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.

Phasing SNPs and Indels

skhalid7skhalid7 GatechMember

I was looking into tools for phasing indels and SNPs. It seems that ReadBackPhasing only supports phasing of SNPs. I'm working on data from TCGA, and according to your docs HaplotypeCaller which can produce phased output, is not recommended for tumor samples. Is there any work around for this problem? Can MuTect phase the variants?

Best Answer


  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    Have a look at this thread. The user there did not submit data, but if you can, that would be very helpful for the developers.


Sign In or Register to comment.