User Tools

Site Tools


gatk-software

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

gatk-software [2017/02/06 10:50] (current)
joguya created
Line 1: Line 1:
 +====== Genome Analysis ToolKit(GATK) ======
 +
 +GATK offers a wide variety of tools with a primary focus on variant discovery and genotyping.
 +
 +===== Information =====
 +
 +  * Latest Version: 3.7.0
 +  * Updated: February, 2017
 +  * Added: May, 2014
 +  * Link: https://​software.broadinstitute.org/​gatk/​
 +
 +===== Usage =====
 +
 +See which versions of GATK are available:
 +<​code>​$ module avail gatk</​code>​
 +
 +Load gatk
 +<​code>​$ module load gatk/​3.7.0</​code>​
 +
 +===== Installation ======
 +
 +Notes from the sysadmin during installation:​
 +<​code>​
 +$ 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/​
 +</​code>​
 +
 +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<​code>#​!/​usr/​bin/​env bash
 +
 +readonly PREFIX=$(dirname $0)
 +
 +java -jar $PREFIX/​GenomeAnalysisTK.jar $*
 +</​code>​
  
gatk-software.txt · Last modified: 2017/02/06 10:50 by joguya