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bio-phasing-imputation-imputation-qc

100 / 100 · Low risk

Fine to try.

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

Assesses and filters phasing/imputation output - the quality metrics (Beagle DR2, Minimac R2 and EmpRsq, IMPUTE/GLIMPSE INFO), MAF-stratified filtering, true accuracy by masking, the differential-imputation confound, dosage-based downstream usage, and phasing switch-error QC. Covers why every routine quality score is an ESTIMATE of r2 from the posterior spread (not validation against truth), why it is confounded with MAF so a flat INFO>=0.3 cutoff is a hidden rare-variant filter, why concordanc…

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