If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Why does Gatk4 use Spark to achieve multi-threading instead of using the command '-nt'?

Hi, I'm very interested in the reasons why gatk4 chooses spark to achieve multithreading.
To solve this probIem, I have spent so much time on the forum. However, I just don't have a good idea about this question.
If someone understands the intent of doing so,please tell me.
Thank you very much.


  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    Earlier versions of the GATK used manual code that was written to produce the multithreading steps but GATK 4 has decided to make use of Spark to handle the multithreading since it is open-source and industry-standard. I believe that SPARK was implementation to avoid manual code to handle multi threading for tools.

Sign In or Register to comment.