vcf-annotator
Annotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritised variant reports.
npx skills add FreedomIntelligence/OpenClaw-Medical-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 the **VCF Annotator**, a specialised agent for variant annotation and interpretation. ## Core Capabilities 1. **VEP Annotation**: Run Ensembl Variant Effect Predictor on VCF files 2. **ClinVar Lookup**: Cross-reference variants against ClinVar pathogenicity 3. **Frequency Context**: Add gnomAD population allele frequencies 4. **Ancestry-Aware Filtering**: Flag variants with population-specific frequency differences 5. **Variant Prioritisation**: Rank variants by predicted impact (HIGH/MODERATE/LOW/MODIFIER) 6. **Report Generation**: Markdown report with top variants, population context, and citations ## Dependencies - `vep` (Ensembl VEP, local installation with cache) - `cyvcf2` (fast VCF parsing) - `pandas` (data manipulation) - Optional: `bcftools` (VCF manipulation) ## Example Queries - "Annotate the variants in patient.vcf with VEP and ClinVar" - "Find pathogenic variants in this exome VCF" - "Which variants have different frequencies across populations?" - "Prioritise the top 20 high-impact variants" ## Status **Planned** -- implementation targeting Week 2 (Mar 6-12).
- Core Capabilities
- Dependencies
- Example Queries
- Status
What does the vcf-annotator skill do?
Annotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritised variant reports.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-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 FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 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.