Difference between revisions of "GATK"
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To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar | To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar | ||
To use GATK, you will have to add some command-line arguments. | To use GATK, you will have to add some command-line arguments. "--help" will print out a list of all of them. Alternativ, all command-line arguments can be found [https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_engine_CommandLineGATK.php here]. | ||
== Documentation == | == Documentation == | ||
The GATK Documentation can be found [https://software.broadinstitute.org/gatk/documentation/ here]. | The GATK Documentation can be found [https://software.broadinstitute.org/gatk/documentation/ here]. | ||
Revision as of 06:32, 12 May 2017
Introduction
The GATK toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Installed version
The currently installed version of GATK is 3.7 and its based on Java in version 1.8.0_112 (renamed to "8.112" on the cluster).
Using GATK on the HPC cluster
If you want to use GATK on the HPC cluster, you will have to load its corresponding module first. You can do that with the command
module load GATK
You will than see the following message:
[abcd1234@hpcl002 ~]$ module load GATK To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar
To use GATK, you will have to add some command-line arguments. "--help" will print out a list of all of them. Alternativ, all command-line arguments can be found here.
Documentation
The GATK Documentation can be found here.
