High AF with Mutect2 in tumor only mode - should I filter?
I'm trying to run Mutect2 in tumor only mode without a PoN on some WES samples. I am well aware that these are not optimal conditions but I do not have access to a panel of normal obtained with the same protocol (putting together some 1000G samples would be better than nothing?) and neither a matched normal is available, I know that I'm facing a high number of false germline calls and I would like to know which additional filters seems to work best in this setup.
I followed the pre-processing bestpractices and am using "--germline-resource af-only-gnomad.hg38.vcf.gz --af-of-alleles-not-in-resource 0.0000025".
In one of the samples (the numbers are pretty similar for other ones) I am getting 2962 passed mutations starting from
I am filtering some mutations with POP_AF=1, believing that they are SNPs where the reference has the minor allele, all gnomad samples could then be listed as having the alternate allele probably...nevertheless they are listed as PASS with NaN risk of being germline.
The distribution of the AF I get has two peaks: one on lower AFs and one around 1: should I remove all the latter
ones considering them as germline and/or technical artifacts that were not filtered due to the lack of a matched normal and/or PoN?
What other parameters should I consider?
Thank you very much, I know fairly well that I am in a not supported context but right now this is everything that I have,