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