GATK Variant Caller Skill
SkillDev toolsGATK best practices skill for germline and somatic variant calling with joint genotyping
Use GATK Variant Caller Skill in Claude, ChatGPT or Ahel Desktop
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Also: Claude Code · Cursor · Codex
Then ask your AI: use the GATK Variant Caller Skill
Details
Instructions available. Your AI can read the instructions. Execution depends on the setup they require.
Account requirements not reviewed. Check the skill instructions before use; Ahel provides instructions and does not run this skill.
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Add Ahel to your AI once: Claude, ChatGPT, Cursor, Claude Code or Codex. Then ask it to use this.
What this skill tells your AI
The instructions your AI receives, as published by a5c-ai/babysitter in library/specializations/domains/science/bioinformatics/skills/gatk-variant-caller/SKILL.md and read by Ahel’s review.
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)
Signals
- GitHub stars
- 2k
- Forks
- 113
- Last commit
- Sep 2026
Advanced
- Item type
- skill
- Key
gatk-variant-caller- Source
- github.com/a5c-ai/babysitter
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