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gatk-software [2017/02/06 07:50] – created joguyagatk-software [2023/05/11 09:59] (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: 4.4.0.0
-  * Updated: February, 2017+
   * Added: May, 2014   * Added: May, 2014
-  * Link: https://software.broadinstitute.org/gatk/+  * Updated: May, 2023 
 +  * Link: https://github.com/broadinstitute/gatk
  
 ===== Usage ===== ===== Usage =====
  
-See which versions of GATK are available:+See which versions are available:
 <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/4.4.0.0 
 +$ gatk</code> 
 + 
 +**Note:** The HaplotypeCaller step can scale to multiple CPUs/threads. Please use the ''-nct'' option to set the number of threads launched by GATK. This number should be the same number of CPUs requested in your SLURM batch job.
  
 ===== 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 $* +<code>cd /tmp 
-</code>+$ wget https://github.com/broadinstitute/gatk/releases/download/4.4.0.0/gatk-4.4.0.0.zip 
 +unzip gatk-4.4.0.0.zip 
 +$ sed -i 's/python/python3/' gatk-4.4.0.0/gatk 
 +$ sudo cp -r gatk-4.4.0.0 /export/apps/gatk/4.4.0.0</code>
  
 +**Note (2023-05-11):** we are not currently satisfying Python or R dependencies here because I think most users are not using those features. See [[https://github.com/broadinstitute/gatk#requirements|the GATK requirements]] for more information.
gatk-software.1486367444.txt.gz · Last modified: 2017/02/06 07:50 by joguya