter({'__filtered': 2025, 'comp': 15, 'base': 10}) -2022-08-25 00:31:16,951 [INFO] Stats: { - "TP-base": 6, - "TP-call": 6, - "FP": 4, - "FN": 4, - "precision": 0.6, - "recall": 0.6, - "f1": 0.6, - "base cnt": 10, - "call cnt": 10, - "TP-call_TP-gt": 4, - "TP-call_FP-gt": 2, - "TP-base_TP-gt": 4, - "TP-base_FP-gt": 2, - "gt_concordance": 0.6666666666666666, - "gt_matrix": { - "(1, 1)": { - "(1, 0)": 1, - "(1, 1)": 2 - }, - "(0, 1)": { - "(1, 1)": 1, - "(1, 0)": 1 - }, - "(1, 0)": { - "(1, 0)": 1 - } - } -} -2022-08-25 00:31:16,955 [INFO] Finished bench diff --git a/repo_utils/test_files/answer_key/bench13_extend/summary.txt b/repo_utils/test_files/answer_key/bench13_extend/summary.txt deleted file mode 100644 index f10b9ff8..00000000 --- a/repo_utils/test_files/answer_key/bench13_extend/summary.txt +++ /dev/null @@ -1,29 +0,0 @@ -{ - "TP-base": 6, - "TP-call": 6, - "FP": 4, - "FN": 4, - "precision": 0.6, - "recall": 0.6, - "f1": 0.6, - "base cnt": 10, - "call cnt": 10, - "TP-call_TP-gt": 4, - "TP-call_FP-gt": 2, - "TP-base_TP-gt": 4, - "TP-base_FP-gt": 2, - "gt_concordance": 0.6666666666666666, - "gt_matrix": { - "(1, 1)": { - "(1, 0)": 1, - "(1, 1)": 2 - }, - "(0, 1)": { - "(1, 1)": 1, - "(1, 0)": 1 - }, - "(1, 0)": { - "(1, 0)": 1 - } - } -} \ No newline at end of file diff --git a/repo_utils/test_files/answer_key/bench13_extend/tp-base.vcf b/repo_utils/test_files/answer_key/bench13_extend/tp-base.vcf deleted file mode 100644 index 869fbf46..00000000 --- a/repo_utils/test_files/answer_key/bench13_extend/tp-base.vcf +++ /dev/null @@ -1,55 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 -chr20 149013 . A ACCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=127907;QSTRAND=+;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=1.0.0 GT:PL:DP 1/1:8,8,5:15,29 -chr20 306268 . A ACCAGGCTGGAGTGCAGTGGCTCACTGCGTGGCTCGCTACAGCCTACAACTCCTGGGCTCCAGCAATCCTGCTGCCCCAGCCTCCTGTGTAACTGAGACTACAGGCACGCACCACCACACCCAGCTAATTTTTTCTTTCTTTTTTTTTTTTTTGAGATGAACTCTCACTCTGTTGC 60 . QNAME=HG002-S9-H1-000001F;QSTART=285475;QSTRAND=+;SVTYPE=INS;SVLEN=175;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=100;MatchId=4.0.0 GT:PL:DP 1/1:2,7,2:17,31 -chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCCATCCCCCGTCCGCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 61 . QNAME=HG002-S9-H2-000001F;QSTART=374905;QSTRAND=+;SVTYPE=INS;SVLEN=227;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=6.0.0 GT:PL 0/1:. -chr20 613783 . TGTGTGCTGAGTCCAGCTCAAGTCCCTTGGTTCCCACTGCTGCTAAGCATGCACG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=593293;QSTRAND=+;SVTYPE=DEL;SVLEN=-54;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=100;MatchId=7.0.0 GT:PL:DP 1/1:6,8,8:40,41 -chr20 642300 . G GCCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGC 60 . QNAME=HG002-S9-H1-000001F;QSTART=621812;QSTRAND=+;SVTYPE=INS;SVLEN=408;PctSeqSimilarity=0.8906;PctSizeSimilarity=0.7892;PctRecOverlap=0.6724;SizeDiff=86;StartDistance=-91;EndDistance=-91;GTMatch;TruScore=78;MatchId=8.1.4 GT:PL:DP 1/0:5,10,5:44,36 -chr20 949516 . CTCTGAAGAGGTAACATTTGAACTGAGATGTAGAGGGAGAGAAGGAACTAGCCATGTGGAGATCTGGGGGAGGAGCATTCCAGGCAGAGGGGATAGCAAGTGCA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=905663;QSTRAND=+;SVTYPE=DEL;SVLEN=-103;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=100;MatchId=10.0.0 GT:PL:DP 0/1:6,6,1:34,8 diff --git a/repo_utils/test_files/answer_key/bench13_extend/tp-call.vcf b/repo_utils/test_files/answer_key/bench13_extend/tp-call.vcf deleted file mode 100644 index e5243eae..00000000 --- a/repo_utils/test_files/answer_key/bench13_extend/tp-call.vcf +++ /dev/null @@ -1,54 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__v12_HG00733_hgsvc_pbsq2-clr_1000-flye.h1-un.arrow-p1.fasta.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__v12_HG00733_hgsvc_pbsq2-clr_1000-flye.h2-un.arrow-p1.fasta.gz.vcf.gz; Date=Thu Jul 22 20:41:33 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/unused_samples/grch38/HG00733/exact.vcf.gz; Date=Mon Aug 16 16:57:27 2021 -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00733 -chr20 149013 . A ACCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGAC 60 . QNAME=cluster23_scaffold_3;QSTART=25562871;QSTRAND=-;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=1.0.0 GT 1/0 -chr20 306268 . A ACCAGGCTGGAGTGCAGTGGCTCACTGCGTGGCTCGCTACAGCCTACAACTCCTGGGCTCCAGCAATCCTGCTGCCCCAGCCTCCTGTGTAACTGAGACTACAGGCACGCACCACCACACCCAGCTAATTTTTTCTTTCTTTTTTTTTTTTTTGAGATGAACTCTCACTCTGTTGC 60 . QNAME=cluster23_scaffold_3;QSTART=25405192;QSTRAND=-;SVTYPE=INS;SVLEN=175;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=100;MatchId=4.0.0 GT 1/1 -chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCCATCCCCCGTCCGCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 60 . QNAME=cluster23_scaffold_3;QSTART=25290548;QSTRAND=-;SVTYPE=INS;SVLEN=227;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=6.0.0 GT 1/1 -chr20 613783 . TGTGTGCTGAGTCCAGCTCAAGTCCCTTGGTTCCCACTGCTGCTAAGCATGCACG T 60 . QNAME=cluster23_scaffold_3;QSTART=25097419;QSTRAND=-;SVTYPE=DEL;SVLEN=-54;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=100;MatchId=7.0.0 GT 1/1 -chr20 642391 . G GGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGGC 60 . QNAME=cluster23_scaffold_3;QSTART=25068286;QSTRAND=-;SVTYPE=INS;SVLEN=322;PctSeqSimilarity=0.8906;PctSizeSimilarity=0.7892;PctRecOverlap=0.6724;SizeDiff=86;StartDistance=-91;EndDistance=-91;GTMatch;TruScore=78;MatchId=8.1.4 GT 1/0 -chr20 949516 . CTCTGAAGAGGTAACATTTGAACTGAGATGTAGAGGGAGAGAAGGAACTAGCCATGTGGAGATCTGGGGGAGGAGCATTCCAGGCAGAGGGGATAGCAAGTGCA C 60 . QNAME=cluster23_scaffold_3;QSTART=24759935;QSTRAND=-;SVTYPE=DEL;SVLEN=-103;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=100;MatchId=10.0.0 GT 1/0 diff --git a/repo_utils/test_files/answer_key/bench13_includebed/fn.vcf b/repo_utils/test_files/answer_key/bench13_includebed/fn.vcf deleted file mode 100644 index d9be0297..00000000 --- a/repo_utils/test_files/answer_key/bench13_includebed/fn.vcf +++ /dev/null @@ -1,54 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 -chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCATCCCCCGTCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 60 . QNAME=HG002-S9-H1-000001F;QSTART=400044;QSTRAND=+;SVTYPE=INS;SVLEN=226;PctSeqSimilarity=0.9956;PctSizeSimilarity=0.9956;PctRecOverlap=1;SizeDiff=-1;StartDistance=0;EndDistance=0;TruScore=99;MatchId=5.1.0;Multi GT:PL:DP 1/0:4,8,6:32,9 -chr20 642207 . T TGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGG 60 . QNAME=HG002-S9-H2-000001F;QSTART=596630;QSTRAND=+;SVTYPE=INS;SVLEN=501;PctSeqSimilarity=0.7159;PctSizeSimilarity=0.4511;PctRecOverlap=0.4531;SizeDiff=275;StartDistance=-123;EndDistance=-123;GTMatch;TruScore=54;MatchId=7.0.2 GT:PL:DP 0/1:5,9,1:7,43 -chr20 642300 . G GCCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGC 60 . QNAME=HG002-S9-H1-000001F;QSTART=621812;QSTRAND=+;SVTYPE=INS;SVLEN=408;PctSeqSimilarity=0.7834;PctSizeSimilarity=0.6299;PctRecOverlap=0.6284;SizeDiff=151;StartDistance=29;EndDistance=29;GTMatch;TruScore=68;MatchId=7.1.1 GT:PL:DP 1/0:5,10,5:44,36 -chr20 642330 . G GGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597257;QSTRAND=+;SVTYPE=INS;SVLEN=66;PctSeqSimilarity=0.8835;PctSizeSimilarity=0.5116;PctRecOverlap=0;SizeDiff=-63;StartDistance=262;EndDistance=262;GTMatch;TruScore=46;MatchId=7.2.0 GT:PL:DP 0/1:6,1,9:20,25 -chr20 709830 . G GACACTGCTCGGTCCTCCGCTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCGCTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGAACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGA 60 . QNAME=HG002-S9-H1-000001F;QSTART=689726;QSTRAND=+;SVTYPE=INS;SVLEN=465;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=8.0._ GT:PL:DP 1/0:4,8,7:50,48 diff --git a/repo_utils/test_files/answer_key/bench13_includebed/fp.vcf b/repo_utils/test_files/answer_key/bench13_includebed/fp.vcf deleted file mode 100644 index ad52ea4a..00000000 --- a/repo_utils/test_files/answer_key/bench13_includebed/fp.vcf +++ /dev/null @@ -1,52 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__v12_HG00733_hgsvc_pbsq2-clr_1000-flye.h1-un.arrow-p1.fasta.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__v12_HG00733_hgsvc_pbsq2-clr_1000-flye.h2-un.arrow-p1.fasta.gz.vcf.gz; Date=Thu Jul 22 20:41:33 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/unused_samples/grch38/HG00733/exact.vcf.gz; Date=Mon Aug 16 16:57:27 2021 -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00733 -chr20 149073 . G GAATCCTGACCCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCA 60 . QNAME=cluster23_scaffold_2;QSTART=25547471;QSTRAND=-;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=0.9962;PctSizeSimilarity=1;PctRecOverlap=0.1304;SizeDiff=0;StartDistance=-60;EndDistance=-60;TruScore=70;MatchId=1.0.1;Multi GT 0/1 -chr20 642068 . G GTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCC 60 . QNAME=cluster23_scaffold_2;QSTART=25053097;QSTRAND=-;SVTYPE=INS;SVLEN=129;PctSeqSimilarity=0.8835;PctSizeSimilarity=0.5116;PctRecOverlap=0;SizeDiff=-63;StartDistance=262;EndDistance=262;GTMatch;TruScore=46;MatchId=7.2.0 GT 0/1 -chr20 642271 . G GGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGC 60 . QNAME=cluster23_scaffold_3;QSTART=25068731;QSTRAND=-;SVTYPE=INS;SVLEN=257;PctSeqSimilarity=0.7834;PctSizeSimilarity=0.6299;PctRecOverlap=0.6284;SizeDiff=151;StartDistance=29;EndDistance=29;GTMatch;TruScore=68;MatchId=7.1.1 GT 1/0 -chr20 642330 . G GCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGGGC 60 . QNAME=cluster23_scaffold_2;QSTART=25052609;QSTRAND=-;SVTYPE=INS;SVLEN=226;PctSeqSimilarity=0.7159;PctSizeSimilarity=0.4511;PctRecOverlap=0.4531;SizeDiff=275;StartDistance=-123;EndDistance=-123;GTMatch;TruScore=54;MatchId=7.0.2 GT 0/1 diff --git a/repo_utils/test_files/answer_key/bench13_includebed/log.txt b/repo_utils/test_files/answer_key/bench13_includebed/log.txt deleted file mode 100644 index f6221c7c..00000000 --- a/repo_utils/test_files/answer_key/bench13_includebed/log.txt +++ /dev/null @@ -1,64 +0,0 @@ -2022-08-25 00:31:14,425 [INFO] Running /data/truvari/__main__.py bench -b repo_utils/test_files/input1.vcf.gz -c repo_utils/test_files/input3.vcf.gz -f repo_utils/test_files/reference.fa -o test_results/bench13_includebed/ --includebed repo_utils/test_files/include.bed -2022-08-25 00:31:14,426 [INFO] Params: -{ - "base": "repo_utils/test_files/input1.vcf.gz", - "comp": "repo_utils/test_files/input3.vcf.gz", - "output": "test_results/bench13_includebed/", - "reference": "repo_utils/test_files/reference.fa", - "giabreport": false, - "debug": false, - "prog": false, - "refdist": 500, - "unroll": false, - "pctsim": 0.7, - "minhaplen": 50, - "pctsize": 0.7, - "pctovl": 0.0, - "typeignore": false, - "dup_to_ins": false, - "use_lev": false, - "chunksize": 1000, - "gtcomp": false, - "bSample": null, - "cSample": null, - "sizemin": 50, - "sizefilt": 30, - "sizemax": 50000, - "passonly": false, - "no_ref": false, - "includebed": "repo_utils/test_files/include.bed", - "extend": 0, - "multimatch": false -} -2022-08-25 00:31:14,426 [INFO] Truvari version: 3.5.0-dev -2022-08-25 00:31:14,449 [INFO] Including 11 bed regions -2022-08-25 00:31:14,450 [INFO] Found 1 chromosomes with overlapping regions -2022-08-25 00:31:14,576 [INFO] Zipped 2030 variants Counter({'base': 1130, 'comp': 900}) -2022-08-25 00:31:14,577 [INFO] 10 chunks of 2030 variants Counter({'__filtered': 2009, 'comp': 11, 'base': 10}) -2022-08-25 00:31:14,580 [INFO] Stats: { - "TP-base": 5, - "TP-call": 5, - "FP": 4, - "FN": 5, - "precision": 0.5555555555555556, - "recall": 0.5, - "f1": 0.5263157894736842, - "base cnt": 10, - "call cnt": 9, - "TP-call_TP-gt": 3, - "TP-call_FP-gt": 2, - "TP-base_TP-gt": 3, - "TP-base_FP-gt": 2, - "gt_concordance": 0.6, - "gt_matrix": { - "(1, 1)": { - "(1, 0)": 1, - "(1, 1)": 2 - }, - "(0, 1)": { - "(1, 1)": 1, - "(1, 0)": 1 - } - } -} -2022-08-25 00:31:14,583 [INFO] Finished bench diff --git a/repo_utils/test_files/answer_key/bench13_includebed/summary.txt b/repo_utils/test_files/answer_key/bench13_includebed/summary.txt deleted file mode 100644 index 5fa733cd..00000000 --- a/repo_utils/test_files/answer_key/bench13_includebed/summary.txt +++ /dev/null @@ -1,26 +0,0 @@ -{ - "TP-base": 5, - "TP-call": 5, - "FP": 4, - "FN": 5, - "precision": 0.5555555555555556, - "recall": 0.5, - "f1": 0.5263157894736842, - "base cnt": 10, - "call cnt": 9, - "TP-call_TP-gt": 3, - "TP-call_FP-gt": 2, - "TP-base_TP-gt": 3, - "TP-base_FP-gt": 2, - "gt_concordance": 0.6, - "gt_matrix": { - "(1, 1)": { - "(1, 0)": 1, - "(1, 1)": 2 - }, - "(0, 1)": { - "(1, 1)": 1, - "(1, 0)": 1 - } - } -} \ No newline at end of file diff --git a/repo_utils/test_files/answer_key/bench13_includebed/tp-base.vcf b/repo_utils/test_files/answer_key/bench13_includebed/tp-base.vcf deleted file mode 100644 index a9dfeb2d..00000000 --- a/repo_utils/test_files/answer_key/bench13_includebed/tp-base.vcf +++ /dev/null @@ -1,54 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 -chr20 149013 . A ACCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=127907;QSTRAND=+;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=1.0.0 GT:PL:DP 1/1:8,8,5:15,29 -chr20 306268 . A ACCAGGCTGGAGTGCAGTGGCTCACTGCGTGGCTCGCTACAGCCTACAACTCCTGGGCTCCAGCAATCCTGCTGCCCCAGCCTCCTGTGTAACTGAGACTACAGGCACGCACCACCACACCCAGCTAATTTTTTCTTTCTTTTTTTTTTTTTTGAGATGAACTCTCACTCTGTTGC 60 . QNAME=HG002-S9-H1-000001F;QSTART=285475;QSTRAND=+;SVTYPE=INS;SVLEN=175;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=100;MatchId=3.0.0 GT:PL:DP 1/1:2,7,2:17,31 -chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCCATCCCCCGTCCGCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 61 . QNAME=HG002-S9-H2-000001F;QSTART=374905;QSTRAND=+;SVTYPE=INS;SVLEN=227;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=5.0.0 GT:PL 0/1:. -chr20 613783 . TGTGTGCTGAGTCCAGCTCAAGTCCCTTGGTTCCCACTGCTGCTAAGCATGCACG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=593293;QSTRAND=+;SVTYPE=DEL;SVLEN=-54;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=100;MatchId=6.0.0 GT:PL:DP 1/1:6,8,8:40,41 -chr20 949516 . CTCTGAAGAGGTAACATTTGAACTGAGATGTAGAGGGAGAGAAGGAACTAGCCATGTGGAGATCTGGGGGAGGAGCATTCCAGGCAGAGGGGATAGCAAGTGCA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=905663;QSTRAND=+;SVTYPE=DEL;SVLEN=-103;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=100;MatchId=9.0.0 GT:PL:DP 0/1:6,6,1:34,8 diff --git a/repo_utils/test_files/answer_key/bench13_includebed/tp-call.vcf b/repo_utils/test_files/answer_key/bench13_includebed/tp-call.vcf deleted file mode 100644 index e773ebdc..00000000 --- a/repo_utils/test_files/answer_key/bench13_includebed/tp-call.vcf +++ /dev/null @@ -1,53 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__v12_HG00733_hgsvc_pbsq2-clr_1000-flye.h1-un.arrow-p1.fasta.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__v12_HG00733_hgsvc_pbsq2-clr_1000-flye.h2-un.arrow-p1.fasta.gz.vcf.gz; Date=Thu Jul 22 20:41:33 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/unused_samples/grch38/HG00733/exact.vcf.gz; Date=Mon Aug 16 16:57:27 2021 -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00733 -chr20 149013 . A ACCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGAC 60 . QNAME=cluster23_scaffold_3;QSTART=25562871;QSTRAND=-;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=1.0.0 GT 1/0 -chr20 306268 . A ACCAGGCTGGAGTGCAGTGGCTCACTGCGTGGCTCGCTACAGCCTACAACTCCTGGGCTCCAGCAATCCTGCTGCCCCAGCCTCCTGTGTAACTGAGACTACAGGCACGCACCACCACACCCAGCTAATTTTTTCTTTCTTTTTTTTTTTTTTGAGATGAACTCTCACTCTGTTGC 60 . QNAME=cluster23_scaffold_3;QSTART=25405192;QSTRAND=-;SVTYPE=INS;SVLEN=175;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=100;MatchId=3.0.0 GT 1/1 -chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCCATCCCCCGTCCGCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 60 . QNAME=cluster23_scaffold_3;QSTART=25290548;QSTRAND=-;SVTYPE=INS;SVLEN=227;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=5.0.0 GT 1/1 -chr20 613783 . TGTGTGCTGAGTCCAGCTCAAGTCCCTTGGTTCCCACTGCTGCTAAGCATGCACG T 60 . QNAME=cluster23_scaffold_3;QSTART=25097419;QSTRAND=-;SVTYPE=DEL;SVLEN=-54;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=100;MatchId=6.0.0 GT 1/1 -chr20 949516 . CTCTGAAGAGGTAACATTTGAACTGAGATGTAGAGGGAGAGAAGGAACTAGCCATGTGGAGATCTGGGGGAGGAGCATTCCAGGCAGAGGGGATAGCAAGTGCA C 60 . QNAME=cluster23_scaffold_3;QSTART=24759935;QSTRAND=-;SVTYPE=DEL;SVLEN=-103;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=100;MatchId=9.0.0 GT 1/0 diff --git a/repo_utils/test_files/answer_key/bench23/fn.vcf b/repo_utils/test_files/answer_key/bench23/fn.vcf deleted file mode 100644 index dc8093b4..00000000 --- a/repo_utils/test_files/answer_key/bench23/fn.vcf +++ /dev/null @@ -1,53 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__v12_NA12878_giab_pbsq2-ccs_1000-pereg.h1-un.racon-p2.fasta.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__v12_NA12878_giab_pbsq2-ccs_1000-pereg.h2-un.racon-p2.fasta.gz.vcf.gz; Date=Thu Jul 22 20:43:36 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/unused_samples/grch38/NA12878/exact.vcf.gz; Date=Mon Aug 16 16:58:00 2021 -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 -chr20 380878 . T TGATTAGCTCCGGTTTGCATCACCCGGACCGGGGGATTAGCTCCGGTTTGCATCACCCGGACCGGGG 60 . QNAME=cluster19_000000F;QSTART=25381150;QSTRAND=-;SVTYPE=INS;SVLEN=66;PctSeqSimilarity=0.0294;PctSizeSimilarity=0.5;PctRecOverlap=0.5075;SizeDiff=33;StartDistance=0;EndDistance=-33;GTMatch;TruScore=34;MatchId=7.0.0 GT:PL:AD 1/0:8,3,9:38,14 -chr20 642207 . T TGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGG 60 . QNAME=cluster19_000000F;QSTART=602404;QSTRAND=+;SVTYPE=INS;SVLEN=630;PctSeqSimilarity=0.764;PctSizeSimilarity=0.5111;PctRecOverlap=0.4643;SizeDiff=308;StartDistance=-184;EndDistance=-184;GTMatch;TruScore=57;MatchId=10.0.4 GT:PL:AD 0/1:2,1,9:9,12 -chr20 642230 . T TGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTG 60 . QNAME=cluster19_000000F;QSTART=25119065;QSTRAND=-;SVTYPE=INS;SVLEN=632;PctSeqSimilarity=0.7543;PctSizeSimilarity=0.5095;PctRecOverlap=0.5008;SizeDiff=310;StartDistance=-161;EndDistance=-161;GTMatch;TruScore=58;MatchId=10.1.4 GT:PL:AD 1/0:7,5,6:16,7 -chr20 764537 . A AGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAT 60 . QNAME=cluster19_000000F;QSTART=725358;QSTRAND=+;SVTYPE=INS;SVLEN=117;PctSeqSimilarity=0.8992;PctSizeSimilarity=0.6667;PctRecOverlap=0.0256;SizeDiff=39;StartDistance=95;EndDistance=95;GTMatch;TruScore=53;MatchId=13.1.0 GT:PL:AD 0/1:7,8,4:13,5 diff --git a/repo_utils/test_files/answer_key/bench23/fp.vcf b/repo_utils/test_files/answer_key/bench23/fp.vcf deleted file mode 100644 index 80f20c59..00000000 --- a/repo_utils/test_files/answer_key/bench23/fp.vcf +++ /dev/null @@ -1,57 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__v12_HG00733_hgsvc_pbsq2-clr_1000-flye.h1-un.arrow-p1.fasta.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__v12_HG00733_hgsvc_pbsq2-clr_1000-flye.h2-un.arrow-p1.fasta.gz.vcf.gz; Date=Thu Jul 22 20:41:33 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/unused_samples/grch38/HG00733/exact.vcf.gz; Date=Mon Aug 16 16:57:27 2021 -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00733 -chr20 278930 . C CGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGCGGGAG 60 . QNAME=cluster23_scaffold_2;QSTART=25417363;QSTRAND=-;SVTYPE=INS;SVLEN=188;PctSeqSimilarity=0.6489;PctSizeSimilarity=0.3462;PctRecOverlap=0.3481;SizeDiff=355;StartDistance=139;EndDistance=139;TruScore=44;MatchId=4.0.0 GT 0/1 -chr20 279098 . G GGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGCGGGACGGAGGGAGGGACGGAGGGCGGGACGGAGGGAC 60 . QNAME=cluster23_scaffold_3;QSTART=25432493;QSTRAND=-;SVTYPE=INS;SVLEN=179;PctSeqSimilarity=0.5332;PctSizeSimilarity=0.3297;PctRecOverlap=0.3297;SizeDiff=364;StartDistance=-29;EndDistance=-29;TruScore=39;MatchId=4.0.2 GT 1/0 -chr20 280211 . CAACAACAACAATTGTACTTCCCTAAGGTTACACCCAGCAGGTGCATAAAACCTACAGTAACAAT C 60 . QNAME=cluster23_scaffold_3;QSTART=25431380;QSTRAND=-;SVTYPE=DEL;SVLEN=-64;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=5._.0 GT 1/0 -chr20 641906 . G GGCGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCT 60 . QNAME=cluster23_scaffold_2;QSTART=25053389;QSTRAND=-;SVTYPE=INS;SVLEN=163;PctSeqSimilarity=0.6657;PctSizeSimilarity=0.2587;PctRecOverlap=0.1521;SizeDiff=467;StartDistance=301;EndDistance=301;GTMatch;TruScore=35;MatchId=10.0.0 GT 0/1 -chr20 642068 . G GTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCC 60 . QNAME=cluster23_scaffold_2;QSTART=25053097;QSTRAND=-;SVTYPE=INS;SVLEN=129;PctSeqSimilarity=0.5373;PctSizeSimilarity=0.2041;PctRecOverlap=0.2038;SizeDiff=503;StartDistance=162;EndDistance=162;GTMatch;TruScore=31;MatchId=10.1.1 GT 0/1 -chr20 642271 . G GGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGC 60 . QNAME=cluster23_scaffold_3;QSTART=25068731;QSTRAND=-;SVTYPE=INS;SVLEN=257;PctSeqSimilarity=0.6332;PctSizeSimilarity=0.4079;PctRecOverlap=0.4073;SizeDiff=373;StartDistance=-64;EndDistance=-64;GTMatch;TruScore=48;MatchId=10.0.2 GT 1/0 -chr20 642330 . G GCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGGGC 60 . QNAME=cluster23_scaffold_2;QSTART=25052609;QSTRAND=-;SVTYPE=INS;SVLEN=226;PctSeqSimilarity=0.6341;PctSizeSimilarity=0.3587;PctRecOverlap=0.3597;SizeDiff=404;StartDistance=-123;EndDistance=-123;GTMatch;TruScore=45;MatchId=10.0.3 GT 0/1 -chr20 642391 . G GGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGGC 60 . QNAME=cluster23_scaffold_3;QSTART=25068286;QSTRAND=-;SVTYPE=INS;SVLEN=322;PctSeqSimilarity=0.7543;PctSizeSimilarity=0.5095;PctRecOverlap=0.5008;SizeDiff=310;StartDistance=-161;EndDistance=-161;GTMatch;TruScore=58;MatchId=10.1.4 GT 1/0 -chr20 949516 . CTCTGAAGAGGTAACATTTGAACTGAGATGTAGAGGGAGAGAAGGAACTAGCCATGTGGAGATCTGGGGGAGGAGCATTCCAGGCAGAGGGGATAGCAAGTGCA C 60 . QNAME=cluster23_scaffold_3;QSTART=24759935;QSTRAND=-;SVTYPE=DEL;SVLEN=-103;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=14._.0 GT 1/0 diff --git a/repo_utils/test_files/answer_key/bench23/log.txt b/repo_utils/test_files/answer_key/bench23/log.txt deleted file mode 100644 index 949aaf05..00000000 --- a/repo_utils/test_files/answer_key/bench23/log.txt +++ /dev/null @@ -1,62 +0,0 @@ -2022-08-25 00:31:12,093 [INFO] Running /data/truvari/__main__.py bench -b repo_utils/test_files/input2.vcf.gz -c repo_utils/test_files/input3.vcf.gz -f repo_utils/test_files/reference.fa -o test_results/bench23/ --multimatch -2022-08-25 00:31:12,094 [INFO] Params: -{ - "base": "repo_utils/test_files/input2.vcf.gz", - "comp": "repo_utils/test_files/input3.vcf.gz", - "output": "test_results/bench23/", - "reference": "repo_utils/test_files/reference.fa", - "giabreport": false, - "debug": false, - "prog": false, - "refdist": 500, - "unroll": false, - "pctsim": 0.7, - "minhaplen": 50, - "pctsize": 0.7, - "pctovl": 0.0, - "typeignore": false, - "dup_to_ins": false, - "use_lev": false, - "chunksize": 1000, - "gtcomp": false, - "bSample": null, - "cSample": null, - "sizemin": 50, - "sizefilt": 30, - "sizemax": 50000, - "passonly": false, - "no_ref": false, - "includebed": null, - "extend": 0, - "multimatch": true -} -2022-08-25 00:31:12,095 [INFO] Truvari version: 3.5.0-dev -2022-08-25 00:31:12,196 [INFO] Zipped 3848 variants Counter({'comp': 2065, 'base': 1783}) -2022-08-25 00:31:12,198 [INFO] 15 chunks of 3848 variants Counter({'__filtered': 3816, 'comp': 21, 'base': 11}) -2022-08-25 00:31:12,202 [INFO] Stats: { - "TP-base": 7, - "TP-call": 8, - "FP": 9, - "FN": 4, - "precision": 0.47058823529411764, - "recall": 0.6363636363636364, - "f1": 0.5410628019323671, - "base cnt": 11, - "call cnt": 17, - "TP-call_TP-gt": 3, - "TP-call_FP-gt": 5, - "TP-base_TP-gt": 3, - "TP-base_FP-gt": 4, - "gt_concordance": 0.375, - "gt_matrix": { - "(1, 1)": { - "(0, 1)": 2, - "(1, 1)": 2 - }, - "(1, 0)": { - "(1, 1)": 2, - "(1, 0)": 1 - } - } -} -2022-08-25 00:31:12,205 [INFO] Finished bench diff --git a/repo_utils/test_files/answer_key/bench23/summary.txt b/repo_utils/test_files/answer_key/bench23/summary.txt deleted file mode 100644 index 4da8a094..00000000 --- a/repo_utils/test_files/answer_key/bench23/summary.txt +++ /dev/null @@ -1,26 +0,0 @@ -{ - "TP-base": 7, - "TP-call": 8, - "FP": 9, - "FN": 4, - "precision": 0.47058823529411764, - "recall": 0.6363636363636364, - "f1": 0.5410628019323671, - "base cnt": 11, - "call cnt": 17, - "TP-call_TP-gt": 3, - "TP-call_FP-gt": 5, - "TP-base_TP-gt": 3, - "TP-base_FP-gt": 4, - "gt_concordance": 0.375, - "gt_matrix": { - "(1, 1)": { - "(0, 1)": 2, - "(1, 1)": 2 - }, - "(1, 0)": { - "(1, 1)": 2, - "(1, 0)": 1 - } - } -} \ No newline at end of file diff --git a/repo_utils/test_files/answer_key/bench23/tp-base.vcf b/repo_utils/test_files/answer_key/bench23/tp-base.vcf deleted file mode 100644 index 694f3b6e..00000000 --- a/repo_utils/test_files/answer_key/bench23/tp-base.vcf +++ /dev/null @@ -1,56 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__v12_NA12878_giab_pbsq2-ccs_1000-pereg.h1-un.racon-p2.fasta.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__v12_NA12878_giab_pbsq2-ccs_1000-pereg.h2-un.racon-p2.fasta.gz.vcf.gz; Date=Thu Jul 22 20:43:36 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/unused_samples/grch38/NA12878/exact.vcf.gz; Date=Mon Aug 16 16:58:00 2021 -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 -chr20 149095 . G GGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGACCCATATTTGGGAA 60 . QNAME=cluster19_000000F;QSTART=25613718;QSTRAND=-;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=0.9891;PctSizeSimilarity=1;PctRecOverlap=0.6812;SizeDiff=0;StartDistance=22;EndDistance=22;TruScore=89;MatchId=1.0.1 GT:PL:AD 1/1:10,5,10:30,43 -chr20 279069 . A AGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGC 60 . QNAME=cluster19_000000F;QSTART=25483168;QSTRAND=-;SVTYPE=INS;SVLEN=543;PctSeqSimilarity=0.932;PctSizeSimilarity=0.9466;PctRecOverlap=0.9484;SizeDiff=29;StartDistance=0;EndDistance=0;TruScore=94;MatchId=4.0.1 GT:PL:AD 1/1:8,1,10:40,42 -chr20 306268 . A ACCAGGCTGGAGTGCAGTGGCTCACTGCGTGGCTCGCTACAGCCTACAACTCCTGGGCTCCAGCAATCCTGCTGCCCCAGCCTCCTGTGTAACTGAGACTACAGGCACGCACCACCACACCCAGCTAATGTTTTCTTTCTTTTTTTTTTTTTTGAGATGAACTCTCACTCTGTTGC 60 . QNAME=cluster19_000000F;QSTART=25455794;QSTRAND=-;SVTYPE=INS;SVLEN=175;PctSeqSimilarity=0.9972;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=99;MatchId=6.0.0 GT:PL:AD 1/1:4,10,2:26,18 -chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCATCCCCCGTCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 60 . QNAME=cluster19_000000F;QSTART=25341211;QSTRAND=-;SVTYPE=INS;SVLEN=226;PctSeqSimilarity=0.9956;PctSizeSimilarity=0.9956;PctRecOverlap=1;SizeDiff=-1;StartDistance=0;EndDistance=0;GTMatch;TruScore=99;MatchId=8.0.0 GT:PL:AD 1/1:7,10,5:44,42 -chr20 613783 . TGTGTGCTGAGTCCAGCTCAAGTCCCTTGGTTCCCACTGCTGCTAAGCATGCACG T 60 . QNAME=cluster19_000000F;QSTART=25148089;QSTRAND=-;SVTYPE=DEL;SVLEN=-54;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=9.0.0 GT:PL:AD 1/0:3,1,8:9,32 -chr20 709759 . AGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCC A 60 . QNAME=cluster19_000000F;QSTART=25051525;QSTRAND=-;SVTYPE=DEL;SVLEN=-93;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=11.0.0 GT:PL:AD 1/0:8,10,9:32,27 -chr20 764537 . A AGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAT 60 . QNAME=cluster19_000000F;QSTART=24996803;QSTRAND=-;SVTYPE=INS;SVLEN=78;PctSeqSimilarity=0.9971;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=95;EndDistance=95;GTMatch;TruScore=66;MatchId=13.0.0 GT:PL:AD 1/0:5,4,9:13,8 diff --git a/repo_utils/test_files/answer_key/bench23/tp-call.vcf b/repo_utils/test_files/answer_key/bench23/tp-call.vcf deleted file mode 100644 index 2d0ca88e..00000000 --- a/repo_utils/test_files/answer_key/bench23/tp-call.vcf +++ /dev/null @@ -1,56 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__v12_HG00733_hgsvc_pbsq2-clr_1000-flye.h1-un.arrow-p1.fasta.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__v12_HG00733_hgsvc_pbsq2-clr_1000-flye.h2-un.arrow-p1.fasta.gz.vcf.gz; Date=Thu Jul 22 20:41:33 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/unused_samples/grch38/HG00733/exact.vcf.gz; Date=Mon Aug 16 16:57:27 2021 -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00733 -chr20 149013 . A ACCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGAC 60 . QNAME=cluster23_scaffold_3;QSTART=25562871;QSTRAND=-;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=0.9967;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=82;EndDistance=82;TruScore=66;MatchId=1.0.0 GT 1/0 -chr20 149073 . G GAATCCTGACCCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCA 60 . QNAME=cluster23_scaffold_2;QSTART=25547471;QSTRAND=-;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=0.9891;PctSizeSimilarity=1;PctRecOverlap=0.6812;SizeDiff=0;StartDistance=22;EndDistance=22;TruScore=89;MatchId=1.0.1 GT 0/1 -chr20 279069 . A AGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGCGGGACGGAGGGAGGGC 60 . QNAME=cluster23_scaffold_2;QSTART=25416710;QSTRAND=-;SVTYPE=INS;SVLEN=514;PctSeqSimilarity=0.932;PctSizeSimilarity=0.9466;PctRecOverlap=0.9484;SizeDiff=29;StartDistance=0;EndDistance=0;TruScore=94;MatchId=4.0.1 GT 0/1 -chr20 306268 . A ACCAGGCTGGAGTGCAGTGGCTCACTGCGTGGCTCGCTACAGCCTACAACTCCTGGGCTCCAGCAATCCTGCTGCCCCAGCCTCCTGTGTAACTGAGACTACAGGCACGCACCACCACACCCAGCTAATTTTTTCTTTCTTTTTTTTTTTTTTGAGATGAACTCTCACTCTGTTGC 60 . QNAME=cluster23_scaffold_3;QSTART=25405192;QSTRAND=-;SVTYPE=INS;SVLEN=175;PctSeqSimilarity=0.9972;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=99;MatchId=6.0.0 GT 1/1 -chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCCATCCCCCGTCCGCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 60 . QNAME=cluster23_scaffold_3;QSTART=25290548;QSTRAND=-;SVTYPE=INS;SVLEN=227;PctSeqSimilarity=0.9956;PctSizeSimilarity=0.9956;PctRecOverlap=1;SizeDiff=-1;StartDistance=0;EndDistance=0;GTMatch;TruScore=99;MatchId=8.0.0 GT 1/1 -chr20 613783 . TGTGTGCTGAGTCCAGCTCAAGTCCCTTGGTTCCCACTGCTGCTAAGCATGCACG T 60 . QNAME=cluster23_scaffold_3;QSTART=25097419;QSTRAND=-;SVTYPE=DEL;SVLEN=-54;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=9.0.0 GT 1/1 -chr20 709759 . AGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCC A 60 . QNAME=cluster23_scaffold_3;QSTART=25000888;QSTRAND=-;SVTYPE=DEL;SVLEN=-93;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=11.0.0 GT 1/1 -chr20 764442 . A AGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGG 60 . QNAME=cluster23_scaffold_3;QSTART=24946242;QSTRAND=-;SVTYPE=INS;SVLEN=78;PctSeqSimilarity=0.9971;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=95;EndDistance=95;GTMatch;TruScore=66;MatchId=13.0.0 GT 1/0 diff --git a/repo_utils/test_files/answer_key/bench_giab_report.txt b/repo_utils/test_files/answer_key/bench_giab_report.txt deleted file mode 100644 index b436b316..00000000 --- a/repo_utils/test_files/answer_key/bench_giab_report.txt +++ /dev/null @@ -1,78 +0,0 @@ -# Performance -recall: 0.0 -precision: 0.0 -f1: 0 -gt_concordance: 0 - state -fp 16 -fn 8 -tpbase 0 -tp 0 - - -# State by SizeCat and SVTYPE -sizecat SVTYPE tpbase fn tp fp pct -50to99 DEL 0 3 0 0 0.0 -50to99 INS 0 1 0 0 0.0 -100to299 DEL 0 1 0 0 0.0 -100to299 INS 0 3 0 0 0.0 -300to999 DEL 0 0 0 0 -300to999 INS 0 0 0 0 -gt1000 DEL 0 0 0 0 -gt1000 INS 0 0 0 0 - - -# State by REPTYPE -REPTYPE tpbase fn tp fp pct -DUP 0 2 0 0 0.0 -SIMPLEDEL 0 4 0 0 0.0 -SIMPLEINS 0 2 0 0 0.0 - - -# State by Tech -tech_str tpbase fn tp fp pct -Ill+CG 0 1 0 0 0.0 -Ill+TenX+CG 0 2 0 0 0.0 -PB 0 1 0 0 0.0 -PB+TenX 0 4 0 0 0.0 - - -# State by Genotype -state HET HOM NON REF TOT -tpbase 0.0 0.0 0.0 0.0 0.0 -fn 2.0 4.0 1.0 1.0 8.0 -tp 0.0 0.0 0.0 0.0 0.0 -fp 12.0 4.0 0.0 0.0 16.0 -total 14.0 8.0 1.0 1.0 24.0 -recall 0.0 0.0 0.0 0.0 0.0 -precision 0.0 0.0 0.0 - - -# Args -bSample None -base repo_utils/test_files/giab.vcf.gz -cSample None -chunksize 1000 -comp repo_utils/test_files/input1.vcf.gz -debug False -dup_to_ins False -extend 0 -giabreport True -gtcomp False -includebed repo_utils/test_files/giab.bed -minhaplen 50 -multimatch True -no_ref False -output test_results/bench_giab/ -passonly False -pctovl 0.0 -pctsim 0.7 -pctsize 0.7 -prog True -refdist 500 -reference repo_utils/test_files/reference.fa -sizefilt 30 -sizemax 50000 -sizemin 50 -typeignore False -use_lev False diff --git a/repo_utils/test_files/answer_key/bench_unroll/fn.vcf b/repo_utils/test_files/answer_key/bench_unroll/fn.vcf deleted file mode 100644 index 289edcec..00000000 --- a/repo_utils/test_files/answer_key/bench_unroll/fn.vcf +++ /dev/null @@ -1,59 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##fileDate=20201127 -##source=PAV (HGSVC2) -##reference=ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC2/technical/reference/20200513_hg38_NoALT/hg38.no_alt.fa.gz -##contig= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##INFO= -##INFO= -##bcftools_viewVersion=1.8+htslib-1.8 -##bcftools_viewCommand=view -s NA12878 variants_freeze4_sv_insdel_alt.vcf.gz; Date=Wed Aug 3 14:45:56 2022 -##bcftools_viewCommand=view -i 'INFO/AC >=1' -O z -o GM12878_variants_freeze4_sv_insdel_alt.vcf.gz; Date=Wed Aug 3 14:45:56 2022 -##bcftools_viewCommand=view -r chr21 GM12878_variants_freeze4_sv_insdel_alt.vcf.gz; Date=Thu Aug 11 15:17:10 2022 -##bcftools_viewCommand=view -r chr21:14000000-19000000 GM12878.chr21.true.vcf.gz; Date=Sun Aug 21 18:37:08 2022 -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 -chr21 14088112 chr21-14088113-DEL-223 ATAATTATATATAATATATAAATATATTATATATAATTATATATAATTTATAAATATATTATATATATAAATATATAATATATTTTTATATATTATATAATTATATATAATATATAAATATATTATATATATAAATATATAATATATTTTTATATAATATATAATTATAAATATATAATATATTTTTATATATTATATATAATTATAAATTATTATATATAATC A . . ID=chr21-14088113-DEL-223;VARTYPE=SV;SVTYPE=DEL;SVLEN=-223;SAMPLE=HG00731;TIG_REGION=cluster2_000000F:13803594-13803594;QUERY_STRAND=-;REF_SD=0.92;REF_TRF;AC=1;AN=2;PctSeqSimilarity=0.0089;PctSizeSimilarity=0.4305;PctRecOverlap=0.433;SizeDiff=127;StartDistance=-153;EndDistance=70;TruScore=29;MatchId=1.1.0;Multi GT 1|0 -chr21 14088467 chr21-14088468-DEL-1069 TCGTTTTAATAAATGAATAGAATTCATCACCTAACTTCTAAAGCTACTTCTCCCGATGAAAGTCCGGGCACTTAGGAGTCAACAGTGGTGTATTGAGTGTATGACTCTTGCTCACAGGTGCTTCTCTTCTGTCCCACGGCAGGCGGCACCAACAGAAGGCTTCTGCAAAGCTGAGAGCTCCTTTTACCCATGGATCAGGAGCAGAGTTTGCAGCTACACTGTCAGGCTGTGTTTGGATGTTAGCAGTTAGTTTAGCTTTGCGTCTTCAGAGCAATTGTTCTTAGCTACTTAAAAAAAGAAAAGAAAAGAAAGGAAAATTTAAAATTTTCTTCATTGATCATTCAGGAGCATGTTTAATTTCCATGTATTTGTACAATTTCAAAAGTTCACCTTGTTGTTGACTTCTAGTTTTATTCCATTGTGGTCAGGAAAGATACTCGATATAATTTCAATTATTTTAAATTTGTTGAGACTTGTTTTGTGGCCTAACATATGGTCTATTCTGGAGAATGTTTCTTGTGCTGATGAAAGAATGTGTTTTTTGCATCTGTTGGATGAAATGTTCTGTAAATGTCTCTTTGTTAGTCTAAAATGCAGTTTTTTGTTTTTTGTTTTTTTAGGAGAGTCTCACTCTGTTGCCCAGGCTGGAGTGCAGTAGCATGATCTTGACTCACTGCAACCTCCACCTCCCAGGTTCAAGCAATTCTCATGCCTCAGCCTCCCAAGTAGCTGGAATTACAGATGCCCACCACCACACCCAGCCAATTTTTGTATTTTTAGTAGAGACAGTGTTTTACCATGCTGGCCAGGCTGGTCTCAAACTCCTGGCCTCAAGGGATCCGCCTGCCTTGGCCTCCCAAGGTGCTGGTACTATAGGTGTGAGCCACCGCATCCAGCCTAAAGTACAGTATAAATCTAATGTTTTGTTTTTGATCTTCTATCTAGACAATCTGTTCAGTGCTGAGAATGGGGTATTGAATTCCCCAGCTATTGTATTGGCATCTATATCTCCCTTTAGACCTAATAATATTTGGTTTATATTATATATCTCGGTGCTCCAGTGTTGGGTG T . . ID=chr21-14088468-DEL-1069;VARTYPE=SV;SVTYPE=DEL;SVLEN=-1069;SAMPLE=HG00512;TIG_REGION=cluster23_000000F:32670904-32670904;QUERY_STRAND=-;REF_SD=0.92;AC=1;AN=2;PctSeqSimilarity=0.0019;PctSizeSimilarity=0.0898;PctRecOverlap=0;SizeDiff=973;StartDistance=202;EndDistance=1271;TruScore=3;MatchId=1.2.0;Multi GT 1|0 -chr21 14439480 chr21-14439481-INS-12597 C CGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATAACAGGCGTGAGCCACCGCGCCCGGTCGAAATGGTGGCATTCTTTTACGTTGGCATGAGATAGGAATGTTTATATTTAATTTGTGAACCCCAAAATGTGATCTTGAAGCAAAGATTGATAGCAATGGAAGTAGCAGGTGAAATCACCTGCTGGAGCTCTACCTGATGCCCCTTCAACTAATGCACCATAAAAATTCTCATCCTCTTCTTAGTCAGATCTAGAGGGAAACCCACTTCACTACGTTGTCTGAATGTGACTTGCAGTGAACTAAAAAAAATATGAAATTCTCATCCTTCGTTTAAGATAAGTTCCTCATTGAAAAGAACTAGGAAATAGTATATCAATCTTCAATCATTTGAACAAAATGTTCATGATGGTAAATAGGAGGTCTTCTTGAATCATCCCGATAACTTCTTCAGGATTCCACTTCTTGTTATGATGACTGGGCATCTCACATTGCATCTGTTTTGAGATTGTCACCAAACTAAATAGGCATGAGAACGACTATAGTAGAGGGAAGCAAATTCTTTGTGTTAACAGTTGTTACCTGTTTTGCTAAAATCAGTAGCAGAAGGATTGTGATGAGGTTATTTAACTGGACAGTGAATAGGTCTCATTAGGCTAGAATTTTGTAAGGGGTTCTGCTTACTTGGTTTTACTTCCTTTGGCCAATAGATTAGTGATTCTAATAGCCAGCAATGGTCTACCTGATCTGGGTAGCTACCTAGAAATATGATTGCAGAGATTCTTTAACTTAAGATTTTACAATATTATACAAATATATTTCTGTGAATAACTGAGTCCACATTTTCTATATACAGTTATTACATGCAAAAATTTTAAATCACTCATAATCTCAGCATTTTTAACCACTAAAAAATTAGTTTACCTACTTTCATTCTCCTTCAACTCCACATCACTGTAATCACTGTAAATTATTTTATGAGTATATATTTCCTGGGTTTTAATTTTATTTTGTTTTAAATTGACAGGTAATAATTGTACATATTAATGGGGTACAGAGTGATGTTTTGATACATGTATACATTATGTAATGAGCAAACCAGGATAATTAGCATATCCATCACCGTGAACACTTGTCATTTCTTTGTGGTAAGAATATTCAAAATTCCCTCTTCTAACTATTTTGAAATATACGGTACATTATTTTTTAACTATAGTCATCCTACTGTGCAATAGAACACCAGAACTTACTCCTTCTATCTAACTGTAACTTTGTGCGTGTTGACCAACCTCTCCCCATTCTTCCCTCTCCCCTGTTCTCCCCAGCCTCTGGTAACCACCATTCTACACTTTACTTCTATAAGATCAGCTTTTTAAAATTCCACATATAAGTTAGATCATGTGGTATTTGTACCTCTGTGCTTGGAAACTTTTATTTAACATAACGTTCTCTAGGTTAACTATGTTGTTGCAAATGACAGGATTTCATTATTTTTTATGGCTGGATAGTATTCCATTGTGTACATACACCCATTTTTTAATCCATTCATCCATTAATGAACACTTAGGTTGTTCCTATATTTTGCCTATTGTGAATAATGCTGCAATAAACATGGGGGTGCAGATATCTCTTCAACATATTGATTTCATTTCCTTTGGTTATATACCCAAAATAGGGGTTGCTGGGTCTTAGTGTAGTTCTGTTGTTAATTTTTTAAGAAAACTCCATGCTGTTTTCCATAATGCCTGCTCCAATTTACCTTCCCACCAACAGTGGCTAAGTGCTCTCCTTTTTCTACATCCTCACCAACATTTGTTATTTTTTTTTATCTTTTTGATAGTCACTATTCTAACTGGGGTATGGTGACATCTCATTGAGGTTCTGATTTGCATTTTCCTGATGATTAGTGATATTGAGCATATTTTCATACACCTGTTGTCATTTGTATGTCTTCTTTTGAGAAATCTCTCTTCAGATCTTTTGCCCATTTTCAAAGTGAATTTATTTATTTCCTTTTCTGTTGAGTTGTTTGAGTTTCATATATATTCTGGATCTTAACCGCTTGTCAAATGCATAGTTTGTGACTATTTTCTTTCATTCTGTAGGCTATCTCGTCAACTCTGTTTATTGAGGTTTTGCTGTGTAGAAGCCTTTCAGTTTGATGTAATCCCATGTGTGCCTATTTTTACTTTGTTTTCTGTGCTTTTGAGGTCTTACTCCAAAAATTCCTTGCCCAAGCCAATGTCATAAGCATTTATCCAATTTTTTCCTCTAGTAGTTTTATAGTTTCGGATCTTACATTTAAGTCTTTAGTCCACTCTGAGTTGACTTTTGTTAAGTGGTGAGAGGTAGGAGTCTAGTTTCATTCTTCTGCATGTTTAGATTCAGTTTCCCAGCACCATTTATTGAAGAAACTGTTCTTTCCCCAGTGTGTGTTCTTGGCACCTTTATTGAAATTCAGTTGGCTTAAATGTGTGAATTTTTTTCTGGATAGTCTATTAATTTTTGTATTCATTGTAGAGACGGGGTTTTGCTATGTTGCTCAGGAGGGTCTCGAACTCCTGGACTCAAGCAATTTGCCTGCCTCAGCCTCCCAAAGTGCTGGGACTACAGGTGTGATCCACTGTGCCTGGCCTATAGTTTTTATTGTAGAGACCTTTCACCTCCTTGGTCAAATTCATTCATCGGTATTTTGTTGGTTTTATAGCTATTGTAAATGGGATTCTGTTCTTGATTTCTTTTTTTAGAAAATTCGTTGTTGGCATATAGAAACATTACGGATTTTTGTGTTTATTATGTATACAGCAACTTTACTGAATTTGTTTATTAGTTCCAGTAGTTTTTTGGTTGATTCTATAGGTTTTTTTATAATTAAGATCATGTCTTCTGCAAACAGAGACAACTTGACTCTCAATTTGACAATTGAGGAGCATGTCATTTAATTTCCATGTAGTTGTACAGTTTCCAAAGTTCCTAATGTTATTGATATCTAGATTTTTTTCCCTTGTGGTCAGAAAAGATACTTGATATGATTTTGATTTTTAAAAATTTGTGAAGACTTTTTTGTGGTCTAACATATGATCTGTCCTCGAGAATGAGAGTATTTCATTTGCTGTTGATTCTTCTTTTGTTTTTTTCTTCTTCCGTTCATTCTTTTCACCTTTTTAGTTTTCTTGCCTAATTGCTCTAGCTAAGACTACTAGTACTACATTGAATAGAAGTGGTGAAAACGAACATCCTTGTCTTGTTCCAGAATTTAGAAGTAAAGCTTTTAACATGTTTCCAGTCAGTAAGATGTTAGCTCTGGGTCTTTCCATATATGGCCTTATAGTGTTGAGGTACATTCCTTCTGTAACTAATTTGTTTAGGGTTTTTCTCATAAAGGAATGCTAAATTTTATTGAATGCTTTTTCTTTGTCTATTGGGATGATCATTTGGTTTACTTCCTTCATTCTGTTGATGTGATATATCACATTTATTTGATTTTCATACGTTTGAACATTCTTGCATCCCTGAGTTGAATCCTATTTGATCATGGTGAATGATCTTTTCAATGTGCTGTTGGATTCAGTTTGATAATATTTTGTTGATGATTTTTAAATTCATTTTCAACAGGAATATTGACCTGTAGTTTTCTTTTTTTTTTCTTGTGTCCTTGTCAGATTTTGGTATCAGAGTAATAATGGCCTTGGAGGATGAATTTGGAAGAATTCTCTCCAATTTTTCATCATGGTTTGAGAAGAATTGGCATTTGTTCTTTAAATATTGGTAGAATTTGGCAATGAAATCATTCAAACCTGGGCTTTTATTTGATGGGAGGCATTTTATTACTAATTCAATTTAGTTACTTGTTATTGGTCTGTTCAGGCTTTCTATTTCTTTGTGATTCAATCTCAGTAGTTTGTATGTGTCCAGGAAATTGTCCATTTATGTCAGGTTCTCCAATTTGTTGATGGTTAGTTGTTCATAATTGTCTCTAATGATCTTCTGAATTTCTGTAGTATTGGTTGTGATGCCTCCTGTTTCATCTCTTATTTTATTTATTCAAGTAGCCTTTTTCCTTAATTGGCATAGCTAAGGGTTTGTCAATTTTGTTAAAAAAGCAACTACTCATTTTATTGATCTTTTGTATTTTTTTAGTCTCTATTTTGTTTATTTCTGGTCTAATCTTTATTATTTCTTTCCTTCTATTTTTGAAGTTAGTTTGTTCTGGCTTTTCTAGTATTTTGAGATGAAACATTATGTTATTTGAAATATTTCTACATTTTGATGTAGGCATTCATTGCTAAAAACTTTCTTCTTAGAACTGTTTTTGCTGTATCTGATACATTTGTGATATATTGTGTTTCCATTTTCATTTGACTCAAGAATTTTTTTAATTAAAAATAAAATAAAATGTCTTAATTAAAAAATTTTTAAATTAACACACTAGTTATTGAGGAGCTTGTCATTTAATTTCCATGTAGTTGTACAGTTTCCAAAGTCCCTAATGTTATTGATATCTAGATTTTTTTCCCTTGTGGTCAGAAAAGATACTTGATATGATTTTGATTTTTAAAAATTTGTGAAGACTTGTTTTGTGGTCTAACATATGATCCGTCCTCGAGAATGAGAGTATTCCATTTGCTGTTGAGAAGAAGGTGTATTCTGTGGCTGTTGGATGGAACACTCTATAAATGTCTGTTAGGTCCATTTGGACTAGAGTGTGGTTTAACTGTACTGTTTTCTTGTTCAATTTTTGTCTAGATCACCTGTCCATTGCTGGATTTAGGTTGTTGAAGTTCACTACAATTATAGTATTACAGTCCTTATCTCCTTTTAGGTCTGTTAACATTTGCTTTATATATTTATTCTTCAACATAAGAAAACATTTTATATTGGGTGAATATAAAATTGTTATATCCTCTTGCTGTATTTACCCCTTTATAATTATATTATGGCCTTCATTGTTTCTTTTCACAGTTTTTGTTTAAGGTCTCTTTTTTTCTGATGTAAGTATAGCTGCTCCCACTTTCTTATGGTTTTCATTTGCATAGAATATCTTTTTTTCTATTCCTTCACTTTCAATCTATGTATCCTTACAGGTGAAGTGAGTCTCTTAGGGACAGCATATAATTGGGTATTGTTTTCTTCTCCATTCAGCCCCTCTGCTATAGTTTGGATACTTGACCCTCCAAAAATCATGTTGAAATTTGATCCCTAATGTTAGAGTGGAGCCTACTGGGAGGTGTTTGGGTCATGGAGGTGAAATGCCTTCCCTGGCATTGGGGTGTGTATGAGTTCTCATTCTGTGAATTCCCATAAGGGGTGGTTGTTAAAAAGAGCCTGGTACCTCCCCTTTCCCTCACTTTGCTCTTGCTGTGTGATGTCTGCACATGCTAGCTCCCATTTGCCTTCTGCCATGAGTGGAAGCAGTTTGAGGCCCTCATCAGAAGCAGATATCGACCCTATGCTTCTTGTACAGGCTGCAGAACAGTGAGCCAAATAATCCTCTTTTAAAATTACCTACCCTAAAGTATTGCTTTATAGCAACAAAAACAAACTAAGACATCTTCTATCTCTGTTAATTGGAGATTTACTTTGAATGCAAAGCCAATTTACATTCAAGGGAATTATTGATAGGCAAAGTCTAACTACTGCCACTTTGTTACTTATTTTCTAATTGTTTTGTAGGCTCCTTTTTTCTTTCTTCCTCTCTTACAGTCTTCTTTTGAGGTTAAGTGATTTTCACTAGTTGTATGTTTTGATTCCTTGCTTTTTTATTTTTAGTGTATCTTTTATAGGTTTTTGCTTTGTGGTTACTGTGAGGCTTTCAAATGCCAAGCTATAGTTATGGCAAGTTACTTTAAAATGATAACAACTTAACTACAATTGCAAAGAAAAAAAAGGAATAAAAAAAGCTGTACATTTTAACTACATTCTCATCCCAAATTTTGAATTTTTATTATCATAATTTCAATTTTTATATTGCCTGTTTCTTAATGAATTATTATAATTATTAATTTTGATAATTTTGTCTTATAGTTTTATACTAAAGATATGTGTTTTCAGAATCATAAGTTATCTATTATTGCAGTATTTGAATAACAATCATGGTACCATCAATTTCCTTTGGTTTGTAGAACTCTCTGTAGCATTTTTCATAGGACAGGTCTGGTAGCAATAAGTTTCCTCAGTTTTTGTTTGTCTGGGAATGTCTTTATTTCTCCTTCATTTTTGAAGCTTACTAGGTAAAATATTTTTGGTTGACAGTTGTTTTTATTCAGCATTCTGAATATATTATCGTATTATCTTCTGGCCTGCAAGATTTCTGCTGAGAAGTCTTCTGCCTGGCATATTAGATCTCCATTATATGCTATTTGCTTCTTTTTTCTCACTGCTTTCAGGAATCTTTTTTTGTTTAGACCTTTGAGAGTTTGATTATAATGTATCTTAGAGTATTCTTATTTGGGTTGAATCTAATTAGTGACCTATGATCTTCCTAACCTGAATAATTTTATCCTTCTACAGATTTGGGAAATTTTGTGCTATTATTTCTTTGATTTATCATTCCACCCCTTTGTCTTTCTCATTTTCCTTTTTAACTTAATTAACCCAAATATTTGCTCTTTTGATGTAGTTCCATAGATCCTATATGCTTTCTGTGTTCCGTTTTGTTTTTTTCTCTTTTATTGTCTATGTATTTTCAAATATGCTTTCTTTGAGCTTACTGACTCTTTCTTCTGTTTGATCAATTCTGCTGTTCATGGTCTTTATTACATTTTTCATTTTATTCATTGTATTTTTGGCTCCAGGATTTCTGTTTGGTGTTTTTATTATTTTAATCTCTCTGTTAAGTTTATGTTAAATTTCTGATTTTTTTGTTTTACTGAATTTTGCTGAGCTTCCTTAAAACAGCTATTTTGAATTCCTTGCATAAGAGATCGCACATCTCCATCACTGTAGGGTCTGTTATTGGTGTTTTATTTTGTCATTTTGATGAGGTTACATTTTCCTAAATGGTCTTGTTGCTTATGGATGTGTGATGATATCTGCCCATTGAAGATTGTGTTATGTTTCCTGAGTTCGTAACCACTGCAGCTATCTCAACACTAGAGGATGCTCTAAGCCCAGATTTGCCATGAGTCGCATGAGGATGCCAAGGATGTGGTGACTCTGGCAGGGATGAATCCGAGGAAGGTCCAAGAAGGTACCCAGGCTGTGAGGGAAAGCTAACCAGGAACCAGAAGACGAAGAGATGCCTTCCAGCAGATCCCTACACACGCAGGATAGGTTTTTGACTGTAGCCTAAATAAGCATGCCTTCCAGCAGATCCACATGCAGGATAGGTTTTTTACTGTAGCGAGAGGAGCTGGAGCTGAGACTGGGTCCCCTTGGGATCTCCTGTGGAAGGGTGGGAGGTGAGCTCATTTTGTTATCTCAGAGAGGCATGTCTTGAATTTTTGTTAATTGGCTTCCTTTTTACTCTCTCTAGCCTTTTCTTGTAGAAATCATACTGTATGAATGTTGGGCTCTTGGGAATTTTTCTCTGTCTCTTGATGGTTTATTTTCTGTTTTGAAACTGTATTTATTTTCTATGTGTTCTGGGAAAATTCTCCCATCTTCTCTTCCAACTCACTGATTTTCTTTTCAGCAGTGGATATTTGGACTATATATTAAGTTTTTTTTTTAATTTTAGCAAATATACTTTGCTCTTTTTTCATAACCTTCTATGATACTTCCTACATAAAATATCGCCTGCATCACTTTGAGGATAATTATCTTTTCTGGTTACTTAACTATCAATACCTTTTGTGTGTTTTTTTTTTTCTCAGGGTGTTGCTTTTCATCAAAACTCATCTATGAACTGAGAATTTCTGCTGAACTGTCAGCAGCCAGCCTCAGAGGAAAGGTGGAATCACCTGCCAAGGGCTTATACTTCATATTGTTTTTAGTTAGAGTAAAGGGATGGGAGTAATGTCTCAGCAACTGGTTTTCTGACTCTAATTTCTTTTCTCTTTTTTTTTTGGACATGAAAATGGGTTTATTTATTTATTTTTATTTTATTATTATTTATTATACTTTAAGTTTTAGGGTACATGTGCACAACGTGCCGGTTTGTTACATATGTATACATGTGCCATGTTGGTGTGCTGCACCCATTAACTCGTCATTTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCCCCATCCCCCACCCCACAACTGTCCCCGGTGTGTGATGTTCCCCTTCCTGTATCCATGTGTTCTCATTGTTCAGTTCCCACCTATGAGTGAGAACATGCGGTGTTTGGTTTTTCGTCCTTGAGATAGTTTGCTGAGAATGATGGTTTCCAGCTCCATCCATGTCCCTACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTATTCTATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCACTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAGTGCCACAATAAACATACGTGTGCATGTGTCTTTATAGCATCATGATTTATAATTCTTTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCGCCACACTGTCTTCCACAATGGTGGAACTAGTTTACAGTCCCACGAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATCGCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTCTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATATCCTTCACCCACTTTTTGATGGAGTTTTTTGTTTTTTTCTTGTGAATTTGTTTGAGTTCATTATAGATTCTGGATATTAGCCCTTTGTCAGGTGAGTAGGTTGCAAAAATTTTCTCCCATTCTGTAGGTTGCCTGTTCACTCTGACGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAATTTTGGCTTTTGTTGCCATGCTTTTGGTGTTTTAGACATGAGGTCCTTGCCCGTGCCTATGTCCTGAATGGTATTGCCTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAACATCTAAGTCTTTAATCTATCTTGAATTAATTTTTGTATAAGGTGTAAGGAAGGGATCCGGTTTCAGCTTTCTACATATGGCTAACCAGTTTTCCCAGCACCATTTATTAAATAGGGAATCCTTTCCCCATTGCTTGTTTTTGTCAGGTTTTTCAAAGATCAGATAGTTGTAGATATGTGGCATTATTTCTGAGGGCTCTGTTCTGTTCCATTGATCTATATCTCTGTTTTGGTACCAGTACCATGCTGTTTTGGTTACTGTAGCCTTGTAGTATAGTGTGAAGTCAGGTAGCATGATGCCTCCAGCTTTGTTCTTTTGGCTTAGGATTGACTTGGGAATGCGGGCACTTTTTTGGTTCCATATGAACTTTAAAGTAATTTTTTCCAATTCTATGAAGAAAGTCATTGGTAGCTTGATGGGGATGGCATTGAATCTATAAATTACCTTGGGCAGTATGGCCATTTTCACGATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTCCCATTTGTTTGTATCCTCTTTTATCTCAATGAGCAGTGGTTTGTAGTTCTCCTTGAAGAGTTCCTTCACATCACTTGTAAGTTGGATTCCTAGGTATTTTATTCTTGAAGCAATTGTGAATGGGAGTTCACTCATGATTTGGCTGTCTGTCTGTTATTGGTGTATAAGAATGCTTGTGATTTTTGCACATCGATTTTGTATCCTGAAACTTTTCTGAAGTTACATATCAGCTTAAGGAGATTTAGGGCTGAGACAATGGGGTTTTCTAGATATACAATCATGTCATCTGCAAACAGGTACAATTTGACTTCCTCTTTTCCTAATTGAATGCTCTTTATTTCCTTCTCCTGCCTGATTGCCCTGGCCGGAACTTCCAACACTATGTTGAATAGGAGTGGTGAGAGAGGGCATCCCTGTCTTGTGCCAGTTTTCAAAGGGAATACTTCTAGTTTTTGTCCATTCAGTATGATATTGGCTGTGGGTTTGTCATAGATAGCTCTTATTATTTTGAGATACGTCCCATCAATACCTAATTTATGGAGAGTTTTTAGCATGAAGGGTTGTTGAATTTTGTCAAAGGCCTTTTCTGCATCTATTGAGATAATCATGTGGTTTTTGTCTTTGATTCTGTTAATATGCTGGATTACGTTTATTGATTTTCATATGTTGAACCAGCCTTGCATCCCAGGGATGAAGCCCACTTGATCATGGTGGATAAGCTTTTTGATATGTTGCTGGATTTGGTTTGCCAGTATTTTATTGAGGATTTTTGCATCAATGTTCATCAAGGATATTGGTCTAAAATTCTCTTTTTTGGTTGTGTCTCTGCCAGTCTTTGTTATCAGGATGATGCTGGCCTCATAAAATGAGTTAGGGAAGATTCCCTCTTTTTCTATTGATTAGAATGGTTTCAGAAGGAATGGTACCATCTCCTCCTTGTACCTCTGGTAGAATTCGGCTGTGAACCCATCTGGTCCTGGACTATTTTTGGTTGGTAAGCTATTAATTATTGCCTCAATTTCGTAGCCTGTTATTGTTCTATTCAGAGATTCAACTTCTTCCTGGTTTAGTCTTGGGAGGGTGTATGTGTCGAGGAATTTATCCATTTTTTCTAGATTTTCTAGTTTATTCGCTTAGAGGTGTTTATAGTATTCTCTGATGGTAACTTGTATTTCTGTGGGATTGGTGGTGATATCCCCTTTGTCATTTTTTATTGCATCTATTTTATTCTTTTCTCTTTTCTTCTTTATTAGTCTTGTTAGTGGTCTATCAATTTTGTTGATCTTTTCAAAAAACCAGCTCCTGGATTCACTGATTTTTTGAAGGGTTTTTTGTGTCTCTATCTCCTTCAGTTCTGCTCTGATCTTAGTTATTTCTTGCCTTCTGCTAGCTTTTGAATGTGTTTGCTCTTGCTTCTCTAGTTCTTTTAGTTGTGATGTTAGGGTGTCAATTTTAGATCTTTCCTGCTTTCTCTTGTGGGCATTTAGTGCTATAAATTTCCCTCTACACACTGCTTTCAATGAGTCCCAGAGATTCTGGTATTTTGTGTCTGACTCTAATTTCTGCCTAGTCCCCCATGGGGTCATCACTCATCTGGGTTAACACTATGTTCCTTTGGCCCAAACACAATGTCCAATCCTGGAGACAAAGCCTACTGACATTACAGGGACATGACACACAAGGGTGTATGGTTGCAGAGTCAGCCAATGTGGATGCTCTCCTTGTAGTAACAAAGTAATCTTGTCAATTGAACCATGTTCTGCATAATAGTGAGAAGATTGCTGTTAGCATTTAACAATGTATTTAGAACATATTTCTAGGTGTTTTTTTCTGTGACTGCACAATATTCCATTCTATACCTGTATTATGATGTGTGTAATTACTCCCTGGTAGTTTTCAATTTTTTTTTTTTTCGAGATGGAGTTTCACCCTTTCACCCAGGCTAGAGTGAAGTGACACAATCTCAGCTCACTGCAGCCTCTGCCTCCTAGGTTCAAGCAATTCTCCTGCCTCTGCTTCCTGAGTAGCTGGGATTATAGGCACCCGCCGCCATGTCTGGCTAATTTTTGTATTTTTTTAGTAGAGATGGGGTTTCAGCATTTTGGCAAGGCTGGTCTTCAACTCCTGACCTCTGGTGATCCACCTGCCTTGGGCTCCCAAAGTGCTAGGATTACAGGCGTGAGCCACTGCGTCAGGCCAAAAAGTTTTTTTTAGTAGAGATGGGGTCTCATTGTCTTGTCCAGGCTGATCTTGAAATCACCTCAAGCATGCCTTTCAGTTTGGCCTCCCAAAGTGCTGGGATTATAGTTCTGAGCCATTGCACCCAGCCCCTGGTAAATTTTTAAGTTGTTTCTAGTATTATGCTATTGTAAACAGCAATAGCATAATAGATATTTGACTAGATATTCTTGGCATCAGCTTTGTAGAATATATTCTTAGAAGTACAATTGCTGGGTCATAAAGCCTACACATTTTTAAACAATTTGTACTCCCATCAACAATGTAGGAGAGCATGTTCTTCCACTTTCAAATCAAACCTAACCTTTTTAATTTGCCAAGCTGATACAGGAAAAATGGTATCTGACTATTATATTGCCTTATATTGCTTCCATTATAAAAATTTTCTGTTATATTTCTTTCTAGTATGATTACAATTTTGTTGTTTTCACATTTACGTTTTTTGTTGTTGAGATGGAGTTTTGCTCTTGTTGCCCAGGCTGGAGTGCAACGGCACAATCTCAGCTCACCATGACCTCTGCCTCCTGGGTTCAAGCGATTCTCTGGACTCAGCCTCCTGAGTAGCTGGAATTACAGGGATTCGCCACCATGCCCAGCTAATTTTGTATGTTTCGTAGAGACAGGGTTTCTCCAAATTGGTCAGGCTGGTCTCGAACTCCCGACCTCAG . . ID=chr21-14439481-INS-12597;VARTYPE=SV;SVTYPE=INS;SVLEN=12597;SAMPLE=HG00731;TIG_REGION=cluster2_000000F:13452460-13465056;QUERY_STRAND=-;AC=2;AN=2;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=5.0._ GT 1|1 -chr21 15030991 chr21-15030992-INS-50 G GCTCGGAGGGTCACTACATTCCCTTTCTATGTGTGTACACTCTGGAAGGCA . . ID=chr21-15030992-INS-50;VARTYPE=SV;SVTYPE=INS;SVLEN=50;SAMPLE=HG00731;TIG_REGION=cluster2_000000F:12848462-12848511;QUERY_STRAND=-;REF_TRF;AC=1;AN=2;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=11.0._ GT 0|1 -chr21 15031103 chr21-15031104-INS-350 C CACATTCCCTTTCTATGTGTATACACTCTGGAAGGCGCTCGGAGGATCACCACATTCCCTTTCTATGTGTATACACTCTGGAAGGCGCTCGGAGGATCACCACATTCCCTTTCTATGTGTGTACACTCTGGAAGGCGCTCGGAGGATCACCACATTCCCTTTCTATGTGTGTACACTCTGGAAGGCGCTCGGAGGGTCACTACATTCCCTTTCTATGTGTGTACACTCTGGAAGGCACTCAGAGGATCACCACATTCCCTTTCTATGTGTATACACTCTGGAAGGTGTTCAGAGGTTCACCACATTCCCTTTCTATGTGTATACACTCTGGAAGGCGGTTGGAGGTTCACT . . ID=chr21-15031104-INS-350;VARTYPE=SV;SVTYPE=INS;SVLEN=350;SAMPLE=HG00513;TIG_REGION=cluster21_000000F:1189317-1189666;QUERY_STRAND=+;REF_TRF;AC=1;AN=2;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=11.1._ GT 0|1 -chr21 15089463 chr21-15089464-INS-277 T TATTCACTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAACAG . . ID=chr21-15089464-INS-277;VARTYPE=SV;SVTYPE=INS;SVLEN=277;SAMPLE=HG00513;TIG_REGION=cluster21_000000F:1248003-1248279;QUERY_STRAND=+;AC=1;AN=2;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=12.0._ GT 1|0 -chr21 15556507 chr21-15556508-INS-390 T TAAGAAAATGTGGCACATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGTAGGGACATGGATGAAATTGGAAACCATCATTCTCAGTAAACTATCGCAAGAACAAAAAACCAAACACCGCATATTCTCACTCATAGGTGGGAATTGAACAATGAGATCACATGGACACAGGAAGGGGAATATCACACTCTGGGGACTGTGGTGGGGTCGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGACACGTTAGTGGGTGCAGTGCACCAGCATGGCACATGTATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAACTTAAAGTACAATTAAAAAAAAAAAAAAAA . . ID=chr21-15556508-INS-390;VARTYPE=SV;SVTYPE=INS;SVLEN=390;SAMPLE=NA12878;TIG_REGION=cluster7_000001F:1546884-1547273;QUERY_STRAND=+;AC=1;AN=2;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=13.0._ GT 0|1 -chr21 16187359 chr21-16187360-INS-166 T TTTCTTCCCAATTTGTGAGTTTTCTCCATTCTCTATTGTGTAAATGTCTCCATTTTTTTCTATCTGAATCAAACTTGTGCTTTCCAACCACTCTAGCTTTCTCAACCTCCTTTACCATCATCGCCAGTCCAGTCAGACCATTTTCTATATTCTGCTCTAAAATCTCC . . ID=chr21-16187360-INS-166;VARTYPE=SV;SVTYPE=INS;SVLEN=166;SAMPLE=HG00731;TIG_REGION=cluster2_000000F:11691909-11692074;QUERY_STRAND=-;AC=2;AN=2;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=14.0._ GT 1|1 -chr21 16730888 chr21-16730889-DEL-691 TATATACCCAGTAATGGGATGGCTGGGTCAAACGGTATTTCTAGTTCTAGATCCCTGAGGAATCACCACACTGACTTCCACAATGGTGAAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTTTTTTTTTTTTTGCTTTCATTTTTATTTTTTTATTATACTTTAAGTTTTAGGGTACATGTGCACAACGTGCAGGTTTGTTACATATGTATACATGTGCCATGTTGGTGTGCTGAACCCATTAACTTGTCATTTAACATTAGGTATACCTCCTAATGCTATCCCTCCCCCCTCCCCCAACCCCATAATAGGCCCCAGAGTGTGATGTTCCCCTTCCTGTGTCCATGTGTTCTCATTGTTCAATACCCACCTATGAGTGAGAATATGCGGTGTTTGGTTTTTTGTCCTTGCGATAGTTTGCTGAGAATGATGGTTTCCAGCTTCATCCATGTCCCTACAAAGGACATGAACTCATCATCTTTTATGGCTACATAGTATTCCATGGTGTATATGTGCCACATTTTCTTGATACAGTCTATCACTGTTGGACATTTGGGTTGGTTCCAAGTCTGTGCTATTGTGAATAGTGCTACAATAAACATACATGTGCATGTGTCTTTATAGCAGCATGTTTTGTAATCCTTTGGGC T . . ID=chr21-16730889-DEL-691;VARTYPE=SV;SVTYPE=DEL;SVLEN=-691;SAMPLE=HG00731;TIG_REGION=cluster2_000000F:11148248-11148248;QUERY_STRAND=-;REF_TRF;AC=2;AN=2;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=17.0._ GT 1|1 -chr21 16925120 chr21-16925121-DEL-51 CAGAACATGTATAACATTGGCTTGGAGTAAGAGTCAAGGACAGAAGTTAGGT C . . ID=chr21-16925121-DEL-51;VARTYPE=SV;SVTYPE=DEL;SVLEN=-51;SAMPLE=HG00731;TIG_REGION=cluster2_000000F:10954631-10954631;QUERY_STRAND=-;REF_TRF;AC=1;AN=2;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=19.0._ GT 1|0 -chr21 16972599 chr21-16972600-INS-99 C CACTATAGTATATATAATACACTATAGTATATATACTATAGTATATATAATACACTATAGTATATATACTATAGTATATATAATACACTATAGTATATAT . . ID=chr21-16972600-INS-99;VARTYPE=SV;SVTYPE=INS;SVLEN=99;SAMPLE=HG00731;TIG_REGION=cluster2_000000F:10907116-10907214;QUERY_STRAND=-;REF_TRF;AC=2;AN=2;PctSeqSimilarity=0.7806;PctSizeSimilarity=0.7279;PctRecOverlap=0;SizeDiff=-37;StartDistance=-314;EndDistance=-314;TruScore=50;MatchId=20.0.0;Multi GT 1|1 -chr21 17240011 chr21-17240012-DEL-1304 AATAATAATTATAAAAACTATGGAAGAAATGACTGTTGCTGAGGGCTGTCATTTCACTGGAGAAAGACAATGGAAAACTGGAGATAATTAATTACCAATTTAAAGTAAGTGTGAAAACCACAGGGATTGTTTGGCAGCATATGAAGAATCTCTGCCCCAGGGTGGTTGGCAAGATGGCCAAATAGAAACAGCTCCGGTCTGCAGCTCCCAGTGAGATCAACGCAGAAGGCAGGTGACTTCTGCATTTCCAACTGAGGTACTCGGCTCATCTCACCGGGAGTGATTAGACAGTAGGTGCAGCCCACAGAGGGCAAGACAAAGCAGGGTGGGGTGTCGCCTCACCTGGGAAGCACAAGGGGTCAAAGAGCTCCTTTCCCTAGCCAAGGGAAGCAATGAGAGACTGTGCCATAAGGAACAACGAATTCTGGCCCAGAAACTATGCTTTCCCCACAGTCTTCACAACCTGCAGACCAAGAGATTCCCTCAAGTGGCTACACCATCAGGGCCCTAGGTTTCAAGCACAAAACTGGGTGGCCATTTAGGCAGGCACTGAGCTAGCTGCAGGAGTTTTTTTCATACCCCAGTGGCACCTGGAATGCCAGTGAGACAGAACCATTCATTCCCCTGGAAAGAGGGCTGAAGCCAGGAAGCCAAGTGGTCTAGCTCAGTGGATCCCACCCCCATGGAGCCCAGCAAGCTAAGATCCACTGGCTTGAAATGCTTGCTGCCAGCACAACAGTTTGAAGTCAACCTGGGATGCTCGAGCTTGGTGGGGTAGGGGTGTCCAGCATTACTGAGACTCGAGAAAGCTGTTTTCCCCTTACAGTGTAAACAAAGCTGCCAGGAAGTTCAGACTGGGCAGAGCCCATCACAGCTTGGCAAAGCTGCTATAGCCAGCCTTCCTCTCTAGATTTCTCCTCTCTGGGCAAGGCATCTCTGAAAGAAAGGCACCAGCCCCTGTTAGGGGCTTATAGATAAAACTCCCATCTCCTTGGGACAGAGCACCTGGGGGAAAAGAGGGCTGTGGACACAGGTTTAGCAGACTTAAACATTCCTGCCTGCCAGCTCTGAAGAGAGTGGCAGATCTCCTAGCATAGCGCTCGAGCTCTGCTAAGGGACAGACTGCCTCCTCAAGTGGGTCTCTGACCCCCATGTCTCCTGACTGGGAGACACCTCCTAGCAGGGGTCGACAGACATGTCATAGAGGAGAGCTCCGGCTGGCATCTGGTGGGTGCCCCTCTGGGAAGAAGCTTCCAGAGGCAGCAAAAGGCAGCAATCTTAGCTGCTCTGCAGCCTCCACTGGTG A . . ID=chr21-17240012-DEL-1304;VARTYPE=SV;SVTYPE=DEL;SVLEN=-1304;SAMPLE=HG00731;TIG_REGION=cluster2_000001F:10635695-10635695;QUERY_STRAND=-;AC=1;AN=2;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=23.0._ GT 0|1 -chr21 17292196 chr21-17292197-INS-1030 A ACCCCCACCTCCCTCCTGGACGGGGCGGCTGGCCGGGTGGGGGGCCGACACCCCCACCTCCCTCCCGGACGGGGTGGCTGGCCGGGCAGAGGGGCTCCTCACTTCCCAGTAGGGGCGGCCGGGCAGAGGCGCCCCTCACCTCCCGGACGGGGCGGCTGGCCGGGCAGGGGGGCTGACCCCCGCCACCTCCCTCCCGGATGGGGCGGCTGGCCGGGCGGGGGGCCGACACCCCCACCTCCCTCCCGGACACGCCGGCTGGCCGGGCAGAGGGGCTCCTCACTTCCCAGTAGGGGCGGCCGGGCAGAGGCGCCCCTCACCTCCCAGACGGGGCGGCTGGCCGGGCGGAGGGCTGACCCCCCCACCTCCCTCCCGGACAGGGCGGCTGGCCAGGCGGAGGGCTGACCCCCCCACCTCCCTCCCGGACGGGGCGGCTGGCCGGGCAGAGGGGCTCCTCACTTCCCAGTAGGGGCGGCCGGGCAGAGGCGCCCCTCACCTCCCAGACAGGGCGGCTGGCCGGGCGGAGGGCTGACCCCCCCACCTCCCTCCCGGACAGGGCGGCTGGCCAGGTGGGGGGCTGACCCCCCCACCTCCCTCCCGGACGGGGCGGCTGGCCGGGCAGAGGGGCTCCTCACTTCCCAGTAGGGGCGGCCGGGCAGAGGCGCCCCTCACCTCCCAGACAGGGCGGCTGGCCGGGCGGAGGGCTGACCCCCCCACCTCCCTCCCGGACAGGGCGGCTGGCCAGGTGGGGGGCTGACCCCCCCACCTCCCTCCCGGACGGGGCGGCTGGCTGGGCTGAGGGGCTCCTCACTTCCCAGTAGGGGCGGCCGGGCAGAGGCACCTCTCACCTCCCGGACGGGGCGGCTGGCCGGGCGGGGGGCTGACCCCCCCACCTCCCTCCCGGACGGCACGGCTGGCCAGGTGGGGGGCTGACCCCCCAACCTCCCTCCCGGATGGCACGGCTGGCCGGTCGGGGGGGCTGACCCCCCACCTCCCTCCCAGATGGGGCGGCTGGCCGGGCGGGGGGTTGACCC . . ID=chr21-17292197-INS-1030;VARTYPE=SV;SVTYPE=INS;SVLEN=1030;SAMPLE=HG00731;TIG_REGION=cluster2_000000F:10584195-10585224;QUERY_STRAND=-;REF_TRF;AC=2;AN=2;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=24.0._ GT 1|1 -chr21 17400106 chr21-17400107-INS-125 A AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG . . ID=chr21-17400107-INS-125;VARTYPE=SV;SVTYPE=INS;SVLEN=125;SAMPLE=HG00731;TIG_REGION=cluster2_000000F:10475264-10475388;QUERY_STRAND=-;REF_TRF;AC=2;AN=2;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=25.0._ GT 1|1 -chr21 17501573 chr21-17501574-DEL-53 ACTATGCAAACATTGAGTTAAGCCCAGCATCTTTGATCTATAATGCCCACAGCG A . . ID=chr21-17501574-DEL-53;VARTYPE=SV;SVTYPE=DEL;SVLEN=-53;SAMPLE=NA19238;TIG_REGION=cluster4_000001F:3643326-3643326;QUERY_STRAND=+;REF_TRF;AC=1;AN=2;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=28.0._ GT 0|1 -chr21 17696940 chr21-17696941-INS-314 A AAGTACCTTCTTAAGGGTGGGGGAATATCACAAAGTACCTTCTTAAGGGCGGGGGAATATCACAAAGTACCTTCTTAAGGGCGGGGGAATATCACAAAGTACCTTCTTAAGGGCGGGGGAATATCACAAGTACCTTCTTAAGGGTGGGTGAATATCACAAGTAACTTCTTAAGGCGGGGGAATATCACAAAGTACCTTCTTAAGGGCGGGGGAATATCACAAAGTACCTTCTTAAGGGCAGGGGAATATCACAAAGTACCTTCTTAAGGGCAGGGGAATATCACAAGTACCTTCTTAAGGGCAGGGGAATATCAC . . ID=chr21-17696941-INS-314;VARTYPE=SV;SVTYPE=INS;SVLEN=314;SAMPLE=HG00513;TIG_REGION=cluster21_000000F:3856585-3856898;QUERY_STRAND=+;REF_TRF;AC=1;AN=2;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=30.0._ GT 0|1 -chr21 17719506 chr21-17719507-DEL-486 ACCCCCCCACCTCCCTCCCGGACGGGGCGGCTGGCCGGGCAGAGGGGCTCCTCACTTCCCAGTAGGGGCGGCCGGGCAGAGGTGCCCCTCACCTCCCGGACGGGGCGGCTGGCCGGGCAGGGGGGCTGACCCCCCCCACCTCCTTCAGGACGGGGTGTCTGGCCGGGCGGGGGGGCTGACCCCCCCACCTCCCTCCCGGACGGGGCGGCTGGCCGGGCAGAGGGGCTCCTCACTTCCCAGTAGGGGCGGCCGGGCAGAGGCGCCCCTCACCTCCCGGATGGGGCTGCTGGCCGGGCAGGGGGGCTGACCCCCCCCACCTCCCTCCCGGACGGGGTGGCTGGCCGGGCGGGGGGCTGACCCCCCCACCTCCCTCCCGGACGGGGCGGCTGGCCGGGCAGAGGGGCTCCTCACTTCCCAGTAGGGGCAGCCGGGCAGAGGTGCCCCTCACCTCCCGGACGGGGCGGCTGGCCGGGCAGGGGGGCTAAAC A . . ID=chr21-17719507-DEL-486;VARTYPE=SV;SVTYPE=DEL;SVLEN=-486;SAMPLE=HG00732;TIG_REGION=cluster1_000000F:3127564-3127564;QUERY_STRAND=+;REF_TRF;AC=1;AN=2;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=31.0._ GT 0|1 -chr21 17719675 chr21-17719676-INS-97 G GGGGGCCGACCCCCCCACCTCCCTCCCGGACGGGGCGGCTGGCCGGGCGGGGGGCCGAGCCCCCCACCTCCCTCCCAGACAGGGCGGCTGGCCGGGCA . . ID=chr21-17719676-INS-97;VARTYPE=SV;SVTYPE=INS;SVLEN=97;SAMPLE=HG00731;TIG_REGION=cluster2_000000F:10155302-10155398;QUERY_STRAND=-;REF_TRF;AC=1;AN=2;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=31.1._ GT 1|0 -chr21 17720053 chr21-17720054-DEL-452 CCCTCCCAGACGGGGCGGCTGGCCGGGCAGGGGGGCTAAACCCCCCCCACCTCCCTCCCGGACGGGGCGGCTGGCCGGGCGGGGGGCCGAGCCCCCCACCTCCCTCCCAGACAGGGCGGCTGGCCGGGCGGGGGGCTGACCCCCCAACCTCCCTCCCGGACGGGGCGGCTGGCCGGGCAGAGGGGCTCGTCACTTCCCAGTAGGGGCGGCCGGGCAGAGGCGCCCCTCACCTCCCAGACGGGGCGGCTGGCCGGGCGGAGGGCTGACCCCCCCACCTCCTCCGGACGGGGCGGCTGGCCAGGCAGGGGCTGACCCCCCCCACCTCCCTCCCGGACGGGGCGACTGGCCGGGTGGGGGGGCTGACCCCCCCATCTCCCTCCCGGACGGGGTGGCTGGCCGGGCTGAGGGGCTCCTCACTTCCCAGTAGGGGCAGCCGGGCAGAGGCACCCCTCA C . . ID=chr21-17720054-DEL-452;VARTYPE=SV;SVTYPE=DEL;SVLEN=-452;SAMPLE=HG03125;TIG_REGION=cluster19_000001F:10241353-10241353;QUERY_STRAND=-;REF_TRF;AC=1;AN=2;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=31.2._ GT 0|1 -chr21 17720091 chr21-17720092-INS-229 A AACCCCCCCCACCTCCCTCCCGGACGGGCGGCTGGCCGGGCGGGGGGCTGACCCCCCCACCTCCCTCCCGGACGGGGCGGCTGGCCGGGCAGAGGGGCTCCTCACTTCCCAGTAGGGGCGGCCGGGCAGAGGTGCCCCTCACCTCCCGGACGGGGCGGCTGGCCGGGCAGGGGGGCTGACCCCCCCCCCACCTCCCTCCCGGACGGGGCGGCTGGCCGGGCGGGGGGCCG . . ID=chr21-17720092-INS-229;VARTYPE=SV;SVTYPE=INS;SVLEN=229;SAMPLE=HG00731;TIG_REGION=cluster2_000000F:10154789-10155017;QUERY_STRAND=-;REF_TRF;AC=1;AN=2;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=31.3._ GT 1|0 -chr21 17730247 chr21-17730248-INS-3975 C CCGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGAGAAACCCCGTCTCTACTAAAAATACAAAAAAATTAGCCGGGGGTAGTGGCGGGCACCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAAGCGGAGCTGGCAGTGAGCCGAGACGGCGCCACTGCACTCCAGCCTGGAATTCCAACAAACTTAAATGTGGCAGTGAGAACCGCTTAGGAGATACATGTGGCCTTCTGAAATATGCTGAGTGGGGAACACTGAGCTGTATCACCGCTGTGCTATAGTTGATTCACTTATTTGGTCCTGTGGGTGCAATCTGCTGTTCTGAACACTAGCCCTTGTACCGTTGTCAATATCTTTGCTGGCCCAGTTCCCCGTTATGTATCGTGCTGGCTGAAATTTTATCTACCCTTTAAAGTTGATTCCAAATACTACCTGCTCCATAAAACCTTTCTTAAGTCCACCCCCTGCCAGCCTTGCATGTTGTTTTGAAGTTGGATAACATATTGCAGCAGGCAAAGTAGAAATAGCAATGGGCTGGGGACCACACCAAGCTCCAGTTCTGTGCAAACCAATAGCATCGGAGCATGTATACTCATAATCAGTTTTTGTTGAATGGCTGCATGACTGACTAAATGGATGAATCGGTTGCCTTGGACGAGAAACTTTTGGAGCCTTAATATCTTTATCTGTGGAATAAGGTCATTATAAAGAACTTCCTTTCCCTAAAAGTGGTCCTTGAAATACCTGGTTCTTGTTTAATGGTGAGTCTCATCCTTCTATCGGAACCAGAATCACTGGGGGCCTGAGAATCTGTGTTTAACATATACCGTTGGTGATCATTATACTCAATAAAATTGGAAAAGCATTGAACTGGTGGTTATCTGTTCAATCAAAGCAATGTGATGGCAGTTGCAAATGTATGACCTTGTTTATAAAGATGAGAAATTCCTTTTTTTTTTTTTTTTTTTGAGATGTTGTCTCACTGTTTTGCCCAGGCTGGAATGCAGTGGTGCAATCTCAGCTCACTGCAACCTCTGCCTCCCAGGTTCAAGTGATTCTCCTGCCTTACCCTCCCGAGTAGCTGGGATTATAGGTGTGTGCCACCATGCCCAGCTAATTTTTGTATTTTTAGTAGAGACGAGGTTTCATCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCGCAAGTGATCCGCTCACCTTGGCCTCCCAAAGAGCTGGGATTCCAGGCGTGAGCCACCACACCCAACCAGAGAAATTCTTTTTGTTAAAGGAACGTGGAAGAAATCTCCTGGTTGAAAAAACATGTAAGTAGTGGGAAAAACCTGAAATACTCCAGGAATATTAGGATTGTCTCCAGGTAGAGTTAAGTTGGGGCAGAGTGAGAATGACACATATGAATATCATTAATTATTCACATATCCTTCCCCTTTACAGTCAATGATTATGCATTAATTACCTGGTCATCTGGCTAAGCCAAGCACTGAGGATAAAGGAATGATTTTTGCCATAACCTTTTTATGTAGATGTGGCCTTTATTATTATTCATCCTTGATGATGTCAGCCCCAGAACCAGGAACAGAAGCCCTCGGATGTAATTGAGTCCTATTTCCAAAATACTCCACTGTCCCACTGTCTTCTTACAGAGTCTGGAACTATGAATTGGAACTTCTTGCCTGCCTGCCTGCCTGCCTGCCTGCTTTCTTTCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTTCTTTCTTTCTTTTTTTCTGATGGGGTCTTGCTCTGTTGCCTAGGCTGGAGTGCAGTGGTGTGATCATAGCTCATTGTAGCCTTGACCTTCTGGGCTCAAGAGATCCTCCCAGCCCACCCTCCCAAGTAGCTAGAGCTATAGGTGCATGCCACCATACCAGCTAGCTACGTATTGTTTAATTGGGATCTATGGATTCTGTTTTCCATAGGAACAACTCTCTGAATTTTATAAATGAGATCGGTGGGGAAGAATGAGATTTTCTTTATAGGGTTTTTTTTTTTTAAGCTATCTTTGCTGTAATGTACCAAATCTAAGGGAGGATTACAAGTTATGTTACAGGTTTTTGGACTGAAAATCTTCTAAAGATAATAAGTCACCAGCCATGAAGACTTTATTCCTTCCCAAATCAGTATTCAACTTCAGACGAATTTTCTAGTCATCAAAGAAAGAGTGGACTTGCTGTGTTTCTGATTAATTTTCAGTGGCTTTCTTGTTAGAAAAACTAGCTTCTATTTCTGACTGTATCACTGAGCCACCGTGTGACCTTAAGTATGTTAAAACGCTTTGGGATATCTTGGTTTCACATTCTGTAAAGTGGAGATAAAACATATTGCATACATCTTTCAGAAACAACATGAGGATTAATGAGATAATGTTATTAGGCATATTAAAGTCACTCAACTTTTTTCATACTTAGATTTCTAAATCATTTCCTAATACTAAAATAGGGTCAGGTATTAAAATAGAAAGCAAACGACTATGGAGGATTAAGATTATAGTGAGCTGTCATAGTTATTTCCCAAAAAGAATGAACAGATGACAAATAGGATTATGAAGCTTCTATATATAAATCCTATATATAAATCTTTCATTTTACTTTAATTCTATGTTTCACTAATACTTTGGAAGAGAGAATCTTTTAGAGTTCAAGGAATCTTGATCCATATGCCAGGCTGTCTGCTTAATTTAAAAATTACCGAAAGGAACTAAAACCTTACATTGTCAATAATAATTTGCTTTACTGGGTAATGAGGGTGTTATCCCTAAGCAAGCATTCAGCCCAGAGCCCAGCCGCTGGTAGAGTGTTATCTCTGGGACAACTCAGTCCTTGCTGGAGGAAACCCATGAACCAAAATTCAGAGGGGCTATCCATCACTGCTGGCCCATCCATCATGCTGTTGCTCCACCTTGAACAGGGAATTTGCCTGCCATGAATTTCATCATTGGCTGTATTTCCTAAGTCGAGGCTGGTAATCAGACAGGGTCACCCTGCAATCCCTTCTGGTGAGTGAGGCATCACGCGGCTGCATTTCTCTTCTGGATTGATGGCATTTCCCAGCATCTGGAGGTTTTAAAGGTATGAAAAGCAGCTTAGAAAAGGCCAAGGGAGCAGCTCTGCTAGCACATACGTGGACACAAACAATAGGAATTGGAGATTGGGTGGGAGGAGAGGGGCTGGAGGGTGGAAAAAAGAGGGAAGAGGAAAAGCAGAAAATAAAAAGAAAAAATATAAGTCAGGTGGGAGGAAGGAGATCACAGAATTCTACATAAAAGTAGGGATAAAGGCCAGGCACGGTGGCTTGTGCCTGTAATCTCAGCACTCTGGGGCCAAGGGGGGGATCACGAGGTCAGGAGATCGAGATTATTCTGGCCAACGTGGTGAAACCCTGTCTCTACTAAAAATACAAAAATTAGCCTGGTGGCAGTGGCACGTGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAAGCAGAGGTTGCAGTGAGCCGAGATCACGCCACTGCACTCCAGCCTGGGCAACAGAGCAAGACTCTGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTGGGGATAAAAGGAAAACAGCACAGATGGTGTGATAAACCAGAAAGTTACAGAAAGTTACTTACGTTTATATTTACTGAGATGATAGGTTTGGGAGGTGGCAAGTCGACCTGTACCTATTTTCTCAAGAGTGTTTCATTTTCAAGCTGTTTACTTATATGCACCCCATTGGAGCCTTTCCATAAGATAGGCCAATATTATCCCTTTTTCATATGTTAAAATAAAAGAGGCCGGGCGCGATGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGATACGGGCGGATCA . . ID=chr21-17730248-INS-3975;VARTYPE=SV;SVTYPE=INS;SVLEN=3975;SAMPLE=HG00731;TIG_REGION=cluster2_000000F:10144400-10148374;QUERY_STRAND=-;AC=2;AN=2;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=32.0._ GT 1|1 -chr21 17903116 chr21-17903117-INS-98 A AAAAATAAATAGAACAGTCATGGTTTTTTAGTTTTAAGAAATACATTGTGCAAGTTTTTTTTTTTTTTCCTCCACATAAACTTGAAGTAATGTTGCTAT . . ID=chr21-17903117-INS-98;VARTYPE=SV;SVTYPE=INS;SVLEN=98;SAMPLE=HG00731;TIG_REGION=cluster2_000000F:9967512-9967609;QUERY_STRAND=-;AC=1;AN=2;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=33.0._ GT 0|1 -chr21 18144979 chr21-18144980-INS-3404 A ATGACTAATTTCAATTTTTTTTTTTTTTTTTTATTATACTCTAAGTTTTAGGGTACATGTGCACATTGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCACTGCACCCACTAATGTGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCCCCTCCCCCGACCCCACCACAGTCCCCAGAGTGTGATATTCCCCTTCCTGTGTCCATGTGATCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGTGTTTGGTTTTTTGTTCTTGCGATAGTTTACTGAGAATGATGGTTTCCAATTTCATCCATGTCCCTACAAAGGATATGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATTGTTGGGCATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAGTGCCGCAATAAACATACGTGTGCATGTGTCTTTATAGCAGCATGATTTATACTCATTTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCGCATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATTGCCATTCTAACTGGTGTGAGATGATATCTCATAGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTCTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCAGATGAGTAGGTTGCAAAAATTTTCTCCCATGTTGTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAATTTTGTCTTTTGTTGCCATTGCTTTTGGTGTTTTGGACATGAAGTCCTTGCCCACGCCTATGTCCTGAATGGTAATGCCTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTTTAACGTTTAAATCTTTAATCCATCTTGAATTGATTTTTGTATAAGGTGTAAGGAAGGGATCCAGTTTCAGCTTTCTACATATGGCTAGCCAGTTTTCCCAGCACCATTTATTAAATAGGGAATCCTTTCCCCATTGCTTGTTTTTCTCAGGTTTGTCAAAGATCAGATAGTTGTAGATATGCGGCATTATTTCTGAGGGCTCTGTTCTGTTCCATTGATCTATATCTCTGTTTTGGTACCAGTACCATGCTGTTTTGGTTACTGTAGCCTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTCCAGCTTTGTTCTTTTGGCTTAGGATTGACTTGGCAATGCGGGCTCTTTTTTGGTTCCATATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGTCATTGGTAGCTTGATGGGGATGGCATTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACGATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTCCATTTGTTTGTCTCCTCTTTTATTTCCTTGAGCAGTGGTTTGTAGTTCTCCTTGAAGAGGTCCTTCACATCCCTTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAATTGTGAATGGGAGTTCACCCATGATTTGGCTCTCTGTTTGTCTGTTGTTGGTGTATAAGAATGCTTGTGATTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGGAGATTTTGGGCTGAGACGATGGGGTTTTCTAGATAAACAATCATGTCGTCTGCAAACAGGGACAATTTGACTTCCTCTTTTCCTAATTGAATACCCTTTATTTCCTTCTCCTGCCTGATTGCCCTGGCCAGAACTTCCAACACTATGTTGAATAGGAGTGGTGAGAGAGGGCATCCCTGTCTTGTGCCGGTTTTCAAAGGGAATGCTTCCAGTTTTTGCCCATTCAGTATGATATTGGCTGTGGGTTTGTCATAGATAGCTCTTATTATTTTGAAATACGTCCCATCAATACCTAATTTATTGAGAGTTTTTAGCATGAAGGGTTGTTGAATTTTGTCAAAGGCTTTTTCTGCATCTATTGAGATAATCATGTGGTTTTTGTCTTTGGCTCTGTTTATATGCTGGATTACATTTATTGATTTGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGCCCACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATTCGGTTTGCCAGTATTTTATTGAGGATTTTTGCATCAATGTTCATCAAGGATATTGGTCTAAAATTCTCTTTTTTGGTTGTGTCTCTGCCCGGCTTTGGTATCAGTATGATGCTGGCCTCATAAAATGAGTTAGGGAGGATTCCCTCTTTTTCTATTGATTGGAATAGTTTCAGAAGGAATGGTACCAGTTCCTCCTTGTACCTCTGGTAGAATTCGGCTGTGAATCCATCTGGTCCTGGACTCTTTTTGGTTGGTAAACTATTGATTATTGCCACAATTTCAGAGCCTGTTATTGGTCGATTCAGAGATTCAACTTCTTCCTGGTTTAGTCTTGGGAGAGTGTATGTGTCGAGGAATGTATCCATTTCTTCTAGATTTTCTAGTTTATTTGCATAGAGGTGTTTGTAGTATTCTCTGATGGTAGTTTGTATTTCTGTGGGATCGGTGGTGATATCCCCTTTATCATTTTTTATTGTGTCTATTTGATTCTTCTCTCTTTTTTTCTTTATTAGTCTTGCTAGCGGTCTATCAATTTTGTTGATCCTTTCAAAAAACCAGCTCCTGGATTCATTGATTTTTTGAAGGGTTTTTTGTGTCTCTATTTCCTTCAGTTCTGCTCTGATTTTAGTTATTTCTTGCCTTCTGCTAGCTTTTGAATGTGTTTGCTCTTGCTTTTCTAGTTCTTTTAATTGTGATGTTAGGGTGTCAATTTTGGATCTTTCCTGCTTTCTCTTGTAGGCATTTAGTGCTATAAATTTCCCTCTACACACTGCTTTGAGTGCGTCCCAGAGATTCTGGTATGTGGTGTCTTTGTTCTCGTTGGTTTCAAAGAACATCTTTATTTCTGCCTTCATTTCGTTATGTACCCAGTAGTCATTCAGGAGCAGGTTGTTCAGTTTCCATGTAGTTGAGCGGCTTTGAGTGAGATTCTTAATCCTGAGTTCTAGTTTGATTGCACTGTGGTCTGAGAGATAGTTTGTTATAATTTC . . ID=chr21-18144980-INS-3404;VARTYPE=SV;SVTYPE=INS;SVLEN=3404;SAMPLE=HG00731;TIG_REGION=cluster2_000000F:9728077-9731480;QUERY_STRAND=-;AC=2;AN=2;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=34.0._ GT 1|1 -chr21 18587126 chr21-18587127-DEL-50 CGTTACCTGCATCAGTGACTGATCAGAATGGGGTAAGGCACGCCATTCCCT C . . ID=chr21-18587127-DEL-50;VARTYPE=SV;SVTYPE=DEL;SVLEN=-50;SAMPLE=HG00732;TIG_REGION=cluster1_000000F:4002436-4002436;QUERY_STRAND=+;REF_TRF;AC=1;AN=2;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=40.0._ GT 1|0 -chr21 18859199 chr21-18859200-DEL-70 TTCTATATATATATATATATATATATATGTATATATATATATATATATATATATATATATGTATATATATA T . . ID=chr21-18859200-DEL-70;VARTYPE=SV;SVTYPE=DEL;SVLEN=-70;SAMPLE=HG00512;TIG_REGION=cluster23_000000F:27856470-27856470;QUERY_STRAND=-;REF_TRF;AC=1;AN=2;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=42.0._ GT 1|0 diff --git a/repo_utils/test_files/answer_key/bench_unroll/fp.vcf b/repo_utils/test_files/answer_key/bench_unroll/fp.vcf deleted file mode 100644 index 2abbbe4e..00000000 --- a/repo_utils/test_files/answer_key/bench_unroll/fp.vcf +++ /dev/null @@ -1,42 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##source=cuteSV-1.0.13 -##fileDate=2022-08-21 18:02:57 0-CST -##reference=ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC2/technical/reference/20200513_hg38_NoALT/hg38.no_alt.fa.gz -##contig= -##ALT= -##ALT= -##ALT= -##ALT= -##ALT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FILTER= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##CommandLine="cuteSV --max_cluster_bias_INS 100 --diff_ratio_merging_INS 0.3 --max_cluster_bias_DEL 100 --diff_ratio_merging_DEL 0.3 lra.chr21.14-19_wr.bam chr21.fa lra.chr21.14-19_wr.vcf ./workdir_lra" -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NULL -chr21 20288212 cuteSV.INS.9 A AATTATATATTATATATAAAATATATTATATATATTATATAATATATATAAAATATATTATATATATTATATAATATATATAAAATATATTATATTATATATTATATAATATATATAAAATATATTTATTATATATTATATAATATATATATAAATATATTATATTATATATTATATAATATATATATAATATATTATATTATTATATAATATATATAAAATATATTATATTATATATTATATTATATAT . PASS PRECISE;SVTYPE=INS;SVLEN=249;CIPOS=-21,21;CILEN=-13,13;RE=12;RNAMES=NULL;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=45._.0 GT:DR:DV:PL:GQ ./.:.:12:.,.,.:. diff --git a/repo_utils/test_files/answer_key/bench_unroll/log.txt b/repo_utils/test_files/answer_key/bench_unroll/log.txt deleted file mode 100644 index 6d05142d..00000000 --- a/repo_utils/test_files/answer_key/bench_unroll/log.txt +++ /dev/null @@ -1,62 +0,0 @@ -2022-08-28 06:10:22,809 [INFO] Running /data/truvari/__main__.py bench -b repo_utils/test_files/real_small_base.vcf.gz -c repo_utils/test_files/real_small_comp.vcf.gz -o test_results/bench_unroll/ -2022-08-28 06:10:22,810 [INFO] Params: -{ - "base": "repo_utils/test_files/real_small_base.vcf.gz", - "comp": "repo_utils/test_files/real_small_comp.vcf.gz", - "output": "test_results/bench_unroll/", - "reference": null, - "giabreport": false, - "debug": false, - "prog": false, - "refdist": 500, - "pctsim": 0.7, - "minhaplen": 50, - "pctsize": 0.7, - "pctovl": 0.0, - "typeignore": false, - "dup_to_ins": false, - "use_lev": false, - "chunksize": 1000, - "gtcomp": false, - "bSample": null, - "cSample": null, - "sizemin": 50, - "sizefilt": 30, - "sizemax": 50000, - "passonly": false, - "no_ref": false, - "includebed": null, - "extend": 0, - "multimatch": false -} -2022-08-28 06:10:22,811 [INFO] Truvari version: 4.0.0-dev -2022-08-28 06:10:22,853 [INFO] Zipped 71 variants Counter({'base': 43, 'comp': 28}) -2022-08-28 06:10:22,853 [INFO] 45 chunks of 71 variants Counter({'base': 43, 'comp': 28}) -2022-08-28 06:10:22,879 [INFO] Stats: { - "TP-base": 18, - "TP-call": 18, - "FP": 1, - "FN": 25, - "precision": 0.9473684210526315, - "recall": 0.4186046511627907, - "f1": 0.5806451612903226, - "base cnt": 43, - "call cnt": 19, - "TP-call_TP-gt": 0, - "TP-call_FP-gt": 18, - "TP-base_TP-gt": 0, - "TP-base_FP-gt": 18, - "gt_concordance": 0.0, - "gt_matrix": { - "(0, 1)": { - "(None, None)": 9 - }, - "(1, 0)": { - "(None, None)": 3 - }, - "(1, 1)": { - "(None, None)": 6 - } - } -} -2022-08-28 06:10:22,884 [INFO] Finished bench diff --git a/repo_utils/test_files/answer_key/bench_unroll/summary.txt b/repo_utils/test_files/answer_key/bench_unroll/summary.txt deleted file mode 100644 index dae6c003..00000000 --- a/repo_utils/test_files/answer_key/bench_unroll/summary.txt +++ /dev/null @@ -1,27 +0,0 @@ -{ - "TP-base": 18, - "TP-call": 18, - "FP": 1, - "FN": 25, - "precision": 0.9473684210526315, - "recall": 0.4186046511627907, - "f1": 0.5806451612903226, - "base cnt": 43, - "call cnt": 19, - "TP-call_TP-gt": 0, - "TP-call_FP-gt": 18, - "TP-base_TP-gt": 0, - "TP-base_FP-gt": 18, - "gt_concordance": 0.0, - "gt_matrix": { - "(0, 1)": { - "(None, None)": 9 - }, - "(1, 0)": { - "(None, None)": 3 - }, - "(1, 1)": { - "(None, None)": 6 - } - } -} \ No newline at end of file diff --git a/repo_utils/test_files/answer_key/bench_unroll/tp-base.vcf b/repo_utils/test_files/answer_key/bench_unroll/tp-base.vcf deleted file mode 100644 index 2cb058ed..00000000 --- a/repo_utils/test_files/answer_key/bench_unroll/tp-base.vcf +++ /dev/null @@ -1,52 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##fileDate=20201127 -##source=PAV (HGSVC2) -##reference=ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC2/technical/reference/20200513_hg38_NoALT/hg38.no_alt.fa.gz -##contig= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##INFO= -##INFO= -##bcftools_viewVersion=1.8+htslib-1.8 -##bcftools_viewCommand=view -s NA12878 variants_freeze4_sv_insdel_alt.vcf.gz; Date=Wed Aug 3 14:45:56 2022 -##bcftools_viewCommand=view -i 'INFO/AC >=1' -O z -o GM12878_variants_freeze4_sv_insdel_alt.vcf.gz; Date=Wed Aug 3 14:45:56 2022 -##bcftools_viewCommand=view -r chr21 GM12878_variants_freeze4_sv_insdel_alt.vcf.gz; Date=Thu Aug 11 15:17:10 2022 -##bcftools_viewCommand=view -r chr21:14000000-19000000 GM12878.chr21.true.vcf.gz; Date=Sun Aug 21 18:37:08 2022 -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 -chr21 14088108 chr21-14088109-INS-132 A ATATATAATTATATATAATATATTTATATATATTATATAAATATATAATATATTTTTATATATTATATATAATTATATATAATATATAAATATATTATATATATAAATATATATATAATATATTTTTATATAT . . ID=chr21-14088109-INS-132;VARTYPE=SV;SVTYPE=INS;SVLEN=132;SAMPLE=HG00731;TIG_REGION=cluster2_000001F:13799958-13800089;QUERY_STRAND=-;REF_SD=0.92;REF_TRF;AC=1;AN=2;PctSeqSimilarity=0.8348;PctSizeSimilarity=0.7273;PctRecOverlap=0;SizeDiff=36;StartDistance=-157;EndDistance=-157;TruScore=52;MatchId=1.0.0 GT 0|1 -chr21 14161792 chr21-14161793-DEL-97 TTATTATATATTAATGTATAATATATACAAATATATATTAATATATAATATATACATTATTATATATAATTACATATAATATAACATATATTATATTA T . . ID=chr21-14161793-DEL-97;VARTYPE=SV;SVTYPE=DEL;SVLEN=-97;SAMPLE=HG00731;TIG_REGION=cluster2_000001F:13726108-13726108;QUERY_STRAND=-;REF_TRF;AC=1;AN=2;PctSeqSimilarity=0.8863;PctSizeSimilarity=0.8661;PctRecOverlap=0;SizeDiff=-15;StartDistance=122;EndDistance=107;TruScore=58;MatchId=2.0.0 GT 0|1 -chr21 14261798 chr21-14261799-INS-78 A AGTTCAGAAATAGACACAATGGATTATGATAATTTAGAATATAAAGAAGTACACATTGAATATTGGTGAGCTGAAGAAG . . ID=chr21-14261799-INS-78;VARTYPE=SV;SVTYPE=INS;SVLEN=78;SAMPLE=HG00732;TIG_REGION=cluster1_000002F:4395817-4395894;QUERY_STRAND=-;REF_TRF;AC=1;AN=2;PctSeqSimilarity=0.7244;PctSizeSimilarity=0.9744;PctRecOverlap=0.7215;SizeDiff=2;StartDistance=21;EndDistance=21;TruScore=80;MatchId=4.0.0 GT 1|0 -chr21 14475149 chr21-14475150-DEL-65 CATTTAATTATTAATTAAATAATTTAATTTATTTATTATTATAAATTTATTAATATAAATTAAATA C . . ID=chr21-14475150-DEL-65;VARTYPE=SV;SVTYPE=DEL;SVLEN=-65;SAMPLE=HG00731;TIG_REGION=cluster2_000001F:13400230-13400230;QUERY_STRAND=-;REF_TRF;AC=1;AN=2;PctSeqSimilarity=0.9302;PctSizeSimilarity=0.9538;PctRecOverlap=0.8788;SizeDiff=3;StartDistance=-8;EndDistance=-5;TruScore=92;MatchId=6.0.0 GT 0|1 -chr21 14902961 chr21-14902962-DEL-79 TTGCAGTGAGCCGAGATCGTGCCACTGCACGCCAGCCTGGGGACAGAGCAAGACGCTGTTTCAAAAAAAAAAAATAATAA T . . ID=chr21-14902962-DEL-79;VARTYPE=SV;SVTYPE=DEL;SVLEN=-79;SAMPLE=HG00731;TIG_REGION=cluster2_000000F:12976402-12976402;QUERY_STRAND=-;AC=1;AN=2;PctSeqSimilarity=0.9873;PctSizeSimilarity=0.9747;PctRecOverlap=0.975;SizeDiff=2;StartDistance=-2;EndDistance=0;TruScore=97;MatchId=10.0.0 GT 0|1 -chr21 16359641 chr21-16359642-DEL-139 GTATATTATATATAATATTTATATATTATATATATTTATGTATATTATATATAATATTTATATATTATATATATTTATGTATATTATATATAATATTTATATATTATATGTATTTATGTATATTATATATAATATTTATA G . . ID=chr21-16359642-DEL-139;VARTYPE=SV;SVTYPE=DEL;SVLEN=-139;SAMPLE=HG00731;TIG_REGION=cluster2_000000F:11519424-11519424;QUERY_STRAND=-;REF_TRF;AC=2;AN=2;PctSeqSimilarity=0.9647;PctSizeSimilarity=0.9789;PctRecOverlap=0.9161;SizeDiff=-3;StartDistance=-9;EndDistance=-12;TruScore=95;MatchId=15.0.0 GT 1|1 -chr21 16564734 chr21-16564735-INS-72 T TTGCTGTGTCGAAATCAAGCCAGTCAGGAAACTCATCCCACCCTTGATAACCAGAAGCAGTAATTCAGCAAAG . . ID=chr21-16564735-INS-72;VARTYPE=SV;SVTYPE=INS;SVLEN=72;SAMPLE=HG00731;TIG_REGION=cluster2_000000F:11314483-11314554;QUERY_STRAND=-;AC=2;AN=2;PctSeqSimilarity=0.9103;PctSizeSimilarity=0.9861;PctRecOverlap=0.9726;SizeDiff=1;StartDistance=0;EndDistance=0;TruScore=95;MatchId=16.0.0 GT 1|1 -chr21 16747500 chr21-16747501-INS-54 A ATATGTATATATATACATATACACTGTATATATGTATATATATACATATACAGTG . . ID=chr21-16747501-INS-54;VARTYPE=SV;SVTYPE=INS;SVLEN=54;SAMPLE=HG00731;TIG_REGION=cluster2_000000F:11132329-11132382;QUERY_STRAND=-;REF_TRF;AC=2;AN=2;PctSeqSimilarity=0.8571;PctSizeSimilarity=0.9643;PctRecOverlap=0.7544;SizeDiff=-2;StartDistance=-13;EndDistance=-13;TruScore=85;MatchId=18.0.0 GT 1|1 -chr21 16972886 chr21-16972887-INS-144 T TTATATATAATATATTATATATTACTATATATAATATATTATATATTACTATATATAATATATTATATATTACTATATATAATATATTATATATTACTATATATAATATATTATATATTACTATATATAATATATTATATATTAC . . ID=chr21-16972887-INS-144;VARTYPE=SV;SVTYPE=INS;SVLEN=144;SAMPLE=HG00731;TIG_REGION=cluster2_000000F:10906730-10906873;QUERY_STRAND=-;REF_TRF;AC=2;AN=2;PctSeqSimilarity=0.9149;PctSizeSimilarity=0.9444;PctRecOverlap=0.7862;SizeDiff=8;StartDistance=-27;EndDistance=-27;TruScore=88;MatchId=20.1.0 GT 1|1 -chr21 17069140 chr21-17069141-DEL-56 GTATATATATATATATATACACATATATATGTGTGTATATATATATACATATATATA G . . ID=chr21-17069141-DEL-56;VARTYPE=SV;SVTYPE=DEL;SVLEN=-56;SAMPLE=HG00731;TIG_REGION=cluster2_000000F:10810373-10810373;QUERY_STRAND=-;REF_TRF;AC=1;AN=2;PctSeqSimilarity=0.9735;PctSizeSimilarity=0.9821;PctRecOverlap=0.8246;SizeDiff=1;StartDistance=-10;EndDistance=-9;TruScore=92;MatchId=21.0.0 GT 0|1 -chr21 17085169 chr21-17085170-DEL-52 CATATATATATATATATATATATATATATATATATATATATATATATATATAT C . . ID=chr21-17085170-DEL-52;VARTYPE=SV;SVTYPE=DEL;SVLEN=-52;SAMPLE=HG00731;TIG_REGION=cluster2_000000F:10794400-10794400;QUERY_STRAND=-;REF_TRF;AC=2;AN=2;PctSeqSimilarity=0.913;PctSizeSimilarity=0.8525;PctRecOverlap=0.7581;SizeDiff=-9;StartDistance=-6;EndDistance=-15;TruScore=84;MatchId=22.0.0 GT 1|1 -chr21 17453487 chr21-17453488-DEL-62 ATTTTTTTGCTAAAAGAATCATCAATGGCTCTTGAATTTTTTTTTTTTTTTTTTTTTTTTTTT A . . ID=chr21-17453488-DEL-62;VARTYPE=SV;SVTYPE=DEL;SVLEN=-62;SAMPLE=HG00732;TIG_REGION=cluster1_000002F:1189547-1189547;QUERY_STRAND=-;REF_TRF;AC=1;AN=2;PctSeqSimilarity=0.9453;PctSizeSimilarity=0.9688;PctRecOverlap=0.8923;SizeDiff=-2;StartDistance=-5;EndDistance=-7;TruScore=93;MatchId=27.0.0 GT 0|1 -chr21 17682679 chr21-17682680-DEL-78 CAGCTGGCAGCCCTCCAAGAGGGAGAGAAGAGGAGGCCTGGCTAGAAAAGTTGGTCTTGTTATGTAGGTGAAAATTCAT C . . ID=chr21-17682680-DEL-78;VARTYPE=SV;SVTYPE=DEL;SVLEN=-78;SAMPLE=NA19239;TIG_REGION=cluster8_000001F:10232994-10232994;QUERY_STRAND=-;REF_TRF;AC=1;AN=2;PctSeqSimilarity=0.9419;PctSizeSimilarity=0.9615;PctRecOverlap=0.7722;SizeDiff=3;StartDistance=-18;EndDistance=-15;TruScore=89;MatchId=29.0.0 GT 0|1 -chr21 18174133 chr21-18174134-INS-96 A ATATATATATATATATATATATATCTTGGTATATATATATATATATCTTGGTATATATATATATATCTTGGTATATATATATATATATATATCTTGG . . ID=chr21-18174134-INS-96;VARTYPE=SV;SVTYPE=INS;SVLEN=96;SAMPLE=HG00512;TIG_REGION=cluster23_000000F:28541340-28541435;QUERY_STRAND=-;REF_TRF;AC=1;AN=2;PctSeqSimilarity=0.9194;PctSizeSimilarity=0.9167;PctRecOverlap=0.7835;SizeDiff=8;StartDistance=17;EndDistance=17;TruScore=87;MatchId=35.0.0 GT 1|0 -chr21 18251498 chr21-18251499-INS-448 A ATATTTATTTTAATATATAAAATAAATATTTATTTTAATATATAAAATAAATATTTATTTTAATATATAAAATAAATATTTATTTAATATATAAAATAAATATTTATTTTAATATTAAAATAAATATTTATTTTATATATAAAATAAATATTTATTTAATATATAAAATAAATATTTATTTTAATATATAAAATAAATATTTATTTTAATATATAAAATATTTATTTTAATATATAAAATATTTATTTTAATATATAAAATATTTATTTTAATATATAAAATAAATATTTATTTTAATATATAAAATAAATATTTATTTTAATATATAAAATAAATATTTATTTTAATATATAAAATAAATATTTATTTTAATATATAAAATAAATATTTATTTTAATATATAAAATAAATATTTATTTTATTTATTTTAATATATAAAATATTTTATT . . ID=chr21-18251499-INS-448;VARTYPE=SV;SVTYPE=INS;SVLEN=448;SAMPLE=HG00731;TIG_REGION=cluster2_000000F:9618190-9618637;QUERY_STRAND=-;REF_TRF;AC=2;AN=2;PctSeqSimilarity=0.9383;PctSizeSimilarity=0.9451;PctRecOverlap=0.9453;SizeDiff=-26;StartDistance=-4;EndDistance=-4;TruScore=94;MatchId=36.0.0 GT 1|1 -chr21 18315405 chr21-18315406-DEL-175 ATGGGTGCAGCACACCAACATGGCACATGTATACACAATAACAAACCTGCACGTTGTGCACATGTACCGTAGAACTTAAAGTATAATAAAATATATATATATAAAATAATAAACATGAGTCCTTTGCCACAGCTCAAGGTGGAGCTAGCTTTGATACTGAGTAAATGACGAGTTAG A . . ID=chr21-18315406-DEL-175;VARTYPE=SV;SVTYPE=DEL;SVLEN=-175;SAMPLE=HG00731;TIG_REGION=cluster2_000001F:9555439-9555439;QUERY_STRAND=-;REF_TRF;AC=1;AN=2;PctSeqSimilarity=0.9771;PctSizeSimilarity=0.9886;PctRecOverlap=0.6193;SizeDiff=2;StartDistance=-67;EndDistance=-65;TruScore=86;MatchId=37.0.0 GT 0|1 -chr21 18541734 chr21-18541735-DEL-341 ATTTTTGCATTGTTTTTGATCAATTCTTATCTTCTTTTATTTAATTTTAAAAACCAAATGGCAGATATTTTGTATGAAAAACTATTAATATAGATTTATTCCCTAAATAGTAATATTTTATTCCACAACTTGTTGTTTTGTTTGAGTCTACCATTTAGTTGGAGGGTATATCACCAGATTTTAATCTTGCCTTTACTTCTTGTATTTATTGATCTATACCCAGTTCAGCTGGCCCCTAGGGTTCATACCGTCATGCACAATTGAAAGTATATGTTAATTACCAGAGACCATCATCCTTGGTGGATCCTTACCTTCAGTTTTTATTTGTCAAGCACTATAAAC A . . ID=chr21-18541735-DEL-341;VARTYPE=SV;SVTYPE=DEL;SVLEN=-341;SAMPLE=HG00512;TIG_REGION=cluster23_000000F:28173468-28173468;QUERY_STRAND=-;AC=1;AN=2;PctSeqSimilarity=0.9971;PctSizeSimilarity=0.9971;PctRecOverlap=0.9912;SizeDiff=1;StartDistance=2;EndDistance=3;TruScore=99;MatchId=39.0.0 GT 0|1 -chr21 18674563 chr21-18674564-INS-364 T TATATATATTCTAGGAATATATATATGTATATATATATACATATATATATTCTAGGAATATATATATGTATATATATATACATATATATATTCTAGGAATATATATATGTATATATATATACATATATATATTCTAGGAATATATATATGTATATATATATACATATATATATTCTAGGAATATATATATGTATATATATATACATATATATATTCTAGGAATATATATATGTATATATATACATACACATATATATTCTAGGAATATATATATACACATATATATTCTAGGAATATATATATACACATATATATTCTAGGAATATATATATACACATATATATTCTAGGAATATATATATATAC . . ID=chr21-18674564-INS-364;VARTYPE=SV;SVTYPE=INS;SVLEN=364;SAMPLE=HG00732;TIG_REGION=cluster1_000000F:4089824-4090187;QUERY_STRAND=+;REF_TRF;AC=1;AN=2;PctSeqSimilarity=0.9354;PctSizeSimilarity=0.9093;PctRecOverlap=0.7644;SizeDiff=33;StartDistance=-69;EndDistance=-69;TruScore=86;MatchId=41.0.0 GT 1|0 diff --git a/repo_utils/test_files/answer_key/bench_unroll/tp-call.vcf b/repo_utils/test_files/answer_key/bench_unroll/tp-call.vcf deleted file mode 100644 index 84aa7d79..00000000 --- a/repo_utils/test_files/answer_key/bench_unroll/tp-call.vcf +++ /dev/null @@ -1,59 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##source=cuteSV-1.0.13 -##fileDate=2022-08-21 18:02:57 0-CST -##reference=ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC2/technical/reference/20200513_hg38_NoALT/hg38.no_alt.fa.gz -##contig= -##ALT= -##ALT= -##ALT= -##ALT= -##ALT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FILTER= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##CommandLine="cuteSV --max_cluster_bias_INS 100 --diff_ratio_merging_INS 0.3 --max_cluster_bias_DEL 100 --diff_ratio_merging_DEL 0.3 lra.chr21.14-19_wr.bam chr21.fa lra.chr21.14-19_wr.vcf ./workdir_lra" -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NULL -chr21 14088265 cuteSV.INS.0 A AAATATATAAATATATTATATATAATTATATATAATATATAAATATAGTATATATATAAATATATAATATATTTTATATTATATAATTATATATAAT . PASS PRECISE;SVTYPE=INS;SVLEN=96;CIPOS=-19,19;CILEN=-15,15;RE=8;RNAMES=NULL;PctSeqSimilarity=0.8348;PctSizeSimilarity=0.7273;PctRecOverlap=0;SizeDiff=36;StartDistance=-157;EndDistance=-157;TruScore=52;MatchId=1.0.0 GT:DR:DV:PL:GQ ./.:.:8:.,.,.:. -chr21 14161670 cuteSV.DEL.0 TATACATTATTATATATTAATGTATAATATATACATTATTATATATTAATATATAATATATACATTATTATATATTAATATATAATATATACATTATTATATATTAATATATA T . PASS PRECISE;SVTYPE=DEL;SVLEN=-112;CIPOS=-18,18;CILEN=-3,3;RE=15;RNAMES=NULL;STRAND=+-;PctSeqSimilarity=0.8863;PctSizeSimilarity=0.8661;PctRecOverlap=0;SizeDiff=-15;StartDistance=122;EndDistance=107;TruScore=58;MatchId=2.0.0 GT:DR:DV:PL:GQ ./.:.:15:.,.,.:. -chr21 14261777 cuteSV.INS.1 G GTCAGAAATAGACACAATGGATTATGATAATTTAGAATATAAAAGTACACATTGAATATTAATTGAGCTGAAGAAAG . PASS PRECISE;SVTYPE=INS;SVLEN=76;CIPOS=-27,27;CILEN=-1,1;RE=14;RNAMES=NULL;PctSeqSimilarity=0.7244;PctSizeSimilarity=0.9744;PctRecOverlap=0.7215;SizeDiff=2;StartDistance=21;EndDistance=21;TruScore=80;MatchId=4.0.0 GT:DR:DV:PL:GQ ./.:.:14:.,.,.:. -chr21 14475157 cuteSV.DEL.2 TATTAATTAAATAATTTAATTTATTTATTATTATAAATTTATTAATATAAATTAAATAATAAT T . PASS PRECISE;SVTYPE=DEL;SVLEN=-62;CIPOS=-6,6;CILEN=-4,4;RE=11;RNAMES=NULL;STRAND=+-;PctSeqSimilarity=0.9302;PctSizeSimilarity=0.9538;PctRecOverlap=0.8788;SizeDiff=3;StartDistance=-8;EndDistance=-5;TruScore=92;MatchId=6.0.0 GT:DR:DV:PL:GQ ./.:.:11:.,.,.:. -chr21 14902963 cuteSV.DEL.5 GCAGTGAGCCGAGATCGTGCCACTGCACGCCAGCCTGGGGACAGAGCAAGACGCTGTTTCAAAAAAAAAAAATAATAA G . PASS PRECISE;SVTYPE=DEL;SVLEN=-77;CIPOS=-2,2;CILEN=-2,2;RE=12;RNAMES=NULL;STRAND=+-;PctSeqSimilarity=0.9873;PctSizeSimilarity=0.9747;PctRecOverlap=0.975;SizeDiff=2;StartDistance=-2;EndDistance=0;TruScore=97;MatchId=10.0.0 GT:DR:DV:PL:GQ ./.:.:12:.,.,.:. -chr21 16359650 cuteSV.DEL.6 ATATAATATTTATATATTATATATATTTATGTATATTATATATAATATTTATATATTATATATATTTATGTATATTATATATAATATTTATATATTATATGTATTTATGTATATTATATATAATATTTATATATTATATGTAT A . PASS PRECISE;SVTYPE=DEL;SVLEN=-142;CIPOS=-14,14;CILEN=-5,5;RE=22;RNAMES=NULL;STRAND=+-;PctSeqSimilarity=0.9647;PctSizeSimilarity=0.9789;PctRecOverlap=0.9161;SizeDiff=-3;StartDistance=-9;EndDistance=-12;TruScore=95;MatchId=15.0.0 GT:DR:DV:PL:GQ ./.:.:22:.,.,.:. -chr21 16564734 cuteSV.INS.3 T TTTGCTGTGTCGAAATCAAACCAGTCAGGAAACTCATCCCACCATCAAATATACAGAGCAGTAATTCTGTAA . PASS PRECISE;SVTYPE=INS;SVLEN=71;CIPOS=0,0;CILEN=0,0;RE=26;RNAMES=NULL;PctSeqSimilarity=0.9103;PctSizeSimilarity=0.9861;PctRecOverlap=0.9726;SizeDiff=1;StartDistance=0;EndDistance=0;TruScore=95;MatchId=16.0.0 GT:DR:DV:PL:GQ ./.:.:26:.,.,.:. -chr21 16747513 cuteSV.INS.4 T TTGTATATATATACATATACACTGTATATATGTATATATATACATATATTATGTATA . PASS PRECISE;SVTYPE=INS;SVLEN=56;CIPOS=-16,16;CILEN=-1,1;RE=8;RNAMES=NULL;PctSeqSimilarity=0.8571;PctSizeSimilarity=0.9643;PctRecOverlap=0.7544;SizeDiff=-2;StartDistance=-13;EndDistance=-13;TruScore=85;MatchId=18.0.0 GT:DR:DV:PL:GQ ./.:.:8:.,.,.:. -chr21 16972913 cuteSV.INS.5 T TATTATATATTATATATATAAATATATATATTTATATAATATATTTATATATTTATATATATAATATATTATATATATATATAATATATTATATATTATATATATAATATATTATATATTCTATATAATATATTATA . PASS PRECISE;SVTYPE=INS;SVLEN=136;CIPOS=-47,47;CILEN=-16,16;RE=20;RNAMES=NULL;PctSeqSimilarity=0.9149;PctSizeSimilarity=0.9444;PctRecOverlap=0.7862;SizeDiff=8;StartDistance=-27;EndDistance=-27;TruScore=88;MatchId=20.1.0 GT:DR:DV:PL:GQ ./.:.:20:.,.,.:. -chr21 17069150 cuteSV.DEL.8 ATATATATACACATATATATGTGTGTATATATATATACATATATATATATATATAT A . PASS PRECISE;SVTYPE=DEL;SVLEN=-55;CIPOS=-4,4;CILEN=-1,1;RE=14;RNAMES=NULL;STRAND=+-;PctSeqSimilarity=0.9735;PctSizeSimilarity=0.9821;PctRecOverlap=0.8246;SizeDiff=1;StartDistance=-10;EndDistance=-9;TruScore=92;MatchId=21.0.0 GT:DR:DV:PL:GQ ./.:.:14:.,.,.:. -chr21 17085175 cuteSV.DEL.9 TATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATA T . PASS PRECISE;SVTYPE=DEL;SVLEN=-61;CIPOS=-2,2;CILEN=-1,1;RE=23;RNAMES=NULL;STRAND=+-;PctSeqSimilarity=0.913;PctSizeSimilarity=0.8525;PctRecOverlap=0.7581;SizeDiff=-9;StartDistance=-6;EndDistance=-15;TruScore=84;MatchId=22.0.0 GT:DR:DV:PL:GQ ./.:.:23:.,.,.:. -chr21 17453492 cuteSV.DEL.11 TTTGCTAAAAGAATCATCAATGGCTCTTGAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT T . PASS PRECISE;SVTYPE=DEL;SVLEN=-64;CIPOS=-1,1;CILEN=-1,1;RE=12;RNAMES=NULL;STRAND=+-;PctSeqSimilarity=0.9453;PctSizeSimilarity=0.9688;PctRecOverlap=0.8923;SizeDiff=-2;StartDistance=-5;EndDistance=-7;TruScore=93;MatchId=27.0.0 GT:DR:DV:PL:GQ ./.:.:12:.,.,.:. -chr21 17682697 cuteSV.DEL.12 GAGGGAGAGAAGAGGAGGCCTGGCTAGAAAAGTTGGTCTTGTTATGTAGGTGAAAATTCATAGCTGGCAGCCCTCC G . PASS PRECISE;SVTYPE=DEL;SVLEN=-75;CIPOS=-15,15;CILEN=-1,1;RE=11;RNAMES=NULL;STRAND=+-;PctSeqSimilarity=0.9419;PctSizeSimilarity=0.9615;PctRecOverlap=0.7722;SizeDiff=3;StartDistance=-18;EndDistance=-15;TruScore=89;MatchId=29.0.0 GT:DR:DV:PL:GQ ./.:.:11:.,.,.:. -chr21 18174116 cuteSV.INS.6 T TTATATATATATATCTTATATATATATATATATATCTTGGTATATATATATATATCTTGGTATATATATATATATATATATATATATCT . PASS PRECISE;SVTYPE=INS;SVLEN=88;CIPOS=-8,8;CILEN=-7,7;RE=17;RNAMES=NULL;PctSeqSimilarity=0.9194;PctSizeSimilarity=0.9167;PctRecOverlap=0.7835;SizeDiff=8;StartDistance=17;EndDistance=17;TruScore=87;MatchId=35.0.0 GT:DR:DV:PL:GQ ./.:.:17:.,.,.:. -chr21 18251502 cuteSV.INS.7 T TTATTTTAATATATAAAATAAATATTTATTTTAATATATAAAATAAATATTTATTTAATATATAAAATAAATATTTATTTTAATATTAAAATAAATATTTATTTTATATATAAAATAAATATTTATTTAATATATAAAATAAATATTATTTTAATATATAAAATAAATATTTATTTAATATATAAAATATTTATTTTAATATATAAAATAAATATTTATTTTAATATATAAAATAAATATTTATTTTAATATATAAAATAAATATTTATTTTAATATATAAAATAAATATTTATTTTAATATATAAAATAAATATTTATTTAATATATAAAATAAATATTTATTTTAATATATAAAATAAATATTTATTTTAATATATAAAATAAATATTTATTTTAATATATTAAAATAAATATTTATTTTATTTATTTTAATATATAAAATATTTTTATTTATTTATTTTAATATATAAAATA . PASS PRECISE;SVTYPE=INS;SVLEN=474;CIPOS=-6,6;CILEN=-4,4;RE=13;RNAMES=NULL;PctSeqSimilarity=0.9383;PctSizeSimilarity=0.9451;PctRecOverlap=0.9453;SizeDiff=-26;StartDistance=-4;EndDistance=-4;TruScore=94;MatchId=36.0.0 GT:DR:DV:PL:GQ ./.:.:13:.,.,.:. -chr21 18315472 cuteSV.DEL.13 CGTAGAACTTAAAGTATAATAAAATATATATATATAAAATAATAAACATGAGTCCTTTGCCACAGCTCAAGGTGGAGCTAGCTTTGATACTGAGTAAATGACGAGTTAGTGGGTGCAGCACACCAACATGGCACATGTATACACATATAACAAACCTGCACGTTGTGCACATGT C . PASS PRECISE;SVTYPE=DEL;SVLEN=-173;CIPOS=-31,31;CILEN=0,0;RE=18;RNAMES=NULL;STRAND=+-;PctSeqSimilarity=0.9771;PctSizeSimilarity=0.9886;PctRecOverlap=0.6193;SizeDiff=2;StartDistance=-67;EndDistance=-65;TruScore=86;MatchId=37.0.0 GT:DR:DV:PL:GQ ./.:.:18:.,.,.:. -chr21 18541732 cuteSV.DEL.15 AAATTTTTGCATTGTTTTTGATCAATTCTTATCTTCTTTTATTTAATTTTAAAAACCAAATGGCAGATATTTTGTATGAAAAACTATTAATATAGATTTATTCCCTAAATAGTAATATTTTATTCCACAACTTGTTGTTTTGTTTGAGTCTACCATTTAGTTGGAGGGTATATCACCAGATTTTAATCTTGCCTTTACTTCTTGTATTTATTGATCTATACCCAGTTCAGCTGGCCCCTAGGGTTCATACCGTCATGCACAATTGAAAGTATATGTTAATTACCAGAGACCATCATCCTTGGTGGATCCTTACCTTCAGTTTTTATTTGTCAAGCACTATA A . PASS PRECISE;SVTYPE=DEL;SVLEN=-340;CIPOS=-1,1;CILEN=-1,1;RE=16;RNAMES=NULL;STRAND=+-;PctSeqSimilarity=0.9971;PctSizeSimilarity=0.9971;PctRecOverlap=0.9912;SizeDiff=1;StartDistance=2;EndDistance=3;TruScore=99;MatchId=39.0.0 GT:DR:DV:PL:GQ ./.:.:16:.,.,.:. -chr21 18674632 cuteSV.INS.8 T TTATGTATATATATATACATATATATATTCTAGAATATATATATATGTATATATATATATACATATATATATTCTAGAATATATATATGTATATATATATACATATATATATTCTAGGAATATATATATGTATATATATACATACACATATATATTCTAGAATATATATATATACACATATATATTCTAGGAATATATATATACACATATATATTCTAGGAATATATATATACACATATATATTCTAGGAATATATATATATACATATATATTCTAGAATATATATATACACATATATATTCTAGAATATATATATACACATATATAATTTA . PASS PRECISE;SVTYPE=INS;SVLEN=331;CIPOS=-18,18;CILEN=-7,7;RE=22;RNAMES=NULL;PctSeqSimilarity=0.9354;PctSizeSimilarity=0.9093;PctRecOverlap=0.7644;SizeDiff=33;StartDistance=-69;EndDistance=-69;TruScore=86;MatchId=41.0.0 GT:DR:DV:PL:GQ ./.:.:22:.,.,.:. diff --git a/repo_utils/test_files/answer_key/consistency.json b/repo_utils/test_files/answer_key/consistency.json deleted file mode 100644 index 7d667c3e..00000000 --- a/repo_utils/test_files/answer_key/consistency.json +++ /dev/null @@ -1,89 +0,0 @@ -{ - "vcfs": [ - "repo_utils/test_files/input1.vcf.gz", - "repo_utils/test_files/input2.vcf.gz", - "repo_utils/test_files/input3.vcf.gz" - ], - "total_calls": 3513, - "num_vcfs": 3, - "vcf_counts": { - "repo_utils/test_files/input1.vcf.gz": 2151, - "repo_utils/test_files/input2.vcf.gz": 1783, - "repo_utils/test_files/input3.vcf.gz": 2065 - }, - "shared": [ - { - "vcf_count": 3, - "num_calls": 701, - "call_pct": 0.1995445488186735 - }, - { - "vcf_count": 2, - "num_calls": 1084, - "call_pct": 0.3085681753487048 - }, - { - "vcf_count": 1, - "num_calls": 1728, - "call_pct": 0.4918872758326217 - } - ], - "detailed": [ - { - "group": "111", - "total": 701, - "total_pct": 0.1995445488186735, - "0": 0.32589493258949326, - "1": 0.393157599551318, - "2": 0.3394673123486683 - }, - { - "group": "001", - "total": 645, - "total_pct": 0.18360375747224594, - "0": 0, - "1": 0, - "2": 0.31234866828087166 - }, - { - "group": "100", - "total": 598, - "total_pct": 0.17022487902077996, - "0": 0.2780102278010228, - "1": 0, - "2": 0 - }, - { - "group": "101", - "total": 487, - "total_pct": 0.1386279533162539, - "0": 0.22640632264063226, - "1": 0, - "2": 0.2358353510895884 - }, - { - "group": "010", - "total": 485, - "total_pct": 0.13805863933959578, - "0": 0, - "1": 0.27201346045989905, - "2": 0 - }, - { - "group": "110", - "total": 365, - "total_pct": 0.10389980074010817, - "0": 0.1696885169688517, - "1": 0.2047111609646663, - "2": 0 - }, - { - "group": "011", - "total": 232, - "total_pct": 0.06604042129234272, - "0": 0, - "1": 0.13011777902411667, - "2": 0.11234866828087167 - } - ] -} diff --git a/repo_utils/test_files/answer_key/consistency.txt b/repo_utils/test_files/answer_key/consistency.txt deleted file mode 100644 index ad71f80b..00000000 --- a/repo_utils/test_files/answer_key/consistency.txt +++ /dev/null @@ -1,25 +0,0 @@ -# -# Total 3513 calls across 3 VCFs -# -#File NumCalls -repo_utils/test_files/input1.vcf.gz 2151 -repo_utils/test_files/input2.vcf.gz 1783 -repo_utils/test_files/input3.vcf.gz 2065 -# -# Summary of consistency -# -#VCFs Calls Pct -3 701 19.95% -2 1084 30.86% -1 1728 49.19% -# -# Breakdown of VCFs' consistency -# -#Group Total TotalPct PctOfFileCalls -111 701 19.95% 32.59% 39.32% 33.95% -001 645 18.36% 0% 0% 31.23% -100 598 17.02% 27.80% 0% 0% -101 487 13.86% 22.64% 0% 23.58% -010 485 13.81% 0% 27.20% 0% -110 365 10.39% 16.97% 20.47% 0% -011 232 6.60% 0% 13.01% 11.23% diff --git a/repo_utils/test_files/answer_key/divided/multi_00000000.vcf b/repo_utils/test_files/answer_key/divided/multi_00000000.vcf deleted file mode 100644 index ad4034b3..00000000 --- a/repo_utils/test_files/answer_key/divided/multi_00000000.vcf +++ /dev/null @@ -1,157 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##bcftools_mergeVersion=1.12+htslib-1.12 -##bcftools_mergeCommand=merge -O z -f x -m none input1.vcf.gz input2.vcf.gz input3.vcf.gz; Date=Mon Aug 16 18:05:13 2021 -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 63971 . TTCCATTCCAC T 60 . QNAME=cluster19_000000F;QSTART=25698928;QSTRAND=- GT:DP:AD ./.:17:12,5 1|0:42:24,18 ./.:33:14,19 -chr20 64506 . C CTCCAT 60 . QNAME=cluster19_000000F;QSTART=25698398;QSTRAND=- GT:DP:AD ./.:35:13,22 1|0:30:14,16 ./.:21:12,9 -chr20 66141 . AATTCC A 60 . QNAME=cluster23_scaffold_3;QSTART=25645835;QSTRAND=- GT:DP:AD ./.:18:10,8 ./.:43:18,25 1|1:32:16,16 -chr20 66235 . C CGACTCCACTCCATT 60 . QNAME=HG002-S9-H1-000001F;QSTART=45138;QSTRAND=+ GT:DP:AD 1|1:42:20,22 1|1:27:5,22 1|1:33:22,11 -chr20 66369 . C T 60 . QNAME=cluster19_000000F;QSTART=25696521;QSTRAND=- GT:DP:AD ./.:34:21,13 1|0:30:21,9 ./.:41:16,25 -chr20 67373 . G GAAATGTGAT 60 . QNAME=cluster23_scaffold_2;QSTART=25629267;QSTRAND=- GT:DP:AD ./.:38:18,20 ./.:37:20,17 0|1:29:20,9 -chr20 68303 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=47219;QSTRAND=+ GT:DP:AD 1|1:41:18,23 0|1:43:18,25 1|1:29:15,14 -chr20 72450 . G A 60 . QNAME=cluster19_000000F;QSTART=25690440;QSTRAND=- GT:DP:AD ./.:16:6,10 1|0:23:10,13 ./.:33:15,18 -chr20 72765 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=51682;QSTRAND=+ GT:DP:AD 1|1:14:9,5 0|1:33:10,23 1|0:36:18,18 -chr20 72765 . TA T 60 . QNAME=cluster19_000000F;QSTART=25690125;QSTRAND=- GT:DP:AD ./.:39:16,23 1|0:48:24,24 ./.:24:15,9 -chr20 72765 . T TAA 60 . QNAME=cluster23_scaffold_2;QSTART=25623873;QSTRAND=- GT:DP:AD ./.:43:18,25 ./.:15:6,9 0|1:31:13,18 -chr20 72982 . A C 60 . QNAME=cluster19_000000F;QSTART=25689909;QSTRAND=- GT:DP:AD ./.:43:18,25 1|0:32:23,9 ./.:17:6,11 -chr20 73765 . C A 60 . QNAME=cluster19_000000F;QSTART=25689126;QSTRAND=- GT:DP:AD ./.:26:6,20 1|0:22:9,13 ./.:14:8,6 -chr20 75250 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25621388;QSTRAND=- GT:DP:AD ./.:19:8,11 ./.:16:5,11 0|1:18:11,7 -chr20 76709 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25635256;QSTRAND=- GT:DP:AD ./.:27:7,20 ./.:37:25,12 1|0:43:25,18 -chr20 77005 . A G 60 . QNAME=cluster19_000000F;QSTART=25685886;QSTRAND=- GT:DP:AD ./.:27:7,20 1|0:14:6,8 ./.:32:13,19 -chr20 77736 . CA C 60 . QNAME=cluster19_000000F;QSTART=25685155;QSTRAND=- GT:DP:AD ./.:34:11,23 1|0:30:14,16 ./.:41:25,16 -chr20 77736 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25618901;QSTRAND=- GT:DP:AD ./.:47:23,24 ./.:28:13,15 0|1:36:17,19 -chr20 78705 . A T 60 . QNAME=cluster19_000000F;QSTART=25684187;QSTRAND=- GT:DP:AD ./.:38:14,24 1|0:45:22,23 ./.:45:21,24 -chr20 80457 . C T 60 . QNAME=cluster19_000000F;QSTART=25682435;QSTRAND=- GT:DP:AD ./.:30:18,12 1|0:33:12,21 ./.:41:17,24 -chr20 80497 . C CT 60 . QNAME=cluster19_000000F;QSTART=25682394;QSTRAND=- GT:DP:AD ./.:37:13,24 1|0:32:20,12 ./.:26:16,10 -chr20 81154 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=60071;QSTRAND=+ GT:DP:AD 1|1:11:5,6 0|1:36:16,20 1|1:27:16,11 -chr20 82603 . A C 60 . QNAME=cluster19_000000F;QSTART=25680288;QSTRAND=- GT:DP:AD ./.:19:6,13 1|0:24:11,13 ./.:24:12,12 -chr20 83158 . C T 60 . QNAME=cluster19_000000F;QSTART=25679733;QSTRAND=- GT:DP:AD ./.:25:8,17 1|0:31:11,20 ./.:32:10,22 -chr20 85259 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=64176;QSTRAND=+ GT:DP:AD 1|1:24:11,13 0|1:38:19,19 1|1:31:19,12 -chr20 85729 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=64646;QSTRAND=+ GT:DP:AD 1|1:25:17,8 0|1:30:16,14 1|1:31:14,17 -chr20 86079 . C A 60 . QNAME=cluster19_000000F;QSTART=45136;QSTRAND=+ GT:DP:AD ./.:15:7,8 0|1:34:14,20 ./.:29:15,14 -chr20 86859 . T TTGGTATCTAG 60 . QNAME=HG002-S9-H1-000001F;QSTART=65777;QSTRAND=+ GT:DP:AD 1|1:34:25,9 0|1:36:19,17 1|1:38:17,21 -chr20 88108 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=67035;QSTRAND=+ GT:DP:AD 1|1:20:7,13 1|1:40:24,16 1|1:33:11,22 -chr20 88453 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25623502;QSTRAND=- GT:DP:AD ./.:24:12,12 ./.:24:10,14 1|0:33:22,11 -chr20 88865 . G GACACAC 60 . QNAME=cluster19_000000F;QSTART=47933;QSTRAND=+ GT:DP:AD ./.:18:9,9 0|1:30:12,18 1|0:38:17,21 -chr20 88865 . G GACAC 60 . QNAME=cluster19_000000F;QSTART=25674022;QSTRAND=- GT:DP:AD ./.:44:23,21 1|0:32:21,11 ./.:45:23,22 -chr20 89843 . CTCTT C 60 . QNAME=cluster19_000000F;QSTART=25673044;QSTRAND=- GT:DP:AD ./.:28:13,15 1|0:15:6,9 ./.:37:23,14 -chr20 90339 . G A 60 . QNAME=cluster19_000000F;QSTART=25672552;QSTRAND=- GT:DP:AD ./.:32:20,12 1|0:30:15,15 ./.:25:18,7 -chr20 91463 . TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=70391;QSTRAND=+ GT:DP:AD 1|1:38:15,23 1|0:37:25,12 ./.:23:10,13 -chr20 92251 . G A 60 . QNAME=cluster19_000000F;QSTART=25670641;QSTRAND=- GT:DP:AD ./.:37:18,19 1|0:41:25,16 ./.:36:12,24 -chr20 92395 . C CT 60 . QNAME=cluster19_000000F;QSTART=25670496;QSTRAND=- GT:DP:AD ./.:15:8,7 1|0:24:19,5 ./.:35:17,18 -chr20 92969 . CTT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=71896;QSTRAND=+ GT:DP:AD 1|1:43:20,23 ./.:35:17,18 ./.:43:20,23 -chr20 92969 . CT C 60 . QNAME=cluster19_000000F;QSTART=25669922;QSTRAND=- GT:DP:AD ./.:39:16,23 1|1:40:15,25 ./.:23:7,16 -chr20 92969 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25618979;QSTRAND=- GT:DP:AD ./.:32:12,20 ./.:28:13,15 1|0:30:17,13 -chr20 93706 . G A 60 . QNAME=cluster19_000000F;QSTART=52778;QSTRAND=+ GT:DP:AD ./.:31:21,10 0|1:31:21,10 ./.:38:18,20 -chr20 94088 . G GT 60 . QNAME=HG002-S9-H1-000001F;QSTART=73013;QSTRAND=+ GT:DP:AD 1|1:27:20,7 1|0:26:8,18 ./.:39:21,18 -chr20 94613 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=73538;QSTRAND=+ GT:DP:AD 1|1:27:21,6 ./.:21:15,6 ./.:20:13,7 -chr20 96130 . C T 60 . QNAME=cluster19_000000F;QSTART=25666761;QSTRAND=- GT:DP:AD ./.:39:14,25 1|0:34:22,12 ./.:32:7,25 -chr20 96321 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=75246;QSTRAND=+ GT:DP:AD 1|1:35:19,16 1|1:28:12,16 ./.:33:23,10 -chr20 97324 . G GT 60 . QNAME=HG002-S9-H1-000001F;QSTART=76250;QSTRAND=+ GT:DP:AD 1|1:20:15,5 ./.:33:8,25 ./.:24:12,12 -chr20 98593 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=77519;QSTRAND=+ GT:DP:AD 1|1:27:14,13 1|0:30:9,21 ./.:26:8,18 -chr20 99430 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=78356;QSTRAND=+ GT:DP:AD 1|1:37:17,20 ./.:49:24,25 ./.:31:17,14 -chr20 99840 . G C 60 . QNAME=cluster19_000000F;QSTART=25663051;QSTRAND=- GT:DP:AD ./.:37:19,18 1|0:41:19,22 ./.:24:5,19 -chr20 100014 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=78940;QSTRAND=+ GT:DP:AD 1|1:21:11,10 1|1:32:10,22 1|1:11:5,6 -chr20 101338 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=54816;QSTRAND=+ GT:DP:AD 0|1:21:5,16 ./.:16:7,9 ./.:14:6,8 -chr20 101341 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25610607;QSTRAND=- GT:DP:AD ./.:46:25,21 ./.:48:25,23 1|0:31:6,25 -chr20 101371 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=80297;QSTRAND=+ GT:DP:AD 1|0:14:6,8 0|1:34:17,17 ./.:28:8,20 -chr20 101433 . A C 60 . QNAME=cluster19_000000F;QSTART=25661458;QSTRAND=- GT:DP:AD ./.:36:14,22 1|1:30:12,18 ./.:24:11,13 -chr20 101438 . G A 60 . QNAME=cluster19_000000F;QSTART=25661453;QSTRAND=- GT:DP:AD ./.:30:22,8 1|1:47:22,25 ./.:27:8,19 -chr20 101498 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25610450;QSTRAND=- GT:DP:AD ./.:21:6,15 ./.:36:21,15 1|0:25:9,16 -chr20 101505 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=54983;QSTRAND=+ GT:DP:AD 0|1:47:25,22 ./.:31:7,24 1|0:36:25,11 -chr20 101576 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=80502;QSTRAND=+ GT:DP:AD 1|1:19:10,9 1|1:30:10,20 0|1:18:6,12 -chr20 102609 . CTGTGTGTGTGTGTGTGTGTGTG C 60 . QNAME=HG002-S9-H1-000001F;QSTART=81536;QSTRAND=+ GT:DP:AD 1|0:22:16,6 ./.:44:20,24 ./.:28:21,7 -chr20 102609 . CTG C 60 . QNAME=HG002-S9-H2-000001F;QSTART=56088;QSTRAND=+ GT:DP:AD 0|1:45:20,25 ./.:15:6,9 ./.:17:5,12 -chr20 102609 . CTGTGTGTG C 60 . QNAME=cluster19_000000F;QSTART=25660282;QSTRAND=- GT:DP:AD ./.:43:19,24 1|1:26:12,14 1|0:31:23,8 -chr20 102609 . C CTGTG 60 . QNAME=cluster23_scaffold_2;QSTART=25594014;QSTRAND=- GT:DP:AD ./.:19:5,14 ./.:21:6,15 0|1:30:14,16 -chr20 102613 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=56089;QSTRAND=+ GT:DP:AD 0|1:25:14,11 ./.:39:20,19 ./.:35:11,24 -chr20 102619 . G C 60 . QNAME=cluster19_000000F;QSTART=25660280;QSTRAND=- GT:DP:AD ./.:41:21,20 1|1:40:16,24 1|0:29:18,11 -chr20 102621 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25609335;QSTRAND=- GT:DP:AD ./.:49:25,24 ./.:37:22,15 1|0:28:15,13 -chr20 102623 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25609333;QSTRAND=- GT:DP:AD ./.:30:15,15 ./.:38:23,15 1|0:34:16,18 -chr20 102633 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=81537;QSTRAND=+ GT:DP:AD 1|0:45:25,20 ./.:14:6,8 ./.:23:12,11 -chr20 102634 . T C 60 . QNAME=cluster19_000000F;QSTART=25660265;QSTRAND=- GT:DP:AD ./.:24:7,17 1|1:31:22,9 ./.:13:7,6 -chr20 105364 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=84269;QSTRAND=+ GT:DP:AD 1|1:33:12,21 ./.:31:13,18 ./.:42:24,18 -chr20 105364 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25591258;QSTRAND=- GT:DP:AD ./.:39:16,23 ./.:28:16,12 0|1:24:8,16 -chr20 106471 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=85374;QSTRAND=+ GT:DP:AD 1|1:40:18,22 ./.:31:8,23 ./.:27:5,22 -chr20 106775 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=85678;QSTRAND=+ GT:DP:AD 1|1:20:7,13 ./.:41:19,22 0|1:20:15,5 -chr20 107149 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25589473;QSTRAND=- GT:DP:AD ./.:23:11,12 ./.:22:12,10 0|1:28:22,6 -chr20 107514 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25589108;QSTRAND=- GT:DP:AD ./.:36:19,17 ./.:38:15,23 0|1:15:10,5 -chr20 109367 . C A 60 . QNAME=cluster19_000000F;QSTART=25653532;QSTRAND=- GT:DP:AD ./.:35:11,24 1|1:38:23,15 ./.:12:6,6 -chr20 110447 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=89350;QSTRAND=+ GT:DP:AD 1|1:30:5,25 1|1:20:6,14 0|1:31:23,8 -chr20 110867 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=89770;QSTRAND=+ GT:DP:AD 1|1:26:18,8 1|1:29:9,20 0|1:24:15,9 -chr20 111066 . C T 60 . QNAME=cluster19_000000F;QSTART=70130;QSTRAND=+ GT:DP:AD ./.:33:11,22 0|1:37:14,23 ./.:43:24,19 -chr20 111725 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=90628;QSTRAND=+ GT:DP:AD 1|1:18:6,12 ./.:22:17,5 ./.:32:7,25 -chr20 111886 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=90789;QSTRAND=+ GT:DP:AD 1|1:45:24,21 1|1:36:11,25 0|1:32:14,18 -chr20 112799 . A G 60 . QNAME=cluster19_000000F;QSTART=25650100;QSTRAND=- GT:DP:AD ./.:19:5,14 1|0:31:7,24 ./.:47:22,25 -chr20 113005 . C CT 60 . QNAME=cluster19_000000F;QSTART=25649893;QSTRAND=- GT:DP:AD ./.:24:13,11 1|0:19:14,5 ./.:35:11,24 -chr20 113290 . G A 60 . QNAME=cluster19_000000F;QSTART=25649608;QSTRAND=- GT:DP:AD ./.:19:10,9 1|0:27:21,6 ./.:29:9,20 -chr20 115856 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=25580766;QSTRAND=- GT:DP:AD ./.:33:20,13 ./.:25:16,9 0|1:46:21,25 -chr20 120058 . C T 60 . QNAME=cluster19_000000F;QSTART=25642840;QSTRAND=- GT:DP:AD ./.:25:10,15 1|0:32:22,10 ./.:21:16,5 -chr20 120721 . G A 60 . QNAME=cluster19_000000F;QSTART=79785;QSTRAND=+ GT:DP:AD ./.:36:12,24 0|1:15:6,9 ./.:40:24,16 -chr20 121264 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=74739;QSTRAND=+ GT:DP:AD 0|1:32:20,12 ./.:19:9,10 ./.:34:16,18 -chr20 121439 . TATTCTTCAGCTGTCAAA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=100343;QSTRAND=+ GT:DP:AD 1|1:36:18,18 ./.:32:8,24 ./.:39:14,25 -chr20 121540 . T C 60 . QNAME=cluster19_000000F;QSTART=25641358;QSTRAND=- GT:DP:AD ./.:26:11,15 1|0:28:5,23 ./.:32:18,14 -chr20 122158 . G A 60 . QNAME=cluster19_000000F;QSTART=25640740;QSTRAND=- GT:DP:AD ./.:20:7,13 1|0:27:20,7 ./.:26:7,19 -chr20 122876 . A T 60 . QNAME=cluster19_000000F;QSTART=25640022;QSTRAND=- GT:DP:AD ./.:26:21,5 1|0:30:19,11 ./.:34:9,25 -chr20 124258 . C T 60 . QNAME=cluster19_000000F;QSTART=25638640;QSTRAND=- GT:DP:AD ./.:37:13,24 1|0:33:21,12 ./.:39:19,20 -chr20 125994 . G A 60 . QNAME=cluster19_000000F;QSTART=25636904;QSTRAND=- GT:DP:AD ./.:47:23,24 1|0:13:8,5 ./.:36:11,25 -chr20 126062 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=104949;QSTRAND=+ GT:DP:AD 1|0:41:25,16 0|1:33:20,13 1|1:45:24,21 -chr20 126062 . C CTTT 60 . QNAME=cluster19_000000F;QSTART=25636833;QSTRAND=- GT:DP:AD ./.:45:24,21 1|0:29:9,20 ./.:31:18,13 -chr20 127645 . T G 60 . QNAME=cluster19_000000F;QSTART=25635250;QSTRAND=- GT:DP:AD ./.:28:19,9 1|0:33:15,18 ./.:47:25,22 -chr20 127687 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=106574;QSTRAND=+ GT:DP:AD 1|1:32:17,15 1|1:31:8,23 0|1:32:11,21 -chr20 128317 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=107204;QSTRAND=+ GT:DP:AD 1|1:39:15,24 ./.:41:18,23 ./.:13:6,7 -chr20 128517 . C CAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=107405;QSTRAND=+ GT:DP:AD 1|0:18:8,10 ./.:48:25,23 1|0:38:22,16 -chr20 128517 . C CA 60 . QNAME=HG002-S9-H2-000001F;QSTART=81976;QSTRAND=+ GT:DP:AD 0|1:31:12,19 0|1:21:6,15 ./.:41:16,25 -chr20 128517 . CA C 60 . QNAME=cluster19_000000F;QSTART=25634378;QSTRAND=- GT:DP:AD ./.:26:21,5 1|0:19:10,9 ./.:45:20,25 -chr20 129417 . G C 60 . QNAME=cluster19_000000F;QSTART=25633479;QSTRAND=- GT:DP:AD ./.:31:6,25 1|0:38:19,19 ./.:32:13,19 -chr20 129457 . A G 60 . QNAME=cluster19_000000F;QSTART=25633439;QSTRAND=- GT:DP:AD ./.:34:15,19 1|0:41:24,17 ./.:31:10,21 -chr20 130061 . C T 60 . QNAME=cluster19_000000F;QSTART=25632835;QSTRAND=- GT:DP:AD ./.:17:10,7 1|0:36:17,19 ./.:27:13,14 -chr20 130282 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=83741;QSTRAND=+ GT:DP:AD 0|1:32:14,18 ./.:36:19,17 ./.:24:10,14 -chr20 130329 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=109218;QSTRAND=+ GT:DP:AD 1|1:27:7,20 ./.:47:24,23 ./.:35:16,19 -chr20 130338 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=109227;QSTRAND=+ GT:DP:AD 1|1:21:7,14 0|1:48:23,25 0|1:34:24,10 -chr20 130338 . A G 60 . QNAME=cluster19_000000F;QSTART=25632558;QSTRAND=- GT:DP:AD ./.:35:19,16 1|0:25:17,8 ./.:20:5,15 -chr20 130339 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=109228;QSTRAND=+ GT:DP:AD 1|1:34:14,20 0|1:41:22,19 0|1:44:19,25 -chr20 130636 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25565985;QSTRAND=- GT:DP:AD ./.:39:16,23 ./.:42:20,22 0|1:24:13,11 -chr20 130736 . A C 60 . QNAME=cluster19_000000F;QSTART=25632160;QSTRAND=- GT:DP:AD ./.:20:8,12 1|0:21:10,11 ./.:40:24,16 -chr20 130742 . T C 60 . QNAME=cluster19_000000F;QSTART=25632154;QSTRAND=- GT:DP:AD ./.:38:25,13 1|0:21:12,9 ./.:37:23,14 -chr20 131163 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=110052;QSTRAND=+ GT:DP:AD 1|1:28:13,15 ./.:39:25,14 ./.:27:22,5 -chr20 131230 . A G 60 . QNAME=cluster19_000000F;QSTART=25631666;QSTRAND=- GT:DP:AD ./.:35:14,21 1|0:30:9,21 ./.:35:21,14 -chr20 131374 . G A 60 . QNAME=cluster19_000000F;QSTART=25631522;QSTRAND=- GT:DP:AD ./.:13:6,7 1|0:38:16,22 ./.:21:6,15 -chr20 132236 . C T 60 . QNAME=cluster19_000000F;QSTART=91302;QSTRAND=+ GT:DP:AD ./.:32:7,25 0|1:29:23,6 ./.:36:20,16 diff --git a/repo_utils/test_files/answer_key/divided/multi_00000001.vcf b/repo_utils/test_files/answer_key/divided/multi_00000001.vcf deleted file mode 100644 index b6ebc52a..00000000 --- a/repo_utils/test_files/answer_key/divided/multi_00000001.vcf +++ /dev/null @@ -1,240 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##bcftools_mergeVersion=1.12+htslib-1.12 -##bcftools_mergeCommand=merge -O z -f x -m none input1.vcf.gz input2.vcf.gz input3.vcf.gz; Date=Mon Aug 16 18:05:13 2021 -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 133539 . T C 60 . QNAME=cluster19_000000F;QSTART=25629357;QSTRAND=- GT:DP:AD ./.:23:8,15 1|0:35:21,14 ./.:47:25,22 -chr20 133631 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25562990;QSTRAND=- GT:DP:AD ./.:32:16,16 ./.:37:23,14 0|1:44:19,25 -chr20 133700 . C A 60 . QNAME=cluster19_000000F;QSTART=25629196;QSTRAND=- GT:DP:AD ./.:28:16,12 1|0:35:12,23 ./.:35:17,18 -chr20 134275 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25562346;QSTRAND=- GT:DP:AD ./.:27:19,8 ./.:29:11,18 0|1:27:20,7 -chr20 134452 . A C 60 . QNAME=cluster19_000000F;QSTART=25628444;QSTRAND=- GT:DP:AD ./.:19:12,7 1|0:25:15,10 ./.:22:10,12 -chr20 134675 . C CA 60 . QNAME=cluster19_000000F;QSTART=25628220;QSTRAND=- GT:DP:AD ./.:16:5,11 1|0:24:6,18 ./.:36:23,13 -chr20 134915 . G A 60 . QNAME=cluster19_000000F;QSTART=25627980;QSTRAND=- GT:DP:AD ./.:17:6,11 1|0:37:15,22 ./.:36:13,23 -chr20 135005 . T C 60 . QNAME=cluster19_000000F;QSTART=25627890;QSTRAND=- GT:DP:AD ./.:43:20,23 1|0:22:17,5 ./.:27:19,8 -chr20 135211 . C CA 60 . QNAME=cluster19_000000F;QSTART=25627683;QSTRAND=- GT:DP:AD ./.:31:23,8 1|0:40:19,21 ./.:23:5,18 -chr20 135293 . C G 60 . QNAME=cluster19_000000F;QSTART=25627601;QSTRAND=- GT:DP:AD ./.:15:5,10 1|0:30:5,25 ./.:35:13,22 -chr20 135387 . G A 60 . QNAME=cluster19_000000F;QSTART=94453;QSTRAND=+ GT:DP:AD ./.:24:16,8 0|1:28:23,5 ./.:30:22,8 -chr20 135595 . A G 60 . QNAME=cluster19_000000F;QSTART=25627299;QSTRAND=- GT:DP:AD ./.:40:25,15 1|0:28:13,15 ./.:29:7,22 -chr20 135764 . G A 60 . QNAME=cluster19_000000F;QSTART=25627130;QSTRAND=- GT:DP:AD ./.:45:24,21 1|0:34:23,11 ./.:28:11,17 -chr20 135904 . G A 60 . QNAME=cluster19_000000F;QSTART=25626990;QSTRAND=- GT:DP:AD ./.:36:25,11 1|0:36:24,12 ./.:17:10,7 -chr20 136146 . A G 60 . QNAME=cluster19_000000F;QSTART=25626748;QSTRAND=- GT:DP:AD ./.:31:13,18 1|0:20:12,8 ./.:30:11,19 -chr20 136216 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=89675;QSTRAND=+ GT:DP:AD 0|1:42:23,19 ./.:27:20,7 ./.:27:5,22 -chr20 136668 . G GCAGGATTTCAT 60 . QNAME=cluster19_000000F;QSTART=25626215;QSTRAND=- GT:DP:AD ./.:22:7,15 1|0:24:7,17 ./.:32:10,22 -chr20 139004 . G GT 60 . QNAME=cluster19_000000F;QSTART=25623878;QSTRAND=- GT:DP:AD ./.:19:8,11 1|1:41:21,20 ./.:23:7,16 -chr20 139481 . A AAG 60 . QNAME=HG002-S9-H1-000001F;QSTART=118371;QSTRAND=+ GT:DP:AD 1|1:29:23,6 1|1:31:17,14 0|1:28:8,20 -chr20 139830 . A G 60 . QNAME=cluster19_000000F;QSTART=25623050;QSTRAND=- GT:DP:AD ./.:32:12,20 1|0:20:9,11 ./.:33:13,20 -chr20 140109 . C CAATT 60 . QNAME=HG002-S9-H1-000001F;QSTART=119001;QSTRAND=+ GT:DP:AD 1|1:35:15,20 1|1:28:17,11 0|1:31:7,24 -chr20 140669 . A C 60 . QNAME=cluster19_000000F;QSTART=25622207;QSTRAND=- GT:DP:AD ./.:41:20,21 1|0:32:15,17 ./.:31:19,12 -chr20 140837 . C A 60 . QNAME=cluster19_000000F;QSTART=25622039;QSTRAND=- GT:DP:AD ./.:24:16,8 1|0:45:20,25 ./.:36:17,19 -chr20 140838 . G GT 60 . QNAME=cluster23_scaffold_3;QSTART=25571114;QSTRAND=- GT:DP:AD ./.:36:20,16 ./.:38:16,22 1|0:24:16,8 -chr20 140859 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=94325;QSTRAND=+ GT:DP:AD 0|1:27:6,21 1|0:23:18,5 ./.:29:11,18 -chr20 140859 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25571092;QSTRAND=- GT:DP:AD ./.:44:21,23 ./.:29:6,23 1|1:33:15,18 -chr20 141183 . C T 60 . QNAME=cluster19_000000F;QSTART=25621694;QSTRAND=- GT:DP:AD ./.:40:24,16 1|0:14:9,5 ./.:39:19,20 -chr20 141335 . G A 60 . QNAME=cluster19_000000F;QSTART=25621542;QSTRAND=- GT:DP:AD ./.:21:6,15 1|0:32:14,18 ./.:29:22,7 -chr20 141634 . GA G 60 . QNAME=cluster19_000000F;QSTART=25621243;QSTRAND=- GT:DP:AD ./.:43:22,21 1|0:36:18,18 ./.:30:8,22 -chr20 141867 . G A 60 . QNAME=cluster19_000000F;QSTART=25621011;QSTRAND=- GT:DP:AD ./.:36:12,24 1|0:37:12,25 ./.:34:24,10 -chr20 142165 . T TTA 60 . QNAME=cluster19_000000F;QSTART=25620711;QSTRAND=- GT:DP:AD ./.:20:11,9 1|0:26:15,11 ./.:26:7,19 -chr20 143010 . G GT 60 . QNAME=cluster19_000000F;QSTART=102084;QSTRAND=+ GT:DP:AD ./.:33:21,12 0|1:21:13,8 0|1:28:18,10 -chr20 143661 . A C 60 . QNAME=cluster19_000000F;QSTART=25619215;QSTRAND=- GT:DP:AD ./.:33:22,11 1|0:34:12,22 ./.:28:9,19 -chr20 143771 . C T 60 . QNAME=cluster19_000000F;QSTART=25619105;QSTRAND=- GT:DP:AD ./.:28:5,23 1|0:13:7,6 ./.:23:18,5 -chr20 144480 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=123375;QSTRAND=+ GT:DP:AD 1|1:33:11,22 ./.:17:10,7 ./.:29:13,16 -chr20 144897 . G C 60 . QNAME=cluster19_000000F;QSTART=25617979;QSTRAND=- GT:DP:AD ./.:27:8,19 1|0:31:7,24 ./.:33:13,20 -chr20 145514 . GCAAA G 60 . QNAME=cluster19_000000F;QSTART=25617362;QSTRAND=- GT:DP:AD ./.:22:13,9 1|0:33:22,11 ./.:40:21,19 -chr20 145669 . ACC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=124565;QSTRAND=+ GT:DP:AD 1|1:31:20,11 1|0:32:17,15 1|0:19:10,9 -chr20 145888 . G A 60 . QNAME=cluster19_000000F;QSTART=25616994;QSTRAND=- GT:DP:AD ./.:22:15,7 1|1:26:5,21 ./.:25:6,19 -chr20 145959 . C A 60 . QNAME=cluster19_000000F;QSTART=25616923;QSTRAND=- GT:DP:AD ./.:35:25,10 1|1:34:10,24 ./.:37:20,17 -chr20 145973 . T C 60 . QNAME=cluster19_000000F;QSTART=25616909;QSTRAND=- GT:DP:AD ./.:32:11,21 1|1:13:7,6 ./.:29:18,11 -chr20 146089 . C T 60 . QNAME=cluster19_000000F;QSTART=25616793;QSTRAND=- GT:DP:AD ./.:22:6,16 1|1:38:18,20 ./.:30:24,6 -chr20 146119 . C T 60 . QNAME=cluster19_000000F;QSTART=25616763;QSTRAND=- GT:DP:AD ./.:25:17,8 1|1:24:19,5 ./.:29:18,11 -chr20 146282 . C A 60 . QNAME=cluster19_000000F;QSTART=25616600;QSTRAND=- GT:DP:AD ./.:28:13,15 1|1:22:6,16 ./.:23:7,16 -chr20 146289 . A T 60 . QNAME=cluster19_000000F;QSTART=25616593;QSTRAND=- GT:DP:AD ./.:30:17,13 1|1:45:22,23 ./.:39:25,14 -chr20 147079 . A C 60 . QNAME=cluster19_000000F;QSTART=25615803;QSTRAND=- GT:DP:AD ./.:35:11,24 1|1:24:16,8 ./.:20:14,6 -chr20 147311 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25564642;QSTRAND=- GT:DP:AD ./.:45:21,24 ./.:17:7,10 1|1:36:18,18 -chr20 148061 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=101523;QSTRAND=+ GT:DP:AD 0|1:33:25,8 ./.:27:19,8 ./.:21:16,5 -chr20 148072 . C G 60 . QNAME=cluster19_000000F;QSTART=25614810;QSTRAND=- GT:DP:AD ./.:33:24,9 1|1:31:23,8 ./.:24:10,14 -chr20 148222 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25563731;QSTRAND=- GT:DP:AD ./.:40:18,22 ./.:41:16,25 1|1:42:22,20 -chr20 148422 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25563531;QSTRAND=- GT:DP:AD ./.:42:24,18 ./.:44:19,25 1|1:20:6,14 -chr20 148972 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=127865;QSTRAND=+ GT:DP:AD 1|1:23:9,14 1|1:33:15,18 1|1:23:16,7 -chr20 148994 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=127887;QSTRAND=+ GT:DP:AD 1|1:20:12,8 ./.:39:24,15 ./.:26:5,21 -chr20 149013 . A ACCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=127907;QSTRAND=+;SVTYPE=INS;SVLEN=69 GT:DP:AD 1/1:35:19,16 ./.:31:21,10 1/0:17:8,9 -chr20 149073 . G GAATCCTGACCCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCA 60 . QNAME=cluster23_scaffold_2;QSTART=25547471;QSTRAND=-;SVTYPE=INS;SVLEN=69 GT:DP:AD ./.:44:25,19 ./.:36:12,24 0/1:27:20,7 -chr20 149095 . G GGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGACCCATATTTGGGAA 60 . QNAME=cluster19_000000F;QSTART=25613718;QSTRAND=-;SVTYPE=INS;SVLEN=69 GT:DP:AD ./.:36:13,23 1/1:14:7,7 ./.:40:19,21 -chr20 149223 . C T 60 . QNAME=cluster19_000000F;QSTART=25613590;QSTRAND=- GT:DP:AD ./.:26:5,21 1|1:42:19,23 ./.:38:21,17 -chr20 150418 . T A 60 . QNAME=cluster23_scaffold_2;QSTART=25546126;QSTRAND=- GT:DP:AD ./.:22:14,8 ./.:28:18,10 0|1:35:25,10 -chr20 150492 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25561392;QSTRAND=- GT:DP:AD ./.:39:17,22 ./.:37:20,17 1|0:29:9,20 -chr20 150721 . C T 60 . QNAME=cluster19_000000F;QSTART=25612092;QSTRAND=- GT:DP:AD ./.:30:24,6 1|1:14:5,9 ./.:33:17,16 -chr20 150854 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=129816;QSTRAND=+ GT:DP:AD 1|1:41:20,21 1|1:31:13,18 1|1:29:16,13 -chr20 150864 . CTCT C 60 . QNAME=cluster19_000000F;QSTART=25611949;QSTRAND=- GT:DP:AD ./.:30:12,18 1|1:14:5,9 ./.:25:19,6 -chr20 151016 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=129978;QSTRAND=+ GT:DP:AD 1|1:25:5,20 1|1:40:18,22 1|1:42:17,25 -chr20 151307 . C CCA 60 . QNAME=cluster19_000000F;QSTART=25611507;QSTRAND=- GT:DP:AD ./.:21:11,10 1|1:22:17,5 ./.:31:10,21 -chr20 151663 . TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=130626;QSTRAND=+ GT:DP:AD 1|1:32:14,18 1|1:31:9,22 1|1:29:24,5 -chr20 151898 . A T 60 . QNAME=cluster23_scaffold_2;QSTART=25544647;QSTRAND=- GT:DP:AD ./.:30:25,5 ./.:25:13,12 0|1:37:20,17 -chr20 152134 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=131095;QSTRAND=+ GT:DP:AD 1|1:37:20,17 ./.:34:24,10 ./.:43:18,25 -chr20 152450 . CAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=131412;QSTRAND=+ GT:DP:AD 1|1:11:5,6 ./.:27:12,15 1|0:43:18,25 -chr20 152450 . C CA 60 . QNAME=cluster19_000000F;QSTART=25610364;QSTRAND=- GT:DP:AD ./.:50:25,25 1|1:30:23,7 ./.:33:15,18 -chr20 152450 . CAA C 60 . QNAME=cluster23_scaffold_2;QSTART=25544095;QSTRAND=- GT:DP:AD ./.:40:25,15 ./.:28:7,21 0|1:36:13,23 -chr20 152517 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=131475;QSTRAND=+ GT:DP:AD 1|1:14:8,6 1|1:33:19,14 1|1:16:7,9 -chr20 152792 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=131750;QSTRAND=+ GT:DP:AD 1|0:25:5,20 ./.:32:17,15 1|1:21:11,10 -chr20 153098 . G GT 60 . QNAME=HG002-S9-H1-000001F;QSTART=132057;QSTRAND=+ GT:DP:AD 1|0:49:24,25 ./.:27:21,6 1|1:39:23,16 -chr20 153259 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=132218;QSTRAND=+ GT:DP:AD 1|0:31:15,16 ./.:26:12,14 1|1:32:18,14 -chr20 153376 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=106903;QSTRAND=+ GT:DP:AD 0|1:23:12,11 1|1:27:6,21 ./.:38:23,15 -chr20 153555 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25558332;QSTRAND=- GT:DP:AD ./.:35:17,18 ./.:26:5,21 1|1:45:22,23 -chr20 153640 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25558247;QSTRAND=- GT:DP:AD ./.:25:20,5 ./.:32:25,7 1|1:49:24,25 -chr20 153643 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=132602;QSTRAND=+ GT:DP:AD 1|1:45:20,25 1|1:16:6,10 1|1:25:14,11 -chr20 153725 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=132684;QSTRAND=+ GT:DP:AD 1|1:35:11,24 1|1:25:6,19 1|1:15:5,10 -chr20 153759 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=132718;QSTRAND=+ GT:DP:AD 1|0:33:17,16 ./.:32:14,18 1|0:36:23,13 -chr20 153780 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=132739;QSTRAND=+ GT:DP:AD 1|1:26:19,7 1|1:31:6,25 1|1:29:5,24 -chr20 153787 . CAAAAAAAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=132747;QSTRAND=+ GT:DP:AD 1|1:36:19,17 1|1:23:11,12 1|1:20:13,7 -chr20 153835 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=132785;QSTRAND=+ GT:DP:AD 1|1:21:15,6 1|1:30:9,21 1|1:14:7,7 -chr20 153898 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=132848;QSTRAND=+ GT:DP:AD 1|0:20:13,7 ./.:30:25,5 1|0:36:16,20 -chr20 154002 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=132952;QSTRAND=+ GT:DP:AD 1|1:38:17,21 1|1:27:9,18 1|1:40:25,15 -chr20 154128 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=133079;QSTRAND=+ GT:DP:AD 1|0:25:6,19 ./.:33:16,17 1|1:22:17,5 -chr20 154203 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=133154;QSTRAND=+ GT:DP:AD 1|1:26:12,14 1|1:37:13,24 1|1:27:6,21 -chr20 154290 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=133241;QSTRAND=+ GT:DP:AD 1|1:29:6,23 1|1:33:10,23 1|1:37:17,20 -chr20 154474 . G GTTTGCATTCACAGGAAGACTATAAATAAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=133426;QSTRAND=+;SVTYPE=INS;SVLEN=29 GT:DP:AD 1/1:24:18,6 1/1:18:11,7 1/1:19:9,10 -chr20 154475 . TGCTC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=133456;QSTRAND=+ GT:DP:AD 1|1:33:8,25 1|1:36:21,15 1|1:28:20,8 -chr20 154847 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=133823;QSTRAND=+ GT:DP:AD 1|1:35:14,21 1|1:27:9,18 1|1:22:7,15 -chr20 155384 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=134360;QSTRAND=+ GT:DP:AD 1|0:24:13,11 ./.:25:12,13 1|1:17:7,10 -chr20 155733 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=134709;QSTRAND=+ GT:DP:AD 1|0:17:10,7 ./.:25:13,12 1|1:36:24,12 -chr20 155813 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=134789;QSTRAND=+ GT:DP:AD 1|0:37:15,22 ./.:27:11,16 1|1:23:5,18 -chr20 156080 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=135056;QSTRAND=+ GT:DP:AD 1|0:26:12,14 ./.:21:15,6 1|1:28:21,7 -chr20 156287 . G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=135264;QSTRAND=+ GT:DP:AD 1|0:31:12,19 ./.:49:25,24 1|1:20:8,12 -chr20 156473 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=135450;QSTRAND=+ GT:DP:AD 1|0:30:13,17 ./.:41:25,16 1|1:35:10,25 -chr20 156486 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=110029;QSTRAND=+ GT:DP:AD 0|1:31:9,22 1|1:31:8,23 ./.:31:19,12 -chr20 156669 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=135646;QSTRAND=+ GT:DP:AD 1|0:37:25,12 ./.:32:17,15 1|1:21:14,7 -chr20 156813 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=135790;QSTRAND=+ GT:DP:AD 1|0:19:9,10 ./.:25:14,11 1|1:36:13,23 -chr20 156877 . GTA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=135855;QSTRAND=+ GT:DP:AD 1|1:35:19,16 1|1:19:8,11 1|1:39:16,23 -chr20 156881 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=135856;QSTRAND=+ GT:DP:AD 1|0:50:25,25 ./.:35:14,21 1|1:33:9,24 -chr20 157033 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=110574;QSTRAND=+ GT:DP:AD 0|1:15:6,9 1|1:34:19,15 ./.:38:17,21 -chr20 157259 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=136234;QSTRAND=+ GT:DP:AD 1|0:25:6,19 ./.:25:14,11 1|1:34:21,13 -chr20 157292 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=136267;QSTRAND=+ GT:DP:AD 1|1:30:11,19 1|1:21:14,7 1|1:35:25,10 -chr20 157363 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=136338;QSTRAND=+ GT:DP:AD 1|1:18:9,9 1|1:20:12,8 1|1:33:24,9 -chr20 157484 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=136459;QSTRAND=+ GT:DP:AD 1|0:25:19,6 ./.:25:7,18 1|1:21:6,15 -chr20 157507 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=136482;QSTRAND=+ GT:DP:AD 1|0:29:17,12 ./.:44:22,22 1|1:27:6,21 -chr20 157537 . GC G 60 . QNAME=HG002-S9-H2-000001F;QSTART=111079;QSTRAND=+ GT:DP:AD 0|1:39:15,24 1|1:15:7,8 ./.:41:22,19 -chr20 157819 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=136794;QSTRAND=+ GT:DP:AD 1|0:32:10,22 ./.:17:10,7 1|1:26:13,13 -chr20 157914 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=136889;QSTRAND=+ GT:DP:AD 1|0:31:10,21 ./.:35:23,12 1|1:16:8,8 -chr20 157922 . AATAT A 60 . QNAME=cluster23_scaffold_2;QSTART=25538608;QSTRAND=- GT:DP:AD ./.:19:12,7 ./.:33:17,16 0|1:27:5,22 -chr20 157927 . ATATATGTG A 60 . QNAME=HG002-S9-H1-000001F;QSTART=136903;QSTRAND=+ GT:DP:AD 1|0:23:7,16 ./.:26:8,18 ./.:42:24,18 -chr20 157927 . ATATATG A 60 . QNAME=cluster23_scaffold_3;QSTART=25553944;QSTRAND=- GT:DP:AD ./.:33:10,23 ./.:19:9,10 1|0:36:12,24 -chr20 157929 . ATATGTGTG A 60 . QNAME=HG002-S9-H2-000001F;QSTART=111470;QSTRAND=+ GT:DP:AD 0|1:41:18,23 1|1:32:16,16 ./.:15:10,5 -chr20 157960 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=111492;QSTRAND=+ GT:DP:AD 0|1:26:9,17 1|1:24:10,14 ./.:32:20,12 -chr20 157962 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=111494;QSTRAND=+ GT:DP:AD 0|1:32:15,17 1|1:30:18,12 ./.:35:24,11 -chr20 157965 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=136932;QSTRAND=+ GT:DP:AD 1|0:13:8,5 ./.:38:21,17 1|1:27:17,10 -chr20 157974 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=136941;QSTRAND=+ GT:DP:AD 1|0:31:25,6 ./.:33:21,12 1|1:30:14,16 -chr20 157979 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=136946;QSTRAND=+ GT:DP:AD 1|0:39:25,14 ./.:46:21,25 1|1:15:7,8 -chr20 158513 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=137480;QSTRAND=+ GT:DP:AD 1|0:31:8,23 ./.:22:5,17 1|1:44:23,21 -chr20 158532 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=137499;QSTRAND=+ GT:DP:AD 1|0:27:18,9 ./.:49:24,25 1|0:33:22,11 -chr20 158721 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=112253;QSTRAND=+ GT:DP:AD 0|1:30:17,13 1|1:14:6,8 ./.:43:20,23 -chr20 158768 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=137735;QSTRAND=+ GT:DP:AD 1|0:36:24,12 ./.:26:15,11 1|1:31:8,23 -chr20 158815 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=137782;QSTRAND=+ GT:DP:AD 1|0:38:17,21 ./.:25:13,12 1|1:39:16,23 -chr20 158935 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=137902;QSTRAND=+ GT:DP:AD 1|0:19:14,5 ./.:36:23,13 1|1:41:25,16 -chr20 159104 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=138071;QSTRAND=+ GT:DP:AD 1|1:35:25,10 1|1:24:6,18 1|1:19:6,13 -chr20 159197 . A T 60 . QNAME=cluster23_scaffold_2;QSTART=25537337;QSTRAND=- GT:DP:AD ./.:24:10,14 ./.:26:17,9 0|1:28:22,6 -chr20 159200 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=112732;QSTRAND=+ GT:DP:AD 0|1:26:6,20 1|1:44:24,20 ./.:31:22,9 -chr20 159274 . T TAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=138242;QSTRAND=+ GT:DP:AD 1|0:24:13,11 ./.:23:6,17 1|1:19:13,6 -chr20 159274 . T TAA 60 . QNAME=HG002-S9-H2-000001F;QSTART=112807;QSTRAND=+ GT:DP:AD 0|1:21:6,15 1|1:31:11,20 ./.:31:23,8 -chr20 159286 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=138259;QSTRAND=+ GT:DP:AD 1|0:28:13,15 ./.:25:15,10 1|1:29:18,11 -chr20 159445 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=112979;QSTRAND=+ GT:DP:AD 0|1:26:5,21 1|1:35:15,20 ./.:31:17,14 -chr20 159495 . G GAATGGCATAAACT 60 . QNAME=HG002-S9-H1-000001F;QSTART=138469;QSTRAND=+ GT:DP:AD 1|0:25:6,19 ./.:27:14,13 1|1:26:13,13 -chr20 159530 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=138516;QSTRAND=+ GT:DP:AD 1|0:39:22,17 ./.:24:15,9 1|1:37:12,25 -chr20 159639 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=113173;QSTRAND=+ GT:DP:AD 0|1:44:21,23 1|1:22:6,16 ./.:32:16,16 -chr20 159755 . TTTG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=138742;QSTRAND=+ GT:DP:AD 1|1:29:17,12 1|1:24:7,17 1|1:38:18,20 -chr20 159864 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=138847;QSTRAND=+ GT:DP:AD 1|0:21:15,6 ./.:41:18,23 1|1:34:16,18 -chr20 159865 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=138848;QSTRAND=+ GT:DP:AD 1|0:21:13,8 ./.:37:16,21 1|1:39:16,23 -chr20 159952 . AG A 60 . QNAME=HG002-S9-H1-000001F;QSTART=138936;QSTRAND=+ GT:DP:AD 1|0:44:20,24 ./.:27:6,21 1|1:23:15,8 -chr20 160054 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=139036;QSTRAND=+ GT:DP:AD 1|0:24:19,5 ./.:48:23,25 1|1:19:11,8 -chr20 160212 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=139194;QSTRAND=+ GT:DP:AD 1|0:30:9,21 ./.:42:20,22 1|1:25:16,9 -chr20 160282 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=139264;QSTRAND=+ GT:DP:AD 1|0:32:14,18 ./.:41:17,24 1|1:24:17,7 -chr20 160312 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=139294;QSTRAND=+ GT:DP:AD 1|0:30:14,16 ./.:33:20,13 1|1:28:10,18 -chr20 160384 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=139366;QSTRAND=+ GT:DP:AD 1|0:34:19,15 ./.:30:10,20 1|1:22:17,5 -chr20 160388 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=139370;QSTRAND=+ GT:DP:AD 1|0:29:24,5 ./.:31:20,11 1|1:22:15,7 -chr20 160408 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=139390;QSTRAND=+ GT:DP:AD 1|0:35:16,19 ./.:20:12,8 1|1:35:10,25 -chr20 160413 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=139395;QSTRAND=+ GT:DP:AD 1|0:14:8,6 ./.:26:10,16 1|1:20:6,14 -chr20 160433 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=139415;QSTRAND=+ GT:DP:AD 1|0:37:16,21 ./.:18:9,9 1|1:32:11,21 -chr20 160558 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=139540;QSTRAND=+ GT:DP:AD 1|0:42:24,18 ./.:29:12,17 1|0:36:25,11 -chr20 160625 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=139607;QSTRAND=+ GT:DP:AD 1|0:22:7,15 ./.:35:11,24 1|1:34:10,24 -chr20 160727 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=139709;QSTRAND=+ GT:DP:AD 1|0:46:25,21 ./.:24:14,10 1|1:27:21,6 -chr20 160731 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=139713;QSTRAND=+ GT:DP:AD 1|0:31:9,22 ./.:40:22,18 1|1:18:8,10 -chr20 160873 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=139855;QSTRAND=+ GT:DP:AD 1|0:28:19,9 ./.:29:9,20 1|1:23:5,18 -chr20 160889 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=139871;QSTRAND=+ GT:DP:AD 1|0:29:13,16 ./.:20:12,8 1|1:31:10,21 -chr20 160956 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=139938;QSTRAND=+ GT:DP:AD 1|0:19:11,8 ./.:28:19,9 1|1:32:18,14 -chr20 160967 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=139949;QSTRAND=+ GT:DP:AD 1|0:29:20,9 ./.:38:22,16 1|1:17:10,7 -chr20 161128 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140110;QSTRAND=+ GT:DP:AD 1|0:30:12,18 ./.:28:11,17 1|1:20:10,10 -chr20 161181 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140163;QSTRAND=+ GT:DP:AD 1|0:17:8,9 ./.:41:24,17 1|1:32:7,25 -chr20 161221 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140203;QSTRAND=+ GT:DP:AD 1|0:32:16,16 ./.:15:7,8 1|1:19:14,5 -chr20 161380 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=140362;QSTRAND=+ GT:DP:AD 1|1:15:8,7 1|1:36:17,19 1|1:23:18,5 -chr20 161451 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=140433;QSTRAND=+ GT:DP:AD 1|0:30:9,21 ./.:25:13,12 1|1:32:16,16 -chr20 161571 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=140553;QSTRAND=+ GT:DP:AD 1|0:22:12,10 ./.:17:8,9 1|1:26:20,6 -chr20 161588 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140570;QSTRAND=+ GT:DP:AD 1|1:18:5,13 1|1:45:22,23 1|1:39:19,20 -chr20 161621 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=140603;QSTRAND=+ GT:DP:AD 1|0:27:6,21 ./.:15:9,6 1|1:29:9,20 -chr20 161638 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=140620;QSTRAND=+ GT:DP:AD 1|1:34:12,22 1|1:37:13,24 1|1:33:25,8 -chr20 161698 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140680;QSTRAND=+ GT:DP:AD 1|0:43:18,25 ./.:34:18,16 1|1:38:17,21 -chr20 161730 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=140712;QSTRAND=+ GT:DP:AD 1|0:32:11,21 ./.:35:15,20 1|1:28:16,12 -chr20 161734 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=140716;QSTRAND=+ GT:DP:AD 1|0:45:20,25 ./.:31:21,10 1|1:26:12,14 -chr20 161770 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140752;QSTRAND=+ GT:DP:AD 1|0:19:7,12 ./.:39:16,23 1|1:29:12,17 -chr20 161914 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=140896;QSTRAND=+ GT:DP:AD 1|0:32:12,20 ./.:25:20,5 1|1:20:7,13 -chr20 161918 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=115449;QSTRAND=+ GT:DP:AD 0|1:25:5,20 1|1:27:16,11 ./.:40:17,23 -chr20 161991 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140973;QSTRAND=+ GT:DP:AD 1|0:28:22,6 ./.:29:16,13 1|1:32:21,11 -chr20 162151 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=141133;QSTRAND=+ GT:DP:AD 1|1:40:19,21 1|1:25:8,17 1|1:32:8,24 -chr20 162224 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=141206;QSTRAND=+ GT:DP:AD 1|0:34:15,19 ./.:21:16,5 1|1:30:12,18 -chr20 162225 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=141207;QSTRAND=+ GT:DP:AD 1|0:42:17,25 ./.:28:13,15 1|1:23:10,13 -chr20 162228 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=141210;QSTRAND=+ GT:DP:AD 1|0:26:10,16 ./.:27:5,22 1|1:41:21,20 -chr20 162268 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=141250;QSTRAND=+ GT:DP:AD 1|0:37:19,18 ./.:44:25,19 1|1:42:23,19 -chr20 162455 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=141437;QSTRAND=+ GT:DP:AD 1|0:15:7,8 ./.:39:20,19 1|1:18:6,12 -chr20 162806 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=116337;QSTRAND=+ GT:DP:AD 0|1:48:24,24 1|1:31:12,19 ./.:30:24,6 -chr20 162854 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=141836;QSTRAND=+ GT:DP:AD 1|0:44:25,19 ./.:24:14,10 1|1:23:11,12 -chr20 162932 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=141914;QSTRAND=+ GT:DP:AD 1|0:19:14,5 ./.:39:25,14 1|1:36:11,25 -chr20 163082 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=142064;QSTRAND=+ GT:DP:AD 1|0:45:22,23 ./.:16:8,8 1|1:28:10,18 -chr20 163113 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=142095;QSTRAND=+ GT:DP:AD 1|0:14:7,7 ./.:29:11,18 1|1:24:12,12 -chr20 163277 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=142259;QSTRAND=+ GT:DP:AD 1|1:15:9,6 1|1:49:25,24 1|1:46:24,22 -chr20 163741 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=117272;QSTRAND=+ GT:DP:AD 0|1:23:9,14 1|1:26:7,19 ./.:28:10,18 -chr20 163894 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=117425;QSTRAND=+ GT:DP:AD 0|1:30:18,12 1|1:26:18,8 ./.:17:6,11 -chr20 163919 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=117450;QSTRAND=+ GT:DP:AD 0|1:45:22,23 1|1:22:14,8 ./.:35:15,20 -chr20 163929 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=117460;QSTRAND=+ GT:DP:AD 0|1:35:14,21 1|1:34:25,9 ./.:31:21,10 -chr20 164191 . C CT 60 . QNAME=HG002-S9-H2-000001F;QSTART=117723;QSTRAND=+ GT:DP:AD 0|1:35:19,16 1|1:25:18,7 ./.:36:17,19 -chr20 164243 . CCTT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=117776;QSTRAND=+ GT:DP:AD 0|1:30:7,23 1|1:28:9,19 ./.:31:20,11 -chr20 164258 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=117787;QSTRAND=+ GT:DP:AD 0|1:28:21,7 1|1:26:20,6 ./.:26:5,21 -chr20 164569 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=143551;QSTRAND=+ GT:DP:AD 1|1:37:22,15 1|1:37:20,17 1|1:30:21,9 -chr20 164616 . G GC 60 . QNAME=HG002-S9-H2-000001F;QSTART=118146;QSTRAND=+ GT:DP:AD 0|1:17:5,12 1|1:25:11,14 ./.:23:11,12 -chr20 164772 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=118302;QSTRAND=+ GT:DP:AD 0|1:44:21,23 1|1:20:13,7 ./.:40:20,20 -chr20 165108 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=118638;QSTRAND=+ GT:DP:AD 0|1:30:20,10 1|1:22:12,10 ./.:26:9,17 -chr20 165108 . C CAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=144091;QSTRAND=+ GT:DP:AD 1|0:27:9,18 ./.:26:9,17 ./.:24:9,15 -chr20 165108 . C CACAT 60 . QNAME=cluster23_scaffold_3;QSTART=25546750;QSTRAND=- GT:DP:AD ./.:31:19,12 ./.:39:20,19 1|1:35:16,19 -chr20 165212 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=144196;QSTRAND=+ GT:DP:AD 1|0:23:12,11 ./.:43:24,19 1|1:26:16,10 diff --git a/repo_utils/test_files/answer_key/divided/multi_00000002.vcf b/repo_utils/test_files/answer_key/divided/multi_00000002.vcf deleted file mode 100644 index 2b42ac9d..00000000 --- a/repo_utils/test_files/answer_key/divided/multi_00000002.vcf +++ /dev/null @@ -1,197 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##bcftools_mergeVersion=1.12+htslib-1.12 -##bcftools_mergeCommand=merge -O z -f x -m none input1.vcf.gz input2.vcf.gz input3.vcf.gz; Date=Mon Aug 16 18:05:13 2021 -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 166310 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=145294;QSTRAND=+ GT:DP:AD 1|0:41:16,25 ./.:45:25,20 1|1:14:6,8 -chr20 166354 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=119884;QSTRAND=+ GT:DP:AD 0|1:40:15,25 1|1:29:20,9 ./.:37:13,24 -chr20 166856 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=145840;QSTRAND=+ GT:DP:AD 1|0:30:9,21 ./.:33:25,8 1|1:44:23,21 -chr20 166960 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=145945;QSTRAND=+ GT:DP:AD 1|0:40:20,20 ./.:30:15,15 1|1:46:21,25 -chr20 167044 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=146027;QSTRAND=+ GT:DP:AD 1|0:17:10,7 ./.:33:15,18 1|1:42:23,19 -chr20 167104 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25529412;QSTRAND=- GT:DP:AD ./.:42:18,24 ./.:33:25,8 0|1:15:10,5 -chr20 167274 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=146257;QSTRAND=+ GT:DP:AD 1|0:29:16,13 ./.:36:21,15 1|1:36:22,14 -chr20 167276 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=146259;QSTRAND=+ GT:DP:AD 1|0:35:10,25 ./.:38:15,23 1|1:25:12,13 -chr20 167443 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=146426;QSTRAND=+ GT:DP:AD 1|1:20:14,6 1|1:15:6,9 1|1:35:12,23 -chr20 167839 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=146822;QSTRAND=+ GT:DP:AD 1|1:21:7,14 1|1:26:5,21 1|1:23:10,13 -chr20 168062 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=147045;QSTRAND=+ GT:DP:AD 1|0:30:8,22 ./.:25:14,11 1|1:26:16,10 -chr20 168478 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=147462;QSTRAND=+ GT:DP:AD 1|0:31:11,20 ./.:16:8,8 1|1:36:25,11 -chr20 168766 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=122296;QSTRAND=+ GT:DP:AD 0|1:29:18,11 1|1:29:19,10 ./.:30:13,17 -chr20 169334 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=122864;QSTRAND=+ GT:DP:AD 0|1:20:8,12 1|1:36:17,19 ./.:25:15,10 -chr20 170008 . CTACA C 60 . QNAME=cluster23_scaffold_2;QSTART=25526509;QSTRAND=- GT:DP:AD ./.:40:15,25 ./.:31:10,21 0|1:23:12,11 -chr20 170689 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=124219;QSTRAND=+ GT:DP:AD 0|1:27:9,18 1|1:25:10,15 ./.:27:18,9 -chr20 171892 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=125422;QSTRAND=+ GT:DP:AD 0|1:29:6,23 1|1:22:8,14 ./.:40:17,23 -chr20 171929 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=125459;QSTRAND=+ GT:DP:AD 0|1:36:22,14 1|1:39:15,24 0|1:36:11,25 -chr20 172156 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=125686;QSTRAND=+ GT:DP:AD 0|1:20:8,12 1|0:28:20,8 ./.:21:8,13 -chr20 172258 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=25539602;QSTRAND=- GT:DP:AD ./.:35:19,16 ./.:31:9,22 1|0:36:23,13 -chr20 172331 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=125861;QSTRAND=+ GT:DP:AD 0|1:26:13,13 1|1:42:23,19 0|1:19:13,6 -chr20 172351 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=125881;QSTRAND=+ GT:DP:AD 0|1:41:16,25 1|1:32:7,25 0|1:27:19,8 -chr20 172626 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=126156;QSTRAND=+ GT:DP:AD 0|1:27:22,5 1|1:16:5,11 0|1:34:24,10 -chr20 172657 . T TTC 60 . QNAME=HG002-S9-H2-000001F;QSTART=126188;QSTRAND=+ GT:DP:AD 0|1:40:25,15 1|1:38:16,22 0|1:19:5,14 -chr20 172752 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=126284;QSTRAND=+ GT:DP:AD 0|1:37:22,15 1|1:36:11,25 ./.:41:24,17 -chr20 172789 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=25523730;QSTRAND=- GT:DP:AD ./.:29:11,18 ./.:38:20,18 0|1:36:25,11 -chr20 173036 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25523483;QSTRAND=- GT:DP:AD ./.:46:24,22 ./.:17:12,5 0|1:36:22,14 -chr20 173050 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=126582;QSTRAND=+ GT:DP:AD 0|1:32:13,19 1|1:16:6,10 ./.:32:12,20 -chr20 173133 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25523386;QSTRAND=- GT:DP:AD ./.:28:12,16 ./.:40:24,16 0|1:38:14,24 -chr20 173215 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=152197;QSTRAND=+ GT:DP:AD 1|0:29:12,17 ./.:15:10,5 ./.:34:12,22 -chr20 173791 . CCTT C 60 . QNAME=cluster23_scaffold_2;QSTART=25522728;QSTRAND=- GT:DP:AD ./.:32:23,9 ./.:44:19,25 0|1:44:19,25 -chr20 173973 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=127505;QSTRAND=+ GT:DP:AD 0|1:35:24,11 1|1:42:17,25 ./.:35:11,24 -chr20 174069 . G A 60 . QNAME=cluster19_000000F;QSTART=133216;QSTRAND=+ GT:DP:AD ./.:36:16,20 0|1:19:12,7 ./.:49:24,25 -chr20 174270 . TC T 60 . QNAME=cluster23_scaffold_2;QSTART=25522252;QSTRAND=- GT:DP:AD ./.:40:16,24 ./.:15:10,5 0|1:26:6,20 -chr20 174280 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25522243;QSTRAND=- GT:DP:AD ./.:23:18,5 ./.:31:7,24 0|1:45:24,21 -chr20 174737 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25521786;QSTRAND=- GT:DP:AD ./.:34:10,24 ./.:18:5,13 0|1:31:7,24 -chr20 174986 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25521537;QSTRAND=- GT:DP:AD ./.:32:20,12 ./.:48:23,25 0|1:44:24,20 -chr20 175210 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25521313;QSTRAND=- GT:DP:AD ./.:24:11,13 ./.:38:16,22 0|1:23:11,12 -chr20 175239 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25521284;QSTRAND=- GT:DP:AD ./.:23:17,6 ./.:25:8,17 0|1:41:16,25 -chr20 175269 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=128801;QSTRAND=+ GT:DP:AD 0|1:28:8,20 1|1:23:13,10 0|1:36:12,24 -chr20 175314 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=128846;QSTRAND=+ GT:DP:AD 0|1:28:18,10 1|1:19:13,6 ./.:42:17,25 -chr20 175375 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25521148;QSTRAND=- GT:DP:AD ./.:30:14,16 ./.:26:15,11 0|1:38:21,17 -chr20 175501 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25521022;QSTRAND=- GT:DP:AD ./.:27:10,17 ./.:31:19,12 0|1:18:7,11 -chr20 175524 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=129056;QSTRAND=+ GT:DP:AD 0|1:30:23,7 1|1:21:13,8 0|1:25:16,9 -chr20 175532 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=129064;QSTRAND=+ GT:DP:AD 0|1:43:25,18 1|1:36:21,15 0|1:28:17,11 -chr20 175563 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25520960;QSTRAND=- GT:DP:AD ./.:14:5,9 ./.:29:6,23 0|1:18:5,13 -chr20 175565 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25520958;QSTRAND=- GT:DP:AD ./.:15:8,7 ./.:29:20,9 0|1:37:24,13 -chr20 175595 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25520928;QSTRAND=- GT:DP:AD ./.:26:15,11 ./.:35:21,14 0|1:30:17,13 -chr20 175658 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25520865;QSTRAND=- GT:DP:AD ./.:32:25,7 ./.:16:10,6 0|1:47:25,22 -chr20 175659 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25520864;QSTRAND=- GT:DP:AD ./.:18:10,8 ./.:33:12,21 0|1:29:19,10 -chr20 175676 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25520847;QSTRAND=- GT:DP:AD ./.:26:18,8 ./.:38:15,23 0|1:35:14,21 -chr20 175688 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=129220;QSTRAND=+ GT:DP:AD 0|1:30:13,17 1|1:38:17,21 0|1:24:18,6 -chr20 175689 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=129221;QSTRAND=+ GT:DP:AD 0|1:28:7,21 1|1:31:13,18 0|1:27:5,22 -chr20 175813 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25520710;QSTRAND=- GT:DP:AD ./.:30:25,5 ./.:35:18,17 0|1:26:17,9 -chr20 175893 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=129425;QSTRAND=+ GT:DP:AD 0|1:38:19,19 1|1:34:14,20 0|1:23:17,6 -chr20 175897 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=129429;QSTRAND=+ GT:DP:AD 0|1:20:11,9 1|1:31:11,20 0|1:46:25,21 -chr20 176011 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=129543;QSTRAND=+ GT:DP:AD 0|1:35:25,10 1|1:40:16,24 ./.:42:21,21 -chr20 176015 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=129547;QSTRAND=+ GT:DP:AD 0|1:29:22,7 1|1:26:10,16 ./.:30:18,12 -chr20 176015 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25520508;QSTRAND=- GT:DP:AD ./.:25:10,15 ./.:36:18,18 0|1:38:19,19 -chr20 176128 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=25520395;QSTRAND=- GT:DP:AD ./.:28:12,16 ./.:18:5,13 0|1:41:17,24 -chr20 176156 . A T 60 . QNAME=cluster23_scaffold_2;QSTART=25520367;QSTRAND=- GT:DP:AD ./.:25:20,5 ./.:31:17,14 0|1:37:24,13 -chr20 176325 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25520198;QSTRAND=- GT:DP:AD ./.:27:14,13 ./.:29:9,20 0|1:39:23,16 -chr20 176400 . G GCCC 60 . QNAME=cluster23_scaffold_2;QSTART=25520120;QSTRAND=- GT:DP:AD ./.:42:25,17 ./.:19:10,9 0|1:20:7,13 -chr20 176406 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25520114;QSTRAND=- GT:DP:AD ./.:31:10,21 ./.:21:5,16 0|1:25:9,16 -chr20 176516 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=130048;QSTRAND=+ GT:DP:AD 0|1:36:14,22 1|1:35:19,16 0|1:23:12,11 -chr20 176631 . C T 60 . QNAME=cluster19_000000F;QSTART=135778;QSTRAND=+ GT:DP:AD ./.:36:20,16 0|1:29:24,5 ./.:25:8,17 -chr20 176881 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=130413;QSTRAND=+ GT:DP:AD 0|1:24:13,11 1|0:31:23,8 ./.:39:14,25 -chr20 177105 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=130637;QSTRAND=+ GT:DP:AD 0|1:26:6,20 1|1:17:6,11 0|1:18:9,9 -chr20 177210 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25519310;QSTRAND=- GT:DP:AD ./.:25:20,5 ./.:23:18,5 0|1:40:19,21 -chr20 177334 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25519186;QSTRAND=- GT:DP:AD ./.:33:15,18 ./.:47:24,23 0|1:23:5,18 -chr20 177335 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=130867;QSTRAND=+ GT:DP:AD 0|1:27:16,11 1|1:18:9,9 0|1:18:13,5 -chr20 177343 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25519177;QSTRAND=- GT:DP:AD ./.:38:22,16 ./.:28:7,21 0|1:29:14,15 -chr20 177473 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=131005;QSTRAND=+ GT:DP:AD 0|1:37:17,20 1|1:43:18,25 0|1:29:23,6 -chr20 177674 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=131206;QSTRAND=+ GT:DP:AD 0|1:37:17,20 1|1:20:9,11 ./.:25:19,6 -chr20 177749 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25518771;QSTRAND=- GT:DP:AD ./.:26:21,5 ./.:23:7,16 0|1:20:5,15 -chr20 177793 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=131325;QSTRAND=+ GT:DP:AD 0|1:34:20,14 1|1:25:14,11 ./.:32:7,25 -chr20 177854 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=131386;QSTRAND=+ GT:DP:AD 0|1:35:12,23 1|1:31:19,12 0|1:20:11,9 -chr20 178043 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25518477;QSTRAND=- GT:DP:AD ./.:20:15,5 ./.:29:19,10 0|1:27:14,13 -chr20 178049 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25518471;QSTRAND=- GT:DP:AD ./.:22:5,17 ./.:35:16,19 0|1:28:15,13 -chr20 178343 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25518177;QSTRAND=- GT:DP:AD ./.:28:15,13 ./.:26:16,10 0|1:43:21,22 -chr20 178456 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25518064;QSTRAND=- GT:DP:AD ./.:29:7,22 ./.:42:20,22 0|1:28:11,17 -chr20 178604 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25517916;QSTRAND=- GT:DP:AD ./.:22:7,15 ./.:40:24,16 0|1:40:17,23 -chr20 178648 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=132180;QSTRAND=+ GT:DP:AD 0|1:20:5,15 1|1:27:12,15 ./.:27:6,21 -chr20 178883 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25517637;QSTRAND=- GT:DP:AD ./.:33:19,14 ./.:21:9,12 0|1:22:16,6 -chr20 179104 . A C 60 . QNAME=cluster23_scaffold_2;QSTART=25517416;QSTRAND=- GT:DP:AD ./.:33:11,22 ./.:28:6,22 0|1:37:16,21 -chr20 179470 . A AT 60 . QNAME=HG002-S9-H2-000001F;QSTART=133003;QSTRAND=+ GT:DP:AD 0|1:25:8,17 1|1:27:5,22 0|1:42:25,17 -chr20 179567 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=133100;QSTRAND=+ GT:DP:AD 0|1:26:8,18 1|1:24:11,13 0|1:27:20,7 -chr20 179575 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25516944;QSTRAND=- GT:DP:AD ./.:41:16,25 ./.:23:9,14 0|1:38:20,18 -chr20 179892 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=133425;QSTRAND=+ GT:DP:AD 0|1:33:16,17 1|1:29:21,8 ./.:26:6,20 -chr20 179910 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=133443;QSTRAND=+ GT:DP:AD 0|1:22:17,5 1|1:30:20,10 0|1:44:20,24 -chr20 180809 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=134342;QSTRAND=+ GT:DP:AD 0|1:33:25,8 1|1:46:24,22 0|1:49:25,24 -chr20 180861 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25515658;QSTRAND=- GT:DP:AD ./.:28:7,21 ./.:41:17,24 0|1:33:25,8 -chr20 180945 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25515574;QSTRAND=- GT:DP:AD ./.:21:16,5 ./.:28:8,20 0|1:23:7,16 -chr20 181095 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25515424;QSTRAND=- GT:DP:AD ./.:19:12,7 ./.:27:17,10 0|1:12:7,5 -chr20 181461 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25515058;QSTRAND=- GT:DP:AD ./.:28:7,21 ./.:15:6,9 0|1:31:8,23 -chr20 181576 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25514943;QSTRAND=- GT:DP:AD ./.:40:15,25 ./.:19:9,10 0|1:35:20,15 -chr20 181650 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25514869;QSTRAND=- GT:DP:AD ./.:32:15,17 ./.:23:13,10 0|1:17:10,7 -chr20 181651 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25514868;QSTRAND=- GT:DP:AD ./.:38:16,22 ./.:16:7,9 0|1:28:21,7 -chr20 181704 . AAAAT A 60 . QNAME=cluster23_scaffold_2;QSTART=25514815;QSTRAND=- GT:DP:AD ./.:37:24,13 ./.:38:17,21 0|1:38:25,13 -chr20 182042 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=135575;QSTRAND=+ GT:DP:AD 0|1:36:22,14 1|1:38:15,23 ./.:27:11,16 -chr20 182056 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=25514467;QSTRAND=- GT:DP:AD ./.:34:21,13 ./.:36:13,23 0|1:32:13,19 -chr20 182966 . A AAT 60 . QNAME=HG002-S9-H2-000001F;QSTART=136500;QSTRAND=+ GT:DP:AD 0|1:22:7,15 1|1:33:25,8 0|1:39:14,25 -chr20 182982 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25513539;QSTRAND=- GT:DP:AD ./.:50:25,25 ./.:31:8,23 0|1:35:18,17 -chr20 183100 . T TACACAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=136636;QSTRAND=+ GT:DP:AD 0|1:46:22,24 1|1:24:19,5 ./.:23:14,9 -chr20 183100 . T TAC 60 . QNAME=cluster23_scaffold_2;QSTART=25513419;QSTRAND=- GT:DP:AD ./.:43:22,21 ./.:22:6,16 0|1:26:20,6 -chr20 183442 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25513077;QSTRAND=- GT:DP:AD ./.:42:20,22 ./.:26:11,15 0|1:32:22,10 -chr20 183617 . G GGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAA 60 . QNAME=cluster23_scaffold_2;QSTART=25512867;QSTRAND=-;SVTYPE=INS;SVLEN=35 GT:DP:AD ./.:35:16,19 ./.:32:20,12 0/1:24:11,13 -chr20 183638 . G GAAAAC 60 . QNAME=cluster19_000000F;QSTART=142795;QSTRAND=+ GT:DP:AD ./.:30:6,24 0|1:45:25,20 ./.:40:19,21 -chr20 183643 . G C 60 . QNAME=cluster19_000000F;QSTART=142804;QSTRAND=+ GT:DP:AD ./.:37:17,20 0|1:33:24,9 ./.:27:12,15 -chr20 183643 . G GAAAAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=137185;QSTRAND=+ GT:DP:AD 0|1:41:22,19 1|0:40:25,15 ./.:30:17,13 -chr20 183699 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=137245;QSTRAND=+ GT:DP:AD 0|1:31:23,8 1|1:37:21,16 ./.:47:24,23 -chr20 183795 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25512689;QSTRAND=- GT:DP:AD ./.:23:18,5 ./.:31:7,24 0|1:49:24,25 -chr20 184483 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25512001;QSTRAND=- GT:DP:AD ./.:32:10,22 ./.:43:23,20 0|1:30:19,11 -chr20 184792 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25511692;QSTRAND=- GT:DP:AD ./.:18:9,9 ./.:23:7,16 0|1:38:13,25 -chr20 184838 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25511646;QSTRAND=- GT:DP:AD ./.:42:25,17 ./.:28:15,13 0|1:17:7,10 -chr20 185161 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=25511323;QSTRAND=- GT:DP:AD ./.:29:13,16 ./.:21:11,10 0|1:31:11,20 -chr20 185267 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=138813;QSTRAND=+ GT:DP:AD 0|1:31:22,9 1|1:49:24,25 0|1:44:19,25 -chr20 185522 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25510962;QSTRAND=- GT:DP:AD ./.:41:24,17 ./.:47:24,23 0|1:23:7,16 -chr20 185547 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25510937;QSTRAND=- GT:DP:AD ./.:23:11,12 ./.:48:24,24 0|1:30:22,8 -chr20 185835 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25510648;QSTRAND=- GT:DP:AD ./.:33:20,13 ./.:19:6,13 0|1:37:18,19 -chr20 186086 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=139632;QSTRAND=+ GT:DP:AD 0|1:24:18,6 1|1:43:22,21 ./.:30:15,15 -chr20 186099 . C CAA 60 . QNAME=cluster23_scaffold_2;QSTART=25510382;QSTRAND=- GT:DP:AD ./.:22:6,16 ./.:21:14,7 0|1:41:25,16 -chr20 186183 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=139729;QSTRAND=+ GT:DP:AD 0|1:34:18,16 1|1:25:7,18 ./.:24:7,17 -chr20 186577 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25509904;QSTRAND=- GT:DP:AD ./.:20:12,8 ./.:18:7,11 0|1:23:7,16 -chr20 186669 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=140215;QSTRAND=+ GT:DP:AD 0|1:40:23,17 1|1:29:21,8 ./.:31:14,17 -chr20 186684 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=25509797;QSTRAND=- GT:DP:AD ./.:24:17,7 ./.:28:9,19 0|1:28:15,13 -chr20 186790 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=140336;QSTRAND=+ GT:DP:AD 0|1:28:18,10 1|1:10:5,5 0|1:23:10,13 -chr20 186800 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25509681;QSTRAND=- GT:DP:AD ./.:28:19,9 ./.:19:13,6 0|1:31:8,23 -chr20 186814 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25509667;QSTRAND=- GT:DP:AD ./.:24:17,7 ./.:46:21,25 0|1:39:21,18 -chr20 187006 . T A 60 . QNAME=cluster23_scaffold_2;QSTART=25509475;QSTRAND=- GT:DP:AD ./.:41:16,25 ./.:33:25,8 0|1:35:22,13 -chr20 187133 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25509348;QSTRAND=- GT:DP:AD ./.:30:17,13 ./.:41:24,17 0|1:46:23,23 -chr20 187259 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=25509222;QSTRAND=- GT:DP:AD ./.:32:18,14 ./.:28:13,15 0|1:34:22,12 -chr20 187379 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25509102;QSTRAND=- GT:DP:AD ./.:34:15,19 ./.:28:13,15 0|1:22:9,13 -chr20 187439 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=140985;QSTRAND=+ GT:DP:AD 0|1:33:14,19 1|1:26:15,11 ./.:24:13,11 -chr20 187498 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25508983;QSTRAND=- GT:DP:AD ./.:20:5,15 ./.:18:13,5 0|1:35:21,14 -chr20 187600 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25508881;QSTRAND=- GT:DP:AD ./.:15:7,8 ./.:36:18,18 0|1:23:10,13 -chr20 187825 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=141371;QSTRAND=+ GT:DP:AD 0|1:31:12,19 1|1:16:8,8 ./.:41:24,17 -chr20 188087 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=141633;QSTRAND=+ GT:DP:AD 0|1:20:13,7 1|1:41:23,18 0|1:25:15,10 -chr20 188490 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25507991;QSTRAND=- GT:DP:AD ./.:18:7,11 ./.:18:7,11 0|1:26:21,5 -chr20 189060 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=142606;QSTRAND=+ GT:DP:AD 0|1:14:8,6 1|1:42:18,24 ./.:30:6,24 -chr20 189354 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=142900;QSTRAND=+ GT:DP:AD 0|1:24:9,15 1|1:21:11,10 0|1:34:21,13 -chr20 189473 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25507008;QSTRAND=- GT:DP:AD ./.:33:17,16 ./.:34:23,11 0|1:48:25,23 -chr20 189948 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=143494;QSTRAND=+ GT:DP:AD 0|1:23:6,17 1|1:40:19,21 0|1:26:21,5 -chr20 190001 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=143547;QSTRAND=+ GT:DP:AD 0|1:14:6,8 1|1:44:20,24 0|1:29:10,19 -chr20 190548 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=144094;QSTRAND=+ GT:DP:AD 0|1:34:13,21 1|1:41:18,23 ./.:37:19,18 -chr20 190675 . C CTT 60 . QNAME=HG002-S9-H2-000001F;QSTART=144222;QSTRAND=+ GT:DP:AD 0|1:23:7,16 1|1:36:25,11 ./.:45:20,25 -chr20 190675 . C CT 60 . QNAME=cluster23_scaffold_2;QSTART=25505805;QSTRAND=- GT:DP:AD ./.:26:6,20 ./.:27:9,18 0|1:24:11,13 -chr20 190950 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=144498;QSTRAND=+ GT:DP:AD 0|1:26:8,18 1|1:28:20,8 ./.:45:24,21 -chr20 190986 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=144534;QSTRAND=+ GT:DP:AD 0|1:37:24,13 1|1:42:21,21 ./.:33:23,10 -chr20 191069 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25505411;QSTRAND=- GT:DP:AD ./.:35:24,11 ./.:24:13,11 0|1:24:5,19 -chr20 191221 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=170203;QSTRAND=+ GT:DP:AD 1|0:43:20,23 ./.:25:7,18 ./.:44:21,23 -chr20 191726 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=145275;QSTRAND=+ GT:DP:AD 0|1:33:20,13 1|1:34:19,15 ./.:24:13,11 -chr20 191726 . C CTT 60 . QNAME=cluster23_scaffold_3;QSTART=25520132;QSTRAND=- GT:DP:AD ./.:32:18,14 ./.:17:5,12 1|0:23:15,8 -chr20 191726 . CTT C 60 . QNAME=cluster23_scaffold_2;QSTART=25504754;QSTRAND=- GT:DP:AD ./.:16:8,8 ./.:41:22,19 0|1:43:24,19 -chr20 191877 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=145424;QSTRAND=+ GT:DP:AD 0|1:38:25,13 1|1:48:25,23 0|1:40:16,24 -chr20 192100 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=145647;QSTRAND=+ GT:DP:AD 0|1:21:8,13 1|1:23:17,6 0|1:32:16,16 diff --git a/repo_utils/test_files/answer_key/divided/multi_00000003.vcf b/repo_utils/test_files/answer_key/divided/multi_00000003.vcf deleted file mode 100644 index a798977e..00000000 --- a/repo_utils/test_files/answer_key/divided/multi_00000003.vcf +++ /dev/null @@ -1,373 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##bcftools_mergeVersion=1.12+htslib-1.12 -##bcftools_mergeCommand=merge -O z -f x -m none input1.vcf.gz input2.vcf.gz input3.vcf.gz; Date=Mon Aug 16 18:05:13 2021 -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 193110 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=146657;QSTRAND=+ GT:DP:AD 0|1:30:23,7 1|1:12:5,7 0|1:22:16,6 -chr20 193428 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=146975;QSTRAND=+ GT:DP:AD 0|1:35:16,19 1|1:30:19,11 0|1:27:19,8 -chr20 193735 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25502747;QSTRAND=- GT:DP:AD ./.:17:8,9 ./.:29:23,6 0|1:39:19,20 -chr20 193942 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=25502540;QSTRAND=- GT:DP:AD ./.:26:18,8 ./.:19:10,9 0|1:20:8,12 -chr20 193996 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25502486;QSTRAND=- GT:DP:AD ./.:37:23,14 ./.:43:22,21 0|1:39:17,22 -chr20 194746 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=148293;QSTRAND=+ GT:DP:AD 0|1:24:11,13 1|1:38:19,19 0|1:27:12,15 -chr20 195745 . CGTGTGT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=149293;QSTRAND=+ GT:DP:AD 0|1:22:8,14 1|1:25:13,12 ./.:42:24,18 -chr20 195745 . CGTGT C 60 . QNAME=cluster23_scaffold_3;QSTART=25516113;QSTRAND=- GT:DP:AD ./.:39:19,20 ./.:43:19,24 1|0:20:6,14 -chr20 195745 . C CGT 60 . QNAME=cluster23_scaffold_2;QSTART=25500735;QSTRAND=- GT:DP:AD ./.:41:19,22 ./.:25:8,17 0|1:26:12,14 -chr20 195977 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25500503;QSTRAND=- GT:DP:AD ./.:20:8,12 ./.:39:25,14 0|1:45:22,23 -chr20 196106 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25515756;QSTRAND=- GT:DP:AD ./.:18:7,11 ./.:35:23,12 1|0:28:16,12 -chr20 196584 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=175566;QSTRAND=+ GT:DP:AD 1|0:29:19,10 ./.:23:17,6 1|1:20:7,13 -chr20 196609 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=175591;QSTRAND=+ GT:DP:AD 1|0:20:13,7 ./.:20:14,6 1|0:20:15,5 -chr20 198088 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25513774;QSTRAND=- GT:DP:AD ./.:40:24,16 ./.:34:23,11 1|0:45:23,22 -chr20 198171 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=177153;QSTRAND=+ GT:DP:AD 1|0:27:19,8 ./.:38:17,21 1|1:23:18,5 -chr20 198174 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=177156;QSTRAND=+ GT:DP:AD 1|0:34:11,23 ./.:42:22,20 1|0:14:8,6 -chr20 198215 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=177197;QSTRAND=+ GT:DP:AD 1|0:33:20,13 ./.:31:13,18 1|1:33:9,24 -chr20 198433 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25498047;QSTRAND=- GT:DP:AD ./.:31:7,24 ./.:27:20,7 0|1:25:14,11 -chr20 198814 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=177796;QSTRAND=+ GT:DP:AD 1|0:31:18,13 ./.:17:7,10 1|0:21:9,12 -chr20 198921 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=177903;QSTRAND=+ GT:DP:AD 1|0:15:9,6 ./.:12:5,7 1|1:31:8,23 -chr20 199123 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=178105;QSTRAND=+ GT:DP:AD 1|0:34:18,16 ./.:33:19,14 1|0:36:18,18 -chr20 199139 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=178122;QSTRAND=+ GT:DP:AD 1|0:20:12,8 ./.:48:24,24 ./.:24:9,15 -chr20 199139 . C CTT 60 . QNAME=cluster23_scaffold_3;QSTART=25512721;QSTRAND=- GT:DP:AD ./.:18:5,13 ./.:33:9,24 1|1:44:19,25 -chr20 199741 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25496737;QSTRAND=- GT:DP:AD ./.:44:20,24 ./.:34:9,25 0|1:15:10,5 -chr20 200997 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=179980;QSTRAND=+ GT:DP:AD 1|0:28:10,18 ./.:34:12,22 1|0:26:12,14 -chr20 201076 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25510784;QSTRAND=- GT:DP:AD ./.:27:20,7 ./.:33:18,15 1|0:35:12,23 -chr20 201326 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=180309;QSTRAND=+ GT:DP:AD 1|0:36:14,22 ./.:25:20,5 1|0:36:17,19 -chr20 201372 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=180355;QSTRAND=+ GT:DP:AD 1|0:39:20,19 ./.:20:11,9 1|1:41:23,18 -chr20 201418 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=180401;QSTRAND=+ GT:DP:AD 1|0:28:17,11 ./.:38:18,20 1|0:31:24,7 -chr20 201525 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25494953;QSTRAND=- GT:DP:AD ./.:36:16,20 ./.:15:10,5 0|1:43:21,22 -chr20 201908 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25494570;QSTRAND=- GT:DP:AD ./.:19:6,13 ./.:27:20,7 0|1:17:12,5 -chr20 201932 . C CAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=180916;QSTRAND=+ GT:DP:AD 1|0:31:17,14 ./.:28:9,19 1|0:34:16,18 -chr20 201932 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=155474;QSTRAND=+ GT:DP:AD 0|1:29:21,8 ./.:24:17,7 ./.:30:7,23 -chr20 201932 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25494545;QSTRAND=- GT:DP:AD ./.:17:10,7 ./.:30:16,14 0|1:21:10,11 -chr20 202581 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=181568;QSTRAND=+ GT:DP:AD 1|0:24:14,10 ./.:39:24,15 1|0:21:8,13 -chr20 203580 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=182567;QSTRAND=+ GT:DP:AD 1|0:34:13,21 ./.:13:7,6 1|0:37:22,15 -chr20 203602 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=182589;QSTRAND=+ GT:DP:AD 1|0:32:18,14 ./.:24:8,16 ./.:36:24,12 -chr20 203620 . TCCCTCCC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=182608;QSTRAND=+ GT:DP:AD 1|0:32:8,24 ./.:22:5,17 1|0:28:5,23 -chr20 203847 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=182827;QSTRAND=+ GT:DP:AD 1|0:26:18,8 ./.:34:15,19 1|0:48:24,24 -chr20 204090 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=183070;QSTRAND=+ GT:DP:AD 1|0:21:6,15 ./.:15:10,5 1|0:30:13,17 -chr20 205285 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=184265;QSTRAND=+ GT:DP:AD 1|0:44:23,21 ./.:46:23,23 1|0:42:21,21 -chr20 205764 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=184744;QSTRAND=+ GT:DP:AD 1|0:22:6,16 ./.:38:15,23 1|1:22:17,5 -chr20 206102 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25490375;QSTRAND=- GT:DP:AD ./.:18:6,12 ./.:49:25,24 0|1:29:18,11 -chr20 206175 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=185156;QSTRAND=+ GT:DP:AD 1|0:40:24,16 ./.:13:5,8 ./.:28:10,18 -chr20 206175 . TAAAA T 60 . QNAME=cluster23_scaffold_2;QSTART=25490302;QSTRAND=- GT:DP:AD ./.:39:23,16 ./.:28:19,9 0|1:39:21,18 -chr20 206197 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25490284;QSTRAND=- GT:DP:AD ./.:37:15,22 ./.:16:9,7 0|1:33:21,12 -chr20 206446 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25490035;QSTRAND=- GT:DP:AD ./.:12:5,7 ./.:21:7,14 0|1:40:19,21 -chr20 207202 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=186184;QSTRAND=+ GT:DP:AD 1|0:36:11,25 ./.:25:17,8 1|1:34:21,13 -chr20 207307 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25489173;QSTRAND=- GT:DP:AD ./.:25:10,15 ./.:39:22,17 0|1:25:12,13 -chr20 207389 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=186371;QSTRAND=+ GT:DP:AD 1|0:37:19,18 ./.:33:18,15 1|1:32:19,13 -chr20 207466 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25489014;QSTRAND=- GT:DP:AD ./.:36:14,22 ./.:31:12,19 0|1:21:14,7 -chr20 208792 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=187775;QSTRAND=+ GT:DP:AD 1|0:39:21,18 ./.:39:22,17 1|1:45:20,25 -chr20 209694 . A C 60 . QNAME=cluster23_scaffold_2;QSTART=25486787;QSTRAND=- GT:DP:AD ./.:43:21,22 ./.:25:7,18 0|1:40:21,19 -chr20 210024 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25486457;QSTRAND=- GT:DP:AD ./.:27:22,5 ./.:29:6,23 0|1:44:22,22 -chr20 211156 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=190137;QSTRAND=+ GT:DP:AD 1|0:13:5,8 ./.:24:7,17 1|1:28:19,9 -chr20 211168 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=190149;QSTRAND=+ GT:DP:AD 1|0:26:10,16 ./.:25:19,6 1|1:27:12,15 -chr20 211428 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=190409;QSTRAND=+ GT:DP:AD 1|0:43:22,21 ./.:22:7,15 1|1:31:7,24 -chr20 212919 . AC A 60 . QNAME=cluster23_scaffold_2;QSTART=25483562;QSTRAND=- GT:DP:AD ./.:34:21,13 ./.:18:10,8 0|1:30:15,15 -chr20 212994 . A AT 60 . QNAME=HG002-S9-H2-000001F;QSTART=166535;QSTRAND=+ GT:DP:AD 0|1:36:16,20 ./.:47:25,22 0|1:24:15,9 -chr20 213120 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25483361;QSTRAND=- GT:DP:AD ./.:37:15,22 ./.:32:7,25 0|1:38:15,23 -chr20 213126 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25483355;QSTRAND=- GT:DP:AD ./.:36:25,11 ./.:16:5,11 0|1:35:19,16 -chr20 213223 . G C 60 . QNAME=cluster23_scaffold_2;QSTART=25483258;QSTRAND=- GT:DP:AD ./.:27:7,20 ./.:31:6,25 0|1:20:13,7 -chr20 213244 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25483237;QSTRAND=- GT:DP:AD ./.:30:17,13 ./.:17:5,12 0|1:21:5,16 -chr20 213641 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25498222;QSTRAND=- GT:DP:AD ./.:42:22,20 ./.:39:20,19 1|0:43:18,25 -chr20 213649 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=192630;QSTRAND=+ GT:DP:AD 1|0:35:21,14 ./.:12:6,6 ./.:12:6,6 -chr20 213886 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=192867;QSTRAND=+ GT:DP:AD 1|0:23:11,12 ./.:26:16,10 ./.:27:20,7 -chr20 214444 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=193425;QSTRAND=+ GT:DP:AD 1|0:42:20,22 ./.:25:12,13 ./.:28:15,13 -chr20 214461 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=193442;QSTRAND=+ GT:DP:AD 1|0:35:14,21 ./.:40:20,20 ./.:35:16,19 -chr20 214646 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=193627;QSTRAND=+ GT:DP:AD 1|0:40:21,19 ./.:17:5,12 ./.:31:24,7 -chr20 214796 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=193778;QSTRAND=+ GT:DP:AD 1|0:34:14,20 ./.:30:21,9 ./.:24:10,14 -chr20 214824 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=193804;QSTRAND=+ GT:DP:AD 1|0:33:8,25 ./.:34:14,20 ./.:23:16,7 -chr20 214879 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=193859;QSTRAND=+ GT:DP:AD 1|0:22:8,14 ./.:40:25,15 ./.:30:21,9 -chr20 214962 . A AT 60 . QNAME=cluster23_scaffold_2;QSTART=25481518;QSTRAND=- GT:DP:AD ./.:30:19,11 ./.:32:20,12 0|1:17:6,11 -chr20 215031 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25496832;QSTRAND=- GT:DP:AD ./.:30:17,13 ./.:26:18,8 1|0:29:6,23 -chr20 215055 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=194035;QSTRAND=+ GT:DP:AD 1|0:30:12,18 ./.:42:17,25 1|1:43:20,23 -chr20 215963 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=194943;QSTRAND=+ GT:DP:AD 1|0:20:13,7 ./.:17:8,9 ./.:27:16,11 -chr20 217163 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25479317;QSTRAND=- GT:DP:AD ./.:37:13,24 ./.:25:20,5 0|1:44:22,22 -chr20 217714 . ATATG A 60 . QNAME=cluster23_scaffold_2;QSTART=25478766;QSTRAND=- GT:DP:AD ./.:14:8,6 ./.:16:7,9 0|1:24:5,19 -chr20 217754 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=196734;QSTRAND=+ GT:DP:AD 1|1:37:21,16 1|1:31:18,13 0|1:18:9,9 -chr20 217756 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25494107;QSTRAND=- GT:DP:AD ./.:25:11,14 ./.:27:7,20 1|0:41:20,21 -chr20 219501 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=198481;QSTRAND=+ GT:DP:AD 1|0:26:15,11 ./.:32:20,12 0|1:27:6,21 -chr20 220972 . CTT C 60 . QNAME=cluster23_scaffold_2;QSTART=25475512;QSTRAND=- GT:DP:AD ./.:28:12,16 ./.:14:8,6 0|1:41:17,24 -chr20 221511 . GGGAA G 60 . QNAME=cluster23_scaffold_3;QSTART=25490352;QSTRAND=- GT:DP:AD ./.:19:10,9 ./.:18:5,13 1|1:37:12,25 -chr20 224189 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=203169;QSTRAND=+ GT:DP:AD 1|0:32:9,23 ./.:41:16,25 0|1:26:12,14 -chr20 225761 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=204741;QSTRAND=+ GT:DP:AD 1|0:22:5,17 ./.:35:16,19 0|1:33:14,19 -chr20 225955 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=204935;QSTRAND=+ GT:DP:AD 1|1:28:22,6 1|1:31:19,12 1|1:37:25,12 -chr20 226775 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=205755;QSTRAND=+ GT:DP:AD 1|0:25:12,13 ./.:36:22,14 0|1:46:23,23 -chr20 227248 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=206228;QSTRAND=+ GT:DP:AD 1|0:14:9,5 ./.:17:11,6 ./.:38:16,22 -chr20 227262 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25484605;QSTRAND=- GT:DP:AD ./.:33:15,18 ./.:25:9,16 1|0:16:11,5 -chr20 227527 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=206507;QSTRAND=+ GT:DP:AD 1|0:41:20,21 ./.:44:23,21 1|1:23:17,6 -chr20 227692 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=25484175;QSTRAND=- GT:DP:AD ./.:28:15,13 ./.:38:19,19 1|0:32:14,18 -chr20 227704 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=206684;QSTRAND=+ GT:DP:AD 1|0:31:6,25 ./.:29:22,7 1|1:29:7,22 -chr20 227705 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25484162;QSTRAND=- GT:DP:AD ./.:27:14,13 ./.:26:17,9 1|0:35:23,12 -chr20 227706 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25484161;QSTRAND=- GT:DP:AD ./.:21:5,16 ./.:27:11,16 1|0:12:5,7 -chr20 227707 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25484160;QSTRAND=- GT:DP:AD ./.:29:13,16 ./.:25:7,18 1|0:24:5,19 -chr20 227909 . T G 60 . QNAME=cluster23_scaffold_3;QSTART=25483958;QSTRAND=- GT:DP:AD ./.:13:6,7 ./.:32:19,13 1|0:22:8,14 -chr20 228044 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25483823;QSTRAND=- GT:DP:AD ./.:28:14,14 ./.:20:8,12 1|0:38:17,21 -chr20 228258 . GCTTCTAATGTTTTTAT G 60 . QNAME=cluster23_scaffold_2;QSTART=25468232;QSTRAND=- GT:DP:AD ./.:49:25,24 ./.:19:12,7 0|1:28:5,23 -chr20 228763 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25467743;QSTRAND=- GT:DP:AD ./.:39:20,19 ./.:38:17,21 0|1:24:7,17 -chr20 229210 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25482657;QSTRAND=- GT:DP:AD ./.:39:23,16 ./.:27:5,22 1|0:27:10,17 -chr20 229265 . T TCTC 60 . QNAME=cluster23_scaffold_3;QSTART=25482599;QSTRAND=- GT:DP:AD ./.:33:14,19 ./.:29:9,20 1|0:38:25,13 -chr20 229420 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=208400;QSTRAND=+ GT:DP:AD 1|0:33:17,16 ./.:24:9,15 ./.:38:24,14 -chr20 229665 . C G 60 . QNAME=cluster23_scaffold_3;QSTART=25482199;QSTRAND=- GT:DP:AD ./.:15:7,8 ./.:37:18,19 1|1:38:17,21 -chr20 229898 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25481966;QSTRAND=- GT:DP:AD ./.:30:19,11 ./.:36:14,22 1|0:32:13,19 -chr20 229993 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25481871;QSTRAND=- GT:DP:AD ./.:26:8,18 ./.:31:22,9 1|0:47:24,23 -chr20 230118 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25466388;QSTRAND=- GT:DP:AD ./.:33:22,11 ./.:18:7,11 0|1:22:8,14 -chr20 230234 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=209214;QSTRAND=+ GT:DP:AD 1|0:27:9,18 ./.:42:18,24 ./.:29:20,9 -chr20 230273 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25481591;QSTRAND=- GT:DP:AD ./.:47:22,25 ./.:28:17,11 1|0:32:9,23 -chr20 230354 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25481510;QSTRAND=- GT:DP:AD ./.:27:21,6 ./.:38:15,23 1|0:38:18,20 -chr20 230514 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25481350;QSTRAND=- GT:DP:AD ./.:32:18,14 ./.:20:14,6 1|0:31:23,8 -chr20 230790 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25481074;QSTRAND=- GT:DP:AD ./.:27:9,18 ./.:44:21,23 1|0:18:9,9 -chr20 230868 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=209848;QSTRAND=+ GT:DP:AD 1|0:31:7,24 ./.:25:20,5 0|1:22:16,6 -chr20 230923 . T C 60 . QNAME=cluster19_000000F;QSTART=190079;QSTRAND=+ GT:DP:AD ./.:33:12,21 0|1:20:13,7 ./.:41:20,21 -chr20 231070 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=210050;QSTRAND=+ GT:DP:AD 1|0:39:23,16 ./.:27:6,21 0|1:28:10,18 -chr20 231318 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=210298;QSTRAND=+ GT:DP:AD 1|0:26:9,17 ./.:27:13,14 ./.:28:5,23 -chr20 231710 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=210690;QSTRAND=+ GT:DP:AD 1|0:32:10,22 ./.:46:24,22 1|1:22:16,6 -chr20 231898 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=185439;QSTRAND=+ GT:DP:AD 0|1:29:6,23 1|1:39:17,22 1|0:44:24,20 -chr20 231900 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=185441;QSTRAND=+ GT:DP:AD 0|1:23:10,13 1|1:40:19,21 1|0:34:17,17 -chr20 232009 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25479855;QSTRAND=- GT:DP:AD ./.:27:10,17 ./.:23:16,7 1|0:42:24,18 -chr20 232033 . A AAAATAAAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=211014;QSTRAND=+ GT:DP:AD 1|1:33:15,18 ./.:22:14,8 ./.:19:12,7 -chr20 232033 . A AAAATAAATAAAT 60 . QNAME=cluster19_000000F;QSTART=25530755;QSTRAND=- GT:DP:AD ./.:26:10,16 1|0:26:11,15 1|0:39:16,23 -chr20 232033 . A AAAAT 60 . QNAME=cluster19_000000F;QSTART=191190;QSTRAND=+ GT:DP:AD ./.:24:12,12 0|1:28:12,16 0|1:39:16,23 -chr20 232468 . C CTT 60 . QNAME=cluster23_scaffold_3;QSTART=25479382;QSTRAND=- GT:DP:AD ./.:36:23,13 ./.:33:19,14 1|0:44:23,21 -chr20 232484 . TG T 60 . QNAME=cluster23_scaffold_3;QSTART=25479366;QSTRAND=- GT:DP:AD ./.:43:25,18 ./.:32:7,25 1|0:26:11,15 -chr20 232614 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25479237;QSTRAND=- GT:DP:AD ./.:38:14,24 ./.:19:5,14 1|0:34:24,10 -chr20 232882 . A C 60 . QNAME=cluster23_scaffold_3;QSTART=25478969;QSTRAND=- GT:DP:AD ./.:18:6,12 ./.:29:12,17 1|0:32:19,13 -chr20 233198 . TGACGG T 60 . QNAME=cluster23_scaffold_3;QSTART=25478653;QSTRAND=- GT:DP:AD ./.:30:7,23 ./.:31:12,19 1|0:20:7,13 -chr20 233213 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25478643;QSTRAND=- GT:DP:AD ./.:32:15,17 ./.:28:9,19 1|0:34:23,11 -chr20 233246 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25478610;QSTRAND=- GT:DP:AD ./.:17:12,5 ./.:36:13,23 1|0:26:14,12 -chr20 233732 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=212720;QSTRAND=+ GT:DP:AD 1|1:13:8,5 1|0:26:15,11 1|1:31:25,6 -chr20 234020 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25477836;QSTRAND=- GT:DP:AD ./.:33:22,11 ./.:25:16,9 1|0:26:8,18 -chr20 234023 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=25477833;QSTRAND=- GT:DP:AD ./.:36:24,12 ./.:36:18,18 1|0:26:11,15 -chr20 234144 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=213133;QSTRAND=+ GT:DP:AD 1|1:31:9,22 1|1:28:20,8 ./.:18:6,12 -chr20 234144 . CTTTT C 60 . QNAME=cluster23_scaffold_3;QSTART=25477712;QSTRAND=- GT:DP:AD ./.:30:13,17 ./.:24:17,7 1|0:36:15,21 -chr20 234239 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=213226;QSTRAND=+ GT:DP:AD 1|0:26:15,11 ./.:27:22,5 ./.:37:16,21 -chr20 234441 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=213428;QSTRAND=+ GT:DP:AD 1|1:21:16,5 1|0:20:11,9 ./.:37:22,15 -chr20 234630 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25477230;QSTRAND=- GT:DP:AD ./.:36:25,11 ./.:22:17,5 1|0:44:23,21 -chr20 234736 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25477124;QSTRAND=- GT:DP:AD ./.:20:6,14 ./.:17:12,5 1|0:37:19,18 -chr20 234758 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25477102;QSTRAND=- GT:DP:AD ./.:31:22,9 ./.:26:10,16 1|0:39:15,24 -chr20 234803 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=25477057;QSTRAND=- GT:DP:AD ./.:20:8,12 ./.:32:18,14 1|0:43:22,21 -chr20 234949 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25476911;QSTRAND=- GT:DP:AD ./.:34:10,24 ./.:23:6,17 1|0:20:7,13 -chr20 235000 . T G 60 . QNAME=cluster23_scaffold_3;QSTART=25476860;QSTRAND=- GT:DP:AD ./.:41:16,25 ./.:25:9,16 1|0:32:14,18 -chr20 235023 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25476837;QSTRAND=- GT:DP:AD ./.:30:9,21 ./.:30:21,9 1|0:31:14,17 -chr20 235274 . T G 60 . QNAME=cluster23_scaffold_2;QSTART=25461228;QSTRAND=- GT:DP:AD ./.:21:13,8 ./.:27:20,7 0|1:49:25,24 -chr20 235380 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=25476480;QSTRAND=- GT:DP:AD ./.:32:18,14 ./.:20:9,11 1|0:23:10,13 -chr20 235457 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25476403;QSTRAND=- GT:DP:AD ./.:21:12,9 ./.:34:16,18 1|1:25:18,7 -chr20 235579 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25476281;QSTRAND=- GT:DP:AD ./.:40:24,16 ./.:21:11,10 1|0:28:16,12 -chr20 235581 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25476279;QSTRAND=- GT:DP:AD ./.:45:23,22 ./.:16:5,11 1|0:34:9,25 -chr20 235682 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25476178;QSTRAND=- GT:DP:AD ./.:37:12,25 ./.:29:22,7 1|0:32:12,20 -chr20 236006 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25475854;QSTRAND=- GT:DP:AD ./.:31:6,25 ./.:29:18,11 1|0:29:15,14 -chr20 236109 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=215096;QSTRAND=+ GT:DP:AD 1|1:16:7,9 1|1:38:17,21 1|1:18:11,7 -chr20 236170 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=215157;QSTRAND=+ GT:DP:AD 1|1:34:22,12 1|0:23:16,7 1|1:26:8,18 -chr20 236273 . CTAAG C 60 . QNAME=cluster23_scaffold_3;QSTART=25475587;QSTRAND=- GT:DP:AD ./.:37:21,16 ./.:25:11,14 1|0:33:19,14 -chr20 236433 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=215420;QSTRAND=+ GT:DP:AD 1|1:41:22,19 1|0:29:19,10 0|1:39:25,14 -chr20 236640 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=215627;QSTRAND=+ GT:DP:AD 1|1:29:7,22 1|0:43:23,20 0|1:28:14,14 -chr20 236959 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=215947;QSTRAND=+ GT:DP:AD 1|1:44:19,25 1|0:15:7,8 ./.:31:25,6 -chr20 236959 . CTT C 60 . QNAME=cluster23_scaffold_3;QSTART=25474905;QSTRAND=- GT:DP:AD ./.:23:8,15 ./.:38:15,23 1|0:38:24,14 -chr20 237090 . A C 60 . QNAME=cluster23_scaffold_3;QSTART=25474776;QSTRAND=- GT:DP:AD ./.:33:14,19 ./.:37:12,25 1|0:26:12,14 -chr20 237210 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=216198;QSTRAND=+ GT:DP:AD 1|1:29:21,8 1|1:25:15,10 1|1:26:19,7 -chr20 237614 . A AG 60 . QNAME=HG002-S9-H1-000001F;QSTART=216603;QSTRAND=+ GT:DP:AD 1|1:23:13,10 1|0:18:5,13 1|0:18:13,5 -chr20 238142 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25473723;QSTRAND=- GT:DP:AD ./.:31:19,12 ./.:29:8,21 1|1:27:17,10 -chr20 238370 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=217359;QSTRAND=+ GT:DP:AD 1|1:41:20,21 1|0:19:7,12 1|1:25:9,16 -chr20 238458 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=217447;QSTRAND=+ GT:DP:AD 1|1:19:14,5 1|0:19:8,11 ./.:20:6,14 -chr20 238622 . ACAAGGT A 60 . QNAME=cluster23_scaffold_3;QSTART=25473243;QSTRAND=- GT:DP:AD ./.:33:24,9 ./.:49:24,25 1|1:41:22,19 -chr20 238634 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=25473237;QSTRAND=- GT:DP:AD ./.:31:19,12 ./.:26:18,8 1|1:37:20,17 -chr20 238645 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=25473226;QSTRAND=- GT:DP:AD ./.:33:20,13 ./.:28:19,9 1|1:29:20,9 -chr20 238721 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=217710;QSTRAND=+ GT:DP:AD 1|1:49:25,24 1|0:22:6,16 ./.:38:18,20 -chr20 238845 . G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=217835;QSTRAND=+ GT:DP:AD 1|1:14:5,9 1|0:29:13,16 1|1:49:25,24 -chr20 239021 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25472849;QSTRAND=- GT:DP:AD ./.:40:22,18 ./.:43:19,24 1|1:36:17,19 -chr20 239041 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25457466;QSTRAND=- GT:DP:AD ./.:16:8,8 ./.:41:18,23 0|1:30:16,14 -chr20 239418 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=218408;QSTRAND=+ GT:DP:AD 1|1:41:21,20 1|0:25:6,19 ./.:25:9,16 -chr20 239441 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25457065;QSTRAND=- GT:DP:AD ./.:18:10,8 ./.:33:21,12 0|1:33:11,22 -chr20 239444 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=218434;QSTRAND=+ GT:DP:AD 1|1:10:5,5 1|0:24:16,8 ./.:24:18,6 -chr20 239451 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=218441;QSTRAND=+ GT:DP:AD 1|1:18:5,13 1|0:12:6,6 ./.:38:13,25 -chr20 239556 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=218546;QSTRAND=+ GT:DP:AD 1|1:20:7,13 1|0:29:11,18 1|1:29:15,14 -chr20 239563 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=218553;QSTRAND=+ GT:DP:AD 1|1:48:24,24 1|0:21:11,10 1|1:33:25,8 -chr20 239613 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25456893;QSTRAND=- GT:DP:AD ./.:26:19,7 ./.:35:19,16 0|1:15:7,8 -chr20 239649 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25472221;QSTRAND=- GT:DP:AD ./.:17:12,5 ./.:39:16,23 1|1:31:25,6 -chr20 239662 . A C 60 . QNAME=cluster23_scaffold_3;QSTART=25472208;QSTRAND=- GT:DP:AD ./.:16:6,10 ./.:32:22,10 1|1:20:12,8 -chr20 239803 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=218793;QSTRAND=+ GT:DP:AD 1|1:40:23,17 1|0:26:10,16 ./.:29:21,8 -chr20 239945 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25471925;QSTRAND=- GT:DP:AD ./.:10:5,5 ./.:28:8,20 1|0:38:19,19 -chr20 239951 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=25471919;QSTRAND=- GT:DP:AD ./.:29:21,8 ./.:31:24,7 1|1:24:12,12 -chr20 240008 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25471862;QSTRAND=- GT:DP:AD ./.:24:10,14 ./.:24:16,8 1|1:39:20,19 -chr20 240075 . C CAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=219066;QSTRAND=+ GT:DP:AD 1|1:34:25,9 1|0:24:8,16 ./.:40:22,18 -chr20 240075 . C CAA 60 . QNAME=cluster23_scaffold_3;QSTART=25471793;QSTRAND=- GT:DP:AD ./.:17:8,9 ./.:32:19,13 1|1:39:22,17 -chr20 240116 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25471752;QSTRAND=- GT:DP:AD ./.:49:24,25 ./.:33:8,25 1|1:39:18,21 -chr20 240166 . T G 60 . QNAME=cluster23_scaffold_3;QSTART=25471702;QSTRAND=- GT:DP:AD ./.:45:23,22 ./.:15:5,10 1|1:24:18,6 -chr20 240377 . T G 60 . QNAME=cluster23_scaffold_3;QSTART=25471491;QSTRAND=- GT:DP:AD ./.:24:6,18 ./.:32:21,11 1|1:16:8,8 -chr20 240458 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25471410;QSTRAND=- GT:DP:AD ./.:28:11,17 ./.:39:23,16 1|1:25:7,18 -chr20 240477 . G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=219471;QSTRAND=+ GT:DP:AD 1|1:48:25,23 1|0:25:10,15 ./.:38:21,17 -chr20 240477 . G GAA 60 . QNAME=cluster23_scaffold_3;QSTART=25471389;QSTRAND=- GT:DP:AD ./.:40:18,22 ./.:17:11,6 1|0:37:16,21 -chr20 240477 . G GAAA 60 . QNAME=cluster23_scaffold_2;QSTART=25456024;QSTRAND=- GT:DP:AD ./.:28:8,20 ./.:23:9,14 0|1:30:6,24 -chr20 240872 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25470994;QSTRAND=- GT:DP:AD ./.:26:12,14 ./.:34:23,11 1|1:36:25,11 -chr20 241191 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25470675;QSTRAND=- GT:DP:AD ./.:31:13,18 ./.:28:12,16 1|1:35:19,16 -chr20 241301 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=220295;QSTRAND=+ GT:DP:AD 1|1:23:11,12 1|0:31:17,14 1|1:30:24,6 -chr20 241898 . C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=220893;QSTRAND=+ GT:DP:AD 1|1:22:6,16 1|0:36:18,18 ./.:16:8,8 -chr20 241991 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25469875;QSTRAND=- GT:DP:AD ./.:39:14,25 ./.:32:17,15 1|1:38:20,18 -chr20 242033 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=221028;QSTRAND=+ GT:DP:AD 1|1:26:14,12 1|0:44:23,21 ./.:36:20,16 -chr20 242067 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=221062;QSTRAND=+ GT:DP:AD 1|1:40:25,15 1|0:39:21,18 ./.:40:20,20 -chr20 242195 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=221190;QSTRAND=+ GT:DP:AD 1|1:37:18,19 1|0:30:12,18 1|1:28:9,19 -chr20 242353 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=221348;QSTRAND=+ GT:DP:AD 1|1:23:6,17 1|0:22:9,13 ./.:29:18,11 -chr20 242531 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=221526;QSTRAND=+ GT:DP:AD 1|1:26:13,13 1|0:19:11,8 ./.:27:21,6 -chr20 242614 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=221609;QSTRAND=+ GT:DP:AD 1|1:26:15,11 1|0:39:22,17 ./.:30:13,17 -chr20 242798 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=221793;QSTRAND=+ GT:DP:AD 1|1:25:15,10 1|0:24:13,11 ./.:27:9,18 -chr20 242897 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=221892;QSTRAND=+ GT:DP:AD 1|1:36:25,11 1|0:39:17,22 1|1:33:16,17 -chr20 243066 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25468800;QSTRAND=- GT:DP:AD ./.:21:15,6 ./.:26:6,20 1|1:38:16,22 -chr20 243217 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=222212;QSTRAND=+ GT:DP:AD 1|1:33:15,18 1|0:24:19,5 1|1:41:25,16 -chr20 243487 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=222482;QSTRAND=+ GT:DP:AD 1|1:25:15,10 1|0:33:13,20 ./.:25:8,17 -chr20 243532 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=222527;QSTRAND=+ GT:DP:AD 1|1:29:5,24 1|0:19:11,8 1|1:23:13,10 -chr20 243817 . AAG A 60 . QNAME=cluster23_scaffold_3;QSTART=25468049;QSTRAND=- GT:DP:AD ./.:23:5,18 ./.:17:11,6 1|1:14:7,7 -chr20 243818 . AG A 60 . QNAME=HG002-S9-H1-000001F;QSTART=222814;QSTRAND=+ GT:DP:AD 1|1:30:7,23 1|0:29:24,5 ./.:31:17,14 -chr20 243960 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=222954;QSTRAND=+ GT:DP:AD 1|1:45:25,20 1|0:25:10,15 ./.:30:11,19 -chr20 244104 . GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=223099;QSTRAND=+ GT:DP:AD 1|1:17:8,9 1|0:18:6,12 ./.:24:19,5 -chr20 244300 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=223293;QSTRAND=+ GT:DP:AD 1|1:13:5,8 1|0:27:10,17 1|1:32:17,15 -chr20 244330 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=223323;QSTRAND=+ GT:DP:AD 1|1:32:13,19 1|0:41:21,20 1|1:17:9,8 -chr20 244417 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=223410;QSTRAND=+ GT:DP:AD 1|1:31:15,16 1|0:29:19,10 1|1:17:5,12 -chr20 244771 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=223764;QSTRAND=+ GT:DP:AD 1|1:43:23,20 1|0:46:22,24 ./.:17:10,7 -chr20 244773 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25467095;QSTRAND=- GT:DP:AD ./.:20:8,12 ./.:20:8,12 1|1:33:14,19 -chr20 244803 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=223796;QSTRAND=+ GT:DP:AD 1|1:27:13,14 1|0:40:21,19 ./.:29:5,24 -chr20 244964 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25466904;QSTRAND=- GT:DP:AD ./.:30:6,24 ./.:21:7,14 1|1:21:15,6 -chr20 244981 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25466887;QSTRAND=- GT:DP:AD ./.:33:12,21 ./.:34:14,20 1|1:30:11,19 -chr20 245127 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=224120;QSTRAND=+ GT:DP:AD 1|1:36:15,21 1|0:17:6,11 ./.:19:8,11 -chr20 245425 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25466443;QSTRAND=- GT:DP:AD ./.:20:13,7 ./.:27:8,19 1|1:36:21,15 -chr20 245437 . GTGTATGTATA G 60 . QNAME=cluster23_scaffold_3;QSTART=25466431;QSTRAND=- GT:DP:AD ./.:30:21,9 ./.:22:11,11 1|1:39:17,22 -chr20 245443 . GTA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=224437;QSTRAND=+ GT:DP:AD 1|0:47:24,23 ./.:29:19,10 ./.:30:22,8 -chr20 245443 . GTATATATA G 60 . QNAME=cluster19_000000F;QSTART=204603;QSTRAND=+ GT:DP:AD ./.:23:13,10 0|1:32:14,18 ./.:42:23,19 -chr20 245470 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=224461;QSTRAND=+ GT:DP:AD 1|0:30:8,22 ./.:26:19,7 ./.:38:23,15 -chr20 245472 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=224463;QSTRAND=+ GT:DP:AD 1|0:35:20,15 ./.:14:6,8 1|0:26:9,17 -chr20 245474 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=199028;QSTRAND=+ GT:DP:AD 0|1:28:9,19 ./.:17:8,9 ./.:16:8,8 -chr20 245512 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25466366;QSTRAND=- GT:DP:AD ./.:31:20,11 ./.:30:18,12 1|1:32:25,7 -chr20 245789 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25466089;QSTRAND=- GT:DP:AD ./.:31:25,6 ./.:42:20,22 1|1:20:12,8 -chr20 245803 . A G 60 . QNAME=cluster19_000000F;QSTART=204954;QSTRAND=+ GT:DP:AD ./.:45:20,25 0|1:39:23,16 ./.:24:11,13 -chr20 245877 . G A 60 . QNAME=cluster19_000000F;QSTART=205028;QSTRAND=+ GT:DP:AD ./.:27:5,22 0|1:49:24,25 ./.:31:9,22 -chr20 245928 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25465950;QSTRAND=- GT:DP:AD ./.:34:9,25 ./.:26:17,9 1|1:30:22,8 -chr20 246148 . T A 60 . QNAME=cluster19_000000F;QSTART=205299;QSTRAND=+ GT:DP:AD ./.:36:21,15 0|1:24:13,11 1|1:29:20,9 -chr20 246383 . G A 60 . QNAME=cluster19_000000F;QSTART=205534;QSTRAND=+ GT:DP:AD ./.:20:10,10 0|1:22:9,13 ./.:33:23,10 -chr20 246501 . G T 60 . QNAME=cluster19_000000F;QSTART=205652;QSTRAND=+ GT:DP:AD ./.:36:22,14 0|1:18:9,9 ./.:35:22,13 -chr20 246605 . A G 60 . QNAME=cluster19_000000F;QSTART=205756;QSTRAND=+ GT:DP:AD ./.:22:6,16 0|1:48:23,25 1|1:24:9,15 -chr20 246926 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25449587;QSTRAND=- GT:DP:AD ./.:35:25,10 ./.:45:22,23 0|1:24:14,10 -chr20 246986 . G GCACA 60 . QNAME=cluster23_scaffold_3;QSTART=25464888;QSTRAND=- GT:DP:AD ./.:25:8,17 ./.:32:13,19 1|1:33:13,20 -chr20 247326 . G A 60 . QNAME=cluster19_000000F;QSTART=206477;QSTRAND=+ GT:DP:AD ./.:40:16,24 0|1:26:5,21 1|1:39:16,23 -chr20 247501 . AAAAGAAAAAG A 60 . QNAME=cluster23_scaffold_3;QSTART=25464373;QSTRAND=- GT:DP:AD ./.:43:22,21 ./.:49:25,24 1|0:27:19,8 -chr20 247505 . GAA G 60 . QNAME=cluster23_scaffold_2;QSTART=25449004;QSTRAND=- GT:DP:AD ./.:24:14,10 ./.:44:19,25 0|1:18:12,6 -chr20 247512 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25448999;QSTRAND=- GT:DP:AD ./.:22:16,6 ./.:29:8,21 0|1:14:7,7 -chr20 247516 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25448995;QSTRAND=- GT:DP:AD ./.:26:14,12 ./.:27:9,18 0|1:14:9,5 -chr20 247516 . AAAGG A 60 . QNAME=HG002-S9-H1-000001F;QSTART=226508;QSTRAND=+ GT:DP:AD 1|1:23:15,8 1|0:14:6,8 ./.:23:6,17 -chr20 247516 . AAAGGAAGG A 60 . QNAME=cluster19_000000F;QSTART=206668;QSTRAND=+ GT:DP:AD ./.:27:15,12 0|1:28:5,23 ./.:36:23,13 -chr20 247565 . A C 60 . QNAME=cluster19_000000F;QSTART=206708;QSTRAND=+ GT:DP:AD ./.:32:17,15 0|1:27:9,18 1|1:27:15,12 -chr20 247714 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25464170;QSTRAND=- GT:DP:AD ./.:29:12,17 ./.:30:25,5 1|1:27:11,16 -chr20 247936 . G A 60 . QNAME=cluster19_000000F;QSTART=207079;QSTRAND=+ GT:DP:AD ./.:32:16,16 0|1:13:6,7 1|1:21:10,11 -chr20 248065 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25463819;QSTRAND=- GT:DP:AD ./.:46:22,24 ./.:30:9,21 1|1:19:13,6 -chr20 248099 . T A 60 . QNAME=cluster23_scaffold_3;QSTART=25463785;QSTRAND=- GT:DP:AD ./.:33:19,14 ./.:16:11,5 1|1:34:16,18 -chr20 248173 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25463711;QSTRAND=- GT:DP:AD ./.:32:19,13 ./.:29:11,18 1|1:11:5,6 -chr20 248248 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=25463636;QSTRAND=- GT:DP:AD ./.:14:7,7 ./.:36:16,20 1|1:18:12,6 -chr20 248357 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25463527;QSTRAND=- GT:DP:AD ./.:31:22,9 ./.:28:15,13 1|1:38:24,14 -chr20 248371 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25463513;QSTRAND=- GT:DP:AD ./.:25:5,20 ./.:20:14,6 1|1:22:11,11 -chr20 248716 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25447795;QSTRAND=- GT:DP:AD ./.:42:21,21 ./.:33:12,21 0|1:48:25,23 -chr20 248740 . C CA 60 . QNAME=cluster19_000000F;QSTART=207884;QSTRAND=+ GT:DP:AD ./.:48:24,24 0|1:35:16,19 ./.:21:6,15 -chr20 248740 . CA C 60 . QNAME=cluster23_scaffold_3;QSTART=25463144;QSTRAND=- GT:DP:AD ./.:22:8,14 ./.:28:5,23 1|0:22:17,5 -chr20 248815 . G A 60 . QNAME=cluster19_000000F;QSTART=207959;QSTRAND=+ GT:DP:AD ./.:35:13,22 0|1:17:7,10 ./.:35:14,21 -chr20 248838 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25463047;QSTRAND=- GT:DP:AD ./.:25:15,10 ./.:18:12,6 1|0:45:24,21 -chr20 248854 . T C 60 . QNAME=cluster19_000000F;QSTART=207998;QSTRAND=+ GT:DP:AD ./.:37:24,13 0|1:47:25,22 1|1:22:17,5 -chr20 249081 . T C 60 . QNAME=cluster19_000000F;QSTART=208225;QSTRAND=+ GT:DP:AD ./.:23:18,5 0|1:39:18,21 1|1:34:17,17 -chr20 249089 . C CAA 60 . QNAME=cluster19_000000F;QSTART=208234;QSTRAND=+ GT:DP:AD ./.:24:19,5 0|1:48:24,24 0|1:27:11,16 -chr20 249089 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25462795;QSTRAND=- GT:DP:AD ./.:36:12,24 ./.:20:7,13 1|0:35:20,15 -chr20 249337 . G C 60 . QNAME=cluster19_000000F;QSTART=208483;QSTRAND=+ GT:DP:AD ./.:25:11,14 0|1:25:6,19 ./.:26:12,14 -chr20 249412 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=202962;QSTRAND=+ GT:DP:AD 0|1:24:11,13 1|0:29:9,20 ./.:40:22,18 -chr20 249417 . CAT C 60 . QNAME=cluster19_000000F;QSTART=208564;QSTRAND=+ GT:DP:AD ./.:39:24,15 0|1:34:11,23 ./.:24:6,18 -chr20 249417 . CATA C 60 . QNAME=cluster23_scaffold_3;QSTART=25462467;QSTRAND=- GT:DP:AD ./.:33:22,11 ./.:15:5,10 1|1:29:20,9 -chr20 249536 . A T 60 . QNAME=cluster19_000000F;QSTART=208680;QSTRAND=+ GT:DP:AD ./.:27:20,7 0|1:41:25,16 ./.:20:9,11 -chr20 249875 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=228862;QSTRAND=+ GT:DP:AD 1|0:21:6,15 0|1:30:7,23 1|1:31:12,19 -chr20 249900 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=228887;QSTRAND=+ GT:DP:AD 1|0:26:12,14 0|1:32:23,9 1|1:24:18,6 -chr20 250218 . C T 60 . QNAME=cluster19_000000F;QSTART=209362;QSTRAND=+ GT:DP:AD ./.:26:9,17 0|1:21:12,9 ./.:19:8,11 -chr20 250342 . C T 60 . QNAME=cluster19_000000F;QSTART=209486;QSTRAND=+ GT:DP:AD ./.:25:9,16 0|1:30:8,22 ./.:17:11,6 -chr20 250449 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=229436;QSTRAND=+ GT:DP:AD 1|0:26:7,19 0|1:28:13,15 1|1:33:19,14 -chr20 250472 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=229459;QSTRAND=+ GT:DP:AD 1|0:27:9,18 ./.:26:14,12 1|1:28:13,15 -chr20 250554 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=229541;QSTRAND=+ GT:DP:AD 1|0:35:19,16 ./.:25:20,5 1|1:29:14,15 -chr20 250671 . A C 60 . QNAME=cluster19_000000F;QSTART=209815;QSTRAND=+ GT:DP:AD ./.:28:8,20 0|1:19:9,10 ./.:40:24,16 -chr20 250864 . G A 60 . QNAME=cluster19_000000F;QSTART=210008;QSTRAND=+ GT:DP:AD ./.:27:9,18 0|1:38:25,13 ./.:38:19,19 -chr20 251035 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=230022;QSTRAND=+ GT:DP:AD 1|0:40:23,17 ./.:33:23,10 1|1:35:10,25 -chr20 251370 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=230357;QSTRAND=+ GT:DP:AD 1|0:39:20,19 ./.:45:21,24 1|0:36:17,19 -chr20 251466 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=230453;QSTRAND=+ GT:DP:AD 1|0:24:10,14 0|1:16:5,11 1|1:35:10,25 -chr20 251699 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=230686;QSTRAND=+ GT:DP:AD 1|0:37:15,22 ./.:35:15,20 1|1:28:19,9 -chr20 251939 . G C 60 . QNAME=cluster19_000000F;QSTART=211083;QSTRAND=+ GT:DP:AD ./.:45:25,20 0|1:18:7,11 ./.:34:24,10 -chr20 251993 . T TACACACACACACACAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=230981;QSTRAND=+ GT:DP:AD 1|0:41:17,24 ./.:28:9,19 ./.:23:8,15 -chr20 251993 . T TACACAC 60 . QNAME=cluster19_000000F;QSTART=211138;QSTRAND=+ GT:DP:AD ./.:32:12,20 0|1:30:5,25 ./.:42:22,20 -chr20 251993 . T TACACACACAC 60 . QNAME=cluster23_scaffold_3;QSTART=25459884;QSTRAND=- GT:DP:AD ./.:16:10,6 ./.:31:10,21 1|0:38:25,13 -chr20 251993 . T TACACACACACACAC 60 . QNAME=cluster23_scaffold_2;QSTART=25444505;QSTRAND=- GT:DP:AD ./.:18:6,12 ./.:20:8,12 0|1:28:18,10 -chr20 252833 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=231836;QSTRAND=+ GT:DP:AD 1|0:32:8,24 ./.:40:20,20 1|1:16:10,6 -chr20 252834 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=231837;QSTRAND=+ GT:DP:AD 1|0:42:18,24 ./.:29:12,17 1|1:30:10,20 -chr20 252881 . GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=231885;QSTRAND=+ GT:DP:AD 1|0:32:10,22 ./.:21:16,5 1|1:47:24,23 -chr20 252982 . A T 60 . QNAME=cluster19_000000F;QSTART=212132;QSTRAND=+ GT:DP:AD ./.:36:25,11 0|1:28:12,16 ./.:37:24,13 -chr20 253238 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=232240;QSTRAND=+ GT:DP:AD 1|1:42:18,24 1|1:44:20,24 1|1:36:17,19 -chr20 253538 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=232540;QSTRAND=+ GT:DP:AD 1|0:48:23,25 0|1:35:24,11 1|1:34:22,12 -chr20 253719 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=232721;QSTRAND=+ GT:DP:AD 1|0:15:7,8 0|1:28:15,13 1|1:39:24,15 -chr20 253968 . A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25457909;QSTRAND=- GT:DP:AD ./.:23:13,10 ./.:45:21,24 1|0:24:14,10 -chr20 254466 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=233468;QSTRAND=+ GT:DP:AD 1|0:16:6,10 0|1:30:21,9 1|1:27:16,11 -chr20 255081 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=234083;QSTRAND=+ GT:DP:AD 1|0:24:10,14 0|1:27:18,9 1|1:16:10,6 -chr20 255329 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=234331;QSTRAND=+ GT:DP:AD 1|0:26:17,9 0|1:42:17,25 1|1:30:25,5 -chr20 255356 . C CAAAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=234359;QSTRAND=+ GT:DP:AD 1|0:37:19,18 0|1:36:21,15 ./.:25:11,14 -chr20 255356 . C CAAAAAAAAA 60 . QNAME=cluster23_scaffold_3;QSTART=25456512;QSTRAND=- GT:DP:AD ./.:27:15,12 ./.:13:6,7 1|1:39:21,18 -chr20 255447 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=234457;QSTRAND=+ GT:DP:AD 1|0:23:12,11 0|1:30:6,24 1|1:34:11,23 -chr20 255527 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=234537;QSTRAND=+ GT:DP:AD 1|0:33:14,19 0|1:35:23,12 1|1:43:19,24 -chr20 255597 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=234607;QSTRAND=+ GT:DP:AD 1|0:36:21,15 0|1:22:16,6 1|1:24:12,12 -chr20 255645 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=234655;QSTRAND=+ GT:DP:AD 1|0:44:22,22 0|1:27:18,9 1|1:17:12,5 -chr20 255687 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=234697;QSTRAND=+ GT:DP:AD 1|0:38:17,21 0|1:32:11,21 1|1:36:19,17 -chr20 255778 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=234788;QSTRAND=+ GT:DP:AD 1|0:38:21,17 0|1:36:25,11 1|1:43:18,25 -chr20 255818 . GAT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=234829;QSTRAND=+ GT:DP:AD 1|0:30:6,24 ./.:25:9,16 1|1:26:13,13 -chr20 255818 . G GAT 60 . QNAME=cluster19_000000F;QSTART=25506967;QSTRAND=- GT:DP:AD ./.:32:7,25 1|0:24:15,9 ./.:39:18,21 -chr20 256161 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=235169;QSTRAND=+ GT:DP:AD 1|0:46:25,21 0|1:18:7,11 1|1:32:16,16 -chr20 256351 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=235359;QSTRAND=+ GT:DP:AD 1|0:21:5,16 0|1:16:7,9 1|1:37:14,23 -chr20 256411 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=235419;QSTRAND=+ GT:DP:AD 1|0:45:23,22 0|1:30:12,18 1|1:25:18,7 -chr20 256777 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=235785;QSTRAND=+ GT:DP:AD 1|0:28:17,11 0|1:33:15,18 1|1:19:7,12 -chr20 256856 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=235864;QSTRAND=+ GT:DP:AD 1|0:34:15,19 0|1:27:13,14 1|1:25:8,17 -chr20 256904 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=235912;QSTRAND=+ GT:DP:AD 1|0:22:10,12 0|1:18:11,7 1|1:36:12,24 -chr20 256928 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=235936;QSTRAND=+ GT:DP:AD 1|0:18:6,12 0|1:19:6,13 1|1:22:10,12 -chr20 256977 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=235985;QSTRAND=+ GT:DP:AD 1|0:18:7,11 0|1:21:13,8 1|1:12:6,6 -chr20 257008 . CAGAT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=236017;QSTRAND=+ GT:DP:AD 1|1:26:20,6 0|1:36:18,18 1|1:35:15,20 -chr20 257036 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=236040;QSTRAND=+ GT:DP:AD 1|0:33:20,13 0|1:36:19,17 1|1:35:25,10 -chr20 257175 . A AT 60 . QNAME=HG002-S9-H1-000001F;QSTART=236180;QSTRAND=+ GT:DP:AD 1|0:37:24,13 0|1:23:9,14 1|1:31:22,9 -chr20 257379 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=236384;QSTRAND=+ GT:DP:AD 1|0:27:22,5 0|1:19:6,13 1|1:39:18,21 -chr20 257794 . CTGGTCT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=236800;QSTRAND=+ GT:DP:AD 1|0:28:21,7 0|1:43:19,24 1|1:36:20,16 -chr20 257866 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=236865;QSTRAND=+ GT:DP:AD 1|0:20:13,7 0|1:29:14,15 1|1:22:6,16 -chr20 257889 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=236888;QSTRAND=+ GT:DP:AD 1|0:36:12,24 0|1:24:7,17 1|1:36:14,22 -chr20 257899 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=236898;QSTRAND=+ GT:DP:AD 1|0:28:21,7 0|1:11:5,6 1|1:47:23,24 -chr20 258096 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=237095;QSTRAND=+ GT:DP:AD 1|0:33:8,25 0|1:23:18,5 1|1:17:9,8 -chr20 258653 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=237652;QSTRAND=+ GT:DP:AD 1|0:28:7,21 0|1:16:10,6 1|1:24:18,6 -chr20 258767 . A ACTGTGAAGACCTGGTCCCCACCCCCGTTTTTAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=237767;QSTRAND=+;SVTYPE=INS;SVLEN=33 GT:DP:AD 1/0:20:13,7 0/1:41:19,22 1/1:25:12,13 -chr20 258770 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=237802;QSTRAND=+ GT:DP:AD 1|0:24:12,12 0|1:48:25,23 1|1:32:7,25 -chr20 259023 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=238055;QSTRAND=+ GT:DP:AD 1|0:39:24,15 0|1:20:5,15 1|1:31:22,9 -chr20 259047 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=238079;QSTRAND=+ GT:DP:AD 1|0:27:20,7 0|1:15:9,6 1|1:34:10,24 -chr20 259056 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=238088;QSTRAND=+ GT:DP:AD 1|0:43:20,23 0|1:21:6,15 1|1:29:7,22 diff --git a/repo_utils/test_files/answer_key/divided/multi_00000004.vcf b/repo_utils/test_files/answer_key/divided/multi_00000004.vcf deleted file mode 100644 index 4e0462f1..00000000 --- a/repo_utils/test_files/answer_key/divided/multi_00000004.vcf +++ /dev/null @@ -1,224 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##bcftools_mergeVersion=1.12+htslib-1.12 -##bcftools_mergeCommand=merge -O z -f x -m none input1.vcf.gz input2.vcf.gz input3.vcf.gz; Date=Mon Aug 16 18:05:13 2021 -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 260063 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=239095;QSTRAND=+ GT:DP:AD 1|0:44:21,23 0|1:38:17,21 1|1:42:21,21 -chr20 260065 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=239097;QSTRAND=+ GT:DP:AD 1|0:35:20,15 0|1:28:11,17 1|1:31:18,13 -chr20 260593 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=239625;QSTRAND=+ GT:DP:AD 1|0:42:19,23 0|1:37:15,22 1|1:36:22,14 -chr20 260725 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=239757;QSTRAND=+ GT:DP:AD 1|0:19:5,14 0|1:18:7,11 1|1:25:19,6 -chr20 260755 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=239787;QSTRAND=+ GT:DP:AD 1|0:46:21,25 ./.:14:6,8 1|1:18:7,11 -chr20 260997 . G A 60 . QNAME=cluster19_000000F;QSTART=220179;QSTRAND=+ GT:DP:AD ./.:29:7,22 0|1:38:25,13 ./.:46:21,25 -chr20 261185 . TTTTG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=240218;QSTRAND=+ GT:DP:AD 1|0:20:7,13 ./.:22:17,5 1|1:19:9,10 -chr20 261768 . G A 60 . QNAME=cluster19_000000F;QSTART=220950;QSTRAND=+ GT:DP:AD ./.:34:10,24 0|1:35:14,21 ./.:19:14,5 -chr20 261944 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=240972;QSTRAND=+ GT:DP:AD 1|0:20:12,8 ./.:34:19,15 1|1:26:11,15 -chr20 261974 . G T 60 . QNAME=cluster19_000000F;QSTART=221156;QSTRAND=+ GT:DP:AD ./.:16:11,5 0|1:32:22,10 ./.:32:25,7 -chr20 262044 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=241072;QSTRAND=+ GT:DP:AD 1|0:31:8,23 0|1:40:19,21 1|1:40:25,15 -chr20 262053 . T C 60 . QNAME=cluster19_000000F;QSTART=221235;QSTRAND=+ GT:DP:AD ./.:39:19,20 0|1:37:12,25 ./.:30:16,14 -chr20 262157 . C T 60 . QNAME=cluster19_000000F;QSTART=221339;QSTRAND=+ GT:DP:AD ./.:48:23,25 0|1:21:11,10 ./.:33:14,19 -chr20 262198 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25434273;QSTRAND=- GT:DP:AD ./.:16:6,10 ./.:28:11,17 0|1:29:15,14 -chr20 262582 . C CT 60 . QNAME=cluster19_000000F;QSTART=221765;QSTRAND=+ GT:DP:AD ./.:30:25,5 0|1:27:16,11 ./.:22:10,12 -chr20 262711 . G T 60 . QNAME=cluster19_000000F;QSTART=221894;QSTRAND=+ GT:DP:AD ./.:24:7,17 0|1:29:9,20 ./.:45:22,23 -chr20 262757 . G C 60 . QNAME=cluster19_000000F;QSTART=221940;QSTRAND=+ GT:DP:AD ./.:11:5,6 0|1:39:21,18 ./.:37:13,24 -chr20 263038 . A C 60 . QNAME=cluster19_000000F;QSTART=222221;QSTRAND=+ GT:DP:AD ./.:19:11,8 0|1:28:20,8 ./.:44:19,25 -chr20 263283 . C A 60 . QNAME=cluster19_000000F;QSTART=222466;QSTRAND=+ GT:DP:AD ./.:31:16,15 0|1:30:9,21 ./.:15:7,8 -chr20 263451 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=242479;QSTRAND=+ GT:DP:AD 1|0:33:13,20 0|1:43:23,20 1|1:31:24,7 -chr20 263479 . G GGT 60 . QNAME=cluster19_000000F;QSTART=222663;QSTRAND=+ GT:DP:AD ./.:24:9,15 0|1:23:6,17 ./.:33:10,23 -chr20 263497 . TGTGTGTGC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=242526;QSTRAND=+ GT:DP:AD 1|0:40:24,16 ./.:31:24,7 1|1:26:7,19 -chr20 263505 . C T 60 . QNAME=cluster19_000000F;QSTART=222690;QSTRAND=+ GT:DP:AD ./.:25:15,10 0|1:22:7,15 ./.:18:13,5 -chr20 263692 . A G 60 . QNAME=cluster19_000000F;QSTART=222877;QSTRAND=+ GT:DP:AD ./.:25:18,7 0|1:18:9,9 ./.:22:8,14 -chr20 263732 . C T 60 . QNAME=cluster19_000000F;QSTART=222917;QSTRAND=+ GT:DP:AD ./.:27:22,5 0|1:26:11,15 ./.:26:21,5 -chr20 263776 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=242796;QSTRAND=+ GT:DP:AD 1|0:39:14,25 ./.:12:5,7 1|1:29:7,22 -chr20 264344 . G A 60 . QNAME=cluster19_000000F;QSTART=223529;QSTRAND=+ GT:DP:AD ./.:32:21,11 0|1:30:7,23 ./.:39:14,25 -chr20 264825 . T G 60 . QNAME=cluster19_000000F;QSTART=224010;QSTRAND=+ GT:DP:AD ./.:29:9,20 0|1:41:21,20 ./.:38:16,22 -chr20 265021 . G T 60 . QNAME=cluster19_000000F;QSTART=224206;QSTRAND=+ GT:DP:AD ./.:24:8,16 0|1:41:20,21 ./.:26:17,9 -chr20 265021 . G GT 60 . QNAME=HG002-S9-H2-000001F;QSTART=218568;QSTRAND=+ GT:DP:AD 0|1:18:13,5 1|0:24:9,15 0|1:48:24,24 -chr20 265021 . GT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=244042;QSTRAND=+ GT:DP:AD 1|0:20:9,11 ./.:41:21,20 ./.:23:16,7 -chr20 265024 . T G 60 . QNAME=cluster19_000000F;QSTART=224209;QSTRAND=+ GT:DP:AD ./.:36:13,23 0|1:36:20,16 ./.:47:25,22 -chr20 265028 . T G 60 . QNAME=cluster19_000000F;QSTART=224213;QSTRAND=+ GT:DP:AD ./.:31:20,11 0|1:36:12,24 ./.:12:6,6 -chr20 265032 . T G 60 . QNAME=cluster19_000000F;QSTART=224217;QSTRAND=+ GT:DP:AD ./.:35:25,10 0|1:27:6,21 ./.:22:8,14 -chr20 265049 . C T 60 . QNAME=cluster19_000000F;QSTART=224234;QSTRAND=+ GT:DP:AD ./.:41:24,17 0|1:28:12,16 ./.:19:9,10 -chr20 265294 . G T 60 . QNAME=cluster19_000000F;QSTART=224479;QSTRAND=+ GT:DP:AD ./.:21:15,6 0|1:27:19,8 ./.:39:17,22 -chr20 265390 . AAAG A 60 . QNAME=HG002-S9-H1-000001F;QSTART=244410;QSTRAND=+ GT:DP:AD 1|0:25:15,10 ./.:35:12,23 1|1:26:9,17 -chr20 265614 . C T 60 . QNAME=cluster19_000000F;QSTART=224799;QSTRAND=+ GT:DP:AD ./.:27:22,5 0|1:16:8,8 ./.:31:8,23 -chr20 265842 . T TTAAA 60 . QNAME=cluster19_000000F;QSTART=225028;QSTRAND=+ GT:DP:AD ./.:27:6,21 0|1:20:5,15 1|1:42:20,22 -chr20 266980 . CCT C 60 . QNAME=cluster23_scaffold_3;QSTART=25444877;QSTRAND=- GT:DP:AD ./.:32:23,9 ./.:22:8,14 1|1:29:12,17 -chr20 267423 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25429056;QSTRAND=- GT:DP:AD ./.:32:20,12 ./.:34:19,15 0|1:35:10,25 -chr20 268285 . C A 60 . QNAME=cluster23_scaffold_2;QSTART=25428194;QSTRAND=- GT:DP:AD ./.:20:5,15 ./.:27:9,18 0|1:37:21,16 -chr20 268294 . A T 60 . QNAME=cluster23_scaffold_2;QSTART=25428185;QSTRAND=- GT:DP:AD ./.:28:17,11 ./.:21:8,13 0|1:23:12,11 -chr20 268599 . T A 60 . QNAME=cluster23_scaffold_3;QSTART=25443260;QSTRAND=- GT:DP:AD ./.:32:9,23 ./.:24:13,11 1|1:29:8,21 -chr20 269435 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25442424;QSTRAND=- GT:DP:AD ./.:38:25,13 ./.:41:22,19 1|1:28:5,23 -chr20 269686 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=223234;QSTRAND=+ GT:DP:AD 0|1:31:10,21 ./.:37:16,21 ./.:27:20,7 -chr20 269844 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=223390;QSTRAND=+ GT:DP:AD 0|1:34:11,23 ./.:11:6,5 ./.:30:20,10 -chr20 270732 . ACTT A 60 . QNAME=cluster19_000000F;QSTART=229922;QSTRAND=+ GT:DP:AD ./.:24:17,7 0|1:25:19,6 ./.:30:11,19 -chr20 271440 . GCATACACACACA G 60 . QNAME=cluster23_scaffold_3;QSTART=25440419;QSTRAND=- GT:DP:AD ./.:42:22,20 ./.:20:14,6 1|0:24:14,10 -chr20 271443 . TACAC T 60 . QNAME=cluster19_000000F;QSTART=25491341;QSTRAND=- GT:DP:AD ./.:32:22,10 1|0:32:12,20 ./.:47:25,22 -chr20 271443 . T TAC 60 . QNAME=cluster23_scaffold_2;QSTART=25425034;QSTRAND=- GT:DP:AD ./.:31:21,10 ./.:13:6,7 0|1:25:13,12 -chr20 271455 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=25440416;QSTRAND=- GT:DP:AD ./.:49:25,24 ./.:46:21,25 1|0:30:23,7 -chr20 271524 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25440347;QSTRAND=- GT:DP:AD ./.:21:14,7 ./.:36:19,17 1|0:33:9,24 -chr20 271615 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25440256;QSTRAND=- GT:DP:AD ./.:34:22,12 ./.:22:13,9 1|0:18:10,8 -chr20 272116 . A AC 60 . QNAME=cluster23_scaffold_3;QSTART=25439754;QSTRAND=- GT:DP:AD ./.:27:21,6 ./.:42:23,19 1|0:36:15,21 -chr20 272200 . TA T 60 . QNAME=cluster23_scaffold_3;QSTART=25439670;QSTRAND=- GT:DP:AD ./.:23:12,11 ./.:27:12,15 1|0:46:21,25 -chr20 272348 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25439523;QSTRAND=- GT:DP:AD ./.:28:9,19 ./.:21:7,14 1|0:40:16,24 -chr20 272493 . C A 60 . QNAME=cluster23_scaffold_2;QSTART=25423984;QSTRAND=- GT:DP:AD ./.:26:20,6 ./.:15:6,9 0|1:25:13,12 -chr20 273372 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=252388;QSTRAND=+ GT:DP:AD 1|0:26:11,15 ./.:35:19,16 1|0:36:16,20 -chr20 273876 . C CAAGAA 60 . QNAME=cluster23_scaffold_3;QSTART=25437990;QSTRAND=- GT:DP:AD ./.:24:12,12 ./.:23:16,7 1|0:31:20,11 -chr20 273894 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25437972;QSTRAND=- GT:DP:AD ./.:22:13,9 ./.:30:24,6 1|0:47:24,23 -chr20 273903 . A AAGGGAGGG 60 . QNAME=HG002-S9-H2-000001F;QSTART=227450;QSTRAND=+ GT:DP:AD 0|1:41:24,17 1|1:19:5,14 ./.:34:19,15 -chr20 273903 . AAGGGAGGG A 60 . QNAME=cluster23_scaffold_3;QSTART=25437963;QSTRAND=- GT:DP:AD ./.:42:18,24 ./.:36:20,16 1|0:31:13,18 -chr20 273903 . AAGGG A 60 . QNAME=cluster23_scaffold_2;QSTART=25422574;QSTRAND=- GT:DP:AD ./.:32:21,11 ./.:24:10,14 0|1:22:13,9 -chr20 274125 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=253141;QSTRAND=+ GT:DP:AD 1|0:16:9,7 ./.:12:6,6 ./.:36:20,16 -chr20 274210 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=253226;QSTRAND=+ GT:DP:AD 1|0:22:7,15 ./.:27:14,13 1|0:18:11,7 -chr20 274599 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=253615;QSTRAND=+ GT:DP:AD 1|0:17:11,6 ./.:39:16,23 ./.:26:16,10 -chr20 274820 . TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=253837;QSTRAND=+ GT:DP:AD 1|0:17:12,5 ./.:39:14,25 ./.:48:25,23 -chr20 274829 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25437045;QSTRAND=- GT:DP:AD ./.:47:25,22 ./.:41:22,19 1|0:38:13,25 -chr20 274893 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25436981;QSTRAND=- GT:DP:AD ./.:24:6,18 ./.:27:7,20 1|0:28:6,22 -chr20 275122 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=25436752;QSTRAND=- GT:DP:AD ./.:33:17,16 ./.:41:20,21 1|0:21:5,16 -chr20 275241 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=254256;QSTRAND=+ GT:DP:AD 1|0:35:17,18 ./.:36:13,23 1|0:39:18,21 -chr20 275322 . C CG 60 . QNAME=cluster23_scaffold_3;QSTART=25436551;QSTRAND=- GT:DP:AD ./.:26:19,7 ./.:13:7,6 1|0:35:22,13 -chr20 275361 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25436512;QSTRAND=- GT:DP:AD ./.:25:16,9 ./.:49:24,25 1|0:28:11,17 -chr20 275466 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=254481;QSTRAND=+ GT:DP:AD 1|0:31:7,24 ./.:34:12,22 ./.:32:19,13 -chr20 275606 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25436267;QSTRAND=- GT:DP:AD ./.:25:12,13 ./.:34:11,23 1|0:32:22,10 -chr20 275918 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25435955;QSTRAND=- GT:DP:AD ./.:42:22,20 ./.:37:12,25 1|0:30:17,13 -chr20 275932 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=254947;QSTRAND=+ GT:DP:AD 1|0:25:6,19 ./.:43:23,20 1|0:29:21,8 -chr20 276086 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=255101;QSTRAND=+ GT:DP:AD 1|0:21:9,12 ./.:26:10,16 1|0:29:6,23 -chr20 276119 . G GA 60 . QNAME=cluster23_scaffold_3;QSTART=25435753;QSTRAND=- GT:DP:AD ./.:22:6,16 ./.:31:6,25 1|0:33:23,10 -chr20 276122 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25435750;QSTRAND=- GT:DP:AD ./.:42:24,18 ./.:39:18,21 1|0:39:25,14 -chr20 276225 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=255240;QSTRAND=+ GT:DP:AD 1|0:34:12,22 ./.:35:17,18 1|0:32:14,18 -chr20 276245 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=255260;QSTRAND=+ GT:DP:AD 1|0:30:5,25 ./.:14:5,9 ./.:24:18,6 -chr20 276351 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=255366;QSTRAND=+ GT:DP:AD 1|0:30:13,17 ./.:33:14,19 1|0:41:17,24 -chr20 276391 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=255406;QSTRAND=+ GT:DP:AD 1|0:25:6,19 ./.:40:15,25 1|0:39:19,20 -chr20 276679 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=255694;QSTRAND=+ GT:DP:AD 1|0:27:21,6 ./.:32:11,21 1|0:32:15,17 -chr20 277092 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=256107;QSTRAND=+ GT:DP:AD 1|0:22:9,13 ./.:37:23,14 1|0:32:14,18 -chr20 277162 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=256177;QSTRAND=+ GT:DP:AD 1|0:21:15,6 ./.:45:23,22 ./.:30:23,7 -chr20 277171 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=256186;QSTRAND=+ GT:DP:AD 1|1:15:7,8 ./.:19:13,6 1|0:28:9,19 -chr20 277550 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=256565;QSTRAND=+ GT:DP:AD 1|0:14:5,9 ./.:28:22,6 1|0:31:20,11 -chr20 277574 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=256589;QSTRAND=+ GT:DP:AD 1|0:30:21,9 ./.:21:6,15 1|0:35:23,12 -chr20 277654 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=256669;QSTRAND=+ GT:DP:AD 1|0:20:13,7 ./.:18:7,11 1|0:24:10,14 -chr20 277664 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=256679;QSTRAND=+ GT:DP:AD 1|0:31:7,24 ./.:26:10,16 1|0:43:18,25 -chr20 277800 . C CAG 60 . QNAME=HG002-S9-H1-000001F;QSTART=256816;QSTRAND=+ GT:DP:AD 1|0:29:21,8 ./.:21:11,10 1|0:43:20,23 -chr20 277808 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=256825;QSTRAND=+ GT:DP:AD 1|0:34:15,19 ./.:21:14,7 1|0:23:13,10 -chr20 277915 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=256932;QSTRAND=+ GT:DP:AD 1|0:35:16,19 ./.:32:22,10 1|0:33:12,21 -chr20 278070 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=257087;QSTRAND=+ GT:DP:AD 1|0:19:9,10 ./.:23:10,13 1|0:42:22,20 -chr20 278107 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25433763;QSTRAND=- GT:DP:AD ./.:31:8,23 ./.:30:25,5 1|0:30:14,16 -chr20 278224 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=257241;QSTRAND=+ GT:DP:AD 1|0:46:25,21 ./.:30:25,5 1|0:21:6,15 -chr20 278515 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=257532;QSTRAND=+ GT:DP:AD 1|0:29:16,13 ./.:29:24,5 ./.:33:13,20 -chr20 278561 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25433309;QSTRAND=- GT:DP:AD ./.:34:18,16 ./.:13:7,6 1|0:39:18,21 -chr20 278930 . C CGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAG 60 . QNAME=HG002-S9-H2-000001F;QSTART=232485;QSTRAND=+;SVTYPE=INS;SVLEN=184 GT:DP:AD 0/1:29:9,20 ./.:22:16,6 ./.:24:5,19 -chr20 278930 . C CGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGCGGGAG 60 . QNAME=cluster23_scaffold_2;QSTART=25417363;QSTRAND=-;SVTYPE=INS;SVLEN=188 GT:DP:AD ./.:19:11,8 ./.:33:12,21 0/1:36:12,24 -chr20 278962 . G GGGAGGGAGGGACGGAGGGAGGAAGGGCGGGAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=257980;QSTRAND=+;SVTYPE=INS;SVLEN=32 GT:DP:AD 1/0:42:17,25 ./.:17:10,7 ./.:20:9,11 -chr20 278966 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=258015;QSTRAND=+ GT:DP:AD 1|0:15:5,10 ./.:38:13,25 ./.:42:17,25 -chr20 278977 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=258026;QSTRAND=+ GT:DP:AD 1|0:28:5,23 ./.:26:12,14 ./.:12:7,5 -chr20 279062 . G GGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGTGGGAGGGAGGGAGGGAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=258112;QSTRAND=+;SVTYPE=INS;SVLEN=139 GT:DP:AD 1/0:29:6,23 ./.:40:23,17 ./.:32:9,23 -chr20 279069 . A AGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGCGGGACGGAGGGAGGGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=232808;QSTRAND=+;SVTYPE=INS;SVLEN=438 GT:DP:AD 0/1:26:5,21 ./.:30:8,22 ./.:38:15,23 -chr20 279069 . A AGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGC 60 . QNAME=cluster19_000000F;QSTART=25483168;QSTRAND=-;SVTYPE=INS;SVLEN=543 GT:DP:AD ./.:37:13,24 1/1:24:6,18 ./.:42:19,23 -chr20 279069 . A AGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGCGGGACGGAGGGAGGGC 60 . QNAME=cluster23_scaffold_2;QSTART=25416710;QSTRAND=-;SVTYPE=INS;SVLEN=514 GT:DP:AD ./.:39:23,16 ./.:26:5,21 0/1:21:11,10 -chr20 279098 . G GGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGCGGGACGGAGGGAGGGACGGAGGGCGGGACGGAGGGAC 60 . QNAME=cluster23_scaffold_3;QSTART=25432493;QSTRAND=-;SVTYPE=INS;SVLEN=179 GT:DP:AD ./.:25:20,5 ./.:28:17,11 1/0:23:13,10 -chr20 279102 . C G 60 . QNAME=cluster23_scaffold_3;QSTART=25432489;QSTRAND=- GT:DP:AD ./.:40:22,18 ./.:29:22,7 1|0:42:19,23 -chr20 279177 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=258365;QSTRAND=+ GT:DP:AD 1|1:30:10,20 ./.:29:6,23 0|1:32:15,17 -chr20 279328 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=258516;QSTRAND=+ GT:DP:AD 1|0:14:6,8 ./.:17:8,9 1|0:12:5,7 -chr20 279759 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=258947;QSTRAND=+ GT:DP:AD 1|0:33:13,20 ./.:47:25,22 1|0:35:19,16 -chr20 279880 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=259068;QSTRAND=+ GT:DP:AD 1|0:33:13,20 ./.:37:23,14 1|0:21:9,12 -chr20 280083 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=25431508;QSTRAND=- GT:DP:AD ./.:29:15,14 ./.:30:13,17 1|0:25:18,7 -chr20 280211 . CAACAACAACAATTGTACTTCCCTAAGGTTACACCCAGCAGGTGCATAAAACCTACAGTAACAAT C 60 . QNAME=cluster23_scaffold_3;QSTART=25431380;QSTRAND=-;SVTYPE=DEL;SVLEN=-64 GT:DP:AD ./.:42:24,18 ./.:45:20,25 1/0:39:24,15 -chr20 280230 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=259418;QSTRAND=+ GT:DP:AD 1|0:28:7,21 ./.:32:11,21 ./.:15:5,10 -chr20 280339 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=259527;QSTRAND=+ GT:DP:AD 1|0:47:22,25 ./.:25:17,8 ./.:35:23,12 -chr20 280403 . TAAC T 60 . QNAME=cluster23_scaffold_3;QSTART=25431252;QSTRAND=- GT:DP:AD ./.:20:15,5 ./.:31:23,8 1|0:39:16,23 -chr20 280418 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25431240;QSTRAND=- GT:DP:AD ./.:41:25,16 ./.:18:5,13 1|0:42:25,17 -chr20 280635 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25431023;QSTRAND=- GT:DP:AD ./.:41:18,23 ./.:29:21,8 1|0:34:10,24 -chr20 281010 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=260198;QSTRAND=+ GT:DP:AD 1|0:45:23,22 ./.:44:20,24 ./.:28:10,18 -chr20 281470 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=260658;QSTRAND=+ GT:DP:AD 1|0:27:7,20 ./.:38:23,15 1|0:26:8,18 -chr20 281585 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25430073;QSTRAND=- GT:DP:AD ./.:45:24,21 ./.:31:6,25 1|0:20:15,5 -chr20 281929 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=261117;QSTRAND=+ GT:DP:AD 1|0:29:16,13 ./.:43:20,23 1|0:32:14,18 -chr20 282596 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=261784;QSTRAND=+ GT:DP:AD 1|0:13:5,8 ./.:44:23,21 ./.:27:22,5 -chr20 282775 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=261963;QSTRAND=+ GT:DP:AD 1|0:35:24,11 ./.:35:12,23 ./.:26:8,18 -chr20 283019 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=262207;QSTRAND=+ GT:DP:AD 1|0:39:19,20 ./.:17:8,9 ./.:20:10,10 -chr20 283328 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=262516;QSTRAND=+ GT:DP:AD 1|0:29:6,23 ./.:19:5,14 ./.:30:20,10 -chr20 283411 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=262599;QSTRAND=+ GT:DP:AD 1|0:14:6,8 ./.:32:18,14 ./.:37:21,16 -chr20 283535 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=262723;QSTRAND=+ GT:DP:AD 1|0:18:7,11 ./.:37:17,20 ./.:28:7,21 -chr20 283694 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=262883;QSTRAND=+ GT:DP:AD 1|0:31:21,10 ./.:37:20,17 ./.:26:5,21 -chr20 283724 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=262913;QSTRAND=+ GT:DP:AD 1|0:19:13,6 ./.:24:5,19 ./.:26:14,12 -chr20 283802 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25427856;QSTRAND=- GT:DP:AD ./.:37:14,23 ./.:27:16,11 1|0:35:18,17 -chr20 283857 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=263046;QSTRAND=+ GT:DP:AD 1|0:30:25,5 ./.:22:14,8 ./.:29:7,22 -chr20 284338 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=263527;QSTRAND=+ GT:DP:AD 1|0:37:12,25 ./.:45:24,21 ./.:22:8,14 -chr20 284356 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=263545;QSTRAND=+ GT:DP:AD 1|0:28:12,16 ./.:29:5,24 ./.:35:11,24 -chr20 284597 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=263786;QSTRAND=+ GT:DP:AD 1|0:17:11,6 ./.:30:17,13 1|0:39:20,19 -chr20 284724 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=263913;QSTRAND=+ GT:DP:AD 1|0:32:18,14 ./.:25:13,12 1|0:28:15,13 -chr20 284881 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=264070;QSTRAND=+ GT:DP:AD 1|0:41:16,25 ./.:42:23,19 1|0:17:9,8 -chr20 285327 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=264516;QSTRAND=+ GT:DP:AD 1|0:30:12,18 ./.:43:19,24 1|0:26:15,11 -chr20 285600 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=264789;QSTRAND=+ GT:DP:AD 1|0:35:12,23 ./.:38:17,21 1|0:26:18,8 -chr20 285621 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=264810;QSTRAND=+ GT:DP:AD 1|0:39:21,18 ./.:22:15,7 1|0:39:21,18 -chr20 285738 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=264927;QSTRAND=+ GT:DP:AD 1|0:37:16,21 ./.:40:21,19 ./.:40:24,16 -chr20 286151 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=265340;QSTRAND=+ GT:DP:AD 1|0:11:5,6 ./.:39:23,16 ./.:20:8,12 -chr20 286163 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=265353;QSTRAND=+ GT:DP:AD 1|0:13:6,7 ./.:19:10,9 ./.:18:12,6 -chr20 286710 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=265898;QSTRAND=+ GT:DP:AD 1|0:14:8,6 ./.:21:12,9 1|0:28:5,23 -chr20 286812 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=266000;QSTRAND=+ GT:DP:AD 1|0:29:19,10 ./.:28:7,21 1|0:43:21,22 -chr20 287237 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=266425;QSTRAND=+ GT:DP:AD 1|0:25:20,5 ./.:36:17,19 1|0:37:24,13 -chr20 287305 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=266493;QSTRAND=+ GT:DP:AD 1|0:37:19,18 ./.:30:14,16 1|0:33:23,10 -chr20 287629 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=266817;QSTRAND=+ GT:DP:AD 1|0:18:8,10 ./.:36:23,13 1|0:39:14,25 -chr20 287833 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=267021;QSTRAND=+ GT:DP:AD 1|0:14:8,6 ./.:27:6,21 1|0:30:16,14 -chr20 287837 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=267025;QSTRAND=+ GT:DP:AD 1|0:19:6,13 ./.:32:13,19 ./.:31:20,11 -chr20 287876 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=267064;QSTRAND=+ GT:DP:AD 1|0:24:15,9 ./.:26:15,11 1|0:20:14,6 -chr20 287908 . C CAAAAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=267097;QSTRAND=+ GT:DP:AD 1|0:26:10,16 ./.:30:17,13 ./.:44:21,23 -chr20 287908 . C CAAAAAAAA 60 . QNAME=cluster23_scaffold_3;QSTART=25423742;QSTRAND=- GT:DP:AD ./.:40:18,22 ./.:38:21,17 1|0:29:24,5 -chr20 287932 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=267129;QSTRAND=+ GT:DP:AD 1|0:32:15,17 ./.:27:14,13 ./.:23:14,9 -chr20 288158 . C CTTTCTTTTTCTT 60 . QNAME=HG002-S9-H1-000001F;QSTART=267356;QSTRAND=+ GT:DP:AD 1|0:36:16,20 ./.:34:16,18 ./.:30:5,25 -chr20 288174 . C CTTTTTCTTTTTCTT 60 . QNAME=cluster23_scaffold_3;QSTART=25423462;QSTRAND=- GT:DP:AD ./.:27:11,16 ./.:31:8,23 1|0:41:16,25 -chr20 288174 . C CT 60 . QNAME=cluster23_scaffold_2;QSTART=25407604;QSTRAND=- GT:DP:AD ./.:23:6,17 ./.:33:11,22 0|1:46:25,21 -chr20 288365 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=267574;QSTRAND=+ GT:DP:AD 1|0:32:7,25 ./.:44:21,23 1|0:39:18,21 -chr20 288516 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=267725;QSTRAND=+ GT:DP:AD 1|0:18:13,5 ./.:25:9,16 1|0:32:16,16 -chr20 289049 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=268258;QSTRAND=+ GT:DP:AD 1|0:22:5,17 ./.:39:16,23 1|0:24:14,10 -chr20 289196 . A ACC 60 . QNAME=HG002-S9-H1-000001F;QSTART=268406;QSTRAND=+ GT:DP:AD 1|0:37:12,25 ./.:27:19,8 ./.:28:23,5 -chr20 289196 . A ACCC 60 . QNAME=cluster23_scaffold_3;QSTART=25422437;QSTRAND=- GT:DP:AD ./.:28:5,23 ./.:28:15,13 1|0:44:21,23 -chr20 289773 . TC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=268985;QSTRAND=+ GT:DP:AD 1|0:29:19,10 ./.:35:22,13 1|0:27:6,21 -chr20 289787 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=268997;QSTRAND=+ GT:DP:AD 1|0:34:22,12 ./.:27:17,10 1|0:30:18,12 -chr20 289993 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=269203;QSTRAND=+ GT:DP:AD 1|0:43:25,18 ./.:29:6,23 1|0:41:23,18 -chr20 290134 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=269344;QSTRAND=+ GT:DP:AD 1|0:46:23,23 ./.:48:24,24 1|0:18:13,5 -chr20 290494 . G GC 60 . QNAME=HG002-S9-H2-000001F;QSTART=244671;QSTRAND=+ GT:DP:AD 0|1:18:12,6 1|1:47:22,25 0|1:30:5,25 -chr20 290563 . A ATT 60 . QNAME=cluster23_scaffold_2;QSTART=25405212;QSTRAND=- GT:DP:AD ./.:40:20,20 ./.:33:10,23 0|1:27:15,12 -chr20 290584 . T TTA 60 . QNAME=HG002-S9-H1-000001F;QSTART=269795;QSTRAND=+ GT:DP:AD 1|0:16:10,6 ./.:32:16,16 ./.:18:10,8 -chr20 290584 . T TTTA 60 . QNAME=cluster23_scaffold_3;QSTART=25421047;QSTRAND=- GT:DP:AD ./.:44:24,20 ./.:23:10,13 1|0:27:17,10 -chr20 291169 . TTCTC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=270382;QSTRAND=+ GT:DP:AD 1|0:41:25,16 ./.:27:21,6 1|0:30:13,17 -chr20 291796 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=271004;QSTRAND=+ GT:DP:AD 1|0:30:23,7 ./.:11:6,5 1|0:27:14,13 -chr20 291952 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=271160;QSTRAND=+ GT:DP:AD 1|1:25:15,10 1|1:23:5,18 1|1:37:23,14 -chr20 292806 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=272015;QSTRAND=+ GT:DP:AD 1|0:33:17,16 ./.:28:7,21 1|0:22:12,10 -chr20 293331 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25418305;QSTRAND=- GT:DP:AD ./.:45:25,20 ./.:44:24,20 1|0:20:15,5 -chr20 293433 . GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=272641;QSTRAND=+ GT:DP:AD 1|0:36:16,20 ./.:22:17,5 ./.:32:25,7 -chr20 293692 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=272898;QSTRAND=+ GT:DP:AD 1|0:35:25,10 ./.:29:8,21 1|0:17:5,12 -chr20 294073 . AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=273280;QSTRAND=+ GT:DP:AD 1|0:32:23,9 ./.:34:20,14 ./.:46:22,24 diff --git a/repo_utils/test_files/answer_key/divided/multi_00000005.vcf b/repo_utils/test_files/answer_key/divided/multi_00000005.vcf deleted file mode 100644 index 76d472df..00000000 --- a/repo_utils/test_files/answer_key/divided/multi_00000005.vcf +++ /dev/null @@ -1,142 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##bcftools_mergeVersion=1.12+htslib-1.12 -##bcftools_mergeCommand=merge -O z -f x -m none input1.vcf.gz input2.vcf.gz input3.vcf.gz; Date=Mon Aug 16 18:05:13 2021 -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 296976 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=251153;QSTRAND=+ GT:DP:AD 0|1:33:17,16 1|1:21:16,5 0|1:25:8,17 -chr20 297051 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=251228;QSTRAND=+ GT:DP:AD 0|1:24:6,18 1|1:26:10,16 0|1:25:15,10 -chr20 297191 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=251368;QSTRAND=+ GT:DP:AD 0|1:43:24,19 1|1:32:10,22 0|1:30:9,21 -chr20 297482 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=276688;QSTRAND=+ GT:DP:AD 1|0:23:7,16 ./.:29:23,6 1|0:40:16,24 -chr20 297874 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=252051;QSTRAND=+ GT:DP:AD 0|1:18:13,5 1|1:44:23,21 0|1:23:6,17 -chr20 298162 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=277366;QSTRAND=+ GT:DP:AD 1|0:24:19,5 ./.:25:8,17 0|1:36:25,11 -chr20 298541 . C T 60 . QNAME=cluster19_000000F;QSTART=258279;QSTRAND=+ GT:DP:AD ./.:30:6,24 0|1:40:23,17 ./.:21:5,16 -chr20 298839 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=278043;QSTRAND=+ GT:DP:AD 1|0:33:9,24 ./.:44:19,25 1|0:26:15,11 -chr20 299130 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=278334;QSTRAND=+ GT:DP:AD 1|0:36:15,21 ./.:50:25,25 1|0:40:20,20 -chr20 301074 . G C 60 . QNAME=cluster23_scaffold_2;QSTART=25394701;QSTRAND=- GT:DP:AD ./.:35:20,15 ./.:19:5,14 0|1:25:5,20 -chr20 301778 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=280982;QSTRAND=+ GT:DP:AD 1|0:22:17,5 ./.:32:25,7 1|0:32:25,7 -chr20 302639 . T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=281844;QSTRAND=+ GT:DP:AD 1|0:26:20,6 ./.:40:21,19 1|0:30:24,6 -chr20 302891 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=282096;QSTRAND=+ GT:DP:AD 1|1:36:12,24 1|1:41:21,20 1|1:20:6,14 -chr20 303233 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=282438;QSTRAND=+ GT:DP:AD 1|1:26:18,8 1|1:47:22,25 1|1:26:12,14 -chr20 303404 . C A 60 . QNAME=cluster19_000000F;QSTART=263142;QSTRAND=+ GT:DP:AD ./.:24:17,7 0|1:39:22,17 ./.:28:18,10 -chr20 303430 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=282635;QSTRAND=+ GT:DP:AD 1|1:25:16,9 1|0:22:9,13 1|1:43:18,25 -chr20 304111 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=283316;QSTRAND=+ GT:DP:AD 1|1:27:17,10 1|0:30:7,23 1|1:46:25,21 -chr20 304170 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=283375;QSTRAND=+ GT:DP:AD 1|1:29:6,23 1|1:16:7,9 1|1:26:14,12 -chr20 304190 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=283395;QSTRAND=+ GT:DP:AD 1|1:43:23,20 ./.:25:7,18 1|1:14:7,7 -chr20 304257 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=258434;QSTRAND=+ GT:DP:AD 0|1:37:22,15 1|0:20:5,15 0|1:17:12,5 -chr20 304335 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=258512;QSTRAND=+ GT:DP:AD 0|1:33:12,21 1|0:34:15,19 0|1:28:23,5 -chr20 304365 . G C 60 . QNAME=cluster19_000000F;QSTART=264103;QSTRAND=+ GT:DP:AD ./.:39:19,20 0|1:32:12,20 ./.:24:7,17 -chr20 304375 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25391400;QSTRAND=- GT:DP:AD ./.:20:6,14 ./.:29:7,22 0|1:40:21,19 -chr20 304376 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=258553;QSTRAND=+ GT:DP:AD 0|1:39:16,23 1|1:33:15,18 ./.:36:24,12 -chr20 304377 . G C 60 . QNAME=cluster23_scaffold_2;QSTART=25391398;QSTRAND=- GT:DP:AD ./.:23:10,13 ./.:28:5,23 0|1:28:22,6 -chr20 304450 . T C 60 . QNAME=cluster19_000000F;QSTART=264188;QSTRAND=+ GT:DP:AD ./.:37:18,19 0|1:23:14,9 ./.:31:25,6 -chr20 304460 . T C 60 . QNAME=cluster19_000000F;QSTART=264198;QSTRAND=+ GT:DP:AD ./.:34:15,19 0|1:33:19,14 ./.:36:13,23 -chr20 304461 . T C 60 . QNAME=cluster19_000000F;QSTART=264199;QSTRAND=+ GT:DP:AD ./.:35:22,13 0|1:32:18,14 ./.:24:7,17 -chr20 304463 . A T 60 . QNAME=cluster19_000000F;QSTART=264201;QSTRAND=+ GT:DP:AD ./.:29:13,16 0|1:49:24,25 ./.:17:12,5 -chr20 304504 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=258682;QSTRAND=+ GT:DP:AD 0|1:39:22,17 1|0:41:25,16 0|1:16:8,8 -chr20 304679 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=283884;QSTRAND=+ GT:DP:AD 1|0:32:8,24 ./.:42:23,19 1|0:26:5,21 -chr20 304705 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=258881;QSTRAND=+ GT:DP:AD 0|1:28:8,20 1|1:31:25,6 0|1:15:9,6 -chr20 305012 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=284217;QSTRAND=+ GT:DP:AD 1|1:35:15,20 1|1:20:6,14 1|1:33:12,21 -chr20 305384 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=284589;QSTRAND=+ GT:DP:AD 1|0:29:19,10 0|1:21:14,7 1|0:35:23,12 -chr20 305403 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=284608;QSTRAND=+ GT:DP:AD 1|1:35:11,24 1|1:21:7,14 1|1:43:23,20 -chr20 305843 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=260019;QSTRAND=+ GT:DP:AD 0|1:29:20,9 1|0:30:17,13 0|1:38:15,23 -chr20 305871 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=260047;QSTRAND=+ GT:DP:AD 0|1:39:20,19 1|1:44:23,21 0|1:24:12,12 -chr20 305882 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=260058;QSTRAND=+ GT:DP:AD 0|1:21:10,11 1|1:48:25,23 0|1:29:19,10 -chr20 305943 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=285148;QSTRAND=+ GT:DP:AD 1|1:43:19,24 1|1:34:16,18 1|1:22:13,9 -chr20 306004 . TAAATA T 60 . QNAME=cluster19_000000F;QSTART=265743;QSTRAND=+ GT:DP:AD ./.:38:19,19 0|1:14:8,6 ./.:45:24,21 -chr20 306194 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=285399;QSTRAND=+ GT:DP:AD 1|1:32:18,14 1|1:41:17,24 1|1:39:23,16 -chr20 306232 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=285438;QSTRAND=+ GT:DP:AD 1|0:29:12,17 0|1:23:6,17 1|0:23:5,18 -chr20 306268 . A ACCAGGCTGGAGTGCAGTGGCTCACTGCGTGGCTCGCTACAGCCTACAACTCCTGGGCTCCAGCAATCCTGCTGCCCCAGCCTCCTGTGTAACTGAGACTACAGGCACGCACCACCACACCCAGCTAATTTTTTCTTTCTTTTTTTTTTTTTTGAGATGAACTCTCACTCTGTTGC 60 . QNAME=HG002-S9-H1-000001F;QSTART=285475;QSTRAND=+;SVTYPE=INS;SVLEN=175 GT:DP:AD 1/1:34:18,16 ./.:32:19,13 1/1:25:13,12 -chr20 306268 . A ACCAGGCTGGAGTGCAGTGGCTCACTGCGTGGCTCGCTACAGCCTACAACTCCTGGGCTCCAGCAATCCTGCTGCCCCAGCCTCCTGTGTAACTGAGACTACAGGCACGCACCACCACACCCAGCTAATGTTTTCTTTCTTTTTTTTTTTTTTGAGATGAACTCTCACTCTGTTGC 60 . QNAME=cluster19_000000F;QSTART=25455794;QSTRAND=-;SVTYPE=INS;SVLEN=175 GT:DP:AD ./.:33:15,18 1/1:35:11,24 ./.:34:9,25 -chr20 306413 . T TC 60 . QNAME=cluster23_scaffold_2;QSTART=25389187;QSTRAND=- GT:DP:AD ./.:32:25,7 ./.:21:7,14 0|1:26:11,15 -chr20 306414 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=260765;QSTRAND=+ GT:DP:AD 0|1:37:21,16 1|0:46:25,21 ./.:36:11,25 -chr20 306535 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=260886;QSTRAND=+ GT:DP:AD 0|1:36:22,14 1|0:37:14,23 0|1:16:11,5 -chr20 306582 . A G 60 . QNAME=cluster19_000000F;QSTART=266491;QSTRAND=+ GT:DP:AD ./.:33:9,24 0|1:22:12,10 ./.:20:11,9 -chr20 306627 . T G 60 . QNAME=cluster19_000000F;QSTART=25455435;QSTRAND=- GT:DP:AD ./.:33:15,18 1|0:30:22,8 ./.:24:13,11 -chr20 306642 . T C 60 . QNAME=cluster19_000000F;QSTART=25455420;QSTRAND=- GT:DP:AD ./.:32:10,22 1|1:27:15,12 ./.:29:12,17 -chr20 306653 . C T 60 . QNAME=cluster19_000000F;QSTART=25455409;QSTRAND=- GT:DP:AD ./.:49:24,25 1|0:33:13,20 ./.:19:6,13 -chr20 306667 . T C 60 . QNAME=cluster19_000000F;QSTART=25455395;QSTRAND=- GT:DP:AD ./.:28:5,23 1|0:45:22,23 ./.:35:21,14 -chr20 306742 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=261093;QSTRAND=+ GT:DP:AD 0|1:25:15,10 ./.:32:9,23 0|1:14:6,8 -chr20 306776 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=286157;QSTRAND=+ GT:DP:AD 1|0:33:23,10 ./.:21:11,10 1|0:33:13,20 -chr20 306885 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=286266;QSTRAND=+ GT:DP:AD 1|1:27:9,18 1|1:31:23,8 1|1:31:17,14 -chr20 306993 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=286374;QSTRAND=+ GT:DP:AD 1|0:30:25,5 1|1:25:18,7 1|0:27:18,9 -chr20 307589 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=286970;QSTRAND=+ GT:DP:AD 1|1:32:12,20 1|0:31:16,15 1|1:26:16,10 -chr20 307693 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=262044;QSTRAND=+ GT:DP:AD 0|1:34:25,9 ./.:19:13,6 ./.:33:10,23 -chr20 307712 . CA C 60 . QNAME=cluster19_000000F;QSTART=25454350;QSTRAND=- GT:DP:AD ./.:36:20,16 1|0:33:9,24 0|1:21:13,8 -chr20 308128 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=262479;QSTRAND=+ GT:DP:AD 0|1:18:11,7 0|1:40:25,15 ./.:41:18,23 -chr20 308132 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=287513;QSTRAND=+ GT:DP:AD 1|1:43:21,22 1|1:24:8,16 1|1:29:13,16 -chr20 308261 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=262612;QSTRAND=+ GT:DP:AD 0|1:25:9,16 0|1:30:5,25 ./.:37:25,12 -chr20 308278 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=262629;QSTRAND=+ GT:DP:AD 0|1:24:12,12 1|1:32:10,22 0|1:45:22,23 -chr20 308352 . T C 60 . QNAME=cluster19_000000F;QSTART=25453711;QSTRAND=- GT:DP:AD ./.:16:8,8 1|0:33:13,20 0|1:27:22,5 -chr20 308718 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=263069;QSTRAND=+ GT:DP:AD 0|1:23:15,8 1|1:23:17,6 0|1:24:7,17 -chr20 308968 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=288349;QSTRAND=+ GT:DP:AD 1|1:23:7,16 1|1:17:6,11 1|1:11:6,5 -chr20 309141 . A G 60 . QNAME=cluster19_000000F;QSTART=25452922;QSTRAND=- GT:DP:AD ./.:27:10,17 1|0:37:12,25 0|1:33:14,19 -chr20 309613 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=263964;QSTRAND=+ GT:DP:AD 0|1:38:22,16 ./.:22:16,6 ./.:34:22,12 -chr20 309637 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=289018;QSTRAND=+ GT:DP:AD 1|1:29:24,5 ./.:12:7,5 1|0:39:24,15 -chr20 309639 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=289020;QSTRAND=+ GT:DP:AD 1|1:36:18,18 ./.:25:9,16 1|0:41:21,20 -chr20 309653 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=289034;QSTRAND=+ GT:DP:AD 1|1:46:24,22 ./.:15:8,7 1|0:32:23,9 -chr20 309674 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=289055;QSTRAND=+ GT:DP:AD 1|1:39:16,23 1|1:35:14,21 1|1:37:25,12 -chr20 310521 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=289902;QSTRAND=+ GT:DP:AD 1|1:21:6,15 1|0:34:20,14 0|1:13:7,6 -chr20 310522 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=289903;QSTRAND=+ GT:DP:AD 1|1:19:9,10 1|0:29:8,21 0|1:42:21,21 -chr20 310523 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=289904;QSTRAND=+ GT:DP:AD 1|1:27:20,7 1|0:21:13,8 0|1:23:18,5 -chr20 310719 . A AT 60 . QNAME=HG002-S9-H1-000001F;QSTART=290101;QSTRAND=+ GT:DP:AD 1|1:35:20,15 1|0:31:6,25 0|1:45:24,21 -chr20 311107 . C G 60 . QNAME=cluster19_000000F;QSTART=271016;QSTRAND=+ GT:DP:AD ./.:35:22,13 0|1:32:12,20 1|0:38:25,13 -chr20 311145 . T G 60 . QNAME=cluster19_000000F;QSTART=271054;QSTRAND=+ GT:DP:AD ./.:33:10,23 0|1:32:13,19 1|0:30:7,23 -chr20 311237 . C T 60 . QNAME=cluster19_000000F;QSTART=271146;QSTRAND=+ GT:DP:AD ./.:39:21,18 0|1:28:8,20 1|0:25:8,17 -chr20 311327 . G C 60 . QNAME=cluster19_000000F;QSTART=271236;QSTRAND=+ GT:DP:AD ./.:31:24,7 0|1:30:10,20 1|0:34:21,13 -chr20 311347 . C CATTATT 60 . QNAME=cluster19_000000F;QSTART=271257;QSTRAND=+ GT:DP:AD ./.:21:11,10 0|1:32:12,20 1|0:19:8,11 -chr20 311683 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=291065;QSTRAND=+ GT:DP:AD 1|0:39:20,19 1|0:46:22,24 0|1:40:16,24 -chr20 311774 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=291156;QSTRAND=+ GT:DP:AD 1|0:29:21,8 1|1:16:7,9 0|1:18:12,6 -chr20 311791 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=291173;QSTRAND=+ GT:DP:AD 1|1:32:17,15 1|1:22:14,8 1|1:34:17,17 -chr20 312718 . A AT 60 . QNAME=cluster23_scaffold_2;QSTART=25382881;QSTRAND=- GT:DP:AD ./.:46:21,25 ./.:18:10,8 0|1:25:15,10 -chr20 314417 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=293799;QSTRAND=+ GT:DP:AD 1|0:18:7,11 ./.:16:9,7 ./.:43:19,24 -chr20 314431 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=293813;QSTRAND=+ GT:DP:AD 1|0:48:23,25 ./.:40:23,17 ./.:25:16,9 -chr20 314495 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=268847;QSTRAND=+ GT:DP:AD 0|1:31:6,25 ./.:34:24,10 ./.:38:22,16 -chr20 314567 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25381032;QSTRAND=- GT:DP:AD ./.:21:7,14 ./.:41:18,23 0|1:18:9,9 -chr20 314595 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=268947;QSTRAND=+ GT:DP:AD 0|1:30:15,15 ./.:36:15,21 1|0:27:12,15 -chr20 314668 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=269020;QSTRAND=+ GT:DP:AD 0|1:40:19,21 ./.:27:7,20 1|0:33:11,22 -chr20 314877 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=269229;QSTRAND=+ GT:DP:AD 0|1:21:13,8 ./.:15:6,9 1|0:37:25,12 -chr20 314905 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=269258;QSTRAND=+ GT:DP:AD 0|1:34:9,25 ./.:19:6,13 ./.:24:15,9 -chr20 314905 . C CTT 60 . QNAME=cluster23_scaffold_2;QSTART=25380692;QSTRAND=- GT:DP:AD ./.:37:25,12 ./.:21:14,7 0|1:30:22,8 -chr20 315222 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=269573;QSTRAND=+ GT:DP:AD 0|1:47:25,22 ./.:35:23,12 1|0:26:6,20 -chr20 315528 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=269879;QSTRAND=+ GT:DP:AD 0|1:30:20,10 ./.:28:14,14 1|0:32:7,25 -chr20 315724 . G GTATTAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=270076;QSTRAND=+ GT:DP:AD 0|1:40:23,17 ./.:35:14,21 1|0:28:16,12 -chr20 316587 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=295969;QSTRAND=+ GT:DP:AD 1|0:39:14,25 ./.:23:5,18 ./.:37:17,20 -chr20 316724 . GTT G 60 . QNAME=HG002-S9-H2-000001F;QSTART=271082;QSTRAND=+ GT:DP:AD 0|1:12:5,7 ./.:21:13,8 ./.:44:19,25 -chr20 316724 . GTTT G 60 . QNAME=cluster23_scaffold_3;QSTART=25394724;QSTRAND=- GT:DP:AD ./.:31:19,12 ./.:23:13,10 1|0:31:14,17 -chr20 316724 . G GT 60 . QNAME=cluster23_scaffold_2;QSTART=25378872;QSTRAND=- GT:DP:AD ./.:17:5,12 ./.:34:11,23 0|1:34:12,22 diff --git a/repo_utils/test_files/answer_key/divided/multi_00000006.vcf b/repo_utils/test_files/answer_key/divided/multi_00000006.vcf deleted file mode 100644 index 1df46068..00000000 --- a/repo_utils/test_files/answer_key/divided/multi_00000006.vcf +++ /dev/null @@ -1,304 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##bcftools_mergeVersion=1.12+htslib-1.12 -##bcftools_mergeCommand=merge -O z -f x -m none input1.vcf.gz input2.vcf.gz input3.vcf.gz; Date=Mon Aug 16 18:05:13 2021 -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 317772 . GA G 60 . QNAME=HG002-S9-H2-000001F;QSTART=272128;QSTRAND=+ GT:DP:AD 0|1:28:8,20 ./.:34:13,21 1|0:22:7,15 -chr20 318091 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=272445;QSTRAND=+ GT:DP:AD 0|1:35:17,18 ./.:30:16,14 1|0:31:18,13 -chr20 318388 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=272742;QSTRAND=+ GT:DP:AD 0|1:26:5,21 ./.:18:11,7 1|0:16:11,5 -chr20 318854 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=273208;QSTRAND=+ GT:DP:AD 0|1:17:10,7 1|1:26:10,16 1|1:15:9,6 -chr20 318941 . AC A 60 . QNAME=HG002-S9-H2-000001F;QSTART=273296;QSTRAND=+ GT:DP:AD 0|1:35:15,20 1|1:21:15,6 1|1:31:8,23 -chr20 318943 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=273296;QSTRAND=+ GT:DP:AD 0|1:44:23,21 1|1:22:16,6 1|1:29:16,13 -chr20 318971 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=298353;QSTRAND=+ GT:DP:AD 1|1:43:19,24 1|1:38:21,17 1|0:31:10,21 -chr20 319115 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=273468;QSTRAND=+ GT:DP:AD 0|1:41:22,19 1|1:29:12,17 1|0:16:5,11 -chr20 319367 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=298749;QSTRAND=+ GT:DP:AD 1|0:33:11,22 ./.:28:7,21 ./.:30:17,13 -chr20 319623 . G C 60 . QNAME=cluster19_000000F;QSTART=25442440;QSTRAND=- GT:DP:AD ./.:37:23,14 1|0:24:5,19 ./.:27:5,22 -chr20 319633 . CCA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=299016;QSTRAND=+ GT:DP:AD 1|1:47:22,25 0|1:36:13,23 1|0:37:15,22 -chr20 319838 . G A 60 . QNAME=cluster19_000000F;QSTART=25442225;QSTRAND=- GT:DP:AD ./.:16:9,7 1|0:37:15,22 ./.:29:12,17 -chr20 320255 . CA C 60 . QNAME=cluster23_scaffold_2;QSTART=25375342;QSTRAND=- GT:DP:AD ./.:27:9,18 ./.:37:25,12 0|1:31:9,22 -chr20 321250 . A G 60 . QNAME=cluster19_000000F;QSTART=25440813;QSTRAND=- GT:DP:AD ./.:32:11,21 1|0:31:15,16 ./.:37:23,14 -chr20 326089 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=305469;QSTRAND=+ GT:DP:AD 1|0:33:14,19 0|1:44:19,25 ./.:31:20,11 -chr20 328517 . ATT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=307898;QSTRAND=+ GT:DP:AD 1|1:29:22,7 ./.:41:23,18 1|0:33:25,8 -chr20 328517 . AT A 60 . QNAME=cluster19_000000F;QSTART=25433546;QSTRAND=- GT:DP:AD ./.:31:20,11 1|1:29:5,24 0|1:20:5,15 -chr20 328569 . GA G 60 . QNAME=cluster19_000000F;QSTART=25433495;QSTRAND=- GT:DP:AD ./.:17:9,8 1|0:46:25,21 ./.:28:21,7 -chr20 328569 . G GA 60 . QNAME=cluster23_scaffold_3;QSTART=25382887;QSTRAND=- GT:DP:AD ./.:38:15,23 ./.:39:21,18 1|0:31:7,24 -chr20 328717 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25382739;QSTRAND=- GT:DP:AD ./.:32:24,8 ./.:37:24,13 1|0:37:21,16 -chr20 336200 . C CTCTTCT 60 . QNAME=HG002-S9-H1-000001F;QSTART=315579;QSTRAND=+ GT:DP:AD 1|0:34:11,23 0|1:25:14,11 ./.:46:21,25 -chr20 336200 . CTCTTCTTCT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=290550;QSTRAND=+ GT:DP:AD 0|1:43:21,22 ./.:31:14,17 ./.:34:22,12 -chr20 336200 . C CTCT 60 . QNAME=cluster23_scaffold_3;QSTART=25375253;QSTRAND=- GT:DP:AD ./.:37:25,12 ./.:34:23,11 1|0:26:17,9 -chr20 336200 . CTCT C 60 . QNAME=cluster23_scaffold_2;QSTART=25359399;QSTRAND=- GT:DP:AD ./.:38:17,21 ./.:24:13,11 0|1:26:18,8 -chr20 336263 . TTC T 60 . QNAME=cluster19_000000F;QSTART=25425802;QSTRAND=- GT:DP:AD ./.:27:20,7 1|0:34:18,16 ./.:29:11,18 -chr20 336308 . CTCTTCCTCTTCT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=315693;QSTRAND=+ GT:DP:AD 1|1:30:20,10 0|1:42:25,17 0|1:31:24,7 -chr20 336308 . CTCTTCCTCTTCTTCT C 60 . QNAME=cluster23_scaffold_3;QSTART=25375145;QSTRAND=- GT:DP:AD ./.:28:5,23 ./.:41:24,17 1|0:33:8,25 -chr20 336336 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25375132;QSTRAND=- GT:DP:AD ./.:31:24,7 ./.:26:16,10 1|0:37:13,24 -chr20 338577 . A ATG 60 . QNAME=HG002-S9-H1-000001F;QSTART=317950;QSTRAND=+ GT:DP:AD 1|0:48:24,24 0|1:33:16,17 1|1:37:17,20 -chr20 340238 . CTTTCT C 60 . QNAME=cluster23_scaffold_2;QSTART=25355374;QSTRAND=- GT:DP:AD ./.:34:24,10 ./.:35:18,17 0|1:16:7,9 -chr20 340763 . C T 60 . QNAME=cluster19_000000F;QSTART=25421304;QSTRAND=- GT:DP:AD ./.:30:11,19 1|0:24:16,8 ./.:34:16,18 -chr20 340858 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=295186;QSTRAND=+ GT:DP:AD 0|1:18:11,7 ./.:32:15,17 ./.:16:10,6 -chr20 340865 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=295193;QSTRAND=+ GT:DP:AD 0|1:25:7,18 ./.:38:13,25 ./.:36:21,15 -chr20 341112 . T TCACACA 60 . QNAME=HG002-S9-H2-000001F;QSTART=295441;QSTRAND=+ GT:DP:AD 0|1:38:21,17 ./.:29:15,14 ./.:20:11,9 -chr20 341505 . AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=320880;QSTRAND=+ GT:DP:AD 1|0:29:19,10 ./.:16:11,5 ./.:15:10,5 -chr20 341505 . ATTTTT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=295840;QSTRAND=+ GT:DP:AD 0|1:28:23,5 ./.:34:16,18 ./.:37:20,17 -chr20 341968 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=296297;QSTRAND=+ GT:DP:AD 0|1:15:5,10 1|0:34:19,15 ./.:32:11,21 -chr20 342602 . C CTTT 60 . QNAME=HG002-S9-H1-000001F;QSTART=321976;QSTRAND=+ GT:DP:AD 1|0:26:9,17 ./.:30:5,25 ./.:30:21,9 -chr20 342602 . CTTTTTTTT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=296932;QSTRAND=+ GT:DP:AD 0|1:20:15,5 ./.:39:25,14 ./.:25:12,13 -chr20 342602 . C CTTTTT 60 . QNAME=cluster19_000000F;QSTART=302510;QSTRAND=+ GT:DP:AD ./.:30:9,21 0|1:44:19,25 ./.:46:21,25 -chr20 342602 . C CTTTTTTTT 60 . QNAME=cluster23_scaffold_3;QSTART=25368856;QSTRAND=- GT:DP:AD ./.:22:15,7 ./.:19:10,9 1|0:31:25,6 -chr20 342602 . C CTTTTTTT 60 . QNAME=cluster23_scaffold_2;QSTART=25353008;QSTRAND=- GT:DP:AD ./.:32:14,18 ./.:45:25,20 0|1:26:5,21 -chr20 342621 . T TTTC 60 . QNAME=cluster19_000000F;QSTART=25419443;QSTRAND=- GT:DP:AD ./.:44:19,25 1|0:35:16,19 ./.:24:7,17 -chr20 342641 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=296962;QSTRAND=+ GT:DP:AD 0|1:29:8,21 ./.:41:21,20 ./.:32:8,24 -chr20 342664 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=296985;QSTRAND=+ GT:DP:AD 0|1:46:24,22 ./.:33:18,15 ./.:29:16,13 -chr20 342939 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=297260;QSTRAND=+ GT:DP:AD 0|1:36:22,14 ./.:42:25,17 ./.:39:21,18 -chr20 343326 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=297647;QSTRAND=+ GT:DP:AD 0|1:36:16,20 ./.:34:9,25 ./.:46:25,21 -chr20 343479 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=297800;QSTRAND=+ GT:DP:AD 0|1:42:23,19 ./.:26:11,15 ./.:26:5,21 -chr20 343825 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=298146;QSTRAND=+ GT:DP:AD 0|1:46:23,23 ./.:34:24,10 ./.:45:22,23 -chr20 343865 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=298186;QSTRAND=+ GT:DP:AD 0|1:17:12,5 ./.:15:8,7 ./.:36:22,14 -chr20 343893 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=298214;QSTRAND=+ GT:DP:AD 0|1:36:21,15 ./.:27:15,12 ./.:17:10,7 -chr20 344097 . C CAA 60 . QNAME=HG002-S9-H2-000001F;QSTART=298419;QSTRAND=+ GT:DP:AD 0|1:39:24,15 ./.:29:6,23 ./.:42:17,25 -chr20 344097 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25367360;QSTRAND=- GT:DP:AD ./.:37:19,18 ./.:37:23,14 1|0:34:20,14 -chr20 344354 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=298677;QSTRAND=+ GT:DP:AD 0|1:33:10,23 ./.:22:6,16 ./.:32:10,22 -chr20 344458 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=298781;QSTRAND=+ GT:DP:AD 0|1:40:22,18 ./.:30:17,13 ./.:43:22,21 -chr20 344798 . T G 60 . QNAME=cluster23_scaffold_3;QSTART=25366659;QSTRAND=- GT:DP:AD ./.:25:9,16 ./.:32:13,19 1|0:21:14,7 -chr20 345372 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=299695;QSTRAND=+ GT:DP:AD 0|1:34:15,19 ./.:19:9,10 ./.:31:22,9 -chr20 345506 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=299829;QSTRAND=+ GT:DP:AD 0|1:23:6,17 ./.:29:23,6 ./.:36:15,21 -chr20 345647 . T TACAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=299971;QSTRAND=+ GT:DP:AD 0|1:22:5,17 ./.:19:14,5 ./.:44:23,21 -chr20 348484 . C CGTGTGTGTGT 60 . QNAME=HG002-S9-H1-000001F;QSTART=327861;QSTRAND=+ GT:DP:AD 1|0:34:21,13 ./.:25:5,20 1|0:26:6,20 -chr20 348484 . CGTGTGT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=302812;QSTRAND=+ GT:DP:AD 0|1:35:15,20 ./.:34:23,11 ./.:17:12,5 -chr20 348484 . C CGTGTGTGTGTGT 60 . QNAME=cluster19_000000F;QSTART=308397;QSTRAND=+ GT:DP:AD ./.:34:21,13 0|1:26:15,11 0|1:16:5,11 -chr20 349198 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=303519;QSTRAND=+ GT:DP:AD 0|1:35:14,21 ./.:31:20,11 ./.:17:6,11 -chr20 350477 . TA T 60 . QNAME=HG002-S9-H2-000001F;QSTART=304799;QSTRAND=+ GT:DP:AD 0|1:21:14,7 ./.:34:10,24 ./.:39:14,25 -chr20 350477 . T TA 60 . QNAME=cluster23_scaffold_3;QSTART=25360969;QSTRAND=- GT:DP:AD ./.:30:9,21 ./.:28:11,17 1|0:31:22,9 -chr20 350646 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=330033;QSTRAND=+ GT:DP:AD 1|0:32:20,12 1|1:40:22,18 ./.:33:22,11 -chr20 350646 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25360799;QSTRAND=- GT:DP:AD ./.:30:15,15 ./.:12:7,5 1|0:27:7,20 -chr20 350660 . AAAAAAAAAAAAAAAAAG A 60 . QNAME=HG002-S9-H2-000001F;QSTART=304981;QSTRAND=+ GT:DP:AD 0|1:17:5,12 ./.:21:9,12 ./.:26:17,9 -chr20 351164 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=305467;QSTRAND=+ GT:DP:AD 0|1:36:13,23 ./.:43:23,20 ./.:29:21,8 -chr20 352819 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=332204;QSTRAND=+ GT:DP:AD 1|0:42:19,23 1|1:38:23,15 1|1:22:12,10 -chr20 353673 . TC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=333059;QSTRAND=+ GT:DP:AD 1|0:31:16,15 1|1:40:18,22 1|1:44:19,25 -chr20 354581 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=308884;QSTRAND=+ GT:DP:AD 0|1:35:16,19 ./.:14:8,6 ./.:24:18,6 -chr20 355283 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=309586;QSTRAND=+ GT:DP:AD 0|1:20:5,15 ./.:41:25,16 ./.:32:19,13 -chr20 356342 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=335727;QSTRAND=+ GT:DP:AD 1|0:36:24,12 1|1:21:11,10 1|1:28:13,15 -chr20 356748 . ACC A 60 . QNAME=cluster19_000000F;QSTART=25405319;QSTRAND=- GT:DP:AD ./.:30:18,12 1|0:26:12,14 ./.:44:23,21 -chr20 356924 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=336307;QSTRAND=+ GT:DP:AD 1|1:30:8,22 1|1:14:9,5 1|1:18:10,8 -chr20 358579 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=337963;QSTRAND=+ GT:DP:AD 1|0:33:17,16 1|0:34:14,20 ./.:41:16,25 -chr20 358579 . CTT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=312883;QSTRAND=+ GT:DP:AD 0|1:27:19,8 ./.:26:10,16 ./.:18:12,6 -chr20 358585 . T C 60 . QNAME=cluster19_000000F;QSTART=25403485;QSTRAND=- GT:DP:AD ./.:11:6,5 1|0:26:10,16 ./.:25:19,6 -chr20 358586 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=312887;QSTRAND=+ GT:DP:AD 0|1:35:24,11 ./.:34:9,25 ./.:44:20,24 -chr20 358841 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=338223;QSTRAND=+ GT:DP:AD 1|0:16:10,6 0|1:28:8,20 1|1:26:5,21 -chr20 359400 . GCAC G 60 . QNAME=HG002-S9-H1-000001F;QSTART=338783;QSTRAND=+ GT:DP:AD 1|0:25:8,17 0|1:32:14,18 1|1:31:13,18 -chr20 359869 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=314170;QSTRAND=+ GT:DP:AD 0|1:24:14,10 1|0:41:16,25 ./.:17:10,7 -chr20 359913 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=314214;QSTRAND=+ GT:DP:AD 0|1:43:19,24 1|0:36:23,13 ./.:31:7,24 -chr20 359914 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=314215;QSTRAND=+ GT:DP:AD 0|1:21:12,9 1|0:34:19,15 ./.:20:12,8 -chr20 359916 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=314217;QSTRAND=+ GT:DP:AD 0|1:22:14,8 1|0:37:21,16 ./.:42:22,20 -chr20 359924 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=314225;QSTRAND=+ GT:DP:AD 0|1:30:22,8 1|0:28:5,23 ./.:24:11,13 -chr20 359930 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=314231;QSTRAND=+ GT:DP:AD 0|1:37:20,17 1|0:37:18,19 ./.:28:17,11 -chr20 359931 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=314232;QSTRAND=+ GT:DP:AD 0|1:18:10,8 1|0:25:13,12 ./.:34:22,12 -chr20 359947 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=314248;QSTRAND=+ GT:DP:AD 0|1:22:7,15 1|0:43:23,20 ./.:12:5,7 -chr20 359953 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=314254;QSTRAND=+ GT:DP:AD 0|1:11:6,5 1|0:26:16,10 ./.:30:20,10 -chr20 359954 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=314255;QSTRAND=+ GT:DP:AD 0|1:40:22,18 1|0:44:19,25 ./.:26:19,7 -chr20 359955 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=314256;QSTRAND=+ GT:DP:AD 0|1:30:15,15 1|0:26:9,17 ./.:31:16,15 -chr20 359960 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=314261;QSTRAND=+ GT:DP:AD 0|1:32:7,25 1|0:31:25,6 ./.:42:22,20 -chr20 359969 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=314270;QSTRAND=+ GT:DP:AD 0|1:27:8,19 1|0:31:21,10 ./.:39:15,24 -chr20 359998 . C CA 60 . QNAME=HG002-S9-H2-000001F;QSTART=314300;QSTRAND=+ GT:DP:AD 0|1:40:23,17 ./.:35:17,18 1|0:31:14,17 -chr20 360554 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=314856;QSTRAND=+ GT:DP:AD 0|1:26:9,17 1|0:32:13,19 ./.:28:15,13 -chr20 360556 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=314858;QSTRAND=+ GT:DP:AD 0|1:38:20,18 1|0:36:18,18 ./.:24:15,9 -chr20 360622 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=314924;QSTRAND=+ GT:DP:AD 0|1:11:6,5 1|0:32:20,12 ./.:29:15,14 -chr20 361302 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=315604;QSTRAND=+ GT:DP:AD 0|1:48:23,25 1|0:34:25,9 ./.:24:15,9 -chr20 362051 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=316353;QSTRAND=+ GT:DP:AD 0|1:33:11,22 1|0:38:18,20 ./.:29:16,13 -chr20 362052 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=316354;QSTRAND=+ GT:DP:AD 0|1:40:24,16 1|0:34:14,20 ./.:29:8,21 -chr20 362185 . G GA 60 . QNAME=cluster23_scaffold_3;QSTART=25349263;QSTRAND=- GT:DP:AD ./.:37:17,20 ./.:31:12,19 1|0:26:12,14 -chr20 362679 . A ATG 60 . QNAME=HG002-S9-H2-000001F;QSTART=316982;QSTRAND=+ GT:DP:AD 0|1:19:8,11 1|0:21:15,6 ./.:39:24,15 -chr20 363003 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=317307;QSTRAND=+ GT:DP:AD 0|1:28:10,18 1|0:41:21,20 ./.:15:5,10 -chr20 363114 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=317418;QSTRAND=+ GT:DP:AD 0|1:32:7,25 1|0:32:7,25 ./.:40:16,24 -chr20 363119 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=317423;QSTRAND=+ GT:DP:AD 0|1:34:21,13 1|0:36:22,14 ./.:35:12,23 -chr20 363245 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=342624;QSTRAND=+ GT:DP:AD 1|0:23:15,8 0|1:41:19,22 1|0:23:8,15 -chr20 363435 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=317739;QSTRAND=+ GT:DP:AD 0|1:24:14,10 1|0:22:7,15 ./.:38:17,21 -chr20 363987 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=318291;QSTRAND=+ GT:DP:AD 0|1:38:13,25 1|0:11:6,5 ./.:41:18,23 -chr20 364755 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=319059;QSTRAND=+ GT:DP:AD 0|1:11:5,6 1|0:35:23,12 ./.:34:20,14 -chr20 364763 . C CAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=344143;QSTRAND=+ GT:DP:AD 1|1:17:11,6 1|1:29:10,19 1|1:35:10,25 -chr20 365042 . G A 60 . QNAME=cluster19_000000F;QSTART=25397024;QSTRAND=- GT:DP:AD ./.:30:12,18 1|0:32:25,7 ./.:21:6,15 -chr20 365220 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=344601;QSTRAND=+ GT:DP:AD 1|1:22:5,17 1|1:33:25,8 1|1:35:17,18 -chr20 365798 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=345180;QSTRAND=+ GT:DP:AD 1|1:35:14,21 ./.:29:17,12 0|1:21:8,13 -chr20 365798 . CTT C 60 . QNAME=cluster19_000000F;QSTART=25396268;QSTRAND=- GT:DP:AD ./.:26:13,13 1|0:29:8,21 ./.:33:9,24 -chr20 366032 . C T 60 . QNAME=cluster19_000000F;QSTART=25396036;QSTRAND=- GT:DP:AD ./.:24:5,19 1|0:28:9,19 ./.:13:8,5 -chr20 366058 . AGCCTCCCAAAGGAG A 60 . QNAME=cluster19_000000F;QSTART=25396010;QSTRAND=- GT:DP:AD ./.:12:5,7 1|0:13:8,5 ./.:32:23,9 -chr20 366107 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=345487;QSTRAND=+ GT:DP:AD 1|1:12:6,6 1|1:42:23,19 1|1:31:25,6 -chr20 366279 . C T 60 . QNAME=cluster19_000000F;QSTART=25395803;QSTRAND=- GT:DP:AD ./.:45:24,21 1|0:43:21,22 ./.:34:14,20 -chr20 366317 . A G 60 . QNAME=cluster19_000000F;QSTART=25395765;QSTRAND=- GT:DP:AD ./.:40:22,18 1|0:46:22,24 ./.:33:16,17 -chr20 366341 . A G 60 . QNAME=cluster19_000000F;QSTART=25395741;QSTRAND=- GT:DP:AD ./.:40:19,21 1|0:33:14,19 ./.:14:7,7 -chr20 366365 . C A 60 . QNAME=cluster19_000000F;QSTART=25395717;QSTRAND=- GT:DP:AD ./.:18:12,6 1|0:30:12,18 ./.:31:13,18 -chr20 366711 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=346091;QSTRAND=+ GT:DP:AD 1|0:25:11,14 ./.:23:8,15 1|1:29:18,11 -chr20 367006 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=346386;QSTRAND=+ GT:DP:AD 1|1:29:17,12 1|0:44:22,22 1|1:37:23,14 -chr20 367079 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=346459;QSTRAND=+ GT:DP:AD 1|0:45:23,22 ./.:26:15,11 1|1:11:5,6 -chr20 367082 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=346462;QSTRAND=+ GT:DP:AD 1|0:44:25,19 ./.:32:16,16 1|1:31:20,11 -chr20 367106 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=346486;QSTRAND=+ GT:DP:AD 1|0:36:24,12 ./.:25:9,16 1|1:34:13,21 -chr20 367141 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=346521;QSTRAND=+ GT:DP:AD 1|0:33:16,17 1|0:20:14,6 1|1:48:24,24 -chr20 367164 . TCGCA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=346545;QSTRAND=+ GT:DP:AD 1|0:43:21,22 ./.:20:14,6 1|1:18:10,8 -chr20 367176 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=346552;QSTRAND=+ GT:DP:AD 1|0:26:14,12 ./.:42:17,25 1|1:36:14,22 -chr20 367214 . AAAACAAAC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=346591;QSTRAND=+ GT:DP:AD 1|0:23:6,17 ./.:36:24,12 1|1:45:20,25 -chr20 367226 . A C 60 . QNAME=cluster19_000000F;QSTART=25394856;QSTRAND=- GT:DP:AD ./.:30:20,10 1|0:43:21,22 ./.:44:20,24 -chr20 367234 . A AAAAC 60 . QNAME=cluster19_000000F;QSTART=25394844;QSTRAND=- GT:DP:AD ./.:29:8,21 1|0:36:24,12 ./.:28:17,11 -chr20 367235 . C A 60 . QNAME=cluster19_000000F;QSTART=25394843;QSTRAND=- GT:DP:AD ./.:21:12,9 1|0:41:21,20 ./.:29:13,16 -chr20 367244 . AAAC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=346613;QSTRAND=+ GT:DP:AD 1|0:43:23,20 ./.:29:23,6 1|1:29:6,23 -chr20 367252 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=346617;QSTRAND=+ GT:DP:AD 1|0:46:22,24 ./.:31:20,11 1|1:37:20,17 -chr20 367264 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=321569;QSTRAND=+ GT:DP:AD 0|1:36:12,24 1|1:17:7,10 ./.:34:10,24 -chr20 367521 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=346886;QSTRAND=+ GT:DP:AD 1|0:35:25,10 0|1:38:17,21 ./.:11:6,5 -chr20 367522 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=346887;QSTRAND=+ GT:DP:AD 1|0:24:18,6 ./.:15:5,10 ./.:38:16,22 -chr20 367522 . G C 60 . QNAME=cluster19_000000F;QSTART=327442;QSTRAND=+ GT:DP:AD ./.:23:15,8 0|1:17:9,8 ./.:35:18,17 -chr20 367544 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=321849;QSTRAND=+ GT:DP:AD 0|1:40:23,17 ./.:34:14,20 1|0:20:8,12 -chr20 367675 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=347040;QSTRAND=+ GT:DP:AD 1|0:18:12,6 ./.:45:21,24 0|1:34:19,15 -chr20 367690 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=321995;QSTRAND=+ GT:DP:AD 0|1:20:10,10 ./.:30:10,20 0|1:35:14,21 -chr20 367721 . G GT 60 . QNAME=HG002-S9-H1-000001F;QSTART=347087;QSTRAND=+ GT:DP:AD 1|0:37:15,22 0|1:34:25,9 1|0:28:19,9 -chr20 367877 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=347243;QSTRAND=+ GT:DP:AD 1|0:22:11,11 ./.:37:17,20 ./.:30:24,6 -chr20 368132 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=322437;QSTRAND=+ GT:DP:AD 0|1:23:11,12 1|0:19:9,10 ./.:32:14,18 -chr20 368260 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=322565;QSTRAND=+ GT:DP:AD 0|1:13:7,6 1|0:20:11,9 ./.:28:6,22 -chr20 368284 . CTT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=322590;QSTRAND=+ GT:DP:AD 0|1:38:17,21 1|0:36:21,15 ./.:20:12,8 -chr20 368410 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=322713;QSTRAND=+ GT:DP:AD 0|1:18:5,13 1|0:41:23,18 ./.:29:23,6 -chr20 368474 . C T 60 . QNAME=cluster19_000000F;QSTART=328395;QSTRAND=+ GT:DP:AD ./.:22:14,8 0|1:40:21,19 1|0:40:17,23 -chr20 368491 . G A 60 . QNAME=cluster19_000000F;QSTART=328412;QSTRAND=+ GT:DP:AD ./.:25:7,18 0|1:21:8,13 ./.:26:10,16 -chr20 368580 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=322883;QSTRAND=+ GT:DP:AD 0|1:26:7,19 1|0:29:22,7 ./.:33:13,20 -chr20 368662 . G C 60 . QNAME=cluster19_000000F;QSTART=25393418;QSTRAND=- GT:DP:AD ./.:46:21,25 1|0:29:15,14 ./.:36:11,25 -chr20 368677 . ACT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=322981;QSTRAND=+ GT:DP:AD 0|1:26:9,17 1|0:39:20,19 ./.:23:15,8 -chr20 369093 . T C 60 . QNAME=cluster19_000000F;QSTART=25392989;QSTRAND=- GT:DP:AD ./.:17:7,10 1|0:32:19,13 ./.:38:25,13 -chr20 369284 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25342176;QSTRAND=- GT:DP:AD ./.:46:25,21 ./.:19:7,12 1|0:27:16,11 -chr20 369514 . G A 60 . QNAME=cluster19_000000F;QSTART=25392568;QSTRAND=- GT:DP:AD ./.:37:12,25 1|0:26:11,15 ./.:25:20,5 -chr20 369594 . T A 60 . QNAME=cluster23_scaffold_3;QSTART=25341866;QSTRAND=- GT:DP:AD ./.:27:6,21 ./.:32:21,11 1|0:37:18,19 -chr20 369657 . CAAAAAA C 60 . QNAME=cluster19_000000F;QSTART=25392425;QSTRAND=- GT:DP:AD ./.:22:14,8 1|0:44:22,22 ./.:40:19,21 -chr20 369657 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25341802;QSTRAND=- GT:DP:AD ./.:37:20,17 ./.:13:8,5 1|1:31:11,20 -chr20 369846 . T C 60 . QNAME=cluster19_000000F;QSTART=25392242;QSTRAND=- GT:DP:AD ./.:31:11,20 1|0:32:9,23 1|0:33:25,8 -chr20 369998 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=349364;QSTRAND=+ GT:DP:AD 1|0:28:7,21 ./.:31:11,20 ./.:48:25,23 -chr20 370237 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=349603;QSTRAND=+ GT:DP:AD 1|0:28:18,10 0|1:31:8,23 ./.:38:16,22 -chr20 370371 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=349737;QSTRAND=+ GT:DP:AD 1|0:30:5,25 1|1:20:12,8 ./.:18:13,5 -chr20 371300 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=350666;QSTRAND=+ GT:DP:AD 1|0:31:10,21 0|1:35:22,13 ./.:39:19,20 -chr20 371526 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=350892;QSTRAND=+ GT:DP:AD 1|0:33:8,25 1|1:25:16,9 ./.:16:7,9 -chr20 372007 . T C 60 . QNAME=cluster19_000000F;QSTART=25390081;QSTRAND=- GT:DP:AD ./.:25:8,17 1|0:42:18,24 ./.:29:12,17 -chr20 372073 . A G 60 . QNAME=cluster19_000000F;QSTART=25390015;QSTRAND=- GT:DP:AD ./.:24:8,16 1|0:28:19,9 ./.:16:8,8 -chr20 372441 . A G 60 . QNAME=cluster19_000000F;QSTART=25389647;QSTRAND=- GT:DP:AD ./.:26:12,14 1|0:23:16,7 ./.:20:12,8 -chr20 372564 . A C 60 . QNAME=cluster19_000000F;QSTART=25389524;QSTRAND=- GT:DP:AD ./.:48:23,25 1|0:31:17,14 ./.:28:14,14 -chr20 372676 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=352042;QSTRAND=+ GT:DP:AD 1|0:35:19,16 1|1:37:25,12 ./.:12:7,5 -chr20 372735 . G T 60 . QNAME=cluster19_000000F;QSTART=25389353;QSTRAND=- GT:DP:AD ./.:30:6,24 1|0:31:18,13 ./.:44:20,24 -chr20 373053 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=352419;QSTRAND=+ GT:DP:AD 1|0:23:6,17 1|1:28:10,18 ./.:22:12,10 -chr20 373694 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=353060;QSTRAND=+ GT:DP:AD 1|0:29:20,9 0|1:13:5,8 ./.:22:5,17 -chr20 373749 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=353115;QSTRAND=+ GT:DP:AD 1|0:28:22,6 0|1:38:15,23 ./.:26:11,15 -chr20 374221 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=353587;QSTRAND=+ GT:DP:AD 1|0:27:21,6 0|1:32:13,19 ./.:31:23,8 -chr20 374323 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=353689;QSTRAND=+ GT:DP:AD 1|0:18:11,7 1|1:25:6,19 ./.:27:17,10 -chr20 374523 . A G 60 . QNAME=cluster19_000000F;QSTART=25387565;QSTRAND=- GT:DP:AD ./.:35:20,15 1|0:47:23,24 ./.:36:21,15 -chr20 374580 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=353946;QSTRAND=+ GT:DP:AD 1|0:22:6,16 0|1:30:13,17 ./.:20:15,5 -chr20 374601 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=353967;QSTRAND=+ GT:DP:AD 1|0:28:17,11 0|1:29:21,8 ./.:34:20,14 -chr20 374675 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=354041;QSTRAND=+ GT:DP:AD 1|0:31:19,12 1|1:42:17,25 ./.:35:17,18 -chr20 374716 . C T 60 . QNAME=cluster19_000000F;QSTART=334637;QSTRAND=+ GT:DP:AD ./.:31:18,13 0|1:23:8,15 ./.:32:23,9 -chr20 374726 . C T 60 . QNAME=cluster19_000000F;QSTART=334647;QSTRAND=+ GT:DP:AD ./.:19:10,9 0|1:42:23,19 ./.:39:19,20 -chr20 374740 . G GGT 60 . QNAME=HG002-S9-H1-000001F;QSTART=354107;QSTRAND=+ GT:DP:AD 1|0:30:11,19 0|1:36:22,14 ./.:15:8,7 -chr20 374743 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=354111;QSTRAND=+ GT:DP:AD 1|0:17:9,8 0|1:33:14,19 ./.:29:14,15 -chr20 374744 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=354112;QSTRAND=+ GT:DP:AD 1|0:19:11,8 0|1:10:5,5 ./.:27:10,17 -chr20 374747 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=354115;QSTRAND=+ GT:DP:AD 1|0:30:25,5 0|1:34:19,15 ./.:12:7,5 -chr20 374754 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=354122;QSTRAND=+ GT:DP:AD 1|0:36:17,19 0|1:31:19,12 ./.:28:5,23 -chr20 374836 . T C 60 . QNAME=cluster19_000000F;QSTART=25387252;QSTRAND=- GT:DP:AD ./.:34:22,12 1|0:20:7,13 ./.:24:14,10 -chr20 374900 . C G 60 . QNAME=cluster19_000000F;QSTART=25387188;QSTRAND=- GT:DP:AD ./.:16:7,9 1|0:24:19,5 ./.:26:17,9 -chr20 374905 . A AC 60 . QNAME=HG002-S9-H1-000001F;QSTART=354274;QSTRAND=+ GT:DP:AD 1|0:23:10,13 1|1:39:19,20 ./.:27:5,22 -chr20 375120 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=354489;QSTRAND=+ GT:DP:AD 1|0:29:23,6 1|1:41:22,19 ./.:23:13,10 -chr20 375218 . GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=354588;QSTRAND=+ GT:DP:AD 1|0:26:18,8 ./.:43:21,22 ./.:24:10,14 -chr20 375218 . G GA 60 . QNAME=cluster19_000000F;QSTART=335143;QSTRAND=+ GT:DP:AD ./.:29:19,10 0|1:29:12,17 ./.:22:14,8 -chr20 375359 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=354727;QSTRAND=+ GT:DP:AD 1|0:28:20,8 1|1:34:18,16 ./.:48:23,25 -chr20 375590 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=354958;QSTRAND=+ GT:DP:AD 1|0:34:14,20 0|1:41:17,24 ./.:36:25,11 -chr20 376026 . T TCAAA 60 . QNAME=cluster19_000000F;QSTART=25386057;QSTRAND=- GT:DP:AD ./.:26:18,8 1|0:32:17,15 ./.:21:14,7 -chr20 376031 . A C 60 . QNAME=cluster19_000000F;QSTART=25386052;QSTRAND=- GT:DP:AD ./.:18:9,9 1|0:44:21,23 ./.:32:19,13 -chr20 376031 . A AAAAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=355400;QSTRAND=+ GT:DP:AD 1|0:42:25,17 0|1:20:7,13 ./.:32:23,9 -chr20 376141 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=355513;QSTRAND=+ GT:DP:AD 1|0:18:7,11 1|1:36:17,19 ./.:24:9,15 -chr20 376217 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=355589;QSTRAND=+ GT:DP:AD 1|0:24:7,17 1|1:43:25,18 ./.:29:20,9 -chr20 376406 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=355778;QSTRAND=+ GT:DP:AD 1|0:47:22,25 1|1:18:7,11 ./.:27:20,7 -chr20 376484 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=355856;QSTRAND=+ GT:DP:AD 1|0:38:24,14 1|1:36:14,22 ./.:25:6,19 -chr20 376926 . T C 60 . QNAME=cluster19_000000F;QSTART=25385157;QSTRAND=- GT:DP:AD ./.:28:8,20 1|0:12:7,5 ./.:21:10,11 -chr20 376988 . C T 60 . QNAME=cluster19_000000F;QSTART=25385095;QSTRAND=- GT:DP:AD ./.:41:16,25 1|0:31:14,17 ./.:23:10,13 -chr20 377035 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=356407;QSTRAND=+ GT:DP:AD 1|0:27:14,13 1|1:32:23,9 ./.:47:24,23 -chr20 377056 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=356428;QSTRAND=+ GT:DP:AD 1|0:16:9,7 1|1:34:17,17 ./.:28:6,22 -chr20 377153 . AT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=331455;QSTRAND=+ GT:DP:AD 0|1:43:20,23 ./.:18:11,7 ./.:36:21,15 -chr20 377153 . ATTTTTT A 60 . QNAME=cluster19_000000F;QSTART=25384930;QSTRAND=- GT:DP:AD ./.:31:20,11 1|0:30:19,11 ./.:39:14,25 -chr20 377184 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=356556;QSTRAND=+ GT:DP:AD 1|0:24:12,12 1|1:35:11,24 ./.:27:9,18 -chr20 377366 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=356738;QSTRAND=+ GT:DP:AD 1|0:43:22,21 1|1:25:7,18 ./.:33:24,9 -chr20 377503 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=356876;QSTRAND=+ GT:DP:AD 1|0:19:5,14 1|1:24:6,18 ./.:34:25,9 -chr20 377680 . GT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=357052;QSTRAND=+ GT:DP:AD 1|1:42:25,17 1|1:17:7,10 ./.:24:16,8 -chr20 377680 . G GT 60 . QNAME=cluster23_scaffold_2;QSTART=25317935;QSTRAND=- GT:DP:AD ./.:42:19,23 ./.:30:16,14 0|1:19:10,9 -chr20 377737 . T C 60 . QNAME=cluster19_000000F;QSTART=25384354;QSTRAND=- GT:DP:AD ./.:26:9,17 1|1:26:10,16 ./.:48:25,23 -chr20 377922 . G A 60 . QNAME=cluster19_000000F;QSTART=25384169;QSTRAND=- GT:DP:AD ./.:25:6,19 1|1:35:17,18 ./.:31:14,17 -chr20 377975 . A G 60 . QNAME=cluster19_000000F;QSTART=25384116;QSTRAND=- GT:DP:AD ./.:25:13,12 1|1:14:9,5 ./.:37:12,25 -chr20 378291 . C T 60 . QNAME=cluster19_000000F;QSTART=25383800;QSTRAND=- GT:DP:AD ./.:25:8,17 1|1:25:14,11 ./.:31:12,19 -chr20 378708 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=333008;QSTRAND=+ GT:DP:AD 0|1:31:24,7 ./.:35:11,24 ./.:15:5,10 -chr20 378907 . T A 60 . QNAME=cluster19_000000F;QSTART=338834;QSTRAND=+ GT:DP:AD ./.:24:18,6 0|1:47:24,23 ./.:44:21,23 -chr20 379030 . C T 60 . QNAME=cluster19_000000F;QSTART=25383061;QSTRAND=- GT:DP:AD ./.:21:7,14 1|1:49:24,25 ./.:27:10,17 -chr20 379398 . G A 60 . QNAME=cluster19_000000F;QSTART=25382693;QSTRAND=- GT:DP:AD ./.:37:15,22 1|1:25:13,12 ./.:32:14,18 -chr20 379418 . T C 60 . QNAME=cluster19_000000F;QSTART=25382673;QSTRAND=- GT:DP:AD ./.:24:13,11 1|0:41:16,25 ./.:41:21,20 -chr20 379468 . G A 60 . QNAME=cluster19_000000F;QSTART=25382623;QSTRAND=- GT:DP:AD ./.:23:5,18 1|1:36:17,19 ./.:43:22,21 -chr20 379581 . A C 60 . QNAME=cluster19_000000F;QSTART=25382510;QSTRAND=- GT:DP:AD ./.:31:9,22 1|0:35:24,11 ./.:32:16,16 -chr20 379662 . T C 60 . QNAME=cluster19_000000F;QSTART=25382429;QSTRAND=- GT:DP:AD ./.:36:12,24 1|1:39:18,21 ./.:29:20,9 -chr20 379675 . G GA 60 . QNAME=cluster19_000000F;QSTART=339603;QSTRAND=+ GT:DP:AD ./.:27:10,17 0|1:21:15,6 ./.:29:5,24 -chr20 379699 . G C 60 . QNAME=cluster19_000000F;QSTART=25382392;QSTRAND=- GT:DP:AD ./.:24:13,11 1|1:16:5,11 ./.:39:22,17 -chr20 379759 . T C 60 . QNAME=cluster19_000000F;QSTART=25382332;QSTRAND=- GT:DP:AD ./.:36:20,16 1|1:45:20,25 ./.:25:13,12 -chr20 379794 . T C 60 . QNAME=cluster19_000000F;QSTART=25382297;QSTRAND=- GT:DP:AD ./.:19:13,6 1|1:16:7,9 ./.:32:19,13 -chr20 379816 . C T 60 . QNAME=cluster19_000000F;QSTART=25382275;QSTRAND=- GT:DP:AD ./.:37:12,25 1|1:31:6,25 ./.:39:16,23 -chr20 379966 . G T 60 . QNAME=cluster19_000000F;QSTART=25382125;QSTRAND=- GT:DP:AD ./.:37:22,15 1|1:40:15,25 ./.:32:18,14 -chr20 380070 . G C 60 . QNAME=cluster19_000000F;QSTART=25382021;QSTRAND=- GT:DP:AD ./.:39:17,22 1|1:34:18,16 ./.:22:16,6 -chr20 380078 . G C 60 . QNAME=cluster19_000000F;QSTART=25382013;QSTRAND=- GT:DP:AD ./.:32:21,11 1|1:38:13,25 ./.:22:8,14 -chr20 380145 . T C 60 . QNAME=cluster19_000000F;QSTART=340073;QSTRAND=+ GT:DP:AD ./.:38:24,14 0|1:25:18,7 ./.:37:19,18 -chr20 380283 . TAA T 60 . QNAME=cluster19_000000F;QSTART=25381808;QSTRAND=- GT:DP:AD ./.:28:9,19 1|1:32:14,18 ./.:33:22,11 -chr20 380289 . A C 60 . QNAME=cluster19_000000F;QSTART=25381804;QSTRAND=- GT:DP:AD ./.:31:20,11 1|1:17:8,9 ./.:28:21,7 -chr20 380548 . T C 60 . QNAME=cluster19_000000F;QSTART=25381545;QSTRAND=- GT:DP:AD ./.:25:13,12 1|1:24:17,7 ./.:23:7,16 -chr20 380662 . G A 60 . QNAME=cluster19_000000F;QSTART=25381431;QSTRAND=- GT:DP:AD ./.:24:8,16 1|1:43:22,21 1|0:15:6,9 -chr20 380663 . C A 60 . QNAME=cluster19_000000F;QSTART=25381430;QSTRAND=- GT:DP:AD ./.:22:9,13 1|1:40:16,24 1|0:23:7,16 -chr20 380672 . A G 60 . QNAME=cluster19_000000F;QSTART=25381421;QSTRAND=- GT:DP:AD ./.:22:8,14 1|1:17:5,12 1|0:27:12,15 -chr20 380679 . T C 60 . QNAME=cluster19_000000F;QSTART=25381414;QSTRAND=- GT:DP:AD ./.:32:10,22 1|1:34:24,10 1|0:23:18,5 -chr20 380684 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=360055;QSTRAND=+ GT:DP:AD 1|0:15:10,5 1|1:31:9,22 ./.:24:14,10 -chr20 380684 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25330774;QSTRAND=- GT:DP:AD ./.:42:25,17 ./.:28:9,19 1|0:38:25,13 -chr20 380878 . T TGATTAGCTCCGGTTTGCATCACCCGGACCGGGGGATTAGCTCCGGTTTGCATCACCCGGACCGGGG 60 . QNAME=cluster19_000000F;QSTART=25381150;QSTRAND=-;SVTYPE=INS;SVLEN=66 GT:DP:AD ./.:21:9,12 1/0:15:8,7 ./.:25:20,5 -chr20 380878 . TGATTAGCTCCGGTTTGCATCACCCGGACCGGGG T 60 . QNAME=cluster23_scaffold_3;QSTART=25330580;QSTRAND=-;SVTYPE=DEL;SVLEN=-33 GT:DP:AD ./.:13:5,8 ./.:24:18,6 1/0:18:13,5 -chr20 381233 . G A 60 . QNAME=cluster19_000000F;QSTART=25380795;QSTRAND=- GT:DP:AD ./.:43:23,20 1|0:24:7,17 ./.:34:10,24 -chr20 381358 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=360727;QSTRAND=+ GT:DP:AD 1|0:28:17,11 ./.:23:6,17 ./.:31:23,8 -chr20 381423 . C G 60 . QNAME=cluster23_scaffold_3;QSTART=25330068;QSTRAND=- GT:DP:AD ./.:26:6,20 ./.:36:14,22 1|0:40:19,21 -chr20 381585 . AG A 60 . QNAME=cluster23_scaffold_3;QSTART=25329906;QSTRAND=- GT:DP:AD ./.:24:6,18 ./.:32:17,15 1|0:33:22,11 -chr20 381637 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=361006;QSTRAND=+ GT:DP:AD 1|0:41:21,20 1|1:36:16,20 0|1:26:13,13 -chr20 381684 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=361053;QSTRAND=+ GT:DP:AD 1|0:29:11,18 0|1:31:10,21 1|0:34:25,9 -chr20 381742 . T TG 60 . QNAME=HG002-S9-H2-000001F;QSTART=336041;QSTRAND=+ GT:DP:AD 0|1:35:16,19 1|0:28:6,22 1|0:20:15,5 -chr20 381797 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=336096;QSTRAND=+ GT:DP:AD 0|1:28:23,5 0|1:32:8,24 1|0:33:8,25 -chr20 382099 . C CTG 60 . QNAME=cluster19_000000F;QSTART=25379926;QSTRAND=- GT:DP:AD ./.:39:24,15 1|0:19:12,7 ./.:39:18,21 -chr20 382099 . C CTGTGTGTG 60 . QNAME=cluster23_scaffold_3;QSTART=25329384;QSTRAND=- GT:DP:AD ./.:26:20,6 ./.:26:8,18 1|0:40:16,24 -chr20 382124 . TGTGC T 60 . QNAME=cluster23_scaffold_2;QSTART=25313491;QSTRAND=- GT:DP:AD ./.:22:6,16 ./.:35:12,23 0|1:26:8,18 -chr20 383089 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25328394;QSTRAND=- GT:DP:AD ./.:31:14,17 ./.:14:7,7 1|0:36:15,21 -chr20 383651 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=363020;QSTRAND=+ GT:DP:AD 1|0:44:20,24 1|0:34:13,21 0|1:30:16,14 -chr20 384031 . A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25327451;QSTRAND=- GT:DP:AD ./.:14:9,5 ./.:29:15,14 1|0:21:16,5 -chr20 384050 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25311569;QSTRAND=- GT:DP:AD ./.:42:23,19 ./.:33:12,21 0|1:29:16,13 -chr20 384103 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=25327379;QSTRAND=- GT:DP:AD ./.:38:22,16 ./.:20:11,9 1|0:44:23,21 diff --git a/repo_utils/test_files/answer_key/divided/multi_00000007.vcf b/repo_utils/test_files/answer_key/divided/multi_00000007.vcf deleted file mode 100644 index 5746eadb..00000000 --- a/repo_utils/test_files/answer_key/divided/multi_00000007.vcf +++ /dev/null @@ -1,179 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##bcftools_mergeVersion=1.12+htslib-1.12 -##bcftools_mergeCommand=merge -O z -f x -m none input1.vcf.gz input2.vcf.gz input3.vcf.gz; Date=Mon Aug 16 18:05:13 2021 -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 385414 . AT A 60 . QNAME=cluster19_000000F;QSTART=345340;QSTRAND=+ GT:DP:AD ./.:24:13,11 0|1:37:13,24 1|0:39:17,22 -chr20 385860 . A AT 60 . QNAME=cluster23_scaffold_2;QSTART=25309758;QSTRAND=- GT:DP:AD ./.:45:22,23 ./.:43:20,23 0|1:25:10,15 -chr20 385969 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=365338;QSTRAND=+ GT:DP:AD 1|0:17:7,10 ./.:19:5,14 0|1:41:18,23 -chr20 386036 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=365405;QSTRAND=+ GT:DP:AD 1|0:25:16,9 1|1:50:25,25 1|1:48:24,24 -chr20 386320 . T C 60 . QNAME=cluster19_000000F;QSTART=346244;QSTRAND=+ GT:DP:AD ./.:24:5,19 0|1:35:25,10 1|0:25:7,18 -chr20 387554 . GA G 60 . QNAME=cluster19_000000F;QSTART=347479;QSTRAND=+ GT:DP:AD ./.:44:21,23 0|1:24:6,18 ./.:24:13,11 -chr20 391001 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=345301;QSTRAND=+ GT:DP:AD 0|1:27:22,5 1|0:15:5,10 0|1:30:25,5 -chr20 391001 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25320481;QSTRAND=- GT:DP:AD ./.:29:17,12 ./.:26:19,7 1|0:31:19,12 -chr20 391003 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=345301;QSTRAND=+ GT:DP:AD 0|1:46:24,22 1|0:40:19,21 0|1:36:24,12 -chr20 391137 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=345435;QSTRAND=+ GT:DP:AD 0|1:39:18,21 1|0:28:23,5 0|1:46:25,21 -chr20 391138 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=345436;QSTRAND=+ GT:DP:AD 0|1:32:25,7 1|0:42:17,25 0|1:40:24,16 -chr20 391328 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=345626;QSTRAND=+ GT:DP:AD 0|1:36:24,12 1|0:39:23,16 0|1:18:6,12 -chr20 392021 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=346320;QSTRAND=+ GT:DP:AD 0|1:40:17,23 ./.:27:22,5 ./.:17:5,12 -chr20 392557 . A AT 60 . QNAME=HG002-S9-H2-000001F;QSTART=346855;QSTRAND=+ GT:DP:AD 0|1:26:15,11 1|0:29:12,17 1|1:26:21,5 -chr20 393192 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=347407;QSTRAND=+ GT:DP:AD 0|1:13:6,7 1|0:35:20,15 0|1:13:8,5 -chr20 393337 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=347553;QSTRAND=+ GT:DP:AD 0|1:24:18,6 1|0:23:9,14 1|1:23:7,16 -chr20 393417 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=347631;QSTRAND=+ GT:DP:AD 0|1:21:12,9 1|0:38:16,22 0|1:28:11,17 -chr20 393740 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=347954;QSTRAND=+ GT:DP:AD 0|1:13:5,8 1|0:44:21,23 0|1:23:14,9 -chr20 393795 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=348009;QSTRAND=+ GT:DP:AD 0|1:17:9,8 1|0:40:19,21 0|1:39:17,22 -chr20 394032 . C CT 60 . QNAME=HG002-S9-H2-000001F;QSTART=348247;QSTRAND=+ GT:DP:AD 0|1:39:18,21 1|0:30:12,18 0|1:15:8,7 -chr20 394119 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=348334;QSTRAND=+ GT:DP:AD 0|1:33:8,25 1|0:31:15,16 0|1:26:18,8 -chr20 394301 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=348516;QSTRAND=+ GT:DP:AD 0|1:11:5,6 ./.:28:17,11 0|1:31:6,25 -chr20 394462 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=348677;QSTRAND=+ GT:DP:AD 0|1:14:8,6 1|1:44:21,23 0|1:21:14,7 -chr20 394799 . G GA 60 . QNAME=cluster23_scaffold_3;QSTART=25316682;QSTRAND=- GT:DP:AD ./.:37:17,20 ./.:46:23,23 1|0:35:10,25 -chr20 394955 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=349170;QSTRAND=+ GT:DP:AD 0|1:25:11,14 ./.:31:22,9 0|1:24:14,10 -chr20 395162 . CT C 60 . QNAME=cluster19_000000F;QSTART=25366946;QSTRAND=- GT:DP:AD ./.:21:10,11 1|0:22:8,14 ./.:41:22,19 -chr20 396582 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=350797;QSTRAND=+ GT:DP:AD 0|1:16:10,6 1|0:30:13,17 0|1:50:25,25 -chr20 397598 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=351813;QSTRAND=+ GT:DP:AD 0|1:38:24,14 1|0:43:21,22 0|1:21:14,7 -chr20 397600 . T A 60 . QNAME=cluster23_scaffold_2;QSTART=25298101;QSTRAND=- GT:DP:AD ./.:30:25,5 ./.:39:24,15 0|1:14:8,6 -chr20 397886 . A AC 60 . QNAME=cluster23_scaffold_3;QSTART=25313594;QSTRAND=- GT:DP:AD ./.:23:13,10 ./.:41:16,25 1|0:23:10,13 -chr20 398287 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=352502;QSTRAND=+ GT:DP:AD 0|1:44:20,24 1|0:28:5,23 0|1:33:24,9 -chr20 398312 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=352527;QSTRAND=+ GT:DP:AD 0|1:46:23,23 1|0:32:13,19 0|1:24:14,10 -chr20 398313 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=352528;QSTRAND=+ GT:DP:AD 0|1:33:24,9 1|0:32:18,14 0|1:14:6,8 -chr20 398315 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=352530;QSTRAND=+ GT:DP:AD 0|1:31:21,10 1|0:13:7,6 0|1:28:13,15 -chr20 398320 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=352535;QSTRAND=+ GT:DP:AD 0|1:41:20,21 1|0:25:20,5 0|1:35:19,16 -chr20 398324 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=352539;QSTRAND=+ GT:DP:AD 0|1:35:13,22 1|0:39:16,23 0|1:36:23,13 -chr20 398327 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=352542;QSTRAND=+ GT:DP:AD 0|1:29:24,5 1|0:31:21,10 0|1:40:19,21 -chr20 398334 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=352549;QSTRAND=+ GT:DP:AD 0|1:36:21,15 1|0:16:11,5 0|1:31:22,9 -chr20 398897 . C T 60 . QNAME=cluster19_000000F;QSTART=25363212;QSTRAND=- GT:DP:AD ./.:22:13,9 1|0:20:8,12 ./.:16:5,11 -chr20 399283 . A G 60 . QNAME=cluster19_000000F;QSTART=25362826;QSTRAND=- GT:DP:AD ./.:29:8,21 1|1:36:14,22 1|1:27:13,14 -chr20 399958 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=379327;QSTRAND=+ GT:DP:AD 1|0:30:7,23 1|0:48:25,23 ./.:23:6,17 -chr20 400146 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=379516;QSTRAND=+ GT:DP:AD 1|0:18:5,13 1|1:30:7,23 1|0:19:12,7 -chr20 400336 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=379706;QSTRAND=+ GT:DP:AD 1|0:22:7,15 1|1:41:25,16 1|0:20:12,8 -chr20 400547 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=379917;QSTRAND=+ GT:DP:AD 1|0:44:25,19 1|1:14:6,8 1|0:36:20,16 -chr20 400677 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=380047;QSTRAND=+ GT:DP:AD 1|0:31:17,14 1|1:32:25,7 1|0:27:6,21 -chr20 400755 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=380125;QSTRAND=+ GT:DP:AD 1|0:32:7,25 1|0:24:15,9 ./.:22:17,5 -chr20 400797 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=380167;QSTRAND=+ GT:DP:AD 1|0:23:10,13 1|1:23:9,14 1|0:34:10,24 -chr20 400887 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=380257;QSTRAND=+ GT:DP:AD 1|0:32:25,7 1|1:38:16,22 1|0:18:5,13 -chr20 401685 . C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=381056;QSTRAND=+ GT:DP:AD 1|0:34:24,10 1|1:23:18,5 ./.:38:25,13 -chr20 401685 . C CAA 60 . QNAME=cluster23_scaffold_3;QSTART=25309792;QSTRAND=- GT:DP:AD ./.:27:19,8 ./.:28:12,16 1|0:19:11,8 -chr20 401702 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=381073;QSTRAND=+ GT:DP:AD 1|0:38:23,15 1|1:26:14,12 1|0:47:25,22 -chr20 401915 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=381286;QSTRAND=+ GT:DP:AD 1|0:35:20,15 1|1:42:19,23 1|0:44:25,19 -chr20 401983 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=381354;QSTRAND=+ GT:DP:AD 1|0:40:22,18 1|1:20:11,9 1|0:25:17,8 -chr20 402232 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=381603;QSTRAND=+ GT:DP:AD 1|0:43:19,24 1|1:35:20,15 1|0:39:14,25 -chr20 402478 . CAAAAAAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=381850;QSTRAND=+ GT:DP:AD 1|0:16:8,8 1|0:37:16,21 ./.:34:13,21 -chr20 402478 . C CAA 60 . QNAME=HG002-S9-H2-000001F;QSTART=356694;QSTRAND=+ GT:DP:AD 0|1:28:13,15 ./.:32:12,20 ./.:25:13,12 -chr20 402478 . C CAAA 60 . QNAME=cluster23_scaffold_2;QSTART=25293220;QSTRAND=- GT:DP:AD ./.:41:24,17 ./.:38:17,21 0|1:35:18,17 -chr20 402492 . A AT 60 . QNAME=cluster19_000000F;QSTART=362418;QSTRAND=+ GT:DP:AD ./.:36:15,21 0|1:14:5,9 1|0:16:6,10 -chr20 402498 . A T 60 . QNAME=cluster19_000000F;QSTART=362424;QSTRAND=+ GT:DP:AD ./.:39:20,19 0|1:43:18,25 1|0:23:5,18 -chr20 402504 . A T 60 . QNAME=cluster19_000000F;QSTART=362430;QSTRAND=+ GT:DP:AD ./.:28:12,16 0|1:30:15,15 1|0:34:24,10 -chr20 402509 . A T 60 . QNAME=cluster19_000000F;QSTART=362435;QSTRAND=+ GT:DP:AD ./.:19:14,5 0|1:32:11,21 1|0:28:22,6 -chr20 403076 . C T 60 . QNAME=cluster19_000000F;QSTART=363002;QSTRAND=+ GT:DP:AD ./.:22:16,6 0|1:38:15,23 1|0:38:16,22 -chr20 403697 . A G 60 . QNAME=cluster19_000000F;QSTART=363623;QSTRAND=+ GT:DP:AD ./.:39:17,22 0|1:17:8,9 1|0:13:8,5 -chr20 403859 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=383222;QSTRAND=+ GT:DP:AD 1|0:38:18,20 1|0:45:24,21 ./.:20:6,14 -chr20 404000 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=383363;QSTRAND=+ GT:DP:AD 1|0:14:7,7 1|1:30:11,19 1|0:25:19,6 -chr20 404254 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=383617;QSTRAND=+ GT:DP:AD 1|0:21:7,14 1|0:34:11,23 ./.:25:12,13 -chr20 404408 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=383771;QSTRAND=+ GT:DP:AD 1|0:35:24,11 1|1:16:10,6 1|0:38:22,16 -chr20 404596 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=383959;QSTRAND=+ GT:DP:AD 1|1:37:12,25 1|1:40:21,19 1|1:20:15,5 -chr20 405155 . T TCACA 60 . QNAME=cluster19_000000F;QSTART=365082;QSTRAND=+ GT:DP:AD ./.:29:16,13 0|1:33:21,12 1|0:17:11,6 -chr20 405155 . TCA T 60 . QNAME=cluster19_000000F;QSTART=25356960;QSTRAND=- GT:DP:AD ./.:35:23,12 1|0:39:17,22 ./.:28:5,23 -chr20 405220 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=384583;QSTRAND=+ GT:DP:AD 1|0:27:14,13 1|1:28:16,12 1|0:33:11,22 -chr20 405345 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=384709;QSTRAND=+ GT:DP:AD 1|0:27:11,16 1|0:38:20,18 ./.:23:5,18 -chr20 405478 . C T 60 . QNAME=cluster19_000000F;QSTART=365408;QSTRAND=+ GT:DP:AD ./.:31:13,18 0|1:30:16,14 1|0:22:12,10 -chr20 405820 . A G 60 . QNAME=cluster19_000000F;QSTART=365750;QSTRAND=+ GT:DP:AD ./.:33:17,16 0|1:46:22,24 1|0:31:15,16 -chr20 405931 . GTTCT G 60 . QNAME=cluster19_000000F;QSTART=365862;QSTRAND=+ GT:DP:AD ./.:26:6,20 0|1:31:7,24 1|0:33:14,19 -chr20 405942 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=360160;QSTRAND=+ GT:DP:AD 0|1:16:6,10 ./.:30:19,11 ./.:24:19,5 -chr20 406708 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=360925;QSTRAND=+ GT:DP:AD 0|1:35:13,22 ./.:39:20,19 ./.:22:10,12 -chr20 406708 . CAAA C 60 . QNAME=cluster19_000000F;QSTART=366635;QSTRAND=+ GT:DP:AD ./.:26:14,12 0|1:41:23,18 1|0:29:11,18 -chr20 406708 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25288989;QSTRAND=- GT:DP:AD ./.:21:6,15 ./.:45:21,24 0|1:16:6,10 -chr20 406732 . A AAAAAAAAAAAAG 60 . QNAME=HG002-S9-H1-000001F;QSTART=386097;QSTRAND=+ GT:DP:AD 1|0:14:8,6 ./.:37:20,17 ./.:34:24,10 -chr20 406732 . A AAAAAAAAAAG 60 . QNAME=cluster19_000000F;QSTART=25355374;QSTRAND=- GT:DP:AD ./.:45:21,24 1|0:30:23,7 ./.:36:12,24 -chr20 407013 . G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=386390;QSTRAND=+ GT:DP:AD 1|0:39:24,15 1|1:36:14,22 1|0:29:12,17 -chr20 407083 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=386460;QSTRAND=+ GT:DP:AD 1|0:24:10,14 1|0:41:17,24 ./.:34:9,25 -chr20 407113 . A G 60 . QNAME=cluster19_000000F;QSTART=367037;QSTRAND=+ GT:DP:AD ./.:41:20,21 0|1:33:8,25 1|0:36:14,22 -chr20 407171 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=386548;QSTRAND=+ GT:DP:AD 1|0:33:24,9 1|0:39:20,19 ./.:21:6,15 -chr20 407872 . C T 60 . QNAME=cluster19_000000F;QSTART=367796;QSTRAND=+ GT:DP:AD ./.:33:23,10 0|1:33:8,25 1|0:18:11,7 -chr20 407964 . CG C 60 . QNAME=HG002-S9-H1-000001F;QSTART=387342;QSTRAND=+ GT:DP:AD 1|0:40:24,16 1|0:12:5,7 ./.:30:8,22 -chr20 407977 . CG C 60 . QNAME=HG002-S9-H1-000001F;QSTART=387354;QSTRAND=+ GT:DP:AD 1|0:25:6,19 1|0:21:8,13 ./.:24:9,15 -chr20 408008 . GC G 60 . QNAME=HG002-S9-H1-000001F;QSTART=387384;QSTRAND=+ GT:DP:AD 1|0:30:16,14 ./.:19:6,13 ./.:33:8,25 -chr20 408028 . G GGCCCCGCCC 60 . QNAME=HG002-S9-H2-000001F;QSTART=362274;QSTRAND=+ GT:DP:AD 0|1:18:11,7 ./.:31:18,13 0|1:35:22,13 -chr20 408029 . G GCCCCGCCCA 60 . QNAME=cluster19_000000F;QSTART=367992;QSTRAND=+ GT:DP:AD ./.:12:6,6 0|1:20:9,11 1|0:25:9,16 -chr20 408057 . T TC 60 . QNAME=HG002-S9-H1-000001F;QSTART=387432;QSTRAND=+ GT:DP:AD 1|1:23:13,10 1|1:34:24,10 1|1:24:15,9 -chr20 408812 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=363067;QSTRAND=+ GT:DP:AD 0|1:33:15,18 0|1:50:25,25 1|1:24:18,6 -chr20 409237 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=363492;QSTRAND=+ GT:DP:AD 0|1:30:22,8 0|1:19:5,14 1|1:42:18,24 -chr20 409291 . AT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=363547;QSTRAND=+ GT:DP:AD 0|1:42:22,20 ./.:29:24,5 ./.:19:14,5 -chr20 409340 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=363594;QSTRAND=+ GT:DP:AD 0|1:34:23,11 0|1:27:13,14 1|1:47:24,23 -chr20 409466 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=363721;QSTRAND=+ GT:DP:AD 0|1:28:10,18 ./.:28:19,9 ./.:26:20,6 -chr20 410526 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=364779;QSTRAND=+ GT:DP:AD 0|1:26:10,16 0|1:39:16,23 1|1:23:5,18 -chr20 412325 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=366579;QSTRAND=+ GT:DP:AD 0|1:17:11,6 ./.:42:17,25 ./.:31:23,8 -chr20 413334 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=367586;QSTRAND=+ GT:DP:AD 0|1:40:15,25 0|1:17:12,5 1|1:34:19,15 -chr20 413917 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=368170;QSTRAND=+ GT:DP:AD 0|1:41:24,17 0|1:38:24,14 1|1:21:16,5 -chr20 413941 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=368192;QSTRAND=+ GT:DP:AD 0|1:26:12,14 0|1:27:20,7 1|1:22:13,9 -chr20 414091 . C CA 60 . QNAME=HG002-S9-H2-000001F;QSTART=368343;QSTRAND=+ GT:DP:AD 0|1:31:21,10 0|1:39:21,18 1|1:13:6,7 -chr20 414091 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=393467;QSTRAND=+ GT:DP:AD 1|0:40:15,25 ./.:37:12,25 ./.:37:19,18 -chr20 414317 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=368569;QSTRAND=+ GT:DP:AD 0|1:27:15,12 0|1:19:12,7 1|1:20:12,8 -chr20 415178 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=369430;QSTRAND=+ GT:DP:AD 0|1:29:24,5 0|1:29:23,6 1|1:22:14,8 -chr20 415379 . A AAAAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=394754;QSTRAND=+ GT:DP:AD 1|1:24:5,19 1|1:32:20,12 1|1:17:6,11 -chr20 415512 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=394890;QSTRAND=+ GT:DP:AD 1|0:15:9,6 1|0:20:8,12 ./.:28:15,13 -chr20 416154 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25295271;QSTRAND=- GT:DP:AD ./.:40:15,25 ./.:30:21,9 1|0:25:19,6 -chr20 416334 . G T 60 . QNAME=cluster19_000000F;QSTART=376310;QSTRAND=+ GT:DP:AD ./.:44:20,24 0|1:22:12,10 1|0:41:21,20 -chr20 417284 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=396662;QSTRAND=+ GT:DP:AD 1|1:43:21,22 1|1:40:18,22 1|1:34:17,17 -chr20 417395 . T TTG 60 . QNAME=cluster23_scaffold_3;QSTART=25294028;QSTRAND=- GT:DP:AD ./.:24:16,8 ./.:32:21,11 1|1:38:13,25 -chr20 417634 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=397012;QSTRAND=+ GT:DP:AD 1|0:41:16,25 1|0:40:20,20 ./.:28:18,10 -chr20 418430 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=397808;QSTRAND=+ GT:DP:AD 1|0:36:22,14 1|0:31:9,22 ./.:39:16,23 -chr20 418432 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=397810;QSTRAND=+ GT:DP:AD 1|0:15:6,9 1|0:31:24,7 ./.:28:9,19 -chr20 418579 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=372835;QSTRAND=+ GT:DP:AD 0|1:27:15,12 ./.:18:12,6 1|1:28:14,14 -chr20 418601 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=372857;QSTRAND=+ GT:DP:AD 0|1:37:25,12 ./.:35:24,11 1|1:49:24,25 -chr20 418603 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=372859;QSTRAND=+ GT:DP:AD 0|1:36:17,19 ./.:36:21,15 1|1:16:9,7 -chr20 418658 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=372914;QSTRAND=+ GT:DP:AD 0|1:35:24,11 ./.:40:17,23 1|1:15:9,6 -chr20 419117 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=398495;QSTRAND=+ GT:DP:AD 1|1:25:10,15 1|0:35:25,10 1|1:27:8,19 -chr20 419860 . AGTGACCCTGCACCTGGCT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=374117;QSTRAND=+ GT:DP:AD 0|1:24:19,5 ./.:14:7,7 1|1:27:8,19 -chr20 420228 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=374466;QSTRAND=+ GT:DP:AD 0|1:36:17,19 ./.:25:11,14 1|1:29:10,19 -chr20 420465 . A AG 60 . QNAME=HG002-S9-H2-000001F;QSTART=374704;QSTRAND=+ GT:DP:AD 0|1:19:11,8 ./.:22:8,14 1|1:24:5,19 -chr20 420561 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=399939;QSTRAND=+ GT:DP:AD 1|1:31:17,14 1|0:37:21,16 1|1:47:25,22 -chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCATCCCCCGTCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 60 . QNAME=HG002-S9-H1-000001F;QSTART=400044;QSTRAND=+;SVTYPE=INS;SVLEN=226 GT:DP:AD 1/0:45:21,24 1/1:27:20,7 ./.:31:15,16 -chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCCATCCCCCGTCCGCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 61 . QNAME=HG002-S9-H2-000001F;QSTART=374905;QSTRAND=+;SVTYPE=INS;SVLEN=227 GT:DP:AD 0/1:27:19,8 ./.:40:20,20 1/1:23:7,16 -chr20 421409 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=401013;QSTRAND=+ GT:DP:AD 1|1:29:23,6 1|0:33:15,18 1|1:17:6,11 -chr20 421527 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=375993;QSTRAND=+ GT:DP:AD 0|1:29:24,5 ./.:36:17,19 1|1:37:13,24 -chr20 422066 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=401670;QSTRAND=+ GT:DP:AD 1|1:31:24,7 1|0:40:16,24 1|1:30:23,7 -chr20 422277 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=376743;QSTRAND=+ GT:DP:AD 0|1:44:23,21 ./.:42:22,20 1|1:29:14,15 -chr20 422514 . GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=402119;QSTRAND=+ GT:DP:AD 1|0:42:17,25 1|0:50:25,25 ./.:20:5,15 -chr20 422548 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=402151;QSTRAND=+ GT:DP:AD 1|0:26:8,18 1|0:30:22,8 ./.:34:19,15 -chr20 422567 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=402170;QSTRAND=+ GT:DP:AD 1|0:26:11,15 1|0:38:15,23 ./.:32:13,19 -chr20 423009 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=402612;QSTRAND=+ GT:DP:AD 1|1:40:21,19 1|0:26:20,6 1|1:31:20,11 -chr20 423705 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=403308;QSTRAND=+ GT:DP:AD 1|1:22:17,5 1|0:38:15,23 1|1:43:22,21 -chr20 423763 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=403366;QSTRAND=+ GT:DP:AD 1|1:40:20,20 1|0:30:25,5 1|1:17:7,10 -chr20 424272 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=403875;QSTRAND=+ GT:DP:AD 1|1:34:17,17 1|0:47:25,22 1|1:26:17,9 -chr20 424413 . A AC 60 . QNAME=HG002-S9-H1-000001F;QSTART=404017;QSTRAND=+ GT:DP:AD 1|0:38:17,21 1|0:21:6,15 1|0:31:19,12 diff --git a/repo_utils/test_files/answer_key/divided/multi_00000008.vcf b/repo_utils/test_files/answer_key/divided/multi_00000008.vcf deleted file mode 100644 index 546abb77..00000000 --- a/repo_utils/test_files/answer_key/divided/multi_00000008.vcf +++ /dev/null @@ -1,142 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##bcftools_mergeVersion=1.12+htslib-1.12 -##bcftools_mergeCommand=merge -O z -f x -m none input1.vcf.gz input2.vcf.gz input3.vcf.gz; Date=Mon Aug 16 18:05:13 2021 -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 425626 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=405231;QSTRAND=+ GT:DP:AD 1|1:14:6,8 1|0:31:21,10 1|1:41:16,25 -chr20 426816 . C CT 60 . QNAME=cluster19_000000F;QSTART=25335060;QSTRAND=- GT:DP:AD ./.:16:9,7 1|0:27:22,5 1|0:40:22,18 -chr20 429226 . AT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=383692;QSTRAND=+ GT:DP:AD 0|1:31:21,10 ./.:32:16,16 ./.:33:15,18 -chr20 429226 . A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25281985;QSTRAND=- GT:DP:AD ./.:31:23,8 ./.:34:24,10 1|1:31:10,21 -chr20 429249 . G A 60 . QNAME=cluster19_000000F;QSTART=389451;QSTRAND=+ GT:DP:AD ./.:36:17,19 0|1:30:10,20 ./.:17:9,8 -chr20 431198 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=410801;QSTRAND=+ GT:DP:AD 1|1:33:8,25 1|0:34:24,10 1|1:36:13,23 -chr20 433739 . AGGCTACCCACACTTCCTG A 60 . QNAME=HG002-S9-H1-000001F;QSTART=413343;QSTRAND=+ GT:DP:AD 1|1:46:21,25 1|0:32:15,17 1|1:43:23,20 -chr20 433902 . T C 60 . QNAME=cluster19_000000F;QSTART=25327992;QSTRAND=- GT:DP:AD ./.:46:25,21 1|0:27:9,18 ./.:15:8,7 -chr20 434000 . G GT 60 . QNAME=cluster23_scaffold_3;QSTART=25277228;QSTRAND=- GT:DP:AD ./.:14:5,9 ./.:15:9,6 1|1:20:8,12 -chr20 434001 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=413586;QSTRAND=+ GT:DP:AD 1|1:16:9,7 1|0:36:12,24 1|1:28:12,16 -chr20 434561 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=414146;QSTRAND=+ GT:DP:AD 1|1:49:24,25 1|0:39:23,16 1|1:13:8,5 -chr20 435505 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=415090;QSTRAND=+ GT:DP:AD 1|1:30:10,20 1|0:25:18,7 1|1:45:20,25 -chr20 436968 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=416553;QSTRAND=+ GT:DP:AD 1|1:25:19,6 1|0:28:19,9 1|1:13:5,8 -chr20 437555 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=417140;QSTRAND=+ GT:DP:AD 1|1:43:21,22 1|0:38:17,21 1|1:26:19,7 -chr20 438423 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=418008;QSTRAND=+ GT:DP:AD 1|1:32:25,7 1|0:39:22,17 ./.:38:24,14 -chr20 439461 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=419046;QSTRAND=+ GT:DP:AD 1|1:41:22,19 1|0:36:25,11 ./.:30:18,12 -chr20 441161 . T TCCA 60 . QNAME=HG002-S9-H1-000001F;QSTART=420747;QSTRAND=+ GT:DP:AD 1|1:32:17,15 1|0:31:18,13 ./.:12:6,6 -chr20 443554 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=423142;QSTRAND=+ GT:DP:AD 1|0:28:18,10 1|0:36:16,20 ./.:38:24,14 -chr20 443921 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=423509;QSTRAND=+ GT:DP:AD 1|0:27:17,10 1|0:19:9,10 ./.:36:11,25 -chr20 444453 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=424041;QSTRAND=+ GT:DP:AD 1|0:48:25,23 1|0:18:13,5 ./.:27:17,10 -chr20 444562 . GTTTT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=424151;QSTRAND=+ GT:DP:AD 1|0:39:14,25 1|0:34:13,21 ./.:29:7,22 -chr20 444790 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=424374;QSTRAND=+ GT:DP:AD 1|0:30:20,10 1|0:45:23,22 ./.:29:16,13 -chr20 444962 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=424546;QSTRAND=+ GT:DP:AD 1|0:40:20,20 1|0:21:11,10 ./.:34:17,17 -chr20 445789 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=425373;QSTRAND=+ GT:DP:AD 1|0:42:22,20 1|0:35:17,18 ./.:20:7,13 -chr20 446426 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=426010;QSTRAND=+ GT:DP:AD 1|0:17:8,9 1|0:39:24,15 ./.:26:17,9 -chr20 446529 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=426113;QSTRAND=+ GT:DP:AD 1|0:21:8,13 1|0:17:6,11 ./.:26:18,8 -chr20 446943 . AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=426528;QSTRAND=+ GT:DP:AD 1|1:35:19,16 1|0:25:8,17 ./.:16:9,7 -chr20 446943 . A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25264284;QSTRAND=- GT:DP:AD ./.:17:9,8 ./.:40:20,20 1|1:36:22,14 -chr20 447123 . A AT 60 . QNAME=cluster23_scaffold_2;QSTART=25248333;QSTRAND=- GT:DP:AD ./.:23:16,7 ./.:40:20,20 0|1:15:8,7 -chr20 447395 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=426978;QSTRAND=+ GT:DP:AD 1|0:28:8,20 1|0:22:17,5 ./.:31:17,14 -chr20 448123 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=427706;QSTRAND=+ GT:DP:AD 1|0:36:13,23 1|0:24:12,12 ./.:39:22,17 -chr20 448284 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=427867;QSTRAND=+ GT:DP:AD 1|0:26:8,18 1|0:29:7,22 ./.:21:11,10 -chr20 448552 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=428135;QSTRAND=+ GT:DP:AD 1|0:22:7,15 1|0:22:11,11 ./.:24:7,17 -chr20 448689 . GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=428273;QSTRAND=+ GT:DP:AD 1|0:31:10,21 ./.:44:25,19 ./.:19:12,7 -chr20 448689 . G GA 60 . QNAME=cluster19_000000F;QSTART=25313206;QSTRAND=- GT:DP:AD ./.:31:7,24 1|0:47:25,22 1|0:41:17,24 -chr20 448841 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25262384;QSTRAND=- GT:DP:AD ./.:38:13,25 ./.:28:21,7 1|0:37:18,19 -chr20 449078 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=428660;QSTRAND=+ GT:DP:AD 1|0:36:21,15 1|0:30:15,15 ./.:37:21,16 -chr20 449153 . C CTT 60 . QNAME=HG002-S9-H1-000001F;QSTART=428736;QSTRAND=+ GT:DP:AD 1|0:32:25,7 1|0:27:18,9 ./.:31:15,16 -chr20 449266 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=428850;QSTRAND=+ GT:DP:AD 1|0:35:11,24 1|0:25:9,16 ./.:34:25,9 -chr20 449285 . T TAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=428870;QSTRAND=+ GT:DP:AD 1|0:26:18,8 1|0:21:7,14 ./.:20:8,12 -chr20 449285 . T TA 60 . QNAME=cluster19_000000F;QSTART=409488;QSTRAND=+ GT:DP:AD ./.:21:9,12 0|1:23:7,16 ./.:33:18,15 -chr20 449362 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25261863;QSTRAND=- GT:DP:AD ./.:38:20,18 ./.:28:15,13 1|0:39:21,18 -chr20 449514 . GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=429105;QSTRAND=+ GT:DP:AD 1|1:30:11,19 1|0:18:5,13 1|1:29:10,19 -chr20 450092 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=429681;QSTRAND=+ GT:DP:AD 1|0:40:24,16 1|0:44:24,20 ./.:24:9,15 -chr20 450315 . A AT 60 . QNAME=cluster23_scaffold_2;QSTART=25245141;QSTRAND=- GT:DP:AD ./.:29:6,23 ./.:34:25,9 0|1:34:23,11 -chr20 450858 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=430447;QSTRAND=+ GT:DP:AD 1|0:39:18,21 1|0:49:24,25 ./.:28:18,10 -chr20 452042 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=431631;QSTRAND=+ GT:DP:AD 1|0:17:12,5 1|0:33:11,22 ./.:32:7,25 -chr20 452135 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=431724;QSTRAND=+ GT:DP:AD 1|0:20:7,13 1|0:44:25,19 ./.:22:17,5 -chr20 453153 . CAAAAAAAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=432743;QSTRAND=+ GT:DP:AD 1|0:30:17,13 1|0:30:21,9 ./.:30:18,12 -chr20 453153 . C CAA 60 . QNAME=cluster23_scaffold_3;QSTART=25258071;QSTRAND=- GT:DP:AD ./.:29:20,9 ./.:10:5,5 1|0:28:20,8 -chr20 453153 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25242302;QSTRAND=- GT:DP:AD ./.:40:24,16 ./.:33:17,16 0|1:39:23,16 -chr20 453460 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=433040;QSTRAND=+ GT:DP:AD 1|0:44:21,23 1|0:13:6,7 ./.:30:19,11 -chr20 453539 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=433120;QSTRAND=+ GT:DP:AD 1|0:50:25,25 1|0:29:19,10 ./.:26:19,7 -chr20 453540 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=433121;QSTRAND=+ GT:DP:AD 1|0:36:16,20 1|0:21:12,9 ./.:30:18,12 -chr20 453540 . A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25257683;QSTRAND=- GT:DP:AD ./.:42:17,25 ./.:32:15,17 1|1:32:14,18 -chr20 453995 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=433576;QSTRAND=+ GT:DP:AD 1|0:35:11,24 1|0:15:6,9 ./.:44:24,20 -chr20 454087 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=433668;QSTRAND=+ GT:DP:AD 1|0:32:17,15 1|0:21:6,15 ./.:16:9,7 -chr20 454236 . CAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=433818;QSTRAND=+ GT:DP:AD 1|0:21:13,8 ./.:43:19,24 ./.:37:14,23 -chr20 454236 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=408684;QSTRAND=+ GT:DP:AD 0|1:21:13,8 ./.:22:11,11 ./.:21:11,10 -chr20 454236 . CAA C 60 . QNAME=cluster19_000000F;QSTART=25307660;QSTRAND=- GT:DP:AD ./.:36:13,23 1|0:38:22,16 ./.:40:23,17 -chr20 454295 . G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=433874;QSTRAND=+ GT:DP:AD 1|0:33:15,18 1|0:24:11,13 ./.:20:12,8 -chr20 454614 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=434193;QSTRAND=+ GT:DP:AD 1|0:20:9,11 1|0:37:20,17 ./.:35:22,13 -chr20 454650 . C CATTATT 60 . QNAME=HG002-S9-H1-000001F;QSTART=434230;QSTRAND=+ GT:DP:AD 1|0:29:12,17 1|0:21:7,14 ./.:33:22,11 -chr20 454798 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=434383;QSTRAND=+ GT:DP:AD 1|0:14:5,9 1|0:20:10,10 ./.:25:20,5 -chr20 456053 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=435638;QSTRAND=+ GT:DP:AD 1|0:38:19,19 1|0:25:18,7 ./.:15:10,5 -chr20 456337 . TTTCATCCA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=435923;QSTRAND=+ GT:DP:AD 1|0:45:23,22 1|0:29:10,19 ./.:28:23,5 -chr20 456571 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=411018;QSTRAND=+ GT:DP:AD 0|1:28:18,10 ./.:14:7,7 ./.:37:20,17 -chr20 456603 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=436180;QSTRAND=+ GT:DP:AD 1|0:32:12,20 ./.:20:14,6 ./.:29:6,23 -chr20 456818 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=436395;QSTRAND=+ GT:DP:AD 1|0:12:5,7 1|0:42:17,25 ./.:24:18,6 -chr20 456933 . AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=436511;QSTRAND=+ GT:DP:AD 1|0:39:21,18 ./.:44:20,24 ./.:25:11,14 -chr20 456933 . ATTTT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=411379;QSTRAND=+ GT:DP:AD 0|1:35:22,13 ./.:11:5,6 ./.:31:15,16 -chr20 456933 . ATTT A 60 . QNAME=cluster19_000000F;QSTART=417137;QSTRAND=+ GT:DP:AD ./.:41:24,17 0|1:40:17,23 1|1:34:16,18 -chr20 458314 . A AT 60 . QNAME=cluster23_scaffold_2;QSTART=25237142;QSTRAND=- GT:DP:AD ./.:41:18,23 ./.:35:25,10 0|1:25:15,10 -chr20 458331 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=412772;QSTRAND=+ GT:DP:AD 0|1:38:20,18 0|1:28:5,23 1|1:26:16,10 -chr20 458461 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=412902;QSTRAND=+ GT:DP:AD 0|1:46:22,24 0|1:24:13,11 1|1:35:16,19 -chr20 459799 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=414240;QSTRAND=+ GT:DP:AD 0|1:33:11,22 0|1:45:21,24 1|1:32:19,13 -chr20 460434 . CAAA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=414876;QSTRAND=+ GT:DP:AD 0|1:43:23,20 0|1:32:16,16 1|1:25:10,15 -chr20 460464 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=414902;QSTRAND=+ GT:DP:AD 0|1:33:11,22 0|1:23:11,12 1|1:24:12,12 -chr20 461679 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=416117;QSTRAND=+ GT:DP:AD 0|1:28:18,10 0|1:31:18,13 1|1:22:9,13 -chr20 462293 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=416731;QSTRAND=+ GT:DP:AD 0|1:42:18,24 0|1:28:7,21 1|1:44:24,20 -chr20 463154 . A G 60 . QNAME=cluster19_000000F;QSTART=423351;QSTRAND=+ GT:DP:AD ./.:21:16,5 0|1:36:13,23 1|1:47:25,22 -chr20 463252 . C G 60 . QNAME=cluster19_000000F;QSTART=423449;QSTRAND=+ GT:DP:AD ./.:41:18,23 0|1:35:13,22 1|1:36:13,23 -chr20 463841 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=418279;QSTRAND=+ GT:DP:AD 0|1:34:11,23 ./.:37:24,13 ./.:26:12,14 -chr20 465665 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=445241;QSTRAND=+ GT:DP:AD 1|1:35:18,17 1|1:41:24,17 1|1:38:23,15 -chr20 465676 . GC G 60 . QNAME=HG002-S9-H1-000001F;QSTART=445253;QSTRAND=+ GT:DP:AD 1|1:27:17,10 1|1:27:6,21 1|1:23:6,17 -chr20 466029 . A AAAAT 60 . QNAME=HG002-S9-H2-000001F;QSTART=420467;QSTRAND=+ GT:DP:AD 0|1:22:14,8 ./.:15:10,5 ./.:47:23,24 -chr20 466637 . GTA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=446213;QSTRAND=+ GT:DP:AD 1|0:26:18,8 1|0:29:5,24 ./.:32:19,13 -chr20 466637 . G GTGTATATATA 60 . QNAME=HG002-S9-H2-000001F;QSTART=421079;QSTRAND=+ GT:DP:AD 0|1:47:23,24 ./.:28:22,6 ./.:31:23,8 -chr20 466637 . G GTATA 60 . QNAME=cluster19_000000F;QSTART=426834;QSTRAND=+ GT:DP:AD ./.:28:7,21 0|1:22:14,8 1|0:19:14,5 -chr20 466637 . G GTA 60 . QNAME=cluster23_scaffold_2;QSTART=25228821;QSTRAND=- GT:DP:AD ./.:21:15,6 ./.:16:10,6 0|1:22:15,7 -chr20 467024 . C CT 60 . QNAME=cluster23_scaffold_2;QSTART=25228433;QSTRAND=- GT:DP:AD ./.:36:15,21 ./.:32:23,9 0|1:43:24,19 -chr20 468015 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=447588;QSTRAND=+ GT:DP:AD 1|1:28:14,14 1|1:32:19,13 1|1:26:10,16 -chr20 468269 . C A 60 . QNAME=cluster19_000000F;QSTART=428469;QSTRAND=+ GT:DP:AD ./.:25:8,17 0|1:39:14,25 1|1:40:15,25 -chr20 469249 . G A 60 . QNAME=cluster19_000000F;QSTART=429449;QSTRAND=+ GT:DP:AD ./.:26:7,19 0|1:30:21,9 1|1:28:17,11 -chr20 469257 . A T 60 . QNAME=cluster19_000000F;QSTART=429457;QSTRAND=+ GT:DP:AD ./.:27:8,19 0|1:37:25,12 1|1:33:19,14 -chr20 470060 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=424511;QSTRAND=+ GT:DP:AD 0|1:18:7,11 ./.:30:24,6 ./.:27:18,9 -chr20 471168 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=425619;QSTRAND=+ GT:DP:AD 0|1:22:10,12 ./.:38:23,15 ./.:17:9,8 -chr20 472424 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=451997;QSTRAND=+ GT:DP:AD 1|0:37:18,19 ./.:17:7,10 ./.:44:25,19 -chr20 472457 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=452030;QSTRAND=+ GT:DP:AD 1|1:22:8,14 1|1:28:8,20 1|1:22:8,14 -chr20 475460 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=429912;QSTRAND=+ GT:DP:AD 0|1:35:25,10 ./.:28:10,18 ./.:31:14,17 -chr20 475460 . CAAAAA C 60 . QNAME=cluster19_000000F;QSTART=435661;QSTRAND=+ GT:DP:AD ./.:34:25,9 0|1:32:15,17 ./.:34:15,19 diff --git a/repo_utils/test_files/answer_key/divided/multi_00000009.vcf b/repo_utils/test_files/answer_key/divided/multi_00000009.vcf deleted file mode 100644 index 8e0cc86e..00000000 --- a/repo_utils/test_files/answer_key/divided/multi_00000009.vcf +++ /dev/null @@ -1,142 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##bcftools_mergeVersion=1.12+htslib-1.12 -##bcftools_mergeCommand=merge -O z -f x -m none input1.vcf.gz input2.vcf.gz input3.vcf.gz; Date=Mon Aug 16 18:05:13 2021 -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 477729 . C T 60 . QNAME=cluster19_000000F;QSTART=25284173;QSTRAND=- GT:DP:AD ./.:35:17,18 1|0:24:14,10 1|1:29:15,14 -chr20 478540 . TC T 60 . QNAME=HG002-S9-H2-000001F;QSTART=432991;QSTRAND=+ GT:DP:AD 0|1:33:10,23 ./.:22:14,8 ./.:31:14,17 -chr20 480234 . T G 60 . QNAME=cluster23_scaffold_3;QSTART=25230992;QSTRAND=- GT:DP:AD ./.:25:15,10 ./.:28:23,5 1|0:25:6,19 -chr20 484694 . T TTG 60 . QNAME=cluster19_000000F;QSTART=25277206;QSTRAND=- GT:DP:AD ./.:41:22,19 1|0:23:12,11 ./.:24:19,5 -chr20 484991 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=464564;QSTRAND=+ GT:DP:AD 1|0:25:13,12 ./.:44:20,24 ./.:35:17,18 -chr20 485066 . CAAAA C 60 . QNAME=cluster23_scaffold_3;QSTART=25226160;QSTRAND=- GT:DP:AD ./.:21:10,11 ./.:27:20,7 1|0:22:12,10 -chr20 485088 . AAAAAAAAAAAAAAAAAAAAAAATATATATATAT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=464662;QSTRAND=+;SVTYPE=DEL;SVLEN=-33 GT:DP:AD 1/0:26:11,15 ./.:21:12,9 ./.:20:14,6 -chr20 485103 . A ATATATATATAT 60 . QNAME=cluster23_scaffold_2;QSTART=25210343;QSTRAND=- GT:DP:AD ./.:32:7,25 ./.:26:9,17 0|1:19:7,12 -chr20 485105 . A T 60 . QNAME=cluster23_scaffold_2;QSTART=25210341;QSTRAND=- GT:DP:AD ./.:36:20,16 ./.:44:24,20 0|1:26:18,8 -chr20 485105 . A ATAATATATATATAT 60 . QNAME=HG002-S9-H2-000001F;QSTART=439555;QSTRAND=+ GT:DP:AD 0|1:31:16,15 ./.:16:9,7 ./.:16:5,11 -chr20 485105 . A ATATATATATAT 60 . QNAME=cluster19_000000F;QSTART=25276784;QSTRAND=- GT:DP:AD ./.:32:13,19 1|0:26:11,15 ./.:23:7,16 -chr20 485107 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=439570;QSTRAND=+ GT:DP:AD 0|1:15:8,7 1|0:46:23,23 1|1:21:15,6 -chr20 485109 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=439572;QSTRAND=+ GT:DP:AD 0|1:23:7,16 1|0:28:19,9 1|1:22:7,15 -chr20 485110 . ATAT A 60 . QNAME=cluster19_000000F;QSTART=445306;QSTRAND=+ GT:DP:AD ./.:33:12,21 0|1:25:15,10 ./.:26:21,5 -chr20 485115 . T A 60 . QNAME=cluster19_000000F;QSTART=445307;QSTRAND=+ GT:DP:AD ./.:16:7,9 0|1:32:13,19 ./.:13:6,7 -chr20 485117 . T A 60 . QNAME=cluster19_000000F;QSTART=445309;QSTRAND=+ GT:DP:AD ./.:49:25,24 0|1:18:10,8 ./.:18:12,6 -chr20 485138 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=439601;QSTRAND=+ GT:DP:AD 0|1:35:14,21 ./.:40:17,23 ./.:31:21,10 -chr20 485139 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=439602;QSTRAND=+ GT:DP:AD 0|1:32:23,9 ./.:31:25,6 ./.:37:15,22 -chr20 487542 . G A 60 . QNAME=cluster19_000000F;QSTART=447734;QSTRAND=+ GT:DP:AD ./.:38:19,19 0|1:33:14,19 ./.:13:5,8 -chr20 488040 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25223189;QSTRAND=- GT:DP:AD ./.:41:23,18 ./.:36:17,19 1|1:29:14,15 -chr20 490335 . C CT 60 . QNAME=cluster19_000000F;QSTART=25271553;QSTRAND=- GT:DP:AD ./.:38:19,19 1|0:33:12,21 ./.:29:5,24 -chr20 490909 . A C 60 . QNAME=cluster19_000000F;QSTART=25270979;QSTRAND=- GT:DP:AD ./.:31:18,13 1|0:17:11,6 ./.:32:25,7 -chr20 493202 . A T 60 . QNAME=cluster19_000000F;QSTART=25268686;QSTRAND=- GT:DP:AD ./.:43:20,23 1|0:42:24,18 1|1:36:22,14 -chr20 494543 . T C 60 . QNAME=cluster19_000000F;QSTART=25267345;QSTRAND=- GT:DP:AD ./.:33:16,17 1|0:43:21,22 ./.:37:17,20 -chr20 498335 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=452799;QSTRAND=+ GT:DP:AD 0|1:28:6,22 ./.:30:18,12 ./.:46:22,24 -chr20 498335 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25212893;QSTRAND=- GT:DP:AD ./.:28:10,18 ./.:30:15,15 1|1:16:7,9 -chr20 498901 . T C 60 . QNAME=cluster19_000000F;QSTART=459093;QSTRAND=+ GT:DP:AD ./.:20:6,14 0|1:31:12,19 ./.:28:19,9 -chr20 499958 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25195485;QSTRAND=- GT:DP:AD ./.:31:17,14 ./.:19:5,14 0|1:26:15,11 -chr20 500634 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25210593;QSTRAND=- GT:DP:AD ./.:25:17,8 ./.:39:20,19 1|0:41:19,22 -chr20 501285 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=480825;QSTRAND=+ GT:DP:AD 1|0:19:5,14 ./.:17:11,6 ./.:29:17,12 -chr20 504037 . G GC 60 . QNAME=HG002-S9-H2-000001F;QSTART=458500;QSTRAND=+ GT:DP:AD 0|1:29:17,12 ./.:21:9,12 ./.:31:19,12 -chr20 505351 . G GT 60 . QNAME=cluster19_000000F;QSTART=25256536;QSTRAND=- GT:DP:AD ./.:25:18,7 1|0:29:21,8 1|0:38:19,19 -chr20 505587 . C G 60 . QNAME=cluster19_000000F;QSTART=465779;QSTRAND=+ GT:DP:AD ./.:44:22,22 0|1:11:6,5 ./.:26:15,11 -chr20 505869 . AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=485410;QSTRAND=+ GT:DP:AD 1|0:19:5,14 ./.:20:5,15 ./.:22:12,10 -chr20 505869 . A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25205356;QSTRAND=- GT:DP:AD ./.:37:20,17 ./.:31:25,6 1|0:37:21,16 -chr20 505905 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25205320;QSTRAND=- GT:DP:AD ./.:32:14,18 ./.:14:8,6 1|0:38:17,21 -chr20 506070 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=485609;QSTRAND=+ GT:DP:AD 1|0:29:8,21 ./.:33:16,17 0|1:44:25,19 -chr20 506079 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=485618;QSTRAND=+ GT:DP:AD 1|0:17:11,6 ./.:32:9,23 0|1:29:14,15 -chr20 506080 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=485619;QSTRAND=+ GT:DP:AD 1|0:35:15,20 ./.:18:11,7 0|1:37:18,19 -chr20 506097 . C T 60 . QNAME=cluster19_000000F;QSTART=25255790;QSTRAND=- GT:DP:AD ./.:25:10,15 1|0:45:20,25 1|0:15:9,6 -chr20 506098 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=485637;QSTRAND=+ GT:DP:AD 1|0:16:8,8 ./.:20:10,10 0|1:33:13,20 -chr20 506127 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25205098;QSTRAND=- GT:DP:AD ./.:27:20,7 ./.:26:14,12 1|0:32:12,20 -chr20 507967 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=487506;QSTRAND=+ GT:DP:AD 1|1:35:14,21 1|1:29:21,8 1|1:37:13,24 -chr20 508286 . C T 60 . QNAME=cluster19_000000F;QSTART=25253601;QSTRAND=- GT:DP:AD ./.:33:22,11 1|0:33:20,13 1|1:35:21,14 -chr20 508793 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25186650;QSTRAND=- GT:DP:AD ./.:22:16,6 ./.:39:19,20 0|1:34:24,10 -chr20 511703 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=466166;QSTRAND=+ GT:DP:AD 0|1:16:8,8 ./.:27:6,21 ./.:45:22,23 -chr20 511705 . C T 60 . QNAME=cluster19_000000F;QSTART=25250182;QSTRAND=- GT:DP:AD ./.:46:24,22 1|0:41:25,16 1|1:15:5,10 -chr20 512561 . G T 60 . QNAME=cluster19_000000F;QSTART=25249326;QSTRAND=- GT:DP:AD ./.:16:7,9 1|0:30:14,16 1|1:18:7,11 -chr20 512965 . T C 60 . QNAME=cluster19_000000F;QSTART=25248922;QSTRAND=- GT:DP:AD ./.:25:18,7 1|0:35:16,19 ./.:37:18,19 -chr20 514164 . C T 60 . QNAME=cluster19_000000F;QSTART=25247723;QSTRAND=- GT:DP:AD ./.:45:24,21 1|0:20:8,12 1|1:24:5,19 -chr20 518713 . ATT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=498253;QSTRAND=+ GT:DP:AD 1|0:22:7,15 1|0:44:24,20 0|1:27:6,21 -chr20 518713 . AT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=473177;QSTRAND=+ GT:DP:AD 0|1:25:10,15 0|1:37:21,16 1|0:20:15,5 -chr20 518933 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=473396;QSTRAND=+ GT:DP:AD 0|1:41:19,22 ./.:36:24,12 ./.:17:7,10 -chr20 518933 . C CT 60 . QNAME=cluster23_scaffold_2;QSTART=25176511;QSTRAND=- GT:DP:AD ./.:15:7,8 ./.:28:22,6 0|1:28:18,10 -chr20 522293 . C T 60 . QNAME=cluster19_000000F;QSTART=25239596;QSTRAND=- GT:DP:AD ./.:19:14,5 1|0:31:12,19 1|1:37:18,19 -chr20 523858 . C CA 60 . QNAME=cluster19_000000F;QSTART=25238030;QSTRAND=- GT:DP:AD ./.:37:22,15 1|0:48:24,24 0|1:31:7,24 -chr20 523869 . A C 60 . QNAME=cluster19_000000F;QSTART=484060;QSTRAND=+ GT:DP:AD ./.:19:5,14 0|1:21:15,6 ./.:33:13,20 -chr20 524145 . C T 60 . QNAME=cluster19_000000F;QSTART=25237743;QSTRAND=- GT:DP:AD ./.:32:23,9 1|1:33:8,25 1|1:26:12,14 -chr20 524654 . T C 60 . QNAME=cluster19_000000F;QSTART=25237234;QSTRAND=- GT:DP:AD ./.:31:6,25 1|0:37:23,14 ./.:29:21,8 -chr20 524708 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=504246;QSTRAND=+ GT:DP:AD 1|0:36:14,22 1|0:28:16,12 0|1:19:8,11 -chr20 524708 . CAA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=479170;QSTRAND=+ GT:DP:AD 0|1:26:14,12 0|1:26:19,7 ./.:42:21,21 -chr20 525133 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=504669;QSTRAND=+ GT:DP:AD 1|0:34:11,23 ./.:32:24,8 ./.:45:21,24 -chr20 525391 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=504927;QSTRAND=+ GT:DP:AD 1|0:37:12,25 ./.:21:6,15 ./.:20:13,7 -chr20 525650 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=505187;QSTRAND=+ GT:DP:AD 1|0:29:13,16 ./.:27:11,16 ./.:35:13,22 -chr20 525836 . TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=505372;QSTRAND=+ GT:DP:AD 1|0:30:25,5 ./.:31:20,11 ./.:34:16,18 -chr20 525836 . T TA 60 . QNAME=cluster23_scaffold_2;QSTART=25169607;QSTRAND=- GT:DP:AD ./.:45:22,23 ./.:40:24,16 0|1:33:21,12 -chr20 526238 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=505772;QSTRAND=+ GT:DP:AD 1|0:29:23,6 1|0:39:15,24 1|1:36:15,21 -chr20 526685 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=506219;QSTRAND=+ GT:DP:AD 1|0:34:12,22 ./.:27:14,13 ./.:33:21,12 -chr20 526949 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=506484;QSTRAND=+ GT:DP:AD 1|0:37:21,16 ./.:49:25,24 ./.:41:24,17 -chr20 527001 . C CAGAGAGAGAG 60 . QNAME=cluster19_000000F;QSTART=25234878;QSTRAND=- GT:DP:AD ./.:41:17,24 1|0:34:19,15 ./.:23:6,17 -chr20 527001 . C CAGAG 60 . QNAME=cluster23_scaffold_3;QSTART=25184221;QSTRAND=- GT:DP:AD ./.:30:19,11 ./.:23:6,17 1|0:35:20,15 -chr20 527001 . C CAG 60 . QNAME=cluster23_scaffold_2;QSTART=25168440;QSTRAND=- GT:DP:AD ./.:25:13,12 ./.:23:14,9 0|1:26:16,10 -chr20 527003 . G GAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=506537;QSTRAND=+ GT:DP:AD 1|0:33:21,12 ./.:39:14,25 ./.:32:22,10 -chr20 527729 . G A 60 . QNAME=cluster19_000000F;QSTART=487918;QSTRAND=+ GT:DP:AD ./.:47:22,25 0|1:23:14,9 ./.:35:13,22 -chr20 527782 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=507317;QSTRAND=+ GT:DP:AD 1|0:21:12,9 ./.:29:12,17 ./.:37:20,17 -chr20 528449 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=507984;QSTRAND=+ GT:DP:AD 1|0:35:13,22 ./.:26:21,5 ./.:28:6,22 -chr20 528594 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=508130;QSTRAND=+ GT:DP:AD 1|0:18:6,12 ./.:28:23,5 ./.:29:18,11 -chr20 529190 . A AT 60 . QNAME=cluster19_000000F;QSTART=25232688;QSTRAND=- GT:DP:AD ./.:43:24,19 1|0:18:5,13 1|1:32:14,18 -chr20 530468 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=510003;QSTRAND=+ GT:DP:AD 1|0:33:10,23 ./.:26:13,13 ./.:35:12,23 -chr20 531253 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=510788;QSTRAND=+ GT:DP:AD 1|0:21:10,11 ./.:32:16,16 ./.:44:21,23 -chr20 532330 . ATT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=511866;QSTRAND=+ GT:DP:AD 1|0:21:10,11 ./.:17:10,7 ./.:17:6,11 -chr20 532352 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=511885;QSTRAND=+ GT:DP:AD 1|0:25:12,13 ./.:14:9,5 ./.:31:14,17 -chr20 533815 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=513348;QSTRAND=+ GT:DP:AD 1|0:42:19,23 ./.:36:15,21 ./.:26:5,21 -chr20 535034 . CAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=514568;QSTRAND=+ GT:DP:AD 1|0:12:6,6 ./.:22:13,9 ./.:39:16,23 -chr20 535034 . C CA 60 . QNAME=cluster19_000000F;QSTART=495224;QSTRAND=+ GT:DP:AD ./.:30:7,23 0|1:20:13,7 ./.:24:18,6 -chr20 535629 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=515160;QSTRAND=+ GT:DP:AD 1|0:34:16,18 ./.:48:24,24 ./.:29:12,17 -chr20 535685 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=515216;QSTRAND=+ GT:DP:AD 1|0:29:19,10 ./.:24:6,18 ./.:33:19,14 -chr20 535739 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=515271;QSTRAND=+ GT:DP:AD 1|0:15:8,7 ./.:24:18,6 ./.:26:15,11 -chr20 537243 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=516773;QSTRAND=+ GT:DP:AD 1|0:34:21,13 ./.:29:24,5 ./.:17:6,11 -chr20 537496 . G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=517027;QSTRAND=+ GT:DP:AD 1|0:27:8,19 ./.:24:14,10 ./.:29:13,16 -chr20 537963 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=517495;QSTRAND=+ GT:DP:AD 1|0:45:20,25 ./.:13:8,5 ./.:34:16,18 -chr20 538108 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=517640;QSTRAND=+ GT:DP:AD 1|0:47:25,22 1|0:17:5,12 1|1:30:13,17 -chr20 539053 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=518585;QSTRAND=+ GT:DP:AD 1|0:42:22,20 ./.:21:9,12 ./.:33:8,25 -chr20 539493 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25155947;QSTRAND=- GT:DP:AD ./.:26:12,14 ./.:16:11,5 0|1:24:9,15 -chr20 541244 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=520776;QSTRAND=+ GT:DP:AD 1|0:39:16,23 ./.:16:10,6 ./.:16:7,9 -chr20 541502 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=521034;QSTRAND=+ GT:DP:AD 1|0:37:25,12 ./.:27:12,15 ./.:39:25,14 -chr20 542623 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=522155;QSTRAND=+ GT:DP:AD 1|0:47:22,25 ./.:24:18,6 ./.:22:11,11 -chr20 544402 . G GT 60 . QNAME=cluster19_000000F;QSTART=25217475;QSTRAND=- GT:DP:AD ./.:42:22,20 1|0:25:12,13 1|1:23:10,13 -chr20 545973 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=525505;QSTRAND=+ GT:DP:AD 1|0:25:20,5 ./.:40:15,25 ./.:35:19,16 -chr20 546122 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25149317;QSTRAND=- GT:DP:AD ./.:14:8,6 ./.:29:9,20 0|1:17:11,6 -chr20 546487 . ACT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=526020;QSTRAND=+ GT:DP:AD 1|0:34:13,21 ./.:26:21,5 ./.:19:13,6 diff --git a/repo_utils/test_files/answer_key/divided/multi_00000010.vcf b/repo_utils/test_files/answer_key/divided/multi_00000010.vcf deleted file mode 100644 index b467aa4e..00000000 --- a/repo_utils/test_files/answer_key/divided/multi_00000010.vcf +++ /dev/null @@ -1,159 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##bcftools_mergeVersion=1.12+htslib-1.12 -##bcftools_mergeCommand=merge -O z -f x -m none input1.vcf.gz input2.vcf.gz input3.vcf.gz; Date=Mon Aug 16 18:05:13 2021 -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 547548 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=527078;QSTRAND=+ GT:DP:AD 1|0:32:15,17 ./.:21:9,12 ./.:30:23,7 -chr20 548222 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=527752;QSTRAND=+ GT:DP:AD 1|0:29:16,13 0|1:37:25,12 ./.:19:6,13 -chr20 548575 . ATATTTT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=528106;QSTRAND=+ GT:DP:AD 1|0:20:14,6 ./.:26:19,7 ./.:41:21,20 -chr20 548577 . A AT 60 . QNAME=cluster19_000000F;QSTART=25213299;QSTRAND=- GT:DP:AD ./.:26:9,17 1|0:18:11,7 0|1:16:9,7 -chr20 548577 . A ATT 60 . QNAME=cluster23_scaffold_3;QSTART=25162641;QSTRAND=- GT:DP:AD ./.:27:16,11 ./.:24:18,6 1|0:17:8,9 -chr20 548971 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=528495;QSTRAND=+ GT:DP:AD 1|0:27:9,18 ./.:27:8,19 ./.:29:15,14 -chr20 549092 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=528616;QSTRAND=+ GT:DP:AD 1|0:46:23,23 ./.:17:12,5 ./.:31:11,20 -chr20 549227 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=528751;QSTRAND=+ GT:DP:AD 1|0:37:20,17 ./.:14:9,5 ./.:33:12,21 -chr20 549649 . GGAAA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=529174;QSTRAND=+ GT:DP:AD 1|0:24:9,15 ./.:33:11,22 ./.:47:22,25 -chr20 549670 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=529190;QSTRAND=+ GT:DP:AD 1|0:39:20,19 ./.:30:20,10 ./.:18:12,6 -chr20 550104 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=529624;QSTRAND=+ GT:DP:AD 1|0:42:25,17 ./.:19:13,6 ./.:35:12,23 -chr20 550577 . C T 60 . QNAME=cluster19_000000F;QSTART=25211299;QSTRAND=- GT:DP:AD ./.:31:8,23 1|0:23:8,15 1|1:35:22,13 -chr20 551334 . C A 60 . QNAME=cluster19_000000F;QSTART=25210542;QSTRAND=- GT:DP:AD ./.:13:6,7 1|0:42:18,24 1|1:22:7,15 -chr20 551415 . T A 60 . QNAME=cluster19_000000F;QSTART=25210461;QSTRAND=- GT:DP:AD ./.:32:14,18 1|0:32:22,10 1|1:33:25,8 -chr20 551424 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=530944;QSTRAND=+ GT:DP:AD 1|0:30:24,6 1|0:36:11,25 1|1:24:17,7 -chr20 551459 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=530979;QSTRAND=+ GT:DP:AD 1|0:29:5,24 1|0:18:9,9 1|1:23:15,8 -chr20 552161 . G A 60 . QNAME=cluster19_000000F;QSTART=25209715;QSTRAND=- GT:DP:AD ./.:28:18,10 1|0:26:16,10 1|1:35:14,21 -chr20 552253 . C T 60 . QNAME=cluster19_000000F;QSTART=25209623;QSTRAND=- GT:DP:AD ./.:39:16,23 1|0:42:18,24 1|1:32:22,10 -chr20 552281 . A G 60 . QNAME=cluster19_000000F;QSTART=25209595;QSTRAND=- GT:DP:AD ./.:38:19,19 1|0:24:16,8 1|1:29:11,18 -chr20 552720 . CT C 60 . QNAME=cluster19_000000F;QSTART=25209156;QSTRAND=- GT:DP:AD ./.:38:23,15 1|0:25:12,13 1|1:39:24,15 -chr20 553245 . C G 60 . QNAME=cluster19_000000F;QSTART=25208632;QSTRAND=- GT:DP:AD ./.:33:24,9 1|0:48:23,25 1|1:25:13,12 -chr20 553335 . C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=532856;QSTRAND=+ GT:DP:AD 1|0:25:15,10 ./.:23:17,6 ./.:40:25,15 -chr20 553335 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=507795;QSTRAND=+ GT:DP:AD 0|1:48:23,25 ./.:41:16,25 ./.:31:8,23 -chr20 553335 . C CAAA 60 . QNAME=cluster19_000000F;QSTART=25208539;QSTRAND=- GT:DP:AD ./.:27:11,16 1|0:25:14,11 1|1:26:5,21 -chr20 553919 . C T 60 . QNAME=cluster19_000000F;QSTART=25207955;QSTRAND=- GT:DP:AD ./.:32:15,17 1|0:37:22,15 1|1:23:7,16 -chr20 554853 . T A 60 . QNAME=cluster19_000000F;QSTART=25207021;QSTRAND=- GT:DP:AD ./.:33:19,14 1|0:19:14,5 1|1:32:11,21 -chr20 555892 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=535413;QSTRAND=+ GT:DP:AD 1|1:40:17,23 1|1:37:18,19 1|1:22:8,14 -chr20 556119 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=535640;QSTRAND=+ GT:DP:AD 1|0:22:6,16 0|1:17:12,5 1|1:22:15,7 -chr20 556141 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=535662;QSTRAND=+ GT:DP:AD 1|1:22:6,16 1|1:34:21,13 1|1:28:6,22 -chr20 556215 . G A 60 . QNAME=cluster19_000000F;QSTART=516405;QSTRAND=+ GT:DP:AD ./.:16:10,6 0|1:41:21,20 1|1:20:9,11 -chr20 556356 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=535877;QSTRAND=+ GT:DP:AD 1|0:22:17,5 ./.:22:15,7 ./.:32:10,22 -chr20 556431 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=510889;QSTRAND=+ GT:DP:AD 0|1:16:11,5 1|0:34:17,17 ./.:33:9,24 -chr20 556435 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=535956;QSTRAND=+ GT:DP:AD 1|0:34:15,19 0|1:39:20,19 1|1:43:22,21 -chr20 556632 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=536153;QSTRAND=+ GT:DP:AD 1|1:39:17,22 1|1:38:13,25 1|1:20:9,11 -chr20 556794 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=536315;QSTRAND=+ GT:DP:AD 1|1:25:18,7 1|1:32:10,22 1|1:48:25,23 -chr20 556861 . C A 60 . QNAME=cluster19_000000F;QSTART=517051;QSTRAND=+ GT:DP:AD ./.:20:9,11 0|1:28:19,9 1|1:44:25,19 -chr20 556869 . C CAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=536391;QSTRAND=+ GT:DP:AD 1|1:50:25,25 1|0:27:5,22 ./.:46:25,21 -chr20 556869 . C CAAAAAA 60 . QNAME=cluster23_scaffold_3;QSTART=25154341;QSTRAND=- GT:DP:AD ./.:35:23,12 ./.:42:25,17 1|0:36:13,23 -chr20 556869 . C CAAAAA 60 . QNAME=cluster23_scaffold_2;QSTART=25138562;QSTRAND=- GT:DP:AD ./.:32:15,17 ./.:44:25,19 0|1:15:6,9 -chr20 556881 . A AAAAAAT 60 . QNAME=cluster19_000000F;QSTART=517072;QSTRAND=+ GT:DP:AD ./.:28:9,19 0|1:33:16,17 ./.:16:11,5 -chr20 556883 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=536407;QSTRAND=+ GT:DP:AD 1|1:26:6,20 1|0:29:5,24 ./.:33:17,16 -chr20 556885 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=536409;QSTRAND=+ GT:DP:AD 1|1:21:14,7 1|0:11:6,5 ./.:17:8,9 -chr20 556887 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=536411;QSTRAND=+ GT:DP:AD 1|1:29:13,16 1|0:38:25,13 ./.:16:5,11 -chr20 557034 . T C 60 . QNAME=cluster19_000000F;QSTART=517230;QSTRAND=+ GT:DP:AD ./.:14:9,5 0|1:28:13,15 1|1:41:22,19 -chr20 557559 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=537083;QSTRAND=+ GT:DP:AD 1|1:37:14,23 1|0:23:14,9 ./.:35:18,17 -chr20 557586 . C T 60 . QNAME=cluster19_000000F;QSTART=517782;QSTRAND=+ GT:DP:AD ./.:11:5,6 0|1:18:6,12 1|1:28:21,7 -chr20 557591 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=537115;QSTRAND=+ GT:DP:AD 1|1:47:22,25 1|1:14:8,6 1|1:41:24,17 -chr20 557603 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=537127;QSTRAND=+ GT:DP:AD 1|1:20:14,6 1|0:21:14,7 ./.:24:14,10 -chr20 557995 . C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=537520;QSTRAND=+ GT:DP:AD 1|1:43:25,18 1|1:45:22,23 1|1:23:18,5 -chr20 558185 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=537710;QSTRAND=+ GT:DP:AD 1|1:46:22,24 1|0:21:8,13 ./.:41:25,16 -chr20 558374 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=537899;QSTRAND=+ GT:DP:AD 1|1:14:8,6 1|0:20:14,6 ./.:28:22,6 -chr20 558479 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=538004;QSTRAND=+ GT:DP:AD 1|1:37:14,23 1|0:31:11,20 ./.:25:12,13 -chr20 558579 . ATTTT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=538105;QSTRAND=+ GT:DP:AD 1|1:23:18,5 1|0:22:10,12 ./.:42:19,23 -chr20 558719 . G A 60 . QNAME=cluster19_000000F;QSTART=518916;QSTRAND=+ GT:DP:AD ./.:21:11,10 0|1:16:9,7 1|1:39:15,24 -chr20 558928 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=538449;QSTRAND=+ GT:DP:AD 1|1:42:24,18 1|0:34:24,10 ./.:33:22,11 -chr20 559006 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=538527;QSTRAND=+ GT:DP:AD 1|1:29:16,13 1|1:35:15,20 1|1:35:12,23 -chr20 559112 . G GT 60 . QNAME=HG002-S9-H1-000001F;QSTART=538634;QSTRAND=+ GT:DP:AD 1|1:38:25,13 1|0:21:9,12 ./.:39:25,14 -chr20 559189 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=538711;QSTRAND=+ GT:DP:AD 1|1:37:22,15 1|1:34:10,24 1|1:28:21,7 -chr20 559234 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=538756;QSTRAND=+ GT:DP:AD 1|1:36:23,13 1|0:38:20,18 1|0:15:10,5 -chr20 559282 . G T 60 . QNAME=cluster19_000000F;QSTART=519479;QSTRAND=+ GT:DP:AD ./.:42:21,21 0|1:34:19,15 0|1:36:16,20 -chr20 559554 . T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=539077;QSTRAND=+ GT:DP:AD 1|1:17:10,7 1|1:35:15,20 1|1:30:9,21 -chr20 560062 . AC A 60 . QNAME=HG002-S9-H2-000001F;QSTART=514523;QSTRAND=+ GT:DP:AD 0|1:33:18,15 ./.:15:7,8 ./.:37:22,15 -chr20 560063 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=539586;QSTRAND=+ GT:DP:AD 1|0:33:21,12 1|0:18:12,6 ./.:28:6,22 -chr20 560078 . CAA C 60 . QNAME=cluster19_000000F;QSTART=520277;QSTRAND=+ GT:DP:AD ./.:38:25,13 0|1:35:10,25 1|1:18:7,11 -chr20 560086 . C G 60 . QNAME=cluster19_000000F;QSTART=520282;QSTRAND=+ GT:DP:AD ./.:31:10,21 0|1:31:20,11 1|1:29:20,9 -chr20 560086 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=539610;QSTRAND=+ GT:DP:AD 1|1:24:8,16 1|0:38:19,19 ./.:35:23,12 -chr20 560087 . A C 60 . QNAME=cluster19_000000F;QSTART=520283;QSTRAND=+ GT:DP:AD ./.:35:17,18 0|1:29:21,8 1|1:33:25,8 -chr20 560103 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=539625;QSTRAND=+ GT:DP:AD 1|1:39:18,21 1|1:28:10,18 1|1:17:5,12 -chr20 560343 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=514801;QSTRAND=+ GT:DP:AD 0|1:25:7,18 1|0:39:25,14 ./.:20:14,6 -chr20 560618 . G T 60 . QNAME=cluster19_000000F;QSTART=520814;QSTRAND=+ GT:DP:AD ./.:39:19,20 0|1:22:7,15 1|1:37:16,21 -chr20 560691 . G A 60 . QNAME=cluster19_000000F;QSTART=520887;QSTRAND=+ GT:DP:AD ./.:28:9,19 0|1:32:23,9 1|1:28:22,6 -chr20 560945 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=540467;QSTRAND=+ GT:DP:AD 1|1:28:9,19 1|0:27:16,11 ./.:15:5,10 -chr20 561211 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=540733;QSTRAND=+ GT:DP:AD 1|1:26:14,12 1|1:20:10,10 1|1:21:14,7 -chr20 562030 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=541552;QSTRAND=+ GT:DP:AD 1|1:16:11,5 1|1:38:23,15 1|1:34:22,12 -chr20 562133 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=541655;QSTRAND=+ GT:DP:AD 1|1:22:12,10 1|1:31:23,8 1|1:43:21,22 -chr20 562219 . A G 60 . QNAME=cluster19_000000F;QSTART=522415;QSTRAND=+ GT:DP:AD ./.:31:14,17 0|1:33:24,9 1|1:27:11,16 -chr20 562642 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=542164;QSTRAND=+ GT:DP:AD 1|1:23:9,14 1|1:23:11,12 1|1:33:17,16 -chr20 562657 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=542179;QSTRAND=+ GT:DP:AD 1|1:29:22,7 1|1:45:20,25 1|1:36:18,18 -chr20 562994 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=542516;QSTRAND=+ GT:DP:AD 1|1:32:11,21 1|1:26:5,21 1|1:36:17,19 -chr20 563100 . C T 60 . QNAME=cluster19_000000F;QSTART=523296;QSTRAND=+ GT:DP:AD ./.:34:23,11 0|1:25:14,11 1|1:33:16,17 -chr20 563396 . C T 60 . QNAME=cluster19_000000F;QSTART=25198477;QSTRAND=- GT:DP:AD ./.:17:6,11 1|0:25:14,11 ./.:29:13,16 -chr20 563773 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=543295;QSTRAND=+ GT:DP:AD 1|1:32:25,7 1|0:22:10,12 ./.:32:9,23 -chr20 564270 . G A 60 . QNAME=cluster19_000000F;QSTART=25197603;QSTRAND=- GT:DP:AD ./.:24:19,5 1|1:29:12,17 1|1:28:9,19 -chr20 564271 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=543793;QSTRAND=+ GT:DP:AD 1|1:28:9,19 ./.:27:16,11 ./.:20:14,6 -chr20 564553 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=519011;QSTRAND=+ GT:DP:AD 0|1:30:16,14 1|1:21:6,15 1|1:32:15,17 -chr20 564560 . GTGTT G 60 . QNAME=cluster23_scaffold_3;QSTART=25146650;QSTRAND=- GT:DP:AD ./.:38:13,25 ./.:30:17,13 1|0:25:14,11 -chr20 564629 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25130802;QSTRAND=- GT:DP:AD ./.:24:19,5 ./.:23:17,6 0|1:25:11,14 -chr20 565205 . A AT 60 . QNAME=cluster19_000000F;QSTART=25196667;QSTRAND=- GT:DP:AD ./.:37:14,23 1|1:33:8,25 1|1:30:25,5 -chr20 565232 . C T 60 . QNAME=cluster19_000000F;QSTART=25196640;QSTRAND=- GT:DP:AD ./.:27:6,21 1|1:47:22,25 1|0:39:24,15 -chr20 565534 . T A 60 . QNAME=cluster19_000000F;QSTART=25196338;QSTRAND=- GT:DP:AD ./.:23:18,5 1|1:23:15,8 1|1:25:5,20 -chr20 565902 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=545424;QSTRAND=+ GT:DP:AD 1|0:29:8,21 ./.:16:5,11 ./.:21:6,15 -chr20 565980 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=545502;QSTRAND=+ GT:DP:AD 1|1:30:24,6 ./.:26:6,20 ./.:33:9,24 -chr20 566018 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25145195;QSTRAND=- GT:DP:AD ./.:21:5,16 ./.:31:21,10 1|0:44:24,20 -chr20 566096 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=545618;QSTRAND=+ GT:DP:AD 1|1:31:25,6 ./.:25:18,7 ./.:34:11,23 -chr20 566178 . AAAAAAT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=545701;QSTRAND=+ GT:DP:AD 1|1:22:9,13 ./.:27:14,13 ./.:34:22,12 -chr20 567105 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=546621;QSTRAND=+ GT:DP:AD 1|0:35:15,20 ./.:32:24,8 ./.:23:17,6 -chr20 568286 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=522738;QSTRAND=+ GT:DP:AD 0|1:38:21,17 ./.:18:13,5 ./.:40:22,18 -chr20 568720 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=523172;QSTRAND=+ GT:DP:AD 0|1:35:14,21 ./.:34:17,17 ./.:24:17,7 -chr20 568936 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25142277;QSTRAND=- GT:DP:AD ./.:19:6,13 ./.:38:16,22 1|0:40:18,22 -chr20 569261 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=523713;QSTRAND=+ GT:DP:AD 0|1:32:13,19 ./.:36:18,18 ./.:28:17,11 -chr20 569263 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=548779;QSTRAND=+ GT:DP:AD 1|0:24:12,12 ./.:16:6,10 ./.:16:11,5 -chr20 569274 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=523726;QSTRAND=+ GT:DP:AD 0|1:32:21,11 ./.:40:21,19 ./.:35:16,19 -chr20 569446 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=523898;QSTRAND=+ GT:DP:AD 0|1:28:6,22 1|0:31:23,8 ./.:31:8,23 -chr20 569520 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=523972;QSTRAND=+ GT:DP:AD 0|1:36:22,14 1|1:32:21,11 1|1:36:15,21 -chr20 569616 . A C 60 . QNAME=cluster19_000000F;QSTART=25192256;QSTRAND=- GT:DP:AD ./.:25:15,10 1|1:42:24,18 1|1:28:7,21 -chr20 569956 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=524408;QSTRAND=+ GT:DP:AD 0|1:32:17,15 ./.:26:15,11 ./.:24:11,13 -chr20 570171 . A C 60 . QNAME=cluster19_000000F;QSTART=25191701;QSTRAND=- GT:DP:AD ./.:36:24,12 1|1:15:5,10 1|1:23:11,12 -chr20 570174 . T C 60 . QNAME=cluster19_000000F;QSTART=25191698;QSTRAND=- GT:DP:AD ./.:27:9,18 1|1:37:15,22 1|1:26:21,5 -chr20 570223 . C CT 60 . QNAME=cluster19_000000F;QSTART=25191648;QSTRAND=- GT:DP:AD ./.:44:24,20 1|1:24:11,13 0|1:44:20,24 -chr20 570223 . C CTT 60 . QNAME=cluster23_scaffold_3;QSTART=25140988;QSTRAND=- GT:DP:AD ./.:24:7,17 ./.:28:16,12 1|0:36:12,24 -chr20 570243 . G A 60 . QNAME=cluster19_000000F;QSTART=25191628;QSTRAND=- GT:DP:AD ./.:28:17,11 1|1:41:22,19 1|1:37:19,18 -chr20 570390 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=524842;QSTRAND=+ GT:DP:AD 0|1:27:19,8 1|1:26:16,10 1|1:29:8,21 -chr20 570410 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=524862;QSTRAND=+ GT:DP:AD 0|1:43:18,25 ./.:38:16,22 ./.:28:7,21 -chr20 570752 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=525204;QSTRAND=+ GT:DP:AD 0|1:38:18,20 1|1:33:18,15 1|1:38:20,18 -chr20 571051 . C CT 60 . QNAME=HG002-S9-H2-000001F;QSTART=525504;QSTRAND=+ GT:DP:AD 0|1:21:15,6 1|1:31:9,22 1|1:34:15,19 -chr20 571277 . T C 60 . QNAME=cluster19_000000F;QSTART=25190593;QSTRAND=- GT:DP:AD ./.:21:13,8 1|1:19:14,5 1|1:34:23,11 -chr20 571843 . G A 60 . QNAME=cluster19_000000F;QSTART=25190027;QSTRAND=- GT:DP:AD ./.:36:24,12 1|0:36:22,14 ./.:12:6,6 -chr20 571992 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=551509;QSTRAND=+ GT:DP:AD 1|0:43:23,20 ./.:48:23,25 ./.:31:17,14 diff --git a/repo_utils/test_files/answer_key/divided/multi_00000011.vcf b/repo_utils/test_files/answer_key/divided/multi_00000011.vcf deleted file mode 100644 index 5d817164..00000000 --- a/repo_utils/test_files/answer_key/divided/multi_00000011.vcf +++ /dev/null @@ -1,149 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##bcftools_mergeVersion=1.12+htslib-1.12 -##bcftools_mergeCommand=merge -O z -f x -m none input1.vcf.gz input2.vcf.gz input3.vcf.gz; Date=Mon Aug 16 18:05:13 2021 -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 573141 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=552656;QSTRAND=+ GT:DP:AD 1|0:43:21,22 ./.:44:25,19 ./.:29:11,18 -chr20 574599 . C CT 60 . QNAME=cluster19_000000F;QSTART=25187270;QSTRAND=- GT:DP:AD ./.:25:12,13 1|0:29:14,15 ./.:29:19,10 -chr20 574632 . G A 60 . QNAME=cluster19_000000F;QSTART=25187237;QSTRAND=- GT:DP:AD ./.:37:12,25 1|0:30:12,18 ./.:31:7,24 -chr20 574708 . G A 60 . QNAME=cluster19_000000F;QSTART=25187161;QSTRAND=- GT:DP:AD ./.:24:7,17 1|1:38:16,22 ./.:43:19,24 -chr20 577333 . G A 60 . QNAME=cluster19_000000F;QSTART=537532;QSTRAND=+ GT:DP:AD ./.:36:19,17 0|1:30:8,22 ./.:32:19,13 -chr20 577957 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=557473;QSTRAND=+ GT:DP:AD 1|1:34:16,18 ./.:40:17,23 0|1:26:20,6 -chr20 577957 . CAA C 60 . QNAME=cluster19_000000F;QSTART=25183912;QSTRAND=- GT:DP:AD ./.:23:7,16 1|1:22:15,7 ./.:34:20,14 -chr20 578654 . T TAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=533107;QSTRAND=+ GT:DP:AD 0|1:31:14,17 ./.:32:23,9 1|1:25:8,17 -chr20 578654 . TAC T 60 . QNAME=cluster19_000000F;QSTART=25183217;QSTRAND=- GT:DP:AD ./.:46:24,22 1|1:30:14,16 ./.:25:13,12 -chr20 578790 . T C 60 . QNAME=cluster19_000000F;QSTART=25183083;QSTRAND=- GT:DP:AD ./.:31:15,16 1|1:32:8,24 ./.:28:22,6 -chr20 580481 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=559995;QSTRAND=+ GT:DP:AD 1|1:32:16,16 1|1:36:12,24 0|1:42:24,18 -chr20 580899 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=560413;QSTRAND=+ GT:DP:AD 1|0:35:17,18 1|1:25:8,17 ./.:31:20,11 -chr20 581272 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=560786;QSTRAND=+ GT:DP:AD 1|0:22:9,13 1|0:28:13,15 ./.:33:14,19 -chr20 581577 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=536031;QSTRAND=+ GT:DP:AD 0|1:46:22,24 ./.:40:24,16 ./.:35:21,14 -chr20 581670 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=561184;QSTRAND=+ GT:DP:AD 1|1:20:11,9 1|1:36:18,18 ./.:18:5,13 -chr20 581801 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=561315;QSTRAND=+ GT:DP:AD 1|1:27:17,10 1|1:28:17,11 1|0:26:9,17 -chr20 581995 . GT G 60 . QNAME=HG002-S9-H2-000001F;QSTART=536450;QSTRAND=+ GT:DP:AD 0|1:29:7,22 ./.:17:6,11 1|1:29:16,13 -chr20 581995 . GTTT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=561510;QSTRAND=+ GT:DP:AD 1|0:17:8,9 ./.:29:11,18 ./.:29:21,8 -chr20 581995 . GTT G 60 . QNAME=cluster19_000000F;QSTART=25179878;QSTRAND=- GT:DP:AD ./.:29:9,20 1|1:29:7,22 ./.:45:23,22 -chr20 582041 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=536494;QSTRAND=+ GT:DP:AD 0|1:20:12,8 ./.:10:5,5 0|1:46:22,24 -chr20 582389 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=536842;QSTRAND=+ GT:DP:AD 0|1:38:20,18 ./.:20:10,10 0|1:28:11,17 -chr20 583353 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=562864;QSTRAND=+ GT:DP:AD 1|0:20:7,13 1|1:26:15,11 ./.:26:21,5 -chr20 583466 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=537919;QSTRAND=+ GT:DP:AD 0|1:29:14,15 ./.:40:18,22 0|1:39:21,18 -chr20 583895 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=538348;QSTRAND=+ GT:DP:AD 0|1:29:9,20 ./.:31:14,17 0|1:36:20,16 -chr20 584249 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=563760;QSTRAND=+ GT:DP:AD 1|1:17:8,9 1|1:39:22,17 0|1:30:17,13 -chr20 584433 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=538886;QSTRAND=+ GT:DP:AD 0|1:37:22,15 ./.:19:10,9 0|1:22:6,16 -chr20 584664 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=539117;QSTRAND=+ GT:DP:AD 0|1:45:23,22 ./.:33:21,12 0|1:38:19,19 -chr20 584861 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=539314;QSTRAND=+ GT:DP:AD 0|1:23:5,18 ./.:30:11,19 0|1:16:9,7 -chr20 585289 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=564800;QSTRAND=+ GT:DP:AD 1|1:42:21,21 1|1:21:9,12 0|1:24:13,11 -chr20 585341 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=539794;QSTRAND=+ GT:DP:AD 0|1:42:17,25 ./.:11:6,5 0|1:33:14,19 -chr20 585726 . A ATATATGTATATGTACG 60 . QNAME=HG002-S9-H2-000001F;QSTART=540180;QSTRAND=+ GT:DP:AD 0|1:17:11,6 ./.:35:12,23 0|1:15:9,6 -chr20 585739 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=540208;QSTRAND=+ GT:DP:AD 0|1:28:16,12 ./.:34:20,14 0|1:27:12,15 -chr20 585749 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=540218;QSTRAND=+ GT:DP:AD 0|1:24:18,6 ./.:22:5,17 0|1:38:17,21 -chr20 585766 . GTA G 60 . QNAME=HG002-S9-H2-000001F;QSTART=540236;QSTRAND=+ GT:DP:AD 0|1:34:22,12 ./.:28:13,15 0|1:30:20,10 -chr20 586045 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=540513;QSTRAND=+ GT:DP:AD 0|1:26:16,10 ./.:28:13,15 0|1:50:25,25 -chr20 586045 . C CT 60 . QNAME=cluster19_000000F;QSTART=25175829;QSTRAND=- GT:DP:AD ./.:33:13,20 1|1:33:10,23 1|0:11:6,5 -chr20 586124 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=540590;QSTRAND=+ GT:DP:AD 0|1:30:17,13 ./.:32:18,14 0|1:20:7,13 -chr20 586280 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=565791;QSTRAND=+ GT:DP:AD 1|0:32:15,17 1|1:41:16,25 ./.:25:18,7 -chr20 586536 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=541002;QSTRAND=+ GT:DP:AD 0|1:31:8,23 ./.:19:8,11 0|1:38:21,17 -chr20 588052 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=542518;QSTRAND=+ GT:DP:AD 0|1:32:7,25 ./.:39:15,24 0|1:15:7,8 -chr20 588077 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=542543;QSTRAND=+ GT:DP:AD 0|1:32:12,20 ./.:44:19,25 0|1:40:16,24 -chr20 588283 . A ATT 60 . QNAME=HG002-S9-H2-000001F;QSTART=542750;QSTRAND=+ GT:DP:AD 0|1:33:24,9 ./.:24:15,9 0|1:25:7,18 -chr20 588283 . A AT 60 . QNAME=cluster19_000000F;QSTART=25173590;QSTRAND=- GT:DP:AD ./.:28:11,17 1|1:44:20,24 ./.:39:17,22 -chr20 590301 . AAC A 60 . QNAME=HG002-S9-H2-000001F;QSTART=544770;QSTRAND=+ GT:DP:AD 0|1:21:8,13 ./.:13:7,6 0|1:21:13,8 -chr20 590301 . A AAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=569813;QSTRAND=+ GT:DP:AD 1|0:46:21,25 ./.:29:24,5 ./.:34:13,21 -chr20 590301 . A AACAC 60 . QNAME=cluster19_000000F;QSTART=25171568;QSTRAND=- GT:DP:AD ./.:35:12,23 1|1:11:6,5 ./.:21:5,16 -chr20 590927 . G C 60 . QNAME=cluster23_scaffold_2;QSTART=25104488;QSTRAND=- GT:DP:AD ./.:28:23,5 ./.:49:25,24 0|1:31:6,25 -chr20 591644 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=546111;QSTRAND=+ GT:DP:AD 0|1:37:17,20 ./.:20:11,9 ./.:33:20,13 -chr20 592228 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=546693;QSTRAND=+ GT:DP:AD 0|1:32:10,22 ./.:34:19,15 0|1:33:10,23 -chr20 592392 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=546857;QSTRAND=+ GT:DP:AD 0|1:27:6,21 ./.:14:6,8 0|1:23:7,16 -chr20 593097 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=547562;QSTRAND=+ GT:DP:AD 0|1:30:6,24 ./.:18:11,7 0|1:13:7,6 -chr20 593103 . T TTA 60 . QNAME=cluster19_000000F;QSTART=25168764;QSTRAND=- GT:DP:AD ./.:20:6,14 1|0:20:12,8 ./.:34:16,18 -chr20 593121 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25118087;QSTRAND=- GT:DP:AD ./.:20:8,12 ./.:36:13,23 1|0:31:16,15 -chr20 593121 . A ATATATATTTTT 60 . QNAME=HG002-S9-H2-000001F;QSTART=547587;QSTRAND=+ GT:DP:AD 0|1:34:23,11 ./.:36:22,14 ./.:29:16,13 -chr20 593121 . A ATATATTTTTTT 60 . QNAME=cluster23_scaffold_2;QSTART=25102283;QSTRAND=- GT:DP:AD ./.:13:6,7 ./.:47:22,25 0|1:38:16,22 -chr20 593122 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=572636;QSTRAND=+ GT:DP:AD 1|0:31:18,13 0|1:34:22,12 ./.:40:16,24 -chr20 593123 . T A 60 . QNAME=cluster19_000000F;QSTART=25168744;QSTRAND=- GT:DP:AD ./.:27:7,20 1|0:36:21,15 ./.:27:10,17 -chr20 593266 . CTTTTTTT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=572781;QSTRAND=+ GT:DP:AD 1|0:29:24,5 1|1:27:5,22 ./.:46:25,21 -chr20 593638 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=548114;QSTRAND=+ GT:DP:AD 0|1:39:18,21 ./.:30:24,6 0|1:21:14,7 -chr20 593664 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=548140;QSTRAND=+ GT:DP:AD 0|1:26:9,17 ./.:29:9,20 0|1:11:6,5 -chr20 594618 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=549095;QSTRAND=+ GT:DP:AD 0|1:34:25,9 ./.:33:9,24 ./.:25:19,6 -chr20 594618 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25100785;QSTRAND=- GT:DP:AD ./.:30:9,21 ./.:24:15,9 0|1:25:8,17 -chr20 595396 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=549872;QSTRAND=+ GT:DP:AD 0|1:25:20,5 ./.:43:24,19 ./.:27:22,5 -chr20 595643 . T TTTA 60 . QNAME=HG002-S9-H1-000001F;QSTART=575151;QSTRAND=+ GT:DP:AD 1|0:19:6,13 1|1:30:19,11 ./.:46:22,24 -chr20 596470 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25114738;QSTRAND=- GT:DP:AD ./.:31:9,22 ./.:43:25,18 1|0:36:13,23 -chr20 596536 . G GAAAACA 60 . QNAME=cluster23_scaffold_3;QSTART=25114666;QSTRAND=- GT:DP:AD ./.:26:8,18 ./.:10:5,5 1|0:46:24,22 -chr20 596656 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=576166;QSTRAND=+ GT:DP:AD 1|0:30:22,8 1|1:40:15,25 ./.:38:14,24 -chr20 596715 . C T 60 . QNAME=cluster19_000000F;QSTART=556911;QSTRAND=+ GT:DP:AD ./.:10:5,5 0|1:36:22,14 ./.:38:22,16 -chr20 597212 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=576722;QSTRAND=+ GT:DP:AD 1|0:33:24,9 1|1:24:17,7 ./.:32:8,24 -chr20 597374 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=576884;QSTRAND=+ GT:DP:AD 1|0:36:19,17 1|1:25:18,7 ./.:23:5,18 -chr20 597779 . C T 60 . QNAME=cluster19_000000F;QSTART=557975;QSTRAND=+ GT:DP:AD ./.:47:22,25 0|1:42:22,20 ./.:29:6,23 -chr20 598186 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25113016;QSTRAND=- GT:DP:AD ./.:21:14,7 ./.:36:15,21 1|0:17:7,10 -chr20 598263 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=552737;QSTRAND=+ GT:DP:AD 0|1:28:22,6 ./.:17:6,11 0|1:24:10,14 -chr20 598702 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25112500;QSTRAND=- GT:DP:AD ./.:30:7,23 ./.:15:6,9 1|0:24:15,9 -chr20 599013 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=578523;QSTRAND=+ GT:DP:AD 1|0:26:14,12 1|1:30:14,16 1|1:30:19,11 -chr20 599169 . AT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=553644;QSTRAND=+ GT:DP:AD 0|1:38:19,19 1|1:24:5,19 1|0:25:18,7 -chr20 599169 . ATT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=578680;QSTRAND=+ GT:DP:AD 1|0:33:8,25 ./.:26:6,20 0|1:39:24,15 -chr20 599421 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=578929;QSTRAND=+ GT:DP:AD 1|0:18:8,10 1|1:34:10,24 ./.:22:7,15 -chr20 600604 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=580112;QSTRAND=+ GT:DP:AD 1|1:23:15,8 1|1:42:18,24 1|1:34:14,20 -chr20 600839 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=580347;QSTRAND=+ GT:DP:AD 1|0:22:17,5 1|1:32:16,16 ./.:15:5,10 -chr20 600991 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=580499;QSTRAND=+ GT:DP:AD 1|0:44:19,25 1|1:33:14,19 ./.:18:13,5 -chr20 601642 . G A 60 . QNAME=cluster19_000000F;QSTART=25160230;QSTRAND=- GT:DP:AD ./.:23:13,10 1|0:37:15,22 ./.:29:5,24 -chr20 601683 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=581192;QSTRAND=+ GT:DP:AD 1|0:44:25,19 1|1:44:22,22 0|1:42:22,20 -chr20 601683 . T TAA 60 . QNAME=cluster23_scaffold_3;QSTART=25109518;QSTRAND=- GT:DP:AD ./.:45:25,20 ./.:40:21,19 1|0:14:9,5 -chr20 601733 . GC G 60 . QNAME=cluster23_scaffold_3;QSTART=25109468;QSTRAND=- GT:DP:AD ./.:24:6,18 ./.:40:25,15 1|1:20:5,15 -chr20 602460 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=581969;QSTRAND=+ GT:DP:AD 1|0:12:6,6 1|1:33:22,11 ./.:25:5,20 -chr20 602943 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25108259;QSTRAND=- GT:DP:AD ./.:44:21,23 ./.:30:12,18 1|1:28:15,13 -chr20 606311 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=585820;QSTRAND=+ GT:DP:AD 1|1:28:13,15 1|1:42:25,17 1|1:23:13,10 -chr20 606780 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=586289;QSTRAND=+ GT:DP:AD 1|0:25:17,8 ./.:22:9,13 1|1:24:9,15 -chr20 607272 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=561745;QSTRAND=+ GT:DP:AD 0|1:38:17,21 ./.:14:5,9 ./.:28:10,18 -chr20 607445 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=586954;QSTRAND=+ GT:DP:AD 1|1:37:18,19 ./.:31:25,6 1|1:37:19,18 -chr20 607522 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=587031;QSTRAND=+ GT:DP:AD 1|0:37:13,24 ./.:40:17,23 1|1:15:5,10 -chr20 607633 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=562106;QSTRAND=+ GT:DP:AD 0|1:39:14,25 ./.:29:17,12 ./.:29:22,7 -chr20 607790 . A C 60 . QNAME=cluster19_000000F;QSTART=567986;QSTRAND=+ GT:DP:AD ./.:20:10,10 0|1:23:9,14 ./.:25:12,13 -chr20 608989 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=588498;QSTRAND=+ GT:DP:AD 1|0:33:14,19 ./.:33:14,19 1|1:12:5,7 -chr20 609812 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=589321;QSTRAND=+ GT:DP:AD 1|1:28:9,19 ./.:26:6,20 1|1:31:10,21 -chr20 609898 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=589407;QSTRAND=+ GT:DP:AD 1|1:16:11,5 1|1:28:17,11 1|1:39:25,14 -chr20 609899 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=589408;QSTRAND=+ GT:DP:AD 1|1:19:5,14 1|1:19:8,11 1|1:22:16,6 -chr20 610256 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=589765;QSTRAND=+ GT:DP:AD 1|1:20:7,13 ./.:38:15,23 1|1:28:6,22 -chr20 610966 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=590475;QSTRAND=+ GT:DP:AD 1|0:29:20,9 ./.:35:23,12 1|1:18:13,5 -chr20 611394 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=590903;QSTRAND=+ GT:DP:AD 1|1:42:23,19 ./.:25:13,12 1|1:32:15,17 -chr20 611826 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=566299;QSTRAND=+ GT:DP:AD 0|1:45:20,25 ./.:31:23,8 ./.:37:17,20 -chr20 611881 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=591390;QSTRAND=+ GT:DP:AD 1|1:13:6,7 ./.:39:20,19 1|1:35:17,18 -chr20 612157 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=591666;QSTRAND=+ GT:DP:AD 1|1:24:8,16 ./.:22:6,16 1|1:32:19,13 -chr20 612432 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=591941;QSTRAND=+ GT:DP:AD 1|1:41:21,20 ./.:27:22,5 1|1:25:20,5 -chr20 612561 . AG A 60 . QNAME=cluster19_000000F;QSTART=25149310;QSTRAND=- GT:DP:AD ./.:33:17,16 1|0:18:13,5 ./.:27:18,9 -chr20 612664 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=592173;QSTRAND=+ GT:DP:AD 1|1:31:23,8 ./.:25:19,6 1|1:40:18,22 -chr20 612674 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=592183;QSTRAND=+ GT:DP:AD 1|0:20:12,8 ./.:21:12,9 1|1:29:19,10 diff --git a/repo_utils/test_files/answer_key/divided/multi_00000012.vcf b/repo_utils/test_files/answer_key/divided/multi_00000012.vcf deleted file mode 100644 index aa729f35..00000000 --- a/repo_utils/test_files/answer_key/divided/multi_00000012.vcf +++ /dev/null @@ -1,212 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##bcftools_mergeVersion=1.12+htslib-1.12 -##bcftools_mergeCommand=merge -O z -f x -m none input1.vcf.gz input2.vcf.gz input3.vcf.gz; Date=Mon Aug 16 18:05:13 2021 -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 613783 . TGTGTGCTGAGTCCAGCTCAAGTCCCTTGGTTCCCACTGCTGCTAAGCATGCACG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=593293;QSTRAND=+;SVTYPE=DEL;SVLEN=-54 GT:DP:AD 1/1:46:24,22 1/0:29:14,15 1/1:43:19,24 -chr20 614136 . T C 60 . QNAME=cluster19_000000F;QSTART=574332;QSTRAND=+ GT:DP:AD ./.:33:9,24 0|1:39:15,24 ./.:35:23,12 -chr20 614408 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=568827;QSTRAND=+ GT:DP:AD 0|1:31:6,25 ./.:27:10,17 ./.:39:18,21 -chr20 614449 . ATCTC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=593905;QSTRAND=+ GT:DP:AD 1|0:30:5,25 ./.:22:8,14 1|1:43:22,21 -chr20 614473 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=593924;QSTRAND=+ GT:DP:AD 1|0:18:8,10 ./.:15:5,10 ./.:33:10,23 -chr20 614475 . A C 60 . QNAME=cluster19_000000F;QSTART=574671;QSTRAND=+ GT:DP:AD ./.:16:11,5 0|1:45:21,24 ./.:28:15,13 -chr20 614477 . A C 60 . QNAME=cluster19_000000F;QSTART=574673;QSTRAND=+ GT:DP:AD ./.:25:8,17 0|1:40:17,23 ./.:25:9,16 -chr20 614492 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=593943;QSTRAND=+ GT:DP:AD 1|0:34:16,18 ./.:47:25,22 1|1:22:15,7 -chr20 614492 . T TAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=568912;QSTRAND=+ GT:DP:AD 0|1:18:10,8 ./.:18:5,13 ./.:29:16,13 -chr20 614494 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=593945;QSTRAND=+ GT:DP:AD 1|0:29:14,15 ./.:30:16,14 1|1:42:19,23 -chr20 614496 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=568917;QSTRAND=+ GT:DP:AD 0|1:22:7,15 ./.:16:7,9 ./.:30:23,7 -chr20 614517 . G GTA 60 . QNAME=cluster23_scaffold_3;QSTART=25096741;QSTRAND=- GT:DP:AD ./.:27:12,15 ./.:35:17,18 1|1:41:22,19 -chr20 614555 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=594006;QSTRAND=+ GT:DP:AD 1|0:38:23,15 ./.:19:6,13 1|1:23:9,14 -chr20 614561 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=594012;QSTRAND=+ GT:DP:AD 1|0:44:24,20 ./.:36:21,15 1|1:20:6,14 -chr20 614710 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=594161;QSTRAND=+ GT:DP:AD 1|0:45:25,20 ./.:34:18,16 1|1:15:6,9 -chr20 615045 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=569466;QSTRAND=+ GT:DP:AD 0|1:39:19,20 ./.:23:5,18 ./.:25:18,7 -chr20 615409 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=594860;QSTRAND=+ GT:DP:AD 1|0:18:5,13 ./.:28:6,22 1|1:28:7,21 -chr20 615455 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=569876;QSTRAND=+ GT:DP:AD 0|1:31:6,25 ./.:31:13,18 ./.:33:24,9 -chr20 615471 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=594922;QSTRAND=+ GT:DP:AD 1|1:16:7,9 ./.:32:7,25 1|1:27:17,10 -chr20 615863 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=570284;QSTRAND=+ GT:DP:AD 0|1:29:14,15 ./.:26:20,6 ./.:50:25,25 -chr20 616031 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=570452;QSTRAND=+ GT:DP:AD 0|1:32:16,16 ./.:44:20,24 ./.:35:19,16 -chr20 616321 . G GT 60 . QNAME=HG002-S9-H1-000001F;QSTART=595773;QSTRAND=+ GT:DP:AD 1|0:26:16,10 ./.:41:20,21 1|1:17:11,6 -chr20 616321 . G GTT 60 . QNAME=HG002-S9-H2-000001F;QSTART=570743;QSTRAND=+ GT:DP:AD 0|1:40:18,22 ./.:34:11,23 ./.:31:23,8 -chr20 616559 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=570982;QSTRAND=+ GT:DP:AD 0|1:28:17,11 ./.:36:11,25 ./.:34:24,10 -chr20 616743 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=571166;QSTRAND=+ GT:DP:AD 0|1:28:22,6 ./.:35:14,21 ./.:30:5,25 -chr20 617022 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=571445;QSTRAND=+ GT:DP:AD 0|1:24:9,15 ./.:31:21,10 ./.:23:10,13 -chr20 617094 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=596546;QSTRAND=+ GT:DP:AD 1|1:35:14,21 ./.:33:18,15 1|1:25:11,14 -chr20 617427 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=571850;QSTRAND=+ GT:DP:AD 0|1:34:11,23 ./.:26:6,20 ./.:10:5,5 -chr20 617634 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=597086;QSTRAND=+ GT:DP:AD 1|0:34:18,16 ./.:37:22,15 1|1:11:5,6 -chr20 617892 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=597344;QSTRAND=+ GT:DP:AD 1|1:25:13,12 ./.:22:16,6 1|1:27:8,19 -chr20 618050 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=597502;QSTRAND=+ GT:DP:AD 1|0:38:21,17 ./.:32:19,13 1|1:35:15,20 -chr20 618051 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=572474;QSTRAND=+ GT:DP:AD 0|1:42:20,22 ./.:20:10,10 ./.:39:18,21 -chr20 619223 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=573646;QSTRAND=+ GT:DP:AD 0|1:23:13,10 ./.:36:16,20 ./.:43:23,20 -chr20 620320 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=599772;QSTRAND=+ GT:DP:AD 1|1:46:24,22 ./.:32:9,23 1|1:33:20,13 -chr20 620391 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=599843;QSTRAND=+ GT:DP:AD 1|1:40:24,16 ./.:26:13,13 1|1:31:15,16 -chr20 621742 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=576165;QSTRAND=+ GT:DP:AD 0|1:38:25,13 ./.:41:22,19 ./.:29:10,19 -chr20 622380 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=601832;QSTRAND=+ GT:DP:AD 1|0:41:25,16 ./.:29:8,21 1|1:38:21,17 -chr20 622562 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=576985;QSTRAND=+ GT:DP:AD 0|1:26:5,21 ./.:10:5,5 ./.:26:8,18 -chr20 622615 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=602067;QSTRAND=+ GT:DP:AD 1|1:38:23,15 ./.:28:11,17 1|1:36:17,19 -chr20 622976 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=577399;QSTRAND=+ GT:DP:AD 0|1:25:18,7 ./.:11:5,6 0|1:23:13,10 -chr20 624131 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=578554;QSTRAND=+ GT:DP:AD 0|1:17:5,12 ./.:34:24,10 ./.:35:11,24 -chr20 624618 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=579041;QSTRAND=+ GT:DP:AD 0|1:31:23,8 ./.:37:14,23 ./.:41:16,25 -chr20 624679 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=604131;QSTRAND=+ GT:DP:AD 1|1:44:21,23 ./.:25:16,9 1|1:31:9,22 -chr20 625245 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=604697;QSTRAND=+ GT:DP:AD 1|0:39:19,20 ./.:30:16,14 1|1:44:24,20 -chr20 625293 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=604745;QSTRAND=+ GT:DP:AD 1|1:28:12,16 ./.:34:25,9 1|1:29:5,24 -chr20 626070 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=580493;QSTRAND=+ GT:DP:AD 0|1:18:10,8 1|1:36:12,24 ./.:38:20,18 -chr20 626301 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=605753;QSTRAND=+ GT:DP:AD 1|0:29:23,6 ./.:41:25,16 1|1:20:6,14 -chr20 626305 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=605757;QSTRAND=+ GT:DP:AD 1|0:43:22,21 ./.:25:7,18 1|1:28:5,23 -chr20 626441 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=605893;QSTRAND=+ GT:DP:AD 1|0:36:20,16 ./.:34:13,21 1|1:22:10,12 -chr20 626569 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=580992;QSTRAND=+ GT:DP:AD 0|1:34:23,11 ./.:37:16,21 ./.:32:23,9 -chr20 626821 . A AC 60 . QNAME=HG002-S9-H1-000001F;QSTART=606274;QSTRAND=+ GT:DP:AD 1|0:31:13,18 ./.:33:20,13 1|0:17:12,5 -chr20 626950 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=606403;QSTRAND=+ GT:DP:AD 1|0:34:19,15 ./.:44:20,24 1|0:36:13,23 -chr20 627161 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=606614;QSTRAND=+ GT:DP:AD 1|0:24:17,7 ./.:33:14,19 1|1:29:18,11 -chr20 627348 . A G 60 . QNAME=cluster19_000000F;QSTART=25134578;QSTRAND=- GT:DP:AD ./.:28:14,14 1|0:31:9,22 ./.:29:17,12 -chr20 628116 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=607569;QSTRAND=+ GT:DP:AD 1|0:32:25,7 ./.:19:7,12 1|0:31:6,25 -chr20 628203 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=607656;QSTRAND=+ GT:DP:AD 1|1:43:19,24 ./.:33:14,19 1|1:43:25,18 -chr20 628339 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=607792;QSTRAND=+ GT:DP:AD 1|1:30:24,6 ./.:40:22,18 1|1:37:22,15 -chr20 628481 . G C 60 . QNAME=cluster23_scaffold_2;QSTART=25066979;QSTRAND=- GT:DP:AD ./.:30:16,14 ./.:37:19,18 0|1:41:25,16 -chr20 628698 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=608151;QSTRAND=+ GT:DP:AD 1|0:26:12,14 ./.:31:15,16 1|0:41:17,24 -chr20 628723 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=608176;QSTRAND=+ GT:DP:AD 1|0:10:5,5 ./.:35:19,16 1|0:25:17,8 -chr20 628961 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=608414;QSTRAND=+ GT:DP:AD 1|0:26:11,15 ./.:31:18,13 1|1:17:11,6 -chr20 629302 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=608755;QSTRAND=+ GT:DP:AD 1|0:25:17,8 ./.:38:15,23 1|1:26:11,15 -chr20 629494 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=608947;QSTRAND=+ GT:DP:AD 1|0:25:19,6 ./.:27:19,8 ./.:32:16,16 -chr20 629610 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25065850;QSTRAND=- GT:DP:AD ./.:19:8,11 ./.:32:25,7 0|1:31:15,16 -chr20 629678 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=609131;QSTRAND=+ GT:DP:AD 1|0:36:20,16 ./.:23:5,18 1|1:42:19,23 -chr20 629911 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=609364;QSTRAND=+ GT:DP:AD 1|0:31:11,20 ./.:30:14,16 1|1:27:18,9 -chr20 629941 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=609394;QSTRAND=+ GT:DP:AD 1|0:34:13,21 ./.:27:15,12 1|1:21:15,6 -chr20 630017 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=609470;QSTRAND=+ GT:DP:AD 1|0:36:12,24 ./.:13:7,6 1|1:32:10,22 -chr20 630420 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=609873;QSTRAND=+ GT:DP:AD 1|0:17:11,6 ./.:37:14,23 ./.:27:21,6 -chr20 630592 . CAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=610046;QSTRAND=+ GT:DP:AD 1|0:24:15,9 ./.:24:17,7 1|0:31:6,25 -chr20 630592 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=585016;QSTRAND=+ GT:DP:AD 0|1:47:22,25 ./.:26:10,16 0|1:45:22,23 -chr20 630708 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=610158;QSTRAND=+ GT:DP:AD 1|0:21:6,15 ./.:25:14,11 1|1:20:5,15 -chr20 631945 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=611395;QSTRAND=+ GT:DP:AD 1|0:40:25,15 ./.:43:19,24 ./.:28:8,20 -chr20 632007 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=611457;QSTRAND=+ GT:DP:AD 1|0:17:6,11 ./.:36:25,11 ./.:23:18,5 -chr20 632024 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=611474;QSTRAND=+ GT:DP:AD 1|0:21:14,7 ./.:23:15,8 ./.:33:11,22 -chr20 632038 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=611488;QSTRAND=+ GT:DP:AD 1|0:24:7,17 ./.:28:8,20 ./.:35:17,18 -chr20 632119 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=611569;QSTRAND=+ GT:DP:AD 1|0:37:19,18 ./.:33:25,8 ./.:31:15,16 -chr20 633319 . A G 60 . QNAME=cluster19_000000F;QSTART=25128607;QSTRAND=- GT:DP:AD ./.:24:12,12 1|0:26:14,12 0|1:17:9,8 -chr20 633850 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=613300;QSTRAND=+ GT:DP:AD 1|0:38:13,25 ./.:32:14,18 ./.:17:10,7 -chr20 634306 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=613756;QSTRAND=+ GT:DP:AD 1|0:23:16,7 ./.:33:22,11 ./.:37:13,24 -chr20 634343 . C T 60 . QNAME=cluster19_000000F;QSTART=25127583;QSTRAND=- GT:DP:AD ./.:24:6,18 1|0:26:16,10 0|1:27:21,6 -chr20 634367 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=613817;QSTRAND=+ GT:DP:AD 1|0:40:15,25 1|0:36:11,25 0|1:35:25,10 -chr20 634490 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=613940;QSTRAND=+ GT:DP:AD 1|0:46:24,22 ./.:44:19,25 ./.:23:18,5 -chr20 634534 . G A 60 . QNAME=cluster19_000000F;QSTART=25127392;QSTRAND=- GT:DP:AD ./.:25:12,13 1|0:31:15,16 0|1:28:15,13 -chr20 634915 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=614365;QSTRAND=+ GT:DP:AD 1|0:19:9,10 ./.:25:10,15 ./.:30:23,7 -chr20 637164 . T C 60 . QNAME=cluster19_000000F;QSTART=25124762;QSTRAND=- GT:DP:AD ./.:13:8,5 1|0:45:22,23 ./.:23:12,11 -chr20 637615 . T C 60 . QNAME=cluster19_000000F;QSTART=25124311;QSTRAND=- GT:DP:AD ./.:46:24,22 1|0:27:5,22 ./.:31:19,12 -chr20 638468 . TA T 60 . QNAME=cluster19_000000F;QSTART=25123458;QSTRAND=- GT:DP:AD ./.:27:12,15 1|0:35:19,16 ./.:28:9,19 -chr20 638468 . T TA 60 . QNAME=cluster23_scaffold_3;QSTART=25072790;QSTRAND=- GT:DP:AD ./.:32:14,18 ./.:35:13,22 1|1:21:5,16 -chr20 638748 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=618198;QSTRAND=+ GT:DP:AD 1|0:26:20,6 1|0:23:10,13 ./.:39:16,23 -chr20 638918 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=618368;QSTRAND=+ GT:DP:AD 1|0:31:11,20 ./.:34:15,19 ./.:16:8,8 -chr20 639104 . A AT 60 . QNAME=HG002-S9-H1-000001F;QSTART=618555;QSTRAND=+ GT:DP:AD 1|0:35:12,23 ./.:18:9,9 1|1:35:18,17 -chr20 639255 . T C 60 . QNAME=cluster19_000000F;QSTART=25122672;QSTRAND=- GT:DP:AD ./.:39:24,15 1|0:33:16,17 ./.:15:9,6 -chr20 639552 . T C 60 . QNAME=cluster19_000000F;QSTART=25122375;QSTRAND=- GT:DP:AD ./.:10:5,5 1|0:28:22,6 0|1:33:13,20 -chr20 639866 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25055593;QSTRAND=- GT:DP:AD ./.:40:25,15 ./.:22:6,16 0|1:16:5,11 -chr20 640046 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=619497;QSTRAND=+ GT:DP:AD 1|0:10:5,5 ./.:33:15,18 ./.:32:22,10 -chr20 640049 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=619500;QSTRAND=+ GT:DP:AD 1|1:28:12,16 ./.:29:5,24 1|0:31:19,12 -chr20 640284 . T TC 60 . QNAME=cluster23_scaffold_2;QSTART=25055174;QSTRAND=- GT:DP:AD ./.:19:8,11 ./.:48:23,25 0|1:34:25,9 -chr20 641878 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621329;QSTRAND=+ GT:DP:AD 1|0:17:11,6 ./.:15:9,6 0|1:33:12,21 -chr20 641905 . T TG 60 . QNAME=cluster23_scaffold_3;QSTART=25069351;QSTRAND=- GT:DP:AD ./.:29:5,24 ./.:18:8,10 1|0:18:7,11 -chr20 641906 . G GGCGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCT 60 . QNAME=cluster23_scaffold_2;QSTART=25053389;QSTRAND=-;SVTYPE=INS;SVLEN=163 GT:DP:AD ./.:13:6,7 ./.:34:21,13 0/1:27:16,11 -chr20 641913 . G GGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGA 60 . QNAME=HG002-S9-H1-000001F;QSTART=621365;QSTRAND=+;SVTYPE=INS;SVLEN=66 GT:DP:AD 1/0:34:18,16 ./.:32:17,15 ./.:36:16,20 -chr20 641930 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25053365;QSTRAND=- GT:DP:AD ./.:33:16,17 ./.:15:6,9 0|1:27:13,14 -chr20 641944 . GGA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621462;QSTRAND=+ GT:DP:AD 1|0:30:16,14 ./.:47:25,22 ./.:32:13,19 -chr20 641970 . T TG 60 . QNAME=cluster23_scaffold_2;QSTART=25053324;QSTRAND=- GT:DP:AD ./.:30:14,16 ./.:26:16,10 0|1:31:12,19 -chr20 641977 . G T 60 . QNAME=cluster19_000000F;QSTART=25119950;QSTRAND=- GT:DP:AD ./.:34:16,18 1|0:24:7,17 ./.:28:20,8 -chr20 642012 . GGT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621528;QSTRAND=+ GT:DP:AD 1|0:20:10,10 ./.:35:18,17 ./.:33:16,17 -chr20 642037 . T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=621551;QSTRAND=+ GT:DP:AD 1|0:41:18,23 ./.:44:19,25 ./.:35:18,17 -chr20 642067 . T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=621582;QSTRAND=+ GT:DP:AD 1|0:25:9,16 ./.:38:22,16 ./.:27:21,6 -chr20 642068 . G GTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCC 60 . QNAME=cluster23_scaffold_2;QSTART=25053097;QSTRAND=-;SVTYPE=INS;SVLEN=129 GT:DP:AD ./.:34:24,10 ./.:30:19,11 0/1:18:11,7 -chr20 642069 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621584;QSTRAND=+ GT:DP:AD 1|0:33:20,13 ./.:15:10,5 ./.:27:19,8 -chr20 642076 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25053089;QSTRAND=- GT:DP:AD ./.:31:22,9 ./.:36:21,15 0|1:29:21,8 -chr20 642100 . T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=621616;QSTRAND=+ GT:DP:AD 1|0:30:22,8 ./.:39:21,18 ./.:45:25,20 -chr20 642123 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=621639;QSTRAND=+ GT:DP:AD 1|0:46:23,23 ./.:21:6,15 0|1:42:20,22 -chr20 642130 . T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=621647;QSTRAND=+ GT:DP:AD 1|0:34:15,19 ./.:16:8,8 ./.:23:8,15 -chr20 642132 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=25053033;QSTRAND=- GT:DP:AD ./.:13:6,7 ./.:30:7,23 0|1:35:13,22 -chr20 642171 . GGA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621689;QSTRAND=+ GT:DP:AD 1|0:43:23,20 ./.:40:20,20 0|1:40:18,22 -chr20 642205 . GGT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621721;QSTRAND=+ GT:DP:AD 1|0:33:11,22 ./.:22:5,17 0|1:30:12,18 -chr20 642207 . T TGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGG 60 . QNAME=HG002-S9-H2-000001F;QSTART=596630;QSTRAND=+;SVTYPE=INS;SVLEN=501 GT:DP:AD 0/1:27:12,15 ./.:20:10,10 ./.:22:17,5 -chr20 642207 . T TGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGG 60 . QNAME=cluster19_000000F;QSTART=602404;QSTRAND=+;SVTYPE=INS;SVLEN=630 GT:DP:AD ./.:28:16,12 0/1:27:13,14 ./.:24:18,6 -chr20 642230 . T TGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTG 60 . QNAME=cluster19_000000F;QSTART=25119065;QSTRAND=-;SVTYPE=INS;SVLEN=632 GT:DP:AD ./.:35:18,17 1/0:33:10,23 ./.:44:25,19 -chr20 642230 . T TG 60 . QNAME=cluster23_scaffold_3;QSTART=25069025;QSTRAND=- GT:DP:AD ./.:25:9,16 ./.:21:6,15 1|1:42:23,19 -chr20 642259 . CTG C 60 . QNAME=HG002-S9-H1-000001F;QSTART=621773;QSTRAND=+ GT:DP:AD 1|0:19:6,13 ./.:30:7,23 ./.:16:7,9 -chr20 642261 . GTGGT G 60 . QNAME=cluster23_scaffold_3;QSTART=25068994;QSTRAND=- GT:DP:AD ./.:34:17,17 ./.:27:20,7 1|0:46:25,21 -chr20 642265 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621776;QSTRAND=+ GT:DP:AD 1|1:37:12,25 0|1:27:9,18 ./.:36:22,14 -chr20 642271 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=621782;QSTRAND=+ GT:DP:AD 1|0:34:25,9 ./.:27:11,16 ./.:40:24,16 -chr20 642271 . G GC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597195;QSTRAND=+ GT:DP:AD 0|1:17:6,11 1|1:22:17,5 0|1:22:17,5 -chr20 642271 . G GGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGC 60 . QNAME=cluster23_scaffold_3;QSTART=25068731;QSTRAND=-;SVTYPE=INS;SVLEN=257 GT:DP:AD ./.:36:19,17 ./.:28:5,23 1/0:27:18,9 -chr20 642277 . G A 60 . QNAME=cluster19_000000F;QSTART=603104;QSTRAND=+ GT:DP:AD ./.:25:6,19 0|1:46:25,21 ./.:25:18,7 -chr20 642284 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621795;QSTRAND=+ GT:DP:AD 1|1:16:5,11 1|1:24:8,16 1|1:25:16,9 -chr20 642300 . G GGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597225;QSTRAND=+ GT:DP:AD 0|1:27:11,16 0|1:40:18,22 1|1:15:6,9 -chr20 642300 . G GCCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGC 60 . QNAME=HG002-S9-H1-000001F;QSTART=621812;QSTRAND=+;SVTYPE=INS;SVLEN=408 GT:DP:AD 1/0:44:19,25 ./.:35:12,23 ./.:42:17,25 -chr20 642300 . G GC 60 . QNAME=cluster19_000000F;QSTART=25118993;QSTRAND=- GT:DP:AD ./.:31:7,24 1|0:45:25,20 ./.:37:25,12 -chr20 642330 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=622249;QSTRAND=+ GT:DP:AD 1|0:34:14,20 ./.:33:15,18 1|0:21:13,8 -chr20 642330 . G GGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597257;QSTRAND=+;SVTYPE=INS;SVLEN=66 GT:DP:AD 0/1:18:11,7 ./.:23:10,13 ./.:25:12,13 -chr20 642330 . G GC 60 . QNAME=cluster19_000000F;QSTART=25118962;QSTRAND=- GT:DP:AD ./.:30:14,16 1|1:45:20,25 ./.:24:18,6 -chr20 642330 . G GCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGGGC 60 . QNAME=cluster23_scaffold_2;QSTART=25052609;QSTRAND=-;SVTYPE=INS;SVLEN=226 GT:DP:AD ./.:41:21,20 ./.:28:9,19 0/1:18:12,6 -chr20 642353 . T G 60 . QNAME=cluster23_scaffold_2;QSTART=25052586;QSTRAND=- GT:DP:AD ./.:23:15,8 ./.:16:6,10 0|1:24:17,7 -chr20 642362 . G C 60 . QNAME=cluster23_scaffold_2;QSTART=25052577;QSTRAND=- GT:DP:AD ./.:48:24,24 ./.:26:12,14 0|1:12:7,5 -chr20 642362 . G GC 60 . QNAME=HG002-S9-H1-000001F;QSTART=622282;QSTRAND=+ GT:DP:AD 1|1:25:14,11 1|1:32:16,16 1|0:30:7,23 -chr20 642391 . G GC 60 . QNAME=HG002-S9-H1-000001F;QSTART=622312;QSTRAND=+ GT:DP:AD 1|1:27:9,18 1|1:16:9,7 0|1:20:15,5 -chr20 642391 . G GGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGGC 60 . QNAME=cluster23_scaffold_3;QSTART=25068286;QSTRAND=-;SVTYPE=INS;SVLEN=322 GT:DP:AD ./.:21:9,12 ./.:41:25,16 1/0:14:6,8 -chr20 642420 . G GC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597415;QSTRAND=+ GT:DP:AD 0|1:14:9,5 1|1:39:25,14 1|0:28:11,17 -chr20 642420 . G GGC 60 . QNAME=HG002-S9-H1-000001F;QSTART=622342;QSTRAND=+ GT:DP:AD 1|0:36:19,17 ./.:30:25,5 ./.:34:25,9 -chr20 642420 . G GGGC 60 . QNAME=cluster23_scaffold_2;QSTART=25052515;QSTRAND=- GT:DP:AD ./.:30:22,8 ./.:36:25,11 0|1:39:16,23 -chr20 642746 . C CGGGGTGCGGGT 60 . QNAME=cluster19_000000F;QSTART=603580;QSTRAND=+ GT:DP:AD ./.:43:22,21 0|1:42:23,19 ./.:20:13,7 -chr20 642746 . C CGGGGGTGCGGGT 60 . QNAME=cluster23_scaffold_2;QSTART=25052177;QSTRAND=- GT:DP:AD ./.:24:12,12 ./.:23:6,17 0|1:23:11,12 -chr20 642861 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=622784;QSTRAND=+ GT:DP:AD 1|0:50:25,25 ./.:32:14,18 ./.:33:22,11 -chr20 642893 . GTGA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=622817;QSTRAND=+ GT:DP:AD 1|0:18:8,10 ./.:40:15,25 ./.:39:22,17 -chr20 643742 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25051181;QSTRAND=- GT:DP:AD ./.:45:22,23 ./.:40:19,21 0|1:32:8,24 -chr20 643827 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=623747;QSTRAND=+ GT:DP:AD 1|0:30:24,6 ./.:47:23,24 ./.:38:15,23 -chr20 644129 . T A 60 . QNAME=cluster23_scaffold_2;QSTART=25050794;QSTRAND=- GT:DP:AD ./.:16:7,9 ./.:22:14,8 0|1:27:14,13 -chr20 644264 . TA T 60 . QNAME=cluster23_scaffold_2;QSTART=25050659;QSTRAND=- GT:DP:AD ./.:40:21,19 ./.:24:16,8 0|1:26:18,8 -chr20 644423 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=624343;QSTRAND=+ GT:DP:AD 1|0:33:20,13 ./.:30:25,5 ./.:37:12,25 -chr20 644731 . T TA 60 . QNAME=cluster23_scaffold_2;QSTART=25050192;QSTRAND=- GT:DP:AD ./.:25:13,12 ./.:27:18,9 0|1:26:20,6 -chr20 645244 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25049678;QSTRAND=- GT:DP:AD ./.:22:9,13 ./.:27:7,20 0|1:30:25,5 -chr20 645246 . A AT 60 . QNAME=HG002-S9-H1-000001F;QSTART=625167;QSTRAND=+ GT:DP:AD 1|0:41:19,22 ./.:36:22,14 ./.:26:6,20 -chr20 645378 . A AG 60 . QNAME=HG002-S9-H1-000001F;QSTART=625300;QSTRAND=+ GT:DP:AD 1|1:23:13,10 ./.:36:17,19 1|1:13:8,5 -chr20 645437 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=625359;QSTRAND=+ GT:DP:AD 1|0:26:12,14 ./.:18:8,10 1|0:12:7,5 -chr20 645520 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=625442;QSTRAND=+ GT:DP:AD 1|1:27:18,9 ./.:23:14,9 1|0:36:19,17 -chr20 645645 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=625567;QSTRAND=+ GT:DP:AD 1|0:15:9,6 ./.:31:20,11 ./.:33:18,15 -chr20 646133 . T TCTA 60 . QNAME=HG002-S9-H1-000001F;QSTART=626056;QSTRAND=+ GT:DP:AD 1|1:33:11,22 ./.:35:10,25 1|1:43:21,22 -chr20 646134 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=626059;QSTRAND=+ GT:DP:AD 1|1:25:13,12 ./.:18:9,9 1|1:22:15,7 -chr20 646331 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=626256;QSTRAND=+ GT:DP:AD 1|0:20:8,12 ./.:33:14,19 1|0:44:24,20 -chr20 646515 . C CAAAAAAAAAAAAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=626441;QSTRAND=+ GT:DP:AD 1|0:34:24,10 ./.:40:21,19 ./.:31:20,11 -chr20 646515 . C CAAAAAAAAAAAAAAAA 60 . QNAME=HG002-S9-H2-000001F;QSTART=601515;QSTRAND=+ GT:DP:AD 0|1:30:16,14 ./.:34:14,20 ./.:32:10,22 -chr20 646515 . C CA 60 . QNAME=cluster19_000000F;QSTART=25114773;QSTRAND=- GT:DP:AD ./.:33:21,12 1|0:16:6,10 ./.:35:18,17 -chr20 646515 . C CAAAAAAAAAAAAAAAAAA 60 . QNAME=cluster23_scaffold_3;QSTART=25064139;QSTRAND=- GT:DP:AD ./.:34:14,20 ./.:44:21,23 1|1:31:12,19 -chr20 646526 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=626468;QSTRAND=+ GT:DP:AD 1|0:30:11,19 ./.:31:6,25 1|0:21:10,11 -chr20 646614 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=601630;QSTRAND=+ GT:DP:AD 0|1:10:5,5 ./.:17:7,10 ./.:36:23,13 -chr20 646770 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25048130;QSTRAND=- GT:DP:AD ./.:29:6,23 ./.:36:18,18 0|1:25:9,16 diff --git a/repo_utils/test_files/answer_key/divided/multi_00000013.vcf b/repo_utils/test_files/answer_key/divided/multi_00000013.vcf deleted file mode 100644 index beb75be4..00000000 --- a/repo_utils/test_files/answer_key/divided/multi_00000013.vcf +++ /dev/null @@ -1,173 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##bcftools_mergeVersion=1.12+htslib-1.12 -##bcftools_mergeCommand=merge -O z -f x -m none input1.vcf.gz input2.vcf.gz input3.vcf.gz; Date=Mon Aug 16 18:05:13 2021 -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 648246 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=628188;QSTRAND=+ GT:DP:AD 1|1:32:24,8 ./.:18:10,8 1|0:27:14,13 -chr20 648569 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=628511;QSTRAND=+ GT:DP:AD 1|1:40:22,18 ./.:26:17,9 1|0:29:19,10 -chr20 649005 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=628947;QSTRAND=+ GT:DP:AD 1|0:28:12,16 ./.:31:8,23 1|0:25:17,8 -chr20 649182 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=604196;QSTRAND=+ GT:DP:AD 0|1:30:10,20 ./.:31:8,23 ./.:28:18,10 -chr20 649701 . CAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=629644;QSTRAND=+ GT:DP:AD 1|0:16:11,5 ./.:49:24,25 ./.:31:19,12 -chr20 649701 . CA C 60 . QNAME=cluster23_scaffold_3;QSTART=25060953;QSTRAND=- GT:DP:AD ./.:50:25,25 ./.:28:6,22 1|0:23:15,8 -chr20 649716 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=604730;QSTRAND=+ GT:DP:AD 0|1:38:23,15 ./.:13:8,5 ./.:45:24,21 -chr20 649983 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=629923;QSTRAND=+ GT:DP:AD 1|0:39:14,25 ./.:27:19,8 1|0:37:15,22 -chr20 650241 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25044659;QSTRAND=- GT:DP:AD ./.:28:16,12 ./.:19:9,10 0|1:30:15,15 -chr20 650254 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=605268;QSTRAND=+ GT:DP:AD 0|1:32:22,10 ./.:34:14,20 0|1:17:5,12 -chr20 650326 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=630266;QSTRAND=+ GT:DP:AD 1|1:17:8,9 ./.:25:10,15 1|1:29:16,13 -chr20 650473 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=630413;QSTRAND=+ GT:DP:AD 1|0:17:8,9 ./.:30:11,19 1|0:26:20,6 -chr20 650495 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25044405;QSTRAND=- GT:DP:AD ./.:41:18,23 ./.:22:9,13 0|1:48:24,24 -chr20 650525 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=605539;QSTRAND=+ GT:DP:AD 0|1:24:12,12 ./.:27:16,11 ./.:38:15,23 -chr20 650651 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=605665;QSTRAND=+ GT:DP:AD 0|1:19:8,11 ./.:20:7,13 ./.:30:21,9 -chr20 650723 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=605737;QSTRAND=+ GT:DP:AD 0|1:36:17,19 ./.:26:9,17 ./.:20:11,9 -chr20 650781 . C A 60 . QNAME=cluster19_000000F;QSTART=25110507;QSTRAND=- GT:DP:AD ./.:12:6,6 1|0:30:7,23 ./.:22:5,17 -chr20 651264 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=631204;QSTRAND=+ GT:DP:AD 1|1:33:12,21 ./.:27:21,6 1|1:32:15,17 -chr20 651683 . TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=631624;QSTRAND=+ GT:DP:AD 1|0:42:17,25 ./.:48:23,25 ./.:43:25,18 -chr20 651860 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=606874;QSTRAND=+ GT:DP:AD 0|1:23:13,10 ./.:38:19,19 0|1:41:18,23 -chr20 651923 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=25042977;QSTRAND=- GT:DP:AD ./.:31:25,6 ./.:11:6,5 0|1:38:14,24 -chr20 652315 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=632254;QSTRAND=+ GT:DP:AD 1|0:28:16,12 ./.:31:13,18 1|1:39:25,14 -chr20 652505 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=632444;QSTRAND=+ GT:DP:AD 1|0:38:14,24 ./.:32:21,11 1|1:29:23,6 -chr20 652904 . GACCTCCCTCCTCCGGCA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=632844;QSTRAND=+ GT:DP:AD 1|1:34:10,24 ./.:28:5,23 ./.:46:24,22 -chr20 653259 . CG C 60 . QNAME=HG002-S9-H1-000001F;QSTART=633182;QSTRAND=+ GT:DP:AD 1|0:32:19,13 ./.:33:23,10 ./.:28:13,15 -chr20 653265 . G GT 60 . QNAME=cluster23_scaffold_2;QSTART=25041634;QSTRAND=- GT:DP:AD ./.:41:18,23 ./.:26:10,16 0|1:41:21,20 -chr20 653266 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=25041633;QSTRAND=- GT:DP:AD ./.:30:8,22 ./.:21:10,11 0|1:22:8,14 -chr20 653324 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=633245;QSTRAND=+ GT:DP:AD 1|0:33:10,23 ./.:33:8,25 1|1:32:19,13 -chr20 653378 . C T 60 . QNAME=cluster19_000000F;QSTART=25107910;QSTRAND=- GT:DP:AD ./.:19:6,13 1|0:29:21,8 0|1:25:10,15 -chr20 653790 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=633711;QSTRAND=+ GT:DP:AD 1|1:37:13,24 ./.:19:12,7 1|0:22:12,10 -chr20 653820 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=633741;QSTRAND=+ GT:DP:AD 1|1:34:12,22 ./.:25:19,6 ./.:34:25,9 -chr20 653977 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=608974;QSTRAND=+ GT:DP:AD 0|1:19:14,5 ./.:13:5,8 ./.:24:17,7 -chr20 654666 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=609663;QSTRAND=+ GT:DP:AD 0|1:19:12,7 ./.:28:7,21 ./.:42:21,21 -chr20 655173 . C CAGAAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=635095;QSTRAND=+ GT:DP:AD 1|1:26:19,7 1|1:21:7,14 1|1:30:19,11 -chr20 656194 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=636124;QSTRAND=+ GT:DP:AD 1|0:38:22,16 ./.:37:19,18 ./.:22:15,7 -chr20 658219 . G A 60 . QNAME=cluster19_000000F;QSTART=25103060;QSTRAND=- GT:DP:AD ./.:29:16,13 1|0:42:23,19 1|0:43:23,20 -chr20 658277 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=613283;QSTRAND=+ GT:DP:AD 0|1:17:7,10 ./.:32:19,13 ./.:29:10,19 -chr20 659380 . T TGGAG 60 . QNAME=HG002-S9-H2-000001F;QSTART=614387;QSTRAND=+ GT:DP:AD 0|1:18:10,8 ./.:27:19,8 ./.:38:13,25 -chr20 659768 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=639698;QSTRAND=+ GT:DP:AD 1|0:40:21,19 ./.:45:20,25 ./.:15:10,5 -chr20 659929 . C T 60 . QNAME=cluster19_000000F;QSTART=25101350;QSTRAND=- GT:DP:AD ./.:19:7,12 1|0:36:17,19 1|0:26:16,10 -chr20 660098 . C A 60 . QNAME=cluster19_000000F;QSTART=620951;QSTRAND=+ GT:DP:AD ./.:47:23,24 0|1:12:6,6 ./.:21:11,10 -chr20 660145 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=640075;QSTRAND=+ GT:DP:AD 1|1:35:13,22 1|1:22:13,9 1|0:17:11,6 -chr20 660346 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=640276;QSTRAND=+ GT:DP:AD 1|0:35:15,20 0|1:34:10,24 ./.:20:14,6 -chr20 660450 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25050195;QSTRAND=- GT:DP:AD ./.:28:10,18 ./.:35:16,19 1|0:32:13,19 -chr20 660628 . C CAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=640559;QSTRAND=+ GT:DP:AD 1|0:44:20,24 ./.:23:7,16 ./.:21:12,9 -chr20 660628 . C CA 60 . QNAME=cluster19_000000F;QSTART=621482;QSTRAND=+ GT:DP:AD ./.:33:19,14 0|1:29:19,10 ./.:14:6,8 -chr20 660640 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=640572;QSTRAND=+ GT:DP:AD 1|1:33:25,8 0|1:21:14,7 ./.:28:20,8 -chr20 660909 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=615919;QSTRAND=+ GT:DP:AD 0|1:16:7,9 ./.:33:25,8 ./.:38:16,22 -chr20 661249 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=641181;QSTRAND=+ GT:DP:AD 1|1:29:11,18 1|1:15:9,6 1|0:49:25,24 -chr20 662494 . C CG 60 . QNAME=cluster23_scaffold_2;QSTART=25032395;QSTRAND=- GT:DP:AD ./.:36:18,18 ./.:32:14,18 0|1:31:10,21 -chr20 663033 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=642965;QSTRAND=+ GT:DP:AD 1|0:26:20,6 0|1:29:22,7 1|1:31:6,25 -chr20 663218 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25047427;QSTRAND=- GT:DP:AD ./.:29:20,9 ./.:29:24,5 1|0:42:24,18 -chr20 663275 . T C 60 . QNAME=cluster19_000000F;QSTART=624129;QSTRAND=+ GT:DP:AD ./.:28:6,22 0|1:43:18,25 0|1:36:16,20 -chr20 663449 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25047196;QSTRAND=- GT:DP:AD ./.:39:17,22 ./.:20:8,12 1|0:47:24,23 -chr20 663558 . A C 60 . QNAME=cluster19_000000F;QSTART=624412;QSTRAND=+ GT:DP:AD ./.:21:16,5 0|1:23:6,17 ./.:11:6,5 -chr20 664220 . G GC 60 . QNAME=cluster23_scaffold_2;QSTART=25030668;QSTRAND=- GT:DP:AD ./.:10:5,5 ./.:42:17,25 0|1:21:10,11 -chr20 665209 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=645141;QSTRAND=+ GT:DP:AD 1|1:35:21,14 1|1:26:13,13 1|1:32:8,24 -chr20 665270 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=645202;QSTRAND=+ GT:DP:AD 1|0:35:17,18 ./.:34:23,11 ./.:33:23,10 -chr20 665483 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=645415;QSTRAND=+ GT:DP:AD 1|1:12:7,5 1|1:22:12,10 0|1:26:14,12 -chr20 666690 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=646622;QSTRAND=+ GT:DP:AD 1|0:22:11,11 ./.:38:14,24 ./.:37:25,12 -chr20 667092 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=647024;QSTRAND=+ GT:DP:AD 1|1:31:15,16 1|1:27:7,20 1|1:29:23,6 -chr20 667181 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=647113;QSTRAND=+ GT:DP:AD 1|0:29:14,15 ./.:40:21,19 ./.:45:20,25 -chr20 667787 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=647719;QSTRAND=+ GT:DP:AD 1|0:24:19,5 ./.:29:9,20 ./.:18:7,11 -chr20 668165 . A ATTG 60 . QNAME=HG002-S9-H1-000001F;QSTART=648098;QSTRAND=+ GT:DP:AD 1|0:44:25,19 ./.:22:7,15 1|1:37:13,24 -chr20 668172 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=648107;QSTRAND=+ GT:DP:AD 1|0:27:12,15 ./.:24:12,12 1|1:30:19,11 -chr20 668176 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=648111;QSTRAND=+ GT:DP:AD 1|0:18:13,5 ./.:46:22,24 1|1:40:17,23 -chr20 668345 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=648280;QSTRAND=+ GT:DP:AD 1|0:42:17,25 ./.:25:5,20 1|1:27:22,5 -chr20 669291 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=649226;QSTRAND=+ GT:DP:AD 1|0:21:10,11 ./.:18:11,7 1|1:19:14,5 -chr20 670996 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=650931;QSTRAND=+ GT:DP:AD 1|0:37:20,17 ./.:37:22,15 1|1:30:19,11 -chr20 671453 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=651388;QSTRAND=+ GT:DP:AD 1|0:33:18,15 ./.:14:5,9 1|1:31:9,22 -chr20 671595 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=651530;QSTRAND=+ GT:DP:AD 1|0:34:22,12 ./.:36:17,19 1|1:25:9,16 -chr20 672290 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=652225;QSTRAND=+ GT:DP:AD 1|0:35:19,16 ./.:50:25,25 1|1:32:25,7 -chr20 672388 . CGT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=652324;QSTRAND=+ GT:DP:AD 1|0:37:15,22 ./.:39:21,18 1|1:42:18,24 -chr20 672422 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=652355;QSTRAND=+ GT:DP:AD 1|0:48:24,24 ./.:19:10,9 1|1:34:10,24 -chr20 672619 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=652552;QSTRAND=+ GT:DP:AD 1|0:31:19,12 ./.:27:7,20 1|1:38:18,20 -chr20 673008 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=652941;QSTRAND=+ GT:DP:AD 1|0:40:21,19 ./.:32:22,10 1|1:20:14,6 -chr20 673547 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=653480;QSTRAND=+ GT:DP:AD 1|0:24:9,15 ./.:37:20,17 1|1:42:22,20 -chr20 674399 . TCACA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=654333;QSTRAND=+ GT:DP:AD 1|0:28:16,12 ./.:22:11,11 0|1:30:10,20 -chr20 674399 . TCACACA T 60 . QNAME=cluster23_scaffold_3;QSTART=25036245;QSTRAND=- GT:DP:AD ./.:29:12,17 ./.:36:13,23 1|0:30:25,5 -chr20 674405 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=654334;QSTRAND=+ GT:DP:AD 1|0:26:12,14 ./.:40:18,22 0|1:28:14,14 -chr20 674407 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=654336;QSTRAND=+ GT:DP:AD 1|0:18:9,9 ./.:34:18,16 1|1:26:10,16 -chr20 674409 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=654338;QSTRAND=+ GT:DP:AD 1|0:21:14,7 ./.:42:18,24 1|1:39:18,21 -chr20 674411 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=654340;QSTRAND=+ GT:DP:AD 1|0:48:24,24 ./.:25:19,6 1|1:34:17,17 -chr20 674413 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=654342;QSTRAND=+ GT:DP:AD 1|0:22:12,10 ./.:24:17,7 1|0:38:14,24 -chr20 674688 . A AGT 60 . QNAME=HG002-S9-H2-000001F;QSTART=629699;QSTRAND=+ GT:DP:AD 0|1:37:20,17 1|1:37:23,14 ./.:36:11,25 -chr20 674713 . GTGTGTGTGTGTGTGTGTGTA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=654643;QSTRAND=+ GT:DP:AD 1|0:33:14,19 ./.:36:15,21 1|1:36:14,22 -chr20 675537 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25019374;QSTRAND=- GT:DP:AD ./.:29:16,13 ./.:20:6,14 0|1:21:7,14 -chr20 675763 . T TGGC 60 . QNAME=cluster19_000000F;QSTART=25085511;QSTRAND=- GT:DP:AD ./.:16:11,5 1|1:40:21,19 ./.:23:15,8 -chr20 676166 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=656075;QSTRAND=+ GT:DP:AD 1|0:19:10,9 ./.:39:17,22 1|1:31:23,8 -chr20 676254 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25034416;QSTRAND=- GT:DP:AD ./.:20:5,15 ./.:35:21,14 1|1:19:11,8 -chr20 677116 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25033554;QSTRAND=- GT:DP:AD ./.:16:10,6 ./.:34:12,22 1|1:34:13,21 -chr20 677219 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=632231;QSTRAND=+ GT:DP:AD 0|1:40:20,20 ./.:20:11,9 1|1:27:20,7 -chr20 677414 . TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=657324;QSTRAND=+ GT:DP:AD 1|0:34:16,18 0|1:21:16,5 1|1:26:19,7 -chr20 677414 . TAA T 60 . QNAME=HG002-S9-H2-000001F;QSTART=632427;QSTRAND=+ GT:DP:AD 0|1:49:25,24 ./.:29:8,21 ./.:28:16,12 -chr20 677478 . G A 60 . QNAME=cluster19_000000F;QSTART=638336;QSTRAND=+ GT:DP:AD ./.:33:17,16 0|1:27:6,21 ./.:16:8,8 -chr20 677582 . A AAATAATAAT 60 . QNAME=HG002-S9-H2-000001F;QSTART=632593;QSTRAND=+ GT:DP:AD 0|1:24:14,10 ./.:29:18,11 ./.:20:9,11 -chr20 677689 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25032982;QSTRAND=- GT:DP:AD ./.:14:9,5 ./.:26:7,19 1|1:35:25,10 -chr20 677734 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25032937;QSTRAND=- GT:DP:AD ./.:43:20,23 ./.:38:14,24 1|1:28:6,22 -chr20 677799 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=25032872;QSTRAND=- GT:DP:AD ./.:37:17,20 ./.:32:19,13 1|1:43:24,19 -chr20 677892 . AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=657801;QSTRAND=+ GT:DP:AD 1|0:24:17,7 ./.:23:12,11 ./.:14:5,9 -chr20 677892 . A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25032778;QSTRAND=- GT:DP:AD ./.:20:7,13 ./.:27:8,19 1|1:17:12,5 -chr20 678014 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25032656;QSTRAND=- GT:DP:AD ./.:28:11,17 ./.:45:25,20 1|1:29:14,15 -chr20 678015 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25032655;QSTRAND=- GT:DP:AD ./.:18:9,9 ./.:28:16,12 1|1:18:10,8 -chr20 678191 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=658098;QSTRAND=+ GT:DP:AD 1|1:34:15,19 1|1:47:22,25 1|1:27:11,16 -chr20 678230 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=633249;QSTRAND=+ GT:DP:AD 0|1:23:16,7 ./.:26:16,10 1|1:30:6,24 -chr20 678305 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=633324;QSTRAND=+ GT:DP:AD 0|1:32:8,24 ./.:18:8,10 ./.:18:6,12 -chr20 678433 . C G 60 . QNAME=cluster23_scaffold_3;QSTART=25032237;QSTRAND=- GT:DP:AD ./.:31:11,20 ./.:41:23,18 1|1:39:22,17 -chr20 678642 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25032028;QSTRAND=- GT:DP:AD ./.:38:13,25 ./.:37:24,13 1|1:23:17,6 -chr20 678678 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25031992;QSTRAND=- GT:DP:AD ./.:31:16,15 ./.:28:5,23 1|1:12:6,6 -chr20 678706 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25031964;QSTRAND=- GT:DP:AD ./.:24:18,6 ./.:34:15,19 1|1:19:7,12 -chr20 678778 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25031892;QSTRAND=- GT:DP:AD ./.:13:6,7 ./.:16:8,8 1|1:23:9,14 -chr20 678797 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25031873;QSTRAND=- GT:DP:AD ./.:30:22,8 ./.:44:20,24 1|1:31:13,18 -chr20 678839 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=633858;QSTRAND=+ GT:DP:AD 0|1:31:23,8 ./.:29:24,5 1|1:27:13,14 -chr20 679151 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25031519;QSTRAND=- GT:DP:AD ./.:41:20,21 ./.:37:20,17 1|1:48:24,24 -chr20 679482 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=634501;QSTRAND=+ GT:DP:AD 0|1:11:6,5 ./.:30:5,25 1|1:31:13,18 -chr20 679483 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=634502;QSTRAND=+ GT:DP:AD 0|1:15:5,10 ./.:34:9,25 1|1:34:14,20 -chr20 680009 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25030661;QSTRAND=- GT:DP:AD ./.:29:7,22 ./.:25:5,20 1|1:24:5,19 -chr20 680029 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25030641;QSTRAND=- GT:DP:AD ./.:33:8,25 ./.:33:10,23 1|1:21:5,16 -chr20 680047 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=635066;QSTRAND=+ GT:DP:AD 0|1:18:13,5 ./.:26:19,7 ./.:26:5,21 -chr20 680149 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25030521;QSTRAND=- GT:DP:AD ./.:34:12,22 ./.:45:21,24 1|1:28:8,20 -chr20 680216 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25014695;QSTRAND=- GT:DP:AD ./.:41:25,16 ./.:21:5,16 0|1:27:20,7 -chr20 680257 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25030413;QSTRAND=- GT:DP:AD ./.:28:16,12 ./.:34:20,14 1|1:44:20,24 -chr20 680491 . G GA 60 . QNAME=cluster23_scaffold_3;QSTART=25030178;QSTRAND=- GT:DP:AD ./.:38:15,23 ./.:45:24,21 1|1:24:5,19 -chr20 680625 . T A 60 . QNAME=cluster23_scaffold_3;QSTART=25030044;QSTRAND=- GT:DP:AD ./.:32:14,18 ./.:27:16,11 1|1:17:10,7 -chr20 680841 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25029828;QSTRAND=- GT:DP:AD ./.:37:24,13 ./.:25:11,14 1|1:44:24,20 -chr20 681789 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25028880;QSTRAND=- GT:DP:AD ./.:24:11,13 ./.:24:6,18 1|1:29:15,14 -chr20 681958 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25028711;QSTRAND=- GT:DP:AD ./.:25:16,9 ./.:26:15,11 1|1:27:15,12 -chr20 682463 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=637482;QSTRAND=+ GT:DP:AD 0|1:48:24,24 ./.:45:25,20 1|1:34:18,16 -chr20 682684 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25027985;QSTRAND=- GT:DP:AD ./.:15:10,5 ./.:25:16,9 1|1:26:6,20 -chr20 683486 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25027183;QSTRAND=- GT:DP:AD ./.:27:22,5 ./.:37:20,17 1|1:34:15,19 -chr20 683498 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=638517;QSTRAND=+ GT:DP:AD 0|1:38:19,19 0|1:43:18,25 1|1:16:6,10 -chr20 683582 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25027087;QSTRAND=- GT:DP:AD ./.:26:12,14 ./.:15:7,8 1|1:41:21,20 diff --git a/repo_utils/test_files/answer_key/divided/multi_00000014.vcf b/repo_utils/test_files/answer_key/divided/multi_00000014.vcf deleted file mode 100644 index 75d98ce9..00000000 --- a/repo_utils/test_files/answer_key/divided/multi_00000014.vcf +++ /dev/null @@ -1,156 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##bcftools_mergeVersion=1.12+htslib-1.12 -##bcftools_mergeCommand=merge -O z -f x -m none input1.vcf.gz input2.vcf.gz input3.vcf.gz; Date=Mon Aug 16 18:05:13 2021 -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 684734 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=639753;QSTRAND=+ GT:DP:AD 0|1:22:7,15 ./.:24:14,10 1|1:42:22,20 -chr20 684907 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=639926;QSTRAND=+ GT:DP:AD 0|1:22:13,9 ./.:33:20,13 ./.:24:13,11 -chr20 685089 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25025580;QSTRAND=- GT:DP:AD ./.:29:23,6 ./.:20:13,7 1|1:34:12,22 -chr20 685645 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25025024;QSTRAND=- GT:DP:AD ./.:32:8,24 ./.:26:18,8 1|1:22:13,9 -chr20 685696 . AAATAAT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=665604;QSTRAND=+ GT:DP:AD 1|0:10:5,5 1|0:13:8,5 ./.:26:6,20 -chr20 685696 . AAATAATAATAAT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=640716;QSTRAND=+ GT:DP:AD 0|1:36:19,17 0|1:25:17,8 ./.:15:6,9 -chr20 685696 . AAATAATAAT A 60 . QNAME=cluster23_scaffold_3;QSTART=25024973;QSTRAND=- GT:DP:AD ./.:21:16,5 ./.:28:8,20 1|1:41:25,16 -chr20 686394 . C T 60 . QNAME=cluster19_000000F;QSTART=25074886;QSTRAND=- GT:DP:AD ./.:29:9,20 1|0:36:22,14 ./.:35:19,16 -chr20 686439 . C CAAAAAAAAAAAAAA 60 . QNAME=HG002-S9-H2-000001F;QSTART=641447;QSTRAND=+ GT:DP:AD 0|1:25:10,15 ./.:31:18,13 ./.:37:18,19 -chr20 686455 . A AAAAAAAAAAAAAAAAAAAAAAAAAAT 60 . QNAME=cluster23_scaffold_3;QSTART=25024197;QSTRAND=-;SVTYPE=INS;SVLEN=26 GT:DP:AD ./.:33:22,11 ./.:29:7,22 1/0:41:25,16 -chr20 686455 . A AAAAAAAAAAAAAAAAAAAAAAAAAT 60 . QNAME=cluster23_scaffold_2;QSTART=25008439;QSTRAND=-;SVTYPE=INS;SVLEN=25 GT:DP:AD ./.:31:13,18 ./.:34:16,18 0/1:16:5,11 -chr20 686794 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=641815;QSTRAND=+ GT:DP:AD 0|1:34:23,11 0|1:29:22,7 1|1:34:11,23 -chr20 687380 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=642401;QSTRAND=+ GT:DP:AD 0|1:16:11,5 ./.:23:6,17 ./.:43:19,24 -chr20 687915 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=667816;QSTRAND=+ GT:DP:AD 1|1:14:7,7 1|1:41:20,21 ./.:27:13,14 -chr20 688002 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=667903;QSTRAND=+ GT:DP:AD 1|1:39:20,19 1|1:21:15,6 ./.:37:15,22 -chr20 688657 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25006237;QSTRAND=- GT:DP:AD ./.:16:11,5 ./.:22:7,15 0|1:37:16,21 -chr20 688666 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=25006228;QSTRAND=- GT:DP:AD ./.:33:12,21 ./.:33:24,9 0|1:42:19,23 -chr20 689007 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=668908;QSTRAND=+ GT:DP:AD 1|0:23:13,10 1|1:43:18,25 0|1:37:20,17 -chr20 689613 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=669514;QSTRAND=+ GT:DP:AD 1|0:34:17,17 1|1:45:22,23 0|1:22:7,15 -chr20 689671 . G A 60 . QNAME=cluster19_000000F;QSTART=650517;QSTRAND=+ GT:DP:AD ./.:24:16,8 0|1:31:22,9 ./.:26:10,16 -chr20 690105 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=670006;QSTRAND=+ GT:DP:AD 1|0:27:17,10 1|1:40:18,22 0|1:39:15,24 -chr20 690819 . AGTGT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=670721;QSTRAND=+ GT:DP:AD 1|0:17:9,8 1|1:41:23,18 0|1:25:18,7 -chr20 690819 . A AGT 60 . QNAME=HG002-S9-H2-000001F;QSTART=645841;QSTRAND=+ GT:DP:AD 0|1:23:7,16 ./.:20:13,7 1|0:30:14,16 -chr20 690853 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=670750;QSTRAND=+ GT:DP:AD 1|0:30:12,18 1|1:35:18,17 ./.:40:19,21 -chr20 690931 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25003967;QSTRAND=- GT:DP:AD ./.:47:25,22 ./.:29:6,23 0|1:26:10,16 -chr20 690947 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=670844;QSTRAND=+ GT:DP:AD 1|0:34:16,18 1|1:21:7,14 ./.:21:6,15 -chr20 691419 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25003479;QSTRAND=- GT:DP:AD ./.:31:7,24 ./.:27:7,20 0|1:42:25,17 -chr20 691923 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=671820;QSTRAND=+ GT:DP:AD 1|0:32:18,14 0|1:41:17,24 ./.:26:17,9 -chr20 692698 . C CTT 60 . QNAME=HG002-S9-H1-000001F;QSTART=672596;QSTRAND=+ GT:DP:AD 1|0:26:20,6 0|1:31:22,9 ./.:30:16,14 -chr20 692996 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=672895;QSTRAND=+ GT:DP:AD 1|0:23:15,8 1|1:23:8,15 0|1:33:24,9 -chr20 693104 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=673003;QSTRAND=+ GT:DP:AD 1|0:19:12,7 1|1:28:22,6 0|1:26:6,20 -chr20 693463 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=673362;QSTRAND=+ GT:DP:AD 1|0:18:11,7 1|1:41:22,19 0|1:30:21,9 -chr20 694203 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=649226;QSTRAND=+ GT:DP:AD 0|1:41:16,25 ./.:34:25,9 ./.:31:19,12 -chr20 694318 . A G 60 . QNAME=cluster19_000000F;QSTART=25066966;QSTRAND=- GT:DP:AD ./.:11:5,6 1|0:48:25,23 0|1:19:7,12 -chr20 694678 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=674577;QSTRAND=+ GT:DP:AD 1|0:37:20,17 0|1:43:19,24 ./.:41:19,22 -chr20 695001 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=674900;QSTRAND=+ GT:DP:AD 1|0:41:21,20 1|1:35:20,15 0|1:21:15,6 -chr20 695004 . G C 60 . QNAME=cluster19_000000F;QSTART=25066280;QSTRAND=- GT:DP:AD ./.:26:14,12 1|0:33:10,23 0|1:35:19,16 -chr20 695155 . G GTA 60 . QNAME=cluster19_000000F;QSTART=656000;QSTRAND=+ GT:DP:AD ./.:37:23,14 0|1:43:24,19 ./.:47:24,23 -chr20 695259 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=675158;QSTRAND=+ GT:DP:AD 1|0:18:12,6 1|1:37:17,20 0|1:35:10,25 -chr20 695798 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=675697;QSTRAND=+ GT:DP:AD 1|0:13:5,8 0|1:24:19,5 ./.:42:23,19 -chr20 695931 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=675830;QSTRAND=+ GT:DP:AD 1|0:23:16,7 1|1:27:14,13 0|1:35:11,24 -chr20 696160 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=676059;QSTRAND=+ GT:DP:AD 1|0:35:10,25 0|1:29:13,16 ./.:16:6,10 -chr20 697221 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=677120;QSTRAND=+ GT:DP:AD 1|0:29:20,9 0|1:32:17,15 ./.:42:20,22 -chr20 697409 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=677308;QSTRAND=+ GT:DP:AD 1|0:45:24,21 0|1:19:12,7 ./.:18:13,5 -chr20 697409 . G T 60 . QNAME=cluster19_000000F;QSTART=25063875;QSTRAND=- GT:DP:AD ./.:21:6,15 1|0:25:12,13 0|1:41:19,22 -chr20 697934 . C G 60 . QNAME=cluster19_000000F;QSTART=25063350;QSTRAND=- GT:DP:AD ./.:26:21,5 1|0:22:13,9 0|1:26:10,16 -chr20 698083 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=677982;QSTRAND=+ GT:DP:AD 1|0:15:5,10 ./.:30:5,25 ./.:39:18,21 -chr20 698123 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=678022;QSTRAND=+ GT:DP:AD 1|0:20:9,11 1|1:27:8,19 0|1:49:25,24 -chr20 698533 . C T 60 . QNAME=cluster19_000000F;QSTART=659379;QSTRAND=+ GT:DP:AD ./.:35:21,14 0|1:22:13,9 ./.:19:14,5 -chr20 698627 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=653650;QSTRAND=+ GT:DP:AD 0|1:33:11,22 1|0:33:24,9 0|1:32:8,24 -chr20 698723 . G A 60 . QNAME=cluster19_000000F;QSTART=25062561;QSTRAND=- GT:DP:AD ./.:46:25,21 1|0:28:21,7 0|1:28:16,12 -chr20 699085 . C T 60 . QNAME=cluster19_000000F;QSTART=25062199;QSTRAND=- GT:DP:AD ./.:41:22,19 1|0:30:25,5 0|1:38:21,17 -chr20 699214 . CAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=679114;QSTRAND=+ GT:DP:AD 1|0:37:13,24 ./.:28:7,21 ./.:38:21,17 -chr20 699214 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=654238;QSTRAND=+ GT:DP:AD 0|1:27:12,15 ./.:45:21,24 ./.:35:20,15 -chr20 699214 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25011435;QSTRAND=- GT:DP:AD ./.:30:25,5 ./.:30:12,18 1|0:19:12,7 -chr20 700520 . C T 60 . QNAME=cluster19_000000F;QSTART=25060764;QSTRAND=- GT:DP:AD ./.:24:10,14 1|0:31:8,23 0|1:23:6,17 -chr20 700649 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=655672;QSTRAND=+ GT:DP:AD 0|1:14:7,7 ./.:38:20,18 ./.:30:10,20 -chr20 700649 . C CT 60 . QNAME=cluster19_000000F;QSTART=25060634;QSTRAND=- GT:DP:AD ./.:23:15,8 1|0:29:14,15 0|1:34:10,24 -chr20 701307 . A G 60 . QNAME=cluster19_000000F;QSTART=25059976;QSTRAND=- GT:DP:AD ./.:24:18,6 1|0:20:10,10 0|1:16:6,10 -chr20 701558 . C T 60 . QNAME=cluster19_000000F;QSTART=25059725;QSTRAND=- GT:DP:AD ./.:48:23,25 1|0:26:18,8 0|1:17:12,5 -chr20 702627 . G A 60 . QNAME=cluster19_000000F;QSTART=25058656;QSTRAND=- GT:DP:AD ./.:45:23,22 1|0:42:22,20 0|1:46:23,23 -chr20 702901 . T C 60 . QNAME=cluster19_000000F;QSTART=25058382;QSTRAND=- GT:DP:AD ./.:17:8,9 1|0:28:9,19 0|1:19:6,13 -chr20 702972 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=682868;QSTRAND=+ GT:DP:AD 1|0:33:10,23 0|1:30:7,23 ./.:20:12,8 -chr20 704472 . A G 60 . QNAME=cluster19_000000F;QSTART=25056811;QSTRAND=- GT:DP:AD ./.:39:17,22 1|0:19:10,9 0|1:24:17,7 -chr20 704662 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=659683;QSTRAND=+ GT:DP:AD 0|1:26:18,8 ./.:35:23,12 ./.:27:10,17 -chr20 704704 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=684600;QSTRAND=+ GT:DP:AD 1|0:32:10,22 1|1:27:9,18 1|0:34:14,20 -chr20 705070 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=684966;QSTRAND=+ GT:DP:AD 1|0:20:12,8 1|1:33:15,18 ./.:39:22,17 -chr20 705212 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=660233;QSTRAND=+ GT:DP:AD 0|1:23:12,11 ./.:39:17,22 1|0:27:9,18 -chr20 705650 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=685546;QSTRAND=+ GT:DP:AD 1|0:40:24,16 1|0:41:21,20 ./.:49:24,25 -chr20 706757 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=661778;QSTRAND=+ GT:DP:AD 0|1:22:13,9 ./.:45:25,20 1|0:20:10,10 -chr20 707000 . T TAA 60 . QNAME=cluster23_scaffold_2;QSTART=24987895;QSTRAND=- GT:DP:AD ./.:44:24,20 ./.:33:8,25 0|1:21:8,13 -chr20 707128 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=687024;QSTRAND=+ GT:DP:AD 1|1:32:10,22 1|0:40:16,24 1|1:19:5,14 -chr20 707704 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=662725;QSTRAND=+ GT:DP:AD 0|1:33:8,25 ./.:24:12,12 1|0:26:21,5 -chr20 708199 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=688095;QSTRAND=+ GT:DP:AD 1|0:29:22,7 1|0:26:11,15 0|1:48:24,24 -chr20 708250 . C CTTTTGT 60 . QNAME=cluster19_000000F;QSTART=669097;QSTRAND=+ GT:DP:AD ./.:38:18,20 0|1:40:21,19 ./.:31:21,10 -chr20 708422 . AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=688319;QSTRAND=+ GT:DP:AD 1|0:28:16,12 1|0:27:7,20 ./.:30:6,24 -chr20 708422 . A ATT 60 . QNAME=HG002-S9-H2-000001F;QSTART=663444;QSTRAND=+ GT:DP:AD 0|1:31:14,17 ./.:17:11,6 1|0:18:11,7 -chr20 708747 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=688642;QSTRAND=+ GT:DP:AD 1|0:37:12,25 1|0:21:10,11 ./.:23:13,10 -chr20 708784 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=688679;QSTRAND=+ GT:DP:AD 1|0:37:24,13 1|0:13:5,8 ./.:22:16,6 -chr20 709051 . TC T 60 . QNAME=cluster23_scaffold_2;QSTART=24985844;QSTRAND=- GT:DP:AD ./.:13:5,8 ./.:19:7,12 0|1:21:8,13 -chr20 709759 . AGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCC A 60 . QNAME=HG002-S9-H2-000001F;QSTART=664783;QSTRAND=+;SVTYPE=DEL;SVLEN=-93 GT:DP:AD 0/1:16:7,9 1/0:26:21,5 1/1:41:23,18 -chr20 709830 . G GACACTGCTCGGTCCTCCGCTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCGCTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGAACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGA 60 . QNAME=HG002-S9-H1-000001F;QSTART=689726;QSTRAND=+;SVTYPE=INS;SVLEN=465 GT:DP:AD 1/0:41:16,25 ./.:30:18,12 ./.:21:10,11 -chr20 709916 . T TG 60 . QNAME=cluster19_000000F;QSTART=670769;QSTRAND=+ GT:DP:AD ./.:37:21,16 0|1:33:16,17 ./.:18:10,8 -chr20 710119 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24984870;QSTRAND=- GT:DP:AD ./.:45:23,22 ./.:20:10,10 0|1:21:12,9 -chr20 710584 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24984405;QSTRAND=- GT:DP:AD ./.:42:24,18 ./.:15:10,5 0|1:18:6,12 -chr20 710789 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=691149;QSTRAND=+ GT:DP:AD 1|0:39:24,15 1|1:26:15,11 1|1:30:10,20 -chr20 710948 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=691308;QSTRAND=+ GT:DP:AD 1|0:29:13,16 0|1:44:25,19 1|0:15:5,10 -chr20 711068 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24983921;QSTRAND=- GT:DP:AD ./.:37:17,20 ./.:46:22,24 0|1:41:18,23 -chr20 711120 . G GGT 60 . QNAME=HG002-S9-H2-000001F;QSTART=666051;QSTRAND=+ GT:DP:AD 0|1:26:10,16 ./.:32:11,21 ./.:26:18,8 -chr20 711120 . G GGTGT 60 . QNAME=cluster23_scaffold_2;QSTART=24983865;QSTRAND=- GT:DP:AD ./.:41:16,25 ./.:35:19,16 0|1:33:9,24 -chr20 711177 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=691537;QSTRAND=+ GT:DP:AD 1|0:41:21,20 1|1:38:19,19 1|1:28:19,9 -chr20 711562 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=691922;QSTRAND=+ GT:DP:AD 1|1:27:12,15 1|1:22:13,9 1|0:34:12,22 -chr20 711631 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=691991;QSTRAND=+ GT:DP:AD 1|1:27:9,18 1|1:20:11,9 1|1:28:19,9 -chr20 712402 . GT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=692763;QSTRAND=+ GT:DP:AD 1|1:22:15,7 ./.:16:8,8 ./.:21:15,6 -chr20 712536 . C T 60 . QNAME=cluster19_000000F;QSTART=25048841;QSTRAND=- GT:DP:AD ./.:37:14,23 1|0:36:19,17 ./.:42:20,22 -chr20 712711 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=693071;QSTRAND=+ GT:DP:AD 1|0:33:13,20 ./.:15:10,5 ./.:22:8,14 -chr20 712711 . C CT 60 . QNAME=cluster19_000000F;QSTART=25048665;QSTRAND=- GT:DP:AD ./.:40:25,15 1|0:45:20,25 ./.:32:7,25 -chr20 712944 . T C 60 . QNAME=cluster19_000000F;QSTART=25048432;QSTRAND=- GT:DP:AD ./.:41:21,20 1|0:35:22,13 ./.:26:6,20 -chr20 712978 . G A 60 . QNAME=cluster19_000000F;QSTART=25048398;QSTRAND=- GT:DP:AD ./.:29:7,22 1|0:32:7,25 ./.:18:13,5 -chr20 713101 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=693459;QSTRAND=+ GT:DP:AD 1|1:41:24,17 ./.:32:16,16 ./.:27:16,11 -chr20 713206 . T A 60 . QNAME=cluster19_000000F;QSTART=25048170;QSTRAND=- GT:DP:AD ./.:14:7,7 1|0:35:14,21 ./.:24:12,12 -chr20 713207 . T A 60 . QNAME=cluster19_000000F;QSTART=25048169;QSTRAND=- GT:DP:AD ./.:28:20,8 1|0:20:14,6 ./.:39:19,20 -chr20 713208 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=693566;QSTRAND=+ GT:DP:AD 1|1:21:11,10 1|0:30:21,9 ./.:31:17,14 -chr20 713417 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=693775;QSTRAND=+ GT:DP:AD 1|1:14:6,8 1|1:16:10,6 1|0:26:11,15 -chr20 713874 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24981111;QSTRAND=- GT:DP:AD ./.:24:15,9 ./.:33:17,16 0|1:16:9,7 -chr20 713943 . T C 60 . QNAME=cluster19_000000F;QSTART=25047433;QSTRAND=- GT:DP:AD ./.:23:7,16 1|0:34:19,15 ./.:25:7,18 -chr20 713965 . G A 60 . QNAME=cluster19_000000F;QSTART=25047411;QSTRAND=- GT:DP:AD ./.:19:5,14 1|0:27:16,11 ./.:35:13,22 -chr20 714250 . T C 60 . QNAME=cluster19_000000F;QSTART=25047126;QSTRAND=- GT:DP:AD ./.:36:25,11 1|0:34:11,23 ./.:29:8,21 -chr20 714816 . A G 60 . QNAME=cluster19_000000F;QSTART=675669;QSTRAND=+ GT:DP:AD ./.:24:15,9 0|1:26:5,21 1|0:28:22,6 -chr20 715026 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=695384;QSTRAND=+ GT:DP:AD 1|1:25:17,8 0|1:45:23,22 1|0:39:20,19 -chr20 715559 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=695917;QSTRAND=+ GT:DP:AD 1|1:33:10,23 1|1:42:18,24 1|0:27:14,13 -chr20 715567 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=695925;QSTRAND=+ GT:DP:AD 1|1:29:23,6 1|1:37:18,19 1|0:23:15,8 -chr20 715736 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24979249;QSTRAND=- GT:DP:AD ./.:46:21,25 ./.:27:16,11 0|1:16:11,5 -chr20 715825 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=24994915;QSTRAND=- GT:DP:AD ./.:41:20,21 ./.:49:24,25 1|0:15:5,10 -chr20 715836 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=696194;QSTRAND=+ GT:DP:AD 1|1:36:20,16 1|0:25:8,17 1|0:34:24,10 diff --git a/repo_utils/test_files/answer_key/divided/multi_00000015.vcf b/repo_utils/test_files/answer_key/divided/multi_00000015.vcf deleted file mode 100644 index 1209e506..00000000 --- a/repo_utils/test_files/answer_key/divided/multi_00000015.vcf +++ /dev/null @@ -1,169 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##bcftools_mergeVersion=1.12+htslib-1.12 -##bcftools_mergeCommand=merge -O z -f x -m none input1.vcf.gz input2.vcf.gz input3.vcf.gz; Date=Mon Aug 16 18:05:13 2021 -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 716956 . T C 60 . QNAME=cluster19_000000F;QSTART=677809;QSTRAND=+ GT:DP:AD ./.:34:15,19 0|1:30:6,24 1|0:24:8,16 -chr20 717158 . ATT A 60 . QNAME=cluster19_000000F;QSTART=678012;QSTRAND=+ GT:DP:AD ./.:36:18,18 0|1:30:23,7 ./.:47:24,23 -chr20 717272 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=697630;QSTRAND=+ GT:DP:AD 1|0:28:18,10 ./.:38:20,18 0|1:19:6,13 -chr20 717541 . C T 60 . QNAME=cluster19_000000F;QSTART=678392;QSTRAND=+ GT:DP:AD ./.:19:6,13 0|1:17:9,8 ./.:32:9,23 -chr20 717932 . G C 60 . QNAME=cluster19_000000F;QSTART=25043444;QSTRAND=- GT:DP:AD ./.:34:11,23 1|0:37:16,21 ./.:22:8,14 -chr20 718343 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=698701;QSTRAND=+ GT:DP:AD 1|0:30:16,14 ./.:37:23,14 0|1:18:6,12 -chr20 718374 . C G 60 . QNAME=cluster19_000000F;QSTART=25043002;QSTRAND=- GT:DP:AD ./.:23:12,11 1|1:28:14,14 ./.:29:16,13 -chr20 718391 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=698749;QSTRAND=+ GT:DP:AD 1|0:29:21,8 1|1:37:25,12 0|1:44:24,20 -chr20 718820 . T A 60 . QNAME=cluster19_000000F;QSTART=679671;QSTRAND=+ GT:DP:AD ./.:26:7,19 0|1:28:9,19 ./.:39:21,18 -chr20 719274 . C T 60 . QNAME=cluster19_000000F;QSTART=680125;QSTRAND=+ GT:DP:AD ./.:26:15,11 0|1:22:8,14 ./.:37:13,24 -chr20 719464 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=699822;QSTRAND=+ GT:DP:AD 1|0:24:13,11 1|1:36:15,21 1|1:36:20,16 -chr20 719532 . T C 60 . QNAME=cluster19_000000F;QSTART=25041844;QSTRAND=- GT:DP:AD ./.:19:11,8 1|0:28:7,21 ./.:37:20,17 -chr20 720367 . C G 60 . QNAME=cluster19_000000F;QSTART=681218;QSTRAND=+ GT:DP:AD ./.:23:11,12 0|1:18:8,10 ./.:41:23,18 -chr20 720501 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=700859;QSTRAND=+ GT:DP:AD 1|0:39:21,18 1|1:35:17,18 0|1:31:16,15 -chr20 720677 . C G 60 . QNAME=cluster19_000000F;QSTART=25040699;QSTRAND=- GT:DP:AD ./.:24:14,10 1|1:32:11,21 ./.:44:20,24 -chr20 720868 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=701226;QSTRAND=+ GT:DP:AD 1|0:35:16,19 0|1:29:6,23 0|1:26:19,7 -chr20 720953 . A G 60 . QNAME=cluster19_000000F;QSTART=25040423;QSTRAND=- GT:DP:AD ./.:35:24,11 1|1:27:13,14 ./.:37:15,22 -chr20 720987 . T C 60 . QNAME=cluster19_000000F;QSTART=25040389;QSTRAND=- GT:DP:AD ./.:34:10,24 1|1:28:11,17 ./.:41:25,16 -chr20 721070 . T C 60 . QNAME=cluster19_000000F;QSTART=25040306;QSTRAND=- GT:DP:AD ./.:28:7,21 1|0:39:22,17 ./.:44:19,25 -chr20 721315 . A T 60 . QNAME=cluster19_000000F;QSTART=25040061;QSTRAND=- GT:DP:AD ./.:36:11,25 1|1:16:10,6 ./.:26:16,10 -chr20 721448 . C T 60 . QNAME=cluster19_000000F;QSTART=25039928;QSTRAND=- GT:DP:AD ./.:33:25,8 1|1:36:17,19 ./.:21:15,6 -chr20 721653 . G A 60 . QNAME=cluster19_000000F;QSTART=25039723;QSTRAND=- GT:DP:AD ./.:22:13,9 1|1:28:12,16 ./.:31:19,12 -chr20 721675 . G C 60 . QNAME=cluster19_000000F;QSTART=25039701;QSTRAND=- GT:DP:AD ./.:33:8,25 1|1:23:10,13 ./.:14:7,7 -chr20 721926 . C T 60 . QNAME=cluster19_000000F;QSTART=25039450;QSTRAND=- GT:DP:AD ./.:35:21,14 1|1:30:15,15 ./.:34:10,24 -chr20 722151 . T C 60 . QNAME=cluster19_000000F;QSTART=683002;QSTRAND=+ GT:DP:AD ./.:25:11,14 0|1:42:23,19 ./.:30:12,18 -chr20 722203 . T C 60 . QNAME=cluster19_000000F;QSTART=25039173;QSTRAND=- GT:DP:AD ./.:21:6,15 1|1:25:7,18 ./.:18:9,9 -chr20 722204 . G A 60 . QNAME=cluster19_000000F;QSTART=683055;QSTRAND=+ GT:DP:AD ./.:30:22,8 0|1:22:9,13 ./.:33:8,25 -chr20 722214 . G T 60 . QNAME=cluster19_000000F;QSTART=25039162;QSTRAND=- GT:DP:AD ./.:22:9,13 1|1:28:7,21 ./.:22:5,17 -chr20 722255 . T C 60 . QNAME=cluster19_000000F;QSTART=25039121;QSTRAND=- GT:DP:AD ./.:41:18,23 1|1:33:14,19 ./.:27:17,10 -chr20 722277 . C T 60 . QNAME=cluster19_000000F;QSTART=25039099;QSTRAND=- GT:DP:AD ./.:41:20,21 1|1:36:24,12 ./.:17:9,8 -chr20 722412 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=702770;QSTRAND=+ GT:DP:AD 1|0:23:6,17 ./.:28:22,6 0|1:21:6,15 -chr20 723134 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=703492;QSTRAND=+ GT:DP:AD 1|0:22:8,14 ./.:21:16,5 0|1:33:25,8 -chr20 723311 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=703669;QSTRAND=+ GT:DP:AD 1|1:33:24,9 1|1:36:18,18 1|1:20:10,10 -chr20 723429 . CTCT C 60 . QNAME=cluster19_000000F;QSTART=684281;QSTRAND=+ GT:DP:AD ./.:41:21,20 0|1:33:17,16 ./.:26:10,16 -chr20 723467 . C CTTTCT 60 . QNAME=cluster19_000000F;QSTART=684316;QSTRAND=+ GT:DP:AD ./.:23:16,7 0|1:33:20,13 ./.:35:11,24 -chr20 723709 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=704067;QSTRAND=+ GT:DP:AD 1|0:32:22,10 0|1:23:6,17 0|1:17:7,10 -chr20 723727 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=704085;QSTRAND=+ GT:DP:AD 1|0:27:18,9 ./.:31:10,21 0|1:19:10,9 -chr20 723799 . G A 60 . QNAME=cluster19_000000F;QSTART=25037577;QSTRAND=- GT:DP:AD ./.:20:12,8 1|0:41:20,21 ./.:17:12,5 -chr20 723808 . G A 60 . QNAME=cluster19_000000F;QSTART=684661;QSTRAND=+ GT:DP:AD ./.:44:22,22 0|1:22:13,9 ./.:36:19,17 -chr20 723875 . G A 60 . QNAME=cluster19_000000F;QSTART=684728;QSTRAND=+ GT:DP:AD ./.:26:13,13 0|1:38:20,18 ./.:42:17,25 -chr20 723915 . A G 60 . QNAME=cluster19_000000F;QSTART=25037461;QSTRAND=- GT:DP:AD ./.:19:13,6 1|0:35:25,10 ./.:28:20,8 -chr20 724055 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=704413;QSTRAND=+ GT:DP:AD 1|0:22:6,16 0|1:13:8,5 0|1:27:18,9 -chr20 724660 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=705019;QSTRAND=+ GT:DP:AD 1|0:40:15,25 ./.:31:17,14 0|1:19:12,7 -chr20 725763 . T G 60 . QNAME=cluster19_000000F;QSTART=686616;QSTRAND=+ GT:DP:AD ./.:34:9,25 0|1:31:18,13 ./.:14:7,7 -chr20 726010 . CAAAAAAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=706370;QSTRAND=+ GT:DP:AD 1|0:33:15,18 ./.:36:17,19 0|1:33:8,25 -chr20 726010 . C CA 60 . QNAME=HG002-S9-H2-000001F;QSTART=680942;QSTRAND=+ GT:DP:AD 0|1:12:6,6 1|0:33:12,21 ./.:29:13,16 -chr20 726010 . C CAAAAAAA 60 . QNAME=cluster19_000000F;QSTART=686864;QSTRAND=+ GT:DP:AD ./.:41:18,23 0|1:23:16,7 ./.:29:6,23 -chr20 726075 . G A 60 . QNAME=cluster19_000000F;QSTART=686935;QSTRAND=+ GT:DP:AD ./.:34:16,18 0|1:33:20,13 ./.:19:11,8 -chr20 726115 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=706466;QSTRAND=+ GT:DP:AD 1|0:31:23,8 0|1:27:16,11 0|1:44:20,24 -chr20 726166 . T C 60 . QNAME=cluster19_000000F;QSTART=687026;QSTRAND=+ GT:DP:AD ./.:32:11,21 0|1:28:6,22 ./.:26:18,8 -chr20 726847 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=707198;QSTRAND=+ GT:DP:AD 1|0:25:5,20 ./.:30:5,25 0|1:34:20,14 -chr20 727050 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=707401;QSTRAND=+ GT:DP:AD 1|0:41:19,22 ./.:18:7,11 0|1:18:11,7 -chr20 727183 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=707534;QSTRAND=+ GT:DP:AD 1|0:36:11,25 ./.:48:24,24 0|1:30:14,16 -chr20 727236 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=707587;QSTRAND=+ GT:DP:AD 1|0:36:23,13 ./.:39:19,20 0|1:34:18,16 -chr20 727293 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=24983447;QSTRAND=- GT:DP:AD ./.:22:13,9 ./.:37:15,22 1|0:35:19,16 -chr20 727295 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=707646;QSTRAND=+ GT:DP:AD 1|0:30:7,23 ./.:37:17,20 ./.:20:15,5 -chr20 727508 . TATATCTAATATATATAATATCTAATATATATA T 60 . QNAME=cluster19_000000F;QSTART=25033867;QSTRAND=-;SVTYPE=DEL;SVLEN=-32 GT:DP:AD ./.:15:10,5 1/0:29:9,20 ./.:30:15,15 -chr20 727508 . TATATCTAATATATATAATATCTAATATATATAATATCTAATATATATA T 60 . QNAME=cluster19_000000F;QSTART=688369;QSTRAND=+;SVTYPE=DEL;SVLEN=-48 GT:DP:AD ./.:38:18,20 0/1:34:22,12 ./.:28:13,15 -chr20 727556 . AATATCTAATATATATAATATCTAATATATATAAT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=682489;QSTRAND=+;SVTYPE=DEL;SVLEN=-34 GT:DP:AD 0/1:26:8,18 ./.:41:17,24 1/0:30:17,13 -chr20 727600 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=24983174;QSTRAND=- GT:DP:AD ./.:32:21,11 ./.:42:25,17 1|0:33:12,21 -chr20 727602 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=24983172;QSTRAND=- GT:DP:AD ./.:42:23,19 ./.:29:22,7 1|0:32:13,19 -chr20 727613 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=707964;QSTRAND=+ GT:DP:AD 1|0:35:21,14 1|1:33:25,8 0|1:14:7,7 -chr20 727615 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=707966;QSTRAND=+ GT:DP:AD 1|0:35:11,24 1|1:25:16,9 0|1:38:24,14 -chr20 727615 . C CGA 60 . QNAME=HG002-S9-H2-000001F;QSTART=682514;QSTRAND=+ GT:DP:AD 0|1:35:11,24 ./.:38:16,22 ./.:19:7,12 -chr20 727774 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=682674;QSTRAND=+ GT:DP:AD 0|1:13:7,6 1|1:45:21,24 ./.:28:11,17 -chr20 727786 . ATT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=682687;QSTRAND=+ GT:DP:AD 0|1:28:6,22 1|0:37:16,21 ./.:23:15,8 -chr20 727786 . AT A 60 . QNAME=cluster23_scaffold_3;QSTART=24982988;QSTRAND=- GT:DP:AD ./.:19:13,6 ./.:30:10,20 1|0:14:7,7 -chr20 727926 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=708277;QSTRAND=+ GT:DP:AD 1|0:17:12,5 1|0:35:11,24 ./.:36:15,21 -chr20 727962 . GGC G 60 . QNAME=cluster23_scaffold_3;QSTART=24982813;QSTRAND=- GT:DP:AD ./.:41:24,17 ./.:26:18,8 1|0:42:25,17 -chr20 728062 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=708413;QSTRAND=+ GT:DP:AD 1|1:37:25,12 1|1:37:21,16 0|1:29:10,19 -chr20 728326 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=708677;QSTRAND=+ GT:DP:AD 1|0:26:10,16 0|1:24:13,11 ./.:34:25,9 -chr20 728330 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=708681;QSTRAND=+ GT:DP:AD 1|0:37:13,24 0|1:35:18,17 ./.:36:11,25 -chr20 728371 . G A 60 . QNAME=cluster19_000000F;QSTART=689183;QSTRAND=+ GT:DP:AD ./.:33:16,17 0|1:13:8,5 ./.:20:7,13 -chr20 728488 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=683386;QSTRAND=+ GT:DP:AD 0|1:41:17,24 1|0:33:20,13 0|1:31:19,12 -chr20 728626 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=24966366;QSTRAND=- GT:DP:AD ./.:26:21,5 ./.:31:12,19 0|1:38:17,21 -chr20 728679 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=709030;QSTRAND=+ GT:DP:AD 1|1:37:13,24 1|0:18:8,10 1|1:45:24,21 -chr20 728689 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=709040;QSTRAND=+ GT:DP:AD 1|1:34:16,18 1|0:34:19,15 0|1:20:15,5 -chr20 728722 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=709073;QSTRAND=+ GT:DP:AD 1|1:37:19,18 1|0:47:24,23 1|1:20:9,11 -chr20 728924 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=709275;QSTRAND=+ GT:DP:AD 1|1:33:19,14 1|0:32:12,20 0|1:39:22,17 -chr20 729045 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=709396;QSTRAND=+ GT:DP:AD 1|1:18:11,7 1|0:42:23,19 1|1:39:21,18 -chr20 729328 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=709679;QSTRAND=+ GT:DP:AD 1|1:34:14,20 1|0:27:8,19 1|1:15:8,7 -chr20 729751 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=684649;QSTRAND=+ GT:DP:AD 0|1:32:10,22 1|0:38:21,17 0|1:44:24,20 -chr20 729893 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=684791;QSTRAND=+ GT:DP:AD 0|1:43:20,23 1|0:25:11,14 0|1:40:24,16 -chr20 730190 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=710541;QSTRAND=+ GT:DP:AD 1|0:27:14,13 ./.:47:23,24 1|0:50:25,25 -chr20 730755 . A AG 60 . QNAME=HG002-S9-H1-000001F;QSTART=711107;QSTRAND=+ GT:DP:AD 1|1:23:15,8 1|1:40:17,23 1|1:23:12,11 -chr20 731406 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=686305;QSTRAND=+ GT:DP:AD 0|1:18:6,12 1|0:33:20,13 0|1:30:18,12 -chr20 731541 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=711893;QSTRAND=+ GT:DP:AD 1|1:41:21,20 1|0:31:6,25 1|1:35:19,16 -chr20 732158 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=687057;QSTRAND=+ GT:DP:AD 0|1:26:8,18 1|0:30:12,18 0|1:16:10,6 -chr20 732263 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=687162;QSTRAND=+ GT:DP:AD 0|1:39:21,18 1|0:27:10,17 0|1:37:15,22 -chr20 732533 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=712885;QSTRAND=+ GT:DP:AD 1|1:38:16,22 1|0:32:20,12 1|1:33:13,20 -chr20 733181 . T TTATG 60 . QNAME=HG002-S9-H1-000001F;QSTART=713534;QSTRAND=+ GT:DP:AD 1|0:32:13,19 ./.:40:23,17 ./.:30:25,5 -chr20 733364 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=713720;QSTRAND=+ GT:DP:AD 1|1:34:25,9 1|0:28:5,23 1|1:34:16,18 -chr20 733492 . TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=713849;QSTRAND=+ GT:DP:AD 1|1:27:20,7 1|1:16:8,8 1|1:31:11,20 -chr20 733573 . AAAAAC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=713929;QSTRAND=+ GT:DP:AD 1|0:42:24,18 ./.:17:7,10 ./.:23:18,5 -chr20 733573 . A AAAAACAAAAC 60 . QNAME=cluster23_scaffold_3;QSTART=24977194;QSTRAND=- GT:DP:AD ./.:25:12,13 ./.:47:24,23 1|0:15:8,7 -chr20 733617 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=713967;QSTRAND=+ GT:DP:AD 1|0:22:5,17 ./.:22:6,16 1|0:32:7,25 -chr20 733672 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=714022;QSTRAND=+ GT:DP:AD 1|0:15:5,10 ./.:26:12,14 ./.:33:24,9 -chr20 733818 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=714168;QSTRAND=+ GT:DP:AD 1|1:23:6,17 1|1:29:18,11 1|1:29:20,9 -chr20 733903 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24976864;QSTRAND=- GT:DP:AD ./.:44:24,20 ./.:22:13,9 1|0:27:7,20 -chr20 734373 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=714723;QSTRAND=+ GT:DP:AD 1|0:21:6,15 ./.:36:23,13 ./.:35:22,13 -chr20 734383 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=714733;QSTRAND=+ GT:DP:AD 1|0:14:6,8 ./.:16:11,5 ./.:23:16,7 -chr20 734531 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=714881;QSTRAND=+ GT:DP:AD 1|1:43:21,22 1|0:28:9,19 1|1:23:14,9 -chr20 734610 . G GGTGTGT 60 . QNAME=HG002-S9-H1-000001F;QSTART=714961;QSTRAND=+ GT:DP:AD 1|0:29:17,12 1|0:36:12,24 1|1:33:15,18 -chr20 734610 . G GGTGTGTGT 60 . QNAME=HG002-S9-H2-000001F;QSTART=689509;QSTRAND=+ GT:DP:AD 0|1:33:14,19 ./.:13:6,7 ./.:25:15,10 -chr20 734610 . G GGT 60 . QNAME=cluster19_000000F;QSTART=695423;QSTRAND=+ GT:DP:AD ./.:49:24,25 0|1:35:13,22 ./.:23:17,6 -chr20 734650 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=24976111;QSTRAND=- GT:DP:AD ./.:28:23,5 ./.:29:16,13 1|0:13:8,5 -chr20 735203 . C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=715560;QSTRAND=+ GT:DP:AD 1|1:33:11,22 1|1:28:19,9 1|1:30:18,12 -chr20 735555 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=715912;QSTRAND=+ GT:DP:AD 1|1:32:20,12 1|0:33:19,14 1|1:30:23,7 -chr20 735589 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=690496;QSTRAND=+ GT:DP:AD 0|1:26:5,21 1|0:26:18,8 1|1:26:7,19 -chr20 736154 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24974606;QSTRAND=- GT:DP:AD ./.:23:15,8 ./.:47:24,23 1|0:31:11,20 -chr20 736400 . A C 60 . QNAME=cluster23_scaffold_3;QSTART=24974360;QSTRAND=- GT:DP:AD ./.:27:8,19 ./.:34:10,24 1|0:30:21,9 -chr20 736444 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=716801;QSTRAND=+ GT:DP:AD 1|1:30:20,10 1|0:47:23,24 1|1:35:10,25 -chr20 736736 . CAA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=691644;QSTRAND=+ GT:DP:AD 0|1:18:13,5 1|0:20:11,9 1|1:42:22,20 -chr20 736736 . CA C 60 . QNAME=cluster19_000000F;QSTART=697552;QSTRAND=+ GT:DP:AD ./.:50:25,25 0|1:36:24,12 ./.:12:7,5 -chr20 736925 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=691830;QSTRAND=+ GT:DP:AD 0|1:37:17,20 1|0:29:19,10 0|1:40:15,25 -chr20 737005 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=691910;QSTRAND=+ GT:DP:AD 0|1:34:10,24 1|0:24:13,11 0|1:32:11,21 -chr20 737174 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=717531;QSTRAND=+ GT:DP:AD 1|1:16:10,6 1|1:46:21,25 1|1:20:14,6 -chr20 737624 . A AAAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=717982;QSTRAND=+ GT:DP:AD 1|0:38:15,23 ./.:20:7,13 ./.:21:8,13 -chr20 737624 . A AAATAAT 60 . QNAME=cluster19_000000F;QSTART=698439;QSTRAND=+ GT:DP:AD ./.:33:21,12 0|1:29:18,11 ./.:36:25,11 -chr20 737624 . AAATAAT A 60 . QNAME=cluster23_scaffold_3;QSTART=24973138;QSTRAND=- GT:DP:AD ./.:36:24,12 ./.:25:13,12 1|0:47:24,23 -chr20 737898 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=718258;QSTRAND=+ GT:DP:AD 1|0:44:25,19 ./.:32:25,7 ./.:35:10,25 -chr20 738059 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=718419;QSTRAND=+ GT:DP:AD 1|1:24:11,13 1|1:30:25,5 1|1:26:6,20 -chr20 738091 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=718451;QSTRAND=+ GT:DP:AD 1|1:44:23,21 1|1:16:5,11 1|1:30:18,12 -chr20 738584 . C CA 60 . QNAME=cluster19_000000F;QSTART=699405;QSTRAND=+ GT:DP:AD ./.:23:9,14 0|1:32:9,23 ./.:26:16,10 -chr20 738739 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=693644;QSTRAND=+ GT:DP:AD 0|1:25:17,8 1|0:32:12,20 0|1:38:22,16 -chr20 739096 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=719456;QSTRAND=+ GT:DP:AD 1|1:15:6,9 1|0:38:25,13 1|1:30:6,24 -chr20 739210 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=719570;QSTRAND=+ GT:DP:AD 1|1:42:20,22 1|0:22:15,7 1|1:32:18,14 -chr20 739239 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=719599;QSTRAND=+ GT:DP:AD 1|1:40:24,16 1|0:35:10,25 1|1:35:16,19 diff --git a/repo_utils/test_files/answer_key/divided/multi_00000016.vcf b/repo_utils/test_files/answer_key/divided/multi_00000016.vcf deleted file mode 100644 index 143fe1ae..00000000 --- a/repo_utils/test_files/answer_key/divided/multi_00000016.vcf +++ /dev/null @@ -1,146 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##bcftools_mergeVersion=1.12+htslib-1.12 -##bcftools_mergeCommand=merge -O z -f x -m none input1.vcf.gz input2.vcf.gz input3.vcf.gz; Date=Mon Aug 16 18:05:13 2021 -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 740272 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=695177;QSTRAND=+ GT:DP:AD 0|1:29:18,11 1|0:33:14,19 0|1:28:11,17 -chr20 740467 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=720827;QSTRAND=+ GT:DP:AD 1|1:38:17,21 1|1:29:7,22 1|1:20:9,11 -chr20 741153 . T G 60 . QNAME=cluster23_scaffold_3;QSTART=24969615;QSTRAND=- GT:DP:AD ./.:17:12,5 ./.:13:6,7 1|0:44:23,21 -chr20 741453 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=721813;QSTRAND=+ GT:DP:AD 1|0:24:12,12 ./.:39:21,18 ./.:32:22,10 -chr20 741767 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=696672;QSTRAND=+ GT:DP:AD 0|1:20:5,15 1|0:42:18,24 0|1:24:17,7 -chr20 741939 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=696844;QSTRAND=+ GT:DP:AD 0|1:30:6,24 1|0:15:7,8 1|1:35:23,12 -chr20 742416 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=24968352;QSTRAND=- GT:DP:AD ./.:33:17,16 ./.:29:15,14 1|0:32:9,23 -chr20 742511 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=722871;QSTRAND=+ GT:DP:AD 1|0:41:17,24 ./.:34:25,9 ./.:34:9,25 -chr20 742657 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=24968111;QSTRAND=- GT:DP:AD ./.:31:14,17 ./.:30:16,14 1|0:42:22,20 -chr20 743121 . GTCTCTCTC G 60 . QNAME=HG002-S9-H2-000001F;QSTART=698027;QSTRAND=+ GT:DP:AD 0|1:40:16,24 ./.:29:13,16 ./.:26:20,6 -chr20 743121 . GTCTC G 60 . QNAME=cluster19_000000F;QSTART=25018283;QSTRAND=- GT:DP:AD ./.:30:9,21 1|0:40:24,16 ./.:24:14,10 -chr20 743121 . G GTCTCTCTCTC 60 . QNAME=cluster19_000000F;QSTART=703943;QSTRAND=+ GT:DP:AD ./.:23:14,9 0|1:47:22,25 ./.:25:13,12 -chr20 743153 . C CACACACACACACA 60 . QNAME=HG002-S9-H1-000001F;QSTART=723514;QSTRAND=+ GT:DP:AD 1|0:28:18,10 ./.:23:7,16 ./.:12:5,7 -chr20 743153 . CTCTCTCTCTCT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=723527;QSTRAND=+ GT:DP:AD 1|0:26:20,6 ./.:37:12,25 ./.:38:22,16 -chr20 743160 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=698057;QSTRAND=+ GT:DP:AD 0|1:28:15,13 ./.:31:9,22 ./.:27:12,15 -chr20 743160 . T TCACACA 60 . QNAME=cluster23_scaffold_3;QSTART=24967602;QSTRAND=- GT:DP:AD ./.:36:24,12 ./.:31:16,15 1|0:31:14,17 -chr20 743162 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=698059;QSTRAND=+ GT:DP:AD 0|1:36:17,19 1|0:22:16,6 1|0:19:5,14 -chr20 743162 . T TCA 60 . QNAME=cluster23_scaffold_2;QSTART=24951823;QSTRAND=- GT:DP:AD ./.:27:6,21 ./.:27:14,13 0|1:35:11,24 -chr20 743164 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=698061;QSTRAND=+ GT:DP:AD 0|1:30:15,15 1|0:39:25,14 1|1:29:24,5 -chr20 743734 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=724096;QSTRAND=+ GT:DP:AD 1|0:36:18,18 ./.:31:11,20 ./.:29:22,7 -chr20 743803 . A AG 60 . QNAME=HG002-S9-H1-000001F;QSTART=724166;QSTRAND=+ GT:DP:AD 1|1:39:14,25 1|0:31:7,24 1|1:47:23,24 -chr20 743934 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=24966827;QSTRAND=- GT:DP:AD ./.:34:13,21 ./.:37:15,22 1|0:28:18,10 -chr20 744816 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=725179;QSTRAND=+ GT:DP:AD 1|1:34:9,25 1|1:25:11,14 1|1:31:9,22 -chr20 745347 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=725710;QSTRAND=+ GT:DP:AD 1|1:16:9,7 1|0:37:14,23 1|1:27:21,6 -chr20 745631 . CAGA C 60 . QNAME=cluster19_000000F;QSTART=706463;QSTRAND=+ GT:DP:AD ./.:12:6,6 0|1:29:12,17 ./.:31:7,24 -chr20 745642 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=726005;QSTRAND=+ GT:DP:AD 1|0:38:22,16 ./.:30:14,16 ./.:33:20,13 -chr20 746583 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24964178;QSTRAND=- GT:DP:AD ./.:17:11,6 ./.:29:7,22 1|0:21:11,10 -chr20 746687 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=701585;QSTRAND=+ GT:DP:AD 0|1:37:19,18 1|1:26:15,11 0|1:27:7,20 -chr20 746832 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=701730;QSTRAND=+ GT:DP:AD 0|1:30:12,18 1|0:29:16,13 0|1:25:14,11 -chr20 746873 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=701772;QSTRAND=+ GT:DP:AD 0|1:30:13,17 1|1:45:20,25 1|1:34:9,25 -chr20 746873 . C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=727237;QSTRAND=+ GT:DP:AD 1|0:30:14,16 ./.:20:5,15 ./.:30:15,15 -chr20 746937 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=24963825;QSTRAND=- GT:DP:AD ./.:41:18,23 ./.:13:5,8 1|0:44:25,19 -chr20 747249 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=702146;QSTRAND=+ GT:DP:AD 0|1:40:24,16 1|1:33:9,24 0|1:19:8,11 -chr20 747381 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=702278;QSTRAND=+ GT:DP:AD 0|1:27:19,8 1|1:29:16,13 0|1:38:15,23 -chr20 747855 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=702752;QSTRAND=+ GT:DP:AD 0|1:18:6,12 1|1:29:23,6 0|1:25:15,10 -chr20 748018 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=24962744;QSTRAND=- GT:DP:AD ./.:50:25,25 ./.:31:12,19 1|0:37:25,12 -chr20 748207 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=703105;QSTRAND=+ GT:DP:AD 0|1:39:17,22 1|0:27:14,13 0|1:43:24,19 -chr20 748212 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=703108;QSTRAND=+ GT:DP:AD 0|1:25:18,7 1|1:31:22,9 0|1:32:15,17 -chr20 748246 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=728611;QSTRAND=+ GT:DP:AD 1|0:36:13,23 0|1:30:14,16 ./.:14:8,6 -chr20 748431 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=703327;QSTRAND=+ GT:DP:AD 0|1:34:23,11 1|0:26:17,9 0|1:26:7,19 -chr20 748452 . AT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=703349;QSTRAND=+ GT:DP:AD 0|1:41:25,16 1|0:30:23,7 1|1:32:8,24 -chr20 748776 . G A 60 . QNAME=cluster19_000000F;QSTART=709602;QSTRAND=+ GT:DP:AD ./.:37:24,13 0|1:37:13,24 ./.:11:5,6 -chr20 749061 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24961702;QSTRAND=- GT:DP:AD ./.:38:23,15 ./.:17:6,11 1|0:28:20,8 -chr20 749346 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=704241;QSTRAND=+ GT:DP:AD 0|1:44:19,25 1|0:35:20,15 0|1:24:5,19 -chr20 749546 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=704441;QSTRAND=+ GT:DP:AD 0|1:26:9,17 1|0:23:6,17 0|1:30:10,20 -chr20 749854 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=730217;QSTRAND=+ GT:DP:AD 1|1:39:17,22 1|1:31:15,16 1|1:29:12,17 -chr20 750249 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=705144;QSTRAND=+ GT:DP:AD 0|1:39:21,18 1|0:30:24,6 0|1:30:19,11 -chr20 750361 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=705256;QSTRAND=+ GT:DP:AD 0|1:14:5,9 1|0:29:15,14 0|1:25:13,12 -chr20 750494 . C CA 60 . QNAME=cluster19_000000F;QSTART=25010915;QSTRAND=- GT:DP:AD ./.:19:6,13 1|0:35:15,20 1|1:16:8,8 -chr20 750546 . T G 60 . QNAME=cluster23_scaffold_3;QSTART=24960216;QSTRAND=- GT:DP:AD ./.:43:23,20 ./.:37:23,14 1|0:38:19,19 -chr20 750567 . C A 60 . QNAME=cluster19_000000F;QSTART=711393;QSTRAND=+ GT:DP:AD ./.:36:16,20 0|1:39:22,17 ./.:31:22,9 -chr20 751100 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=705995;QSTRAND=+ GT:DP:AD 0|1:29:6,23 1|0:32:11,21 0|1:27:10,17 -chr20 751283 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=706178;QSTRAND=+ GT:DP:AD 0|1:25:18,7 1|0:14:5,9 0|1:36:20,16 -chr20 751473 . CTTTATTTTATTTTATTTTATTTTAT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=706369;QSTRAND=+;SVTYPE=DEL;SVLEN=-25 GT:DP:AD 0/1:34:11,23 1/0:35:12,23 0/1:35:13,22 -chr20 751473 . CTTTATTTTAT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=731837;QSTRAND=+ GT:DP:AD 1|0:27:7,20 0|1:15:10,5 ./.:25:12,13 -chr20 751473 . CTTTAT C 60 . QNAME=cluster23_scaffold_3;QSTART=24959289;QSTRAND=- GT:DP:AD ./.:21:12,9 ./.:36:15,21 1|0:27:5,22 -chr20 751519 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=706389;QSTRAND=+ GT:DP:AD 0|1:39:24,15 1|0:39:20,19 0|1:20:15,5 -chr20 751627 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=706497;QSTRAND=+ GT:DP:AD 0|1:32:13,19 1|0:35:20,15 0|1:33:19,14 -chr20 751651 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=706521;QSTRAND=+ GT:DP:AD 0|1:43:18,25 1|0:30:6,24 0|1:34:13,21 -chr20 751755 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=706625;QSTRAND=+ GT:DP:AD 0|1:32:15,17 1|0:30:18,12 0|1:48:24,24 -chr20 752069 . ATCTT A 60 . QNAME=cluster23_scaffold_3;QSTART=24958698;QSTRAND=- GT:DP:AD ./.:44:19,25 ./.:29:7,22 1|0:43:21,22 -chr20 752120 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=706990;QSTRAND=+ GT:DP:AD 0|1:36:15,21 1|0:18:11,7 0|1:29:13,16 -chr20 752235 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=707105;QSTRAND=+ GT:DP:AD 0|1:32:9,23 1|0:30:21,9 0|1:31:20,11 -chr20 752300 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=707170;QSTRAND=+ GT:DP:AD 0|1:19:14,5 1|0:29:6,23 0|1:14:5,9 -chr20 752450 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=732803;QSTRAND=+ GT:DP:AD 1|1:24:11,13 1|1:16:5,11 1|1:21:10,11 -chr20 752821 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=707691;QSTRAND=+ GT:DP:AD 0|1:20:8,12 1|0:28:8,20 0|1:44:25,19 -chr20 753097 . G GAAGAAAGAAAGAAAGAAAAGA 60 . QNAME=cluster19_000000F;QSTART=25008316;QSTRAND=- GT:DP:AD ./.:34:25,9 1|0:31:7,24 ./.:29:18,11 -chr20 753097 . G GAAGA 60 . QNAME=cluster23_scaffold_3;QSTART=24957670;QSTRAND=- GT:DP:AD ./.:34:20,14 ./.:42:24,18 1|0:38:23,15 -chr20 753109 . A AAAGAAAAGAAAGAAAGAAAGAAAAGAAAGAAAG 60 . QNAME=HG002-S9-H2-000001F;QSTART=707980;QSTRAND=+;SVTYPE=INS;SVLEN=33 GT:DP:AD 0/1:30:6,24 ./.:29:16,13 ./.:32:20,12 -chr20 753109 . A AAAGAAAAGAAAGAAAGAAAGAAAAG 60 . QNAME=cluster23_scaffold_2;QSTART=24941877;QSTRAND=-;SVTYPE=INS;SVLEN=25 GT:DP:AD ./.:45:25,20 ./.:22:10,12 0/1:42:24,18 -chr20 753112 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=733465;QSTRAND=+ GT:DP:AD 1|0:32:21,11 0|1:30:13,17 ./.:34:15,19 -chr20 753113 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=733466;QSTRAND=+ GT:DP:AD 1|0:25:15,10 0|1:28:13,15 ./.:19:7,12 -chr20 753141 . GAAAGAAAGAAAGAAAGAA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=733495;QSTRAND=+ GT:DP:AD 1|0:21:10,11 ./.:43:19,24 ./.:28:13,15 -chr20 753148 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=708051;QSTRAND=+ GT:DP:AD 0|1:38:19,19 1|0:22:5,17 0|1:32:9,23 -chr20 753159 . A AAG 60 . QNAME=HG002-S9-H2-000001F;QSTART=708063;QSTRAND=+ GT:DP:AD 0|1:30:5,25 1|1:38:21,17 0|1:30:23,7 -chr20 753159 . A AAAGAAAG 60 . QNAME=cluster23_scaffold_3;QSTART=24957601;QSTRAND=- GT:DP:AD ./.:37:21,16 ./.:29:6,23 1|0:20:13,7 -chr20 753194 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=708099;QSTRAND=+ GT:DP:AD 0|1:30:16,14 1|0:30:10,20 0|1:40:17,23 -chr20 753319 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=708224;QSTRAND=+ GT:DP:AD 0|1:22:10,12 1|0:27:19,8 0|1:32:16,16 -chr20 753350 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24957410;QSTRAND=- GT:DP:AD ./.:36:19,17 ./.:16:5,11 1|0:37:12,25 -chr20 753848 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=24956912;QSTRAND=- GT:DP:AD ./.:32:7,25 ./.:22:5,17 1|0:48:24,24 -chr20 753849 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=24956911;QSTRAND=- GT:DP:AD ./.:27:16,11 ./.:34:20,14 1|0:37:20,17 -chr20 753973 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=708878;QSTRAND=+ GT:DP:AD 0|1:44:20,24 1|0:44:24,20 0|1:34:12,22 -chr20 754002 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=734337;QSTRAND=+ GT:DP:AD 1|0:28:16,12 ./.:26:8,18 ./.:17:12,5 -chr20 754073 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=24956687;QSTRAND=- GT:DP:AD ./.:48:23,25 ./.:32:9,23 1|0:41:21,20 -chr20 754124 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=734459;QSTRAND=+ GT:DP:AD 1|1:26:5,21 1|0:38:25,13 1|1:34:20,14 -chr20 754553 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=709458;QSTRAND=+ GT:DP:AD 0|1:47:22,25 1|0:36:22,14 0|1:23:15,8 -chr20 755158 . G T 60 . QNAME=cluster19_000000F;QSTART=25006253;QSTRAND=- GT:DP:AD ./.:31:6,25 1|0:16:6,10 ./.:24:6,18 -chr20 755213 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=735548;QSTRAND=+ GT:DP:AD 1|1:19:12,7 1|1:25:5,20 1|1:41:24,17 -chr20 755214 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=735549;QSTRAND=+ GT:DP:AD 1|0:12:5,7 ./.:28:12,16 ./.:16:7,9 -chr20 755269 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=735605;QSTRAND=+ GT:DP:AD 1|1:35:10,25 1|1:36:19,17 1|1:46:25,21 -chr20 755467 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=735803;QSTRAND=+ GT:DP:AD 1|0:28:22,6 ./.:37:21,16 ./.:35:16,19 -chr20 755545 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=24955214;QSTRAND=- GT:DP:AD ./.:18:8,10 ./.:37:21,16 1|0:34:25,9 -chr20 755581 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=710487;QSTRAND=+ GT:DP:AD 0|1:37:24,13 1|1:32:12,20 1|1:29:12,17 -chr20 755749 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=736085;QSTRAND=+ GT:DP:AD 1|0:35:10,25 ./.:15:6,9 ./.:33:22,11 -chr20 755803 . A G 60 . QNAME=cluster19_000000F;QSTART=716622;QSTRAND=+ GT:DP:AD ./.:31:11,20 0|1:25:14,11 ./.:30:22,8 -chr20 756000 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=736336;QSTRAND=+ GT:DP:AD 1|1:31:20,11 1|1:33:11,22 0|1:12:6,6 -chr20 756217 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=736553;QSTRAND=+ GT:DP:AD 1|0:20:15,5 ./.:19:11,8 ./.:46:23,23 -chr20 756388 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=24954371;QSTRAND=- GT:DP:AD ./.:39:17,22 ./.:36:16,20 1|0:20:14,6 -chr20 756408 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=736744;QSTRAND=+ GT:DP:AD 1|0:20:15,5 ./.:24:8,16 ./.:34:12,22 -chr20 756478 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=24954281;QSTRAND=- GT:DP:AD ./.:34:18,16 ./.:18:10,8 1|0:16:10,6 -chr20 756575 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=736912;QSTRAND=+ GT:DP:AD 1|1:21:16,5 1|1:23:14,9 0|1:35:18,17 -chr20 756637 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=24954122;QSTRAND=- GT:DP:AD ./.:21:7,14 ./.:34:22,12 1|0:28:5,23 -chr20 756764 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=24953995;QSTRAND=- GT:DP:AD ./.:28:14,14 ./.:26:11,15 1|0:28:5,23 -chr20 756872 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=737208;QSTRAND=+ GT:DP:AD 1|1:47:22,25 1|1:35:17,18 1|0:31:21,10 -chr20 756909 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=737243;QSTRAND=+ GT:DP:AD 1|1:21:11,10 1|1:49:24,25 1|1:15:5,10 diff --git a/repo_utils/test_files/answer_key/divided/multi_00000017.vcf b/repo_utils/test_files/answer_key/divided/multi_00000017.vcf deleted file mode 100644 index 9268578b..00000000 --- a/repo_utils/test_files/answer_key/divided/multi_00000017.vcf +++ /dev/null @@ -1,408 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##bcftools_mergeVersion=1.12+htslib-1.12 -##bcftools_mergeCommand=merge -O z -f x -m none input1.vcf.gz input2.vcf.gz input3.vcf.gz; Date=Mon Aug 16 18:05:13 2021 -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 758241 . A AT 60 . QNAME=HG002-S9-H1-000001F;QSTART=738576;QSTRAND=+ GT:DP:AD 1|1:28:10,18 1|1:20:8,12 0|1:24:19,5 -chr20 758241 . A ATTT 60 . QNAME=cluster23_scaffold_3;QSTART=24952516;QSTRAND=- GT:DP:AD ./.:28:19,9 ./.:24:16,8 1|0:21:12,9 -chr20 758268 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=738603;QSTRAND=+ GT:DP:AD 1|0:33:14,19 ./.:28:9,19 ./.:20:8,12 -chr20 758339 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=738674;QSTRAND=+ GT:DP:AD 1|0:33:17,16 ./.:16:10,6 ./.:32:21,11 -chr20 758391 . A C 60 . QNAME=cluster23_scaffold_3;QSTART=24952366;QSTRAND=- GT:DP:AD ./.:14:5,9 ./.:19:12,7 1|0:18:5,13 -chr20 758562 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=24952195;QSTRAND=- GT:DP:AD ./.:32:21,11 ./.:25:5,20 1|0:27:16,11 -chr20 758620 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=713525;QSTRAND=+ GT:DP:AD 0|1:21:11,10 1|0:39:24,15 0|1:24:12,12 -chr20 758664 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=24952093;QSTRAND=- GT:DP:AD ./.:31:6,25 ./.:33:24,9 1|0:32:12,20 -chr20 758808 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=739143;QSTRAND=+ GT:DP:AD 1|1:28:14,14 1|1:30:12,18 1|1:19:9,10 -chr20 758874 . C G 60 . QNAME=cluster19_000000F;QSTART=719692;QSTRAND=+ GT:DP:AD ./.:38:16,22 0|1:34:10,24 ./.:33:18,15 -chr20 758972 . CGTGTGTGT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=713878;QSTRAND=+ GT:DP:AD 0|1:22:9,13 1|1:33:22,11 0|1:15:7,8 -chr20 758972 . CGTGTGTGTGT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=739308;QSTRAND=+ GT:DP:AD 1|0:22:14,8 ./.:31:10,21 ./.:17:6,11 -chr20 758972 . CGTGT C 60 . QNAME=cluster23_scaffold_3;QSTART=24951785;QSTRAND=- GT:DP:AD ./.:45:23,22 ./.:35:25,10 1|0:27:12,15 -chr20 759048 . AC A 60 . QNAME=cluster23_scaffold_3;QSTART=24951713;QSTRAND=- GT:DP:AD ./.:45:23,22 ./.:29:18,11 1|0:26:21,5 -chr20 759464 . C CA 60 . QNAME=HG002-S9-H2-000001F;QSTART=714362;QSTRAND=+ GT:DP:AD 0|1:23:14,9 1|1:41:23,18 0|1:25:20,5 -chr20 760189 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=715087;QSTRAND=+ GT:DP:AD 0|1:32:18,14 1|0:26:19,7 0|1:18:8,10 -chr20 760275 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=740600;QSTRAND=+ GT:DP:AD 1|1:24:6,18 1|1:32:25,7 1|1:25:6,19 -chr20 761203 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=741528;QSTRAND=+ GT:DP:AD 1|1:38:16,22 0|1:24:13,11 1|1:38:19,19 -chr20 761573 . C G 60 . QNAME=cluster19_000000F;QSTART=24999845;QSTRAND=- GT:DP:AD ./.:43:24,19 1|0:32:17,15 1|0:46:24,22 -chr20 761593 . G A 60 . QNAME=cluster19_000000F;QSTART=24999825;QSTRAND=- GT:DP:AD ./.:12:6,6 1|1:23:11,12 ./.:25:10,15 -chr20 761595 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=741920;QSTRAND=+ GT:DP:AD 1|1:38:21,17 1|1:22:12,10 1|1:21:15,6 -chr20 761987 . A G 60 . QNAME=cluster19_000000F;QSTART=24999431;QSTRAND=- GT:DP:AD ./.:31:15,16 1|0:42:18,24 1|1:36:12,24 -chr20 762072 . A C 60 . QNAME=cluster23_scaffold_3;QSTART=24948690;QSTRAND=- GT:DP:AD ./.:30:22,8 ./.:31:23,8 1|0:26:12,14 -chr20 762187 . G T 60 . QNAME=cluster19_000000F;QSTART=24999231;QSTRAND=- GT:DP:AD ./.:18:9,9 1|0:34:17,17 1|0:36:11,25 -chr20 762374 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=742699;QSTRAND=+ GT:DP:AD 1|1:22:13,9 1|1:29:13,16 1|0:41:17,24 -chr20 762480 . C G 60 . QNAME=cluster19_000000F;QSTART=24998938;QSTRAND=- GT:DP:AD ./.:43:21,22 1|0:17:7,10 1|0:17:5,12 -chr20 762486 . C T 60 . QNAME=cluster19_000000F;QSTART=24998932;QSTRAND=- GT:DP:AD ./.:47:24,23 1|0:14:8,6 1|0:33:25,8 -chr20 762576 . T C 60 . QNAME=cluster19_000000F;QSTART=24998842;QSTRAND=- GT:DP:AD ./.:25:16,9 1|0:25:6,19 1|0:42:23,19 -chr20 762628 . C T 60 . QNAME=cluster19_000000F;QSTART=24998790;QSTRAND=- GT:DP:AD ./.:31:20,11 1|0:33:9,24 1|0:27:21,6 -chr20 763183 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=743508;QSTRAND=+ GT:DP:AD 1|1:19:12,7 1|1:17:10,7 1|0:16:7,9 -chr20 763406 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=743731;QSTRAND=+ GT:DP:AD 1|1:48:24,24 0|1:28:11,17 ./.:30:15,15 -chr20 763806 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=744131;QSTRAND=+ GT:DP:AD 1|1:33:23,10 1|1:26:21,5 1|0:36:17,19 -chr20 764018 . A ACAGGTCAAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=744344;QSTRAND=+ GT:DP:AD 1|1:22:16,6 0|1:27:5,22 ./.:35:10,25 -chr20 764203 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=744537;QSTRAND=+ GT:DP:AD 1|1:38:16,22 1|1:38:16,22 1|0:28:23,5 -chr20 764230 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=744564;QSTRAND=+ GT:DP:AD 1|1:20:5,15 1|1:36:22,14 1|0:22:14,8 -chr20 764442 . A AGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGG 60 . QNAME=cluster23_scaffold_3;QSTART=24946242;QSTRAND=-;SVTYPE=INS;SVLEN=78 GT:DP:AD ./.:30:19,11 ./.:35:14,21 1/0:46:22,24 -chr20 764537 . A AGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=744872;QSTRAND=+;SVTYPE=INS;SVLEN=117 GT:DP:AD 1/1:23:18,5 0/1:14:6,8 ./.:45:20,25 -chr20 764537 . A AGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAT 60 . QNAME=cluster19_000000F;QSTART=24996803;QSTRAND=-;SVTYPE=INS;SVLEN=78 GT:DP:AD ./.:25:14,11 1/0:43:20,23 ./.:30:22,8 -chr20 764800 . C A 60 . QNAME=cluster23_scaffold_2;QSTART=24930190;QSTRAND=- GT:DP:AD ./.:34:22,12 ./.:29:16,13 0|1:35:24,11 -chr20 765454 . G A 60 . QNAME=cluster19_000000F;QSTART=24995886;QSTRAND=- GT:DP:AD ./.:42:17,25 1|0:24:12,12 ./.:41:18,23 -chr20 765937 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=746389;QSTRAND=+ GT:DP:AD 1|1:40:25,15 0|1:13:5,8 ./.:23:11,12 -chr20 766211 . A AG 60 . QNAME=HG002-S9-H1-000001F;QSTART=746664;QSTRAND=+ GT:DP:AD 1|1:35:10,25 1|1:20:10,10 1|0:47:22,25 -chr20 766216 . G T 60 . QNAME=cluster19_000000F;QSTART=24995123;QSTRAND=- GT:DP:AD ./.:27:16,11 1|0:28:16,12 ./.:25:7,18 -chr20 766241 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=746694;QSTRAND=+ GT:DP:AD 1|1:33:22,11 1|1:24:12,12 1|0:34:22,12 -chr20 766308 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=746761;QSTRAND=+ GT:DP:AD 1|1:45:25,20 1|1:42:20,22 1|0:18:10,8 -chr20 766512 . C A 60 . QNAME=cluster19_000000F;QSTART=24994827;QSTRAND=- GT:DP:AD ./.:40:15,25 1|0:20:10,10 ./.:21:7,14 -chr20 766576 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=747029;QSTRAND=+ GT:DP:AD 1|1:22:10,12 1|1:32:11,21 1|1:32:18,14 -chr20 766899 . T TA 60 . QNAME=cluster23_scaffold_2;QSTART=24928090;QSTRAND=- GT:DP:AD ./.:24:10,14 ./.:26:16,10 0|1:43:21,22 -chr20 767023 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=747476;QSTRAND=+ GT:DP:AD 1|1:45:23,22 0|1:40:24,16 ./.:27:16,11 -chr20 767036 . A ATAG 60 . QNAME=cluster19_000000F;QSTART=24994300;QSTRAND=- GT:DP:AD ./.:27:18,9 1|0:34:19,15 ./.:30:24,6 -chr20 767191 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=747644;QSTRAND=+ GT:DP:AD 1|1:31:8,23 1|1:37:17,20 1|0:21:14,7 -chr20 767349 . C T 60 . QNAME=cluster19_000000F;QSTART=24993987;QSTRAND=- GT:DP:AD ./.:36:22,14 1|0:24:16,8 ./.:25:17,8 -chr20 767359 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=24943323;QSTRAND=- GT:DP:AD ./.:21:7,14 ./.:39:25,14 1|0:14:7,7 -chr20 767376 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=747829;QSTRAND=+ GT:DP:AD 1|1:35:12,23 1|1:39:24,15 1|0:19:11,8 -chr20 767966 . T C 60 . QNAME=cluster19_000000F;QSTART=24993370;QSTRAND=- GT:DP:AD ./.:48:24,24 1|0:32:11,21 ./.:26:12,14 -chr20 768267 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=748720;QSTRAND=+ GT:DP:AD 1|1:21:15,6 0|1:43:22,21 ./.:27:22,5 -chr20 768330 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=748783;QSTRAND=+ GT:DP:AD 1|1:23:14,9 1|1:22:16,6 1|0:27:5,22 -chr20 769651 . C G 60 . QNAME=cluster23_scaffold_3;QSTART=24941031;QSTRAND=- GT:DP:AD ./.:34:17,17 ./.:15:6,9 1|0:25:14,11 -chr20 769672 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=750125;QSTRAND=+ GT:DP:AD 1|1:42:17,25 0|1:22:17,5 ./.:19:14,5 -chr20 769904 . A C 60 . QNAME=cluster19_000000F;QSTART=730843;QSTRAND=+ GT:DP:AD ./.:23:15,8 0|1:35:14,21 ./.:26:16,10 -chr20 770094 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=750547;QSTRAND=+ GT:DP:AD 1|1:43:22,21 1|1:23:16,7 1|0:21:7,14 -chr20 770601 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24940081;QSTRAND=- GT:DP:AD ./.:34:15,19 ./.:45:20,25 1|0:36:15,21 -chr20 771027 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=751480;QSTRAND=+ GT:DP:AD 1|1:30:18,12 0|1:37:16,21 ./.:26:10,16 -chr20 771420 . CTT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=751874;QSTRAND=+ GT:DP:AD 1|1:33:20,13 ./.:32:19,13 ./.:39:22,17 -chr20 771488 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=24939194;QSTRAND=- GT:DP:AD ./.:27:15,12 ./.:39:19,20 1|0:35:19,16 -chr20 771669 . G GAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=752121;QSTRAND=+ GT:DP:AD 1|1:28:11,17 ./.:23:6,17 ./.:32:23,9 -chr20 771669 . GA G 60 . QNAME=cluster19_000000F;QSTART=24989667;QSTRAND=- GT:DP:AD ./.:17:7,10 1|0:34:18,16 ./.:17:5,12 -chr20 771669 . G GA 60 . QNAME=cluster19_000000F;QSTART=732609;QSTRAND=+ GT:DP:AD ./.:17:7,10 0|1:19:6,13 ./.:44:20,24 -chr20 771669 . G GAA 60 . QNAME=cluster23_scaffold_3;QSTART=24939011;QSTRAND=- GT:DP:AD ./.:42:17,25 ./.:23:16,7 1|0:34:20,14 -chr20 771724 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=752178;QSTRAND=+ GT:DP:AD 1|1:20:8,12 1|1:22:12,10 1|0:42:20,22 -chr20 771989 . T G 60 . QNAME=cluster19_000000F;QSTART=24989348;QSTRAND=- GT:DP:AD ./.:23:8,15 1|1:35:12,23 1|0:22:11,11 -chr20 772587 . GT G 60 . QNAME=cluster19_000000F;QSTART=24988750;QSTRAND=- GT:DP:AD ./.:48:23,25 1|1:26:10,16 ./.:19:5,14 -chr20 772587 . G GT 60 . QNAME=cluster23_scaffold_3;QSTART=24938092;QSTRAND=- GT:DP:AD ./.:42:22,20 ./.:28:9,19 1|0:32:20,12 -chr20 772587 . GTT G 60 . QNAME=cluster23_scaffold_2;QSTART=24922402;QSTRAND=- GT:DP:AD ./.:16:8,8 ./.:21:15,6 0|1:27:5,22 -chr20 772599 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=753053;QSTRAND=+ GT:DP:AD 1|0:34:10,24 1|1:30:24,6 ./.:27:20,7 -chr20 772666 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=24938013;QSTRAND=- GT:DP:AD ./.:25:10,15 ./.:23:7,16 1|0:27:16,11 -chr20 772719 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=753173;QSTRAND=+ GT:DP:AD 1|1:21:7,14 1|1:33:25,8 1|1:23:14,9 -chr20 772824 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=753278;QSTRAND=+ GT:DP:AD 1|1:40:16,24 1|1:39:15,24 1|0:24:6,18 -chr20 772843 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=753297;QSTRAND=+ GT:DP:AD 1|1:33:18,15 1|1:47:23,24 1|1:28:15,13 -chr20 772872 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=753326;QSTRAND=+ GT:DP:AD 1|1:41:25,16 0|1:34:16,18 1|0:28:13,15 -chr20 773095 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=753549;QSTRAND=+ GT:DP:AD 1|1:37:16,21 0|1:28:5,23 ./.:29:16,13 -chr20 773193 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24921798;QSTRAND=- GT:DP:AD ./.:24:11,13 ./.:23:14,9 0|1:36:16,20 -chr20 773273 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24921718;QSTRAND=- GT:DP:AD ./.:26:5,21 ./.:37:24,13 0|1:41:19,22 -chr20 773723 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=754177;QSTRAND=+ GT:DP:AD 1|1:42:25,17 1|1:22:11,11 1|1:23:12,11 -chr20 773737 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=754191;QSTRAND=+ GT:DP:AD 1|1:25:14,11 1|1:36:15,21 1|1:18:11,7 -chr20 774159 . G A 60 . QNAME=cluster19_000000F;QSTART=735098;QSTRAND=+ GT:DP:AD ./.:47:25,22 0|1:29:5,24 ./.:38:24,14 -chr20 774304 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=729331;QSTRAND=+ GT:DP:AD 0|1:38:13,25 ./.:46:23,23 ./.:42:19,23 -chr20 774383 . T C 60 . QNAME=cluster19_000000F;QSTART=735322;QSTRAND=+ GT:DP:AD ./.:33:14,19 0|1:32:16,16 ./.:38:17,21 -chr20 774574 . A G 60 . QNAME=cluster19_000000F;QSTART=735513;QSTRAND=+ GT:DP:AD ./.:30:10,20 0|1:33:15,18 ./.:49:25,24 -chr20 775268 . CTTTTTTTTTTT C 60 . QNAME=cluster19_000000F;QSTART=24986070;QSTRAND=- GT:DP:AD ./.:24:8,16 1|0:27:15,12 1|1:16:10,6 -chr20 775268 . CTTTTTTTT C 60 . QNAME=cluster19_000000F;QSTART=736208;QSTRAND=+ GT:DP:AD ./.:16:7,9 0|1:30:14,16 ./.:42:21,21 -chr20 775431 . G A 60 . QNAME=cluster19_000000F;QSTART=24985918;QSTRAND=- GT:DP:AD ./.:16:6,10 1|0:38:20,18 1|1:38:17,21 -chr20 775463 . T C 60 . QNAME=cluster19_000000F;QSTART=24985886;QSTRAND=- GT:DP:AD ./.:42:19,23 1|1:27:18,9 1|1:36:16,20 -chr20 775534 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=755988;QSTRAND=+ GT:DP:AD 1|1:37:15,22 1|1:20:11,9 1|1:38:25,13 -chr20 775539 . A G 60 . QNAME=cluster19_000000F;QSTART=24985810;QSTRAND=- GT:DP:AD ./.:30:20,10 1|1:27:17,10 1|1:44:24,20 -chr20 775876 . A G 60 . QNAME=cluster19_000000F;QSTART=24985473;QSTRAND=- GT:DP:AD ./.:25:19,6 1|1:36:24,12 1|1:27:22,5 -chr20 775888 . A G 60 . QNAME=cluster19_000000F;QSTART=736819;QSTRAND=+ GT:DP:AD ./.:46:22,24 0|1:23:13,10 ./.:22:13,9 -chr20 776848 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=757302;QSTRAND=+ GT:DP:AD 1|0:40:25,15 0|1:28:16,12 ./.:32:11,21 -chr20 776855 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=757309;QSTRAND=+ GT:DP:AD 1|1:19:7,12 1|1:28:6,22 1|1:38:25,13 -chr20 776856 . TG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=757311;QSTRAND=+ GT:DP:AD 1|0:28:5,23 1|0:20:11,9 1|1:26:8,18 -chr20 776863 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=731890;QSTRAND=+ GT:DP:AD 0|1:40:23,17 ./.:27:14,13 ./.:21:7,14 -chr20 776921 . T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=757375;QSTRAND=+ GT:DP:AD 1|1:23:12,11 0|1:42:23,19 ./.:34:13,21 -chr20 777272 . C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=757727;QSTRAND=+ GT:DP:AD 1|1:22:9,13 1|0:45:20,25 1|1:14:9,5 -chr20 777276 . A AC 60 . QNAME=cluster19_000000F;QSTART=738209;QSTRAND=+ GT:DP:AD ./.:21:13,8 0|1:23:18,5 ./.:27:5,22 -chr20 777343 . A G 60 . QNAME=cluster19_000000F;QSTART=738276;QSTRAND=+ GT:DP:AD ./.:46:25,21 0|1:38:21,17 ./.:31:11,20 -chr20 777391 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=757846;QSTRAND=+ GT:DP:AD 1|1:36:21,15 ./.:24:19,5 ./.:30:17,13 -chr20 778013 . CT C 60 . QNAME=cluster19_000000F;QSTART=738947;QSTRAND=+ GT:DP:AD ./.:26:15,11 0|1:28:13,15 ./.:22:16,6 -chr20 778013 . C CT 60 . QNAME=cluster23_scaffold_2;QSTART=24916988;QSTRAND=- GT:DP:AD ./.:24:8,16 ./.:41:23,18 0|1:44:25,19 -chr20 778339 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=758794;QSTRAND=+ GT:DP:AD 1|1:38:25,13 1|1:46:21,25 1|1:32:16,16 -chr20 778729 . C CT 60 . QNAME=cluster19_000000F;QSTART=24982619;QSTRAND=- GT:DP:AD ./.:30:15,15 1|0:44:20,24 ./.:27:12,15 -chr20 778749 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24916252;QSTRAND=- GT:DP:AD ./.:24:18,6 ./.:30:7,23 0|1:29:17,12 -chr20 778880 . A G 60 . QNAME=cluster19_000000F;QSTART=24982468;QSTRAND=- GT:DP:AD ./.:36:24,12 1|1:18:5,13 1|1:31:7,24 -chr20 779208 . T C 60 . QNAME=cluster19_000000F;QSTART=24982140;QSTRAND=- GT:DP:AD ./.:26:5,21 1|1:29:6,23 1|1:30:10,20 -chr20 779804 . T C 60 . QNAME=cluster19_000000F;QSTART=24981544;QSTRAND=- GT:DP:AD ./.:29:15,14 1|0:21:15,6 ./.:20:6,14 -chr20 780086 . G A 60 . QNAME=cluster19_000000F;QSTART=741018;QSTRAND=+ GT:DP:AD ./.:35:17,18 0|1:27:16,11 ./.:27:14,13 -chr20 780364 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=760819;QSTRAND=+ GT:DP:AD 1|1:30:17,13 ./.:28:21,7 ./.:39:16,23 -chr20 781143 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=761598;QSTRAND=+ GT:DP:AD 1|1:26:6,20 1|1:27:11,16 1|1:31:24,7 -chr20 781912 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=762367;QSTRAND=+ GT:DP:AD 1|1:19:6,13 1|1:19:12,7 1|1:33:22,11 -chr20 782053 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=762508;QSTRAND=+ GT:DP:AD 1|1:34:21,13 1|1:23:13,10 1|1:23:12,11 -chr20 782135 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=762590;QSTRAND=+ GT:DP:AD 1|1:30:11,19 1|1:43:18,25 1|1:33:25,8 -chr20 782243 . T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=762699;QSTRAND=+ GT:DP:AD 1|0:28:6,22 ./.:30:14,16 ./.:49:24,25 -chr20 782250 . G GA 60 . QNAME=HG002-S9-H2-000001F;QSTART=737280;QSTRAND=+ GT:DP:AD 0|1:35:25,10 1|1:30:10,20 1|1:19:13,6 -chr20 782334 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=762790;QSTRAND=+ GT:DP:AD 1|1:43:22,21 1|1:31:9,22 1|1:18:10,8 -chr20 782552 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=763008;QSTRAND=+ GT:DP:AD 1|1:41:21,20 1|1:24:16,8 1|1:19:13,6 -chr20 782748 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=763204;QSTRAND=+ GT:DP:AD 1|1:17:10,7 1|1:34:13,21 1|1:32:14,18 -chr20 782898 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=763354;QSTRAND=+ GT:DP:AD 1|1:28:21,7 1|1:31:12,19 1|1:33:14,19 -chr20 783008 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=763464;QSTRAND=+ GT:DP:AD 1|1:36:21,15 1|1:24:18,6 1|1:43:21,22 -chr20 783188 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=763644;QSTRAND=+ GT:DP:AD 1|1:35:20,15 1|1:15:5,10 1|1:21:16,5 -chr20 783194 . C T 60 . QNAME=cluster19_000000F;QSTART=24978153;QSTRAND=- GT:DP:AD ./.:30:5,25 1|0:45:21,24 1|1:30:22,8 -chr20 783195 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=763651;QSTRAND=+ GT:DP:AD 1|1:35:14,21 1|1:48:24,24 1|1:25:12,13 -chr20 783325 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=763781;QSTRAND=+ GT:DP:AD 1|1:27:7,20 1|1:11:6,5 1|1:40:15,25 -chr20 783424 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=763880;QSTRAND=+ GT:DP:AD 1|1:29:10,19 1|1:41:25,16 1|1:23:12,11 -chr20 783447 . A G 60 . QNAME=cluster19_000000F;QSTART=24977900;QSTRAND=- GT:DP:AD ./.:42:19,23 1|0:19:13,6 1|1:42:17,25 -chr20 783450 . C T 60 . QNAME=cluster19_000000F;QSTART=744383;QSTRAND=+ GT:DP:AD ./.:27:12,15 0|1:18:6,12 ./.:25:15,10 -chr20 783488 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=763944;QSTRAND=+ GT:DP:AD 1|1:24:15,9 ./.:28:8,20 ./.:25:14,11 -chr20 783520 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=763976;QSTRAND=+ GT:DP:AD 1|1:41:18,23 1|1:23:15,8 1|1:45:25,20 -chr20 783739 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=764195;QSTRAND=+ GT:DP:AD 1|1:36:22,14 1|1:28:23,5 1|1:19:12,7 -chr20 783834 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=764290;QSTRAND=+ GT:DP:AD 1|1:14:7,7 1|1:46:23,23 1|1:34:23,11 -chr20 783937 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=764393;QSTRAND=+ GT:DP:AD 1|1:39:23,16 1|1:41:22,19 1|1:33:15,18 -chr20 784114 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=764570;QSTRAND=+ GT:DP:AD 1|1:31:11,20 1|0:21:16,5 1|1:43:25,18 -chr20 784189 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=764645;QSTRAND=+ GT:DP:AD 1|1:18:9,9 1|1:35:23,12 1|1:43:25,18 -chr20 784244 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=764700;QSTRAND=+ GT:DP:AD 1|1:39:15,24 1|1:28:13,15 1|1:22:6,16 -chr20 784245 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=764701;QSTRAND=+ GT:DP:AD 1|1:15:5,10 1|1:33:18,15 1|1:35:21,14 -chr20 784337 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=764793;QSTRAND=+ GT:DP:AD 1|1:22:6,16 1|1:43:19,24 1|1:21:5,16 -chr20 784347 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=764803;QSTRAND=+ GT:DP:AD 1|1:46:23,23 1|1:31:16,15 1|1:29:23,6 -chr20 784686 . G T 60 . QNAME=cluster19_000000F;QSTART=24976661;QSTRAND=- GT:DP:AD ./.:31:24,7 1|0:19:14,5 1|1:35:21,14 -chr20 784695 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=765151;QSTRAND=+ GT:DP:AD 1|1:26:18,8 1|1:26:15,11 1|1:21:7,14 -chr20 784821 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=765277;QSTRAND=+ GT:DP:AD 1|1:21:7,14 1|1:25:7,18 1|1:24:15,9 -chr20 784842 . A G 60 . QNAME=cluster19_000000F;QSTART=745775;QSTRAND=+ GT:DP:AD ./.:35:18,17 0|1:20:13,7 ./.:14:9,5 -chr20 785145 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=765601;QSTRAND=+ GT:DP:AD 1|1:20:14,6 0|1:22:17,5 ./.:16:8,8 -chr20 785294 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=765750;QSTRAND=+ GT:DP:AD 1|1:43:23,20 1|1:35:19,16 1|1:41:24,17 -chr20 785303 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=765759;QSTRAND=+ GT:DP:AD 1|1:30:20,10 1|1:32:12,20 1|1:28:23,5 -chr20 785581 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=766037;QSTRAND=+ GT:DP:AD 1|1:13:6,7 1|1:32:18,14 1|1:18:13,5 -chr20 785647 . G A 60 . QNAME=cluster19_000000F;QSTART=24975700;QSTRAND=- GT:DP:AD ./.:24:8,16 1|0:27:6,21 1|1:36:17,19 -chr20 785693 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=766149;QSTRAND=+ GT:DP:AD 1|1:27:19,8 1|1:46:22,24 1|1:30:11,19 -chr20 785803 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=766259;QSTRAND=+ GT:DP:AD 1|1:47:24,23 1|1:24:13,11 1|1:15:9,6 -chr20 786660 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24924029;QSTRAND=- GT:DP:AD ./.:34:20,14 ./.:35:18,17 1|0:32:23,9 -chr20 787077 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=767533;QSTRAND=+ GT:DP:AD 1|1:33:15,18 1|1:46:22,24 1|1:23:16,7 -chr20 787239 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=767696;QSTRAND=+ GT:DP:AD 1|1:30:12,18 ./.:31:21,10 1|0:30:21,9 -chr20 787239 . CTT C 60 . QNAME=cluster23_scaffold_2;QSTART=24907761;QSTRAND=- GT:DP:AD ./.:32:18,14 ./.:24:6,18 0|1:26:9,17 -chr20 787512 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=767968;QSTRAND=+ GT:DP:AD 1|1:24:9,15 1|1:40:22,18 1|0:38:20,18 -chr20 787930 . A T 60 . QNAME=cluster19_000000F;QSTART=24973418;QSTRAND=- GT:DP:AD ./.:23:17,6 1|0:46:25,21 1|1:35:10,25 -chr20 788431 . T C 60 . QNAME=cluster19_000000F;QSTART=24972917;QSTRAND=- GT:DP:AD ./.:23:5,18 1|0:41:21,20 1|1:33:8,25 -chr20 788945 . T C 60 . QNAME=cluster19_000000F;QSTART=24972403;QSTRAND=- GT:DP:AD ./.:36:18,18 1|0:45:24,21 1|1:41:21,20 -chr20 789027 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=769481;QSTRAND=+ GT:DP:AD 1|1:19:13,6 1|0:27:17,10 1|1:34:20,14 -chr20 789716 . G A 60 . QNAME=cluster19_000000F;QSTART=750648;QSTRAND=+ GT:DP:AD ./.:28:21,7 0|1:32:24,8 ./.:40:18,22 -chr20 789908 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=770362;QSTRAND=+ GT:DP:AD 1|1:22:14,8 1|1:39:24,15 1|1:39:18,21 -chr20 789995 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=770449;QSTRAND=+ GT:DP:AD 1|1:39:20,19 ./.:18:9,9 ./.:18:11,7 -chr20 790219 . T C 60 . QNAME=cluster19_000000F;QSTART=24971129;QSTRAND=- GT:DP:AD ./.:36:21,15 1|0:40:24,16 1|1:29:14,15 -chr20 790252 . G A 60 . QNAME=cluster19_000000F;QSTART=24971096;QSTRAND=- GT:DP:AD ./.:32:11,21 1|0:22:17,5 1|1:15:5,10 -chr20 790270 . C G 60 . QNAME=cluster19_000000F;QSTART=24971078;QSTRAND=- GT:DP:AD ./.:23:5,18 1|0:44:19,25 1|1:39:23,16 -chr20 790371 . CAAAAAAA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=745400;QSTRAND=+ GT:DP:AD 0|1:35:25,10 1|0:38:19,19 0|1:35:17,18 -chr20 790371 . CAAAAAAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=770826;QSTRAND=+ GT:DP:AD 1|0:36:20,16 ./.:15:10,5 1|0:17:6,11 -chr20 790371 . C CAAAAAAAAAAAA 60 . QNAME=cluster19_000000F;QSTART=751304;QSTRAND=+ GT:DP:AD ./.:23:11,12 0|1:23:12,11 ./.:41:17,24 -chr20 790626 . T G 60 . QNAME=cluster19_000000F;QSTART=24970729;QSTRAND=- GT:DP:AD ./.:36:13,23 1|0:22:8,14 1|1:40:24,16 -chr20 790639 . C T 60 . QNAME=cluster19_000000F;QSTART=24970716;QSTRAND=- GT:DP:AD ./.:28:20,8 1|0:31:22,9 1|1:16:8,8 -chr20 791233 . A G 60 . QNAME=cluster19_000000F;QSTART=24970122;QSTRAND=- GT:DP:AD ./.:14:5,9 1|0:24:14,10 1|1:33:22,11 -chr20 791888 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=772334;QSTRAND=+ GT:DP:AD 1|1:34:13,21 ./.:30:10,20 ./.:29:6,23 -chr20 791971 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=772417;QSTRAND=+ GT:DP:AD 1|1:30:21,9 1|1:19:12,7 1|1:14:5,9 -chr20 792261 . T C 60 . QNAME=cluster19_000000F;QSTART=753205;QSTRAND=+ GT:DP:AD ./.:27:21,6 0|1:29:11,18 ./.:24:17,7 -chr20 792795 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=773241;QSTRAND=+ GT:DP:AD 1|1:30:20,10 1|1:42:17,25 1|1:29:19,10 -chr20 792866 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=773312;QSTRAND=+ GT:DP:AD 1|1:43:19,24 1|1:31:22,9 1|1:17:10,7 -chr20 792873 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=773319;QSTRAND=+ GT:DP:AD 1|1:40:24,16 1|1:23:6,17 1|1:20:11,9 -chr20 792876 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=773322;QSTRAND=+ GT:DP:AD 1|1:20:6,14 1|1:47:23,24 1|1:42:23,19 -chr20 792903 . A G 60 . QNAME=cluster19_000000F;QSTART=24968452;QSTRAND=- GT:DP:AD ./.:19:8,11 1|1:26:5,21 ./.:35:25,10 -chr20 793346 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24917353;QSTRAND=- GT:DP:AD ./.:25:19,6 ./.:32:21,11 1|0:15:8,7 -chr20 793395 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=773841;QSTRAND=+ GT:DP:AD 1|1:23:6,17 1|1:36:25,11 1|1:14:7,7 -chr20 793450 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=748471;QSTRAND=+ GT:DP:AD 0|1:27:13,14 ./.:33:23,10 ./.:17:7,10 -chr20 793500 . C T 60 . QNAME=cluster19_000000F;QSTART=24967855;QSTRAND=- GT:DP:AD ./.:34:21,13 1|0:21:14,7 ./.:11:5,6 -chr20 793560 . C CG 60 . QNAME=HG002-S9-H2-000001F;QSTART=748582;QSTRAND=+ GT:DP:AD 0|1:17:12,5 ./.:33:15,18 ./.:29:18,11 -chr20 793560 . CGG C 60 . QNAME=cluster19_000000F;QSTART=24967795;QSTRAND=- GT:DP:AD ./.:29:5,24 1|0:41:19,22 1|1:39:15,24 -chr20 793560 . CG C 60 . QNAME=cluster19_000000F;QSTART=754505;QSTRAND=+ GT:DP:AD ./.:28:13,15 0|1:25:7,18 ./.:39:17,22 -chr20 793678 . C G 60 . QNAME=cluster19_000000F;QSTART=754621;QSTRAND=+ GT:DP:AD ./.:30:8,22 0|1:44:20,24 ./.:29:20,9 -chr20 793771 . T G 60 . QNAME=cluster19_000000F;QSTART=24967586;QSTRAND=- GT:DP:AD ./.:27:20,7 1|0:18:13,5 1|1:26:18,8 -chr20 794325 . T C 60 . QNAME=cluster19_000000F;QSTART=24967032;QSTRAND=- GT:DP:AD ./.:33:22,11 1|0:27:18,9 0|1:24:16,8 -chr20 794444 . A G 60 . QNAME=cluster19_000000F;QSTART=24966913;QSTRAND=- GT:DP:AD ./.:41:21,20 1|0:30:7,23 1|1:28:7,21 -chr20 794733 . T G 60 . QNAME=cluster19_000000F;QSTART=24966624;QSTRAND=- GT:DP:AD ./.:27:7,20 1|0:31:19,12 1|1:40:21,19 -chr20 795199 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24915502;QSTRAND=- GT:DP:AD ./.:30:9,21 ./.:26:6,20 1|0:17:6,11 -chr20 795434 . C A 60 . QNAME=cluster19_000000F;QSTART=24965923;QSTRAND=- GT:DP:AD ./.:30:9,21 1|0:32:17,15 1|1:35:19,16 -chr20 795539 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24915162;QSTRAND=- GT:DP:AD ./.:28:18,10 ./.:22:13,9 1|0:29:8,21 -chr20 795540 . C G 60 . QNAME=cluster23_scaffold_3;QSTART=24915161;QSTRAND=- GT:DP:AD ./.:24:18,6 ./.:14:9,5 1|0:34:25,9 -chr20 795731 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=750753;QSTRAND=+ GT:DP:AD 0|1:38:16,22 ./.:32:13,19 ./.:23:15,8 -chr20 795805 . G A 60 . QNAME=cluster19_000000F;QSTART=24965552;QSTRAND=- GT:DP:AD ./.:33:16,17 1|0:32:13,19 ./.:18:7,11 -chr20 795876 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=776322;QSTRAND=+ GT:DP:AD 1|1:33:18,15 ./.:22:5,17 1|0:15:9,6 -chr20 795985 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24899026;QSTRAND=- GT:DP:AD ./.:35:18,17 ./.:38:21,17 0|1:24:13,11 -chr20 796225 . T G 60 . QNAME=cluster19_000000F;QSTART=24965132;QSTRAND=- GT:DP:AD ./.:32:19,13 1|0:20:10,10 ./.:27:10,17 -chr20 796289 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=24898722;QSTRAND=- GT:DP:AD ./.:34:16,18 ./.:33:15,18 0|1:30:25,5 -chr20 796344 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=751366;QSTRAND=+ GT:DP:AD 0|1:42:25,17 1|1:35:19,16 ./.:17:7,10 -chr20 796564 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=751586;QSTRAND=+ GT:DP:AD 0|1:36:20,16 ./.:37:14,23 ./.:35:21,14 -chr20 797048 . A G 60 . QNAME=cluster19_000000F;QSTART=757991;QSTRAND=+ GT:DP:AD ./.:42:18,24 0|1:39:17,22 ./.:31:9,22 -chr20 797400 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=777846;QSTRAND=+ GT:DP:AD 1|0:20:8,12 ./.:34:10,24 ./.:17:10,7 -chr20 797739 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=778185;QSTRAND=+ GT:DP:AD 1|0:24:18,6 ./.:36:12,24 ./.:34:11,23 -chr20 797871 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=752893;QSTRAND=+ GT:DP:AD 0|1:34:16,18 0|1:31:6,25 ./.:43:22,21 -chr20 798053 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=753075;QSTRAND=+ GT:DP:AD 0|1:47:23,24 0|1:28:11,17 ./.:27:15,12 -chr20 798278 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=753300;QSTRAND=+ GT:DP:AD 0|1:19:12,7 0|1:26:8,18 ./.:24:5,19 -chr20 798467 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=753489;QSTRAND=+ GT:DP:AD 0|1:40:20,20 0|1:36:17,19 ./.:28:17,11 -chr20 798479 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=778925;QSTRAND=+ GT:DP:AD 1|1:22:11,11 0|1:31:16,15 ./.:19:9,10 -chr20 798594 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=753616;QSTRAND=+ GT:DP:AD 0|1:38:22,16 0|1:39:21,18 ./.:27:5,22 -chr20 798717 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=753739;QSTRAND=+ GT:DP:AD 0|1:36:15,21 ./.:34:22,12 ./.:22:6,16 -chr20 798853 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=779299;QSTRAND=+ GT:DP:AD 1|0:46:25,21 ./.:24:5,19 ./.:35:16,19 -chr20 799277 . C CAAAA 60 . QNAME=HG002-S9-H2-000001F;QSTART=754300;QSTRAND=+ GT:DP:AD 0|1:26:18,8 ./.:27:19,8 ./.:26:12,14 -chr20 799277 . C CAA 60 . QNAME=cluster19_000000F;QSTART=24962078;QSTRAND=- GT:DP:AD ./.:18:6,12 1|0:25:15,10 1|1:33:10,23 -chr20 799300 . C T 60 . QNAME=cluster19_000000F;QSTART=24962055;QSTRAND=- GT:DP:AD ./.:39:17,22 1|0:26:21,5 1|1:24:7,17 -chr20 799510 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=779956;QSTRAND=+ GT:DP:AD 1|1:31:16,15 1|0:30:25,5 1|1:28:6,22 -chr20 799644 . G A 60 . QNAME=cluster19_000000F;QSTART=24961711;QSTRAND=- GT:DP:AD ./.:26:19,7 1|0:33:9,24 1|1:43:20,23 -chr20 799744 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=780190;QSTRAND=+ GT:DP:AD 1|0:27:5,22 ./.:14:8,6 ./.:18:6,12 -chr20 800427 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=780873;QSTRAND=+ GT:DP:AD 1|0:29:23,6 ./.:24:11,13 ./.:13:5,8 -chr20 800494 . TCGATTACCTGCTCCACCCTGACTCACTC T 60 . QNAME=HG002-S9-H2-000001F;QSTART=755521;QSTRAND=+;SVTYPE=DEL;SVLEN=-28 GT:DP:AD 0/1:22:7,15 1/0:22:13,9 1/1:29:24,5 -chr20 800604 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781050;QSTRAND=+ GT:DP:AD 1|0:39:25,14 ./.:32:25,7 ./.:34:19,15 -chr20 800640 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781086;QSTRAND=+ GT:DP:AD 1|0:27:17,10 ./.:32:20,12 ./.:39:16,23 -chr20 800671 . GCACTCACCCCAT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=781118;QSTRAND=+ GT:DP:AD 1|0:25:17,8 ./.:39:24,15 ./.:15:7,8 -chr20 800707 . G A 60 . QNAME=cluster19_000000F;QSTART=24960676;QSTRAND=- GT:DP:AD ./.:31:15,16 1|0:35:10,25 1|1:12:7,5 -chr20 800818 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781252;QSTRAND=+ GT:DP:AD 1|1:19:14,5 1|0:30:21,9 1|1:17:7,10 -chr20 800884 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=781318;QSTRAND=+ GT:DP:AD 1|0:27:15,12 ./.:28:17,11 ./.:31:23,8 -chr20 800927 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=781361;QSTRAND=+ GT:DP:AD 1|0:22:12,10 ./.:32:12,20 ./.:22:13,9 -chr20 800955 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=781389;QSTRAND=+ GT:DP:AD 1|0:24:19,5 ./.:43:24,19 ./.:36:21,15 -chr20 800960 . CCTT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781395;QSTRAND=+ GT:DP:AD 1|0:37:25,12 ./.:25:17,8 ./.:34:22,12 -chr20 801002 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781433;QSTRAND=+ GT:DP:AD 1|0:17:10,7 ./.:29:18,11 ./.:30:18,12 -chr20 801097 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781528;QSTRAND=+ GT:DP:AD 1|0:41:18,23 ./.:36:15,21 ./.:37:15,22 -chr20 801205 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781636;QSTRAND=+ GT:DP:AD 1|0:35:15,20 ./.:27:6,21 ./.:32:18,14 -chr20 801403 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=781834;QSTRAND=+ GT:DP:AD 1|0:23:7,16 ./.:41:22,19 ./.:21:13,8 -chr20 801427 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781858;QSTRAND=+ GT:DP:AD 1|0:21:7,14 ./.:27:8,19 ./.:23:7,16 -chr20 801488 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781919;QSTRAND=+ GT:DP:AD 1|0:18:13,5 1|0:35:13,22 1|1:23:7,16 -chr20 801793 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=782224;QSTRAND=+ GT:DP:AD 1|0:36:13,23 ./.:32:14,18 ./.:29:16,13 -chr20 801807 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=782238;QSTRAND=+ GT:DP:AD 1|0:35:20,15 ./.:46:22,24 ./.:36:25,11 -chr20 801853 . CAAATAAAT C 60 . QNAME=cluster19_000000F;QSTART=24959530;QSTRAND=- GT:DP:AD ./.:37:13,24 1|0:30:13,17 0|1:39:16,23 -chr20 801853 . CAAAT C 60 . QNAME=cluster23_scaffold_3;QSTART=24908874;QSTRAND=- GT:DP:AD ./.:23:16,7 ./.:29:24,5 1|0:25:16,9 -chr20 801854 . AAATAAAT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=782286;QSTRAND=+ GT:DP:AD 1|0:33:14,19 ./.:40:15,25 ./.:41:23,18 -chr20 801893 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=782317;QSTRAND=+ GT:DP:AD 1|0:42:21,21 ./.:36:24,12 ./.:30:19,11 -chr20 802063 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=782487;QSTRAND=+ GT:DP:AD 1|0:20:6,14 ./.:23:7,16 ./.:23:7,16 -chr20 802155 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=757153;QSTRAND=+ GT:DP:AD 0|1:33:20,13 1|0:37:18,19 1|1:30:11,19 -chr20 802331 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=782755;QSTRAND=+ GT:DP:AD 1|1:26:15,11 1|0:29:8,21 ./.:46:21,25 -chr20 802369 . G A 60 . QNAME=cluster19_000000F;QSTART=763312;QSTRAND=+ GT:DP:AD ./.:22:6,16 0|1:37:18,19 ./.:23:9,14 -chr20 802531 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=757529;QSTRAND=+ GT:DP:AD 0|1:39:16,23 ./.:28:5,23 ./.:24:19,5 -chr20 802606 . C CA 60 . QNAME=HG002-S9-H2-000001F;QSTART=757605;QSTRAND=+ GT:DP:AD 0|1:43:24,19 ./.:38:20,18 0|1:24:12,12 -chr20 802739 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=757738;QSTRAND=+ GT:DP:AD 0|1:38:14,24 0|1:33:24,9 1|0:43:21,22 -chr20 803221 . C T 60 . QNAME=cluster19_000000F;QSTART=24958170;QSTRAND=- GT:DP:AD ./.:14:6,8 1|1:26:10,16 1|1:48:25,23 -chr20 803367 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=783791;QSTRAND=+ GT:DP:AD 1|1:30:14,16 1|1:28:10,18 1|1:17:9,8 -chr20 803419 . C T 60 . QNAME=cluster19_000000F;QSTART=24957972;QSTRAND=- GT:DP:AD ./.:21:13,8 1|1:29:5,24 1|1:34:22,12 -chr20 803499 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=783923;QSTRAND=+ GT:DP:AD 1|0:36:17,19 ./.:15:6,9 ./.:23:10,13 -chr20 803703 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=784127;QSTRAND=+ GT:DP:AD 1|1:27:13,14 1|1:25:5,20 1|1:16:11,5 -chr20 803760 . C T 60 . QNAME=cluster19_000000F;QSTART=24957631;QSTRAND=- GT:DP:AD ./.:37:15,22 1|1:34:15,19 1|1:21:13,8 -chr20 804087 . G A 60 . QNAME=cluster19_000000F;QSTART=24957304;QSTRAND=- GT:DP:AD ./.:30:15,15 1|1:16:6,10 1|1:41:20,21 -chr20 804255 . C T 60 . QNAME=cluster19_000000F;QSTART=24957136;QSTRAND=- GT:DP:AD ./.:29:6,23 1|1:30:9,21 1|1:29:21,8 -chr20 804315 . C G 60 . QNAME=cluster19_000000F;QSTART=24957076;QSTRAND=- GT:DP:AD ./.:47:22,25 1|1:29:10,19 1|1:33:25,8 -chr20 804381 . C T 60 . QNAME=cluster19_000000F;QSTART=24957010;QSTRAND=- GT:DP:AD ./.:43:20,23 1|1:48:24,24 1|1:39:16,23 -chr20 804444 . G A 60 . QNAME=cluster19_000000F;QSTART=24956947;QSTRAND=- GT:DP:AD ./.:22:9,13 1|1:37:12,25 1|1:33:25,8 -chr20 804465 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=784889;QSTRAND=+ GT:DP:AD 1|1:25:8,17 ./.:27:7,20 ./.:40:21,19 -chr20 804804 . A AT 60 . QNAME=HG002-S9-H1-000001F;QSTART=785229;QSTRAND=+ GT:DP:AD 1|0:27:22,5 ./.:33:17,16 ./.:23:11,12 -chr20 804804 . AT A 60 . QNAME=cluster19_000000F;QSTART=24956587;QSTRAND=- GT:DP:AD ./.:34:19,15 1|1:27:16,11 1|1:34:19,15 -chr20 805255 . T C 60 . QNAME=cluster19_000000F;QSTART=24956137;QSTRAND=- GT:DP:AD ./.:46:25,21 1|1:30:19,11 1|1:23:5,18 -chr20 805274 . T C 60 . QNAME=cluster19_000000F;QSTART=24956118;QSTRAND=- GT:DP:AD ./.:27:13,14 1|1:16:7,9 1|1:43:23,20 -chr20 805356 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=785781;QSTRAND=+ GT:DP:AD 1|1:27:22,5 1|1:27:16,11 1|1:40:24,16 -chr20 805464 . C G 60 . QNAME=cluster19_000000F;QSTART=24955928;QSTRAND=- GT:DP:AD ./.:28:11,17 1|1:41:24,17 1|1:46:25,21 -chr20 805609 . AAG A 60 . QNAME=cluster19_000000F;QSTART=24955783;QSTRAND=- GT:DP:AD ./.:48:25,23 1|1:29:21,8 1|1:17:10,7 -chr20 805627 . AT A 60 . QNAME=cluster23_scaffold_2;QSTART=24889420;QSTRAND=- GT:DP:AD ./.:21:12,9 ./.:26:14,12 0|1:18:11,7 -chr20 805812 . C T 60 . QNAME=cluster19_000000F;QSTART=24955582;QSTRAND=- GT:DP:AD ./.:36:25,11 1|1:34:17,17 1|1:37:12,25 -chr20 806032 . T TA 60 . QNAME=cluster23_scaffold_2;QSTART=24889015;QSTRAND=- GT:DP:AD ./.:28:20,8 ./.:31:21,10 0|1:15:9,6 -chr20 806060 . A G 60 . QNAME=cluster19_000000F;QSTART=24955334;QSTRAND=- GT:DP:AD ./.:30:25,5 1|1:30:8,22 1|1:31:18,13 -chr20 806121 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=786547;QSTRAND=+ GT:DP:AD 1|1:35:11,24 1|1:30:6,24 1|1:35:21,14 -chr20 806416 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=786842;QSTRAND=+ GT:DP:AD 1|1:29:18,11 1|1:42:20,22 1|1:36:18,18 -chr20 806539 . CT C 60 . QNAME=cluster23_scaffold_2;QSTART=24888507;QSTRAND=- GT:DP:AD ./.:41:18,23 ./.:23:7,16 0|1:20:15,5 -chr20 806698 . A G 60 . QNAME=cluster19_000000F;QSTART=24954695;QSTRAND=- GT:DP:AD ./.:33:22,11 1|1:29:20,9 1|1:19:8,11 -chr20 806714 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24904019;QSTRAND=- GT:DP:AD ./.:32:21,11 ./.:29:10,19 1|0:19:8,11 -chr20 807227 . T TTTTATTTATTTATTTATTTA 60 . QNAME=cluster19_000000F;QSTART=24954146;QSTRAND=- GT:DP:AD ./.:36:21,15 1|1:40:20,20 1|1:27:12,15 -chr20 807315 . A G 60 . QNAME=cluster19_000000F;QSTART=24954058;QSTRAND=- GT:DP:AD ./.:40:18,22 1|1:38:16,22 1|1:24:11,13 -chr20 807395 . C T 60 . QNAME=cluster19_000000F;QSTART=24953978;QSTRAND=- GT:DP:AD ./.:28:6,22 1|1:42:23,19 1|1:46:23,23 -chr20 807886 . CT C 60 . QNAME=cluster23_scaffold_2;QSTART=24887141;QSTRAND=- GT:DP:AD ./.:34:14,20 ./.:16:8,8 0|1:25:15,10 -chr20 808070 . G A 60 . QNAME=cluster19_000000F;QSTART=24953303;QSTRAND=- GT:DP:AD ./.:46:25,21 1|1:34:24,10 1|1:15:6,9 -chr20 808486 . C T 60 . QNAME=cluster19_000000F;QSTART=24952887;QSTRAND=- GT:DP:AD ./.:25:10,15 1|1:39:16,23 1|1:41:21,20 -chr20 808580 . CT C 60 . QNAME=cluster23_scaffold_2;QSTART=24886448;QSTRAND=- GT:DP:AD ./.:33:20,13 ./.:29:24,5 0|1:35:23,12 -chr20 808747 . T C 60 . QNAME=cluster19_000000F;QSTART=24952626;QSTRAND=- GT:DP:AD ./.:50:25,25 1|1:35:19,16 1|1:46:23,23 -chr20 808798 . T TG 60 . QNAME=cluster23_scaffold_2;QSTART=24886230;QSTRAND=- GT:DP:AD ./.:40:20,20 ./.:29:15,14 0|1:20:14,6 -chr20 808973 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=789399;QSTRAND=+ GT:DP:AD 1|1:35:24,11 1|1:28:5,23 1|1:16:8,8 -chr20 809124 . T TA 60 . QNAME=cluster19_000000F;QSTART=24952248;QSTRAND=- GT:DP:AD ./.:31:11,20 1|1:31:9,22 1|0:26:5,21 -chr20 809124 . T TAA 60 . QNAME=cluster23_scaffold_2;QSTART=24885902;QSTRAND=- GT:DP:AD ./.:28:18,10 ./.:30:6,24 0|1:32:17,15 -chr20 809392 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=789818;QSTRAND=+ GT:DP:AD 1|1:14:8,6 1|1:45:25,20 1|1:34:22,12 -chr20 809449 . C A 60 . QNAME=cluster19_000000F;QSTART=24951923;QSTRAND=- GT:DP:AD ./.:22:8,14 1|1:13:6,7 1|1:18:5,13 -chr20 809476 . C T 60 . QNAME=cluster19_000000F;QSTART=24951896;QSTRAND=- GT:DP:AD ./.:26:15,11 1|1:31:12,19 1|1:23:13,10 -chr20 809653 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=790079;QSTRAND=+ GT:DP:AD 1|1:48:23,25 ./.:29:16,13 ./.:21:5,16 -chr20 809775 . T G 60 . QNAME=cluster19_000000F;QSTART=24951597;QSTRAND=- GT:DP:AD ./.:20:14,6 1|0:35:21,14 ./.:37:21,16 -chr20 810079 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=790505;QSTRAND=+ GT:DP:AD 1|1:25:16,9 1|1:33:8,25 1|1:43:21,22 -chr20 810083 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=790509;QSTRAND=+ GT:DP:AD 1|1:31:25,6 ./.:38:19,19 ./.:20:9,11 -chr20 810565 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=790991;QSTRAND=+ GT:DP:AD 1|1:42:22,20 1|1:27:11,16 1|1:33:17,16 -chr20 810659 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=791085;QSTRAND=+ GT:DP:AD 1|1:24:13,11 1|1:28:23,5 1|1:20:7,13 -chr20 810742 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=791168;QSTRAND=+ GT:DP:AD 1|1:20:14,6 ./.:28:23,5 ./.:24:7,17 -chr20 811032 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=791458;QSTRAND=+ GT:DP:AD 1|1:22:16,6 ./.:34:22,12 ./.:32:18,14 -chr20 811102 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=791528;QSTRAND=+ GT:DP:AD 1|1:20:12,8 ./.:30:9,21 ./.:42:25,17 -chr20 811314 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=791740;QSTRAND=+ GT:DP:AD 1|1:14:8,6 1|1:30:5,25 1|1:27:8,19 -chr20 811539 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=791965;QSTRAND=+ GT:DP:AD 1|1:37:14,23 ./.:26:19,7 ./.:25:6,19 -chr20 811587 . G A 60 . QNAME=cluster19_000000F;QSTART=24949785;QSTRAND=- GT:DP:AD ./.:12:5,7 1|1:36:12,24 1|1:46:22,24 -chr20 811839 . A AG 60 . QNAME=cluster23_scaffold_2;QSTART=24883186;QSTRAND=- GT:DP:AD ./.:34:12,22 ./.:11:6,5 0|1:30:6,24 -chr20 812140 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=792566;QSTRAND=+ GT:DP:AD 1|1:35:22,13 ./.:36:18,18 ./.:31:13,18 -chr20 812429 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=792855;QSTRAND=+ GT:DP:AD 1|1:25:8,17 ./.:28:15,13 ./.:37:23,14 -chr20 812492 . A C 60 . QNAME=cluster19_000000F;QSTART=24948880;QSTRAND=- GT:DP:AD ./.:30:20,10 1|1:14:9,5 1|1:50:25,25 -chr20 813255 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=793681;QSTRAND=+ GT:DP:AD 1|1:40:21,19 ./.:38:15,23 1|0:35:23,12 -chr20 813573 . C T 60 . QNAME=cluster19_000000F;QSTART=24947799;QSTRAND=- GT:DP:AD ./.:37:19,18 1|1:42:18,24 0|1:35:11,24 -chr20 813792 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=794218;QSTRAND=+ GT:DP:AD 1|1:22:13,9 ./.:20:14,6 1|0:25:20,5 -chr20 813863 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=794289;QSTRAND=+ GT:DP:AD 1|1:33:16,17 1|1:39:14,25 1|1:44:22,22 -chr20 814342 . T TG 60 . QNAME=cluster23_scaffold_2;QSTART=24880682;QSTRAND=- GT:DP:AD ./.:36:17,19 ./.:27:18,9 0|1:38:15,23 -chr20 814479 . AT A 60 . QNAME=cluster23_scaffold_2;QSTART=24880545;QSTRAND=- GT:DP:AD ./.:37:23,14 ./.:23:13,10 0|1:28:12,16 -chr20 814505 . T TTTTATTTA 60 . QNAME=HG002-S9-H1-000001F;QSTART=794932;QSTRAND=+ GT:DP:AD 1|1:40:15,25 ./.:25:12,13 1|0:33:24,9 -chr20 814505 . T TTTTA 60 . QNAME=cluster19_000000F;QSTART=24946863;QSTRAND=- GT:DP:AD ./.:24:15,9 1|1:15:10,5 0|1:42:23,19 -chr20 815073 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=795507;QSTRAND=+ GT:DP:AD 1|1:34:23,11 ./.:30:13,17 1|0:17:5,12 -chr20 815387 . A T 60 . QNAME=cluster19_000000F;QSTART=24945981;QSTRAND=- GT:DP:AD ./.:26:10,16 1|1:14:6,8 0|1:39:14,25 -chr20 815789 . C A 60 . QNAME=cluster19_000000F;QSTART=24945579;QSTRAND=- GT:DP:AD ./.:36:23,13 1|1:27:9,18 ./.:37:23,14 -chr20 816179 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=796613;QSTRAND=+ GT:DP:AD 1|1:38:19,19 ./.:17:11,6 1|0:27:14,13 -chr20 816272 . CT C 60 . QNAME=cluster23_scaffold_2;QSTART=24878749;QSTRAND=- GT:DP:AD ./.:19:11,8 ./.:24:19,5 0|1:22:9,13 -chr20 816693 . GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=797128;QSTRAND=+ GT:DP:AD 1|0:17:7,10 1|1:23:15,8 1|0:28:17,11 -chr20 816723 . TTGTGCG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=797157;QSTRAND=+ GT:DP:AD 1|0:42:21,21 ./.:44:24,20 1|0:30:8,22 -chr20 816728 . CGT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=771737;QSTRAND=+ GT:DP:AD 0|1:15:10,5 ./.:14:7,7 ./.:30:14,16 -chr20 816728 . C CGTGT 60 . QNAME=cluster23_scaffold_2;QSTART=24878290;QSTRAND=- GT:DP:AD ./.:27:18,9 ./.:26:7,19 0|1:36:16,20 -chr20 816757 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=797184;QSTRAND=+ GT:DP:AD 1|0:33:16,17 ./.:19:5,14 1|0:14:8,6 -chr20 817397 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24877621;QSTRAND=- GT:DP:AD ./.:40:20,20 ./.:20:15,5 0|1:33:16,17 -chr20 817512 . A G 60 . QNAME=cluster19_000000F;QSTART=24943857;QSTRAND=- GT:DP:AD ./.:32:8,24 1|0:10:5,5 ./.:17:8,9 -chr20 817544 . G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=797972;QSTRAND=+ GT:DP:AD 1|0:35:25,10 ./.:27:12,15 1|0:27:6,21 -chr20 817544 . GA G 60 . QNAME=HG002-S9-H2-000001F;QSTART=772551;QSTRAND=+ GT:DP:AD 0|1:28:12,16 0|1:35:21,14 ./.:23:10,13 -chr20 817544 . GAA G 60 . QNAME=cluster19_000000F;QSTART=24943825;QSTRAND=- GT:DP:AD ./.:24:12,12 1|0:24:7,17 0|1:30:23,7 -chr20 817584 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=798012;QSTRAND=+ GT:DP:AD 1|0:27:7,20 ./.:35:15,20 1|0:18:13,5 -chr20 817587 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=798015;QSTRAND=+ GT:DP:AD 1|0:34:13,21 ./.:37:15,22 1|0:19:8,11 -chr20 817664 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=798092;QSTRAND=+ GT:DP:AD 1|0:23:8,15 ./.:20:12,8 1|0:33:21,12 -chr20 817690 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=798118;QSTRAND=+ GT:DP:AD 1|0:27:12,15 1|1:32:21,11 1|1:26:8,18 -chr20 817718 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=798146;QSTRAND=+ GT:DP:AD 1|0:31:15,16 ./.:11:5,6 1|0:37:23,14 -chr20 817808 . T C 60 . QNAME=cluster19_000000F;QSTART=24943563;QSTRAND=- GT:DP:AD ./.:27:21,6 1|1:38:25,13 ./.:41:25,16 -chr20 817809 . T A 60 . QNAME=cluster19_000000F;QSTART=24943562;QSTRAND=- GT:DP:AD ./.:35:23,12 1|1:13:5,8 ./.:26:19,7 -chr20 817850 . G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=798279;QSTRAND=+ GT:DP:AD 1|0:41:22,19 ./.:17:8,9 ./.:41:22,19 -chr20 817871 . G GA 60 . QNAME=cluster23_scaffold_2;QSTART=24877148;QSTRAND=- GT:DP:AD ./.:24:18,6 ./.:37:14,23 0|1:26:13,13 -chr20 818023 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=798452;QSTRAND=+ GT:DP:AD 1|0:36:24,12 ./.:21:7,14 1|0:29:18,11 -chr20 818055 . T TG 60 . QNAME=cluster23_scaffold_2;QSTART=24876963;QSTRAND=- GT:DP:AD ./.:21:9,12 ./.:43:19,24 0|1:29:19,10 -chr20 818068 . T TG 60 . QNAME=cluster23_scaffold_2;QSTART=24876949;QSTRAND=- GT:DP:AD ./.:30:8,22 ./.:27:11,16 0|1:26:20,6 -chr20 818085 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=798514;QSTRAND=+ GT:DP:AD 1|0:31:14,17 ./.:17:11,6 1|0:28:9,19 -chr20 818112 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=798541;QSTRAND=+ GT:DP:AD 1|0:21:12,9 1|1:24:5,19 1|1:35:14,21 -chr20 818177 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24876840;QSTRAND=- GT:DP:AD ./.:25:12,13 ./.:18:13,5 0|1:40:24,16 -chr20 818388 . A AG 60 . QNAME=cluster23_scaffold_3;QSTART=24892321;QSTRAND=- GT:DP:AD ./.:48:24,24 ./.:36:14,22 1|0:48:23,25 -chr20 818488 . A ATT 60 . QNAME=HG002-S9-H1-000001F;QSTART=798918;QSTRAND=+ GT:DP:AD 1|0:14:9,5 ./.:27:21,6 ./.:28:10,18 -chr20 818488 . A AT 60 . QNAME=HG002-S9-H2-000001F;QSTART=773494;QSTRAND=+ GT:DP:AD 0|1:33:24,9 ./.:14:5,9 ./.:33:15,18 -chr20 818644 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=799075;QSTRAND=+ GT:DP:AD 1|1:23:11,12 ./.:32:16,16 1|0:45:25,20 -chr20 818794 . C CTT 60 . QNAME=HG002-S9-H1-000001F;QSTART=799226;QSTRAND=+ GT:DP:AD 1|1:21:11,10 ./.:30:10,20 1|0:19:9,10 -chr20 818794 . CT C 60 . QNAME=cluster23_scaffold_2;QSTART=24876223;QSTRAND=- GT:DP:AD ./.:17:10,7 ./.:31:13,18 0|1:34:14,20 -chr20 818839 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=24876179;QSTRAND=- GT:DP:AD ./.:19:13,6 ./.:44:20,24 0|1:36:14,22 -chr20 818891 . A G 60 . QNAME=cluster19_000000F;QSTART=24942480;QSTRAND=- GT:DP:AD ./.:34:9,25 1|1:26:20,6 ./.:20:7,13 -chr20 818898 . T TC 60 . QNAME=cluster23_scaffold_2;QSTART=24876119;QSTRAND=- GT:DP:AD ./.:21:9,12 ./.:44:21,23 0|1:33:10,23 -chr20 818940 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=799373;QSTRAND=+ GT:DP:AD 1|1:35:13,22 ./.:42:18,24 1|1:32:15,17 -chr20 818970 . G C 60 . QNAME=cluster19_000000F;QSTART=24942401;QSTRAND=- GT:DP:AD ./.:27:13,14 1|1:28:21,7 ./.:21:5,16 -chr20 819017 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=774025;QSTRAND=+ GT:DP:AD 0|1:29:14,15 ./.:31:25,6 ./.:27:15,12 -chr20 819249 . T C 60 . QNAME=cluster19_000000F;QSTART=780213;QSTRAND=+ GT:DP:AD ./.:24:7,17 0|1:25:5,20 ./.:28:5,23 -chr20 819251 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=774259;QSTRAND=+ GT:DP:AD 0|1:34:21,13 ./.:27:17,10 ./.:27:20,7 diff --git a/repo_utils/test_files/answer_key/divided/multi_00000018.vcf b/repo_utils/test_files/answer_key/divided/multi_00000018.vcf deleted file mode 100644 index 38b9a27d..00000000 --- a/repo_utils/test_files/answer_key/divided/multi_00000018.vcf +++ /dev/null @@ -1,159 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##bcftools_mergeVersion=1.12+htslib-1.12 -##bcftools_mergeCommand=merge -O z -f x -m none input1.vcf.gz input2.vcf.gz input3.vcf.gz; Date=Mon Aug 16 18:05:13 2021 -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 820514 . T TTTC 60 . QNAME=HG002-S9-H1-000001F;QSTART=802126;QSTRAND=+ GT:DP:AD 1|1:23:14,9 1|1:36:23,13 1|1:25:9,16 -chr20 820545 . T TTC 60 . QNAME=cluster19_000000F;QSTART=24937541;QSTRAND=- GT:DP:AD ./.:17:10,7 1|1:29:10,19 ./.:23:15,8 -chr20 820587 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=802201;QSTRAND=+ GT:DP:AD 1|1:31:16,15 ./.:31:16,15 1|0:27:18,9 -chr20 820752 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=802366;QSTRAND=+ GT:DP:AD 1|1:39:24,15 ./.:40:24,16 1|0:37:20,17 -chr20 821376 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=24871732;QSTRAND=- GT:DP:AD ./.:28:20,8 ./.:16:5,11 0|1:22:17,5 -chr20 821480 . G T 60 . QNAME=cluster19_000000F;QSTART=24936606;QSTRAND=- GT:DP:AD ./.:35:17,18 1|1:41:18,23 0|1:17:10,7 -chr20 822153 . ATTTT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=803768;QSTRAND=+ GT:DP:AD 1|1:27:11,16 ./.:34:18,16 1|0:29:8,21 -chr20 822153 . ATTT A 60 . QNAME=cluster19_000000F;QSTART=24935933;QSTRAND=- GT:DP:AD ./.:47:23,24 1|1:26:15,11 ./.:48:23,25 -chr20 822153 . A AT 60 . QNAME=cluster23_scaffold_2;QSTART=24870954;QSTRAND=- GT:DP:AD ./.:41:23,18 ./.:36:23,13 0|1:23:12,11 -chr20 822622 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24870485;QSTRAND=- GT:DP:AD ./.:36:12,24 ./.:36:17,19 0|1:25:6,19 -chr20 823109 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=804719;QSTRAND=+ GT:DP:AD 1|1:38:15,23 1|1:39:16,23 1|1:28:9,19 -chr20 824454 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=806064;QSTRAND=+ GT:DP:AD 1|1:40:22,18 1|1:18:9,9 1|1:38:24,14 -chr20 825318 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=806928;QSTRAND=+ GT:DP:AD 1|1:16:10,6 ./.:33:23,10 1|0:24:17,7 -chr20 825338 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=806948;QSTRAND=+ GT:DP:AD 1|1:40:19,21 ./.:21:12,9 1|0:32:21,11 -chr20 825828 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=807438;QSTRAND=+ GT:DP:AD 1|1:34:23,11 1|1:27:5,22 1|1:39:14,25 -chr20 826034 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=807644;QSTRAND=+ GT:DP:AD 1|1:46:25,21 1|1:20:8,12 1|1:47:24,23 -chr20 826235 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=807845;QSTRAND=+ GT:DP:AD 1|1:35:15,20 1|1:48:23,25 1|1:40:17,23 -chr20 826944 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=808554;QSTRAND=+ GT:DP:AD 1|1:36:23,13 ./.:35:20,15 1|0:23:12,11 -chr20 827056 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=808666;QSTRAND=+ GT:DP:AD 1|1:41:22,19 ./.:19:11,8 1|0:29:24,5 -chr20 827617 . C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=809228;QSTRAND=+ GT:DP:AD 1|1:25:12,13 ./.:20:5,15 1|0:24:11,13 -chr20 827617 . C CAA 60 . QNAME=cluster19_000000F;QSTART=24930470;QSTRAND=- GT:DP:AD ./.:39:24,15 1|1:45:24,21 0|1:44:23,21 -chr20 827787 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=809398;QSTRAND=+ GT:DP:AD 1|1:40:16,24 1|1:48:23,25 1|1:34:20,14 -chr20 827840 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24865265;QSTRAND=- GT:DP:AD ./.:40:25,15 ./.:33:14,19 0|1:40:19,21 -chr20 827959 . G A 60 . QNAME=cluster19_000000F;QSTART=24930128;QSTRAND=- GT:DP:AD ./.:24:9,15 1|1:32:25,7 ./.:27:11,16 -chr20 828060 . G GAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=809672;QSTRAND=+ GT:DP:AD 1|1:25:6,19 1|1:39:17,22 0|1:32:19,13 -chr20 828060 . G GAAAAA 60 . QNAME=cluster23_scaffold_3;QSTART=24881385;QSTRAND=- GT:DP:AD ./.:26:11,15 ./.:31:16,15 1|0:24:9,15 -chr20 828725 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=810340;QSTRAND=+ GT:DP:AD 1|1:18:5,13 1|1:39:23,16 1|1:39:18,21 -chr20 828856 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=810471;QSTRAND=+ GT:DP:AD 1|1:33:21,12 1|1:28:13,15 1|1:37:23,14 -chr20 828857 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=810472;QSTRAND=+ GT:DP:AD 1|1:49:25,24 1|1:42:23,19 1|1:43:21,22 -chr20 828946 . C T 60 . QNAME=cluster19_000000F;QSTART=24929137;QSTRAND=- GT:DP:AD ./.:29:15,14 1|1:27:9,18 ./.:34:20,14 -chr20 829194 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24863907;QSTRAND=- GT:DP:AD ./.:29:13,16 ./.:26:15,11 0|1:49:24,25 -chr20 829287 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=810902;QSTRAND=+ GT:DP:AD 1|1:23:6,17 1|1:33:11,22 1|1:38:23,15 -chr20 830064 . A G 60 . QNAME=cluster19_000000F;QSTART=24928019;QSTRAND=- GT:DP:AD ./.:21:7,14 1|1:43:24,19 0|1:14:6,8 -chr20 830268 . C CTT 60 . QNAME=cluster23_scaffold_2;QSTART=24862831;QSTRAND=- GT:DP:AD ./.:37:12,25 ./.:29:21,8 0|1:38:15,23 -chr20 830270 . T C 60 . QNAME=cluster19_000000F;QSTART=24927813;QSTRAND=- GT:DP:AD ./.:33:12,21 1|1:36:20,16 ./.:16:8,8 -chr20 830311 . A G 60 . QNAME=cluster19_000000F;QSTART=24927772;QSTRAND=- GT:DP:AD ./.:24:13,11 1|1:48:25,23 0|1:17:12,5 -chr20 830449 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=812065;QSTRAND=+ GT:DP:AD 1|0:30:7,23 ./.:36:16,20 ./.:21:10,11 -chr20 830449 . C CTT 60 . QNAME=cluster19_000000F;QSTART=24927632;QSTRAND=- GT:DP:AD ./.:37:23,14 1|1:28:6,22 0|1:33:13,20 -chr20 830787 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=812401;QSTRAND=+ GT:DP:AD 1|1:17:7,10 1|1:29:8,21 1|1:37:18,19 -chr20 830864 . G A 60 . QNAME=cluster19_000000F;QSTART=24927217;QSTRAND=- GT:DP:AD ./.:30:10,20 1|1:29:23,6 0|1:49:24,25 -chr20 831203 . G C 60 . QNAME=cluster19_000000F;QSTART=24926878;QSTRAND=- GT:DP:AD ./.:26:14,12 1|1:28:9,19 ./.:30:7,23 -chr20 831231 . T C 60 . QNAME=cluster19_000000F;QSTART=24926850;QSTRAND=- GT:DP:AD ./.:28:23,5 1|1:29:5,24 0|1:31:10,21 -chr20 831257 . C CA 60 . QNAME=cluster19_000000F;QSTART=795540;QSTRAND=+ GT:DP:AD ./.:24:12,12 0|1:45:22,23 1|1:45:22,23 -chr20 831332 . T C 60 . QNAME=cluster19_000000F;QSTART=24926749;QSTRAND=- GT:DP:AD ./.:20:7,13 1|1:31:25,6 0|1:29:9,20 -chr20 831358 . A T 60 . QNAME=cluster19_000000F;QSTART=24926723;QSTRAND=- GT:DP:AD ./.:33:13,20 1|1:33:22,11 0|1:39:14,25 -chr20 831366 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24861730;QSTRAND=- GT:DP:AD ./.:38:14,24 ./.:38:18,20 0|1:22:17,5 -chr20 832087 . A C 60 . QNAME=cluster19_000000F;QSTART=24925994;QSTRAND=- GT:DP:AD ./.:28:13,15 1|1:28:13,15 0|1:41:21,20 -chr20 833024 . A G 60 . QNAME=cluster19_000000F;QSTART=24925057;QSTRAND=- GT:DP:AD ./.:29:13,16 1|0:34:14,20 ./.:29:6,23 -chr20 833025 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=814639;QSTRAND=+ GT:DP:AD 1|1:29:14,15 0|1:23:7,16 0|1:24:9,15 -chr20 833025 . AG A 60 . QNAME=cluster19_000000F;QSTART=24925056;QSTRAND=- GT:DP:AD ./.:29:14,15 1|0:28:6,22 ./.:17:8,9 -chr20 833026 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=814640;QSTRAND=+ GT:DP:AD 1|1:26:11,15 0|1:28:11,17 0|1:23:11,12 -chr20 833026 . G GA 60 . QNAME=cluster23_scaffold_3;QSTART=24876417;QSTRAND=- GT:DP:AD ./.:36:20,16 ./.:21:8,13 1|0:24:9,15 -chr20 833108 . C G 60 . QNAME=cluster19_000000F;QSTART=24924974;QSTRAND=- GT:DP:AD ./.:39:15,24 1|1:33:15,18 0|1:38:22,16 -chr20 835141 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24857955;QSTRAND=- GT:DP:AD ./.:23:10,13 ./.:29:19,10 0|1:34:14,20 -chr20 835164 . A ATC 60 . QNAME=HG002-S9-H1-000001F;QSTART=816779;QSTRAND=+ GT:DP:AD 1|1:37:21,16 ./.:41:17,24 ./.:24:7,17 -chr20 835200 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=24874243;QSTRAND=- GT:DP:AD ./.:36:12,24 ./.:37:22,15 1|0:37:19,18 -chr20 835200 . C CTCTATA 60 . QNAME=cluster23_scaffold_2;QSTART=24857890;QSTRAND=- GT:DP:AD ./.:19:6,13 ./.:38:18,20 0|1:33:24,9 -chr20 835202 . A C 60 . QNAME=cluster19_000000F;QSTART=24922880;QSTRAND=- GT:DP:AD ./.:21:7,14 1|1:21:5,16 ./.:40:18,22 -chr20 836246 . TG T 60 . QNAME=cluster19_000000F;QSTART=24921836;QSTRAND=- GT:DP:AD ./.:36:12,24 1|1:31:12,19 0|1:32:20,12 -chr20 837045 . G GTT 60 . QNAME=cluster23_scaffold_2;QSTART=24856044;QSTRAND=- GT:DP:AD ./.:44:25,19 ./.:41:16,25 0|1:19:5,14 -chr20 838387 . G C 60 . QNAME=cluster23_scaffold_2;QSTART=24854702;QSTRAND=- GT:DP:AD ./.:25:19,6 ./.:21:9,12 0|1:29:24,5 -chr20 841266 . C T 60 . QNAME=cluster19_000000F;QSTART=805548;QSTRAND=+ GT:DP:AD ./.:30:19,11 0|1:21:11,10 0|1:21:6,15 -chr20 842793 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24850296;QSTRAND=- GT:DP:AD ./.:29:21,8 ./.:38:17,21 0|1:43:22,21 -chr20 842861 . T G 60 . QNAME=cluster23_scaffold_2;QSTART=24850228;QSTRAND=- GT:DP:AD ./.:36:17,19 ./.:19:6,13 0|1:12:6,6 -chr20 843131 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24849958;QSTRAND=- GT:DP:AD ./.:27:18,9 ./.:30:13,17 0|1:41:25,16 -chr20 843133 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24849956;QSTRAND=- GT:DP:AD ./.:35:22,13 ./.:29:17,12 0|1:44:22,22 -chr20 843148 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=824764;QSTRAND=+ GT:DP:AD 1|0:36:13,23 ./.:35:22,13 ./.:17:6,11 -chr20 843149 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=824765;QSTRAND=+ GT:DP:AD 1|0:32:12,20 ./.:38:22,16 ./.:38:21,17 -chr20 843779 . C A 60 . QNAME=cluster23_scaffold_2;QSTART=24849310;QSTRAND=- GT:DP:AD ./.:31:11,20 ./.:35:23,12 0|1:30:17,13 -chr20 843805 . T C 60 . QNAME=cluster19_000000F;QSTART=808087;QSTRAND=+ GT:DP:AD ./.:36:18,18 0|1:28:17,11 ./.:24:12,12 -chr20 843879 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=24849210;QSTRAND=- GT:DP:AD ./.:35:23,12 ./.:19:7,12 0|1:16:8,8 -chr20 844439 . TGCCCAGGTC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=826056;QSTRAND=+ GT:DP:AD 1|1:26:11,15 1|1:28:12,16 1|1:29:14,15 -chr20 844675 . C CT 60 . QNAME=HG002-S9-H2-000001F;QSTART=800823;QSTRAND=+ GT:DP:AD 0|1:39:22,17 0|1:26:5,21 1|1:35:15,20 -chr20 845035 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=826642;QSTRAND=+ GT:DP:AD 1|1:32:21,11 1|1:28:21,7 1|1:29:7,22 -chr20 845849 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=827456;QSTRAND=+ GT:DP:AD 1|1:36:24,12 ./.:21:10,11 1|1:42:19,23 -chr20 845870 . C G 60 . QNAME=cluster19_000000F;QSTART=810144;QSTRAND=+ GT:DP:AD ./.:13:7,6 0|1:34:12,22 ./.:36:17,19 -chr20 846023 . G T 60 . QNAME=cluster19_000000F;QSTART=24912069;QSTRAND=- GT:DP:AD ./.:41:19,22 1|0:25:13,12 ./.:19:12,7 -chr20 846067 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=827674;QSTRAND=+ GT:DP:AD 1|1:22:17,5 ./.:30:10,20 1|1:44:23,21 -chr20 846626 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=828233;QSTRAND=+ GT:DP:AD 1|1:26:21,5 ./.:28:6,22 1|1:26:18,8 -chr20 847610 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=829217;QSTRAND=+ GT:DP:AD 1|1:17:6,11 ./.:30:7,23 1|1:21:7,14 -chr20 847932 . C T 60 . QNAME=cluster19_000000F;QSTART=812206;QSTRAND=+ GT:DP:AD ./.:23:10,13 0|1:37:16,21 ./.:37:22,15 -chr20 847948 . C T 60 . QNAME=cluster19_000000F;QSTART=812222;QSTRAND=+ GT:DP:AD ./.:36:21,15 0|1:20:7,13 ./.:32:14,18 -chr20 848007 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=829614;QSTRAND=+ GT:DP:AD 1|1:43:22,21 ./.:11:5,6 1|1:34:13,21 -chr20 848148 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=829755;QSTRAND=+ GT:DP:AD 1|1:27:6,21 0|1:27:17,10 0|1:20:14,6 -chr20 848655 . G GCCC 60 . QNAME=cluster19_000000F;QSTART=812930;QSTRAND=+ GT:DP:AD ./.:21:7,14 0|1:20:15,5 ./.:13:6,7 -chr20 848655 . G GC 60 . QNAME=cluster23_scaffold_2;QSTART=24844441;QSTRAND=- GT:DP:AD ./.:31:15,16 ./.:29:24,5 0|1:45:24,21 -chr20 848966 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=830573;QSTRAND=+ GT:DP:AD 1|1:16:5,11 ./.:20:6,14 1|1:15:7,8 -chr20 849159 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=830766;QSTRAND=+ GT:DP:AD 1|1:29:18,11 ./.:22:17,5 1|1:21:11,10 -chr20 849210 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=830817;QSTRAND=+ GT:DP:AD 1|1:40:22,18 1|1:40:25,15 1|1:26:14,12 -chr20 849245 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=830852;QSTRAND=+ GT:DP:AD 1|1:40:17,23 ./.:47:23,24 1|1:13:8,5 -chr20 849258 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=830866;QSTRAND=+ GT:DP:AD 1|1:31:18,13 0|1:43:24,19 1|1:21:16,5 -chr20 849509 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=831115;QSTRAND=+ GT:DP:AD 1|1:28:14,14 ./.:40:25,15 1|1:45:23,22 -chr20 849655 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=831261;QSTRAND=+ GT:DP:AD 1|1:37:24,13 ./.:29:21,8 1|1:16:10,6 -chr20 849665 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=831271;QSTRAND=+ GT:DP:AD 1|1:24:13,11 ./.:31:22,9 1|1:27:5,22 -chr20 849770 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=831376;QSTRAND=+ GT:DP:AD 1|1:25:17,8 ./.:28:19,9 1|1:17:8,9 -chr20 849895 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=831501;QSTRAND=+ GT:DP:AD 1|1:17:5,12 ./.:32:19,13 1|1:28:8,20 -chr20 850094 . T TACACAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=831701;QSTRAND=+ GT:DP:AD 1|0:34:11,23 ./.:35:14,21 0|1:30:5,25 -chr20 850094 . T TACACACACAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=806242;QSTRAND=+ GT:DP:AD 0|1:16:10,6 ./.:26:13,13 ./.:21:12,9 -chr20 850134 . C CACACAT 60 . QNAME=cluster19_000000F;QSTART=24907952;QSTRAND=- GT:DP:AD ./.:41:17,24 1|0:22:9,13 1|0:16:5,11 -chr20 850134 . C CACACACACACAT 60 . QNAME=cluster19_000000F;QSTART=814411;QSTRAND=+ GT:DP:AD ./.:43:25,18 0|1:34:24,10 ./.:33:16,17 -chr20 850182 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=831794;QSTRAND=+ GT:DP:AD 1|1:30:23,7 ./.:27:12,15 1|1:33:11,22 -chr20 850404 . C T 60 . QNAME=cluster19_000000F;QSTART=814692;QSTRAND=+ GT:DP:AD ./.:31:8,23 0|1:38:25,13 ./.:34:15,19 -chr20 850450 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=832062;QSTRAND=+ GT:DP:AD 1|1:40:20,20 0|1:28:14,14 1|1:26:6,20 -chr20 850608 . A G 60 . QNAME=cluster19_000000F;QSTART=814896;QSTRAND=+ GT:DP:AD ./.:31:17,14 0|1:33:18,15 ./.:30:8,22 -chr20 850762 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=832374;QSTRAND=+ GT:DP:AD 1|1:32:16,16 ./.:39:23,16 1|1:21:12,9 -chr20 850818 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=832430;QSTRAND=+ GT:DP:AD 1|1:30:12,18 0|1:37:19,18 1|1:43:22,21 -chr20 851565 . G A 60 . QNAME=cluster19_000000F;QSTART=815853;QSTRAND=+ GT:DP:AD ./.:31:7,24 0|1:22:9,13 ./.:30:22,8 -chr20 851698 . C T 60 . QNAME=cluster19_000000F;QSTART=24906388;QSTRAND=- GT:DP:AD ./.:32:18,14 1|0:42:17,25 ./.:38:24,14 -chr20 852010 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=833622;QSTRAND=+ GT:DP:AD 1|1:43:24,19 ./.:33:21,12 1|1:29:20,9 -chr20 852120 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=833732;QSTRAND=+ GT:DP:AD 1|1:44:23,21 ./.:29:7,22 1|1:39:14,25 -chr20 852153 . C T 60 . QNAME=cluster19_000000F;QSTART=816441;QSTRAND=+ GT:DP:AD ./.:42:19,23 0|1:44:20,24 ./.:40:22,18 -chr20 852155 . T C 60 . QNAME=cluster19_000000F;QSTART=816443;QSTRAND=+ GT:DP:AD ./.:32:25,7 0|1:16:10,6 ./.:37:15,22 -chr20 852165 . G A 60 . QNAME=cluster19_000000F;QSTART=816453;QSTRAND=+ GT:DP:AD ./.:33:11,22 0|1:34:11,23 ./.:29:14,15 -chr20 852596 . ACT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=834209;QSTRAND=+ GT:DP:AD 1|1:20:11,9 0|1:28:5,23 1|1:42:20,22 -chr20 852714 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=834324;QSTRAND=+ GT:DP:AD 1|1:41:22,19 0|1:13:5,8 1|1:33:10,23 -chr20 852722 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=834332;QSTRAND=+ GT:DP:AD 1|1:30:17,13 ./.:42:19,23 1|1:37:12,25 -chr20 853509 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=835119;QSTRAND=+ GT:DP:AD 1|1:22:10,12 ./.:34:25,9 1|1:31:11,20 -chr20 853837 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=835447;QSTRAND=+ GT:DP:AD 1|1:41:24,17 ./.:35:14,21 1|1:27:6,21 diff --git a/repo_utils/test_files/answer_key/divided/multi_00000019.vcf b/repo_utils/test_files/answer_key/divided/multi_00000019.vcf deleted file mode 100644 index bb3b1e4e..00000000 --- a/repo_utils/test_files/answer_key/divided/multi_00000019.vcf +++ /dev/null @@ -1,183 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##bcftools_mergeVersion=1.12+htslib-1.12 -##bcftools_mergeCommand=merge -O z -f x -m none input1.vcf.gz input2.vcf.gz input3.vcf.gz; Date=Mon Aug 16 18:05:13 2021 -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 854857 . TTGTG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=836468;QSTRAND=+ GT:DP:AD 1|0:17:7,10 1|1:19:5,14 ./.:29:13,16 -chr20 854857 . TTGTGTG T 60 . QNAME=HG002-S9-H2-000001F;QSTART=811013;QSTRAND=+ GT:DP:AD 0|1:26:12,14 ./.:24:13,11 1|1:26:5,21 -chr20 855703 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=837309;QSTRAND=+ GT:DP:AD 1|0:34:11,23 1|1:32:20,12 1|1:36:21,15 -chr20 855883 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=812032;QSTRAND=+ GT:DP:AD 0|1:42:18,24 ./.:46:24,22 ./.:16:7,9 -chr20 856057 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=837663;QSTRAND=+ GT:DP:AD 1|1:33:9,24 1|1:49:24,25 1|1:26:21,5 -chr20 856168 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=837774;QSTRAND=+ GT:DP:AD 1|0:24:10,14 0|1:31:7,24 ./.:23:11,12 -chr20 856433 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=838039;QSTRAND=+ GT:DP:AD 1|1:34:15,19 1|1:29:18,11 1|1:43:18,25 -chr20 856781 . G A 60 . QNAME=cluster19_000000F;QSTART=821063;QSTRAND=+ GT:DP:AD ./.:46:25,21 0|1:13:7,6 ./.:39:17,22 -chr20 857157 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=838763;QSTRAND=+ GT:DP:AD 1|1:17:6,11 1|1:25:13,12 1|1:27:21,6 -chr20 857179 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=838785;QSTRAND=+ GT:DP:AD 1|1:16:10,6 1|1:29:7,22 1|1:24:17,7 -chr20 857617 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=839223;QSTRAND=+ GT:DP:AD 1|1:40:17,23 1|1:22:11,11 1|1:33:22,11 -chr20 858872 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=840478;QSTRAND=+ GT:DP:AD 1|1:32:12,20 1|1:41:23,18 1|1:28:9,19 -chr20 858925 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=840531;QSTRAND=+ GT:DP:AD 1|1:26:13,13 1|1:29:22,7 1|1:35:15,20 -chr20 859762 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=841368;QSTRAND=+ GT:DP:AD 1|1:33:11,22 1|1:16:8,8 1|1:41:25,16 -chr20 860453 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=842059;QSTRAND=+ GT:DP:AD 1|0:23:10,13 0|1:30:22,8 ./.:18:5,13 -chr20 860488 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=816637;QSTRAND=+ GT:DP:AD 0|1:19:6,13 1|0:21:5,16 1|1:21:13,8 -chr20 861973 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=843579;QSTRAND=+ GT:DP:AD 1|1:42:23,19 1|1:35:15,20 1|1:32:19,13 -chr20 861975 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=843581;QSTRAND=+ GT:DP:AD 1|1:39:18,21 1|1:25:9,16 1|1:14:7,7 -chr20 862051 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=843657;QSTRAND=+ GT:DP:AD 1|1:15:10,5 1|1:29:8,21 1|1:37:20,17 -chr20 862053 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=843659;QSTRAND=+ GT:DP:AD 1|1:16:7,9 1|1:19:11,8 1|1:30:25,5 -chr20 862244 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=818394;QSTRAND=+ GT:DP:AD 0|1:24:15,9 1|0:35:10,25 1|0:13:6,7 -chr20 862244 . CTT C 60 . QNAME=cluster23_scaffold_2;QSTART=24830855;QSTRAND=- GT:DP:AD ./.:39:25,14 ./.:31:14,17 0|1:15:10,5 -chr20 862270 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=843876;QSTRAND=+ GT:DP:AD 1|1:42:24,18 1|0:45:24,21 1|1:44:19,25 -chr20 862270 . T TA 60 . QNAME=cluster19_000000F;QSTART=826553;QSTRAND=+ GT:DP:AD ./.:21:11,10 0|1:37:15,22 ./.:37:23,14 -chr20 862295 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=843901;QSTRAND=+ GT:DP:AD 1|1:31:6,25 1|1:32:15,17 1|1:27:5,22 -chr20 862400 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=818548;QSTRAND=+ GT:DP:AD 0|1:34:19,15 1|0:15:9,6 1|1:45:23,22 -chr20 863200 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=844806;QSTRAND=+ GT:DP:AD 1|0:31:8,23 0|1:35:22,13 ./.:37:15,22 -chr20 863302 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=819450;QSTRAND=+ GT:DP:AD 0|1:15:6,9 1|0:29:16,13 1|1:28:12,16 -chr20 863798 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=845405;QSTRAND=+ GT:DP:AD 1|1:45:23,22 1|1:28:21,7 1|1:30:12,18 -chr20 864029 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=820176;QSTRAND=+ GT:DP:AD 0|1:31:17,14 1|0:39:21,18 1|1:24:8,16 -chr20 864049 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=820196;QSTRAND=+ GT:DP:AD 0|1:40:22,18 1|0:47:22,25 1|1:44:22,22 -chr20 864080 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=845685;QSTRAND=+ GT:DP:AD 1|1:30:9,21 1|1:13:6,7 1|1:24:12,12 -chr20 865132 . AAGCAGAAAAGC A 60 . QNAME=cluster23_scaffold_2;QSTART=24827970;QSTRAND=- GT:DP:AD ./.:15:7,8 ./.:37:20,17 0|1:30:8,22 -chr20 865868 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=847474;QSTRAND=+ GT:DP:AD 1|0:46:24,22 0|1:43:23,20 ./.:22:6,16 -chr20 866330 . A AC 60 . QNAME=HG002-S9-H1-000001F;QSTART=847937;QSTRAND=+ GT:DP:AD 1|0:26:10,16 0|1:32:13,19 ./.:40:18,22 -chr20 866340 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=847947;QSTRAND=+ GT:DP:AD 1|0:35:15,20 0|1:15:5,10 ./.:28:19,9 -chr20 866636 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=848243;QSTRAND=+ GT:DP:AD 1|0:28:10,18 0|1:42:22,20 ./.:39:23,16 -chr20 866712 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=848319;QSTRAND=+ GT:DP:AD 1|0:33:10,23 0|1:38:25,13 ./.:42:23,19 -chr20 866777 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=848384;QSTRAND=+ GT:DP:AD 1|0:34:11,23 0|1:45:24,21 ./.:24:15,9 -chr20 866852 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=848459;QSTRAND=+ GT:DP:AD 1|0:28:20,8 0|1:18:10,8 ./.:26:12,14 -chr20 867420 . GTA G 60 . QNAME=cluster19_000000F;QSTART=24890672;QSTRAND=- GT:DP:AD ./.:23:6,17 1|0:33:19,14 ./.:40:22,18 -chr20 867422 . ATATG A 60 . QNAME=cluster23_scaffold_2;QSTART=24825691;QSTRAND=- GT:DP:AD ./.:24:8,16 ./.:37:23,14 0|1:25:13,12 -chr20 867424 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=823571;QSTRAND=+ GT:DP:AD 0|1:37:14,23 ./.:27:5,22 1|0:41:18,23 -chr20 867424 . ATG A 60 . QNAME=cluster19_000000F;QSTART=831709;QSTRAND=+ GT:DP:AD ./.:14:9,5 0|1:36:25,11 ./.:24:9,15 -chr20 867469 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=849076;QSTRAND=+ GT:DP:AD 1|0:27:19,8 1|1:24:11,13 0|1:13:6,7 -chr20 867469 . T TGA 60 . QNAME=HG002-S9-H2-000001F;QSTART=823617;QSTRAND=+ GT:DP:AD 0|1:31:18,13 ./.:31:6,25 1|0:16:8,8 -chr20 867728 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=849335;QSTRAND=+ GT:DP:AD 1|0:19:12,7 