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Genome Analysis ToolKit(GATK)

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 gatk

$ module load gatk/3.7.0


Notes from the sysadmin during installation:

$ cd /tmp
$ wget -qO- "" | 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.


#!/usr/bin/env bash

readonly PREFIX=$(dirname $0)

java -jar $PREFIX/GenomeAnalysisTK.jar $*
gatk-software.1486367444.txt.gz · Last modified: 2017/02/06 07:50 by joguya