Parabricks on the Genomics Compute Cluster
How to run Parabricks, the licensed GPU version of GATK 4, on the Genomics Compute Cluster on Quest.
NVIDIA’s Clara Parabricks is a licensed GPU version of GATK 4 which runs 10x faster than the open-source CPU version of GATK, and is available to genomics researchers at Northwestern who are members of the Genomics Compute Cluster. To run the CPU version of GATK 4, load the gatk/4.1.0 module. Information on running Parabrick's GPU version of GATK 4 is below.
Checking out Parabricks Licenses
sbatch -L parabricks:2 <submission_script.sh>In this example, two Parabricks licenses are being checked out for this job. The scheduler will keep track of checked out licenses and your job will not begin unless licenses are available for it. Run your Parabricks job on two GPU cards, using two Parabricks licenses.
Running Parabricks on Quest
module load python/anaconda3.6 module load singularity
Fastq to Bam example script
sbatch -L parabricks:2 /projects/b1042/Parabricks_Training/fq2bam_quest.sh
Deep Variant example script
sbatch -L parabricks:2 /projects/b1042/Parabricks_Training/dv.sh