GATK

Owned by Simon Alexander
Last updated: Dec 21, 2022 by Joshua Cook (Unlicensed)
1 min read
1 Overview | 2 Using | 2.1 Multicore

Overview

  • GATK: Genome Analysis Toolkit Variant Discovery in High-Throughput Sequencing Data. Developed in the Data Sciences Platform at the Broad Institute, the 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.

    • The User Guide can be found at the general homepage.

Using

Use the module name gatk to discover versions available and to load the application.

Use gatk --list to get a list of tools installed with that version of gatk.

Multicore

Tools built with Spark are capable of running with multiple cores. Tools built with Spark have Spark at the end of the tool name or mention that they are built with Spark in their description. For a full list of the tools that come with GATK please refer to the output of running gatk --list.

 

Note: Although ARCC happily takes responsibility for setting up, installing, and testing the software it is running, this is a very feature-rich application and we are unable to test every feature and all the parameter settings. To assist us, and other users, we would sincerely appreciate feedback from users that we can share with the wider research community.