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.
Rat's snpdb file
I would like to run mutect for Rat. is it essential to provide dbSNP file? Rat dpSNP file does not provide information on which is Somatic and which is germ line. All SAO=0.
Did mutect use germ line SNVs in dpSNP file to filter out germ line mutation from output.??If so, I think Rat dbSNP will not provide helpful information as many somatic mutations might excluded because of ambigius SAO flag
One more thing is that dpSNP file is in rn5 not latest rat assembly rn6.