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Vep variant annotator

Skill a5c-ai/babysitter/library/specializations/domains/science/bioinformatics/skills/vep-variant-annotator

Variant Effect Predictor skill for comprehensive variant annotation with clinical database integrationFrom its SKILL.md

Install
npx -y skills add a5c-ai/babysitter --skill vep-variant-annotator

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SKILL.md

1.7 KB, 199 tokens by cl100k_base, as published. Nobody here has run it

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)

What ships with it

Read from the repository

Just SKILL.md. No reference files, no scripts.

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