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.