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

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-8
• GATK/4.1.8.1-GCCcore-8.3.0-Java-8

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:

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.