Agent-Skills.md

Agent Skills: GATK Variant Caller Skill

GATK best practices skill for germline and somatic variant calling with joint genotyping

bioinformaticsID: a5c-ai/babysitter/gatk-variant-caller

Repository

a5c-ai/babysitter
a5c-aiLicense: MIT
244

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pnpm dlx add-skill https://github.com/a5c-ai/babysitter/tree/HEAD/plugins/babysitter/skills/babysit/process/specializations/domains/science/bioinformatics/skills/gatk-variant-caller

Skill Files

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plugins/babysitter/skills/babysit/process/specializations/domains/science/bioinformatics/skills/gatk-variant-caller/SKILL.md

Skill Metadata

Name
gatk-variant-caller
Description
GATK best practices skill for germline and somatic variant calling with joint genotyping

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)