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.
Why are dbSNP indels excluded from indel realignment?
According to the known variants documentation (https://software.broadinstitute.org/gatk/guide/article?id=1247), only Mills indels and 1KG indels are recommended for indel realignment (RealignerTargetCreator and IndelRealigner). Although dbSNP contains indels (including 1KG indels) and is also in the bundle, it is not recommended. Why not? Is there a problem with using too many known indels or that may contain too many false positives?