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.
Difference between GATK Bundle and Files from Original Sources
Hi GATK Team,
I am Mia Yang. Would like to ask you some questions regarding the resources from GATK bundle.
(1) Is there any differences between the original files (HapMap, 1000G, Mills, etc..) and the one that we can download directly from the GATK bundle? And are these resources compatible with other variant re-calibration tools available out there?
(2) I can see that there are some labelled with hg19 at the back of the file names. Does this means that the files are only compatible with hg19 genome or it is optimized for hg19 and not the others (example hg38 etc..)?
Thank you in advance and have a nice day!