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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, MA admin
    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.

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    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.

  • egeulgenegeulgen USMember

    That seems reasonable to me :) Thanks for your kind comment!

    @Geraldine_VdAuwera said:
    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.

  • AlvaAlva SwitzerlandMember ✭✭
    edited February 2016

    @egeulgen : Could you please share the command line here where you used Tumor and matching Normal samples to get the Somatic mutations using GATK variant finding tool. I want to use the same for my RNA-seq data.
    Thank you
    /A

  • SheilaSheila Broad InstituteMember, Broadie admin

    @Alva
    Hi A,

    This MuTect2 documentation should help.

    -Sheila

  • AlvaAlva SwitzerlandMember ✭✭

    @Sheila
    Thanks Shelia, I have another question regarding Mutect2 output file..Could you please take a look ito that..

  • SheilaSheila Broad InstituteMember, Broadie admin

    @Alva
    Hi,

    I think your question was answered here :smiley:

    -Sheila

  • AlvaAlva SwitzerlandMember ✭✭
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