gatk-variant-caller
GATK best practices skill for germline and somatic variant calling with joint genotyping
npx skills add a5c-ai/babysitter --skill gatk-variant-caller --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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)
- Purpose
- Capabilities
- Usage Guidelines
- Dependencies
- Process Integration
What does the gatk-variant-caller skill do?
GATK best practices skill for germline and somatic variant calling with joint genotyping
How do I install it?
Run `npx skills add a5c-ai/babysitter --skill gatk-variant-caller --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From a5c-ai/babysitter, a repository with 1,642 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.