0|1:41:23,18 ./.:37:24,13 -chr20 867974 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=824123;QSTRAND=+ GT:DP:AD 0|1:19:7,12 1|0:30:18,12 1|1:39:22,17 -chr20 868254 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=849861;QSTRAND=+ GT:DP:AD 1|1:10:5,5 1|1:44:22,22 1|1:42:21,21 -chr20 868526 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=850133;QSTRAND=+ GT:DP:AD 1|0:37:15,22 0|1:45:23,22 ./.:25:16,9 -chr20 868606 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=850213;QSTRAND=+ GT:DP:AD 1|0:30:14,16 0|1:48:23,25 ./.:40:22,18 -chr20 868745 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=824894;QSTRAND=+ GT:DP:AD 0|1:24:9,15 1|0:44:19,25 1|1:29:23,6 -chr20 868950 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=850558;QSTRAND=+ GT:DP:AD 1|0:30:5,25 0|1:28:12,16 ./.:24:19,5 -chr20 868955 . TC T 60 . QNAME=HG002-S9-H2-000001F;QSTART=825105;QSTRAND=+ GT:DP:AD 0|1:37:21,16 ./.:31:17,14 ./.:28:18,10 -chr20 868956 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=850564;QSTRAND=+ GT:DP:AD 1|0:32:24,8 1|1:34:21,13 1|1:13:7,6 -chr20 869010 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=850618;QSTRAND=+ GT:DP:AD 1|1:24:15,9 1|1:37:12,25 1|1:42:18,24 -chr20 869733 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=851341;QSTRAND=+ GT:DP:AD 1|1:35:13,22 1|1:19:6,13 1|1:31:17,14 -chr20 869777 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=851385;QSTRAND=+ GT:DP:AD 1|1:29:24,5 1|1:29:17,12 1|1:33:12,21 -chr20 871966 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=828114;QSTRAND=+ GT:DP:AD 0|1:27:6,21 1|0:27:19,8 1|1:21:7,14 -chr20 871969 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=828117;QSTRAND=+ GT:DP:AD 0|1:31:23,8 1|0:28:6,22 1|1:38:23,15 -chr20 872450 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=828598;QSTRAND=+ GT:DP:AD 0|1:32:19,13 1|0:24:15,9 1|1:17:10,7 -chr20 872792 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=854400;QSTRAND=+ GT:DP:AD 1|1:39:19,20 1|1:24:13,11 1|1:32:17,15 -chr20 873491 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=855099;QSTRAND=+ GT:DP:AD 1|0:27:19,8 0|1:31:25,6 ./.:40:15,25 -chr20 873608 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=855216;QSTRAND=+ GT:DP:AD 1|0:41:22,19 0|1:25:19,6 ./.:35:25,10 -chr20 873920 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=855528;QSTRAND=+ GT:DP:AD 1|0:17:7,10 0|1:29:19,10 0|1:18:13,5 -chr20 873956 . C A 60 . QNAME=cluster19_000000F;QSTART=24884138;QSTRAND=- GT:DP:AD ./.:37:17,20 1|0:31:24,7 ./.:38:18,20 -chr20 874038 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=855646;QSTRAND=+ GT:DP:AD 1|0:36:22,14 0|1:33:12,21 0|1:18:6,12 -chr20 874111 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=855719;QSTRAND=+ GT:DP:AD 1|0:25:16,9 0|1:25:13,12 0|1:25:20,5 -chr20 874297 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=855905;QSTRAND=+ GT:DP:AD 1|0:22:15,7 0|1:34:13,21 0|1:32:11,21 -chr20 874696 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=856304;QSTRAND=+ GT:DP:AD 1|0:21:15,6 0|1:32:25,7 0|1:23:13,10 -chr20 875035 . TC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=856644;QSTRAND=+ GT:DP:AD 1|0:40:24,16 0|1:42:17,25 0|1:29:6,23 -chr20 875568 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=857175;QSTRAND=+ GT:DP:AD 1|0:46:22,24 0|1:14:9,5 ./.:24:5,19 -chr20 875568 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=24817550;QSTRAND=- GT:DP:AD ./.:24:13,11 ./.:19:14,5 0|1:27:17,10 -chr20 875920 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=857527;QSTRAND=+ GT:DP:AD 1|0:39:20,19 0|1:19:11,8 0|1:17:7,10 -chr20 876104 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=857711;QSTRAND=+ GT:DP:AD 1|0:23:12,11 0|1:38:24,14 0|1:45:21,24 -chr20 876144 . CAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=857752;QSTRAND=+ GT:DP:AD 1|0:32:13,19 0|1:22:14,8 0|1:24:8,16 -chr20 876144 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=24833309;QSTRAND=- GT:DP:AD ./.:30:9,21 ./.:28:19,9 1|0:16:7,9 -chr20 876194 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=857799;QSTRAND=+ GT:DP:AD 1|0:37:24,13 0|1:36:25,11 0|1:42:22,20 -chr20 876734 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24816386;QSTRAND=- GT:DP:AD ./.:46:24,22 ./.:24:14,10 0|1:24:18,6 -chr20 878979 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24814141;QSTRAND=- GT:DP:AD ./.:21:13,8 ./.:18:5,13 0|1:34:17,17 -chr20 879508 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=861113;QSTRAND=+ GT:DP:AD 1|0:15:7,8 0|1:27:17,10 ./.:21:10,11 -chr20 880111 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=861716;QSTRAND=+ GT:DP:AD 1|0:18:9,9 0|1:44:20,24 ./.:37:17,20 -chr20 880159 . G A 60 . QNAME=cluster19_000000F;QSTART=24877935;QSTRAND=- GT:DP:AD ./.:41:23,18 1|0:33:20,13 ./.:37:24,13 -chr20 880302 . A AG 60 . QNAME=HG002-S9-H1-000001F;QSTART=861908;QSTRAND=+ GT:DP:AD 1|0:30:8,22 0|1:35:10,25 ./.:28:18,10 -chr20 880463 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24812657;QSTRAND=- GT:DP:AD ./.:29:14,15 ./.:34:23,11 0|1:19:11,8 -chr20 880587 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=862194;QSTRAND=+ GT:DP:AD 1|0:26:16,10 ./.:25:17,8 ./.:25:9,16 -chr20 880587 . C CA 60 . QNAME=cluster19_000000F;QSTART=24877506;QSTRAND=- GT:DP:AD ./.:19:13,6 1|0:23:17,6 ./.:14:5,9 -chr20 880743 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=862348;QSTRAND=+ GT:DP:AD 1|0:16:9,7 0|1:13:8,5 0|1:33:10,23 -chr20 881100 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=24812020;QSTRAND=- GT:DP:AD ./.:46:21,25 ./.:18:5,13 0|1:28:9,19 -chr20 881114 . G GGGAA 60 . QNAME=cluster23_scaffold_2;QSTART=24812002;QSTRAND=- GT:DP:AD ./.:25:20,5 ./.:32:11,21 0|1:27:5,22 -chr20 881524 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24811592;QSTRAND=- GT:DP:AD ./.:31:16,15 ./.:35:20,15 0|1:30:11,19 -chr20 881561 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24811555;QSTRAND=- GT:DP:AD ./.:29:17,12 ./.:30:15,15 0|1:40:17,23 -chr20 882074 . T G 60 . QNAME=cluster23_scaffold_2;QSTART=24811042;QSTRAND=- GT:DP:AD ./.:35:24,11 ./.:39:20,19 0|1:47:22,25 -chr20 882180 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24810936;QSTRAND=- GT:DP:AD ./.:11:5,6 ./.:24:14,10 0|1:40:22,18 -chr20 882348 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=863953;QSTRAND=+ GT:DP:AD 1|0:39:15,24 0|1:19:10,9 ./.:31:9,22 -chr20 882505 . C CTAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=864111;QSTRAND=+ GT:DP:AD 1|0:37:22,15 0|1:39:15,24 ./.:18:5,13 -chr20 882628 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=864236;QSTRAND=+ GT:DP:AD 1|0:45:25,20 0|1:36:17,19 ./.:28:8,20 -chr20 882865 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=864473;QSTRAND=+ GT:DP:AD 1|0:32:23,9 0|1:32:10,22 ./.:30:6,24 -chr20 883063 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=864671;QSTRAND=+ GT:DP:AD 1|0:39:20,19 0|1:31:23,8 0|1:28:20,8 -chr20 883101 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=864709;QSTRAND=+ GT:DP:AD 1|0:39:18,21 0|1:29:17,12 ./.:31:17,14 -chr20 883203 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24809913;QSTRAND=- GT:DP:AD ./.:24:19,5 ./.:23:16,7 0|1:26:21,5 -chr20 883230 . C T 60 . QNAME=cluster19_000000F;QSTART=24874863;QSTRAND=- GT:DP:AD ./.:27:13,14 1|0:30:25,5 ./.:13:5,8 -chr20 883431 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24809685;QSTRAND=- GT:DP:AD ./.:39:23,16 ./.:20:8,12 0|1:19:7,12 -chr20 883556 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=865164;QSTRAND=+ GT:DP:AD 1|0:15:10,5 0|1:42:21,21 ./.:32:13,19 -chr20 883658 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=24809458;QSTRAND=- GT:DP:AD ./.:37:25,12 ./.:33:10,23 0|1:41:18,23 -chr20 883812 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=865420;QSTRAND=+ GT:DP:AD 1|0:42:17,25 0|1:16:7,9 0|1:28:23,5 -chr20 883869 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=24809247;QSTRAND=- GT:DP:AD ./.:31:19,12 ./.:11:5,6 0|1:28:23,5 -chr20 883997 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=865605;QSTRAND=+ GT:DP:AD 1|0:19:14,5 0|1:41:21,20 0|1:28:11,17 -chr20 884017 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=865625;QSTRAND=+ GT:DP:AD 1|0:34:10,24 0|1:25:6,19 0|1:34:17,17 -chr20 884411 . G C 60 . QNAME=cluster23_scaffold_2;QSTART=24808705;QSTRAND=- GT:DP:AD ./.:17:8,9 ./.:18:5,13 0|1:46:25,21 -chr20 884723 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=866331;QSTRAND=+ GT:DP:AD 1|0:42:24,18 0|1:26:9,17 0|1:37:19,18 -chr20 884894 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24808222;QSTRAND=- GT:DP:AD ./.:26:21,5 ./.:37:19,18 0|1:37:21,16 -chr20 885021 . TC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=866630;QSTRAND=+ GT:DP:AD 1|0:34:22,12 0|1:38:21,17 ./.:20:11,9 -chr20 885587 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=867194;QSTRAND=+ GT:DP:AD 1|0:25:12,13 0|1:18:8,10 ./.:17:9,8 -chr20 885689 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=867296;QSTRAND=+ GT:DP:AD 1|0:32:16,16 0|1:23:9,14 ./.:36:16,20 -chr20 885707 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=867314;QSTRAND=+ GT:DP:AD 1|0:27:19,8 0|1:31:7,24 ./.:28:16,12 -chr20 885722 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=867329;QSTRAND=+ GT:DP:AD 1|0:18:6,12 0|1:15:8,7 ./.:16:11,5 -chr20 886137 . AG A 60 . QNAME=cluster23_scaffold_2;QSTART=24806979;QSTRAND=- GT:DP:AD ./.:24:14,10 ./.:36:13,23 0|1:43:18,25 -chr20 886620 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=868227;QSTRAND=+ GT:DP:AD 1|0:27:5,22 0|1:36:19,17 ./.:33:19,14 -chr20 886681 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=868288;QSTRAND=+ GT:DP:AD 1|0:36:23,13 0|1:41:19,22 0|1:42:21,21 -chr20 886694 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=868301;QSTRAND=+ GT:DP:AD 1|0:44:23,21 0|1:19:10,9 ./.:15:6,9 -chr20 887636 . CTTTT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=869244;QSTRAND=+ GT:DP:AD 1|0:29:19,10 0|1:31:20,11 ./.:15:10,5 -chr20 887636 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=843785;QSTRAND=+ GT:DP:AD 0|1:15:8,7 1|0:47:23,24 ./.:35:11,24 -chr20 887636 . CTTT C 60 . QNAME=cluster23_scaffold_2;QSTART=24805481;QSTRAND=- GT:DP:AD ./.:11:6,5 ./.:32:21,11 0|1:23:8,15 -chr20 887887 . G GAGGA 60 . QNAME=cluster23_scaffold_2;QSTART=24805229;QSTRAND=- GT:DP:AD ./.:42:22,20 ./.:32:10,22 0|1:22:11,11 -chr20 887996 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=869599;QSTRAND=+ GT:DP:AD 1|0:35:16,19 0|1:29:24,5 0|1:37:12,25 -chr20 888753 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=870356;QSTRAND=+ GT:DP:AD 1|0:23:14,9 0|1:39:21,18 ./.:34:22,12 -chr20 889503 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=871106;QSTRAND=+ GT:DP:AD 1|0:20:7,13 0|1:34:10,24 0|1:42:17,25 -chr20 889671 . C G 60 . QNAME=cluster23_scaffold_3;QSTART=24819782;QSTRAND=- GT:DP:AD ./.:32:10,22 ./.:39:14,25 1|0:22:9,13 -chr20 890514 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=872117;QSTRAND=+ GT:DP:AD 1|0:32:19,13 0|1:29:18,11 ./.:35:18,17 -chr20 890614 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=872217;QSTRAND=+ GT:DP:AD 1|0:46:23,23 ./.:40:15,25 ./.:30:18,12 -chr20 891187 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=872790;QSTRAND=+ GT:DP:AD 1|0:34:9,25 ./.:28:16,12 ./.:32:21,11 -chr20 891480 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=873083;QSTRAND=+ GT:DP:AD 1|0:39:15,24 ./.:27:22,5 ./.:35:24,11 -chr20 891653 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24801463;QSTRAND=- GT:DP:AD ./.:18:9,9 ./.:31:13,18 0|1:36:11,25 -chr20 892108 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=873711;QSTRAND=+ GT:DP:AD 1|0:31:15,16 ./.:48:24,24 ./.:44:24,20 -chr20 892511 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=874114;QSTRAND=+ GT:DP:AD 1|0:32:21,11 ./.:28:15,13 ./.:26:11,15 -chr20 892634 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=874237;QSTRAND=+ GT:DP:AD 1|0:25:20,5 ./.:29:10,19 ./.:33:12,21 -chr20 892840 . C T 60 . QNAME=cluster19_000000F;QSTART=24865254;QSTRAND=- GT:DP:AD ./.:42:19,23 1|0:35:10,25 ./.:32:8,24 -chr20 893106 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=874709;QSTRAND=+ GT:DP:AD 1|0:13:8,5 ./.:32:21,11 ./.:24:9,15 -chr20 893464 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=875067;QSTRAND=+ GT:DP:AD 1|0:40:15,25 ./.:28:23,5 ./.:13:7,6 -chr20 893483 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=875086;QSTRAND=+ GT:DP:AD 1|0:36:25,11 ./.:28:18,10 ./.:35:25,10 -chr20 894385 . C T 60 . QNAME=cluster19_000000F;QSTART=24863709;QSTRAND=- GT:DP:AD ./.:37:22,15 1|0:28:11,17 ./.:40:24,16 diff --git a/repo_utils/test_files/answer_key/divided/multi_00000020.vcf b/repo_utils/test_files/answer_key/divided/multi_00000020.vcf deleted file mode 100644 index b4c52284..00000000 --- a/repo_utils/test_files/answer_key/divided/multi_00000020.vcf +++ /dev/null @@ -1,160 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##bcftools_mergeVersion=1.12+htslib-1.12 -##bcftools_mergeCommand=merge -O z -f x -m none input1.vcf.gz input2.vcf.gz input3.vcf.gz; Date=Mon Aug 16 18:05:13 2021 -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 895490 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=877093;QSTRAND=+ GT:DP:AD 1|0:42:25,17 ./.:39:25,14 ./.:39:24,15 -chr20 895600 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=877203;QSTRAND=+ GT:DP:AD 1|0:27:15,12 ./.:12:6,6 ./.:40:20,20 -chr20 896059 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=877662;QSTRAND=+ GT:DP:AD 1|0:18:6,12 ./.:19:10,9 ./.:29:14,15 -chr20 896562 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=878165;QSTRAND=+ GT:DP:AD 1|0:43:23,20 ./.:20:12,8 ./.:47:22,25 -chr20 896997 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=878600;QSTRAND=+ GT:DP:AD 1|0:37:13,24 ./.:29:11,18 ./.:32:18,14 -chr20 899093 . T C 60 . QNAME=cluster19_000000F;QSTART=24859001;QSTRAND=- GT:DP:AD ./.:32:23,9 1|0:28:6,22 ./.:34:9,25 -chr20 899180 . T A 60 . QNAME=cluster19_000000F;QSTART=24858914;QSTRAND=- GT:DP:AD ./.:25:6,19 1|0:32:23,9 ./.:20:11,9 -chr20 899195 . C G 60 . QNAME=cluster19_000000F;QSTART=24858899;QSTRAND=- GT:DP:AD ./.:19:11,8 1|0:29:10,19 ./.:32:19,13 -chr20 899251 . AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=880855;QSTRAND=+ GT:DP:AD 1|1:36:11,25 ./.:13:5,8 ./.:35:24,11 -chr20 899252 . T A 60 . QNAME=cluster19_000000F;QSTART=24858842;QSTRAND=- GT:DP:AD ./.:35:16,19 1|0:28:8,20 ./.:39:22,17 -chr20 899447 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=881049;QSTRAND=+ GT:DP:AD 1|1:31:22,9 1|1:30:25,5 1|1:16:8,8 -chr20 899533 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=855679;QSTRAND=+ GT:DP:AD 0|1:32:23,9 ./.:16:8,8 ./.:40:17,23 -chr20 900321 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=856467;QSTRAND=+ GT:DP:AD 0|1:36:19,17 ./.:13:5,8 ./.:35:13,22 -chr20 900721 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=856867;QSTRAND=+ GT:DP:AD 0|1:31:25,6 ./.:36:25,11 ./.:36:25,11 -chr20 900932 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=857078;QSTRAND=+ GT:DP:AD 0|1:22:7,15 ./.:37:13,24 ./.:32:10,22 -chr20 900977 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=857123;QSTRAND=+ GT:DP:AD 0|1:29:13,16 ./.:22:5,17 ./.:21:8,13 -chr20 901001 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=857147;QSTRAND=+ GT:DP:AD 0|1:24:7,17 ./.:46:21,25 ./.:37:25,12 -chr20 901060 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=857206;QSTRAND=+ GT:DP:AD 0|1:48:25,23 ./.:33:24,9 ./.:18:12,6 -chr20 901437 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=857583;QSTRAND=+ GT:DP:AD 0|1:32:13,19 ./.:45:21,24 ./.:37:13,24 -chr20 901786 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=857932;QSTRAND=+ GT:DP:AD 0|1:41:16,25 0|1:19:9,10 ./.:38:24,14 -chr20 902160 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=858306;QSTRAND=+ GT:DP:AD 0|1:31:10,21 ./.:19:7,12 ./.:17:10,7 -chr20 902357 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=858503;QSTRAND=+ GT:DP:AD 0|1:33:16,17 ./.:33:21,12 ./.:32:25,7 -chr20 902728 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=858874;QSTRAND=+ GT:DP:AD 0|1:11:5,6 ./.:32:19,13 ./.:32:12,20 -chr20 903001 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=859147;QSTRAND=+ GT:DP:AD 0|1:33:12,21 ./.:15:10,5 ./.:25:16,9 -chr20 903427 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=859573;QSTRAND=+ GT:DP:AD 0|1:22:17,5 ./.:28:15,13 ./.:27:20,7 -chr20 903489 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=859635;QSTRAND=+ GT:DP:AD 0|1:34:12,22 ./.:38:14,24 ./.:31:18,13 -chr20 904502 . A AC 60 . QNAME=HG002-S9-H2-000001F;QSTART=860649;QSTRAND=+ GT:DP:AD 0|1:27:6,21 ./.:26:19,7 ./.:30:12,18 -chr20 905359 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=861506;QSTRAND=+ GT:DP:AD 0|1:25:14,11 ./.:32:8,24 ./.:15:5,10 -chr20 905407 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=861554;QSTRAND=+ GT:DP:AD 0|1:42:17,25 ./.:30:17,13 ./.:29:18,11 -chr20 905736 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=861883;QSTRAND=+ GT:DP:AD 0|1:24:8,16 ./.:29:22,7 ./.:23:6,17 -chr20 906213 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=862360;QSTRAND=+ GT:DP:AD 0|1:31:14,17 ./.:43:20,23 ./.:36:23,13 -chr20 906268 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=862415;QSTRAND=+ GT:DP:AD 0|1:17:7,10 ./.:25:17,8 ./.:21:7,14 -chr20 906812 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=862959;QSTRAND=+ GT:DP:AD 0|1:33:11,22 ./.:30:9,21 ./.:21:6,15 -chr20 906878 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=863025;QSTRAND=+ GT:DP:AD 0|1:28:23,5 ./.:24:7,17 ./.:22:17,5 -chr20 907157 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=863304;QSTRAND=+ GT:DP:AD 0|1:42:25,17 ./.:40:15,25 ./.:29:18,11 -chr20 907880 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=864027;QSTRAND=+ GT:DP:AD 0|1:37:17,20 ./.:37:15,22 0|1:26:15,11 -chr20 908674 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=864821;QSTRAND=+ GT:DP:AD 0|1:40:19,21 ./.:23:12,11 0|1:36:13,23 -chr20 909226 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24783890;QSTRAND=- GT:DP:AD ./.:25:14,11 ./.:13:5,8 0|1:35:20,15 -chr20 909261 . C A 60 . QNAME=cluster19_000000F;QSTART=873540;QSTRAND=+ GT:DP:AD ./.:32:9,23 0|1:24:11,13 ./.:36:11,25 -chr20 909371 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24783745;QSTRAND=- GT:DP:AD ./.:22:16,6 ./.:29:15,14 0|1:44:22,22 -chr20 909453 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=891055;QSTRAND=+ GT:DP:AD 1|0:37:14,23 ./.:33:23,10 ./.:39:14,25 -chr20 909635 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=24783481;QSTRAND=- GT:DP:AD ./.:36:23,13 ./.:30:6,24 0|1:39:23,16 -chr20 909706 . G C 60 . QNAME=cluster19_000000F;QSTART=873985;QSTRAND=+ GT:DP:AD ./.:21:5,16 0|1:46:21,25 ./.:38:21,17 -chr20 911795 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=893397;QSTRAND=+ GT:DP:AD 1|0:23:17,6 ./.:27:5,22 ./.:36:24,12 -chr20 911823 . AGACAGAGAGAGGGAGAGAGG A 60 . QNAME=HG002-S9-H1-000001F;QSTART=893426;QSTRAND=+ GT:DP:AD 1|0:26:6,20 ./.:21:13,8 ./.:30:18,12 -chr20 912080 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=893662;QSTRAND=+ GT:DP:AD 1|0:19:8,11 ./.:25:5,20 ./.:41:23,18 -chr20 912305 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=893887;QSTRAND=+ GT:DP:AD 1|0:13:8,5 ./.:28:13,15 ./.:29:13,16 -chr20 913482 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=895064;QSTRAND=+ GT:DP:AD 1|0:32:20,12 ./.:31:8,23 ./.:25:12,13 -chr20 914079 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=895661;QSTRAND=+ GT:DP:AD 1|0:16:10,6 1|0:24:7,17 ./.:25:11,14 -chr20 914238 . A G 60 . QNAME=cluster19_000000F;QSTART=24843856;QSTRAND=- GT:DP:AD ./.:45:23,22 1|0:23:13,10 ./.:25:13,12 -chr20 914324 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=895906;QSTRAND=+ GT:DP:AD 1|1:37:14,23 1|1:32:18,14 1|0:24:14,10 -chr20 914682 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=896264;QSTRAND=+ GT:DP:AD 1|1:35:20,15 1|0:34:14,20 1|1:27:15,12 -chr20 914775 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=870922;QSTRAND=+ GT:DP:AD 0|1:25:16,9 ./.:27:10,17 1|0:17:9,8 -chr20 914780 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=896362;QSTRAND=+ GT:DP:AD 1|0:36:18,18 1|0:38:24,14 0|1:32:20,12 -chr20 914814 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=870961;QSTRAND=+ GT:DP:AD 0|1:26:15,11 ./.:16:6,10 1|0:29:19,10 -chr20 915350 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=896932;QSTRAND=+ GT:DP:AD 1|0:33:10,23 ./.:36:22,14 ./.:28:14,14 -chr20 915369 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=896951;QSTRAND=+ GT:DP:AD 1|1:37:14,23 1|0:14:8,6 1|0:18:5,13 -chr20 915656 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=897238;QSTRAND=+ GT:DP:AD 1|1:12:6,6 1|0:30:22,8 1|1:26:12,14 -chr20 916110 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=872257;QSTRAND=+ GT:DP:AD 0|1:23:8,15 ./.:40:15,25 ./.:35:15,20 -chr20 916419 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=898001;QSTRAND=+ GT:DP:AD 1|1:37:17,20 1|1:20:5,15 1|1:28:5,23 -chr20 916452 . A C 60 . QNAME=cluster19_000000F;QSTART=880731;QSTRAND=+ GT:DP:AD ./.:34:21,13 0|1:34:19,15 ./.:38:22,16 -chr20 916852 . C T 60 . QNAME=cluster19_000000F;QSTART=881131;QSTRAND=+ GT:DP:AD ./.:29:23,6 0|1:28:5,23 ./.:29:18,11 -chr20 916971 . C T 60 . QNAME=cluster19_000000F;QSTART=881250;QSTRAND=+ GT:DP:AD ./.:37:17,20 0|1:30:20,10 ./.:23:6,17 -chr20 917534 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=873681;QSTRAND=+ GT:DP:AD 0|1:22:11,11 ./.:23:8,15 ./.:27:14,13 -chr20 917575 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=899157;QSTRAND=+ GT:DP:AD 1|1:39:21,18 1|1:24:7,17 1|1:33:16,17 -chr20 917906 . T G 60 . QNAME=cluster19_000000F;QSTART=882185;QSTRAND=+ GT:DP:AD ./.:20:9,11 0|1:27:14,13 ./.:19:9,10 -chr20 918736 . G A 60 . QNAME=cluster19_000000F;QSTART=883015;QSTRAND=+ GT:DP:AD ./.:41:25,16 0|1:24:8,16 ./.:28:14,14 -chr20 919146 . CTCTT C 60 . QNAME=cluster19_000000F;QSTART=883426;QSTRAND=+ GT:DP:AD ./.:46:22,24 0|1:34:25,9 ./.:21:9,12 -chr20 919167 . C CTT 60 . QNAME=cluster23_scaffold_2;QSTART=24773947;QSTRAND=- GT:DP:AD ./.:33:9,24 ./.:13:7,6 0|1:28:13,15 -chr20 919371 . G C 60 . QNAME=cluster19_000000F;QSTART=883646;QSTRAND=+ GT:DP:AD ./.:38:18,20 0|1:32:8,24 ./.:31:9,22 -chr20 919990 . TG T 60 . QNAME=cluster19_000000F;QSTART=24838104;QSTRAND=- GT:DP:AD ./.:32:19,13 1|0:35:22,13 ./.:32:24,8 -chr20 919994 . T C 60 . QNAME=cluster19_000000F;QSTART=24838101;QSTRAND=- GT:DP:AD ./.:39:25,14 1|0:35:12,23 ./.:46:24,22 -chr20 920055 . T TC 60 . QNAME=HG002-S9-H1-000001F;QSTART=901638;QSTRAND=+ GT:DP:AD 1|1:13:7,6 1|1:23:8,15 1|1:29:18,11 -chr20 920188 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=901771;QSTRAND=+ GT:DP:AD 1|0:32:11,21 1|0:41:25,16 ./.:24:8,16 -chr20 920292 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=901875;QSTRAND=+ GT:DP:AD 1|0:23:17,6 1|0:20:9,11 ./.:22:13,9 -chr20 920391 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=901974;QSTRAND=+ GT:DP:AD 1|0:16:10,6 ./.:25:12,13 ./.:21:11,10 -chr20 921033 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=902616;QSTRAND=+ GT:DP:AD 1|1:27:10,17 1|1:38:16,22 1|1:37:15,22 -chr20 921239 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=902822;QSTRAND=+ GT:DP:AD 1|1:38:20,18 1|1:16:6,10 1|1:11:6,5 -chr20 921288 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=902871;QSTRAND=+ GT:DP:AD 1|1:20:5,15 1|0:38:17,21 1|1:42:21,21 -chr20 921359 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=877507;QSTRAND=+ GT:DP:AD 0|1:17:8,9 ./.:21:14,7 ./.:35:10,25 -chr20 921417 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=877565;QSTRAND=+ GT:DP:AD 0|1:18:10,8 1|0:32:23,9 0|1:32:13,19 -chr20 921417 . T TG 60 . QNAME=cluster19_000000F;QSTART=885694;QSTRAND=+ GT:DP:AD ./.:38:17,21 0|1:28:7,21 ./.:31:23,8 -chr20 921667 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=903250;QSTRAND=+ GT:DP:AD 1|0:31:18,13 0|1:29:23,6 0|1:38:21,17 -chr20 922254 . C G 60 . QNAME=cluster19_000000F;QSTART=886531;QSTRAND=+ GT:DP:AD ./.:34:13,21 0|1:18:6,12 0|1:39:24,15 -chr20 922377 . G A 60 . QNAME=cluster19_000000F;QSTART=886654;QSTRAND=+ GT:DP:AD ./.:31:8,23 0|1:19:8,11 0|1:34:19,15 -chr20 923331 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=24769781;QSTRAND=- GT:DP:AD ./.:25:18,7 ./.:13:6,7 0|1:47:22,25 -chr20 923875 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=24769236;QSTRAND=- GT:DP:AD ./.:33:23,10 ./.:45:20,25 0|1:24:16,8 -chr20 924499 . C T 60 . QNAME=cluster19_000000F;QSTART=888776;QSTRAND=+ GT:DP:AD ./.:23:12,11 0|1:38:17,21 0|1:19:12,7 -chr20 925913 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=882062;QSTRAND=+ GT:DP:AD 0|1:47:22,25 ./.:31:16,15 ./.:32:24,8 -chr20 928807 . G C 60 . QNAME=cluster19_000000F;QSTART=893084;QSTRAND=+ GT:DP:AD ./.:27:21,6 0|1:34:22,12 0|1:26:19,7 -chr20 929128 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=885275;QSTRAND=+ GT:DP:AD 0|1:48:24,24 1|1:19:11,8 0|1:38:13,25 -chr20 929177 . T C 60 . QNAME=cluster19_000000F;QSTART=893454;QSTRAND=+ GT:DP:AD ./.:41:19,22 0|1:37:18,19 ./.:44:20,24 -chr20 929220 . A T 60 . QNAME=cluster19_000000F;QSTART=893497;QSTRAND=+ GT:DP:AD ./.:38:18,20 0|1:18:13,5 ./.:25:6,19 -chr20 929302 . TTA T 60 . QNAME=cluster19_000000F;QSTART=24828792;QSTRAND=- GT:DP:AD ./.:34:24,10 1|0:49:25,24 ./.:12:6,6 -chr20 929302 . TTATGG T 60 . QNAME=cluster19_000000F;QSTART=893580;QSTRAND=+ GT:DP:AD ./.:36:17,19 0|1:19:14,5 ./.:20:15,5 -chr20 929491 . A C 60 . QNAME=cluster19_000000F;QSTART=24828605;QSTRAND=- GT:DP:AD ./.:22:9,13 1|1:29:17,12 ./.:24:9,15 -chr20 929623 . T C 60 . QNAME=cluster19_000000F;QSTART=24828473;QSTRAND=- GT:DP:AD ./.:25:14,11 1|1:38:18,20 ./.:44:24,20 -chr20 929701 . T G 60 . QNAME=cluster19_000000F;QSTART=24828395;QSTRAND=- GT:DP:AD ./.:36:11,25 1|1:25:6,19 ./.:36:11,25 -chr20 931616 . C T 60 . QNAME=cluster19_000000F;QSTART=24826480;QSTRAND=- GT:DP:AD ./.:40:22,18 1|1:18:10,8 ./.:33:11,22 -chr20 931983 . A G 60 . QNAME=cluster19_000000F;QSTART=24826113;QSTRAND=- GT:DP:AD ./.:39:21,18 1|1:16:8,8 ./.:26:14,12 -chr20 932022 . T C 60 . QNAME=cluster19_000000F;QSTART=24826074;QSTRAND=- GT:DP:AD ./.:30:21,9 1|1:36:17,19 ./.:45:24,21 -chr20 932357 . T C 60 . QNAME=cluster19_000000F;QSTART=24825739;QSTRAND=- GT:DP:AD ./.:27:7,20 1|1:42:18,24 ./.:20:11,9 -chr20 932610 . G A 60 . QNAME=cluster19_000000F;QSTART=24825486;QSTRAND=- GT:DP:AD ./.:29:10,19 1|1:30:21,9 ./.:21:15,6 -chr20 932660 . A AT 60 . QNAME=cluster19_000000F;QSTART=24825435;QSTRAND=- GT:DP:AD ./.:31:19,12 1|1:47:24,23 ./.:18:9,9 -chr20 932698 . G A 60 . QNAME=cluster19_000000F;QSTART=24825397;QSTRAND=- GT:DP:AD ./.:38:17,21 1|1:33:10,23 ./.:34:13,21 -chr20 932824 . G A 60 . QNAME=cluster19_000000F;QSTART=24825271;QSTRAND=- GT:DP:AD ./.:37:13,24 1|1:26:6,20 ./.:30:16,14 -chr20 933093 . C T 60 . QNAME=cluster19_000000F;QSTART=24825002;QSTRAND=- GT:DP:AD ./.:33:10,23 1|1:31:6,25 ./.:21:16,5 -chr20 933764 . G T 60 . QNAME=cluster19_000000F;QSTART=24824331;QSTRAND=- GT:DP:AD ./.:43:25,18 1|1:42:19,23 ./.:23:5,18 -chr20 933777 . T G 60 . QNAME=cluster19_000000F;QSTART=24824318;QSTRAND=- GT:DP:AD ./.:28:13,15 1|1:38:15,23 ./.:29:18,11 -chr20 934006 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=890153;QSTRAND=+ GT:DP:AD 0|1:31:22,9 ./.:43:25,18 ./.:43:18,25 -chr20 934616 . G A 60 . QNAME=cluster19_000000F;QSTART=24823479;QSTRAND=- GT:DP:AD ./.:23:17,6 1|1:33:11,22 ./.:24:8,16 -chr20 935220 . C A 60 . QNAME=cluster19_000000F;QSTART=24822875;QSTRAND=- GT:DP:AD ./.:29:24,5 1|1:20:14,6 ./.:23:7,16 -chr20 935920 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24757191;QSTRAND=- GT:DP:AD ./.:35:24,11 ./.:30:18,12 0|1:40:18,22 -chr20 936160 . A C 60 . QNAME=cluster19_000000F;QSTART=24821935;QSTRAND=- GT:DP:AD ./.:41:24,17 1|0:39:16,23 ./.:41:21,20 -chr20 937152 . A T 60 . QNAME=cluster19_000000F;QSTART=24820943;QSTRAND=- GT:DP:AD ./.:31:7,24 1|0:46:22,24 ./.:40:25,15 -chr20 937174 . C T 60 . QNAME=cluster19_000000F;QSTART=24820921;QSTRAND=- GT:DP:AD ./.:33:11,22 1|0:17:6,11 ./.:27:16,11 -chr20 937837 . T A 60 . QNAME=cluster19_000000F;QSTART=24820258;QSTRAND=- GT:DP:AD ./.:23:10,13 1|0:33:23,10 ./.:43:18,25 -chr20 937941 . A G 60 . QNAME=cluster19_000000F;QSTART=24820154;QSTRAND=- GT:DP:AD ./.:31:11,20 1|0:25:19,6 ./.:28:19,9 -chr20 938380 . G A 60 . QNAME=cluster19_000000F;QSTART=24819715;QSTRAND=- GT:DP:AD ./.:34:16,18 1|0:34:20,14 ./.:32:9,23 diff --git a/repo_utils/test_files/answer_key/divided/multi_00000021.vcf b/repo_utils/test_files/answer_key/divided/multi_00000021.vcf deleted file mode 100644 index b21990a3..00000000 --- a/repo_utils/test_files/answer_key/divided/multi_00000021.vcf +++ /dev/null @@ -1,166 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##bcftools_mergeVersion=1.12+htslib-1.12 -##bcftools_mergeCommand=merge -O z -f x -m none input1.vcf.gz input2.vcf.gz input3.vcf.gz; Date=Mon Aug 16 18:05:13 2021 -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 940109 . A G 60 . QNAME=cluster19_000000F;QSTART=24817986;QSTRAND=- GT:DP:AD ./.:40:20,20 1|1:31:16,15 ./.:25:13,12 -chr20 940207 . G A 60 . QNAME=cluster19_000000F;QSTART=24817888;QSTRAND=- GT:DP:AD ./.:31:12,19 1|1:15:10,5 ./.:23:8,15 -chr20 941328 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=897475;QSTRAND=+ GT:DP:AD 0|1:27:9,18 1|1:22:16,6 0|1:31:10,21 -chr20 942095 . C CA 60 . QNAME=cluster19_000000F;QSTART=906369;QSTRAND=+ GT:DP:AD ./.:26:11,15 0|1:34:20,14 ./.:30:11,19 -chr20 942273 . A AT 60 . QNAME=HG002-S9-H2-000001F;QSTART=898421;QSTRAND=+ GT:DP:AD 0|1:33:8,25 1|1:34:12,22 0|1:21:11,10 -chr20 942277 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=898425;QSTRAND=+ GT:DP:AD 0|1:17:8,9 1|1:37:22,15 0|1:31:20,11 -chr20 942358 . C T 60 . QNAME=cluster19_000000F;QSTART=24815736;QSTRAND=- GT:DP:AD ./.:34:10,24 1|1:47:22,25 0|1:26:14,12 -chr20 942424 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=898572;QSTRAND=+ GT:DP:AD 0|1:25:9,16 ./.:26:13,13 ./.:20:9,11 -chr20 942563 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=898711;QSTRAND=+ GT:DP:AD 0|1:32:18,14 ./.:28:20,8 ./.:21:14,7 -chr20 942659 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=898807;QSTRAND=+ GT:DP:AD 0|1:21:12,9 1|1:37:24,13 0|1:32:13,19 -chr20 943015 . G A 60 . QNAME=cluster19_000000F;QSTART=24815079;QSTRAND=- GT:DP:AD ./.:36:11,25 1|1:39:16,23 0|1:31:16,15 -chr20 943016 . C A 60 . QNAME=cluster19_000000F;QSTART=24815078;QSTRAND=- GT:DP:AD ./.:28:16,12 1|1:14:8,6 0|1:46:24,22 -chr20 943950 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=900098;QSTRAND=+ GT:DP:AD 0|1:42:23,19 ./.:33:14,19 ./.:27:8,19 -chr20 943984 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=900132;QSTRAND=+ GT:DP:AD 0|1:34:25,9 1|1:32:17,15 0|1:41:18,23 -chr20 944018 . GCT G 60 . QNAME=cluster19_000000F;QSTART=24814076;QSTRAND=- GT:DP:AD ./.:14:8,6 1|1:21:10,11 0|1:21:13,8 -chr20 944028 . TC T 60 . QNAME=HG002-S9-H2-000001F;QSTART=900177;QSTRAND=+ GT:DP:AD 0|1:27:18,9 ./.:11:6,5 ./.:21:8,13 -chr20 944029 . C CTT 60 . QNAME=cluster23_scaffold_3;QSTART=24765421;QSTRAND=- GT:DP:AD ./.:39:18,21 ./.:40:25,15 1|0:42:25,17 -chr20 944093 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24765357;QSTRAND=- GT:DP:AD ./.:27:18,9 ./.:36:21,15 1|0:25:16,9 -chr20 944094 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=24765356;QSTRAND=- GT:DP:AD ./.:13:6,7 ./.:19:10,9 1|0:26:15,11 -chr20 945682 . T C 60 . QNAME=cluster19_000000F;QSTART=909955;QSTRAND=+ GT:DP:AD ./.:25:7,18 0|1:45:20,25 0|1:22:5,17 -chr20 945711 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=901858;QSTRAND=+ GT:DP:AD 0|1:40:19,21 0|1:27:13,14 0|1:41:22,19 -chr20 945754 . G A 60 . QNAME=cluster19_000000F;QSTART=910027;QSTRAND=+ GT:DP:AD ./.:34:17,17 0|1:33:25,8 0|1:34:10,24 -chr20 945942 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=902089;QSTRAND=+ GT:DP:AD 0|1:31:8,23 0|1:15:8,7 0|1:27:13,14 -chr20 946505 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=928088;QSTRAND=+ GT:DP:AD 1|0:25:10,15 0|1:27:16,11 0|1:30:10,20 -chr20 946814 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=902961;QSTRAND=+ GT:DP:AD 0|1:18:13,5 ./.:44:22,22 1|0:32:24,8 -chr20 946899 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=903046;QSTRAND=+ GT:DP:AD 0|1:35:16,19 ./.:30:7,23 1|0:22:6,16 -chr20 947202 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=903349;QSTRAND=+ GT:DP:AD 0|1:36:21,15 ./.:18:7,11 1|0:26:17,9 -chr20 947218 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=903365;QSTRAND=+ GT:DP:AD 0|1:20:12,8 ./.:31:14,17 1|0:38:18,20 -chr20 947585 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=903732;QSTRAND=+ GT:DP:AD 0|1:23:16,7 ./.:18:7,11 1|0:30:23,7 -chr20 947624 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=903771;QSTRAND=+ GT:DP:AD 0|1:30:20,10 ./.:32:25,7 1|0:47:25,22 -chr20 947782 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=903929;QSTRAND=+ GT:DP:AD 0|1:35:15,20 ./.:26:7,19 1|0:28:23,5 -chr20 947795 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=903942;QSTRAND=+ GT:DP:AD 0|1:38:20,18 ./.:14:9,5 1|0:26:7,19 -chr20 947914 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=904061;QSTRAND=+ GT:DP:AD 0|1:22:8,14 ./.:36:16,20 1|0:20:5,15 -chr20 948357 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=904504;QSTRAND=+ GT:DP:AD 0|1:27:13,14 ./.:29:22,7 1|0:34:10,24 -chr20 948492 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=904639;QSTRAND=+ GT:DP:AD 0|1:16:8,8 ./.:33:24,9 1|0:19:9,10 -chr20 948493 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=904640;QSTRAND=+ GT:DP:AD 0|1:29:19,10 ./.:31:17,14 1|0:13:8,5 -chr20 948861 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=905008;QSTRAND=+ GT:DP:AD 0|1:36:19,17 ./.:37:19,18 1|0:33:23,10 -chr20 949016 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=905163;QSTRAND=+ GT:DP:AD 0|1:27:20,7 ./.:32:13,19 1|0:24:18,6 -chr20 949377 . GA G 60 . QNAME=HG002-S9-H2-000001F;QSTART=905525;QSTRAND=+ GT:DP:AD 0|1:45:20,25 ./.:20:15,5 1|0:15:7,8 -chr20 949516 . CTCTGAAGAGGTAACATTTGAACTGAGATGTAGAGGGAGAGAAGGAACTAGCCATGTGGAGATCTGGGGGAGGAGCATTCCAGGCAGAGGGGATAGCAAGTGCA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=905663;QSTRAND=+;SVTYPE=DEL;SVLEN=-103 GT:DP:AD 0/1:29:9,20 ./.:28:7,21 1/0:34:12,22 -chr20 949837 . C T 60 . QNAME=cluster19_000000F;QSTART=914110;QSTRAND=+ GT:DP:AD ./.:12:6,6 0|1:41:23,18 0|1:24:15,9 -chr20 949917 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=905960;QSTRAND=+ GT:DP:AD 0|1:40:25,15 ./.:31:9,22 1|0:38:18,20 -chr20 950840 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=906883;QSTRAND=+ GT:DP:AD 0|1:40:18,22 ./.:15:5,10 1|0:25:5,20 -chr20 950981 . A AAAATAAAT 60 . QNAME=HG002-S9-H2-000001F;QSTART=907025;QSTRAND=+ GT:DP:AD 0|1:40:25,15 ./.:30:22,8 1|0:32:9,23 -chr20 951023 . A AAAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=907075;QSTRAND=+ GT:DP:AD 0|1:25:7,18 ./.:29:16,13 1|0:40:19,21 -chr20 951100 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=907154;QSTRAND=+ GT:DP:AD 0|1:42:17,25 ./.:24:10,14 1|0:19:11,8 -chr20 951130 . A ATT 60 . QNAME=HG002-S9-H1-000001F;QSTART=932714;QSTRAND=+ GT:DP:AD 1|0:37:24,13 ./.:38:13,25 ./.:20:6,14 -chr20 951130 . ATTTTTTTTTTTTT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=907185;QSTRAND=+ GT:DP:AD 0|1:32:18,14 ./.:34:12,22 ./.:38:18,20 -chr20 951130 . ATTTTTTTTTTTT A 60 . QNAME=cluster19_000000F;QSTART=24806966;QSTRAND=- GT:DP:AD ./.:47:24,23 1|0:48:24,24 1|0:24:7,17 -chr20 951130 . A ATTT 60 . QNAME=cluster19_000000F;QSTART=915404;QSTRAND=+ GT:DP:AD ./.:39:17,22 0|1:40:15,25 ./.:36:18,18 -chr20 951130 . A ATTTTT 60 . QNAME=cluster23_scaffold_2;QSTART=24741977;QSTRAND=- GT:DP:AD ./.:15:9,6 ./.:31:25,6 0|1:24:9,15 -chr20 951172 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=907213;QSTRAND=+ GT:DP:AD 0|1:36:21,15 ./.:31:9,22 1|0:32:8,24 -chr20 951188 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=907229;QSTRAND=+ GT:DP:AD 0|1:20:13,7 ./.:27:6,21 1|0:24:7,17 -chr20 951376 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=932961;QSTRAND=+ GT:DP:AD 1|1:29:20,9 0|1:42:23,19 1|1:31:6,25 -chr20 951397 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=932982;QSTRAND=+ GT:DP:AD 1|0:39:21,18 ./.:37:18,19 ./.:28:22,6 -chr20 951428 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=933013;QSTRAND=+ GT:DP:AD 1|0:32:10,22 ./.:31:8,23 ./.:41:25,16 -chr20 951612 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=933197;QSTRAND=+ GT:DP:AD 1|0:34:15,19 ./.:32:10,22 ./.:31:11,20 -chr20 951687 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=933272;QSTRAND=+ GT:DP:AD 1|0:39:18,21 ./.:29:15,14 ./.:28:8,20 -chr20 951756 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=933341;QSTRAND=+ GT:DP:AD 1|0:30:25,5 ./.:28:13,15 ./.:36:25,11 -chr20 951868 . C T 60 . QNAME=cluster19_000000F;QSTART=916144;QSTRAND=+ GT:DP:AD ./.:15:6,9 0|1:25:11,14 1|1:27:19,8 -chr20 951868 . CGT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=907910;QSTRAND=+ GT:DP:AD 0|1:30:13,17 ./.:24:14,10 ./.:37:18,19 -chr20 951870 . T C 60 . QNAME=cluster19_000000F;QSTART=916146;QSTRAND=+ GT:DP:AD ./.:19:12,7 0|1:15:8,7 1|1:34:25,9 -chr20 951975 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=908014;QSTRAND=+ GT:DP:AD 0|1:20:8,12 0|1:29:24,5 1|1:34:23,11 -chr20 952317 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=933902;QSTRAND=+ GT:DP:AD 1|0:22:12,10 ./.:42:23,19 ./.:27:5,22 -chr20 952372 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=933957;QSTRAND=+ GT:DP:AD 1|0:34:13,21 ./.:30:11,19 ./.:38:15,23 -chr20 952391 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=908430;QSTRAND=+ GT:DP:AD 0|1:17:9,8 0|1:22:8,14 1|1:16:7,9 -chr20 952475 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=934060;QSTRAND=+ GT:DP:AD 1|0:30:10,20 ./.:26:18,8 ./.:27:8,19 -chr20 952558 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=908597;QSTRAND=+ GT:DP:AD 0|1:21:16,5 0|1:40:25,15 1|1:47:24,23 -chr20 952594 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=934179;QSTRAND=+ GT:DP:AD 1|0:41:25,16 ./.:17:8,9 ./.:38:13,25 -chr20 952909 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=934494;QSTRAND=+ GT:DP:AD 1|0:35:14,21 ./.:33:24,9 ./.:12:7,5 -chr20 953115 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=909154;QSTRAND=+ GT:DP:AD 0|1:20:6,14 1|1:37:14,23 1|1:40:23,17 -chr20 953327 . GTTAT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=934913;QSTRAND=+ GT:DP:AD 1|1:35:16,19 1|1:22:6,16 1|1:34:11,23 -chr20 953360 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=934941;QSTRAND=+ GT:DP:AD 1|0:31:24,7 ./.:31:6,25 ./.:20:12,8 -chr20 953456 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=935037;QSTRAND=+ GT:DP:AD 1|0:37:17,20 ./.:29:8,21 ./.:39:20,19 -chr20 953490 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=935071;QSTRAND=+ GT:DP:AD 1|1:32:19,13 1|1:30:21,9 1|1:30:7,23 -chr20 953507 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=935088;QSTRAND=+ GT:DP:AD 1|0:30:15,15 ./.:35:10,25 ./.:41:22,19 -chr20 953510 . A AT 60 . QNAME=HG002-S9-H2-000001F;QSTART=909546;QSTRAND=+ GT:DP:AD 0|1:30:8,22 1|1:32:11,21 1|1:35:17,18 -chr20 953670 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=909706;QSTRAND=+ GT:DP:AD 0|1:37:24,13 1|1:17:5,12 0|1:31:21,10 -chr20 953787 . AC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=935369;QSTRAND=+ GT:DP:AD 1|0:10:5,5 ./.:39:21,18 ./.:23:8,15 -chr20 953831 . T TC 60 . QNAME=HG002-S9-H1-000001F;QSTART=935412;QSTRAND=+ GT:DP:AD 1|0:26:15,11 ./.:23:13,10 ./.:32:21,11 -chr20 953857 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=935438;QSTRAND=+ GT:DP:AD 1|0:29:12,17 ./.:33:15,18 ./.:36:16,20 -chr20 953954 . CG C 60 . QNAME=HG002-S9-H1-000001F;QSTART=935536;QSTRAND=+ GT:DP:AD 1|0:29:23,6 ./.:16:9,7 ./.:25:13,12 -chr20 953974 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=935554;QSTRAND=+ GT:DP:AD 1|0:43:20,23 ./.:21:16,5 ./.:38:22,16 -chr20 954305 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=935885;QSTRAND=+ GT:DP:AD 1|1:30:8,22 1|1:25:7,18 0|1:17:12,5 -chr20 954418 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=910454;QSTRAND=+ GT:DP:AD 0|1:27:12,15 1|1:37:16,21 0|1:44:20,24 -chr20 954610 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=24738500;QSTRAND=- GT:DP:AD ./.:24:6,18 ./.:32:12,20 0|1:39:25,14 -chr20 954684 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=936264;QSTRAND=+ GT:DP:AD 1|1:35:19,16 1|1:26:21,5 1|1:25:6,19 -chr20 954686 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=936266;QSTRAND=+ GT:DP:AD 1|1:17:5,12 1|1:45:25,20 0|1:46:22,24 -chr20 954688 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=936268;QSTRAND=+ GT:DP:AD 1|0:24:11,13 ./.:44:23,21 ./.:47:22,25 -chr20 954692 . CAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=936273;QSTRAND=+ GT:DP:AD 1|1:41:22,19 1|1:33:19,14 1|1:39:20,19 -chr20 955001 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=936579;QSTRAND=+ GT:DP:AD 1|0:44:22,22 ./.:28:12,16 ./.:42:21,21 -chr20 956302 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=937880;QSTRAND=+ GT:DP:AD 1|0:24:8,16 ./.:35:13,22 ./.:41:20,21 -chr20 956624 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=938202;QSTRAND=+ GT:DP:AD 1|1:24:8,16 1|1:42:21,21 1|1:31:12,19 -chr20 956630 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=938208;QSTRAND=+ GT:DP:AD 1|0:43:23,20 ./.:12:7,5 ./.:23:10,13 -chr20 957046 . C T 60 . QNAME=cluster19_000000F;QSTART=24801067;QSTRAND=- GT:DP:AD ./.:32:14,18 1|0:13:5,8 ./.:27:13,14 -chr20 957302 . G GTA 60 . QNAME=HG002-S9-H1-000001F;QSTART=938881;QSTRAND=+ GT:DP:AD 1|0:46:22,24 ./.:37:25,12 ./.:35:12,23 -chr20 957320 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=938900;QSTRAND=+ GT:DP:AD 1|0:26:6,20 ./.:46:22,24 ./.:38:14,24 -chr20 957322 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=938902;QSTRAND=+ GT:DP:AD 1|0:30:14,16 ./.:35:18,17 ./.:20:9,11 -chr20 957387 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=938967;QSTRAND=+ GT:DP:AD 1|1:24:19,5 1|1:39:19,20 0|1:43:21,22 -chr20 957642 . C CAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=939223;QSTRAND=+ GT:DP:AD 1|0:24:6,18 ./.:42:17,25 ./.:39:15,24 -chr20 957677 . T TAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=939264;QSTRAND=+ GT:DP:AD 1|0:28:8,20 ./.:13:5,8 ./.:45:22,23 -chr20 958217 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=939805;QSTRAND=+ GT:DP:AD 1|0:26:21,5 ./.:39:21,18 ./.:21:12,9 -chr20 958300 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=939888;QSTRAND=+ GT:DP:AD 1|0:32:14,18 ./.:34:11,23 ./.:27:15,12 -chr20 958487 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=940075;QSTRAND=+ GT:DP:AD 1|0:24:9,15 ./.:30:11,19 ./.:36:11,25 -chr20 958518 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=940106;QSTRAND=+ GT:DP:AD 1|0:42:17,25 ./.:21:11,10 ./.:30:6,24 -chr20 958523 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=940111;QSTRAND=+ GT:DP:AD 1|0:27:21,6 ./.:25:19,6 ./.:27:17,10 -chr20 958650 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24734462;QSTRAND=- GT:DP:AD ./.:46:24,22 ./.:23:7,16 0|1:28:5,23 -chr20 958880 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=940468;QSTRAND=+ GT:DP:AD 1|0:32:24,8 ./.:29:17,12 ./.:13:7,6 -chr20 959105 . GAGTGTGGTGGTGGGTGTGGGGC G 60 . QNAME=HG002-S9-H1-000001F;QSTART=940694;QSTRAND=+ GT:DP:AD 1|0:27:14,13 ./.:47:22,25 ./.:39:22,17 -chr20 959171 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=940737;QSTRAND=+ GT:DP:AD 1|0:16:11,5 ./.:35:22,13 ./.:44:22,22 -chr20 959315 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=940881;QSTRAND=+ GT:DP:AD 1|0:36:19,17 ./.:35:22,13 ./.:27:8,19 -chr20 959563 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=941129;QSTRAND=+ GT:DP:AD 1|0:21:11,10 ./.:27:7,20 ./.:34:15,19 -chr20 959871 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=941437;QSTRAND=+ GT:DP:AD 1|0:48:23,25 ./.:23:14,9 ./.:18:9,9 -chr20 960669 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=942235;QSTRAND=+ GT:DP:AD 1|0:20:5,15 ./.:30:20,10 ./.:50:25,25 -chr20 960776 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=942342;QSTRAND=+ GT:DP:AD 1|0:33:18,15 ./.:22:5,17 ./.:41:17,24 -chr20 960856 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=942422;QSTRAND=+ GT:DP:AD 1|0:39:22,17 ./.:42:21,21 ./.:25:5,20 -chr20 961022 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=942588;QSTRAND=+ GT:DP:AD 1|0:27:9,18 ./.:33:11,22 ./.:31:20,11 -chr20 961081 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=942647;QSTRAND=+ GT:DP:AD 1|1:31:21,10 1|1:32:14,18 1|1:37:17,20 -chr20 961455 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=943021;QSTRAND=+ GT:DP:AD 1|0:29:16,13 ./.:37:15,22 ./.:18:7,11 -chr20 961789 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=943355;QSTRAND=+ GT:DP:AD 1|0:40:19,21 ./.:30:15,15 ./.:36:20,16 -chr20 961809 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=943375;QSTRAND=+ GT:DP:AD 1|0:30:18,12 ./.:22:7,15 ./.:15:6,9 -chr20 962027 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=943593;QSTRAND=+ GT:DP:AD 1|0:10:5,5 ./.:17:7,10 ./.:16:5,11 -chr20 962140 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=943706;QSTRAND=+ GT:DP:AD 1|0:22:8,14 ./.:20:9,11 ./.:37:20,17 -chr20 962739 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=944305;QSTRAND=+ GT:DP:AD 1|0:32:8,24 ./.:21:5,16 ./.:24:14,10 -chr20 962818 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=944384;QSTRAND=+ GT:DP:AD 1|0:41:18,23 ./.:32:25,7 ./.:28:13,15 diff --git a/repo_utils/test_files/answer_key/divided/multi_00000022.vcf b/repo_utils/test_files/answer_key/divided/multi_00000022.vcf deleted file mode 100644 index b8f481a4..00000000 --- a/repo_utils/test_files/answer_key/divided/multi_00000022.vcf +++ /dev/null @@ -1,116 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##bcftools_mergeVersion=1.12+htslib-1.12 -##bcftools_mergeCommand=merge -O z -f x -m none input1.vcf.gz input2.vcf.gz input3.vcf.gz; Date=Mon Aug 16 18:05:13 2021 -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 964006 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=945572;QSTRAND=+ GT:DP:AD 1|0:31:19,12 ./.:35:25,10 ./.:35:19,16 -chr20 964368 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=945934;QSTRAND=+ GT:DP:AD 1|0:45:23,22 ./.:32:14,18 ./.:43:24,19 -chr20 964461 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=946027;QSTRAND=+ GT:DP:AD 1|0:28:8,20 ./.:32:17,15 ./.:27:8,19 -chr20 964587 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=946153;QSTRAND=+ GT:DP:AD 1|0:29:24,5 ./.:21:10,11 ./.:37:13,24 -chr20 964681 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=946247;QSTRAND=+ GT:DP:AD 1|0:26:12,14 ./.:20:11,9 ./.:35:13,22 -chr20 964763 . T TAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=946330;QSTRAND=+ GT:DP:AD 1|0:24:11,13 ./.:34:13,21 ./.:22:13,9 -chr20 964805 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=946373;QSTRAND=+ GT:DP:AD 1|0:25:18,7 ./.:30:16,14 ./.:30:10,20 -chr20 964823 . CACACACACATAT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=946392;QSTRAND=+ GT:DP:AD 1|0:23:8,15 ./.:24:13,11 ./.:34:9,25 -chr20 964827 . CACACAT C 60 . QNAME=cluster23_scaffold_3;QSTART=24744733;QSTRAND=- GT:DP:AD ./.:26:19,7 ./.:23:12,11 1|0:42:24,18 -chr20 964831 . CAT C 60 . QNAME=cluster19_000000F;QSTART=24793282;QSTRAND=- GT:DP:AD ./.:23:17,6 1|1:25:14,11 0|1:25:16,9 -chr20 965654 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=947210;QSTRAND=+ GT:DP:AD 1|0:38:13,25 ./.:38:15,23 ./.:12:5,7 -chr20 965660 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=947216;QSTRAND=+ GT:DP:AD 1|0:19:6,13 ./.:37:22,15 ./.:45:20,25 -chr20 965819 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=947375;QSTRAND=+ GT:DP:AD 1|0:29:11,18 ./.:18:6,12 ./.:35:14,21 -chr20 965855 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=947411;QSTRAND=+ GT:DP:AD 1|0:31:15,16 ./.:31:24,7 ./.:40:22,18 -chr20 966123 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=947679;QSTRAND=+ GT:DP:AD 1|0:17:11,6 ./.:19:7,12 ./.:22:14,8 -chr20 966156 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=947712;QSTRAND=+ GT:DP:AD 1|0:26:5,21 ./.:34:14,20 ./.:43:22,21 -chr20 966449 . G GTC 60 . QNAME=HG002-S9-H1-000001F;QSTART=948006;QSTRAND=+ GT:DP:AD 1|0:30:13,17 ./.:33:21,12 ./.:24:5,19 -chr20 966451 . CT C 60 . QNAME=cluster23_scaffold_2;QSTART=24726663;QSTRAND=- GT:DP:AD ./.:45:23,22 ./.:16:6,10 0|1:23:15,8 -chr20 966507 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=948065;QSTRAND=+ GT:DP:AD 1|0:19:12,7 ./.:12:6,6 ./.:35:12,23 -chr20 966840 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=948398;QSTRAND=+ GT:DP:AD 1|0:28:10,18 ./.:19:9,10 ./.:47:24,23 -chr20 966858 . AAAACAAGC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=948417;QSTRAND=+ GT:DP:AD 1|0:29:9,20 ./.:27:21,6 ./.:30:11,19 -chr20 970054 . TC T 60 . QNAME=cluster23_scaffold_2;QSTART=24723061;QSTRAND=- GT:DP:AD ./.:29:17,12 ./.:24:15,9 0|1:29:16,13 -chr20 971192 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=952742;QSTRAND=+ GT:DP:AD 1|0:14:8,6 ./.:19:10,9 ./.:38:23,15 -chr20 971309 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=927343;QSTRAND=+ GT:DP:AD 0|1:34:15,19 ./.:18:7,11 ./.:30:9,21 -chr20 971575 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=927609;QSTRAND=+ GT:DP:AD 0|1:31:12,19 ./.:22:14,8 ./.:39:23,16 -chr20 972263 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=953813;QSTRAND=+ GT:DP:AD 1|1:28:11,17 ./.:40:18,22 ./.:40:24,16 -chr20 972407 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=953957;QSTRAND=+ GT:DP:AD 1|1:34:24,10 ./.:13:7,6 ./.:33:23,10 -chr20 972507 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=928541;QSTRAND=+ GT:DP:AD 0|1:21:10,11 ./.:14:8,6 ./.:24:5,19 -chr20 972633 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=954183;QSTRAND=+ GT:DP:AD 1|1:28:7,21 ./.:35:15,20 ./.:35:20,15 -chr20 972877 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=954427;QSTRAND=+ GT:DP:AD 1|1:13:8,5 ./.:29:22,7 ./.:44:22,22 -chr20 972959 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=954509;QSTRAND=+ GT:DP:AD 1|1:22:13,9 ./.:27:10,17 ./.:21:14,7 -chr20 973165 . TGG T 60 . QNAME=cluster23_scaffold_3;QSTART=24736401;QSTRAND=- GT:DP:AD ./.:28:11,17 ./.:22:17,5 1|0:32:23,9 -chr20 973459 . ATTGT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=955010;QSTRAND=+ GT:DP:AD 1|1:22:11,11 ./.:35:17,18 ./.:31:15,16 -chr20 973459 . A ATTGT 60 . QNAME=cluster19_000000F;QSTART=24784652;QSTRAND=- GT:DP:AD ./.:30:8,22 1|0:34:22,12 1|0:40:20,20 -chr20 973633 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=955179;QSTRAND=+ GT:DP:AD 1|1:33:13,20 ./.:27:8,19 ./.:22:8,14 -chr20 974110 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=930140;QSTRAND=+ GT:DP:AD 0|1:32:11,21 ./.:30:17,13 ./.:43:23,20 -chr20 974769 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=956315;QSTRAND=+ GT:DP:AD 1|1:31:18,13 ./.:35:20,15 ./.:36:14,22 -chr20 975693 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=957239;QSTRAND=+ GT:DP:AD 1|0:29:11,18 ./.:20:13,7 ./.:45:24,21 -chr20 976042 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=957588;QSTRAND=+ GT:DP:AD 1|1:47:24,23 ./.:30:12,18 1|0:34:15,19 -chr20 976694 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=958240;QSTRAND=+ GT:DP:AD 1|0:47:23,24 ./.:20:13,7 ./.:38:14,24 -chr20 977237 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=958783;QSTRAND=+ GT:DP:AD 1|0:16:9,7 ./.:22:11,11 ./.:22:12,10 -chr20 977764 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=959310;QSTRAND=+ GT:DP:AD 1|0:20:8,12 ./.:34:24,10 ./.:28:23,5 -chr20 978561 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=24714555;QSTRAND=- GT:DP:AD ./.:23:18,5 ./.:17:5,12 0|1:32:25,7 -chr20 978696 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=960242;QSTRAND=+ GT:DP:AD 1|0:33:18,15 ./.:42:18,24 ./.:32:7,25 -chr20 979248 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=960794;QSTRAND=+ GT:DP:AD 1|0:24:11,13 ./.:31:24,7 ./.:14:6,8 -chr20 980145 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=961691;QSTRAND=+ GT:DP:AD 1|0:39:16,23 ./.:29:17,12 ./.:36:18,18 -chr20 980577 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=936607;QSTRAND=+ GT:DP:AD 0|1:16:9,7 1|0:26:15,11 ./.:37:19,18 -chr20 980652 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=962198;QSTRAND=+ GT:DP:AD 1|0:27:14,13 ./.:46:21,25 ./.:26:6,20 -chr20 980884 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=962430;QSTRAND=+ GT:DP:AD 1|0:20:9,11 ./.:32:19,13 ./.:30:10,20 -chr20 981108 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=962654;QSTRAND=+ GT:DP:AD 1|0:38:17,21 ./.:25:13,12 ./.:23:7,16 -chr20 981138 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=962684;QSTRAND=+ GT:DP:AD 1|0:16:7,9 ./.:34:20,14 ./.:26:20,6 -chr20 984922 . C CCCAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=966469;QSTRAND=+ GT:DP:AD 1|0:33:12,21 ./.:18:5,13 0|1:34:25,9 -chr20 990421 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=971971;QSTRAND=+ GT:DP:AD 1|0:32:22,10 ./.:31:15,16 ./.:40:24,16 -chr20 991150 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=972700;QSTRAND=+ GT:DP:AD 1|0:29:19,10 ./.:30:13,17 ./.:29:7,22 -chr20 991319 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=972869;QSTRAND=+ GT:DP:AD 1|0:26:17,9 ./.:13:7,6 ./.:42:20,22 -chr20 991428 . A AT 60 . QNAME=cluster19_000000F;QSTART=955698;QSTRAND=+ GT:DP:AD ./.:24:18,6 0|1:32:21,11 ./.:33:10,23 -chr20 992032 . G GGGAC 60 . QNAME=cluster23_scaffold_3;QSTART=24717528;QSTRAND=- GT:DP:AD ./.:40:15,25 ./.:24:17,7 1|1:10:5,5 -chr20 992091 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=973641;QSTRAND=+ GT:DP:AD 1|0:39:14,25 ./.:26:21,5 ./.:31:8,23 -chr20 992263 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=24717296;QSTRAND=- GT:DP:AD ./.:44:21,23 ./.:22:11,11 1|0:34:9,25 -chr20 992288 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=973838;QSTRAND=+ GT:DP:AD 1|0:29:6,23 ./.:34:15,19 ./.:35:14,21 -chr20 992532 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=974082;QSTRAND=+ GT:DP:AD 1|0:26:20,6 ./.:31:15,16 ./.:40:21,19 -chr20 992797 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=974347;QSTRAND=+ GT:DP:AD 1|0:18:8,10 ./.:32:22,10 ./.:25:19,6 -chr20 993026 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=974576;QSTRAND=+ GT:DP:AD 1|0:26:16,10 ./.:30:22,8 ./.:36:18,18 -chr20 993059 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=974609;QSTRAND=+ GT:DP:AD 1|0:29:9,20 ./.:29:12,17 ./.:34:14,20 -chr20 993443 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=974993;QSTRAND=+ GT:DP:AD 1|0:26:17,9 ./.:31:16,15 ./.:27:21,6 -chr20 993795 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=975345;QSTRAND=+ GT:DP:AD 1|0:41:24,17 ./.:36:19,17 ./.:40:20,20 -chr20 993846 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=975396;QSTRAND=+ GT:DP:AD 1|0:41:16,25 ./.:40:19,21 ./.:32:25,7 -chr20 993854 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=975404;QSTRAND=+ GT:DP:AD 1|0:29:13,16 ./.:32:15,17 ./.:41:24,17 -chr20 993856 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=975406;QSTRAND=+ GT:DP:AD 1|0:22:6,16 ./.:20:14,6 ./.:24:5,19 -chr20 994379 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=975929;QSTRAND=+ GT:DP:AD 1|1:48:23,25 1|0:31:21,10 1|1:19:8,11 -chr20 994584 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=976134;QSTRAND=+ GT:DP:AD 1|0:32:25,7 ./.:19:6,13 ./.:30:7,23 -chr20 994605 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=976155;QSTRAND=+ GT:DP:AD 1|0:40:16,24 ./.:35:22,13 ./.:17:5,12 -chr20 995547 . GA G 60 . QNAME=cluster23_scaffold_2;QSTART=24697561;QSTRAND=- GT:DP:AD ./.:31:20,11 ./.:21:9,12 0|1:37:22,15 -chr20 996521 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=978071;QSTRAND=+ GT:DP:AD 1|0:17:10,7 ./.:39:24,15 ./.:26:14,12 -chr20 999077 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=980627;QSTRAND=+ GT:DP:AD 1|0:19:8,11 ./.:27:14,13 ./.:40:16,24 diff --git a/repo_utils/test_files/answer_key/help.txt b/repo_utils/test_files/answer_key/help.txt deleted file mode 100644 index 78846db3..00000000 --- a/repo_utils/test_files/answer_key/help.txt +++ /dev/null @@ -1,22 +0,0 @@ -usage: truvari [-h] CMD ... - -Truvari v3.5.1 Structural Variant Benchmarking and Annotation - -Available commands: - bench Performance metrics from comparison of two VCFs - collapse Collapse possibly redundant VCF entries - anno Annotate a VCF - consistency Consistency report between multiple VCFs - vcf2df Turn a VCF into a pandas DataFrame - segment Normalization of SVs into disjointed genomic regions - divide Divide a VCF into multiple parts - phab Phased variant benchmarking using MSA - version Print the Truvari version and exit - -positional arguments: - CMD Command to execute - OPTIONS Options to pass to the command - -options: - -h, --help show this help message and exit - diff --git a/repo_utils/test_files/answer_key/multi_vcf2df.jl b/repo_utils/test_files/answer_key/multi_vcf2df.jl deleted file mode 100644 index ae8b4ecd..00000000 Binary files a/repo_utils/test_files/answer_key/multi_vcf2df.jl and /dev/null differ diff --git a/repo_utils/test_files/answer_key/phab_result.vcf.gz b/repo_utils/test_files/answer_key/phab_result.vcf.gz deleted file mode 100644 index a968a82d..00000000 Binary files a/repo_utils/test_files/answer_key/phab_result.vcf.gz and /dev/null differ diff --git a/repo_utils/test_files/answer_key/segment.vcf b/repo_utils/test_files/answer_key/segment.vcf deleted file mode 100644 index 17bb2779..00000000 --- a/repo_utils/test_files/answer_key/segment.vcf +++ /dev/null @@ -1,3567 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##INFO= -##INFO= -##INFO= -##FORMAT= -##bcftools_mergeVersion=1.10.2+htslib-1.10.2 -##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021 -##INFO= -##INFO= -##bcftools_viewVersion=1.12+htslib-1.12 -##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021 -##bcftools_mergeVersion=1.12+htslib-1.12 -##bcftools_mergeCommand=merge -O z -f x -m none input1.vcf.gz input2.vcf.gz input3.vcf.gz; Date=Mon Aug 16 18:05:13 2021 -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO== 0x,5x,10x,15x"> -##INFO== 0x,5x,10x,15x"> -##INFO= -##INFO= -##FORMAT= ploidy)"> -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385 NA12878 HG00733 -chr20 63971 . TTCCATTCCAC T 60 . QNAME=cluster19_000000F;QSTART=25698928;QSTRAND=-;GCPCT=45;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.747459 GT:DP:AD ./.:17:12,5 1|0:42:24,18 ./.:33:14,19 -chr20 64506 . C CTCCAT 60 . QNAME=cluster19_000000F;QSTART=25698398;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.729574 GT:DP:AD ./.:35:13,22 1|0:30:14,16 ./.:21:12,9 -chr20 66141 . AATTCC A 60 . QNAME=cluster23_scaffold_3;QSTART=25645835;QSTRAND=-;GCPCT=33;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.792481 GT:DP:AD ./.:18:10,8 ./.:43:18,25 1|1:32:16,16 -chr20 66235 . C CGACTCCACTCCATT 60 . QNAME=HG002-S9-H1-000001F;QSTART=45138;QSTRAND=+;GCPCT=53;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.873233 GT:DP:AD 1|1:42:20,22 1|1:27:5,22 1|1:33:22,11 -chr20 66369 . C T 60 . QNAME=cluster19_000000F;QSTART=25696521;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:34:21,13 1|0:30:21,9 ./.:41:16,25 -chr20 67373 . G GAAATGTGAT 60 . QNAME=cluster23_scaffold_2;QSTART=25629267;QSTRAND=-;GCPCT=30;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.785475 GT:DP:AD ./.:38:18,20 ./.:37:20,17 0|1:29:20,9 -chr20 68303 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=47219;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:41:18,23 0|1:43:18,25 1|1:29:15,14 -chr20 72450 . G A 60 . QNAME=cluster19_000000F;QSTART=25690440;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:16:6,10 1|0:23:10,13 ./.:33:15,18 -chr20 72765 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=51682;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|1:14:9,5 0|1:33:10,23 1|0:36:18,18 -chr20 72765 . T TAA 60 . QNAME=cluster23_scaffold_2;QSTART=25623873;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.459148 GT:DP:AD ./.:43:18,25 ./.:15:6,9 0|1:31:13,18 -chr20 72765 . TA T 60 . QNAME=cluster19_000000F;QSTART=25690125;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:39:16,23 1|0:48:24,24 ./.:24:15,9 -chr20 72982 . A C 60 . QNAME=cluster19_000000F;QSTART=25689909;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:43:18,25 1|0:32:23,9 ./.:17:6,11 -chr20 73765 . C A 60 . QNAME=cluster19_000000F;QSTART=25689126;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:26:6,20 1|0:22:9,13 ./.:14:8,6 -chr20 75250 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25621388;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:19:8,11 ./.:16:5,11 0|1:18:11,7 -chr20 76709 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25635256;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:27:7,20 ./.:37:25,12 1|0:43:25,18 -chr20 77005 . A G 60 . QNAME=cluster19_000000F;QSTART=25685886;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:27:7,20 1|0:14:6,8 ./.:32:13,19 -chr20 77736 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25618901;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:47:23,24 ./.:28:13,15 0|1:36:17,19 -chr20 77736 . CA C 60 . QNAME=cluster19_000000F;QSTART=25685155;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:34:11,23 1|0:30:14,16 ./.:41:25,16 -chr20 78705 . A T 60 . QNAME=cluster19_000000F;QSTART=25684187;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:38:14,24 1|0:45:22,23 ./.:45:21,24 -chr20 80457 . C T 60 . QNAME=cluster19_000000F;QSTART=25682435;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:30:18,12 1|0:33:12,21 ./.:41:17,24 -chr20 80497 . C CT 60 . QNAME=cluster19_000000F;QSTART=25682394;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD ./.:37:13,24 1|0:32:20,12 ./.:26:16,10 -chr20 81154 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=60071;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:11:5,6 0|1:36:16,20 1|1:27:16,11 -chr20 82603 . A C 60 . QNAME=cluster19_000000F;QSTART=25680288;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD ./.:19:6,13 1|0:24:11,13 ./.:24:12,12 -chr20 83158 . C T 60 . QNAME=cluster19_000000F;QSTART=25679733;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:25:8,17 1|0:31:11,20 ./.:32:10,22 -chr20 85259 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=64176;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:24:11,13 0|1:38:19,19 1|1:31:19,12 -chr20 85729 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=64646;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:25:17,8 0|1:30:16,14 1|1:31:14,17 -chr20 86079 . C A 60 . QNAME=cluster19_000000F;QSTART=45136;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:15:7,8 0|1:34:14,20 ./.:29:15,14 -chr20 86859 . T TTGGTATCTAG 60 . QNAME=HG002-S9-H1-000001F;QSTART=65777;QSTRAND=+;GCPCT=36;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.894965 GT:DP:AD 1|1:34:25,9 0|1:36:19,17 1|1:38:17,21 -chr20 88108 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=67035;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:20:7,13 1|1:40:24,16 1|1:33:11,22 -chr20 88453 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25623502;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD ./.:24:12,12 ./.:24:10,14 1|0:33:22,11 -chr20 88865 . G GACAC 60 . QNAME=cluster19_000000F;QSTART=25674022;QSTRAND=-;GCPCT=60;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.760964 GT:DP:AD ./.:44:23,21 1|0:32:21,11 ./.:45:23,22 -chr20 88865 . G GACACAC 60 . QNAME=cluster19_000000F;QSTART=47933;QSTRAND=+;GCPCT=57;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.724408 GT:DP:AD ./.:18:9,9 0|1:30:12,18 1|0:38:17,21 -chr20 89843 . CTCTT C 60 . QNAME=cluster19_000000F;QSTART=25673044;QSTRAND=-;GCPCT=40;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.485475 GT:DP:AD ./.:28:13,15 1|0:15:6,9 ./.:37:23,14 -chr20 90339 . G A 60 . QNAME=cluster19_000000F;QSTART=25672552;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:32:20,12 1|0:30:15,15 ./.:25:18,7 -chr20 91463 . TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=70391;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD 1|1:38:15,23 1|0:37:25,12 ./.:23:10,13 -chr20 92251 . G A 60 . QNAME=cluster19_000000F;QSTART=25670641;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:37:18,19 1|0:41:25,16 ./.:36:12,24 -chr20 92395 . C CT 60 . QNAME=cluster19_000000F;QSTART=25670496;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD ./.:15:8,7 1|0:24:19,5 ./.:35:17,18 -chr20 92969 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25618979;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:32:12,20 ./.:28:13,15 1|0:30:17,13 -chr20 92969 . CT C 60 . QNAME=cluster19_000000F;QSTART=25669922;QSTRAND=-;GCPCT=50;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:39:16,23 1|1:40:15,25 ./.:23:7,16 -chr20 92969 . CTT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=71896;QSTRAND=+;GCPCT=33;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.459148 GT:DP:AD 1|1:43:20,23 ./.:35:17,18 ./.:43:20,23 -chr20 93706 . G A 60 . QNAME=cluster19_000000F;QSTART=52778;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:31:21,10 0|1:31:21,10 ./.:38:18,20 -chr20 94088 . G GT 60 . QNAME=HG002-S9-H1-000001F;QSTART=73013;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|1:27:20,7 1|0:26:8,18 ./.:39:21,18 -chr20 94613 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=73538;QSTRAND=+;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0 GT:DP:AD 1|1:27:21,6 ./.:21:15,6 ./.:20:13,7 -chr20 96130 . C T 60 . QNAME=cluster19_000000F;QSTART=25666761;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:39:14,25 1|0:34:22,12 ./.:32:7,25 -chr20 96321 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=75246;QSTRAND=+;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:35:19,16 1|1:28:12,16 ./.:33:23,10 -chr20 97324 . G GT 60 . QNAME=HG002-S9-H1-000001F;QSTART=76250;QSTRAND=+;GCPCT=50;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|1:20:15,5 ./.:33:8,25 ./.:24:12,12 -chr20 98593 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=77519;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:27:14,13 1|0:30:9,21 ./.:26:8,18 -chr20 99430 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=78356;QSTRAND=+;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:37:17,20 ./.:49:24,25 ./.:31:17,14 -chr20 99840 . G C 60 . QNAME=cluster19_000000F;QSTART=25663051;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:37:19,18 1|0:41:19,22 ./.:24:5,19 -chr20 100014 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=78940;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:21:11,10 1|1:32:10,22 1|1:11:5,6 -chr20 101338 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=54816;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:21:5,16 ./.:16:7,9 ./.:14:6,8 -chr20 101341 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25610607;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:46:25,21 ./.:48:25,23 1|0:31:6,25 -chr20 101371 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=80297;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:14:6,8 0|1:34:17,17 ./.:28:8,20 -chr20 101433 . A C 60 . QNAME=cluster19_000000F;QSTART=25661458;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:36:14,22 1|1:30:12,18 ./.:24:11,13 -chr20 101438 . G A 60 . QNAME=cluster19_000000F;QSTART=25661453;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:30:22,8 1|1:47:22,25 ./.:27:8,19 -chr20 101498 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25610450;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:21:6,15 ./.:36:21,15 1|0:25:9,16 -chr20 101505 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=54983;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:47:25,22 ./.:31:7,24 1|0:36:25,11 -chr20 101576 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=80502;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:19:10,9 1|1:30:10,20 0|1:18:6,12 -chr20 102609 . C CTGTG 60 . QNAME=cluster23_scaffold_2;QSTART=25594014;QSTRAND=-;GCPCT=60;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.760964 GT:DP:AD ./.:19:5,14 ./.:21:6,15 0|1:30:14,16 -chr20 102609 . CTG C 60 . QNAME=HG002-S9-H2-000001F;QSTART=56088;QSTRAND=+;GCPCT=66;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.792481 GT:DP:AD 0|1:45:20,25 ./.:15:6,9 ./.:17:5,12 -chr20 102609 . CTGTGTGTG C 60 . QNAME=cluster19_000000F;QSTART=25660282;QSTRAND=-;GCPCT=55;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.696074 GT:DP:AD ./.:43:19,24 1|1:26:12,14 1|0:31:23,8 -chr20 102609 . CTGTGTGTGTGTGTGTGTGTGTG C 60 . QNAME=HG002-S9-H1-000001F;QSTART=81536;QSTRAND=+;GCPCT=52;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.60727 GT:DP:AD 1|0:22:16,6 ./.:44:20,24 ./.:28:21,7 -chr20 102613 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=56089;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:25:14,11 ./.:39:20,19 ./.:35:11,24 -chr20 102619 . G C 60 . QNAME=cluster19_000000F;QSTART=25660280;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:41:21,20 1|1:40:16,24 1|0:29:18,11 -chr20 102621 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25609335;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:49:25,24 ./.:37:22,15 1|0:28:15,13 -chr20 102623 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25609333;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:30:15,15 ./.:38:23,15 1|0:34:16,18 -chr20 102633 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=81537;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:45:25,20 ./.:14:6,8 ./.:23:12,11 -chr20 102634 . T C 60 . QNAME=cluster19_000000F;QSTART=25660265;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:24:7,17 1|1:31:22,9 ./.:13:7,6 -chr20 105364 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25591258;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:39:16,23 ./.:28:16,12 0|1:24:8,16 -chr20 105364 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=84269;QSTRAND=+;GCPCT=50;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 1|1:33:12,21 ./.:31:13,18 ./.:42:24,18 -chr20 106471 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=85374;QSTRAND=+;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:40:18,22 ./.:31:8,23 ./.:27:5,22 -chr20 106775 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=85678;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:20:7,13 ./.:41:19,22 0|1:20:15,5 -chr20 107149 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25589473;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:23:11,12 ./.:22:12,10 0|1:28:22,6 -chr20 107514 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25589108;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:36:19,17 ./.:38:15,23 0|1:15:10,5 -chr20 109367 . C A 60 . QNAME=cluster19_000000F;QSTART=25653532;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:35:11,24 1|1:38:23,15 ./.:12:6,6 -chr20 110447 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=89350;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:30:5,25 1|1:20:6,14 0|1:31:23,8 -chr20 110867 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=89770;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:26:18,8 1|1:29:9,20 0|1:24:15,9 -chr20 111066 . C T 60 . QNAME=cluster19_000000F;QSTART=70130;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:33:11,22 0|1:37:14,23 ./.:43:24,19 -chr20 111725 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=90628;QSTRAND=+;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:18:6,12 ./.:22:17,5 ./.:32:7,25 -chr20 111886 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=90789;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:45:24,21 1|1:36:11,25 0|1:32:14,18 -chr20 112799 . A G 60 . QNAME=cluster19_000000F;QSTART=25650100;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:19:5,14 1|0:31:7,24 ./.:47:22,25 -chr20 113005 . C CT 60 . QNAME=cluster19_000000F;QSTART=25649893;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:24:13,11 1|0:19:14,5 ./.:35:11,24 -chr20 113290 . G A 60 . QNAME=cluster19_000000F;QSTART=25649608;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:19:10,9 1|0:27:21,6 ./.:29:9,20 -chr20 115856 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=25580766;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:33:20,13 ./.:25:16,9 0|1:46:21,25 -chr20 120058 . C T 60 . QNAME=cluster19_000000F;QSTART=25642840;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:25:10,15 1|0:32:22,10 ./.:21:16,5 -chr20 120721 . G A 60 . QNAME=cluster19_000000F;QSTART=79785;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:36:12,24 0|1:15:6,9 ./.:40:24,16 -chr20 121264 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=74739;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:32:20,12 ./.:19:9,10 ./.:34:16,18 -chr20 121439 . TATTCTTCAGCTGTCAAA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=100343;QSTRAND=+;GCPCT=33;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.93882 GT:DP:AD 1|1:36:18,18 ./.:32:8,24 ./.:39:14,25 -chr20 121540 . T C 60 . QNAME=cluster19_000000F;QSTART=25641358;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:26:11,15 1|0:28:5,23 ./.:32:18,14 -chr20 122158 . G A 60 . QNAME=cluster19_000000F;QSTART=25640740;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:20:7,13 1|0:27:20,7 ./.:26:7,19 -chr20 122876 . A T 60 . QNAME=cluster19_000000F;QSTART=25640022;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:26:21,5 1|0:30:19,11 ./.:34:9,25 -chr20 124258 . C T 60 . QNAME=cluster19_000000F;QSTART=25638640;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:37:13,24 1|0:33:21,12 ./.:39:19,20 -chr20 125994 . G A 60 . QNAME=cluster19_000000F;QSTART=25636904;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:47:23,24 1|0:13:8,5 ./.:36:11,25 -chr20 126062 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=104949;QSTRAND=+;GCPCT=50;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 1|0:41:25,16 0|1:33:20,13 1|1:45:24,21 -chr20 126062 . C CTTT 60 . QNAME=cluster19_000000F;QSTART=25636833;QSTRAND=-;GCPCT=25;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.405639 GT:DP:AD ./.:45:24,21 1|0:29:9,20 ./.:31:18,13 -chr20 127645 . T G 60 . QNAME=cluster19_000000F;QSTART=25635250;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:28:19,9 1|0:33:15,18 ./.:47:25,22 -chr20 127687 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=106574;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:32:17,15 1|1:31:8,23 0|1:32:11,21 -chr20 128317 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=107204;QSTRAND=+;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:39:15,24 ./.:41:18,23 ./.:13:6,7 -chr20 128517 . C CA 60 . QNAME=HG002-S9-H2-000001F;QSTART=81976;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 0|1:31:12,19 0|1:21:6,15 ./.:41:16,25 -chr20 128517 . C CAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=107405;QSTRAND=+;GCPCT=33;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.459148 GT:DP:AD 1|0:18:8,10 ./.:48:25,23 1|0:38:22,16 -chr20 128517 . CA C 60 . QNAME=cluster19_000000F;QSTART=25634378;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD ./.:26:21,5 1|0:19:10,9 ./.:45:20,25 -chr20 129417 . G C 60 . QNAME=cluster19_000000F;QSTART=25633479;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:31:6,25 1|0:38:19,19 ./.:32:13,19 -chr20 129457 . A G 60 . QNAME=cluster19_000000F;QSTART=25633439;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:34:15,19 1|0:41:24,17 ./.:31:10,21 -chr20 130061 . C T 60 . QNAME=cluster19_000000F;QSTART=25632835;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:17:10,7 1|0:36:17,19 ./.:27:13,14 -chr20 130282 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=83741;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:32:14,18 ./.:36:19,17 ./.:24:10,14 -chr20 130329 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=109218;QSTRAND=+;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:27:7,20 ./.:47:24,23 ./.:35:16,19 -chr20 130338 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=109227;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:21:7,14 0|1:48:23,25 0|1:34:24,10 -chr20 130338 . A G 60 . QNAME=cluster19_000000F;QSTART=25632558;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:35:19,16 1|0:25:17,8 ./.:20:5,15 -chr20 130339 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=109228;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:34:14,20 0|1:41:22,19 0|1:44:19,25 -chr20 130636 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25565985;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:39:16,23 ./.:42:20,22 0|1:24:13,11 -chr20 130736 . A C 60 . QNAME=cluster19_000000F;QSTART=25632160;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:20:8,12 1|0:21:10,11 ./.:40:24,16 -chr20 130742 . T C 60 . QNAME=cluster19_000000F;QSTART=25632154;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:38:25,13 1|0:21:12,9 ./.:37:23,14 -chr20 131163 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=110052;QSTRAND=+;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:28:13,15 ./.:39:25,14 ./.:27:22,5 -chr20 131230 . A G 60 . QNAME=cluster19_000000F;QSTART=25631666;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:35:14,21 1|0:30:9,21 ./.:35:21,14 -chr20 131374 . G A 60 . QNAME=cluster19_000000F;QSTART=25631522;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:13:6,7 1|0:38:16,22 ./.:21:6,15 -chr20 132236 . C T 60 . QNAME=cluster19_000000F;QSTART=91302;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:32:7,25 0|1:29:23,6 ./.:36:20,16 -chr20 133539 . T C 60 . QNAME=cluster19_000000F;QSTART=25629357;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:23:8,15 1|0:35:21,14 ./.:47:25,22 -chr20 133631 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25562990;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:32:16,16 ./.:37:23,14 0|1:44:19,25 -chr20 133700 . C A 60 . QNAME=cluster19_000000F;QSTART=25629196;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:28:16,12 1|0:35:12,23 ./.:35:17,18 -chr20 134275 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25562346;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:27:19,8 ./.:29:11,18 0|1:27:20,7 -chr20 134452 . A C 60 . QNAME=cluster19_000000F;QSTART=25628444;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:19:12,7 1|0:25:15,10 ./.:22:10,12 -chr20 134675 . C CA 60 . QNAME=cluster19_000000F;QSTART=25628220;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD ./.:16:5,11 1|0:24:6,18 ./.:36:23,13 -chr20 134915 . G A 60 . QNAME=cluster19_000000F;QSTART=25627980;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:17:6,11 1|0:37:15,22 ./.:36:13,23 -chr20 135005 . T C 60 . QNAME=cluster19_000000F;QSTART=25627890;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:43:20,23 1|0:22:17,5 ./.:27:19,8 -chr20 135211 . C CA 60 . QNAME=cluster19_000000F;QSTART=25627683;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:31:23,8 1|0:40:19,21 ./.:23:5,18 -chr20 135293 . C G 60 . QNAME=cluster19_000000F;QSTART=25627601;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:15:5,10 1|0:30:5,25 ./.:35:13,22 -chr20 135387 . G A 60 . QNAME=cluster19_000000F;QSTART=94453;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0 GT:DP:AD ./.:24:16,8 0|1:28:23,5 ./.:30:22,8 -chr20 135595 . A G 60 . QNAME=cluster19_000000F;QSTART=25627299;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:40:25,15 1|0:28:13,15 ./.:29:7,22 -chr20 135764 . G A 60 . QNAME=cluster19_000000F;QSTART=25627130;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:45:24,21 1|0:34:23,11 ./.:28:11,17 -chr20 135904 . G A 60 . QNAME=cluster19_000000F;QSTART=25626990;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:36:25,11 1|0:36:24,12 ./.:17:10,7 -chr20 136146 . A G 60 . QNAME=cluster19_000000F;QSTART=25626748;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:31:13,18 1|0:20:12,8 ./.:30:11,19 -chr20 136216 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=89675;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:42:23,19 ./.:27:20,7 ./.:27:5,22 -chr20 136668 . G GCAGGATTTCAT 60 . QNAME=cluster19_000000F;QSTART=25626215;QSTRAND=-;GCPCT=41;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.979574 GT:DP:AD ./.:22:7,15 1|0:24:7,17 ./.:32:10,22 -chr20 139004 . G GT 60 . QNAME=cluster19_000000F;QSTART=25623878;QSTRAND=-;GCPCT=50;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:19:8,11 1|1:41:21,20 ./.:23:7,16 -chr20 139481 . A AAG 60 . QNAME=HG002-S9-H1-000001F;QSTART=118371;QSTRAND=+;GCPCT=33;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.459148 GT:DP:AD 1|1:29:23,6 1|1:31:17,14 0|1:28:8,20 -chr20 139830 . A G 60 . QNAME=cluster19_000000F;QSTART=25623050;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:32:12,20 1|0:20:9,11 ./.:33:13,20 -chr20 140109 . C CAATT 60 . QNAME=HG002-S9-H1-000001F;QSTART=119001;QSTRAND=+;GCPCT=20;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.760964 GT:DP:AD 1|1:35:15,20 1|1:28:17,11 0|1:31:7,24 -chr20 140669 . A C 60 . QNAME=cluster19_000000F;QSTART=25622207;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:41:20,21 1|0:32:15,17 ./.:31:19,12 -chr20 140837 . C A 60 . QNAME=cluster19_000000F;QSTART=25622039;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:24:16,8 1|0:45:20,25 ./.:36:17,19 -chr20 140838 . G GT 60 . QNAME=cluster23_scaffold_3;QSTART=25571114;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:36:20,16 ./.:38:16,22 1|0:24:16,8 -chr20 140859 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25571092;QSTRAND=-;GCPCT=50;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:44:21,23 ./.:29:6,23 1|1:33:15,18 -chr20 140859 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=94325;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 0|1:27:6,21 1|0:23:18,5 ./.:29:11,18 -chr20 141183 . C T 60 . QNAME=cluster19_000000F;QSTART=25621694;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:40:24,16 1|0:14:9,5 ./.:39:19,20 -chr20 141335 . G A 60 . QNAME=cluster19_000000F;QSTART=25621542;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:21:6,15 1|0:32:14,18 ./.:29:22,7 -chr20 141634 . GA G 60 . QNAME=cluster19_000000F;QSTART=25621243;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:43:22,21 1|0:36:18,18 ./.:30:8,22 -chr20 141867 . G A 60 . QNAME=cluster19_000000F;QSTART=25621011;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:36:12,24 1|0:37:12,25 ./.:34:24,10 -chr20 142165 . T TTA 60 . QNAME=cluster19_000000F;QSTART=25620711;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.459148 GT:DP:AD ./.:20:11,9 1|0:26:15,11 ./.:26:7,19 -chr20 143010 . G GT 60 . QNAME=cluster19_000000F;QSTART=102084;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.5 GT:DP:AD ./.:33:21,12 0|1:21:13,8 0|1:28:18,10 -chr20 143661 . A C 60 . QNAME=cluster19_000000F;QSTART=25619215;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:33:22,11 1|0:34:12,22 ./.:28:9,19 -chr20 143771 . C T 60 . QNAME=cluster19_000000F;QSTART=25619105;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:28:5,23 1|0:13:7,6 ./.:23:18,5 -chr20 144480 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=123375;QSTRAND=+;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:33:11,22 ./.:17:10,7 ./.:29:13,16 -chr20 144897 . G C 60 . QNAME=cluster19_000000F;QSTART=25617979;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:27:8,19 1|0:31:7,24 ./.:33:13,20 -chr20 145514 . GCAAA G 60 . QNAME=cluster19_000000F;QSTART=25617362;QSTRAND=-;GCPCT=40;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.685475 GT:DP:AD ./.:22:13,9 1|0:33:22,11 ./.:40:21,19 -chr20 145669 . ACC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=124565;QSTRAND=+;GCPCT=66;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.459148 GT:DP:AD 1|1:31:20,11 1|0:32:17,15 1|0:19:10,9 -chr20 145888 . G A 60 . QNAME=cluster19_000000F;QSTART=25616994;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:22:15,7 1|1:26:5,21 ./.:25:6,19 -chr20 145959 . C A 60 . QNAME=cluster19_000000F;QSTART=25616923;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:35:25,10 1|1:34:10,24 ./.:37:20,17 -chr20 145973 . T C 60 . QNAME=cluster19_000000F;QSTART=25616909;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:32:11,21 1|1:13:7,6 ./.:29:18,11 -chr20 146089 . C T 60 . QNAME=cluster19_000000F;QSTART=25616793;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:22:6,16 1|1:38:18,20 ./.:30:24,6 -chr20 146119 . C T 60 . QNAME=cluster19_000000F;QSTART=25616763;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:25:17,8 1|1:24:19,5 ./.:29:18,11 -chr20 146282 . C A 60 . QNAME=cluster19_000000F;QSTART=25616600;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:28:13,15 1|1:22:6,16 ./.:23:7,16 -chr20 146289 . A T 60 . QNAME=cluster19_000000F;QSTART=25616593;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:30:17,13 1|1:45:22,23 ./.:39:25,14 -chr20 147079 . A C 60 . QNAME=cluster19_000000F;QSTART=25615803;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:35:11,24 1|1:24:16,8 ./.:20:14,6 -chr20 147311 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25564642;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:45:21,24 ./.:17:7,10 1|1:36:18,18 -chr20 148061 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=101523;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0 GT:DP:AD 0|1:33:25,8 ./.:27:19,8 ./.:21:16,5 -chr20 148072 . C G 60 . QNAME=cluster19_000000F;QSTART=25614810;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:33:24,9 1|1:31:23,8 ./.:24:10,14 -chr20 148222 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25563731;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:40:18,22 ./.:41:16,25 1|1:42:22,20 -chr20 148422 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25563531;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:42:24,18 ./.:44:19,25 1|1:20:6,14 -chr20 148972 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=127865;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:23:9,14 1|1:33:15,18 1|1:23:16,7 -chr20 148994 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=127887;QSTRAND=+;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:20:12,8 ./.:39:24,15 ./.:26:5,21 -chr20 149013 . A ACCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=127907;QSTRAND=+;SVTYPE=INS;SVLEN=69;HOMPCT=31.7;REMAP=tandem;REMAPHits=chr20:149012-149082.100,chr20:149081-149151.100,chr20:149150-149220.100;GCPCT=48;GTCNT=1,0,1,1;NumNeighbors=2;NeighId=0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.98203 GT:DP:AD 1/1:35:19,16 ./.:31:21,10 1/0:17:8,9 -chr20 149073 . G GAATCCTGACCCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCA 60 . QNAME=cluster23_scaffold_2;QSTART=25547471;QSTRAND=-;SVTYPE=INS;SVLEN=69;HOMPCT=31.7;REMAP=tandem;REMAPHits=chr20:149013-149073.85,chr20:149072-149142.100,chr20:149141-149211.100;GCPCT=48;GTCNT=2,0,1,0;NumNeighbors=2;NeighId=0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.98203 GT:DP:AD ./.:44:25,19 ./.:36:12,24 0/1:27:20,7 -chr20 149095 . G GGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGACCCATATTTGGGAA 60 . QNAME=cluster19_000000F;QSTART=25613718;QSTRAND=-;SVTYPE=INS;SVLEN=69;HOMPCT=31.7;REMAP=tandem;REMAPHits=chr20:149163-149220.81,chr20:149025-149095.100,chr20:149094-149164.100;GCPCT=48;GTCNT=2,0,0,1;NumNeighbors=2;NeighId=0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0.98203 GT:DP:AD ./.:36:13,23 1/1:14:7,7 ./.:40:19,21 -chr20 149223 . C T 60 . QNAME=cluster19_000000F;QSTART=25613590;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:26:5,21 1|1:42:19,23 ./.:38:21,17 -chr20 150418 . T A 60 . QNAME=cluster23_scaffold_2;QSTART=25546126;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:22:14,8 ./.:28:18,10 0|1:35:25,10 -chr20 150492 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25561392;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:39:17,22 ./.:37:20,17 1|0:29:9,20 -chr20 150721 . C T 60 . QNAME=cluster19_000000F;QSTART=25612092;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:30:24,6 1|1:14:5,9 ./.:33:17,16 -chr20 150854 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=129816;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:41:20,21 1|1:31:13,18 1|1:29:16,13 -chr20 150864 . CTCT C 60 . QNAME=cluster19_000000F;QSTART=25611949;QSTRAND=-;GCPCT=50;GTCNT=2,0,0,1;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD ./.:30:12,18 1|1:14:5,9 ./.:25:19,6 -chr20 151016 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=129978;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:25:5,20 1|1:40:18,22 1|1:42:17,25 -chr20 151307 . C CCA 60 . QNAME=cluster19_000000F;QSTART=25611507;QSTRAND=-;GCPCT=66;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.459148 GT:DP:AD ./.:21:11,10 1|1:22:17,5 ./.:31:10,21 -chr20 151663 . TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=130626;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|1:32:14,18 1|1:31:9,22 1|1:29:24,5 -chr20 151898 . A T 60 . QNAME=cluster23_scaffold_2;QSTART=25544647;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:30:25,5 ./.:25:13,12 0|1:37:20,17 -chr20 152134 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=131095;QSTRAND=+;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:37:20,17 ./.:34:24,10 ./.:43:18,25 -chr20 152450 . C CA 60 . QNAME=cluster19_000000F;QSTART=25610364;QSTRAND=-;GCPCT=50;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:50:25,25 1|1:30:23,7 ./.:33:15,18 -chr20 152450 . CAA C 60 . QNAME=cluster23_scaffold_2;QSTART=25544095;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.459148 GT:DP:AD ./.:40:25,15 ./.:28:7,21 0|1:36:13,23 -chr20 152450 . CAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=131412;QSTRAND=+;GCPCT=25;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0.405639 GT:DP:AD 1|1:11:5,6 ./.:27:12,15 1|0:43:18,25 -chr20 152517 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=131475;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|1:14:8,6 1|1:33:19,14 1|1:16:7,9 -chr20 152792 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=131750;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:25:5,20 ./.:32:17,15 1|1:21:11,10 -chr20 153098 . G GT 60 . QNAME=HG002-S9-H1-000001F;QSTART=132057;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|0:49:24,25 ./.:27:21,6 1|1:39:23,16 -chr20 153259 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=132218;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:31:15,16 ./.:26:12,14 1|1:32:18,14 -chr20 153376 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=106903;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:23:12,11 1|1:27:6,21 ./.:38:23,15 -chr20 153555 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25558332;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:35:17,18 ./.:26:5,21 1|1:45:22,23 -chr20 153640 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25558247;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:25:20,5 ./.:32:25,7 1|1:49:24,25 -chr20 153643 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=132602;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:45:20,25 1|1:16:6,10 1|1:25:14,11 -chr20 153725 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=132684;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:35:11,24 1|1:25:6,19 1|1:15:5,10 -chr20 153759 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=132718;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:33:17,16 ./.:32:14,18 1|0:36:23,13 -chr20 153780 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=132739;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:26:19,7 1|1:31:6,25 1|1:29:5,24 -chr20 153787 . CAAAAAAAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=132747;QSTRAND=+;GCPCT=10;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.234498 GT:DP:AD 1|1:36:19,17 1|1:23:11,12 1|1:20:13,7 -chr20 153835 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=132785;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:21:15,6 1|1:30:9,21 1|1:14:7,7 -chr20 153898 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=132848;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:20:13,7 ./.:30:25,5 1|0:36:16,20 -chr20 154002 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=132952;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:38:17,21 1|1:27:9,18 1|1:40:25,15 -chr20 154128 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=133079;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|0:25:6,19 ./.:33:16,17 1|1:22:17,5 -chr20 154203 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=133154;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:26:12,14 1|1:37:13,24 1|1:27:6,21 -chr20 154290 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=133241;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:29:6,23 1|1:33:10,23 1|1:37:17,20 -chr20 154474 . G GTTTGCATTCACAGGAAGACTATAAATAAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=133426;QSTRAND=+;SVTYPE=INS;SVLEN=29;GCPCT=33;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0.949465 GT:DP:AD 1/1:24:18,6 1/1:18:11,7 1/1:19:9,10 -chr20 154475 . TGCTC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=133456;QSTRAND=+;GCPCT=60;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.760964 GT:DP:AD 1|1:33:8,25 1|1:36:21,15 1|1:28:20,8 -chr20 154847 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=133823;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:35:14,21 1|1:27:9,18 1|1:22:7,15 -chr20 155384 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=134360;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD 1|0:24:13,11 ./.:25:12,13 1|1:17:7,10 -chr20 155733 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=134709;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:17:10,7 ./.:25:13,12 1|1:36:24,12 -chr20 155813 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=134789;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:37:15,22 ./.:27:11,16 1|1:23:5,18 -chr20 156080 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=135056;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:26:12,14 ./.:21:15,6 1|1:28:21,7 -chr20 156287 . G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=135264;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 1|0:31:12,19 ./.:49:25,24 1|1:20:8,12 -chr20 156473 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=135450;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:30:13,17 ./.:41:25,16 1|1:35:10,25 -chr20 156486 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=110029;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:31:9,22 1|1:31:8,23 ./.:31:19,12 -chr20 156669 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=135646;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:37:25,12 ./.:32:17,15 1|1:21:14,7 -chr20 156813 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=135790;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:19:9,10 ./.:25:14,11 1|1:36:13,23 -chr20 156877 . GTA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=135855;QSTRAND=+;GCPCT=33;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.792481 GT:DP:AD 1|1:35:19,16 1|1:19:8,11 1|1:39:16,23 -chr20 156881 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=135856;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:50:25,25 ./.:35:14,21 1|1:33:9,24 -chr20 157033 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=110574;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:15:6,9 1|1:34:19,15 ./.:38:17,21 -chr20 157259 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=136234;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:25:6,19 ./.:25:14,11 1|1:34:21,13 -chr20 157292 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=136267;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:30:11,19 1|1:21:14,7 1|1:35:25,10 -chr20 157363 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=136338;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0 GT:DP:AD 1|1:18:9,9 1|1:20:12,8 1|1:33:24,9 -chr20 157484 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=136459;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:25:19,6 ./.:25:7,18 1|1:21:6,15 -chr20 157507 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=136482;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:29:17,12 ./.:44:22,22 1|1:27:6,21 -chr20 157537 . GC G 60 . QNAME=HG002-S9-H2-000001F;QSTART=111079;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 0|1:39:15,24 1|1:15:7,8 ./.:41:22,19 -chr20 157819 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=136794;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:32:10,22 ./.:17:10,7 1|1:26:13,13 -chr20 157914 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=136889;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:31:10,21 ./.:35:23,12 1|1:16:8,8 -chr20 157922 . AATAT A 60 . QNAME=cluster23_scaffold_2;QSTART=25538608;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.485475 GT:DP:AD ./.:19:12,7 ./.:33:17,16 0|1:27:5,22 -chr20 157927 . ATATATG A 60 . QNAME=cluster23_scaffold_3;QSTART=25553944;QSTRAND=-;GCPCT=14;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.724408 GT:DP:AD ./.:33:10,23 ./.:19:9,10 1|0:36:12,24 -chr20 157927 . ATATATGTG A 60 . QNAME=HG002-S9-H1-000001F;QSTART=136903;QSTRAND=+;GCPCT=22;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.765247 GT:DP:AD 1|0:23:7,16 ./.:26:8,18 ./.:42:24,18 -chr20 157929 . ATATGTGTG A 60 . QNAME=HG002-S9-H2-000001F;QSTART=111470;QSTRAND=+;GCPCT=33;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.765247 GT:DP:AD 0|1:41:18,23 1|1:32:16,16 ./.:15:10,5 -chr20 157960 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=111492;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:26:9,17 1|1:24:10,14 ./.:32:20,12 -chr20 157962 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=111494;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:32:15,17 1|1:30:18,12 ./.:35:24,11 -chr20 157965 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=136932;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:13:8,5 ./.:38:21,17 1|1:27:17,10 -chr20 157974 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=136941;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:31:25,6 ./.:33:21,12 1|1:30:14,16 -chr20 157979 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=136946;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:39:25,14 ./.:46:21,25 1|1:15:7,8 -chr20 158513 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=137480;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:31:8,23 ./.:22:5,17 1|1:44:23,21 -chr20 158532 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=137499;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:27:18,9 ./.:49:24,25 1|0:33:22,11 -chr20 158721 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=112253;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:30:17,13 1|1:14:6,8 ./.:43:20,23 -chr20 158768 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=137735;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:36:24,12 ./.:26:15,11 1|1:31:8,23 -chr20 158815 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=137782;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:38:17,21 ./.:25:13,12 1|1:39:16,23 -chr20 158935 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=137902;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:19:14,5 ./.:36:23,13 1|1:41:25,16 -chr20 159104 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=138071;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:35:25,10 1|1:24:6,18 1|1:19:6,13 -chr20 159197 . A T 60 . QNAME=cluster23_scaffold_2;QSTART=25537337;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:24:10,14 ./.:26:17,9 0|1:28:22,6 -chr20 159200 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=112732;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:26:6,20 1|1:44:24,20 ./.:31:22,9 -chr20 159274 . T TAA 60 . QNAME=HG002-S9-H2-000001F;QSTART=112807;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.459148 GT:DP:AD 0|1:21:6,15 1|1:31:11,20 ./.:31:23,8 -chr20 159274 . T TAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=138242;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.295836 GT:DP:AD 1|0:24:13,11 ./.:23:6,17 1|1:19:13,6 -chr20 159286 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=138259;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:28:13,15 ./.:25:15,10 1|1:29:18,11 -chr20 159445 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=112979;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:26:5,21 1|1:35:15,20 ./.:31:17,14 -chr20 159495 . G GAATGGCATAAACT 60 . QNAME=HG002-S9-H1-000001F;QSTART=138469;QSTRAND=+;GCPCT=35;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.938694 GT:DP:AD 1|0:25:6,19 ./.:27:14,13 1|1:26:13,13 -chr20 159530 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=138516;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:39:22,17 ./.:24:15,9 1|1:37:12,25 -chr20 159639 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=113173;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:44:21,23 1|1:22:6,16 ./.:32:16,16 -chr20 159755 . TTTG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=138742;QSTRAND=+;GCPCT=25;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.405639 GT:DP:AD 1|1:29:17,12 1|1:24:7,17 1|1:38:18,20 -chr20 159864 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=138847;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:21:15,6 ./.:41:18,23 1|1:34:16,18 -chr20 159865 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=138848;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:21:13,8 ./.:37:16,21 1|1:39:16,23 -chr20 159952 . AG A 60 . QNAME=HG002-S9-H1-000001F;QSTART=138936;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|0:44:20,24 ./.:27:6,21 1|1:23:15,8 -chr20 160054 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=139036;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:24:19,5 ./.:48:23,25 1|1:19:11,8 -chr20 160212 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=139194;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:30:9,21 ./.:42:20,22 1|1:25:16,9 -chr20 160282 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=139264;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:32:14,18 ./.:41:17,24 1|1:24:17,7 -chr20 160312 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=139294;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:30:14,16 ./.:33:20,13 1|1:28:10,18 -chr20 160384 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=139366;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:34:19,15 ./.:30:10,20 1|1:22:17,5 -chr20 160388 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=139370;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:29:24,5 ./.:31:20,11 1|1:22:15,7 -chr20 160408 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=139390;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:35:16,19 ./.:20:12,8 1|1:35:10,25 -chr20 160413 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=139395;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:14:8,6 ./.:26:10,16 1|1:20:6,14 -chr20 160433 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=139415;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:37:16,21 ./.:18:9,9 1|1:32:11,21 -chr20 160558 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=139540;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:42:24,18 ./.:29:12,17 1|0:36:25,11 -chr20 160625 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=139607;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:22:7,15 ./.:35:11,24 1|1:34:10,24 -chr20 160727 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=139709;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:46:25,21 ./.:24:14,10 1|1:27:21,6 -chr20 160731 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=139713;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:31:9,22 ./.:40:22,18 1|1:18:8,10 -chr20 160873 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=139855;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:28:19,9 ./.:29:9,20 1|1:23:5,18 -chr20 160889 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=139871;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:29:13,16 ./.:20:12,8 1|1:31:10,21 -chr20 160956 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=139938;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:19:11,8 ./.:28:19,9 1|1:32:18,14 -chr20 160967 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=139949;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:29:20,9 ./.:38:22,16 1|1:17:10,7 -chr20 161128 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140110;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:30:12,18 ./.:28:11,17 1|1:20:10,10 -chr20 161181 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140163;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:17:8,9 ./.:41:24,17 1|1:32:7,25 -chr20 161221 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140203;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:32:16,16 ./.:15:7,8 1|1:19:14,5 -chr20 161380 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=140362;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:15:8,7 1|1:36:17,19 1|1:23:18,5 -chr20 161451 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=140433;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:30:9,21 ./.:25:13,12 1|1:32:16,16 -chr20 161571 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=140553;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:22:12,10 ./.:17:8,9 1|1:26:20,6 -chr20 161588 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140570;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:18:5,13 1|1:45:22,23 1|1:39:19,20 -chr20 161621 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=140603;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:27:6,21 ./.:15:9,6 1|1:29:9,20 -chr20 161638 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=140620;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:34:12,22 1|1:37:13,24 1|1:33:25,8 -chr20 161698 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140680;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:43:18,25 ./.:34:18,16 1|1:38:17,21 -chr20 161730 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=140712;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:32:11,21 ./.:35:15,20 1|1:28:16,12 -chr20 161734 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=140716;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:45:20,25 ./.:31:21,10 1|1:26:12,14 -chr20 161770 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140752;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:19:7,12 ./.:39:16,23 1|1:29:12,17 -chr20 161914 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=140896;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:32:12,20 ./.:25:20,5 1|1:20:7,13 -chr20 161918 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=115449;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:25:5,20 1|1:27:16,11 ./.:40:17,23 -chr20 161991 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=140973;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:28:22,6 ./.:29:16,13 1|1:32:21,11 -chr20 162151 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=141133;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:40:19,21 1|1:25:8,17 1|1:32:8,24 -chr20 162224 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=141206;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:34:15,19 ./.:21:16,5 1|1:30:12,18 -chr20 162225 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=141207;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:42:17,25 ./.:28:13,15 1|1:23:10,13 -chr20 162228 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=141210;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:26:10,16 ./.:27:5,22 1|1:41:21,20 -chr20 162268 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=141250;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:37:19,18 ./.:44:25,19 1|1:42:23,19 -chr20 162455 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=141437;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:15:7,8 ./.:39:20,19 1|1:18:6,12 -chr20 162806 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=116337;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:48:24,24 1|1:31:12,19 ./.:30:24,6 -chr20 162854 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=141836;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:44:25,19 ./.:24:14,10 1|1:23:11,12 -chr20 162932 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=141914;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:19:14,5 ./.:39:25,14 1|1:36:11,25 -chr20 163082 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=142064;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:45:22,23 ./.:16:8,8 1|1:28:10,18 -chr20 163113 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=142095;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:14:7,7 ./.:29:11,18 1|1:24:12,12 -chr20 163277 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=142259;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:15:9,6 1|1:49:25,24 1|1:46:24,22 -chr20 163741 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=117272;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:23:9,14 1|1:26:7,19 ./.:28:10,18 -chr20 163894 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=117425;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 0|1:30:18,12 1|1:26:18,8 ./.:17:6,11 -chr20 163919 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=117450;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:45:22,23 1|1:22:14,8 ./.:35:15,20 -chr20 163929 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=117460;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:35:14,21 1|1:34:25,9 ./.:31:21,10 -chr20 164191 . C CT 60 . QNAME=HG002-S9-H2-000001F;QSTART=117723;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 0|1:35:19,16 1|1:25:18,7 ./.:36:17,19 -chr20 164243 . CCTT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=117776;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 0|1:30:7,23 1|1:28:9,19 ./.:31:20,11 -chr20 164258 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=117787;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:28:21,7 1|1:26:20,6 ./.:26:5,21 -chr20 164569 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=143551;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:37:22,15 1|1:37:20,17 1|1:30:21,9 -chr20 164616 . G GC 60 . QNAME=HG002-S9-H2-000001F;QSTART=118146;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0.5 GT:DP:AD 0|1:17:5,12 1|1:25:11,14 ./.:23:11,12 -chr20 164772 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=118302;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:44:21,23 1|1:20:13,7 ./.:40:20,20 -chr20 165108 . C CACAT 60 . QNAME=cluster23_scaffold_3;QSTART=25546750;QSTRAND=-;GCPCT=40;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.760964 GT:DP:AD ./.:31:19,12 ./.:39:20,19 1|1:35:16,19 -chr20 165108 . C CAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=144091;QSTRAND=+;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.792481 GT:DP:AD 1|0:27:9,18 ./.:26:9,17 ./.:24:9,15 -chr20 165108 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=118638;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:30:20,10 1|1:22:12,10 ./.:26:9,17 -chr20 165212 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=144196;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:23:12,11 ./.:43:24,19 1|1:26:16,10 -chr20 166310 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=145294;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:41:16,25 ./.:45:25,20 1|1:14:6,8 -chr20 166354 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=119884;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:40:15,25 1|1:29:20,9 ./.:37:13,24 -chr20 166856 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=145840;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:30:9,21 ./.:33:25,8 1|1:44:23,21 -chr20 166960 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=145945;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 1|0:40:20,20 ./.:30:15,15 1|1:46:21,25 -chr20 167044 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=146027;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:17:10,7 ./.:33:15,18 1|1:42:23,19 -chr20 167104 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25529412;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:42:18,24 ./.:33:25,8 0|1:15:10,5 -chr20 167274 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=146257;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:29:16,13 ./.:36:21,15 1|1:36:22,14 -chr20 167276 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=146259;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:35:10,25 ./.:38:15,23 1|1:25:12,13 -chr20 167443 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=146426;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:20:14,6 1|1:15:6,9 1|1:35:12,23 -chr20 167839 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=146822;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:21:7,14 1|1:26:5,21 1|1:23:10,13 -chr20 168062 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=147045;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:30:8,22 ./.:25:14,11 1|1:26:16,10 -chr20 168478 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=147462;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|0:31:11,20 ./.:16:8,8 1|1:36:25,11 -chr20 168766 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=122296;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:29:18,11 1|1:29:19,10 ./.:30:13,17 -chr20 169334 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=122864;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:20:8,12 1|1:36:17,19 ./.:25:15,10 -chr20 170008 . CTACA C 60 . QNAME=cluster23_scaffold_2;QSTART=25526509;QSTRAND=-;GCPCT=40;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.760964 GT:DP:AD ./.:40:15,25 ./.:31:10,21 0|1:23:12,11 -chr20 170689 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=124219;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:27:9,18 1|1:25:10,15 ./.:27:18,9 -chr20 171892 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=125422;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:29:6,23 1|1:22:8,14 ./.:40:17,23 -chr20 171929 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=125459;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:36:22,14 1|1:39:15,24 0|1:36:11,25 -chr20 172156 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=125686;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 0|1:20:8,12 1|0:28:20,8 ./.:21:8,13 -chr20 172258 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=25539602;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:35:19,16 ./.:31:9,22 1|0:36:23,13 -chr20 172331 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=125861;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:26:13,13 1|1:42:23,19 0|1:19:13,6 -chr20 172351 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=125881;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:41:16,25 1|1:32:7,25 0|1:27:19,8 -chr20 172626 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=126156;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 0|1:27:22,5 1|1:16:5,11 0|1:34:24,10 -chr20 172657 . T TTC 60 . QNAME=HG002-S9-H2-000001F;QSTART=126188;QSTRAND=+;GCPCT=33;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.459148 GT:DP:AD 0|1:40:25,15 1|1:38:16,22 0|1:19:5,14 -chr20 172752 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=126284;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:37:22,15 1|1:36:11,25 ./.:41:24,17 -chr20 172789 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=25523730;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:29:11,18 ./.:38:20,18 0|1:36:25,11 -chr20 173036 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25523483;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:46:24,22 ./.:17:12,5 0|1:36:22,14 -chr20 173050 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=126582;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:32:13,19 1|1:16:6,10 ./.:32:12,20 -chr20 173133 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25523386;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:28:12,16 ./.:40:24,16 0|1:38:14,24 -chr20 173215 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=152197;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:29:12,17 ./.:15:10,5 ./.:34:12,22 -chr20 173791 . CCTT C 60 . QNAME=cluster23_scaffold_2;QSTART=25522728;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:32:23,9 ./.:44:19,25 0|1:44:19,25 -chr20 173973 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=127505;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:35:24,11 1|1:42:17,25 ./.:35:11,24 -chr20 174069 . G A 60 . QNAME=cluster19_000000F;QSTART=133216;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:36:16,20 0|1:19:12,7 ./.:49:24,25 -chr20 174270 . TC T 60 . QNAME=cluster23_scaffold_2;QSTART=25522252;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:40:16,24 ./.:15:10,5 0|1:26:6,20 -chr20 174280 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25522243;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:23:18,5 ./.:31:7,24 0|1:45:24,21 -chr20 174737 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25521786;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:34:10,24 ./.:18:5,13 0|1:31:7,24 -chr20 174986 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25521537;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:32:20,12 ./.:48:23,25 0|1:44:24,20 -chr20 175210 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25521313;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:24:11,13 ./.:38:16,22 0|1:23:11,12 -chr20 175239 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25521284;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:23:17,6 ./.:25:8,17 0|1:41:16,25 -chr20 175269 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=128801;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:28:8,20 1|1:23:13,10 0|1:36:12,24 -chr20 175314 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=128846;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:28:18,10 1|1:19:13,6 ./.:42:17,25 -chr20 175375 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25521148;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:30:14,16 ./.:26:15,11 0|1:38:21,17 -chr20 175501 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25521022;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:27:10,17 ./.:31:19,12 0|1:18:7,11 -chr20 175524 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=129056;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0 GT:DP:AD 0|1:30:23,7 1|1:21:13,8 0|1:25:16,9 -chr20 175532 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=129064;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:43:25,18 1|1:36:21,15 0|1:28:17,11 -chr20 175563 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25520960;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:14:5,9 ./.:29:6,23 0|1:18:5,13 -chr20 175565 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25520958;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:15:8,7 ./.:29:20,9 0|1:37:24,13 -chr20 175595 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25520928;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD ./.:26:15,11 ./.:35:21,14 0|1:30:17,13 -chr20 175658 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25520865;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:32:25,7 ./.:16:10,6 0|1:47:25,22 -chr20 175659 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25520864;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:18:10,8 ./.:33:12,21 0|1:29:19,10 -chr20 175676 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25520847;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:26:18,8 ./.:38:15,23 0|1:35:14,21 -chr20 175688 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=129220;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:30:13,17 1|1:38:17,21 0|1:24:18,6 -chr20 175689 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=129221;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:28:7,21 1|1:31:13,18 0|1:27:5,22 -chr20 175813 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25520710;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:30:25,5 ./.:35:18,17 0|1:26:17,9 -chr20 175893 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=129425;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:38:19,19 1|1:34:14,20 0|1:23:17,6 -chr20 175897 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=129429;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:20:11,9 1|1:31:11,20 0|1:46:25,21 -chr20 176011 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=129543;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:35:25,10 1|1:40:16,24 ./.:42:21,21 -chr20 176015 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=129547;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:29:22,7 1|1:26:10,16 ./.:30:18,12 -chr20 176015 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25520508;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:25:10,15 ./.:36:18,18 0|1:38:19,19 -chr20 176128 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=25520395;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:28:12,16 ./.:18:5,13 0|1:41:17,24 -chr20 176156 . A T 60 . QNAME=cluster23_scaffold_2;QSTART=25520367;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:25:20,5 ./.:31:17,14 0|1:37:24,13 -chr20 176325 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25520198;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:27:14,13 ./.:29:9,20 0|1:39:23,16 -chr20 176400 . G GCCC 60 . QNAME=cluster23_scaffold_2;QSTART=25520120;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.405639 GT:DP:AD ./.:42:25,17 ./.:19:10,9 0|1:20:7,13 -chr20 176406 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25520114;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:31:10,21 ./.:21:5,16 0|1:25:9,16 -chr20 176516 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=130048;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:36:14,22 1|1:35:19,16 0|1:23:12,11 -chr20 176631 . C T 60 . QNAME=cluster19_000000F;QSTART=135778;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:36:20,16 0|1:29:24,5 ./.:25:8,17 -chr20 176881 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=130413;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:24:13,11 1|0:31:23,8 ./.:39:14,25 -chr20 177105 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=130637;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:26:6,20 1|1:17:6,11 0|1:18:9,9 -chr20 177210 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25519310;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:25:20,5 ./.:23:18,5 0|1:40:19,21 -chr20 177334 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25519186;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:33:15,18 ./.:47:24,23 0|1:23:5,18 -chr20 177335 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=130867;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 0|1:27:16,11 1|1:18:9,9 0|1:18:13,5 -chr20 177343 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25519177;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:38:22,16 ./.:28:7,21 0|1:29:14,15 -chr20 177473 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=131005;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:37:17,20 1|1:43:18,25 0|1:29:23,6 -chr20 177674 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=131206;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:37:17,20 1|1:20:9,11 ./.:25:19,6 -chr20 177749 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25518771;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:26:21,5 ./.:23:7,16 0|1:20:5,15 -chr20 177793 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=131325;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:34:20,14 1|1:25:14,11 ./.:32:7,25 -chr20 177854 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=131386;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:35:12,23 1|1:31:19,12 0|1:20:11,9 -chr20 178043 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25518477;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:20:15,5 ./.:29:19,10 0|1:27:14,13 -chr20 178049 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25518471;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:22:5,17 ./.:35:16,19 0|1:28:15,13 -chr20 178343 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25518177;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:28:15,13 ./.:26:16,10 0|1:43:21,22 -chr20 178456 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25518064;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:29:7,22 ./.:42:20,22 0|1:28:11,17 -chr20 178604 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25517916;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:22:7,15 ./.:40:24,16 0|1:40:17,23 -chr20 178648 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=132180;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:20:5,15 1|1:27:12,15 ./.:27:6,21 -chr20 178883 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25517637;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:33:19,14 ./.:21:9,12 0|1:22:16,6 -chr20 179104 . A C 60 . QNAME=cluster23_scaffold_2;QSTART=25517416;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:33:11,22 ./.:28:6,22 0|1:37:16,21 -chr20 179470 . A AT 60 . QNAME=HG002-S9-H2-000001F;QSTART=133003;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 0|1:25:8,17 1|1:27:5,22 0|1:42:25,17 -chr20 179567 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=133100;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:26:8,18 1|1:24:11,13 0|1:27:20,7 -chr20 179575 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25516944;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:41:16,25 ./.:23:9,14 0|1:38:20,18 -chr20 179892 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=133425;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:33:16,17 1|1:29:21,8 ./.:26:6,20 -chr20 179910 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=133443;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:22:17,5 1|1:30:20,10 0|1:44:20,24 -chr20 180809 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=134342;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:33:25,8 1|1:46:24,22 0|1:49:25,24 -chr20 180861 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25515658;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:28:7,21 ./.:41:17,24 0|1:33:25,8 -chr20 180945 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25515574;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:21:16,5 ./.:28:8,20 0|1:23:7,16 -chr20 181095 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25515424;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:19:12,7 ./.:27:17,10 0|1:12:7,5 -chr20 181461 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25515058;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:28:7,21 ./.:15:6,9 0|1:31:8,23 -chr20 181576 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25514943;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:40:15,25 ./.:19:9,10 0|1:35:20,15 -chr20 181650 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25514869;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:32:15,17 ./.:23:13,10 0|1:17:10,7 -chr20 181651 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25514868;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:38:16,22 ./.:16:7,9 0|1:28:21,7 -chr20 181704 . AAAAT A 60 . QNAME=cluster23_scaffold_2;QSTART=25514815;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.360964 GT:DP:AD ./.:37:24,13 ./.:38:17,21 0|1:38:25,13 -chr20 182042 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=135575;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:36:22,14 1|1:38:15,23 ./.:27:11,16 -chr20 182056 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=25514467;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:34:21,13 ./.:36:13,23 0|1:32:13,19 -chr20 182966 . A AAT 60 . QNAME=HG002-S9-H2-000001F;QSTART=136500;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.459148 GT:DP:AD 0|1:22:7,15 1|1:33:25,8 0|1:39:14,25 -chr20 182982 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25513539;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:50:25,25 ./.:31:8,23 0|1:35:18,17 -chr20 183100 . T TAC 60 . QNAME=cluster23_scaffold_2;QSTART=25513419;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.792481 GT:DP:AD ./.:43:22,21 ./.:22:6,16 0|1:26:20,6 -chr20 183100 . T TACACAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=136636;QSTRAND=+;GCPCT=42;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.724408 GT:DP:AD 0|1:46:22,24 1|1:24:19,5 ./.:23:14,9 -chr20 183442 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25513077;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:42:20,22 ./.:26:11,15 0|1:32:22,10 -chr20 183617 . G GGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAA 60 . QNAME=cluster23_scaffold_2;QSTART=25512867;QSTRAND=-;SVTYPE=INS;SVLEN=35;GCPCT=22;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.382102 GT:DP:AD ./.:35:16,19 ./.:32:20,12 0/1:24:11,13 -chr20 183638 . G GAAAAC 60 . QNAME=cluster19_000000F;QSTART=142795;QSTRAND=+;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.625815 GT:DP:AD ./.:30:6,24 0|1:45:25,20 ./.:40:19,21 -chr20 183643 . G C 60 . QNAME=cluster19_000000F;QSTART=142804;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:37:17,20 0|1:33:24,9 ./.:27:12,15 -chr20 183643 . G GAAAAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=137185;QSTRAND=+;GCPCT=33;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.625815 GT:DP:AD 0|1:41:22,19 1|0:40:25,15 ./.:30:17,13 -chr20 183699 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=137245;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:31:23,8 1|1:37:21,16 ./.:47:24,23 -chr20 183795 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25512689;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:23:18,5 ./.:31:7,24 0|1:49:24,25 -chr20 184483 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25512001;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:32:10,22 ./.:43:23,20 0|1:30:19,11 -chr20 184792 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25511692;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:18:9,9 ./.:23:7,16 0|1:38:13,25 -chr20 184838 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25511646;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:42:25,17 ./.:28:15,13 0|1:17:7,10 -chr20 185161 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=25511323;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:29:13,16 ./.:21:11,10 0|1:31:11,20 -chr20 185267 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=138813;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:31:22,9 1|1:49:24,25 0|1:44:19,25 -chr20 185522 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25510962;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:41:24,17 ./.:47:24,23 0|1:23:7,16 -chr20 185547 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25510937;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:23:11,12 ./.:48:24,24 0|1:30:22,8 -chr20 185835 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25510648;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD ./.:33:20,13 ./.:19:6,13 0|1:37:18,19 -chr20 186086 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=139632;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:24:18,6 1|1:43:22,21 ./.:30:15,15 -chr20 186099 . C CAA 60 . QNAME=cluster23_scaffold_2;QSTART=25510382;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.459148 GT:DP:AD ./.:22:6,16 ./.:21:14,7 0|1:41:25,16 -chr20 186183 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=139729;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:34:18,16 1|1:25:7,18 ./.:24:7,17 -chr20 186577 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25509904;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:20:12,8 ./.:18:7,11 0|1:23:7,16 -chr20 186669 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=140215;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:40:23,17 1|1:29:21,8 ./.:31:14,17 -chr20 186684 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=25509797;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:24:17,7 ./.:28:9,19 0|1:28:15,13 -chr20 186790 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=140336;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,1,2;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 0|1:28:18,10 1|1:10:5,5 0|1:23:10,13 -chr20 186800 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25509681;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:28:19,9 ./.:19:13,6 0|1:31:8,23 -chr20 186814 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25509667;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:24:17,7 ./.:46:21,25 0|1:39:21,18 -chr20 187006 . T A 60 . QNAME=cluster23_scaffold_2;QSTART=25509475;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:41:16,25 ./.:33:25,8 0|1:35:22,13 -chr20 187133 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25509348;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:30:17,13 ./.:41:24,17 0|1:46:23,23 -chr20 187259 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=25509222;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:32:18,14 ./.:28:13,15 0|1:34:22,12 -chr20 187379 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25509102;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:34:15,19 ./.:28:13,15 0|1:22:9,13 -chr20 187439 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=140985;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:33:14,19 1|1:26:15,11 ./.:24:13,11 -chr20 187498 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25508983;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:20:5,15 ./.:18:13,5 0|1:35:21,14 -chr20 187600 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25508881;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:15:7,8 ./.:36:18,18 0|1:23:10,13 -chr20 187825 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=141371;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:31:12,19 1|1:16:8,8 ./.:41:24,17 -chr20 188087 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=141633;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:20:13,7 1|1:41:23,18 0|1:25:15,10 -chr20 188490 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25507991;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:18:7,11 ./.:18:7,11 0|1:26:21,5 -chr20 189060 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=142606;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:14:8,6 1|1:42:18,24 ./.:30:6,24 -chr20 189354 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=142900;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:24:9,15 1|1:21:11,10 0|1:34:21,13 -chr20 189473 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25507008;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:33:17,16 ./.:34:23,11 0|1:48:25,23 -chr20 189948 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=143494;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:23:6,17 1|1:40:19,21 0|1:26:21,5 -chr20 190001 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=143547;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:14:6,8 1|1:44:20,24 0|1:29:10,19 -chr20 190548 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=144094;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:34:13,21 1|1:41:18,23 ./.:37:19,18 -chr20 190675 . C CT 60 . QNAME=cluster23_scaffold_2;QSTART=25505805;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:26:6,20 ./.:27:9,18 0|1:24:11,13 -chr20 190675 . C CTT 60 . QNAME=HG002-S9-H2-000001F;QSTART=144222;QSTRAND=+;GCPCT=33;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.459148 GT:DP:AD 0|1:23:7,16 1|1:36:25,11 ./.:45:20,25 -chr20 190950 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=144498;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:26:8,18 1|1:28:20,8 ./.:45:24,21 -chr20 190986 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=144534;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:37:24,13 1|1:42:21,21 ./.:33:23,10 -chr20 191069 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25505411;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:35:24,11 ./.:24:13,11 0|1:24:5,19 -chr20 191221 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=170203;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:43:20,23 ./.:25:7,18 ./.:44:21,23 -chr20 191726 . C CTT 60 . QNAME=cluster23_scaffold_3;QSTART=25520132;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.459148 GT:DP:AD ./.:32:18,14 ./.:17:5,12 1|0:23:15,8 -chr20 191726 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=145275;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD 0|1:33:20,13 1|1:34:19,15 ./.:24:13,11 -chr20 191726 . CTT C 60 . QNAME=cluster23_scaffold_2;QSTART=25504754;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.459148 GT:DP:AD ./.:16:8,8 ./.:41:22,19 0|1:43:24,19 -chr20 191877 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=145424;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:38:25,13 1|1:48:25,23 0|1:40:16,24 -chr20 192100 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=145647;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:21:8,13 1|1:23:17,6 0|1:32:16,16 -chr20 193110 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=146657;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,1,2;ADCNT=0,3,0,0;LCR=0 GT:DP:AD 0|1:30:23,7 1|1:12:5,7 0|1:22:16,6 -chr20 193428 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=146975;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:35:16,19 1|1:30:19,11 0|1:27:19,8 -chr20 193735 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25502747;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:17:8,9 ./.:29:23,6 0|1:39:19,20 -chr20 193942 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=25502540;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:26:18,8 ./.:19:10,9 0|1:20:8,12 -chr20 193996 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25502486;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:37:23,14 ./.:43:22,21 0|1:39:17,22 -chr20 194746 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=148293;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:24:11,13 1|1:38:19,19 0|1:27:12,15 -chr20 195745 . C CGT 60 . QNAME=cluster23_scaffold_2;QSTART=25500735;QSTRAND=-;GCPCT=66;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.792481 GT:DP:AD ./.:41:19,22 ./.:25:8,17 0|1:26:12,14 -chr20 195745 . CGTGT C 60 . QNAME=cluster23_scaffold_3;QSTART=25516113;QSTRAND=-;GCPCT=60;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.760964 GT:DP:AD ./.:39:19,20 ./.:43:19,24 1|0:20:6,14 -chr20 195745 . CGTGTGT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=149293;QSTRAND=+;GCPCT=57;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.724408 GT:DP:AD 0|1:22:8,14 1|1:25:13,12 ./.:42:24,18 -chr20 195977 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25500503;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:20:8,12 ./.:39:25,14 0|1:45:22,23 -chr20 196106 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25515756;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD ./.:18:7,11 ./.:35:23,12 1|0:28:16,12 -chr20 196584 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=175566;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:29:19,10 ./.:23:17,6 1|1:20:7,13 -chr20 196609 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=175591;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0 GT:DP:AD 1|0:20:13,7 ./.:20:14,6 1|0:20:15,5 -chr20 198088 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25513774;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:40:24,16 ./.:34:23,11 1|0:45:23,22 -chr20 198171 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=177153;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:27:19,8 ./.:38:17,21 1|1:23:18,5 -chr20 198174 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=177156;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:34:11,23 ./.:42:22,20 1|0:14:8,6 -chr20 198215 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=177197;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:33:20,13 ./.:31:13,18 1|1:33:9,24 -chr20 198433 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25498047;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:31:7,24 ./.:27:20,7 0|1:25:14,11 -chr20 198814 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=177796;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD 1|0:31:18,13 ./.:17:7,10 1|0:21:9,12 -chr20 198921 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=177903;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:15:9,6 ./.:12:5,7 1|1:31:8,23 -chr20 199123 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=178105;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:34:18,16 ./.:33:19,14 1|0:36:18,18 -chr20 199139 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=178122;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|0:20:12,8 ./.:48:24,24 ./.:24:9,15 -chr20 199139 . C CTT 60 . QNAME=cluster23_scaffold_3;QSTART=25512721;QSTRAND=-;GCPCT=33;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.459148 GT:DP:AD ./.:18:5,13 ./.:33:9,24 1|1:44:19,25 -chr20 199741 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25496737;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:44:20,24 ./.:34:9,25 0|1:15:10,5 -chr20 200997 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=179980;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:28:10,18 ./.:34:12,22 1|0:26:12,14 -chr20 201076 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25510784;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:27:20,7 ./.:33:18,15 1|0:35:12,23 -chr20 201326 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=180309;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:36:14,22 ./.:25:20,5 1|0:36:17,19 -chr20 201372 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=180355;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:39:20,19 ./.:20:11,9 1|1:41:23,18 -chr20 201418 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=180401;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:28:17,11 ./.:38:18,20 1|0:31:24,7 -chr20 201525 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25494953;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:36:16,20 ./.:15:10,5 0|1:43:21,22 -chr20 201908 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25494570;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:19:6,13 ./.:27:20,7 0|1:17:12,5 -chr20 201932 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25494545;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.5 GT:DP:AD ./.:17:10,7 ./.:30:16,14 0|1:21:10,11 -chr20 201932 . C CAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=180916;QSTRAND=+;GCPCT=20;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.360964 GT:DP:AD 1|0:31:17,14 ./.:28:9,19 1|0:34:16,18 -chr20 201932 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=155474;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD 0|1:29:21,8 ./.:24:17,7 ./.:30:7,23 -chr20 202581 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=181568;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:24:14,10 ./.:39:24,15 1|0:21:8,13 -chr20 203580 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=182567;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:34:13,21 ./.:13:7,6 1|0:37:22,15 -chr20 203602 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=182589;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:32:18,14 ./.:24:8,16 ./.:36:24,12 -chr20 203620 . TCCCTCCC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=182608;QSTRAND=+;GCPCT=75;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.405639 GT:DP:AD 1|0:32:8,24 ./.:22:5,17 1|0:28:5,23 -chr20 203847 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=182827;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:26:18,8 ./.:34:15,19 1|0:48:24,24 -chr20 204090 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=183070;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:21:6,15 ./.:15:10,5 1|0:30:13,17 -chr20 205285 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=184265;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:44:23,21 ./.:46:23,23 1|0:42:21,21 -chr20 205764 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=184744;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:22:6,16 ./.:38:15,23 1|1:22:17,5 -chr20 206102 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25490375;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:18:6,12 ./.:49:25,24 0|1:29:18,11 -chr20 206175 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=185156;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|0:40:24,16 ./.:13:5,8 ./.:28:10,18 -chr20 206175 . TAAAA T 60 . QNAME=cluster23_scaffold_2;QSTART=25490302;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.360964 GT:DP:AD ./.:39:23,16 ./.:28:19,9 0|1:39:21,18 -chr20 206197 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25490284;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:37:15,22 ./.:16:9,7 0|1:33:21,12 -chr20 206446 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25490035;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:12:5,7 ./.:21:7,14 0|1:40:19,21 -chr20 207202 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=186184;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|0:36:11,25 ./.:25:17,8 1|1:34:21,13 -chr20 207307 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25489173;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:25:10,15 ./.:39:22,17 0|1:25:12,13 -chr20 207389 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=186371;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:37:19,18 ./.:33:18,15 1|1:32:19,13 -chr20 207466 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25489014;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:36:14,22 ./.:31:12,19 0|1:21:14,7 -chr20 208792 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=187775;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 1|0:39:21,18 ./.:39:22,17 1|1:45:20,25 -chr20 209694 . A C 60 . QNAME=cluster23_scaffold_2;QSTART=25486787;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:43:21,22 ./.:25:7,18 0|1:40:21,19 -chr20 210024 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25486457;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:27:22,5 ./.:29:6,23 0|1:44:22,22 -chr20 211156 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=190137;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:13:5,8 ./.:24:7,17 1|1:28:19,9 -chr20 211168 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=190149;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:26:10,16 ./.:25:19,6 1|1:27:12,15 -chr20 211428 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=190409;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:43:22,21 ./.:22:7,15 1|1:31:7,24 -chr20 212919 . AC A 60 . QNAME=cluster23_scaffold_2;QSTART=25483562;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:34:21,13 ./.:18:10,8 0|1:30:15,15 -chr20 212994 . A AT 60 . QNAME=HG002-S9-H2-000001F;QSTART=166535;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 0|1:36:16,20 ./.:47:25,22 0|1:24:15,9 -chr20 213120 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25483361;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:37:15,22 ./.:32:7,25 0|1:38:15,23 -chr20 213126 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25483355;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:36:25,11 ./.:16:5,11 0|1:35:19,16 -chr20 213223 . G C 60 . QNAME=cluster23_scaffold_2;QSTART=25483258;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:27:7,20 ./.:31:6,25 0|1:20:13,7 -chr20 213244 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25483237;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:30:17,13 ./.:17:5,12 0|1:21:5,16 -chr20 213641 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25498222;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:42:22,20 ./.:39:20,19 1|0:43:18,25 -chr20 213649 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=192630;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,2,1;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:35:21,14 ./.:12:6,6 ./.:12:6,6 -chr20 213886 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=192867;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:23:11,12 ./.:26:16,10 ./.:27:20,7 -chr20 214444 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=193425;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:42:20,22 ./.:25:12,13 ./.:28:15,13 -chr20 214461 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=193442;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:35:14,21 ./.:40:20,20 ./.:35:16,19 -chr20 214646 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=193627;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:40:21,19 ./.:17:5,12 ./.:31:24,7 -chr20 214796 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=193778;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|0:34:14,20 ./.:30:21,9 ./.:24:10,14 -chr20 214824 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=193804;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:33:8,25 ./.:34:14,20 ./.:23:16,7 -chr20 214879 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=193859;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:22:8,14 ./.:40:25,15 ./.:30:21,9 -chr20 214962 . A AT 60 . QNAME=cluster23_scaffold_2;QSTART=25481518;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0.5 GT:DP:AD ./.:30:19,11 ./.:32:20,12 0|1:17:6,11 -chr20 215031 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25496832;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:30:17,13 ./.:26:18,8 1|0:29:6,23 -chr20 215055 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=194035;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:30:12,18 ./.:42:17,25 1|1:43:20,23 -chr20 215963 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=194943;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:20:13,7 ./.:17:8,9 ./.:27:16,11 -chr20 217163 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25479317;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:37:13,24 ./.:25:20,5 0|1:44:22,22 -chr20 217714 . ATATG A 60 . QNAME=cluster23_scaffold_2;QSTART=25478766;QSTRAND=-;GCPCT=20;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0.760964 GT:DP:AD ./.:14:8,6 ./.:16:7,9 0|1:24:5,19 -chr20 217754 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=196734;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:37:21,16 1|1:31:18,13 0|1:18:9,9 -chr20 217756 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25494107;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:25:11,14 ./.:27:7,20 1|0:41:20,21 -chr20 219501 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=198481;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:26:15,11 ./.:32:20,12 0|1:27:6,21 -chr20 220972 . CTT C 60 . QNAME=cluster23_scaffold_2;QSTART=25475512;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0.459148 GT:DP:AD ./.:28:12,16 ./.:14:8,6 0|1:41:17,24 -chr20 221511 . GGGAA G 60 . QNAME=cluster23_scaffold_3;QSTART=25490352;QSTRAND=-;GCPCT=60;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.485475 GT:DP:AD ./.:19:10,9 ./.:18:5,13 1|1:37:12,25 -chr20 224189 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=203169;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:32:9,23 ./.:41:16,25 0|1:26:12,14 -chr20 225761 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=204741;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:22:5,17 ./.:35:16,19 0|1:33:14,19 -chr20 225955 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=204935;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|1:28:22,6 1|1:31:19,12 1|1:37:25,12 -chr20 226775 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=205755;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:25:12,13 ./.:36:22,14 0|1:46:23,23 -chr20 227248 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=206228;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:14:9,5 ./.:17:11,6 ./.:38:16,22 -chr20 227262 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25484605;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:33:15,18 ./.:25:9,16 1|0:16:11,5 -chr20 227527 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=206507;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:41:20,21 ./.:44:23,21 1|1:23:17,6 -chr20 227692 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=25484175;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:28:15,13 ./.:38:19,19 1|0:32:14,18 -chr20 227704 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=206684;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:31:6,25 ./.:29:22,7 1|1:29:7,22 -chr20 227705 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25484162;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:27:14,13 ./.:26:17,9 1|0:35:23,12 -chr20 227706 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25484161;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:21:5,16 ./.:27:11,16 1|0:12:5,7 -chr20 227707 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25484160;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:29:13,16 ./.:25:7,18 1|0:24:5,19 -chr20 227909 . T G 60 . QNAME=cluster23_scaffold_3;QSTART=25483958;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:13:6,7 ./.:32:19,13 1|0:22:8,14 -chr20 228044 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25483823;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:28:14,14 ./.:20:8,12 1|0:38:17,21 -chr20 228258 . GCTTCTAATGTTTTTAT G 60 . QNAME=cluster23_scaffold_2;QSTART=25468232;QSTRAND=-;GCPCT=23;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.809197 GT:DP:AD ./.:49:25,24 ./.:19:12,7 0|1:28:5,23 -chr20 228763 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25467743;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:39:20,19 ./.:38:17,21 0|1:24:7,17 -chr20 229210 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25482657;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:39:23,16 ./.:27:5,22 1|0:27:10,17 -chr20 229265 . T TCTC 60 . QNAME=cluster23_scaffold_3;QSTART=25482599;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:33:14,19 ./.:29:9,20 1|0:38:25,13 -chr20 229420 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=208400;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:33:17,16 ./.:24:9,15 ./.:38:24,14 -chr20 229665 . C G 60 . QNAME=cluster23_scaffold_3;QSTART=25482199;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:15:7,8 ./.:37:18,19 1|1:38:17,21 -chr20 229898 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25481966;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:30:19,11 ./.:36:14,22 1|0:32:13,19 -chr20 229993 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25481871;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:26:8,18 ./.:31:22,9 1|0:47:24,23 -chr20 230118 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25466388;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD ./.:33:22,11 ./.:18:7,11 0|1:22:8,14 -chr20 230234 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=209214;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:27:9,18 ./.:42:18,24 ./.:29:20,9 -chr20 230273 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25481591;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:47:22,25 ./.:28:17,11 1|0:32:9,23 -chr20 230354 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25481510;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:27:21,6 ./.:38:15,23 1|0:38:18,20 -chr20 230514 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25481350;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:32:18,14 ./.:20:14,6 1|0:31:23,8 -chr20 230790 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25481074;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:27:9,18 ./.:44:21,23 1|0:18:9,9 -chr20 230868 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=209848;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:31:7,24 ./.:25:20,5 0|1:22:16,6 -chr20 230923 . T C 60 . QNAME=cluster19_000000F;QSTART=190079;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:33:12,21 0|1:20:13,7 ./.:41:20,21 -chr20 231070 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=210050;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:39:23,16 ./.:27:6,21 0|1:28:10,18 -chr20 231318 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=210298;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:26:9,17 ./.:27:13,14 ./.:28:5,23 -chr20 231710 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=210690;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:32:10,22 ./.:46:24,22 1|1:22:16,6 -chr20 231898 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=185439;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:29:6,23 1|1:39:17,22 1|0:44:24,20 -chr20 231900 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=185441;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:23:10,13 1|1:40:19,21 1|0:34:17,17 -chr20 232009 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25479855;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:27:10,17 ./.:23:16,7 1|0:42:24,18 -chr20 232033 . A AAAAT 60 . QNAME=cluster19_000000F;QSTART=191190;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.360964 GT:DP:AD ./.:24:12,12 0|1:28:12,16 0|1:39:16,23 -chr20 232033 . A AAAATAAAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=211014;QSTRAND=+;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.382102 GT:DP:AD 1|1:33:15,18 ./.:22:14,8 ./.:19:12,7 -chr20 232033 . A AAAATAAATAAAT 60 . QNAME=cluster19_000000F;QSTART=25530755;QSTRAND=-;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.389675 GT:DP:AD ./.:26:10,16 1|0:26:11,15 1|0:39:16,23 -chr20 232468 . C CTT 60 . QNAME=cluster23_scaffold_3;QSTART=25479382;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.459148 GT:DP:AD ./.:36:23,13 ./.:33:19,14 1|0:44:23,21 -chr20 232484 . TG T 60 . QNAME=cluster23_scaffold_3;QSTART=25479366;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:43:25,18 ./.:32:7,25 1|0:26:11,15 -chr20 232614 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25479237;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:38:14,24 ./.:19:5,14 1|0:34:24,10 -chr20 232882 . A C 60 . QNAME=cluster23_scaffold_3;QSTART=25478969;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:18:6,12 ./.:29:12,17 1|0:32:19,13 -chr20 233198 . TGACGG T 60 . QNAME=cluster23_scaffold_3;QSTART=25478653;QSTRAND=-;GCPCT=66;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.896241 GT:DP:AD ./.:30:7,23 ./.:31:12,19 1|0:20:7,13 -chr20 233213 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25478643;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:32:15,17 ./.:28:9,19 1|0:34:23,11 -chr20 233246 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25478610;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:17:12,5 ./.:36:13,23 1|0:26:14,12 -chr20 233732 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=212720;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|1:13:8,5 1|0:26:15,11 1|1:31:25,6 -chr20 234020 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25477836;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:33:22,11 ./.:25:16,9 1|0:26:8,18 -chr20 234023 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=25477833;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:36:24,12 ./.:36:18,18 1|0:26:11,15 -chr20 234144 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=213133;QSTRAND=+;GCPCT=50;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|1:31:9,22 1|1:28:20,8 ./.:18:6,12 -chr20 234144 . CTTTT C 60 . QNAME=cluster23_scaffold_3;QSTART=25477712;QSTRAND=-;GCPCT=20;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.360964 GT:DP:AD ./.:30:13,17 ./.:24:17,7 1|0:36:15,21 -chr20 234239 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=213226;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:26:15,11 ./.:27:22,5 ./.:37:16,21 -chr20 234441 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=213428;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:21:16,5 1|0:20:11,9 ./.:37:22,15 -chr20 234630 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25477230;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:36:25,11 ./.:22:17,5 1|0:44:23,21 -chr20 234736 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25477124;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:20:6,14 ./.:17:12,5 1|0:37:19,18 -chr20 234758 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25477102;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:31:22,9 ./.:26:10,16 1|0:39:15,24 -chr20 234803 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=25477057;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:20:8,12 ./.:32:18,14 1|0:43:22,21 -chr20 234949 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25476911;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:34:10,24 ./.:23:6,17 1|0:20:7,13 -chr20 235000 . T G 60 . QNAME=cluster23_scaffold_3;QSTART=25476860;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:41:16,25 ./.:25:9,16 1|0:32:14,18 -chr20 235023 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25476837;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:30:9,21 ./.:30:21,9 1|0:31:14,17 -chr20 235274 . T G 60 . QNAME=cluster23_scaffold_2;QSTART=25461228;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:21:13,8 ./.:27:20,7 0|1:49:25,24 -chr20 235380 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=25476480;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD ./.:32:18,14 ./.:20:9,11 1|0:23:10,13 -chr20 235457 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25476403;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:21:12,9 ./.:34:16,18 1|1:25:18,7 -chr20 235579 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25476281;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:40:24,16 ./.:21:11,10 1|0:28:16,12 -chr20 235581 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25476279;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:45:23,22 ./.:16:5,11 1|0:34:9,25 -chr20 235682 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25476178;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:37:12,25 ./.:29:22,7 1|0:32:12,20 -chr20 236006 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25475854;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:31:6,25 ./.:29:18,11 1|0:29:15,14 -chr20 236109 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=215096;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:16:7,9 1|1:38:17,21 1|1:18:11,7 -chr20 236170 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=215157;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:34:22,12 1|0:23:16,7 1|1:26:8,18 -chr20 236273 . CTAAG C 60 . QNAME=cluster23_scaffold_3;QSTART=25475587;QSTRAND=-;GCPCT=40;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.960964 GT:DP:AD ./.:37:21,16 ./.:25:11,14 1|0:33:19,14 -chr20 236433 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=215420;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:41:22,19 1|0:29:19,10 0|1:39:25,14 -chr20 236640 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=215627;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:29:7,22 1|0:43:23,20 0|1:28:14,14 -chr20 236959 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=215947;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD 1|1:44:19,25 1|0:15:7,8 ./.:31:25,6 -chr20 236959 . CTT C 60 . QNAME=cluster23_scaffold_3;QSTART=25474905;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.459148 GT:DP:AD ./.:23:8,15 ./.:38:15,23 1|0:38:24,14 -chr20 237090 . A C 60 . QNAME=cluster23_scaffold_3;QSTART=25474776;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:33:14,19 ./.:37:12,25 1|0:26:12,14 -chr20 237210 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=216198;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|1:29:21,8 1|1:25:15,10 1|1:26:19,7 -chr20 237614 . A AG 60 . QNAME=HG002-S9-H1-000001F;QSTART=216603;QSTRAND=+;GCPCT=50;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.5 GT:DP:AD 1|1:23:13,10 1|0:18:5,13 1|0:18:13,5 -chr20 238142 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25473723;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:31:19,12 ./.:29:8,21 1|1:27:17,10 -chr20 238370 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=217359;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:41:20,21 1|0:19:7,12 1|1:25:9,16 -chr20 238458 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=217447;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|1:19:14,5 1|0:19:8,11 ./.:20:6,14 -chr20 238622 . ACAAGGT A 60 . QNAME=cluster23_scaffold_3;QSTART=25473243;QSTRAND=-;GCPCT=42;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.921185 GT:DP:AD ./.:33:24,9 ./.:49:24,25 1|1:41:22,19 -chr20 238634 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=25473237;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:31:19,12 ./.:26:18,8 1|1:37:20,17 -chr20 238645 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=25473226;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:33:20,13 ./.:28:19,9 1|1:29:20,9 -chr20 238721 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=217710;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:49:25,24 1|0:22:6,16 ./.:38:18,20 -chr20 238845 . G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=217835;QSTRAND=+;GCPCT=50;GTCNT=0,0,1,2;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|1:14:5,9 1|0:29:13,16 1|1:49:25,24 -chr20 239021 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25472849;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:40:22,18 ./.:43:19,24 1|1:36:17,19 -chr20 239041 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25457466;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:16:8,8 ./.:41:18,23 0|1:30:16,14 -chr20 239418 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=218408;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:41:21,20 1|0:25:6,19 ./.:25:9,16 -chr20 239441 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25457065;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:18:10,8 ./.:33:21,12 0|1:33:11,22 -chr20 239444 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=218434;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,3,0,0;LCR=0 GT:DP:AD 1|1:10:5,5 1|0:24:16,8 ./.:24:18,6 -chr20 239451 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=218441;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:18:5,13 1|0:12:6,6 ./.:38:13,25 -chr20 239556 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=218546;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:20:7,13 1|0:29:11,18 1|1:29:15,14 -chr20 239563 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=218553;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:48:24,24 1|0:21:11,10 1|1:33:25,8 -chr20 239613 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25456893;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:26:19,7 ./.:35:19,16 0|1:15:7,8 -chr20 239649 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25472221;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:17:12,5 ./.:39:16,23 1|1:31:25,6 -chr20 239662 . A C 60 . QNAME=cluster23_scaffold_3;QSTART=25472208;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:16:6,10 ./.:32:22,10 1|1:20:12,8 -chr20 239803 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=218793;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:40:23,17 1|0:26:10,16 ./.:29:21,8 -chr20 239945 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25471925;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:10:5,5 ./.:28:8,20 1|0:38:19,19 -chr20 239951 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=25471919;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:29:21,8 ./.:31:24,7 1|1:24:12,12 -chr20 240008 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25471862;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:24:10,14 ./.:24:16,8 1|1:39:20,19 -chr20 240075 . C CAA 60 . QNAME=cluster23_scaffold_3;QSTART=25471793;QSTRAND=-;GCPCT=33;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.459148 GT:DP:AD ./.:17:8,9 ./.:32:19,13 1|1:39:22,17 -chr20 240075 . C CAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=219066;QSTRAND=+;GCPCT=25;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.405639 GT:DP:AD 1|1:34:25,9 1|0:24:8,16 ./.:40:22,18 -chr20 240116 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25471752;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:49:24,25 ./.:33:8,25 1|1:39:18,21 -chr20 240166 . T G 60 . QNAME=cluster23_scaffold_3;QSTART=25471702;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:45:23,22 ./.:15:5,10 1|1:24:18,6 -chr20 240377 . T G 60 . QNAME=cluster23_scaffold_3;QSTART=25471491;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:24:6,18 ./.:32:21,11 1|1:16:8,8 -chr20 240458 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25471410;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:28:11,17 ./.:39:23,16 1|1:25:7,18 -chr20 240477 . G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=219471;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 1|1:48:25,23 1|0:25:10,15 ./.:38:21,17 -chr20 240477 . G GAA 60 . QNAME=cluster23_scaffold_3;QSTART=25471389;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.459148 GT:DP:AD ./.:40:18,22 ./.:17:11,6 1|0:37:16,21 -chr20 240477 . G GAAA 60 . QNAME=cluster23_scaffold_2;QSTART=25456024;QSTRAND=-;GCPCT=25;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.405639 GT:DP:AD ./.:28:8,20 ./.:23:9,14 0|1:30:6,24 -chr20 240872 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25470994;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD ./.:26:12,14 ./.:34:23,11 1|1:36:25,11 -chr20 241191 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25470675;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:31:13,18 ./.:28:12,16 1|1:35:19,16 -chr20 241301 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=220295;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|1:23:11,12 