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Panel Of Normals for MuTect

I am wondering if there is a public repository from which one can build a panel of normals?
A couple of questions about that:
1. Must all the sample for a PON come from the same platform?
2. if not, is there a publicly available PON?

Many thanks

Issue · Github
by Sheila

Issue Number
539
State
closed
Last Updated
Closed By
vdauwera

Best Answer

Answers

  • bracha25bracha25 Member

    Thank you! Obviously we are trying to make a PON in the absence of available normals in our samples. But I guess we will have to use 1000genomes or SRA.

  • EugenieEugenie Member

    @Geraldine_VdAuwera
    Hello Geraldine,
    I have a question concerning Mutect PON creation and I am not sure where to post it as there are several similar threads related to the topic, hope it's ok to ask here.

    Both for Mutect1 and Mutect2 it's recommended to create a PON by calling normals with Mutect itself.
    And I am wondering what are the advantages of this approach compared to using a germline caller (eg Haplotype caller or samtools).
    Or, if I rephrase it: is there an advantage of calling normals as tumors for this specific purpose?
    One guess I have is that by treating normal as tumor Mutect would detect variants with allele frequency far below 50% and the created PON will therefore include some artifacts as well as true germline variants (eg artifacts coming from consistent misalignment).
    Does it make sense?

    From my experience the Mutect-created PON is much efficient than the one based on 1000genomes or HapMap (even when working with just 10/20/30 normal-tumor pairs).
    Which can be of course due to the small numbers of samples from the relevant population in these datasets but I think it's more than that.
    The reason I am particularly interested in this now is that I am going to analyse a big dataset for which germline mutations are already available and I am thinking whether it's enough or should I create a new PON.

    I would greatly appreciate if Mutect developers could comment on it.

    Thank you!

    Eugenie

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @Eugenie
    Hi Eugenie,

    Have a look at this thread. Also, this article may help too.

    -Sheila

  • EugenieEugenie Member

    @Sheila said:
    @Eugenie
    Hi Eugenie,

    Have a look at this thread. Also, this article may help too.

    -Sheila

    Thank you, Sheila, that's exactly what I was looking for;)
    Sorry I missed that thread somehow

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