Most of my samples show a private.germline.all count of 0. However, there are tons of germline mutations that are not filtered out, as the PureCN log files show. Why is the private germline count 0? I checked one sample's germline mutations manually to see if in fact all of them occurred in another sample, and they do not, although I did not do all the filtering that PureCN did. However, the PureCN filtering removed a fairly small number of mutations compared to the overall total.
This is a feature for tumor-only analyses. It is the count of mutations not in dbSNP (or whatever database you use for annotation), but predicted to be germline. If you have matched normals, dbSNP status is ignored and the SOMATIC info flag is used instead.
I use this mainly as a QC check in tumor-only. Private germline rates should be roughly constant across individuals, so if you have outliers here, the germline vs somatic classification is likely poor (most often happens in hyper mutated samples of very high purity when lots of somatic variants are wrongly classified as germline).
But good question, that should be made clear in the documentation.