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.

GenomicsDBImport / CreateSomaticPanelOfNormals interval list

Good afternoon

I am using the latest version of GATK and trying to prepare PanelOfNormals as described at

and I see that it changed from 4.0 version.

Step 1 worked just fine, but step 2 complains that "A large number of intervals were specified. Using more than 100 intervals in a single import is not recommended and can cause performance to suffer."

Could you please tell me which intervals to use? I always use the same interval list which was used to capture targets for the library prep.

Indeed, the process taking very long time now, whereas for older version it took a few minutes

Thank you


Best Answer


Sign In or Register to comment.