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bio-workflows-gwas-pipeline

95 / 100 · Low risk

Fine to try.

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

Orchestrates the GWAS pipeline from genotypes to association results, chaining PLINK2 QC (variant-then-sample missingness, controls-only HWE, KING relatedness), panel harmonization + joint phasing/imputation to dosages, long-range-LD-excluded PCA, and an engine chosen by sample structure (PLINK2-GLM / regenie / SAIGE / BOLT-LMM), with LDSC-intercept diagnostics. Use when committing the genome build + ancestry-matched imputation panel once (ancestry match > panel size), running the strand/allele…

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-workflows-gwas-pipeline' ] || [ -L ~/.agents/skills/'bio-workflows-gwas-pipeline' ]; then echo 'A skill folder named bio-workflows-gwas-pipeline 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 "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-workflows-gwas-pipeline' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-workflows-gwas-pipeline' ~/.agents/skills/'bio-workflows-gwas-pipeline' && 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-workflows-gwas-pipeline' ~/.claude/skills/'bio-workflows-gwas-pipeline' (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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