# Giab Benchmark Validator

> Genome in a Bottle benchmark validation skill for pipeline accuracy assessment

- Skill: `a5c-ai/giab-benchmark-validator` (Agent Skill)
- Install (CLI): `npx skillmds@latest add a5c-ai/giab-benchmark-validator`
- Raw SKILL.md: https://api.skillmd.com/api/skills/a5c-ai/giab-benchmark-validator/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: DevOps & Infra
- Author: a5c-ai (https://skillmd.com/u/a5c-ai)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/a5c-ai/giab-benchmark-validator

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# 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)