# Gatk4 Somatic Variant Caller

> Executes GATK4 Mutect2 tumor-normal paired variant calling, applies LearnReadOrientationModel, and runs FilterMutectCalls for somatic SNV filtering.

- Skill: `yulianuzhnenko/gatk4-somatic-variant-caller` (Agent Skill)
- Install (CLI): `npx skillmds@latest add yulianuzhnenko/gatk4-somatic-variant-caller`
- Raw SKILL.md: https://api.skillmd.com/api/skills/yulianuzhnenko/gatk4-somatic-variant-caller/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: YuliaNuzhnenko (https://skillmd.com/u/yulianuzhnenko)
- Updated: 2026-09-22
- Page: https://skillmd.com/skills/yulianuzhnenko/gatk4-somatic-variant-caller

---


# Agent Skill: GATK4 Mutect2 Somatic Variant Calling Skill

[![Domain](https://img.shields.io/badge/Domain-Somatic%20Genomics-00f0ff?style=flat-square)](#)
[![Version](https://img.shields.io/badge/Version-1.0.0-green?style=flat-square)](#)

## 📌 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`:
1. **Input Validation**: Verify that the required input files or coordinates are supplied.
2. **Environment Check**: Ensure dependencies (`GATK4, SAMtools, Picard, BCFtools`) are installed.
3. **Execution**: Run the protocol pipeline snippet below.
4. **Output Generation**: Produce actionable Markdown/JSON summaries with publication figures.

---

## 💻 Protocol Code Snippet

```python
# 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.