agentsclimarketplace
Sign in

Giab benchmark validator

Skill a5c-ai/babysitter/library/specializations/domains/science/bioinformatics/skills/giab-benchmark-validator

Genome in a Bottle benchmark validation skill for pipeline accuracy assessmentFrom its SKILL.md

Install
npx -y skills add a5c-ai/babysitter --skill giab-benchmark-validator

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

1.4 KB, 159 tokens by cl100k_base, as published. Nobody here has run it

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)

What ships with it

Read from the repository

Just SKILL.md. No reference files, no scripts.

Keep looking

Skills are one crate of 325,949. Ordering is by how many stacks a row turns up in, so the top of any crate is what has actually been picked rather than what has the most stars.