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gatk-variant-caller

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

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Source SKILL.md: https://github.com/a5c-ai/babysitter/blob/HEAD/library/specializations/domains/science/bioinformatics/skills/gatk-variant-caller/SKILL.md

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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)