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 re…