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

We would like to know how does GATK handle the situation where an insert in a library is sequenced from both ends (read 1 and read 2), and the insert is sufficiently short that the reads overlap. This gives rise to a situation where the same stretch of DNA from the same insert is read twice, so it is effectively a duplicated (sub)read. Ideally the overlap should only be counted once for the purposes of polymorphism discovery. We understand that GATK now has functionality to handle this situation by merging the fragments when they overlap before doing SNP calling; is this the case?


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