1|0:31:17,14 1|1:30:24,6 -chr20 241898 . C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=220893;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|1:22:6,16 1|0:36:18,18 ./.:16:8,8 -chr20 241991 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25469875;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:39:14,25 ./.:32:17,15 1|1:38:20,18 -chr20 242033 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=221028;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:26:14,12 1|0:44:23,21 ./.:36:20,16 -chr20 242067 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=221062;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:40:25,15 1|0:39:21,18 ./.:40:20,20 -chr20 242195 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=221190;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:37:18,19 1|0:30:12,18 1|1:28:9,19 -chr20 242353 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=221348;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:23:6,17 1|0:22:9,13 ./.:29:18,11 -chr20 242531 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=221526;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|1:26:13,13 1|0:19:11,8 ./.:27:21,6 -chr20 242614 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=221609;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:26:15,11 1|0:39:22,17 ./.:30:13,17 -chr20 242798 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=221793;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:25:15,10 1|0:24:13,11 ./.:27:9,18 -chr20 242897 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=221892;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:36:25,11 1|0:39:17,22 1|1:33:16,17 -chr20 243066 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25468800;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:21:15,6 ./.:26:6,20 1|1:38:16,22 -chr20 243217 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=222212;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:33:15,18 1|0:24:19,5 1|1:41:25,16 -chr20 243487 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=222482;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:25:15,10 1|0:33:13,20 ./.:25:8,17 -chr20 243532 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=222527;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:29:5,24 1|0:19:11,8 1|1:23:13,10 -chr20 243817 . AAG A 60 . QNAME=cluster23_scaffold_3;QSTART=25468049;QSTRAND=-;GCPCT=33;GTCNT=2,0,0,1;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0.459148 GT:DP:AD ./.:23:5,18 ./.:17:11,6 1|1:14:7,7 -chr20 243818 . AG A 60 . QNAME=HG002-S9-H1-000001F;QSTART=222814;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|1:30:7,23 1|0:29:24,5 ./.:31:17,14 -chr20 243960 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=222954;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:45:25,20 1|0:25:10,15 ./.:30:11,19 -chr20 244104 . GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=223099;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0.5 GT:DP:AD 1|1:17:8,9 1|0:18:6,12 ./.:24:19,5 -chr20 244300 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=223293;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:13:5,8 1|0:27:10,17 1|1:32:17,15 -chr20 244330 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=223323;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:32:13,19 1|0:41:21,20 1|1:17:9,8 -chr20 244417 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=223410;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:31:15,16 1|0:29:19,10 1|1:17:5,12 -chr20 244771 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=223764;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:43:23,20 1|0:46:22,24 ./.:17:10,7 -chr20 244773 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25467095;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:20:8,12 ./.:20:8,12 1|1:33:14,19 -chr20 244803 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=223796;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:27:13,14 1|0:40:21,19 ./.:29:5,24 -chr20 244964 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25466904;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:30:6,24 ./.:21:7,14 1|1:21:15,6 -chr20 244981 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25466887;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:33:12,21 ./.:34:14,20 1|1:30:11,19 -chr20 245127 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=224120;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:36:15,21 1|0:17:6,11 ./.:19:8,11 -chr20 245425 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25466443;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:20:13,7 ./.:27:8,19 1|1:36:21,15 -chr20 245437 . GTGTATGTATA G 60 . QNAME=cluster23_scaffold_3;QSTART=25466431;QSTRAND=-;GCPCT=27;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.769742 GT:DP:AD ./.:30:21,9 ./.:22:11,11 1|1:39:17,22 -chr20 245443 . GTA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=224437;QSTRAND=+;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.792481 GT:DP:AD 1|0:47:24,23 ./.:29:19,10 ./.:30:22,8 -chr20 245443 . GTATATATA G 60 . QNAME=cluster19_000000F;QSTART=204603;QSTRAND=+;GCPCT=11;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.696074 GT:DP:AD ./.:23:13,10 0|1:32:14,18 ./.:42:23,19 -chr20 245470 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=224461;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:30:8,22 ./.:26:19,7 ./.:38:23,15 -chr20 245472 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=224463;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:35:20,15 ./.:14:6,8 1|0:26:9,17 -chr20 245474 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=199028;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:28:9,19 ./.:17:8,9 ./.:16:8,8 -chr20 245512 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25466366;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:31:20,11 ./.:30:18,12 1|1:32:25,7 -chr20 245789 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25466089;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:31:25,6 ./.:42:20,22 1|1:20:12,8 -chr20 245803 . A G 60 . QNAME=cluster19_000000F;QSTART=204954;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:45:20,25 0|1:39:23,16 ./.:24:11,13 -chr20 245877 . G A 60 . QNAME=cluster19_000000F;QSTART=205028;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:27:5,22 0|1:49:24,25 ./.:31:9,22 -chr20 245928 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25465950;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:34:9,25 ./.:26:17,9 1|1:30:22,8 -chr20 246148 . T A 60 . QNAME=cluster19_000000F;QSTART=205299;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:36:21,15 0|1:24:13,11 1|1:29:20,9 -chr20 246383 . G A 60 . QNAME=cluster19_000000F;QSTART=205534;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD ./.:20:10,10 0|1:22:9,13 ./.:33:23,10 -chr20 246501 . G T 60 . QNAME=cluster19_000000F;QSTART=205652;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:36:22,14 0|1:18:9,9 ./.:35:22,13 -chr20 246605 . A G 60 . QNAME=cluster19_000000F;QSTART=205756;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:22:6,16 0|1:48:23,25 1|1:24:9,15 -chr20 246926 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25449587;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:35:25,10 ./.:45:22,23 0|1:24:14,10 -chr20 246986 . G GCACA 60 . QNAME=cluster23_scaffold_3;QSTART=25464888;QSTRAND=-;GCPCT=60;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.760964 GT:DP:AD ./.:25:8,17 ./.:32:13,19 1|1:33:13,20 -chr20 247326 . G A 60 . QNAME=cluster19_000000F;QSTART=206477;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:40:16,24 0|1:26:5,21 1|1:39:16,23 -chr20 247501 . AAAAGAAAAAG A 60 . QNAME=cluster23_scaffold_3;QSTART=25464373;QSTRAND=-;GCPCT=18;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.342019 GT:DP:AD ./.:43:22,21 ./.:49:25,24 1|0:27:19,8 -chr20 247505 . GAA G 60 . QNAME=cluster23_scaffold_2;QSTART=25449004;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.459148 GT:DP:AD ./.:24:14,10 ./.:44:19,25 0|1:18:12,6 -chr20 247512 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25448999;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:22:16,6 ./.:29:8,21 0|1:14:7,7 -chr20 247516 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25448995;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:26:14,12 ./.:27:9,18 0|1:14:9,5 -chr20 247516 . AAAGG A 60 . QNAME=HG002-S9-H1-000001F;QSTART=226508;QSTRAND=+;GCPCT=40;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0.485475 GT:DP:AD 1|1:23:15,8 1|0:14:6,8 ./.:23:6,17 -chr20 247516 . AAAGGAAGG A 60 . QNAME=cluster19_000000F;QSTART=206668;QSTRAND=+;GCPCT=44;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.495538 GT:DP:AD ./.:27:15,12 0|1:28:5,23 ./.:36:23,13 -chr20 247565 . A C 60 . QNAME=cluster19_000000F;QSTART=206708;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:32:17,15 0|1:27:9,18 1|1:27:15,12 -chr20 247714 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25464170;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:29:12,17 ./.:30:25,5 1|1:27:11,16 -chr20 247936 . G A 60 . QNAME=cluster19_000000F;QSTART=207079;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:32:16,16 0|1:13:6,7 1|1:21:10,11 -chr20 248065 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25463819;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:46:22,24 ./.:30:9,21 1|1:19:13,6 -chr20 248099 . T A 60 . QNAME=cluster23_scaffold_3;QSTART=25463785;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:33:19,14 ./.:16:11,5 1|1:34:16,18 -chr20 248173 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25463711;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:32:19,13 ./.:29:11,18 1|1:11:5,6 -chr20 248248 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=25463636;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:14:7,7 ./.:36:16,20 1|1:18:12,6 -chr20 248357 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25463527;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:31:22,9 ./.:28:15,13 1|1:38:24,14 -chr20 248371 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25463513;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:25:5,20 ./.:20:14,6 1|1:22:11,11 -chr20 248716 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25447795;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:42:21,21 ./.:33:12,21 0|1:48:25,23 -chr20 248740 . C CA 60 . QNAME=cluster19_000000F;QSTART=207884;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:48:24,24 0|1:35:16,19 ./.:21:6,15 -chr20 248740 . CA C 60 . QNAME=cluster23_scaffold_3;QSTART=25463144;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:22:8,14 ./.:28:5,23 1|0:22:17,5 -chr20 248815 . G A 60 . QNAME=cluster19_000000F;QSTART=207959;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:35:13,22 0|1:17:7,10 ./.:35:14,21 -chr20 248838 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25463047;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:25:15,10 ./.:18:12,6 1|0:45:24,21 -chr20 248854 . T C 60 . QNAME=cluster19_000000F;QSTART=207998;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:37:24,13 0|1:47:25,22 1|1:22:17,5 -chr20 249081 . T C 60 . QNAME=cluster19_000000F;QSTART=208225;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:23:18,5 0|1:39:18,21 1|1:34:17,17 -chr20 249089 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25462795;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:36:12,24 ./.:20:7,13 1|0:35:20,15 -chr20 249089 . C CAA 60 . QNAME=cluster19_000000F;QSTART=208234;QSTRAND=+;GCPCT=33;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.459148 GT:DP:AD ./.:24:19,5 0|1:48:24,24 0|1:27:11,16 -chr20 249337 . G C 60 . QNAME=cluster19_000000F;QSTART=208483;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:25:11,14 0|1:25:6,19 ./.:26:12,14 -chr20 249412 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=202962;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:24:11,13 1|0:29:9,20 ./.:40:22,18 -chr20 249417 . CAT C 60 . QNAME=cluster19_000000F;QSTART=208564;QSTRAND=+;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.792481 GT:DP:AD ./.:39:24,15 0|1:34:11,23 ./.:24:6,18 -chr20 249417 . CATA C 60 . QNAME=cluster23_scaffold_3;QSTART=25462467;QSTRAND=-;GCPCT=25;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.75 GT:DP:AD ./.:33:22,11 ./.:15:5,10 1|1:29:20,9 -chr20 249536 . A T 60 . QNAME=cluster19_000000F;QSTART=208680;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:27:20,7 0|1:41:25,16 ./.:20:9,11 -chr20 249875 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=228862;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:21:6,15 0|1:30:7,23 1|1:31:12,19 -chr20 249900 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=228887;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:26:12,14 0|1:32:23,9 1|1:24:18,6 -chr20 250218 . C T 60 . QNAME=cluster19_000000F;QSTART=209362;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:26:9,17 0|1:21:12,9 ./.:19:8,11 -chr20 250342 . C T 60 . QNAME=cluster19_000000F;QSTART=209486;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:25:9,16 0|1:30:8,22 ./.:17:11,6 -chr20 250449 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=229436;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:26:7,19 0|1:28:13,15 1|1:33:19,14 -chr20 250472 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=229459;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:27:9,18 ./.:26:14,12 1|1:28:13,15 -chr20 250554 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=229541;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:35:19,16 ./.:25:20,5 1|1:29:14,15 -chr20 250671 . A C 60 . QNAME=cluster19_000000F;QSTART=209815;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:28:8,20 0|1:19:9,10 ./.:40:24,16 -chr20 250864 . G A 60 . QNAME=cluster19_000000F;QSTART=210008;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:27:9,18 0|1:38:25,13 ./.:38:19,19 -chr20 251035 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=230022;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:40:23,17 ./.:33:23,10 1|1:35:10,25 -chr20 251370 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=230357;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:39:20,19 ./.:45:21,24 1|0:36:17,19 -chr20 251466 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=230453;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:24:10,14 0|1:16:5,11 1|1:35:10,25 -chr20 251699 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=230686;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:37:15,22 ./.:35:15,20 1|1:28:19,9 -chr20 251939 . G C 60 . QNAME=cluster19_000000F;QSTART=211083;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:45:25,20 0|1:18:7,11 ./.:34:24,10 -chr20 251993 . T TACACAC 60 . QNAME=cluster19_000000F;QSTART=211138;QSTRAND=+;GCPCT=42;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.724408 GT:DP:AD ./.:32:12,20 0|1:30:5,25 ./.:42:22,20 -chr20 251993 . T TACACACACAC 60 . QNAME=cluster23_scaffold_3;QSTART=25459884;QSTRAND=-;GCPCT=45;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.674294 GT:DP:AD ./.:16:10,6 ./.:31:10,21 1|0:38:25,13 -chr20 251993 . T TACACACACACACAC 60 . QNAME=cluster23_scaffold_2;QSTART=25444505;QSTRAND=-;GCPCT=46;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0.643346 GT:DP:AD ./.:18:6,12 ./.:20:8,12 0|1:28:18,10 -chr20 251993 . T TACACACACACACACAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=230981;QSTRAND=+;GCPCT=47;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.631967 GT:DP:AD 1|0:41:17,24 ./.:28:9,19 ./.:23:8,15 -chr20 252833 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=231836;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:32:8,24 ./.:40:20,20 1|1:16:10,6 -chr20 252834 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=231837;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:42:18,24 ./.:29:12,17 1|1:30:10,20 -chr20 252881 . GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=231885;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|0:32:10,22 ./.:21:16,5 1|1:47:24,23 -chr20 252982 . A T 60 . QNAME=cluster19_000000F;QSTART=212132;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:36:25,11 0|1:28:12,16 ./.:37:24,13 -chr20 253238 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=232240;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:42:18,24 1|1:44:20,24 1|1:36:17,19 -chr20 253538 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=232540;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:48:23,25 0|1:35:24,11 1|1:34:22,12 -chr20 253719 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=232721;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:15:7,8 0|1:28:15,13 1|1:39:24,15 -chr20 253968 . A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25457909;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD ./.:23:13,10 ./.:45:21,24 1|0:24:14,10 -chr20 254466 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=233468;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:16:6,10 0|1:30:21,9 1|1:27:16,11 -chr20 255081 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=234083;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:24:10,14 0|1:27:18,9 1|1:16:10,6 -chr20 255329 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=234331;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:26:17,9 0|1:42:17,25 1|1:30:25,5 -chr20 255356 . C CAAAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=234359;QSTRAND=+;GCPCT=11;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.251629 GT:DP:AD 1|0:37:19,18 0|1:36:21,15 ./.:25:11,14 -chr20 255356 . C CAAAAAAAAA 60 . QNAME=cluster23_scaffold_3;QSTART=25456512;QSTRAND=-;GCPCT=10;GTCNT=2,0,0,1;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0.234498 GT:DP:AD ./.:27:15,12 ./.:13:6,7 1|1:39:21,18 -chr20 255447 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=234457;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:23:12,11 0|1:30:6,24 1|1:34:11,23 -chr20 255527 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=234537;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:33:14,19 0|1:35:23,12 1|1:43:19,24 -chr20 255597 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=234607;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:36:21,15 0|1:22:16,6 1|1:24:12,12 -chr20 255645 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=234655;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:44:22,22 0|1:27:18,9 1|1:17:12,5 -chr20 255687 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=234697;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:38:17,21 0|1:32:11,21 1|1:36:19,17 -chr20 255778 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=234788;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:38:21,17 0|1:36:25,11 1|1:43:18,25 -chr20 255818 . G GAT 60 . QNAME=cluster19_000000F;QSTART=25506967;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.792481 GT:DP:AD ./.:32:7,25 1|0:24:15,9 ./.:39:18,21 -chr20 255818 . GAT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=234829;QSTRAND=+;GCPCT=33;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.792481 GT:DP:AD 1|0:30:6,24 ./.:25:9,16 1|1:26:13,13 -chr20 256161 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=235169;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:46:25,21 0|1:18:7,11 1|1:32:16,16 -chr20 256351 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=235359;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:21:5,16 0|1:16:7,9 1|1:37:14,23 -chr20 256411 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=235419;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:45:23,22 0|1:30:12,18 1|1:25:18,7 -chr20 256777 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=235785;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:28:17,11 0|1:33:15,18 1|1:19:7,12 -chr20 256856 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=235864;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:34:15,19 0|1:27:13,14 1|1:25:8,17 -chr20 256904 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=235912;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:22:10,12 0|1:18:11,7 1|1:36:12,24 -chr20 256928 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=235936;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD 1|0:18:6,12 0|1:19:6,13 1|1:22:10,12 -chr20 256977 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=235985;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:18:7,11 0|1:21:13,8 1|1:12:6,6 -chr20 257008 . CAGAT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=236017;QSTRAND=+;GCPCT=40;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.960964 GT:DP:AD 1|1:26:20,6 0|1:36:18,18 1|1:35:15,20 -chr20 257036 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=236040;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:33:20,13 0|1:36:19,17 1|1:35:25,10 -chr20 257175 . A AT 60 . QNAME=HG002-S9-H1-000001F;QSTART=236180;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.5 GT:DP:AD 1|0:37:24,13 0|1:23:9,14 1|1:31:22,9 -chr20 257379 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=236384;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:27:22,5 0|1:19:6,13 1|1:39:18,21 -chr20 257794 . CTGGTCT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=236800;QSTRAND=+;GCPCT=57;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.778328 GT:DP:AD 1|0:28:21,7 0|1:43:19,24 1|1:36:20,16 -chr20 257866 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=236865;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:20:13,7 0|1:29:14,15 1|1:22:6,16 -chr20 257889 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=236888;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:36:12,24 0|1:24:7,17 1|1:36:14,22 -chr20 257899 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=236898;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:28:21,7 0|1:11:5,6 1|1:47:23,24 -chr20 258096 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=237095;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:33:8,25 0|1:23:18,5 1|1:17:9,8 -chr20 258653 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=237652;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:28:7,21 0|1:16:10,6 1|1:24:18,6 -chr20 258767 . A ACTGTGAAGACCTGGTCCCCACCCCCGTTTTTAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=237767;QSTRAND=+;SVTYPE=INS;SVLEN=33;GCPCT=55;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.960576 GT:DP:AD 1/0:20:13,7 0/1:41:19,22 1/1:25:12,13 -chr20 258770 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=237802;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:24:12,12 0|1:48:25,23 1|1:32:7,25 -chr20 259023 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=238055;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:39:24,15 0|1:20:5,15 1|1:31:22,9 -chr20 259047 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=238079;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:27:20,7 0|1:15:9,6 1|1:34:10,24 -chr20 259056 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=238088;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:43:20,23 0|1:21:6,15 1|1:29:7,22 -chr20 260063 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=239095;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:44:21,23 0|1:38:17,21 1|1:42:21,21 -chr20 260065 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=239097;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:35:20,15 0|1:28:11,17 1|1:31:18,13 -chr20 260593 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=239625;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:42:19,23 0|1:37:15,22 1|1:36:22,14 -chr20 260725 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=239757;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:19:5,14 0|1:18:7,11 1|1:25:19,6 -chr20 260755 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=239787;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:46:21,25 ./.:14:6,8 1|1:18:7,11 -chr20 260997 . G A 60 . QNAME=cluster19_000000F;QSTART=220179;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:29:7,22 0|1:38:25,13 ./.:46:21,25 -chr20 261185 . TTTTG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=240218;QSTRAND=+;GCPCT=20;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.360964 GT:DP:AD 1|0:20:7,13 ./.:22:17,5 1|1:19:9,10 -chr20 261768 . G A 60 . QNAME=cluster19_000000F;QSTART=220950;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:34:10,24 0|1:35:14,21 ./.:19:14,5 -chr20 261944 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=240972;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:20:12,8 ./.:34:19,15 1|1:26:11,15 -chr20 261974 . G T 60 . QNAME=cluster19_000000F;QSTART=221156;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:16:11,5 0|1:32:22,10 ./.:32:25,7 -chr20 262044 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=241072;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:31:8,23 0|1:40:19,21 1|1:40:25,15 -chr20 262053 . T C 60 . QNAME=cluster19_000000F;QSTART=221235;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:39:19,20 0|1:37:12,25 ./.:30:16,14 -chr20 262157 . C T 60 . QNAME=cluster19_000000F;QSTART=221339;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:48:23,25 0|1:21:11,10 ./.:33:14,19 -chr20 262198 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25434273;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD ./.:16:6,10 ./.:28:11,17 0|1:29:15,14 -chr20 262582 . C CT 60 . QNAME=cluster19_000000F;QSTART=221765;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.5 GT:DP:AD ./.:30:25,5 0|1:27:16,11 ./.:22:10,12 -chr20 262711 . G T 60 . QNAME=cluster19_000000F;QSTART=221894;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:24:7,17 0|1:29:9,20 ./.:45:22,23 -chr20 262757 . G C 60 . QNAME=cluster19_000000F;QSTART=221940;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:11:5,6 0|1:39:21,18 ./.:37:13,24 -chr20 263038 . A C 60 . QNAME=cluster19_000000F;QSTART=222221;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:19:11,8 0|1:28:20,8 ./.:44:19,25 -chr20 263283 . C A 60 . QNAME=cluster19_000000F;QSTART=222466;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:31:16,15 0|1:30:9,21 ./.:15:7,8 -chr20 263451 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=242479;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:33:13,20 0|1:43:23,20 1|1:31:24,7 -chr20 263479 . G GGT 60 . QNAME=cluster19_000000F;QSTART=222663;QSTRAND=+;GCPCT=66;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.459148 GT:DP:AD ./.:24:9,15 0|1:23:6,17 ./.:33:10,23 -chr20 263497 . TGTGTGTGC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=242526;QSTRAND=+;GCPCT=55;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.696074 GT:DP:AD 1|0:40:24,16 ./.:31:24,7 1|1:26:7,19 -chr20 263505 . C T 60 . QNAME=cluster19_000000F;QSTART=222690;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:25:15,10 0|1:22:7,15 ./.:18:13,5 -chr20 263692 . A G 60 . QNAME=cluster19_000000F;QSTART=222877;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:25:18,7 0|1:18:9,9 ./.:22:8,14 -chr20 263732 . C T 60 . QNAME=cluster19_000000F;QSTART=222917;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:27:22,5 0|1:26:11,15 ./.:26:21,5 -chr20 263776 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=242796;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:39:14,25 ./.:12:5,7 1|1:29:7,22 -chr20 264344 . G A 60 . QNAME=cluster19_000000F;QSTART=223529;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:32:21,11 0|1:30:7,23 ./.:39:14,25 -chr20 264825 . T G 60 . QNAME=cluster19_000000F;QSTART=224010;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:29:9,20 0|1:41:21,20 ./.:38:16,22 -chr20 265021 . G GT 60 . QNAME=HG002-S9-H2-000001F;QSTART=218568;QSTRAND=+;GCPCT=50;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 0|1:18:13,5 1|0:24:9,15 0|1:48:24,24 -chr20 265021 . G T 60 . QNAME=cluster19_000000F;QSTART=224206;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:24:8,16 0|1:41:20,21 ./.:26:17,9 -chr20 265021 . GT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=244042;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|0:20:9,11 ./.:41:21,20 ./.:23:16,7 -chr20 265024 . T G 60 . QNAME=cluster19_000000F;QSTART=224209;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:36:13,23 0|1:36:20,16 ./.:47:25,22 -chr20 265028 . T G 60 . QNAME=cluster19_000000F;QSTART=224213;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:31:20,11 0|1:36:12,24 ./.:12:6,6 -chr20 265032 . T G 60 . QNAME=cluster19_000000F;QSTART=224217;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:35:25,10 0|1:27:6,21 ./.:22:8,14 -chr20 265049 . C T 60 . QNAME=cluster19_000000F;QSTART=224234;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:41:24,17 0|1:28:12,16 ./.:19:9,10 -chr20 265294 . G T 60 . QNAME=cluster19_000000F;QSTART=224479;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:21:15,6 0|1:27:19,8 ./.:39:17,22 -chr20 265390 . AAAG A 60 . QNAME=HG002-S9-H1-000001F;QSTART=244410;QSTRAND=+;GCPCT=25;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.405639 GT:DP:AD 1|0:25:15,10 ./.:35:12,23 1|1:26:9,17 -chr20 265614 . C T 60 . QNAME=cluster19_000000F;QSTART=224799;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:27:22,5 0|1:16:8,8 ./.:31:8,23 -chr20 265842 . T TTAAA 60 . QNAME=cluster19_000000F;QSTART=225028;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.485475 GT:DP:AD ./.:27:6,21 0|1:20:5,15 1|1:42:20,22 -chr20 266980 . CCT C 60 . QNAME=cluster23_scaffold_3;QSTART=25444877;QSTRAND=-;GCPCT=66;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.459148 GT:DP:AD ./.:32:23,9 ./.:22:8,14 1|1:29:12,17 -chr20 267423 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25429056;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:32:20,12 ./.:34:19,15 0|1:35:10,25 -chr20 268285 . C A 60 . QNAME=cluster23_scaffold_2;QSTART=25428194;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:20:5,15 ./.:27:9,18 0|1:37:21,16 -chr20 268294 . A T 60 . QNAME=cluster23_scaffold_2;QSTART=25428185;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD ./.:28:17,11 ./.:21:8,13 0|1:23:12,11 -chr20 268599 . T A 60 . QNAME=cluster23_scaffold_3;QSTART=25443260;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:32:9,23 ./.:24:13,11 1|1:29:8,21 -chr20 269435 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25442424;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:38:25,13 ./.:41:22,19 1|1:28:5,23 -chr20 269686 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=223234;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 0|1:31:10,21 ./.:37:16,21 ./.:27:20,7 -chr20 269844 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=223390;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:34:11,23 ./.:11:6,5 ./.:30:20,10 -chr20 270732 . ACTT A 60 . QNAME=cluster19_000000F;QSTART=229922;QSTRAND=+;GCPCT=25;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.75 GT:DP:AD ./.:24:17,7 0|1:25:19,6 ./.:30:11,19 -chr20 271440 . GCATACACACACA G 60 . QNAME=cluster23_scaffold_3;QSTART=25440419;QSTRAND=-;GCPCT=46;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.807165 GT:DP:AD ./.:42:22,20 ./.:20:14,6 1|0:24:14,10 -chr20 271443 . T TAC 60 . QNAME=cluster23_scaffold_2;QSTART=25425034;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,2,0;LCR=0.792481 GT:DP:AD ./.:31:21,10 ./.:13:6,7 0|1:25:13,12 -chr20 271443 . TACAC T 60 . QNAME=cluster19_000000F;QSTART=25491341;QSTRAND=-;GCPCT=40;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.760964 GT:DP:AD ./.:32:22,10 1|0:32:12,20 ./.:47:25,22 -chr20 271455 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=25440416;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:49:25,24 ./.:46:21,25 1|0:30:23,7 -chr20 271524 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25440347;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:21:14,7 ./.:36:19,17 1|0:33:9,24 -chr20 271615 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25440256;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:34:22,12 ./.:22:13,9 1|0:18:10,8 -chr20 272116 . A AC 60 . QNAME=cluster23_scaffold_3;QSTART=25439754;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:27:21,6 ./.:42:23,19 1|0:36:15,21 -chr20 272200 . TA T 60 . QNAME=cluster23_scaffold_3;QSTART=25439670;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:23:12,11 ./.:27:12,15 1|0:46:21,25 -chr20 272348 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25439523;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:28:9,19 ./.:21:7,14 1|0:40:16,24 -chr20 272493 . C A 60 . QNAME=cluster23_scaffold_2;QSTART=25423984;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:26:20,6 ./.:15:6,9 0|1:25:13,12 -chr20 273372 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=252388;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:26:11,15 ./.:35:19,16 1|0:36:16,20 -chr20 273876 . C CAAGAA 60 . QNAME=cluster23_scaffold_3;QSTART=25437990;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.625815 GT:DP:AD ./.:24:12,12 ./.:23:16,7 1|0:31:20,11 -chr20 273894 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25437972;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:22:13,9 ./.:30:24,6 1|0:47:24,23 -chr20 273903 . A AAGGGAGGG 60 . QNAME=HG002-S9-H2-000001F;QSTART=227450;QSTRAND=+;GCPCT=66;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.459148 GT:DP:AD 0|1:41:24,17 1|1:19:5,14 ./.:34:19,15 -chr20 273903 . AAGGG A 60 . QNAME=cluster23_scaffold_2;QSTART=25422574;QSTRAND=-;GCPCT=60;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.485475 GT:DP:AD ./.:32:21,11 ./.:24:10,14 0|1:22:13,9 -chr20 273903 . AAGGGAGGG A 60 . QNAME=cluster23_scaffold_3;QSTART=25437963;QSTRAND=-;GCPCT=66;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.459148 GT:DP:AD ./.:42:18,24 ./.:36:20,16 1|0:31:13,18 -chr20 274125 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=253141;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:16:9,7 ./.:12:6,6 ./.:36:20,16 -chr20 274210 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=253226;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:22:7,15 ./.:27:14,13 1|0:18:11,7 -chr20 274599 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=253615;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:17:11,6 ./.:39:16,23 ./.:26:16,10 -chr20 274820 . TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=253837;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|0:17:12,5 ./.:39:14,25 ./.:48:25,23 -chr20 274829 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25437045;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:47:25,22 ./.:41:22,19 1|0:38:13,25 -chr20 274893 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25436981;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:24:6,18 ./.:27:7,20 1|0:28:6,22 -chr20 275122 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=25436752;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:33:17,16 ./.:41:20,21 1|0:21:5,16 -chr20 275241 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=254256;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:35:17,18 ./.:36:13,23 1|0:39:18,21 -chr20 275322 . C CG 60 . QNAME=cluster23_scaffold_3;QSTART=25436551;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0.5 GT:DP:AD ./.:26:19,7 ./.:13:7,6 1|0:35:22,13 -chr20 275361 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25436512;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:25:16,9 ./.:49:24,25 1|0:28:11,17 -chr20 275466 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=254481;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:31:7,24 ./.:34:12,22 ./.:32:19,13 -chr20 275606 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25436267;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:25:12,13 ./.:34:11,23 1|0:32:22,10 -chr20 275918 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25435955;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:42:22,20 ./.:37:12,25 1|0:30:17,13 -chr20 275932 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=254947;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:25:6,19 ./.:43:23,20 1|0:29:21,8 -chr20 276086 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=255101;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:21:9,12 ./.:26:10,16 1|0:29:6,23 -chr20 276119 . G GA 60 . QNAME=cluster23_scaffold_3;QSTART=25435753;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:22:6,16 ./.:31:6,25 1|0:33:23,10 -chr20 276122 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25435750;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:42:24,18 ./.:39:18,21 1|0:39:25,14 -chr20 276225 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=255240;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:34:12,22 ./.:35:17,18 1|0:32:14,18 -chr20 276245 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=255260;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:30:5,25 ./.:14:5,9 ./.:24:18,6 -chr20 276351 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=255366;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:30:13,17 ./.:33:14,19 1|0:41:17,24 -chr20 276391 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=255406;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:25:6,19 ./.:40:15,25 1|0:39:19,20 -chr20 276679 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=255694;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:27:21,6 ./.:32:11,21 1|0:32:15,17 -chr20 277092 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=256107;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:22:9,13 ./.:37:23,14 1|0:32:14,18 -chr20 277162 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=256177;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:21:15,6 ./.:45:23,22 ./.:30:23,7 -chr20 277171 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=256186;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:15:7,8 ./.:19:13,6 1|0:28:9,19 -chr20 277550 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=256565;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:14:5,9 ./.:28:22,6 1|0:31:20,11 -chr20 277574 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=256589;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:30:21,9 ./.:21:6,15 1|0:35:23,12 -chr20 277654 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=256669;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:20:13,7 ./.:18:7,11 1|0:24:10,14 -chr20 277664 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=256679;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:31:7,24 ./.:26:10,16 1|0:43:18,25 -chr20 277800 . C CAG 60 . QNAME=HG002-S9-H1-000001F;QSTART=256816;QSTRAND=+;GCPCT=66;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.792481 GT:DP:AD 1|0:29:21,8 ./.:21:11,10 1|0:43:20,23 -chr20 277808 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=256825;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:34:15,19 ./.:21:14,7 1|0:23:13,10 -chr20 277915 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=256932;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:35:16,19 ./.:32:22,10 1|0:33:12,21 -chr20 278070 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=257087;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:19:9,10 ./.:23:10,13 1|0:42:22,20 -chr20 278107 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25433763;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:31:8,23 ./.:30:25,5 1|0:30:14,16 -chr20 278224 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=257241;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:46:25,21 ./.:30:25,5 1|0:21:6,15 -chr20 278515 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=257532;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:29:16,13 ./.:29:24,5 ./.:33:13,20 -chr20 278561 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25433309;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:34:18,16 ./.:13:7,6 1|0:39:18,21 -chr20 278930 . C CGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGCGGGAG 60 . QNAME=cluster23_scaffold_2;QSTART=25417363;QSTRAND=-;SVTYPE=INS;SVLEN=188;HOMPCT=3.2;REMAP=partial;GCPCT=80;GTCNT=2,0,1,0;NumNeighbors=6;NeighId=1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.591695 GT:DP:AD ./.:19:11,8 ./.:33:12,21 0/1:36:12,24 -chr20 278930 . C CGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAG 60 . QNAME=HG002-S9-H2-000001F;QSTART=232485;QSTRAND=+;SVTYPE=INS;SVLEN=184;HOMPCT=3.2;REMAP=partial;GCPCT=80;GTCNT=2,0,1,0;NumNeighbors=6;NeighId=1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.591756 GT:DP:AD 0/1:29:9,20 ./.:22:16,6 ./.:24:5,19 -chr20 278962 . G GGGAGGGAGGGACGGAGGGAGGAAGGGCGGGAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=257980;QSTRAND=+;SVTYPE=INS;SVLEN=32;GCPCT=75;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.60004 GT:DP:AD 1/0:42:17,25 ./.:17:10,7 ./.:20:9,11 -chr20 278966 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=258015;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:15:5,10 ./.:38:13,25 ./.:42:17,25 -chr20 278977 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=258026;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:28:5,23 ./.:26:12,14 ./.:12:7,5 -chr20 279062 . G GGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGTGGGAGGGAGGGAGGGAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=258112;QSTRAND=+;SVTYPE=INS;SVLEN=139;HOMPCT=3.2;REMAP=tandem;REMAPHits=chr20:279033-279148.87,chr20:278941-279082.100;GCPCT=77;GTCNT=2,0,1,0;NumNeighbors=6;NeighId=1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.591759 GT:DP:AD 1/0:29:6,23 ./.:40:23,17 ./.:32:9,23 -chr20 279069 . A AGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGC 60 . QNAME=cluster19_000000F;QSTART=25483168;QSTRAND=-;SVTYPE=INS;SVLEN=543;HOMPCT=3.2;REMAP=partial;GCPCT=79;GTCNT=2,0,0,1;NumNeighbors=6;NeighId=1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.592739 GT:DP:AD ./.:37:13,24 1/1:24:6,18 ./.:42:19,23 -chr20 279069 . A AGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGCGGGACGGAGGGAGGGC 60 . QNAME=cluster23_scaffold_2;QSTART=25416710;QSTRAND=-;SVTYPE=INS;SVLEN=514;HOMPCT=3.2;REMAP=partial;GCPCT=78;GTCNT=2,0,1,0;NumNeighbors=6;NeighId=1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.582903 GT:DP:AD ./.:39:23,16 ./.:26:5,21 0/1:21:11,10 -chr20 279069 . A AGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGCGGGACGGAGGGAGGGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=232808;QSTRAND=+;SVTYPE=INS;SVLEN=438;HOMPCT=3.2;REMAP=partial;GCPCT=79;GTCNT=2,0,1,0;NumNeighbors=6;NeighId=1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.589779 GT:DP:AD 0/1:26:5,21 ./.:30:8,22 ./.:38:15,23 -chr20 279098 . G GGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGCGGGACGGAGGGAGGGACGGAGGGCGGGACGGAGGGAC 60 . QNAME=cluster23_scaffold_3;QSTART=25432493;QSTRAND=-;SVTYPE=INS;SVLEN=179;HOMPCT=3.2;REMAP=tandem;REMAPHits=chr20:278929-279088.81,chr20:278933-279100.92;GCPCT=78;GTCNT=2,0,1,0;NumNeighbors=6;NeighId=1;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.590685 GT:DP:AD ./.:25:20,5 ./.:28:17,11 1/0:23:13,10 -chr20 279102 . C G 60 . QNAME=cluster23_scaffold_3;QSTART=25432489;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:40:22,18 ./.:29:22,7 1|0:42:19,23 -chr20 279177 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=258365;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:30:10,20 ./.:29:6,23 0|1:32:15,17 -chr20 279328 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=258516;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,2,1;ADCNT=0,3,0,0;LCR=0 GT:DP:AD 1|0:14:6,8 ./.:17:8,9 1|0:12:5,7 -chr20 279759 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=258947;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:33:13,20 ./.:47:25,22 1|0:35:19,16 -chr20 279880 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=259068;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:33:13,20 ./.:37:23,14 1|0:21:9,12 -chr20 280083 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=25431508;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:29:15,14 ./.:30:13,17 1|0:25:18,7 -chr20 280230 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=259418;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:28:7,21 ./.:32:11,21 ./.:15:5,10 -chr20 280339 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=259527;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:47:22,25 ./.:25:17,8 ./.:35:23,12 -chr20 280403 . TAAC T 60 . QNAME=cluster23_scaffold_3;QSTART=25431252;QSTRAND=-;GCPCT=25;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.75 GT:DP:AD ./.:20:15,5 ./.:31:23,8 1|0:39:16,23 -chr20 280418 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25431240;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:41:25,16 ./.:18:5,13 1|0:42:25,17 -chr20 280635 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25431023;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:41:18,23 ./.:29:21,8 1|0:34:10,24 -chr20 281010 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=260198;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:45:23,22 ./.:44:20,24 ./.:28:10,18 -chr20 281470 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=260658;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:27:7,20 ./.:38:23,15 1|0:26:8,18 -chr20 281585 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25430073;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:45:24,21 ./.:31:6,25 1|0:20:15,5 -chr20 281929 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=261117;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:29:16,13 ./.:43:20,23 1|0:32:14,18 -chr20 282596 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=261784;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:13:5,8 ./.:44:23,21 ./.:27:22,5 -chr20 282775 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=261963;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:35:24,11 ./.:35:12,23 ./.:26:8,18 -chr20 283019 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=262207;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:39:19,20 ./.:17:8,9 ./.:20:10,10 -chr20 283328 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=262516;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:29:6,23 ./.:19:5,14 ./.:30:20,10 -chr20 283411 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=262599;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:14:6,8 ./.:32:18,14 ./.:37:21,16 -chr20 283535 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=262723;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:18:7,11 ./.:37:17,20 ./.:28:7,21 -chr20 283694 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=262883;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 1|0:31:21,10 ./.:37:20,17 ./.:26:5,21 -chr20 283724 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=262913;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:19:13,6 ./.:24:5,19 ./.:26:14,12 -chr20 283802 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25427856;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:37:14,23 ./.:27:16,11 1|0:35:18,17 -chr20 283857 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=263046;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:30:25,5 ./.:22:14,8 ./.:29:7,22 -chr20 284338 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=263527;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:37:12,25 ./.:45:24,21 ./.:22:8,14 -chr20 284356 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=263545;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:28:12,16 ./.:29:5,24 ./.:35:11,24 -chr20 284597 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=263786;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:17:11,6 ./.:30:17,13 1|0:39:20,19 -chr20 284724 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=263913;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD 1|0:32:18,14 ./.:25:13,12 1|0:28:15,13 -chr20 284881 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=264070;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:41:16,25 ./.:42:23,19 1|0:17:9,8 -chr20 285327 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=264516;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:30:12,18 ./.:43:19,24 1|0:26:15,11 -chr20 285600 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=264789;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:35:12,23 ./.:38:17,21 1|0:26:18,8 -chr20 285621 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=264810;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:39:21,18 ./.:22:15,7 1|0:39:21,18 -chr20 285738 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=264927;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:37:16,21 ./.:40:21,19 ./.:40:24,16 -chr20 286151 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=265340;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:11:5,6 ./.:39:23,16 ./.:20:8,12 -chr20 286163 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=265353;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,3,0,0;LCR=0.5 GT:DP:AD 1|0:13:6,7 ./.:19:10,9 ./.:18:12,6 -chr20 286710 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=265898;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:14:8,6 ./.:21:12,9 1|0:28:5,23 -chr20 286812 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=266000;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:29:19,10 ./.:28:7,21 1|0:43:21,22 -chr20 287237 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=266425;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:25:20,5 ./.:36:17,19 1|0:37:24,13 -chr20 287305 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=266493;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:37:19,18 ./.:30:14,16 1|0:33:23,10 -chr20 287629 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=266817;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:18:8,10 ./.:36:23,13 1|0:39:14,25 -chr20 287833 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=267021;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:14:8,6 ./.:27:6,21 1|0:30:16,14 -chr20 287837 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=267025;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:19:6,13 ./.:32:13,19 ./.:31:20,11 -chr20 287876 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=267064;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:24:15,9 ./.:26:15,11 1|0:20:14,6 -chr20 287908 . C CAAAAAAAA 60 . QNAME=cluster23_scaffold_3;QSTART=25423742;QSTRAND=-;GCPCT=11;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.251629 GT:DP:AD ./.:40:18,22 ./.:38:21,17 1|0:29:24,5 -chr20 287908 . C CAAAAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=267097;QSTRAND=+;GCPCT=10;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.234498 GT:DP:AD 1|0:26:10,16 ./.:30:17,13 ./.:44:21,23 -chr20 287932 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=267129;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:32:15,17 ./.:27:14,13 ./.:23:14,9 -chr20 288158 . C CTTTCTTTTTCTT 60 . QNAME=HG002-S9-H1-000001F;QSTART=267356;QSTRAND=+;GCPCT=23;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.389675 GT:DP:AD 1|0:36:16,20 ./.:34:16,18 ./.:30:5,25 -chr20 288174 . C CT 60 . QNAME=cluster23_scaffold_2;QSTART=25407604;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:23:6,17 ./.:33:11,22 0|1:46:25,21 -chr20 288174 . C CTTTTTCTTTTTCTT 60 . QNAME=cluster23_scaffold_3;QSTART=25423462;QSTRAND=-;GCPCT=20;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.360964 GT:DP:AD ./.:27:11,16 ./.:31:8,23 1|0:41:16,25 -chr20 288365 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=267574;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:32:7,25 ./.:44:21,23 1|0:39:18,21 -chr20 288516 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=267725;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:18:13,5 ./.:25:9,16 1|0:32:16,16 -chr20 289049 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=268258;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:22:5,17 ./.:39:16,23 1|0:24:14,10 -chr20 289196 . A ACC 60 . QNAME=HG002-S9-H1-000001F;QSTART=268406;QSTRAND=+;GCPCT=66;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.459148 GT:DP:AD 1|0:37:12,25 ./.:27:19,8 ./.:28:23,5 -chr20 289196 . A ACCC 60 . QNAME=cluster23_scaffold_3;QSTART=25422437;QSTRAND=-;GCPCT=75;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.405639 GT:DP:AD ./.:28:5,23 ./.:28:15,13 1|0:44:21,23 -chr20 289773 . TC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=268985;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD 1|0:29:19,10 ./.:35:22,13 1|0:27:6,21 -chr20 289787 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=268997;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD 1|0:34:22,12 ./.:27:17,10 1|0:30:18,12 -chr20 289993 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=269203;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:43:25,18 ./.:29:6,23 1|0:41:23,18 -chr20 290134 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=269344;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:46:23,23 ./.:48:24,24 1|0:18:13,5 -chr20 290494 . G GC 60 . QNAME=HG002-S9-H2-000001F;QSTART=244671;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 0|1:18:12,6 1|1:47:22,25 0|1:30:5,25 -chr20 290563 . A ATT 60 . QNAME=cluster23_scaffold_2;QSTART=25405212;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.459148 GT:DP:AD ./.:40:20,20 ./.:33:10,23 0|1:27:15,12 -chr20 290584 . T TTA 60 . QNAME=HG002-S9-H1-000001F;QSTART=269795;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.459148 GT:DP:AD 1|0:16:10,6 ./.:32:16,16 ./.:18:10,8 -chr20 290584 . T TTTA 60 . QNAME=cluster23_scaffold_3;QSTART=25421047;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.405639 GT:DP:AD ./.:44:24,20 ./.:23:10,13 1|0:27:17,10 -chr20 291169 . TTCTC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=270382;QSTRAND=+;GCPCT=40;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.485475 GT:DP:AD 1|0:41:25,16 ./.:27:21,6 1|0:30:13,17 -chr20 291796 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=271004;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:30:23,7 ./.:11:6,5 1|0:27:14,13 -chr20 291952 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=271160;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:25:15,10 1|1:23:5,18 1|1:37:23,14 -chr20 292806 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=272015;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 1|0:33:17,16 ./.:28:7,21 1|0:22:12,10 -chr20 293331 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25418305;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:45:25,20 ./.:44:24,20 1|0:20:15,5 -chr20 293433 . GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=272641;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD 1|0:36:16,20 ./.:22:17,5 ./.:32:25,7 -chr20 293692 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=272898;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:35:25,10 ./.:29:8,21 1|0:17:5,12 -chr20 294073 . AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=273280;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|0:32:23,9 ./.:34:20,14 ./.:46:22,24 -chr20 296976 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=251153;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:33:17,16 1|1:21:16,5 0|1:25:8,17 -chr20 297051 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=251228;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:24:6,18 1|1:26:10,16 0|1:25:15,10 -chr20 297191 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=251368;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:43:24,19 1|1:32:10,22 0|1:30:9,21 -chr20 297482 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=276688;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|0:23:7,16 ./.:29:23,6 1|0:40:16,24 -chr20 297874 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=252051;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:18:13,5 1|1:44:23,21 0|1:23:6,17 -chr20 298162 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=277366;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:24:19,5 ./.:25:8,17 0|1:36:25,11 -chr20 298541 . C T 60 . QNAME=cluster19_000000F;QSTART=258279;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:30:6,24 0|1:40:23,17 ./.:21:5,16 -chr20 298839 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=278043;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:33:9,24 ./.:44:19,25 1|0:26:15,11 -chr20 299130 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=278334;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:36:15,21 ./.:50:25,25 1|0:40:20,20 -chr20 301074 . G C 60 . QNAME=cluster23_scaffold_2;QSTART=25394701;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:35:20,15 ./.:19:5,14 0|1:25:5,20 -chr20 301778 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=280982;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0 GT:DP:AD 1|0:22:17,5 ./.:32:25,7 1|0:32:25,7 -chr20 302639 . T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=281844;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD 1|0:26:20,6 ./.:40:21,19 1|0:30:24,6 -chr20 302891 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=282096;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:36:12,24 1|1:41:21,20 1|1:20:6,14 -chr20 303233 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=282438;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:26:18,8 1|1:47:22,25 1|1:26:12,14 -chr20 303404 . C A 60 . QNAME=cluster19_000000F;QSTART=263142;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:24:17,7 0|1:39:22,17 ./.:28:18,10 -chr20 303430 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=282635;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:25:16,9 1|0:22:9,13 1|1:43:18,25 -chr20 304111 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=283316;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:27:17,10 1|0:30:7,23 1|1:46:25,21 -chr20 304170 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=283375;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:29:6,23 1|1:16:7,9 1|1:26:14,12 -chr20 304190 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=283395;QSTRAND=+;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:43:23,20 ./.:25:7,18 1|1:14:7,7 -chr20 304257 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=258434;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:37:22,15 1|0:20:5,15 0|1:17:12,5 -chr20 304335 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=258512;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:33:12,21 1|0:34:15,19 0|1:28:23,5 -chr20 304365 . G C 60 . QNAME=cluster19_000000F;QSTART=264103;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:39:19,20 0|1:32:12,20 ./.:24:7,17 -chr20 304375 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25391400;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:20:6,14 ./.:29:7,22 0|1:40:21,19 -chr20 304376 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=258553;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:39:16,23 1|1:33:15,18 ./.:36:24,12 -chr20 304377 . G C 60 . QNAME=cluster23_scaffold_2;QSTART=25391398;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:23:10,13 ./.:28:5,23 0|1:28:22,6 -chr20 304450 . T C 60 . QNAME=cluster19_000000F;QSTART=264188;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:37:18,19 0|1:23:14,9 ./.:31:25,6 -chr20 304460 . T C 60 . QNAME=cluster19_000000F;QSTART=264198;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:34:15,19 0|1:33:19,14 ./.:36:13,23 -chr20 304461 . T C 60 . QNAME=cluster19_000000F;QSTART=264199;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:35:22,13 0|1:32:18,14 ./.:24:7,17 -chr20 304463 . A T 60 . QNAME=cluster19_000000F;QSTART=264201;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:29:13,16 0|1:49:24,25 ./.:17:12,5 -chr20 304504 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=258682;QSTRAND=+;GCPCT=50;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 0|1:39:22,17 1|0:41:25,16 0|1:16:8,8 -chr20 304679 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=283884;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:32:8,24 ./.:42:23,19 1|0:26:5,21 -chr20 304705 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=258881;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:28:8,20 1|1:31:25,6 0|1:15:9,6 -chr20 305012 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=284217;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:35:15,20 1|1:20:6,14 1|1:33:12,21 -chr20 305384 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=284589;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:29:19,10 0|1:21:14,7 1|0:35:23,12 -chr20 305403 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=284608;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:35:11,24 1|1:21:7,14 1|1:43:23,20 -chr20 305843 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=260019;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:29:20,9 1|0:30:17,13 0|1:38:15,23 -chr20 305871 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=260047;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:39:20,19 1|1:44:23,21 0|1:24:12,12 -chr20 305882 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=260058;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:21:10,11 1|1:48:25,23 0|1:29:19,10 -chr20 305943 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=285148;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:43:19,24 1|1:34:16,18 1|1:22:13,9 -chr20 306004 . TAAATA T 60 . QNAME=cluster19_000000F;QSTART=265743;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0.459148 GT:DP:AD ./.:38:19,19 0|1:14:8,6 ./.:45:24,21 -chr20 306194 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=285399;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:32:18,14 1|1:41:17,24 1|1:39:23,16 -chr20 306232 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=285438;QSTRAND=+;GCPCT=50;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 1|0:29:12,17 0|1:23:6,17 1|0:23:5,18 -chr20 306268 . A ACCAGGCTGGAGTGCAGTGGCTCACTGCGTGGCTCGCTACAGCCTACAACTCCTGGGCTCCAGCAATCCTGCTGCCCCAGCCTCCTGTGTAACTGAGACTACAGGCACGCACCACCACACCCAGCTAATGTTTTCTTTCTTTTTTTTTTTTTTGAGATGAACTCTCACTCTGTTGC 60 . QNAME=cluster19_000000F;QSTART=25455794;QSTRAND=-;SVTYPE=INS;SVLEN=175;HOMPCT=33.3;REMAP=tandem;REMAPHits=chr20:306267-306420.86;GCPCT=52;GTCNT=2,0,0,1;NumNeighbors=1;NeighId=3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.982307 GT:DP:AD ./.:33:15,18 1/1:35:11,24 ./.:34:9,25 -chr20 306268 . A ACCAGGCTGGAGTGCAGTGGCTCACTGCGTGGCTCGCTACAGCCTACAACTCCTGGGCTCCAGCAATCCTGCTGCCCCAGCCTCCTGTGTAACTGAGACTACAGGCACGCACCACCACACCCAGCTAATTTTTTCTTTCTTTTTTTTTTTTTTGAGATGAACTCTCACTCTGTTGC 60 . QNAME=HG002-S9-H1-000001F;QSTART=285475;QSTRAND=+;SVTYPE=INS;SVLEN=175;HOMPCT=33.3;REMAP=tandem;REMAPHits=chr20:306267-306420.86;GCPCT=51;GTCNT=1,0,0,2;NumNeighbors=1;NeighId=3;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.980782 GT:DP:AD 1/1:34:18,16 ./.:32:19,13 1/1:25:13,12 -chr20 306413 . T TC 60 . QNAME=cluster23_scaffold_2;QSTART=25389187;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:32:25,7 ./.:21:7,14 0|1:26:11,15 -chr20 306414 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=260765;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:37:21,16 1|0:46:25,21 ./.:36:11,25 -chr20 306535 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=260886;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:36:22,14 1|0:37:14,23 0|1:16:11,5 -chr20 306582 . A G 60 . QNAME=cluster19_000000F;QSTART=266491;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:33:9,24 0|1:22:12,10 ./.:20:11,9 -chr20 306627 . T G 60 . QNAME=cluster19_000000F;QSTART=25455435;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:33:15,18 1|0:30:22,8 ./.:24:13,11 -chr20 306642 . T C 60 . QNAME=cluster19_000000F;QSTART=25455420;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:32:10,22 1|1:27:15,12 ./.:29:12,17 -chr20 306653 . C T 60 . QNAME=cluster19_000000F;QSTART=25455409;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:49:24,25 1|0:33:13,20 ./.:19:6,13 -chr20 306667 . T C 60 . QNAME=cluster19_000000F;QSTART=25455395;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:28:5,23 1|0:45:22,23 ./.:35:21,14 -chr20 306742 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=261093;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:25:15,10 ./.:32:9,23 0|1:14:6,8 -chr20 306776 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=286157;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:33:23,10 ./.:21:11,10 1|0:33:13,20 -chr20 306885 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=286266;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:27:9,18 1|1:31:23,8 1|1:31:17,14 -chr20 306993 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=286374;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0 GT:DP:AD 1|0:30:25,5 1|1:25:18,7 1|0:27:18,9 -chr20 307589 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=286970;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:32:12,20 1|0:31:16,15 1|1:26:16,10 -chr20 307693 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=262044;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:34:25,9 ./.:19:13,6 ./.:33:10,23 -chr20 307712 . CA C 60 . QNAME=cluster19_000000F;QSTART=25454350;QSTRAND=-;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:36:20,16 1|0:33:9,24 0|1:21:13,8 -chr20 308128 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=262479;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:18:11,7 0|1:40:25,15 ./.:41:18,23 -chr20 308132 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=287513;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:43:21,22 1|1:24:8,16 1|1:29:13,16 -chr20 308261 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=262612;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:25:9,16 0|1:30:5,25 ./.:37:25,12 -chr20 308278 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=262629;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:24:12,12 1|1:32:10,22 0|1:45:22,23 -chr20 308352 . T C 60 . QNAME=cluster19_000000F;QSTART=25453711;QSTRAND=-;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:16:8,8 1|0:33:13,20 0|1:27:22,5 -chr20 308718 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=263069;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:23:15,8 1|1:23:17,6 0|1:24:7,17 -chr20 308968 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=288349;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:23:7,16 1|1:17:6,11 1|1:11:6,5 -chr20 309141 . A G 60 . QNAME=cluster19_000000F;QSTART=25452922;QSTRAND=-;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:27:10,17 1|0:37:12,25 0|1:33:14,19 -chr20 309613 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=263964;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:38:22,16 ./.:22:16,6 ./.:34:22,12 -chr20 309637 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=289018;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:29:24,5 ./.:12:7,5 1|0:39:24,15 -chr20 309639 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=289020;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:36:18,18 ./.:25:9,16 1|0:41:21,20 -chr20 309653 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=289034;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:46:24,22 ./.:15:8,7 1|0:32:23,9 -chr20 309674 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=289055;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:39:16,23 1|1:35:14,21 1|1:37:25,12 -chr20 310521 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=289902;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:21:6,15 1|0:34:20,14 0|1:13:7,6 -chr20 310522 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=289903;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:19:9,10 1|0:29:8,21 0|1:42:21,21 -chr20 310523 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=289904;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0 GT:DP:AD 1|1:27:20,7 1|0:21:13,8 0|1:23:18,5 -chr20 310719 . A AT 60 . QNAME=HG002-S9-H1-000001F;QSTART=290101;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 1|1:35:20,15 1|0:31:6,25 0|1:45:24,21 -chr20 311107 . C G 60 . QNAME=cluster19_000000F;QSTART=271016;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:35:22,13 0|1:32:12,20 1|0:38:25,13 -chr20 311145 . T G 60 . QNAME=cluster19_000000F;QSTART=271054;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:33:10,23 0|1:32:13,19 1|0:30:7,23 -chr20 311237 . C T 60 . QNAME=cluster19_000000F;QSTART=271146;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:39:21,18 0|1:28:8,20 1|0:25:8,17 -chr20 311327 . G C 60 . QNAME=cluster19_000000F;QSTART=271236;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:31:24,7 0|1:30:10,20 1|0:34:21,13 -chr20 311347 . C CATTATT 60 . QNAME=cluster19_000000F;QSTART=271257;QSTRAND=+;GCPCT=14;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.689392 GT:DP:AD ./.:21:11,10 0|1:32:12,20 1|0:19:8,11 -chr20 311683 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=291065;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:39:20,19 1|0:46:22,24 0|1:40:16,24 -chr20 311774 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=291156;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0 GT:DP:AD 1|0:29:21,8 1|1:16:7,9 0|1:18:12,6 -chr20 311791 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=291173;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:32:17,15 1|1:22:14,8 1|1:34:17,17 -chr20 312718 . A AT 60 . QNAME=cluster23_scaffold_2;QSTART=25382881;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:46:21,25 ./.:18:10,8 0|1:25:15,10 -chr20 314417 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=293799;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:18:7,11 ./.:16:9,7 ./.:43:19,24 -chr20 314431 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=293813;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:48:23,25 ./.:40:23,17 ./.:25:16,9 -chr20 314495 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=268847;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:31:6,25 ./.:34:24,10 ./.:38:22,16 -chr20 314567 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25381032;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:21:7,14 ./.:41:18,23 0|1:18:9,9 -chr20 314595 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=268947;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:30:15,15 ./.:36:15,21 1|0:27:12,15 -chr20 314668 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=269020;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:40:19,21 ./.:27:7,20 1|0:33:11,22 -chr20 314877 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=269229;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 0|1:21:13,8 ./.:15:6,9 1|0:37:25,12 -chr20 314905 . C CTT 60 . QNAME=cluster23_scaffold_2;QSTART=25380692;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0.459148 GT:DP:AD ./.:37:25,12 ./.:21:14,7 0|1:30:22,8 -chr20 314905 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=269258;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 0|1:34:9,25 ./.:19:6,13 ./.:24:15,9 -chr20 315222 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=269573;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:47:25,22 ./.:35:23,12 1|0:26:6,20 -chr20 315528 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=269879;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:30:20,10 ./.:28:14,14 1|0:32:7,25 -chr20 315724 . G GTATTAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=270076;QSTRAND=+;GCPCT=28;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.921185 GT:DP:AD 0|1:40:23,17 ./.:35:14,21 1|0:28:16,12 -chr20 316587 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=295969;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:39:14,25 ./.:23:5,18 ./.:37:17,20 -chr20 316724 . G GT 60 . QNAME=cluster23_scaffold_2;QSTART=25378872;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:17:5,12 ./.:34:11,23 0|1:34:12,22 -chr20 316724 . GTT G 60 . QNAME=HG002-S9-H2-000001F;QSTART=271082;QSTRAND=+;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0.459148 GT:DP:AD 0|1:12:5,7 ./.:21:13,8 ./.:44:19,25 -chr20 316724 . GTTT G 60 . QNAME=cluster23_scaffold_3;QSTART=25394724;QSTRAND=-;GCPCT=25;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.405639 GT:DP:AD ./.:31:19,12 ./.:23:13,10 1|0:31:14,17 -chr20 317772 . GA G 60 . QNAME=HG002-S9-H2-000001F;QSTART=272128;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 0|1:28:8,20 ./.:34:13,21 1|0:22:7,15 -chr20 318091 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=272445;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:35:17,18 ./.:30:16,14 1|0:31:18,13 -chr20 318388 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=272742;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:26:5,21 ./.:18:11,7 1|0:16:11,5 -chr20 318854 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=273208;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:17:10,7 1|1:26:10,16 1|1:15:9,6 -chr20 318941 . AC A 60 . QNAME=HG002-S9-H2-000001F;QSTART=273296;QSTRAND=+;GCPCT=50;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 0|1:35:15,20 1|1:21:15,6 1|1:31:8,23 -chr20 318943 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=273296;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:44:23,21 1|1:22:16,6 1|1:29:16,13 -chr20 318971 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=298353;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:43:19,24 1|1:38:21,17 1|0:31:10,21 -chr20 319115 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=273468;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:41:22,19 1|1:29:12,17 1|0:16:5,11 -chr20 319367 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=298749;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:33:11,22 ./.:28:7,21 ./.:30:17,13 -chr20 319623 . G C 60 . QNAME=cluster19_000000F;QSTART=25442440;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:37:23,14 1|0:24:5,19 ./.:27:5,22 -chr20 319633 . CCA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=299016;QSTRAND=+;GCPCT=66;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.459148 GT:DP:AD 1|1:47:22,25 0|1:36:13,23 1|0:37:15,22 -chr20 319838 . G A 60 . QNAME=cluster19_000000F;QSTART=25442225;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:16:9,7 1|0:37:15,22 ./.:29:12,17 -chr20 320255 . CA C 60 . QNAME=cluster23_scaffold_2;QSTART=25375342;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:27:9,18 ./.:37:25,12 0|1:31:9,22 -chr20 321250 . A G 60 . QNAME=cluster19_000000F;QSTART=25440813;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:32:11,21 1|0:31:15,16 ./.:37:23,14 -chr20 326089 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=305469;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:33:14,19 0|1:44:19,25 ./.:31:20,11 -chr20 328517 . AT A 60 . QNAME=cluster19_000000F;QSTART=25433546;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:31:20,11 1|1:29:5,24 0|1:20:5,15 -chr20 328517 . ATT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=307898;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.459148 GT:DP:AD 1|1:29:22,7 ./.:41:23,18 1|0:33:25,8 -chr20 328569 . G GA 60 . QNAME=cluster23_scaffold_3;QSTART=25382887;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:38:15,23 ./.:39:21,18 1|0:31:7,24 -chr20 328569 . GA G 60 . QNAME=cluster19_000000F;QSTART=25433495;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD ./.:17:9,8 1|0:46:25,21 ./.:28:21,7 -chr20 328717 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25382739;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:32:24,8 ./.:37:24,13 1|0:37:21,16 -chr20 336200 . C CTCT 60 . QNAME=cluster23_scaffold_3;QSTART=25375253;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.5 GT:DP:AD ./.:37:25,12 ./.:34:23,11 1|0:26:17,9 -chr20 336200 . C CTCTTCT 60 . QNAME=HG002-S9-H1-000001F;QSTART=315579;QSTRAND=+;GCPCT=42;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.492614 GT:DP:AD 1|0:34:11,23 0|1:25:14,11 ./.:46:21,25 -chr20 336200 . CTCT C 60 . QNAME=cluster23_scaffold_2;QSTART=25359399;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:38:17,21 ./.:24:13,11 0|1:26:18,8 -chr20 336200 . CTCTTCTTCT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=290550;QSTRAND=+;GCPCT=40;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.485475 GT:DP:AD 0|1:43:21,22 ./.:31:14,17 ./.:34:22,12 -chr20 336263 . TTC T 60 . QNAME=cluster19_000000F;QSTART=25425802;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.459148 GT:DP:AD ./.:27:20,7 1|0:34:18,16 ./.:29:11,18 -chr20 336308 . CTCTTCCTCTTCT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=315693;QSTRAND=+;GCPCT=46;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.497864 GT:DP:AD 1|1:30:20,10 0|1:42:25,17 0|1:31:24,7 -chr20 336308 . CTCTTCCTCTTCTTCT C 60 . QNAME=cluster23_scaffold_3;QSTART=25375145;QSTRAND=-;GCPCT=43;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.49435 GT:DP:AD ./.:28:5,23 ./.:41:24,17 1|0:33:8,25 -chr20 336336 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25375132;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:31:24,7 ./.:26:16,10 1|0:37:13,24 -chr20 338577 . A ATG 60 . QNAME=HG002-S9-H1-000001F;QSTART=317950;QSTRAND=+;GCPCT=33;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.792481 GT:DP:AD 1|0:48:24,24 0|1:33:16,17 1|1:37:17,20 -chr20 340238 . CTTTCT C 60 . QNAME=cluster23_scaffold_2;QSTART=25355374;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.459148 GT:DP:AD ./.:34:24,10 ./.:35:18,17 0|1:16:7,9 -chr20 340763 . C T 60 . QNAME=cluster19_000000F;QSTART=25421304;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:30:11,19 1|0:24:16,8 ./.:34:16,18 -chr20 340858 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=295186;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:18:11,7 ./.:32:15,17 ./.:16:10,6 -chr20 340865 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=295193;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:25:7,18 ./.:38:13,25 ./.:36:21,15 -chr20 341112 . T TCACACA 60 . QNAME=HG002-S9-H2-000001F;QSTART=295441;QSTRAND=+;GCPCT=42;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.724408 GT:DP:AD 0|1:38:21,17 ./.:29:15,14 ./.:20:11,9 -chr20 341505 . AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=320880;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0.5 GT:DP:AD 1|0:29:19,10 ./.:16:11,5 ./.:15:10,5 -chr20 341505 . ATTTTT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=295840;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.325011 GT:DP:AD 0|1:28:23,5 ./.:34:16,18 ./.:37:20,17 -chr20 341968 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=296297;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:15:5,10 1|0:34:19,15 ./.:32:11,21 -chr20 342602 . C CTTT 60 . QNAME=HG002-S9-H1-000001F;QSTART=321976;QSTRAND=+;GCPCT=25;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.405639 GT:DP:AD 1|0:26:9,17 ./.:30:5,25 ./.:30:21,9 -chr20 342602 . C CTTTTT 60 . QNAME=cluster19_000000F;QSTART=302510;QSTRAND=+;GCPCT=16;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.325011 GT:DP:AD ./.:30:9,21 0|1:44:19,25 ./.:46:21,25 -chr20 342602 . C CTTTTTTT 60 . QNAME=cluster23_scaffold_2;QSTART=25353008;QSTRAND=-;GCPCT=12;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.271782 GT:DP:AD ./.:32:14,18 ./.:45:25,20 0|1:26:5,21 -chr20 342602 . C CTTTTTTTT 60 . QNAME=cluster23_scaffold_3;QSTART=25368856;QSTRAND=-;GCPCT=11;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0.251629 GT:DP:AD ./.:22:15,7 ./.:19:10,9 1|0:31:25,6 -chr20 342602 . CTTTTTTTT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=296932;QSTRAND=+;GCPCT=11;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.251629 GT:DP:AD 0|1:20:15,5 ./.:39:25,14 ./.:25:12,13 -chr20 342621 . T TTTC 60 . QNAME=cluster19_000000F;QSTART=25419443;QSTRAND=-;GCPCT=25;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.405639 GT:DP:AD ./.:44:19,25 1|0:35:16,19 ./.:24:7,17 -chr20 342641 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=296962;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:29:8,21 ./.:41:21,20 ./.:32:8,24 -chr20 342664 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=296985;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:46:24,22 ./.:33:18,15 ./.:29:16,13 -chr20 342939 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=297260;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:36:22,14 ./.:42:25,17 ./.:39:21,18 -chr20 343326 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=297647;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:36:16,20 ./.:34:9,25 ./.:46:25,21 -chr20 343479 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=297800;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:42:23,19 ./.:26:11,15 ./.:26:5,21 -chr20 343825 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=298146;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:46:23,23 ./.:34:24,10 ./.:45:22,23 -chr20 343865 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=298186;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 0|1:17:12,5 ./.:15:8,7 ./.:36:22,14 -chr20 343893 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=298214;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:36:21,15 ./.:27:15,12 ./.:17:10,7 -chr20 344097 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25367360;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD ./.:37:19,18 ./.:37:23,14 1|0:34:20,14 -chr20 344097 . C CAA 60 . QNAME=HG002-S9-H2-000001F;QSTART=298419;QSTRAND=+;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.459148 GT:DP:AD 0|1:39:24,15 ./.:29:6,23 ./.:42:17,25 -chr20 344354 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=298677;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:33:10,23 ./.:22:6,16 ./.:32:10,22 -chr20 344458 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=298781;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:40:22,18 ./.:30:17,13 ./.:43:22,21 -chr20 344798 . T G 60 . QNAME=cluster23_scaffold_3;QSTART=25366659;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:25:9,16 ./.:32:13,19 1|0:21:14,7 -chr20 345372 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=299695;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:34:15,19 ./.:19:9,10 ./.:31:22,9 -chr20 345506 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=299829;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:23:6,17 ./.:29:23,6 ./.:36:15,21 -chr20 345647 . T TACAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=299971;QSTRAND=+;GCPCT=40;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.760964 GT:DP:AD 0|1:22:5,17 ./.:19:14,5 ./.:44:23,21 -chr20 348484 . C CGTGTGTGTGT 60 . QNAME=HG002-S9-H1-000001F;QSTART=327861;QSTRAND=+;GCPCT=54;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.674294 GT:DP:AD 1|0:34:21,13 ./.:25:5,20 1|0:26:6,20 -chr20 348484 . C CGTGTGTGTGTGT 60 . QNAME=cluster19_000000F;QSTART=308397;QSTRAND=+;GCPCT=53;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0.65716 GT:DP:AD ./.:34:21,13 0|1:26:15,11 0|1:16:5,11 -chr20 348484 . CGTGTGT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=302812;QSTRAND=+;GCPCT=57;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.724408 GT:DP:AD 0|1:35:15,20 ./.:34:23,11 ./.:17:12,5 -chr20 349198 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=303519;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:35:14,21 ./.:31:20,11 ./.:17:6,11 -chr20 350477 . T TA 60 . QNAME=cluster23_scaffold_3;QSTART=25360969;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:30:9,21 ./.:28:11,17 1|0:31:22,9 -chr20 350477 . TA T 60 . QNAME=HG002-S9-H2-000001F;QSTART=304799;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 0|1:21:14,7 ./.:34:10,24 ./.:39:14,25 -chr20 350646 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25360799;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:30:15,15 ./.:12:7,5 1|0:27:7,20 -chr20 350646 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=330033;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD 1|0:32:20,12 1|1:40:22,18 ./.:33:22,11 -chr20 350660 . AAAAAAAAAAAAAAAAAG A 60 . QNAME=HG002-S9-H2-000001F;QSTART=304981;QSTRAND=+;GCPCT=5;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.154772 GT:DP:AD 0|1:17:5,12 ./.:21:9,12 ./.:26:17,9 -chr20 351164 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=305467;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:36:13,23 ./.:43:23,20 ./.:29:21,8 -chr20 352819 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=332204;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:42:19,23 1|1:38:23,15 1|1:22:12,10 -chr20 353673 . TC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=333059;QSTRAND=+;GCPCT=50;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 1|0:31:16,15 1|1:40:18,22 1|1:44:19,25 -chr20 354581 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=308884;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:35:16,19 ./.:14:8,6 ./.:24:18,6 -chr20 355283 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=309586;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:20:5,15 ./.:41:25,16 ./.:32:19,13 -chr20 356342 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=335727;QSTRAND=+;GCPCT=50;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD 1|0:36:24,12 1|1:21:11,10 1|1:28:13,15 -chr20 356748 . ACC A 60 . QNAME=cluster19_000000F;QSTART=25405319;QSTRAND=-;GCPCT=66;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.459148 GT:DP:AD ./.:30:18,12 1|0:26:12,14 ./.:44:23,21 -chr20 356924 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=336307;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:30:8,22 1|1:14:9,5 1|1:18:10,8 -chr20 358579 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=337963;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 1|0:33:17,16 1|0:34:14,20 ./.:41:16,25 -chr20 358579 . CTT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=312883;QSTRAND=+;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.459148 GT:DP:AD 0|1:27:19,8 ./.:26:10,16 ./.:18:12,6 -chr20 358585 . T C 60 . QNAME=cluster19_000000F;QSTART=25403485;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:11:6,5 1|0:26:10,16 ./.:25:19,6 -chr20 358586 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=312887;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:35:24,11 ./.:34:9,25 ./.:44:20,24 -chr20 358841 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=338223;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:16:10,6 0|1:28:8,20 1|1:26:5,21 -chr20 359400 . GCAC G 60 . QNAME=HG002-S9-H1-000001F;QSTART=338783;QSTRAND=+;GCPCT=75;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.75 GT:DP:AD 1|0:25:8,17 0|1:32:14,18 1|1:31:13,18 -chr20 359869 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=314170;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:24:14,10 1|0:41:16,25 ./.:17:10,7 -chr20 359913 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=314214;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:43:19,24 1|0:36:23,13 ./.:31:7,24 -chr20 359914 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=314215;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:21:12,9 1|0:34:19,15 ./.:20:12,8 -chr20 359916 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=314217;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:22:14,8 1|0:37:21,16 ./.:42:22,20 -chr20 359924 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=314225;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:30:22,8 1|0:28:5,23 ./.:24:11,13 -chr20 359930 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=314231;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:37:20,17 1|0:37:18,19 ./.:28:17,11 -chr20 359931 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=314232;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 0|1:18:10,8 1|0:25:13,12 ./.:34:22,12 -chr20 359947 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=314248;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:22:7,15 1|0:43:23,20 ./.:12:5,7 -chr20 359953 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=314254;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 0|1:11:6,5 1|0:26:16,10 ./.:30:20,10 -chr20 359954 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=314255;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:40:22,18 1|0:44:19,25 ./.:26:19,7 -chr20 359955 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=314256;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:30:15,15 1|0:26:9,17 ./.:31:16,15 -chr20 359960 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=314261;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:32:7,25 1|0:31:25,6 ./.:42:22,20 -chr20 359969 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=314270;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:27:8,19 1|0:31:21,10 ./.:39:15,24 -chr20 359998 . C CA 60 . QNAME=HG002-S9-H2-000001F;QSTART=314300;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 0|1:40:23,17 ./.:35:17,18 1|0:31:14,17 -chr20 360554 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=314856;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:26:9,17 1|0:32:13,19 ./.:28:15,13 -chr20 360556 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=314858;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:38:20,18 1|0:36:18,18 ./.:24:15,9 -chr20 360622 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=314924;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 0|1:11:6,5 1|0:32:20,12 ./.:29:15,14 -chr20 361302 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=315604;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:48:23,25 1|0:34:25,9 ./.:24:15,9 -chr20 362051 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=316353;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:33:11,22 1|0:38:18,20 ./.:29:16,13 -chr20 362052 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=316354;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:40:24,16 1|0:34:14,20 ./.:29:8,21 -chr20 362185 . G GA 60 . QNAME=cluster23_scaffold_3;QSTART=25349263;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:37:17,20 ./.:31:12,19 1|0:26:12,14 -chr20 362679 . A ATG 60 . QNAME=HG002-S9-H2-000001F;QSTART=316982;QSTRAND=+;GCPCT=33;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.792481 GT:DP:AD 0|1:19:8,11 1|0:21:15,6 ./.:39:24,15 -chr20 363003 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=317307;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:28:10,18 1|0:41:21,20 ./.:15:5,10 -chr20 363114 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=317418;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:32:7,25 1|0:32:7,25 ./.:40:16,24 -chr20 363119 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=317423;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:34:21,13 1|0:36:22,14 ./.:35:12,23 -chr20 363245 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=342624;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:23:15,8 0|1:41:19,22 1|0:23:8,15 -chr20 363435 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=317739;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:24:14,10 1|0:22:7,15 ./.:38:17,21 -chr20 363987 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=318291;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:38:13,25 1|0:11:6,5 ./.:41:18,23 -chr20 364755 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=319059;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 0|1:11:5,6 1|0:35:23,12 ./.:34:20,14 -chr20 364763 . C CAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=344143;QSTRAND=+;GCPCT=33;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.459148 GT:DP:AD 1|1:17:11,6 1|1:29:10,19 1|1:35:10,25 -chr20 365042 . G A 60 . QNAME=cluster19_000000F;QSTART=25397024;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:30:12,18 1|0:32:25,7 ./.:21:6,15 -chr20 365220 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=344601;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:22:5,17 1|1:33:25,8 1|1:35:17,18 -chr20 365798 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=345180;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD 1|1:35:14,21 ./.:29:17,12 0|1:21:8,13 -chr20 365798 . CTT C 60 . QNAME=cluster19_000000F;QSTART=25396268;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.459148 GT:DP:AD ./.:26:13,13 1|0:29:8,21 ./.:33:9,24 -chr20 366032 . C T 60 . QNAME=cluster19_000000F;QSTART=25396036;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:24:5,19 1|0:28:9,19 ./.:13:8,5 -chr20 366058 . AGCCTCCCAAAGGAG A 60 . QNAME=cluster19_000000F;QSTART=25396010;QSTRAND=-;GCPCT=60;GTCNT=2,0,1,0;DPCNT=0,0,2,1;ADCNT=0,3,0,0;LCR=0.912803 GT:DP:AD ./.:12:5,7 1|0:13:8,5 ./.:32:23,9 -chr20 366107 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=345487;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:12:6,6 1|1:42:23,19 1|1:31:25,6 -chr20 366279 . C T 60 . QNAME=cluster19_000000F;QSTART=25395803;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:45:24,21 1|0:43:21,22 ./.:34:14,20 -chr20 366317 . A G 60 . QNAME=cluster19_000000F;QSTART=25395765;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:40:22,18 1|0:46:22,24 ./.:33:16,17 -chr20 366341 . A G 60 . QNAME=cluster19_000000F;QSTART=25395741;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:40:19,21 1|0:33:14,19 ./.:14:7,7 -chr20 366365 . C A 60 . QNAME=cluster19_000000F;QSTART=25395717;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:18:12,6 1|0:30:12,18 ./.:31:13,18 -chr20 366711 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=346091;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:25:11,14 ./.:23:8,15 1|1:29:18,11 -chr20 367006 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=346386;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:29:17,12 1|0:44:22,22 1|1:37:23,14 -chr20 367079 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=346459;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:45:23,22 ./.:26:15,11 1|1:11:5,6 -chr20 367082 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=346462;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:44:25,19 ./.:32:16,16 1|1:31:20,11 -chr20 367106 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=346486;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:36:24,12 ./.:25:9,16 1|1:34:13,21 -chr20 367141 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=346521;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:33:16,17 1|0:20:14,6 1|1:48:24,24 -chr20 367164 . TCGCA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=346545;QSTRAND=+;GCPCT=60;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.960964 GT:DP:AD 1|0:43:21,22 ./.:20:14,6 1|1:18:10,8 -chr20 367176 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=346552;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:26:14,12 ./.:42:17,25 1|1:36:14,22 -chr20 367214 . AAAACAAAC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=346591;QSTRAND=+;GCPCT=22;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.382102 GT:DP:AD 1|0:23:6,17 ./.:36:24,12 1|1:45:20,25 -chr20 367226 . A C 60 . QNAME=cluster19_000000F;QSTART=25394856;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:30:20,10 1|0:43:21,22 ./.:44:20,24 -chr20 367234 . A AAAAC 60 . QNAME=cluster19_000000F;QSTART=25394844;QSTRAND=-;GCPCT=20;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.360964 GT:DP:AD ./.:29:8,21 1|0:36:24,12 ./.:28:17,11 -chr20 367235 . C A 60 . QNAME=cluster19_000000F;QSTART=25394843;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:21:12,9 1|0:41:21,20 ./.:29:13,16 -chr20 367244 . AAAC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=346613;QSTRAND=+;GCPCT=25;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.405639 GT:DP:AD 1|0:43:23,20 ./.:29:23,6 1|1:29:6,23 -chr20 367252 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=346617;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:46:22,24 ./.:31:20,11 1|1:37:20,17 -chr20 367264 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=321569;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:36:12,24 1|1:17:7,10 ./.:34:10,24 -chr20 367521 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=346886;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:35:25,10 0|1:38:17,21 ./.:11:6,5 -chr20 367522 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=346887;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:24:18,6 ./.:15:5,10 ./.:38:16,22 -chr20 367522 . G C 60 . QNAME=cluster19_000000F;QSTART=327442;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:23:15,8 0|1:17:9,8 ./.:35:18,17 -chr20 367544 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=321849;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:40:23,17 ./.:34:14,20 1|0:20:8,12 -chr20 367675 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=347040;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:18:12,6 ./.:45:21,24 0|1:34:19,15 -chr20 367690 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=321995;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:20:10,10 ./.:30:10,20 0|1:35:14,21 -chr20 367721 . G GT 60 . QNAME=HG002-S9-H1-000001F;QSTART=347087;QSTRAND=+;GCPCT=50;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD 1|0:37:15,22 0|1:34:25,9 1|0:28:19,9 -chr20 367877 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=347243;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:22:11,11 ./.:37:17,20 ./.:30:24,6 -chr20 368132 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=322437;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:23:11,12 1|0:19:9,10 ./.:32:14,18 -chr20 368260 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=322565;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:13:7,6 1|0:20:11,9 ./.:28:6,22 -chr20 368284 . CTT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=322590;QSTRAND=+;GCPCT=33;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.459148 GT:DP:AD 0|1:38:17,21 1|0:36:21,15 ./.:20:12,8 -chr20 368410 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=322713;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:18:5,13 1|0:41:23,18 ./.:29:23,6 -chr20 368474 . C T 60 . QNAME=cluster19_000000F;QSTART=328395;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:22:14,8 0|1:40:21,19 1|0:40:17,23 -chr20 368491 . G A 60 . QNAME=cluster19_000000F;QSTART=328412;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:25:7,18 0|1:21:8,13 ./.:26:10,16 -chr20 368580 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=322883;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:26:7,19 1|0:29:22,7 ./.:33:13,20 -chr20 368662 . G C 60 . QNAME=cluster19_000000F;QSTART=25393418;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:46:21,25 1|0:29:15,14 ./.:36:11,25 -chr20 368677 . ACT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=322981;QSTRAND=+;GCPCT=33;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.792481 GT:DP:AD 0|1:26:9,17 1|0:39:20,19 ./.:23:15,8 -chr20 369093 . T C 60 . QNAME=cluster19_000000F;QSTART=25392989;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD ./.:17:7,10 1|0:32:19,13 ./.:38:25,13 -chr20 369284 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25342176;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:46:25,21 ./.:19:7,12 1|0:27:16,11 -chr20 369514 . G A 60 . QNAME=cluster19_000000F;QSTART=25392568;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:37:12,25 1|0:26:11,15 ./.:25:20,5 -chr20 369594 . T A 60 . QNAME=cluster23_scaffold_3;QSTART=25341866;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:27:6,21 ./.:32:21,11 1|0:37:18,19 -chr20 369657 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25341802;QSTRAND=-;GCPCT=50;GTCNT=2,0,0,1;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:37:20,17 ./.:13:8,5 1|1:31:11,20 -chr20 369657 . CAAAAAA C 60 . QNAME=cluster19_000000F;QSTART=25392425;QSTRAND=-;GCPCT=14;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.295836 GT:DP:AD ./.:22:14,8 1|0:44:22,22 ./.:40:19,21 -chr20 369846 . T C 60 . QNAME=cluster19_000000F;QSTART=25392242;QSTRAND=-;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:31:11,20 1|0:32:9,23 1|0:33:25,8 -chr20 369998 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=349364;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:28:7,21 ./.:31:11,20 ./.:48:25,23 -chr20 370237 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=349603;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:28:18,10 0|1:31:8,23 ./.:38:16,22 -chr20 370371 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=349737;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:30:5,25 1|1:20:12,8 ./.:18:13,5 -chr20 371300 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=350666;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:31:10,21 0|1:35:22,13 ./.:39:19,20 -chr20 371526 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=350892;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:33:8,25 1|1:25:16,9 ./.:16:7,9 -chr20 372007 . T C 60 . QNAME=cluster19_000000F;QSTART=25390081;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:25:8,17 1|0:42:18,24 ./.:29:12,17 -chr20 372073 . A G 60 . QNAME=cluster19_000000F;QSTART=25390015;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:24:8,16 1|0:28:19,9 ./.:16:8,8 -chr20 372441 . A G 60 . QNAME=cluster19_000000F;QSTART=25389647;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:26:12,14 1|0:23:16,7 ./.:20:12,8 -chr20 372564 . A C 60 . QNAME=cluster19_000000F;QSTART=25389524;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:48:23,25 1|0:31:17,14 ./.:28:14,14 -chr20 372676 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=352042;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:35:19,16 1|1:37:25,12 ./.:12:7,5 -chr20 372735 . G T 60 . QNAME=cluster19_000000F;QSTART=25389353;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:30:6,24 1|0:31:18,13 ./.:44:20,24 -chr20 373053 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=352419;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:23:6,17 1|1:28:10,18 ./.:22:12,10 -chr20 373694 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=353060;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:29:20,9 0|1:13:5,8 ./.:22:5,17 -chr20 373749 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=353115;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:28:22,6 0|1:38:15,23 ./.:26:11,15 -chr20 374221 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=353587;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:27:21,6 0|1:32:13,19 ./.:31:23,8 -chr20 374323 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=353689;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:18:11,7 1|1:25:6,19 ./.:27:17,10 -chr20 374523 . A G 60 . QNAME=cluster19_000000F;QSTART=25387565;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:35:20,15 1|0:47:23,24 ./.:36:21,15 -chr20 374580 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=353946;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:22:6,16 0|1:30:13,17 ./.:20:15,5 -chr20 374601 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=353967;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:28:17,11 0|1:29:21,8 ./.:34:20,14 -chr20 374675 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=354041;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:31:19,12 1|1:42:17,25 ./.:35:17,18 -chr20 374716 . C T 60 . QNAME=cluster19_000000F;QSTART=334637;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:31:18,13 0|1:23:8,15 ./.:32:23,9 -chr20 374726 . C T 60 . QNAME=cluster19_000000F;QSTART=334647;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:19:10,9 0|1:42:23,19 ./.:39:19,20 -chr20 374740 . G GGT 60 . QNAME=HG002-S9-H1-000001F;QSTART=354107;QSTRAND=+;GCPCT=66;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.459148 GT:DP:AD 1|0:30:11,19 0|1:36:22,14 ./.:15:8,7 -chr20 374743 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=354111;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:17:9,8 0|1:33:14,19 ./.:29:14,15 -chr20 374744 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=354112;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:19:11,8 0|1:10:5,5 ./.:27:10,17 -chr20 374747 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=354115;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:30:25,5 0|1:34:19,15 ./.:12:7,5 -chr20 374754 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=354122;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:36:17,19 0|1:31:19,12 ./.:28:5,23 -chr20 374836 . T C 60 . QNAME=cluster19_000000F;QSTART=25387252;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD ./.:34:22,12 1|0:20:7,13 ./.:24:14,10 -chr20 374900 . C G 60 . QNAME=cluster19_000000F;QSTART=25387188;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0 GT:DP:AD ./.:16:7,9 1|0:24:19,5 ./.:26:17,9 -chr20 374905 . A AC 60 . QNAME=HG002-S9-H1-000001F;QSTART=354274;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 1|0:23:10,13 1|1:39:19,20 ./.:27:5,22 -chr20 375120 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=354489;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:29:23,6 1|1:41:22,19 ./.:23:13,10 -chr20 375218 . G GA 60 . QNAME=cluster19_000000F;QSTART=335143;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:29:19,10 0|1:29:12,17 ./.:22:14,8 -chr20 375218 . GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=354588;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|0:26:18,8 ./.:43:21,22 ./.:24:10,14 -chr20 375359 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=354727;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:28:20,8 1|1:34:18,16 ./.:48:23,25 -chr20 375590 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=354958;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:34:14,20 0|1:41:17,24 ./.:36:25,11 -chr20 376026 . T TCAAA 60 . QNAME=cluster19_000000F;QSTART=25386057;QSTRAND=-;GCPCT=20;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.685475 GT:DP:AD ./.:26:18,8 1|0:32:17,15 ./.:21:14,7 -chr20 376031 . A AAAAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=355400;QSTRAND=+;GCPCT=20;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.360964 GT:DP:AD 1|0:42:25,17 0|1:20:7,13 ./.:32:23,9 -chr20 376031 . A C 60 . QNAME=cluster19_000000F;QSTART=25386052;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:18:9,9 1|0:44:21,23 ./.:32:19,13 -chr20 376141 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=355513;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:18:7,11 1|1:36:17,19 ./.:24:9,15 -chr20 376217 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=355589;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:24:7,17 1|1:43:25,18 ./.:29:20,9 -chr20 376406 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=355778;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:47:22,25 1|1:18:7,11 ./.:27:20,7 -chr20 376484 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=355856;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:38:24,14 1|1:36:14,22 ./.:25:6,19 -chr20 376926 . T C 60 . QNAME=cluster19_000000F;QSTART=25385157;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:28:8,20 1|0:12:7,5 ./.:21:10,11 -chr20 376988 . C T 60 . QNAME=cluster19_000000F;QSTART=25385095;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:41:16,25 1|0:31:14,17 ./.:23:10,13 -chr20 377035 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=356407;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:27:14,13 1|1:32:23,9 ./.:47:24,23 -chr20 377056 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=356428;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:16:9,7 1|1:34:17,17 ./.:28:6,22 -chr20 377153 . AT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=331455;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 0|1:43:20,23 ./.:18:11,7 ./.:36:21,15 -chr20 377153 . ATTTTTT A 60 . QNAME=cluster19_000000F;QSTART=25384930;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.295836 GT:DP:AD ./.:31:20,11 1|0:30:19,11 ./.:39:14,25 -chr20 377184 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=356556;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:24:12,12 1|1:35:11,24 ./.:27:9,18 -chr20 377366 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=356738;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:43:22,21 1|1:25:7,18 ./.:33:24,9 -chr20 377503 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=356876;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|0:19:5,14 1|1:24:6,18 ./.:34:25,9 -chr20 377680 . G GT 60 . QNAME=cluster23_scaffold_2;QSTART=25317935;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:42:19,23 ./.:30:16,14 0|1:19:10,9 -chr20 377680 . GT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=357052;QSTRAND=+;GCPCT=50;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|1:42:25,17 1|1:17:7,10 ./.:24:16,8 -chr20 377737 . T C 60 . QNAME=cluster19_000000F;QSTART=25384354;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:26:9,17 1|1:26:10,16 ./.:48:25,23 -chr20 377922 . G A 60 . QNAME=cluster19_000000F;QSTART=25384169;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:25:6,19 1|1:35:17,18 ./.:31:14,17 -chr20 377975 . A G 60 . QNAME=cluster19_000000F;QSTART=25384116;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:25:13,12 1|1:14:9,5 ./.:37:12,25 -chr20 378291 . C T 60 . QNAME=cluster19_000000F;QSTART=25383800;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:25:8,17 1|1:25:14,11 ./.:31:12,19 -chr20 378708 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=333008;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 0|1:31:24,7 ./.:35:11,24 ./.:15:5,10 -chr20 378907 . T A 60 . QNAME=cluster19_000000F;QSTART=338834;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:24:18,6 0|1:47:24,23 ./.:44:21,23 -chr20 379030 . C T 60 . QNAME=cluster19_000000F;QSTART=25383061;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:21:7,14 1|1:49:24,25 ./.:27:10,17 -chr20 379398 . G A 60 . QNAME=cluster19_000000F;QSTART=25382693;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:37:15,22 1|1:25:13,12 ./.:32:14,18 -chr20 379418 . T C 60 . QNAME=cluster19_000000F;QSTART=25382673;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:24:13,11 1|0:41:16,25 ./.:41:21,20 -chr20 379468 . G A 60 . QNAME=cluster19_000000F;QSTART=25382623;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:23:5,18 1|1:36:17,19 ./.:43:22,21 -chr20 379581 . A C 60 . QNAME=cluster19_000000F;QSTART=25382510;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:31:9,22 1|0:35:24,11 ./.:32:16,16 -chr20 379662 . T C 60 . QNAME=cluster19_000000F;QSTART=25382429;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:36:12,24 1|1:39:18,21 ./.:29:20,9 -chr20 379675 . G GA 60 . QNAME=cluster19_000000F;QSTART=339603;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:27:10,17 0|1:21:15,6 ./.:29:5,24 -chr20 379699 . G C 60 . QNAME=cluster19_000000F;QSTART=25382392;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:24:13,11 1|1:16:5,11 ./.:39:22,17 -chr20 379759 . T C 60 . QNAME=cluster19_000000F;QSTART=25382332;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:36:20,16 1|1:45:20,25 ./.:25:13,12 -chr20 379794 . T C 60 . QNAME=cluster19_000000F;QSTART=25382297;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:19:13,6 1|1:16:7,9 ./.:32:19,13 -chr20 379816 . C T 60 . QNAME=cluster19_000000F;QSTART=25382275;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:37:12,25 1|1:31:6,25 ./.:39:16,23 -chr20 379966 . G T 60 . QNAME=cluster19_000000F;QSTART=25382125;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:37:22,15 1|1:40:15,25 ./.:32:18,14 -chr20 380070 . G C 60 . QNAME=cluster19_000000F;QSTART=25382021;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:39:17,22 1|1:34:18,16 ./.:22:16,6 -chr20 380078 . G C 60 . QNAME=cluster19_000000F;QSTART=25382013;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:32:21,11 1|1:38:13,25 ./.:22:8,14 -chr20 380145 . T C 60 . QNAME=cluster19_000000F;QSTART=340073;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:38:24,14 0|1:25:18,7 ./.:37:19,18 -chr20 380283 . TAA T 60 . QNAME=cluster19_000000F;QSTART=25381808;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.459148 GT:DP:AD ./.:28:9,19 1|1:32:14,18 ./.:33:22,11 -chr20 380289 . A C 60 . QNAME=cluster19_000000F;QSTART=25381804;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:31:20,11 1|1:17:8,9 ./.:28:21,7 -chr20 380548 . T C 60 . QNAME=cluster19_000000F;QSTART=25381545;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:25:13,12 1|1:24:17,7 ./.:23:7,16 -chr20 380662 . G A 60 . QNAME=cluster19_000000F;QSTART=25381431;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:24:8,16 1|1:43:22,21 1|0:15:6,9 -chr20 380663 . C A 60 . QNAME=cluster19_000000F;QSTART=25381430;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:22:9,13 1|1:40:16,24 1|0:23:7,16 -chr20 380672 . A G 60 . QNAME=cluster19_000000F;QSTART=25381421;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:22:8,14 1|1:17:5,12 1|0:27:12,15 -chr20 380679 . T C 60 . QNAME=cluster19_000000F;QSTART=25381414;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:32:10,22 1|1:34:24,10 1|0:23:18,5 -chr20 380684 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25330774;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:42:25,17 ./.:28:9,19 1|0:38:25,13 -chr20 380684 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=360055;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|0:15:10,5 1|1:31:9,22 ./.:24:14,10 -chr20 380878 . T TGATTAGCTCCGGTTTGCATCACCCGGACCGGGGGATTAGCTCCGGTTTGCATCACCCGGACCGGGG 60 . QNAME=cluster19_000000F;QSTART=25381150;QSTRAND=-;SVTYPE=INS;SVLEN=66;HOMPCT=1.7;REMAP=tandem;REMAPHits=chr20:380877-380944.100,chr20:380910-380977.100;GCPCT=62;GTCNT=2,0,1,0;NumNeighbors=0;NeighId=4;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0.970592 GT:DP:AD ./.:21:9,12 1/0:15:8,7 ./.:25:20,5 -chr20 381233 . G A 60 . QNAME=cluster19_000000F;QSTART=25380795;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:43:23,20 1|0:24:7,17 ./.:34:10,24 -chr20 381358 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=360727;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:28:17,11 ./.:23:6,17 ./.:31:23,8 -chr20 381423 . C G 60 . QNAME=cluster23_scaffold_3;QSTART=25330068;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:26:6,20 ./.:36:14,22 1|0:40:19,21 -chr20 381585 . AG A 60 . QNAME=cluster23_scaffold_3;QSTART=25329906;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:24:6,18 ./.:32:17,15 1|0:33:22,11 -chr20 381637 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=361006;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:41:21,20 1|1:36:16,20 0|1:26:13,13 -chr20 381684 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=361053;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:29:11,18 0|1:31:10,21 1|0:34:25,9 -chr20 381742 . T TG 60 . QNAME=HG002-S9-H2-000001F;QSTART=336041;QSTRAND=+;GCPCT=50;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 0|1:35:16,19 1|0:28:6,22 1|0:20:15,5 -chr20 381797 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=336096;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:28:23,5 0|1:32:8,24 1|0:33:8,25 -chr20 382099 . C CTG 60 . QNAME=cluster19_000000F;QSTART=25379926;QSTRAND=-;GCPCT=66;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.792481 GT:DP:AD ./.:39:24,15 1|0:19:12,7 ./.:39:18,21 -chr20 382099 . C CTGTGTGTG 60 . QNAME=cluster23_scaffold_3;QSTART=25329384;QSTRAND=-;GCPCT=55;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.696074 GT:DP:AD ./.:26:20,6 ./.:26:8,18 1|0:40:16,24 -chr20 382124 . TGTGC T 60 . QNAME=cluster23_scaffold_2;QSTART=25313491;QSTRAND=-;GCPCT=60;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.760964 GT:DP:AD ./.:22:6,16 ./.:35:12,23 0|1:26:8,18 -chr20 383089 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25328394;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:31:14,17 ./.:14:7,7 1|0:36:15,21 -chr20 383651 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=363020;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:44:20,24 1|0:34:13,21 0|1:30:16,14 -chr20 384031 . A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25327451;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0.5 GT:DP:AD ./.:14:9,5 ./.:29:15,14 1|0:21:16,5 -chr20 384050 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25311569;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:42:23,19 ./.:33:12,21 0|1:29:16,13 -chr20 384103 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=25327379;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:38:22,16 ./.:20:11,9 1|0:44:23,21 -chr20 385414 . AT A 60 . QNAME=cluster19_000000F;QSTART=345340;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:24:13,11 0|1:37:13,24 1|0:39:17,22 -chr20 385860 . A AT 60 . QNAME=cluster23_scaffold_2;QSTART=25309758;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:45:22,23 ./.:43:20,23 0|1:25:10,15 -chr20 385969 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=365338;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:17:7,10 ./.:19:5,14 0|1:41:18,23 -chr20 386036 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=365405;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:25:16,9 1|1:50:25,25 1|1:48:24,24 -chr20 386320 . T C 60 . QNAME=cluster19_000000F;QSTART=346244;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:24:5,19 0|1:35:25,10 1|0:25:7,18 -chr20 387554 . GA G 60 . QNAME=cluster19_000000F;QSTART=347479;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:44:21,23 0|1:24:6,18 ./.:24:13,11 -chr20 391001 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25320481;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.5 GT:DP:AD ./.:29:17,12 ./.:26:19,7 1|0:31:19,12 -chr20 391001 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=345301;QSTRAND=+;GCPCT=50;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0.5 GT:DP:AD 0|1:27:22,5 1|0:15:5,10 0|1:30:25,5 -chr20 391003 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=345301;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:46:24,22 1|0:40:19,21 0|1:36:24,12 -chr20 391137 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=345435;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:39:18,21 1|0:28:23,5 0|1:46:25,21 -chr20 391138 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=345436;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:32:25,7 1|0:42:17,25 0|1:40:24,16 -chr20 391328 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=345626;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:36:24,12 1|0:39:23,16 0|1:18:6,12 -chr20 392021 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=346320;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 0|1:40:17,23 ./.:27:22,5 ./.:17:5,12 -chr20 392557 . A AT 60 . QNAME=HG002-S9-H2-000001F;QSTART=346855;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 0|1:26:15,11 1|0:29:12,17 1|1:26:21,5 -chr20 393192 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=347407;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,2,1;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:13:6,7 1|0:35:20,15 0|1:13:8,5 -chr20 393337 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=347553;QSTRAND=+;GCPCT=50;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 0|1:24:18,6 1|0:23:9,14 1|1:23:7,16 -chr20 393417 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=347631;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:21:12,9 1|0:38:16,22 0|1:28:11,17 -chr20 393740 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=347954;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:13:5,8 1|0:44:21,23 0|1:23:14,9 -chr20 393795 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=348009;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:17:9,8 1|0:40:19,21 0|1:39:17,22 -chr20 394032 . C CT 60 . QNAME=HG002-S9-H2-000001F;QSTART=348247;QSTRAND=+;GCPCT=50;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 0|1:39:18,21 1|0:30:12,18 0|1:15:8,7 -chr20 394119 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=348334;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:33:8,25 1|0:31:15,16 0|1:26:18,8 -chr20 394301 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=348516;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:11:5,6 ./.:28:17,11 0|1:31:6,25 -chr20 394462 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=348677;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:14:8,6 1|1:44:21,23 0|1:21:14,7 -chr20 394799 . G GA 60 . QNAME=cluster23_scaffold_3;QSTART=25316682;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:37:17,20 ./.:46:23,23 1|0:35:10,25 -chr20 394955 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=349170;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 0|1:25:11,14 ./.:31:22,9 0|1:24:14,10 -chr20 395162 . CT C 60 . QNAME=cluster19_000000F;QSTART=25366946;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD ./.:21:10,11 1|0:22:8,14 ./.:41:22,19 -chr20 396582 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=350797;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:16:10,6 1|0:30:13,17 0|1:50:25,25 -chr20 397598 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=351813;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:38:24,14 1|0:43:21,22 0|1:21:14,7 -chr20 397600 . T A 60 . QNAME=cluster23_scaffold_2;QSTART=25298101;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:30:25,5 ./.:39:24,15 0|1:14:8,6 -chr20 397886 . A AC 60 . QNAME=cluster23_scaffold_3;QSTART=25313594;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD ./.:23:13,10 ./.:41:16,25 1|0:23:10,13 -chr20 398287 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=352502;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:44:20,24 1|0:28:5,23 0|1:33:24,9 -chr20 398312 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=352527;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:46:23,23 1|0:32:13,19 0|1:24:14,10 -chr20 398313 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=352528;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 0|1:33:24,9 1|0:32:18,14 0|1:14:6,8 -chr20 398315 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=352530;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:31:21,10 1|0:13:7,6 0|1:28:13,15 -chr20 398320 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=352535;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:41:20,21 1|0:25:20,5 0|1:35:19,16 -chr20 398324 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=352539;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:35:13,22 1|0:39:16,23 0|1:36:23,13 -chr20 398327 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=352542;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:29:24,5 1|0:31:21,10 0|1:40:19,21 -chr20 398334 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=352549;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:36:21,15 1|0:16:11,5 0|1:31:22,9 -chr20 398897 . C T 60 . QNAME=cluster19_000000F;QSTART=25363212;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:22:13,9 1|0:20:8,12 ./.:16:5,11 -chr20 399283 . A G 60 . QNAME=cluster19_000000F;QSTART=25362826;QSTRAND=-;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:29:8,21 1|1:36:14,22 1|1:27:13,14 -chr20 399958 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=379327;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:30:7,23 1|0:48:25,23 ./.:23:6,17 -chr20 400146 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=379516;QSTRAND=+;GCPCT=50;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|0:18:5,13 1|1:30:7,23 1|0:19:12,7 -chr20 400336 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=379706;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:22:7,15 1|1:41:25,16 1|0:20:12,8 -chr20 400547 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=379917;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:44:25,19 1|1:14:6,8 1|0:36:20,16 -chr20 400677 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=380047;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:31:17,14 1|1:32:25,7 1|0:27:6,21 -chr20 400755 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=380125;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:32:7,25 1|0:24:15,9 ./.:22:17,5 -chr20 400797 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=380167;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:23:10,13 1|1:23:9,14 1|0:34:10,24 -chr20 400887 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=380257;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:32:25,7 1|1:38:16,22 1|0:18:5,13 -chr20 401685 . C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=381056;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.5 GT:DP:AD 1|0:34:24,10 1|1:23:18,5 ./.:38:25,13 -chr20 401685 . C CAA 60 . QNAME=cluster23_scaffold_3;QSTART=25309792;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.459148 GT:DP:AD ./.:27:19,8 ./.:28:12,16 1|0:19:11,8 -chr20 401702 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=381073;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:38:23,15 1|1:26:14,12 1|0:47:25,22 -chr20 401915 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=381286;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:35:20,15 1|1:42:19,23 1|0:44:25,19 -chr20 401983 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=381354;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:40:22,18 1|1:20:11,9 1|0:25:17,8 -chr20 402232 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=381603;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:43:19,24 1|1:35:20,15 1|0:39:14,25 -chr20 402478 . C CAA 60 . QNAME=HG002-S9-H2-000001F;QSTART=356694;QSTRAND=+;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.459148 GT:DP:AD 0|1:28:13,15 ./.:32:12,20 ./.:25:13,12 -chr20 402478 . C CAAA 60 . QNAME=cluster23_scaffold_2;QSTART=25293220;QSTRAND=-;GCPCT=25;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.405639 GT:DP:AD ./.:41:24,17 ./.:38:17,21 0|1:35:18,17 -chr20 402478 . CAAAAAAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=381850;QSTRAND=+;GCPCT=11;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.251629 GT:DP:AD 1|0:16:8,8 1|0:37:16,21 ./.:34:13,21 -chr20 402492 . A AT 60 . QNAME=cluster19_000000F;QSTART=362418;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:36:15,21 0|1:14:5,9 1|0:16:6,10 -chr20 402498 . A T 60 . QNAME=cluster19_000000F;QSTART=362424;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:39:20,19 0|1:43:18,25 1|0:23:5,18 -chr20 402504 . A T 60 . QNAME=cluster19_000000F;QSTART=362430;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:28:12,16 0|1:30:15,15 1|0:34:24,10 -chr20 402509 . A T 60 . QNAME=cluster19_000000F;QSTART=362435;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:19:14,5 0|1:32:11,21 1|0:28:22,6 -chr20 403076 . C T 60 . QNAME=cluster19_000000F;QSTART=363002;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:22:16,6 0|1:38:15,23 1|0:38:16,22 -chr20 403697 . A G 60 . QNAME=cluster19_000000F;QSTART=363623;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:39:17,22 0|1:17:8,9 1|0:13:8,5 -chr20 403859 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=383222;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:38:18,20 1|0:45:24,21 ./.:20:6,14 -chr20 404000 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=383363;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:14:7,7 1|1:30:11,19 1|0:25:19,6 -chr20 404254 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=383617;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:21:7,14 1|0:34:11,23 ./.:25:12,13 -chr20 404408 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=383771;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:35:24,11 1|1:16:10,6 1|0:38:22,16 -chr20 404596 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=383959;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:37:12,25 1|1:40:21,19 1|1:20:15,5 -chr20 405155 . T TCACA 60 . QNAME=cluster19_000000F;QSTART=365082;QSTRAND=+;GCPCT=40;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.760964 GT:DP:AD ./.:29:16,13 0|1:33:21,12 1|0:17:11,6 -chr20 405155 . TCA T 60 . QNAME=cluster19_000000F;QSTART=25356960;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.792481 GT:DP:AD ./.:35:23,12 1|0:39:17,22 ./.:28:5,23 -chr20 405220 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=384583;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:27:14,13 1|1:28:16,12 1|0:33:11,22 -chr20 405345 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=384709;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 1|0:27:11,16 1|0:38:20,18 ./.:23:5,18 -chr20 405478 . C T 60 . QNAME=cluster19_000000F;QSTART=365408;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:31:13,18 0|1:30:16,14 1|0:22:12,10 -chr20 405820 . A G 60 . QNAME=cluster19_000000F;QSTART=365750;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:33:17,16 0|1:46:22,24 1|0:31:15,16 -chr20 405931 . GTTCT G 60 . QNAME=cluster19_000000F;QSTART=365862;QSTRAND=+;GCPCT=40;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.685475 GT:DP:AD ./.:26:6,20 0|1:31:7,24 1|0:33:14,19 -chr20 405942 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=360160;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.5 GT:DP:AD 0|1:16:6,10 ./.:30:19,11 ./.:24:19,5 -chr20 406708 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25288989;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:21:6,15 ./.:45:21,24 0|1:16:6,10 -chr20 406708 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=360925;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 0|1:35:13,22 ./.:39:20,19 ./.:22:10,12 -chr20 406708 . CAAA C 60 . QNAME=cluster19_000000F;QSTART=366635;QSTRAND=+;GCPCT=25;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.405639 GT:DP:AD ./.:26:14,12 0|1:41:23,18 1|0:29:11,18 -chr20 406732 . A AAAAAAAAAAAAG 60 . QNAME=HG002-S9-H1-000001F;QSTART=386097;QSTRAND=+;GCPCT=7;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0.195622 GT:DP:AD 1|0:14:8,6 ./.:37:20,17 ./.:34:24,10 -chr20 406732 . A AAAAAAAAAAG 60 . QNAME=cluster19_000000F;QSTART=25355374;QSTRAND=-;GCPCT=9;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.219748 GT:DP:AD ./.:45:21,24 1|0:30:23,7 ./.:36:12,24 -chr20 407013 . G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=386390;QSTRAND=+;GCPCT=50;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 1|0:39:24,15 1|1:36:14,22 1|0:29:12,17 -chr20 407083 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=386460;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:24:10,14 1|0:41:17,24 ./.:34:9,25 -chr20 407113 . A G 60 . QNAME=cluster19_000000F;QSTART=367037;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:41:20,21 0|1:33:8,25 1|0:36:14,22 -chr20 407171 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=386548;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:33:24,9 1|0:39:20,19 ./.:21:6,15 -chr20 407872 . C T 60 . QNAME=cluster19_000000F;QSTART=367796;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:33:23,10 0|1:33:8,25 1|0:18:11,7 -chr20 407964 . CG C 60 . QNAME=HG002-S9-H1-000001F;QSTART=387342;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|0:40:24,16 1|0:12:5,7 ./.:30:8,22 -chr20 407977 . CG C 60 . QNAME=HG002-S9-H1-000001F;QSTART=387354;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 1|0:25:6,19 1|0:21:8,13 ./.:24:9,15 -chr20 408008 . GC G 60 . QNAME=HG002-S9-H1-000001F;QSTART=387384;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD 1|0:30:16,14 ./.:19:6,13 ./.:33:8,25 -chr20 408028 . G GGCCCCGCCC 60 . QNAME=HG002-S9-H2-000001F;QSTART=362274;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.440645 GT:DP:AD 0|1:18:11,7 ./.:31:18,13 0|1:35:22,13 -chr20 408029 . G GCCCCGCCCA 60 . QNAME=cluster19_000000F;QSTART=367992;QSTRAND=+;GCPCT=90;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0.57839 GT:DP:AD ./.:12:6,6 0|1:20:9,11 1|0:25:9,16 -chr20 408057 . T TC 60 . QNAME=HG002-S9-H1-000001F;QSTART=387432;QSTRAND=+;GCPCT=50;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.5 GT:DP:AD 1|1:23:13,10 1|1:34:24,10 1|1:24:15,9 -chr20 408812 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=363067;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:33:15,18 0|1:50:25,25 1|1:24:18,6 -chr20 409237 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=363492;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:30:22,8 0|1:19:5,14 1|1:42:18,24 -chr20 409291 . AT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=363547;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD 0|1:42:22,20 ./.:29:24,5 ./.:19:14,5 -chr20 409340 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=363594;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:34:23,11 0|1:27:13,14 1|1:47:24,23 -chr20 409466 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=363721;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD 0|1:28:10,18 ./.:28:19,9 ./.:26:20,6 -chr20 410526 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=364779;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:26:10,16 0|1:39:16,23 1|1:23:5,18 -chr20 412325 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=366579;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD 0|1:17:11,6 ./.:42:17,25 ./.:31:23,8 -chr20 413334 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=367586;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:40:15,25 0|1:17:12,5 1|1:34:19,15 -chr20 413917 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=368170;QSTRAND=+;GCPCT=50;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 0|1:41:24,17 0|1:38:24,14 1|1:21:16,5 -chr20 413941 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=368192;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 0|1:26:12,14 0|1:27:20,7 1|1:22:13,9 -chr20 414091 . C CA 60 . QNAME=HG002-S9-H2-000001F;QSTART=368343;QSTRAND=+;GCPCT=50;GTCNT=0,0,2,1;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 0|1:31:21,10 0|1:39:21,18 1|1:13:6,7 -chr20 414091 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=393467;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 1|0:40:15,25 ./.:37:12,25 ./.:37:19,18 -chr20 414317 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=368569;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 0|1:27:15,12 0|1:19:12,7 1|1:20:12,8 -chr20 415178 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=369430;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0 GT:DP:AD 0|1:29:24,5 0|1:29:23,6 1|1:22:14,8 -chr20 415379 . A AAAAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=394754;QSTRAND=+;GCPCT=20;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.360964 GT:DP:AD 1|1:24:5,19 1|1:32:20,12 1|1:17:6,11 -chr20 415512 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=394890;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:15:9,6 1|0:20:8,12 ./.:28:15,13 -chr20 416154 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25295271;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD ./.:40:15,25 ./.:30:21,9 1|0:25:19,6 -chr20 416334 . G T 60 . QNAME=cluster19_000000F;QSTART=376310;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:44:20,24 0|1:22:12,10 1|0:41:21,20 -chr20 417284 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=396662;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:43:21,22 1|1:40:18,22 1|1:34:17,17 -chr20 417395 . T TTG 60 . QNAME=cluster23_scaffold_3;QSTART=25294028;QSTRAND=-;GCPCT=33;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.459148 GT:DP:AD ./.:24:16,8 ./.:32:21,11 1|1:38:13,25 -chr20 417634 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=397012;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:41:16,25 1|0:40:20,20 ./.:28:18,10 -chr20 418430 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=397808;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:36:22,14 1|0:31:9,22 ./.:39:16,23 -chr20 418432 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=397810;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:15:6,9 1|0:31:24,7 ./.:28:9,19 -chr20 418579 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=372835;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 0|1:27:15,12 ./.:18:12,6 1|1:28:14,14 -chr20 418601 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=372857;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:37:25,12 ./.:35:24,11 1|1:49:24,25 -chr20 418603 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=372859;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:36:17,19 ./.:36:21,15 1|1:16:9,7 -chr20 418658 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=372914;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:35:24,11 ./.:40:17,23 1|1:15:9,6 -chr20 419117 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=398495;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:25:10,15 1|0:35:25,10 1|1:27:8,19 -chr20 419860 . AGTGACCCTGCACCTGGCT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=374117;QSTRAND=+;GCPCT=63;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0.965648 GT:DP:AD 0|1:24:19,5 ./.:14:7,7 1|1:27:8,19 -chr20 420228 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=374466;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:36:17,19 ./.:25:11,14 1|1:29:10,19 -chr20 420465 . A AG 60 . QNAME=HG002-S9-H2-000001F;QSTART=374704;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 0|1:19:11,8 ./.:22:8,14 1|1:24:5,19 -chr20 420561 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=399939;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:31:17,14 1|0:37:21,16 1|1:47:25,22 -chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCATCCCCCGTCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 60 . QNAME=HG002-S9-H1-000001F;QSTART=400044;QSTRAND=+;SVTYPE=INS;SVLEN=226;HOMPCT=37;REMAP=partial;GCPCT=76;GTCNT=1,0,1,1;NumNeighbors=1;NeighId=5;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.67651 GT:DP:AD 1/0:45:21,24 1/1:27:20,7 ./.:31:15,16 -chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCCATCCCCCGTCCGCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 61 . QNAME=HG002-S9-H2-000001F;QSTART=374905;QSTRAND=+;SVTYPE=INS;SVLEN=227;HOMPCT=37;REMAP=partial;GCPCT=76;GTCNT=1,0,1,1;NumNeighbors=1;NeighId=5;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.681844 GT:DP:AD 0/1:27:19,8 ./.:40:20,20 1/1:23:7,16 -chr20 421409 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=401013;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:29:23,6 1|0:33:15,18 1|1:17:6,11 -chr20 421527 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=375993;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:29:24,5 ./.:36:17,19 1|1:37:13,24 -chr20 422066 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=401670;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:31:24,7 1|0:40:16,24 1|1:30:23,7 -chr20 422277 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=376743;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:44:23,21 ./.:42:22,20 1|1:29:14,15 -chr20 422514 . GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=402119;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 1|0:42:17,25 1|0:50:25,25 ./.:20:5,15 -chr20 422548 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=402151;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:26:8,18 1|0:30:22,8 ./.:34:19,15 -chr20 422567 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=402170;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:26:11,15 1|0:38:15,23 ./.:32:13,19 -chr20 423009 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=402612;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:40:21,19 1|0:26:20,6 1|1:31:20,11 -chr20 423705 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=403308;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:22:17,5 1|0:38:15,23 1|1:43:22,21 -chr20 423763 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=403366;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:40:20,20 1|0:30:25,5 1|1:17:7,10 -chr20 424272 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=403875;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:34:17,17 1|0:47:25,22 1|1:26:17,9 -chr20 424413 . A AC 60 . QNAME=HG002-S9-H1-000001F;QSTART=404017;QSTRAND=+;GCPCT=50;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 1|0:38:17,21 1|0:21:6,15 1|0:31:19,12 -chr20 425626 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=405231;QSTRAND=+;GCPCT=50;GTCNT=0,0,1,2;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|1:14:6,8 1|0:31:21,10 1|1:41:16,25 -chr20 426816 . C CT 60 . QNAME=cluster19_000000F;QSTART=25335060;QSTRAND=-;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD ./.:16:9,7 1|0:27:22,5 1|0:40:22,18 -chr20 429226 . A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25281985;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:31:23,8 ./.:34:24,10 1|1:31:10,21 -chr20 429226 . AT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=383692;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 0|1:31:21,10 ./.:32:16,16 ./.:33:15,18 -chr20 429249 . G A 60 . QNAME=cluster19_000000F;QSTART=389451;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:36:17,19 0|1:30:10,20 ./.:17:9,8 -chr20 431198 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=410801;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:33:8,25 1|0:34:24,10 1|1:36:13,23 -chr20 433739 . AGGCTACCCACACTTCCTG A 60 . QNAME=HG002-S9-H1-000001F;QSTART=413343;QSTRAND=+;GCPCT=57;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.946204 GT:DP:AD 1|1:46:21,25 1|0:32:15,17 1|1:43:23,20 -chr20 433902 . T C 60 . QNAME=cluster19_000000F;QSTART=25327992;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:46:25,21 1|0:27:9,18 ./.:15:8,7 -chr20 434000 . G GT 60 . QNAME=cluster23_scaffold_3;QSTART=25277228;QSTRAND=-;GCPCT=50;GTCNT=2,0,0,1;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0.5 GT:DP:AD ./.:14:5,9 ./.:15:9,6 1|1:20:8,12 -chr20 434001 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=413586;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:16:9,7 1|0:36:12,24 1|1:28:12,16 -chr20 434561 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=414146;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:49:24,25 1|0:39:23,16 1|1:13:8,5 -chr20 435505 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=415090;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:30:10,20 1|0:25:18,7 1|1:45:20,25 -chr20 436968 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=416553;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,1,2;ADCNT=0,3,0,0;LCR=0 GT:DP:AD 1|1:25:19,6 1|0:28:19,9 1|1:13:5,8 -chr20 437555 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=417140;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:43:21,22 1|0:38:17,21 1|1:26:19,7 -chr20 438423 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=418008;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:32:25,7 1|0:39:22,17 ./.:38:24,14 -chr20 439461 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=419046;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:41:22,19 1|0:36:25,11 ./.:30:18,12 -chr20 441161 . T TCCA 60 . QNAME=HG002-S9-H1-000001F;QSTART=420747;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0.75 GT:DP:AD 1|1:32:17,15 1|0:31:18,13 ./.:12:6,6 -chr20 443554 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=423142;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:28:18,10 1|0:36:16,20 ./.:38:24,14 -chr20 443921 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=423509;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:27:17,10 1|0:19:9,10 ./.:36:11,25 -chr20 444453 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=424041;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:48:25,23 1|0:18:13,5 ./.:27:17,10 -chr20 444562 . GTTTT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=424151;QSTRAND=+;GCPCT=20;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.360964 GT:DP:AD 1|0:39:14,25 1|0:34:13,21 ./.:29:7,22 -chr20 444790 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=424374;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:30:20,10 1|0:45:23,22 ./.:29:16,13 -chr20 444962 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=424546;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:40:20,20 1|0:21:11,10 ./.:34:17,17 -chr20 445789 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=425373;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:42:22,20 1|0:35:17,18 ./.:20:7,13 -chr20 446426 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=426010;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:17:8,9 1|0:39:24,15 ./.:26:17,9 -chr20 446529 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=426113;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:21:8,13 1|0:17:6,11 ./.:26:18,8 -chr20 446943 . A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25264284;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:17:9,8 ./.:40:20,20 1|1:36:22,14 -chr20 446943 . AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=426528;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|1:35:19,16 1|0:25:8,17 ./.:16:9,7 -chr20 447123 . A AT 60 . QNAME=cluster23_scaffold_2;QSTART=25248333;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD ./.:23:16,7 ./.:40:20,20 0|1:15:8,7 -chr20 447395 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=426978;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:28:8,20 1|0:22:17,5 ./.:31:17,14 -chr20 448123 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=427706;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:36:13,23 1|0:24:12,12 ./.:39:22,17 -chr20 448284 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=427867;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:26:8,18 1|0:29:7,22 ./.:21:11,10 -chr20 448552 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=428135;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:22:7,15 1|0:22:11,11 ./.:24:7,17 -chr20 448689 . G GA 60 . QNAME=cluster19_000000F;QSTART=25313206;QSTRAND=-;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:31:7,24 1|0:47:25,22 1|0:41:17,24 -chr20 448689 . GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=428273;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|0:31:10,21 ./.:44:25,19 ./.:19:12,7 -chr20 448841 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25262384;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:38:13,25 ./.:28:21,7 1|0:37:18,19 -chr20 449078 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=428660;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:36:21,15 1|0:30:15,15 ./.:37:21,16 -chr20 449153 . C CTT 60 . QNAME=HG002-S9-H1-000001F;QSTART=428736;QSTRAND=+;GCPCT=33;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.459148 GT:DP:AD 1|0:32:25,7 1|0:27:18,9 ./.:31:15,16 -chr20 449266 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=428850;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:35:11,24 1|0:25:9,16 ./.:34:25,9 -chr20 449285 . T TA 60 . QNAME=cluster19_000000F;QSTART=409488;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:21:9,12 0|1:23:7,16 ./.:33:18,15 -chr20 449285 . T TAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=428870;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.295836 GT:DP:AD 1|0:26:18,8 1|0:21:7,14 ./.:20:8,12 -chr20 449362 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25261863;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:38:20,18 ./.:28:15,13 1|0:39:21,18 -chr20 449514 . GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=429105;QSTRAND=+;GCPCT=50;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 1|1:30:11,19 1|0:18:5,13 1|1:29:10,19 -chr20 450092 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=429681;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:40:24,16 1|0:44:24,20 ./.:24:9,15 -chr20 450315 . A AT 60 . QNAME=cluster23_scaffold_2;QSTART=25245141;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:29:6,23 ./.:34:25,9 0|1:34:23,11 -chr20 450858 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=430447;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:39:18,21 1|0:49:24,25 ./.:28:18,10 -chr20 452042 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=431631;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:17:12,5 1|0:33:11,22 ./.:32:7,25 -chr20 452135 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=431724;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:20:7,13 1|0:44:25,19 ./.:22:17,5 -chr20 453153 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25242302;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:40:24,16 ./.:33:17,16 0|1:39:23,16 -chr20 453153 . C CAA 60 . QNAME=cluster23_scaffold_3;QSTART=25258071;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,3,0,0;LCR=0.459148 GT:DP:AD ./.:29:20,9 ./.:10:5,5 1|0:28:20,8 -chr20 453153 . CAAAAAAAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=432743;QSTRAND=+;GCPCT=10;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.234498 GT:DP:AD 1|0:30:17,13 1|0:30:21,9 ./.:30:18,12 -chr20 453460 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=433040;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:44:21,23 1|0:13:6,7 ./.:30:19,11 -chr20 453539 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=433120;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|0:50:25,25 1|0:29:19,10 ./.:26:19,7 -chr20 453540 . A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25257683;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:42:17,25 ./.:32:15,17 1|1:32:14,18 -chr20 453540 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=433121;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:36:16,20 1|0:21:12,9 ./.:30:18,12 -chr20 453995 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=433576;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:35:11,24 1|0:15:6,9 ./.:44:24,20 -chr20 454087 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=433668;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:32:17,15 1|0:21:6,15 ./.:16:9,7 -chr20 454236 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=408684;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.5 GT:DP:AD 0|1:21:13,8 ./.:22:11,11 ./.:21:11,10 -chr20 454236 . CAA C 60 . QNAME=cluster19_000000F;QSTART=25307660;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.459148 GT:DP:AD ./.:36:13,23 1|0:38:22,16 ./.:40:23,17 -chr20 454236 . CAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=433818;QSTRAND=+;GCPCT=25;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.405639 GT:DP:AD 1|0:21:13,8 ./.:43:19,24 ./.:37:14,23 -chr20 454295 . G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=433874;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|0:33:15,18 1|0:24:11,13 ./.:20:12,8 -chr20 454614 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=434193;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:20:9,11 1|0:37:20,17 ./.:35:22,13 -chr20 454650 . C CATTATT 60 . QNAME=HG002-S9-H1-000001F;QSTART=434230;QSTRAND=+;GCPCT=14;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.689392 GT:DP:AD 1|0:29:12,17 1|0:21:7,14 ./.:33:22,11 -chr20 454798 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=434383;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:14:5,9 1|0:20:10,10 ./.:25:20,5 -chr20 456053 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=435638;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:38:19,19 1|0:25:18,7 ./.:15:10,5 -chr20 456337 . TTTCATCCA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=435923;QSTRAND=+;GCPCT=33;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.765247 GT:DP:AD 1|0:45:23,22 1|0:29:10,19 ./.:28:23,5 -chr20 456571 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=411018;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 0|1:28:18,10 ./.:14:7,7 ./.:37:20,17 -chr20 456603 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=436180;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:32:12,20 ./.:20:14,6 ./.:29:6,23 -chr20 456818 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=436395;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:12:5,7 1|0:42:17,25 ./.:24:18,6 -chr20 456933 . AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=436511;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 1|0:39:21,18 ./.:44:20,24 ./.:25:11,14 -chr20 456933 . ATTT A 60 . QNAME=cluster19_000000F;QSTART=417137;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.405639 GT:DP:AD ./.:41:24,17 0|1:40:17,23 1|1:34:16,18 -chr20 456933 . ATTTT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=411379;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0.360964 GT:DP:AD 0|1:35:22,13 ./.:11:5,6 ./.:31:15,16 -chr20 458314 . A AT 60 . QNAME=cluster23_scaffold_2;QSTART=25237142;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD ./.:41:18,23 ./.:35:25,10 0|1:25:15,10 -chr20 458331 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=412772;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:38:20,18 0|1:28:5,23 1|1:26:16,10 -chr20 458461 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=412902;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:46:22,24 0|1:24:13,11 1|1:35:16,19 -chr20 459799 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=414240;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:33:11,22 0|1:45:21,24 1|1:32:19,13 -chr20 460434 . CAAA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=414876;QSTRAND=+;GCPCT=25;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.405639 GT:DP:AD 0|1:43:23,20 0|1:32:16,16 1|1:25:10,15 -chr20 460464 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=414902;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:33:11,22 0|1:23:11,12 1|1:24:12,12 -chr20 461679 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=416117;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD 0|1:28:18,10 0|1:31:18,13 1|1:22:9,13 -chr20 462293 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=416731;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:42:18,24 0|1:28:7,21 1|1:44:24,20 -chr20 463154 . A G 60 . QNAME=cluster19_000000F;QSTART=423351;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:21:16,5 0|1:36:13,23 1|1:47:25,22 -chr20 463252 . C G 60 . QNAME=cluster19_000000F;QSTART=423449;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:41:18,23 0|1:35:13,22 1|1:36:13,23 -chr20 463841 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=418279;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:34:11,23 ./.:37:24,13 ./.:26:12,14 -chr20 465665 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=445241;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:35:18,17 1|1:41:24,17 1|1:38:23,15 -chr20 465676 . GC G 60 . QNAME=HG002-S9-H1-000001F;QSTART=445253;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 1|1:27:17,10 1|1:27:6,21 1|1:23:6,17 -chr20 466029 . A AAAAT 60 . QNAME=HG002-S9-H2-000001F;QSTART=420467;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.360964 GT:DP:AD 0|1:22:14,8 ./.:15:10,5 ./.:47:23,24 -chr20 466637 . G GTA 60 . QNAME=cluster23_scaffold_2;QSTART=25228821;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0.792481 GT:DP:AD ./.:21:15,6 ./.:16:10,6 0|1:22:15,7 -chr20 466637 . G GTATA 60 . QNAME=cluster19_000000F;QSTART=426834;QSTRAND=+;GCPCT=20;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.760964 GT:DP:AD ./.:28:7,21 0|1:22:14,8 1|0:19:14,5 -chr20 466637 . G GTGTATATATA 60 . QNAME=HG002-S9-H2-000001F;QSTART=421079;QSTRAND=+;GCPCT=18;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.747459 GT:DP:AD 0|1:47:23,24 ./.:28:22,6 ./.:31:23,8 -chr20 466637 . GTA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=446213;QSTRAND=+;GCPCT=33;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.792481 GT:DP:AD 1|0:26:18,8 1|0:29:5,24 ./.:32:19,13 -chr20 467024 . C CT 60 . QNAME=cluster23_scaffold_2;QSTART=25228433;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:36:15,21 ./.:32:23,9 0|1:43:24,19 -chr20 468015 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=447588;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:28:14,14 1|1:32:19,13 1|1:26:10,16 -chr20 468269 . C A 60 . QNAME=cluster19_000000F;QSTART=428469;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:25:8,17 0|1:39:14,25 1|1:40:15,25 -chr20 469249 . G A 60 . QNAME=cluster19_000000F;QSTART=429449;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:26:7,19 0|1:30:21,9 1|1:28:17,11 -chr20 469257 . A T 60 . QNAME=cluster19_000000F;QSTART=429457;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:27:8,19 0|1:37:25,12 1|1:33:19,14 -chr20 470060 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=424511;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 0|1:18:7,11 ./.:30:24,6 ./.:27:18,9 -chr20 471168 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=425619;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:22:10,12 ./.:38:23,15 ./.:17:9,8 -chr20 472424 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=451997;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:37:18,19 ./.:17:7,10 ./.:44:25,19 -chr20 472457 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=452030;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:22:8,14 1|1:28:8,20 1|1:22:8,14 -chr20 475460 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=429912;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 0|1:35:25,10 ./.:28:10,18 ./.:31:14,17 -chr20 475460 . CAAAAA C 60 . QNAME=cluster19_000000F;QSTART=435661;QSTRAND=+;GCPCT=16;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.325011 GT:DP:AD ./.:34:25,9 0|1:32:15,17 ./.:34:15,19 -chr20 477729 . C T 60 . QNAME=cluster19_000000F;QSTART=25284173;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:35:17,18 1|0:24:14,10 1|1:29:15,14 -chr20 478540 . TC T 60 . QNAME=HG002-S9-H2-000001F;QSTART=432991;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 0|1:33:10,23 ./.:22:14,8 ./.:31:14,17 -chr20 480234 . T G 60 . QNAME=cluster23_scaffold_3;QSTART=25230992;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:25:15,10 ./.:28:23,5 1|0:25:6,19 -chr20 484694 . T TTG 60 . QNAME=cluster19_000000F;QSTART=25277206;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.459148 GT:DP:AD ./.:41:22,19 1|0:23:12,11 ./.:24:19,5 -chr20 484991 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=464564;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:25:13,12 ./.:44:20,24 ./.:35:17,18 -chr20 485066 . CAAAA C 60 . QNAME=cluster23_scaffold_3;QSTART=25226160;QSTRAND=-;GCPCT=20;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.360964 GT:DP:AD ./.:21:10,11 ./.:27:20,7 1|0:22:12,10 -chr20 485103 . A ATATATATATAT 60 . QNAME=cluster23_scaffold_2;QSTART=25210343;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:32:7,25 ./.:26:9,17 0|1:19:7,12 -chr20 485105 . A ATAATATATATATAT 60 . QNAME=HG002-S9-H2-000001F;QSTART=439555;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.498396 GT:DP:AD 0|1:31:16,15 ./.:16:9,7 ./.:16:5,11 -chr20 485105 . A ATATATATATAT 60 . QNAME=cluster19_000000F;QSTART=25276784;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:32:13,19 1|0:26:11,15 ./.:23:7,16 -chr20 485105 . A T 60 . QNAME=cluster23_scaffold_2;QSTART=25210341;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:36:20,16 ./.:44:24,20 0|1:26:18,8 -chr20 485107 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=439570;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:15:8,7 1|0:46:23,23 1|1:21:15,6 -chr20 485109 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=439572;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:23:7,16 1|0:28:19,9 1|1:22:7,15 -chr20 485110 . ATAT A 60 . QNAME=cluster19_000000F;QSTART=445306;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:33:12,21 0|1:25:15,10 ./.:26:21,5 -chr20 485115 . T A 60 . QNAME=cluster19_000000F;QSTART=445307;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:16:7,9 0|1:32:13,19 ./.:13:6,7 -chr20 485117 . T A 60 . QNAME=cluster19_000000F;QSTART=445309;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:49:25,24 0|1:18:10,8 ./.:18:12,6 -chr20 485138 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=439601;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:35:14,21 ./.:40:17,23 ./.:31:21,10 -chr20 485139 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=439602;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:32:23,9 ./.:31:25,6 ./.:37:15,22 -chr20 487542 . G A 60 . QNAME=cluster19_000000F;QSTART=447734;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:38:19,19 0|1:33:14,19 ./.:13:5,8 -chr20 488040 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25223189;QSTRAND=-;GCPCT=50;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:41:23,18 ./.:36:17,19 1|1:29:14,15 -chr20 490335 . C CT 60 . QNAME=cluster19_000000F;QSTART=25271553;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:38:19,19 1|0:33:12,21 ./.:29:5,24 -chr20 490909 . A C 60 . QNAME=cluster19_000000F;QSTART=25270979;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:31:18,13 1|0:17:11,6 ./.:32:25,7 -chr20 493202 . A T 60 . QNAME=cluster19_000000F;QSTART=25268686;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:43:20,23 1|0:42:24,18 1|1:36:22,14 -chr20 494543 . T C 60 . QNAME=cluster19_000000F;QSTART=25267345;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:33:16,17 1|0:43:21,22 ./.:37:17,20 -chr20 498335 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25212893;QSTRAND=-;GCPCT=50;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:28:10,18 ./.:30:15,15 1|1:16:7,9 -chr20 498335 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=452799;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 0|1:28:6,22 ./.:30:18,12 ./.:46:22,24 -chr20 498901 . T C 60 . QNAME=cluster19_000000F;QSTART=459093;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:20:6,14 0|1:31:12,19 ./.:28:19,9 -chr20 499958 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25195485;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0.5 GT:DP:AD ./.:31:17,14 ./.:19:5,14 0|1:26:15,11 -chr20 500634 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=25210593;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:25:17,8 ./.:39:20,19 1|0:41:19,22 -chr20 501285 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=480825;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:19:5,14 ./.:17:11,6 ./.:29:17,12 -chr20 504037 . G GC 60 . QNAME=HG002-S9-H2-000001F;QSTART=458500;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0.5 GT:DP:AD 0|1:29:17,12 ./.:21:9,12 ./.:31:19,12 -chr20 505351 . G GT 60 . QNAME=cluster19_000000F;QSTART=25256536;QSTRAND=-;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD ./.:25:18,7 1|0:29:21,8 1|0:38:19,19 -chr20 505587 . C G 60 . QNAME=cluster19_000000F;QSTART=465779;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:44:22,22 0|1:11:6,5 ./.:26:15,11 -chr20 505869 . A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25205356;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:37:20,17 ./.:31:25,6 1|0:37:21,16 -chr20 505869 . AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=485410;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD 1|0:19:5,14 ./.:20:5,15 ./.:22:12,10 -chr20 505905 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25205320;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:32:14,18 ./.:14:8,6 1|0:38:17,21 -chr20 506070 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=485609;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:29:8,21 ./.:33:16,17 0|1:44:25,19 -chr20 506079 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=485618;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:17:11,6 ./.:32:9,23 0|1:29:14,15 -chr20 506080 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=485619;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:35:15,20 ./.:18:11,7 0|1:37:18,19 -chr20 506097 . C T 60 . QNAME=cluster19_000000F;QSTART=25255790;QSTRAND=-;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:25:10,15 1|0:45:20,25 1|0:15:9,6 -chr20 506098 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=485637;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:16:8,8 ./.:20:10,10 0|1:33:13,20 -chr20 506127 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25205098;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:27:20,7 ./.:26:14,12 1|0:32:12,20 -chr20 507967 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=487506;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:35:14,21 1|1:29:21,8 1|1:37:13,24 -chr20 508286 . C T 60 . QNAME=cluster19_000000F;QSTART=25253601;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD ./.:33:22,11 1|0:33:20,13 1|1:35:21,14 -chr20 508793 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25186650;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:22:16,6 ./.:39:19,20 0|1:34:24,10 -chr20 511703 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=466166;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:16:8,8 ./.:27:6,21 ./.:45:22,23 -chr20 511705 . C T 60 . QNAME=cluster19_000000F;QSTART=25250182;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:46:24,22 1|0:41:25,16 1|1:15:5,10 -chr20 512561 . G T 60 . QNAME=cluster19_000000F;QSTART=25249326;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:16:7,9 1|0:30:14,16 1|1:18:7,11 -chr20 512965 . T C 60 . QNAME=cluster19_000000F;QSTART=25248922;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:25:18,7 1|0:35:16,19 ./.:37:18,19 -chr20 514164 . C T 60 . QNAME=cluster19_000000F;QSTART=25247723;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:45:24,21 1|0:20:8,12 1|1:24:5,19 -chr20 518713 . AT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=473177;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 0|1:25:10,15 0|1:37:21,16 1|0:20:15,5 -chr20 518713 . ATT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=498253;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.459148 GT:DP:AD 1|0:22:7,15 1|0:44:24,20 0|1:27:6,21 -chr20 518933 . C CT 60 . QNAME=cluster23_scaffold_2;QSTART=25176511;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0.5 GT:DP:AD ./.:15:7,8 ./.:28:22,6 0|1:28:18,10 -chr20 518933 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=473396;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD 0|1:41:19,22 ./.:36:24,12 ./.:17:7,10 -chr20 522293 . C T 60 . QNAME=cluster19_000000F;QSTART=25239596;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:19:14,5 1|0:31:12,19 1|1:37:18,19 -chr20 523858 . C CA 60 . QNAME=cluster19_000000F;QSTART=25238030;QSTRAND=-;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:37:22,15 1|0:48:24,24 0|1:31:7,24 -chr20 523869 . A C 60 . QNAME=cluster19_000000F;QSTART=484060;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:19:5,14 0|1:21:15,6 ./.:33:13,20 -chr20 524145 . C T 60 . QNAME=cluster19_000000F;QSTART=25237743;QSTRAND=-;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:32:23,9 1|1:33:8,25 1|1:26:12,14 -chr20 524654 . T C 60 . QNAME=cluster19_000000F;QSTART=25237234;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:31:6,25 1|0:37:23,14 ./.:29:21,8 -chr20 524708 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=504246;QSTRAND=+;GCPCT=50;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD 1|0:36:14,22 1|0:28:16,12 0|1:19:8,11 -chr20 524708 . CAA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=479170;QSTRAND=+;GCPCT=33;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.459148 GT:DP:AD 0|1:26:14,12 0|1:26:19,7 ./.:42:21,21 -chr20 525133 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=504669;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:34:11,23 ./.:32:24,8 ./.:45:21,24 -chr20 525391 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=504927;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:37:12,25 ./.:21:6,15 ./.:20:13,7 -chr20 525650 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=505187;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 1|0:29:13,16 ./.:27:11,16 ./.:35:13,22 -chr20 525836 . T TA 60 . QNAME=cluster23_scaffold_2;QSTART=25169607;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:45:22,23 ./.:40:24,16 0|1:33:21,12 -chr20 525836 . TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=505372;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|0:30:25,5 ./.:31:20,11 ./.:34:16,18 -chr20 526238 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=505772;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:29:23,6 1|0:39:15,24 1|1:36:15,21 -chr20 526685 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=506219;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:34:12,22 ./.:27:14,13 ./.:33:21,12 -chr20 526949 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=506484;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 1|0:37:21,16 ./.:49:25,24 ./.:41:24,17 -chr20 527001 . C CAG 60 . QNAME=cluster23_scaffold_2;QSTART=25168440;QSTRAND=-;GCPCT=66;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.792481 GT:DP:AD ./.:25:13,12 ./.:23:14,9 0|1:26:16,10 -chr20 527001 . C CAGAG 60 . QNAME=cluster23_scaffold_3;QSTART=25184221;QSTRAND=-;GCPCT=60;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.760964 GT:DP:AD ./.:30:19,11 ./.:23:6,17 1|0:35:20,15 -chr20 527001 . C CAGAGAGAGAG 60 . QNAME=cluster19_000000F;QSTART=25234878;QSTRAND=-;GCPCT=54;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.674294 GT:DP:AD ./.:41:17,24 1|0:34:19,15 ./.:23:6,17 -chr20 527003 . G GAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=506537;QSTRAND=+;GCPCT=66;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.792481 GT:DP:AD 1|0:33:21,12 ./.:39:14,25 ./.:32:22,10 -chr20 527729 . G A 60 . QNAME=cluster19_000000F;QSTART=487918;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:47:22,25 0|1:23:14,9 ./.:35:13,22 -chr20 527782 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=507317;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:21:12,9 ./.:29:12,17 ./.:37:20,17 -chr20 528449 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=507984;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:35:13,22 ./.:26:21,5 ./.:28:6,22 -chr20 528594 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=508130;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.5 GT:DP:AD 1|0:18:6,12 ./.:28:23,5 ./.:29:18,11 -chr20 529190 . A AT 60 . QNAME=cluster19_000000F;QSTART=25232688;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:43:24,19 1|0:18:5,13 1|1:32:14,18 -chr20 530468 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=510003;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 1|0:33:10,23 ./.:26:13,13 ./.:35:12,23 -chr20 531253 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=510788;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:21:10,11 ./.:32:16,16 ./.:44:21,23 -chr20 532330 . ATT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=511866;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.459148 GT:DP:AD 1|0:21:10,11 ./.:17:10,7 ./.:17:6,11 -chr20 532352 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=511885;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:25:12,13 ./.:14:9,5 ./.:31:14,17 -chr20 533815 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=513348;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:42:19,23 ./.:36:15,21 ./.:26:5,21 -chr20 535034 . C CA 60 . QNAME=cluster19_000000F;QSTART=495224;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD ./.:30:7,23 0|1:20:13,7 ./.:24:18,6 -chr20 535034 . CAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=514568;QSTRAND=+;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0.459148 GT:DP:AD 1|0:12:6,6 ./.:22:13,9 ./.:39:16,23 -chr20 535629 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=515160;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:34:16,18 ./.:48:24,24 ./.:29:12,17 -chr20 535685 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=515216;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:29:19,10 ./.:24:6,18 ./.:33:19,14 -chr20 535739 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=515271;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0.5 GT:DP:AD 1|0:15:8,7 ./.:24:18,6 ./.:26:15,11 -chr20 537243 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=516773;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:34:21,13 ./.:29:24,5 ./.:17:6,11 -chr20 537496 . G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=517027;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 1|0:27:8,19 ./.:24:14,10 ./.:29:13,16 -chr20 537963 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=517495;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|0:45:20,25 ./.:13:8,5 ./.:34:16,18 -chr20 538108 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=517640;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:47:25,22 1|0:17:5,12 1|1:30:13,17 -chr20 539053 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=518585;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:42:22,20 ./.:21:9,12 ./.:33:8,25 -chr20 539493 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25155947;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:26:12,14 ./.:16:11,5 0|1:24:9,15 -chr20 541244 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=520776;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:39:16,23 ./.:16:10,6 ./.:16:7,9 -chr20 541502 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=521034;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:37:25,12 ./.:27:12,15 ./.:39:25,14 -chr20 542623 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=522155;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:47:22,25 ./.:24:18,6 ./.:22:11,11 -chr20 544402 . G GT 60 . QNAME=cluster19_000000F;QSTART=25217475;QSTRAND=-;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD ./.:42:22,20 1|0:25:12,13 1|1:23:10,13 -chr20 545973 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=525505;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:25:20,5 ./.:40:15,25 ./.:35:19,16 -chr20 546122 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25149317;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:14:8,6 ./.:29:9,20 0|1:17:11,6 -chr20 546487 . ACT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=526020;QSTRAND=+;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.792481 GT:DP:AD 1|0:34:13,21 ./.:26:21,5 ./.:19:13,6 -chr20 547548 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=527078;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:32:15,17 ./.:21:9,12 ./.:30:23,7 -chr20 548222 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=527752;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD 1|0:29:16,13 0|1:37:25,12 ./.:19:6,13 -chr20 548575 . ATATTTT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=528106;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.43156 GT:DP:AD 1|0:20:14,6 ./.:26:19,7 ./.:41:21,20 -chr20 548577 . A AT 60 . QNAME=cluster19_000000F;QSTART=25213299;QSTRAND=-;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD ./.:26:9,17 1|0:18:11,7 0|1:16:9,7 -chr20 548577 . A ATT 60 . QNAME=cluster23_scaffold_3;QSTART=25162641;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0.459148 GT:DP:AD ./.:27:16,11 ./.:24:18,6 1|0:17:8,9 -chr20 548971 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=528495;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:27:9,18 ./.:27:8,19 ./.:29:15,14 -chr20 549092 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=528616;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:46:23,23 ./.:17:12,5 ./.:31:11,20 -chr20 549227 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=528751;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:37:20,17 ./.:14:9,5 ./.:33:12,21 -chr20 549649 . GGAAA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=529174;QSTRAND=+;GCPCT=40;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.485475 GT:DP:AD 1|0:24:9,15 ./.:33:11,22 ./.:47:22,25 -chr20 549670 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=529190;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:39:20,19 ./.:30:20,10 ./.:18:12,6 -chr20 550104 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=529624;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:42:25,17 ./.:19:13,6 ./.:35:12,23 -chr20 550577 . C T 60 . QNAME=cluster19_000000F;QSTART=25211299;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:31:8,23 1|0:23:8,15 1|1:35:22,13 -chr20 551334 . C A 60 . QNAME=cluster19_000000F;QSTART=25210542;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:13:6,7 1|0:42:18,24 1|1:22:7,15 -chr20 551415 . T A 60 . QNAME=cluster19_000000F;QSTART=25210461;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:32:14,18 1|0:32:22,10 1|1:33:25,8 -chr20 551424 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=530944;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:30:24,6 1|0:36:11,25 1|1:24:17,7 -chr20 551459 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=530979;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:29:5,24 1|0:18:9,9 1|1:23:15,8 -chr20 552161 . G A 60 . QNAME=cluster19_000000F;QSTART=25209715;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:28:18,10 1|0:26:16,10 1|1:35:14,21 -chr20 552253 . C T 60 . QNAME=cluster19_000000F;QSTART=25209623;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:39:16,23 1|0:42:18,24 1|1:32:22,10 -chr20 552281 . A G 60 . QNAME=cluster19_000000F;QSTART=25209595;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:38:19,19 1|0:24:16,8 1|1:29:11,18 -chr20 552720 . CT C 60 . QNAME=cluster19_000000F;QSTART=25209156;QSTRAND=-;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:38:23,15 1|0:25:12,13 1|1:39:24,15 -chr20 553245 . C G 60 . QNAME=cluster19_000000F;QSTART=25208632;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:33:24,9 1|0:48:23,25 1|1:25:13,12 -chr20 553335 . C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=532856;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|0:25:15,10 ./.:23:17,6 ./.:40:25,15 -chr20 553335 . C CAAA 60 . QNAME=cluster19_000000F;QSTART=25208539;QSTRAND=-;GCPCT=25;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.405639 GT:DP:AD ./.:27:11,16 1|0:25:14,11 1|1:26:5,21 -chr20 553335 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=507795;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 0|1:48:23,25 ./.:41:16,25 ./.:31:8,23 -chr20 553919 . C T 60 . QNAME=cluster19_000000F;QSTART=25207955;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:32:15,17 1|0:37:22,15 1|1:23:7,16 -chr20 554853 . T A 60 . QNAME=cluster19_000000F;QSTART=25207021;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:33:19,14 1|0:19:14,5 1|1:32:11,21 -chr20 555892 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=535413;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:40:17,23 1|1:37:18,19 1|1:22:8,14 -chr20 556119 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=535640;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:22:6,16 0|1:17:12,5 1|1:22:15,7 -chr20 556141 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=535662;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:22:6,16 1|1:34:21,13 1|1:28:6,22 -chr20 556215 . G A 60 . QNAME=cluster19_000000F;QSTART=516405;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:16:10,6 0|1:41:21,20 1|1:20:9,11 -chr20 556356 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=535877;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:22:17,5 ./.:22:15,7 ./.:32:10,22 -chr20 556431 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=510889;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:16:11,5 1|0:34:17,17 ./.:33:9,24 -chr20 556435 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=535956;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:34:15,19 0|1:39:20,19 1|1:43:22,21 -chr20 556632 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=536153;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:39:17,22 1|1:38:13,25 1|1:20:9,11 -chr20 556794 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=536315;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:25:18,7 1|1:32:10,22 1|1:48:25,23 -chr20 556861 . C A 60 . QNAME=cluster19_000000F;QSTART=517051;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:20:9,11 0|1:28:19,9 1|1:44:25,19 -chr20 556869 . C CAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=536391;QSTRAND=+;GCPCT=25;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.405639 GT:DP:AD 1|1:50:25,25 1|0:27:5,22 ./.:46:25,21 -chr20 556869 . C CAAAAA 60 . QNAME=cluster23_scaffold_2;QSTART=25138562;QSTRAND=-;GCPCT=16;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.325011 GT:DP:AD ./.:32:15,17 ./.:44:25,19 0|1:15:6,9 -chr20 556869 . C CAAAAAA 60 . QNAME=cluster23_scaffold_3;QSTART=25154341;QSTRAND=-;GCPCT=14;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.295836 GT:DP:AD ./.:35:23,12 ./.:42:25,17 1|0:36:13,23 -chr20 556881 . A AAAAAAT 60 . QNAME=cluster19_000000F;QSTART=517072;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.295836 GT:DP:AD ./.:28:9,19 0|1:33:16,17 ./.:16:11,5 -chr20 556883 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=536407;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:26:6,20 1|0:29:5,24 ./.:33:17,16 -chr20 556885 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=536409;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,3,0,0;LCR=0 GT:DP:AD 1|1:21:14,7 1|0:11:6,5 ./.:17:8,9 -chr20 556887 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=536411;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:29:13,16 1|0:38:25,13 ./.:16:5,11 -chr20 557034 . T C 60 . QNAME=cluster19_000000F;QSTART=517230;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:14:9,5 0|1:28:13,15 1|1:41:22,19 -chr20 557559 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=537083;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:37:14,23 1|0:23:14,9 ./.:35:18,17 -chr20 557586 . C T 60 . QNAME=cluster19_000000F;QSTART=517782;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:11:5,6 0|1:18:6,12 1|1:28:21,7 -chr20 557591 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=537115;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:47:22,25 1|1:14:8,6 1|1:41:24,17 -chr20 557603 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=537127;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|1:20:14,6 1|0:21:14,7 ./.:24:14,10 -chr20 557995 . C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=537520;QSTRAND=+;GCPCT=50;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|1:43:25,18 1|1:45:22,23 1|1:23:18,5 -chr20 558185 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=537710;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:46:22,24 1|0:21:8,13 ./.:41:25,16 -chr20 558374 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=537899;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,3,0,0;LCR=0 GT:DP:AD 1|1:14:8,6 1|0:20:14,6 ./.:28:22,6 -chr20 558479 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=538004;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:37:14,23 1|0:31:11,20 ./.:25:12,13 -chr20 558579 . ATTTT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=538105;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.360964 GT:DP:AD 1|1:23:18,5 1|0:22:10,12 ./.:42:19,23 -chr20 558719 . G A 60 . QNAME=cluster19_000000F;QSTART=518916;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:21:11,10 0|1:16:9,7 1|1:39:15,24 -chr20 558928 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=538449;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:42:24,18 1|0:34:24,10 ./.:33:22,11 -chr20 559006 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=538527;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:29:16,13 1|1:35:15,20 1|1:35:12,23 -chr20 559112 . G GT 60 . QNAME=HG002-S9-H1-000001F;QSTART=538634;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0.5 GT:DP:AD 1|1:38:25,13 1|0:21:9,12 ./.:39:25,14 -chr20 559189 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=538711;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:37:22,15 1|1:34:10,24 1|1:28:21,7 -chr20 559234 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=538756;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:36:23,13 1|0:38:20,18 1|0:15:10,5 -chr20 559282 . G T 60 . QNAME=cluster19_000000F;QSTART=519479;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:42:21,21 0|1:34:19,15 0|1:36:16,20 -chr20 559554 . T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=539077;QSTRAND=+;GCPCT=50;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|1:17:10,7 1|1:35:15,20 1|1:30:9,21 -chr20 560062 . AC A 60 . QNAME=HG002-S9-H2-000001F;QSTART=514523;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 0|1:33:18,15 ./.:15:7,8 ./.:37:22,15 -chr20 560063 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=539586;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:33:21,12 1|0:18:12,6 ./.:28:6,22 -chr20 560078 . CAA C 60 . QNAME=cluster19_000000F;QSTART=520277;QSTRAND=+;GCPCT=33;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.459148 GT:DP:AD ./.:38:25,13 0|1:35:10,25 1|1:18:7,11 -chr20 560086 . C G 60 . QNAME=cluster19_000000F;QSTART=520282;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:31:10,21 0|1:31:20,11 1|1:29:20,9 -chr20 560086 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=539610;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 1|1:24:8,16 1|0:38:19,19 ./.:35:23,12 -chr20 560087 . A C 60 . QNAME=cluster19_000000F;QSTART=520283;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:35:17,18 0|1:29:21,8 1|1:33:25,8 -chr20 560103 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=539625;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:39:18,21 1|1:28:10,18 1|1:17:5,12 -chr20 560343 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=514801;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:25:7,18 1|0:39:25,14 ./.:20:14,6 -chr20 560618 . G T 60 . QNAME=cluster19_000000F;QSTART=520814;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:39:19,20 0|1:22:7,15 1|1:37:16,21 -chr20 560691 . G A 60 . QNAME=cluster19_000000F;QSTART=520887;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:28:9,19 0|1:32:23,9 1|1:28:22,6 -chr20 560945 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=540467;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:28:9,19 1|0:27:16,11 ./.:15:5,10 -chr20 561211 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=540733;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|1:26:14,12 1|1:20:10,10 1|1:21:14,7 -chr20 562030 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=541552;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:16:11,5 1|1:38:23,15 1|1:34:22,12 -chr20 562133 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=541655;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:22:12,10 1|1:31:23,8 1|1:43:21,22 -chr20 562219 . A G 60 . QNAME=cluster19_000000F;QSTART=522415;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:31:14,17 0|1:33:24,9 1|1:27:11,16 -chr20 562642 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=542164;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:23:9,14 1|1:23:11,12 1|1:33:17,16 -chr20 562657 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=542179;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:29:22,7 1|1:45:20,25 1|1:36:18,18 -chr20 562994 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=542516;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:32:11,21 1|1:26:5,21 1|1:36:17,19 -chr20 563100 . C T 60 . QNAME=cluster19_000000F;QSTART=523296;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:34:23,11 0|1:25:14,11 1|1:33:16,17 -chr20 563396 . C T 60 . QNAME=cluster19_000000F;QSTART=25198477;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:17:6,11 1|0:25:14,11 ./.:29:13,16 -chr20 563773 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=543295;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:32:25,7 1|0:22:10,12 ./.:32:9,23 -chr20 564270 . G A 60 . QNAME=cluster19_000000F;QSTART=25197603;QSTRAND=-;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:24:19,5 1|1:29:12,17 1|1:28:9,19 -chr20 564271 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=543793;QSTRAND=+;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:28:9,19 ./.:27:16,11 ./.:20:14,6 -chr20 564553 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=519011;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:30:16,14 1|1:21:6,15 1|1:32:15,17 -chr20 564560 . GTGTT G 60 . QNAME=cluster23_scaffold_3;QSTART=25146650;QSTRAND=-;GCPCT=40;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.485475 GT:DP:AD ./.:38:13,25 ./.:30:17,13 1|0:25:14,11 -chr20 564629 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25130802;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:24:19,5 ./.:23:17,6 0|1:25:11,14 -chr20 565205 . A AT 60 . QNAME=cluster19_000000F;QSTART=25196667;QSTRAND=-;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:37:14,23 1|1:33:8,25 1|1:30:25,5 -chr20 565232 . C T 60 . QNAME=cluster19_000000F;QSTART=25196640;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:27:6,21 1|1:47:22,25 1|0:39:24,15 -chr20 565534 . T A 60 . QNAME=cluster19_000000F;QSTART=25196338;QSTRAND=-;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:23:18,5 1|1:23:15,8 1|1:25:5,20 -chr20 565902 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=545424;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:29:8,21 ./.:16:5,11 ./.:21:6,15 -chr20 565980 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=545502;QSTRAND=+;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:30:24,6 ./.:26:6,20 ./.:33:9,24 -chr20 566018 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25145195;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:21:5,16 ./.:31:21,10 1|0:44:24,20 -chr20 566096 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=545618;QSTRAND=+;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:31:25,6 ./.:25:18,7 ./.:34:11,23 -chr20 566178 . AAAAAAT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=545701;QSTRAND=+;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0.295836 GT:DP:AD 1|1:22:9,13 ./.:27:14,13 ./.:34:22,12 -chr20 567105 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=546621;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:35:15,20 ./.:32:24,8 ./.:23:17,6 -chr20 568286 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=522738;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:38:21,17 ./.:18:13,5 ./.:40:22,18 -chr20 568720 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=523172;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:35:14,21 ./.:34:17,17 ./.:24:17,7 -chr20 568936 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25142277;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:19:6,13 ./.:38:16,22 1|0:40:18,22 -chr20 569261 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=523713;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:32:13,19 ./.:36:18,18 ./.:28:17,11 -chr20 569263 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=548779;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:24:12,12 ./.:16:6,10 ./.:16:11,5 -chr20 569274 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=523726;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:32:21,11 ./.:40:21,19 ./.:35:16,19 -chr20 569446 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=523898;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:28:6,22 1|0:31:23,8 ./.:31:8,23 -chr20 569520 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=523972;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:36:22,14 1|1:32:21,11 1|1:36:15,21 -chr20 569616 . A C 60 . QNAME=cluster19_000000F;QSTART=25192256;QSTRAND=-;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:25:15,10 1|1:42:24,18 1|1:28:7,21 -chr20 569956 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=524408;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:32:17,15 ./.:26:15,11 ./.:24:11,13 -chr20 570171 . A C 60 . QNAME=cluster19_000000F;QSTART=25191701;QSTRAND=-;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD ./.:36:24,12 1|1:15:5,10 1|1:23:11,12 -chr20 570174 . T C 60 . QNAME=cluster19_000000F;QSTART=25191698;QSTRAND=-;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:27:9,18 1|1:37:15,22 1|1:26:21,5 -chr20 570223 . C CT 60 . QNAME=cluster19_000000F;QSTART=25191648;QSTRAND=-;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:44:24,20 1|1:24:11,13 0|1:44:20,24 -chr20 570223 . C CTT 60 . QNAME=cluster23_scaffold_3;QSTART=25140988;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.459148 GT:DP:AD ./.:24:7,17 ./.:28:16,12 1|0:36:12,24 -chr20 570243 . G A 60 . QNAME=cluster19_000000F;QSTART=25191628;QSTRAND=-;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:28:17,11 1|1:41:22,19 1|1:37:19,18 -chr20 570390 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=524842;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:27:19,8 1|1:26:16,10 1|1:29:8,21 -chr20 570410 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=524862;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:43:18,25 ./.:38:16,22 ./.:28:7,21 -chr20 570752 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=525204;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:38:18,20 1|1:33:18,15 1|1:38:20,18 -chr20 571051 . C CT 60 . QNAME=HG002-S9-H2-000001F;QSTART=525504;QSTRAND=+;GCPCT=50;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 0|1:21:15,6 1|1:31:9,22 1|1:34:15,19 -chr20 571277 . T C 60 . QNAME=cluster19_000000F;QSTART=25190593;QSTRAND=-;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:21:13,8 1|1:19:14,5 1|1:34:23,11 -chr20 571843 . G A 60 . QNAME=cluster19_000000F;QSTART=25190027;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:36:24,12 1|0:36:22,14 ./.:12:6,6 -chr20 571992 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=551509;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 1|0:43:23,20 ./.:48:23,25 ./.:31:17,14 -chr20 573141 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=552656;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:43:21,22 ./.:44:25,19 ./.:29:11,18 -chr20 574599 . C CT 60 . QNAME=cluster19_000000F;QSTART=25187270;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD ./.:25:12,13 1|0:29:14,15 ./.:29:19,10 -chr20 574632 . G A 60 . QNAME=cluster19_000000F;QSTART=25187237;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:37:12,25 1|0:30:12,18 ./.:31:7,24 -chr20 574708 . G A 60 . QNAME=cluster19_000000F;QSTART=25187161;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:24:7,17 1|1:38:16,22 ./.:43:19,24 -chr20 577333 . G A 60 . QNAME=cluster19_000000F;QSTART=537532;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:36:19,17 0|1:30:8,22 ./.:32:19,13 -chr20 577957 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=557473;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|1:34:16,18 ./.:40:17,23 0|1:26:20,6 -chr20 577957 . CAA C 60 . QNAME=cluster19_000000F;QSTART=25183912;QSTRAND=-;GCPCT=33;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.459148 GT:DP:AD ./.:23:7,16 1|1:22:15,7 ./.:34:20,14 -chr20 578654 . T TAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=533107;QSTRAND=+;GCPCT=33;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.792481 GT:DP:AD 0|1:31:14,17 ./.:32:23,9 1|1:25:8,17 -chr20 578654 . TAC T 60 . QNAME=cluster19_000000F;QSTART=25183217;QSTRAND=-;GCPCT=33;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.792481 GT:DP:AD ./.:46:24,22 1|1:30:14,16 ./.:25:13,12 -chr20 578790 . T C 60 . QNAME=cluster19_000000F;QSTART=25183083;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:31:15,16 1|1:32:8,24 ./.:28:22,6 -chr20 580481 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=559995;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:32:16,16 1|1:36:12,24 0|1:42:24,18 -chr20 580899 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=560413;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:35:17,18 1|1:25:8,17 ./.:31:20,11 -chr20 581272 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=560786;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:22:9,13 1|0:28:13,15 ./.:33:14,19 -chr20 581577 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=536031;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:46:22,24 ./.:40:24,16 ./.:35:21,14 -chr20 581670 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=561184;QSTRAND=+;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:20:11,9 1|1:36:18,18 ./.:18:5,13 -chr20 581801 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=561315;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:27:17,10 1|1:28:17,11 1|0:26:9,17 -chr20 581995 . GT G 60 . QNAME=HG002-S9-H2-000001F;QSTART=536450;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD 0|1:29:7,22 ./.:17:6,11 1|1:29:16,13 -chr20 581995 . GTT G 60 . QNAME=cluster19_000000F;QSTART=25179878;QSTRAND=-;GCPCT=33;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.459148 GT:DP:AD ./.:29:9,20 1|1:29:7,22 ./.:45:23,22 -chr20 581995 . GTTT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=561510;QSTRAND=+;GCPCT=25;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.405639 GT:DP:AD 1|0:17:8,9 ./.:29:11,18 ./.:29:21,8 -chr20 582041 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=536494;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:20:12,8 ./.:10:5,5 0|1:46:22,24 -chr20 582389 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=536842;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:38:20,18 ./.:20:10,10 0|1:28:11,17 -chr20 583353 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=562864;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:20:7,13 1|1:26:15,11 ./.:26:21,5 -chr20 583466 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=537919;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:29:14,15 ./.:40:18,22 0|1:39:21,18 -chr20 583895 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=538348;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:29:9,20 ./.:31:14,17 0|1:36:20,16 -chr20 584249 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=563760;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:17:8,9 1|1:39:22,17 0|1:30:17,13 -chr20 584433 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=538886;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:37:22,15 ./.:19:10,9 0|1:22:6,16 -chr20 584664 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=539117;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:45:23,22 ./.:33:21,12 0|1:38:19,19 -chr20 584861 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=539314;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:23:5,18 ./.:30:11,19 0|1:16:9,7 -chr20 585289 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=564800;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:42:21,21 1|1:21:9,12 0|1:24:13,11 -chr20 585341 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=539794;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:42:17,25 ./.:11:6,5 0|1:33:14,19 -chr20 585726 . A ATATATGTATATGTACG 60 . QNAME=HG002-S9-H2-000001F;QSTART=540180;QSTRAND=+;GCPCT=23;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.869727 GT:DP:AD 0|1:17:11,6 ./.:35:12,23 0|1:15:9,6 -chr20 585739 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=540208;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:28:16,12 ./.:34:20,14 0|1:27:12,15 -chr20 585749 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=540218;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:24:18,6 ./.:22:5,17 0|1:38:17,21 -chr20 585766 . GTA G 60 . QNAME=HG002-S9-H2-000001F;QSTART=540236;QSTRAND=+;GCPCT=33;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.792481 GT:DP:AD 0|1:34:22,12 ./.:28:13,15 0|1:30:20,10 -chr20 586045 . C CT 60 . QNAME=cluster19_000000F;QSTART=25175829;QSTRAND=-;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:33:13,20 1|1:33:10,23 1|0:11:6,5 -chr20 586045 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=540513;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 0|1:26:16,10 ./.:28:13,15 0|1:50:25,25 -chr20 586124 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=540590;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD 0|1:30:17,13 ./.:32:18,14 0|1:20:7,13 -chr20 586280 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=565791;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:32:15,17 1|1:41:16,25 ./.:25:18,7 -chr20 586536 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=541002;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:31:8,23 ./.:19:8,11 0|1:38:21,17 -chr20 588052 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=542518;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:32:7,25 ./.:39:15,24 0|1:15:7,8 -chr20 588077 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=542543;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:32:12,20 ./.:44:19,25 0|1:40:16,24 -chr20 588283 . A AT 60 . QNAME=cluster19_000000F;QSTART=25173590;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:28:11,17 1|1:44:20,24 ./.:39:17,22 -chr20 588283 . A ATT 60 . QNAME=HG002-S9-H2-000001F;QSTART=542750;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.459148 GT:DP:AD 0|1:33:24,9 ./.:24:15,9 0|1:25:7,18 -chr20 590301 . A AAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=569813;QSTRAND=+;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.459148 GT:DP:AD 1|0:46:21,25 ./.:29:24,5 ./.:34:13,21 -chr20 590301 . A AACAC 60 . QNAME=cluster19_000000F;QSTART=25171568;QSTRAND=-;GCPCT=40;GTCNT=2,0,0,1;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0.485475 GT:DP:AD ./.:35:12,23 1|1:11:6,5 ./.:21:5,16 -chr20 590301 . AAC A 60 . QNAME=HG002-S9-H2-000001F;QSTART=544770;QSTRAND=+;GCPCT=33;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0.459148 GT:DP:AD 0|1:21:8,13 ./.:13:7,6 0|1:21:13,8 -chr20 590927 . G C 60 . QNAME=cluster23_scaffold_2;QSTART=25104488;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:28:23,5 ./.:49:25,24 0|1:31:6,25 -chr20 591644 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=546111;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 0|1:37:17,20 ./.:20:11,9 ./.:33:20,13 -chr20 592228 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=546693;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:32:10,22 ./.:34:19,15 0|1:33:10,23 -chr20 592392 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=546857;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:27:6,21 ./.:14:6,8 0|1:23:7,16 -chr20 593097 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=547562;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:30:6,24 ./.:18:11,7 0|1:13:7,6 -chr20 593103 . T TTA 60 . QNAME=cluster19_000000F;QSTART=25168764;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.459148 GT:DP:AD ./.:20:6,14 1|0:20:12,8 ./.:34:16,18 -chr20 593121 . A ATATATATTTTT 60 . QNAME=HG002-S9-H2-000001F;QSTART=547587;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0.459148 GT:DP:AD 0|1:34:23,11 ./.:36:22,14 ./.:29:16,13 -chr20 593121 . A ATATATTTTTTT 60 . QNAME=cluster23_scaffold_2;QSTART=25102283;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0.405639 GT:DP:AD ./.:13:6,7 ./.:47:22,25 0|1:38:16,22 -chr20 593121 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25118087;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:20:8,12 ./.:36:13,23 1|0:31:16,15 -chr20 593122 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=572636;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD 1|0:31:18,13 0|1:34:22,12 ./.:40:16,24 -chr20 593123 . T A 60 . QNAME=cluster19_000000F;QSTART=25168744;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:27:7,20 1|0:36:21,15 ./.:27:10,17 -chr20 593266 . CTTTTTTT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=572781;QSTRAND=+;GCPCT=12;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.271782 GT:DP:AD 1|0:29:24,5 1|1:27:5,22 ./.:46:25,21 -chr20 593638 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=548114;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:39:18,21 ./.:30:24,6 0|1:21:14,7 -chr20 593664 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=548140;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:26:9,17 ./.:29:9,20 0|1:11:6,5 -chr20 594618 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25100785;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:30:9,21 ./.:24:15,9 0|1:25:8,17 -chr20 594618 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=549095;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD 0|1:34:25,9 ./.:33:9,24 ./.:25:19,6 -chr20 595396 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=549872;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD 0|1:25:20,5 ./.:43:24,19 ./.:27:22,5 -chr20 595643 . T TTTA 60 . QNAME=HG002-S9-H1-000001F;QSTART=575151;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.405639 GT:DP:AD 1|0:19:6,13 1|1:30:19,11 ./.:46:22,24 -chr20 596470 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25114738;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:31:9,22 ./.:43:25,18 1|0:36:13,23 -chr20 596536 . G GAAAACA 60 . QNAME=cluster23_scaffold_3;QSTART=25114666;QSTRAND=-;GCPCT=28;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0.574417 GT:DP:AD ./.:26:8,18 ./.:10:5,5 1|0:46:24,22 -chr20 596656 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=576166;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:30:22,8 1|1:40:15,25 ./.:38:14,24 -chr20 596715 . C T 60 . QNAME=cluster19_000000F;QSTART=556911;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:10:5,5 0|1:36:22,14 ./.:38:22,16 -chr20 597212 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=576722;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:33:24,9 1|1:24:17,7 ./.:32:8,24 -chr20 597374 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=576884;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:36:19,17 1|1:25:18,7 ./.:23:5,18 -chr20 597779 . C T 60 . QNAME=cluster19_000000F;QSTART=557975;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:47:22,25 0|1:42:22,20 ./.:29:6,23 -chr20 598186 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25113016;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:21:14,7 ./.:36:15,21 1|0:17:7,10 -chr20 598263 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=552737;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 0|1:28:22,6 ./.:17:6,11 0|1:24:10,14 -chr20 598702 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25112500;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:30:7,23 ./.:15:6,9 1|0:24:15,9 -chr20 599013 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=578523;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:26:14,12 1|1:30:14,16 1|1:30:19,11 -chr20 599169 . AT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=553644;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 0|1:38:19,19 1|1:24:5,19 1|0:25:18,7 -chr20 599169 . ATT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=578680;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.459148 GT:DP:AD 1|0:33:8,25 ./.:26:6,20 0|1:39:24,15 -chr20 599421 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=578929;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:18:8,10 1|1:34:10,24 ./.:22:7,15 -chr20 600604 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=580112;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:23:15,8 1|1:42:18,24 1|1:34:14,20 -chr20 600839 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=580347;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:22:17,5 1|1:32:16,16 ./.:15:5,10 -chr20 600991 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=580499;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:44:19,25 1|1:33:14,19 ./.:18:13,5 -chr20 601642 . G A 60 . QNAME=cluster19_000000F;QSTART=25160230;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:23:13,10 1|0:37:15,22 ./.:29:5,24 -chr20 601683 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=581192;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 1|0:44:25,19 1|1:44:22,22 0|1:42:22,20 -chr20 601683 . T TAA 60 . QNAME=cluster23_scaffold_3;QSTART=25109518;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0.459148 GT:DP:AD ./.:45:25,20 ./.:40:21,19 1|0:14:9,5 -chr20 601733 . GC G 60 . QNAME=cluster23_scaffold_3;QSTART=25109468;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:24:6,18 ./.:40:25,15 1|1:20:5,15 -chr20 602460 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=581969;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:12:6,6 1|1:33:22,11 ./.:25:5,20 -chr20 602943 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25108259;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:44:21,23 ./.:30:12,18 1|1:28:15,13 -chr20 606311 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=585820;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:28:13,15 1|1:42:25,17 1|1:23:13,10 -chr20 606780 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=586289;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:25:17,8 ./.:22:9,13 1|1:24:9,15 -chr20 607272 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=561745;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:38:17,21 ./.:14:5,9 ./.:28:10,18 -chr20 607445 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=586954;QSTRAND=+;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:37:18,19 ./.:31:25,6 1|1:37:19,18 -chr20 607522 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=587031;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:37:13,24 ./.:40:17,23 1|1:15:5,10 -chr20 607633 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=562106;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:39:14,25 ./.:29:17,12 ./.:29:22,7 -chr20 607790 . A C 60 . QNAME=cluster19_000000F;QSTART=567986;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD ./.:20:10,10 0|1:23:9,14 ./.:25:12,13 -chr20 608989 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=588498;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:33:14,19 ./.:33:14,19 1|1:12:5,7 -chr20 609812 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=589321;QSTRAND=+;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:28:9,19 ./.:26:6,20 1|1:31:10,21 -chr20 609898 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=589407;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|1:16:11,5 1|1:28:17,11 1|1:39:25,14 -chr20 609899 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=589408;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|1:19:5,14 1|1:19:8,11 1|1:22:16,6 -chr20 610256 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=589765;QSTRAND=+;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:20:7,13 ./.:38:15,23 1|1:28:6,22 -chr20 610966 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=590475;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:29:20,9 ./.:35:23,12 1|1:18:13,5 -chr20 611394 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=590903;QSTRAND=+;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:42:23,19 ./.:25:13,12 1|1:32:15,17 -chr20 611826 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=566299;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:45:20,25 ./.:31:23,8 ./.:37:17,20 -chr20 611881 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=591390;QSTRAND=+;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:13:6,7 ./.:39:20,19 1|1:35:17,18 -chr20 612157 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=591666;QSTRAND=+;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:24:8,16 ./.:22:6,16 1|1:32:19,13 -chr20 612432 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=591941;QSTRAND=+;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:41:21,20 ./.:27:22,5 1|1:25:20,5 -chr20 612561 . AG A 60 . QNAME=cluster19_000000F;QSTART=25149310;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD ./.:33:17,16 1|0:18:13,5 ./.:27:18,9 -chr20 612664 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=592173;QSTRAND=+;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:31:23,8 ./.:25:19,6 1|1:40:18,22 -chr20 612674 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=592183;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:20:12,8 ./.:21:12,9 1|1:29:19,10 -chr20 614136 . T C 60 . QNAME=cluster19_000000F;QSTART=574332;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:33:9,24 0|1:39:15,24 ./.:35:23,12 -chr20 614408 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=568827;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:31:6,25 ./.:27:10,17 ./.:39:18,21 -chr20 614449 . ATCTC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=593905;QSTRAND=+;GCPCT=40;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.760964 GT:DP:AD 1|0:30:5,25 ./.:22:8,14 1|1:43:22,21 -chr20 614473 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=593924;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:18:8,10 ./.:15:5,10 ./.:33:10,23 -chr20 614475 . A C 60 . QNAME=cluster19_000000F;QSTART=574671;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:16:11,5 0|1:45:21,24 ./.:28:15,13 -chr20 614477 . A C 60 . QNAME=cluster19_000000F;QSTART=574673;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:25:8,17 0|1:40:17,23 ./.:25:9,16 -chr20 614492 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=593943;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:34:16,18 ./.:47:25,22 1|1:22:15,7 -chr20 614492 . T TAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=568912;QSTRAND=+;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.792481 GT:DP:AD 0|1:18:10,8 ./.:18:5,13 ./.:29:16,13 -chr20 614494 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=593945;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:29:14,15 ./.:30:16,14 1|1:42:19,23 -chr20 614496 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=568917;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:22:7,15 ./.:16:7,9 ./.:30:23,7 -chr20 614517 . G GTA 60 . QNAME=cluster23_scaffold_3;QSTART=25096741;QSTRAND=-;GCPCT=33;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.792481 GT:DP:AD ./.:27:12,15 ./.:35:17,18 1|1:41:22,19 -chr20 614555 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=594006;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:38:23,15 ./.:19:6,13 1|1:23:9,14 -chr20 614561 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=594012;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:44:24,20 ./.:36:21,15 1|1:20:6,14 -chr20 614710 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=594161;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:45:25,20 ./.:34:18,16 1|1:15:6,9 -chr20 615045 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=569466;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:39:19,20 ./.:23:5,18 ./.:25:18,7 -chr20 615409 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=594860;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:18:5,13 ./.:28:6,22 1|1:28:7,21 -chr20 615455 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=569876;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:31:6,25 ./.:31:13,18 ./.:33:24,9 -chr20 615471 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=594922;QSTRAND=+;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:16:7,9 ./.:32:7,25 1|1:27:17,10 -chr20 615863 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=570284;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:29:14,15 ./.:26:20,6 ./.:50:25,25 -chr20 616031 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=570452;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:32:16,16 ./.:44:20,24 ./.:35:19,16 -chr20 616321 . G GT 60 . QNAME=HG002-S9-H1-000001F;QSTART=595773;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|0:26:16,10 ./.:41:20,21 1|1:17:11,6 -chr20 616321 . G GTT 60 . QNAME=HG002-S9-H2-000001F;QSTART=570743;QSTRAND=+;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.459148 GT:DP:AD 0|1:40:18,22 ./.:34:11,23 ./.:31:23,8 -chr20 616559 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=570982;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:28:17,11 ./.:36:11,25 ./.:34:24,10 -chr20 616743 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=571166;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:28:22,6 ./.:35:14,21 ./.:30:5,25 -chr20 617022 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=571445;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:24:9,15 ./.:31:21,10 ./.:23:10,13 -chr20 617094 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=596546;QSTRAND=+;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:35:14,21 ./.:33:18,15 1|1:25:11,14 -chr20 617427 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=571850;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:34:11,23 ./.:26:6,20 ./.:10:5,5 -chr20 617634 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=597086;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:34:18,16 ./.:37:22,15 1|1:11:5,6 -chr20 617892 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=597344;QSTRAND=+;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:25:13,12 ./.:22:16,6 1|1:27:8,19 -chr20 618050 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=597502;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:38:21,17 ./.:32:19,13 1|1:35:15,20 -chr20 618051 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=572474;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:42:20,22 ./.:20:10,10 ./.:39:18,21 -chr20 619223 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=573646;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:23:13,10 ./.:36:16,20 ./.:43:23,20 -chr20 620320 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=599772;QSTRAND=+;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:46:24,22 ./.:32:9,23 1|1:33:20,13 -chr20 620391 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=599843;QSTRAND=+;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:40:24,16 ./.:26:13,13 1|1:31:15,16 -chr20 621742 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=576165;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:38:25,13 ./.:41:22,19 ./.:29:10,19 -chr20 622380 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=601832;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:41:25,16 ./.:29:8,21 1|1:38:21,17 -chr20 622562 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=576985;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:26:5,21 ./.:10:5,5 ./.:26:8,18 -chr20 622615 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=602067;QSTRAND=+;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:38:23,15 ./.:28:11,17 1|1:36:17,19 -chr20 622976 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=577399;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 0|1:25:18,7 ./.:11:5,6 0|1:23:13,10 -chr20 624131 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=578554;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:17:5,12 ./.:34:24,10 ./.:35:11,24 -chr20 624618 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=579041;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:31:23,8 ./.:37:14,23 ./.:41:16,25 -chr20 624679 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=604131;QSTRAND=+;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:44:21,23 ./.:25:16,9 1|1:31:9,22 -chr20 625245 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=604697;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:39:19,20 ./.:30:16,14 1|1:44:24,20 -chr20 625293 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=604745;QSTRAND=+;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:28:12,16 ./.:34:25,9 1|1:29:5,24 -chr20 626070 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=580493;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:18:10,8 1|1:36:12,24 ./.:38:20,18 -chr20 626301 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=605753;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:29:23,6 ./.:41:25,16 1|1:20:6,14 -chr20 626305 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=605757;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:43:22,21 ./.:25:7,18 1|1:28:5,23 -chr20 626441 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=605893;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:36:20,16 ./.:34:13,21 1|1:22:10,12 -chr20 626569 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=580992;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:34:23,11 ./.:37:16,21 ./.:32:23,9 -chr20 626821 . A AC 60 . QNAME=HG002-S9-H1-000001F;QSTART=606274;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|0:31:13,18 ./.:33:20,13 1|0:17:12,5 -chr20 626950 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=606403;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:34:19,15 ./.:44:20,24 1|0:36:13,23 -chr20 627161 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=606614;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:24:17,7 ./.:33:14,19 1|1:29:18,11 -chr20 627348 . A G 60 . QNAME=cluster19_000000F;QSTART=25134578;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:28:14,14 1|0:31:9,22 ./.:29:17,12 -chr20 628116 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=607569;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:32:25,7 ./.:19:7,12 1|0:31:6,25 -chr20 628203 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=607656;QSTRAND=+;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:43:19,24 ./.:33:14,19 1|1:43:25,18 -chr20 628339 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=607792;QSTRAND=+;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:30:24,6 ./.:40:22,18 1|1:37:22,15 -chr20 628481 . G C 60 . QNAME=cluster23_scaffold_2;QSTART=25066979;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:30:16,14 ./.:37:19,18 0|1:41:25,16 -chr20 628698 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=608151;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:26:12,14 ./.:31:15,16 1|0:41:17,24 -chr20 628723 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=608176;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:10:5,5 ./.:35:19,16 1|0:25:17,8 -chr20 628961 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=608414;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:26:11,15 ./.:31:18,13 1|1:17:11,6 -chr20 629302 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=608755;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:25:17,8 ./.:38:15,23 1|1:26:11,15 -chr20 629494 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=608947;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:25:19,6 ./.:27:19,8 ./.:32:16,16 -chr20 629610 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25065850;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:19:8,11 ./.:32:25,7 0|1:31:15,16 -chr20 629678 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=609131;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:36:20,16 ./.:23:5,18 1|1:42:19,23 -chr20 629911 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=609364;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:31:11,20 ./.:30:14,16 1|1:27:18,9 -chr20 629941 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=609394;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:34:13,21 ./.:27:15,12 1|1:21:15,6 -chr20 630017 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=609470;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:36:12,24 ./.:13:7,6 1|1:32:10,22 -chr20 630420 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=609873;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:17:11,6 ./.:37:14,23 ./.:27:21,6 -chr20 630592 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=585016;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 0|1:47:22,25 ./.:26:10,16 0|1:45:22,23 -chr20 630592 . CAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=610046;QSTRAND=+;GCPCT=25;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.405639 GT:DP:AD 1|0:24:15,9 ./.:24:17,7 1|0:31:6,25 -chr20 630708 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=610158;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:21:6,15 ./.:25:14,11 1|1:20:5,15 -chr20 631945 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=611395;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:40:25,15 ./.:43:19,24 ./.:28:8,20 -chr20 632007 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=611457;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:17:6,11 ./.:36:25,11 ./.:23:18,5 -chr20 632024 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=611474;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:21:14,7 ./.:23:15,8 ./.:33:11,22 -chr20 632038 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=611488;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:24:7,17 ./.:28:8,20 ./.:35:17,18 -chr20 632119 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=611569;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:37:19,18 ./.:33:25,8 ./.:31:15,16 -chr20 633319 . A G 60 . QNAME=cluster19_000000F;QSTART=25128607;QSTRAND=-;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:24:12,12 1|0:26:14,12 0|1:17:9,8 -chr20 633850 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=613300;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:38:13,25 ./.:32:14,18 ./.:17:10,7 -chr20 634306 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=613756;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:23:16,7 ./.:33:22,11 ./.:37:13,24 -chr20 634343 . C T 60 . QNAME=cluster19_000000F;QSTART=25127583;QSTRAND=-;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:24:6,18 1|0:26:16,10 0|1:27:21,6 -chr20 634367 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=613817;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:40:15,25 1|0:36:11,25 0|1:35:25,10 -chr20 634490 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=613940;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:46:24,22 ./.:44:19,25 ./.:23:18,5 -chr20 634534 . G A 60 . QNAME=cluster19_000000F;QSTART=25127392;QSTRAND=-;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:25:12,13 1|0:31:15,16 0|1:28:15,13 -chr20 634915 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=614365;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:19:9,10 ./.:25:10,15 ./.:30:23,7 -chr20 637164 . T C 60 . QNAME=cluster19_000000F;QSTART=25124762;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:13:8,5 1|0:45:22,23 ./.:23:12,11 -chr20 637615 . T C 60 . QNAME=cluster19_000000F;QSTART=25124311;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:46:24,22 1|0:27:5,22 ./.:31:19,12 -chr20 638468 . T TA 60 . QNAME=cluster23_scaffold_3;QSTART=25072790;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:32:14,18 ./.:35:13,22 1|1:21:5,16 -chr20 638468 . TA T 60 . QNAME=cluster19_000000F;QSTART=25123458;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:27:12,15 1|0:35:19,16 ./.:28:9,19 -chr20 638748 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=618198;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:26:20,6 1|0:23:10,13 ./.:39:16,23 -chr20 638918 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=618368;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:31:11,20 ./.:34:15,19 ./.:16:8,8 -chr20 639104 . A AT 60 . QNAME=HG002-S9-H1-000001F;QSTART=618555;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|0:35:12,23 ./.:18:9,9 1|1:35:18,17 -chr20 639255 . T C 60 . QNAME=cluster19_000000F;QSTART=25122672;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:39:24,15 1|0:33:16,17 ./.:15:9,6 -chr20 639552 . T C 60 . QNAME=cluster19_000000F;QSTART=25122375;QSTRAND=-;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:10:5,5 1|0:28:22,6 0|1:33:13,20 -chr20 639866 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25055593;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:40:25,15 ./.:22:6,16 0|1:16:5,11 -chr20 640046 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=619497;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:10:5,5 ./.:33:15,18 ./.:32:22,10 -chr20 640049 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=619500;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:28:12,16 ./.:29:5,24 1|0:31:19,12 -chr20 640284 . T TC 60 . QNAME=cluster23_scaffold_2;QSTART=25055174;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:19:8,11 ./.:48:23,25 0|1:34:25,9 -chr20 641878 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621329;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:17:11,6 ./.:15:9,6 0|1:33:12,21 -chr20 641905 . T TG 60 . QNAME=cluster23_scaffold_3;QSTART=25069351;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD ./.:29:5,24 ./.:18:8,10 1|0:18:7,11 -chr20 641906 . G GGCGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCT 60 . QNAME=cluster23_scaffold_2;QSTART=25053389;QSTRAND=-;SVTYPE=INS;SVLEN=163;HOMPCT=13.6;REMAP=tandem;REMAPHits=chr20:642292-642433.93,chr20:641878-642037.96,chr20:642038-642197.98,chr20:642101-642260.98,chr20:641905-642067.100,chr20:641938-642100.100,chr20:642005-642163.100,chr20:642131-642292.100,chr20:642198-642351.100;GCPCT=81;GTCNT=2,0,1,0;NumNeighbors=10;NeighId=7;DPCNT=0,0,1,2;ADCNT=0,1,2,0;LCR=0.756033 GT:DP:AD ./.:13:6,7 ./.:34:21,13 0/1:27:16,11 -chr20 641913 . G GGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGA 60 . QNAME=HG002-S9-H1-000001F;QSTART=621365;QSTRAND=+;SVTYPE=INS;SVLEN=66;HOMPCT=13.6;REMAP=tandem;REMAPHits=chr20:641879-641946.100,chr20:641911-641979.100,chr20:641944-642013.100,chr20:641978-642046.100,chr20:642011-642076.100,chr20:642041-642109.100,chr20:642137-642206.100,chr20:642171-642239.100,chr20:642234-642301.100,chr20:642325-642392.100;GCPCT=80;GTCNT=2,0,1,0;NumNeighbors=10;NeighId=7;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.75613 GT:DP:AD 1/0:34:18,16 ./.:32:17,15 ./.:36:16,20 -chr20 641930 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25053365;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:33:16,17 ./.:15:6,9 0|1:27:13,14 -chr20 641944 . GGA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621462;QSTRAND=+;GCPCT=66;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.459148 GT:DP:AD 1|0:30:16,14 ./.:47:25,22 ./.:32:13,19 -chr20 641970 . T TG 60 . QNAME=cluster23_scaffold_2;QSTART=25053324;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:30:14,16 ./.:26:16,10 0|1:31:12,19 -chr20 641977 . G T 60 . QNAME=cluster19_000000F;QSTART=25119950;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:34:16,18 1|0:24:7,17 ./.:28:20,8 -chr20 642012 . GGT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621528;QSTRAND=+;GCPCT=66;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.459148 GT:DP:AD 1|0:20:10,10 ./.:35:18,17 ./.:33:16,17 -chr20 642037 . T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=621551;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 1|0:41:18,23 ./.:44:19,25 ./.:35:18,17 -chr20 642067 . T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=621582;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|0:25:9,16 ./.:38:22,16 ./.:27:21,6 -chr20 642068 . G GTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCC 60 . QNAME=cluster23_scaffold_2;QSTART=25053097;QSTRAND=-;SVTYPE=INS;SVLEN=129;HOMPCT=13.6;REMAP=tandem;REMAPHits=chr20:641878-642003.94,chr20:642292-642411.96,chr20:642037-642162.96,chr20:641938-642066.98,chr20:642005-642129.98,chr20:642131-642259.98,chr20:642198-642320.98,chr20:641903-642036.100,chr20:641970-642099.100;GCPCT=82;GTCNT=2,0,1,0;NumNeighbors=10;NeighId=7;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.731111 GT:DP:AD ./.:34:24,10 ./.:30:19,11 0/1:18:11,7 -chr20 642069 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621584;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:33:20,13 ./.:15:10,5 ./.:27:19,8 -chr20 642076 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25053089;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:31:22,9 ./.:36:21,15 0|1:29:21,8 -chr20 642100 . T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=621616;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|0:30:22,8 ./.:39:21,18 ./.:45:25,20 -chr20 642123 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=621639;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:46:23,23 ./.:21:6,15 0|1:42:20,22 -chr20 642130 . T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=621647;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|0:34:15,19 ./.:16:8,8 ./.:23:8,15 -chr20 642132 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=25053033;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:13:6,7 ./.:30:7,23 0|1:35:13,22 -chr20 642171 . GGA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621689;QSTRAND=+;GCPCT=66;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.459148 GT:DP:AD 1|0:43:23,20 ./.:40:20,20 0|1:40:18,22 -chr20 642205 . GGT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621721;QSTRAND=+;GCPCT=66;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.459148 GT:DP:AD 1|0:33:11,22 ./.:22:5,17 0|1:30:12,18 -chr20 642207 . T TGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGG 60 . QNAME=cluster19_000000F;QSTART=602404;QSTRAND=+;SVTYPE=INS;SVLEN=630;HOMPCT=13.8;REMAP=tandem;REMAPHits=chr20:641866-642420.87,chr20:641881-642435.87;GCPCT=79;GTCNT=2,0,1,0;NumNeighbors=10;NeighId=7;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.773177 GT:DP:AD ./.:28:16,12 0/1:27:13,14 ./.:24:18,6 -chr20 642207 . T TGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGG 60 . QNAME=HG002-S9-H2-000001F;QSTART=596630;QSTRAND=+;SVTYPE=INS;SVLEN=501;HOMPCT=13.8;REMAP=tandem;REMAPHits=chr20:642013-642429.83,chr20:641881-642391.100;GCPCT=80;GTCNT=2,0,1,0;NumNeighbors=10;NeighId=7;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.762331 GT:DP:AD 0/1:27:12,15 ./.:20:10,10 ./.:22:17,5 -chr20 642230 . T TG 60 . QNAME=cluster23_scaffold_3;QSTART=25069025;QSTRAND=-;GCPCT=50;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:25:9,16 ./.:21:6,15 1|1:42:23,19 -chr20 642230 . T TGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTG 60 . QNAME=cluster19_000000F;QSTART=25119065;QSTRAND=-;SVTYPE=INS;SVLEN=632;HOMPCT=13.8;REMAP=tandem;REMAPHits=chr20:641866-642420.87;GCPCT=79;GTCNT=2,0,1,0;NumNeighbors=10;NeighId=7;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.771876 GT:DP:AD ./.:35:18,17 1/0:33:10,23 ./.:44:25,19 -chr20 642259 . CTG C 60 . QNAME=HG002-S9-H1-000001F;QSTART=621773;QSTRAND=+;GCPCT=66;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.792481 GT:DP:AD 1|0:19:6,13 ./.:30:7,23 ./.:16:7,9 -chr20 642261 . GTGGT G 60 . QNAME=cluster23_scaffold_3;QSTART=25068994;QSTRAND=-;GCPCT=60;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.485475 GT:DP:AD ./.:34:17,17 ./.:27:20,7 1|0:46:25,21 -chr20 642265 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621776;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:37:12,25 0|1:27:9,18 ./.:36:22,14 -chr20 642271 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=621782;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:34:25,9 ./.:27:11,16 ./.:40:24,16 -chr20 642271 . G GC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597195;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0.5 GT:DP:AD 0|1:17:6,11 1|1:22:17,5 0|1:22:17,5 -chr20 642271 . G GGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGC 60 . QNAME=cluster23_scaffold_3;QSTART=25068731;QSTRAND=-;SVTYPE=INS;SVLEN=257;HOMPCT=13.8;REMAP=tandem;REMAPHits=chr20:641881-642138.99,chr20:642076-642331.100;GCPCT=80;GTCNT=2,0,1,0;NumNeighbors=10;NeighId=7;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.76612 GT:DP:AD ./.:36:19,17 ./.:28:5,23 1/0:27:18,9 -chr20 642277 . G A 60 . QNAME=cluster19_000000F;QSTART=603104;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:25:6,19 0|1:46:25,21 ./.:25:18,7 -chr20 642284 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=621795;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:16:5,11 1|1:24:8,16 1|1:25:16,9 -chr20 642300 . G GC 60 . QNAME=cluster19_000000F;QSTART=25118993;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:31:7,24 1|0:45:25,20 ./.:37:25,12 -chr20 642300 . G GCCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGC 60 . QNAME=HG002-S9-H1-000001F;QSTART=621812;QSTRAND=+;SVTYPE=INS;SVLEN=408;HOMPCT=13.8;REMAP=tandem;REMAPHits=chr20:642076-642435.88,chr20:641881-642300.99,chr20:641913-642332.100,chr20:641946-642363.100;GCPCT=80;GTCNT=2,0,1,0;NumNeighbors=10;NeighId=7;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.763885 GT:DP:AD 1/0:44:19,25 ./.:35:12,23 ./.:42:17,25 -chr20 642300 . G GGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597225;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.459148 GT:DP:AD 0|1:27:11,16 0|1:40:18,22 1|1:15:6,9 -chr20 642330 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=622249;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:34:14,20 ./.:33:15,18 1|0:21:13,8 -chr20 642330 . G GC 60 . QNAME=cluster19_000000F;QSTART=25118962;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:30:14,16 1|1:45:20,25 ./.:24:18,6 -chr20 642330 . G GCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGGGC 60 . QNAME=cluster23_scaffold_2;QSTART=25052609;QSTRAND=-;SVTYPE=INS;SVLEN=226;HOMPCT=13.8;REMAP=tandem;REMAPHits=chr20:641882-642108.97,chr20:642014-642238.97,chr20:642077-642300.97,chr20:642207-642420.97,chr20:642140-642362.98;GCPCT=79;GTCNT=2,0,1,0;NumNeighbors=10;NeighId=7;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.77591 GT:DP:AD ./.:41:21,20 ./.:28:9,19 0/1:18:12,6 -chr20 642330 . G GGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597257;QSTRAND=+;SVTYPE=INS;SVLEN=66;HOMPCT=13.8;REMAP=tandem;REMAPHits=chr20:642076-642138.97,chr20:641913-641980.100,chr20:641946-642014.100,chr20:641980-642046.100,chr20:642043-642109.100,chr20:642139-642207.100,chr20:642173-642239.100,chr20:642206-642272.100,chr20:642236-642301.100,chr20:642297-642361.100;GCPCT=77;GTCNT=2,0,1,0;NumNeighbors=10;NeighId=7;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.792073 GT:DP:AD 0/1:18:11,7 ./.:23:10,13 ./.:25:12,13 -chr20 642353 . T G 60 . QNAME=cluster23_scaffold_2;QSTART=25052586;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:23:15,8 ./.:16:6,10 0|1:24:17,7 -chr20 642362 . G C 60 . QNAME=cluster23_scaffold_2;QSTART=25052577;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:48:24,24 ./.:26:12,14 0|1:12:7,5 -chr20 642362 . G GC 60 . QNAME=HG002-S9-H1-000001F;QSTART=622282;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 1|1:25:14,11 1|1:32:16,16 1|0:30:7,23 -chr20 642391 . G GC 60 . QNAME=HG002-S9-H1-000001F;QSTART=622312;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD 1|1:27:9,18 1|1:16:9,7 0|1:20:15,5 -chr20 642391 . G GGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGGC 60 . QNAME=cluster23_scaffold_3;QSTART=25068286;QSTRAND=-;SVTYPE=INS;SVLEN=322;HOMPCT=13.8;REMAP=tandem;REMAPHits=chr20:642139-642435.94,chr20:641881-642209.100,chr20:641946-642273.100,chr20:641980-642301.100,chr20:642043-642364.100;GCPCT=78;GTCNT=2,0,1,0;NumNeighbors=10;NeighId=7;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0.778434 GT:DP:AD ./.:21:9,12 ./.:41:25,16 1/0:14:6,8 -chr20 642420 . G GC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597415;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 0|1:14:9,5 1|1:39:25,14 1|0:28:11,17 -chr20 642420 . G GGC 60 . QNAME=HG002-S9-H1-000001F;QSTART=622342;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.459148 GT:DP:AD 1|0:36:19,17 ./.:30:25,5 ./.:34:25,9 -chr20 642420 . G GGGC 60 . QNAME=cluster23_scaffold_2;QSTART=25052515;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.405639 GT:DP:AD ./.:30:22,8 ./.:36:25,11 0|1:39:16,23 -chr20 642746 . C CGGGGGTGCGGGT 60 . QNAME=cluster23_scaffold_2;QSTART=25052177;QSTRAND=-;GCPCT=84;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.599092 GT:DP:AD ./.:24:12,12 ./.:23:6,17 0|1:23:11,12 -chr20 642746 . C CGGGGTGCGGGT 60 . QNAME=cluster19_000000F;QSTART=603580;QSTRAND=+;GCPCT=83;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.625815 GT:DP:AD ./.:43:22,21 0|1:42:23,19 ./.:20:13,7 -chr20 642861 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=622784;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:50:25,25 ./.:32:14,18 ./.:33:22,11 -chr20 642893 . GTGA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=622817;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.75 GT:DP:AD 1|0:18:8,10 ./.:40:15,25 ./.:39:22,17 -chr20 643742 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25051181;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:45:22,23 ./.:40:19,21 0|1:32:8,24 -chr20 643827 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=623747;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:30:24,6 ./.:47:23,24 ./.:38:15,23 -chr20 644129 . T A 60 . QNAME=cluster23_scaffold_2;QSTART=25050794;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:16:7,9 ./.:22:14,8 0|1:27:14,13 -chr20 644264 . TA T 60 . QNAME=cluster23_scaffold_2;QSTART=25050659;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD ./.:40:21,19 ./.:24:16,8 0|1:26:18,8 -chr20 644423 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=624343;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:33:20,13 ./.:30:25,5 ./.:37:12,25 -chr20 644731 . T TA 60 . QNAME=cluster23_scaffold_2;QSTART=25050192;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0.5 GT:DP:AD ./.:25:13,12 ./.:27:18,9 0|1:26:20,6 -chr20 645244 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=25049678;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:22:9,13 ./.:27:7,20 0|1:30:25,5 -chr20 645246 . A AT 60 . QNAME=HG002-S9-H1-000001F;QSTART=625167;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 1|0:41:19,22 ./.:36:22,14 ./.:26:6,20 -chr20 645378 . A AG 60 . QNAME=HG002-S9-H1-000001F;QSTART=625300;QSTRAND=+;GCPCT=50;GTCNT=1,0,0,2;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|1:23:13,10 ./.:36:17,19 1|1:13:8,5 -chr20 645437 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=625359;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:26:12,14 ./.:18:8,10 1|0:12:7,5 -chr20 645520 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=625442;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:27:18,9 ./.:23:14,9 1|0:36:19,17 -chr20 645645 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=625567;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:15:9,6 ./.:31:20,11 ./.:33:18,15 -chr20 646133 . T TCTA 60 . QNAME=HG002-S9-H1-000001F;QSTART=626056;QSTRAND=+;GCPCT=25;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.75 GT:DP:AD 1|1:33:11,22 ./.:35:10,25 1|1:43:21,22 -chr20 646134 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=626059;QSTRAND=+;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|1:25:13,12 ./.:18:9,9 1|1:22:15,7 -chr20 646331 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=626256;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:20:8,12 ./.:33:14,19 1|0:44:24,20 -chr20 646515 . C CA 60 . QNAME=cluster19_000000F;QSTART=25114773;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD ./.:33:21,12 1|0:16:6,10 ./.:35:18,17 -chr20 646515 . C CAAAAAAAAAAAAAAAA 60 . QNAME=HG002-S9-H2-000001F;QSTART=601515;QSTRAND=+;GCPCT=5;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.161378 GT:DP:AD 0|1:30:16,14 ./.:34:14,20 ./.:32:10,22 -chr20 646515 . C CAAAAAAAAAAAAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=626441;QSTRAND=+;GCPCT=5;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.154772 GT:DP:AD 1|0:34:24,10 ./.:40:21,19 ./.:31:20,11 -chr20 646515 . C CAAAAAAAAAAAAAAAAAA 60 . QNAME=cluster23_scaffold_3;QSTART=25064139;QSTRAND=-;GCPCT=5;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.148736 GT:DP:AD ./.:34:14,20 ./.:44:21,23 1|1:31:12,19 -chr20 646526 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=626468;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:30:11,19 ./.:31:6,25 1|0:21:10,11 -chr20 646614 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=601630;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,2,0;LCR=0.5 GT:DP:AD 0|1:10:5,5 ./.:17:7,10 ./.:36:23,13 -chr20 646770 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25048130;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:29:6,23 ./.:36:18,18 0|1:25:9,16 -chr20 648246 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=628188;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|1:32:24,8 ./.:18:10,8 1|0:27:14,13 -chr20 648569 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=628511;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:40:22,18 ./.:26:17,9 1|0:29:19,10 -chr20 649005 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=628947;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:28:12,16 ./.:31:8,23 1|0:25:17,8 -chr20 649182 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=604196;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:30:10,20 ./.:31:8,23 ./.:28:18,10 -chr20 649701 . CA C 60 . QNAME=cluster23_scaffold_3;QSTART=25060953;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:50:25,25 ./.:28:6,22 1|0:23:15,8 -chr20 649701 . CAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=629644;QSTRAND=+;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.459148 GT:DP:AD 1|0:16:11,5 ./.:49:24,25 ./.:31:19,12 -chr20 649716 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=604730;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:38:23,15 ./.:13:8,5 ./.:45:24,21 -chr20 649983 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=629923;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:39:14,25 ./.:27:19,8 1|0:37:15,22 -chr20 650241 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=25044659;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:28:16,12 ./.:19:9,10 0|1:30:15,15 -chr20 650254 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=605268;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:32:22,10 ./.:34:14,20 0|1:17:5,12 -chr20 650326 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=630266;QSTRAND=+;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:17:8,9 ./.:25:10,15 1|1:29:16,13 -chr20 650473 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=630413;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:17:8,9 ./.:30:11,19 1|0:26:20,6 -chr20 650495 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25044405;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:41:18,23 ./.:22:9,13 0|1:48:24,24 -chr20 650525 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=605539;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:24:12,12 ./.:27:16,11 ./.:38:15,23 -chr20 650651 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=605665;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 0|1:19:8,11 ./.:20:7,13 ./.:30:21,9 -chr20 650723 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=605737;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:36:17,19 ./.:26:9,17 ./.:20:11,9 -chr20 650781 . C A 60 . QNAME=cluster19_000000F;QSTART=25110507;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:12:6,6 1|0:30:7,23 ./.:22:5,17 -chr20 651264 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=631204;QSTRAND=+;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:33:12,21 ./.:27:21,6 1|1:32:15,17 -chr20 651683 . TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=631624;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 1|0:42:17,25 ./.:48:23,25 ./.:43:25,18 -chr20 651860 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=606874;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:23:13,10 ./.:38:19,19 0|1:41:18,23 -chr20 651923 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=25042977;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:31:25,6 ./.:11:6,5 0|1:38:14,24 -chr20 652315 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=632254;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:28:16,12 ./.:31:13,18 1|1:39:25,14 -chr20 652505 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=632444;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:38:14,24 ./.:32:21,11 1|1:29:23,6 -chr20 652904 . GACCTCCCTCCTCCGGCA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=632844;QSTRAND=+;GCPCT=72;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.842489 GT:DP:AD 1|1:34:10,24 ./.:28:5,23 ./.:46:24,22 -chr20 653259 . CG C 60 . QNAME=HG002-S9-H1-000001F;QSTART=633182;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD 1|0:32:19,13 ./.:33:23,10 ./.:28:13,15 -chr20 653265 . G GT 60 . QNAME=cluster23_scaffold_2;QSTART=25041634;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:41:18,23 ./.:26:10,16 0|1:41:21,20 -chr20 653266 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=25041633;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:30:8,22 ./.:21:10,11 0|1:22:8,14 -chr20 653324 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=633245;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:33:10,23 ./.:33:8,25 1|1:32:19,13 -chr20 653378 . C T 60 . QNAME=cluster19_000000F;QSTART=25107910;QSTRAND=-;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:19:6,13 1|0:29:21,8 0|1:25:10,15 -chr20 653790 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=633711;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:37:13,24 ./.:19:12,7 1|0:22:12,10 -chr20 653820 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=633741;QSTRAND=+;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:34:12,22 ./.:25:19,6 ./.:34:25,9 -chr20 653977 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=608974;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,3,0,0;LCR=0 GT:DP:AD 0|1:19:14,5 ./.:13:5,8 ./.:24:17,7 -chr20 654666 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=609663;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:19:12,7 ./.:28:7,21 ./.:42:21,21 -chr20 655173 . C CAGAAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=635095;QSTRAND=+;GCPCT=20;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.460964 GT:DP:AD 1|1:26:19,7 1|1:21:7,14 1|1:30:19,11 -chr20 656194 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=636124;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:38:22,16 ./.:37:19,18 ./.:22:15,7 -chr20 658219 . G A 60 . QNAME=cluster19_000000F;QSTART=25103060;QSTRAND=-;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:29:16,13 1|0:42:23,19 1|0:43:23,20 -chr20 658277 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=613283;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:17:7,10 ./.:32:19,13 ./.:29:10,19 -chr20 659380 . T TGGAG 60 . QNAME=HG002-S9-H2-000001F;QSTART=614387;QSTRAND=+;GCPCT=60;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.685475 GT:DP:AD 0|1:18:10,8 ./.:27:19,8 ./.:38:13,25 -chr20 659768 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=639698;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:40:21,19 ./.:45:20,25 ./.:15:10,5 -chr20 659929 . C T 60 . QNAME=cluster19_000000F;QSTART=25101350;QSTRAND=-;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:19:7,12 1|0:36:17,19 1|0:26:16,10 -chr20 660098 . C A 60 . QNAME=cluster19_000000F;QSTART=620951;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:47:23,24 0|1:12:6,6 ./.:21:11,10 -chr20 660145 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=640075;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:35:13,22 1|1:22:13,9 1|0:17:11,6 -chr20 660346 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=640276;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:35:15,20 0|1:34:10,24 ./.:20:14,6 -chr20 660450 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25050195;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:28:10,18 ./.:35:16,19 1|0:32:13,19 -chr20 660628 . C CA 60 . QNAME=cluster19_000000F;QSTART=621482;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,2,0;LCR=0.5 GT:DP:AD ./.:33:19,14 0|1:29:19,10 ./.:14:6,8 -chr20 660628 . C CAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=640559;QSTRAND=+;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.459148 GT:DP:AD 1|0:44:20,24 ./.:23:7,16 ./.:21:12,9 -chr20 660640 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=640572;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0 GT:DP:AD 1|1:33:25,8 0|1:21:14,7 ./.:28:20,8 -chr20 660909 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=615919;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:16:7,9 ./.:33:25,8 ./.:38:16,22 -chr20 661249 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=641181;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:29:11,18 1|1:15:9,6 1|0:49:25,24 -chr20 662494 . C CG 60 . QNAME=cluster23_scaffold_2;QSTART=25032395;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:36:18,18 ./.:32:14,18 0|1:31:10,21 -chr20 663033 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=642965;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:26:20,6 0|1:29:22,7 1|1:31:6,25 -chr20 663218 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25047427;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:29:20,9 ./.:29:24,5 1|0:42:24,18 -chr20 663275 . T C 60 . QNAME=cluster19_000000F;QSTART=624129;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:28:6,22 0|1:43:18,25 0|1:36:16,20 -chr20 663449 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25047196;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:39:17,22 ./.:20:8,12 1|0:47:24,23 -chr20 663558 . A C 60 . QNAME=cluster19_000000F;QSTART=624412;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:21:16,5 0|1:23:6,17 ./.:11:6,5 -chr20 664220 . G GC 60 . QNAME=cluster23_scaffold_2;QSTART=25030668;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:10:5,5 ./.:42:17,25 0|1:21:10,11 -chr20 665209 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=645141;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:35:21,14 1|1:26:13,13 1|1:32:8,24 -chr20 665270 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=645202;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:35:17,18 ./.:34:23,11 ./.:33:23,10 -chr20 665483 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=645415;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,1,2;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|1:12:7,5 1|1:22:12,10 0|1:26:14,12 -chr20 666690 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=646622;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:22:11,11 ./.:38:14,24 ./.:37:25,12 -chr20 667092 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=647024;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:31:15,16 1|1:27:7,20 1|1:29:23,6 -chr20 667181 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=647113;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:29:14,15 ./.:40:21,19 ./.:45:20,25 -chr20 667787 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=647719;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:24:19,5 ./.:29:9,20 ./.:18:7,11 -chr20 668165 . A ATTG 60 . QNAME=HG002-S9-H1-000001F;QSTART=648098;QSTRAND=+;GCPCT=25;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.75 GT:DP:AD 1|0:44:25,19 ./.:22:7,15 1|1:37:13,24 -chr20 668172 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=648107;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:27:12,15 ./.:24:12,12 1|1:30:19,11 -chr20 668176 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=648111;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:18:13,5 ./.:46:22,24 1|1:40:17,23 -chr20 668345 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=648280;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:42:17,25 ./.:25:5,20 1|1:27:22,5 -chr20 669291 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=649226;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:21:10,11 ./.:18:11,7 1|1:19:14,5 -chr20 670996 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=650931;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:37:20,17 ./.:37:22,15 1|1:30:19,11 -chr20 671453 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=651388;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:33:18,15 ./.:14:5,9 1|1:31:9,22 -chr20 671595 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=651530;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:34:22,12 ./.:36:17,19 1|1:25:9,16 -chr20 672290 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=652225;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:35:19,16 ./.:50:25,25 1|1:32:25,7 -chr20 672388 . CGT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=652324;QSTRAND=+;GCPCT=66;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.792481 GT:DP:AD 1|0:37:15,22 ./.:39:21,18 1|1:42:18,24 -chr20 672422 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=652355;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:48:24,24 ./.:19:10,9 1|1:34:10,24 -chr20 672619 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=652552;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:31:19,12 ./.:27:7,20 1|1:38:18,20 -chr20 673008 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=652941;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:40:21,19 ./.:32:22,10 1|1:20:14,6 -chr20 673547 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=653480;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:24:9,15 ./.:37:20,17 1|1:42:22,20 -chr20 674399 . TCACA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=654333;QSTRAND=+;GCPCT=40;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.760964 GT:DP:AD 1|0:28:16,12 ./.:22:11,11 0|1:30:10,20 -chr20 674399 . TCACACA T 60 . QNAME=cluster23_scaffold_3;QSTART=25036245;QSTRAND=-;GCPCT=42;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.724408 GT:DP:AD ./.:29:12,17 ./.:36:13,23 1|0:30:25,5 -chr20 674405 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=654334;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:26:12,14 ./.:40:18,22 0|1:28:14,14 -chr20 674407 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=654336;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:18:9,9 ./.:34:18,16 1|1:26:10,16 -chr20 674409 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=654338;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:21:14,7 ./.:42:18,24 1|1:39:18,21 -chr20 674411 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=654340;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:48:24,24 ./.:25:19,6 1|1:34:17,17 -chr20 674413 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=654342;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:22:12,10 ./.:24:17,7 1|0:38:14,24 -chr20 674688 . A AGT 60 . QNAME=HG002-S9-H2-000001F;QSTART=629699;QSTRAND=+;GCPCT=33;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.792481 GT:DP:AD 0|1:37:20,17 1|1:37:23,14 ./.:36:11,25 -chr20 674713 . GTGTGTGTGTGTGTGTGTGTA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=654643;QSTRAND=+;GCPCT=47;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.614288 GT:DP:AD 1|0:33:14,19 ./.:36:15,21 1|1:36:14,22 -chr20 675537 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25019374;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD ./.:29:16,13 ./.:20:6,14 0|1:21:7,14 -chr20 675763 . T TGGC 60 . QNAME=cluster19_000000F;QSTART=25085511;QSTRAND=-;GCPCT=75;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.75 GT:DP:AD ./.:16:11,5 1|1:40:21,19 ./.:23:15,8 -chr20 676166 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=656075;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:19:10,9 ./.:39:17,22 1|1:31:23,8 -chr20 676254 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25034416;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:20:5,15 ./.:35:21,14 1|1:19:11,8 -chr20 677116 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25033554;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:16:10,6 ./.:34:12,22 1|1:34:13,21 -chr20 677219 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=632231;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:40:20,20 ./.:20:11,9 1|1:27:20,7 -chr20 677414 . TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=657324;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD 1|0:34:16,18 0|1:21:16,5 1|1:26:19,7 -chr20 677414 . TAA T 60 . QNAME=HG002-S9-H2-000001F;QSTART=632427;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.459148 GT:DP:AD 0|1:49:25,24 ./.:29:8,21 ./.:28:16,12 -chr20 677478 . G A 60 . QNAME=cluster19_000000F;QSTART=638336;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:33:17,16 0|1:27:6,21 ./.:16:8,8 -chr20 677582 . A AAATAATAAT 60 . QNAME=HG002-S9-H2-000001F;QSTART=632593;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0.440645 GT:DP:AD 0|1:24:14,10 ./.:29:18,11 ./.:20:9,11 -chr20 677689 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25032982;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:14:9,5 ./.:26:7,19 1|1:35:25,10 -chr20 677734 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25032937;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:43:20,23 ./.:38:14,24 1|1:28:6,22 -chr20 677799 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=25032872;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:37:17,20 ./.:32:19,13 1|1:43:24,19 -chr20 677892 . A AT 60 . QNAME=cluster23_scaffold_3;QSTART=25032778;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:20:7,13 ./.:27:8,19 1|1:17:12,5 -chr20 677892 . AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=657801;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0.5 GT:DP:AD 1|0:24:17,7 ./.:23:12,11 ./.:14:5,9 -chr20 678014 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25032656;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:28:11,17 ./.:45:25,20 1|1:29:14,15 -chr20 678015 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25032655;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:18:9,9 ./.:28:16,12 1|1:18:10,8 -chr20 678191 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=658098;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:34:15,19 1|1:47:22,25 1|1:27:11,16 -chr20 678230 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=633249;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:23:16,7 ./.:26:16,10 1|1:30:6,24 -chr20 678305 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=633324;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:32:8,24 ./.:18:8,10 ./.:18:6,12 -chr20 678433 . C G 60 . QNAME=cluster23_scaffold_3;QSTART=25032237;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:31:11,20 ./.:41:23,18 1|1:39:22,17 -chr20 678642 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25032028;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:38:13,25 ./.:37:24,13 1|1:23:17,6 -chr20 678678 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25031992;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:31:16,15 ./.:28:5,23 1|1:12:6,6 -chr20 678706 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25031964;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:24:18,6 ./.:34:15,19 1|1:19:7,12 -chr20 678778 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25031892;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:13:6,7 ./.:16:8,8 1|1:23:9,14 -chr20 678797 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25031873;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:30:22,8 ./.:44:20,24 1|1:31:13,18 -chr20 678839 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=633858;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 0|1:31:23,8 ./.:29:24,5 1|1:27:13,14 -chr20 679151 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25031519;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:41:20,21 ./.:37:20,17 1|1:48:24,24 -chr20 679482 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=634501;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:11:6,5 ./.:30:5,25 1|1:31:13,18 -chr20 679483 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=634502;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:15:5,10 ./.:34:9,25 1|1:34:14,20 -chr20 680009 . A T 60 . QNAME=cluster23_scaffold_3;QSTART=25030661;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:29:7,22 ./.:25:5,20 1|1:24:5,19 -chr20 680029 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25030641;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:33:8,25 ./.:33:10,23 1|1:21:5,16 -chr20 680047 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=635066;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:18:13,5 ./.:26:19,7 ./.:26:5,21 -chr20 680149 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25030521;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:34:12,22 ./.:45:21,24 1|1:28:8,20 -chr20 680216 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25014695;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:41:25,16 ./.:21:5,16 0|1:27:20,7 -chr20 680257 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25030413;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:28:16,12 ./.:34:20,14 1|1:44:20,24 -chr20 680491 . G GA 60 . QNAME=cluster23_scaffold_3;QSTART=25030178;QSTRAND=-;GCPCT=50;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:38:15,23 ./.:45:24,21 1|1:24:5,19 -chr20 680625 . T A 60 . QNAME=cluster23_scaffold_3;QSTART=25030044;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:32:14,18 ./.:27:16,11 1|1:17:10,7 -chr20 680841 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25029828;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:37:24,13 ./.:25:11,14 1|1:44:24,20 -chr20 681789 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25028880;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:24:11,13 ./.:24:6,18 1|1:29:15,14 -chr20 681958 . G C 60 . QNAME=cluster23_scaffold_3;QSTART=25028711;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:25:16,9 ./.:26:15,11 1|1:27:15,12 -chr20 682463 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=637482;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:48:24,24 ./.:45:25,20 1|1:34:18,16 -chr20 682684 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25027985;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:15:10,5 ./.:25:16,9 1|1:26:6,20 -chr20 683486 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=25027183;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:27:22,5 ./.:37:20,17 1|1:34:15,19 -chr20 683498 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=638517;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:38:19,19 0|1:43:18,25 1|1:16:6,10 -chr20 683582 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=25027087;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:26:12,14 ./.:15:7,8 1|1:41:21,20 -chr20 684734 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=639753;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:22:7,15 ./.:24:14,10 1|1:42:22,20 -chr20 684907 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=639926;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 0|1:22:13,9 ./.:33:20,13 ./.:24:13,11 -chr20 685089 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=25025580;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:29:23,6 ./.:20:13,7 1|1:34:12,22 -chr20 685645 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=25025024;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:32:8,24 ./.:26:18,8 1|1:22:13,9 -chr20 685696 . AAATAAT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=665604;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,2,1;ADCNT=0,2,0,1;LCR=0.43156 GT:DP:AD 1|0:10:5,5 1|0:13:8,5 ./.:26:6,20 -chr20 685696 . AAATAATAAT A 60 . QNAME=cluster23_scaffold_3;QSTART=25024973;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.440645 GT:DP:AD ./.:21:16,5 ./.:28:8,20 1|1:41:25,16 -chr20 685696 . AAATAATAATAAT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=640716;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.445246 GT:DP:AD 0|1:36:19,17 0|1:25:17,8 ./.:15:6,9 -chr20 686394 . C T 60 . QNAME=cluster19_000000F;QSTART=25074886;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:29:9,20 1|0:36:22,14 ./.:35:19,16 -chr20 686439 . C CAAAAAAAAAAAAAA 60 . QNAME=HG002-S9-H2-000001F;QSTART=641447;QSTRAND=+;GCPCT=6;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.17668 GT:DP:AD 0|1:25:10,15 ./.:31:18,13 ./.:37:18,19 -chr20 686455 . A AAAAAAAAAAAAAAAAAAAAAAAAAAT 60 . QNAME=cluster23_scaffold_3;QSTART=25024197;QSTRAND=-;SVTYPE=INS;SVLEN=26;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.114269 GT:DP:AD ./.:33:22,11 ./.:29:7,22 1/0:41:25,16 -chr20 686455 . A AAAAAAAAAAAAAAAAAAAAAAAAAT 60 . QNAME=cluster23_scaffold_2;QSTART=25008439;QSTRAND=-;SVTYPE=INS;SVLEN=25;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.117597 GT:DP:AD ./.:31:13,18 ./.:34:16,18 0/1:16:5,11 -chr20 686794 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=641815;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:34:23,11 0|1:29:22,7 1|1:34:11,23 -chr20 687380 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=642401;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:16:11,5 ./.:23:6,17 ./.:43:19,24 -chr20 687915 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=667816;QSTRAND=+;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:14:7,7 1|1:41:20,21 ./.:27:13,14 -chr20 688002 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=667903;QSTRAND=+;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:39:20,19 1|1:21:15,6 ./.:37:15,22 -chr20 688657 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=25006237;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:16:11,5 ./.:22:7,15 0|1:37:16,21 -chr20 688666 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=25006228;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:33:12,21 ./.:33:24,9 0|1:42:19,23 -chr20 689007 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=668908;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:23:13,10 1|1:43:18,25 0|1:37:20,17 -chr20 689613 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=669514;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:34:17,17 1|1:45:22,23 0|1:22:7,15 -chr20 689671 . G A 60 . QNAME=cluster19_000000F;QSTART=650517;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:24:16,8 0|1:31:22,9 ./.:26:10,16 -chr20 690105 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=670006;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:27:17,10 1|1:40:18,22 0|1:39:15,24 -chr20 690819 . A AGT 60 . QNAME=HG002-S9-H2-000001F;QSTART=645841;QSTRAND=+;GCPCT=33;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.792481 GT:DP:AD 0|1:23:7,16 ./.:20:13,7 1|0:30:14,16 -chr20 690819 . AGTGT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=670721;QSTRAND=+;GCPCT=40;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.760964 GT:DP:AD 1|0:17:9,8 1|1:41:23,18 0|1:25:18,7 -chr20 690853 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=670750;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:30:12,18 1|1:35:18,17 ./.:40:19,21 -chr20 690931 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=25003967;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:47:25,22 ./.:29:6,23 0|1:26:10,16 -chr20 690947 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=670844;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:34:16,18 1|1:21:7,14 ./.:21:6,15 -chr20 691419 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=25003479;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:31:7,24 ./.:27:7,20 0|1:42:25,17 -chr20 691923 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=671820;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:32:18,14 0|1:41:17,24 ./.:26:17,9 -chr20 692698 . C CTT 60 . QNAME=HG002-S9-H1-000001F;QSTART=672596;QSTRAND=+;GCPCT=33;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0.459148 GT:DP:AD 1|0:26:20,6 0|1:31:22,9 ./.:30:16,14 -chr20 692996 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=672895;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:23:15,8 1|1:23:8,15 0|1:33:24,9 -chr20 693104 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=673003;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:19:12,7 1|1:28:22,6 0|1:26:6,20 -chr20 693463 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=673362;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:18:11,7 1|1:41:22,19 0|1:30:21,9 -chr20 694203 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=649226;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:41:16,25 ./.:34:25,9 ./.:31:19,12 -chr20 694318 . A G 60 . QNAME=cluster19_000000F;QSTART=25066966;QSTRAND=-;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:11:5,6 1|0:48:25,23 0|1:19:7,12 -chr20 694678 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=674577;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:37:20,17 0|1:43:19,24 ./.:41:19,22 -chr20 695001 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=674900;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:41:21,20 1|1:35:20,15 0|1:21:15,6 -chr20 695004 . G C 60 . QNAME=cluster19_000000F;QSTART=25066280;QSTRAND=-;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:26:14,12 1|0:33:10,23 0|1:35:19,16 -chr20 695155 . G GTA 60 . QNAME=cluster19_000000F;QSTART=656000;QSTRAND=+;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.792481 GT:DP:AD ./.:37:23,14 0|1:43:24,19 ./.:47:24,23 -chr20 695259 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=675158;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:18:12,6 1|1:37:17,20 0|1:35:10,25 -chr20 695798 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=675697;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:13:5,8 0|1:24:19,5 ./.:42:23,19 -chr20 695931 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=675830;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:23:16,7 1|1:27:14,13 0|1:35:11,24 -chr20 696160 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=676059;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:35:10,25 0|1:29:13,16 ./.:16:6,10 -chr20 697221 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=677120;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:29:20,9 0|1:32:17,15 ./.:42:20,22 -chr20 697409 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=677308;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:45:24,21 0|1:19:12,7 ./.:18:13,5 -chr20 697409 . G T 60 . QNAME=cluster19_000000F;QSTART=25063875;QSTRAND=-;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:21:6,15 1|0:25:12,13 0|1:41:19,22 -chr20 697934 . C G 60 . QNAME=cluster19_000000F;QSTART=25063350;QSTRAND=-;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:26:21,5 1|0:22:13,9 0|1:26:10,16 -chr20 698083 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=677982;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:15:5,10 ./.:30:5,25 ./.:39:18,21 -chr20 698123 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=678022;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:20:9,11 1|1:27:8,19 0|1:49:25,24 -chr20 698533 . C T 60 . QNAME=cluster19_000000F;QSTART=659379;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:35:21,14 0|1:22:13,9 ./.:19:14,5 -chr20 698627 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=653650;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:33:11,22 1|0:33:24,9 0|1:32:8,24 -chr20 698723 . G A 60 . QNAME=cluster19_000000F;QSTART=25062561;QSTRAND=-;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:46:25,21 1|0:28:21,7 0|1:28:16,12 -chr20 699085 . C T 60 . QNAME=cluster19_000000F;QSTART=25062199;QSTRAND=-;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:41:22,19 1|0:30:25,5 0|1:38:21,17 -chr20 699214 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=25011435;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD ./.:30:25,5 ./.:30:12,18 1|0:19:12,7 -chr20 699214 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=654238;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 0|1:27:12,15 ./.:45:21,24 ./.:35:20,15 -chr20 699214 . CAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=679114;QSTRAND=+;GCPCT=25;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.405639 GT:DP:AD 1|0:37:13,24 ./.:28:7,21 ./.:38:21,17 -chr20 700520 . C T 60 . QNAME=cluster19_000000F;QSTART=25060764;QSTRAND=-;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:24:10,14 1|0:31:8,23 0|1:23:6,17 -chr20 700649 . C CT 60 . QNAME=cluster19_000000F;QSTART=25060634;QSTRAND=-;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:23:15,8 1|0:29:14,15 0|1:34:10,24 -chr20 700649 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=655672;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 0|1:14:7,7 ./.:38:20,18 ./.:30:10,20 -chr20 701307 . A G 60 . QNAME=cluster19_000000F;QSTART=25059976;QSTRAND=-;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:24:18,6 1|0:20:10,10 0|1:16:6,10 -chr20 701558 . C T 60 . QNAME=cluster19_000000F;QSTART=25059725;QSTRAND=-;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:48:23,25 1|0:26:18,8 0|1:17:12,5 -chr20 702627 . G A 60 . QNAME=cluster19_000000F;QSTART=25058656;QSTRAND=-;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:45:23,22 1|0:42:22,20 0|1:46:23,23 -chr20 702901 . T C 60 . QNAME=cluster19_000000F;QSTART=25058382;QSTRAND=-;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:17:8,9 1|0:28:9,19 0|1:19:6,13 -chr20 702972 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=682868;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:33:10,23 0|1:30:7,23 ./.:20:12,8 -chr20 704472 . A G 60 . QNAME=cluster19_000000F;QSTART=25056811;QSTRAND=-;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:39:17,22 1|0:19:10,9 0|1:24:17,7 -chr20 704662 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=659683;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:26:18,8 ./.:35:23,12 ./.:27:10,17 -chr20 704704 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=684600;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:32:10,22 1|1:27:9,18 1|0:34:14,20 -chr20 705070 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=684966;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:20:12,8 1|1:33:15,18 ./.:39:22,17 -chr20 705212 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=660233;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:23:12,11 ./.:39:17,22 1|0:27:9,18 -chr20 705650 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=685546;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:40:24,16 1|0:41:21,20 ./.:49:24,25 -chr20 706757 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=661778;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:22:13,9 ./.:45:25,20 1|0:20:10,10 -chr20 707000 . T TAA 60 . QNAME=cluster23_scaffold_2;QSTART=24987895;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.459148 GT:DP:AD ./.:44:24,20 ./.:33:8,25 0|1:21:8,13 -chr20 707128 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=687024;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:32:10,22 1|0:40:16,24 1|1:19:5,14 -chr20 707704 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=662725;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:33:8,25 ./.:24:12,12 1|0:26:21,5 -chr20 708199 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=688095;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:29:22,7 1|0:26:11,15 0|1:48:24,24 -chr20 708250 . C CTTTTGT 60 . QNAME=cluster19_000000F;QSTART=669097;QSTRAND=+;GCPCT=28;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.574417 GT:DP:AD ./.:38:18,20 0|1:40:21,19 ./.:31:21,10 -chr20 708422 . A ATT 60 . QNAME=HG002-S9-H2-000001F;QSTART=663444;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.459148 GT:DP:AD 0|1:31:14,17 ./.:17:11,6 1|0:18:11,7 -chr20 708422 . AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=688319;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 1|0:28:16,12 1|0:27:7,20 ./.:30:6,24 -chr20 708747 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=688642;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:37:12,25 1|0:21:10,11 ./.:23:13,10 -chr20 708784 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=688679;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:37:24,13 1|0:13:5,8 ./.:22:16,6 -chr20 709051 . TC T 60 . QNAME=cluster23_scaffold_2;QSTART=24985844;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,2,0;LCR=0.5 GT:DP:AD ./.:13:5,8 ./.:19:7,12 0|1:21:8,13 -chr20 709830 . G GACACTGCTCGGTCCTCCGCTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCGCTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGAACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGA 60 . QNAME=HG002-S9-H1-000001F;QSTART=689726;QSTRAND=+;SVTYPE=INS;SVLEN=465;HOMPCT=19.4;REMAP=partial;GCPCT=67;GTCNT=2,0,1,0;NumNeighbors=1;NeighId=8;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.936881 GT:DP:AD 1/0:41:16,25 ./.:30:18,12 ./.:21:10,11 -chr20 709916 . T TG 60 . QNAME=cluster19_000000F;QSTART=670769;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:37:21,16 0|1:33:16,17 ./.:18:10,8 -chr20 710119 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24984870;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:45:23,22 ./.:20:10,10 0|1:21:12,9 -chr20 710584 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24984405;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:42:24,18 ./.:15:10,5 0|1:18:6,12 -chr20 710789 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=691149;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:39:24,15 1|1:26:15,11 1|1:30:10,20 -chr20 710948 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=691308;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:29:13,16 0|1:44:25,19 1|0:15:5,10 -chr20 711068 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24983921;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:37:17,20 ./.:46:22,24 0|1:41:18,23 -chr20 711120 . G GGT 60 . QNAME=HG002-S9-H2-000001F;QSTART=666051;QSTRAND=+;GCPCT=66;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.459148 GT:DP:AD 0|1:26:10,16 ./.:32:11,21 ./.:26:18,8 -chr20 711120 . G GGTGT 60 . QNAME=cluster23_scaffold_2;QSTART=24983865;QSTRAND=-;GCPCT=60;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.485475 GT:DP:AD ./.:41:16,25 ./.:35:19,16 0|1:33:9,24 -chr20 711177 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=691537;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:41:21,20 1|1:38:19,19 1|1:28:19,9 -chr20 711562 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=691922;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:27:12,15 1|1:22:13,9 1|0:34:12,22 -chr20 711631 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=691991;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:27:9,18 1|1:20:11,9 1|1:28:19,9 -chr20 712402 . GT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=692763;QSTRAND=+;GCPCT=50;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0.5 GT:DP:AD 1|1:22:15,7 ./.:16:8,8 ./.:21:15,6 -chr20 712536 . C T 60 . QNAME=cluster19_000000F;QSTART=25048841;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:37:14,23 1|0:36:19,17 ./.:42:20,22 -chr20 712711 . C CT 60 . QNAME=cluster19_000000F;QSTART=25048665;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:40:25,15 1|0:45:20,25 ./.:32:7,25 -chr20 712711 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=693071;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|0:33:13,20 ./.:15:10,5 ./.:22:8,14 -chr20 712944 . T C 60 . QNAME=cluster19_000000F;QSTART=25048432;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:41:21,20 1|0:35:22,13 ./.:26:6,20 -chr20 712978 . G A 60 . QNAME=cluster19_000000F;QSTART=25048398;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:29:7,22 1|0:32:7,25 ./.:18:13,5 -chr20 713101 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=693459;QSTRAND=+;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:41:24,17 ./.:32:16,16 ./.:27:16,11 -chr20 713206 . T A 60 . QNAME=cluster19_000000F;QSTART=25048170;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:14:7,7 1|0:35:14,21 ./.:24:12,12 -chr20 713207 . T A 60 . QNAME=cluster19_000000F;QSTART=25048169;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:28:20,8 1|0:20:14,6 ./.:39:19,20 -chr20 713208 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=693566;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|1:21:11,10 1|0:30:21,9 ./.:31:17,14 -chr20 713417 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=693775;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:14:6,8 1|1:16:10,6 1|0:26:11,15 -chr20 713874 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24981111;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:24:15,9 ./.:33:17,16 0|1:16:9,7 -chr20 713943 . T C 60 . QNAME=cluster19_000000F;QSTART=25047433;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:23:7,16 1|0:34:19,15 ./.:25:7,18 -chr20 713965 . G A 60 . QNAME=cluster19_000000F;QSTART=25047411;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:19:5,14 1|0:27:16,11 ./.:35:13,22 -chr20 714250 . T C 60 . QNAME=cluster19_000000F;QSTART=25047126;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:36:25,11 1|0:34:11,23 ./.:29:8,21 -chr20 714816 . A G 60 . QNAME=cluster19_000000F;QSTART=675669;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:24:15,9 0|1:26:5,21 1|0:28:22,6 -chr20 715026 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=695384;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:25:17,8 0|1:45:23,22 1|0:39:20,19 -chr20 715559 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=695917;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:33:10,23 1|1:42:18,24 1|0:27:14,13 -chr20 715567 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=695925;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:29:23,6 1|1:37:18,19 1|0:23:15,8 -chr20 715736 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24979249;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:46:21,25 ./.:27:16,11 0|1:16:11,5 -chr20 715825 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=24994915;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:41:20,21 ./.:49:24,25 1|0:15:5,10 -chr20 715836 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=696194;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:36:20,16 1|0:25:8,17 1|0:34:24,10 -chr20 716956 . T C 60 . QNAME=cluster19_000000F;QSTART=677809;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:34:15,19 0|1:30:6,24 1|0:24:8,16 -chr20 717158 . ATT A 60 . QNAME=cluster19_000000F;QSTART=678012;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.459148 GT:DP:AD ./.:36:18,18 0|1:30:23,7 ./.:47:24,23 -chr20 717272 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=697630;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:28:18,10 ./.:38:20,18 0|1:19:6,13 -chr20 717541 . C T 60 . QNAME=cluster19_000000F;QSTART=678392;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:19:6,13 0|1:17:9,8 ./.:32:9,23 -chr20 717932 . G C 60 . QNAME=cluster19_000000F;QSTART=25043444;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:34:11,23 1|0:37:16,21 ./.:22:8,14 -chr20 718343 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=698701;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD 1|0:30:16,14 ./.:37:23,14 0|1:18:6,12 -chr20 718374 . C G 60 . QNAME=cluster19_000000F;QSTART=25043002;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD ./.:23:12,11 1|1:28:14,14 ./.:29:16,13 -chr20 718391 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=698749;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:29:21,8 1|1:37:25,12 0|1:44:24,20 -chr20 718820 . T A 60 . QNAME=cluster19_000000F;QSTART=679671;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:26:7,19 0|1:28:9,19 ./.:39:21,18 -chr20 719274 . C T 60 . QNAME=cluster19_000000F;QSTART=680125;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:26:15,11 0|1:22:8,14 ./.:37:13,24 -chr20 719464 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=699822;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:24:13,11 1|1:36:15,21 1|1:36:20,16 -chr20 719532 . T C 60 . QNAME=cluster19_000000F;QSTART=25041844;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:19:11,8 1|0:28:7,21 ./.:37:20,17 -chr20 720367 . C G 60 . QNAME=cluster19_000000F;QSTART=681218;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:23:11,12 0|1:18:8,10 ./.:41:23,18 -chr20 720501 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=700859;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:39:21,18 1|1:35:17,18 0|1:31:16,15 -chr20 720677 . C G 60 . QNAME=cluster19_000000F;QSTART=25040699;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:24:14,10 1|1:32:11,21 ./.:44:20,24 -chr20 720868 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=701226;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:35:16,19 0|1:29:6,23 0|1:26:19,7 -chr20 720953 . A G 60 . QNAME=cluster19_000000F;QSTART=25040423;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:35:24,11 1|1:27:13,14 ./.:37:15,22 -chr20 720987 . T C 60 . QNAME=cluster19_000000F;QSTART=25040389;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:34:10,24 1|1:28:11,17 ./.:41:25,16 -chr20 721070 . T C 60 . QNAME=cluster19_000000F;QSTART=25040306;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:28:7,21 1|0:39:22,17 ./.:44:19,25 -chr20 721315 . A T 60 . QNAME=cluster19_000000F;QSTART=25040061;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:36:11,25 1|1:16:10,6 ./.:26:16,10 -chr20 721448 . C T 60 . QNAME=cluster19_000000F;QSTART=25039928;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:33:25,8 1|1:36:17,19 ./.:21:15,6 -chr20 721653 . G A 60 . QNAME=cluster19_000000F;QSTART=25039723;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:22:13,9 1|1:28:12,16 ./.:31:19,12 -chr20 721675 . G C 60 . QNAME=cluster19_000000F;QSTART=25039701;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:33:8,25 1|1:23:10,13 ./.:14:7,7 -chr20 721926 . C T 60 . QNAME=cluster19_000000F;QSTART=25039450;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:35:21,14 1|1:30:15,15 ./.:34:10,24 -chr20 722151 . T C 60 . QNAME=cluster19_000000F;QSTART=683002;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:25:11,14 0|1:42:23,19 ./.:30:12,18 -chr20 722203 . T C 60 . QNAME=cluster19_000000F;QSTART=25039173;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:21:6,15 1|1:25:7,18 ./.:18:9,9 -chr20 722204 . G A 60 . QNAME=cluster19_000000F;QSTART=683055;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:30:22,8 0|1:22:9,13 ./.:33:8,25 -chr20 722214 . G T 60 . QNAME=cluster19_000000F;QSTART=25039162;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:22:9,13 1|1:28:7,21 ./.:22:5,17 -chr20 722255 . T C 60 . QNAME=cluster19_000000F;QSTART=25039121;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:41:18,23 1|1:33:14,19 ./.:27:17,10 -chr20 722277 . C T 60 . QNAME=cluster19_000000F;QSTART=25039099;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:41:20,21 1|1:36:24,12 ./.:17:9,8 -chr20 722412 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=702770;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:23:6,17 ./.:28:22,6 0|1:21:6,15 -chr20 723134 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=703492;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:22:8,14 ./.:21:16,5 0|1:33:25,8 -chr20 723311 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=703669;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:33:24,9 1|1:36:18,18 1|1:20:10,10 -chr20 723429 . CTCT C 60 . QNAME=cluster19_000000F;QSTART=684281;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:41:21,20 0|1:33:17,16 ./.:26:10,16 -chr20 723467 . C CTTTCT 60 . QNAME=cluster19_000000F;QSTART=684316;QSTRAND=+;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.459148 GT:DP:AD ./.:23:16,7 0|1:33:20,13 ./.:35:11,24 -chr20 723709 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=704067;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:32:22,10 0|1:23:6,17 0|1:17:7,10 -chr20 723727 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=704085;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:27:18,9 ./.:31:10,21 0|1:19:10,9 -chr20 723799 . G A 60 . QNAME=cluster19_000000F;QSTART=25037577;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:20:12,8 1|0:41:20,21 ./.:17:12,5 -chr20 723808 . G A 60 . QNAME=cluster19_000000F;QSTART=684661;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:44:22,22 0|1:22:13,9 ./.:36:19,17 -chr20 723875 . G A 60 . QNAME=cluster19_000000F;QSTART=684728;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:26:13,13 0|1:38:20,18 ./.:42:17,25 -chr20 723915 . A G 60 . QNAME=cluster19_000000F;QSTART=25037461;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:19:13,6 1|0:35:25,10 ./.:28:20,8 -chr20 724055 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=704413;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:22:6,16 0|1:13:8,5 0|1:27:18,9 -chr20 724660 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=705019;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|0:40:15,25 ./.:31:17,14 0|1:19:12,7 -chr20 725763 . T G 60 . QNAME=cluster19_000000F;QSTART=686616;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:34:9,25 0|1:31:18,13 ./.:14:7,7 -chr20 726010 . C CA 60 . QNAME=HG002-S9-H2-000001F;QSTART=680942;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 0|1:12:6,6 1|0:33:12,21 ./.:29:13,16 -chr20 726010 . C CAAAAAAA 60 . QNAME=cluster19_000000F;QSTART=686864;QSTRAND=+;GCPCT=12;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.271782 GT:DP:AD ./.:41:18,23 0|1:23:16,7 ./.:29:6,23 -chr20 726010 . CAAAAAAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=706370;QSTRAND=+;GCPCT=11;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.251629 GT:DP:AD 1|0:33:15,18 ./.:36:17,19 0|1:33:8,25 -chr20 726075 . G A 60 . QNAME=cluster19_000000F;QSTART=686935;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:34:16,18 0|1:33:20,13 ./.:19:11,8 -chr20 726115 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=706466;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:31:23,8 0|1:27:16,11 0|1:44:20,24 -chr20 726166 . T C 60 . QNAME=cluster19_000000F;QSTART=687026;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:32:11,21 0|1:28:6,22 ./.:26:18,8 -chr20 726847 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=707198;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:25:5,20 ./.:30:5,25 0|1:34:20,14 -chr20 727050 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=707401;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:41:19,22 ./.:18:7,11 0|1:18:11,7 -chr20 727183 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=707534;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:36:11,25 ./.:48:24,24 0|1:30:14,16 -chr20 727236 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=707587;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:36:23,13 ./.:39:19,20 0|1:34:18,16 -chr20 727293 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=24983447;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:22:13,9 ./.:37:15,22 1|0:35:19,16 -chr20 727295 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=707646;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:30:7,23 ./.:37:17,20 ./.:20:15,5 -chr20 727600 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=24983174;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:32:21,11 ./.:42:25,17 1|0:33:12,21 -chr20 727602 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=24983172;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:42:23,19 ./.:29:22,7 1|0:32:13,19 -chr20 727613 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=707964;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:35:21,14 1|1:33:25,8 0|1:14:7,7 -chr20 727615 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=707966;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:35:11,24 1|1:25:16,9 0|1:38:24,14 -chr20 727615 . C CGA 60 . QNAME=HG002-S9-H2-000001F;QSTART=682514;QSTRAND=+;GCPCT=66;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.792481 GT:DP:AD 0|1:35:11,24 ./.:38:16,22 ./.:19:7,12 -chr20 727774 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=682674;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:13:7,6 1|1:45:21,24 ./.:28:11,17 -chr20 727786 . AT A 60 . QNAME=cluster23_scaffold_3;QSTART=24982988;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD ./.:19:13,6 ./.:30:10,20 1|0:14:7,7 -chr20 727786 . ATT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=682687;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.459148 GT:DP:AD 0|1:28:6,22 1|0:37:16,21 ./.:23:15,8 -chr20 727926 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=708277;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:17:12,5 1|0:35:11,24 ./.:36:15,21 -chr20 727962 . GGC G 60 . QNAME=cluster23_scaffold_3;QSTART=24982813;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.459148 GT:DP:AD ./.:41:24,17 ./.:26:18,8 1|0:42:25,17 -chr20 728062 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=708413;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:37:25,12 1|1:37:21,16 0|1:29:10,19 -chr20 728326 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=708677;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:26:10,16 0|1:24:13,11 ./.:34:25,9 -chr20 728330 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=708681;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:37:13,24 0|1:35:18,17 ./.:36:11,25 -chr20 728371 . G A 60 . QNAME=cluster19_000000F;QSTART=689183;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:33:16,17 0|1:13:8,5 ./.:20:7,13 -chr20 728488 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=683386;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:41:17,24 1|0:33:20,13 0|1:31:19,12 -chr20 728626 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=24966366;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:26:21,5 ./.:31:12,19 0|1:38:17,21 -chr20 728679 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=709030;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:37:13,24 1|0:18:8,10 1|1:45:24,21 -chr20 728689 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=709040;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:34:16,18 1|0:34:19,15 0|1:20:15,5 -chr20 728722 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=709073;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:37:19,18 1|0:47:24,23 1|1:20:9,11 -chr20 728924 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=709275;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:33:19,14 1|0:32:12,20 0|1:39:22,17 -chr20 729045 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=709396;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:18:11,7 1|0:42:23,19 1|1:39:21,18 -chr20 729328 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=709679;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:34:14,20 1|0:27:8,19 1|1:15:8,7 -chr20 729751 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=684649;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:32:10,22 1|0:38:21,17 0|1:44:24,20 -chr20 729893 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=684791;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:43:20,23 1|0:25:11,14 0|1:40:24,16 -chr20 730190 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=710541;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:27:14,13 ./.:47:23,24 1|0:50:25,25 -chr20 730755 . A AG 60 . QNAME=HG002-S9-H1-000001F;QSTART=711107;QSTRAND=+;GCPCT=50;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|1:23:15,8 1|1:40:17,23 1|1:23:12,11 -chr20 731406 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=686305;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD 0|1:18:6,12 1|0:33:20,13 0|1:30:18,12 -chr20 731541 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=711893;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:41:21,20 1|0:31:6,25 1|1:35:19,16 -chr20 732158 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=687057;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:26:8,18 1|0:30:12,18 0|1:16:10,6 -chr20 732263 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=687162;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:39:21,18 1|0:27:10,17 0|1:37:15,22 -chr20 732533 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=712885;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:38:16,22 1|0:32:20,12 1|1:33:13,20 -chr20 733181 . T TTATG 60 . QNAME=HG002-S9-H1-000001F;QSTART=713534;QSTRAND=+;GCPCT=20;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.685475 GT:DP:AD 1|0:32:13,19 ./.:40:23,17 ./.:30:25,5 -chr20 733364 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=713720;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:34:25,9 1|0:28:5,23 1|1:34:16,18 -chr20 733492 . TA T 60 . QNAME=HG002-S9-H1-000001F;QSTART=713849;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD 1|1:27:20,7 1|1:16:8,8 1|1:31:11,20 -chr20 733573 . A AAAAACAAAAC 60 . QNAME=cluster23_scaffold_3;QSTART=24977194;QSTRAND=-;GCPCT=18;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.342019 GT:DP:AD ./.:25:12,13 ./.:47:24,23 1|0:15:8,7 -chr20 733573 . AAAAAC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=713929;QSTRAND=+;GCPCT=16;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.325011 GT:DP:AD 1|0:42:24,18 ./.:17:7,10 ./.:23:18,5 -chr20 733617 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=713967;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:22:5,17 ./.:22:6,16 1|0:32:7,25 -chr20 733672 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=714022;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:15:5,10 ./.:26:12,14 ./.:33:24,9 -chr20 733818 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=714168;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:23:6,17 1|1:29:18,11 1|1:29:20,9 -chr20 733903 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24976864;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:44:24,20 ./.:22:13,9 1|0:27:7,20 -chr20 734373 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=714723;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:21:6,15 ./.:36:23,13 ./.:35:22,13 -chr20 734383 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=714733;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,3,0,0;LCR=0 GT:DP:AD 1|0:14:6,8 ./.:16:11,5 ./.:23:16,7 -chr20 734531 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=714881;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:43:21,22 1|0:28:9,19 1|1:23:14,9 -chr20 734610 . G GGT 60 . QNAME=cluster19_000000F;QSTART=695423;QSTRAND=+;GCPCT=66;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.459148 GT:DP:AD ./.:49:24,25 0|1:35:13,22 ./.:23:17,6 -chr20 734610 . G GGTGTGT 60 . QNAME=HG002-S9-H1-000001F;QSTART=714961;QSTRAND=+;GCPCT=57;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.492614 GT:DP:AD 1|0:29:17,12 1|0:36:12,24 1|1:33:15,18 -chr20 734610 . G GGTGTGTGT 60 . QNAME=HG002-S9-H2-000001F;QSTART=689509;QSTRAND=+;GCPCT=55;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0.495538 GT:DP:AD 0|1:33:14,19 ./.:13:6,7 ./.:25:15,10 -chr20 734650 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=24976111;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:28:23,5 ./.:29:16,13 1|0:13:8,5 -chr20 735203 . C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=715560;QSTRAND=+;GCPCT=50;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|1:33:11,22 1|1:28:19,9 1|1:30:18,12 -chr20 735555 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=715912;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|1:32:20,12 1|0:33:19,14 1|1:30:23,7 -chr20 735589 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=690496;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:26:5,21 1|0:26:18,8 1|1:26:7,19 -chr20 736154 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24974606;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:23:15,8 ./.:47:24,23 1|0:31:11,20 -chr20 736400 . A C 60 . QNAME=cluster23_scaffold_3;QSTART=24974360;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:27:8,19 ./.:34:10,24 1|0:30:21,9 -chr20 736444 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=716801;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:30:20,10 1|0:47:23,24 1|1:35:10,25 -chr20 736736 . CA C 60 . QNAME=cluster19_000000F;QSTART=697552;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:50:25,25 0|1:36:24,12 ./.:12:7,5 -chr20 736736 . CAA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=691644;QSTRAND=+;GCPCT=33;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.459148 GT:DP:AD 0|1:18:13,5 1|0:20:11,9 1|1:42:22,20 -chr20 736925 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=691830;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:37:17,20 1|0:29:19,10 0|1:40:15,25 -chr20 737005 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=691910;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:34:10,24 1|0:24:13,11 0|1:32:11,21 -chr20 737174 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=717531;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:16:10,6 1|1:46:21,25 1|1:20:14,6 -chr20 737624 . A AAAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=717982;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.405639 GT:DP:AD 1|0:38:15,23 ./.:20:7,13 ./.:21:8,13 -chr20 737624 . A AAATAAT 60 . QNAME=cluster19_000000F;QSTART=698439;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0.43156 GT:DP:AD ./.:33:21,12 0|1:29:18,11 ./.:36:25,11 -chr20 737624 . AAATAAT A 60 . QNAME=cluster23_scaffold_3;QSTART=24973138;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.43156 GT:DP:AD ./.:36:24,12 ./.:25:13,12 1|0:47:24,23 -chr20 737898 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=718258;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:44:25,19 ./.:32:25,7 ./.:35:10,25 -chr20 738059 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=718419;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:24:11,13 1|1:30:25,5 1|1:26:6,20 -chr20 738091 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=718451;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:44:23,21 1|1:16:5,11 1|1:30:18,12 -chr20 738584 . C CA 60 . QNAME=cluster19_000000F;QSTART=699405;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD ./.:23:9,14 0|1:32:9,23 ./.:26:16,10 -chr20 738739 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=693644;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:25:17,8 1|0:32:12,20 0|1:38:22,16 -chr20 739096 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=719456;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:15:6,9 1|0:38:25,13 1|1:30:6,24 -chr20 739210 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=719570;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:42:20,22 1|0:22:15,7 1|1:32:18,14 -chr20 739239 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=719599;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:40:24,16 1|0:35:10,25 1|1:35:16,19 -chr20 740272 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=695177;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:29:18,11 1|0:33:14,19 0|1:28:11,17 -chr20 740467 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=720827;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:38:17,21 1|1:29:7,22 1|1:20:9,11 -chr20 741153 . T G 60 . QNAME=cluster23_scaffold_3;QSTART=24969615;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:17:12,5 ./.:13:6,7 1|0:44:23,21 -chr20 741453 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=721813;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:24:12,12 ./.:39:21,18 ./.:32:22,10 -chr20 741767 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=696672;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:20:5,15 1|0:42:18,24 0|1:24:17,7 -chr20 741939 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=696844;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:30:6,24 1|0:15:7,8 1|1:35:23,12 -chr20 742416 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=24968352;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:33:17,16 ./.:29:15,14 1|0:32:9,23 -chr20 742511 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=722871;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:41:17,24 ./.:34:25,9 ./.:34:9,25 -chr20 742657 . G T 60 . QNAME=cluster23_scaffold_3;QSTART=24968111;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:31:14,17 ./.:30:16,14 1|0:42:22,20 -chr20 743121 . G GTCTCTCTCTC 60 . QNAME=cluster19_000000F;QSTART=703943;QSTRAND=+;GCPCT=54;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.674294 GT:DP:AD ./.:23:14,9 0|1:47:22,25 ./.:25:13,12 -chr20 743121 . GTCTC G 60 . QNAME=cluster19_000000F;QSTART=25018283;QSTRAND=-;GCPCT=60;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.760964 GT:DP:AD ./.:30:9,21 1|0:40:24,16 ./.:24:14,10 -chr20 743121 . GTCTCTCTC G 60 . QNAME=HG002-S9-H2-000001F;QSTART=698027;QSTRAND=+;GCPCT=55;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.696074 GT:DP:AD 0|1:40:16,24 ./.:29:13,16 ./.:26:20,6 -chr20 743153 . C CACACACACACACA 60 . QNAME=HG002-S9-H1-000001F;QSTART=723514;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|0:28:18,10 ./.:23:7,16 ./.:12:5,7 -chr20 743153 . CTCTCTCTCTCT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=723527;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|0:26:20,6 ./.:37:12,25 ./.:38:22,16 -chr20 743160 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=698057;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:28:15,13 ./.:31:9,22 ./.:27:12,15 -chr20 743160 . T TCACACA 60 . QNAME=cluster23_scaffold_3;QSTART=24967602;QSTRAND=-;GCPCT=42;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.724408 GT:DP:AD ./.:36:24,12 ./.:31:16,15 1|0:31:14,17 -chr20 743162 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=698059;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:36:17,19 1|0:22:16,6 1|0:19:5,14 -chr20 743162 . T TCA 60 . QNAME=cluster23_scaffold_2;QSTART=24951823;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.792481 GT:DP:AD ./.:27:6,21 ./.:27:14,13 0|1:35:11,24 -chr20 743164 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=698061;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:30:15,15 1|0:39:25,14 1|1:29:24,5 -chr20 743734 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=724096;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:36:18,18 ./.:31:11,20 ./.:29:22,7 -chr20 743803 . A AG 60 . QNAME=HG002-S9-H1-000001F;QSTART=724166;QSTRAND=+;GCPCT=50;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 1|1:39:14,25 1|0:31:7,24 1|1:47:23,24 -chr20 743934 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=24966827;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:34:13,21 ./.:37:15,22 1|0:28:18,10 -chr20 744816 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=725179;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:34:9,25 1|1:25:11,14 1|1:31:9,22 -chr20 745347 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=725710;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:16:9,7 1|0:37:14,23 1|1:27:21,6 -chr20 745631 . CAGA C 60 . QNAME=cluster19_000000F;QSTART=706463;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0.75 GT:DP:AD ./.:12:6,6 0|1:29:12,17 ./.:31:7,24 -chr20 745642 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=726005;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:38:22,16 ./.:30:14,16 ./.:33:20,13 -chr20 746583 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24964178;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:17:11,6 ./.:29:7,22 1|0:21:11,10 -chr20 746687 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=701585;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:37:19,18 1|1:26:15,11 0|1:27:7,20 -chr20 746832 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=701730;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:30:12,18 1|0:29:16,13 0|1:25:14,11 -chr20 746873 . C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=727237;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 1|0:30:14,16 ./.:20:5,15 ./.:30:15,15 -chr20 746873 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=701772;QSTRAND=+;GCPCT=50;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 0|1:30:13,17 1|1:45:20,25 1|1:34:9,25 -chr20 746937 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=24963825;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:41:18,23 ./.:13:5,8 1|0:44:25,19 -chr20 747249 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=702146;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:40:24,16 1|1:33:9,24 0|1:19:8,11 -chr20 747381 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=702278;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:27:19,8 1|1:29:16,13 0|1:38:15,23 -chr20 747855 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=702752;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 0|1:18:6,12 1|1:29:23,6 0|1:25:15,10 -chr20 748018 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=24962744;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:50:25,25 ./.:31:12,19 1|0:37:25,12 -chr20 748207 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=703105;QSTRAND=+;GCPCT=50;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 0|1:39:17,22 1|0:27:14,13 0|1:43:24,19 -chr20 748212 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=703108;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:25:18,7 1|1:31:22,9 0|1:32:15,17 -chr20 748246 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=728611;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|0:36:13,23 0|1:30:14,16 ./.:14:8,6 -chr20 748431 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=703327;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:34:23,11 1|0:26:17,9 0|1:26:7,19 -chr20 748452 . AT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=703349;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 0|1:41:25,16 1|0:30:23,7 1|1:32:8,24 -chr20 748776 . G A 60 . QNAME=cluster19_000000F;QSTART=709602;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:37:24,13 0|1:37:13,24 ./.:11:5,6 -chr20 749061 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24961702;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:38:23,15 ./.:17:6,11 1|0:28:20,8 -chr20 749346 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=704241;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:44:19,25 1|0:35:20,15 0|1:24:5,19 -chr20 749546 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=704441;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:26:9,17 1|0:23:6,17 0|1:30:10,20 -chr20 749854 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=730217;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:39:17,22 1|1:31:15,16 1|1:29:12,17 -chr20 750249 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=705144;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:39:21,18 1|0:30:24,6 0|1:30:19,11 -chr20 750361 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=705256;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,1,2;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 0|1:14:5,9 1|0:29:15,14 0|1:25:13,12 -chr20 750494 . C CA 60 . QNAME=cluster19_000000F;QSTART=25010915;QSTRAND=-;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:19:6,13 1|0:35:15,20 1|1:16:8,8 -chr20 750546 . T G 60 . QNAME=cluster23_scaffold_3;QSTART=24960216;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:43:23,20 ./.:37:23,14 1|0:38:19,19 -chr20 750567 . C A 60 . QNAME=cluster19_000000F;QSTART=711393;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:36:16,20 0|1:39:22,17 ./.:31:22,9 -chr20 751100 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=705995;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:29:6,23 1|0:32:11,21 0|1:27:10,17 -chr20 751283 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=706178;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:25:18,7 1|0:14:5,9 0|1:36:20,16 -chr20 751473 . CTTTAT C 60 . QNAME=cluster23_scaffold_3;QSTART=24959289;QSTRAND=-;GCPCT=16;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.625815 GT:DP:AD ./.:21:12,9 ./.:36:15,21 1|0:27:5,22 -chr20 751473 . CTTTATTTTAT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=731837;QSTRAND=+;GCPCT=9;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.547898 GT:DP:AD 1|0:27:7,20 0|1:15:10,5 ./.:25:12,13 -chr20 751519 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=706389;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:39:24,15 1|0:39:20,19 0|1:20:15,5 -chr20 751627 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=706497;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:32:13,19 1|0:35:20,15 0|1:33:19,14 -chr20 751651 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=706521;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:43:18,25 1|0:30:6,24 0|1:34:13,21 -chr20 751755 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=706625;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:32:15,17 1|0:30:18,12 0|1:48:24,24 -chr20 752069 . ATCTT A 60 . QNAME=cluster23_scaffold_3;QSTART=24958698;QSTRAND=-;GCPCT=20;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.685475 GT:DP:AD ./.:44:19,25 ./.:29:7,22 1|0:43:21,22 -chr20 752120 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=706990;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:36:15,21 1|0:18:11,7 0|1:29:13,16 -chr20 752235 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=707105;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:32:9,23 1|0:30:21,9 0|1:31:20,11 -chr20 752300 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=707170;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:19:14,5 1|0:29:6,23 0|1:14:5,9 -chr20 752450 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=732803;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD 1|1:24:11,13 1|1:16:5,11 1|1:21:10,11 -chr20 752821 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=707691;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:20:8,12 1|0:28:8,20 0|1:44:25,19 -chr20 753097 . G GAAGA 60 . QNAME=cluster23_scaffold_3;QSTART=24957670;QSTRAND=-;GCPCT=40;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.485475 GT:DP:AD ./.:34:20,14 ./.:42:24,18 1|0:38:23,15 -chr20 753097 . G GAAGAAAGAAAGAAAGAAAAGA 60 . QNAME=cluster19_000000F;QSTART=25008316;QSTRAND=-;GCPCT=27;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.422675 GT:DP:AD ./.:34:25,9 1|0:31:7,24 ./.:29:18,11 -chr20 753109 . A AAAGAAAAGAAAGAAAGAAAGAAAAG 60 . QNAME=cluster23_scaffold_2;QSTART=24941877;QSTRAND=-;SVTYPE=INS;SVLEN=25;GCPCT=23;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.389675 GT:DP:AD ./.:45:25,20 ./.:22:10,12 0/1:42:24,18 -chr20 753109 . A AAAGAAAAGAAAGAAAGAAAGAAAAGAAAGAAAG 60 . QNAME=HG002-S9-H2-000001F;QSTART=707980;QSTRAND=+;SVTYPE=INS;SVLEN=33;GCPCT=23;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.393563 GT:DP:AD 0/1:30:6,24 ./.:29:16,13 ./.:32:20,12 -chr20 753112 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=733465;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:32:21,11 0|1:30:13,17 ./.:34:15,19 -chr20 753113 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=733466;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:25:15,10 0|1:28:13,15 ./.:19:7,12 -chr20 753141 . GAAAGAAAGAAAGAAAGAA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=733495;QSTRAND=+;GCPCT=26;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.415737 GT:DP:AD 1|0:21:10,11 ./.:43:19,24 ./.:28:13,15 -chr20 753148 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=708051;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:38:19,19 1|0:22:5,17 0|1:32:9,23 -chr20 753159 . A AAAGAAAG 60 . QNAME=cluster23_scaffold_3;QSTART=24957601;QSTRAND=-;GCPCT=25;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.405639 GT:DP:AD ./.:37:21,16 ./.:29:6,23 1|0:20:13,7 -chr20 753159 . A AAG 60 . QNAME=HG002-S9-H2-000001F;QSTART=708063;QSTRAND=+;GCPCT=33;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.459148 GT:DP:AD 0|1:30:5,25 1|1:38:21,17 0|1:30:23,7 -chr20 753194 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=708099;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:30:16,14 1|0:30:10,20 0|1:40:17,23 -chr20 753319 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=708224;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:22:10,12 1|0:27:19,8 0|1:32:16,16 -chr20 753350 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24957410;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:36:19,17 ./.:16:5,11 1|0:37:12,25 -chr20 753848 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=24956912;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:32:7,25 ./.:22:5,17 1|0:48:24,24 -chr20 753849 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=24956911;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:27:16,11 ./.:34:20,14 1|0:37:20,17 -chr20 753973 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=708878;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:44:20,24 1|0:44:24,20 0|1:34:12,22 -chr20 754002 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=734337;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:28:16,12 ./.:26:8,18 ./.:17:12,5 -chr20 754073 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=24956687;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:48:23,25 ./.:32:9,23 1|0:41:21,20 -chr20 754124 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=734459;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:26:5,21 1|0:38:25,13 1|1:34:20,14 -chr20 754553 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=709458;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:47:22,25 1|0:36:22,14 0|1:23:15,8 -chr20 755158 . G T 60 . QNAME=cluster19_000000F;QSTART=25006253;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:31:6,25 1|0:16:6,10 ./.:24:6,18 -chr20 755213 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=735548;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:19:12,7 1|1:25:5,20 1|1:41:24,17 -chr20 755214 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=735549;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:12:5,7 ./.:28:12,16 ./.:16:7,9 -chr20 755269 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=735605;QSTRAND=+;GCPCT=50;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 1|1:35:10,25 1|1:36:19,17 1|1:46:25,21 -chr20 755467 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=735803;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:28:22,6 ./.:37:21,16 ./.:35:16,19 -chr20 755545 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=24955214;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:18:8,10 ./.:37:21,16 1|0:34:25,9 -chr20 755581 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=710487;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:37:24,13 1|1:32:12,20 1|1:29:12,17 -chr20 755749 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=736085;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:35:10,25 ./.:15:6,9 ./.:33:22,11 -chr20 755803 . A G 60 . QNAME=cluster19_000000F;QSTART=716622;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:31:11,20 0|1:25:14,11 ./.:30:22,8 -chr20 756000 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=736336;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:31:20,11 1|1:33:11,22 0|1:12:6,6 -chr20 756217 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=736553;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:20:15,5 ./.:19:11,8 ./.:46:23,23 -chr20 756388 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=24954371;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:39:17,22 ./.:36:16,20 1|0:20:14,6 -chr20 756408 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=736744;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:20:15,5 ./.:24:8,16 ./.:34:12,22 -chr20 756478 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=24954281;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:34:18,16 ./.:18:10,8 1|0:16:10,6 -chr20 756575 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=736912;QSTRAND=+;GCPCT=50;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD 1|1:21:16,5 1|1:23:14,9 0|1:35:18,17 -chr20 756637 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=24954122;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:21:7,14 ./.:34:22,12 1|0:28:5,23 -chr20 756764 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=24953995;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:28:14,14 ./.:26:11,15 1|0:28:5,23 -chr20 756872 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=737208;QSTRAND=+;GCPCT=50;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 1|1:47:22,25 1|1:35:17,18 1|0:31:21,10 -chr20 756909 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=737243;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:21:11,10 1|1:49:24,25 1|1:15:5,10 -chr20 758241 . A AT 60 . QNAME=HG002-S9-H1-000001F;QSTART=738576;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|1:28:10,18 1|1:20:8,12 0|1:24:19,5 -chr20 758241 . A ATTT 60 . QNAME=cluster23_scaffold_3;QSTART=24952516;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0.405639 GT:DP:AD ./.:28:19,9 ./.:24:16,8 1|0:21:12,9 -chr20 758268 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=738603;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:33:14,19 ./.:28:9,19 ./.:20:8,12 -chr20 758339 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=738674;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:33:17,16 ./.:16:10,6 ./.:32:21,11 -chr20 758391 . A C 60 . QNAME=cluster23_scaffold_3;QSTART=24952366;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:14:5,9 ./.:19:12,7 1|0:18:5,13 -chr20 758562 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=24952195;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:32:21,11 ./.:25:5,20 1|0:27:16,11 -chr20 758620 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=713525;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:21:11,10 1|0:39:24,15 0|1:24:12,12 -chr20 758664 . T C 60 . QNAME=cluster23_scaffold_3;QSTART=24952093;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:31:6,25 ./.:33:24,9 1|0:32:12,20 -chr20 758808 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=739143;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:28:14,14 1|1:30:12,18 1|1:19:9,10 -chr20 758874 . C G 60 . QNAME=cluster19_000000F;QSTART=719692;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:38:16,22 0|1:34:10,24 ./.:33:18,15 -chr20 758972 . CGTGT C 60 . QNAME=cluster23_scaffold_3;QSTART=24951785;QSTRAND=-;GCPCT=60;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.760964 GT:DP:AD ./.:45:23,22 ./.:35:25,10 1|0:27:12,15 -chr20 758972 . CGTGTGTGT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=713878;QSTRAND=+;GCPCT=55;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.696074 GT:DP:AD 0|1:22:9,13 1|1:33:22,11 0|1:15:7,8 -chr20 758972 . CGTGTGTGTGT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=739308;QSTRAND=+;GCPCT=54;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.674294 GT:DP:AD 1|0:22:14,8 ./.:31:10,21 ./.:17:6,11 -chr20 759048 . AC A 60 . QNAME=cluster23_scaffold_3;QSTART=24951713;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:45:23,22 ./.:29:18,11 1|0:26:21,5 -chr20 759464 . C CA 60 . QNAME=HG002-S9-H2-000001F;QSTART=714362;QSTRAND=+;GCPCT=50;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD 0|1:23:14,9 1|1:41:23,18 0|1:25:20,5 -chr20 760189 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=715087;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 0|1:32:18,14 1|0:26:19,7 0|1:18:8,10 -chr20 760275 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=740600;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:24:6,18 1|1:32:25,7 1|1:25:6,19 -chr20 761203 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=741528;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:38:16,22 0|1:24:13,11 1|1:38:19,19 -chr20 761573 . C G 60 . QNAME=cluster19_000000F;QSTART=24999845;QSTRAND=-;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:43:24,19 1|0:32:17,15 1|0:46:24,22 -chr20 761593 . G A 60 . QNAME=cluster19_000000F;QSTART=24999825;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:12:6,6 1|1:23:11,12 ./.:25:10,15 -chr20 761595 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=741920;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:38:21,17 1|1:22:12,10 1|1:21:15,6 -chr20 761987 . A G 60 . QNAME=cluster19_000000F;QSTART=24999431;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:31:15,16 1|0:42:18,24 1|1:36:12,24 -chr20 762072 . A C 60 . QNAME=cluster23_scaffold_3;QSTART=24948690;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:30:22,8 ./.:31:23,8 1|0:26:12,14 -chr20 762187 . G T 60 . QNAME=cluster19_000000F;QSTART=24999231;QSTRAND=-;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:18:9,9 1|0:34:17,17 1|0:36:11,25 -chr20 762374 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=742699;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:22:13,9 1|1:29:13,16 1|0:41:17,24 -chr20 762480 . C G 60 . QNAME=cluster19_000000F;QSTART=24998938;QSTRAND=-;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:43:21,22 1|0:17:7,10 1|0:17:5,12 -chr20 762486 . C T 60 . QNAME=cluster19_000000F;QSTART=24998932;QSTRAND=-;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:47:24,23 1|0:14:8,6 1|0:33:25,8 -chr20 762576 . T C 60 . QNAME=cluster19_000000F;QSTART=24998842;QSTRAND=-;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:25:16,9 1|0:25:6,19 1|0:42:23,19 -chr20 762628 . C T 60 . QNAME=cluster19_000000F;QSTART=24998790;QSTRAND=-;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:31:20,11 1|0:33:9,24 1|0:27:21,6 -chr20 763183 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=743508;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0 GT:DP:AD 1|1:19:12,7 1|1:17:10,7 1|0:16:7,9 -chr20 763406 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=743731;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:48:24,24 0|1:28:11,17 ./.:30:15,15 -chr20 763806 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=744131;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:33:23,10 1|1:26:21,5 1|0:36:17,19 -chr20 764018 . A ACAGGTCAAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=744344;QSTRAND=+;GCPCT=40;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.960964 GT:DP:AD 1|1:22:16,6 0|1:27:5,22 ./.:35:10,25 -chr20 764203 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=744537;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:38:16,22 1|1:38:16,22 1|0:28:23,5 -chr20 764230 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=744564;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:20:5,15 1|1:36:22,14 1|0:22:14,8 -chr20 764442 . A AGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGG 60 . QNAME=cluster23_scaffold_3;QSTART=24946242;QSTRAND=-;SVTYPE=INS;SVLEN=78;HOMPCT=50;REMAP=tandem;REMAPHits=chr20:764441-764520.100;GCPCT=63;GTCNT=2,0,1,0;NumNeighbors=2;NeighId=9;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.922364 GT:DP:AD ./.:30:19,11 ./.:35:14,21 1/0:46:22,24 -chr20 764537 . A AGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=744872;QSTRAND=+;SVTYPE=INS;SVLEN=117;HOMPCT=51.4;REMAP=tandem;REMAPHits=chr20:764431-764537.89;GCPCT=63;GTCNT=1,0,1,1;NumNeighbors=2;NeighId=9;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0.930192 GT:DP:AD 1/1:23:18,5 0/1:14:6,8 ./.:45:20,25 -chr20 764537 . A AGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAT 60 . QNAME=cluster19_000000F;QSTART=24996803;QSTRAND=-;SVTYPE=INS;SVLEN=78;HOMPCT=51.4;REMAP=tandem;REMAPHits=chr20:764431-764498.84,chr20:764458-764537.100;GCPCT=63;GTCNT=2,0,1,0;NumNeighbors=2;NeighId=9;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.933711 GT:DP:AD ./.:25:14,11 1/0:43:20,23 ./.:30:22,8 -chr20 764800 . C A 60 . QNAME=cluster23_scaffold_2;QSTART=24930190;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD ./.:34:22,12 ./.:29:16,13 0|1:35:24,11 -chr20 765454 . G A 60 . QNAME=cluster19_000000F;QSTART=24995886;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:42:17,25 1|0:24:12,12 ./.:41:18,23 -chr20 765937 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=746389;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|1:40:25,15 0|1:13:5,8 ./.:23:11,12 -chr20 766211 . A AG 60 . QNAME=HG002-S9-H1-000001F;QSTART=746664;QSTRAND=+;GCPCT=50;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 1|1:35:10,25 1|1:20:10,10 1|0:47:22,25 -chr20 766216 . G T 60 . QNAME=cluster19_000000F;QSTART=24995123;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:27:16,11 1|0:28:16,12 ./.:25:7,18 -chr20 766241 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=746694;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD 1|1:33:22,11 1|1:24:12,12 1|0:34:22,12 -chr20 766308 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=746761;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:45:25,20 1|1:42:20,22 1|0:18:10,8 -chr20 766512 . C A 60 . QNAME=cluster19_000000F;QSTART=24994827;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:40:15,25 1|0:20:10,10 ./.:21:7,14 -chr20 766576 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=747029;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:22:10,12 1|1:32:11,21 1|1:32:18,14 -chr20 766899 . T TA 60 . QNAME=cluster23_scaffold_2;QSTART=24928090;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD ./.:24:10,14 ./.:26:16,10 0|1:43:21,22 -chr20 767023 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=747476;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:45:23,22 0|1:40:24,16 ./.:27:16,11 -chr20 767036 . A ATAG 60 . QNAME=cluster19_000000F;QSTART=24994300;QSTRAND=-;GCPCT=25;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.75 GT:DP:AD ./.:27:18,9 1|0:34:19,15 ./.:30:24,6 -chr20 767191 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=747644;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:31:8,23 1|1:37:17,20 1|0:21:14,7 -chr20 767349 . C T 60 . QNAME=cluster19_000000F;QSTART=24993987;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:36:22,14 1|0:24:16,8 ./.:25:17,8 -chr20 767359 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=24943323;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,2,0;LCR=0.5 GT:DP:AD ./.:21:7,14 ./.:39:25,14 1|0:14:7,7 -chr20 767376 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=747829;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:35:12,23 1|1:39:24,15 1|0:19:11,8 -chr20 767966 . T C 60 . QNAME=cluster19_000000F;QSTART=24993370;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:48:24,24 1|0:32:11,21 ./.:26:12,14 -chr20 768267 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=748720;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:21:15,6 0|1:43:22,21 ./.:27:22,5 -chr20 768330 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=748783;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:23:14,9 1|1:22:16,6 1|0:27:5,22 -chr20 769651 . C G 60 . QNAME=cluster23_scaffold_3;QSTART=24941031;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:34:17,17 ./.:15:6,9 1|0:25:14,11 -chr20 769672 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=750125;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:42:17,25 0|1:22:17,5 ./.:19:14,5 -chr20 769904 . A C 60 . QNAME=cluster19_000000F;QSTART=730843;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:23:15,8 0|1:35:14,21 ./.:26:16,10 -chr20 770094 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=750547;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:43:22,21 1|1:23:16,7 1|0:21:7,14 -chr20 770601 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24940081;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:34:15,19 ./.:45:20,25 1|0:36:15,21 -chr20 771027 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=751480;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:30:18,12 0|1:37:16,21 ./.:26:10,16 -chr20 771420 . CTT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=751874;QSTRAND=+;GCPCT=33;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.459148 GT:DP:AD 1|1:33:20,13 ./.:32:19,13 ./.:39:22,17 -chr20 771488 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=24939194;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:27:15,12 ./.:39:19,20 1|0:35:19,16 -chr20 771669 . G GA 60 . QNAME=cluster19_000000F;QSTART=732609;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD ./.:17:7,10 0|1:19:6,13 ./.:44:20,24 -chr20 771669 . G GAA 60 . QNAME=cluster23_scaffold_3;QSTART=24939011;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.459148 GT:DP:AD ./.:42:17,25 ./.:23:16,7 1|0:34:20,14 -chr20 771669 . G GAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=752121;QSTRAND=+;GCPCT=25;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.405639 GT:DP:AD 1|1:28:11,17 ./.:23:6,17 ./.:32:23,9 -chr20 771669 . GA G 60 . QNAME=cluster19_000000F;QSTART=24989667;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD ./.:17:7,10 1|0:34:18,16 ./.:17:5,12 -chr20 771724 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=752178;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:20:8,12 1|1:22:12,10 1|0:42:20,22 -chr20 771989 . T G 60 . QNAME=cluster19_000000F;QSTART=24989348;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:23:8,15 1|1:35:12,23 1|0:22:11,11 -chr20 772587 . G GT 60 . QNAME=cluster23_scaffold_3;QSTART=24938092;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:42:22,20 ./.:28:9,19 1|0:32:20,12 -chr20 772587 . GT G 60 . QNAME=cluster19_000000F;QSTART=24988750;QSTRAND=-;GCPCT=50;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:48:23,25 1|1:26:10,16 ./.:19:5,14 -chr20 772587 . GTT G 60 . QNAME=cluster23_scaffold_2;QSTART=24922402;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.459148 GT:DP:AD ./.:16:8,8 ./.:21:15,6 0|1:27:5,22 -chr20 772599 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=753053;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:34:10,24 1|1:30:24,6 ./.:27:20,7 -chr20 772666 . G A 60 . QNAME=cluster23_scaffold_3;QSTART=24938013;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:25:10,15 ./.:23:7,16 1|0:27:16,11 -chr20 772719 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=753173;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|1:21:7,14 1|1:33:25,8 1|1:23:14,9 -chr20 772824 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=753278;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:40:16,24 1|1:39:15,24 1|0:24:6,18 -chr20 772843 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=753297;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:33:18,15 1|1:47:23,24 1|1:28:15,13 -chr20 772872 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=753326;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:41:25,16 0|1:34:16,18 1|0:28:13,15 -chr20 773095 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=753549;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:37:16,21 0|1:28:5,23 ./.:29:16,13 -chr20 773193 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24921798;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:24:11,13 ./.:23:14,9 0|1:36:16,20 -chr20 773273 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24921718;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:26:5,21 ./.:37:24,13 0|1:41:19,22 -chr20 773723 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=754177;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:42:25,17 1|1:22:11,11 1|1:23:12,11 -chr20 773737 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=754191;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:25:14,11 1|1:36:15,21 1|1:18:11,7 -chr20 774159 . G A 60 . QNAME=cluster19_000000F;QSTART=735098;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:47:25,22 0|1:29:5,24 ./.:38:24,14 -chr20 774304 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=729331;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:38:13,25 ./.:46:23,23 ./.:42:19,23 -chr20 774383 . T C 60 . QNAME=cluster19_000000F;QSTART=735322;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:33:14,19 0|1:32:16,16 ./.:38:17,21 -chr20 774574 . A G 60 . QNAME=cluster19_000000F;QSTART=735513;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:30:10,20 0|1:33:15,18 ./.:49:25,24 -chr20 775268 . CTTTTTTTT C 60 . QNAME=cluster19_000000F;QSTART=736208;QSTRAND=+;GCPCT=11;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.251629 GT:DP:AD ./.:16:7,9 0|1:30:14,16 ./.:42:21,21 -chr20 775268 . CTTTTTTTTTTT C 60 . QNAME=cluster19_000000F;QSTART=24986070;QSTRAND=-;GCPCT=8;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.206908 GT:DP:AD ./.:24:8,16 1|0:27:15,12 1|1:16:10,6 -chr20 775431 . G A 60 . QNAME=cluster19_000000F;QSTART=24985918;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:16:6,10 1|0:38:20,18 1|1:38:17,21 -chr20 775463 . T C 60 . QNAME=cluster19_000000F;QSTART=24985886;QSTRAND=-;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:42:19,23 1|1:27:18,9 1|1:36:16,20 -chr20 775534 