bio-variant-normalization

95 / 100 · Low risk

Fine to try.

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

Left-align and trim indels to parsimonious canonical form, decompose MNPs (atomize), and split multiallelic variants with bcftools norm. Use when comparing variants across callers or cohorts, preparing a VCF for database annotation or ClinVar/dbSNP matching, merging VCFs, reconciling vt-vs-bcftools representation discordance, or resolving the VCF-left-align vs HGVS-3'-rule clash.

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 14 places.

skills/bio-variant-normalization/SKILL.md, line 85bcftools norm --atomize input.vcf.gz | \
skills/bio-variant-normalization/SKILL.md, line 94bcftools norm -m- input.vcf.gz | \
skills/bio-variant-normalization/SKILL.md, line 120bcftools norm -f reference.fa input.vcf.gz -Oz -o normalized.vcf.gz

Show 11 more

skills/bio-variant-normalization/SKILL.md, line 130bcftools norm -f reference.fa -c w input.vcf.gz > /dev/null
skills/bio-variant-normalization/SKILL.md, line 144bcftools norm -m-any input.vcf.gz -Oz -o split.vcf.gz
skills/bio-variant-normalization/SKILL.md, line 195bcftools norm -m+any input.vcf.gz -Oz -o merged.vcf.gz
skills/bio-variant-normalization/SKILL.md, line 228bcftools norm --atomize input.vcf.gz -Oz -o atomized.vcf.gz
skills/bio-variant-normalization/SKILL.md, line 250bcftools norm --atomize --old-rec-tag ORIGINAL input.vcf.gz -Oz -o atomized.vcf.gz
skills/bio-variant-normalization/SKILL.md, line 274bcftools norm -f reference.fa -c s input.vcf.gz -Oz -o fixed.vcf.gz
skills/bio-variant-normalization/SKILL.md, line 282bcftools norm -f reference.fa -c x input.vcf.gz -Oz -o clean.vcf.gz
skills/bio-variant-normalization/SKILL.md, line 290bcftools norm -d exact input.vcf.gz -Oz -o deduped.vcf.gz
skills/bio-variant-normalization/SKILL.md, line 310for vcf in gatk.vcf.gz freebayes.vcf.gz; do
skills/bio-variant-normalization/SKILL.md, line 326bcftools norm --atomize variants.vcf.gz | \
skills/bio-variant-normalization/SKILL.md, line 339bcftools norm -f reference.fa -m- input.vcf.gz | \

Install

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

if [ -e ~/.agents/skills/'bio-variant-normalization' ] || [ -L ~/.agents/skills/'bio-variant-normalization' ]; then echo 'A skill folder named bio-variant-normalization 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 "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-variant-normalization' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-variant-normalization' ~/.agents/skills/'bio-variant-normalization' && 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-variant-normalization' ~/.claude/skills/'bio-variant-normalization' (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`	95