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.
Will BaseRecalibrator overwrite an existing .grp file? Where are the tmp files stored?
I've been running BaseRecalibrator for a while, and I've just realized that I have an empty file with the same name I've given to BaseRecalibrator as output (it may have been created from a previous aborted run). Will the tool write to this file when it is finished (ETA ~19 hours), or will it exit with an error? Also, are there any intermediate files created in generating the recalibration table, and if so, where should I look for them (output directory, log directory, directory from which I called GATK, ...)?