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

• Latest Version: 3.7.0
• Updated: February, 2017
• Added: May, 2014
• Link: https://software.broadinstitute.org/gatk/

See which versions of GATK are available:

$ module avail gatk

Load gatk

$ module load gatk/3.7.0

Notes from the sysadmin during installation:

$ cd /tmp
$ wget -qO- "https://software.broadinstitute.org/gatk/download/auth?package=GATK" | tar xjv
$ sudo mkdir /export/apps/gatk/3.7.0/
$ sudo chown -R joguya:joguya /export/apps/gatk/3.7.0/
$ sudo cp -rv GenomeAnalysisTK.jar resources/ /export/apps/gatk/3.7.0/

I created a generic GenomeAnalysisTK wrapper shell script for GATK, as it must otherwise be run with java -jar .. and is rather user-unfriendly.

/export/apps/gatk/3.7.0/GenomeAnalysisTK.jar

#!/usr/bin/env bash

readonly PREFIX=$(dirname $0)

java -jar $PREFIX/GenomeAnalysisTK.jar $*