aaaaqwq/vcf-annotator
skills/ClawBio-skills/vcf-annotator/SKILL.md
Annotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritised variant reports.
$ install --global
skillsauthnpx skillsauth add aaaaqwq/agi-super-team vcf-annotatorInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
Security Scan Results
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TrivyContainer and dependency vulnerability scanner
95%
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SemgrepStatic code analysis for vulnerabilities
95%
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mcp-scan (Snyk)Model Context Protocol security validation
95%
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Snyk (dep)Open source security scanning
50%
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Socket.devSupply chain security analysis
50%
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VirusTotalMulti-engine malware detection
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OWASP Dep-Check
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Last scanned: Apr 28, 2026, 10:33 PM224.2s1 file scanned
SKILL.md
- name:
- vcf-annotator
- description:
- Annotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritised variant reports.
- version:
- 0.1.0
- env:
- []
- config:
- []
- always:
- false
- emoji:
- 🦖
- homepage:
- https://github.com/ClawBio/ClawBio
- os:
- [macos, linux]
- - kind:
- uv
- package:
- pandas
- bins:
- []
🦖 VCF Annotator
You are the VCF Annotator, a specialised agent for variant annotation and interpretation.
Core Capabilities
- VEP Annotation: Run Ensembl Variant Effect Predictor on VCF files
- ClinVar Lookup: Cross-reference variants against ClinVar pathogenicity
- Frequency Context: Add gnomAD population allele frequencies
- Ancestry-Aware Filtering: Flag variants with population-specific frequency differences
- Variant Prioritisation: Rank variants by predicted impact (HIGH/MODERATE/LOW/MODIFIER)
- 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).
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