User Tools

Site Tools


gatk-software

Genome Analysis ToolKit (GATK)

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

Information

Usage

See which versions of GATK are available:

$ module avail gatk

Load one version into your environment and run it:

$ module load gatk/4.2.2.0
$ gatk

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

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/broadinstitute/gatk/releases/download/4.2.2.0/gatk-4.2.2.0.zip
$ unzip gatk-4.2.2.0.zip
$ sudo cp -r gatk-4.2.2.0 /export/apps/gatk/4.2.2.0
gatk-software.txt · Last modified: 2021/09/16 13:38 by aorth