I use Mutects of Variant Call for paired Tumor/Normal WES, do I get a credibility (p value) for each call?
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10 weeks ago
field654 ▴ 20

Hi folks,

I have paired T/N samples for variant analysis. For one trial I followed GATK pipeline, where the variant calls were annotated with Funcotator. I have gone through the .maf result but didn't find a column indicating the credibility of the variants. I wonder if there should be one that I missed. VarScan would generate one by calcaulating the reads from T and N that support either the reference or an alternate.

I haven't heard back from GATK people yet. I wonder if anyone's familiar with the issue.

Many thanks.

Field

Mutect2 GATK WES Funcotator • 273 views
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Hi, can you post the link to the question that you posted to the GATK forum? I would recommend taking other metrics from the GATK-produced VCF file - there should be many QC metrics included.

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Yes, absolutely. I didn't initiate a separate question thread. I posted directly below the Funcotator workflow page. Here's the link. https://gatk.broadinstitute.org/hc/en-us/articles/360035889931-Funcotator-Information-and-Tutorial Thank you.

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