# Vep Variant Annotator

> Variant Effect Predictor skill for comprehensive variant annotation with clinical database integration

- Skill: `a5c-ai/vep-variant-annotator` (Agent Skill)
- Install (CLI): `npx skillmds@latest add a5c-ai/vep-variant-annotator`
- Raw SKILL.md: https://api.skillmd.com/api/skills/a5c-ai/vep-variant-annotator/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Integrations & APIs
- Author: a5c-ai (https://skillmd.com/u/a5c-ai)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/a5c-ai/vep-variant-annotator

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# VEP Variant Annotator Skill

## Purpose
Provide comprehensive variant annotation using Variant Effect Predictor with clinical database integration.

## Capabilities
- Functional consequence prediction
- Population frequency annotation (gnomAD)
- Clinical database integration (ClinVar, COSMIC)
- Custom annotation plugins
- Pathogenicity score integration (CADD, REVEL)
- Regulatory region annotation

## Usage Guidelines
- Configure VEP with relevant annotation sources
- Include population frequency databases
- Add clinical databases for interpretation
- Use pathogenicity predictors for prioritization
- Document annotation database versions
- Update annotations regularly

## Dependencies
- Ensembl VEP
- ANNOVAR
- SnpEff

## Process Integration
- Whole Genome Sequencing Pipeline (wgs-analysis-pipeline)
- Clinical Variant Interpretation (clinical-variant-interpretation)
- Pharmacogenomics Analysis (pharmacogenomics-analysis)
- Rare Disease Diagnostic Pipeline (rare-disease-diagnostics)