# gatk

## Summary

+ **Module Name:** gatk
+ **Support Level:** Primary Support
+ **Software Access Level:** Open Access
+ **Home Page:** [https://gatk.broadinstitute.org/hc/en-us](https://gatk.broadinstitute.org/hc/en-us)

## Software Description

From the GATK website:

> A genomic analysis toolkit focused on variant
> discovery. The GATK is the industry standard for identifying SNPs and
> indels in germline DNA and RNAseq data. Its scope is now expanding to
> include somatic short variant calling, and to tackle copy number (CNV)
> and structural variation (SV). In addition to the variant callers
> themselves, the GATK also includes many utilities to perform related
> tasks such as processing and quality control of high-throughput
> sequencing data, and bundles the popular Picard toolkit. These tools
> were primarily designed to process exomes and whole genomes generated
> with Illumina sequencing technology, but they can be adapted to handle a
> variety of other technologies and experimental designs. And although it
> was originally developed for human genetics, the GATK has since evolved
> to handle genome data from any organism, with any level of ploidy. GATK
> consists of many tools each with many parameters. To run GATK
> effectively, review the GATK best practices documentation:

[GATK Homepage](http://www.broadinstitute.org/gatk/)

[Getting started with
GATK](https://gatk.broadinstitute.org/hc/en-us/categories/360002302312)
(includes best practices workflows)
## General Linux

To run this software interactively in a Linux environment run the commands:

	module load gatk
	gatk

This will list the basic options for running GATK.
To see a list of all available GATK tools, use:

	gatk --list

To see options for an individual too, use:

	gatk TOOL_NAME -help

where `TOOL_NAME` is the name of the GATK tool.
For example, to see available options for HaplotypeCaller, run:

	gatk HaplotypeCaller -help

To run HaplotypeCaller, or another GATK tool, use this:

	gatk --java-options "-Xmx4g" TOOL_NAME

The `-Xmx{n}` option specifies the amount of memory available to Java (e.g., 4g, 4096m or 4194304k). If Java exceeds the allocated limit the interactive session will be terminated.

**NOTE:** GATK requires at least 4GB of memory for Java. Java often exceeds memory limits imposed by the `-Xmx{n}` flag, so the default interactive environment only informs Java of a fraction of the memory, reserving the rest for padding.