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bio-population-genetics-linkage-disequilibrium

80 / 100 · Low risk

Fine to try.

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

Computes linkage disequilibrium (r2, D', composite Rogers-Huff r2), prunes correlated variants, clumps GWAS summary statistics to lead SNPs, and defines haplotype blocks with PLINK 1.9/2.0 and scikit-allel. r2 and D' answer different questions - r2 (= chi2/N) is the tagging and GWAS-power currency, D' marks observed recombination and is upward-biased for rare variants. PLINK 2.0 has no bare --r2 (split into --r2-phased and --r2-unphased); pruning (--indep-pairwise, genotype-blind) and clumping …

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