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vcf-annotator

Annotate VCF files with VEP, ClinVar, and gnomAD data.

1.1k|238|Updated Feb 25, 2026
Search Tags:#annotation#vcf#clinvar#gnomad#vep#variant-prioritisation
One-click install
npx skills add https://github.com/ClawBio/ClawBio --skill vcf-annotator
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: vcf-annotator
Source: https://github.com/ClawBio/ClawBio/tree/main/skills/vcf-annotator
Command: npx skills add https://github.com/ClawBio/ClawBio --skill vcf-annotator

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill streamlines the complex, multi-source process of annotating VCF variant calls by combining VEP consequence annotation, ClinVar pathogenicity lookup, gnomAD population frequencies, and ancestry-aware context into a reproducible, prioritised report.

Core Features & Use Cases

  • VEP Annotation: Attach transcript- and consequence-level annotations from Ensembl VEP to each VCF record.
  • ClinVar & Frequency Context: Cross-reference ClinVar pathogenicity and add gnomAD population allele frequencies to inform clinical interpretation.
  • Ancestry-aware Filtering & Prioritisation: Flag variants with population-specific frequency differences and rank variants by predicted impact to produce a focused report for review.
  • Use Case: Annotate an exome VCF to surface ClinVar pathogenic calls, filter common population variants, and produce a top-20 high-impact variants Markdown report for a clinical genetics review.

Quick Start

Annotate patient.vcf with VEP, add ClinVar and gnomAD allele frequencies, and generate a prioritized Markdown variant report.

Frequently Asked Questions about vcf-annotator

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I annotate a VCF file with gnomAD and ClinVar for variant prioritisation?▼

VEP annotation works by attaching transcript- and consequence-level annotations from Ensembl VEP to each VCF record, adding ClinVar pathogenicity and gnomAD population frequencies to inform clinical interpretation.

How do I filter common population variants from an exome VCF?▼

Ancestry-aware filtering flags variants with population-specific frequency differences, ranking them by predicted impact to help you focus on clinically relevant calls for clinical genetics review.

Do I need a local VEP installation to annotate VCF files?▼

Yes, you need a local VEP installation with cache to annotate VCF files, and optionally use cyvcf2, pandas, and bcftools for efficient parsing, annotation, and report generation.

Can I generate a clinical variant prioritisation report from a genome VCF?▼

Yes, you can apply this workflow to genome VCFs for clinical variant prioritisation to surface ClinVar pathogenic calls, filter common variants, and produce a top-20 high-impact variants Markdown report.

What is the best way to combine VEP consequences with gnomAD frequencies?▼

The best way to combine VEP consequences with gnomAD frequencies is to use a reproducible workflow that attaches Ensembl VEP transcript annotations and cross-references gnomAD data, producing a prioritised report.

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