GATK offers a wide variety of tools with a primary focus on variant discovery and genotyping.

• Latest Version: 4.4.0.0
• Added: May, 2014
• Updated: May, 2023
• Link: https://github.com/broadinstitute/gatk

See which versions are available:

$ module avail gatk

Load one version into your environment and run it:

$ module load gatk/4.4.0.0
$ gatk

Note: The HaplotypeCaller step can scale to multiple CPUs/threads. Please use the -nct option to set the number of threads launched by GATK. This number should be the same number of CPUs requested in your SLURM batch job.

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/broadinstitute/gatk/releases/download/4.4.0.0/gatk-4.4.0.0.zip
$ unzip gatk-4.4.0.0.zip
$ sed -i 's/python/python3/' gatk-4.4.0.0/gatk
$ sudo cp -r gatk-4.4.0.0 /export/apps/gatk/4.4.0.0

Note (2023-05-11): we are not currently satisfying Python or R dependencies here because I think most users are not using those features. See the GATK requirements for more information.