# GATK4 Mutect2

**Galaxy Tool ID**: `toolshed.g2.bx.psu.edu/repos/iuc/gatk4_mutect2/gatk4_mutect2/4.1.7.0+galaxy1`
**Version**: 4.1.7.0+galaxy1
**Category**: Variant Calling

> - Call somatic SNVs and indels via local assembly of haplotypes

## Example Query

> "Run GATK4 Mutect2 on my data"

## Run via Galaxy Bridge

```bash
python galaxy_bridge.py --tool-details toolshed.g2.bx.psu.edu/repos/iuc/gatk4_mutect2/gatk4_mutect2/4.1.7.0+galaxy1
python galaxy_bridge.py --run toolshed.g2.bx.psu.edu/repos/iuc/gatk4_mutect2/gatk4_mutect2/4.1.7.0+galaxy1 --input <file> --output <dir>
```

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*Auto-generated from usegalaxy.org tool index*
