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
Usage on Bridges
To see what versions of GATK are available type
module avail gatk
To see what other modules are needed, what commands are available and how to get additional help type
module help gatk
To use GATK, include a command like this in your batch script or interactive session to load the gatk module:
module load gatk
Be sure you also load any other modules needed, as listed by the
module help gatk command.