GATK

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.

Documentation

• GATK web site

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.