Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. 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.

Loss of Heterozygosity and the MNP variants

mscjuliamscjulia United StatesMember

Hello,

I searched around the forum but could not confirm --- whether the MNP annotation used by "SelectVariants" tool actually covers loss of heterozygosity (LOH) on a relative large genome region. (LOH occurs when information in part of one chromosome is replaced by the same region of the other chromosome.) Thanks a lot.

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @mscjulia
    Hi,

    Sorry for the late response. I am not sure I understand your question. I think SelectVariants will only output the MNP sites, but not give any other information related to it.

    -Sheila

Sign In or Register to comment.