From 2c44cb76686ec01c748c6a7bff986798d4e25c52 Mon Sep 17 00:00:00 2001 From: Daniel Nilsson Date: Thu, 24 Oct 2024 09:14:20 +0200 Subject: [PATCH] =?UTF-8?q?changed=20a=20few=20more=20refs=20from=20M?= =?UTF-8?q?=C3=A5ns=20original=20url=20to=20new=20org=20url?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- CITATION.cff | 2 +- docs/index.md | 14 +++++++------- examples/readme.md | 18 +++++++++--------- mkdocs.yml | 2 +- setup.py | 2 +- 5 files changed, 19 insertions(+), 19 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 25cf11f..35f31af 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -13,4 +13,4 @@ identifiers: type: doi value: "10.5281/zenodo.3841142" license: MIT Licence -repository-code: "https://github.com/moonso/genmod" +repository-code: "https://github.com/Clinical-Genomics/genmod" diff --git a/docs/index.md b/docs/index.md index a21355e..d836a71 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,8 +1,8 @@ # Genmod #

- - + +

@@ -24,15 +24,15 @@ whole exome data and whole genome data. ## Installation ## **GENMOD** - +```bash pip install genmod - +``` or - - git clone https://github.com/moonso/genmod.git +```bash + git clone https://github.com/Clinical-Genomics/genmod.git cd genmod python setup.py install - +``` ### Example: ### diff --git a/examples/readme.md b/examples/readme.md index f911ca2..373fb71 100644 --- a/examples/readme.md +++ b/examples/readme.md @@ -12,9 +12,9 @@ If the user want to build own annotations please use **genmod build_annotation** ##Annotate variants for Recessive Family## - +``` genmod annotate examples/test_vcf.vcf -f examples/recessive_trio.ped -o examples/test_vcf_recessive_annotated.vcf - +``` The vcf file have a couple of variants made up so it will be easy to understand how the genetic inheritance patterns are annotated. With the basic command listed above the output should look like the variants in ```examples/test_vcf_recessive_annotated.vcf``` @@ -30,24 +30,24 @@ The following variants are to show how the ``-strict`` flag affects the analysis ##Annotate variants for Dominant Family## - +``` genmod annotate test_data/test_vcf.vcf -f test_data/dominant_trio.ped -o examples/test_vcf_dominant_annotated.vcf - +``` We can now see how the conditions change when one of the parents are affected. For example the recessive pattern for the first variant is not followed since all affected needs to be homozygote alternative if the variant should follow the Autosomal Recessive pattern. ##Annotate variants for Multiple Families## - +``` genmod annotate test_data/test_vcf.vcf -f test_data/multi_family.ped -o examples/test_vcf_multi_annotated.vcf - +``` We can now see how the conditions change when one of the parents are affected. For example the recessive pattern for the first variant is not followed since all affected needs to be homozygote alternative if the variant should follow the Autosomal Recessive pattern. ##Annotate variants with CADD scores and population frequencies## This is another example of how one can annotate with genmod: - +``` genmod annotate examples/test_vcf.vcf --cadd_file examples/small_CADD.tsv.gz --thousand_g examples/small_1000G.vcf.gz +``` - -Please post issues on http://github.com/moonso/genmod if any problems. \ No newline at end of file +Please post issues on http://github.com/Clinical-Genomics/genmod in case of any problems. \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml index 66f7579..65b095b 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -3,7 +3,7 @@ site_name: genmod docs site_description: Project documentation with Markdown site_author: Måns Magnusson -repo_url: https://github.com/moonso/genmod +repo_url: https://github.com/Clinical-Genomics/genmod pages: - Home: index.md diff --git a/setup.py b/setup.py index 505644e..a61e5c0 100644 --- a/setup.py +++ b/setup.py @@ -24,7 +24,7 @@ description='Annotate genetic inheritance models in variant files', author = 'Mans Magnusson', author_email = 'mans.magnusson@scilifelab.se', - url = 'http://github.com/moonso/genmod', + url = 'http://github.com/Clinical-Genomics/genmod', license = 'MIT License', python_requires="~=3.8.0", install_requires=[