Genome Analysis Toolkit (GATK)¶

The Genome Analysis Toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. The gatk bundle packages version 4.4.0.0.

UFS HPC Usage Example¶

The following command can be executed in the terminal to load the bundle:

1	`module load gatk`

The GATK utilities can be run as shown below:

gatk

The gatk_shell commmand can be used to access a shell in the gatk bundle.

1	`gatk_shell`

Performance Notes¶

No performance notes available

Recommended resources per session¶

No recommended resources available

Benchmarks¶

No benchmarks available.

UFS HPC Community Guides and Tutorials¶

No community guides available.

Official site and documentation¶

Licensing Information¶

GATK is licensed under the Apache license.

Primary citation¶

External Guides and Resources¶

If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za