bio-vcf-statistics

80 / 100 · Low risk

Fine to try.

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

Compute and interpret VCF quality-control metrics (Ti/Tv, het/hom, novel/known, missingness, HWE, contamination, relatedness) with bcftools stats, vcftools, plot-vcfstats, and identity tools (somalier, peddy, KING). Use when judging whether a callset is trustworthy, diagnosing a low Ti/Tv or outlier het/hom sample, deciding whether an HWE deviation is error or biology, screening a cohort for sample swaps/contamination/wrong-sex before analysis, or comparing call sets before and after filtering.…

Works with any agent that supports SKILL.md skills.

What this skill can do

Runs commands on your computer

The author does not mention this.

Found in 9 places.

skills/bio-vcf-statistics/SKILL.md, line 55bcftools stats input.vcf.gz > stats.txt # cohort-level
skills/bio-vcf-statistics/SKILL.md, line 64bcftools stats input.vcf.gz | grep "^SN" | cut -f3- # counts
skills/bio-vcf-statistics/SKILL.md, line 86bcftools annotate -a dbsnp.vcf.gz -c ID input.vcf.gz -Oz -o annotated.vcf.gz

Show 6 more

skills/bio-vcf-statistics/SKILL.md, line 98vcftools --gzvcf input.vcf.gz --missing-indv --out sample_miss # .imiss (per-sample)
skills/bio-vcf-statistics/SKILL.md, line 112vcftools --gzvcf controls.vcf.gz --hardy --out hwe # exact-test P per site
skills/bio-vcf-statistics/SKILL.md, line 125bcftools query -i 'GT="het"' -f '[%AD]\n' input.vcf.gz | \
skills/bio-vcf-statistics/SKILL.md, line 144bcftools gtcheck input.vcf.gz > gtcheck.txt # DC lines: query, genotyped, discordance, sites
skills/bio-vcf-statistics/SKILL.md, line 164bcftools stats -R easy_regions.bed input.vcf.gz > easy.txt
skills/bio-vcf-statistics/SKILL.md, line 173bcftools view -H input.vcf.gz | wc -l # total records

Downloads and installs other software

The author does not mention this.

Found in 3 places.

skills/bio-vcf-statistics/SKILL.md, line 205| `plot-vcfstats not found` / no plots | matplotlib missing or not on PATH | `pip install matplotlib`; check `which plot-vcfstats` |
skills/bio-vcf-statistics/usage-guide.md, line 11- somalier (`conda install -c bioconda somalier`) and peddy (`pip install peddy`) for scalable identity/relatedness/sex/ancestry QC
skills/bio-vcf-statistics/usage-guide.md, line 12- cyvcf2 (`pip install cyvcf2`) and numpy for custom per-record statistics in Python

Install

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

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

Date	Version	Score
2026-11-11	`908229c`	80