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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Mutect2 panel of normals design

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    Genevieve Brandt (she/her)

    Hi,

    The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

    Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

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    David Benjamin

    Before answering your questions, we need to point out a few things:

    1. The panel of normals' role is only to clean technical artifacts, not remove germline mutations, which is handled by the germline resource and FilterMutectCalls.
    2. Since you don't have a matched normal, even with strict germline filtering you will end up with a very large number of germline false positives from rare (ie absent from gnomAD and other resources) germline events.  Any given genome will have 30,000 of these or so, and the only way around it is to have a low-purity or low-allele fraction tumor in order to distinguish somatic variants from germline hets.
    3. In most cases using the public panels from our google bucket is better than making your own.

    Now for your questions.

    1. The cancer type is irrelevant since technical artifacts are independent of the biological nature of the sample.
    2. FFPE is okay but I expect it to lead to a slight  (less than 1% if I had to guess) loss of sensitivity even when calling on FFPE samples.
    3. Don't worry about the age of the samples.  The concern is that non-cancerous somatic variation in older samples would lead to real variants getting into the panel, but this doesn't happen enough to be a serious issue.  Normal tissue next to the tumor will be a serious problem if a significant amount of tumor cells contaminate the normal, but not otherwise.
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