ReddRadar
Agent skill
gatk-variant-caller
GATK best practices skill for germline and somatic variant calling with joint genotyping
Install this agent skill to your Project
npx add-skill https://github.com/a5c-ai/babysitter/tree/main/library/specializations/domains/science/bioinformatics/skills/gatk-variant-caller
Metadata
Additional technical details for this skill
- tags
-
variant-analysis gatk snv indel
- version
- 1.0
- category
- bioinformatics
SKILL.md
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)
Recommended Agent Skills
Expand your agent's capabilities with these related and highly-rated skills.
a5c-ai/babysitter
gsd-tools
Central utility skill for GSD operations. Provides config parsing, slug generation, timestamps, path operations, and orchestrates calls to other specialized skills. Acts as the unified entry point that the original gsd-tools.cjs provided via its lib/ modules (commands, config, core, init).
a5c-ai/babysitter
model-profile-resolution
Resolve model profile (quality/balanced/budget) at orchestration start and map agents to specific models. Enables cost/quality tradeoffs by selecting appropriate AI models for each agent role.
a5c-ai/babysitter
verification-suite
Plan structure validation, phase completeness checks, reference integrity verification, and artifact existence confirmation. Provides the structured verification layer ensuring GSD artifacts are well-formed and complete.
a5c-ai/babysitter
state-management
STATE.md reading, writing, and field-level updates. Provides cross-session state persistence via .planning/STATE.md with structured fields for current task, completed phases, blockers, decisions, and quick tasks.
a5c-ai/babysitter
git-integration
Git commit patterns, formats, and conventions for GSD methodology. Provides atomic commits per task, structured commit messages, planning file commits, branch management, and milestone tag operations.
a5c-ai/babysitter
frontmatter-parsing
YAML frontmatter parsing and manipulation for .planning/ documents. Provides read, write, update, query, and validation operations on frontmatter blocks in GSD markdown artifacts.
Didn't find tool you were looking for?