GATK offers a wide variety of tools with a primary focus on variant discovery and genotyping.
See which versions of GATK are available:
$ module avail gatk
Load one version into your environment and run it:
$ module load gatk/4.0.10.1 $ gatk
Notes from the sysadmin during installation:
$ cd /tmp $ wget https://github.com/broadinstitute/gatk/releases/download/4.0.10.1/gatk-4.0.10.1.zip $ unzip gatk-4.0.10.1.zip $ sudo cp -r gatk-4.0.10.1 /export/apps/gatk/4.0.10.1