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=755988;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:37:15,22 1|1:20:11,9 1|1:38:25,13 -chr20 775539 . A G 60 . QNAME=cluster19_000000F;QSTART=24985810;QSTRAND=-;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:30:20,10 1|1:27:17,10 1|1:44:24,20 -chr20 775876 . A G 60 . QNAME=cluster19_000000F;QSTART=24985473;QSTRAND=-;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:25:19,6 1|1:36:24,12 1|1:27:22,5 -chr20 775888 . A G 60 . QNAME=cluster19_000000F;QSTART=736819;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:46:22,24 0|1:23:13,10 ./.:22:13,9 -chr20 776848 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=757302;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:40:25,15 0|1:28:16,12 ./.:32:11,21 -chr20 776855 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=757309;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:19:7,12 1|1:28:6,22 1|1:38:25,13 -chr20 776856 . TG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=757311;QSTRAND=+;GCPCT=50;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|0:28:5,23 1|0:20:11,9 1|1:26:8,18 -chr20 776863 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=731890;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:40:23,17 ./.:27:14,13 ./.:21:7,14 -chr20 776921 . T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=757375;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 1|1:23:12,11 0|1:42:23,19 ./.:34:13,21 -chr20 777272 . C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=757727;QSTRAND=+;GCPCT=50;GTCNT=0,0,1,2;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|1:22:9,13 1|0:45:20,25 1|1:14:9,5 -chr20 777276 . A AC 60 . QNAME=cluster19_000000F;QSTART=738209;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD ./.:21:13,8 0|1:23:18,5 ./.:27:5,22 -chr20 777343 . A G 60 . QNAME=cluster19_000000F;QSTART=738276;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:46:25,21 0|1:38:21,17 ./.:31:11,20 -chr20 777391 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=757846;QSTRAND=+;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:36:21,15 ./.:24:19,5 ./.:30:17,13 -chr20 778013 . C CT 60 . QNAME=cluster23_scaffold_2;QSTART=24916988;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:24:8,16 ./.:41:23,18 0|1:44:25,19 -chr20 778013 . CT C 60 . QNAME=cluster19_000000F;QSTART=738947;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:26:15,11 0|1:28:13,15 ./.:22:16,6 -chr20 778339 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=758794;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:38:25,13 1|1:46:21,25 1|1:32:16,16 -chr20 778729 . C CT 60 . QNAME=cluster19_000000F;QSTART=24982619;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:30:15,15 1|0:44:20,24 ./.:27:12,15 -chr20 778749 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24916252;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:24:18,6 ./.:30:7,23 0|1:29:17,12 -chr20 778880 . A G 60 . QNAME=cluster19_000000F;QSTART=24982468;QSTRAND=-;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:36:24,12 1|1:18:5,13 1|1:31:7,24 -chr20 779208 . T C 60 . QNAME=cluster19_000000F;QSTART=24982140;QSTRAND=-;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:26:5,21 1|1:29:6,23 1|1:30:10,20 -chr20 779804 . T C 60 . QNAME=cluster19_000000F;QSTART=24981544;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:29:15,14 1|0:21:15,6 ./.:20:6,14 -chr20 780086 . G A 60 . QNAME=cluster19_000000F;QSTART=741018;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:35:17,18 0|1:27:16,11 ./.:27:14,13 -chr20 780364 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=760819;QSTRAND=+;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:30:17,13 ./.:28:21,7 ./.:39:16,23 -chr20 781143 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=761598;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:26:6,20 1|1:27:11,16 1|1:31:24,7 -chr20 781912 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=762367;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|1:19:6,13 1|1:19:12,7 1|1:33:22,11 -chr20 782053 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=762508;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD 1|1:34:21,13 1|1:23:13,10 1|1:23:12,11 -chr20 782135 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=762590;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:30:11,19 1|1:43:18,25 1|1:33:25,8 -chr20 782243 . T TG 60 . QNAME=HG002-S9-H1-000001F;QSTART=762699;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 1|0:28:6,22 ./.:30:14,16 ./.:49:24,25 -chr20 782250 . G GA 60 . QNAME=HG002-S9-H2-000001F;QSTART=737280;QSTRAND=+;GCPCT=50;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 0|1:35:25,10 1|1:30:10,20 1|1:19:13,6 -chr20 782334 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=762790;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:43:22,21 1|1:31:9,22 1|1:18:10,8 -chr20 782552 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=763008;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:41:21,20 1|1:24:16,8 1|1:19:13,6 -chr20 782748 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=763204;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:17:10,7 1|1:34:13,21 1|1:32:14,18 -chr20 782898 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=763354;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:28:21,7 1|1:31:12,19 1|1:33:14,19 -chr20 783008 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=763464;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:36:21,15 1|1:24:18,6 1|1:43:21,22 -chr20 783188 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=763644;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:35:20,15 1|1:15:5,10 1|1:21:16,5 -chr20 783194 . C T 60 . QNAME=cluster19_000000F;QSTART=24978153;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:30:5,25 1|0:45:21,24 1|1:30:22,8 -chr20 783195 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=763651;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:35:14,21 1|1:48:24,24 1|1:25:12,13 -chr20 783325 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=763781;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:27:7,20 1|1:11:6,5 1|1:40:15,25 -chr20 783424 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=763880;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:29:10,19 1|1:41:25,16 1|1:23:12,11 -chr20 783447 . A G 60 . QNAME=cluster19_000000F;QSTART=24977900;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:42:19,23 1|0:19:13,6 1|1:42:17,25 -chr20 783450 . C T 60 . QNAME=cluster19_000000F;QSTART=744383;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:27:12,15 0|1:18:6,12 ./.:25:15,10 -chr20 783488 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=763944;QSTRAND=+;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:24:15,9 ./.:28:8,20 ./.:25:14,11 -chr20 783520 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=763976;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:41:18,23 1|1:23:15,8 1|1:45:25,20 -chr20 783739 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=764195;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|1:36:22,14 1|1:28:23,5 1|1:19:12,7 -chr20 783834 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=764290;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:14:7,7 1|1:46:23,23 1|1:34:23,11 -chr20 783937 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=764393;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:39:23,16 1|1:41:22,19 1|1:33:15,18 -chr20 784114 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=764570;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:31:11,20 1|0:21:16,5 1|1:43:25,18 -chr20 784189 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=764645;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:18:9,9 1|1:35:23,12 1|1:43:25,18 -chr20 784244 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=764700;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:39:15,24 1|1:28:13,15 1|1:22:6,16 -chr20 784245 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=764701;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:15:5,10 1|1:33:18,15 1|1:35:21,14 -chr20 784337 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=764793;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:22:6,16 1|1:43:19,24 1|1:21:5,16 -chr20 784347 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=764803;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:46:23,23 1|1:31:16,15 1|1:29:23,6 -chr20 784686 . G T 60 . QNAME=cluster19_000000F;QSTART=24976661;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:31:24,7 1|0:19:14,5 1|1:35:21,14 -chr20 784695 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=765151;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|1:26:18,8 1|1:26:15,11 1|1:21:7,14 -chr20 784821 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=765277;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:21:7,14 1|1:25:7,18 1|1:24:15,9 -chr20 784842 . A G 60 . QNAME=cluster19_000000F;QSTART=745775;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:35:18,17 0|1:20:13,7 ./.:14:9,5 -chr20 785145 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=765601;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0 GT:DP:AD 1|1:20:14,6 0|1:22:17,5 ./.:16:8,8 -chr20 785294 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=765750;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:43:23,20 1|1:35:19,16 1|1:41:24,17 -chr20 785303 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=765759;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:30:20,10 1|1:32:12,20 1|1:28:23,5 -chr20 785581 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=766037;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|1:13:6,7 1|1:32:18,14 1|1:18:13,5 -chr20 785647 . G A 60 . QNAME=cluster19_000000F;QSTART=24975700;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:24:8,16 1|0:27:6,21 1|1:36:17,19 -chr20 785693 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=766149;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:27:19,8 1|1:46:22,24 1|1:30:11,19 -chr20 785803 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=766259;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:47:24,23 1|1:24:13,11 1|1:15:9,6 -chr20 786660 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24924029;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:34:20,14 ./.:35:18,17 1|0:32:23,9 -chr20 787077 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=767533;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:33:15,18 1|1:46:22,24 1|1:23:16,7 -chr20 787239 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=767696;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|1:30:12,18 ./.:31:21,10 1|0:30:21,9 -chr20 787239 . CTT C 60 . QNAME=cluster23_scaffold_2;QSTART=24907761;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.459148 GT:DP:AD ./.:32:18,14 ./.:24:6,18 0|1:26:9,17 -chr20 787512 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=767968;QSTRAND=+;GCPCT=50;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 1|1:24:9,15 1|1:40:22,18 1|0:38:20,18 -chr20 787930 . A T 60 . QNAME=cluster19_000000F;QSTART=24973418;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:23:17,6 1|0:46:25,21 1|1:35:10,25 -chr20 788431 . T C 60 . QNAME=cluster19_000000F;QSTART=24972917;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:23:5,18 1|0:41:21,20 1|1:33:8,25 -chr20 788945 . T C 60 . QNAME=cluster19_000000F;QSTART=24972403;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:36:18,18 1|0:45:24,21 1|1:41:21,20 -chr20 789027 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=769481;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|1:19:13,6 1|0:27:17,10 1|1:34:20,14 -chr20 789716 . G A 60 . QNAME=cluster19_000000F;QSTART=750648;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:28:21,7 0|1:32:24,8 ./.:40:18,22 -chr20 789908 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=770362;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:22:14,8 1|1:39:24,15 1|1:39:18,21 -chr20 789995 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=770449;QSTRAND=+;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:39:20,19 ./.:18:9,9 ./.:18:11,7 -chr20 790219 . T C 60 . QNAME=cluster19_000000F;QSTART=24971129;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:36:21,15 1|0:40:24,16 1|1:29:14,15 -chr20 790252 . G A 60 . QNAME=cluster19_000000F;QSTART=24971096;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:32:11,21 1|0:22:17,5 1|1:15:5,10 -chr20 790270 . C G 60 . QNAME=cluster19_000000F;QSTART=24971078;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:23:5,18 1|0:44:19,25 1|1:39:23,16 -chr20 790371 . C CAAAAAAAAAAAA 60 . QNAME=cluster19_000000F;QSTART=751304;QSTRAND=+;GCPCT=7;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.195622 GT:DP:AD ./.:23:11,12 0|1:23:12,11 ./.:41:17,24 -chr20 790371 . CAAAAAAA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=745400;QSTRAND=+;GCPCT=12;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.271782 GT:DP:AD 0|1:35:25,10 1|0:38:19,19 0|1:35:17,18 -chr20 790371 . CAAAAAAAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=770826;QSTRAND=+;GCPCT=11;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.251629 GT:DP:AD 1|0:36:20,16 ./.:15:10,5 1|0:17:6,11 -chr20 790626 . T G 60 . QNAME=cluster19_000000F;QSTART=24970729;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:36:13,23 1|0:22:8,14 1|1:40:24,16 -chr20 790639 . C T 60 . QNAME=cluster19_000000F;QSTART=24970716;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0 GT:DP:AD ./.:28:20,8 1|0:31:22,9 1|1:16:8,8 -chr20 791233 . A G 60 . QNAME=cluster19_000000F;QSTART=24970122;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:14:5,9 1|0:24:14,10 1|1:33:22,11 -chr20 791888 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=772334;QSTRAND=+;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:34:13,21 ./.:30:10,20 ./.:29:6,23 -chr20 791971 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=772417;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,1,2;ADCNT=0,3,0,0;LCR=0 GT:DP:AD 1|1:30:21,9 1|1:19:12,7 1|1:14:5,9 -chr20 792261 . T C 60 . QNAME=cluster19_000000F;QSTART=753205;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:27:21,6 0|1:29:11,18 ./.:24:17,7 -chr20 792795 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=773241;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:30:20,10 1|1:42:17,25 1|1:29:19,10 -chr20 792866 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=773312;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:43:19,24 1|1:31:22,9 1|1:17:10,7 -chr20 792873 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=773319;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:40:24,16 1|1:23:6,17 1|1:20:11,9 -chr20 792876 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=773322;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:20:6,14 1|1:47:23,24 1|1:42:23,19 -chr20 792903 . A G 60 . QNAME=cluster19_000000F;QSTART=24968452;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:19:8,11 1|1:26:5,21 ./.:35:25,10 -chr20 793346 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24917353;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:25:19,6 ./.:32:21,11 1|0:15:8,7 -chr20 793395 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=773841;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:23:6,17 1|1:36:25,11 1|1:14:7,7 -chr20 793450 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=748471;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD 0|1:27:13,14 ./.:33:23,10 ./.:17:7,10 -chr20 793500 . C T 60 . QNAME=cluster19_000000F;QSTART=24967855;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:34:21,13 1|0:21:14,7 ./.:11:5,6 -chr20 793560 . C CG 60 . QNAME=HG002-S9-H2-000001F;QSTART=748582;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 0|1:17:12,5 ./.:33:15,18 ./.:29:18,11 -chr20 793560 . CG C 60 . QNAME=cluster19_000000F;QSTART=754505;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:28:13,15 0|1:25:7,18 ./.:39:17,22 -chr20 793560 . CGG C 60 . QNAME=cluster19_000000F;QSTART=24967795;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.459148 GT:DP:AD ./.:29:5,24 1|0:41:19,22 1|1:39:15,24 -chr20 793678 . C G 60 . QNAME=cluster19_000000F;QSTART=754621;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:30:8,22 0|1:44:20,24 ./.:29:20,9 -chr20 793771 . T G 60 . QNAME=cluster19_000000F;QSTART=24967586;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0 GT:DP:AD ./.:27:20,7 1|0:18:13,5 1|1:26:18,8 -chr20 794325 . T C 60 . QNAME=cluster19_000000F;QSTART=24967032;QSTRAND=-;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:33:22,11 1|0:27:18,9 0|1:24:16,8 -chr20 794444 . A G 60 . QNAME=cluster19_000000F;QSTART=24966913;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:41:21,20 1|0:30:7,23 1|1:28:7,21 -chr20 794733 . T G 60 . QNAME=cluster19_000000F;QSTART=24966624;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:27:7,20 1|0:31:19,12 1|1:40:21,19 -chr20 795199 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24915502;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:30:9,21 ./.:26:6,20 1|0:17:6,11 -chr20 795434 . C A 60 . QNAME=cluster19_000000F;QSTART=24965923;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:30:9,21 1|0:32:17,15 1|1:35:19,16 -chr20 795539 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24915162;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:28:18,10 ./.:22:13,9 1|0:29:8,21 -chr20 795540 . C G 60 . QNAME=cluster23_scaffold_3;QSTART=24915161;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,3,0,0;LCR=0 GT:DP:AD ./.:24:18,6 ./.:14:9,5 1|0:34:25,9 -chr20 795731 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=750753;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:38:16,22 ./.:32:13,19 ./.:23:15,8 -chr20 795805 . G A 60 . QNAME=cluster19_000000F;QSTART=24965552;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:33:16,17 1|0:32:13,19 ./.:18:7,11 -chr20 795876 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=776322;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:33:18,15 ./.:22:5,17 1|0:15:9,6 -chr20 795985 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24899026;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:35:18,17 ./.:38:21,17 0|1:24:13,11 -chr20 796225 . T G 60 . QNAME=cluster19_000000F;QSTART=24965132;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:32:19,13 1|0:20:10,10 ./.:27:10,17 -chr20 796289 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=24898722;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:34:16,18 ./.:33:15,18 0|1:30:25,5 -chr20 796344 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=751366;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:42:25,17 1|1:35:19,16 ./.:17:7,10 -chr20 796564 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=751586;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:36:20,16 ./.:37:14,23 ./.:35:21,14 -chr20 797048 . A G 60 . QNAME=cluster19_000000F;QSTART=757991;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:42:18,24 0|1:39:17,22 ./.:31:9,22 -chr20 797400 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=777846;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:20:8,12 ./.:34:10,24 ./.:17:10,7 -chr20 797739 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=778185;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:24:18,6 ./.:36:12,24 ./.:34:11,23 -chr20 797871 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=752893;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:34:16,18 0|1:31:6,25 ./.:43:22,21 -chr20 798053 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=753075;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:47:23,24 0|1:28:11,17 ./.:27:15,12 -chr20 798278 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=753300;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:19:12,7 0|1:26:8,18 ./.:24:5,19 -chr20 798467 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=753489;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:40:20,20 0|1:36:17,19 ./.:28:17,11 -chr20 798479 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=778925;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:22:11,11 0|1:31:16,15 ./.:19:9,10 -chr20 798594 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=753616;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:38:22,16 0|1:39:21,18 ./.:27:5,22 -chr20 798717 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=753739;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:36:15,21 ./.:34:22,12 ./.:22:6,16 -chr20 798853 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=779299;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:46:25,21 ./.:24:5,19 ./.:35:16,19 -chr20 799277 . C CAA 60 . QNAME=cluster19_000000F;QSTART=24962078;QSTRAND=-;GCPCT=33;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.459148 GT:DP:AD ./.:18:6,12 1|0:25:15,10 1|1:33:10,23 -chr20 799277 . C CAAAA 60 . QNAME=HG002-S9-H2-000001F;QSTART=754300;QSTRAND=+;GCPCT=20;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0.360964 GT:DP:AD 0|1:26:18,8 ./.:27:19,8 ./.:26:12,14 -chr20 799300 . C T 60 . QNAME=cluster19_000000F;QSTART=24962055;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:39:17,22 1|0:26:21,5 1|1:24:7,17 -chr20 799510 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=779956;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:31:16,15 1|0:30:25,5 1|1:28:6,22 -chr20 799644 . G A 60 . QNAME=cluster19_000000F;QSTART=24961711;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:26:19,7 1|0:33:9,24 1|1:43:20,23 -chr20 799744 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=780190;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:27:5,22 ./.:14:8,6 ./.:18:6,12 -chr20 800427 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=780873;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:29:23,6 ./.:24:11,13 ./.:13:5,8 -chr20 800604 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781050;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:39:25,14 ./.:32:25,7 ./.:34:19,15 -chr20 800640 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781086;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:27:17,10 ./.:32:20,12 ./.:39:16,23 -chr20 800671 . GCACTCACCCCAT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=781118;QSTRAND=+;GCPCT=61;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.83459 GT:DP:AD 1|0:25:17,8 ./.:39:24,15 ./.:15:7,8 -chr20 800707 . G A 60 . QNAME=cluster19_000000F;QSTART=24960676;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:31:15,16 1|0:35:10,25 1|1:12:7,5 -chr20 800818 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781252;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|1:19:14,5 1|0:30:21,9 1|1:17:7,10 -chr20 800884 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=781318;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:27:15,12 ./.:28:17,11 ./.:31:23,8 -chr20 800927 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=781361;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:22:12,10 ./.:32:12,20 ./.:22:13,9 -chr20 800955 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=781389;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:24:19,5 ./.:43:24,19 ./.:36:21,15 -chr20 800960 . CCTT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781395;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.5 GT:DP:AD 1|0:37:25,12 ./.:25:17,8 ./.:34:22,12 -chr20 801002 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781433;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:17:10,7 ./.:29:18,11 ./.:30:18,12 -chr20 801097 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781528;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:41:18,23 ./.:36:15,21 ./.:37:15,22 -chr20 801205 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781636;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:35:15,20 ./.:27:6,21 ./.:32:18,14 -chr20 801403 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=781834;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:23:7,16 ./.:41:22,19 ./.:21:13,8 -chr20 801427 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781858;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:21:7,14 ./.:27:8,19 ./.:23:7,16 -chr20 801488 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=781919;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:18:13,5 1|0:35:13,22 1|1:23:7,16 -chr20 801793 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=782224;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:36:13,23 ./.:32:14,18 ./.:29:16,13 -chr20 801807 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=782238;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:35:20,15 ./.:46:22,24 ./.:36:25,11 -chr20 801853 . CAAAT C 60 . QNAME=cluster23_scaffold_3;QSTART=24908874;QSTRAND=-;GCPCT=20;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0.685475 GT:DP:AD ./.:23:16,7 ./.:29:24,5 1|0:25:16,9 -chr20 801853 . CAAATAAAT C 60 . QNAME=cluster19_000000F;QSTART=24959530;QSTRAND=-;GCPCT=11;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.612197 GT:DP:AD ./.:37:13,24 1|0:30:13,17 0|1:39:16,23 -chr20 801854 . AAATAAAT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=782286;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.405639 GT:DP:AD 1|0:33:14,19 ./.:40:15,25 ./.:41:23,18 -chr20 801893 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=782317;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:42:21,21 ./.:36:24,12 ./.:30:19,11 -chr20 802063 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=782487;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:20:6,14 ./.:23:7,16 ./.:23:7,16 -chr20 802155 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=757153;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:33:20,13 1|0:37:18,19 1|1:30:11,19 -chr20 802331 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=782755;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:26:15,11 1|0:29:8,21 ./.:46:21,25 -chr20 802369 . G A 60 . QNAME=cluster19_000000F;QSTART=763312;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:22:6,16 0|1:37:18,19 ./.:23:9,14 -chr20 802531 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=757529;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:39:16,23 ./.:28:5,23 ./.:24:19,5 -chr20 802606 . C CA 60 . QNAME=HG002-S9-H2-000001F;QSTART=757605;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 0|1:43:24,19 ./.:38:20,18 0|1:24:12,12 -chr20 802739 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=757738;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:38:14,24 0|1:33:24,9 1|0:43:21,22 -chr20 803221 . C T 60 . QNAME=cluster19_000000F;QSTART=24958170;QSTRAND=-;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:14:6,8 1|1:26:10,16 1|1:48:25,23 -chr20 803367 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=783791;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:30:14,16 1|1:28:10,18 1|1:17:9,8 -chr20 803419 . C T 60 . QNAME=cluster19_000000F;QSTART=24957972;QSTRAND=-;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:21:13,8 1|1:29:5,24 1|1:34:22,12 -chr20 803499 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=783923;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:36:17,19 ./.:15:6,9 ./.:23:10,13 -chr20 803703 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=784127;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:27:13,14 1|1:25:5,20 1|1:16:11,5 -chr20 803760 . C T 60 . QNAME=cluster19_000000F;QSTART=24957631;QSTRAND=-;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:37:15,22 1|1:34:15,19 1|1:21:13,8 -chr20 804087 . G A 60 . QNAME=cluster19_000000F;QSTART=24957304;QSTRAND=-;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:30:15,15 1|1:16:6,10 1|1:41:20,21 -chr20 804255 . C T 60 . QNAME=cluster19_000000F;QSTART=24957136;QSTRAND=-;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:29:6,23 1|1:30:9,21 1|1:29:21,8 -chr20 804315 . C G 60 . QNAME=cluster19_000000F;QSTART=24957076;QSTRAND=-;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:47:22,25 1|1:29:10,19 1|1:33:25,8 -chr20 804381 . C T 60 . QNAME=cluster19_000000F;QSTART=24957010;QSTRAND=-;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:43:20,23 1|1:48:24,24 1|1:39:16,23 -chr20 804444 . G A 60 . QNAME=cluster19_000000F;QSTART=24956947;QSTRAND=-;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:22:9,13 1|1:37:12,25 1|1:33:25,8 -chr20 804465 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=784889;QSTRAND=+;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:25:8,17 ./.:27:7,20 ./.:40:21,19 -chr20 804804 . A AT 60 . QNAME=HG002-S9-H1-000001F;QSTART=785229;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|0:27:22,5 ./.:33:17,16 ./.:23:11,12 -chr20 804804 . AT A 60 . QNAME=cluster19_000000F;QSTART=24956587;QSTRAND=-;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:34:19,15 1|1:27:16,11 1|1:34:19,15 -chr20 805255 . T C 60 . QNAME=cluster19_000000F;QSTART=24956137;QSTRAND=-;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:46:25,21 1|1:30:19,11 1|1:23:5,18 -chr20 805274 . T C 60 . QNAME=cluster19_000000F;QSTART=24956118;QSTRAND=-;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:27:13,14 1|1:16:7,9 1|1:43:23,20 -chr20 805356 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=785781;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:27:22,5 1|1:27:16,11 1|1:40:24,16 -chr20 805464 . C G 60 . QNAME=cluster19_000000F;QSTART=24955928;QSTRAND=-;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:28:11,17 1|1:41:24,17 1|1:46:25,21 -chr20 805609 . AAG A 60 . QNAME=cluster19_000000F;QSTART=24955783;QSTRAND=-;GCPCT=33;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.459148 GT:DP:AD ./.:48:25,23 1|1:29:21,8 1|1:17:10,7 -chr20 805627 . AT A 60 . QNAME=cluster23_scaffold_2;QSTART=24889420;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0.5 GT:DP:AD ./.:21:12,9 ./.:26:14,12 0|1:18:11,7 -chr20 805812 . C T 60 . QNAME=cluster19_000000F;QSTART=24955582;QSTRAND=-;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:36:25,11 1|1:34:17,17 1|1:37:12,25 -chr20 806032 . T TA 60 . QNAME=cluster23_scaffold_2;QSTART=24889015;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0.5 GT:DP:AD ./.:28:20,8 ./.:31:21,10 0|1:15:9,6 -chr20 806060 . A G 60 . QNAME=cluster19_000000F;QSTART=24955334;QSTRAND=-;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:30:25,5 1|1:30:8,22 1|1:31:18,13 -chr20 806121 . T TA 60 . QNAME=HG002-S9-H1-000001F;QSTART=786547;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 1|1:35:11,24 1|1:30:6,24 1|1:35:21,14 -chr20 806416 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=786842;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:29:18,11 1|1:42:20,22 1|1:36:18,18 -chr20 806539 . CT C 60 . QNAME=cluster23_scaffold_2;QSTART=24888507;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:41:18,23 ./.:23:7,16 0|1:20:15,5 -chr20 806698 . A G 60 . QNAME=cluster19_000000F;QSTART=24954695;QSTRAND=-;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:33:22,11 1|1:29:20,9 1|1:19:8,11 -chr20 806714 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24904019;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:32:21,11 ./.:29:10,19 1|0:19:8,11 -chr20 807227 . T TTTTATTTATTTATTTATTTA 60 . QNAME=cluster19_000000F;QSTART=24954146;QSTRAND=-;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.395929 GT:DP:AD ./.:36:21,15 1|1:40:20,20 1|1:27:12,15 -chr20 807315 . A G 60 . QNAME=cluster19_000000F;QSTART=24954058;QSTRAND=-;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:40:18,22 1|1:38:16,22 1|1:24:11,13 -chr20 807395 . C T 60 . QNAME=cluster19_000000F;QSTART=24953978;QSTRAND=-;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:28:6,22 1|1:42:23,19 1|1:46:23,23 -chr20 807886 . CT C 60 . QNAME=cluster23_scaffold_2;QSTART=24887141;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:34:14,20 ./.:16:8,8 0|1:25:15,10 -chr20 808070 . G A 60 . QNAME=cluster19_000000F;QSTART=24953303;QSTRAND=-;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:46:25,21 1|1:34:24,10 1|1:15:6,9 -chr20 808486 . C T 60 . QNAME=cluster19_000000F;QSTART=24952887;QSTRAND=-;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:25:10,15 1|1:39:16,23 1|1:41:21,20 -chr20 808580 . CT C 60 . QNAME=cluster23_scaffold_2;QSTART=24886448;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.5 GT:DP:AD ./.:33:20,13 ./.:29:24,5 0|1:35:23,12 -chr20 808747 . T C 60 . QNAME=cluster19_000000F;QSTART=24952626;QSTRAND=-;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:50:25,25 1|1:35:19,16 1|1:46:23,23 -chr20 808798 . T TG 60 . QNAME=cluster23_scaffold_2;QSTART=24886230;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:40:20,20 ./.:29:15,14 0|1:20:14,6 -chr20 808973 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=789399;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:35:24,11 1|1:28:5,23 1|1:16:8,8 -chr20 809124 . T TA 60 . QNAME=cluster19_000000F;QSTART=24952248;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:31:11,20 1|1:31:9,22 1|0:26:5,21 -chr20 809124 . T TAA 60 . QNAME=cluster23_scaffold_2;QSTART=24885902;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.459148 GT:DP:AD ./.:28:18,10 ./.:30:6,24 0|1:32:17,15 -chr20 809392 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=789818;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:14:8,6 1|1:45:25,20 1|1:34:22,12 -chr20 809449 . C A 60 . QNAME=cluster19_000000F;QSTART=24951923;QSTRAND=-;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,1,2;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:22:8,14 1|1:13:6,7 1|1:18:5,13 -chr20 809476 . C T 60 . QNAME=cluster19_000000F;QSTART=24951896;QSTRAND=-;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:26:15,11 1|1:31:12,19 1|1:23:13,10 -chr20 809653 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=790079;QSTRAND=+;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:48:23,25 ./.:29:16,13 ./.:21:5,16 -chr20 809775 . T G 60 . QNAME=cluster19_000000F;QSTART=24951597;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:20:14,6 1|0:35:21,14 ./.:37:21,16 -chr20 810079 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=790505;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:25:16,9 1|1:33:8,25 1|1:43:21,22 -chr20 810083 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=790509;QSTRAND=+;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:31:25,6 ./.:38:19,19 ./.:20:9,11 -chr20 810565 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=790991;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:42:22,20 1|1:27:11,16 1|1:33:17,16 -chr20 810659 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=791085;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|1:24:13,11 1|1:28:23,5 1|1:20:7,13 -chr20 810742 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=791168;QSTRAND=+;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:20:14,6 ./.:28:23,5 ./.:24:7,17 -chr20 811032 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=791458;QSTRAND=+;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|1:22:16,6 ./.:34:22,12 ./.:32:18,14 -chr20 811102 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=791528;QSTRAND=+;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:20:12,8 ./.:30:9,21 ./.:42:25,17 -chr20 811314 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=791740;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:14:8,6 1|1:30:5,25 1|1:27:8,19 -chr20 811539 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=791965;QSTRAND=+;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:37:14,23 ./.:26:19,7 ./.:25:6,19 -chr20 811587 . G A 60 . QNAME=cluster19_000000F;QSTART=24949785;QSTRAND=-;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:12:5,7 1|1:36:12,24 1|1:46:22,24 -chr20 811839 . A AG 60 . QNAME=cluster23_scaffold_2;QSTART=24883186;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:34:12,22 ./.:11:6,5 0|1:30:6,24 -chr20 812140 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=792566;QSTRAND=+;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:35:22,13 ./.:36:18,18 ./.:31:13,18 -chr20 812429 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=792855;QSTRAND=+;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:25:8,17 ./.:28:15,13 ./.:37:23,14 -chr20 812492 . A C 60 . QNAME=cluster19_000000F;QSTART=24948880;QSTRAND=-;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:30:20,10 1|1:14:9,5 1|1:50:25,25 -chr20 813255 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=793681;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:40:21,19 ./.:38:15,23 1|0:35:23,12 -chr20 813573 . C T 60 . QNAME=cluster19_000000F;QSTART=24947799;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:37:19,18 1|1:42:18,24 0|1:35:11,24 -chr20 813792 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=794218;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0 GT:DP:AD 1|1:22:13,9 ./.:20:14,6 1|0:25:20,5 -chr20 813863 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=794289;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:33:16,17 1|1:39:14,25 1|1:44:22,22 -chr20 814342 . T TG 60 . QNAME=cluster23_scaffold_2;QSTART=24880682;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:36:17,19 ./.:27:18,9 0|1:38:15,23 -chr20 814479 . AT A 60 . QNAME=cluster23_scaffold_2;QSTART=24880545;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD ./.:37:23,14 ./.:23:13,10 0|1:28:12,16 -chr20 814505 . T TTTTA 60 . QNAME=cluster19_000000F;QSTART=24946863;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.360964 GT:DP:AD ./.:24:15,9 1|1:15:10,5 0|1:42:23,19 -chr20 814505 . T TTTTATTTA 60 . QNAME=HG002-S9-H1-000001F;QSTART=794932;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.382102 GT:DP:AD 1|1:40:15,25 ./.:25:12,13 1|0:33:24,9 -chr20 815073 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=795507;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:34:23,11 ./.:30:13,17 1|0:17:5,12 -chr20 815387 . A T 60 . QNAME=cluster19_000000F;QSTART=24945981;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:26:10,16 1|1:14:6,8 0|1:39:14,25 -chr20 815789 . C A 60 . QNAME=cluster19_000000F;QSTART=24945579;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:36:23,13 1|1:27:9,18 ./.:37:23,14 -chr20 816179 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=796613;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:38:19,19 ./.:17:11,6 1|0:27:14,13 -chr20 816272 . CT C 60 . QNAME=cluster23_scaffold_2;QSTART=24878749;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0.5 GT:DP:AD ./.:19:11,8 ./.:24:19,5 0|1:22:9,13 -chr20 816693 . GA G 60 . QNAME=HG002-S9-H1-000001F;QSTART=797128;QSTRAND=+;GCPCT=50;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.5 GT:DP:AD 1|0:17:7,10 1|1:23:15,8 1|0:28:17,11 -chr20 816723 . TTGTGCG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=797157;QSTRAND=+;GCPCT=57;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.724408 GT:DP:AD 1|0:42:21,21 ./.:44:24,20 1|0:30:8,22 -chr20 816728 . C CGTGT 60 . QNAME=cluster23_scaffold_2;QSTART=24878290;QSTRAND=-;GCPCT=60;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.760964 GT:DP:AD ./.:27:18,9 ./.:26:7,19 0|1:36:16,20 -chr20 816728 . CGT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=771737;QSTRAND=+;GCPCT=66;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0.792481 GT:DP:AD 0|1:15:10,5 ./.:14:7,7 ./.:30:14,16 -chr20 816757 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=797184;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:33:16,17 ./.:19:5,14 1|0:14:8,6 -chr20 817397 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24877621;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:40:20,20 ./.:20:15,5 0|1:33:16,17 -chr20 817512 . A G 60 . QNAME=cluster19_000000F;QSTART=24943857;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:32:8,24 1|0:10:5,5 ./.:17:8,9 -chr20 817544 . G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=797972;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 1|0:35:25,10 ./.:27:12,15 1|0:27:6,21 -chr20 817544 . GA G 60 . QNAME=HG002-S9-H2-000001F;QSTART=772551;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD 0|1:28:12,16 0|1:35:21,14 ./.:23:10,13 -chr20 817544 . GAA G 60 . QNAME=cluster19_000000F;QSTART=24943825;QSTRAND=-;GCPCT=33;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.459148 GT:DP:AD ./.:24:12,12 1|0:24:7,17 0|1:30:23,7 -chr20 817584 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=798012;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:27:7,20 ./.:35:15,20 1|0:18:13,5 -chr20 817587 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=798015;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:34:13,21 ./.:37:15,22 1|0:19:8,11 -chr20 817664 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=798092;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:23:8,15 ./.:20:12,8 1|0:33:21,12 -chr20 817690 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=798118;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:27:12,15 1|1:32:21,11 1|1:26:8,18 -chr20 817718 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=798146;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:31:15,16 ./.:11:5,6 1|0:37:23,14 -chr20 817808 . T C 60 . QNAME=cluster19_000000F;QSTART=24943563;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:27:21,6 1|1:38:25,13 ./.:41:25,16 -chr20 817809 . T A 60 . QNAME=cluster19_000000F;QSTART=24943562;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:35:23,12 1|1:13:5,8 ./.:26:19,7 -chr20 817850 . G GA 60 . QNAME=HG002-S9-H1-000001F;QSTART=798279;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|0:41:22,19 ./.:17:8,9 ./.:41:22,19 -chr20 817871 . G GA 60 . QNAME=cluster23_scaffold_2;QSTART=24877148;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:24:18,6 ./.:37:14,23 0|1:26:13,13 -chr20 818023 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=798452;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD 1|0:36:24,12 ./.:21:7,14 1|0:29:18,11 -chr20 818055 . T TG 60 . QNAME=cluster23_scaffold_2;QSTART=24876963;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD ./.:21:9,12 ./.:43:19,24 0|1:29:19,10 -chr20 818068 . T TG 60 . QNAME=cluster23_scaffold_2;QSTART=24876949;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:30:8,22 ./.:27:11,16 0|1:26:20,6 -chr20 818085 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=798514;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:31:14,17 ./.:17:11,6 1|0:28:9,19 -chr20 818112 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=798541;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:21:12,9 1|1:24:5,19 1|1:35:14,21 -chr20 818177 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24876840;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:25:12,13 ./.:18:13,5 0|1:40:24,16 -chr20 818388 . A AG 60 . QNAME=cluster23_scaffold_3;QSTART=24892321;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD ./.:48:24,24 ./.:36:14,22 1|0:48:23,25 -chr20 818488 . A AT 60 . QNAME=HG002-S9-H2-000001F;QSTART=773494;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD 0|1:33:24,9 ./.:14:5,9 ./.:33:15,18 -chr20 818488 . A ATT 60 . QNAME=HG002-S9-H1-000001F;QSTART=798918;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0.459148 GT:DP:AD 1|0:14:9,5 ./.:27:21,6 ./.:28:10,18 -chr20 818644 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=799075;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:23:11,12 ./.:32:16,16 1|0:45:25,20 -chr20 818794 . C CTT 60 . QNAME=HG002-S9-H1-000001F;QSTART=799226;QSTRAND=+;GCPCT=33;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.459148 GT:DP:AD 1|1:21:11,10 ./.:30:10,20 1|0:19:9,10 -chr20 818794 . CT C 60 . QNAME=cluster23_scaffold_2;QSTART=24876223;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:17:10,7 ./.:31:13,18 0|1:34:14,20 -chr20 818839 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=24876179;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:19:13,6 ./.:44:20,24 0|1:36:14,22 -chr20 818891 . A G 60 . QNAME=cluster19_000000F;QSTART=24942480;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:34:9,25 1|1:26:20,6 ./.:20:7,13 -chr20 818898 . T TC 60 . QNAME=cluster23_scaffold_2;QSTART=24876119;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:21:9,12 ./.:44:21,23 0|1:33:10,23 -chr20 818940 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=799373;QSTRAND=+;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:35:13,22 ./.:42:18,24 1|1:32:15,17 -chr20 818970 . G C 60 . QNAME=cluster19_000000F;QSTART=24942401;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:27:13,14 1|1:28:21,7 ./.:21:5,16 -chr20 819017 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=774025;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:29:14,15 ./.:31:25,6 ./.:27:15,12 -chr20 819249 . T C 60 . QNAME=cluster19_000000F;QSTART=780213;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:24:7,17 0|1:25:5,20 ./.:28:5,23 -chr20 819251 . C A 60 . QNAME=HG002-S9-H2-000001F;QSTART=774259;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 0|1:34:21,13 ./.:27:17,10 ./.:27:20,7 -chr20 820514 . T TTTC 60 . QNAME=HG002-S9-H1-000001F;QSTART=802126;QSTRAND=+;GCPCT=25;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.405639 GT:DP:AD 1|1:23:14,9 1|1:36:23,13 1|1:25:9,16 -chr20 820545 . T TTC 60 . QNAME=cluster19_000000F;QSTART=24937541;QSTRAND=-;GCPCT=33;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.459148 GT:DP:AD ./.:17:10,7 1|1:29:10,19 ./.:23:15,8 -chr20 820587 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=802201;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:31:16,15 ./.:31:16,15 1|0:27:18,9 -chr20 820752 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=802366;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:39:24,15 ./.:40:24,16 1|0:37:20,17 -chr20 821376 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=24871732;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:28:20,8 ./.:16:5,11 0|1:22:17,5 -chr20 821480 . G T 60 . QNAME=cluster19_000000F;QSTART=24936606;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:35:17,18 1|1:41:18,23 0|1:17:10,7 -chr20 822153 . A AT 60 . QNAME=cluster23_scaffold_2;QSTART=24870954;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD ./.:41:23,18 ./.:36:23,13 0|1:23:12,11 -chr20 822153 . ATTT A 60 . QNAME=cluster19_000000F;QSTART=24935933;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.405639 GT:DP:AD ./.:47:23,24 1|1:26:15,11 ./.:48:23,25 -chr20 822153 . ATTTT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=803768;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.360964 GT:DP:AD 1|1:27:11,16 ./.:34:18,16 1|0:29:8,21 -chr20 822622 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24870485;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:36:12,24 ./.:36:17,19 0|1:25:6,19 -chr20 823109 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=804719;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:38:15,23 1|1:39:16,23 1|1:28:9,19 -chr20 824454 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=806064;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:40:22,18 1|1:18:9,9 1|1:38:24,14 -chr20 825318 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=806928;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|1:16:10,6 ./.:33:23,10 1|0:24:17,7 -chr20 825338 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=806948;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:40:19,21 ./.:21:12,9 1|0:32:21,11 -chr20 825828 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=807438;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:34:23,11 1|1:27:5,22 1|1:39:14,25 -chr20 826034 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=807644;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:46:25,21 1|1:20:8,12 1|1:47:24,23 -chr20 826235 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=807845;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:35:15,20 1|1:48:23,25 1|1:40:17,23 -chr20 826944 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=808554;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:36:23,13 ./.:35:20,15 1|0:23:12,11 -chr20 827056 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=808666;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:41:22,19 ./.:19:11,8 1|0:29:24,5 -chr20 827617 . C CA 60 . QNAME=HG002-S9-H1-000001F;QSTART=809228;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD 1|1:25:12,13 ./.:20:5,15 1|0:24:11,13 -chr20 827617 . C CAA 60 . QNAME=cluster19_000000F;QSTART=24930470;QSTRAND=-;GCPCT=33;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.459148 GT:DP:AD ./.:39:24,15 1|1:45:24,21 0|1:44:23,21 -chr20 827787 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=809398;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:40:16,24 1|1:48:23,25 1|1:34:20,14 -chr20 827840 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24865265;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:40:25,15 ./.:33:14,19 0|1:40:19,21 -chr20 827959 . G A 60 . QNAME=cluster19_000000F;QSTART=24930128;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:24:9,15 1|1:32:25,7 ./.:27:11,16 -chr20 828060 . G GAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=809672;QSTRAND=+;GCPCT=20;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.360964 GT:DP:AD 1|1:25:6,19 1|1:39:17,22 0|1:32:19,13 -chr20 828060 . G GAAAAA 60 . QNAME=cluster23_scaffold_3;QSTART=24881385;QSTRAND=-;GCPCT=16;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.325011 GT:DP:AD ./.:26:11,15 ./.:31:16,15 1|0:24:9,15 -chr20 828725 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=810340;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:18:5,13 1|1:39:23,16 1|1:39:18,21 -chr20 828856 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=810471;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:33:21,12 1|1:28:13,15 1|1:37:23,14 -chr20 828857 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=810472;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:49:25,24 1|1:42:23,19 1|1:43:21,22 -chr20 828946 . C T 60 . QNAME=cluster19_000000F;QSTART=24929137;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:29:15,14 1|1:27:9,18 ./.:34:20,14 -chr20 829194 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24863907;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:29:13,16 ./.:26:15,11 0|1:49:24,25 -chr20 829287 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=810902;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:23:6,17 1|1:33:11,22 1|1:38:23,15 -chr20 830064 . A G 60 . QNAME=cluster19_000000F;QSTART=24928019;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:21:7,14 1|1:43:24,19 0|1:14:6,8 -chr20 830268 . C CTT 60 . QNAME=cluster23_scaffold_2;QSTART=24862831;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.459148 GT:DP:AD ./.:37:12,25 ./.:29:21,8 0|1:38:15,23 -chr20 830270 . T C 60 . QNAME=cluster19_000000F;QSTART=24927813;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:33:12,21 1|1:36:20,16 ./.:16:8,8 -chr20 830311 . A G 60 . QNAME=cluster19_000000F;QSTART=24927772;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:24:13,11 1|1:48:25,23 0|1:17:12,5 -chr20 830449 . C CTT 60 . QNAME=cluster19_000000F;QSTART=24927632;QSTRAND=-;GCPCT=33;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.459148 GT:DP:AD ./.:37:23,14 1|1:28:6,22 0|1:33:13,20 -chr20 830449 . CT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=812065;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 1|0:30:7,23 ./.:36:16,20 ./.:21:10,11 -chr20 830787 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=812401;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:17:7,10 1|1:29:8,21 1|1:37:18,19 -chr20 830864 . G A 60 . QNAME=cluster19_000000F;QSTART=24927217;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:30:10,20 1|1:29:23,6 0|1:49:24,25 -chr20 831203 . G C 60 . QNAME=cluster19_000000F;QSTART=24926878;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:26:14,12 1|1:28:9,19 ./.:30:7,23 -chr20 831231 . T C 60 . QNAME=cluster19_000000F;QSTART=24926850;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:28:23,5 1|1:29:5,24 0|1:31:10,21 -chr20 831257 . C CA 60 . QNAME=cluster19_000000F;QSTART=795540;QSTRAND=+;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:24:12,12 0|1:45:22,23 1|1:45:22,23 -chr20 831332 . T C 60 . QNAME=cluster19_000000F;QSTART=24926749;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:20:7,13 1|1:31:25,6 0|1:29:9,20 -chr20 831358 . A T 60 . QNAME=cluster19_000000F;QSTART=24926723;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:33:13,20 1|1:33:22,11 0|1:39:14,25 -chr20 831366 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24861730;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:38:14,24 ./.:38:18,20 0|1:22:17,5 -chr20 832087 . A C 60 . QNAME=cluster19_000000F;QSTART=24925994;QSTRAND=-;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:28:13,15 1|1:28:13,15 0|1:41:21,20 -chr20 833024 . A G 60 . QNAME=cluster19_000000F;QSTART=24925057;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:29:13,16 1|0:34:14,20 ./.:29:6,23 -chr20 833025 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=814639;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:29:14,15 0|1:23:7,16 0|1:24:9,15 -chr20 833025 . AG A 60 . QNAME=cluster19_000000F;QSTART=24925056;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:29:14,15 1|0:28:6,22 ./.:17:8,9 -chr20 833026 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=814640;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:26:11,15 0|1:28:11,17 0|1:23:11,12 -chr20 833026 . G GA 60 . QNAME=cluster23_scaffold_3;QSTART=24876417;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:36:20,16 ./.:21:8,13 1|0:24:9,15 -chr20 833108 . C G 60 . QNAME=cluster19_000000F;QSTART=24924974;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:39:15,24 1|1:33:15,18 0|1:38:22,16 -chr20 835141 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24857955;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:23:10,13 ./.:29:19,10 0|1:34:14,20 -chr20 835164 . A ATC 60 . QNAME=HG002-S9-H1-000001F;QSTART=816779;QSTRAND=+;GCPCT=33;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.792481 GT:DP:AD 1|1:37:21,16 ./.:41:17,24 ./.:24:7,17 -chr20 835200 . C A 60 . QNAME=cluster23_scaffold_3;QSTART=24874243;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:36:12,24 ./.:37:22,15 1|0:37:19,18 -chr20 835200 . C CTCTATA 60 . QNAME=cluster23_scaffold_2;QSTART=24857890;QSTRAND=-;GCPCT=28;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.778328 GT:DP:AD ./.:19:6,13 ./.:38:18,20 0|1:33:24,9 -chr20 835202 . A C 60 . QNAME=cluster19_000000F;QSTART=24922880;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:21:7,14 1|1:21:5,16 ./.:40:18,22 -chr20 836246 . TG T 60 . QNAME=cluster19_000000F;QSTART=24921836;QSTRAND=-;GCPCT=50;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:36:12,24 1|1:31:12,19 0|1:32:20,12 -chr20 837045 . G GTT 60 . QNAME=cluster23_scaffold_2;QSTART=24856044;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.459148 GT:DP:AD ./.:44:25,19 ./.:41:16,25 0|1:19:5,14 -chr20 838387 . G C 60 . QNAME=cluster23_scaffold_2;QSTART=24854702;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:25:19,6 ./.:21:9,12 0|1:29:24,5 -chr20 841266 . C T 60 . QNAME=cluster19_000000F;QSTART=805548;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:30:19,11 0|1:21:11,10 0|1:21:6,15 -chr20 842793 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24850296;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:29:21,8 ./.:38:17,21 0|1:43:22,21 -chr20 842861 . T G 60 . QNAME=cluster23_scaffold_2;QSTART=24850228;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:36:17,19 ./.:19:6,13 0|1:12:6,6 -chr20 843131 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24849958;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:27:18,9 ./.:30:13,17 0|1:41:25,16 -chr20 843133 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24849956;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:35:22,13 ./.:29:17,12 0|1:44:22,22 -chr20 843148 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=824764;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:36:13,23 ./.:35:22,13 ./.:17:6,11 -chr20 843149 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=824765;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:32:12,20 ./.:38:22,16 ./.:38:21,17 -chr20 843779 . C A 60 . QNAME=cluster23_scaffold_2;QSTART=24849310;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:31:11,20 ./.:35:23,12 0|1:30:17,13 -chr20 843805 . T C 60 . QNAME=cluster19_000000F;QSTART=808087;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:36:18,18 0|1:28:17,11 ./.:24:12,12 -chr20 843879 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=24849210;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:35:23,12 ./.:19:7,12 0|1:16:8,8 -chr20 844439 . TGCCCAGGTC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=826056;QSTRAND=+;GCPCT=70;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.92322 GT:DP:AD 1|1:26:11,15 1|1:28:12,16 1|1:29:14,15 -chr20 844675 . C CT 60 . QNAME=HG002-S9-H2-000001F;QSTART=800823;QSTRAND=+;GCPCT=50;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 0|1:39:22,17 0|1:26:5,21 1|1:35:15,20 -chr20 845035 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=826642;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:32:21,11 1|1:28:21,7 1|1:29:7,22 -chr20 845849 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=827456;QSTRAND=+;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:36:24,12 ./.:21:10,11 1|1:42:19,23 -chr20 845870 . C G 60 . QNAME=cluster19_000000F;QSTART=810144;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:13:7,6 0|1:34:12,22 ./.:36:17,19 -chr20 846023 . G T 60 . QNAME=cluster19_000000F;QSTART=24912069;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:41:19,22 1|0:25:13,12 ./.:19:12,7 -chr20 846067 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=827674;QSTRAND=+;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:22:17,5 ./.:30:10,20 1|1:44:23,21 -chr20 846626 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=828233;QSTRAND=+;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:26:21,5 ./.:28:6,22 1|1:26:18,8 -chr20 847610 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=829217;QSTRAND=+;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:17:6,11 ./.:30:7,23 1|1:21:7,14 -chr20 847932 . C T 60 . QNAME=cluster19_000000F;QSTART=812206;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:23:10,13 0|1:37:16,21 ./.:37:22,15 -chr20 847948 . C T 60 . QNAME=cluster19_000000F;QSTART=812222;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:36:21,15 0|1:20:7,13 ./.:32:14,18 -chr20 848007 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=829614;QSTRAND=+;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:43:22,21 ./.:11:5,6 1|1:34:13,21 -chr20 848148 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=829755;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:27:6,21 0|1:27:17,10 0|1:20:14,6 -chr20 848655 . G GC 60 . QNAME=cluster23_scaffold_2;QSTART=24844441;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:31:15,16 ./.:29:24,5 0|1:45:24,21 -chr20 848655 . G GCCC 60 . QNAME=cluster19_000000F;QSTART=812930;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0.405639 GT:DP:AD ./.:21:7,14 0|1:20:15,5 ./.:13:6,7 -chr20 848966 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=830573;QSTRAND=+;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|1:16:5,11 ./.:20:6,14 1|1:15:7,8 -chr20 849159 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=830766;QSTRAND=+;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|1:29:18,11 ./.:22:17,5 1|1:21:11,10 -chr20 849210 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=830817;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:40:22,18 1|1:40:25,15 1|1:26:14,12 -chr20 849245 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=830852;QSTRAND=+;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:40:17,23 ./.:47:23,24 1|1:13:8,5 -chr20 849258 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=830866;QSTRAND=+;GCPCT=50;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|1:31:18,13 0|1:43:24,19 1|1:21:16,5 -chr20 849509 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=831115;QSTRAND=+;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:28:14,14 ./.:40:25,15 1|1:45:23,22 -chr20 849655 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=831261;QSTRAND=+;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|1:37:24,13 ./.:29:21,8 1|1:16:10,6 -chr20 849665 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=831271;QSTRAND=+;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:24:13,11 ./.:31:22,9 1|1:27:5,22 -chr20 849770 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=831376;QSTRAND=+;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0 GT:DP:AD 1|1:25:17,8 ./.:28:19,9 1|1:17:8,9 -chr20 849895 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=831501;QSTRAND=+;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:17:5,12 ./.:32:19,13 1|1:28:8,20 -chr20 850094 . T TACACAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=831701;QSTRAND=+;GCPCT=42;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.724408 GT:DP:AD 1|0:34:11,23 ./.:35:14,21 0|1:30:5,25 -chr20 850094 . T TACACACACAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=806242;QSTRAND=+;GCPCT=45;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0.674294 GT:DP:AD 0|1:16:10,6 ./.:26:13,13 ./.:21:12,9 -chr20 850134 . C CACACACACACAT 60 . QNAME=cluster19_000000F;QSTART=814411;QSTRAND=+;GCPCT=46;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.65716 GT:DP:AD ./.:43:25,18 0|1:34:24,10 ./.:33:16,17 -chr20 850134 . C CACACAT 60 . QNAME=cluster19_000000F;QSTART=24907952;QSTRAND=-;GCPCT=42;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.724408 GT:DP:AD ./.:41:17,24 1|0:22:9,13 1|0:16:5,11 -chr20 850182 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=831794;QSTRAND=+;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:30:23,7 ./.:27:12,15 1|1:33:11,22 -chr20 850404 . C T 60 . QNAME=cluster19_000000F;QSTART=814692;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:31:8,23 0|1:38:25,13 ./.:34:15,19 -chr20 850450 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=832062;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:40:20,20 0|1:28:14,14 1|1:26:6,20 -chr20 850608 . A G 60 . QNAME=cluster19_000000F;QSTART=814896;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:31:17,14 0|1:33:18,15 ./.:30:8,22 -chr20 850762 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=832374;QSTRAND=+;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:32:16,16 ./.:39:23,16 1|1:21:12,9 -chr20 850818 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=832430;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:30:12,18 0|1:37:19,18 1|1:43:22,21 -chr20 851565 . G A 60 . QNAME=cluster19_000000F;QSTART=815853;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:31:7,24 0|1:22:9,13 ./.:30:22,8 -chr20 851698 . C T 60 . QNAME=cluster19_000000F;QSTART=24906388;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:32:18,14 1|0:42:17,25 ./.:38:24,14 -chr20 852010 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=833622;QSTRAND=+;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:43:24,19 ./.:33:21,12 1|1:29:20,9 -chr20 852120 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=833732;QSTRAND=+;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:44:23,21 ./.:29:7,22 1|1:39:14,25 -chr20 852153 . C T 60 . QNAME=cluster19_000000F;QSTART=816441;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:42:19,23 0|1:44:20,24 ./.:40:22,18 -chr20 852155 . T C 60 . QNAME=cluster19_000000F;QSTART=816443;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:32:25,7 0|1:16:10,6 ./.:37:15,22 -chr20 852165 . G A 60 . QNAME=cluster19_000000F;QSTART=816453;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:33:11,22 0|1:34:11,23 ./.:29:14,15 -chr20 852596 . ACT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=834209;QSTRAND=+;GCPCT=33;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.792481 GT:DP:AD 1|1:20:11,9 0|1:28:5,23 1|1:42:20,22 -chr20 852714 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=834324;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:41:22,19 0|1:13:5,8 1|1:33:10,23 -chr20 852722 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=834332;QSTRAND=+;GCPCT=0;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:30:17,13 ./.:42:19,23 1|1:37:12,25 -chr20 853509 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=835119;QSTRAND=+;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:22:10,12 ./.:34:25,9 1|1:31:11,20 -chr20 853837 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=835447;QSTRAND=+;GCPCT=100;GTCNT=1,0,0,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:41:24,17 ./.:35:14,21 1|1:27:6,21 -chr20 854857 . TTGTG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=836468;QSTRAND=+;GCPCT=40;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.485475 GT:DP:AD 1|0:17:7,10 1|1:19:5,14 ./.:29:13,16 -chr20 854857 . TTGTGTG T 60 . QNAME=HG002-S9-H2-000001F;QSTART=811013;QSTRAND=+;GCPCT=42;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.492614 GT:DP:AD 0|1:26:12,14 ./.:24:13,11 1|1:26:5,21 -chr20 855703 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=837309;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:34:11,23 1|1:32:20,12 1|1:36:21,15 -chr20 855883 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=812032;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:42:18,24 ./.:46:24,22 ./.:16:7,9 -chr20 856057 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=837663;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:33:9,24 1|1:49:24,25 1|1:26:21,5 -chr20 856168 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=837774;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:24:10,14 0|1:31:7,24 ./.:23:11,12 -chr20 856433 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=838039;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:34:15,19 1|1:29:18,11 1|1:43:18,25 -chr20 856781 . G A 60 . QNAME=cluster19_000000F;QSTART=821063;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:46:25,21 0|1:13:7,6 ./.:39:17,22 -chr20 857157 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=838763;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|1:17:6,11 1|1:25:13,12 1|1:27:21,6 -chr20 857179 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=838785;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:16:10,6 1|1:29:7,22 1|1:24:17,7 -chr20 857617 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=839223;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:40:17,23 1|1:22:11,11 1|1:33:22,11 -chr20 858872 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=840478;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:32:12,20 1|1:41:23,18 1|1:28:9,19 -chr20 858925 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=840531;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:26:13,13 1|1:29:22,7 1|1:35:15,20 -chr20 859762 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=841368;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:33:11,22 1|1:16:8,8 1|1:41:25,16 -chr20 860453 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=842059;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:23:10,13 0|1:30:22,8 ./.:18:5,13 -chr20 860488 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=816637;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:19:6,13 1|0:21:5,16 1|1:21:13,8 -chr20 861973 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=843579;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:42:23,19 1|1:35:15,20 1|1:32:19,13 -chr20 861975 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=843581;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:39:18,21 1|1:25:9,16 1|1:14:7,7 -chr20 862051 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=843657;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:15:10,5 1|1:29:8,21 1|1:37:20,17 -chr20 862053 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=843659;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0 GT:DP:AD 1|1:16:7,9 1|1:19:11,8 1|1:30:25,5 -chr20 862244 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=818394;QSTRAND=+;GCPCT=50;GTCNT=0,0,3,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD 0|1:24:15,9 1|0:35:10,25 1|0:13:6,7 -chr20 862244 . CTT C 60 . QNAME=cluster23_scaffold_2;QSTART=24830855;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.459148 GT:DP:AD ./.:39:25,14 ./.:31:14,17 0|1:15:10,5 -chr20 862270 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=843876;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:42:24,18 1|0:45:24,21 1|1:44:19,25 -chr20 862270 . T TA 60 . QNAME=cluster19_000000F;QSTART=826553;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD ./.:21:11,10 0|1:37:15,22 ./.:37:23,14 -chr20 862295 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=843901;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:31:6,25 1|1:32:15,17 1|1:27:5,22 -chr20 862400 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=818548;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:34:19,15 1|0:15:9,6 1|1:45:23,22 -chr20 863200 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=844806;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:31:8,23 0|1:35:22,13 ./.:37:15,22 -chr20 863302 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=819450;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:15:6,9 1|0:29:16,13 1|1:28:12,16 -chr20 863798 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=845405;QSTRAND=+;GCPCT=50;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|1:45:23,22 1|1:28:21,7 1|1:30:12,18 -chr20 864029 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=820176;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:31:17,14 1|0:39:21,18 1|1:24:8,16 -chr20 864049 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=820196;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:40:22,18 1|0:47:22,25 1|1:44:22,22 -chr20 864080 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=845685;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:30:9,21 1|1:13:6,7 1|1:24:12,12 -chr20 865132 . AAGCAGAAAAGC A 60 . QNAME=cluster23_scaffold_2;QSTART=24827970;QSTRAND=-;GCPCT=41;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.692216 GT:DP:AD ./.:15:7,8 ./.:37:20,17 0|1:30:8,22 -chr20 865868 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=847474;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 1|0:46:24,22 0|1:43:23,20 ./.:22:6,16 -chr20 866330 . A AC 60 . QNAME=HG002-S9-H1-000001F;QSTART=847937;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 1|0:26:10,16 0|1:32:13,19 ./.:40:18,22 -chr20 866340 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=847947;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:35:15,20 0|1:15:5,10 ./.:28:19,9 -chr20 866636 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=848243;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:28:10,18 0|1:42:22,20 ./.:39:23,16 -chr20 866712 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=848319;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:33:10,23 0|1:38:25,13 ./.:42:23,19 -chr20 866777 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=848384;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:34:11,23 0|1:45:24,21 ./.:24:15,9 -chr20 866852 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=848459;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:28:20,8 0|1:18:10,8 ./.:26:12,14 -chr20 867420 . GTA G 60 . QNAME=cluster19_000000F;QSTART=24890672;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.792481 GT:DP:AD ./.:23:6,17 1|0:33:19,14 ./.:40:22,18 -chr20 867422 . ATATG A 60 . QNAME=cluster23_scaffold_2;QSTART=24825691;QSTRAND=-;GCPCT=20;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.760964 GT:DP:AD ./.:24:8,16 ./.:37:23,14 0|1:25:13,12 -chr20 867424 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=823571;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:37:14,23 ./.:27:5,22 1|0:41:18,23 -chr20 867424 . ATG A 60 . QNAME=cluster19_000000F;QSTART=831709;QSTRAND=+;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0.792481 GT:DP:AD ./.:14:9,5 0|1:36:25,11 ./.:24:9,15 -chr20 867469 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=849076;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:27:19,8 1|1:24:11,13 0|1:13:6,7 -chr20 867469 . T TGA 60 . QNAME=HG002-S9-H2-000001F;QSTART=823617;QSTRAND=+;GCPCT=33;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.792481 GT:DP:AD 0|1:31:18,13 ./.:31:6,25 1|0:16:8,8 -chr20 867728 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=849335;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:19:12,7 0|1:41:23,18 ./.:37:24,13 -chr20 867974 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=824123;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:19:7,12 1|0:30:18,12 1|1:39:22,17 -chr20 868254 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=849861;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:10:5,5 1|1:44:22,22 1|1:42:21,21 -chr20 868526 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=850133;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:37:15,22 0|1:45:23,22 ./.:25:16,9 -chr20 868606 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=850213;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:30:14,16 0|1:48:23,25 ./.:40:22,18 -chr20 868745 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=824894;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:24:9,15 1|0:44:19,25 1|1:29:23,6 -chr20 868950 . C CT 60 . QNAME=HG002-S9-H1-000001F;QSTART=850558;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|0:30:5,25 0|1:28:12,16 ./.:24:19,5 -chr20 868955 . TC T 60 . QNAME=HG002-S9-H2-000001F;QSTART=825105;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD 0|1:37:21,16 ./.:31:17,14 ./.:28:18,10 -chr20 868956 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=850564;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:32:24,8 1|1:34:21,13 1|1:13:7,6 -chr20 869010 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=850618;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:24:15,9 1|1:37:12,25 1|1:42:18,24 -chr20 869733 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=851341;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:35:13,22 1|1:19:6,13 1|1:31:17,14 -chr20 869777 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=851385;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:29:24,5 1|1:29:17,12 1|1:33:12,21 -chr20 871966 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=828114;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:27:6,21 1|0:27:19,8 1|1:21:7,14 -chr20 871969 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=828117;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:31:23,8 1|0:28:6,22 1|1:38:23,15 -chr20 872450 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=828598;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 0|1:32:19,13 1|0:24:15,9 1|1:17:10,7 -chr20 872792 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=854400;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:39:19,20 1|1:24:13,11 1|1:32:17,15 -chr20 873491 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=855099;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:27:19,8 0|1:31:25,6 ./.:40:15,25 -chr20 873608 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=855216;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:41:22,19 0|1:25:19,6 ./.:35:25,10 -chr20 873920 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=855528;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:17:7,10 0|1:29:19,10 0|1:18:13,5 -chr20 873956 . C A 60 . QNAME=cluster19_000000F;QSTART=24884138;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:37:17,20 1|0:31:24,7 ./.:38:18,20 -chr20 874038 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=855646;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:36:22,14 0|1:33:12,21 0|1:18:6,12 -chr20 874111 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=855719;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:25:16,9 0|1:25:13,12 0|1:25:20,5 -chr20 874297 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=855905;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:22:15,7 0|1:34:13,21 0|1:32:11,21 -chr20 874696 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=856304;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:21:15,6 0|1:32:25,7 0|1:23:13,10 -chr20 875035 . TC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=856644;QSTRAND=+;GCPCT=50;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 1|0:40:24,16 0|1:42:17,25 0|1:29:6,23 -chr20 875568 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=857175;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:46:22,24 0|1:14:9,5 ./.:24:5,19 -chr20 875568 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=24817550;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD ./.:24:13,11 ./.:19:14,5 0|1:27:17,10 -chr20 875920 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=857527;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:39:20,19 0|1:19:11,8 0|1:17:7,10 -chr20 876104 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=857711;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:23:12,11 0|1:38:24,14 0|1:45:21,24 -chr20 876144 . C CA 60 . QNAME=cluster23_scaffold_3;QSTART=24833309;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD ./.:30:9,21 ./.:28:19,9 1|0:16:7,9 -chr20 876144 . CAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=857752;QSTRAND=+;GCPCT=33;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.459148 GT:DP:AD 1|0:32:13,19 0|1:22:14,8 0|1:24:8,16 -chr20 876194 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=857799;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:37:24,13 0|1:36:25,11 0|1:42:22,20 -chr20 876734 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24816386;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:46:24,22 ./.:24:14,10 0|1:24:18,6 -chr20 878979 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24814141;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:21:13,8 ./.:18:5,13 0|1:34:17,17 -chr20 879508 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=861113;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:15:7,8 0|1:27:17,10 ./.:21:10,11 -chr20 880111 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=861716;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:18:9,9 0|1:44:20,24 ./.:37:17,20 -chr20 880159 . G A 60 . QNAME=cluster19_000000F;QSTART=24877935;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:41:23,18 1|0:33:20,13 ./.:37:24,13 -chr20 880302 . A AG 60 . QNAME=HG002-S9-H1-000001F;QSTART=861908;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 1|0:30:8,22 0|1:35:10,25 ./.:28:18,10 -chr20 880463 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24812657;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:29:14,15 ./.:34:23,11 0|1:19:11,8 -chr20 880587 . C CA 60 . QNAME=cluster19_000000F;QSTART=24877506;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,3,0,0;LCR=0.5 GT:DP:AD ./.:19:13,6 1|0:23:17,6 ./.:14:5,9 -chr20 880587 . CA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=862194;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|0:26:16,10 ./.:25:17,8 ./.:25:9,16 -chr20 880743 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=862348;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:16:9,7 0|1:13:8,5 0|1:33:10,23 -chr20 881100 . C G 60 . QNAME=cluster23_scaffold_2;QSTART=24812020;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:46:21,25 ./.:18:5,13 0|1:28:9,19 -chr20 881114 . G GGGAA 60 . QNAME=cluster23_scaffold_2;QSTART=24812002;QSTRAND=-;GCPCT=60;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.485475 GT:DP:AD ./.:25:20,5 ./.:32:11,21 0|1:27:5,22 -chr20 881524 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24811592;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:31:16,15 ./.:35:20,15 0|1:30:11,19 -chr20 881561 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24811555;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:29:17,12 ./.:30:15,15 0|1:40:17,23 -chr20 882074 . T G 60 . QNAME=cluster23_scaffold_2;QSTART=24811042;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:35:24,11 ./.:39:20,19 0|1:47:22,25 -chr20 882180 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24810936;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:11:5,6 ./.:24:14,10 0|1:40:22,18 -chr20 882348 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=863953;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:39:15,24 0|1:19:10,9 ./.:31:9,22 -chr20 882505 . C CTAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=864111;QSTRAND=+;GCPCT=25;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.75 GT:DP:AD 1|0:37:22,15 0|1:39:15,24 ./.:18:5,13 -chr20 882628 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=864236;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:45:25,20 0|1:36:17,19 ./.:28:8,20 -chr20 882865 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=864473;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:32:23,9 0|1:32:10,22 ./.:30:6,24 -chr20 883063 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=864671;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:39:20,19 0|1:31:23,8 0|1:28:20,8 -chr20 883101 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=864709;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:39:18,21 0|1:29:17,12 ./.:31:17,14 -chr20 883203 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24809913;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0 GT:DP:AD ./.:24:19,5 ./.:23:16,7 0|1:26:21,5 -chr20 883230 . C T 60 . QNAME=cluster19_000000F;QSTART=24874863;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:27:13,14 1|0:30:25,5 ./.:13:5,8 -chr20 883431 . T C 60 . QNAME=cluster23_scaffold_2;QSTART=24809685;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:39:23,16 ./.:20:8,12 0|1:19:7,12 -chr20 883556 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=865164;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:15:10,5 0|1:42:21,21 ./.:32:13,19 -chr20 883658 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=24809458;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:37:25,12 ./.:33:10,23 0|1:41:18,23 -chr20 883812 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=865420;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:42:17,25 0|1:16:7,9 0|1:28:23,5 -chr20 883869 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=24809247;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:31:19,12 ./.:11:5,6 0|1:28:23,5 -chr20 883997 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=865605;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:19:14,5 0|1:41:21,20 0|1:28:11,17 -chr20 884017 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=865625;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:34:10,24 0|1:25:6,19 0|1:34:17,17 -chr20 884411 . G C 60 . QNAME=cluster23_scaffold_2;QSTART=24808705;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:17:8,9 ./.:18:5,13 0|1:46:25,21 -chr20 884723 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=866331;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:42:24,18 0|1:26:9,17 0|1:37:19,18 -chr20 884894 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24808222;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:26:21,5 ./.:37:19,18 0|1:37:21,16 -chr20 885021 . TC T 60 . QNAME=HG002-S9-H1-000001F;QSTART=866630;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|0:34:22,12 0|1:38:21,17 ./.:20:11,9 -chr20 885587 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=867194;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:25:12,13 0|1:18:8,10 ./.:17:9,8 -chr20 885689 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=867296;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:32:16,16 0|1:23:9,14 ./.:36:16,20 -chr20 885707 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=867314;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:27:19,8 0|1:31:7,24 ./.:28:16,12 -chr20 885722 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=867329;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:18:6,12 0|1:15:8,7 ./.:16:11,5 -chr20 886137 . AG A 60 . QNAME=cluster23_scaffold_2;QSTART=24806979;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:24:14,10 ./.:36:13,23 0|1:43:18,25 -chr20 886620 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=868227;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:27:5,22 0|1:36:19,17 ./.:33:19,14 -chr20 886681 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=868288;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:36:23,13 0|1:41:19,22 0|1:42:21,21 -chr20 886694 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=868301;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:44:23,21 0|1:19:10,9 ./.:15:6,9 -chr20 887636 . CT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=843785;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 0|1:15:8,7 1|0:47:23,24 ./.:35:11,24 -chr20 887636 . CTTT C 60 . QNAME=cluster23_scaffold_2;QSTART=24805481;QSTRAND=-;GCPCT=25;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0.405639 GT:DP:AD ./.:11:6,5 ./.:32:21,11 0|1:23:8,15 -chr20 887636 . CTTTT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=869244;QSTRAND=+;GCPCT=20;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.360964 GT:DP:AD 1|0:29:19,10 0|1:31:20,11 ./.:15:10,5 -chr20 887887 . G GAGGA 60 . QNAME=cluster23_scaffold_2;QSTART=24805229;QSTRAND=-;GCPCT=60;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.485475 GT:DP:AD ./.:42:22,20 ./.:32:10,22 0|1:22:11,11 -chr20 887996 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=869599;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:35:16,19 0|1:29:24,5 0|1:37:12,25 -chr20 888753 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=870356;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:23:14,9 0|1:39:21,18 ./.:34:22,12 -chr20 889503 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=871106;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:20:7,13 0|1:34:10,24 0|1:42:17,25 -chr20 889671 . C G 60 . QNAME=cluster23_scaffold_3;QSTART=24819782;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:32:10,22 ./.:39:14,25 1|0:22:9,13 -chr20 890514 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=872117;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:32:19,13 0|1:29:18,11 ./.:35:18,17 -chr20 890614 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=872217;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:46:23,23 ./.:40:15,25 ./.:30:18,12 -chr20 891187 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=872790;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:34:9,25 ./.:28:16,12 ./.:32:21,11 -chr20 891480 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=873083;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:39:15,24 ./.:27:22,5 ./.:35:24,11 -chr20 891653 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24801463;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:18:9,9 ./.:31:13,18 0|1:36:11,25 -chr20 892108 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=873711;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:31:15,16 ./.:48:24,24 ./.:44:24,20 -chr20 892511 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=874114;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:32:21,11 ./.:28:15,13 ./.:26:11,15 -chr20 892634 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=874237;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:25:20,5 ./.:29:10,19 ./.:33:12,21 -chr20 892840 . C T 60 . QNAME=cluster19_000000F;QSTART=24865254;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:42:19,23 1|0:35:10,25 ./.:32:8,24 -chr20 893106 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=874709;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:13:8,5 ./.:32:21,11 ./.:24:9,15 -chr20 893464 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=875067;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:40:15,25 ./.:28:23,5 ./.:13:7,6 -chr20 893483 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=875086;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD 1|0:36:25,11 ./.:28:18,10 ./.:35:25,10 -chr20 894385 . C T 60 . QNAME=cluster19_000000F;QSTART=24863709;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:37:22,15 1|0:28:11,17 ./.:40:24,16 -chr20 895490 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=877093;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:42:25,17 ./.:39:25,14 ./.:39:24,15 -chr20 895600 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=877203;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:27:15,12 ./.:12:6,6 ./.:40:20,20 -chr20 896059 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=877662;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:18:6,12 ./.:19:10,9 ./.:29:14,15 -chr20 896562 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=878165;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:43:23,20 ./.:20:12,8 ./.:47:22,25 -chr20 896997 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=878600;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:37:13,24 ./.:29:11,18 ./.:32:18,14 -chr20 899093 . T C 60 . QNAME=cluster19_000000F;QSTART=24859001;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:32:23,9 1|0:28:6,22 ./.:34:9,25 -chr20 899180 . T A 60 . QNAME=cluster19_000000F;QSTART=24858914;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:25:6,19 1|0:32:23,9 ./.:20:11,9 -chr20 899195 . C G 60 . QNAME=cluster19_000000F;QSTART=24858899;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:19:11,8 1|0:29:10,19 ./.:32:19,13 -chr20 899251 . AT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=880855;QSTRAND=+;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|1:36:11,25 ./.:13:5,8 ./.:35:24,11 -chr20 899252 . T A 60 . QNAME=cluster19_000000F;QSTART=24858842;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:35:16,19 1|0:28:8,20 ./.:39:22,17 -chr20 899447 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=881049;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0 GT:DP:AD 1|1:31:22,9 1|1:30:25,5 1|1:16:8,8 -chr20 899533 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=855679;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:32:23,9 ./.:16:8,8 ./.:40:17,23 -chr20 900321 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=856467;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:36:19,17 ./.:13:5,8 ./.:35:13,22 -chr20 900721 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=856867;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 0|1:31:25,6 ./.:36:25,11 ./.:36:25,11 -chr20 900932 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=857078;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:22:7,15 ./.:37:13,24 ./.:32:10,22 -chr20 900977 . T A 60 . QNAME=HG002-S9-H2-000001F;QSTART=857123;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:29:13,16 ./.:22:5,17 ./.:21:8,13 -chr20 901001 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=857147;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:24:7,17 ./.:46:21,25 ./.:37:25,12 -chr20 901060 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=857206;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:48:25,23 ./.:33:24,9 ./.:18:12,6 -chr20 901437 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=857583;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:32:13,19 ./.:45:21,24 ./.:37:13,24 -chr20 901786 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=857932;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:41:16,25 0|1:19:9,10 ./.:38:24,14 -chr20 902160 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=858306;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:31:10,21 ./.:19:7,12 ./.:17:10,7 -chr20 902357 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=858503;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:33:16,17 ./.:33:21,12 ./.:32:25,7 -chr20 902728 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=858874;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:11:5,6 ./.:32:19,13 ./.:32:12,20 -chr20 903001 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=859147;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:33:12,21 ./.:15:10,5 ./.:25:16,9 -chr20 903427 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=859573;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 0|1:22:17,5 ./.:28:15,13 ./.:27:20,7 -chr20 903489 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=859635;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:34:12,22 ./.:38:14,24 ./.:31:18,13 -chr20 904502 . A AC 60 . QNAME=HG002-S9-H2-000001F;QSTART=860649;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 0|1:27:6,21 ./.:26:19,7 ./.:30:12,18 -chr20 905359 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=861506;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:25:14,11 ./.:32:8,24 ./.:15:5,10 -chr20 905407 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=861554;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:42:17,25 ./.:30:17,13 ./.:29:18,11 -chr20 905736 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=861883;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:24:8,16 ./.:29:22,7 ./.:23:6,17 -chr20 906213 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=862360;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:31:14,17 ./.:43:20,23 ./.:36:23,13 -chr20 906268 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=862415;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 0|1:17:7,10 ./.:25:17,8 ./.:21:7,14 -chr20 906812 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=862959;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:33:11,22 ./.:30:9,21 ./.:21:6,15 -chr20 906878 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=863025;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:28:23,5 ./.:24:7,17 ./.:22:17,5 -chr20 907157 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=863304;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:42:25,17 ./.:40:15,25 ./.:29:18,11 -chr20 907880 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=864027;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:37:17,20 ./.:37:15,22 0|1:26:15,11 -chr20 908674 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=864821;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:40:19,21 ./.:23:12,11 0|1:36:13,23 -chr20 909226 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24783890;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:25:14,11 ./.:13:5,8 0|1:35:20,15 -chr20 909261 . C A 60 . QNAME=cluster19_000000F;QSTART=873540;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:32:9,23 0|1:24:11,13 ./.:36:11,25 -chr20 909371 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24783745;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:22:16,6 ./.:29:15,14 0|1:44:22,22 -chr20 909453 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=891055;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:37:14,23 ./.:33:23,10 ./.:39:14,25 -chr20 909635 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=24783481;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:36:23,13 ./.:30:6,24 0|1:39:23,16 -chr20 909706 . G C 60 . QNAME=cluster19_000000F;QSTART=873985;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:21:5,16 0|1:46:21,25 ./.:38:21,17 -chr20 911795 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=893397;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:23:17,6 ./.:27:5,22 ./.:36:24,12 -chr20 911823 . AGACAGAGAGAGGGAGAGAGG A 60 . QNAME=HG002-S9-H1-000001F;QSTART=893426;QSTRAND=+;GCPCT=57;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.610847 GT:DP:AD 1|0:26:6,20 ./.:21:13,8 ./.:30:18,12 -chr20 912080 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=893662;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:19:8,11 ./.:25:5,20 ./.:41:23,18 -chr20 912305 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=893887;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:13:8,5 ./.:28:13,15 ./.:29:13,16 -chr20 913482 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=895064;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:32:20,12 ./.:31:8,23 ./.:25:12,13 -chr20 914079 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=895661;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:16:10,6 1|0:24:7,17 ./.:25:11,14 -chr20 914238 . A G 60 . QNAME=cluster19_000000F;QSTART=24843856;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:45:23,22 1|0:23:13,10 ./.:25:13,12 -chr20 914324 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=895906;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:37:14,23 1|1:32:18,14 1|0:24:14,10 -chr20 914682 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=896264;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:35:20,15 1|0:34:14,20 1|1:27:15,12 -chr20 914775 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=870922;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:25:16,9 ./.:27:10,17 1|0:17:9,8 -chr20 914780 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=896362;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:36:18,18 1|0:38:24,14 0|1:32:20,12 -chr20 914814 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=870961;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD 0|1:26:15,11 ./.:16:6,10 1|0:29:19,10 -chr20 915350 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=896932;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:33:10,23 ./.:36:22,14 ./.:28:14,14 -chr20 915369 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=896951;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:37:14,23 1|0:14:8,6 1|0:18:5,13 -chr20 915656 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=897238;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|1:12:6,6 1|0:30:22,8 1|1:26:12,14 -chr20 916110 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=872257;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:23:8,15 ./.:40:15,25 ./.:35:15,20 -chr20 916419 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=898001;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:37:17,20 1|1:20:5,15 1|1:28:5,23 -chr20 916452 . A C 60 . QNAME=cluster19_000000F;QSTART=880731;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:34:21,13 0|1:34:19,15 ./.:38:22,16 -chr20 916852 . C T 60 . QNAME=cluster19_000000F;QSTART=881131;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:29:23,6 0|1:28:5,23 ./.:29:18,11 -chr20 916971 . C T 60 . QNAME=cluster19_000000F;QSTART=881250;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:37:17,20 0|1:30:20,10 ./.:23:6,17 -chr20 917534 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=873681;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:22:11,11 ./.:23:8,15 ./.:27:14,13 -chr20 917575 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=899157;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:39:21,18 1|1:24:7,17 1|1:33:16,17 -chr20 917906 . T G 60 . QNAME=cluster19_000000F;QSTART=882185;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD ./.:20:9,11 0|1:27:14,13 ./.:19:9,10 -chr20 918736 . G A 60 . QNAME=cluster19_000000F;QSTART=883015;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:41:25,16 0|1:24:8,16 ./.:28:14,14 -chr20 919146 . CTCTT C 60 . QNAME=cluster19_000000F;QSTART=883426;QSTRAND=+;GCPCT=40;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.485475 GT:DP:AD ./.:46:22,24 0|1:34:25,9 ./.:21:9,12 -chr20 919167 . C CTT 60 . QNAME=cluster23_scaffold_2;QSTART=24773947;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0.459148 GT:DP:AD ./.:33:9,24 ./.:13:7,6 0|1:28:13,15 -chr20 919371 . G C 60 . QNAME=cluster19_000000F;QSTART=883646;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:38:18,20 0|1:32:8,24 ./.:31:9,22 -chr20 919990 . TG T 60 . QNAME=cluster19_000000F;QSTART=24838104;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.5 GT:DP:AD ./.:32:19,13 1|0:35:22,13 ./.:32:24,8 -chr20 919994 . T C 60 . QNAME=cluster19_000000F;QSTART=24838101;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:39:25,14 1|0:35:12,23 ./.:46:24,22 -chr20 920055 . T TC 60 . QNAME=HG002-S9-H1-000001F;QSTART=901638;QSTRAND=+;GCPCT=50;GTCNT=0,0,0,3;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD 1|1:13:7,6 1|1:23:8,15 1|1:29:18,11 -chr20 920188 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=901771;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:32:11,21 1|0:41:25,16 ./.:24:8,16 -chr20 920292 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=901875;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:23:17,6 1|0:20:9,11 ./.:22:13,9 -chr20 920391 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=901974;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:16:10,6 ./.:25:12,13 ./.:21:11,10 -chr20 921033 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=902616;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:27:10,17 1|1:38:16,22 1|1:37:15,22 -chr20 921239 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=902822;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:38:20,18 1|1:16:6,10 1|1:11:6,5 -chr20 921288 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=902871;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:20:5,15 1|0:38:17,21 1|1:42:21,21 -chr20 921359 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=877507;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:17:8,9 ./.:21:14,7 ./.:35:10,25 -chr20 921417 . T G 60 . QNAME=HG002-S9-H2-000001F;QSTART=877565;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:18:10,8 1|0:32:23,9 0|1:32:13,19 -chr20 921417 . T TG 60 . QNAME=cluster19_000000F;QSTART=885694;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD ./.:38:17,21 0|1:28:7,21 ./.:31:23,8 -chr20 921667 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=903250;QSTRAND=+;GCPCT=100;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:31:18,13 0|1:29:23,6 0|1:38:21,17 -chr20 922254 . C G 60 . QNAME=cluster19_000000F;QSTART=886531;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:34:13,21 0|1:18:6,12 0|1:39:24,15 -chr20 922377 . G A 60 . QNAME=cluster19_000000F;QSTART=886654;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:31:8,23 0|1:19:8,11 0|1:34:19,15 -chr20 923331 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=24769781;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD ./.:25:18,7 ./.:13:6,7 0|1:47:22,25 -chr20 923875 . C CA 60 . QNAME=cluster23_scaffold_2;QSTART=24769236;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:33:23,10 ./.:45:20,25 0|1:24:16,8 -chr20 924499 . C T 60 . QNAME=cluster19_000000F;QSTART=888776;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:23:12,11 0|1:38:17,21 0|1:19:12,7 -chr20 925913 . CA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=882062;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 0|1:47:22,25 ./.:31:16,15 ./.:32:24,8 -chr20 928807 . G C 60 . QNAME=cluster19_000000F;QSTART=893084;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:27:21,6 0|1:34:22,12 0|1:26:19,7 -chr20 929128 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=885275;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:48:24,24 1|1:19:11,8 0|1:38:13,25 -chr20 929177 . T C 60 . QNAME=cluster19_000000F;QSTART=893454;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:41:19,22 0|1:37:18,19 ./.:44:20,24 -chr20 929220 . A T 60 . QNAME=cluster19_000000F;QSTART=893497;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:38:18,20 0|1:18:13,5 ./.:25:6,19 -chr20 929302 . TTA T 60 . QNAME=cluster19_000000F;QSTART=24828792;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0.459148 GT:DP:AD ./.:34:24,10 1|0:49:25,24 ./.:12:6,6 -chr20 929302 . TTATGG T 60 . QNAME=cluster19_000000F;QSTART=893580;QSTRAND=+;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.729574 GT:DP:AD ./.:36:17,19 0|1:19:14,5 ./.:20:15,5 -chr20 929491 . A C 60 . QNAME=cluster19_000000F;QSTART=24828605;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:22:9,13 1|1:29:17,12 ./.:24:9,15 -chr20 929623 . T C 60 . QNAME=cluster19_000000F;QSTART=24828473;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:25:14,11 1|1:38:18,20 ./.:44:24,20 -chr20 929701 . T G 60 . QNAME=cluster19_000000F;QSTART=24828395;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:36:11,25 1|1:25:6,19 ./.:36:11,25 -chr20 931616 . C T 60 . QNAME=cluster19_000000F;QSTART=24826480;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:40:22,18 1|1:18:10,8 ./.:33:11,22 -chr20 931983 . A G 60 . QNAME=cluster19_000000F;QSTART=24826113;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:39:21,18 1|1:16:8,8 ./.:26:14,12 -chr20 932022 . T C 60 . QNAME=cluster19_000000F;QSTART=24826074;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:30:21,9 1|1:36:17,19 ./.:45:24,21 -chr20 932357 . T C 60 . QNAME=cluster19_000000F;QSTART=24825739;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:27:7,20 1|1:42:18,24 ./.:20:11,9 -chr20 932610 . G A 60 . QNAME=cluster19_000000F;QSTART=24825486;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:29:10,19 1|1:30:21,9 ./.:21:15,6 -chr20 932660 . A AT 60 . QNAME=cluster19_000000F;QSTART=24825435;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:31:19,12 1|1:47:24,23 ./.:18:9,9 -chr20 932698 . G A 60 . QNAME=cluster19_000000F;QSTART=24825397;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:38:17,21 1|1:33:10,23 ./.:34:13,21 -chr20 932824 . G A 60 . QNAME=cluster19_000000F;QSTART=24825271;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:37:13,24 1|1:26:6,20 ./.:30:16,14 -chr20 933093 . C T 60 . QNAME=cluster19_000000F;QSTART=24825002;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:33:10,23 1|1:31:6,25 ./.:21:16,5 -chr20 933764 . G T 60 . QNAME=cluster19_000000F;QSTART=24824331;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:43:25,18 1|1:42:19,23 ./.:23:5,18 -chr20 933777 . T G 60 . QNAME=cluster19_000000F;QSTART=24824318;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:28:13,15 1|1:38:15,23 ./.:29:18,11 -chr20 934006 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=890153;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:31:22,9 ./.:43:25,18 ./.:43:18,25 -chr20 934616 . G A 60 . QNAME=cluster19_000000F;QSTART=24823479;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:23:17,6 1|1:33:11,22 ./.:24:8,16 -chr20 935220 . C A 60 . QNAME=cluster19_000000F;QSTART=24822875;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:29:24,5 1|1:20:14,6 ./.:23:7,16 -chr20 935920 . C T 60 . QNAME=cluster23_scaffold_2;QSTART=24757191;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:35:24,11 ./.:30:18,12 0|1:40:18,22 -chr20 936160 . A C 60 . QNAME=cluster19_000000F;QSTART=24821935;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:41:24,17 1|0:39:16,23 ./.:41:21,20 -chr20 937152 . A T 60 . QNAME=cluster19_000000F;QSTART=24820943;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:31:7,24 1|0:46:22,24 ./.:40:25,15 -chr20 937174 . C T 60 . QNAME=cluster19_000000F;QSTART=24820921;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:33:11,22 1|0:17:6,11 ./.:27:16,11 -chr20 937837 . T A 60 . QNAME=cluster19_000000F;QSTART=24820258;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD ./.:23:10,13 1|0:33:23,10 ./.:43:18,25 -chr20 937941 . A G 60 . QNAME=cluster19_000000F;QSTART=24820154;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:31:11,20 1|0:25:19,6 ./.:28:19,9 -chr20 938380 . G A 60 . QNAME=cluster19_000000F;QSTART=24819715;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:34:16,18 1|0:34:20,14 ./.:32:9,23 -chr20 940109 . A G 60 . QNAME=cluster19_000000F;QSTART=24817986;QSTRAND=-;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:40:20,20 1|1:31:16,15 ./.:25:13,12 -chr20 940207 . G A 60 . QNAME=cluster19_000000F;QSTART=24817888;QSTRAND=-;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:31:12,19 1|1:15:10,5 ./.:23:8,15 -chr20 941328 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=897475;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:27:9,18 1|1:22:16,6 0|1:31:10,21 -chr20 942095 . C CA 60 . QNAME=cluster19_000000F;QSTART=906369;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:26:11,15 0|1:34:20,14 ./.:30:11,19 -chr20 942273 . A AT 60 . QNAME=HG002-S9-H2-000001F;QSTART=898421;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD 0|1:33:8,25 1|1:34:12,22 0|1:21:11,10 -chr20 942277 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=898425;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:17:8,9 1|1:37:22,15 0|1:31:20,11 -chr20 942358 . C T 60 . QNAME=cluster19_000000F;QSTART=24815736;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:34:10,24 1|1:47:22,25 0|1:26:14,12 -chr20 942424 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=898572;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 0|1:25:9,16 ./.:26:13,13 ./.:20:9,11 -chr20 942563 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=898711;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 0|1:32:18,14 ./.:28:20,8 ./.:21:14,7 -chr20 942659 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=898807;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:21:12,9 1|1:37:24,13 0|1:32:13,19 -chr20 943015 . G A 60 . QNAME=cluster19_000000F;QSTART=24815079;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:36:11,25 1|1:39:16,23 0|1:31:16,15 -chr20 943016 . C A 60 . QNAME=cluster19_000000F;QSTART=24815078;QSTRAND=-;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:28:16,12 1|1:14:8,6 0|1:46:24,22 -chr20 943950 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=900098;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:42:23,19 ./.:33:14,19 ./.:27:8,19 -chr20 943984 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=900132;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:34:25,9 1|1:32:17,15 0|1:41:18,23 -chr20 944018 . GCT G 60 . QNAME=cluster19_000000F;QSTART=24814076;QSTRAND=-;GCPCT=66;GTCNT=1,0,1,1;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0.792481 GT:DP:AD ./.:14:8,6 1|1:21:10,11 0|1:21:13,8 -chr20 944028 . TC T 60 . QNAME=HG002-S9-H2-000001F;QSTART=900177;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0.5 GT:DP:AD 0|1:27:18,9 ./.:11:6,5 ./.:21:8,13 -chr20 944029 . C CTT 60 . QNAME=cluster23_scaffold_3;QSTART=24765421;QSTRAND=-;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.459148 GT:DP:AD ./.:39:18,21 ./.:40:25,15 1|0:42:25,17 -chr20 944093 . C T 60 . QNAME=cluster23_scaffold_3;QSTART=24765357;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:27:18,9 ./.:36:21,15 1|0:25:16,9 -chr20 944094 . A G 60 . QNAME=cluster23_scaffold_3;QSTART=24765356;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:13:6,7 ./.:19:10,9 1|0:26:15,11 -chr20 945682 . T C 60 . QNAME=cluster19_000000F;QSTART=909955;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:25:7,18 0|1:45:20,25 0|1:22:5,17 -chr20 945711 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=901858;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:40:19,21 0|1:27:13,14 0|1:41:22,19 -chr20 945754 . G A 60 . QNAME=cluster19_000000F;QSTART=910027;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD ./.:34:17,17 0|1:33:25,8 0|1:34:10,24 -chr20 945942 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=902089;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:31:8,23 0|1:15:8,7 0|1:27:13,14 -chr20 946505 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=928088;QSTRAND=+;GCPCT=0;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:25:10,15 0|1:27:16,11 0|1:30:10,20 -chr20 946814 . A C 60 . QNAME=HG002-S9-H2-000001F;QSTART=902961;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:18:13,5 ./.:44:22,22 1|0:32:24,8 -chr20 946899 . C G 60 . QNAME=HG002-S9-H2-000001F;QSTART=903046;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:35:16,19 ./.:30:7,23 1|0:22:6,16 -chr20 947202 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=903349;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:36:21,15 ./.:18:7,11 1|0:26:17,9 -chr20 947218 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=903365;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:20:12,8 ./.:31:14,17 1|0:38:18,20 -chr20 947585 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=903732;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 0|1:23:16,7 ./.:18:7,11 1|0:30:23,7 -chr20 947624 . G C 60 . QNAME=HG002-S9-H2-000001F;QSTART=903771;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:30:20,10 ./.:32:25,7 1|0:47:25,22 -chr20 947782 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=903929;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:35:15,20 ./.:26:7,19 1|0:28:23,5 -chr20 947795 . A G 60 . QNAME=HG002-S9-H2-000001F;QSTART=903942;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:38:20,18 ./.:14:9,5 1|0:26:7,19 -chr20 947914 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=904061;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:22:8,14 ./.:36:16,20 1|0:20:5,15 -chr20 948357 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=904504;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:27:13,14 ./.:29:22,7 1|0:34:10,24 -chr20 948492 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=904639;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 0|1:16:8,8 ./.:33:24,9 1|0:19:9,10 -chr20 948493 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=904640;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 0|1:29:19,10 ./.:31:17,14 1|0:13:8,5 -chr20 948861 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=905008;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:36:19,17 ./.:37:19,18 1|0:33:23,10 -chr20 949016 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=905163;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 0|1:27:20,7 ./.:32:13,19 1|0:24:18,6 -chr20 949377 . GA G 60 . QNAME=HG002-S9-H2-000001F;QSTART=905525;QSTRAND=+;GCPCT=50;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.5 GT:DP:AD 0|1:45:20,25 ./.:20:15,5 1|0:15:7,8 -chr20 949837 . C T 60 . QNAME=cluster19_000000F;QSTART=914110;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD ./.:12:6,6 0|1:41:23,18 0|1:24:15,9 -chr20 949917 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=905960;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:40:25,15 ./.:31:9,22 1|0:38:18,20 -chr20 950840 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=906883;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:40:18,22 ./.:15:5,10 1|0:25:5,20 -chr20 950981 . A AAAATAAAT 60 . QNAME=HG002-S9-H2-000001F;QSTART=907025;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.382102 GT:DP:AD 0|1:40:25,15 ./.:30:22,8 1|0:32:9,23 -chr20 951023 . A AAAC 60 . QNAME=HG002-S9-H2-000001F;QSTART=907075;QSTRAND=+;GCPCT=25;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.405639 GT:DP:AD 0|1:25:7,18 ./.:29:16,13 1|0:40:19,21 -chr20 951100 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=907154;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:42:17,25 ./.:24:10,14 1|0:19:11,8 -chr20 951130 . A ATT 60 . QNAME=HG002-S9-H1-000001F;QSTART=932714;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.459148 GT:DP:AD 1|0:37:24,13 ./.:38:13,25 ./.:20:6,14 -chr20 951130 . A ATTT 60 . QNAME=cluster19_000000F;QSTART=915404;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.405639 GT:DP:AD ./.:39:17,22 0|1:40:15,25 ./.:36:18,18 -chr20 951130 . A ATTTTT 60 . QNAME=cluster23_scaffold_2;QSTART=24741977;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.325011 GT:DP:AD ./.:15:9,6 ./.:31:25,6 0|1:24:9,15 -chr20 951130 . ATTTTTTTTTTTT A 60 . QNAME=cluster19_000000F;QSTART=24806966;QSTRAND=-;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.195622 GT:DP:AD ./.:47:24,23 1|0:48:24,24 1|0:24:7,17 -chr20 951130 . ATTTTTTTTTTTTT A 60 . QNAME=HG002-S9-H2-000001F;QSTART=907185;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.185616 GT:DP:AD 0|1:32:18,14 ./.:34:12,22 ./.:38:18,20 -chr20 951172 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=907213;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:36:21,15 ./.:31:9,22 1|0:32:8,24 -chr20 951188 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=907229;QSTRAND=+;GCPCT=100;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:20:13,7 ./.:27:6,21 1|0:24:7,17 -chr20 951376 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=932961;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:29:20,9 0|1:42:23,19 1|1:31:6,25 -chr20 951397 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=932982;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:39:21,18 ./.:37:18,19 ./.:28:22,6 -chr20 951428 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=933013;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:32:10,22 ./.:31:8,23 ./.:41:25,16 -chr20 951612 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=933197;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:34:15,19 ./.:32:10,22 ./.:31:11,20 -chr20 951687 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=933272;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:39:18,21 ./.:29:15,14 ./.:28:8,20 -chr20 951756 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=933341;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:30:25,5 ./.:28:13,15 ./.:36:25,11 -chr20 951868 . C T 60 . QNAME=cluster19_000000F;QSTART=916144;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:15:6,9 0|1:25:11,14 1|1:27:19,8 -chr20 951868 . CGT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=907910;QSTRAND=+;GCPCT=66;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.792481 GT:DP:AD 0|1:30:13,17 ./.:24:14,10 ./.:37:18,19 -chr20 951870 . T C 60 . QNAME=cluster19_000000F;QSTART=916146;QSTRAND=+;GCPCT=0;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,3,0,0;LCR=0 GT:DP:AD ./.:19:12,7 0|1:15:8,7 1|1:34:25,9 -chr20 951975 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=908014;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 0|1:20:8,12 0|1:29:24,5 1|1:34:23,11 -chr20 952317 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=933902;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:22:12,10 ./.:42:23,19 ./.:27:5,22 -chr20 952372 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=933957;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:34:13,21 ./.:30:11,19 ./.:38:15,23 -chr20 952391 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=908430;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 0|1:17:9,8 0|1:22:8,14 1|1:16:7,9 -chr20 952475 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=934060;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:30:10,20 ./.:26:18,8 ./.:27:8,19 -chr20 952558 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=908597;QSTRAND=+;GCPCT=0;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:21:16,5 0|1:40:25,15 1|1:47:24,23 -chr20 952594 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=934179;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:41:25,16 ./.:17:8,9 ./.:38:13,25 -chr20 952909 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=934494;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:35:14,21 ./.:33:24,9 ./.:12:7,5 -chr20 953115 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=909154;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:20:6,14 1|1:37:14,23 1|1:40:23,17 -chr20 953327 . GTTAT G 60 . QNAME=HG002-S9-H1-000001F;QSTART=934913;QSTRAND=+;GCPCT=20;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.685475 GT:DP:AD 1|1:35:16,19 1|1:22:6,16 1|1:34:11,23 -chr20 953360 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=934941;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:31:24,7 ./.:31:6,25 ./.:20:12,8 -chr20 953456 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=935037;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:37:17,20 ./.:29:8,21 ./.:39:20,19 -chr20 953490 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=935071;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|1:32:19,13 1|1:30:21,9 1|1:30:7,23 -chr20 953507 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=935088;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:30:15,15 ./.:35:10,25 ./.:41:22,19 -chr20 953510 . A AT 60 . QNAME=HG002-S9-H2-000001F;QSTART=909546;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.5 GT:DP:AD 0|1:30:8,22 1|1:32:11,21 1|1:35:17,18 -chr20 953670 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=909706;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0 GT:DP:AD 0|1:37:24,13 1|1:17:5,12 0|1:31:21,10 -chr20 953787 . AC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=935369;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0.5 GT:DP:AD 1|0:10:5,5 ./.:39:21,18 ./.:23:8,15 -chr20 953831 . T TC 60 . QNAME=HG002-S9-H1-000001F;QSTART=935412;QSTRAND=+;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,3,0;LCR=0.5 GT:DP:AD 1|0:26:15,11 ./.:23:13,10 ./.:32:21,11 -chr20 953857 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=935438;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:29:12,17 ./.:33:15,18 ./.:36:16,20 -chr20 953954 . CG C 60 . QNAME=HG002-S9-H1-000001F;QSTART=935536;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0.5 GT:DP:AD 1|0:29:23,6 ./.:16:9,7 ./.:25:13,12 -chr20 953974 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=935554;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:43:20,23 ./.:21:16,5 ./.:38:22,16 -chr20 954305 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=935885;QSTRAND=+;GCPCT=0;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:30:8,22 1|1:25:7,18 0|1:17:12,5 -chr20 954418 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=910454;QSTRAND=+;GCPCT=100;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 0|1:27:12,15 1|1:37:16,21 0|1:44:20,24 -chr20 954610 . A G 60 . QNAME=cluster23_scaffold_2;QSTART=24738500;QSTRAND=-;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD ./.:24:6,18 ./.:32:12,20 0|1:39:25,14 -chr20 954684 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=936264;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:35:19,16 1|1:26:21,5 1|1:25:6,19 -chr20 954686 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=936266;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:17:5,12 1|1:45:25,20 0|1:46:22,24 -chr20 954688 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=936268;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:24:11,13 ./.:44:23,21 ./.:47:22,25 -chr20 954692 . CAA C 60 . QNAME=HG002-S9-H1-000001F;QSTART=936273;QSTRAND=+;GCPCT=33;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.459148 GT:DP:AD 1|1:41:22,19 1|1:33:19,14 1|1:39:20,19 -chr20 955001 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=936579;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:44:22,22 ./.:28:12,16 ./.:42:21,21 -chr20 956302 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=937880;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:24:8,16 ./.:35:13,22 ./.:41:20,21 -chr20 956624 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=938202;QSTRAND=+;GCPCT=0;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:24:8,16 1|1:42:21,21 1|1:31:12,19 -chr20 956630 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=938208;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:43:23,20 ./.:12:7,5 ./.:23:10,13 -chr20 957046 . C T 60 . QNAME=cluster19_000000F;QSTART=24801067;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD ./.:32:14,18 1|0:13:5,8 ./.:27:13,14 -chr20 957302 . G GTA 60 . QNAME=HG002-S9-H1-000001F;QSTART=938881;QSTRAND=+;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.792481 GT:DP:AD 1|0:46:22,24 ./.:37:25,12 ./.:35:12,23 -chr20 957320 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=938900;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:26:6,20 ./.:46:22,24 ./.:38:14,24 -chr20 957322 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=938902;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:30:14,16 ./.:35:18,17 ./.:20:9,11 -chr20 957387 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=938967;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|1:24:19,5 1|1:39:19,20 0|1:43:21,22 -chr20 957642 . C CAAAAAA 60 . QNAME=HG002-S9-H1-000001F;QSTART=939223;QSTRAND=+;GCPCT=14;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.295836 GT:DP:AD 1|0:24:6,18 ./.:42:17,25 ./.:39:15,24 -chr20 957677 . T TAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=939264;QSTRAND=+;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0.792481 GT:DP:AD 1|0:28:8,20 ./.:13:5,8 ./.:45:22,23 -chr20 958217 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=939805;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:26:21,5 ./.:39:21,18 ./.:21:12,9 -chr20 958300 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=939888;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:32:14,18 ./.:34:11,23 ./.:27:15,12 -chr20 958487 . T A 60 . QNAME=HG002-S9-H1-000001F;QSTART=940075;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:24:9,15 ./.:30:11,19 ./.:36:11,25 -chr20 958518 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=940106;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:42:17,25 ./.:21:11,10 ./.:30:6,24 -chr20 958523 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=940111;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:27:21,6 ./.:25:19,6 ./.:27:17,10 -chr20 958650 . G A 60 . QNAME=cluster23_scaffold_2;QSTART=24734462;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD ./.:46:24,22 ./.:23:7,16 0|1:28:5,23 -chr20 958880 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=940468;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:32:24,8 ./.:29:17,12 ./.:13:7,6 -chr20 959105 . GAGTGTGGTGGTGGGTGTGGGGC G 60 . QNAME=HG002-S9-H1-000001F;QSTART=940694;QSTRAND=+;GCPCT=69;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.650626 GT:DP:AD 1|0:27:14,13 ./.:47:22,25 ./.:39:22,17 -chr20 959171 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=940737;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:16:11,5 ./.:35:22,13 ./.:44:22,22 -chr20 959315 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=940881;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:36:19,17 ./.:35:22,13 ./.:27:8,19 -chr20 959563 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=941129;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:21:11,10 ./.:27:7,20 ./.:34:15,19 -chr20 959871 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=941437;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:48:23,25 ./.:23:14,9 ./.:18:9,9 -chr20 960669 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=942235;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:20:5,15 ./.:30:20,10 ./.:50:25,25 -chr20 960776 . C A 60 . QNAME=HG002-S9-H1-000001F;QSTART=942342;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:33:18,15 ./.:22:5,17 ./.:41:17,24 -chr20 960856 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=942422;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:39:22,17 ./.:42:21,21 ./.:25:5,20 -chr20 961022 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=942588;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:27:9,18 ./.:33:11,22 ./.:31:20,11 -chr20 961081 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=942647;QSTRAND=+;GCPCT=100;GTCNT=0,0,0,3;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:31:21,10 1|1:32:14,18 1|1:37:17,20 -chr20 961455 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=943021;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:29:16,13 ./.:37:15,22 ./.:18:7,11 -chr20 961789 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=943355;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:40:19,21 ./.:30:15,15 ./.:36:20,16 -chr20 961809 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=943375;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:30:18,12 ./.:22:7,15 ./.:15:6,9 -chr20 962027 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=943593;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:10:5,5 ./.:17:7,10 ./.:16:5,11 -chr20 962140 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=943706;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:22:8,14 ./.:20:9,11 ./.:37:20,17 -chr20 962739 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=944305;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:32:8,24 ./.:21:5,16 ./.:24:14,10 -chr20 962818 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=944384;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:41:18,23 ./.:32:25,7 ./.:28:13,15 -chr20 964006 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=945572;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:31:19,12 ./.:35:25,10 ./.:35:19,16 -chr20 964368 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=945934;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:45:23,22 ./.:32:14,18 ./.:43:24,19 -chr20 964461 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=946027;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:28:8,20 ./.:32:17,15 ./.:27:8,19 -chr20 964587 . T G 60 . QNAME=HG002-S9-H1-000001F;QSTART=946153;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:29:24,5 ./.:21:10,11 ./.:37:13,24 -chr20 964681 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=946247;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:26:12,14 ./.:20:11,9 ./.:35:13,22 -chr20 964763 . T TAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=946330;QSTRAND=+;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.792481 GT:DP:AD 1|0:24:11,13 ./.:34:13,21 ./.:22:13,9 -chr20 964805 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=946373;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:25:18,7 ./.:30:16,14 ./.:30:10,20 -chr20 964823 . CACACACACATAT C 60 . QNAME=HG002-S9-H1-000001F;QSTART=946392;QSTRAND=+;GCPCT=38;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.730242 GT:DP:AD 1|0:23:8,15 ./.:24:13,11 ./.:34:9,25 -chr20 964827 . CACACAT C 60 . QNAME=cluster23_scaffold_3;QSTART=24744733;QSTRAND=-;GCPCT=42;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.724408 GT:DP:AD ./.:26:19,7 ./.:23:12,11 1|0:42:24,18 -chr20 964831 . CAT C 60 . QNAME=cluster19_000000F;QSTART=24793282;QSTRAND=-;GCPCT=33;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0.792481 GT:DP:AD ./.:23:17,6 1|1:25:14,11 0|1:25:16,9 -chr20 965654 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=947210;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:38:13,25 ./.:38:15,23 ./.:12:5,7 -chr20 965660 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=947216;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:19:6,13 ./.:37:22,15 ./.:45:20,25 -chr20 965819 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=947375;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:29:11,18 ./.:18:6,12 ./.:35:14,21 -chr20 965855 . G C 60 . QNAME=HG002-S9-H1-000001F;QSTART=947411;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:31:15,16 ./.:31:24,7 ./.:40:22,18 -chr20 966123 . A T 60 . QNAME=HG002-S9-H1-000001F;QSTART=947679;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:17:11,6 ./.:19:7,12 ./.:22:14,8 -chr20 966156 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=947712;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:26:5,21 ./.:34:14,20 ./.:43:22,21 -chr20 966449 . G GTC 60 . QNAME=HG002-S9-H1-000001F;QSTART=948006;QSTRAND=+;GCPCT=66;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.792481 GT:DP:AD 1|0:30:13,17 ./.:33:21,12 ./.:24:5,19 -chr20 966451 . CT C 60 . QNAME=cluster23_scaffold_2;QSTART=24726663;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:45:23,22 ./.:16:6,10 0|1:23:15,8 -chr20 966507 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=948065;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:19:12,7 ./.:12:6,6 ./.:35:12,23 -chr20 966840 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=948398;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:28:10,18 ./.:19:9,10 ./.:47:24,23 -chr20 966858 . AAAACAAGC A 60 . QNAME=HG002-S9-H1-000001F;QSTART=948417;QSTRAND=+;GCPCT=33;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0.612197 GT:DP:AD 1|0:29:9,20 ./.:27:21,6 ./.:30:11,19 -chr20 970054 . TC T 60 . QNAME=cluster23_scaffold_2;QSTART=24723061;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0.5 GT:DP:AD ./.:29:17,12 ./.:24:15,9 0|1:29:16,13 -chr20 971192 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=952742;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:14:8,6 ./.:19:10,9 ./.:38:23,15 -chr20 971309 . A T 60 . QNAME=HG002-S9-H2-000001F;QSTART=927343;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:34:15,19 ./.:18:7,11 ./.:30:9,21 -chr20 971575 . C T 60 . QNAME=HG002-S9-H2-000001F;QSTART=927609;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 0|1:31:12,19 ./.:22:14,8 ./.:39:23,16 -chr20 972263 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=953813;QSTRAND=+;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:28:11,17 ./.:40:18,22 ./.:40:24,16 -chr20 972407 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=953957;QSTRAND=+;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,1,2;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|1:34:24,10 ./.:13:7,6 ./.:33:23,10 -chr20 972507 . G T 60 . QNAME=HG002-S9-H2-000001F;QSTART=928541;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:21:10,11 ./.:14:8,6 ./.:24:5,19 -chr20 972633 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=954183;QSTRAND=+;GCPCT=100;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:28:7,21 ./.:35:15,20 ./.:35:20,15 -chr20 972877 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=954427;QSTRAND=+;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:13:8,5 ./.:29:22,7 ./.:44:22,22 -chr20 972959 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=954509;QSTRAND=+;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|1:22:13,9 ./.:27:10,17 ./.:21:14,7 -chr20 973165 . TGG T 60 . QNAME=cluster23_scaffold_3;QSTART=24736401;QSTRAND=-;GCPCT=66;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.459148 GT:DP:AD ./.:28:11,17 ./.:22:17,5 1|0:32:23,9 -chr20 973459 . A ATTGT 60 . QNAME=cluster19_000000F;QSTART=24784652;QSTRAND=-;GCPCT=20;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.685475 GT:DP:AD ./.:30:8,22 1|0:34:22,12 1|0:40:20,20 -chr20 973459 . ATTGT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=955010;QSTRAND=+;GCPCT=20;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.685475 GT:DP:AD 1|1:22:11,11 ./.:35:17,18 ./.:31:15,16 -chr20 973633 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=955179;QSTRAND=+;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:33:13,20 ./.:27:8,19 ./.:22:8,14 -chr20 974110 . G A 60 . QNAME=HG002-S9-H2-000001F;QSTART=930140;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 0|1:32:11,21 ./.:30:17,13 ./.:43:23,20 -chr20 974769 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=956315;QSTRAND=+;GCPCT=0;GTCNT=2,0,0,1;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|1:31:18,13 ./.:35:20,15 ./.:36:14,22 -chr20 975693 . C G 60 . QNAME=HG002-S9-H1-000001F;QSTART=957239;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:29:11,18 ./.:20:13,7 ./.:45:24,21 -chr20 976042 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=957588;QSTRAND=+;GCPCT=100;GTCNT=1,0,1,1;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|1:47:24,23 ./.:30:12,18 1|0:34:15,19 -chr20 976694 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=958240;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:47:23,24 ./.:20:13,7 ./.:38:14,24 -chr20 977237 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=958783;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:16:9,7 ./.:22:11,11 ./.:22:12,10 -chr20 977764 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=959310;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:20:8,12 ./.:34:24,10 ./.:28:23,5 -chr20 978561 . G T 60 . QNAME=cluster23_scaffold_2;QSTART=24714555;QSTRAND=-;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD ./.:23:18,5 ./.:17:5,12 0|1:32:25,7 -chr20 978696 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=960242;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:33:18,15 ./.:42:18,24 ./.:32:7,25 -chr20 979248 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=960794;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:24:11,13 ./.:31:24,7 ./.:14:6,8 -chr20 980145 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=961691;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:39:16,23 ./.:29:17,12 ./.:36:18,18 -chr20 980577 . T C 60 . QNAME=HG002-S9-H2-000001F;QSTART=936607;QSTRAND=+;GCPCT=0;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 0|1:16:9,7 1|0:26:15,11 ./.:37:19,18 -chr20 980652 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=962198;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:27:14,13 ./.:46:21,25 ./.:26:6,20 -chr20 980884 . A C 60 . QNAME=HG002-S9-H1-000001F;QSTART=962430;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:20:9,11 ./.:32:19,13 ./.:30:10,20 -chr20 981108 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=962654;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:38:17,21 ./.:25:13,12 ./.:23:7,16 -chr20 981138 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=962684;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,1,0;LCR=0 GT:DP:AD 1|0:16:7,9 ./.:34:20,14 ./.:26:20,6 -chr20 984922 . C CCCAT 60 . QNAME=HG002-S9-H1-000001F;QSTART=966469;QSTRAND=+;GCPCT=60;GTCNT=1,0,2,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.685475 GT:DP:AD 1|0:33:12,21 ./.:18:5,13 0|1:34:25,9 -chr20 990421 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=971971;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:32:22,10 ./.:31:15,16 ./.:40:24,16 -chr20 991150 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=972700;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0 GT:DP:AD 1|0:29:19,10 ./.:30:13,17 ./.:29:7,22 -chr20 991319 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=972869;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:26:17,9 ./.:13:7,6 ./.:42:20,22 -chr20 991428 . A AT 60 . QNAME=cluster19_000000F;QSTART=955698;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0.5 GT:DP:AD ./.:24:18,6 0|1:32:21,11 ./.:33:10,23 -chr20 992032 . G GGGAC 60 . QNAME=cluster23_scaffold_3;QSTART=24717528;QSTRAND=-;GCPCT=80;GTCNT=2,0,0,1;DPCNT=0,0,1,2;ADCNT=0,2,0,1;LCR=0.685475 GT:DP:AD ./.:40:15,25 ./.:24:17,7 1|1:10:5,5 -chr20 992091 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=973641;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:39:14,25 ./.:26:21,5 ./.:31:8,23 -chr20 992263 . C CT 60 . QNAME=cluster23_scaffold_3;QSTART=24717296;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,1,2;LCR=0.5 GT:DP:AD ./.:44:21,23 ./.:22:11,11 1|0:34:9,25 -chr20 992288 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=973838;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:29:6,23 ./.:34:15,19 ./.:35:14,21 -chr20 992532 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=974082;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:26:20,6 ./.:31:15,16 ./.:40:21,19 -chr20 992797 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=974347;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,2,0;LCR=0 GT:DP:AD 1|0:18:8,10 ./.:32:22,10 ./.:25:19,6 -chr20 993026 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=974576;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:26:16,10 ./.:30:22,8 ./.:36:18,18 -chr20 993059 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=974609;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:29:9,20 ./.:29:12,17 ./.:34:14,20 -chr20 993443 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=974993;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0 GT:DP:AD 1|0:26:17,9 ./.:31:16,15 ./.:27:21,6 -chr20 993795 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=975345;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:41:24,17 ./.:36:19,17 ./.:40:20,20 -chr20 993846 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=975396;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:41:16,25 ./.:40:19,21 ./.:32:25,7 -chr20 993854 . G A 60 . QNAME=HG002-S9-H1-000001F;QSTART=975404;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0 GT:DP:AD 1|0:29:13,16 ./.:32:15,17 ./.:41:24,17 -chr20 993856 . G T 60 . QNAME=HG002-S9-H1-000001F;QSTART=975406;QSTRAND=+;GCPCT=100;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,0,2;LCR=0 GT:DP:AD 1|0:22:6,16 ./.:20:14,6 ./.:24:5,19 -chr20 994379 . C T 60 . QNAME=HG002-S9-H1-000001F;QSTART=975929;QSTRAND=+;GCPCT=100;GTCNT=0,0,1,2;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|1:48:23,25 1|0:31:21,10 1|1:19:8,11 -chr20 994584 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=976134;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:32:25,7 ./.:19:6,13 ./.:30:7,23 -chr20 994605 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=976155;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:40:16,24 ./.:35:22,13 ./.:17:5,12 -chr20 995547 . GA G 60 . QNAME=cluster23_scaffold_2;QSTART=24697561;QSTRAND=-;GCPCT=50;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0.5 GT:DP:AD ./.:31:20,11 ./.:21:9,12 0|1:37:22,15 -chr20 996521 . A G 60 . QNAME=HG002-S9-H1-000001F;QSTART=978071;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,1,1,1;LCR=0 GT:DP:AD 1|0:17:10,7 ./.:39:24,15 ./.:26:14,12 -chr20 999077 . T C 60 . QNAME=HG002-S9-H1-000001F;QSTART=980627;QSTRAND=+;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,0,2,1;LCR=0 GT:DP:AD 1|0:19:8,11 ./.:27:14,13 ./.:40:16,24 -chr20 280211 . CAACAACAACAATTGTACTTCCCTAAGGTTACACCCAGCAGGTGCATAAAACCTACAGTAACAAT C 60 . QNAME=cluster23_scaffold_3;QSTART=25431380;QSTRAND=-;SVTYPE=DEL;SVLEN=64;HOMPCT=3.3;REMAP=tandem;REMAPHits=chr20:280274-280339.100,chr20:280338-280403.100;GCPCT=40;GTCNT=2,0,1,0;NumNeighbors=0;NeighId=2;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.939062 GT:DP:AD ./.:42:24,18 ./.:45:20,25 1/0:39:24,15 -chr20 380878 . TGATTAGCTCCGGTTTGCATCACCCGGACCGGGG T 60 . QNAME=cluster23_scaffold_3;QSTART=25330580;QSTRAND=-;SVTYPE=DEL;SVLEN=-33;GCPCT=61;GTCNT=2,0,1,0;DPCNT=0,0,1,2;ADCNT=0,3,0,0;LCR=0.971927 GT:DP:AD ./.:13:5,8 ./.:24:18,6 1/0:18:13,5 -chr20 485088 . AAAAAAAAAAAAAAAAAAAAAAATATATATATAT A 60 . QNAME=HG002-S9-H1-000001F;QSTART=464662;QSTRAND=+;SVTYPE=DEL;SVLEN=-33;GCPCT=0;GTCNT=2,0,1,0;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.336147 GT:DP:AD 1/0:26:11,15 ./.:21:12,9 ./.:20:14,6 -chr20 613783 . TGTGTGCTGAGTCCAGCTCAAGTCCCTTGGTTCCCACTGCTGCTAAGCATGCACG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=593293;QSTRAND=+;SVTYPE=DEL;SVLEN=54;HOMPCT=29.3;REMAP=novel;GCPCT=56;GTCNT=0,0,1,2;NumNeighbors=0;NeighId=6;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.982293 GT:DP:AD 1/1:46:24,22 1/0:29:14,15 1/1:43:19,24 -chr20 709759 . AGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCC A 60 . QNAME=HG002-S9-H2-000001F;QSTART=664783;QSTRAND=+;SVTYPE=DEL;SVLEN=93;HOMPCT=19.4;REMAP=tandem;REMAPHits=chr20:709851-709945.100;GCPCT=67;GTCNT=0,0,2,1;NumNeighbors=1;NeighId=8;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.944193 GT:DP:AD 0/1:16:7,9 1/0:26:21,5 1/1:41:23,18 -chr20 727508 . . . . END=727540;SEGCNT=2 GT:SEG 0/0:0 1/1:2 0/0:0 -chr20 727541 . . . . END=727555;SEGCNT=1 GT:SEG 0/0:0 0/1:1 0/0:0 -chr20 727556 . . . . END=727556;SEGCNT=2 GT:SEG 0/1:1 0/1:1 0/1:1 -chr20 727557 . . . . END=727590;SEGCNT=1 GT:SEG 0/1:1 0/0:0 0/1:1 -chr20 751473 . CTTTATTTTATTTTATTTTATTTTAT C 60 . QNAME=HG002-S9-H2-000001F;QSTART=706369;QSTRAND=+;SVTYPE=DEL;SVLEN=-25;GCPCT=3;GTCNT=0,0,3,0;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.464678 GT:DP:AD 0/1:34:11,23 1/0:35:12,23 0/1:35:13,22 -chr20 800494 . TCGATTACCTGCTCCACCCTGACTCACTC T 60 . QNAME=HG002-S9-H2-000001F;QSTART=755521;QSTRAND=+;SVTYPE=DEL;SVLEN=-28;GCPCT=55;GTCNT=0,0,2,1;DPCNT=0,0,0,3;ADCNT=0,2,0,1;LCR=0.903641 GT:DP:AD 0/1:22:7,15 1/0:22:13,9 1/1:29:24,5 -chr20 949516 . CTCTGAAGAGGTAACATTTGAACTGAGATGTAGAGGGAGAGAAGGAACTAGCCATGTGGAGATCTGGGGGAGGAGCATTCCAGGCAGAGGGGATAGCAAGTGCA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=905663;QSTRAND=+;SVTYPE=DEL;SVLEN=103;HOMPCT=5.3;REMAP=tandem;REMAPHits=chr20:949618-949722.100;GCPCT=50;GTCNT=1,0,2,0;NumNeighbors=0;NeighId=10;DPCNT=0,0,0,3;ADCNT=0,0,0,3;LCR=0.941771 GT:DP:AD 0/1:29:9,20 ./.:28:7,21 1/0:34:12,22 diff --git a/repo_utils/test_files/answer_key/single_vcf2df.jl b/repo_utils/test_files/answer_key/single_vcf2df.jl deleted file mode 100644 index 5a47e42c..00000000 Binary files a/repo_utils/test_files/answer_key/single_vcf2df.jl and /dev/null differ diff --git a/repo_utils/test_files/answer_key/subset_vcf2df.jl b/repo_utils/test_files/answer_key/subset_vcf2df.jl deleted file mode 100644 index a3658241..00000000 Binary files a/repo_utils/test_files/answer_key/subset_vcf2df.jl and /dev/null differ diff --git a/repo_utils/test_files/answer_key/truv2df.jl b/repo_utils/test_files/answer_key/truv2df.jl deleted file mode 100644 index b50be6aa..00000000 Binary files a/repo_utils/test_files/answer_key/truv2df.jl and /dev/null differ diff --git a/repo_utils/test_files/answer_key/vcf2df.jl b/repo_utils/test_files/answer_key/vcf2df.jl deleted file mode 100644 index 97457c71..00000000 Binary files a/repo_utils/test_files/answer_key/vcf2df.jl and /dev/null differ diff --git a/repo_utils/test_files/answer_key/vcf2df_bare.jl b/repo_utils/test_files/answer_key/vcf2df_bare.jl deleted file mode 100644 index 2a098931..00000000 Binary files a/repo_utils/test_files/answer_key/vcf2df_bare.jl and /dev/null differ diff --git a/repo_utils/test_files/genome.bed b/repo_utils/test_files/beds/genome.bed similarity index 100% rename from repo_utils/test_files/genome.bed rename to repo_utils/test_files/beds/genome.bed diff --git a/repo_utils/test_files/giab.bed b/repo_utils/test_files/beds/giab.bed similarity index 100% rename from repo_utils/test_files/giab.bed rename to repo_utils/test_files/beds/giab.bed diff --git a/repo_utils/test_files/include.bed b/repo_utils/test_files/beds/include.bed similarity index 100% rename from repo_utils/test_files/include.bed rename to repo_utils/test_files/beds/include.bed diff --git a/repo_utils/test_files/mask.bed b/repo_utils/test_files/beds/mask.bed similarity index 100% rename from repo_utils/test_files/mask.bed rename to repo_utils/test_files/beds/mask.bed diff --git a/repo_utils/test_files/repeats.adotto.bed.gz b/repo_utils/test_files/beds/repeats.adotto.bed.gz similarity index 100% rename from repo_utils/test_files/repeats.adotto.bed.gz rename to repo_utils/test_files/beds/repeats.adotto.bed.gz diff --git a/repo_utils/test_files/repeats.adotto.bed.gz.tbi b/repo_utils/test_files/beds/repeats.adotto.bed.gz.tbi similarity index 100% rename from repo_utils/test_files/repeats.adotto.bed.gz.tbi rename to repo_utils/test_files/beds/repeats.adotto.bed.gz.tbi diff --git a/repo_utils/test_files/simplerepeat.bed.gz b/repo_utils/test_files/beds/simplerepeat.bed.gz similarity index 100% rename from repo_utils/test_files/simplerepeat.bed.gz rename to repo_utils/test_files/beds/simplerepeat.bed.gz diff --git a/repo_utils/test_files/simplerepeat.bed.gz.tbi b/repo_utils/test_files/beds/simplerepeat.bed.gz.tbi similarity index 100% rename from repo_utils/test_files/simplerepeat.bed.gz.tbi rename to repo_utils/test_files/beds/simplerepeat.bed.gz.tbi diff --git a/repo_utils/test_files/external/fake_mafft/README.md b/repo_utils/test_files/external/fake_mafft/README.md new file mode 100644 index 00000000..ef43558c --- /dev/null +++ b/repo_utils/test_files/external/fake_mafft/README.md @@ -0,0 +1,16 @@ +Fake MAFFT + +We need to run MAFFT from inside of truvari when doing functional tests. However, MAFFT is a larger executable and isn't +that easy to install, especially on the instances that the github actions run on. Therefore, we have a fake mafft. + +This works by saving real mafft results and using this fake mafft to simply lookup what the correct result should be. + +Build the results by first soft-linking the directory where the phab results sit with `ln -s` + +Next, run `python make_fake_mafft_results.py soft-link-dir/haps.fa soft-link-dir/*/haps.fa > mafft_results.json` + +This script will warn you when there are conflicting hashes. I assume that's okay because identical inputs make +identical outputs? + +Also, be sure in the ssshtest to update the $PATH to point to this directory so that `mafft` is found in the +environment. See `sub_tests/phab.sh` for an example diff --git a/repo_utils/test_files/external/fake_mafft/mafft b/repo_utils/test_files/external/fake_mafft/mafft new file mode 100755 index 00000000..004e1d31 --- /dev/null +++ b/repo_utils/test_files/external/fake_mafft/mafft @@ -0,0 +1,19 @@ +#!/usr/bin/env python3 +""" +Given a haps.fa, return the pre-computed result +""" +import os +import sys +import json +import hashlib + +fn = sys.argv[-1] +sys.stderr.write(f"Running fake MAFFT for {fn}\n") +m_dir = os.path.dirname(os.path.realpath(__file__)) + +lookup = json.load(open(os.path.join(m_dir, "mafft_results.json"), 'r')) +with open(fn, 'r') as fh: + data = fh.read() + m_key = hashlib.md5(data.encode('utf-8')).hexdigest() + with open(os.path.join(m_dir, lookup[m_key])) as result: + sys.stdout.write(result.read()) diff --git a/repo_utils/test_files/external/fake_mafft/mafft_results.json b/repo_utils/test_files/external/fake_mafft/mafft_results.json new file mode 100644 index 00000000..d1dad6f2 --- /dev/null +++ b/repo_utils/test_files/external/fake_mafft/mafft_results.json @@ -0,0 +1,119 @@ +{ + "0c324d099b6bbbaebedd3244acebe3ee": "refine_one_phab/chr20/chr20:10802676-10802959/msa.fa", + "a786f724af1583217c6c458ac2d0ac4b": "refine_one_phab/chr20/chr20:13848164-13848650/msa.fa", + "ff5942434f750f1959c376b0d249b35f": "refine_one_phab/chr20/chr20:14861937-14862742/msa.fa", + "90e3ace57204decd3e0d3503745a417a": "refine_one_phab/chr20/chr20:16257741-16259346/msa.fa", + "7788e52f913d41b7489017d4d8e2c3b0": "refine_one_phab/chr20/chr20:16395149-16395422/msa.fa", + "77388cae5e8caad9c71ff5210d07e734": "refine_one_phab/chr20/chr20:17081216-17081411/msa.fa", + "f1d0ee7ba962f120b7e239257cb4ad8e": "refine_one_phab/chr20/chr20:18209097-18210728/msa.fa", + "e8cf782f81ea7c68ffef18b6814efa9e": "refine_one_phab/chr20/chr20:20295955-20296566/msa.fa", + "46abaf0008b6dd141ec02666d4c2b0df": "refine_one_phab/chr20/chr20:20320285-20320580/msa.fa", + "114204996ccda7f9bf8f68f25dea2652": 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"refine_one_phab/chr20/chr20:60702942-60703116/msa.fa", + "f7a512fa3890273ced4a77611a8d32bb": "refine_one_phab/chr20/chr20:61100792-61102688/msa.fa", + "da5e0b77d1ed49ea8309e1bbbdea6f61": "refine_one_phab/chr20/chr20:61201683-61202475/msa.fa", + "c4695c9cfc32cec191b00b15864ef2d4": "refine_one_phab/chr20/chr20:61282506-61283670/msa.fa", + "8a27078d4113f18347c233dc20a848db": "refine_one_phab/chr20/chr20:61289625-61290556/msa.fa", + "f7edc77024e3e604256ceafb3f720f41": "refine_one_phab/chr20/chr20:61329258-61329578/msa.fa", + "7b261998207e7bfca0411a5cc48c06f0": "refine_one_phab/chr20/chr20:61561920-61562504/msa.fa", + "81ed053972afef5ed9022d9565f5b2f1": "refine_one_phab/chr20/chr20:61744188-61744655/msa.fa", + "515566a42940386464abce5d9e289a98": "refine_one_phab/chr20/chr20:61783403-61784840/msa.fa", + "0ebf29fe2e2878d4d8b3a2022ef143f1": "refine_one_phab/chr20/chr20:62057573-62059140/msa.fa", + "f1a90d739c54b49478b5e75f6fcb7881": "refine_one_phab/chr20/chr20:62270279-62271095/msa.fa", + "fd096c1b07d012723194c19a877ce386": "refine_one_phab/chr20/chr20:62321031-62321874/msa.fa", + "c44b360a612e0004948f55d93e063e00": "refine_one_phab/chr20/chr20:62349612-62349933/msa.fa", + "3fb2d59f7fbe1514688c43ac01f6e82b": "refine_one_phab/chr20/chr20:62360190-62360713/msa.fa", + "81de1c36504a00bf3e43b22c5042eb5b": "refine_one_phab/chr20/chr20:62830612-62830839/msa.fa", + "7afd9c13b752540983d647b56921e289": "refine_one_phab/chr20/chr20:62875172-62875557/msa.fa", + "cbdce4fa12b4b4224a11c7b9c408bb50": "refine_one_phab/chr20/chr20:63027997-63028167/msa.fa", + "7c2f0be366f5c0c70297e2e75bcbb4e4": "refine_one_phab/chr20/chr20:63028876-63029403/msa.fa", + "d793bca1fbf461fbea52f51840a029c6": "refine_one_phab/chr20/chr20:63049033-63049413/msa.fa", + "80d0fcb456c951b9f9eed09ed235affe": "refine_one_phab/chr20/chr20:63154585-63154996/msa.fa", + "314209c4d123e4c8e37dfa9171930c1b": "refine_one_phab/chr20/chr20:63167387-63167628/msa.fa", + "9dcb83424ac6184926ca764fa6864076": "refine_one_phab/chr20/chr20:63221480-63221877/msa.fa", + "66aeb67e26ee17ecb43d33f616ef18ca": "refine_one_phab/chr20/chr20:63372065-63372692/msa.fa", + "335b0f33a27821052ad5caa94dfa77b9": "refine_one_phab/chr20/chr20:63491589-63493065/msa.fa", + "34ed4b6453b4ba3d8dc34c0d77015d07": "refine_one_phab/chr20/chr20:63535674-63536246/msa.fa", + "d74a5acf914ab7f368aee53949bfdab9": "refine_one_phab/chr20/chr20:63559288-63559964/msa.fa", + "602523ace10eb9e663de79161f074eea": "refine_one_phab/chr20/chr20:63641779-63642136/msa.fa", + "7cd1a765772e934481c122e6c70f09b2": "refine_one_phab/chr20/chr20:63693325-63693885/msa.fa", + "f59bcbbb93b16c07f150882eab2a5a9f": "refine_one_phab/chr20/chr20:63770912-63771104/msa.fa", + "821523a281910ed130dc26d42503968d": "refine_one_phab/chr20/chr20:63948514-63948759/msa.fa", + "1e76ffe1144287008ec813aec2546cdb": "refine_one_phab/chr20/chr20:63964768-63966618/msa.fa", + "9c7871e02d933fa8577fda2df6ec6c44": "refine_one_phab/chr20/chr20:64065853-64066012/msa.fa", + "f772de66e4bcb9af0e00918ce758551e": "refine_one_phab/chr20/chr20:64090704-64091390/msa.fa", + "c245559b8963ad350a10faff14a0a012": "refine_one_phab/chr20/chr20:64096658-64097165/msa.fa", + "52541a8c6ad3133277412bd94ae60ddd": "refine_one_phab/chr20/chr20:64125109-64127975/msa.fa", + "4450be8758f6a58b7e7084105efa10f3": "refine_one_phab/chr20/chr20:64131804-64133956/msa.fa", + "6cd8a9aa3cbf1a8d1f4af866232b3b44": "refine_one_phab/chr20/chr20:64134883-64136387/msa.fa", + "da360a3ec5873ee9925aae684303093f": "refine_one_phab/chr20/chr20:64173409-64176530/msa.fa", + "a65af3043c9451f2dc9fcb414a028b3d": "refine_one_phab/chr20/chr20:641836-642466/msa.fa", + "45b9a2c9d345477119fa4a18c9d9a664": "refine_one_phab/chr20/chr20:7720911-7721004/msa.fa", + "03e4723c466b5d947c9c1c84685d1750": "refine_one_phab/chr20/chr20:8661911-8662658/msa.fa", + "b5ac581b010dfd3269e90a3b6b2e193a": "refine_two_phab/chr20/chr20:14861937-14862742/msa.fa", + "34ee13de078509716ec62820191f8b95": "refine_two_phab/chr20/chr20:18209097-18210728/msa.fa", + "1eee3b6410b0f3e1f2338008f3cb1122": "refine_two_phab/chr20/chr20:20337200-20337708/msa.fa", + "b2ded5ac5cabc1c24a380cde15fc6c11": "refine_two_phab/chr20/chr20:20354570-20358324/msa.fa", + "dcb755c7b841ad9d485646ec920f2743": "refine_two_phab/chr20/chr20:23155504-23155976/msa.fa", + "64d17983536ea90f05ff3ad119dcb18c": "refine_two_phab/chr20/chr20:34235750-34236214/msa.fa", + "f3821391d3081b9b186492bd722b56e0": "refine_two_phab/chr20/chr20:38123590-38124706/msa.fa", + "58befa14d4fe1b3aa5696d486ef8edf0": "refine_two_phab/chr20/chr20:4032219-4033602/msa.fa", + "9eccab6d5dd45aa77f04015d3ce2f2e3": "refine_two_phab/chr20/chr20:53203987-53204474/msa.fa", + "104c122bbe4361465eff126ac485e143": "refine_two_phab/chr20/chr20:55943919-55945808/msa.fa", + "52ec6b6a0642d0784fe70ad1f1b9fb16": "refine_two_phab/chr20/chr20:61201683-61202475/msa.fa", + "dc3fc9adaf2ea03bdf8d55cdb16f5031": "refine_two_phab/chr20/chr20:62057573-62059140/msa.fa", + "e2cb5c913c1deb97fc9d0674d02aa194": "refine_two_phab/chr20/chr20:62270279-62271095/msa.fa", + "606ea3e12198492bcb24c42995206ad8": "refine_two_phab/chr20/chr20:62349612-62349933/msa.fa", + "af5fc900d58a70d9ff398c942c02b276": "refine_two_phab/chr20/chr20:62830612-62830839/msa.fa", + "04db71097a2baf4e35e7511288534684": "refine_two_phab/chr20/chr20:63221480-63221877/msa.fa", + "fb800f2b74ceb8e734172c6de1ae4b4b": "refine_two_phab/chr20/chr20:63491589-63493065/msa.fa", + "c5e1ea5977dd5224b7e17fecb017e1bd": "refine_two_phab/chr20/chr20:63559288-63559964/msa.fa", + "7d7a4ed46ee8796ed3e16d1cfef80e62": "refine_two_phab/chr20/chr20:63641779-63642136/msa.fa", + "4a4a0041c5eefc0bd95758a87e07623b": "refine_two_phab/chr20/chr20:63693325-63693885/msa.fa", + "cacbbdea4bf84054d5f182d3b0700ea9": "refine_two_phab/chr20/chr20:63948514-63948759/msa.fa", + "d5c023b1e77aeac4cd8a84ffc45ae0d6": "refine_two_phab/chr20/chr20:64131804-64133956/msa.fa", + "c09462de46ef1aa5acc040b619c20faf": "refine_two_phab/chr20/chr20:64173409-64176530/msa.fa", + "a055a0c364384c91f3276758fda2c9f9": "refine_two_phab/chr20/chr20:8661911-8662658/msa.fa", + "a91902c4fe6511f5d004ae3cac6ad878": "phab_result/msa.fa" +} diff --git a/repo_utils/test_files/external/fake_mafft/make_fake_mafft_results.py b/repo_utils/test_files/external/fake_mafft/make_fake_mafft_results.py new file mode 100644 index 00000000..2d799e0c --- /dev/null +++ b/repo_utils/test_files/external/fake_mafft/make_fake_mafft_results.py @@ -0,0 +1,25 @@ +""" +Makes a lookup from a haps.fa to the msa.fa output + +This allows us to 'save' the mafft results and fake its functionality +""" +import os +import sys +import glob +import json +import hashlib +# Provide all the haps files +all_haps = sys.argv[1:] + +lookup = {} +for haps in all_haps: + # For every haps.fa, read it in, get a hash key, save hash key to file's msa.fa + with open(haps, 'r') as fh: + data = fh.read() + m_key = hashlib.md5(data.encode('utf-8')).hexdigest() + if m_key in lookup: + sys.stderr.write("!!WARN!! Conflicting key %s on %s with %s\n" % (m_key, haps, lookup[m_key])) + lookup[m_key] = os.path.join(os.path.dirname(haps), 'msa.fa') + +print(json.dumps(lookup, indent=4)) + diff --git a/repo_utils/test_files/external/fake_mafft/phab_result b/repo_utils/test_files/external/fake_mafft/phab_result new file mode 120000 index 00000000..4add0002 --- /dev/null +++ b/repo_utils/test_files/external/fake_mafft/phab_result @@ -0,0 +1 @@ +../../../answer_key/phab/phab_result/ \ No newline at end of file diff --git a/repo_utils/test_files/external/fake_mafft/refine_one_phab b/repo_utils/test_files/external/fake_mafft/refine_one_phab new file mode 120000 index 00000000..86e02578 --- /dev/null +++ b/repo_utils/test_files/external/fake_mafft/refine_one_phab @@ -0,0 +1 @@ +../../../answer_key/refine/refine_output_one/phab \ No newline at end of file diff --git a/repo_utils/test_files/external/fake_mafft/refine_two_phab b/repo_utils/test_files/external/fake_mafft/refine_two_phab new file mode 120000 index 00000000..d02151a9 --- /dev/null +++ b/repo_utils/test_files/external/fake_mafft/refine_two_phab @@ -0,0 +1 @@ +../../../answer_key/refine/refine_output_two/phab \ No newline at end of file diff --git a/repo_utils/test_files/anno.gtf.gz b/repo_utils/test_files/misc/anno.gtf.gz similarity index 100% rename from repo_utils/test_files/anno.gtf.gz rename to repo_utils/test_files/misc/anno.gtf.gz diff --git a/repo_utils/test_files/grpaf.labels.txt b/repo_utils/test_files/misc/grpaf.labels.txt similarity index 100% rename from repo_utils/test_files/grpaf.labels.txt rename to repo_utils/test_files/misc/grpaf.labels.txt diff --git a/repo_utils/test_files/phab_ref.fa b/repo_utils/test_files/references/phab_ref.fa similarity index 100% rename from repo_utils/test_files/phab_ref.fa rename to repo_utils/test_files/references/phab_ref.fa diff --git a/repo_utils/test_files/phab_ref.fa.fai b/repo_utils/test_files/references/phab_ref.fa.fai similarity index 100% rename from repo_utils/test_files/phab_ref.fa.fai rename to repo_utils/test_files/references/phab_ref.fa.fai diff --git a/repo_utils/test_files/reference.fa b/repo_utils/test_files/references/reference.fa similarity index 100% rename from repo_utils/test_files/reference.fa rename to repo_utils/test_files/references/reference.fa diff --git a/repo_utils/test_files/reference.fa.amb b/repo_utils/test_files/references/reference.fa.amb similarity index 100% rename from repo_utils/test_files/reference.fa.amb rename to repo_utils/test_files/references/reference.fa.amb diff --git a/repo_utils/test_files/reference.fa.ann b/repo_utils/test_files/references/reference.fa.ann similarity index 100% rename from repo_utils/test_files/reference.fa.ann rename to repo_utils/test_files/references/reference.fa.ann diff --git a/repo_utils/test_files/reference.fa.bwt b/repo_utils/test_files/references/reference.fa.bwt similarity index 100% rename from repo_utils/test_files/reference.fa.bwt rename to repo_utils/test_files/references/reference.fa.bwt diff --git a/repo_utils/test_files/reference.fa.fai b/repo_utils/test_files/references/reference.fa.fai similarity index 100% rename from repo_utils/test_files/reference.fa.fai rename to repo_utils/test_files/references/reference.fa.fai diff --git a/repo_utils/test_files/reference.fa.pac b/repo_utils/test_files/references/reference.fa.pac similarity index 100% rename from repo_utils/test_files/reference.fa.pac rename to repo_utils/test_files/references/reference.fa.pac diff --git a/repo_utils/test_files/reference.fa.sa b/repo_utils/test_files/references/reference.fa.sa similarity index 100% rename from repo_utils/test_files/reference.fa.sa rename to repo_utils/test_files/references/reference.fa.sa diff --git a/repo_utils/test_files/refine_data/chr20.fa.gz b/repo_utils/test_files/refine_data/chr20.fa.gz new file mode 100644 index 00000000..852a34d2 Binary files /dev/null and b/repo_utils/test_files/refine_data/chr20.fa.gz differ diff --git a/repo_utils/test_files/refine_data/chr20.fa.gz.fai b/repo_utils/test_files/refine_data/chr20.fa.gz.fai new file mode 100644 index 00000000..53f6a504 --- /dev/null +++ b/repo_utils/test_files/refine_data/chr20.fa.gz.fai @@ -0,0 +1 @@ +chr20 64444167 7 60 61 diff --git a/repo_utils/test_files/refine_data/chr20.fa.gz.gzi b/repo_utils/test_files/refine_data/chr20.fa.gz.gzi new file mode 100644 index 00000000..011f7880 Binary files /dev/null and b/repo_utils/test_files/refine_data/chr20.fa.gz.gzi differ diff --git a/repo_utils/test_files/refine_data/h1_hc_tr_hg002.bed b/repo_utils/test_files/refine_data/h1_hc_tr_hg002.bed new file mode 100644 index 00000000..035abe96 --- /dev/null +++ b/repo_utils/test_files/refine_data/h1_hc_tr_hg002.bed @@ -0,0 +1,225 @@ +chr20 278900 279186 [{"chrom": "chr20", "start": 278904, "end": 279155, "period": 20.0, "copies": 13.1, "score": 428, "entropy": 1.3, "repeat": "AGGGAGGGAGGGCGGGACGG"}, {"chrom": "chr20", "start": 278905, "end": 279154, "period": 8.0, "copies": 31.6, "score": 316, "entropy": 1.29, "repeat": "GGCGGGAG"}] +chr20 420555 420770 [{"chrom": "chr20", "start": 420590, "end": 420733, "period": 5.0, "copies": 27.4, "score": 43, "entropy": 1.4, "repeat": "CCTCC"}, {"chrom": "chr20", "start": 420610, "end": 420621, "period": 6.0, "copies": 2.0, "score": 36, "entropy": 1.25, "repeat": "CCACCT"}, {"chrom": "chr20", "start": 420665, "end": 420739, "period": 7.0, "copies": 11.1, "score": 164, "entropy": 1.12, "repeat": "CCCATCC"}, {"chrom": "chr20", "start": 420665, "end": 420739, "period": 20.0, "copies": 3.7, "score": 165, "entropy": 1.12, "repeat": "CCCATCCCCCACCCCCACC"}] +chr20 641836 642465 [{"chrom": "chr20", "start": 641854, "end": 641859, "period": 1.0, "copies": 6.0, "score": 18, "entropy": 0.0, "repeat": "C"}, {"chrom": "chr20", "start": 641866, "end": 642434, "period": 33.0, "copies": 18.0, "score": 1404, "entropy": 1.55, "repeat": "GTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGA"}, {"chrom": "chr20", "start": 641866, "end": 642434, "period": 193.0, "copies": 3.0, "score": 1529, "entropy": 1.55, "repeat": "GTTGCCTGTGGAGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGA"}, {"chrom": "chr20", "start": 641866, "end": 642434, "period": 63.0, "copies": 9.0, "score": 1375, "entropy": 1.55, "repeat": "GTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGA"}, {"chrom": "chr20", "start": 641878, "end": 641882, "period": 1.0, "copies": 5.0, "score": 15, "entropy": 0.0, "repeat": "G"}, {"chrom": "chr20", "start": 641905, "end": 641914, "period": 1.0, "copies": +chr20 709729 709975 [{"chrom": "chr20", "start": 709759, "end": 709944, "period": 93.0, "copies": 2.0, "score": 548, "entropy": 1.86, "repeat": "GTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCC"}, {"chrom": "chr20", "start": 709808, "end": 709829, "period": 1.0, "copies": 22.0, "score": 26, "entropy": 0.87, "repeat": "G"}, {"chrom": "chr20", "start": 709901, "end": 709922, "period": 1.0, "copies": 22.0, "score": 26, "entropy": 0.87, "repeat": "G"}, {"chrom": "chr20", "start": 709935, "end": 709949, "period": 5.0, "copies": 3.0, "score": 35, "entropy": 1.05, "repeat": "CCTCC"}, {"chrom": "chr20", "start": 709935, "end": 709957, "period": 10.0, "copies": 2.3, "score": 52, "entropy": 1.19, "repeat": "CCTCCGCCCG"}] +chr20 1149807 1150220 [{"chrom": "chr20", "start": 1149837, "end": 1150161, "period": 155.0, "copies": 2.1, "score": 955, "entropy": 1.98, "repeat": "CCAGCCTGGGCAACATGGTGAAACTCTGTCTCTATAAATTAGCTGGATGTGGTGGCGTGACCCTGGAGTCCCAACTACTTGAGAGGCTGAGGTGGGAGGATTGCTTGAGCCCAGGAGGTGGAGGTTGTGGTGAGCCATGATCACACCACTGTACT"}, {"chrom": "chr20", "start": 1149950, "end": 1149968, "period": 6.0, "copies": 3.2, "score": 37, "entropy": 1.27, "repeat": "GGAGGT"}, {"chrom": "chr20", "start": 1150040, "end": 1150048, "period": 3.0, "copies": 3.0, "score": 27, "entropy": 0.92, "repeat": "GTG"}, {"chrom": "chr20", "start": 1150105, "end": 1150123, "period": 6.0, "copies": 3.2, "score": 37, "entropy": 1.27, "repeat": "GGAGGT"}, {"chrom": "chr20", "start": 1150179, "end": 1150194, "period": 1.0, "copies": 16.0, "score": 48, "entropy": 0.0, "repeat": "A"}] +chr20 1257933 1260528 [{"chrom": "chr20", "start": 1258009, "end": 1258038, "period": 14.0, "copies": 2.2, "score": 60, "entropy": 1.09, "repeat": "TTTTCTCTTTTG"}, {"chrom": "chr20", "start": 1258009, "end": 1258038, "period": 7.0, "copies": 4.4, "score": 53, "entropy": 1.09, "repeat": "TTTTCTG"}, {"chrom": "chr20", "start": 1258009, "end": 1258038, "period": 13.0, "copies": 2.1, "score": 76, "entropy": 1.09, "repeat": "TTTTCTGCTTTCTGT"}, {"chrom": "chr20", "start": 1258036, "end": 1258051, "period": 5.0, "copies": 3.4, "score": 41, "entropy": 1.2, "repeat": "TTTCA"}, {"chrom": "chr20", "start": 1258065, "end": 1258075, "period": 3.0, "copies": 3.7, "score": 33, "entropy": 0.85, "repeat": "TTA"}, {"chrom": 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20.7, "score": 5532, "entropy": 1.86, "repeat": "CTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACC"}, {"chrom": "chr20", "start": 64131834, "end": 64133924, "period": 135.0, "copies": 15.5, "score": 5552, "entropy": 1.86, "repeat": "CTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGTCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTATAGAGACCCCCTCACTGTCCACCCTCATGGCCTGTAGAGACCCCCTCACTGTCCACC"}] +chr20 64134883 64136386 [{"chrom": "chr20", "start": 64134913, "end": 64136355, "period": 33.0, "copies": 44.9, "score": 3057, "entropy": 1.93, "repeat": "GTGCATCACAAACACACACGCTCCCTCAGTTTT"}, {"chrom": "chr20", "start": 64134913, "end": 64136355, "period": 95.0, "copies": 15.0, "score": 2865, "entropy": 1.93, "repeat": "GTGCATACAACACACACGCTCCCTCAGTTTTGTGCGTCACAAACACACACGCTCCCTCAGTTTTGTGCATCACAAACACACACGCTCCCTCAGTTTT"}, {"chrom": "chr20", "start": 64134919, "end": 64134931, "period": 2.0, "copies": 6.5, "score": 29, "entropy": 1.0, "repeat": "CA"}, {"chrom": "chr20", 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a/repo_utils/test_files/phab_base.vcf.gz b/repo_utils/test_files/variants/phab_base.vcf.gz similarity index 100% rename from repo_utils/test_files/phab_base.vcf.gz rename to repo_utils/test_files/variants/phab_base.vcf.gz diff --git a/repo_utils/test_files/phab_base.vcf.gz.tbi b/repo_utils/test_files/variants/phab_base.vcf.gz.tbi similarity index 100% rename from repo_utils/test_files/phab_base.vcf.gz.tbi rename to repo_utils/test_files/variants/phab_base.vcf.gz.tbi diff --git a/repo_utils/test_files/phab_comp.vcf.gz b/repo_utils/test_files/variants/phab_comp.vcf.gz similarity index 100% rename from repo_utils/test_files/phab_comp.vcf.gz rename to repo_utils/test_files/variants/phab_comp.vcf.gz diff --git a/repo_utils/test_files/phab_comp.vcf.gz.tbi b/repo_utils/test_files/variants/phab_comp.vcf.gz.tbi similarity index 100% rename from repo_utils/test_files/phab_comp.vcf.gz.tbi rename to repo_utils/test_files/variants/phab_comp.vcf.gz.tbi diff --git a/repo_utils/test_files/real_small_base.vcf.gz b/repo_utils/test_files/variants/real_small_base.vcf.gz similarity index 100% rename from repo_utils/test_files/real_small_base.vcf.gz rename to repo_utils/test_files/variants/real_small_base.vcf.gz diff --git a/repo_utils/test_files/real_small_base.vcf.gz.tbi b/repo_utils/test_files/variants/real_small_base.vcf.gz.tbi similarity index 100% rename from repo_utils/test_files/real_small_base.vcf.gz.tbi rename to repo_utils/test_files/variants/real_small_base.vcf.gz.tbi diff --git a/repo_utils/test_files/real_small_comp.vcf.gz b/repo_utils/test_files/variants/real_small_comp.vcf.gz similarity index 100% rename from repo_utils/test_files/real_small_comp.vcf.gz rename to repo_utils/test_files/variants/real_small_comp.vcf.gz diff --git a/repo_utils/test_files/real_small_comp.vcf.gz.tbi b/repo_utils/test_files/variants/real_small_comp.vcf.gz.tbi similarity index 100% rename from repo_utils/test_files/real_small_comp.vcf.gz.tbi rename to repo_utils/test_files/variants/real_small_comp.vcf.gz.tbi diff --git a/repo_utils/truvari_ssshtests.sh b/repo_utils/truvari_ssshtests.sh index cf641513..6f7c17d0 100644 --- a/repo_utils/truvari_ssshtests.sh +++ b/repo_utils/truvari_ssshtests.sh @@ -19,8 +19,10 @@ source $TESTSRC/sub_tests/consistency.sh source $TESTSRC/sub_tests/divide.sh source $TESTSRC/sub_tests/doctests.sh source $TESTSRC/sub_tests/entry_main.sh -#source $TESTSRC/sub_tests/phab.sh +source $TESTSRC/sub_tests/phab.sh +source $TESTSRC/sub_tests/refine.sh source $TESTSRC/sub_tests/segment.sh +source $TESTSRC/sub_tests/stratify.sh source $TESTSRC/sub_tests/vcf2df.sh source $TESTSRC/sub_tests/version.sh @@ -34,3 +36,5 @@ if [ -z "$1" ]; then coverage json --include=truvari/* -o $OD/coverage.json python3 repo_utils/coverage_maker.py $OD/coverage.json fi +# Clean if they're left +rm -f .coverage.