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vcf-basics

combined

View, query, and interpret VCF/BCF variant files with bcftools and cyvcf2. Use when inspecting variants, extracting fields with query format strings, converting VCF/BCF, or correctly reading a field -- QUAL (site) vs GQ (genotype) vs PL/GL likelihoods, AD vs DP and allele balance, GT phasing/ploidy/PS and missing-vs-hom-ref, INFO/FORMAT Number A/R/G semantics, symbolic alleles (<DEL>, <NON_REF>, spanning *) and END, or telling a raw gVCF apart from a filtered callset.

When to use

• inspecting variants
• extracting specific fields
• understanding VCF format structure
• viewing VCF/BCF files
• format conversion
• querying variant data

Skill page

Conflict

The two copies cover the same core task (viewing and querying VCF/BCF files with bcftools and cyvcf2) but the GPTomics copy adds substantial, non-trivial interpretive constraints that the FreedomIntelligence copy lacks: a governing principle about field level and Number semantics, a detailed QUAL vs GQ vs PL/GL comparison, the header contract, and specific traps (missing vs hom-ref, symbolic alleles, gVCF). The FreedomIntelligence copy provides a more complete, step-by-step command reference for bcftools view/query, format conversion, indexing, and cyvcf2 code patterns that the GPTomics copy truncates or omits. Crowning one would hide the other's real value.