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Giab benchmark validator

Skill a5c-ai/babysitter/library/specializations/domains/science/bioinformatics/skills/giab-benchmark-validator

Babysitter enforces obedience on agentic workforces and enables them to manage extremely complex tasks and workflows through deterministic, hallucination-free self-orchestration

Install
npx -y skills add a5c-ai/babysitter --skill giab-benchmark-validator

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Genome in a Bottle benchmark validation skill for pipeline accuracy assessment

SKILL.md

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GIAB Benchmark Validator Skill

Purpose

Enable Genome in a Bottle benchmark validation for pipeline accuracy assessment.

Capabilities

  • Truth set comparison
  • hap.py/vcfeval execution
  • Sensitivity/specificity calculation
  • Stratified performance metrics
  • Difficult region analysis
  • Validation report generation

Usage Guidelines

  • Use appropriate GIAB reference samples
  • Compare against truth sets with hap.py
  • Calculate sensitivity and specificity
  • Stratify by region type and variant class
  • Analyze performance in difficult regions
  • Generate comprehensive validation reports

Dependencies

  • hap.py
  • vcfeval
  • GIAB resources

Process Integration

  • Analysis Pipeline Validation (pipeline-validation)
  • Whole Genome Sequencing Pipeline (wgs-analysis-pipeline)

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