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Vcf annotator

Skill aAAaqwq/AGI-Super-Team/skills/vcf-annotator

Annotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritised variant reports.From its SKILL.md

Install
npx -y skills add aAAaqwq/AGI-Super-Team --skill vcf-annotator

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

1.6 KB, 278 tokens by cl100k_base, as published. Nobody here has run it

🦖 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).

What ships with it

Read from the repository

Just SKILL.md. No reference files, no scripts.

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