CLI for VCF/BCF: filter, merge, annotate, query, normalize, compute stats. Core post-variant-calling: quality filtering, multi-sample merging, rsID annotation, genotype extraction. Samtools companion in HTSlib. Use GATK for complex indel realignment during calling; use VCFtools for population genetics stats.
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bcftools — VCF/BCF Variant Manipulation Toolkit
Overview
bcftools is the standard command-line toolkit for processing VCF (Variant Call Format) and BCF (Binary Call Format) files in the HTSlib ecosystem. It covers the complete post-variant-calling workflow: format conversion, quality filtering, variant normalization, multi-sample merging, annotation with external databases, genotype extraction, and QC statistics. bcftools uses streaming by design — most commands read from stdin and write
[Description truncada. Veja o README completo no GitHub.]
