I found out why my somatic variants are being filtered out by PureCN. It is filtering on the value in the QUAL column of the VCF. My germline variants have a value in the QUAL column, but the somatic variants (in the same VCF file) have "." (missing value) for QUAL. It seems to me they should not be filtered out if they are ".". Couldn't there be a mixture of QUAL, BQ, and MBQ fields for different variants in a VCF file? Shouldn't the filtering code check each one on a variant-by-variant basis?