Notice:
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

Hi,

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.

Thank you.

Tagged:

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    I believe MuTect only checks whether a SNP is present in the dbsnp file, and does not check the SAO flag. To whitelist somatic variants, it uses the COSMIC database.

  • chris2015chris2015 USMember

    Thank you for reply. So when i use mutect with Rat data, it is not necessary to add neither dbsnp file nor COSMIC file (As COSMIC data is for human cancer only).
    What about if i provided only dpsnp file, any call that is in dpsnp file will be excluded wether it is germ or somatic snp??

Sign In or Register to comment.