ReddRadar
Agent skill
giab-benchmark-validator
Genome in a Bottle benchmark validation skill for pipeline accuracy assessment
Install this agent skill to your Project
npx add-skill https://github.com/a5c-ai/babysitter/tree/main/library/specializations/domains/science/bioinformatics/skills/giab-benchmark-validator
Metadata
Additional technical details for this skill
- tags
-
infrastructure validation benchmark giab
- version
- 1.0
- category
- bioinformatics
SKILL.md
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)
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