Differences

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--- gatk-software [2018/10/15 13:25] – aorth
+++ gatk-software [2021/09/16 13:38] – aorth
@@ Line 5: / Line 5: @@
 ===== Information =====
-  * Latest Version: 4.0.10.1
+  * Latest Version: 4.2.2.0
   * Added: May, 2014
-  * Updated: October, 2018
+  * Updated: September, 2021
-  * Link: https://software.broadinstitute.org/gatk/
+  * Link: https://github.com/broadinstitute/gatk
 ===== Usage =====
@@ Line 16: / Line 16: @@
 Load one version into your environment and run it:
-<code>$ module load gatk/4.0.10.1
+<code>$ module load gatk/4.2.2.0
 $ 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 ======
@@ 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/4.2.2.0/gatk-4.2.2.0.zip
-$ unzip gatk-4.0.10.1.zip
+$ unzip gatk-4.2.2.0.zip
-$ sudo cp -r gatk-4.0.10.1 /export/apps/gatk/4.0.10.1</code>
+$ sudo cp -r gatk-4.2.2.0 /export/apps/gatk/4.2.2.0</code>