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bio-phasing-imputation-haplotype-phasing

100 / 100 · Low risk

Fine to try.

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

Estimates haplotype phase from population linkage disequilibrium with SHAPEIT5, SHAPEIT4, Eagle2, or Beagle - turning unphased genotypes (0/1) into phased haplotypes (0|1) for imputation input, compound-heterozygote calls, HLA typing, or population genetics. Covers why statistical phase is an INFERENCE (not a measurement) whose error concentrates at rare variants, why a genome-wide switch-error rate hides catastrophic rare-variant error and must be reported MAC-stratified, the SHAPEIT5 common-s…

Works with any agent that supports SKILL.md skills.

What this skill can do

We found nothing in the files we read that matches our rules. That does not prove the skill is safe: see the limits of static scanning.

Install

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

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