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"]