====== GATK ======

**GATK** is a software module available on **Comet**.

===== GATK overview =====

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$''):

<code lang=text>
  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/
</code>

If there are multiple versions of **GATK** listed, then you can load a //specific// version as follows:
<code lang=bash>
$ module load GATK/version_string
</code>

You can find the most //up to date information// whilst logged on to Comet by running ''module -r spider ^GATK$''.

----

===== GATK Help =====

The module **GATK** has the following embedded help text (''module help GATK''):

<code lang=text>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/

</code>

----

===== GATK Dependencies =====

The //default// version of the module **GATK** has the following dependencies:

   * GCCcore/13.2.0
   * Java/17
   * Python/3.11.5-GCCcore-13.2.0

----

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