Genome Analysis Tool Kit (GATK) is produced by the Broad Institute. GATK offers a wide variety of tools but focuses primarily on variant discovery and genotyping.
Usage on Bridges-2
To see what versions of GATK are available and if there is more than one, which is the default, along with some help, type
module spider gatk
To use GATK, include a command like this in your batch script or interactive session to load the GATK module: (note ‘module load’ is case-sensitive):
module load GATK