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GATK

The Genome Analysis Toolkit or GATK is a software package for analysis of high-throughput sequencing data, developed by the Data Science and Data Engineering group at the Broad Institute. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

Interactive Usage

After connecting to Iceberg (see Establishing a SSH connection), start an interactive sesssion with the qsh or qrsh command.

The latest version of GATK (currently 3.4-46) is made available with the command

module load apps/binapps/GATK

Alternatively, you can load a specific version with

module load apps/binapps/GATK/3.4-46
module load apps/binapps/GATK/2.6-5

Version 3.4-46 of GATK also changes the environment to use Java 1.7 since this is required by GATK 3.4-46. An environment variable called GATKHOME is created by the module command that contains the path to the requested version of GATK.

Thus, you can run the program with the command

java -jar $GATKHOME/GenomeAnalysisTK.jar -h

Which will give a large amount of help, beginning with the version information

---------------------------------------------------------------------------------
The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
Copyright (c) 2010 The Broad Institute
For support and documentation go to http://www.broadinstitute.org/gatk
---------------------------------------------------------------------------------

Documentation

The GATK manual is available online https://www.broadinstitute.org/gatk/guide/

Installation notes

The entire install is just a .jar file. Put it in the install directory and you’re done.

Modulefile

Version 3.4-46

  • The module file is on the system at /usr/local/modulefiles/apps/binapps/GATK/3.4-46

Its contents are

#%Module1.0#####################################################################
##
## GATK 3.4-46 modulefile
##

## Module file logging
source /usr/local/etc/module_logging.tcl
##

#This version of GATK needs Java 1.7
module load apps/java/1.7

proc ModulesHelp { } {
        puts stderr "Makes GATK 3.4-46 available"
}


set version 3.4-46
set GATK_DIR /usr/local/packages6/apps/binapps/GATK/$version

module-whatis   "Makes GATK 3.4-46 available"

prepend-path GATKHOME $GATK_DIR

Version 2.6-5

  • The module file is on the system at /usr/local/modulefiles/apps/binapps/GATK/2.6-5

Its contents are

#%Module1.0#####################################################################
##
## GATK 2.6-5 modulefile
##

## Module file logging
source /usr/local/etc/module_logging.tcl
##

proc ModulesHelp { } {
        puts stderr "Makes GATK 3.4-46 available"
}


set version 2.6.5
set GATK_DIR /usr/local/packages6/apps/binapps/GATK/$version

module-whatis   "Makes GATK 2.6-5 available"

prepend-path GATKHOME $GATK_DIR