====== Genome Analysis ToolKit (GATK) ======

GATK offers a wide variety of tools with a primary focus on variant discovery and genotyping.

===== Information =====

  * Latest Version: 4.4.0.0
  * Added: May, 2014
  * Updated: May, 2023
  * Link: https://github.com/broadinstitute/gatk

===== Usage =====

See which versions are available:
<code>$ module avail gatk</code>

Load one version into your environment and run it:
<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 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.