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gatk-software

Genome Analysis ToolKit(GATK)

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

Information

Usage

See which versions of GATK are available:

$ module avail gatk

Load gatk

$ module load gatk/3.7.0

Installation

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 $*
gatk-software.txt · Last modified: 2017/02/06 10:50 by joguya