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gatk-software [2018/10/15 13:25] aorthgatk-software [2023/05/11 09:59] (current) aorth
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 ===== Information ===== ===== Information =====
  
-  * Latest Version: 4.0.10.1+  * Latest Version: 4.4.0.0
   * Added: May, 2014   * Added: May, 2014
-  * Updated: October2018 +  * Updated: May2023 
-  * Link: https://software.broadinstitute.org/gatk/+  * 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 one version into your environment and run it: Load one version into your environment and run it:
-<code>$ module load gatk/4.0.10.1+<code>$ module load gatk/4.4.0.0
 $ gatk</code> $ 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 ======
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 <code>$ cd /tmp <code>$ cd /tmp
-$ wget https://github.com/broadinstitute/gatk/releases/download/4.0.10.1/gatk-4.0.10.1.zip +$ wget https://github.com/broadinstitute/gatk/releases/download/4.4.0.0/gatk-4.4.0.0.zip 
-$ unzip gatk-4.0.10.1.zip +$ unzip gatk-4.4.0.0.zip 
-$ sudo cp -r gatk-4.0.10.1 /export/apps/gatk/4.0.10.1</code>+$ sed -i 's/python/python3/' gatk-4.4.0.0/gatk 
 +$ sudo cp -r gatk-4.4.0./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.1539609930.txt.gz · Last modified: 2018/10/15 13:25 by aorth