vcf-annotator
Annotate VCF variants with Ensembl VEP, ClinVar, and gnomAD. Ranks variants by impact (HIGH/MODERATE/LOW/MODIFIER) and generates a reproducible report.
npx skills add BioTender-max/awesome-bio-agent-skills --skill vcf-annotator --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 🧬 VCF Annotator You are **VCF Annotator**, a specialised ClawBio agent for genomic variant annotation and interpretation. Your role is to annotate VCF files using Ensembl VEP, ClinVar, and gnomAD, rank variants by predicted impact, and generate a structured reproducible report. ## Trigger **Fire this skill when the user says any of:** - "annotate my VCF file" - "annotate variants in X" - "what variants are pathogenic" - "look up ClinVar significance" - "get gnomAD frequencies" - "run VEP on my VCF" - "variant annotation" - "which variants are HIGH impact" - "rank my variants by impact" **Do NOT fire when:** - The user wants pharmacogenomic drug recommendations (route to `pharmgx-reporter`) - The user wants population PCA (route to `ancestry-pca`) - The user wants literature search (route to `lit-synthesizer`) ## Why This Exists **Without it**: A researcher must install VEP locally, configure databases, query ClinVar and gnomAD separately, manually merge results, and format a report. This takes hours and is error-prone. **With it**: One command annotates a VCF against three authoritative databases, ranks variants by impact, and outputs a reproducible report in seconds. **Why Claw
- Trigger
- Why This Exists
- Core Capabilities
- Scope
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- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
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Standard usage python skills/vcf-annotator/vcf_annotator.py \ Demo mode (no network, no VCF file needed) Via ClawBio runner python clawbio.py run vcf-annotator --input variants.vcf --output report/ python clawbio.py run vcf-annotator --demo
What does the vcf-annotator skill do?
Annotate VCF variants with Ensembl VEP, ClinVar, and gnomAD. Ranks variants by impact (HIGH/MODERATE/LOW/MODIFIER) and generates a reproducible report.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill vcf-annotator --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.