View source for GATK

== Introduction ==

The GATK toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

== Installed version ==

The currently installed version of GATK is '''3.7''' and its based on Java in version '''1.8.0_112''' (renamed to "8.112" on the cluster).

== Using GATK on the HPC cluster ==

If you want to use GATK on the HPC cluster, you will have to load its corresponding module first. You can do that with the command
 module load GATK

You will than see the following message:
 [abcd1234@hpcl002 ~]$ module load GATK
 To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar

To use GATK, you will have to add some command-line arguments. A full list including details for each argument can be found [https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_engine_CommandLineGATK.php here].

== Documentation ==

The GATK Documentation can be found [https://software.broadinstitute.org/gatk/documentation/ here].