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bio-variant-calling-filtering-best-practices

80 / 100 · Low risk

Fine to try.

By lilinji/GeneTind-Life-Skills (GitHub) · other · 17 stars · scanned at commit 908229c

Filters germline and somatic variant callsets at the site and genotype level with GATK VQSR (VQSLOD, truth-sensitivity tranches), VETS/ScoreVariantAnnotations, NVScoreVariants, hard filters with per-annotation thresholds, and bcftools/cyvcf2 expressions, plus Ti/Tv-based QC. Use when deciding between VQSR, hard filtering, and ML recalibration by cohort size and platform, setting SNP vs indel thresholds, replicating the missing-annotation-passes rule so hom-alt sites survive, applying genotype-l…

Works with any agent that supports SKILL.md skills.

What this skill can do

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'bio-variant-calling-filtering-best-practices' ] || [ -L ~/.agents/skills/'bio-variant-calling-filtering-best-practices' ]; then echo 'A skill folder named bio-variant-calling-filtering-best-practices already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/lilinji/GeneTind-Life-Skills' "$d" && git -C "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-variant-calling-filtering-best-practices' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-variant-calling-filtering-best-practices' ~/.agents/skills/'bio-variant-calling-filtering-best-practices' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'bio-variant-calling-filtering-best-practices' ~/.claude/skills/'bio-variant-calling-filtering-best-practices' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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