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.
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.
gatk4 vs gatk3
I'm trying to migrate my pipelines that use gatk tools from gatk3 to gatk4 and encounter some problems. Other than differences among syntaxes and options, some tools available in gatk3 are not valid any more in gatk4. For example, I got a 'RealignerTargetCreator' is not a valid command error. I'm wondering if this could be due to one of two things: either a tool is no longer available at all or the tool may have a different name (or a replacement) in gatk4. So my question is, is there a document listing tools that are totally new in gatk4, removed from gatk4, or have different names (or there're equivalent tools) in gatk4? Thanks.