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Gatk variant caller

Skill a5c-ai/babysitter/library/specializations/domains/science/bioinformatics/skills/gatk-variant-caller

GATK best practices skill for germline and somatic variant calling with joint genotypingFrom its SKILL.md

Install
npx -y skills add a5c-ai/babysitter --skill gatk-variant-caller

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

SKILL.md

1.6 KB, 220 tokens by cl100k_base, as published. Nobody here has run it

GATK Variant Caller Skill

Purpose

Provide GATK best practices for germline and somatic variant calling with joint genotyping support.

Capabilities

  • HaplotypeCaller execution
  • Base quality score recalibration (BQSR)
  • Variant quality score recalibration (VQSR)
  • Joint genotyping across cohorts
  • GVCF generation and management
  • Mutect2 somatic calling

Usage Guidelines

  • Follow GATK best practices workflow
  • Apply BQSR for improved accuracy
  • Use VQSR for quality filtering when sample count permits
  • Generate GVCFs for scalable joint calling
  • Select Mutect2 for somatic variants
  • Document resource bundles and versions

Dependencies

  • GATK4
  • Picard

Process Integration

  • Whole Genome Sequencing Pipeline (wgs-analysis-pipeline)
  • Clinical Variant Interpretation (clinical-variant-interpretation)
  • Tumor Molecular Profiling (tumor-molecular-profiling)
  • Rare Disease Diagnostic Pipeline (rare-disease-diagnostics)

What ships with it

Read from the repository

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

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