Panel of Normal and Match-Normal relation
Hello GATK team ! (again)
I am now doing my pipeline again with more samples, coming from the GDC data portal. So this time I will have a matched-normal for every samples. I am also considering to build a panel of normals.
My question is : Is there any bias that could arise from the fact that the match-normal used for variant calling is also present in the PoN ? It would be of course much more convenient to build only once the PoN and use the same for every variant call...
Another question : how is the filtering step with the PoN achieved ? Are every variants in the PoN filtered out ? (so, by default, present in at least 2 samples used to make the PoN) I mean, is it just a hard-filter or is there any statistical approach behind ?
Thank you very much in advance ! Regards,