In the PureCN.R output file *_variants.csv, am I correct to think that I can get a quick count of the number of somatic variants that PureCN.R saw in the input VCF file by adding the number of entries > 0.9 in column "prior.somatic"? (A log message said that variants marked SOMATIC were found and their prior probability was set to 0.999).
PureCN.R is not seeing most of my somatic variants, or at least is not putting the prior value to 0.999. For one sample, which should have about 120 somatic variants, only 1 variant has prior probability > 0.9.
What filtering might PureCN be applying to my somatic variants? I didn't see log file messages indicating that a bunch of them had been filtered out.