* diff --git a/resources/all_fields2truvbed.py b/resources/all_fields2truvbed.py deleted file mode 100644 index 4596c751..00000000 --- a/resources/all_fields2truvbed.py +++ /dev/null @@ -1,22 +0,0 @@ -print("""##INFO= -#INFO= -#INFO= -#INFO= -#INFO=""") - -# Given an all_fields output from UCSC genome browser simple repeats, make a anno trf bed -import sys - -for line in sys.stdin: - if line.startswith("#"): - index = {x:y for y,x in enumerate(line.strip()[1:].split('\t'))} - continue - data = line.strip().split('\t') - print("\t".join([data[index['chrom']], - data[index['chromStart']], - data[index['chromEnd']], - data[index['period']], - data[index['copyNum']], - data[index['score']], - data[index['entropy']], - data[index['sequence']]])) diff --git a/resources/chm13.simpleRepeat.truvari.bed.gz b/resources/chm13.simpleRepeat.truvari.bed.gz deleted file mode 100644 index b805c1b0..00000000 --- a/resources/chm13.simpleRepeat.truvari.bed.gz +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:12af06674aaf4d6a745021816afd7321cbb967e46b363b77bf636e6f6f059c4a -size 16349104 diff --git a/resources/chm13.simpleRepeat.truvari.bed.gz.tbi b/resources/chm13.simpleRepeat.truvari.bed.gz.tbi deleted file mode 100644 index 87978ad1..00000000 --- a/resources/chm13.simpleRepeat.truvari.bed.gz.tbi +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:ea8d33fda920edd80a709a3f148f0fb457dc4d4bf4bacd7fdfc32b321a4c78c7 -size 1309019 diff --git a/resources/grch37.simpleRepeat.truvari.bed.gz b/resources/grch37.simpleRepeat.truvari.bed.gz deleted file mode 100644 index c656bccf..00000000 --- a/resources/grch37.simpleRepeat.truvari.bed.gz +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:2dde19c1f5d9159a53ee3e011c7de113c62a9627fc4b14ecea8e14d25ab60940 -size 19570458 diff --git a/resources/grch37.simpleRepeat.truvari.bed.gz.tbi b/resources/grch37.simpleRepeat.truvari.bed.gz.tbi deleted file mode 100644 index 5c2b4bad..00000000 --- a/resources/grch37.simpleRepeat.truvari.bed.gz.tbi +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:85b3f0b278e612e67df8fa58b5e9f756bb66ae07d98b95dea7eb555f3f57d496 -size 1390515 diff --git a/resources/grch38.simpleRepeat.truvari.bed.gz b/resources/grch38.simpleRepeat.truvari.bed.gz deleted file mode 100644 index 87e26bdd..00000000 --- a/resources/grch38.simpleRepeat.truvari.bed.gz +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:72c502c54de89034c7cf74be8130aa0fa70ffef431a0dbfc3eb8680467b29ab7 -size 21460635 diff --git a/resources/grch38.simpleRepeat.truvari.bed.gz.tbi b/resources/grch38.simpleRepeat.truvari.bed.gz.tbi deleted file mode 100644 index 005d3919..00000000 --- a/resources/grch38.simpleRepeat.truvari.bed.gz.tbi +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:caaaa9182564f74e4c14aa3d9dbec8986b74fd9160293e7c60e186a2640e334f -size 1414810 diff --git a/setup.py b/setup.py index 9d9f1d64..b5443a08 100644 --- a/setup.py +++ b/setup.py @@ -62,9 +62,7 @@ def _get_repo_hash(): }, install_requires=[ "rich==12.5.1", - "python-Levenshtein==0.12.2", "edlib>=1.3.9", - "progressbar2>=4.0.0", "pysam>=0.15.2", "intervaltree>=3.0.2", "joblib>=1.0.1", diff --git a/truvari/__init__.py b/truvari/__init__.py index 0c26c7ab..be133a7f 100644 --- a/truvari/__init__.py +++ b/truvari/__init__.py @@ -1,25 +1,28 @@ """ + Truvari - SV comparison and annotation toolkit See `help()` of specific functions / objects for details VariantRecord methods: + :meth:`entry_boundaries` -:meth:`entry_create_haplotype` :meth:`entry_distance` :meth:`entry_gt_comp` :meth:`entry_is_filtered` :meth:`entry_is_present` -:meth:`entry_pctsim` :meth:`entry_reciprocal_overlap` :meth:`entry_same_variant_type` +:meth:`entry_shared_ref_context` +:meth:`entry_seq_similarity` :meth:`entry_size` :meth:`entry_size_similarity` -:meth:`entry_to_haplotype` +:meth:`entry_to_hash` :meth:`entry_to_key` :meth:`entry_variant_type` Extra methods: + :meth:`allele_freq_annos` :meth:`bed_ranges` :meth:`build_anno_tree` @@ -35,37 +38,47 @@ :meth:`overlap_percent` :meth:`overlaps` :meth:`phab` +:meth:`phab_multi` :meth:`reciprocal_overlap` :meth:`ref_ranges` :meth:`seqsim` :meth:`sizesim` :meth:`unroll_compare` :meth:`vcf_ranges` -:meth:`weighted_score` Dev methods: + +:meth:`benchdir_count_entries` :meth:`chunker` :meth:`cmd_exe` +:meth:`consolidate_phab_vcfs` +:meth:`count_entries` +:meth:`fchain` :meth:`file_zipper` :meth:`help_unknown_cmd` :meth:`make_temp_filename` :meth:`opt_gz_open` :meth:`optimize_df_memory` +:meth:`performance_metrics` :meth:`restricted_float` :meth:`restricted_int` :meth:`setup_logging` -:meth:`setup_progressbar` :meth:`vcf_to_df` Objects: + +:class:`Bench` +:class:`BenchOutput` :class:`GT` :class:`RegionVCFIterator` :class:`LogFileStderr` :class:`MatchResult` :class:`Matcher` +:class:`StatsBox` :class:`SV` Data: + :data:`truvari.HEADERMAT` :data:`truvari.QUALBINS` :data:`truvari.SVTYTYPE` @@ -74,7 +87,7 @@ :data:`truvari.SZBINTYPE` """ -__version__ = '3.5.1' +__version__ = '4.0.0' from truvari.annotations.af_calc import ( @@ -83,20 +96,26 @@ calc_hwe ) +from truvari.bench import ( + Bench, + BenchOutput, + StatsBox, +) + from truvari.comparisons import ( create_pos_haplotype, entry_boundaries, - entry_create_haplotype, entry_distance, entry_gt_comp, entry_is_filtered, entry_is_present, - entry_pctsim, entry_reciprocal_overlap, entry_same_variant_type, + entry_shared_ref_context, + entry_seq_similarity, entry_size, entry_size_similarity, - entry_to_haplotype, + entry_to_hash, entry_to_key, entry_variant_type, overlap_percent, @@ -105,7 +124,6 @@ seqsim, sizesim, unroll_compare, - weighted_score, ) from truvari.matching import ( @@ -119,8 +137,14 @@ msa2vcf ) +from truvari.pipeline import ( + fchain +) + from truvari.phab import ( - phab + phab, + phab_multi, + consolidate_phab_vcfs ) from truvari.region_vcf_iter import ( @@ -128,6 +152,11 @@ build_anno_tree ) +from truvari.stratify import ( + count_entries, + benchdir_count_entries, +) + from truvari.utils import ( HEADERMAT, LogFileStderr, @@ -137,11 +166,11 @@ help_unknown_cmd, make_temp_filename, opt_gz_open, + performance_metrics, ref_ranges, restricted_float, restricted_int, setup_logging, - setup_progressbar, vcf_ranges, ) diff --git a/truvari/__main__.py b/truvari/__main__.py index 148c40ec..0b0a138c 100755 --- a/truvari/__main__.py +++ b/truvari/__main__.py @@ -4,6 +4,7 @@ """ import sys import argparse +from importlib.metadata import version from rich.console import Console @@ -14,27 +15,31 @@ from truvari.bench import bench_main from truvari.divide import divide_main from truvari.vcf2df import vcf2df_main +from truvari.refine import refine_main from truvari.collapse import collapse_main +from truvari.stratify import stratify_main from truvari.segmentation import segment_main -from truvari.consistency_report import consistency_main +from truvari.consistency import consistency_main -# pylint: disable=unused-argument - - -def version(args): +def flat_version(args): """Print the version""" - print(f"Truvari v{__version__}") - - -TOOLS = {'bench': bench_main, - 'consistency': consistency_main, - 'anno': anno_main, - 'collapse': collapse_main, - 'vcf2df': vcf2df_main, - 'segment': segment_main, - 'divide': divide_main, - 'phab': phab_main, - 'version': version} + if len(args) and args[0].count("-v"): + print(f"Truvari {version('truvari')}") + else: + print(f"Truvari v{__version__}") + + +TOOLS = {"bench": bench_main, + "consistency": consistency_main, + "anno": anno_main, + "collapse": collapse_main, + "vcf2df": vcf2df_main, + "segment": segment_main, + "stratify": stratify_main, + "divide": divide_main, + "phab": phab_main, + "refine": refine_main, + "version": flat_version} USAGE = f"""\ [bold]Truvari v{__version__}[/] Structural Variant Benchmarking and Annotation @@ -46,8 +51,10 @@ def version(args): [bold][cyan]consistency[/][/] Consistency report between multiple VCFs [bold][cyan]vcf2df[/][/] Turn a VCF into a pandas DataFrame [bold][cyan]segment[/][/] Normalization of SVs into disjointed genomic regions - [bold][cyan]divide[/][/] Divide a VCF into multiple parts - [bold][cyan]phab[/][/] Phased variant benchmarking using MSA + [bold][cyan]stratify[/][/] Count variants per-region in vcf + [bold][cyan]divide[/][/] Divide a VCF into independent shards + [bold][cyan]phab[/][/] Variant harmonization using MSA + [bold][cyan]refine[/][/] Automated bench result refinement with phab [bold][cyan]version[/][/] Print the Truvari version and exit """ diff --git a/truvari/anno.py b/truvari/anno.py index 4265b76e..6b385953 100644 --- a/truvari/anno.py +++ b/truvari/anno.py @@ -5,20 +5,23 @@ from rich.console import Console import truvari.annotations as tannos -ANNOS = {"gcpct": ("GC Percent", tannos.gcpct_main), - "gtcnt": ("Genotype Counts", tannos.gtcnt_main), - "trf": ("Tandem Repeats", tannos.trf_main), - "grm": ("Mappability", tannos.grm_main), - "repmask": ("Repeats", tannos.rmk_main), - "remap": ("Allele Remapping", tannos.remap_main), - "hompct": ("Homozygous Percent", tannos.hompct_main), - "numneigh": ("Number of Neighbors", tannos.numneigh_main), - "svinfo": ("SVINFO Fields", tannos.svinfo_main), +ANNOS = { + "addid": ("Set ID field", tannos.addid_main), "bpovl": ("Annotation Intersection", tannos.bpovl_main), "density": ("Variant Density", tannos.density_main), "dpcnt": ("Call Depth Counts", tannos.dpcnt_main), + "gcpct": ("GC Percent", tannos.gcpct_main), + "grm": ("Mappability", tannos.grm_main), + "grpaf": ("Sample Group Allele Frequency", tannos.grpaf_main), + "gtcnt": ("Genotype Counts", tannos.gtcnt_main), + "hompct": ("Homozygous Percent", tannos.hompct_main), "lcr": ("Low-complexity Regions", tannos.lcr_main), - "grpaf": ("Sample Group Allele Frequency", tannos.grpaf_main)} + "numneigh": ("Number of Neighbors", tannos.numneigh_main), + "remap": ("Allele Remapping", tannos.remap_main), + "repmask": ("Repeats", tannos.rmk_main), + "svinfo": ("SVINFO Fields", tannos.svinfo_main), + "trf": ("Tandem Repeats", tannos.trf_main) + } USAGE = "Truvari annotations:\n" + "\n".join([f" [bold][cyan]{k:9}[/][/] {t[0]}" for k,t in ANNOS.items()]) diff --git a/truvari/annotations/__init__.py b/truvari/annotations/__init__.py index beedb9c8..ad9e04f2 100644 --- a/truvari/annotations/__init__.py +++ b/truvari/annotations/__init__.py @@ -1,32 +1,34 @@ """ annotation modules """ +from truvari.annotations.addid import addid_main +from truvari.annotations.bpovl import bpovl_main +from truvari.annotations.density import density_main +from truvari.annotations.dpcnt import dpcnt_main from truvari.annotations.gccontent import gcpct_main -from truvari.annotations.gtcnt import gtcnt_main -from truvari.annotations.trf import trf_main from truvari.annotations.grm import grm_main -from truvari.annotations.repmask import rmk_main -from truvari.annotations.remap import remap_main +from truvari.annotations.grpaf import grpaf_main +from truvari.annotations.gtcnt import gtcnt_main from truvari.annotations.hompct import hompct_main +from truvari.annotations.lcr import lcr_main from truvari.annotations.numneigh import numneigh_main +from truvari.annotations.remap import remap_main +from truvari.annotations.repmask import rmk_main from truvari.annotations.svinfo import svinfo_main -from truvari.annotations.bpovl import bpovl_main -from truvari.annotations.density import density_main -from truvari.annotations.dpcnt import dpcnt_main -from truvari.annotations.lcr import lcr_main -from truvari.annotations.grpaf import grpaf_main +from truvari.annotations.trf import trf_main __all__ = [ + 'addid_main', + 'bpovl_main', + 'density_main', + 'dpcnt_main', 'gcpct_main', - 'gtcnt_main', - 'trf_main', 'grm_main', - 'rmk_main', - 'remap_main', + 'grpaf_main', + 'gtcnt_main', 'hompct_main', + 'lcr_main', 'numneigh_main', + 'remap_main', + 'rmk_main', 'svinfo_main', - 'bpovl_main', - 'density_main', - 'dpcnt_main', - 'lcr_main', - 'grpaf_main' + 'trf_main' ] diff --git a/truvari/annotations/addid.py b/truvari/annotations/addid.py new file mode 100644 index 00000000..b9bb1c08 --- /dev/null +++ b/truvari/annotations/addid.py @@ -0,0 +1,51 @@ +""" +Sets an ID to variants +""" +import logging +import argparse + +import truvari + +def parse_args(args): + """ + Pull the command line parameters + """ + parser = argparse.ArgumentParser(prog="addid", description=__doc__, + formatter_class=argparse.RawDescriptionHelpFormatter) + parser.add_argument("input", nargs="?", type=str, default="/dev/stdin", + help="VCF to annotate (stdin)") + parser.add_argument("-o", "--output", type=str, default="/dev/stdout", + help="Output filename (stdout)") + truvari.setup_logging(show_version=True) + return parser.parse_args(args) + + +def get_idx(line): + """ + Get string's tab positions + """ + ret = [0] + for _ in range(8): + ret.append(line.index('\t', ret[-1] + 1)) + return ret + +def addid_main(cmdargs): + """ + Main method + """ + args = parse_args(cmdargs) + fh = truvari.opt_gz_open(args.input) + + cnt = 0 + with open(args.output, 'w') as fout: + for line in fh: + if line[0] == "#": + fout.write(line) + continue + tabs = get_idx(line) + new_id = line[:tabs[1]].replace('chr','') + hex(cnt) + fout.write(line[:tabs[2] + 1]) + fout.write(new_id) + fout.write(line[tabs[3]:]) + cnt += 1 + logging.info("Finished addid") diff --git a/truvari/annotations/af_calc.py b/truvari/annotations/af_calc.py index 551041f8..3ffd39ea 100644 --- a/truvari/annotations/af_calc.py +++ b/truvari/annotations/af_calc.py @@ -85,7 +85,7 @@ def calc_af(gts): | MAF - minor allele frequency | ExcHet - excess heterozygosity | HWE - hardy weinberg equilibrium - | AC - allele count + | AC - allele count for GT 0 and 1 | MAC - minor allele count | AN - number of called alleles :rtype: dict @@ -104,7 +104,7 @@ def calc_af(gts): n_het += 1 if g[0] != g[1] and None not in g else 0 if an == 0: - return {"AF": 0, "MAF": 0, "ExcHet": 0, "HWE": 0, "MAC": 0, "AC": 0, "AN": 0} + return {"AF": 0, "MAF": 0, "ExcHet": 0, "HWE": 0, "MAC": 0, "AC": [0, 0], "AN": 0} af = cnt[1] / an srt = [(v, k) for k, v in sorted(cnt.items(), key=lambda item: item[1])] ac = [cnt[_] for _ in [0, 1]] @@ -136,7 +136,7 @@ def allele_freq_annos(entry, samples=None): Example >>> import truvari >>> import pysam - >>> v = pysam.VariantFile('repo_utils/test_files/multi.vcf.gz') + >>> v = pysam.VariantFile('repo_utils/test_files/variants/multi.vcf.gz') >>> truvari.allele_freq_annos(next(v)) {'AF': 0.5, 'MAF': 0.5, 'ExcHet': 1.0, 'HWE': 1.0, 'MAC': 1, 'AC': [1, 1], 'AN': 2} """ diff --git a/truvari/annotations/bpovl.py b/truvari/annotations/bpovl.py index 24c992a9..d4dcdba3 100644 --- a/truvari/annotations/bpovl.py +++ b/truvari/annotations/bpovl.py @@ -64,40 +64,40 @@ def bpovl_main(cmdargs): args = parse_args(cmdargs) in_vcf = pysam.VariantFile(args.input) anno_tree, anno_cnt = truvari.build_anno_tree(args.anno, *args.anno_psets) - out_rows = [] logging.info("Loaded %d annotations", anno_cnt) - hit_cnt = 0 - for entry in in_vcf: - has_hit = False + def _transform(): + hit_cnt = 0 + for entry in in_vcf: + has_hit = False - start, end = truvari.entry_boundaries(entry) - span = abs(end - start) - if span > args.spanmax: - continue - svlen = truvari.entry_size(entry) - if svlen < args.sizemin: - continue + start, end = truvari.entry_boundaries(entry) + span = abs(end - start) + if span > args.spanmax: + continue + svlen = truvari.entry_size(entry) + if svlen < args.sizemin: + continue - key = truvari.entry_to_key(entry) - for anno_idx in anno_tree[entry.chrom].at(start): - has_hit = True - out_rows.append([key, 'start_bnd', anno_idx.data]) - - for anno_idx in anno_tree[entry.chrom].at(end): - has_hit = True - out_rows.append([key, 'end_bnd', anno_idx.data]) - - for anno_idx in anno_tree[entry.chrom].overlap(start, end): - if start <= anno_idx.begin and anno_idx.end <= end: + key = truvari.entry_to_hash(entry) + for anno_idx in anno_tree[entry.chrom].at(start): has_hit = True - out_rows.append([key, 'overlaps', anno_idx.data]) - elif anno_idx.begin <= start and end <= anno_idx.end: + yield [key, 'start_bnd', anno_idx.data] + + for anno_idx in anno_tree[entry.chrom].at(end): has_hit = True - out_rows.append([key, 'contains', anno_idx.data]) - hit_cnt += has_hit - logging.info("%d SVs hit annotations", hit_cnt) - out = pd.DataFrame(out_rows, columns=["vcf_key", - "intersection", - "anno_key"]) + yield [key, 'end_bnd', anno_idx.data] + + for anno_idx in anno_tree[entry.chrom].overlap(start, end): + if start <= anno_idx.begin and anno_idx.end <= end: + has_hit = True + yield [key, 'overlaps', anno_idx.data] + elif anno_idx.begin <= start and end <= anno_idx.end: + has_hit = True + yield [key, 'contains', anno_idx.data] + hit_cnt += has_hit + logging.info("%d SVs hit annotations", hit_cnt) + out = pd.DataFrame(_transform(), columns=["vcf_key", + "intersection", + "anno_key"]) joblib.dump(out, args.output) logging.info("Finished bpovl") diff --git a/truvari/annotations/grm.py b/truvari/annotations/grm.py index 96d35300..8b0581cc 100644 --- a/truvari/annotations/grm.py +++ b/truvari/annotations/grm.py @@ -2,7 +2,6 @@ Maps graph edge kmers with BWA to assess Graph Reference Mappability """ # pylint: disable=too-many-locals -import os import sys import re import types @@ -171,7 +170,7 @@ def parse_args(args): help="Size of kmer to map (%(default)s)") parser.add_argument("-m", "--min-size", default=25, type=truvari.restricted_int, help="Minimum size of variants to map (%(default)s)") - parser.add_argument("-t", "--threads", default=os.cpu_count(), type=truvari.restricted_int, + parser.add_argument("-t", "--threads", default=1, type=truvari.restricted_int, help="Number of threads (%(default)s)") parser.add_argument("--debug", action="store_true", help="Verbose logging") diff --git a/truvari/annotations/repmask.py b/truvari/annotations/repmask.py index 75ed1cb7..8ddac84f 100644 --- a/truvari/annotations/repmask.py +++ b/truvari/annotations/repmask.py @@ -1,5 +1,4 @@ """ Wrapper around RepeatMasker to annotate insertion sequences in a VCF """ -import os import sys import logging import argparse @@ -79,7 +78,7 @@ def extract_seqs(self): if self.min_length <= entry_size <= self.max_length: cnt += 1 cntbp += entry_size - if truvari.entry_variant_type(entry) == "INS": + if truvari.entry_variant_type(entry) == truvari.SV.INS: ret.write(f">{pos}\n{entry.alts[0]}\n") else: ret.write(f">{pos}\n{entry.ref}\n") @@ -190,7 +189,7 @@ def parse_args(args): help="Threshold for pct of allele covered (%(default)s)") parser.add_argument("-p", "--params", type=str, default=DEFAULTPARAMS, help="Default parameter string to send to RepeatMasker (%(default)s)") - parser.add_argument("-T", "--threads", type=truvari.restricted_int, default=os.cpu_count(), + parser.add_argument("-T", "--threads", type=truvari.restricted_int, default=1, help="Number of threads to use (%(default)s)") parser.add_argument("--debug", action="store_true", help="Verbose logging") diff --git a/truvari/annotations/svinfo.py b/truvari/annotations/svinfo.py index ed777ee5..9c4525ec 100644 --- a/truvari/annotations/svinfo.py +++ b/truvari/annotations/svinfo.py @@ -24,17 +24,28 @@ def parse_args(args): return parser.parse_args(args) -def edit_header(my_vcf): +def edit_header(header): """ Add INFO for new fields to vcf """ - header = my_vcf.header.copy() header.add_line( '##INFO=') header.add_line( '##INFO=') return header +def add_svinfo(entry, min_size=0, n_header=None): + """ + Add svinfo + """ + sz = truvari.entry_size(entry) + if sz < min_size: + return + if n_header: + entry.translate(n_header) + svtype = truvari.entry_variant_type(entry) + entry.info["SVTYPE"] = svtype.name + entry.info["SVLEN"] = sz def svinfo_main(cmdargs): """ @@ -42,14 +53,9 @@ def svinfo_main(cmdargs): """ args = parse_args(cmdargs) vcf = pysam.VariantFile(args.input) - n_header = edit_header(vcf) + n_header = edit_header(vcf.header.copy()) with pysam.VariantFile(args.output, 'w', header=n_header) as out: for entry in vcf: - sz = truvari.entry_size(entry) - if sz >= args.minsize: - entry.translate(n_header) - svtype = truvari.entry_variant_type(entry) - entry.info["SVTYPE"] = svtype.name - entry.info["SVLEN"] = sz + add_svinfo(entry, args.minsize, n_header) out.write(entry) logging.info("Finished svinfo") diff --git a/truvari/annotations/trf.py b/truvari/annotations/trf.py index dc802dca..965680c7 100644 --- a/truvari/annotations/trf.py +++ b/truvari/annotations/trf.py @@ -58,12 +58,13 @@ class TRFAnno(): Operates on a single TRF region across multiple TRF annotations """ - def __init__(self, region, reference, motif_similarity=0.90): + def __init__(self, region, reference, motif_similarity=0.90, buf=5): """ setup """ self.region = region self.reference = reference self.motif_similarity = motif_similarity self.known_motifs = {_["repeat"]:_["copies"] for _ in self.region["annos"]} + self.buffer = buf def make_seq(self, entry, svtype): """ @@ -92,9 +93,9 @@ def score_annotation(self, var_start, var_end, anno): Scores the annotation. Addes fields in place. if is_new, we calculate the diff """ - ovl_pct = truvari.overlap_percent(var_start, var_end, anno["start"], anno["end"]) + ovl_pct = truvari.overlap_percent(var_start, var_end, anno["start"] - self.buffer, anno["end"] + self.buffer) # has to have overlap - if ovl_pct <= 0: + if ovl_pct == 0: return None anno["ovl_pct"] = ovl_pct @@ -128,7 +129,8 @@ def del_annotate(self, entry, svlen, score_filter=True): scores = [] for anno in self.region["annos"]: # + 1 for anchor base - ovl_pct = truvari.overlap_percent(entry.start + 1, entry.stop, anno["start"], anno["end"]) + ovl_pct = truvari.overlap_percent(entry.start + 1, entry.stop, \ + anno["start"] - self.buffer, anno["end"] + self.buffer) if ovl_pct == 0: continue m_sc = dict(anno) @@ -161,7 +163,6 @@ def ins_annotate(self, entry, annos=None, score_filter=True): annos = annos["key"] self.translate_coords(annos) - scores = [] for anno in annos: m_sc = self.score_annotation(entry.start, entry.stop, anno) @@ -207,7 +208,8 @@ def ins_estimate_anno(self, entry, score_filter=True): scores = [] best_score = {} for anno in self.region["annos"]: - ovl_pct = truvari.overlap_percent(entry.start + 1, entry.stop, anno["start"], anno["end"]) + ovl_pct = truvari.overlap_percent(entry.start + 1, entry.stop, \ + anno["start"] - self.buffer, anno["end"] + self.buffer) if ovl_pct == 0: continue @@ -285,6 +287,15 @@ def run_trf(fa_fn, executable="trf409.linux64", trf_params="2 7 7 80 10 50 500 -m -f -h -d -ngs"): """ Given a fasta file, run TRF and return result + trf_params are + File = sequences input file + Match = matching weight + Mismatch = mismatching penalty + Delta = indel penalty + PM = match probability (whole number) + PI = indel probability (whole number) + Minscore = minimum alignment score to report + MaxPeriod = maximum period size to report """ if "-ngs" not in trf_params: trf_params = trf_params + " -ngs " @@ -352,6 +363,8 @@ def process_ref_region(region): m_fetch = vcf.fetch(region["chrom"], region["start"], region["end"]) except ValueError as e: logging.debug("Skipping VCF fetch %s", e) + return None + m_stack = AnnoStack(list(iter_tr_regions(trfshared.args.repeats, (region["chrom"], region["start"], region["end"]))), @@ -416,7 +429,7 @@ def process_tr_region(region): ref = pysam.FastaFile(trfshared.args.reference) ref_seq = ref.fetch(region["chrom"], region["start"], region["end"]) - tanno = TRFAnno(region, ref_seq, trfshared.args.motif_similarity) + tanno = TRFAnno(region, ref_seq, trfshared.args.motif_similarity, trfshared.args.buffer) vcf = pysam.VariantFile(trfshared.args.input) new_header = edit_header(vcf.header) out = StringIO() @@ -564,6 +577,8 @@ def parse_args(args): help="Default parameters to send to trf (%(default)s)") parser.add_argument("-r", "--repeats", type=str, required=True, help="Reference repeat annotations") + parser.add_argument("--buffer", type=int, default=5, + help="buffer on annotations during intersection (%(default)s)") parser.add_argument("-f", "--reference", type=str, required=True, help="Reference fasta file") parser.add_argument("-s", "--motif-similarity", type=truvari.restricted_float, default=0.90, @@ -576,7 +591,7 @@ def parse_args(args): help="Skip INS estimation procedure and run everything through TRF. (%(default)s)") parser.add_argument("-C", "--chunk-size", type=int, default=5, help="Size (in mbs) of reference chunks for parallelization (%(default)s)") - parser.add_argument("-t", "--threads", type=truvari.restricted_int, default=multiprocessing.cpu_count(), + parser.add_argument("-t", "--threads", type=truvari.restricted_int, default=1, help="Number of threads to use (%(default)s)") parser.add_argument("--debug", action="store_true", help="Verbose logging") @@ -602,6 +617,9 @@ def check_params(args): if not args.repeats.endswith(".bed.gz"): logging.error(f"{args.repeats} isn't compressed bed") check_fail = True + if not os.path.exists(args.repeats): + logging.error(f"{args.repeats} doesn't exit") + check_fail = True if not os.path.exists(args.repeats + '.tbi'): logging.error(f"{args.repeats}.tbi doesn't exit") check_fail = True @@ -624,6 +642,7 @@ def trf_main(cmdargs): m_regions = iter_tr_regions(args.repeats) m_process = process_tr_region else: + # refactor. need streaming mode m_regions = truvari.ref_ranges(args.reference, chunk_size=int(args.chunk_size * 1e6)) m_process = process_ref_region @@ -637,11 +656,8 @@ def trf_main(cmdargs): with open(args.output, 'w') as fout: fout.write(str(new_header)) for i in chunks: - fout.write(i) + if i is not None: + fout.write(i) pool.join() logging.info("Finished trf") - - -if __name__ == '__main__': - trf_main(sys.argv[1:]) diff --git a/truvari/bench.py b/truvari/bench.py index aa5572bf..9926500d 100644 --- a/truvari/bench.py +++ b/truvari/bench.py @@ -1,6 +1,6 @@ """ -Structural variant caller comparison tool -Given a benchmark and callset, calculate the recall/precision/f-measure +Structural variant benchmarking tool +Given baseline and comparison sets of variants, calculate the recall/precision/f-measure """ import os import sys @@ -16,272 +16,10 @@ import numpy as np import truvari -from truvari.giab_report import make_giabreport -class StatsBox(OrderedDict): - """ - Make a blank stats box for counting TP/FP/FN and calculating performance - """ - - def __init__(self): - super().__init__() - self["TP-base"] = 0 - self["TP-call"] = 0 - self["FP"] = 0 - self["FN"] = 0 - self["precision"] = 0 - self["recall"] = 0 - self["f1"] = 0 - self["base cnt"] = 0 - self["call cnt"] = 0 - self["TP-call_TP-gt"] = 0 - self["TP-call_FP-gt"] = 0 - self["TP-base_TP-gt"] = 0 - self["TP-base_FP-gt"] = 0 - self["gt_concordance"] = 0 - self["gt_matrix"] = defaultdict(Counter) - - def calc_performance(self): - """ - Calculate the precision/recall - """ - do_stats_math = True - if self["TP-base"] == 0 and self["FN"] == 0: - logging.warning("No TP or FN calls in base!") - do_stats_math = False - elif self["TP-call"] == 0 and self["FP"] == 0: - logging.warning("No TP or FP calls in comp!") - do_stats_math = False - - # Final calculations - if do_stats_math: - self["precision"] = float(self["TP-call"]) / \ - (self["TP-call"] + self["FP"]) - self["recall"] = float(self["TP-base"]) / \ - (self["TP-base"] + self["FN"]) - if self["TP-call_TP-gt"] + self["TP-call_FP-gt"] != 0: - self["gt_concordance"] = float(self["TP-call_TP-gt"]) / (self["TP-call_TP-gt"] + - self["TP-call_FP-gt"]) - - # f-measure - neum = self["recall"] * self["precision"] - denom = self["recall"] + self["precision"] - if denom != 0: - self["f1"] = 2 * (neum / denom) - -def compare_chunk(chunk): - """ - Given a filtered chunk, (from chunker) compare all of the calls - """ - matcher, chunk_dict, chunk_id = chunk - logging.debug(f"Comparing chunk {chunk_dict}") - - # All FPs - if len(chunk_dict['base']) == 0: - fps = [] - for cid, c in enumerate(chunk_dict['comp']): - ret = truvari.MatchResult() - ret.comp = c - ret.matid = f"{chunk_id}._.{cid}" - fps.append(ret) - logging.debug("All FP chunk -> {ret}") - return fps - - # All FNs - if len(chunk_dict['comp']) == 0: - fns = [] - for bid, b in enumerate(chunk_dict['base']): - ret = truvari.MatchResult() - ret.base = b - ret.matid = f"{chunk_id}.{bid}._" - logging.debug(f"All FN chunk -> {ret}") - fns.append(ret) - return fns - - # Build all v all matrix - # Should allow short-circuiting here. - # If we find a perfect match, don't need to keep comparing. - match_matrix = [] - for bid, b in enumerate(chunk_dict['base']): - base_matches = [] - for cid, c in enumerate(chunk_dict['comp']): - mat = matcher.build_match(b, c, f"{chunk_id}.{bid}.{cid}") - logging.debug(f"Made mat -> {mat}") - base_matches.append(mat) - match_matrix.append(base_matches) - - # For building custom pickers - match_matrix = np.array(match_matrix) - if matcher.params.multimatch == 'KEEPALL': - return match_matrix - # Sort and annotate matches - ret = [] - if matcher.params.multimatch: - ret = pick_multi_matches(match_matrix) - else: - ret = pick_single_matches(match_matrix) - return ret - - -def pick_multi_matches(match_matrix): - """ - Given a numpy array of MatchResults - Pick each base/comp call's best match - """ - ret = [] - for b_max in match_matrix.max(axis=1): - b_max = copy.copy(b_max) - b_max.comp = None - ret.append(b_max) - - for c_max in match_matrix.max(axis=0): - c_max = copy.copy(c_max) - c_max.base = None - ret.append(c_max) - return ret - - -def pick_single_matches(match_matrix): - """ - Given a numpy array of MatchResults - for each base, get its best match and record that the comp call can't be used anymore - Once all best pairs are found, return the remaining - """ - ret = [] - base_cnt, comp_cnt = match_matrix.shape - match_matrix = np.ravel(match_matrix) - match_matrix.sort() - used_comp = set() - used_base = set() - for match in match_matrix[::-1]: - # No more matches to find - if base_cnt == 0 and comp_cnt == 0: - break - - base_is_used = str(match.base) in used_base - comp_is_used = str(match.comp) in used_comp - # Only write the comp - if base_cnt == 0 and not comp_is_used: - to_process = copy.copy(match) - to_process.base = None - to_process.state = False - to_process.multi = True - comp_cnt -= 1 - used_comp.add(str(to_process.comp)) - ret.append(to_process) - # Only write the base - elif comp_cnt == 0 and not base_is_used: - to_process = copy.copy(match) - to_process.comp = None - to_process.state = False - to_process.multi = True - base_cnt -= 1 - used_base.add(str(to_process.base)) - ret.append(to_process) - # Write both - elif not base_is_used and not comp_is_used: - to_process = copy.copy(match) - base_cnt -= 1 - used_base.add(str(to_process.base)) - comp_cnt -= 1 - used_comp.add(str(to_process.comp)) - ret.append(to_process) - return ret - - -############### -# VCF editing # -############### -def edit_header(my_vcf): - """ - Add INFO for new fields to vcf - """ - header = my_vcf.header.copy() - header.add_line(('##INFO=')) - header.add_line(('##INFO=')) - header.add_line(('##INFO=')) - header.add_line(('##INFO=')) - header.add_line(('##INFO=')) - header.add_line(('##INFO=')) - header.add_line(('##INFO=')) - header.add_line(('##INFO=')) - header.add_line(('##INFO=')) - header.add_line(('##INFO=')) - return header - - -def annotate_entry(entry, match, header): - """ - Make a new entry with all the information - """ - entry.translate(header) - entry.info["PctSeqSimilarity"] = round(match.seqsim, 4) if match.seqsim is not None else None - entry.info["PctSizeSimilarity"] = round(match.sizesim, 4) if match.sizesim is not None else None - entry.info["PctRecOverlap"] = round(match.ovlpct, 4) if match.ovlpct is not None else None - entry.info["SizeDiff"] = match.sizediff - entry.info["StartDistance"] = match.st_dist - entry.info["EndDistance"] = match.ed_dist - entry.info["GTMatch"] = match.gt_match - entry.info["TruScore"] = int(match.score) if match.score else None - entry.info["MatchId"] = match.matid - entry.info["Multi"] = match.multi - - -def output_writer(match, outs, sizemin): - """ - Annotate a MatchResults' entries, write to the apppropriate file in outs - and do the stats counting. - Writer is responsible for handling FPs between sizefilt-sizemin - """ - box = outs["stats_box"] - if match.base: - box["base cnt"] += 1 - annotate_entry(match.base, match, outs['n_base_header']) - if match.state: - gtBase = str(match.base_gt) - gtComp = str(match.comp_gt) - box["gt_matrix"][gtBase][gtComp] += 1 - - box["TP-base"] += 1 - outs["tpb_out"].write(match.base) - if match.gt_match: - box["TP-base_TP-gt"] += 1 - else: - box["TP-base_FP-gt"] += 1 - else: - box["FN"] += 1 - outs["fn_out"].write(match.base) - - if match.comp: - annotate_entry(match.comp, match, outs['n_comp_header']) - if match.state: - box["call cnt"] += 1 - box["TP-call"] += 1 - outs["tpc_out"].write(match.comp) - if match.gt_match: - box["TP-call_TP-gt"] += 1 - else: - box["TP-call_FP-gt"] += 1 - elif truvari.entry_size(match.comp) >= sizemin: - # The if is because we don't count FPs between sizefilt-sizemin - box["call cnt"] += 1 - box["FP"] += 1 - outs["fp_out"].write(match.comp) - - -########################## -# Parameters and outputs # -########################## +############## +# Parameters # +############## def parse_args(args): """ Pull the command line parameters @@ -296,60 +34,52 @@ def parse_args(args): parser.add_argument("-o", "--output", type=str, required=True, help="Output directory") parser.add_argument("-f", "--reference", type=str, default=None, - help="Indexed fasta used to call variants") - parser.add_argument("--giabreport", action="store_true", - help="Parse output TPs/FNs for GIAB annotations and create a report") + help="Fasta used to call variants. Turns on reference context sequence comparison") parser.add_argument("--debug", action="store_true", default=False, help="Verbose logging") - parser.add_argument("--prog", action="store_true", - help="Turn on progress monitoring") thresg = parser.add_argument_group("Comparison Threshold Arguments") thresg.add_argument("-r", "--refdist", type=truvari.restricted_int, default=defaults.refdist, - help="Max reference location distance (%(default)s)") - thresg.add_argument("-p", "--pctsim", type=truvari.restricted_float, default=defaults.pctsim, - help="Min percent allele sequence similarity. Set to 0 to ignore. (%(default)s)") - thresg.add_argument("-B", "--minhaplen", type=truvari.restricted_int, default=defaults.minhaplen, - help="Minimum haplotype sequence length to create (%(default)s)") + help="Max reference distance (%(default)s)") + thresg.add_argument("-p", "--pctseq", type=truvari.restricted_float, default=defaults.pctseq, + help="Min sequence similarity. Set to 0 to ignore (%(default)s)") thresg.add_argument("-P", "--pctsize", type=truvari.restricted_float, default=defaults.pctsize, - help="Min pct allele size similarity (minvarsize/maxvarsize) (%(default)s)") + help="Min variant size similarity (%(default)s)") thresg.add_argument("-O", "--pctovl", type=truvari.restricted_float, default=defaults.pctovl, - help="Min pct reciprocal overlap (%(default)s)") + help="Min reciprocal overlap (%(default)s)") thresg.add_argument("-t", "--typeignore", action="store_true", default=defaults.typeignore, - help="Variant types don't need to match to compare (%(default)s)") + help="Don't compare variant types (%(default)s)") + thresg.add_argument("--pick", type=str, default=defaults.pick, choices=PICKERS.keys(), + help="Number of matches reported per-call") thresg.add_argument("--dup-to-ins", action="store_true", help="Assume DUP svtypes are INS (%(default)s)") - thresg.add_argument("--use-lev", action="store_true", - help="Use the Levenshtein distance ratio instead of edlib editDistance ratio (%(default)s)") thresg.add_argument("-C", "--chunksize", type=truvari.restricted_int, default=defaults.chunksize, help="Max reference distance to compare calls (%(default)s)") + thresg.add_argument("-B", "--minhaplen", type=truvari.restricted_int, default=defaults.minhaplen, + help="Min haplotype sequence length to create (%(default)s)") + genoty = parser.add_argument_group("Genotype Comparison Arguments") - genoty.add_argument("--gtcomp", action="store_true", default=defaults.gtcomp, - help="Compare GenoTypes of matching calls") genoty.add_argument("--bSample", type=str, default=None, - help="Baseline calls sample to use (first)") + help="Baseline calls' sample to use (first)") genoty.add_argument("--cSample", type=str, default=None, - help="Comparison calls sample to use (first)") + help="Comparison calls' sample to use (first)") filteg = parser.add_argument_group("Filtering Arguments") + filteg.add_argument("--passonly", action="store_true", default=defaults.passonly, + help="Only consider calls with FILTER == PASS") filteg.add_argument("-s", "--sizemin", type=truvari.restricted_int, default=defaults.sizemin, help="Minimum variant size to consider from --comp (%(default)s)") filteg.add_argument("-S", "--sizefilt", type=truvari.restricted_int, default=None, help="Minimum variant size to consider from --base (30)") filteg.add_argument("--sizemax", type=truvari.restricted_int, default=defaults.sizemax, - help="Maximum variant size to consider for comparison (%(default)s)") - filteg.add_argument("--passonly", action="store_true", default=defaults.passonly, - help="Only consider calls with FILTER == PASS") + help="Maximum variant size to consider (%(default)s)") filteg.add_argument("--no-ref", default=defaults.no_ref, choices=['a', 'b', 'c'], - help="Don't include 0/0 or ./. GT calls from all (a), base (b), or comp (c) vcfs (%(default)s)") + help="Exclude 0/0 or ./. GT calls from all (a), base (b), or comp (c) vcfs (%(default)s)") filteg.add_argument("--includebed", type=str, default=None, - help="Bed file of regions in the genome to include only calls overlapping") + help="Bed file of regions to analyze. Only calls within regions are counted") filteg.add_argument("--extend", type=truvari.restricted_int, default=0, help="Distance to allow comp entries outside of includebed regions (%(default)s)") - filteg.add_argument("--multimatch", action="store_true", default=defaults.multimatch, - help=("Allow base calls to match multiple comparison calls, and vice versa. " - "Output vcfs will have redundant entries. (%(default)s)")) args = parser.parse_args(args) # When sizefilt is not provided and sizemin has been lowered below the default, @@ -360,6 +90,13 @@ def parse_args(args): args.sizefilt = args.sizemin else: args.sizefilt = defaults.sizefilt + + # Setup abspaths + args.base = os.path.abspath(args.base) + args.comp = os.path.abspath(args.comp) + args.includebed = os.path.abspath(args.includebed) if args.includebed else args.includebed + args.reference = os.path.abspath(args.reference) if args.reference else args.reference + return args @@ -403,24 +140,28 @@ def check_params(args): if args.includebed and not os.path.exists(args.includebed): logging.error("Include bed %s does not exist", args.includebed) check_fail = True - + if args.reference and not os.path.exists(args.reference): + logging.error("Reference %s does not exist", args.reference) + check_fail = True return check_fail -def check_sample(vcf_fn, sampleId=None): +def check_sample(vcf_fn, sample_id=None): """ Checks that a sample is inside a vcf Returns True if check failed """ vcf_file = pysam.VariantFile(vcf_fn) check_fail = False - if sampleId is not None and sampleId not in vcf_file.header.samples: - logging.error("Sample %s not found in vcf (%s)", sampleId, vcf_fn) + if sample_id is not None and sample_id not in vcf_file.header.samples: + logging.error("Sample %s not found in vcf (%s)", sample_id, vcf_fn) check_fail = True if len(vcf_file.header.samples) == 0: logging.error("No SAMPLE columns found in vcf (%s)", vcf_fn) check_fail = True - return check_fail + if sample_id is None: + sample_id = vcf_file.header.samples[0] + return check_fail, sample_id def check_inputs(args): @@ -428,93 +169,508 @@ def check_inputs(args): Checks the inputs to ensure expected values are found inside of files Returns True if check failed """ - return check_sample(args.base, args.bSample) or check_sample(args.comp, args.cSample) + b_check, args.bSample = check_sample(args.base, args.bSample) + c_check, args.cSample = check_sample(args.comp, args.cSample) + return b_check or c_check + + +############### +# VCF editing # +############### +def edit_header(my_vcf): + """ + Add INFO for new fields to vcf + """ + header = my_vcf.header.copy() + header.add_line(('##INFO=')) + header.add_line(('##INFO=')) + header.add_line(('##INFO=')) + header.add_line(('##INFO=')) + header.add_line(('##INFO=')) + header.add_line(('##INFO=')) + header.add_line(('##INFO=')) + header.add_line(('##INFO=')) + header.add_line(('##INFO=')) + header.add_line(('##INFO=')) + return header + + +def annotate_entry(entry, match, header): + """ + Make a new entry with all the information + """ + entry.translate(header) + entry.info["PctSeqSimilarity"] = round(match.seqsim, 4) if match.seqsim is not None else None + entry.info["PctSizeSimilarity"] = round(match.sizesim, 4) if match.sizesim is not None else None + entry.info["PctRecOverlap"] = round(match.ovlpct, 4) if match.ovlpct is not None else None + entry.info["SizeDiff"] = match.sizediff + entry.info["StartDistance"] = match.st_dist + entry.info["EndDistance"] = match.ed_dist + entry.info["GTMatch"] = match.gt_match + entry.info["TruScore"] = int(match.score) if match.score else None + entry.info["MatchId"] = match.matid + entry.info["Multi"] = match.multi -def setup_outputs(args): +############# +# Core code # +############# +class StatsBox(OrderedDict): """ - Makes all of the output files - Places the data into the shared space + Make a blank stats box for counting TP/FP/FN and calculating performance """ - os.mkdir(args.output) - truvari.setup_logging(args.debug, truvari.LogFileStderr( - os.path.join(args.output, "log.txt")), show_version=True) - logging.info("Params:\n%s", json.dumps(vars(args), indent=4)) - outputs = {} - outputs["vcf_base"] = pysam.VariantFile(args.base) - outputs["n_base_header"] = edit_header(outputs["vcf_base"]) + def __init__(self): + super().__init__() + self["TP-base"] = 0 + self["TP-comp"] = 0 + self["FP"] = 0 + self["FN"] = 0 + self["precision"] = 0 + self["recall"] = 0 + self["f1"] = 0 + self["base cnt"] = 0 + self["comp cnt"] = 0 + self["TP-comp_TP-gt"] = 0 + self["TP-comp_FP-gt"] = 0 + self["TP-base_TP-gt"] = 0 + self["TP-base_FP-gt"] = 0 + self["gt_concordance"] = 0 + self["gt_matrix"] = defaultdict(Counter) - outputs["vcf_comp"] = pysam.VariantFile(args.comp) - outputs["n_comp_header"] = edit_header(outputs["vcf_comp"]) + def calc_performance(self): + """ + Calculate the precision/recall + """ + if self["TP-base"] == 0 and self["FN"] == 0: + logging.warning("No TP or FN calls in base!") + elif self["TP-comp"] == 0 and self["FP"] == 0: + logging.warning("No TP or FP calls in comp!") - outputs["tpb_out"] = pysam.VariantFile(os.path.join( - args.output, "tp-base.vcf"), 'w', header=outputs["n_base_header"]) - outputs["tpc_out"] = pysam.VariantFile(os.path.join( - args.output, "tp-call.vcf"), 'w', header=outputs["n_comp_header"]) + precision, recall, f1 = truvari.performance_metrics(self["TP-base"], self["TP-comp"], self["FN"], self["FP"]) - outputs["fn_out"] = pysam.VariantFile(os.path.join( - args.output, "fn.vcf"), 'w', header=outputs["n_base_header"]) - outputs["fp_out"] = pysam.VariantFile(os.path.join( - args.output, "fp.vcf"), 'w', header=outputs["n_comp_header"]) + self["precision"] = precision + self["recall"] = recall + self["f1"] = f1 + if self["TP-comp_TP-gt"] + self["TP-comp_FP-gt"] != 0: + self["gt_concordance"] = float(self["TP-comp_TP-gt"]) / (self["TP-comp_TP-gt"] + + self["TP-comp_FP-gt"]) - outputs["stats_box"] = StatsBox() - return outputs + def write_json(self, out_name): + """ + Write stats as json to file + """ + with open(out_name, 'w') as fout: + fout.write(json.dumps(self, indent=4)) -def close_outputs(outputs): +class BenchOutput(): """ - Close all the files + Makes all of the output files for a Bench.run + + The variable `BenchOutput.vcf_filenames` holds a dictonary. The keys are tpb, tpc + for true positive base/comp vcf filename and fn, fp. The variable `stats_box` holds + a :class:`StatsBox`. """ - outputs["tpb_out"].close() - outputs["tpc_out"].close() - outputs["fn_out"].close() - outputs["fp_out"].close() + def __init__(self, bench, matcher): + """ + initialize + """ + self.m_bench = bench + self.m_matcher = matcher + + os.mkdir(self.m_bench.outdir) + param_dict = self.m_bench.param_dict() + param_dict.update(vars(self.m_matcher.params)) + + if self.m_bench.do_logging: + truvari.setup_logging(self.m_bench.debug, truvari.LogFileStderr( + os.path.join(self.m_bench.outdir, "log.txt")), show_version=True) + logging.info("Params:\n%s", json.dumps(param_dict, indent=4)) + + with open(os.path.join(self.m_bench.outdir, 'params.json'), 'w') as fout: + json.dump(param_dict, fout) + + b_vcf = pysam.VariantFile(self.m_bench.base_vcf) + c_vcf = pysam.VariantFile(self.m_bench.comp_vcf) + self.n_headers = {'b':edit_header(b_vcf), + 'c':edit_header(c_vcf)} + + self.vcf_filenames = {'tpb': os.path.join(self.m_bench.outdir, "tp-base.vcf"), + 'tpc': os.path.join(self.m_bench.outdir, "tp-comp.vcf"), + 'fn': os.path.join(self.m_bench.outdir, "fn.vcf"), + 'fp': os.path.join(self.m_bench.outdir, "fp.vcf")} + self.out_vcfs = {} + for key in ['tpb', 'fn']: + self.out_vcfs[key] = pysam.VariantFile(self.vcf_filenames[key], mode='w', header=self.n_headers['b']) + for key in ['tpc', 'fp']: + self.out_vcfs[key] = pysam.VariantFile(self.vcf_filenames[key], mode='w', header=self.n_headers['c']) + + self.stats_box = StatsBox() + + def write_match(self, match): + """ + Annotate a MatchResults' entries then write to the apppropriate file + and do the stats counting. + Writer is responsible for handling FPs between sizefilt-sizemin + """ + box = self.stats_box + if match.base: + box["base cnt"] += 1 + annotate_entry(match.base, match, self.n_headers['b']) + if match.state: + gtBase = str(match.base_gt) + gtComp = str(match.comp_gt) + box["gt_matrix"][gtBase][gtComp] += 1 + + box["TP-base"] += 1 + self.out_vcfs["tpb"].write(match.base) + if match.gt_match == 0: + box["TP-base_TP-gt"] += 1 + else: + box["TP-base_FP-gt"] += 1 + else: + box["FN"] += 1 + self.out_vcfs["fn"].write(match.base) + + if match.comp: + annotate_entry(match.comp, match, self.n_headers['c']) + if match.state: + box["comp cnt"] += 1 + box["TP-comp"] += 1 + self.out_vcfs["tpc"].write(match.comp) + if match.gt_match == 0: + box["TP-comp_TP-gt"] += 1 + else: + box["TP-comp_FP-gt"] += 1 + elif truvari.entry_size(match.comp) >= self.m_matcher.params.sizemin: + # The if is because we don't count FPs between sizefilt-sizemin + box["comp cnt"] += 1 + box["FP"] += 1 + self.out_vcfs["fp"].write(match.comp) + + def close_outputs(self): + """ + Close all the files + """ + for i in self.out_vcfs.values(): + i.close() + for i in self.vcf_filenames.values(): + truvari.compress_index_vcf(i) -def bench_main(cmdargs): + self.stats_box.calc_performance() + self.stats_box.write_json(os.path.join(self.m_bench.outdir, "summary.json")) + + +class Bench(): """ - Main + Object to perform operations of truvari bench + + You can build a Bench worker with default matching parameters via: + + .. code-block:: python + + m_bench = truvari.Bench() + + If you'd like to customize the parameters, build and edit a :class:`Matcher` and pass it to the Bench init + + .. code-block:: python + + matcher = truvari.Matcher() + matcher.params.pctseq = 0.50 + m_bench = truvari.Bench(matcher) + + To run on a chunk of :class:`pysam.VariantRecord` already loaded, pass them in as lists to: + + .. code-block:: python + + matches = m_bench.compare_calls(base_variants, comp_variants) + + For advanced parsing, one can build the match matrix for a chunk of calls with: + + .. code-block:: python + + match_matrix = m_bench.build_matrix(base_variants, comp_variants) + + This can then be used for things such as creating custom match pickers or adding new matching checks. + + If you want to run on existing files, simply supply the arguments to init + + .. code-block:: python + + m_bench = truvari.Bench(matcher, base_vcf, comp_vcf, outdir) + output = m_bench.run() + + Note that running on files must write to an output directory and is the only way to use things like 'includebed'. + However, the returned `BenchOutput` has attributes pointing to all the results. """ - args = parse_args(cmdargs) + def __init__(self, matcher=None, base_vcf=None, comp_vcf=None, outdir=None, + includebed=None, extend=0, debug=False , do_logging=False): + """ + Initilize + """ + self.matcher = matcher if matcher is not None else truvari.Matcher() + self.base_vcf = base_vcf + self.comp_vcf = comp_vcf + self.outdir = outdir + self.includebed = includebed + self.extend = extend + self.debug = debug + self.do_logging = do_logging + + def param_dict(self): + """ + Returns the parameters as a dict + """ + return {'base': self.base_vcf, + "comp": self.comp_vcf, + "output": self.outdir, + "includebed": self.includebed, + "extend": self.extend, + "debug": self.debug} + + def run(self): + """ + Runs bench and returns the resulting :class:`truvari.BenchOutput` + """ + if self.base_vcf is None or self.comp_vcf is None or self.outdir is None: + raise RuntimeError("Cannot call Bench.run without base/comp vcf filenames and outdir") - if check_params(args) or check_inputs(args): - sys.stderr.write("Couldn't run Truvari. Please fix parameters\n") - sys.exit(100) + output = BenchOutput(self, self.matcher) + + base = pysam.VariantFile(self.base_vcf) + comp = pysam.VariantFile(self.comp_vcf) + + regions = truvari.RegionVCFIterator(base, comp, + self.includebed, + self.matcher.params.sizemax) + regions.merge_overlaps() + regions_extended = regions.extend(self.extend) if self.extend else regions + + base_i = regions.iterate(base) + comp_i = regions_extended.iterate(comp) - matcher = truvari.Matcher(args=args) - outputs = setup_outputs(args) + chunks = truvari.chunker(self.matcher, ('base', base_i), ('comp', comp_i)) + for match in itertools.chain.from_iterable(map(self.compare_chunk, chunks)): + # setting non-matched comp variants that are not fully contained in the original regions to None + # These don't count as FP or TP and don't appear in the output vcf files + if self.extend and match.comp is not None and not match.state and not regions.include(match.comp): + match.comp = None + output.write_match(match) + + output.close_outputs() + return output + + def compare_chunk(self, chunk): + """ + Given a filtered chunk, (from chunker) compare all of the calls + """ + _, chunk_dict, chunk_id = chunk + logging.debug("Comparing chunk %s", chunk_id) + return self.compare_calls(chunk_dict["base"], chunk_dict["comp"], chunk_id) + + def compare_calls(self, base_variants, comp_variants, chunk_id=0): + """ + Builds MatchResults, returns them as a numpy matrix if there's at least one base and one comp variant. + Otherwise, returns a list of the variants placed in MatchResults + """ + # All FPs + if len(base_variants) == 0: + fps = [] + for cid, c in enumerate(comp_variants): + ret = truvari.MatchResult() + ret.comp = c + ret.matid = f"{chunk_id}._.{cid}" + fps.append(ret) + logging.debug("All FP -> %s", ret) + return fps + + # All FNs + if len(comp_variants) == 0: + fns = [] + for bid, b in enumerate(base_variants): + ret = truvari.MatchResult() + ret.base = b + ret.matid = f"{chunk_id}.{bid}._" + logging.debug("All FN -> %s", ret) + fns.append(ret) + return fns + + match_matrix = self.build_matrix(base_variants, comp_variants, chunk_id) + if isinstance(match_matrix, list): + return match_matrix + return PICKERS[self.matcher.params.pick](match_matrix) + + def build_matrix(self, base_variants, comp_variants, chunk_id=0, skip_gt=False): + """ + Builds MatchResults, returns them as a numpy matrix + """ + if not base_variants or not comp_variants: + raise RuntimeError("Expected at least one base and one comp variant") + match_matrix = [] + for bid, b in enumerate(base_variants): + base_matches = [] + for cid, c in enumerate(comp_variants): + mat = self.matcher.build_match(b, c, f"{chunk_id}.{bid}.{cid}", skip_gt) + logging.debug("Made mat -> %s", mat) + base_matches.append(mat) + match_matrix.append(base_matches) + + return np.array(match_matrix) + + +################# +# Match Pickers # +################# +def pick_multi_matches(match_matrix): + """ + Given a numpy array of MatchResults + Pick each base/comp call's best match + """ + ret = [] + for b_max in match_matrix.max(axis=1): + b_max = copy.copy(b_max) + b_max.comp = None + ret.append(b_max) - base = pysam.VariantFile(args.base) - comp = pysam.VariantFile(args.comp) + for c_max in match_matrix.max(axis=0): + c_max = copy.copy(c_max) + c_max.base = None + ret.append(c_max) + return ret - regions = truvari.RegionVCFIterator(base, comp, - args.includebed, - args.sizemax) +def pick_ac_matches(match_matrix): + """ + Given a numpy array of MatchResults + Find upto allele count mumber of matches + """ + ret = [] + base_cnt, comp_cnt = match_matrix.shape + match_matrix = np.ravel(match_matrix) + match_matrix.sort() + used_comp = Counter() + used_base = Counter() + for match in match_matrix[::-1]: + # No more matches to find + if base_cnt == 0 and comp_cnt == 0: + break + b_key = str(match.base) + c_key = str(match.comp) + # This is a trick + base_is_used = used_base[b_key] >= match.base_gt_count + comp_is_used = used_comp[c_key] >= match.comp_gt_count + # Only write the comp (FP) + if base_cnt == 0 and not comp_is_used: + to_process = copy.copy(match) + to_process.base = None + to_process.multi = to_process.state + to_process.state = False + comp_cnt -= 1 + if used_comp[c_key] == 0: # Only write as F if it hasn't been a T + ret.append(to_process) + used_comp[c_key] = 9 + # Only write the base (FN) + elif comp_cnt == 0 and not base_is_used: + to_process = copy.copy(match) + to_process.comp = None + to_process.multi = to_process.state + to_process.state = False + base_cnt -= 1 + if used_base[b_key] == 0: # Only write as F if it hasn't been a T + ret.append(to_process) + used_base[b_key] = 9 + # Write both (any state) + elif not base_is_used and not comp_is_used: + to_process = copy.copy(match) + # Don't write twice + if used_base[b_key] != 0: + to_process.base = None + if used_comp[c_key] != 0: + to_process.comp = None + + used_base[b_key] += match.comp_gt_count + used_comp[c_key] += match.base_gt_count + # All used up + if used_base[b_key] >= match.base_gt_count: + base_cnt -= 1 + if used_comp[c_key] >= match.comp_gt_count: + comp_cnt -= 1 + + # Safety edge case check + if to_process.base is not None or to_process.comp is not None: + ret.append(to_process) + return ret - regions.merge_overlaps() - regions_extended = regions.extend(args.extend) if args.extend else regions +def pick_single_matches(match_matrix): + """ + Given a numpy array of MatchResults, find the single best match for calls + Once all best pairs yielded, the unpaired calls are set to FP/FN and yielded + """ + hit_order = np.array(np.unravel_index(np.argsort(match_matrix, axis=None), match_matrix.shape)).T + top_hit_idx = len(hit_order) - 1 + + mask = np.ones(match_matrix.shape, dtype='bool') # True = can use + + used_pairs = [] + while top_hit_idx >= 0 and mask.any(): + idx = tuple(hit_order[top_hit_idx]) + if mask[idx]: + mask[idx[0], :] = False + mask[:, idx[1]] = False + used_pairs.append(idx) + yield match_matrix[idx] + top_hit_idx -= 1 + + used_base, used_comp = zip(*used_pairs) if used_pairs else ([],[]) + # FNs + for base_col in set(range(match_matrix.shape[0])) - set(used_base): + comp_col = match_matrix[base_col].argmax() + to_process = copy.copy(match_matrix[base_col, comp_col]) + to_process.comp = None # The comp will be written elsewhere + to_process.multi = to_process.state + to_process.state = False + yield to_process + + # FPs + for comp_col in set(range(match_matrix.shape[1])) - set(used_comp): + base_col = match_matrix[:, comp_col].argmax() + to_process = copy.copy(match_matrix[base_col, comp_col]) + to_process.base = None # The base will be written elsewhere + to_process.multi = to_process.state + to_process.state = False + yield to_process + +PICKERS = {"single": pick_single_matches, + "ac": pick_ac_matches, + "multi": pick_multi_matches + } - base_i = regions.iterate(base) - comp_i = regions_extended.iterate(comp) - chunks = truvari.chunker(matcher, ('base', base_i), ('comp', comp_i)) - for match in itertools.chain.from_iterable(map(compare_chunk, chunks)): - # setting non-matched comp variants that are not fully contained in the original regions to None - # These don't count as FP or TP and don't appear in the output vcf files - if args.extend and match.comp is not None and not match.state and not regions.include(match.comp): - match.comp = None - output_writer(match, outputs, args.sizemin) +def bench_main(cmdargs): + """ + Main - entry point from command line + """ + args = parse_args(cmdargs) - with open(os.path.join(args.output, "summary.txt"), 'w') as fout: - box = outputs["stats_box"] - box.calc_performance() - fout.write(json.dumps(box, indent=4)) - logging.info("Stats: %s", json.dumps(box, indent=4)) + if check_params(args) or check_inputs(args): + sys.stderr.write("Couldn't run Truvari. Please fix parameters\n") + sys.exit(100) - close_outputs(outputs) + matcher = truvari.Matcher(args) - if args.giabreport: - make_giabreport(args, outputs["stats_box"]) + m_bench = Bench(matcher, args.base, args.comp, args.output, args.includebed, args.extend, args.debug, True) + output = m_bench.run() + logging.info("Stats: %s", json.dumps(output.stats_box, indent=4)) logging.info("Finished bench") diff --git a/truvari/collapse.py b/truvari/collapse.py index ec4a9a12..d8412867 100644 --- a/truvari/collapse.py +++ b/truvari/collapse.py @@ -17,14 +17,13 @@ import truvari import truvari.bench as trubench - def collapse_chunk(chunk): """ For calls in a chunk, separate which ones should be kept from collapsed """ matcher, chunk_dict, chunk_id = chunk calls = chunk_dict['base'] - logging.debug(f"Comparing chunk {calls}") + logging.debug("Collapsing chunk %d", chunk_id) # Need to add a deterministic sort here... calls.sort(key=matcher.sorter) @@ -51,7 +50,8 @@ def collapse_chunk(chunk): mat = matcher.build_match(cur_keep_candidate, cur_collapse_candidate, ret[keep_key][2], - skip_gt=True) + skip_gt=True, + short_circuit=True) if matcher.hap and not hap_resolve(cur_keep_candidate, cur_collapse_candidate): mat.state = False # to collapse @@ -75,8 +75,7 @@ def collapse_chunk(chunk): calls = remaining_calls if matcher.no_consolidate: - for key, val in ret.items(): - logging.debug("Collapsing %s", key) + for val in ret.values(): edited_entry, collapse_cnt = collapse_into_entry(val[0], val[1], matcher.hap) val[0] = edited_entry val[3] = collapse_cnt @@ -84,7 +83,7 @@ def collapse_chunk(chunk): ret = list(ret.values()) for i in chunk_dict['__filtered']: ret.append([i, None, None, 0]) - + ret.sort(key=cmp_to_key(lambda x, y: x[0].pos - y[0].pos)) return ret @@ -128,16 +127,14 @@ def collapse_into_entry(entry, others, hap_mode=False): try: entry.samples[sample][key] = o_entry.samples[sample][key] except TypeError: - logging.warning( - "Unable to set FORMAT %s for sample %s", key, sample) - logging.warning("Kept entry: %s:%d %s", entry.chrom, entry.pos, entry.id) - logging.warning("Colap entry: %s:%d %s", o_entry.chrom, o_entry.pos, o_entry.id) + # Happens for things like PL when one is null but its expecting a tuple + logging.debug("Unable to set FORMAT %s for sample %s", key, sample) + logging.debug("Kept entry: %s:%d %s", entry.chrom, entry.pos, entry.id) + logging.debug("Colap entry: %s:%d %s", o_entry.chrom, o_entry.pos, o_entry.id) except KeyError: logging.debug("Unshared format %s in sample %s ignored for pair %s:%d %s %s:%d %s", key, sample, entry.chrom, entry.pos, entry.id, o_entry.chrom, o_entry.pos, o_entry.id) - - return entry, n_consolidate @@ -247,7 +244,7 @@ def parse_args(args): parser = argparse.ArgumentParser(prog="collapse", description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter) parser.add_argument("-i", "--input", type=str, required=True, - help="Comparison set of calls") + help="Input variants") parser.add_argument("-o", "--output", type=str, default="/dev/stdout", help="Output vcf (stdout)") parser.add_argument("-c", "--collapsed-output", type=str, default="collapsed.vcf", @@ -262,8 +259,8 @@ def parse_args(args): thresg = parser.add_argument_group("Comparison Threshold Arguments") thresg.add_argument("-r", "--refdist", type=truvari.restricted_int, default=500, help="Max reference location distance (%(default)s)") - thresg.add_argument("-p", "--pctsim", type=truvari.restricted_float, default=0.95, - help="Min percent allele sequence similarity. Set to 0 to ignore. (%(default)s)") + thresg.add_argument("-p", "--pctseq", type=truvari.restricted_float, default=0.95, + help="Min percent sequence similarity. Set to 0 to ignore. (%(default)s)") thresg.add_argument("-B", "--minhaplen", type=truvari.restricted_int, default=50, help="Minimum haplotype sequence length to create (%(default)s)") thresg.add_argument("-P", "--pctsize", type=truvari.restricted_float, default=0.95, @@ -332,12 +329,10 @@ def build_collapse_matcher(args): So set it up for us here """ args.chunksize = args.refdist - args.gtcomp = False args.bSample = None args.cSample = None args.sizefilt = args.sizemin args.no_ref = False - args.multimatch = False matcher = truvari.Matcher(args=args) matcher.params.includebed = None matcher.keep = args.keep @@ -345,14 +340,15 @@ def build_collapse_matcher(args): matcher.chain = args.chain matcher.sorter = SORTS[args.keep] matcher.no_consolidate = args.no_consolidate + matcher.picker = 'single' return matcher - def setup_outputs(args): """ - Makes all of the output files - return a ... to get to each of the + Makes all of the output files for collapse + + returns a dictionary holding outputs """ truvari.setup_logging(args.debug, show_version=True) logging.info("Params:\n%s", json.dumps(vars(args), indent=4)) @@ -423,16 +419,6 @@ def collapse_main(args): chunks = truvari.chunker(matcher, ('base', base)) for call in itertools.chain.from_iterable(map(collapse_chunk, chunks)): output_writer(call, outputs) - #with concurrent.futures.ThreadPoolExecutor(max_workers = args.threads) as executor: - # future_chunks = {executor.submit(collapse_chunk, c): c for c in chunks} - # for future in concurrent.futures.as_completed(future_chunks): - # result = None - # try: - # result = future.result() - # except Exception as exc: - # logging.error('%r generated an exception: %s', result, exc) - # else: - # for call in result: close_outputs(outputs) logging.info("Wrote %d Variants", outputs["stats_box"]["out_cnt"]) @@ -440,7 +426,3 @@ def collapse_main(args): outputs["stats_box"]["kept_cnt"]) logging.info("%d samples' FORMAT fields consolidated", outputs["stats_box"]["consol_cnt"]) logging.info("Finished collapse") - - -if __name__ == '__main__': - collapse_main(sys.argv[1:]) diff --git a/truvari/comparisons.py b/truvari/comparisons.py index c2c1995d..d07380c7 100644 --- a/truvari/comparisons.py +++ b/truvari/comparisons.py @@ -3,118 +3,86 @@ that compare events, coordinates, or transform vcf entries """ import re -import logging +import hashlib import edlib -import Levenshtein import truvari -def entry_is_present(entry, sample=None): - """ - Checks if entry's sample genotype is present and is heterozygous or homozygous (a.k.a. present) - - :param `entry`: entry to check - :type `entry`: :class:`pysam.VariantRecord` - :param `sample`: sample name - :type `sample`: string, optional - - :return: True if variant is present in the sample - :rtype: bool - - Example - >>> import truvari - >>> import pysam - >>> v = pysam.VariantFile('repo_utils/test_files/input1.vcf.gz') - >>> truvari.entry_is_present(next(v)) - True - """ - if sample is None: - sample = entry.samples.keys()[0] - return "GT" in entry.samples[sample] and \ - truvari.get_gt(entry.samples[sample]["GT"]) in [ - truvari.GT.HET, truvari.GT.HOM] - - -def entry_to_key(entry, prefix="", bounds=False): +def create_pos_haplotype(a1, a2, ref, min_len=0): """ - Turn a vcf entry into a hashable key string. Use the prefix (base/comp) to indicate the source - VCF when consolidating multiple files' calls. If bounds: call entry_boundaries for start/stop. - - .. warning:: - If a caller redundantly calls a variant exactly the same. It will not have a unique key + Create haplotypes of two allele's regions that are assumed to be overlapping - :param `source`: string to identify vcf from which this entry originates - :type `source`: string - :param `entry`: entry to stringify - :type `entry`: :class:`pysam.VariantRecord` + :param `a1`: tuple of chrom, start, end, seq + :type `a1`: tuple + :param `a2`: tuple of chrom, start, end, seq + :type `a2`: tuple + :param `ref`: Reference genome + :type `ref`: :class:`pysam.FastaFile` + :param `min_len`: Minimum length of the haplotype sequence to create + :type `min_len`: int, optional - :return: hashable string uniquely identifying the variant - :rtype: string + :return: allele haplotype sequences created + :rtupe: tuple (string, string) """ - if prefix: - prefix += '.' - if bounds: - start, end = entry_boundaries(entry) - return f"{prefix}{entry.chrom}:{start}-{end}({entry.ref}|{entry.alts[0]})" + chrom, a1_start, a1_end, a1_seq = a1 + chrom, a2_start, a2_end, a2_seq = a2 + start = min(a1_start, a2_start) + end = max(a1_end, a2_end) - return f"{prefix}{entry.chrom}:{entry.start}-{entry.stop}.{entry.alts[0]}" + hap_len1 = (abs(a1_start - start) + len(a1_seq) + abs(a1_end - end)) + hap_len2 = (abs(a2_start - start) + len(a2_seq) + abs(a2_end - end)) + min_size = min(hap_len1, hap_len2) + if min_size < min_len: + start -= (min_len - min_size) // 2 + end += (min_len + min_size) // 2 + # no negative fetch + start = max(0, start) + hap1_seq = ref.fetch(chrom, start, a1_start) + \ + a1_seq + ref.fetch(chrom, a1_end, end) + hap2_seq = ref.fetch(chrom, start, a2_start) + \ + a2_seq + ref.fetch(chrom, a2_end, end) + return str(hap1_seq), str(hap2_seq) -def sizesim(sizeA, sizeB): +def entry_boundaries(entry, ins_inflate=False): """ - Calculate the size similarity percent and size diff for two sizes + Get the start and end of an entry - :param `sizeA`: first size - :type `sizeA`: int - :param `sizeB`: second size - :type `sizeB`: int + :param `entry`: entry to get bounds + :type `entry`: :class:`pysam.VariantRecord` + :param `ins_inflate`: inflate INS boundaries by sv length + :type `ins_inflate`: bool, optional - :return: size similarity percent and size diff (A - B) - :rtype: (float, int) + :return: start/end + :rtype: tuple (int, int) """ - if sizeA == 0 or sizeB == 0: - if sizeA == sizeB: - return 1, 0 - sizeA = max(sizeA, 1) - sizeB = max(sizeB, 1) - return min(sizeA, sizeB) / float(max(sizeA, sizeB)), sizeA - sizeB + start = entry.start + end = entry.stop + if ins_inflate and entry_variant_type(entry) == truvari.SV.INS: + size = entry_size(entry) + start -= size // 2 + end += size // 2 + return start, end def entry_distance(entryA, entryB): """ - Calculate the start and end distances of the pair - """ - astart, aend = entry_boundaries(entryA) - bstart, bend = entry_boundaries(entryB) - return astart - bstart, aend - bend - - -def entry_size_similarity(entryA, entryB): - """ - Calculate the size similarity percent for two entries + Calculate the start and end distances of the pair. Negative distances + indicate entryA is upstream of entryB :param `entryA`: first entry :type `entryA`: :class:`pysam.VariantRecord` :param `entryB`: second entry :type `entryB`: :class:`pysam.VariantRecord` - :return: size similarity percent and size diff (A - B) - :rtype: (float, int) - - Example - >>> import truvari - >>> import pysam - >>> v = pysam.VariantFile('repo_utils/test_files/input1.vcf.gz') - >>> a = next(v) - >>> b = next(v) - >>> truvari.entry_size_similarity(a, b) - (0.07142857142857142, 13) + :return: starts and ends distance + :rtype: tuple (int, int) """ - sizeA = entry_size(entryA) - sizeB = entry_size(entryB) - return sizesim(sizeA, sizeB) + astart, aend = entry_boundaries(entryA) + bstart, bend = entry_boundaries(entryB) + return astart - bstart, aend - bend def entry_gt_comp(entryA, entryB, sampleA=None, sampleB=None): @@ -124,7 +92,7 @@ def entry_gt_comp(entryA, entryB, sampleA=None, sampleB=None): :param `entryA`: first entry :type `entryA`: :class:`pysam.VariantRecord` :param `entryB`: second entry - :type `entryB`: :class`pysam.VariantRecord` + :type `entryB`: :class:`pysam.VariantRecord` :param `sampleA`: sample of entryA to check :type `sampleA`: string, optional :param `sampleB`: sample of entryB to check @@ -136,7 +104,7 @@ def entry_gt_comp(entryA, entryB, sampleA=None, sampleB=None): Example >>> import truvari >>> import pysam - >>> v = pysam.VariantFile('repo_utils/test_files/input1.vcf.gz') + >>> v = pysam.VariantFile('repo_utils/test_files/variants/input1.vcf.gz') >>> a = next(v) >>> b = next(v) >>> truvari.entry_gt_comp(a, b) @@ -149,97 +117,63 @@ def entry_gt_comp(entryA, entryB, sampleA=None, sampleB=None): return truvari.get_gt(entryA.samples[sampleA]["GT"]) == truvari.get_gt(entryB.samples[sampleB]["GT"]) -def create_pos_haplotype(a1, a2, ref, min_len=0): - """ - Create haplotypes of two allele's regions that are assumed to be overlapping - - :param `a1`: tuple of chrom, start, end, seq - :type `a1`: tuple - :param `a2`: tuple of chrom, start, end, seq - :type `a2`: tuple - :param `ref`: Reference genome - :type `ref`: :class:`pysam.FastaFile` - :param `min_len`: Minimum length of the haplotype sequence to create - :type `min_len`: int, optional - - :return: allele haplotype sequences created - :rtupe: tuple (string, string) +def entry_is_filtered(entry, values=None): """ - chrom, a1_start, a1_end, a1_seq = a1 - chrom, a2_start, a2_end, a2_seq = a2 - start = min(a1_start, a2_start) - end = max(a1_end, a2_end) + Checks if entry should be filtered given the filter values provided. + If values is None, assume that filter must have PASS or be blank '.' - hap_len1 = (abs(a1_start - start) + len(a1_seq) + abs(a1_end - end)) - hap_len2 = (abs(a2_start - start) + len(a2_seq) + abs(a2_end - end)) - min_size = min(hap_len1, hap_len2) - if min_size < min_len: - start -= (min_len - min_size) // 2 - end += (min_len + min_size) // 2 - # no negative fetch - start = max(0, start) - hap1_seq = ref.fetch(chrom, start, a1_start) + \ - a1_seq + ref.fetch(chrom, a1_end, end) - hap2_seq = ref.fetch(chrom, start, a2_start) + \ - a2_seq + ref.fetch(chrom, a2_end, end) - return str(hap1_seq), str(hap2_seq) + :param `entry`: entry to check + :type `entry`: :class:`pysam.VariantRecord` + :param `values`: set of filter values for intersection + :type `values`: set, optional + :return: True if entry should be filtered + :rtype: bool -def entry_create_haplotype(entryA, entryB, ref, use_ref_seq=False, min_len=0): + Example + >>> import truvari + >>> import pysam + >>> v = pysam.VariantFile('repo_utils/test_files/variants/input1.vcf.gz') + >>> truvari.entry_is_filtered(next(v)) # PASS shouldn't be filtered + False + >>> truvari.entry_is_filtered(next(v), set(["lowQ"])) # Call isn't lowQ, so filter + True """ - Turn two entries into their haplotype sequence for comparison + if values is None: + return len(entry.filter) != 0 and 'PASS' not in entry.filter + return len(set(values).intersection(set(entry.filter))) == 0 - :param `entryA`: first entry - :type `entryA`: :class:`pysam.VariantRecord` - :param `entryB`: second entry - :type `entryB`: :class:`pysam.VariantRecord` - :param `ref`: Reference genome - :type `ref`: :class:`pysam.FastaFile` - :param `use_ref_seq`: If True, use the reference genome to get the sequence instead of the vcf entries - :type `use_ref_seq`: bool, optional - :param `min_len`: Minimum length of the haplotype sequence to create - :type `min_len`: int, optional - :return: allele haplotype sequences created - :rtype: tuple : (string, string) +def entry_is_present(entry, sample=None): """ - def get_props(entry): - """ - We compare the longer of the ref/alt sequence to increase comparability - """ - if use_ref_seq and (entry.alts[0] == "" or len(entry.alts[0]) < len(entry.ref)): - return entry.chrom, entry.start, entry.stop, ref.fetch(entry.chrom, entry.start, entry.stop) - return entry.chrom, entry.start, entry.stop, entry.alts[0] - a1 = get_props(entryA) - a2 = get_props(entryB) - return create_pos_haplotype(a1, a2, ref, min_len=min_len) + Checks if entry's sample genotype is present and is heterozygous or homozygous (a.k.a. present) -def entry_to_haplotype(entry, ref, start=None, end=None): - """ - Integrate an entry into the reference and return the sequence. + :param `entry`: entry to check + :type `entry`: :class:`pysam.VariantRecord` + :param `sample`: sample name + :type `sample`: string, optional - :param `entry`: vcf entry - :type `entry: :class:`pysam.VariantRecord` - :param `ref`: reference genome - :type `ref`: :class:`pysam.FastaFile` - :param `start`: beginning region of reference to use - :type `start`: int, optional - :param `end`: beginning region of reference to use - :type `end`: int, optional + :return: True if variant is present in the sample + :rtype: bool - :return: allele haplotype sequence - :rtype: str + Example + >>> import truvari + >>> import pysam + >>> v = pysam.VariantFile('repo_utils/test_files/variants/input1.vcf.gz') + >>> truvari.entry_is_present(next(v)) + True """ - chrom = entry.chrom - a1_start = entry.start - a1_end = entry.stop - hap1_seq = ref.fetch(chrom, start, a1_start) + \ - entry.alts[0] + ref.fetch(chrom, a1_end, end) - return hap1_seq + if sample is None: + sample = entry.samples.keys()[0] + return "GT" in entry.samples[sample] and \ + truvari.get_gt(entry.samples[sample]["GT"]) in [ + truvari.GT.HET, truvari.GT.HOM] -def entry_pctsim(entryA, entryB, ref, min_len=0, use_lev=True): + +def entry_seq_similarity(entryA, entryB, ref=None, min_len=0): """ - Calculate similarity of two entries' haplotype changes + Calculate sequence similarity of two entries. If reference is not None, + compare their shared reference context. Otherwise, use the unroll technique. :param `entryA`: first entry :type `entryA`: :class:`pysam.VariantRecord` @@ -247,10 +181,8 @@ def entry_pctsim(entryA, entryB, ref, min_len=0, use_lev=True): :type `entryB`: :class:`pysam.VariantRecord` :param `ref`: Reference genome :type `ref`: :class:`pysam.FastaFile` - :param `min_len`: Percent of selected region's range length to buffer + :param `min_len`: Minimum length of reference context to generate :type `min_len`: float, optional - :param `use_lev`: Use levenshtein distance by default. Set to False to use the faster edlib - :type `use_lev`: bool, optional :return: sequence similarity :rtype: float @@ -259,104 +191,81 @@ def entry_pctsim(entryA, entryB, ref, min_len=0, use_lev=True): if entryA.ref == entryB.ref and entryA.alts[0] == entryB.alts[0]: return 1.0 + # Inversions handled differently if entry_variant_type(entryA) == truvari.SV.INV and entry_variant_type(entryB) == truvari.SV.INV: allele1 = entryA.alts[0] allele2 = entryB.alts[0] - return seqsim(allele1, allele2, use_lev) + return seqsim(allele1, allele2) - # Handling of breakends should be here - allele1, allele2 = entry_create_haplotype(entryA, entryB, ref, min_len=min_len) - return seqsim(allele1, allele2, use_lev) + a_seq = entryA.ref if entry_variant_type(entryA) == truvari.SV.DEL else entryA.alts[0] + b_seq = entryB.ref if entry_variant_type(entryB) == truvari.SV.DEL else entryB.alts[0] + st_dist, ed_dist = entry_distance(entryA, entryB) + if st_dist == 0 or ed_dist == 0: + return seqsim(a_seq, b_seq) -def seqsim(allele1, allele2, use_lev=False): - """ - Calculate similarity of two sequences + if ref is not None: + allele1, allele2 = entry_shared_ref_context(entryA, entryB, ref, min_len=min_len) + return seqsim(allele1, allele2) - :param `allele1`: first entry - :type `allele1`: :class:`pysam.VariantRecord` - :param `allele2`: second entry - :type `allele2`: :class:`pysam.VariantRecord` - :param `use_lev`: Use levenshtein distance by default. Set to False to use the faster edlib - :type `use_lev`: bool, optional + if st_dist > 0: + return unroll_compare(a_seq, b_seq, st_dist % len(b_seq)) + return unroll_compare(b_seq, a_seq, st_dist % len(a_seq)) - :return: sequence similarity - :rtype: float - """ - allele1 = allele1.upper() - allele2 = allele2.upper() - if use_lev: - return Levenshtein.ratio(allele1, allele2) - scr = edlib.align(allele1, allele2) - totlen = len(allele1) + len(allele2) - return (totlen - scr["editDistance"]) / totlen - - -def overlaps(s1, e1, s2, e2): +def entry_reciprocal_overlap(entry1, entry2): """ - Check if two start/end ranges have overlap - - :param `s1`: range 1 start - :type `s1`: int - :param `e1`: range 1 end - :type `e1`: int - :param `s2`: range 2 start - :type `s2`: int - :param `e2`: range 2 end - :type `e2`: int + Calculates reciprocal overlap of two entries - :return: True if ranges overlap - :rtype: bool - """ - s_cand = max(s1, s2) - e_cand = min(e1, e2) - return s_cand < e_cand + :param `entry1`: First entry + :type `entry1`: :class:`pysam.VariantRecord` + :param `entry2`: Second entry + :type `entry2`: :class:`pysam.VariantRecord` + :return: The reciprocal overlap + :rtype: float -def entry_variant_type(entry): + Example + >>> import truvari + >>> import pysam + >>> v = pysam.VariantFile('repo_utils/test_files/variants/input1.vcf.gz') + >>> a = next(v) + >>> b = next(v) + >>> truvari.entry_reciprocal_overlap(a, b) + 0 """ - Return entry's SVTYPE - - .. note:: - How svtype is determined: - - - Starts by trying to use INFO/SVTYPE - - If SVTYPE is unavailable, infer if entry is a insertion or deletion by \ - looking at the REF/ALT sequence size differences - - If REF/ALT sequences are not available, try to parse the , , \ - etc from the ALT column. - - Otherwise, assume 'UNK' - - :param `entry`: - :type `entry`: :class:`pysam.VariantRecord` + astart, aend = entry_boundaries(entry1, True) + bstart, bend = entry_boundaries(entry2, True) + return reciprocal_overlap(astart, aend, bstart, bend) - :return: SV type - :rtype: :class:`truvari.SV` + +def entry_shared_ref_context(entryA, entryB, ref, use_ref_seq=False, min_len=0): """ - sv_alt_match = re.compile(r"\<(?P.*)\>") + Get the shared reference context of two entries and create the haplotype - ret_type = None - if "SVTYPE" in entry.info: - ret_type = entry.info["SVTYPE"] - if isinstance(ret_type, (list, tuple)): - ret_type = ret_type[0] - return truvari.get_svtype(ret_type) + :param `entryA`: first entry + :type `entryA`: :class:`pysam.VariantRecord` + :param `entryB`: second entry + :type `entryB`: :class:`pysam.VariantRecord` + :param `ref`: Reference genome + :type `ref`: :class:`pysam.FastaFile` + :param `use_ref_seq`: If True, use the reference genome to get the variant sequence instead the entries + :type `use_ref_seq`: bool, optional + :param `min_len`: Minimum length of the reference context to create + :type `min_len`: int, optional - if not (entry.alts[0].count("<") or entry.alts[0].count(":")): - # Doesn't have or BNDs as the alt seq, then we can assume it's sequence resolved..? - if len(entry.ref) < len(entry.alts[0]): - ret_type = "INS" - elif len(entry.ref) > len(entry.alts[0]): - ret_type = "DEL" - elif len(entry.ref) == len(entry.alts[0]): - ret_type = "SNP" if len(entry.ref) == 1 else "UNK" - return truvari.get_svtype(ret_type) - mat = sv_alt_match.match(entry.alts[0]) - if mat is not None: - return truvari.get_svtype(mat.groupdict()["SVTYPE"]) - logging.warning( - "SVTYPE is undetermined for entry, using 'UNK' - %s", str(entry)) - return truvari.get_svtype("UNK") + :return: sequences created + :rtype: tuple : (string, string) + """ + def get_props(entry): + """ + We compare the longer of the ref/alt sequence to increase comparability + """ + if use_ref_seq and (entry.alts[0] == "" or len(entry.alts[0]) < len(entry.ref)): + return entry.chrom, entry.start, entry.stop, ref.fetch(entry.chrom, entry.start, entry.stop) + return entry.chrom, entry.start, entry.stop, entry.alts[0] + a1 = get_props(entryA) + a2 = get_props(entryB) + return create_pos_haplotype(a1, a2, ref, min_len=min_len) def entry_same_variant_type(entryA, entryB, dup_to_ins=False): @@ -382,27 +291,6 @@ def entry_same_variant_type(entryA, entryB, dup_to_ins=False): return a_type == b_type -def entry_boundaries(entry, ins_inflate=False): - """ - Get the start/end of an entry and order (start < end) - - :param `entry`: entry to get bounds - :type `entry`: :class:`pysam.VariantRecord` - :param `ins_inflate`: inflate INS boundaries by sv length - :type `ins_inflate`: bool, optional - - :return: the entry's start/end boundaries - :rtype: tuple (int, int) - """ - start = entry.start - end = entry.stop - if ins_inflate and entry_variant_type(entry) == truvari.SV.INS: - size = entry_size(entry) - start -= size // 2 - end += size // 2 - return start, end - - def entry_size(entry): """ Determine the size of the variant. @@ -428,12 +316,12 @@ def entry_size(entry): size = abs(entry.info["SVLEN"][0]) else: size = abs(entry.info["SVLEN"]) - elif entry.alts[0].count("<"): + elif entry.alts is not None and entry.alts[0].count("<"): start, end = entry_boundaries(entry) size = end - start else: r_len = len(entry.ref) - a_len = len(entry.alts[0]) + a_len = len(entry.alts[0]) if entry.alts is not None else 0 if r_len == a_len: if r_len == 1: size = 0 # SNPs are special @@ -444,31 +332,120 @@ def entry_size(entry): return size -def weighted_score(sim, size, ovl): +def entry_size_similarity(entryA, entryB): + """ + Calculate the size similarity and difference for two entries + + :param `entryA`: first entry + :type `entryA`: :class:`pysam.VariantRecord` + :param `entryB`: second entry + :type `entryB`: :class:`pysam.VariantRecord` + + :return: size similarity and size diff (A - B) + :rtype: (float, int) + + Example + >>> import truvari + >>> import pysam + >>> v = pysam.VariantFile('repo_utils/test_files/variants/input1.vcf.gz') + >>> a = next(v) + >>> b = next(v) + >>> truvari.entry_size_similarity(a, b) + (0.07142857142857142, 13) + """ + sizeA = entry_size(entryA) + sizeB = entry_size(entryB) + return sizesim(sizeA, sizeB) + +def entry_to_hash(entry, hasher=hashlib.sha1): """ - Unite the similarity measures and make a score - `(2*sim + 1*size + 1*ovl) / 3.0` scaled to 0-100 + Turn variant into a key and hash with provided hasher - :param `sim`: - :type `sim`: float - Sequence similarity - :param `size`: - :type `size`: float - Size similarity - :param `ovl`: Reciprocal overlap - :type `ovl`: float + :param `entry`: entry + :type `entry`: :class:`pysam.VariantRecord` + :param `hasher`: hashing function + :type `entry`: method - :return: The score - :rtype: float + :return: hash + :rtype: string """ - score = (sim + size + ovl) / 3.0 * 100 - #new_score = score / 1.333333 * 100 - return score + return hasher(entry_to_key(entry).encode()).hexdigest() -def reciprocal_overlap(astart, aend, bstart, bend): +def entry_to_key(entry, prefix="", bounds=False): """ - Calculates reciprocal overlap of two ranges + Turn a vcf entry into a hashable key string. Use the prefix (base/comp) to indicate the source + VCF when consolidating multiple files' calls. If bounds: call entry_boundaries for start/stop. + + .. warning:: + If a caller redundantly calls a variant exactly the same. It will not have a unique key + + :param `entry`: entry to stringify + :type `entry`: :class:`pysam.VariantRecord` + :param `prefix`: prefix + :type `prefix`: string, optional + :param `bounds`: use entry_boundaries + :type `bounds`: bool, optional + + :return: hashable string uniquely identifying the variant + :rtype: string + """ + if prefix: + prefix += '.' + alt = entry.alts[0] if entry.alts is not None else "." + if bounds: + start, end = entry_boundaries(entry) + return f"{prefix}{entry.chrom}:{start}-{end}({entry.ref}|{alt})" + return f"{prefix}{entry.chrom}:{entry.start}-{entry.stop}.{alt}" + + +def entry_variant_type(entry): + """ + Return entry's SVTYPE + + .. note:: + How svtype is determined: + + - Starts by trying to use INFO/SVTYPE + - If SVTYPE is unavailable, infer if entry is a insertion or deletion by \ + looking at the REF/ALT sequence size differences + - If REF/ALT sequences are not available, try to parse the , , \ + etc from the ALT column. + - Otherwise, assume 'UNK' + + :param `entry`: + :type `entry`: :class:`pysam.VariantRecord` + + :return: SV type + :rtype: :class:`truvari.SV` + """ + sv_alt_match = re.compile(r"\<(?P.*)\>") + + ret_type = None + if "SVTYPE" in entry.info: + ret_type = entry.info["SVTYPE"] + if isinstance(ret_type, (list, tuple)): + ret_type = ret_type[0] + return truvari.get_svtype(ret_type) + + if entry.alts is not None and not (entry.alts[0].count("<") or entry.alts[0].count(":")): + # Doesn't have or BNDs as the alt seq, then we can assume it's sequence resolved..? + if len(entry.ref) < len(entry.alts[0]): + ret_type = "INS" + elif len(entry.ref) > len(entry.alts[0]): + ret_type = "DEL" + elif len(entry.ref) == len(entry.alts[0]): + ret_type = "SNP" if len(entry.ref) == 1 else "UNK" + return truvari.get_svtype(ret_type) + mat = sv_alt_match.match(entry.alts[0]) if entry.alts is not None else None + if mat is not None: + return truvari.get_svtype(mat.groupdict()["SVTYPE"]) + return truvari.get_svtype("UNK") + + +def overlap_percent(astart, aend, bstart, bend): + """ + Calculates the percent of range A which overlaps with range B :param `astart`: First range's start position :type `astart`: int @@ -479,21 +456,45 @@ def reciprocal_overlap(astart, aend, bstart, bend): :param `bend`: Second range's end position :type `bend`: int - :return: reciprocal overlap + :return: overlap percent :rtype: float """ + if astart >= bstart and aend <= bend: + return 1 ovl_start = max(astart, bstart) ovl_end = min(aend, bend) if ovl_start < ovl_end: # Otherwise, they're not overlapping - ovl_pct = float(ovl_end - ovl_start) / \ - max(aend - astart, bend - bstart) + ovl_pct = float(ovl_end - ovl_start) / (aend - astart) else: ovl_pct = 0 return ovl_pct -def overlap_percent(astart, aend, bstart, bend): + +def overlaps(s1, e1, s2, e2): """ - Calculates the percent of range A which overlaps with range B + Check if two start/end ranges have overlap + + :param `s1`: range 1 start + :type `s1`: int + :param `e1`: range 1 end + :type `e1`: int + :param `s2`: range 2 start + :type `s2`: int + :param `e2`: range 2 end + :type `e2`: int + + :return: True if ranges overlap + :rtype: bool + """ + s_cand = max(s1, s2) + e_cand = min(e1, e2) + return s_cand < e_cand + + +def reciprocal_overlap(astart, aend, bstart, bend): + """ + Calculates reciprocal overlap of two ranges + :param `astart`: First range's start position :type `astart`: int :param `aend`: First range's end position @@ -503,70 +504,57 @@ def overlap_percent(astart, aend, bstart, bend): :param `bend`: Second range's end position :type `bend`: int - :return: overlap percent + :return: reciprocal overlap :rtype: float """ - if astart >= bstart and aend <= bend: - return 1 ovl_start = max(astart, bstart) ovl_end = min(aend, bend) if ovl_start < ovl_end: # Otherwise, they're not overlapping - ovl_pct = float(ovl_end - ovl_start) / (aend - astart) + ovl_pct = float(ovl_end - ovl_start) / \ + max(aend - astart, bend - bstart) else: ovl_pct = 0 return ovl_pct -def entry_reciprocal_overlap(entry1, entry2): + +def seqsim(allele1, allele2): """ - Calculates reciprocal overlap of two entries + Calculate similarity of two sequences - :param `entry1`: First entry - :type `entry1`: :class:`pysam.VariantRecord` - :param `entry2`: Second entry - :type `entry2`: :class:`pysam.VariantRecord` + :param `allele1`: first entry + :type `allele1`: :class:`pysam.VariantRecord` + :param `allele2`: second entry + :type `allele2`: :class:`pysam.VariantRecord` - :return: The reciprocal overlap + :return: sequence similarity :rtype: float - - Example - >>> import truvari - >>> import pysam - >>> v = pysam.VariantFile('repo_utils/test_files/input1.vcf.gz') - >>> a = next(v) - >>> b = next(v) - >>> truvari.entry_reciprocal_overlap(a, b) - 0 """ - astart, aend = entry_boundaries(entry1, True) - bstart, bend = entry_boundaries(entry2, True) - return reciprocal_overlap(astart, aend, bstart, bend) + allele1 = allele1.upper() + allele2 = allele2.upper() + scr = edlib.align(allele1, allele2) + totlen = len(allele1) + len(allele2) + return (totlen - scr["editDistance"]) / totlen -def entry_is_filtered(entry, values=None): +def sizesim(sizeA, sizeB): """ - Returns if entry should be filtered given the filter values provided. - If values is None, assume that filter must have PASS or be blank '.' - - :param `entry`: entry to check - :type `entry`: :class:`pysam.VariantRecord` - :param `values`: set of filter values for intersection - :type `values`: set, optional + Calculate the size similarity percent and size diff for two sizes - :return: True if entry should be filtered - :rtype: bool + :param `sizeA`: first size + :type `sizeA`: int + :param `sizeB`: second size + :type `sizeB`: int - Example - >>> import truvari - >>> import pysam - >>> v = pysam.VariantFile('repo_utils/test_files/input1.vcf.gz') - >>> truvari.entry_is_filtered(next(v)) # PASS shouldn't be filtered - False - >>> truvari.entry_is_filtered(next(v), set(["lowQ"])) # Call isn't lowQ, so filter - True + :return: size similarity percent and size diff (A - B) + :rtype: (float, int) """ - if values is None: - return len(entry.filter) != 0 and 'PASS' not in entry.filter - return len(set(values).intersection(set(entry.filter))) == 0 + if sizeA == 0 or sizeB == 0: + if sizeA == sizeB: + return 1, 0 + sizeA = max(sizeA, 1) + sizeB = max(sizeB, 1) + return min(sizeA, sizeB) / float(max(sizeA, sizeB)), sizeA - sizeB + def unroll_compare(seqA, seqB, p): """ @@ -574,8 +562,11 @@ def unroll_compare(seqA, seqB, p): See https://gist.github.com/ACEnglish/1e7421c46ee10c71bee4c03982e5df6c for details :param `seqA`: sequence + :type `seqA`: string :param `seqB`: sequence - :param `p`: positional difference + :type `seqB`: string + :param `p`: positional difference of A from B + :type `p`: integer :return: sequence similarity of seqA vs seqB after unrolling :rtype: float diff --git a/truvari/consistency.py b/truvari/consistency.py new file mode 100644 index 00000000..6ab0bfda --- /dev/null +++ b/truvari/consistency.py @@ -0,0 +1,160 @@ +""" +Over multiple vcfs, calculate their intersection/consistency. + +Calls will match between VCFs if they have a matching key of: + CHROM:POS ID REF ALT +""" +import json +import argparse +from collections import defaultdict, Counter + +import truvari + +def parse_vcf(fn): + """ + Simple vcf reader + """ + fh = truvari.opt_gz_open(fn) + for line in fh: + if line.startswith("#"): + continue + # Only keep the first 5 fields, and use them as key + yield "\t".join(line.split("\t")[:5]) + + +def read_files(allVCFs): + """ + Read all VCFs and mark all (union) calls for their presence + + For each call, we will use and integer and mark a call's presence + at the index of the VCF file as 1. + + For example, if we have 3 VCFs, and the call is present in only the + first VCF, then the integer will be `0 | (1 << 2)`, that is `0b100`, + where the first bit marks that the call appears in the first VCF. + + Returns: + all_presence: dict of all calls, with the integers as values. + The integers are the bitwise OR of all VCFs that have the call. + n_calls_per_vcf: list of the number of calls in each VCF + """ + n_vcfs = len(allVCFs) + # Initialize the integer to 0 + all_presence = defaultdict(lambda: 0) + n_calls_per_vcf = [0] * len(allVCFs) + for i, vcf in enumerate(allVCFs): + for key in parse_vcf(vcf): + n_calls_per_vcf[i] += 1 + all_presence[key] |= (1 << (n_vcfs - i - 1)) + + # We don't care about the calls anyway for stats + # Then this becomes a list of integers, which will save memory + return all_presence.values(), n_calls_per_vcf + + +def parse_args(args): + """ parse args """ + parser = argparse.ArgumentParser(prog="consistency", description=__doc__, + formatter_class=argparse.RawDescriptionHelpFormatter) + parser.add_argument("-j", "--json", action='store_true', + help="Output report in json format") + parser.add_argument("allVCFs", metavar='VCFs', nargs='+', + help="VCFs to intersect") + args = parser.parse_args(args) + return args + + +def make_report(allVCFs, all_presence, n_calls_per_vcf): + """ + Create the report + """ + output = {} + output['vcfs'] = allVCFs + total_unique_calls = len(all_presence) + output['total_calls'] = total_unique_calls + n_vcfs = len(allVCFs) + output['num_vcfs'] = n_vcfs + output['vcf_counts'] = {} + for i, fn in enumerate(allVCFs): + output['vcf_counts'][fn] = n_calls_per_vcf[i] + + output['shared'] = [] + output['detailed'] = [] + + # setup shared + for i in reversed(range(n_vcfs)): + output['shared'].append({'vcf_count': i + 1, 'num_calls': 0, 'call_pct': 0}) + + all_overlap = Counter(all_presence) + for group, ncalls in sorted(all_overlap.items(), key=lambda x: (-x[1], x[0])): + group = bin(group) + shared_calls_vcf_count = group.count("1") + output['shared'][-shared_calls_vcf_count]["num_calls"] += ncalls + + group = group[2:].rjust(n_vcfs, '0') + tot_pct = ncalls / total_unique_calls + c = [(ncalls / n_calls_per_vcf[i]) + if group[i] == "1" + else 0 + for i in range(n_vcfs) + ] + row = {'group': group, + 'total': ncalls, + 'total_pct': tot_pct} + for i, v in enumerate(c): + row[i] = v + output['detailed'].append(row) + + # finish shared + for i in range(n_vcfs): + output['shared'][i]['call_pct'] = output['shared'][i]['num_calls'] / total_unique_calls + return output + + + +def write_report(output): + """ + Write the report + """ + print(f"#\n# Total {output['total_calls']} calls across {output['num_vcfs']} VCFs\n#") + + print("#File\tNumCalls") + for name in output['vcfs']: + print(f"{name}\t{output['vcf_counts'][name]}") + + print("#\n# Summary of consistency\n#") + print("#VCFs\tCalls\tPct") + for row in output['shared']: + print(f"{row['vcf_count']}\t{row['num_calls']}\t{row['call_pct'] * 100:.2f}%") + + print("#\n# Breakdown of VCFs' consistency\n#") + print("#Group\tTotal\tTotalPct\tPctOfFileCalls") + for row in output['detailed']: + group = row['group'] + ncalls = row['total'] + tot_pct = row['total_pct'] * 100 + c_text = " ".join([f"{row[i] * 100:.2f}%" + if row['group'][i] == "1" + else "0%" + for i in range(output['num_vcfs']) + ]) + print(f"{group}\t{ncalls}\t{tot_pct:.2f}%\t{c_text}") + +def consistency_main(args): + """ + Run the program + """ + args = parse_args(args) + + all_presence, n_calls_per_vcf = read_files(args.allVCFs) + data = make_report(args.allVCFs, all_presence, n_calls_per_vcf) + if args.json: + for grp in data['detailed']: + # rename to file + for idx, name in enumerate(args.allVCFs): + pct = grp[idx] + del grp[idx] + grp[name] = pct + print(json.dumps(data, indent=4)) + else: + write_report(data) diff --git a/truvari/consistency_report.py b/truvari/consistency_report.py deleted file mode 100644 index ec9715f4..00000000 --- a/truvari/consistency_report.py +++ /dev/null @@ -1,164 +0,0 @@ -""" -Over multiple vcfs, calculate their intersection/consistency. - -Calls will match between VCFs if they have a matching key of: - CHROM:POS ID REF ALT -""" -# pylint: disable=consider-using-f-string -import io -import gzip -import argparse -import json -from collections import defaultdict, Counter - - -def parse_vcf(fn): - """ - Simple vcf reader - """ - if fn.endswith(".gz"): - fh = io.TextIOWrapper(gzip.open(fn)) - else: - fh = open(fn, 'r') # pylint: disable=consider-using-with - for line in fh: - if line.startswith("#"): - continue - # Only keep the first 5 fields, and use them as key - yield "\t".join(line.split("\t")[:5]) - - -def read_files(allVCFs): - """ - Read all VCFs and mark all (union) calls for their presence - - For each call, we will use and integer and mark a call's presence - at the index of the VCF file as 1. - - For example, if we have 3 VCFs, and the call is present in only the - first VCF, then the integer will be `0 | (1 << 2)`, that is `0b100`, - where the first bit marks that the call appears in the first VCF. - - Returns: - all_presence: dict of all calls, with the integers as values. - The integers are the bitwise OR of all VCFs that have the call. - n_calls_per_vcf: list of the number of calls in each VCF - """ - n_vcfs = len(allVCFs) - # Initialize the integer to 0 - all_presence = defaultdict(lambda: 0) - n_calls_per_vcf = [] - for i, vcf in enumerate(allVCFs): - n_calls_per_vcf.append(0) - for key in parse_vcf(vcf): - n_calls_per_vcf[i] += 1 - all_presence[key] |= (1 << (n_vcfs - i - 1)) - - # We don't care about the calls anyway for stats - # Then this becomes a list of integers, which will save memory - return all_presence.values(), n_calls_per_vcf - - -def get_shared_calls(all_presence, n): - """Get n shared calls from the all_presence dictionary""" - return sum( - 1 for presence in all_presence - if bin(presence).count("1") == n - ) - - -def parse_args(args): - """ parse args """ - parser = argparse.ArgumentParser(prog="consistency", description=__doc__, - formatter_class=argparse.RawDescriptionHelpFormatter) - parser.add_argument("-j", "--json", action='store_true', - help="Output report in json format") - parser.add_argument("allVCFs", metavar='VCFs', nargs='+', - help="VCFs to intersect") - args = parser.parse_args(args) - return args - - -def make_report(allVCFs, all_presence, n_calls_per_vcf): - """ - Create the report - """ - output = {} - output['vcfs'] = allVCFs - total_unique_calls = len(all_presence) - output['total_calls'] = total_unique_calls - n_vcfs = len(allVCFs) - output['num_vcfs'] = n_vcfs - output['vcf_counts'] = {} - for i, fn in enumerate(allVCFs): - output['vcf_counts'][fn] = n_calls_per_vcf[i] - output['shared'] = [] - for i in reversed(range(n_vcfs)): - shared_calls = get_shared_calls(all_presence, i + 1) - call_pct = shared_calls / total_unique_calls - output['shared'].append({'vcf_count': i + 1, 'num_calls': shared_calls, 'call_pct': call_pct}) - output['detailed'] = [] - all_overlap = Counter(all_presence) - for group, ncalls in sorted(all_overlap.items(), key=lambda x: (-x[1], x[0])): - group = bin(group)[2:].rjust(n_vcfs, '0') - tot_pct = ncalls / total_unique_calls - c = [(ncalls / n_calls_per_vcf[i]) - if group[i] == "1" - else 0 - for i in range(n_vcfs) - ] - row = {'group': group, - 'total': ncalls, - 'total_pct': tot_pct} - for i, v in enumerate(c): - row[i] = v - output['detailed'].append(row) - return output - - - -def write_report(output): - """ - Write the report - """ - print("#\n# Total %d calls across %d VCFs\n#" % - (output['total_calls'], output['num_vcfs'])) - - print("#File\tNumCalls") - for name in output['vcfs']: - print("%s\t%d" % (name, output['vcf_counts'][name])) - - print("#\n# Summary of consistency\n#") - print("#VCFs\tCalls\tPct") - for row in output['shared']: - print("%d\t%d\t%.2f%%" % ( - row['vcf_count'], - row['num_calls'], - row['call_pct'] * 100 - )) - - print("#\n# Breakdown of VCFs' consistency\n#") - print("#Group\tTotal\tTotalPct\tPctOfFileCalls") - for row in output['detailed']: - group = row['group'] - ncalls = row['total'] - tot_pct = row['total_pct'] * 100 - c_text = " ".join(["%.2f%%" % (row[i] * 100) - if row['group'][i] == "1" - else "0%" - for i in range(output['num_vcfs']) - ]) - print("%s\t%d\t%.2f%%\t%s" % - (group, ncalls, tot_pct, c_text)) - -def consistency_main(args): - """ - Run the program - """ - args = parse_args(args) - - all_presence, n_calls_per_vcf = read_files(args.allVCFs) - data = make_report(args.allVCFs, all_presence, n_calls_per_vcf) - if args.json: - print(json.dumps(data, indent=4)) - else: - write_report(data) diff --git a/truvari/divide.py b/truvari/divide.py index 9ad9a5fe..fb66c3bf 100644 --- a/truvari/divide.py +++ b/truvari/divide.py @@ -24,7 +24,7 @@ def parse_args(args): help="Output directory to save parts") parser.add_argument("-b", "--buffer", type=truvari.restricted_int, default=1000, help="Buffer to make mini-clusters (%(default)s)") - parser.add_argument("-m", "--min", type=truvari.restricted_int, default=100, + parser.add_argument("-m", "--min", type=truvari.restricted_int, default=50000, help="Minimum number of entries per-vcf (%(default)s)") parser.add_argument("--no-compress", action="store_false", help="Don't attempt to compress/index sub-VCFs") @@ -44,7 +44,7 @@ def flush_stack(in_vcf, stack, out_name, compress=True): cur_out.write(i) cur_out.close() if compress: - truvari.compress_index(out_name) + truvari.compress_index_vcf(out_name) def divide_main(args): """ diff --git a/truvari/giab_report.py b/truvari/giab_report.py deleted file mode 100644 index 3105fe8c..00000000 --- a/truvari/giab_report.py +++ /dev/null @@ -1,92 +0,0 @@ -""" -When running against GIAB SVs, we can make reports -""" -import os - -import joblib -import pandas as pd -import truvari -from truvari.vcf2df import bench_dir_to_df - - -def make_tech(data): - """ - Add tech and tech_str columns to the data frame - """ - flag = {1: "PB", 2: "Ill", 4: "TenX", 8: "CG"} - data['tech'] = 0 - for val, col in enumerate(["PBcalls", "Illcalls", "TenXcalls", "CGcalls"]): - data['tech'] += (data[col] != 0).astype(int) * (val + 1) ** 2 - - def make_tech_str(x): - ret = [] - for key, value in flag.items(): - if x & key: - ret.append(value) - if ret: - return "+".join(ret) - return None - data["tech_str"] = data['tech'].apply(make_tech_str) - - -def make_giabreport(args, stats_box): - """ - Create summaries of the TPs/FNs - """ - out_df = os.path.join(args.output, "giab.jl") - data = bench_dir_to_df(args.output, with_info=True, with_fmt=True, no_prefix=True) - joblib.dump(data, out_df) - sz_type = pd.CategoricalDtype( - categories=["50to99", "100to299", "300to999", "gt1000"], ordered=True) - data["sizecat"] = data["sizecat"].astype(sz_type) - make_tech(data) - with open(os.path.join(args.output, "giab_report.txt"), 'w') as sum_out: - sum_out.write("# Performance\n") - sum_out.write(f"recall: {stats_box['recall']}\n") - sum_out.write(f"precision: {stats_box['precision']}\n") - sum_out.write(f"f1: {stats_box['f1']}\n") - sum_out.write(f"gt_concordance: {stats_box['gt_concordance']}\n") - sum_out.write(data["state"].value_counts().to_csv(sep="\t") + "\n") - sum_out.write("\n") - - base_calls = data["state"].isin(["tpbase", "fn"]) - sum_out.write("# State by SizeCat and SVTYPE\n") - view = data[base_calls].groupby( - ["sizecat", "SVTYPE", "state"]).size().unstack(fill_value=0) - view["pct"] = view["tpbase"] / view.sum(axis=1) - sum_out.write(view.to_csv(sep="\t") + '\n') - sum_out.write("\n") - - sum_out.write("# State by REPTYPE\n") - view = data[base_calls].groupby( - ["REPTYPE", "state"]).size().unstack(fill_value=0) - view["pct"] = view["tpbase"] / (view["fn"] + view["tpbase"]) - view.sort_index(inplace=True) - sum_out.write(view.to_csv(sep="\t") + '\n') - sum_out.write("\n") - - sum_out.write("# State by Tech\n") - view = data[base_calls].groupby( - ["tech_str", "state"]).size().unstack(fill_value=0).sort_index() - view["pct"] = view["tpbase"] / view.sum(axis=1) - sum_out.write(view.to_csv(sep="\t") + '\n') - sum_out.write("\n") - - sum_out.write("# State by Genotype\n") - data["HG002_GT"] = data["GT"].apply(lambda x: truvari.get_gt(x).name if x else None) - view = data.groupby(["state", "HG002_GT"]).size().unstack(fill_value=0) - view.loc["total"] = view.sum(axis=0) - view["TOT"] = view.sum(axis=1) - view.loc["recall"] = view.loc["tpbase"] / \ - (view.loc["tpbase"] + view.loc["fn"]) - view.loc["precision"] = view.loc["tp"] / \ - (view.loc["tp"] + view.loc["fp"]) - view = view.round(decimals=2) - sum_out.write(view.to_csv(sep="\t") + '\n') - sum_out.write("\n") - - sum_out.write("# Args\n") - argd = vars(args) - for key in sorted(argd.keys()): - sum_out.write(f"{key}\t{str(argd[key])}\n") - joblib.dump(data, out_df) diff --git a/truvari/matching.py b/truvari/matching.py index 81a50794..8f9bb2ea 100644 --- a/truvari/matching.py +++ b/truvari/matching.py @@ -1,6 +1,7 @@ """ Comparison engine """ +import sys import types import logging from collections import Counter, defaultdict @@ -13,15 +14,17 @@ class MatchResult(): # pylint: disable=too-many-instance-attributes """ A base/comp match holder """ - __slots__ = ["base", "comp", "base_gt", "comp_gt", "state", "seqsim", "sizesim", - "ovlpct", "sizediff", "st_dist", "ed_dist", "gt_match", "multi", - "score", "matid"] + __slots__ = ["base", "comp", "base_gt", "base_gt_count", "comp_gt", "comp_gt_count", + "state", "seqsim", "sizesim", "ovlpct", "sizediff", "st_dist", "ed_dist", + "gt_match", "multi", "score", "matid"] def __init__(self): self.base = None self.comp = None self.base_gt = None + self.base_gt_count = 0 self.comp_gt = None + self.comp_gt_count = 0 self.matid = None self.seqsim = None self.sizesim = None @@ -30,17 +33,16 @@ def __init__(self): self.st_dist = None self.ed_dist = None self.gt_match = None + self.multi = None self.state = False self.score = None - self.multi = None def calc_score(self): """ - Set self.score to truvari.weighted_score + Unite the similarity measures and make a score """ if None not in [self.seqsim, self.sizesim, self.ovlpct]: - self.score = truvari.weighted_score( - self.seqsim, self.sizesim, self.ovlpct) + self.score = (self.seqsim + self.sizesim + self.ovlpct) / 3.0 * 100 def __lt__(self, other): # Trues are always worth more @@ -67,48 +69,52 @@ class Matcher(): >>> import pysam >>> import truvari >>> mat = truvari.Matcher() - >>> mat.params.pctsim = 0 - >>> v = pysam.VariantFile('repo_utils/test_files/input1.vcf.gz') + >>> mat.params.pctseq = 0 + >>> v = pysam.VariantFile('repo_utils/test_files/variants/input1.vcf.gz') >>> one = next(v); two = next(v) >>> mat.build_match(one, two) + + Look at `Matcher.make_match_params()` for a list of all params and their defaults """ - def __init__(self, params=None, args=None): + def __init__(self, args=None): + """ + Initalize. args is a Namespace from argparse + """ if args is not None: - params = self.make_match_params_from_args(args) - elif params is None: - params = self.make_match_params() + self.params = self.make_match_params_from_args(args) + else: + self.params = self.make_match_params() - self.params = params + self.reference = None + if self.params.reference is not None: + self.reference = pysam.FastaFile(self.params.reference) @staticmethod def make_match_params(): """ - Makes a simple namespace of matching parameters + Makes a simple namespace of matching parameters. Holds defaults """ - ret = types.SimpleNamespace() - ret.reference = None - ret.refdist = 500 - ret.pctsim = 0.70 - ret.minhaplen = 50 - ret.pctsize = 0.70 - ret.pctovl = 0.0 - ret.typeignore = False - ret.use_lev = False - ret.chunksize = 1000 - ret.gtcomp = False - ret.bSample = 0 - ret.cSample = 0 - ret.dup_to_ins = False - # filtering properties - ret.sizemin = 50 - ret.sizefilt = 30 - ret.sizemax = 50000 - ret.passonly = False - ret.no_ref = False - ret.multimatch = False - return ret + params = types.SimpleNamespace() + params.reference = None + params.refdist = 500 + params.pctseq = 0.70 + params.minhaplen = 50 + params.pctsize = 0.70 + params.pctovl = 0.0 + params.typeignore = False + params.chunksize = 1000 + params.bSample = 0 + params.cSample = 0 + params.dup_to_ins = False + params.sizemin = 50 + params.sizefilt = 30 + params.sizemax = 50000 + params.passonly = False + params.no_ref = False + params.pick = 'single' + return params @staticmethod def make_match_params_from_args(args): @@ -116,17 +122,14 @@ def make_match_params_from_args(args): Makes a simple namespace of matching parameters """ ret = types.SimpleNamespace() - ret.reference = pysam.FastaFile( - args.reference) if args.reference else None + ret.reference = args.reference ret.refdist = args.refdist - ret.pctsim = args.pctsim + ret.pctseq = args.pctseq ret.minhaplen = args.minhaplen ret.pctsize = args.pctsize ret.pctovl = args.pctovl ret.typeignore = args.typeignore - ret.use_lev = args.use_lev ret.chunksize = args.chunksize - ret.gtcomp = args.gtcomp ret.bSample = args.bSample if args.bSample else 0 ret.cSample = args.cSample if args.cSample else 0 ret.dup_to_ins = args.dup_to_ins if "dup_to_ins" in args else False @@ -136,7 +139,7 @@ def make_match_params_from_args(args): ret.sizemax = args.sizemax ret.passonly = args.passonly ret.no_ref = args.no_ref - ret.multimatch = args.multimatch + ret.pick = args.pick if "pick" in args else "single" return ret def filter_call(self, entry, base=False): @@ -144,6 +147,9 @@ def filter_call(self, entry, base=False): Returns True if the call should be filtered Base has different filtering requirements, so let the method know """ + if self.params.passonly and truvari.entry_is_filtered(entry): + return True + size = truvari.entry_size(entry) if size > self.params.sizemax: return True @@ -156,17 +162,16 @@ def filter_call(self, entry, base=False): samp = self.params.bSample if base else self.params.cSample prefix = 'b' if base else 'c' - if self.params.no_ref in ["a", prefix] and not truvari.entry_is_present(entry, samp): - return True - - if self.params.passonly and truvari.entry_is_filtered(entry): + if (self.params.no_ref in ["a", prefix] or self.params.pick == 'ac') and not truvari.entry_is_present(entry, samp): return True return False - def build_match(self, base, comp, matid=None, skip_gt=False): + def build_match(self, base, comp, matid=None, skip_gt=False, short_circuit=False): """ Build a MatchResult + if skip_gt, don't do genotype comparison + if short_circuit, return after first failure """ ret = MatchResult() ret.base = base @@ -179,6 +184,8 @@ def build_match(self, base, comp, matid=None, skip_gt=False): logging.debug("%s and %s are not the same SVTYPE", str(base), str(comp)) ret.state = False + if short_circuit: + return ret bstart, bend = truvari.entry_boundaries(base) cstart, cend = truvari.entry_boundaries(comp) @@ -186,47 +193,43 @@ def build_match(self, base, comp, matid=None, skip_gt=False): logging.debug("%s and %s are not within REFDIST", str(base), str(comp)) ret.state = False + if short_circuit: + return ret ret.sizesim, ret.sizediff = truvari.entry_size_similarity(base, comp) if ret.sizesim < self.params.pctsize: logging.debug("%s and %s size similarity is too low (%.3f)", str(base), str(comp), ret.sizesim) ret.state = False + if short_circuit: + return ret if not skip_gt: if "GT" in base.samples[self.params.bSample]: ret.base_gt = base.samples[self.params.bSample]["GT"] + ret.base_gt_count = sum(1 for _ in ret.base_gt if _ == 1) if "GT" in comp.samples[self.params.cSample]: ret.comp_gt = comp.samples[self.params.cSample]["GT"] - ret.gt_match = truvari.get_gt(ret.base_gt) == truvari.get_gt(ret.comp_gt) - if self.params.gtcomp and not ret.gt_match: - logging.debug("%s and %s are not the same genotype", - str(base), str(comp)) - ret.state = False + ret.comp_gt_count = sum(1 for _ in ret.comp_gt if _ == 1) + ret.gt_match = abs(ret.base_gt_count - ret.comp_gt_count) ret.ovlpct = truvari.entry_reciprocal_overlap(base, comp) if ret.ovlpct < self.params.pctovl: logging.debug("%s and %s overlap percent is too low (%.3f)", str(base), str(comp), ret.ovlpct) ret.state = False + if short_circuit: + return ret ret.st_dist, ret.ed_dist = truvari.entry_distance(base, comp) - if self.params.pctsim > 0: - b_seq, c_seq = (base.ref, comp.ref) \ - if truvari.entry_variant_type(base) == truvari.SV.DEL else \ - (base.alts[0], comp.alts[0]) - if ret.st_dist == 0 or ret.ed_dist == 0: - ret.seqsim = truvari.seqsim(b_seq, c_seq, self.params.use_lev) - elif self.params.reference is not None: - ret.seqsim = truvari.entry_pctsim(base, comp, self.params.reference, - self.params.minhaplen, self.params.use_lev) - else: - ret.seqsim = truvari.unroll_compare(c_seq, b_seq, ret.st_dist % len(c_seq)) - - if ret.seqsim < self.params.pctsim: + if self.params.pctseq > 0: + ret.seqsim = truvari.entry_seq_similarity(base, comp, self.reference, self.params.minhaplen) + if ret.seqsim < self.params.pctseq: logging.debug("%s and %s sequence similarity is too low (%.3ff)", str(base), str(comp), ret.seqsim) ret.state = False + if short_circuit: + return ret else: ret.seqsim = 0 @@ -240,48 +243,46 @@ def build_match(self, base, comp, matid=None, skip_gt=False): def file_zipper(*start_files): """ Zip files to yield the entries in order. - Files must be sorted - Each parameter is a tuple of ('key', iterable) + Each file must be sorted in the same order. + start_files is a tuple of ('key', iterable) where key is the identifier (so we know which file the yielded entry came from) - iterable is usually a pysam.VariantFile + and iterable is usually a pysam.VariantFile + yields key, pysam.VariantRecord """ - next_markers = [] - files = [] - names = [] + markers = [] # list of lists: [name, file_handler, top_entry] file_counts = Counter() for name, i in start_files: try: - next_markers.append(next(i)) - names.append(name) - files.append(i) + markers.append([name, i, next(i)]) except StopIteration: # For when there are no variants in the file pass - while next_markers: - sidx = 0 # assume the first is the least - for idx, i in enumerate(next_markers): - if i.chrom < next_markers[sidx].chrom: - sidx = idx - elif i.chrom == next_markers[sidx].chrom and i.start < next_markers[sidx].start: - sidx = idx - entry = next_markers[sidx] - key = names[sidx] - file_counts[key] += 1 + while markers: + # Get the first entry among each of the files' tops + first_idx = 0 + for idx, mk in enumerate(markers[1:]): + idx += 1 + if mk[2].chrom < markers[first_idx][2].chrom or \ + (mk[2].chrom == markers[first_idx][2].chrom and mk[2].start < markers[first_idx][2].start): + first_idx = idx + name, fh, entry = markers[first_idx] + file_counts[name] += 1 try: - next_markers[sidx] = next(files[sidx]) + # update this file's top + markers[first_idx][2] = next(fh) except StopIteration: # This file is done - files.pop(sidx) - names.pop(sidx) - next_markers.pop(sidx) - yield key, entry + markers.pop(first_idx) + yield name, entry logging.info("Zipped %d variants %s", sum(file_counts.values()), file_counts) def chunker(matcher, *files): """ Given a Matcher and multiple files, zip them and create chunks + + Yields tuple of the matcher, the chunk of calls, and an identifier of the chunk """ call_counts = Counter() chunk_count = 0 @@ -289,9 +290,14 @@ def chunker(matcher, *files): cur_end = None cur_chunk = defaultdict(list) for key, entry in file_zipper(*files): + if len(entry.alts) > 1: + logging.error("Cannot compare multi-allelic records. Please split") + logging.error("%s file - line %s", key, str(entry)) + sys.exit(10) if entry.alts is None: # ignore monomorphic reference cur_chunk['__filtered'].append(entry) call_counts['__filtered'] += 1 + cur_chrom = entry.chrom continue new_chrom = cur_chrom and entry.chrom != cur_chrom new_chunk = cur_end and cur_end + matcher.params.chunksize < entry.start @@ -303,9 +309,9 @@ def chunker(matcher, *files): cur_end = None cur_chunk = defaultdict(list) + cur_chrom = entry.chrom if not matcher.filter_call(entry, key == 'base'): logging.debug(f"Adding to {key} -> {entry}") - cur_chrom = entry.chrom cur_end = entry.stop cur_chunk[key].append(entry) call_counts[key] += 1 diff --git a/truvari/msa2vcf.py b/truvari/msa2vcf.py index 4e8e70be..3405827b 100644 --- a/truvari/msa2vcf.py +++ b/truvari/msa2vcf.py @@ -1,8 +1,7 @@ """ Turn an MSA fasta into VCF. Assumes one entry is reference with name >ref_chrom:start-end """ -import sys -import logging +import copy from io import StringIO from collections import defaultdict @@ -20,7 +19,36 @@ def build_header(chrom=None): ret += f"\n##contig=\n" return ret -def msa_to_vars(msa, ref_seq, chrom, start_pos=0): +def decompose_variant(cur_variant): + """ + Left trim and decompose (repl -> indel) variant + returns a list of new variants + """ + def var_to_str(v): + return "\t".join([str(_) for _ in v]) + ref = cur_variant[REFIDX] + alt = cur_variant[ALTIDX] + if ref == alt: + return [] + # If base after anchor base is identical, we have a new anchor base + # Stop when there's only one base left or unmached bases + trim = 0 + while trim < len(ref) - 1 and trim < len(alt) - 1 and ref[trim] == alt[trim]: + trim += 1 + cur_variant[1] += trim + cur_variant[REFIDX] = ref[trim:] + cur_variant[ALTIDX] = alt[trim:] + if len(cur_variant[REFIDX]) == 1 or len(cur_variant[ALTIDX]) == 1: + return [var_to_str(cur_variant)] + + # decompose REPL to INS and DEL - easier for truvari to compare + in_var = copy.copy(cur_variant) + in_var[REFIDX] = in_var[REFIDX][0] + del_var = copy.copy(cur_variant) + del_var[ALTIDX] = del_var[ALTIDX][0] + return [var_to_str(in_var), var_to_str(del_var)] + +def msa_to_vars(msa, ref_seq, chrom, start_pos=0, abs_anchor_base='N'): """ Turn MSA into VCF entries and their presence in samples returns list of sample names parsed and dictionary of variant : samples containing the variant @@ -36,15 +64,11 @@ def msa_to_vars(msa, ref_seq, chrom, start_pos=0): cur_samp_hap = "_".join(alt_key.split('_')[:-1]) sample_names.add("_".join(alt_key.split('_')[:-2])) alt_seq = msa[alt_key].upper() - # Gotta assume the first base is a match (little unsafe) - anchor_base = ref_seq[0] - if anchor_base == '-': - logging.error("MSA starts with an indel in %s. Can't make VCF", alt_key) - # raise RuntimeWarning TODO - fix this, it breaks threads and makes phab hang - sys.exit(1) + + anchor_base = ref_seq[0] if ref_seq[0] != '-' else abs_anchor_base cur_variant = [] - cur_pos = start_pos + cur_pos = start_pos # still have a problem here with anchor base. # This is too long. need to have a separate zip method for ref_base, alt_base in zip(ref_seq, alt_seq): is_ref = ref_base != '-' @@ -59,15 +83,7 @@ def msa_to_vars(msa, ref_seq, chrom, start_pos=0): if ref_base == alt_base: # No variant if cur_variant and is_ref: # back to matching reference - # Anchor base correction - if len(cur_variant[REFIDX]) == len(cur_variant[ALTIDX]): - cur_variant[REFIDX] = cur_variant[REFIDX][1:] - cur_variant[ALTIDX] = cur_variant[ALTIDX][1:] - cur_variant[1] += 1 - key = "\t".join([str(_) for _ in cur_variant]) - # this is a weird edge check - # sometimes reference bases aren't aligned - if cur_variant[REFIDX] != cur_variant[ALTIDX]: + for key in decompose_variant(cur_variant): final_vars[key].append(cur_samp_hap) cur_variant = [] else: @@ -83,15 +99,7 @@ def msa_to_vars(msa, ref_seq, chrom, start_pos=0): anchor_base = ref_base # End Zipping if cur_variant: - # Anchor base correction - if len(cur_variant[REFIDX]) == len(cur_variant[ALTIDX]): - cur_variant[REFIDX] = cur_variant[REFIDX][1:] - cur_variant[ALTIDX] = cur_variant[ALTIDX][1:] - cur_variant[1] += 1 - key = "\t".join([str(_) for _ in cur_variant]) - # this is a weird edge check - # sometimes reference bases aren't aligned - if cur_variant[REFIDX] != cur_variant[ALTIDX]: + for key in decompose_variant(cur_variant): final_vars[key].append(cur_samp_hap) # End alignment sample_names = sorted(list(sample_names)) @@ -120,20 +128,25 @@ def make_vcf(variants, sample_names, header): out.seek(0) return out.read() -def msa2vcf(fn, header=None): +def msa2vcf(fn, header=None, anchor_base=None): """ - Parses an MSA and returns its VCF as a string - Assumes one entry in the MSA has the name ref_${chrom}:${start}-${end} + Parse an MSA file and returns its VCF as a string + + Assumes one entry in the MSA has the name `ref_${chrom}:${start}-${end}` which gives VCF entries coordinates + + VCF can be given a header or a minimal one is created with only file format and a single contig line + Provide anchor_base to prevent 'N' from being used as an anchor base + Returns a string """ msa = pysam.FastaFile(fn) # The ref_key identifies reference ref_key = [_ for _ in msa.references if _.startswith("ref_")][0] # pylint: disable=not-an-iterable ref_seq = msa[ref_key].upper() - chrom = ref_key.split('_')[1] - start_pos = int(ref_key.split('_')[2]) + _, chrom, start_pos, _ = ref_key.split('_') + start_pos = int(start_pos) - sample_names, variants = msa_to_vars(msa, ref_seq, chrom, start_pos) + sample_names, variants = msa_to_vars(msa, ref_seq, chrom, start_pos, anchor_base) if header is None: header = build_header(chrom) diff --git a/truvari/phab.py b/truvari/phab.py index 424bd516..8646e819 100644 --- a/truvari/phab.py +++ b/truvari/phab.py @@ -4,14 +4,19 @@ import os import re import sys +import glob import shutil import logging import argparse +import resource import multiprocessing import pysam +from pysam import bcftools import truvari +DEFAULT_MAFFT_PARAM="--auto --thread 1" + def parse_args(args): """ Pull the command line parameters @@ -31,13 +36,15 @@ def parse_args(args): help="Number of reference bases before/after region to add to MSA (%(default)s)") #parser.add_argument("--add-to", action='store_true', # help="Build the baseMSA independentally of the compMSA, then add the comp") - parser.add_argument("-o", "--output", default="phab_out", - help="Output directory") + parser.add_argument("-o", "--output", type=str, default="phab_out.vcf.gz", + help="Output VCF") + parser.add_argument("-k", "--keep-parts", type=str, default=None, + help="Directory to save intermediate region results") parser.add_argument("--bSamples", type=str, default=None, help="Subset of samples to MSA from base-VCF") parser.add_argument("--cSamples", type=str, default=None, help="Subset of samples to MSA from comp-VCF") - parser.add_argument("-m", "--mafft-params", type=str, default="--retree 2 --maxiterate 0", + parser.add_argument("-m", "--mafft-params", type=str, default=DEFAULT_MAFFT_PARAM, help="Parameters for mafft, wrap in a single quote (%(default)s)") parser.add_argument("-t", "--threads", type=int, default=1, help="Number of threads (%(default)s)") @@ -55,30 +62,41 @@ def parse_regions(argument): if not argument: return ret if os.path.exists(argument): - with open(argument, 'r') as fh: - for i in fh: + for i in truvari.opt_gz_open(argument): + try: chrom, start, end = i.strip().split('\t')[:3] start = int(start) end = int(end) - ret.append((chrom, start, end)) + except Exception: #pylint: disable=broad-except + logging.error("Unable to parse bed line %s", i) + sys.exit(1) + ret.append((chrom, start, end)) else: for i in argument.split(','): - chrom, start, end = re.split(':|-', i) - start = int(start) - end = int(end) + try: + chrom, start, end = re.split(':|-', i) + start = int(start) + end = int(end) + except ValueError: + logging.error("Unable to parse region line %s", i) + sys.exit(1) ret.append((chrom, start, end)) return ret def get_reference(fn, output, chrom, start, end): """ Pull a subset of the reference and put into a file + Returns the anchor base (1bp upstream from start) for msa2vcf """ fasta = pysam.FastaFile(fn) - oseq = fasta.fetch(chrom, start - 1, end) + oseq = fasta.fetch(chrom, start - 2, end) # no need to make it pretty? #oseq = re.sub("(.{60})", "\\1\n", oseq, 0, re.DOTALL) with open(output, 'w') as fout: - fout.write(f">ref_{chrom}_{start}_{end}\n{oseq}\n") + fout.write(f">ref_{chrom}_{start}_{end}\n{oseq[1:]}\n") + with open(output + '.ref.fa', 'w') as fout: + fout.write(f">{chrom}:{start}-{end}\n{oseq[1:]}\n") + return oseq[0] def pull_variants(vcf, region, output, ref, samples=None): """ @@ -99,6 +117,11 @@ def pull_variants(vcf, region, output, ref, samples=None): logging.error("Unable to pull variants from %s", vcf) logging.error(ret.stderr) sys.exit(1) + cnt = 0 + with pysam.VariantFile(output) as fh: + for _ in fh: + cnt += 1 + return cnt def build_consensus(vcf, ref, region, output, samples=None, prefix_name=False): """ @@ -106,9 +129,8 @@ def build_consensus(vcf, ref, region, output, samples=None, prefix_name=False): """ chrom, start, end = region prefix = 'p:' if prefix_name else '' - cmd = """samtools faidx {ref} {chrom}:{start}-{end} | \ -bcftools consensus -H{hap} --sample {sample} --prefix {prefix}{sample}_{hap}_ {vcf} >> {output} -""" + ref = output + '.ref.fa' + cmd = "cat {ref} | bcftools consensus -H{hap} --sample {sample} --prefix {prefix}{sample}_{hap}_ {vcf} >> {output}" for samp in samples: for hap in [1, 2]: m_cmd = cmd.format(ref=ref, @@ -126,20 +148,22 @@ def build_consensus(vcf, ref, region, output, samples=None, prefix_name=False): logging.error(ret.stderr) sys.exit(1) -def run_mafft(seq_fn, output, params="--retree 2 --maxiterate 0"): +def run_mafft(seq_fn, output, params=DEFAULT_MAFFT_PARAM): """ - Run mafft + Run mafft - return True if successful """ cmd = f"mafft {params} {seq_fn} > {output}" ret = truvari.cmd_exe(cmd) - if ret.ret_code != 0: # this doesn't (ever?) exit non-zero + if ret.ret_code != 0: logging.error("Unable to run MAFFT on %s", seq_fn) logging.error(ret.stderr) - sys.exit(1) + return False + return True +# pylint: disable=too-many-locals def phab(base_vcf, reference, output_dir, var_region, buffer=100, comp_vcf=None, bSamples=None, cSamples=None, - mafft_params="--retree 2 --maxiterate 0", prefix_comp=False): + mafft_params=DEFAULT_MAFFT_PARAM, prefix_comp=False): """ Harmonize variants with MSA. @@ -163,11 +187,9 @@ def phab(base_vcf, reference, output_dir, var_region, buffer=100, :type `mafft_params`: :class:`str` :param `prefix_comp`: Ensure unique sample names by prefixing comp samples :type `prefix_comp`: :class:`bool` - - Raises IOError if `output_dir` does not exist """ if not os.path.exists(output_dir): - raise IOError(f"Directory {output_dir} does not exist") + os.makedirs(output_dir) buff_region = (var_region[0], var_region[1] - buffer, var_region[2] + buffer) @@ -176,22 +198,27 @@ def phab(base_vcf, reference, output_dir, var_region, buffer=100, if comp_vcf and cSamples is None: cSamples = list(pysam.VariantFile(comp_vcf).header.samples) + # Make sure there are variants first + subset_base_vcf = os.path.join(output_dir, "base.vcf.gz") + num_vars = pull_variants(base_vcf, var_region, subset_base_vcf, reference, bSamples) + if comp_vcf is not None: + subset_comp_vcf = os.path.join(output_dir, "comp.vcf.gz") + num_vars += pull_variants(comp_vcf, var_region, subset_comp_vcf, reference, cSamples) + + if num_vars == 0: + return + sequences = os.path.join(output_dir, "haps.fa") - get_reference(reference, sequences, *buff_region) + anchor_base = get_reference(reference, sequences, *buff_region) - subset_base_vcf = os.path.join(output_dir, "base.vcf.gz") - pull_variants(base_vcf, var_region, subset_base_vcf, reference, bSamples) build_consensus(subset_base_vcf, reference, buff_region, sequences, bSamples) - # if add-to, we put this elsewhere and revisit for now I'll disable that feature - # because it assumes we already have an MSA if comp_vcf is not None: - subset_comp_vcf = os.path.join(output_dir, "comp.vcf.gz") - pull_variants(comp_vcf, var_region, subset_comp_vcf, reference, cSamples) build_consensus(subset_comp_vcf, reference, buff_region, sequences, cSamples, prefix_comp) msa_output = os.path.join(output_dir, "msa.fa") - run_mafft(sequences, msa_output, mafft_params) + if not run_mafft(sequences, msa_output, mafft_params): + return output_vcf = os.path.join(output_dir, "output.vcf") vcf = pysam.VariantFile(base_vcf) @@ -199,26 +226,128 @@ def phab(base_vcf, reference, output_dir, var_region, buffer=100, n_header += str(vcf.header.contigs[var_region[0]].header_record) with open(output_vcf, 'w') as fout: - fout.write(truvari.msa2vcf(msa_output, n_header)) + try: + fout.write(truvari.msa2vcf(msa_output, n_header, anchor_base)) + except RuntimeWarning: + return truvari.compress_index_vcf(output_vcf) +# pylint: enable=too-many-locals + +def consolidate_phab_vcfs(phab_dir, out_vcf): + """ + Consolidate all the phab output VCFs in a directory and write to compressed indexed vcf + """ + def concat(file_names): + tmp_name = truvari.make_temp_filename(suffix=".vcf.gz") + files = truvari.make_temp_filename(suffix=".txt") + with open(files, 'w') as fout: + fout.write('\n'.join(file_names)) + bcftools.concat("--no-version", "-O", "z", "-a", "-f", files, "-o", tmp_name, catch_stdout=False) + pysam.tabix_index(tmp_name, preset='vcf') + return tmp_name + max_files = (resource.getrlimit(resource.RLIMIT_NOFILE)[0] - 1) // 2 + in_files = glob.glob(os.path.join(phab_dir, "*", "*", "output.vcf.gz")) + in_files.sort() + while len(in_files) > 1: + tmp_names = [] + # bcftools gets weird with more than 1,010 files + for i in range(0, len(in_files), max_files): + tmp_names.append(concat(in_files[i:i+max_files])) + in_files = tmp_names + shutil.move(in_files[0], out_vcf) + shutil.move(in_files[0] + '.tbi', out_vcf + '.tbi') def check_requirements(): """ ensure external programs are in PATH """ check_fail = False - for prog in ["bcftools", "vcf-sort", "bgzip", "tabix", "samtools", "mafft"]: + for prog in ["bcftools", "bgzip", "tabix", "mafft"]: if not shutil.which(prog): logging.error("Unable to find `%s` in PATH", prog) check_fail = True return check_fail -def t_phab(job): +def check_params(args): + """ + Ensure files are okay to use + """ + check_fail = False + if not args.output.endswith(".vcf.gz"): + logging.error("Output file must be a '.vcf.gz', got %s", args.output) + check_fail = True + if args.keep_parts and os.path.isdir(args.keep_parts): + logging.error("Output directory '%s' already exists", args.keep_parts) + check_fail = True + if args.comp is not None and not os.path.exists(args.comp): + logging.error("File %s does not exist", args.comp) + check_fail = True + if not os.path.exists(args.base): + logging.error("File %s does not exist", args.base) + check_fail = True + if args.comp is not None and not args.comp.endswith(".gz"): + logging.error( + "Comparison vcf %s does not end with .gz. Must be bgzip'd", args.comp) + check_fail = True + if args.comp is not None and not os.path.exists(args.comp + '.tbi'): + logging.error( + "Comparison vcf index %s.tbi does not exist. Must be indexed", args.comp) + check_fail = True + if not args.base.endswith(".gz"): + logging.error( + "Base vcf %s does not end with .gz. Must be bgzip'd", args.base) + check_fail = True + if not os.path.exists(args.base + '.tbi'): + logging.error( + "Base vcf index %s.tbi does not exist. Must be indexed", args.base) + check_fail = True + if not os.path.exists(args.reference): + logging.error("Reference %s does not exist", args.reference) + check_fail = True + + return check_fail + +def phab_wrapper(job): + """ + Convience function to call phab (which works no a single region) + job is a tuple of region, output_dir, and kwargs dict + """ + try: + phab(var_region=job[0], output_dir=job[1], **job[2]) + except Exception as e: #pylint: disable=broad-except + logging.critical("phab failed on %s\n%s", str(job[0]), e) + +#pylint: disable=too-many-arguments +# This is just how many arguments it takes +def phab_multi(base_vcf, reference, output_dir, var_regions, buf=100, comp_vcf=None, + bSamples=None, cSamples=None, mafft_params=DEFAULT_MAFFT_PARAM, + prefix_comp=False, threads=1): """ - Hack to mimmic starmap since I can't find a Pool.starmap_unordered + Run phab on multiple regions """ - phab(*job) + if not os.path.exists(output_dir): + os.makedirs(output_dir) + + params = {"base_vcf": base_vcf, + "reference": reference, + "buffer": buf, + "comp_vcf": comp_vcf, + "bSamples": bSamples, + "cSamples": cSamples, + "mafft_params": mafft_params, + "prefix_comp": prefix_comp} + with multiprocessing.Pool(threads, maxtasksperchild=1) as pool: + # build jobs + jobs = [] + for region in var_regions: + m_output = os.path.join(output_dir, region[0], f"{region[0]}:{region[1]}-{region[2]}") + jobs.append((region, m_output, params)) + + pool.imap_unordered(phab_wrapper, jobs) + pool.close() + pool.join() +#pylint: enable=too-many-arguments def phab_main(cmdargs): """ @@ -226,12 +355,11 @@ def phab_main(cmdargs): """ args = parse_args(cmdargs) truvari.setup_logging(args.debug, show_version=True) - if check_requirements(): - sys.exit(1) - #if check_params(args): - # mainly just if files exist - #pass + if check_requirements() or check_params(args): + logging.error("Couldn't run Truvari. Please fix parameters\n") + sys.exit(100) + # Setting up the samples is tricky if args.bSamples is None: args.bSamples = list(pysam.VariantFile(args.base).header.samples) else: @@ -242,29 +370,25 @@ def phab_main(cmdargs): args.cSamples = list(pysam.VariantFile(args.comp).header.samples) else: args.cSamples = args.cSamples.split(',') + prefix_comp = False if args.cSamples and set(args.cSamples) & set(args.bSamples): logging.warning("--cSamples intersect with --bSamples. Output vcf --comp SAMPLE names will have prefix 'p:'") prefix_comp = True all_regions = parse_regions(args.region) - with multiprocessing.Pool(args.threads) as pool: - # build jobs - jobs = [] - for region in all_regions: - m_output = args.output if len(all_regions) == 1 \ - else os.path.join(args.output, f"{region[0]}:{region[1]}-{region[2]}") - try: - os.makedirs(m_output) - except FileExistsError: - logging.error("Output directory %s exists.", args.output) - sys.exit(1) + if args.keep_parts is None: + remove = True # remove at the end + args.keep_parts = truvari.make_temp_filename() + else: + remove = False + phab_multi(args.base, args.reference, args.keep_parts, all_regions, args.buffer, args.comp, + args.bSamples, args.cSamples, args.mafft_params, prefix_comp, args.threads) - jobs.append((args.base, args.reference, m_output, region, args.buffer, - args.comp, args.bSamples, args.cSamples, args.mafft_params, prefix_comp)) - logging.info("%d regions to process", len(jobs)) - pool.imap_unordered(t_phab, jobs) - pool.close() - pool.join() + consolidate_phab_vcfs(args.keep_parts, args.output) + + if remove: + logging.info("Cleaning") + shutil.rmtree(args.keep_parts) logging.info("Finished phab") diff --git a/truvari/pipeline.py b/truvari/pipeline.py new file mode 100644 index 00000000..293ae461 --- /dev/null +++ b/truvari/pipeline.py @@ -0,0 +1,70 @@ +""" +pipeline - Easy function chaining with futures parallelization +""" +#import concurrent.futures as cfuts +import multiprocessing +from functools import partial, reduce + + +def __reduce_wrapper(funcs, data, **kwargs): + """ + This is a wrapper around reduce, which chains the functions + We assume there must always be at least one argument + """ + return reduce(lambda r, f: f(r, **kwargs), funcs, data) + + +def __partial_wrapper(funcs): + """ + Wrap the reduce_wrapper in a partial so it may run multiple times + (i.e. over multiple pieces of data) + """ + return partial(__reduce_wrapper, funcs) + + +def fchain(pipe, data, workers=1): + """ + Runs chained functions over every piece of data using a multiprocessing pool + + * pipe: list of [(function, kwargs), ...] + * each function must be defined with at least `def foobar(data)`. + * kwargs is a dictionary of other parameters the function may need. + * if no parameters are needed, an item in the list can just be a function + * data: list data to process + * data must be hashable + * workers: maximum number of ProcessPoolExecutor workers to create + + For example, the first yield of a 2 step pipe on the first piece of data is + equivalent to:: + + pipe[1][0]( + pipe[0][0](data[0], **pipe[0][1]), + **pipe[1][1] + ) + + Yields results of chained functions called per data. + """ + m_reduce = __partial_wrapper([partial(_[0], **_[1]) if isinstance(_, tuple) else _ for _ in pipe]) + #with cfuts.ProcessPoolExecutor(max_workers=workers) as executor: + with multiprocessing.Pool(workers, maxtasksperchild=1) as pool: + for i in pool.imap_unordered(m_reduce, data): + yield i + pool.close() + pool.join() + # Start the load operations and mark each future with its arg + #future_results = {executor.submit(m_reduce, _): _ for _ in data} + #for future in cfuts.as_completed(future_results): + # my_name = future_results[future] + # try: + # cur_result = future.result() + # except Exception as exc: + # logging.critical('%r generated an exception: %s', my_name, exc) + # for fut in future_results: + # _ = fut.cancel() + # #logging.debug("Dumping Traceback:") + # #exc_type, exc_value, exc_traceback = sys.exc_info() + # #traceback.print_exception(exc_type, exc_value, exc_traceback, file=sys.stderr) + # raise exc + # yield cur_result + # # Can't keep all of these around. Manually remove as you go. + # del future_results[future] diff --git a/truvari/refine.py b/truvari/refine.py new file mode 100644 index 00000000..3aa55a84 --- /dev/null +++ b/truvari/refine.py @@ -0,0 +1,325 @@ +""" +Automated Truvari bench result refinement with phab +""" +import os +import sys +import json +import shutil +import logging +import argparse +from argparse import Namespace +from collections import defaultdict + +import pandas as pd + +from pysam import bcftools +from intervaltree import IntervalTree + +import truvari + +def read_json(fn): + """ + Parse json and return dict + """ + ret = None + with open(fn, 'r') as fh: + ret = json.load(fh) + return ret + +def intersect_beds(bed_a, bed_b): + """ + Return bed_a regions that intersect bed_b regions + """ + shared = {} + count = 0 + for chrom in bed_a: + s_inc = [] + for i in bed_a[chrom]: + if bed_b[chrom].overlaps(i): + count += 1 + s_inc.append(i) + shared[chrom] = IntervalTree(s_inc) + return shared, count + +def tree_to_regions(trees): + """ + turn an anno tree into a list of lists of chrom start end + """ + return [[chrom, intv.begin, intv.end] for chrom, all_intv in trees.items() for intv in all_intv] + +def resolve_regions(params, args): + """ + Figures out or creates the regions we'll be analyzing + """ + if params.includebed is None and args.regions is None: + logging.error("Bench output didn't use `--includebed` and `--regions` not provided") + logging.error("Unable to run refine") + sys.exit(1) + elif args.regions is None: + reeval_trees, new_count = truvari.build_anno_tree(params.includebed, idxfmt="") + logging.info("Evaluating %d regions", new_count) + elif args.regions is not None and params.includebed is not None: + a_trees, regi_count = truvari.build_anno_tree(args.regions, idxfmt="") + b_trees, orig_count = truvari.build_anno_tree(params.includebed, idxfmt="") + if args.use_includebed: + reeval_trees, new_count = intersect_beds(b_trees, a_trees) + logging.info("%d --includebed reduced to %d after intersecting with %d from --regions", + orig_count, new_count, regi_count) + + else: + reeval_trees, new_count = intersect_beds(a_trees, b_trees) + logging.info("%d --regions reduced to %d after intersecting with %d from --includebed", + regi_count, new_count, orig_count) + else: + reeval_trees, count = truvari.build_anno_tree(args.regions, idxfmt="") + logging.info("%d --regions loaded", count) + # might need to merge overlaps. + return reeval_trees + + +def consolidate_bench_vcfs(benchdir): + """ + Pull and consolidate base/comp variants from their regions + """ + bout_name = truvari.make_temp_filename(suffix=".vcf") + output = bcftools.concat("--no-version", *[os.path.join(benchdir, "tp-base.vcf.gz"), + os.path.join(benchdir, "fn.vcf.gz")]) + with open(bout_name, 'w') as fout: + fout.write(output) + truvari.compress_index_vcf(bout_name) + + cout_name = truvari.make_temp_filename(suffix=".vcf") + output = bcftools.concat("--no-version", *[os.path.join(benchdir, "tp-comp.vcf.gz"), + os.path.join(benchdir, "fp.vcf.gz")]) + with open(cout_name, 'w') as fout: + fout.write(output) + truvari.compress_index_vcf(cout_name) + return bout_name + '.gz', cout_name + '.gz' + +def make_variant_report(regions): + """ + Count all the variants, log and write to output + """ + summary = truvari.StatsBox() + summary["TP-base"] = int(regions["out_tpbase"].sum()) + summary["TP-comp"] = int(regions["out_tp"].sum()) + summary["FP"] = int(regions["out_fp"].sum()) + summary["FN"] = int(regions["out_fn"].sum()) + summary["base cnt"] = summary["TP-base"] + summary["FN"] + summary["comp cnt"] = summary["TP-comp"] + summary["FP"] + summary.calc_performance() + return summary + +def make_region_report(data): + """ + Given a refine counts DataFrame, calculate the performance of + PPV, TNR, etc. Also adds 'state' column to regions inplace + """ + false_pos = (data['out_fp'] != 0) + false_neg = (data['out_fn'] != 0) + any_false = false_pos | false_neg + + true_positives = (data['out_tp'] != 0) & (data['out_tpbase'] != 0) & ~any_false + + true_negatives = (data[['out_tpbase', 'out_tp', 'out_fn', 'out_fp']] == 0).all(axis=1) + + + state_map = defaultdict(lambda: 'UNK') + state_map.update({(True, False, False, False): 'TP', + (False, True, False, False): 'TN', + (False, False, True, False): 'FP', + (False, False, False, True): 'FN', + (False, False, True, True): 'FN,FP'}) + + data['state'] = [state_map[_] for _ in zip(true_positives, true_negatives, false_pos, false_neg)] + + tot = (true_positives + false_pos + false_neg + true_negatives).astype(int) + und = data.iloc[tot[tot != 1].index] + + result = {} + + base = (data['out_tpbase'] != 0) | (data['out_fn'] != 0) + baseP = int(base.sum()) + baseN = int((~base).sum()) + comp = (data['out_tp'] != 0) | (data['out_fp'] != 0) + compP = int(comp.sum()) + compN = int((~comp).sum()) + + result["TP"] = int(true_positives.sum()) + result["TN"] = int(true_negatives.sum()) + result["FP"] = int(false_pos.sum()) + result["FN"] = int(false_neg.sum()) + result["base P"] = baseP + result["base N"] = baseN + result["comp P"] = compP + result["comp N"] = compN + # precision + result["PPV"] = result["TP"] / result["comp P"] + # recall + result["TPR"] = result["TP"] / result["base P"] + # specificity + result["TNR"] = result["TN"] / result["base N"] + # negative predictive value + result["NPV"] = result["TN"] / result["comp N"] + # accuracy + result["ACC"] = (result["TP"] + result["TN"]) / (result["base P"] + result["base N"]) + result["BA"] = (result["TPR"] + result["TNR"]) / 2 + result["F1"] = 2 * ((result["PPV"] * result["TPR"]) / (result["PPV"] + result["TPR"])) + result["UND"] = len(und) + + return result + +def parse_args(args): + """ + Pull the command line parameters + """ + parser = argparse.ArgumentParser(prog="refine", description=__doc__, + formatter_class=argparse.RawDescriptionHelpFormatter) + parser.add_argument("benchdir", metavar="DIR", + help="Truvari bench directory") + parser.add_argument("-f", "--reference", type=str, + help="Indexed fasta used to call variants") + parser.add_argument("-r", "--regions", default=None, + help="Regions to process") + parser.add_argument("-I", "--use-includebed", action="store_true", + help="When intersecting includebed with regions, use includebed coordinates") + parser.add_argument("-u", "--use-original", action="store_true", + help="Use original input VCFs instead of filtered tp/fn/fps") + parser.add_argument("-t", "--threads", default=1, type=int, + help="Number of threads to use (%(default)s)") + parser.add_argument("-k", "--keep-phab", action="store_true", + help="Keep the phab intermediate files") + parser.add_argument("--debug", action="store_true", + help="Verbose logging") + args = parser.parse_args(args) + truvari.setup_logging(args.debug, show_version=True) + return args + +def check_params(args): + """ + Sets up all the parameters from the bench/params.json + + Returns as a Namespace + """ + param_path = os.path.join(args.benchdir, "params.json") + if not os.path.exists(param_path): + logging.error("Bench directory %s doesn't have params.json", param_path) + sys.exit(1) + params = read_json(param_path) + + if params["reference"] is None and args.reference is None: + logging.error("Reference not in params.json or given as a parameter to refine") + sys.exit(1) + elif args.reference is None: + args.reference = params["reference"] + + if not os.path.exists(args.reference): + logging.error("Reference %s does not exist", args.reference) + sys.exit(1) + + # Setup prefix + params["cSample"] = "p:" + params["cSample"] + + phdir = os.path.join(args.benchdir, 'phab') + if os.path.exists(phdir): + logging.error("Directory %s exists. Cannot run refine", phdir) + sys.exit(1) + + bhdir = os.path.join(args.benchdir, 'phab_bench') + if os.path.exists(bhdir): + logging.error("Directory %s exists. Cannot run refine", bhdir) + sys.exit(1) + + # Should check that bench dir has compressed/indexed vcfs for fetching + check_fail = False + for i in ["tp-base.vcf.gz", "tp-comp.vcf.gz", "fn.vcf.gz", "fp.vcf.gz"]: + if not os.path.exists(os.path.join(args.benchdir, i)): + logging.error("Benchdir doesn't have compressed/indexed %s", i) + check_fail = True + if check_fail: + sys.exit(1) + + os.makedirs(phdir) + return Namespace(**params) + +def initial_stratify(benchdir, regions): + """ + Get the stratify counts from the initial bench results + """ + counts = truvari.benchdir_count_entries(benchdir, regions, True)[["tpbase", "tp", "fn", "fp"]] + regions = pd.DataFrame(regions, columns=["chrom", "start", "end"]) + counts.index = regions.index + counts.columns = ["in_tpbase", "in_tp", "in_fn", "in_fp"] + regions = regions.join(counts) + return regions + +def refined_stratify(outdir, to_eval_coords, regions): + """ + update regions in-place with the output variant counts + """ + counts = truvari.benchdir_count_entries(outdir, to_eval_coords, True)[["tpbase", "tp", "fn", "fp"]] + counts.index = regions[regions['refined']].index + counts.columns = ["out_tpbase", "out_tp", "out_fn", "out_fp"] + regions = regions.join(counts) + for i in ["tpbase", "tp", "fn", "fp"]: + regions[f"out_{i}"] = regions[f"in_{i}"].where(~regions['refined'], regions[f"out_{i}"]) + return regions + +def refine_main(cmdargs): + """ + Main + """ + args = parse_args(cmdargs) + + params = check_params(args) + + reeval_trees = resolve_regions(params, args) + regions = tree_to_regions(reeval_trees) + + # Stratify. + regions = initial_stratify(args.benchdir, regions) + + + # Figure out which to reevaluate + # Set the input VCFs for phab + if args.use_original: + base_vcf, comp_vcf = params.base, params.comp + regions["refined"] = (regions["in_fn"] > 0) | (regions["in_fp"] > 0) + else: + base_vcf, comp_vcf = consolidate_bench_vcfs(args.benchdir) + regions["refined"] = (regions["in_fn"] > 0) & (regions["in_fp"] > 0) + logging.info("%d regions to be refined", regions["refined"].sum()) + + reeval_bed = truvari.make_temp_filename(suffix=".bed") + regions[regions["refined"]].to_csv(reeval_bed, sep='\t', header=False, index=False) + + # Send the vcfs to phab + to_eval_coords = regions[regions["refined"]][["chrom", "start", "end"]].to_numpy().tolist() + phab_dir = os.path.join(args.benchdir, "phab") + truvari.phab_multi(base_vcf, args.reference, phab_dir, to_eval_coords, + comp_vcf=comp_vcf, prefix_comp=True, threads=args.threads) + + phab_vcf = os.path.join(args.benchdir, "phab.output.vcf.gz") + truvari.consolidate_phab_vcfs(phab_dir, phab_vcf) + + # Now run bench on the phab harmonized variants + matcher = truvari.Matcher(params) + matcher.params.no_ref = 'a' + outdir = os.path.join(args.benchdir, "phab_bench") + m_bench = truvari.Bench(matcher, phab_vcf, phab_vcf, outdir, reeval_bed) + m_bench.run() + + regions = refined_stratify(outdir, to_eval_coords, regions) + + summary = make_variant_report(regions) + summary.write_json(os.path.join(args.benchdir, 'refine.variant_summary.json')) + + report = make_region_report(regions) + regions.to_csv(os.path.join(args.benchdir, 'refine.regions.txt'), sep='\t', index=False) + + with open(os.path.join(args.benchdir, "refine.region_summary.json"), 'w') as fout: + fout.write(json.dumps(report, indent=4)) + + if not args.keep_phab: + shutil.rmtree(phab_dir) + logging.info("Finished refine") diff --git a/truvari/region_vcf_iter.py b/truvari/region_vcf_iter.py index a0301b09..9cb527aa 100644 --- a/truvari/region_vcf_iter.py +++ b/truvari/region_vcf_iter.py @@ -8,7 +8,6 @@ from intervaltree import IntervalTree import truvari -import truvari.comparisons as tcomp class RegionVCFIterator(): @@ -43,7 +42,7 @@ def __build_tree(self, vcfA, vcfB): excluding = contigB_set - contigA_set if excluding: logging.warning( - "Excluding %d contigs present in comparison calls header but not base calls.", len(excluding)) + "Excluding %d contigs present in comparison calls header but not baseline calls.", len(excluding)) for contig in contigA_set: name = vcfA.header.contigs[contig].name @@ -89,13 +88,18 @@ def include(self, entry): Returns if this entry's start and end are within a region that is to be included Here overlap means lies completely within the boundary of an include region """ - astart, aend = tcomp.entry_boundaries(entry) + astart, aend = truvari.entry_boundaries(entry) # Filter these early so we don't have to keep checking overlaps - if self.max_span is None or aend - astart > self.max_span: + if self.max_span is not None and aend - astart > self.max_span: return False if astart == aend - 1: return self.tree[entry.chrom].overlaps(astart) - return len(self.tree[entry.chrom].overlap(astart, aend)) == 1 + m_ovl = self.tree[entry.chrom].overlap(astart, aend) + if len(m_ovl) != 1: + return False + m_ovl = list(m_ovl)[0] + # Edge case - the variant spans the entire include region + return astart >= m_ovl.begin and aend <= m_ovl.end def extend(self, pad): """ @@ -114,6 +118,31 @@ def extend(self, pad): def build_anno_tree(filename, chrom_col=0, start_col=1, end_col=2, one_based=False, comment='#', idxfmt=None): """ Build an dictionary of IntervalTrees for each chromosome from tab-delimited annotation file + + By default, the file is assumed to be a bed-format. If custom chrom/start/end are used, the columns can be + specified. + + idxfmt is a string that will be formatted with the line number from the file (e.g. "num %d" will + make intervals with data="num 0", "num 1". By default the data will be interger line number. + If intervals will be compared between anno_trees, set idxfmt to "" + + :param `filename`: Path to file to parse, can be compressed + :type `filename`: string + :param `chrom_col`: Index of column in file with chromosome + :type `chrom_col`: integer, optional + :param `start_col`: Index of column in file with start + :type `start_col`: integer, optional + :param `end_col`: Index of column in file with end + :type `end_col`: integer, optional + :param `one_based`: True if coordinates are one-based + :type `one_based`: bool, optional + :param `comment`: ignore lines if they start with this string + :type `comment`: string, optional + :param `idxfmt`: Index of column in file with chromosome + :type `idxfmt`: string, optional + + :return: dictionary with chromosome keys and :class:`intervaltree.IntervalTree` values + :rtype: dict """ idx = 0 correction = 1 if one_based else 0 diff --git a/truvari/segmentation.py b/truvari/segmentation.py index 3f80ae69..2fb4c819 100644 --- a/truvari/segmentation.py +++ b/truvari/segmentation.py @@ -10,7 +10,7 @@ from intervaltree import IntervalTree import truvari - +from truvari.annotations import svinfo def parse_args(args): """ @@ -21,22 +21,19 @@ def parse_args(args): parser.add_argument("vcf", metavar="IN", help="VCF to parse") - parser.add_argument("output", metavar="OUT", + parser.add_argument("-o", "--output", default="/dev/stdout", help="Output VCF") - # parser.add_argument("-m", "--min", default=10, type=int, - # help="Minimum span of variants to segment") - # parser.add_argument("--alter", action="store_true", - # help="Add SEG Format field to all variants (false)") + parser.add_argument("--passonly", action="store_true", + help="Only segment PASS variants") args = parser.parse_args(args) truvari.setup_logging(show_version=True) return args -def edit_header(vcf): +def edit_header(header): """ Add new vcf header lines """ - header = vcf.header.copy() header.add_line(('##INFO=')) header.add_line(('##FORMAT='] + new_entry.stop = reg.end + 1 + new_entry.ref = 'N' + svlen = new_entry.stop - new_entry.start - 1 + if svlen > 1: + # assuming they're DEL, but DUP may eventually be seg-able + new_entry.alts = [''] + new_entry.info["SVTYPE"] = 'DEL' + new_entry.info["SVLEN"] = new_entry.stop - new_entry.start - 1 + else: + new_entry.alts = ['.'] new_entry.info["SEGCNT"] = segcnt for samp, dat in zip(new_entry.samples, reg.data[1]): if dat == 0: @@ -99,5 +106,5 @@ def reducer(x, y): else: new_entry.samples[samp]["GT"] = (1, 1) new_entry.samples[samp]["SEG"] = int(dat) - out.write(new_entry) + logging.info("Finished segment") diff --git a/truvari/stratifications.sh b/truvari/stratifications.sh deleted file mode 100644 index afdc5309..00000000 --- a/truvari/stratifications.sh +++ /dev/null @@ -1,42 +0,0 @@ -## Run the GIAB recommended tandem-repeat stratifications analysis -## Arg1 = the Truvari result directory to operate over -## Arg2 = The repeats annotation file - -repeats=`readlink -f $2` -cd $1 -# FN/INS/non-TR -(grep "#" fn.vcf && (grep 'SVTYPE=INS' fn.vcf | grep 'TRgt100=FALSE')) | vcf-sort | bgzip > fn_ins_nonTR.vcf.gz -tabix -p vcf fn_ins_nonTR.vcf.gz -# FN/INS/TR -(grep "#" fn.vcf && (grep 'SVTYPE=INS' fn.vcf | grep 'TRgt100=TRUE')) | vcf-sort | bgzip > fn_ins_TR.vcf.gz -tabix -p vcf fn_ins_TR.vcf.gz - -# FP/INS/non-TR -# grep -v "#" fp.vcf | awk '{if (length($4) - length($5) < 0) print $0}' | bedtools intersect -a stdin \ -(grep "#" fp.vcf && (grep "#" fp.vcf && grep 'SVTYPE=INS' fp.vcf) | bedtools intersect -a stdin \ - -b $repeats -f 0.2 -v) | vcf-sort | bgzip > fp_ins_nonTR.vcf.gz -tabix -p vcf fp_ins_nonTR.vcf.gz - -# FP/INS/TR -# grep -v "#" fp.vcf | awk '{if (length($4) - length($5) < 0) print $0}' | bedtools intersect -a stdin \ -(grep "#" fp.vcf && (grep "#" fp.vcf && grep 'SVTYPE=INS' fp.vcf) | bedtools intersect -a stdin \ - -b $repeats -f 0.2 -u) | vcf-sort | bgzip > fp_ins_TR.vcf.gz -tabix -p vcf fp_ins_TR.vcf.gz - -# FN/DEL/non-TR -(grep "#" fn.vcf && (grep 'SVTYPE=DEL' fn.vcf | grep 'TRgt100=FALSE')) | vcf-sort | bgzip > fn_del_nonTR.vcf.gz -tabix -p vcf fn_del_nonTR.vcf.gz -# FN/DEL/TR -(grep "#" fn.vcf && (grep 'SVTYPE=DEL' fn.vcf | grep 'TRgt100=TRUE')) | vcf-sort | bgzip > fn_del_TR.vcf.gz -tabix -p vcf fn_del_TR.vcf.gz -# FP/DEL/non-TR -# grep -v "#" fp.vcf | awk '{if (length($4) - length($5) > 0) print $0}' | bedtools intersect -a stdin \ -(grep "#" fp.vcf && (grep "#" fp.vcf && grep 'SVTYPE=DEL' fp.vcf) | bedtools intersect -a stdin \ - -b $repeats -f 0.2 -v) | vcf-sort | bgzip > fp_del_nonTR.vcf.gz -tabix -p vcf fp_del_nonTR.vcf.gz -# FP/DEL/TR -# grep -v "#" fp.vcf | awk '{if (length($4) - length($5) > 0) print $0}' | bedtools intersect -a stdin \ -(grep "#" fp.vcf && (grep "#" fp.vcf && grep 'SVTYPE=DEL' fp.vcf) | bedtools intersect -a stdin \ - -b $repeats -f 0.2 -u) | vcf-sort | bgzip > fp_del_TR.vcf.gz -tabix -p vcf fp_del_TR.vcf.gz -cd - diff --git a/truvari/stratify.py b/truvari/stratify.py new file mode 100644 index 00000000..fc60205d --- /dev/null +++ b/truvari/stratify.py @@ -0,0 +1,81 @@ +""" +Count variants per-region in vcf +""" +import os +import argparse + +import pysam +import pandas as pd + +import truvari + +def parse_args(args): + """ + Pull the command line parameters + """ + parser = argparse.ArgumentParser(prog="stratify", description=__doc__, + formatter_class=argparse.RawDescriptionHelpFormatter) + parser.add_argument("regions", metavar="BED", + help="Regions to process") + parser.add_argument("in_vcf", metavar="VCF", + help="Truvari bench result directory or a single VCF") + parser.add_argument("-o", "--output", metavar="OUT", default="/dev/stdout", + help="Output bed-like file") + parser.add_argument("--header", action="store_true", + help="Input regions have header to preserve in output") + parser.add_argument("-w", "--within", action="store_true", + help="Only count variants contained completely within region boundaries") + parser.add_argument("--debug", action="store_true", + help="Verbose logging") + args = parser.parse_args(args) + truvari.setup_logging(args.debug, show_version=True) + return args + +def count_entries(vcf, regions, within): + """ + Count the number of variants per bed region a VCF + regions is a list of lists with sub-lists having 0:3 of chrom, start, end + Returns a list of the counts in the same order as the regions + """ + counts = [0] * len(regions) + for idx, row in enumerate(regions): + for entry in vcf.fetch(row[0], row[1], row[2]): + if within: + ent_start, ent_end = truvari.entry_boundaries(entry) + if not (row[1] <= ent_start and ent_end <= row[2]): + continue + counts[idx] += 1 + return counts + +def benchdir_count_entries(benchdir, regions, within=False): + """ + Count the number of variants per bed region in Truvari bench directory by state + + Returns a pandas dataframe of the counts + """ + vcfs = {'tpbase': pysam.VariantFile(os.path.join(benchdir, 'tp-base.vcf.gz')), + 'tp': pysam.VariantFile(os.path.join(benchdir, 'tp-comp.vcf.gz')), + 'fn': pysam.VariantFile(os.path.join(benchdir, 'fn.vcf.gz')), + 'fp': pysam.VariantFile(os.path.join(benchdir, 'fp.vcf.gz')) + } + data = {} + for name, vcf in vcfs.items(): + data[name] = count_entries(vcf, regions, within) + return pd.DataFrame(data) + +def stratify_main(cmdargs): + """ + stratify + """ + args = parse_args(cmdargs) + read_header = 0 if args.header else None + regions = pd.read_csv(args.regions, sep='\t', header=read_header) + r_list = regions.to_numpy().tolist() # the methods expect lists + if os.path.isdir(args.in_vcf): + counts = benchdir_count_entries(args.in_vcf, r_list, args.within)[["tpbase", "tp", "fn", "fp"]] + else: + counts = count_entries(pysam.VariantFile(args.in_vcf), r_list, args.within) + counts = pd.Series(counts, name="count").to_frame() + counts.index = regions.index + regions = regions.join(counts) + regions.to_csv(args.output, header=args.header, index=False, sep='\t') diff --git a/truvari/utils.py b/truvari/utils.py index 0de1e46c..37fef171 100644 --- a/truvari/utils.py +++ b/truvari/utils.py @@ -16,9 +16,10 @@ from collections import namedtuple from importlib.metadata import version -import Levenshtein import pysam -import progressbar +from pysam import bcftools + +import truvari HEADERMAT = re.compile( r"##\w+=\w+),Number=(?P[\.01AGR]),Type=(?P\w+)") @@ -72,31 +73,6 @@ def restricted_int(x): raise argparse.ArgumentTypeError(f"{x} is < 0") return x -def setup_progressbar(size): - """ - Build a formatted :class:`progressbar.ProgressBar` - - :param `size`: Number of elements in the progress bar - :type `size`: int - - :return: Formatted progress bar - :rtype: progressbar.ProgressBar - - Example - >>> import truvari - >>> import time - >>> bar = truvari.setup_progressbar(4) - >>> for i in range(4): - ... bar.update(i + 1) # The bar animation updates - ... time.sleep(1) - >>> bar.finish() # Final update to the bar - """ - return progressbar.ProgressBar(redirect_stdout=True, max_value=size, widgets=[ - ' [', progressbar.Timer(), ' ', progressbar.Counter(), '/', str(size), '] ', - progressbar.Bar(), - ' (', progressbar.ETA(), ') ', - ]) - class LogFileStderr(): """ Write to stderr and a file @@ -251,7 +227,7 @@ def ref_ranges(reference, chunk_size=10000000): Example >>> import truvari - >>> gen = truvari.ref_ranges("repo_utils/test_files/reference.fa", 1000) + >>> gen = truvari.ref_ranges("repo_utils/test_files/references/reference.fa", 1000) >>> print(len([_ for _ in gen])) 1000 """ @@ -281,7 +257,7 @@ def bed_ranges(bed, chunk_size=10000000): Example >>> import truvari - >>> gen = truvari.bed_ranges("repo_utils/test_files/giab.bed", 1000) + >>> gen = truvari.bed_ranges("repo_utils/test_files/beds/giab.bed", 1000) >>> print(len([_ for _ in gen])) 992 """ @@ -311,7 +287,7 @@ def vcf_ranges(vcf, min_dist=1000): Example >>> import truvari - >>> gen = truvari.vcf_ranges("repo_utils/test_files/input1.vcf.gz") + >>> gen = truvari.vcf_ranges("repo_utils/test_files/variants/input1.vcf.gz") >>> print(len([_ for _ in gen])) 228 """ @@ -343,6 +319,7 @@ def vcf_ranges(vcf, min_dist=1000): def opt_gz_open(in_fn): """ Chooses file handler for plain-text files or `*.gz` files. + returns a generator which yields lines of the file """ def gz_hdlr(fn): @@ -369,7 +346,7 @@ def make_temp_filename(tmpdir=None, suffix=""): fn = os.path.join(tmpdir, next(tempfile._get_candidate_names())) + suffix # pylint: disable=protected-access return fn -def help_unknown_cmd(user_cmd, avail_cmds, threshold=.5): +def help_unknown_cmd(user_cmd, avail_cmds, threshold=0.8): """ Guess the command in avail_cmds that's most similar to user_cmd. If there is no guess below threshold, don't guess. @@ -392,33 +369,60 @@ def help_unknown_cmd(user_cmd, avail_cmds, threshold=.5): """ guesses = [] for real in avail_cmds: - ratio = Levenshtein.ratio(user_cmd, real) - distance = Levenshtein.distance(user_cmd, real) - score = distance - ratio - score2 = 1 - distance / len(real) - dat = (score, real) - if ratio >= threshold and score2 >= threshold: - guesses.append(dat) + score = truvari.seqsim(user_cmd, real) + if score >= threshold: + guesses.append((score, real)) guesses.sort() if not guesses: return None - return guesses[0][1] + return guesses[-1][1] -def compress_index_vcf(fn, remove=True): +def performance_metrics(tpbase, tp, fn, fp): + """ + Calculates precision, recall, and f1 given counts by state + Can return None if values are zero + + :param `tpbase`: found base count + :type `tpbase`: int + :param `tp`: found comp count + :type `tp`: int + :param `fn`: missed base count + :type `fn`: int + :param `fp`: missed comp count + :type `fp`: int + + :return: tuple of precision, recall, f1 + :rtype: tuple, float + """ + base_cnt = tpbase + fn + comp_cnt = tp + fp + if base_cnt == 0 or comp_cnt == 0: + return None, None, None + precision = tp / comp_cnt + recall = tpbase / base_cnt + neum = recall * precision + denom = recall + precision + f1 = 2 * (neum / denom) if denom != 0 else None + return precision, recall, f1 + +def compress_index_vcf(fn, fout=None, remove=True): """ - compress/index a VCF file in place using bgzip and tabix - if remove: take out the old one - Should maybe shutil.which the tools. Probably should raise an exception instead of exiting + Compress and index a vcf. If no fout is provided, write to fn + '.gz' + + :param `fn`: filename of vcf to work on + :type `fn`: string + :param `fout`: output filename + :type `fout`: string, optional + :param `remove`: remove fn after fout is made + :type `remove`: bool """ - logging.debug("compress/index") - ret = cmd_exe(f"vcf-sort {fn} | bgzip > {fn}_tmp", pipefail=True) - os.rename(f"{fn}_tmp", f"{fn}.gz") - if ret.ret_code != 0: - logging.error(ret) - sys.exit(ret.ret_code) - ret = cmd_exe(f"tabix -f {fn}.gz") - if ret.ret_code != 0: - logging.error(ret) - sys.exit(ret.ret_code) + if fout is None: + fout = fn + '.gz' + m_tmp = make_temp_filename(suffix='.vcf') + with open(m_tmp, 'w') as out_hdlr: + out_hdlr.write(bcftools.sort(fn)) + pysam.tabix_compress(m_tmp, fout) + pysam.tabix_index(fout, preset="vcf") if remove: os.remove(fn) + os.remove(m_tmp) diff --git a/truvari/vcf2df.py b/truvari/vcf2df.py index d7faaa8e..064e7de3 100644 --- a/truvari/vcf2df.py +++ b/truvari/vcf2df.py @@ -63,9 +63,9 @@ class SV(Enum): def get_svtype(svtype): """ - Turn to an SV + Turn a SVTYPE string to a :class:`truvari.SV` object - :param `svtype`: SVTYPE string to turn into SV object + :param `svtype`: :type `svtype`: string :return: A :class:`SV` of the SVTYPE @@ -174,16 +174,15 @@ def get_files_from_truvdir(directory): return dictionary of file identifier and path (e.g. "tp-base": "dir/tp-base.vcf.gz") """ ret = {} - pats = [("tpbase", "tp-base.vcf"), ("tp", "tp-call.vcf"), - ("fp", "fp.vcf"), ("fn", "fn.vcf")] + pats = [("tpbase", "tp-base.vcf.gz"), ("tp", "tp-comp.vcf.gz"), + ("fp", "fp.vcf.gz"), ("fn", "fn.vcf.gz")] has_error = False for key, name in pats: fname = os.path.join(directory, name) ret[key] = glob.glob(fname) - ret[key].extend(glob.glob(fname + '.gz')) if len(ret[key]) != 1: logging.error( - "Expected 1 file for %s[.gz] found %d", fname, len(ret[key])) + "Expected 1 file for %s found %d", fname, len(ret[key])) has_error = True if has_error: raise FileNotFoundError((f"Couldn't parse truvari directory {directory}. " @@ -240,7 +239,7 @@ def pres_check(dat, key, multi=False): return columns, ops -def vcf_to_df(fn, with_info=True, with_fmt=True, sample=None, no_prefix=False): +def vcf_to_df(fn, with_info=True, with_format=True, sample=None, no_prefix=False, alleles=False): """ Parse a vcf file and turn it into a dataframe. Tries its best to pull info/format tags from the sample information. @@ -251,32 +250,35 @@ def vcf_to_df(fn, with_info=True, with_fmt=True, sample=None, no_prefix=False): :type `fn`: string :param `with_info`: Add the INFO fields from the VCF to the DataFrame columns :type `with_info`: boolean, optional - :param `with_fmt`: Add the FORMAT fields from the VCF to the DataFrame columns + :param `with_format`: Add the FORMAT fields from the VCF to the DataFrame columns :type `with_info`: boolean, optional - :param `sample`: Sample from the VCF to parse. Only used when with_fmt==True + :param `sample`: Sample from the VCF to parse. Only used when with_format==True :type `sample`: int/string, optional :param `no_prefix`: Don't prefix FORMAT fields with sample name :type `no_prefix`: boolean, optional + :param `alleles`: Add column with allele sequences + :type `alleles`: boolean, optional :return: Converted VCF :rtype: pandas.DataFrame Example >>> import truvari - >>> df = truvari.vcf_to_df("repo_utils/test_files/input2.vcf.gz", True, True) + >>> df = truvari.vcf_to_df("repo_utils/test_files/variants/input2.vcf.gz", True, True) >>> df.columns - Index(['id', 'svtype', 'svlen', 'szbin', 'qual', 'filter', 'is_pass', 'QNAME', - 'QSTART', 'QSTRAND', 'SVTYPE', 'SVLEN', 'NA12878_GT', 'NA12878_PL_ref', - 'NA12878_PL_het', 'NA12878_PL_hom', 'NA12878_AD_ref', 'NA12878_AD_alt'], + Index(['chrom', 'start', 'end', 'id', 'svtype', 'svlen', 'szbin', 'qual', + 'filter', 'is_pass', 'QNAME', 'QSTART', 'QSTRAND', 'SVTYPE', 'SVLEN', + 'NA12878_GT', 'NA12878_PL_ref', 'NA12878_PL_het', 'NA12878_PL_hom', + 'NA12878_AD_ref', 'NA12878_AD_alt'], dtype='object') """ v = pysam.VariantFile(fn) - if with_fmt and not sample: - sample = pull_samples(fn) + if with_format and not sample: + sample = list(v.header.samples) if sample and len(sample) > 1 and no_prefix: raise TypeError("Multiple samples being pulled, must use prefix") - header = ["key", "id", "svtype", "svlen", + header = ["hash", "chrom", "start", "end", "id", "svtype", "svlen", "szbin", "qual", "filter", "is_pass"] info_ops = [] @@ -286,7 +288,7 @@ def vcf_to_df(fn, with_info=True, with_fmt=True, sample=None, no_prefix=False): header.extend(info_header) fmt_ops = [] - if with_fmt: # get all the format fields, and how to parse them from header, add them to the header + if with_format: # get all the format fields, and how to parse them from header, add them to the header fmt_header, fmt_ops = tags_to_ops(v.header.formats.items()) logging.debug(fmt_header) if isinstance(sample, list) and not no_prefix: @@ -302,33 +304,44 @@ def vcf_to_df(fn, with_info=True, with_fmt=True, sample=None, no_prefix=False): sample = [sample] else: sample = [] - - rows = [] - for entry in v: - varsize = truvari.entry_size(entry) - filt = list(entry.filter) - cur_row = [truvari.entry_to_key(entry), - entry.id, - truvari.entry_variant_type(entry).name, - varsize, - truvari.get_sizebin(varsize), - entry.qual, - filt, - not filt or filt[0] == 'PASS' - ] - - for i, op in info_ops: # Need to make OPs for INFOS.. - cur_row.extend(op(entry.info, i)) - - for samp in sample: - for i, op in fmt_ops: - cur_row.extend(op(entry.samples[samp], i)) - - rows.append(cur_row) - ret = pd.DataFrame(rows, columns=header) + if alleles: + header.append("alleles") + + def _transform(): + """ + Yields the rows + """ + for entry in v: + varsize = truvari.entry_size(entry) + cur_row = [truvari.entry_to_hash(entry), + entry.chrom, + entry.start, + entry.stop, + entry.id, + truvari.entry_variant_type(entry).name, + varsize, + truvari.get_sizebin(varsize), + entry.qual, + list(entry.filter), + not truvari.entry_is_filtered(entry) + ] + + for i, op in info_ops: + cur_row.extend(op(entry.info, i)) + + for samp in sample: + for i, op in fmt_ops: + cur_row.extend(op(entry.samples[samp], i)) + + if alleles: + cur_row.append(entry.alleles) + + yield cur_row + + ret = pd.DataFrame(_transform(), columns=header) ret["szbin"] = ret["szbin"].astype(SZBINTYPE) ret["svtype"] = ret["svtype"].astype(SVTYTYPE) - return ret.set_index("key") + return ret.set_index("hash") def optimize_df_memory(df): @@ -409,12 +422,6 @@ def parse_args(args): args.compress = 3 return args -def pull_samples(vcf_fn): - """ - Pull sample names from a vcf - """ - vcf = pysam.VariantFile(vcf_fn) - return list(vcf.header.samples) def vcf2df_main(args): """