Hi,
I have the following project setup 150 matched tumor/normal samples and 100 tumor only samples from the same entity.
I analyzed them all with Mutect2 using a PON which I build up from the normal Samples. While the 150 tumor/normal samples are fine in the analyzes, the 100 tumor only samples producing a lot of rubbish aside to the unknown "real" variants.
Now my problem, since my gatk-workshop in Cambridge last year an idea is swirling around my head and I don't know if it is great or complete dumb ...Can I use my results from the 150 matched tumor/normal samples as a truth set and train my filters on the 150 tumors (only) samples of this set? So I can use my trained filters for the 100 tumor only samples instead of the blunt filtering by AF etc?
Hope somebody can give me an advice or already tried that and can share his/her experience? Otherwise, I will try and report 
Thanks in advance,
EADG