gatk-variant-caller

# 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)