vcf-annotator

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.