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.