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gatk-software [2017/02/06 07:50]
joguya created
gatk-software [2018/10/15 13:25] (current)
aorth
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-====== Genome Analysis ToolKit(GATK) ======+====== Genome Analysis ToolKit (GATK) ======
  
 GATK offers a wide variety of tools with a primary focus on variant discovery and genotyping. GATK offers a wide variety of tools with a primary focus on variant discovery and genotyping.
Line 5: Line 5:
 ===== Information ===== ===== Information =====
  
-  * Latest Version: 3.7.0 +  * Latest Version: 4.0.10.1
-  * Updated: February, 2017+
   * Added: May, 2014   * Added: May, 2014
 +  * Updated: October, 2018
   * Link: https://software.broadinstitute.org/gatk/   * Link: https://software.broadinstitute.org/gatk/
  
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 <code>$ module avail gatk</code> <code>$ module avail gatk</code>
  
-Load gatk +Load one version into your environment and run it: 
-<code>$ module load gatk/3.7.0</code>+<code>$ module load gatk/4.0.10.1 
 +$ gatk</code>
  
 ===== Installation ====== ===== Installation ======
- 
 Notes from the sysadmin during 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> 
  
 +<code>$ 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</code>
gatk-software.1486367444.txt.gz · Last modified: 2017/02/06 07:50 by joguya