GATK4 CNV Runs on Indivisual Set, How Can I tell Which Segments are Somatic

As the title, GATK4 tool CNV runs on individual set, then how can I tell which CNVs are somatic.
Usually there are always some errors, the germline CNVs sometime are not identical in paired samples. How can I identify the germline CNVs from the GATK4 CNV output?