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Add filtering of VEP annotated VCF files using bcftools/view #23

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merged 17 commits into from
Feb 10, 2025

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famosab
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@famosab famosab commented Feb 4, 2025

This adds bcftools/view to enable filtering the VCFs for specific patterns. Mostly to filter through VEP annotation.

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
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@famosab famosab changed the base branch from master to dev February 4, 2025 05:12
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@d4straub d4straub left a comment

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LGTM!

@famosab famosab merged commit 5708e09 into qbic-pipelines:dev Feb 10, 2025
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@famosab famosab deleted the feat/vep-filter branch February 10, 2025 11:51
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2 participants