We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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.
GATK calling on del/ins at same location
I mapped using both BWA and novoalign.
In my sample on gene DHCR7 on chr11, there is Deletion and Insertion at same location. Del of 4 bases (GACG) at chr11: 71,155,132 - 71,155,135 AND insertion of 11 bp CGTCACCGGAC
After alignment in IGV, it shows up as insertion of CGTCACCG between 71,155,131 and 71,155,132 and deletion of bp 71,155,135 (G) . It ends up being called as separate variant which is wrong
IGV is attached. Any inputs of correcting is appreciated. How does GATK algorithm handles this - how about local realignment by haplotyper ?