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.
Base quality score recalibration
Thank you for the great description on detecting SNPs from RNA-seq data.
I am using RNA-seq data to call SNPs but I don't have any known set of SNPs for my species. I am now in the step to recalibrate quality score but when I try to run the command, it gives an error that I need to provide a set of known SNPs. I understand the reason for this because the tool is considering any mismatch to be an error and providing a set of known SNPs, will tell the software to skip these positions but does it mean that I should skip BQSR for my samples?
Thanks for any hint on this.