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.
-known parameter for RealignerTargetCreator and indelrealign
Dear GATK scientists,
when using RealignerTargetCreator and IndelRealigner of gatk, both of these two programs have --known parameter.
if i want to use reads alignment indel information combined with known indel information such as dbsnp to do the indel realign, how to use --known parameter for RealignerTargetCreator and IndelRealigner ? use this parameter in both of the programs?