giab-benchmark-validator

# 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)