Difference between revisions of "GATK"
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== Installed version == | == Installed version == | ||
This version is installed and currently available ... | |||
''... on environment hpc-uniol-env'' | |||
*'''GATK/3.7-Java-8.112''' | |||
''... on environment hpc-env/8.3'' | |||
*''GATK/4.1.4.1-GCCcore-8.3.0-Java-11'' | |||
== Using GATK on the HPC cluster == | == Using GATK on the HPC cluster == | ||
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module load GATK | module load GATK | ||
On environment hpc-uniol-env, you will then see the following message: | |||
[abcd1234@hpcl002 ~]$ module load GATK | [abcd1234@hpcl002 ~]$ module load GATK | ||
To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar | To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar | ||
To use GATK, you will have to add some command-line arguments. "--help" will print out a list of all of them | On environment hpc-env/8.3, a newer GATK version is installed which you can start by just typing | ||
gatk | |||
To use GATK productively, you will have to add some command-line arguments. "--help" will print out a list of all of them. | |||
== Documentation == | == Documentation == | ||
The GATK Documentation can be found [https://software.broadinstitute.org/gatk/documentation/ here]. | The GATK Documentation can be found [https://software.broadinstitute.org/gatk/documentation/ here]. | ||
Revision as of 10:03, 24 April 2020
Introduction
The GATK toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Installed version
This version is installed and currently available ...
... on environment hpc-uniol-env
- GATK/3.7-Java-8.112
... on environment hpc-env/8.3
- GATK/4.1.4.1-GCCcore-8.3.0-Java-11
Using GATK on the HPC cluster
If you want to use GATK on the HPC cluster, you will have to load its corresponding module first. You can do that with the command
module load GATK
On environment hpc-uniol-env, you will then see the following message:
[abcd1234@hpcl002 ~]$ module load GATK To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar
On environment hpc-env/8.3, a newer GATK version is installed which you can start by just typing
gatk
To use GATK productively, you will have to add some command-line arguments. "--help" will print out a list of all of them.
Documentation
The GATK Documentation can be found here.
