GATK: Difference between revisions

For the commands that do use spark, you can request multiple cpus. '''NOTE:''' please provide the exact number of cpus to the spark command, so if you requested 10 cpus, use <code>--spark-master local[10]</code> instead of <code>--spark-master local[*]</code>. If you want to scale the spark calls with multinode SPARK cluster, you have to first [https://docs.computecanada.ca/wiki/Apache_Spark/en deploy an SPARK cluster] and then set up the appropriate variables in the GATK4 spark command.

If you encounter errors like "[https://gatk.broadinstitute.org/hc/en-us/community/posts/360067054832-GATK-4-1-7-0-error-java-lang-IllegalArgumentException-malformed-input-off-17635906-length-1 IllegalArgumentException]" while using the installed modules on our clusters, we recommend you to try another workflow by using the program via [[Singularity]].

A Docker image of GATK can be found [https://hub.docker.com/r/broadinstitute/gatk here] and other versions are available at this [https://hub.docker.com/r/broadinstitute/gatk/tags page]. You will need first to [[Singularity/en#Creating_an_image_using_Docker_Hub|build a Singularity image from the Docker image]].  

For example, to get the latest version, you can run the following commands on the cluster:

<pre>

module load singularity

</pre>

or to get a particular [https://hub.docker.com/r/broadinstitute/gatk/tags version]:

<pre>

module load singularity

</pre>

In your [[Running jobs|SBATCH]] script, you should use something like this:

<pre>

module load singularity

     <path to the image>/gatk.sif gatk [--java-options "-Xmx4G"] ToolName [GATK args]</pre>

For more information about Singularity, you can watch the recorded [https://www.youtube.com/watch?v=kYb0aXS5DEE Singularity webinar].