# Gatk Variant Caller

> GATK best practices skill for germline and somatic variant calling with joint genotyping

- Skill: `a5c-ai/gatk-variant-caller` (Agent Skill)
- Install (CLI): `npx skillmds@latest add a5c-ai/gatk-variant-caller`
- Raw SKILL.md: https://api.skillmd.com/api/skills/a5c-ai/gatk-variant-caller/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: a5c-ai (https://skillmd.com/u/a5c-ai)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/a5c-ai/gatk-variant-caller

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# 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)