Differences

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--- gatk-software [2018/10/15 13:25] – aorth
+++ gatk-software [2026/01/09 09:46] (current) – aorth
@@ Line 5: / Line 5: @@
 ===== Information =====
-  * Latest Version: 4.0.10.1
+  * Latest Version: 4.4.0.0
   * Added: May, 2014
-  * Updated: October, 2018
+  * Updated: May, 2023
-  * Link: https://software.broadinstitute.org/gatk/
+  * 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 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>
+**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 ======
@@ Line 23: / Line 25: @@
 <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-4.4.0.0 /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.