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.

MuTect detection abilities

szyszkaszyszka Member


I am wondering if MuTect is able to detect loss of one allele in the case where the normal sample is heterozygous (AB) and then tumor sample would contain only A or only B allele. Would MuTect keep it as a possible mutation or filter it out? If these mutations are kept are they then marked in a specific way so that it's easier to look for them in the output file?

Thank you in advance for any help.
All the best.


  • kcibulkcibul Cambridge, MAMember, Broadie, Dev ✭✭✭

    Hi -- it's a good question, and does get asked frequently. What you're referring to is often called "Loss of Heterozygosity" or LOH. Mutect does not call these events, as it's focused on point mutations that arise in the tumor and are not in the normal. LOH is really a copy number event, and is best detected by those methods. Also, as a copy number event, one could write a LOH-caller that takes advantage of the fact that all SNPs in a region would be affected thus giving you more power.


Sign In or Register to comment.