Hello GATK Team,
I have a simple question when it comes to creating a somatic PON. Under the 'CreateSomaticPanelOfNormals' description it says that "The tool takes multiple normal sample callsets produced by Mutect2's tumor-only mode and collates sites present in two or more samples into a sites-only VCF". Does this means that a variant present in at least 2 of the total samples used, is going to be introduced into the PON? If so, the more samples used, the more likely variants are going to be common between samples. With this, should there be a reasonable maximum number of samples used to create a PON, so that we don't have false positives in the PON?
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