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Bcftools variant filtering starter

Skill ma-compbio-lab/SkillFoundry/skills/genomics/bcftools-variant-filtering-starter

A framework for discovering, compiling, and validating reusable skills for scientific agents.

Install
npx -y skills add ma-compbio-lab/SkillFoundry --skill bcftools-variant-filtering-starter

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SKILL.md

1.2 KB, 313 tokens by cl100k_base, as published. Nobody here has run it

bcftools Variant Filtering Starter

Use this skill to run a deterministic bcftools view filtering example on a tiny VCF and capture the kept variants in a compact JSON summary.

What it does

  • Runs bcftools view with a configurable include expression against a local VCF.
  • Writes a compressed filtered VCF plus a tabix index.
  • Summarizes the input record count, passing record count, and kept IDs for testing and demos.

When to use it

  • You need a runnable starter for VCF filtering logic.
  • You want a tiny verified example before building cohort-scale post-calling workflows.
  • You need a smoke-testable wrapper around bcftools in the repo-managed genomics environment.

Example

python3 skills/genomics/bcftools-variant-filtering-starter/scripts/run_bcftools_variant_filtering.py \
  --input skills/genomics/bcftools-variant-filtering-starter/examples/toy_variants.vcf \
  --out scratch/genomics/bcftools_variant_filtering_summary.json \
  --filtered-vcf-out scratch/genomics/toy_variants.filtered.vcf.gz

Verification

  • Skill-local tests: python3 -m unittest discover -s skills/genomics/bcftools-variant-filtering-starter/tests -p 'test_*.py'
  • Expected summary: passing_record_count == 2 and kept_ids == ["varA", "varC"]

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