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Babysitter giab-benchmark-validator

Genome in a Bottle benchmark validation skill for pipeline accuracy assessment

install
source · Clone the upstream repo
git clone https://github.com/a5c-ai/babysitter
Claude Code · Install into ~/.claude/skills/
T=$(mktemp -d) && git clone --depth=1 https://github.com/a5c-ai/babysitter "$T" && mkdir -p ~/.claude/skills && cp -r "$T/library/specializations/domains/science/bioinformatics/skills/giab-benchmark-validator" ~/.claude/skills/a5c-ai-babysitter-giab-benchmark-validator && rm -rf "$T"
manifest: library/specializations/domains/science/bioinformatics/skills/giab-benchmark-validator/SKILL.md
tags
#bioinformatics#validation#benchmark#giab#variant-calling#sequence-analysis
source content

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)