gatk-variant-caller
GATK best practices skill for germline and somatic variant calling with joint genotyping
Best use case
gatk-variant-caller is best used when you need a repeatable AI agent workflow instead of a one-off prompt.
GATK best practices skill for germline and somatic variant calling with joint genotyping
Teams using gatk-variant-caller should expect a more consistent output, faster repeated execution, less prompt rewriting.
When to use this skill
- You want a reusable workflow that can be run more than once with consistent structure.
When not to use this skill
- You only need a quick one-off answer and do not need a reusable workflow.
- You cannot install or maintain the underlying files, dependencies, or repository context.
Installation
Claude Code / Cursor / Codex
Manual Installation
- Download SKILL.md from GitHub
- Place it in
.claude/skills/gatk-variant-caller/SKILL.mdinside your project - Restart your AI agent — it will auto-discover the skill
How gatk-variant-caller Compares
| Feature / Agent | gatk-variant-caller | Standard Approach |
|---|---|---|
| Platform Support | Not specified | Limited / Varies |
| Context Awareness | High | Baseline |
| Installation Complexity | Unknown | N/A |
Frequently Asked Questions
What does this skill do?
GATK best practices skill for germline and somatic variant calling with joint genotyping
Where can I find the source code?
You can find the source code on GitHub using the link provided at the top of the page.
SKILL.md Source
# 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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