name: giab-benchmark-validator description: Genome in a Bottle benchmark validation skill for pipeline accuracy assessment allowed-tools:

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• Bash metadata: version: "1.0" category: bioinformatics tags:
  • infrastructure
  • validation
  • benchmark
  • giab

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)