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Phasing SNPs and Indels

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


    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.


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