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

• Latest Version: 4.2.2.0
• Added: May, 2014
• Updated: September, 2021
• Link: https://github.com/broadinstitute/gatk

See which versions of GATK are available:

$ module avail gatk

Load one version into your environment and run it:

$ module load gatk/4.2.2.0
$ gatk

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/broadinstitute/gatk/releases/download/4.2.2.0/gatk-4.2.2.0.zip
$ unzip gatk-4.2.2.0.zip
$ sudo cp -r gatk-4.2.2.0 /export/apps/gatk/4.2.2.0