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

Question

[field654]

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

[Kevin Blighe]

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.

[field654]

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.