Mutect2 PON with one normal sample

I am trying to analyze several tumors and one normal with mutect2. They are not paired. Is it appropriate to use -I normal ? or create pon with one normal sample and use -pon option? Tried to use mutect2 tumor-only mode to call the normal sample and use CreateSomaticPanelOfNormals, the result is an empty vcf with only headers. Any suggestions would be appreciated.

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Best Answer

  • Tom0802Tom0802 Member
    Accepted Answer

    Thanks for response, I am using Mutect2 4.0.1.0 in gatk4, the normal is from normal kidney tissues and tumors are kidney cancers. Unfortunately I have only one normal sample and it is not paired with any tumors. Reading the link you provided above it is not a real pon case, but will it help to generate a pon file using just one sample?

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @Tom0802
    Hi,

    Where did you get the one normal sample from?

    For the PoN, have a look at this article. You may also find the Mutect2 hands-on tutorial helpful (in the Presentations section).

    Which version are you using? We do have some helpful threads on running in tumor-only mode. Have a look also here.

    -Sheila

  • Tom0802Tom0802 Member
    Accepted Answer

    Thanks for response, I am using Mutect2 4.0.1.0 in gatk4, the normal is from normal kidney tissues and tumors are kidney cancers. Unfortunately I have only one normal sample and it is not paired with any tumors. Reading the link you provided above it is not a real pon case, but will it help to generate a pon file using just one sample?

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @Tom0802
    Hi,

    In your case, only having one normal sample is not enough for a PoN. We recommend having at least 40 samples in the PoN. However, if you look at the PoN article I pointed to above, you will see you can make a PoN from normal samples that were sequenced in the same way as your tumor samples. For example, in the hands on tutorial, we used 1000Genomes samples that were sequenced in the same way as our tumor samples in the PoN. If you cannot find enough normal samples that were sequenced in the same way as your tumor samples, you can try running in tumor only mode. The tutorials I linked to above should help with that.

    -Sheila

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