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)