vep-variant-annotator

# 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)