GATK

GATK is a software package for analysis of high-throughput sequencing data. 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.

Availability and Restrictions

The following versions of GATK are available on OSC clusters:

Version Oakley Owens
3.5 X* X*
*: Current default version

You can use  module spider gatk to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access for Academic Users

GATK is available to academic OSC users with proper validation. In order to obtain validation, please contact OSC Help for further instruction. 

Usage on Oakley

Set-up

To configure your environment for use of GATK, run the following command:   module load gatk. The default version will be loaded. To select a particular GATK version, use   module load gatk/version. For example, use  module load gatk/3.5to load GATK 3.5.

Usage

This software is a Java executable .jar file; thus, it is not possible to add to the PATH environment variable.

From module load gatk , a new environment variable, GATK, will be set.

Thus, users can use the software by running the following command: java -jar $GATK {other options}

Usage on Owens

Set-up

To configure your environment for use of GATK, run the following command:   module load gatk. The default version will be loaded. To select a particular GATK version, use   module load gatk/version. For example, use module load gatk/3.5 to load GATK 3.5.

Usage

This software is a Java executable .jar file; thus, it is not possible to add to the PATH environment variable.

From module load gatk, a new environment variable, GATK, will be set.

Thus, users can use the software by running the following command: java -jar $GATK {other options}

Further Reading

Service: 
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