gatk-variant-caller
GATK best practices skill for germline and somatic variant calling with joint genotyping
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技能内容
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)
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原文件路径
library/specializations/domains/science/bioinformatics/skills/gatk-variant-caller/SKILL.md