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 October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.
Any known problems with IndelRealigner code in gsa-stable?
Does anyone know of any known issues with the indelrealigner? The GATK is calling 1000s of SNPs on one genome I have due to bad realignments. It appears the target finder identifies regions of the genome that are essentially perfectly aligned, but when the realigner gets to these areas it remits the reads as a new alignment that is a train-wreck compared to what the re-aligner started with. Am going to investigate further but thought I would check if this rings any bells. I am using the flag -model USE_READS and have no known indels to work with.