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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.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
Using MuTect2 with RNAseq data with a PoN (no matched normal)
I am trying to construct a panel of normals since I don't have any matched normal for my tumour sample to run MuTect2. So as I have read in this forum, this PoN should be built with data that has been obtained through the same protocols (and this point seems to be very important, right?).
As I have RNAseq data for my tumor, my question is : should the PoN be built with other RNAseq "normal" data ? My tumour sample is a human glioblastoma (brain tumor). I have a bunch of RNAseq coming from astrocytes, so would it be a reasonable choice ? I also have RNAseq data coming from meningioma (non-malignant tumor, also in brain), would it be good ?
Other questions : can I put tumor data in this PoN ? Or should I choose only data coming from healthy patient or healthy tissue ?
Another Idea was to use DNAseq data from matched normal but for other tumors. It has been done in the same lab but since it is DNAseq data, it did not follow the same protocol. Would it be a good choice ?
Thanks a lot for your answer ! And for your amazing work ! Cheers,