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)