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Indel realignment multiple cancer samples


It is usually suggested to run individually Tumor normal pair files with indel realignment before we continur for checking for contamination.
I have two questions.

  1. in my case for each patient I have multiple samples, at least 3 tumor and 1 normal. Shall I run indel realignment on all of them at the same time? What do you suggest?

  2. the output of the above command will be a single bam file unless we state the -nWayout option, but still for the contamination we have to use the tumor and the normal vcf files separately. Therefore, we have to use the nWayout option in the indel realignment. Is that correct?

Thank you.

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by Sheila

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  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there, I'm not sure what is our recommendation for dealing with multiple tumor samples, so I'll have to look that up with our cancer analysis experts. It might take a few days before we have a definitive answer for you; in the meantime you may want to look at the literature to see what people usually do for this case.

    But in any case, yes you will need to use the -nWayOut option.

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭


    Which version of MuTect are you planning to use? If using MuTect1, then you can try to run IndelRealigner with all the samples from the same individual together so that the tumor and normal have the same events for eliminating germline events. If using MuTect2, then Indel Realignment probably is not required at all.


  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    Hi again,

    I may not have fully answered your question. As for how to process and call variants on the tumor samples, we do not have experience dealing with multiple tumor samples. The best thing we can tell you is to try running the tumor samples as one sample and as three different samples, then compare the results.
    Let us know what you find!


  • alejandraalejandra spainMember

    Hi Sheila,

    Thank you for the advice. I had a go with both options. Here is what I have.
    When I run indel realignment in pairs T-N and then mutect T-N, everything seems to work fine.
    However, when I run indel realignment All Tumor samples and N, and then mutect with each Tumor sample and Normal, mutect gets an error in the input file.

    Therefore I think that since mutect doesn't allow for multiple inputs, it is better to run indel realignment in pairs.


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Can you clarify what "mutect gets an error in the input file" means? This should t produce an error.

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