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.
GATK4 pipeline in easy bash scripts, please
Hi, I asked this question a while ago and a few times. I know, there is a wonderful WDL platform and fire cloud stuff to run things in parallel and check this and that. But, for someone who are so used to a series of simple BASH commands, can you guys please kindly provide an example script like the one shown here https://gencore.bio.nyu.edu/variant-calling-pipeline/?
Right after I found the above, I found that it is not updated with GATK4, and I would hate to use a pipeline that is based on an outdated version of engine.
I will say "Thank You So Much, GATK". For almost a year, I still could not make GATK run on my own server, although there are a million documentation and tutorial and PPTs googled everywhere.