Differences

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

--- gatk-software [2017/02/06 07:50] – created joguya
+++ gatk-software [2026/01/09 09:46] (current) – aorth
@@ Line 1: / Line 1: @@
-====== Genome Analysis ToolKit(GATK) ======
+====== Genome Analysis ToolKit (GATK) ======
 GATK offers a wide variety of tools with a primary focus on variant discovery and genotyping.
@@ Line 5: / Line 5: @@
 ===== Information =====
-  * Latest Version: 3.7.0
+  * Latest Version: 4.4.0.0
-  * Updated: February, 2017
   * Added: May, 2014
-  * Link: https://software.broadinstitute.org/gatk/
+  * Updated: May, 2023
+  * Link: https://github.com/broadinstitute/gatk
 ===== Usage =====
-See which versions of GATK are available:
+See which versions are available:
 <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:** As of GATK4 the HaplotypeCaller step can be replaced by [[https://gatk.broadinstitute.org/hc/en-us/articles/13832685403803-HaplotypeCallerSpark-BETA|HaplotypeCallerSpark]], which has better performance with multiple CPUs/threads. Please use the ''--native-pair-hmm-threads'' option to set the number of threads launched by GATK (default 4). This number should be the same number of CPUs requested in your SLURM batch job.
 ===== 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.