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name: variant-io description: "Guides agents using pysam VariantFile, VariantHeader, and VariantRecord for VCF/BCF reading, writing, sample subsetting, metadata edits, and coordinate/header troubleshooting." disable-model-invocation: true metadata: disco-role: operating license: MIT

variant-io

Use this sub-skill when a task involves VCF/BCF variant data through pysam.VariantFile, VariantHeader, VariantRecord, INFO/FORMAT/sample fields, record creation, record translation, or random access with fetch.

Read First

• references/api-reference.md for the object model, signatures, modes, and mapping-like containers.
• references/workflows.md for common read/filter/write, header-building, record-editing, sample-subsetting, and translation patterns.
• references/troubleshooting.md for header declarations, INFO/FORMAT mismatches, genotype/allele errors, indexes, coordinates, and VCF/BCF mode choices.
• scripts/variant_smoke.py for a source-free VCF round-trip smoke helper that prints JSON assertions.

Scope

This sub-skill owns VCF/BCF I/O and variant object manipulation: VariantFile, VariantHeader, VariantHeaderRecord, VariantRecord, VariantRecordSample, header metadata mappings, fetch, write, subset_samples, new_record, and translate.

Use sibling sub-skills instead for tabix row parsers and BED/GTF/GFF parsing, bcftools command wrappers, or SAM/BAM/CRAM alignment and pileup workflows.