Genome Analysis Toolkit v3.6

The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance.

Accessing the software

To load the module:

$ module load apps/gatk/v3.6

An example command to include in your job script:

java -jar ${GATK_ROOT}/GenomeAnalysisTK.jar -T <analysis_type> -args <arg_file>

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations


Other Information

The Support Level for this application is An.

Visit the GATK website for more information regarding this application.

Last modified: 23 November 2017