Agent-Skills.md

Agent Skills: VEP Variant Annotator Skill

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

bioinformaticsID: a5c-ai/babysitter/vep-variant-annotator

Repository

a5c-ai/babysitter
a5c-aiLicense: MIT
244

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pnpm dlx add-skill https://github.com/a5c-ai/babysitter/tree/HEAD/plugins/babysitter/skills/babysit/process/specializations/domains/science/bioinformatics/skills/vep-variant-annotator

Skill Files

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plugins/babysitter/skills/babysit/process/specializations/domains/science/bioinformatics/skills/vep-variant-annotator/SKILL.md

Skill Metadata

Name
vep-variant-annotator
Description
Variant Effect Predictor skill for comprehensive variant annotation with clinical database integration

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)