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.
Revert the Split'N'trim step
Hi guys, we are presently building some simulation program in our lab presently and we were wondering if there's already a program known by the community or done by GATK's team to revert back the bam files containing splitted spliced reads like what is outputted by the Split'N'trim step?
I'm asking because we are testing multiple programs to map RNAseq reads and bwa is outputting splitted reads directly and we want to revert them back to reads with N Cigar operators.
Thanks a lot for your help!