GATK - Genome Analysis Toolkit

The GATK is a structured software library that makes writing efficient analysis tools using next-generation sequencing data very easy. Secondly, it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller, and a local realigner.

To run this software interactively in a Linux environment run the commands:
module load gatk
gatk --help


module load gatk
java -Xmx4g -jar /soft/gatk/VER/GenomeAnalysisTK.jar --help
where VER is the module version you are using.  The --help option will list available options for GATK. 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 isub 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 isub environment only informs Java of a fraction of the memory, reserving the rest for padding. 
To ensure sufficient memory is available, launch isub with: 
isub -m 12gb
NOTE: The current default version loaded is 2.7.2.  The GATK 2.X releases include both the addition of brand-new (and often still experimental) tools and updates to the existing stable tools. These updates will require users to change how they are using GATK tools. GATK 2.X is released under a different license that places restrictions on commercial usage.  For more information visit
The old version of GATK can be loaded with:
module load gatk/1.6
GATK also has a a command-line scripting framework for defining multi-stage genomic analysis pipelines combined with an execution manager that runs those pipelines from end-to-end.  This can be run with:
module load gatk-queue
java -jar /soft/gatk-queue/VER/Queue.jar --help

where VER again refers to the module version you are using.  The --help option will list available options for GATK-Queue.

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