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)