GATK is a software module available on Comet.
To access GATK on Comet, run module load GATK. This will load the default version of GATK.
An overview of the module information is shown below (module -r spider ^GATK$):
GATK: GATK/4.6.0.0-GCCcore-13.2.0-Java-17
Description:
The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing
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. Its robust architecture, powerful processing engine and high-performance computing features
make it capable of taking on projects of any size.
This module can be loaded directly: module load GATK/4.6.0.0-GCCcore-13.2.0-Java-17
Help:
Description
===========
The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute
to analyse next-generation resequencing 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. Its robust architecture, powerful processing engine and
high-performance computing features make it capable of taking on projects of any size.
More information
================
- Homepage: https://www.broadinstitute.org/gatk/
If there are multiple versions of GATK listed, then you can load a specific version as follows:
$ module load GATK/version_string
You can find the most up to date information whilst logged on to Comet by running module -r spider ^GATK$.
The module GATK has the following embedded help text (module help GATK):
Description
===========
The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute
to analyse next-generation resequencing 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. Its robust architecture, powerful processing engine and
high-performance computing features make it capable of taking on projects of any size.
More information
================
- Homepage: https://www.broadinstitute.org/gatk/
The default version of the module GATK has the following dependencies: