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.

HaplotypeCaller in Gatk4 vs Gatk3.5

Dear colleagues, I noticed that latest "5 dollar pipeline" uses HaplotypeCaller from gatk3.5 not gatk4.
Could you comment is it OK now to use HaplotypeCaller from gatk4 - if no, what are potential problems with using it?


  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    The pipeline uses 3.5 because at the time of building, GATK4 was not yet validated/ready to use. Now that GATK4 is validated, there should be no issue using it in the pipeline :smile: The team has just not made the switch yet.


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