Individual skill

vcf-variant-filtering

Guide to quality filtering raw VCF files before computing summary stats (Ts/Tv ratio, variant counts, AF distributions). Covers detecting raw VCFs via FILTER column and QUAL inspection, QUAL-based filtering with bcftools, Ts/Tv interpretation, and when NOT to filter. Read before any variant-level QC task. See bcftools-variant-manipulation for advanced filters, gatk-variant-calling for caller config, samtools-bam-processing for upstream alignment QC.

skills/genomics-bioinformatics/variant/vcf-variant-filtering/SKILL.md

Source commit 55c1bd3e863d11bf5a853d24bcdda10c88e6eddf

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Observed behavior

Network or broad shell

Last checked

Nov 5, 2026

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