Gatk Variant Caller

---
name: gatk-variant-caller
description: GATK best practices skill for germline and somatic variant calling with joint genotyping
allowed-tools:
  - Read
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  - Glob
  - Grep
  - Edit
  - WebFetch
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metadata:
  version: "1.0"
  category: bioinformatics
  tags:
    - variant-analysis
    - gatk
    - snv
    - indel
graph:
  domains: [domain:bioinformatics]
  specializations: [specialization:biomedical-informatics]
  skillAreas: [skill-area:statistical-analysis, skill-area:python-data-pipelines, skill-area:data-analysis]
  workflows: [workflow:experiment-design]
  roles: [role:research-engineer, role:biomedical-engineer]
---

# 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)