giab-benchmark-validator

name	giab-benchmark-validator
description	Genome in a Bottle benchmark validation skill for pipeline accuracy assessment
allowed-tools	["Read","Write","Glob","Grep","Edit","WebFetch","WebSearch","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)