YuliaNuzhnenko Agent Skill: GATK4 Mutect2 Somatic Variant Calling Skill
📌 Description
Executes GATK4 Mutect2 tumor-normal paired variant calling, applies LearnReadOrientationModel, and runs FilterMutectCalls for somatic SNV filtering.
🤖 Agent Execution Protocol
When an AI Agent is tasked with gatk4-somatic-variant-caller:
- Input Validation: Verify that the required input files or coordinates are supplied.
- Environment Check: Ensure dependencies (
GATK4, SAMtools, Picard, BCFtools) are installed. - Execution: Run the protocol pipeline snippet below.
- Output Generation: Produce actionable Markdown/JSON summaries with publication figures.
💻 Protocol Code Snippet
# GATK Mutect2 Shell Protocol
gatk Mutect2 -R reference.fasta -I tumor.bam -I normal.bam -O raw_somatic.vcf.gz
📥 Input & Output Specifications
Input Contract
- Target Files: Valid input data matching domain formats.
- Parameters: Quality thresholds and cutoffs.
Output Contract
- Results Table: Structured summary dataframe or matrix.
- Visualization: Rendered SVG/PNG figures.
📄 License
Distributed under the MIT License. See LICENSE for details.