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Use target bed files as regions instead of bait intervals for SNV calling in WES samples #636

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merged 6 commits into from
Oct 25, 2024
Merged

Use target bed files as regions instead of bait intervals for SNV calling in WES samples #636

merged 6 commits into from
Oct 25, 2024

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ramprasadn
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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/raredisease branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
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  • Usage Documentation in docs/usage.md is updated.
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github-actions bot commented Oct 18, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3df34f8

+| ✅ 200 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-22 17:04:23

@ramprasadn ramprasadn marked this pull request as ready for review October 18, 2024 08:06
@jemten jemten linked an issue Oct 20, 2024 that may be closed by this pull request
Some SNV genome variants were found outside of --target_bed file with --bait_padding #631
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jemten commented Oct 20, 2024

I tried running a test case and the bed file presented to deepvariant can't be bgzipped.

I1018 19:16:53.355009 139642998064960 genomics_reader.py:222] Reading ADM997A3_sorted_md.bam with NativeSamReader
I1018 19:16:53.406375 139642998064960 make_examples_core.py:301] Task 18/36: Preparing inputs
I1018 19:16:53.513127 139642998064960 genomics_reader.py:222] Reading ADM997A3_sorted_md.bam with NativeSamReader
I1018 19:16:53.529938 139642998064960 make_examples_core.py:301] Task 18/36: Common contigs are ['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', 'X', 'Y', 'MT']
Traceback (most recent call last):
  File "/home/proj/stage/analysis/cases/cleanshrimp/work/Bazel.runfiles_h0i4nyq0/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 234, in <module>
    app.run(main)
  File "/home/proj/stage/analysis/cases/cleanshrimp/work/Bazel.runfiles_h0i4nyq0/runfiles/absl_py/absl/app.py", line 312, in run
    _run_main(main, args)
  File "/home/proj/stage/analysis/cases/cleanshrimp/work/Bazel.runfiles_h0i4nyq0/runfiles/absl_py/absl/app.py", line 258, in _run_main
    sys.exit(main(argv))
  File "/home/proj/stage/analysis/cases/cleanshrimp/work/Bazel.runfiles_h0i4nyq0/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 224, in main
    make_examples_core.make_examples_runner(options)
  File "/home/proj/stage/analysis/cases/cleanshrimp/work/Bazel.runfiles_h0i4nyq0/runfiles/com_google_deepvariant/deepvariant/make_examples_core.py", line 2739, in make_examples_runner
    regions, calling_regions = processing_regions_from_options(options)
  File "/home/proj/stage/analysis/cases/cleanshrimp/work/Bazel.runfiles_h0i4nyq0/runfiles/com_google_deepvariant/deepvariant/make_examples_core.py", line 2641, in processing_regions_from_options
    calling_regions = build_calling_regions(
  File "/home/proj/stage/analysis/cases/cleanshrimp/work/Bazel.runfiles_h0i4nyq0/runfiles/com_google_deepvariant/deepvariant/make_examples_core.py", line 607, in build_calling_regions
    ranges.RangeSet.from_regions(regions_to_include, contig_dict)
  File "/home/proj/stage/analysis/cases/cleanshrimp/work/Bazel.runfiles_h0i4nyq0/runfiles/com_google_deepvariant/third_party/nucleus/util/ranges.py", line 170, in from_regions
    return cls(ranges=from_regions(regions, contig_map=contig_map))
  File "/home/proj/stage/analysis/cases/cleanshrimp/work/Bazel.runfiles_h0i4nyq0/runfiles/com_google_deepvariant/third_party/nucleus/util/ranges.py", line 117, in __init__
    for i, range_ in enumerate(ranges):
  File "/home/proj/stage/analysis/cases/cleanshrimp/work/Bazel.runfiles_h0i4nyq0/runfiles/co
m_google_deepvariant/third_party/nucleus/util/ranges.py", line 509, in from_regions
    yield parse_literal(region, contig_map)
  File "/home/proj/stage/analysis/cases/cleanshrimp/work/Bazel.runfiles_h0i4nyq0/runfiles/com_google_deepvariant/third_party/nucleus/util/ranges.py", line 597, in parse_literal
    raise ValueError(
ValueError: Could not parse "home.bed.gz" as a region literal.  Region literals should have the form "chr:start-stop" or "chr:start" or just "chr".  A common error is to use the "chr" prefix on inputs that don't have it, or vice-versa.
```
We can use `ch_target_bed_unprocessed` or we have to decompress the bed file again prior to deepvariant.

jemten
jemten reviewed Oct 22, 2024
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jemten
jemten approved these changes Oct 25, 2024
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👍

@ramprasadn ramprasadn merged commit 31249da into dev Oct 25, 2024
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@ramprasadn ramprasadn deleted the targetbedtodeepvariant branch October 31, 2024 22:34
@ramprasadn ramprasadn mentioned this pull request Nov 3, 2024
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Some SNV genome variants were found outside of --target_bed file with --bait_padding
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@ramprasadn @jemten