vcf-variant-filtering
From the author
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.
Install
npx skills add jaechang-hits/SciAgent-Skills --skill vcf-variant-filtering -a claude-code
Installs to .claude/skills/vcf-variant-filtering/ · Each command fetches the skill straight from GitHub with the open skills CLI.
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