GATK Variant Caller Skill

SkillDev tools

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

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.

Add ahel to your AI once: Claude, ChatGPT, Cursor, Claude Code or Codex. Then ask it to use this.

Then ask your AI: use the GATK Variant Caller Skill skill

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: 112
Last commit: Sep 2026

Advanced

Item type: skill
Key: gatk-variant-caller
Source: github.com/a5c-ai/babysitter

github.com/a5c-ai/babysitter