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Tumor-Normal Paired Exome-Sequencing pipeline

Hello,
We're currently running a research project involving exome sequencing of tumors and paired normal blood samples from brain cancer patients.
I'm relatively new to NGS processing but thanks to this forum (and the excellent documentation provided by the Broad) I was able to put together the following pipeline for this project:

I just wanted to check with the Cancer Team that everything looks OK, as well as get any suggestions, if possible.
Looking forward to your valuable response,
-E

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    Accepted Answer

    Looks great, my only comment is that we are going to be releasing MuTect 2, which is a complete rewrite based on HaplotypeCaller that can call both SNPs and indels, fairly soon. The indel calls in particular are vastly superior to those produced by Indelocator, so depending on the timeframe you envision for this project it may be worth it to wait for the M2 release. It's currently in validation phase, and I expect it will be released sometime in the September/October time frame.

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