bio-variant-annotation

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

Annotates VCF variants with functional consequences, population frequencies, and pathogenicity scores using bcftools annotate/csq, Ensembl VEP, SnpEff, and ANNOVAR. Use when deciding which annotation engine and version to pin, which transcript set to report on (RefSeq vs Ensembl vs MANE Select/Plus Clinical, and why VEP --pick is dangerous clinically), how to reconcile HGVS 3'-shifting with VCF left-alignment, which consequence plus NMD status governs PVS1 eligibility, which single calibrated p…

Works with any agent that supports SKILL.md skills.

What this skill can do

Runs commands on your computer

This is disclosed by the author in the skill's SKILL.md or README.

Found in 8 places.

skills/bio-variant-annotation/SKILL.md, line 42bcftools norm -f reference.fa -m-any input.vcf.gz -Oz -o normalized.vcf.gz
skills/bio-variant-annotation/SKILL.md, line 69vep -i norm.vcf --vcf --cache --offline --assembly GRCh38 \
skills/bio-variant-annotation/SKILL.md, line 94vep -i norm.vcf.gz -o out.vcf --vcf --cache --offline \

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skills/bio-variant-annotation/SKILL.md, line 100vep -i norm.vcf.gz -o out.vcf --vcf --cache --offline \
skills/bio-variant-annotation/SKILL.md, line 114snpEff -Xmx8g ann GRCh38.105 norm.vcf > out.vcf
skills/bio-variant-annotation/SKILL.md, line 125table_annovar.pl norm.vcf humandb/ -buildver hg38 -out annotated -remove \
skills/bio-variant-annotation/SKILL.md, line 137bcftools csq -f reference.fa -g genes.gff3.gz norm.vcf.gz -Oz -o csq.vcf.gz # adds BCSQ
skills/bio-variant-annotation/SKILL.md, line 210set -euo pipefail

Downloads and installs other software

The author does not mention this.

Found in 1 place.

skills/bio-variant-annotation/usage-guide.md, line 13- Python parsing: `cyvcf2` (`pip install cyvcf2`)

Sends data to these websites: ftp.ncbi.nih.gov, gnomad-public-us-east-1.s3.amazonaws.com, ftp.ncbi.nlm.nih.gov

The author does not mention this.

Found in 6 places.

skills/bio-variant-annotation/usage-guide.md, line 264wget https://ftp.ncbi.nih.gov/snp/latest_release/VCF/GCF_000001405.40.gz
skills/bio-variant-annotation/usage-guide.md, line 265wget https://ftp.ncbi.nih.gov/snp/latest_release/VCF/GCF_000001405.40.gz.tbi
skills/bio-variant-annotation/usage-guide.md, line 277wget https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr1.vcf.bgz

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skills/bio-variant-annotation/usage-guide.md, line 278wget https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr1.vcf.bgz.tbi
skills/bio-variant-annotation/usage-guide.md, line 292wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz
skills/bio-variant-annotation/usage-guide.md, line 293wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz.tbi

Safer alternatives

Low-risk skills in the same category (other) that look related. Check that one does what you need.

Install

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

if [ -e ~/.agents/skills/'bio-variant-annotation' ] || [ -L ~/.agents/skills/'bio-variant-annotation' ]; then echo 'A skill folder named bio-variant-annotation 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 "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-variant-annotation' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-variant-annotation' ~/.agents/skills/'bio-variant-annotation' && 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-annotation' ~/.claude/skills/'bio-variant-annotation' (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`	77