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.
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 $GATKHOME/GenomeAnalysisTK.jar -h
Which will give a large amount of help, beginning with the version information
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The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
Copyright (c) 2010 The Broad Institute
For support and documentation go to http://www.broadinstitute.org/gatk
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The GATK manual is available online https://www.broadinstitute.org/gatk/guide/
The entire install is just a .jar file. Put it in the install directory and you’re done.
Version 3.4-46
Its contents are
#%Module1.0#####################################################################
##
## GATK 3.4-46 modulefile
##
## Module file logging
source /usr/local/etc/module_logging.tcl
##
#This version of GATK needs Java 1.7
module load apps/java/1.7
proc ModulesHelp { } {
puts stderr "Makes GATK 3.4-46 available"
}
set version 3.4-46
set GATK_DIR /usr/local/packages6/apps/binapps/GATK/$version
module-whatis "Makes GATK 3.4-46 available"
prepend-path GATKHOME $GATK_DIR
Version 2.6-5
Its contents are
#%Module1.0#####################################################################
##
## GATK 2.6-5 modulefile
##
## Module file logging
source /usr/local/etc/module_logging.tcl
##
proc ModulesHelp { } {
puts stderr "Makes GATK 3.4-46 available"
}
set version 2.6.5
set GATK_DIR /usr/local/packages6/apps/binapps/GATK/$version
module-whatis "Makes GATK 2.6-5 available"
prepend-path GATKHOME $GATK_DIR